{"achievements_table":[{"rows":[{"id":"1f1820b4-c7f3-43ba-9ca3-269b7237a1a2","Published":true,"Type":"Publication","Journal":["Springer Link"],"Profiles":"jon-iredell, geoffrey-coombs","URL":"https://link.springer.com/article/10.1007/s40121-023-00835-9","Tags":["Phage Therapy"," Polyclonal Bacteraemia"," Staphylococcus aureus"],"Authors":"Jason P. Gordon, Amer Al Taie, Ryan L. Miller, James W. Dennis, Mark A. T. Blaskovich, Jonathan R. Iredell, John D. Turnidge, Geoffrey W. Coombs, David Charles Grolman & Jacqueline Youssef","Name":"Quantifying the Economic and Clinical Value of Reducing Antimicrobial Resistance in Gram-negative Pathogens Causing Hospital-Acquired Infections in Australia","Date":{"type":"date","start_date":"2023-06-21"},"Created By":[{"id":"5eb42727-2109-44be-b04d-578a4950ef50","firstName":"Jan","lastLame":"Zheng","fullName":"Jan Zheng","profilePhoto":"https://s3-us-west-2.amazonaws.com/public.notion-static.com/6fad563c-6cb2-49c9-8026-fd7827cc57a9/8.31supd_157_sq_sm.jpg"}]},{"id":"8e47e6c1-a6c8-4396-9ed6-9f36717db6e8","format":{"copied_from_pointer":{"id":"1f1820b4-c7f3-43ba-9ca3-269b7237a1a2","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"Published":true,"Type":"Publication","Journal":["BMJ Open"],"Profiles":"ameneh-khatami, david-anthony-foley, morgyn-warner, anton-peleg, jian-li, stephen-stick, nettie-burke, ruby-lin, julia-warning, tom-snelling, steven-tong, jon-iredell","URL":"https://bmjopen.bmj.com/content/12/12/e065401","Tags":["Phage Therapy"," Polyclonal Bacteraemia"," Staphylococcus aureus"],"Authors":"Ameneh Khatami, David A Foley, Morgyn S Warner, Elizabeth H Barnes, Anton Y Peleg, Jian Li, Stephen Stick, Nettie Burke, Ruby C Y Lin, Julia Warning, Thomas L Snelling, Steven Y C Tong, Jonathan Iredell","Name":"Standardised treatment and monitoring protocol to assess safety and tolerability of bacteriophage therapy for adult and paediatric patients (STAMP study): protocol for an open-label, single-arm trial","Date":{"type":"date","start_date":"2023-06-16"},"Created By":[{"id":"5eb42727-2109-44be-b04d-578a4950ef50","firstName":"Jan","lastLame":"Zheng","fullName":"Jan Zheng","profilePhoto":"https://s3-us-west-2.amazonaws.com/public.notion-static.com/6fad563c-6cb2-49c9-8026-fd7827cc57a9/8.31supd_157_sq_sm.jpg"}]},{"id":"dc6dca4a-36fa-4a5f-ba10-2bf3817e00ce","Published":true,"Type":"News","URL":"https://www.youtube.com/watch?v=011UsBTuhxA","Tags":["Phage Therapy"," Polyclonal Bacteraemia"," Staphylococcus aureus"],"Name":"Advanced Therapeutics Webinar 11 - Phage Therapy in Australia: STAMPing out problematic infections","Date":{"type":"date","start_date":"2023-06-03"},"Created By":[{"id":"5eb42727-2109-44be-b04d-578a4950ef50","firstName":"Jan","lastLame":"Zheng","fullName":"Jan Zheng","profilePhoto":"https://s3-us-west-2.amazonaws.com/public.notion-static.com/6fad563c-6cb2-49c9-8026-fd7827cc57a9/8.31supd_157_sq_sm.jpg"}]},{"id":"54f9de99-aa21-4170-8d50-821e22d2a05a","Published":true,"Type":"Publication","Description":"Bacteriophages (phages) are viruses with the ability to infect bacteria, and they have recently attracted substantial attention as potential therapeutic alternatives or adjuvants to antibiotic therapy due to the global urgency of antimicrobial resistance. Antibiotics have been the clinical ‘gold standard’ for treating bacterial infections, and their pharmacokinetics/pharmacodynamics (PK/PD) have been extensively investigated over the past decades. Unfortunately, there has been a significant lack of research on the PK/PD of phage therapy, severely hindering its clinical translation. Recognising this as a major hurdle, excellent reviews summarising the available literature on phage PK/PD have been published over recent years. The aim of this present narrative review is to discuss the PK/PD challenges with the clinical translation of phage therapy and address the voids that need to be filled.","Journal":["Clinical Microbiology and Infection"],"Profiles":"jon-iredell, hak-kim-chan, jian-li, aleksandra-petrovic-fabijan, rachel-yoon-change, sue-nang","URL":"https://www.clinicalmicrobiologyandinfection.com/article/S1198-743X(23)00046-0/fulltext","Tags":["Phage Therapy"," PK/PD"," Review Paper"],"Authors":"Sue C. Nang, Yu-Wei Lin, Aleksandra Petrovic Fabijan, Rachel Y.K. Chang, Gauri G. Rao, Jonathan Iredell, Hak-Kim Chan, Jian Li","Name":"Pharmacokinetics/pharmacodynamics of phage therapy: a major hurdle to clinical translation","Created By":[{"id":"5eb42727-2109-44be-b04d-578a4950ef50","firstName":"Jan","lastLame":"Zheng","fullName":"Jan Zheng","profilePhoto":"https://s3-us-west-2.amazonaws.com/public.notion-static.com/6fad563c-6cb2-49c9-8026-fd7827cc57a9/8.31supd_157_sq_sm.jpg"}]},{"id":"f2430b5c-3cd8-4d4b-b68f-7657eec17ced","Published":true,"Type":"Publication","Description":"Staphylococcus aureus is a leading cause of bacteraemia and endocarditis in which intraclonal genetic variation, but not true polyclonal bacteraemia, is well documented. We describe a case of 36-year-old women with simultaneous and persistent bacteremia from two strains of Staphylococcus aureus that probably would have gone unrecognised because of the identical antibiotic profiles if had we not used bacteriophage susceptibility (“phage typing”) to further characterise the strains. In this patient, the dual bacteraemia was followed months later by another bacteraemia that likely would have been deemed a relapse of the original infection, except that we used similar methods to identify a third and unrelated strain. Our patient eventually responded well to antibiotics, and her bacteriophage therapy probably contributed little to that recovery. However, bacteriophage therapy required that we identify the strain of S. aureus causing her bacteraemia, and that requirement led directly to our identification of dual strains with identical antibiotic susceptibilities. Because of this experience, we alert other clinicians to the possibility of polyclonal infections with S. aureus. When bacteraemia is suspected, clinicians often pick a single colony or a few colonies from the original culture because prompt identification of the organism is critical and this practice provides a faster turnaround time. We caution that it might not identify different strains with different antibiotic sensitivities when polyclonal infections are present.","Journal":["Annals of Internal Medicine"],"Profiles":"aleksandra-petrovic-fabijan, nouri-ben-zakour, ruby-lin, jon-iredell","URL":"https://www.acpjournals.org/doi/epdf/10.7326/L19-0369","Tags":["Phage Therapy"," Polyclonal Bacteraemia"," Staphylococcus aureus"],"Org":"Westmead Hospital, Westmed Institute for Medical Research","Authors":"Aleksandra Petrovic Fabijan, Nouri L. Ben Zakour, Josephine Ho, Ruby CY Lin, Jonathan Iredell, Westmead Bacteriophage Therapy Team (WBTT) and AmpliPhi Biosciences Corporation","Name":"Polyclonal Staphylococcus aureus Bacteraemia","Created By":[{"id":"5eb42727-2109-44be-b04d-578a4950ef50","firstName":"Jan","lastLame":"Zheng","fullName":"Jan Zheng","profilePhoto":"https://s3-us-west-2.amazonaws.com/public.notion-static.com/6fad563c-6cb2-49c9-8026-fd7827cc57a9/8.31supd_157_sq_sm.jpg"}]},{"id":"566ba630-6ef7-4e81-ab1c-1faa915432f6","Published":true,"Type":"Publication","Description":"Bacterial L-forms require specialized culture techniques and are neither widely reported nor well understood in human infections. To date, most of the studies have been conducted on Gram-positive and stable L-form bacteria, which usually require mutagenesis or long-term passages for their generation. Here, using an adapted osmoprotective growth media, we provide evidence that pathogenic E. coli can efficiently switch to L-forms and back to a cell-walled state, proliferating aerobically in supratherapeutic concentrations of antibiotics targeting cell walls with few or no changes in their DNA sequences. Our work demonstrates that L-form switching is an effective adaptive strategy in stressful environments and can be expected to limit the efficacy of β-lactam and phages for many important infections.","Journal":["Microbiology Spectrum"],"Profiles":"aleksandra-petrovic-fabijan, carola-venturini, jonathan-iredell","URL":"https://journals.asm.org/doi/10.1128/spectrum.02419-22","Tags":["L-forms"," Antibiotic resistance"," Phages"," Escherichia coli"],"Org":"Westmead Institute for Medical Research","Authors":"Aleksandra Petrovic Fabijan, David Martinez-Martin, Carola Venturini, Katarzyna Mickiewicz, Neftali Flores-Rodriguez, Jeff Errington, Jonathan Iredell","Name":"L-Form Switching in Escherichia coli as a Common β-Lactam Resistance Mechanism","Date":"","Created By":[{"id":"5eb42727-2109-44be-b04d-578a4950ef50","firstName":"Jan","lastLame":"Zheng","fullName":"Jan Zheng","profilePhoto":"https://s3-us-west-2.amazonaws.com/public.notion-static.com/6fad563c-6cb2-49c9-8026-fd7827cc57a9/8.31supd_157_sq_sm.jpg"}]},{"id":"ea3b3ff3-e4ff-437a-a4ed-6020aec50b12","Published":true,"Type":"Publication","Description":"Bacteriophages (phages) are selective viral predators of bacteria. Abundant and ubiquitous in nature, phages can be used to treat bacterial infections (phage therapy), including refractory infections and those resistant to antibiotics. However, despite an abundance of anecdotal evidence of efficacy, significant hurdles remain before routine implementation of phage therapy into medical practice, including a dearth of robust clinical trial data. Phage–bacterium interactions are complex and diverse, characterized by co-evolution trajectories that are significantly influenced by the environments in which they occur (mammalian body sites, water, soil, etc.). An understanding of the molecular mechanisms underpinning these dynamics is essential for successful clinical translation. This review aims to cover key aspects of bacterium–phage interactions that affect bacterial killing by describing the most relevant published literature and detailing the current knowledge gaps most likely to influence therapeutic success.","Journal":["EMBO Molecular Medicine"],"Profiles":"carola-venturini, aleksandra-petrovic-fabijan, alicia-fajardo-lubian, jonathan-iredell","URL":"https://www.embopress.org/doi/full/10.15252/emmm.202012435","Tags":["Phage biology"," Phage Therapy"," Phage-bacterium dynamics"," Antimicrobials"],"Org":"Westmead Institute for Medical Research","Authors":"Carola Venturini, Aleksandra Petrovic Fabijan, Alicia Fajardo Lubian, Stefanie Barbirz, Jonathan Iredell","Name":"Biological foundations of successful bacteriophage therapy","Date":"","Created By":[{"id":"5eb42727-2109-44be-b04d-578a4950ef50","firstName":"Jan","lastLame":"Zheng","fullName":"Jan Zheng","profilePhoto":"https://s3-us-west-2.amazonaws.com/public.notion-static.com/6fad563c-6cb2-49c9-8026-fd7827cc57a9/8.31supd_157_sq_sm.jpg"}]},{"id":"17fb0201-d8e9-4459-adc7-28a3b5e825aa","Published":true,"Type":"Publication","Description":"The first phage therapy course jointly organised by ESCMID (European Society of Clinical Microbiology and Infectious Diseases) and ESGNTA (ESCMID Study Group for Non-traditional Antibacterial Therapy) and includes four sessions with cutting-edge scientific talks in the field of personalised phage therapy : (1) therapeutic monitoring (2) immune response to bacteriophages (3) formulation and administration of bacteriophages for therapy, and (4) current state and prospects of oral phage therapy, followed by live Q&A sessions and panel discussion.","Journal":["ESCMID Online Course 2022"],"Profiles":"jon-iredell, aleksandra-petrovic-fabijan","URL":"https://eacademy.escmid.org/escmid/#!*menu=6*browseby=3*sortby=2*ce_id=2271","Tags":["Online Course"," Phage therapy"," ESCMID"," ESGNTA"],"Org":"ESCMID, ESGNTA, Westmead Institute for Medical Research","Authors":"Aleksandra Petrovic Fabijan, Jonathan Iredell","Name":"Personalised phage therapy: basic principles of monitoring and treatment","Date":"","Cover":"https://dl.phage.directory/escmid.png","Created By":[{"id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","firstName":"Jessica","lastLame":"Sacher","fullName":"Jessica Sacher","profilePhoto":"https://s3-us-west-2.amazonaws.com/public.notion-static.com/d8e7973f-d27f-46d9-aef2-ab06e1cc2bb3/jess_non_labcoat_photo_cropped_copy.jpg"}]},{"id":"c00e5fcc-bfc6-4440-a8b8-c51e7a181985","format":{"copied_from_pointer":{"id":"d49d38b9-3af5-4b41-8a7d-475b631ce272","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"Published":true,"Type":"News","Description":"Academics plan to roll out therapy widely in Australia: Researchers at the University of Sydney, Western Sydney Local Health District and the Westmead Institute for Medical Research are developing a therapeutic solution to antimicrobial resistance that predates the discovery and wide usage of antibiotics… [Link to Paper](https://www.escmid.org/fileadmin/src/media/PDFs/1Dates_Events/event_flyers/ESGNTA_Course22_web.pdf)","Profiles":"jon-iredell,ameneh-khatami,ruby-lin","URL":"https://www.sydney.edu.au/news-opinion/news/2022/08/31/natural-virus-predators-offer-potential-alternative-to-antibioti.html?campaign=BIENCO&source=twitter&area=medicine-health&a=public&type=p&pid=phage","Tags":["Phage Therapy"],"Name":"Natural virus predators offer potential alternative to antibiotics","Date":{"type":"date","start_date":"2022-08-31"},"Created By":[{"id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","firstName":"Jessica","lastLame":"Sacher","fullName":"Jessica Sacher","profilePhoto":"https://s3-us-west-2.amazonaws.com/public.notion-static.com/d8e7973f-d27f-46d9-aef2-ab06e1cc2bb3/jess_non_labcoat_photo_cropped_copy.jpg"}]},{"id":"90dfc69b-1ce3-4393-8b0c-6170ec50e72e","Published":true,"Type":"News","Description":"An expert team, led by Director of the Centre of Infectious Diseases and Microbiology at the Westmead Institute for Medical Research (WIMR) Professor Jon Iredell, is developing a key alternative to antibiotics and central to the treatment are phages…","Profiles":"jon-iredell,ameneh-khatami,ruby-lin","URL":"https://www.medicalresearch.nsw.gov.au/a-therapy-from-the-past-could-hold-the-key-to-beating-antibiotic-resistance-in-the-future/","Tags":["Phage Therapy"],"Name":"A therapy from the past could hold the key to beating antibiotic resistance in the future","Date":{"type":"date","start_date":"2022-08-17"},"Created By":[{"id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","firstName":"Jessica","lastLame":"Sacher","fullName":"Jessica Sacher","profilePhoto":"https://s3-us-west-2.amazonaws.com/public.notion-static.com/d8e7973f-d27f-46d9-aef2-ab06e1cc2bb3/jess_non_labcoat_photo_cropped_copy.jpg"}]},{"id":"97a5cdd6-0d2f-4cd8-96f8-89bd2ff57778","Published":true,"Type":"Twitter","URL":"https://twitter.com/kids_research/status/1547813178448691201?s=12&t=8j_vJZaMKUf2C_xyIGNxjQ","Tags":["Phage Therapy"],"Name":"

Phage therapy changed the life of this brave Sydney teen, after years of treatment for a stubborn infection. Read more 👇 @SCHNkids @WestSydHealth @WestmeadInst @PhageAustralia #kidsresearch #phagetherapy #phage #cysticfibrosis https://t.co/PMxVPT2B6f
— Kids Research (@kids_research) July 15, 2022

","Date":{"type":"date","start_date":"2022-07-15"},"Created By":[{"id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","firstName":"Jessica","lastLame":"Sacher","fullName":"Jessica Sacher","profilePhoto":"https://s3-us-west-2.amazonaws.com/public.notion-static.com/d8e7973f-d27f-46d9-aef2-ab06e1cc2bb3/jess_non_labcoat_photo_cropped_copy.jpg"}]},{"id":"9b248287-600e-4e70-9fdd-889bf24fa016","Published":true,"Type":"Twitter","Profiles":"anthony-kicic","URL":"https://twitter.com/dranthonykicic/status/1544170888152907776?s=12&t=Nv6DR2JhY15aaHeV8JIN2A","Tags":["Funding","Phage Therapy"],"Name":"

Excited to have received funding to create a phage production facility for those severely ill. @telethonkids @WalyanCentre, @PhageAustralia

Reading: Future Health Research and Innovation Fund - Innovation Seed Fund grant recipients https://t.co/WytRgGSOg9 #Future
— Anthony Kicic (@DrAnthonyKicic) July 5, 2022

","Date":{"type":"date","start_date":"2022-07-05"},"Created By":[{"id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","firstName":"Jessica","lastLame":"Sacher","fullName":"Jessica Sacher","profilePhoto":"https://s3-us-west-2.amazonaws.com/public.notion-static.com/d8e7973f-d27f-46d9-aef2-ab06e1cc2bb3/jess_non_labcoat_photo_cropped_copy.jpg"}]},{"id":"e5e8423a-7b39-45cf-bc82-0d0280eb5b0f","format":{"copied_from_pointer":{"id":"17fb0201-d8e9-4459-adc7-28a3b5e825aa","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"Published":true,"Type":"Publication","Journal":["Clinical Infectious Diseases"],"Profiles":"rebekah-dedrick, jonathan-iredell, ameneh-khatami, brendan-mcmullan, graham-hatfull","URL":"https://academic.oup.com/cid/advance-article/doi/10.1093/cid/ciac453/6604409","Tags":["Phage Therapy"],"Publication date":"June, 2022","Authors":"Rebekah M. Dedrick, Bailey E. Smith, Madison Cristinziano, Krista G. Freeman, Deborah Jacobs-Sera, Yvonne Belessis, A. Whitney Brown, Keira A. Cohen, Rebecca M. Davidson, David van Duin, Andrew Gainey, Cristina Berastegui Garcia, C.R. Robert George, Ghady Haidar, Winnie Ip, Jonathan Iredell, Ameneh Khatami, Jessica S. Little, Kirsi Malmivaara, Brendan J. McMullan, David E. Michalik, Andrea Moscatelli, Jerry A. Nick, Maria G. Tupayachi Ortiz, Hari M. Polenakovik, Paul D. Robinson, Mikael Skurnik, Daniel A. Solomon, James Soothill, Helen Spencer, Peter Wark, Austen Worth, Robert T. Schooley, Constance A. Benson, Graham F. Hatfull","Name":"Phage Therapy of Mycobacterium Infections: Compassionate-use of Phages in Twenty Patients with Drug-Resistant Mycobacterial Disease","Created By":[{"id":"5eb42727-2109-44be-b04d-578a4950ef50","firstName":"Jan","lastLame":"Zheng","fullName":"Jan Zheng","profilePhoto":"https://s3-us-west-2.amazonaws.com/public.notion-static.com/6fad563c-6cb2-49c9-8026-fd7827cc57a9/8.31supd_157_sq_sm.jpg"}]},{"id":"4e4a9019-5988-489b-8ec5-2c9083f50c97","format":{"copied_from_pointer":{"id":"9e715b4e-7164-43e9-aa4c-fad39600314e","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"Published":true,"Type":"News","Description":"Leading the fight against Antimicrobial Resistance (AMR) in Western Australia: The WA Phage website showcases the research journey and outputs of WA researchers from the Wal-yan Respiratory Research Centre at the Telethon Kids Institute. The Phage WA website connects us with our community and provides up to date information on our collective mission to tackle anti-microbial resistance (AMR) through phage therapy.","Profiles":"anthony-kicic","URL":"https://walyanrespiratory.telethonkids.org.au/projects/phage-wa/","Org":"Phage WA","Name":"Phage WA Site Launched","Date":{"type":"date","start_date":"2022-06-17"},"Cover":"https://dl.phage.directory/.attachments/5b1977d4e6052caca5bfa238cc742cfc/b183e50a/current-research-transformed.webp","Created By":[{"id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","firstName":"Jessica","lastLame":"Sacher","fullName":"Jessica Sacher","profilePhoto":"https://s3-us-west-2.amazonaws.com/public.notion-static.com/d8e7973f-d27f-46d9-aef2-ab06e1cc2bb3/jess_non_labcoat_photo_cropped_copy.jpg"}]},{"id":"1238b74d-eb18-4e05-811d-ed0c684762a9","Published":true,"Type":"Publication","Journal":["Nature Microbiology"],"Profiles":"aleksandra-petrovic-fabijan, ruby-lin, susan-maddocks, nouri-ben-zakour, jon-iredell","URL":"https://www.nature.com/articles/s41564-019-0634-z","Tags":["Phage Therapy","Clinical trial","Sepsis"],"Publication date":"2020","Authors":"Aleksandra Petrovic Fabijan, Ruby CY Lin, Josephine Ho, Susan Maddocks, Nouri L. Ben Zakour, and Jonathan R. Iredell.","Name":"Safety of bacteriophage therapy in severe Staphylococcus aureus infection","First author":"Aleksandra Petrovic Fabijan","Created By":[{"id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","firstName":"Jessica","lastLame":"Sacher","fullName":"Jessica Sacher","profilePhoto":"https://s3-us-west-2.amazonaws.com/public.notion-static.com/d8e7973f-d27f-46d9-aef2-ab06e1cc2bb3/jess_non_labcoat_photo_cropped_copy.jpg"}]},{"id":"9e715b4e-7164-43e9-aa4c-fad39600314e","format":{"copied_from_pointer":{"id":"c3d5ee69-8729-4ca9-8e80-2ef574a71805","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"Published":false,"Type":"Twitter","URL":"https://twitter.com/UWAresearch/status/1529722186960777217?s=20&t=dLtH8ywtI-LTM6nbxYo89A","Name":"

Congratulations to @jcarapetis @telethonkids Executive Director & Winthrop Professor at @uwanews - elected as a new Fellow of the prestigious @Science_Academy in recognition of his pioneering, paradigm-shifting expertise in infectious diseases

READ: https://t.co/vZvLYMgEMs pic.twitter.com/iLRyEeh62k
— UWA Research (@UWAresearch) May 26, 2022

","Created By":[{"id":"5eb42727-2109-44be-b04d-578a4950ef50","firstName":"Jan","lastLame":"Zheng","fullName":"Jan Zheng","profilePhoto":"https://s3-us-west-2.amazonaws.com/public.notion-static.com/6fad563c-6cb2-49c9-8026-fd7827cc57a9/8.31supd_157_sq_sm.jpg"}]},{"id":"295ab63b-77d0-451a-aac7-6578b1dcf670","Type":"News","Description":"We just launched the first version of our site!","Profiles":"phage-australia","URL":"https://phageaustralia.org","Org":"Phage Australia","Name":"Website Launched","Date":{"type":"date","start_date":"2022-05-28"},"Created By":[{"id":"5eb42727-2109-44be-b04d-578a4950ef50","firstName":"Jan","lastLame":"Zheng","fullName":"Jan Zheng","profilePhoto":"https://s3-us-west-2.amazonaws.com/public.notion-static.com/6fad563c-6cb2-49c9-8026-fd7827cc57a9/8.31supd_157_sq_sm.jpg"}]},{"id":"21826a6b-86bb-4560-981d-9a23f8d10b62","format":{"copied_from_pointer":{"id":"f1b41dd5-992e-43d1-92c3-8e002242702b","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"Published":true,"Type":"Publication","Journal":["Frontiers in Microbiology"],"Profiles":"ali-khalid, ruby-lin, jon-iredell","URL":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7904893/","Tags":["Phage Therapy","Clinicians","Review paper"],"Publication date":"February, 2021","Authors":"Ali Khalid, Ruby C. Y. Lin and Jonathan R. Iredell","Name":"A Phage Therapy Guide for Clinicians and Basic Scientists: Background and Highlighting Applications for Developing Countries","First author":"Ali Khalid","Created By":[{"id":"5eb42727-2109-44be-b04d-578a4950ef50","firstName":"Jan","lastLame":"Zheng","fullName":"Jan Zheng","profilePhoto":"https://s3-us-west-2.amazonaws.com/public.notion-static.com/6fad563c-6cb2-49c9-8026-fd7827cc57a9/8.31supd_157_sq_sm.jpg"}]},{"id":"646a0c51-7714-489d-b6d8-9b8ed3588b25","format":{"copied_from_pointer":{"id":"d84b0e6f-7ba2-4889-8f5c-a40364a1dabb","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"Published":true,"Type":"Publication","Journal":["Australian Critical Care"],"Profiles":"aleksandra-petrovic-fabijan, ruby-lin, susan-maddocks, jon-iredell","URL":"https://www.australiancriticalcare.com/article/S1036-7314(20)30089-8/fulltext","Tags":["Abstract","Phage Therapy"],"Publication date":"January, 2020","Authors":"Josephine Ho, Aleksandra Petrovic Fabijan, Ruby CY. Lin, Susan Maddocks, Jonathan Iredell","Name":"Bacteriophage therapy in the critically ill","First author":"Josephine Ho","Created By":[{"id":"5eb42727-2109-44be-b04d-578a4950ef50","firstName":"Jan","lastLame":"Zheng","fullName":"Jan Zheng","profilePhoto":"https://s3-us-west-2.amazonaws.com/public.notion-static.com/6fad563c-6cb2-49c9-8026-fd7827cc57a9/8.31supd_157_sq_sm.jpg"}]},{"id":"0811bf6c-0129-40e2-836a-e6ea43e57921","format":{"copied_from_pointer":{"id":"e5cb6e6d-4438-42c9-a3b7-e50e9f6c80d0","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"Published":true,"Type":"Publication","Journal":["Nature Microbiology"],"Profiles":"fernando-gordillo-altamirano, dinesh-subedi, trevor-lithgow, anton-peleg, jeremy-barr","URL":"https://www.nature.com/articles/s41564-020-00830-7","Tags":["Acinetobacter","Phage-resistance","Research paper"],"Publication date":"January, 2021","Authors":"Fernando Gordillo Altamirano, John H. Forsyth, Ruzeen Patwa, Xenia Kostoulias, Michael Trim, Dinesh Subedi, Stuart K. Archer, Faye C. Morris, Cody Oliveira, Luisa Kielty, Denis Korneev, Moira K. O’Bryan, Trevor J. Lithgow, Anton Y. Peleg & Jeremy J. 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resistance in uropathogens across northern Australia 2007–20 and impact on treatment guidelines","First author":"Will Cuningham","Created By":[{"id":"5eb42727-2109-44be-b04d-578a4950ef50","firstName":"Jan","lastLame":"Zheng","fullName":"Jan Zheng","profilePhoto":"https://s3-us-west-2.amazonaws.com/public.notion-static.com/6fad563c-6cb2-49c9-8026-fd7827cc57a9/8.31supd_157_sq_sm.jpg"}]},{"id":"82933f80-4e82-454a-b53a-1f52ae5c4bff","format":{"copied_from_pointer":{"id":"bb70d03f-cb50-4c1e-b8ba-6a2168fecf7b","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"Published":true,"Type":"Publication","Journal":["Current Opinions in Biotechnology"],"Profiles":"phage-australia, jon-iredell, ruby-lin, jessica-sacher, jan-zheng, ali-khalid, pieter-jan-ceyssens","URL":"https://www.sciencedirect.com/science/article/abs/pii/S0958166920302020","Tags":["Phage biobank","Opinion paper"],"Publication date":"April, 2021","Authors":"Ruby CY Lin, Jessica C Sacher, Pieter-Jan Ceyssens, Jan Zheng, Ali Khalid, Jonathan R Iredell, The Australian Phage Biobanking Network.","Name":"Phage Biobank: Present Challenges and Future Perspectives","First author":"Ruby CY Lin","Created By":[{"id":"5eb42727-2109-44be-b04d-578a4950ef50","firstName":"Jan","lastLame":"Zheng","fullName":"Jan Zheng","profilePhoto":"https://s3-us-west-2.amazonaws.com/public.notion-static.com/6fad563c-6cb2-49c9-8026-fd7827cc57a9/8.31supd_157_sq_sm.jpg"}]},{"id":"3b896421-b2fb-47e6-be67-dd0859f312a3","format":{"copied_from_pointer":{"id":"85eb8acd-1e3d-43a1-86db-fa36f6dd637e","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"Published":true,"Type":"Publication","Journal":["Research Square | Pre-print"],"Profiles":"ameneh-khatami, ruby-lin, aleksandra-petrovic-fabijan, sivan-alkalay-oren, ronen-hazan, ran-nir-paz, jon-iredell","URL":"https://assets.researchsquare.com/files/rs-110673/v1/0380f83a-2dc7-43b2-bc80-eaed366cb55c.pdf?c=1631861533","Tags":["Pediatrics","Phage Therapy","Clinical 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aleksandra-petrovic-fabijan","URL":"https://www.publish.csiro.au/ma/pdf/MA19005","Tags":["Phage Therapy","Research paper"],"Publication date":"March, 2019","Authors":"Carola Venturini, Aleksandra Petrovic Fabjian and Ruby CY Lin","Name":"Bacteriophage therapy for severe infections","First author":"Carola Venturini","Created By":[{"id":"5eb42727-2109-44be-b04d-578a4950ef50","firstName":"Jan","lastLame":"Zheng","fullName":"Jan Zheng","profilePhoto":"https://s3-us-west-2.amazonaws.com/public.notion-static.com/6fad563c-6cb2-49c9-8026-fd7827cc57a9/8.31supd_157_sq_sm.jpg"}]},{"id":"3084dc16-ed07-4717-b432-db5229e0de9b","format":{"copied_from_pointer":{"id":"a1b0539e-5391-4237-84b3-79caa7d8ad20","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"Published":true,"Type":"Publication","Journal":["ASM Journal: mSystems"],"Profiles":"jeremy-barr, rhys-dunstan, trevor-lithgow, rebecca-bamert","URL":"https://journals.asm.org/doi/full/10.1128/mSystems.00242-21","Tags":["Research 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Thung, Murray E. White, Wei Dai, Jonathan J. Wilksch, Rebecca S. Bamert, Andrea Rocker, Christopher J. Stubenrauch, Daniel Williams, Cheng Huang, Ralf Schittelhelm, Jeremy J. Barr, Eleanor Jameson, Sheena McGowan, Yanju Zhang, Jiawei Wang, Rhys A. Dunstan, and Trevor Lithgow","Name":"Component Parts of Bacteriophage Virions Accurately Defined by a Machine-Learning Approach Built on Evolutionary Features","First author":"Tze Y. Thung","Created By":[{"id":"5eb42727-2109-44be-b04d-578a4950ef50","firstName":"Jan","lastLame":"Zheng","fullName":"Jan Zheng","profilePhoto":"https://s3-us-west-2.amazonaws.com/public.notion-static.com/6fad563c-6cb2-49c9-8026-fd7827cc57a9/8.31supd_157_sq_sm.jpg"}]},{"id":"de84d7a0-bd01-4c8c-96ec-61a3f988b1cc","format":{"copied_from_pointer":{"id":"81d3d0b3-c281-44c7-82fa-f4cd02d8c7e5","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"Published":true,"Type":"Publication","Journal":["Annals of Internal Medicine"],"Profiles":"steven-tong","URL":"https://www.acpjournals.org/doi/abs/10.7326/M21-1491","Tags":["Staphylococcus","MRSA","Clinical"],"Publication date":"May, 2021","Authors":"Steven Y.C. Tong","Name":"Annals for Hospitalists Inpatient Notes - Clinical Pearls—Methicillin-Resistant Staphylococcus aureus Bacteremia","First author":"Steven Y.C. 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Mitchell & Peter Speck","Name":"Efficacy of phage cocktail AB-SA01 therapy in diabetic mouse wound infections caused by multidrug-resistant Staphylococcus aureus","First author":"Legesse Garedew Kifelew","Created By":[{"id":"5eb42727-2109-44be-b04d-578a4950ef50","firstName":"Jan","lastLame":"Zheng","fullName":"Jan Zheng","profilePhoto":"https://s3-us-west-2.amazonaws.com/public.notion-static.com/6fad563c-6cb2-49c9-8026-fd7827cc57a9/8.31supd_157_sq_sm.jpg"}]},{"id":"b0825bf3-2797-4e2e-b233-7a505d7ae717","format":{"copied_from_pointer":{"id":"7bbf3266-38a8-4f92-bbef-41fa94df1be4","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"Published":true,"Type":"Publication","Journal":["MDPI: Viruses"],"Profiles":"joshua-iszatt, alexander-larcombe, hak-kim-chan, stephen-stick, luke-garratt, anthony-kicic","URL":"https://www.mdpi.com/1999-4915/13/9/1809","Tags":["Review paper","Respiratory Tract infections","Phage Therapy"],"Publication date":"September, 2021","Authors":"Joshua J. Iszatt, Alexander N. Larcombe, Hak-Kim Chan, Stephen M. Stick, Luke W. Garratt and Anthony Kicic.","Name":"Phage Therapy for Multi-Drug Resistant Respiratory Tract Infections","First author":"Joshua J. Iszatt","Created By":[{"id":"5eb42727-2109-44be-b04d-578a4950ef50","firstName":"Jan","lastLame":"Zheng","fullName":"Jan Zheng","profilePhoto":"https://s3-us-west-2.amazonaws.com/public.notion-static.com/6fad563c-6cb2-49c9-8026-fd7827cc57a9/8.31supd_157_sq_sm.jpg"}]},{"id":"da278674-986c-4b72-a559-45f7e2d41789","format":{"copied_from_pointer":{"id":"7ea133e9-5ece-40d4-8082-6a08df8389d2","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"Published":true,"Type":"Publication","Journal":["EMBO Molecular Medicine"],"Profiles":"ameneh-khatami, ruby-lin, aleksandra-petrovic-fabijan, sivan-alkalay-oren, ronen-hazan, ran-nir-paz, jon-iredell","URL":"https://www.embopress.org/doi/full/10.15252/emmm.202113936","Tags":["Clinical trial","Pediatrics","Immune response","Phage Therapy"],"Publication date":"August, 2021","Authors":"Ameneh Khatami, Ruby C Y Lin, Aleksandra Petrovic-Fabijan, Sivan Alkalay-Oren, Sulaiman Almuzam, Philip N Britton, Michael J Brownstein, Quang Dao, Joe Fackler, Ronen Hazan, Bri’Anna Horne, Ran Nir-Paz,\nJonathan R Iredell","Name":"Bacterial lysis, autophagy and innate immune responses during adjunctive phage therapy in a child","First author":"Ameneh Khatami","Created By":[{"id":"5eb42727-2109-44be-b04d-578a4950ef50","firstName":"Jan","lastLame":"Zheng","fullName":"Jan Zheng","profilePhoto":"https://s3-us-west-2.amazonaws.com/public.notion-static.com/6fad563c-6cb2-49c9-8026-fd7827cc57a9/8.31supd_157_sq_sm.jpg"}]},{"id":"ad16047b-db20-4f8a-b082-de3eece67abb","format":{"copied_from_pointer":{"id":"5f5c618b-9192-4490-974c-2f45e0f2170a","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"Published":true,"Type":"Publication","Journal":["International Journal of Infectious Diseases"],"Profiles":"ali-khalid, aleksandra-petrovic-fabijan, susan-maddocks, ruby-lin, jon-iredell","URL":"https://www.ijidonline.com/article/S1201-9712(20)31081-X/fulltext","Tags":["Phage Virulence","Antibiotic synergy","Research paper"],"Publication date":"December, 2020","Authors":"A. Khalid, A.P. Fabijan, S. Maddocks, R.C.Y. Lin\nJ.R. Iredell","Name":"Rapid automated system for bacteriophage virulence and antibiotic synergy testing – The ‘phago-antibiogram’","First author":"A. Khalid","Created By":[{"id":"5eb42727-2109-44be-b04d-578a4950ef50","firstName":"Jan","lastLame":"Zheng","fullName":"Jan Zheng","profilePhoto":"https://s3-us-west-2.amazonaws.com/public.notion-static.com/6fad563c-6cb2-49c9-8026-fd7827cc57a9/8.31supd_157_sq_sm.jpg"}]},{"id":"c85f7b89-d881-46b8-9ccf-f42613c216a9","format":{"copied_from_pointer":{"id":"6edbb051-be39-41bd-ad48-5b6e23f50979","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"Published":true,"Type":"Publication","Journal":["JAMA Network"],"Profiles":"steven-tong","URL":"https://jamanetwork.com/journals/jama/article-abstract/2760737","Tags":["Clinical trial","MRSA","Antibiotics"],"Publication date":"February, 2020","Authors":"Steven Y. C. Tong, David C. Lye, Dafna Yahav","Name":"Effect of Vancomycin or Daptomycin With vs Without an Antistaphylococcal β-Lactam on Mortality, Bacteremia, Relapse, or Treatment Failure in Patients With MRSA Bacteremia\nA Randomized Clinical Trial","First author":"Steven Y. C. Tong","Created By":[{"id":"5eb42727-2109-44be-b04d-578a4950ef50","firstName":"Jan","lastLame":"Zheng","fullName":"Jan Zheng","profilePhoto":"https://s3-us-west-2.amazonaws.com/public.notion-static.com/6fad563c-6cb2-49c9-8026-fd7827cc57a9/8.31supd_157_sq_sm.jpg"}]},{"id":"8b02dcf3-6a60-4dfd-9ad8-cdd1248bd928","format":{"copied_from_pointer":{"id":"61e25c75-cb6e-46d3-8fa4-ea597d4a042f","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"Published":true,"Type":"Publication","Journal":["Journal of Cystic Fibrosis"],"Profiles":"dinesh-subedi, fernando-gordillo-altamirano, jeremy-barr, ameneh-khatami","URL":"https://www.cysticfibrosisjournal.com/article/S1569-1993(20)30334-9/pdf","Tags":["Cystic Fibrosis","Phage isolation","Pseudomonas","Staphylococcus","Pediatrics"],"Publication date":"June, 2020","Authors":"Jagdev Singh, Dinesh Subedi, Fernando Lautaro Gordillo Altamirano, Ruzeen Patwa, Hiran Selvadurai, Jeremy Barr, Ameneh Khatami","Name":"Isolating and characterising phages against Pseudomonas aeruginosa and Staphylococcus aureus in children with cystic fibrosis","First author":"Jagdev Singh","Created By":[{"id":"5eb42727-2109-44be-b04d-578a4950ef50","firstName":"Jan","lastLame":"Zheng","fullName":"Jan Zheng","profilePhoto":"https://s3-us-west-2.amazonaws.com/public.notion-static.com/6fad563c-6cb2-49c9-8026-fd7827cc57a9/8.31supd_157_sq_sm.jpg"}]},{"id":"8edcf394-6873-4857-abb0-129eaabcfe72","format":{"copied_from_pointer":{"id":"63cca4b1-ec58-4b6d-a2a5-5f7a064d8b8e","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"Published":true,"Type":"Publication","Journal":["MDPI: Viruses"],"Profiles":"morgyn-warner, peter-speck","URL":"https://www.mdpi.com/1999-4915/12/5/559","Tags":["Research paper","Biofilms","Staphylococcus","Pseudomonas","Phage Therapy"],"Publication date":"May, 2020","Authors":"Legesse Garedew Kifelew, Morgyn S. Warner, Sandra Morales, Nicky Thomas, David L. Gordon, James G. Mitchell, and Peter G. 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Phage therapy changed the life of this brave Sydney teen, after years of treatment for a stubborn infection. Read more 👇 @SCHNkids @WestSydHealth @WestmeadInst @PhageAustralia #kidsresearch #phagetherapy #phage #cysticfibrosis https://t.co/PMxVPT2B6f
— Kids Research (@kids_research) July 15, 2022

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Excited to have received funding to create a phage production facility for those severely ill. @telethonkids @WalyanCentre, @PhageAustralia

Reading: Future Health Research and Innovation Fund - Innovation Seed Fund grant recipients https://t.co/WytRgGSOg9 #Future
— Anthony Kicic (@DrAnthonyKicic) July 5, 2022

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Congratulations to @jcarapetis @telethonkids Executive Director & Winthrop Professor at @uwanews - elected as a new Fellow of the prestigious @Science_Academy in recognition of his pioneering, paradigm-shifting expertise in infectious diseases

READ: https://t.co/vZvLYMgEMs pic.twitter.com/iLRyEeh62k
— UWA Research (@UWAresearch) May 26, 2022

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Bacteria may be beneficial (e.g. bacteria in the gut to help digest food) or pathogenic (e.g. bacteria causing an infection in the lungs). The bacterium is the singular term for bacteria (plural)."]],"horA":[["Published"]],"title":[["Bacteria"]]},"created_time":1653628860000,"last_edited_time":1654761480000,"parent_id":"bfb058a7-7eb6-4672-8e06-b42a76b43255","parent_table":"collection","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"30b2029b-3035-4b50-ada6-89b96d918ab8","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},{"value":{"id":"186c50e3-8b71-48bf-82f4-c3cd4d1a4fdc","version":416,"type":"page","properties":{"?~_]":[["Also known as phage. Phage is a virus that infects and replicates within bacteria. 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I am interested in implementing genomic (personalised) medicine into healthcare and translate research outcomes into clinical settings. My publications are available in ORCID (0000-0003-4163-511X), Google Scholar and Research Gate (>5300 citations). \n\nI have a BSc in Zoology and MSc (1st Class Hons) in Molecular and Cellular Biology from the University of Canterbury, New Zealand, and a PhD in Medicine (Molecular Genetics) from the University of Sydney, Australia. I was a named NHMRC Peter Doherty Fellow (2005-8) and then a University of NSW Vice-Chancellor Global Research Fellow (2009-2014). I have secured over $6.4 million AUD competitive Category 1 research funding (including several NHMRC project grants, ARC LIEF) in the discipline of cardiovascular diseases, obesity, cancer biology, biobanking, infectious diseases and phage therapy. \n\nI advocate for women in STEMM and do pro bono career coaching. 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CI Khatami’s research career spans 3 continents with a wide network of international collaborators. This started with clinical leadership of vaccine trials carried out with the Oxford Vaccine Group at the University of Oxford, under the supervision of Sir Andrew Pollard. Subsequent experience includes time at New York University, investigating Group B Streptococcus colonisation in women. Since returning to Sydney in 2019 CI Khatami has developed extensive collaborations with respiratory medicine specialists throughout Australia, with a focus on antimicrobial therapies in children with cystic fibrosis (CF).\nCI Khatami is the Phage Therapy Content Expert for the Sydney Children’s Hospitals Network (SCHN) Advanced Therapeutics Steering Committee and was the first clinician in Australia to treat a paediatric patient with intravenous phage therapy (October 2019) for a highly resistant _Pseudomonas aeruginosa_ bone infection with support from CI Iredell. 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He leads the _Staphylococcus aureus_ Network Adaptive Platform trial, an NHMRC funded global adaptive platform trial (GNT #1184238, CIA, 2020-2024, $4.95M; also NZ HRC, Canadian IHR grants for additional $2M) and the Australasian COVID-19 Trial (ASCOT), which has been funded through philanthropy, and has recruited >1,600 participants in Australia, NZ, India, and Nepal. He chairs: the Australasian Society for Infectious Diseases Clinical Research Network; the Translational and Clinical Research discipline at the Doherty Institute; and the Melbourne Academic Centre of Health Infection subcommittee.\nProf Tong has completed clinical trials and other complex projects including CAMERA2, the largest RCT for MRSA bloodstream infections (JAMA 2020). His involvement in REMAP-CAP for COVID has further built capacity for adaptive clinical trials in infectious diseases. 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He moved to the US as a PostDoc, first at the University of Pennsylvania in Philadelphia studying enterotoxigenic _E. coli_, and then at the University of Illinois, Urbana-Champaign studying the genomics and pathogenesis of _Salmonella_, work that he continued as an Assistant Professor at the University of Tennessee Health Sciences Center in Memphis, TN._ _Working with Argonne National Labs and the Fellowship for the Interpretation of Genomes (FIG) he developed the RAST and MG-RAST systems for bacterial genome and metagenome annotation.\nIn 2006, Rob took a position in the Departments of Computer Science and Biology at San Diego State University, and his work there led to breakthroughs in our understanding of how viruses interact with their hosts, and how viruses from around the world carry important genetic information. 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She is an expert in polymer chemistry, organic and inorganic/organic hybrid nanomaterials. She has established herself as a leader in using nanotechnology in the form of nanoparticles for biomedical application.","Category":["Chief Investigator"],"Name":"Hien Duong","Profile":[{"id":"attgDxTB8Y0bysqe5","width":300,"height":300,"url":"https://v5.airtableusercontent.com/v3/u/26/26/1707998400000/MurQQkWg-2BDiD5S4SVyZw/WYu0js0ASlPsyAmQwfRLA-R7OynixRxMUd1gUnfxMkq5R7lZrwy96K8q0y1ClTWHOoUD8JYp9g1ncq48N-oGzigR9JahGyrzxfNTy_hz9pXKRcC8-QYP74vhWMZn9Zi-WHIi6MweMKAIprhCS_2ieDaV9tUbDzlXZ6DeuSMqL9c/3BfTUh1kZoTRBNGv71Ys4EKcucUD0h615c7ygL-Zh3A","filename":"profile photo Hien_1.jpg","size":31031,"type":"image/jpeg","thumbnails":{"small":{"url":"https://v5.airtableusercontent.com/v3/u/26/26/1707998400000/Vs5kW9vA4MCjaFcJ17ApBQ/Ap8tMBXonaAvLWhRWR4kc1S_T54LMvhw-Eu7pB_9VimCuXzLzY-uY_8Td3LsKoxX_KQRpAApBJkZUfeGu_HA7jUWZLETwPcqP115Po9LdGyewDqKXJLLlGfgWtBsbTg_mvLYB0NlIqEJhzm1vL3WRQ/4fZKcrLtDBH5dL9fV0iz6UJemgYbSo9MLopHY_OATbw","width":36,"height":36},"large":{"url":"https://v5.airtableusercontent.com/v3/u/26/26/1707998400000/og4uCkCCmIdCRCS6chIn2g/FZpYDj1ckCCh8Xh2IbPad8DS-gz3k5BblUEDDVgJm2eQIpjUROGq8dTu8NnGzYt5O2D3XZQRGrCP2gpatmvrxDSB91IulvwNq9ge1se274U8kB--s-hsEcuiCrwtYzeLSKMwRbI-6b23kZsy6vwXeQ/JNop2edUkOMKZhm3Rr0rdcxkZyGve2yKhiu8taqpRto","width":300,"height":300},"full":{"url":"https://v5.airtableusercontent.com/v3/u/26/26/1707998400000/kcUJppf8nsAieKbosGrFvg/wa19kCg4b4TpPy7P4uvjXjd0A7yjVDFheoAwBSSp-1mH7Zcz1wVInk78Z4jnHsYSu0xY5kR5nkU0Scv26wp86iHKqS0jCC9w8jEEiOyHJc98rwGtjJaevno5GF4tejh68Hy8KJq1JAv3L2oYWhvphQ/sPVB0ygMD4whVth3O2yCCYoWVcGForxXNnRAqaORLq4","width":3000,"height":3000}}}],"Linked Profiles":["recrVq0k7wusEZKZS"],"Position":"Senior lecturer","Title":"Dr","Status":"Published","Last name":"Duong","Slug":"hien-duong","Location":"Sydney, NSW, or Australia","Description":"** **\nI was awarded my PhD in 2011 from the University of New South Wales. \n\n**RESEARCH OPPORTUNITIES**\n** **\n**i) A description of my role**\n\nAfter I finished my PhD in 2011, I commenced my postdoctoral academic career at the Australian Centre for NanoMedicine (established by UNSW in 2011) in the lab of Profs Tom Davis and Cyrille Boyer, both of whom are world experts in polymer science. There I developed several inorganic and organic nanomaterials with different functionalities that can undergo post-modification via highly efficient and orthogonal chemistry. I gained extensive experience in understanding the interface between nanotechnology and biomedical science.\n\nIn November 2014 I joined the Key Centre for Polymers and Colloids in the School of Chemistry at the University of Sydney, in the lab of A/Profs Brian Hawkett and Chiara Neto. This position was funded through an ARC Linkage grant with Dulux Australia. I worked on the development of Janus nanoparticles with multiple functionalities and complex architecture. These nanoparticles potentially have a wide range of uses, ranging from biomedical applications to the paint industry.\n\nIn May 2016 I joined the Institute for Biomedical Materials & Devices in the School of Mathematical and Physical Sciences, Faculty of Science, University of Technology Sydney, as a Senior Research Fellow in the lab of Prof Dayong Jin. At UTS, I worked on multi-functional polymers to functionalise upconversion nanoparticles for use in diagnostic and therapeutic applications. I was part of the ARC Industry Transformation Research Hub for Integrated Devices for End-User Analysis at Low Levels (IDEAL Hub). \n\nIn February 2017 I took up my current position as lecturer in the School of Pharmacy at the University of Sydney. In this role, I have a typical load for a university-based researcher consisting of 40% teaching, 40% research and 20% administration. \n\nMy administration workload includes coordinating two units of study, being a representative of the School of Pharmacy on the University Executive Student Life Committee for one year and being involved in Pharmacy ECR activities. I hold a leadership role in the School including Sydney Pharmacy School Professionalism Committee.\n\nDespite my substantial non-research activities, I have been building a dynamic research environment with a fresh approach to the development of alternative therapies based on nano-enabled products. In recognition of my research leadership at USyd, I was appointed as leader of Antimicrobial Nanotechnologies theme in Safe-by-Design - Sustainable Nanotechnology, Sydney Nano Grand Challenge from 2019 to 2021. Recently, I was awarded Sydney Infectious Diseases Seed Funding (2022, $25,000) and Sydney Nano Kickstarter (2022, $50,000) to work on bacteriophage conjugates. I am one of the investigators who secured Stage 1 MRFF Frontiers funding for Phage Australia (A$1 million, 06/2021-06/2022) which is led by Prof Jonathan Iredell at the Westmead Institute for Medical Research. The application for MRFF Frontiers Stage 2 bid for $50M will be submitted in June 2022.\nI developed strong understanding of the needs of industry partners through collaborations with Dulux Australia (at USYD) and Minomic International Ltd (through the ARC IDEAL Hub at UTS). This also expanded my understanding of the requirements for business success. \n\n**ii) Research mentoring and facilities**\n** **\nAt the University of Sydney, I have benefited from both formal and informal mentoring by senior colleagues. Through the University’s Academic Planning & Development System, I have received excellent support and mentorship from Profs Mary Collins and Paul Groundwater at the School of Pharmacy. I also receive informal mentoring from other senior researchers within the School and throughout the University including Profs Andrew McLachlan (HoS), Wojciech Chrzanowski, Jonathan Iredell and Gregory Whitwell and senior researchers in the Australian Centre for Microscopy & Microanalysis (ACMM), Charles Perkins Centre (CPC) and Bosch Institute. Earlier in my career, I have received excellent mentorships from all my aforementioned postdoc supervisors.\n\nResearch facilities at the School of Pharmacy include a complete suite of state-of-the-art instruments for the characterization of nanomaterials, including vibrational spectroscopy, microscopy and microanalysis, and facilities for molecular characterization such as NMR, GPC, mass spectrometry, thermogravimetric analysis, differential scanning calorimetry. I have immediate access to instruments for the rapid and routine structural and physical characterization of surfaces required in this Discovery Project. \n\n**RESEARCH ACHIEVEMENTS AND CONTRIBUTIONS**\n** **\n**i) Prizes, honours and awards**\n** **\n 2017\n Early Career Development Fellowship, University of Sydney\n 2015\n Monash Engineering Women's Leadership Award\n 2011\n Runner-up prize for the oral presentation at the International Nanomedicine Conference \n 2009\n Postgraduate Research Student Scholarship\n 2007\n Endeavour Postgraduate Award (Australian Government merit-based scholarship) for a PhD Engineering program (2007-2011).\n 2003\n Australian Development Scholarship for a Masters Engineering program (2003-2005) at UNSW.\n\n **ii) Invited speaker addresses**\n\nI was invited to deliver a talk on innovative nanotechnology for biomedical applications at the 2016 Rural Innovation and Research Symposium, Coffs Harbour. I have given a number of invited departmental seminars as at Macquarie University, UNSW, the University of Sydney and the University of Queensland. I am invited as a Keynote Speaker for the 4th International Seminar on Pharmaceutical Science and Technology in Bandung, Indonesia on 27-28/10/2020.\n \n**iii) Research support income **\n_ _\n· _Ultra-high-performance microbalance, XPR2_, University of Sydney, Faculty of Pharmacy/Equipment Grant 2017.\n· _Novel 3-in-1 formulation for prostate cancer treatment_, India Development Fund (Chief Investigator, $20K, 2017-2018).\n· _Inhaled therapy for chronic lung infections using a “triple hits” nano-in-microparticle formulation_, Usyd-Chinese University of Hong Kong Partnership Collaboration Award (Chief Investigator, $20K, 2018-2019).\n· _Safe-by-Design - Sustainable Nanotechnology_, Sydney Nano Grand Challenge, (co-CI, $75K per year, 2019-2021).\n· _Phage Australia: Integrating Australian Phage Biobanking and therapeutic networks and Delivering Solutions for Antimicrobial Resistance_ (co-CI, $1M, 06/2021-06/2022).\n· _Phage-drug conjugate: solution for antimicrobial resistance, _Sydney ID Seed Funding_ _(Chief Investigator, $25K, 2022)._ _\n· _Bacteriophage nanorobots_, Sydney Nano Kickstarter (Chief Investigator, $50K, 2022)._ _\n· _Freeze Dryer with controllable drying shelf temperature and organic solvent compatibility, _2022 Provost’s Equipment_ _(co-CI, $102K, 2022).\n· _PAVONE –transformative, automated high throughput testing platform for nanomedicine, mechanopharmacology, mechanobiology, and precision, _2022 Provost’s Equipment_ _(co-CI, $217K, 2022).\n\n**iv) Commercial outcomes**\n** **\n1\\. Barraud, N, Boyer, C, and **Duong, HTT** “Anti-Biofilm Polymer”, filed 30 May 2014\n2\\. Vittorio, O, Kavallaris, M, Boyer, C, and **Duong, HTT** “Copper-dependent chemotherapeutics”, filed 30 May 2016.\n3\\. **Duong, H. T. T. T**.; Iredell, J. R.; Huang, H. “Phage-drug conjugate”, filed 29 November 2021.\n \n**v) Other professional activities**\n \nAs a sign of my strong national and international standing in my discipline, from 2011 to 2014, I was one of the team leaders of the organizing committee International Nanomedicine Conference which is held annually in Sydney. In February 2016 I was involved in organizing the 30th Australian Colloid and Surface Science Student Conference in Kiola, NSW. I was invited as co-chair in Career Development Symposium session in the eighth International Conference on Nanoscience and Nanotechnology (ICONN 2020) which is the largest biennial Australian conference series in the field of nanoscience. I am invited as a Keynote Speaker for the 4th International Seminar on Pharmaceutical Science and Technology in Bandung, Indonesia on 27-28/10/2020. I am a regular referee for high-impact scientific journals. \n\n**vi) Advancement of knowledge in my field and relevance of my achievements to this proposal**\n** **\nMy research is multidisciplinary, focusing on new concepts and ideas to engineer novel materials and devices at nanoscale. As a polymer chemist I have developed a broad range of expertise in the application of nanotechnology in biotechnology. I have made a significant contribution to the field of nanotechnology for biomedical applications, which is likely to have a high impact on improved therapy of life-threatening diseases including biofilm-related infectious diseases. I have a strong international reputation for research in nanomedicine, as demonstrated by my publication record (45 peer-reviewed publications, three patents, one book chapter and 8 fully refereed conference proceedings). My leadership is evident by the number of publications with me as first and corresponding authors. \n\n\n","Slug::Auto":"hien-duong","recordId":"rec6yfvVsLeKyo5Uo","Profile Image URL":"https://dl.phage.directory/.attachments/13feab50e64b5be22f9a23f1d2b9d89b/a24970fe/profilephotoHien_1.jpg","Editable Form Link":{"label":"Form Edit 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He also holds specialist qualifications in public health (FAFPHM). He is currently Director of Clinical Microbiology and Infectious Diseases at Royal North Shore Hospital (RNSH) and has been since 2016. A/Prof Hudson oversees the clinical infectious diseases service for RNSH as well as the district-wide service for Northern Sydney Local Health District (NSLHD) and the Clinical Microbiology laboratory at RNSH in his capacity as supervising pathologist (microbiology) for that laboratory. His duties include oversight of all microbiology tests performed on site, including molecular biology, serology, bacteriology, mycobacteriology and mycology. He is responsible for the professional development and training of the division’s consultants, interns and registrars. Microbiology and Infectious Diseases have many links with other clinical specialties. It receives invaluable clinical samples that can be a valuable resource for collaborative research. Since 2018, A/Prof Hudson has collaborated with Professor Holmes at Sydney University in the search for novel pathogens in animals and humans.\n**_Most significant peer reviewed publications in the last 5 years: Prof Hudson has represented RNSH-NSLHD and NSW Health Pathology (NSWHP) as an institutional leader and Principal Investigator in multi-disciplinary projects. He has been the main contributor and subject matter expert reviewer of the data published._**\n1\\. Balachandran H., Phetsouphanh C., Agapiou D….**Hudson B., …** Bull RA., on Behalf of the COSIN Study Group. Maintenance of broad neutralizing antibodies and memory B cells 1 year post-infection is predicted by SARS-CoV-2-speciﬁc CD4+ T cell responses. Cell Reports 38, 110345, February 8, 2022\n\n2\\. Abayasingam A., Balachandran H., Agapiou D….**Hudson B**., Bull RA., on Behalf of the COSIN Study Group. Long-term persistence of RBD+ memory B cells encoding neutralizing antibodies in SARS-CoV-2 infection; Cell Reports Medicine (2021), https://doi.org/10.1016/j.xcrm.2021.100228.\n3\\. Shiel E, Miyakis S, Tennant E, Fernando S, Kizny-Gordon A, Koh B, Findlay M, Garnham K, Pilli S, Segboer H, Tallon J, Kao J, Miller A, Shore T, Maher R, Telford M, Barclay K, Harris B, Newcombe J, **Hudson B**, Figtree M. Clinical Characteristics and Outcomes of COVID-19 in a low-prevalence, well-resourced setting _Internal Medicine Journal_. 2021 Jul 06. [Journal Article] [2021/07/06 13:29].\n4\\. Long-term persistence of RBD+ memory B cells encoding neutralizing antibodies in SARS-CoV-2 infection. Abayasingam A, Balachandran H, Agapiou D, Hammoud M, Rodrigo C, Keoshkerian E, Li H, Brasher NA, Christ D, Rouet R, Burnet D, Grubor-Bauk B, Rawlinson W, Turville S, Aggarwal A, Stella AO, Fichter C, Brilot F, Mina M, Post JJ, **Hudson B**, Gilroy N, Dwyer D, Sasson SC, Tea F, Pilli D, Kelleher A, Tedla N, Lloyd AR, Martinello M, Bull RA, COSIN Study Group. _Cell_ _Reports_ _Medicine_. 2(4):100228, 2021 Apr 20. [Journal Article] [2021/03/22 08:31].\n5\\. Beukers AG, Newton P, Hudson B, Ross K, Gottlieb T, O'Sullivan M, Daley DA, Pang S, Coombs GW, van Hal SJ.A multicentre outbreak of ST45 MRSA containing deletions in the spa gene in New South Wales, Australia. _Journal of Antimicrobial Chemotherapy_. 75(5):1112-1116, 2020 05 01. [Journal Article. Multicenter Study] [2020/02/05 06:00].\n6\\. Contamination of the Surgical Field with Propionibacterium acnes in Primary Shoulder Arthroplasty. Falconer TM, Baba M, Kruse LM, Dorrestijn O, Donaldson MJ, Smith MM, Figtree MC, **Hudson** **BJ**, Cass B, Young AA. _Journal of Bone & Joint Surgery_ - American Volume. 98(20):1722-1728, 2016 Oct 19. [Journal Article] [2016/11/22 06:00].\n7\\. Identification of a Novel Equine Papillomavirus in Semen from a Thoroughbred Stallion with a Penile Lesion. Li CX, Chang WS, Mitsakos K, Rodger J, Holmes EC, **Hudson BJ** _Viruses_. 11(8), 2019 08 04. [Journal Article. Research Support, Non-U.S. Gov't] [2019/08/07 06:00] UI: 31382657.\n**_Research Impact and Support: _**In 2020, A/Prof Hudson has established the first ever Infectious Diseases Clinical Research Unit at Royal North Shore Hospital. This Unit has attracted over $1.25 million in funding for investigation of patients with tickborne disease, using cutting edge genomic and biomarker techniques. Since onset of the SARS-2-CoV/COVID-19 pandemic, the RNSH Microbiology laboratory is consistently in the top 4 government laboratories in NSW by volume for SARS-2-CoV PCR tests performed. A/Prof Hudson is the laboratory expert member of NSLHD COVID-19 Executive and RNSH COVID-19 Executive and co-chair of NSLHD COVID-19 Research Committee, the major steering committees for NSLHD and RNSH during the pandemic. \n1\\. F2G Study (2021-Current): A Phase III, adjudicator-blinded, randomised study to evaluate the efficacy and safety of treatment with olorofim versus treatment with AmBisome® followed by standard of care (SOC) in patients with invasive fungal disease (IFD) caused by Aspergillus species Role: Global Clinical Trials Program Manager and NSWLHD-NSWHP North Coordinating Principal Investigator.\n2\\. ARMATA AP-SA02 (2021-Current): Phase 1b/2a, Randomized, Double-Blind, Placebo-Controlled, Multiple Ascending Dose Escalation Study of the Safety, Tolerability, and Efficacy of Intravenous AP-SA02 as an Adjunct to Best Available Antibiotic Therapy Compared to Best Available Antibiotic Therapy Alone for the Treatment of Adults With Bacteremia Due to Staphylococcus aureus Role: Global Clinical Trials Program Manager and NSLHD-NSWHP North Principal Investigator.\n3\\. Oncology Study (2021-Current): Immune response to COVID vaccination in patients with malignancy. Multicentre Clinical Trials NSLHD-NSWHP North Principal Coordinator.\n4\\. COVID & HCW (2021-2021): Impacts of COVID-19 on NSW Health Care Workers. Clinical Trials Principal Coordinator.\n5\\. Prevalence of Asymptomatic SARS-Cov-2 Infection in Elective Surgical Patients in Australia. Multicentre study (2020-2021). Clinical Trials NSWHP North Principal Investigator.\n6\\. COVID-19 & Biomarker study (2021-2022): Identification of new biomarkers for severity, disease progression and response to treatment for COVID-19. Multicentre Clinical Trials NSWHP North Principal Coordinator.\n7\\. Australasian COVID-19 Trial (ASCOT) ADAptive Platform Trial: Multicentre Clinical Trials NSLHD-NSWHP Principal Investigator.\n8\\. COSIN Study (2020-2022) - Snow Medical Research Foundation: A national biobank of highly characterised samples from symptomatic and asymptomatic COVID-19 positive individuals, jointly led by a national consortium of researchers from the University of Melbourne, UNSW and The University of Sydney. NSLHD-NSWHP North Principal Investigator.\n9\\. Clinical and Laboratory Findings in Patients with Tickborne Diseases (2021-2026) - Snow Medical Research Foundation - Vectorborne Disease Clinical Research Centre Royal North Shore Hospital Northern Sydney Local Health District, University of Sydney, Macquarie University.\n10\\. Single target LOW Positive for SARS-CoV-2 diagnosis (LOW-POS) (2020-Current). Principal Investigator.\n11\\. Improving diagnostics for detection of enterovirus outbreaks by collection and PCR of residual enterovirus-positive samples (2019-2026). NSLHD-NSWHP North Principal Investigator.\n12\\. Pathogen Discovery (2020-Ongoing) – SREI: Centre for Pathogen Discovery, Holmes E, Shi M, Eden J, Sintchenko V, Lo N, Barrs V, Beatty J, Hudson B, Rose K, Rockett R, DVC Research/Sydney Research Excellence Initiative 2020.\n13\\. Next Generation Sequencing for Detection of Tickborne Pathogens in Australia (2018-2021) – NHMRC: Using Metagenomics to Determine the Causative Agents of Tick-Borne Disease in Australia, Holmes E, Bunce M, Hudson B, Lo N, Hansen A, National Health and Medical Research Council (NHMRC)/Project Grants.NSLHD-NSWHP North Principal Investigator.\n**_National and International Scientific Recognition:_** A/Prof Hudson is the founding chair of the Travel Health Advisory Group (THAG) a peak body affiliated with the Australian College of Tropical Medicine that promotes safe and healthy travel to the community as well as sponsoring research studies in travel medicine and health. For over 20 years, A/Prof Hudson has lectured annually as a guest professor at the travel medicine block in the Master of Public Health program at James Cook University, Townsville. For over 10 years, he has also been an invited speaker at the Global Health Program at Sydney University and the Master of Infection and Immunology Program at Westmead Hospital/ICPMR. A/Prof Hudson has been a topic editor for Frontiers in Microbiology and has peer reviewed a number of papers for local and international journals.\n\n\n\n\n\n\n\n","Slug::Auto":"bernard-hudson","recordId":"recrcJmtgkRyi5Z6t","Profile Image URL":"https://dl.phage.directory/.attachments/30e7a1446560da976d4c764c01118e9b/b29c5808/BJH3.PNG","Editable Form Link":{"label":"Form Edit 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Profiles":["recrVq0k7wusEZKZS","recx9glxlGq9WHpzy","recZxKYDdk1HqRfCF","recL7d4MMsRrym7NK","rec8gNmZEjySyHPBx"],"Position":"ID clinician","Affiliation":"WSLHD, Sydney Uni","Title":"Dr","Status":"Published","Last name":"Shetty","Slug":"amith-shetty","Twitter":"https://twitter.com/Docshetty","Location":"Sydney NSW Australia","Description":"# Dr Amith Shetty MBBS, FACEM, PhD\nMob: +61402453061 email: amith.shetty@health.nsw.gov.au\n**Goals**\nThe creation of an effective learning healthcare system through collaboration, sound leadership and integration of knowledge streams capable of delivering safe and high-quality better value care with improved patient experiences and outcomes.\n# Employment\n## Current position\n**_ _**\n**_Clinical Director, Patient Experience and System Performance Support division, NSW Ministry of health (Since July 2019 to now)_**\n## Current role and projects\n \nClinical Lead, COVID-19 Care in the community NSW health and Clinical lead, SIA COVID-19 Capacity Collaborative NSW health modelling group, Member Critical Intelligence Unit and Clinical Council for NSW COVID-19 response teams\nChair, COVID-19 care in the home Community of practice NSW Health\nClinical lead, COVID-19 community risk of deterioration live patient tracker\n## Immediate past appointments\n**_ _**\n**Director, **Hospital in the Home service, Western Sydney Local Health District since September 2016-19\n**Clinical Director, **eHealth NSW 2017-19, Electronic Transitions of care project (Medication Safety), Clinical analytics and Shared learning programs, Real-time risk trigger monitoring program \n**Staff Specialist**, Westmead Hospital Emergency department, Western Sydney Local health district since February 2012\n \n**Honorary Research Fellow**, NHMRC centre for research excellence in critical infection, Westmead Institute for Medical Research (WIMR) since June 2014\n \n**Director**, Westmead Emergency Medical Research unit, Westmead Hospital, Emergency department since January 2014\n \n**Clinical Senior Lecturer**, Sydney Medical School, University of Sydney, Westmead Campus since February 2012\n## Key Achievements (last 5 years)\n### · NSW Ministry of Health\no Clinical director for division comprising of System performance support, System purchasing, performance management and system information and analytics\no Clinical guidance and leadership on key interventions/ programs/ models of care at NSW health\n### · eHealth NSW\no Clinically led the proof of concept of the first electronic medications interoperability project to aid transitions of care and information sharing between disparate ward and ICU clinical information systems\no Clinically leading the first of it’s kind Internet of Things (IoT) project for device integration in NSW with eHealth NSW, NSW pathology and WSLHD\no Clinically leading and implemented the first of its kind algorithm-based risk-harm prediction and reporting system pilot in NSW hospitals\n### · NSW health\no Currently coordinating and designing system level changes needed to deliver on the recent NSW Premier’s priorities for health\no Developing and co-designing novel models of care for care of acute non- emergent patients in NSW hospitals in current role\no State-wide emergency medicine clinical lead for the Sepsis Kills program including designing and implementing a clinical alert system for identifying and predicting sepsis earlier, review member and lead for several root-cause analyses teams, systems review post-safety incidents across NSW.\no State-wide NSW Emergency care institute Research unit medical chair and member of national emergency research committee\n### · WSLHD\no Designed, developed and implemented the direct admission at home model of care for hospital in the home services in Western Sydney\no Designed and implemented Westmead hospital emergency department novel models of care\no Currently leading research initiatives and funding grants in WSLHD themed on use of information technology in healthcare\n# Education\n### Fellow of Australasian College for Emergency Medicine (FACEM) (2012). AHPRA Medical practitioner with general and specialist registration\n### Bachelor of Medicine, Bachelor of Surgery (MBBS) University of Mumbai (1998)\n### \n### International program for Physician Leadership development at Institute for Healthcare Improvement (IHI, Boston) and Harvard School for Public Health, May 2016.\n### Doctor of Philosophy (PhD) University of Sydney (2020) Sepsis screening pathways in Emergency departments.\n### Certificate in Managing Health Care Delivery from Harvard Business School (2020-2021)\n### Certificates in Leadership strategies in Information Technology in Healthcare (2014), Healthcare Project Management (2012), from Harvard School for Public Health.\n### Certificates in Authentic Leadership from London Business School and Leading Innovation at Harvard Business School (part I/III of certificate in management excellence at HBS).\n \n \n**Research and publications**\n**_Key research themes: Models of care, Point of care testing, work-flows and algorithms, risk stratification and patient outcomes and experience measures_**\n**_Publications: top cited _**\n Authors\n Title\n Publication\n Volume\nNumber\nPages\nYear\n Citations\n Shetty, Amith; Gunja, Naren; Byth, Karen; Vukasovic, Matthew; \n Senior streaming assessment further evaluation after triage zone: a novel model of care encompassing various emergency department throughput measures\n Emergency Medicine Australasia\n 24\n4\n374-382\n2012\n 36\n Perveen, Shuhana; Unwin, Danielle; Shetty, Amith Loknath; \n Point of care D-dimer testing in the emergency department: a bioequivalence study\n Annals of laboratory medicine\n 33\n1\n34-38\n2013\n 19\n Grewal, Harjeet; Varshney, Kavita; Thomas, Lee C; Kok, Jen; Shetty, Amith; \n Blood pressure cuffs as a vector for transmission of multi‐resistant organisms: Colonisation rates and effects of disinfection\n Emergency Medicine Australasia\n 25\n3\n222-226\n2013\n 9\n Vaghasiya, Milan R; Murphy, Margaret; O’Flynn, Daniel; Shetty, Amith; \n The emergency department prediction of disposition (EPOD) study\n Australasian Emergency Nursing Journal\n 17\n4\n161-166\n2014\n 13\n Denver, Dominique; Shetty, Amith; Unwin, Danielle; \n Falls and implementation of NEXUS in the elderly (The FINE Study)\n The Journal of emergency medicine\n 49\n3\n294-300\n2015\n 17\n Shetty, Amith L; Brown, Tristam; Booth, Tarra; Van, Kim Linh; Dor‐Shiffer, Daphna E; Vaghasiya, Milan R; Eccleston, Cassanne E; Iredell, Jonathan; \n Systemic inflammatory response syndrome‐based severe sepsis screening algorithms in emergency department patients with suspected sepsis\n Emergency Medicine Australasia\n 28\n3\n287-294\n2016\n 8\n Macdonald, Stephen PJ; Williams, Julian M; Shetty, Amith; Bellomo, Rinaldo; Finfer, Simon; Shapiro, Nathan; Keijzers, Gerben; \n Sepsis in the emergency department–Part 1: Definitions and outcomes\n Emergency Medicine Australasia\n 29\n6\n619-625\n2017\n 14\n Shetty, Amith; MacDonald, Stephen PJ; Williams, Julian M; van Bockxmeer, John; de Groot, Bas; Esteve Cuevas, Laura M; Ansems, Annemieke; Green, Malcolm; Thompson, Kelly; Lander, Harvey; \n Lactate≥ 2 mmol/L plus qSOFA improves utility over qSOFA alone in emergency department patients presenting with suspected sepsis\n Emergency Medicine Australasia\n 29\n6\n626-634\n2017\n 16\n Shetty, Amith L; Thompson, Kelly; Byth, Karen; Macaskill, Petra; Green, Malcolm; Fullick, Mary; Lander, Harvey; Iredell, Jonathan; \n Serum lactate cut-offs as a risk stratification tool for in-hospital adverse outcomes in emergency department patients screened for suspected sepsis\n BMJ open\n 8\n1\ne015492\n2018\n 11\n Shetty, Amith; Macdonald, Stephen PJ; Keijzers, Gerben; Williams, Julian M; Tang, Benjamin; De Groot, Bas; Thompson, Kelly; Fraser, John F; Finfer, Simon; Bellomo, Rinaldo; \n Sepsis in the emergency department–Part 2: Investigations and monitoring\n Emergency Medicine Australasia\n 30\n1\n4-Dec\n2018\n 11\n \n** **\n**Publications for Amith Shetty**\n**2019**\nHerwanto, V., Shetty, A., Nalos, M., Chakraborty, M., McLean, A., Eslick, G., Tang, B. (2019). Accuracy of Quick Sequential Organ Failure Assessment Score to Predict Sepsis Mortality in 121 Studies Including 1,716,017 Individuals: A Systematic Review and Meta-Analysis. _Critical Care Explorations_, 1(9), 1-9. [More Information]\nShaw, T., Janssen, A., Crampton, R., O'Leary, F., Hoyle, P., Jones, A., Shetty, A., Gunja, N., Ritchie, A., Spallek, H., Solman, A., Kay, J., Makeham, M., et al (2019). Attitudes of health professionals to using routinely collected clinical data for performance feedback and personalised professional development. _Medical Journal of Australia_, 210(S6), S17-S21. [More Information]\nLi, L., Rathnayake, K., Green, M., Fullick, M., Shetty, A., Walter, S., Braithwaite, J., Lander, H., Westbrook, J. (2019). Improving the Performance of Clinical Decision Support for Early Detection of Sepsis: A Retrospective Observational Cohort Study. _Studies in Health Technology and Informatics_, 264, 679-683. [More Information]\nNguyen, H., Rebbeck, T., Kifley, A., Jagnoor, J., Dinh, M., Shetty, A., Nicholas, M., Cameron, I. (2019). Positive recovery for low-risk injuries screened by the short form-Orebro musculoskeletal pain screening questionnaire following road traffic injury: Evidence from an inception cohort study in New South Wales, Australia. _BMC Musculoskeletal Disorders_, 20(1), 1-10. [More Information]\nCoggins, A., Nottingham, C., Byth, K., Ho, K., Aulia, F., Murphy, M., Shetty, A., Todd, A., Moore, N. (2019). Randomised controlled trial of simulation-based education for mechanical cardiopulmonary resuscitation training. _Emergency Medicine Journal_, 36(5), 266-272. [More Information]\nChow, M., Nikolic, S., Shetty, A., Lai, K. (2019). Structured Interdisciplinary Bedside Rounds in an Australian tertiary hospital emergency department: Patient satisfaction and staff perspectives. _EMA - Emergency Medicine Australasia_, 31(3), 347-354. [More Information]\nNoori, O., Jackson, M., Shetty, A., Medlow, S., Steinbeck, K. (2019). Transition care and the emergency department. _EMA - Emergency Medicine Australasia_, 31(6), 1125-1127. [More Information]\n**2018**\nPavic, K., Pandya, J., Sebak, S., Shetty, A., Manolios, N. (2018). Acute arthritis: predictive factors and current practice in the approach to diagnosis and management across two hospitals in Sydney. _Internal Medicine Journal_, 48(9), 1087-1095. [More Information]\nShetty, A., Sparenberg, S., Adams, K., Selvedran, S., Tang, B., Hanna, K., Iredell, J. (2018). Arterial to end-tidal carbon dioxide tension difference (CO2 gap) as a prognostic marker for adverse outcomes in emergency department patients presenting with suspected sepsis. _EMA - Emergency Medicine Australasia_, 30(6), 794-801. [More Information]\nBrown, T., Shetty, A., Zhao, D., Harvey, N., Yu, T., Murphy, M. (2018). Association between pain control and patient satisfaction outcomes in the emergency department setting. _EMA - Emergency Medicine Australasia_, 30(4), 523-529. [More Information]\nShetty, A., MACDONALD, S., Keijzers, G., Williams, J., Tang, B., De Groot, B., Thompson, K., Fraser, J., Finfer, S., Bellomo, R., Iredell, J. (2018). Review article: Sepsis in the emergency department - Part 2: Investigations and monitoring. _EMA - Emergency Medicine Australasia_, 30(1), 4-12. [More Information]\nWilliams, J., Keijzers, G., MacDonald, S., Shetty, A., Fraser, J. (2018). Review article: Sepsis in the emergency department - Part 3: Treatment. _EMA - Emergency Medicine Australasia_, 30(2), 144-151. [More Information]\nShetty, A., Thompson, K., Byth Wilson, K., Macaskill, P., Green, M., Fullick, M., Lander, H., Iredell, J. (2018). Serum lactate cut-offs as a risk stratification tool for in-hospital adverse outcomes in emergency department patients screened for suspected sepsis. _BMJ Open_, 8(1), 1-8. [More Information]\nWarmerdam, M., Baris, L., Liebergen, M., Ansems, A., Exteve Cuevas, L., Willeboer, M., Rijpsma, D., Shetty, A., De Groot, B. (2018). The association between systolic blood pressure and in-hospital mortality in older emergency department patients who are hospitalised with a suspected infection. _Emergency Medicine Journal_, 35(10), 619-622. [More Information]\n**2017**\nNoori, O., Batra, S., Shetty, A., Steinbeck, K. (2017). Adolescent presentations to an adult hospital emergency department. _EMA - Emergency Medicine Australasia_, 29(5), 539-544. [More Information]\nShetty, A., Teh, C., Vukasovic, M., Joyce, S., Vaghasiya, M., Forero, R. (2017). Impact of emergency department discharge stream short stay unit performance and hospital bed occupancy rates on access and patient flow measures: A single site study. _EMA - Emergency Medicine Australasia_, 29(4), 407-414. [More Information]\nShetty, A., MACDONALD, S., Williams, J., Van Bockxmeer, J., De Groot, B., Exteve Cuevas, L., Ansems, A., Green, M., Thompson, K., Lander, H., et al (2017). Lactate (>=)2 mmol/L plus qSOFA improves utility over qSOFA alone in emergency department patients presenting with suspected sepsis. _EMA - Emergency Medicine Australasia_, 29(6), 626-634. [More Information]\nFullerton, J., Thompson, K., Shetty, A., Iredell, J., Lander, H., Myburgh, J., Finfer, S. (2017). New sepsis definition changes incidence of sepsis in the intensive care unit. _Critical Care and Resuscitation_, 19(1), 9-13.\nFullerton, J., Thompson, K., Shetty, A., Iredell, J., Lander, H., Myburgh, J., Finfer, S. (2017). New sepsis definition changes incidence of sepsis in the intensive care unit. _Critical Care and Resuscitation_, 19(1), 9-13.\nMACDONALD, S., Williams, J., Shetty, A., Bellomo, R., Finfer, S., Shapiro, N., Keijzers, G. (2017). Review article: Sepsis in the emergency department � Part 1: Definitions and outcomes. _EMA - Emergency Medicine Australasia_, 29(6), 619-625. [More Information]\n**2016**\nNoori, O., Shetty, A., Steinbeck, K. (2016). Adolescent presentations to adult hospital emergency departments: systematic review. _Jacobs Journal of Emergency Medicine_, 3(4), 1-7.\nTse, R., Thompson, N., Moscova, M., Sindhusake, D., Shetty, A., Young, N. (2016). Do delays in radiology lead to breaches in the 4-hour rule? _Clinical Radiology_, 71(6), 523-531. [More Information]\nShetty, A., Vaghasiya, M., Boddy, R., Byth Wilson, K., Unwin, D. (2016). Perceived incivility during emergency department phone consultations. _EMA - Emergency Medicine Australasia_, 28(3), 256-261. [More Information]\nShetty, A., Brown, T., Booth, T., Van, K., Dor-Shiffer, D., Vaghasiya, M., Eccleston, C., Iredell, J. (2016). Systemic inflammatory response syndrome-based severe sepsis screening algorithms in emergency department patients with suspected sepsis. _EMA - Emergency Medicine Australasia_, 28(3), 287-294. [More Information]\n**2015**\nYee, K., Shetty, A., Lai, K. (2015). ABG needle study: a randomised control study comparing 23G versus 25G needle success and pain scores. _Emergency Medicine Journal_, 32(5), 343-347. [More Information]\nShetty, A., Shankar Raju, S., Hermiz, A., Vaghasiya, M., Vukasovic, M. (2015). Age and admission times as predictive factors for failure of admissions to discharge-stream short-stay units. _EMA - Emergency Medicine Australasia_, 27(1), 42-46. [More Information]\nDenver, D., Shetty, A., Unwin, D. (2015). Falls and Implementation of NEXUS in the Elderly (The FINE Study). _The Journal of Emergency Medicine_, 49(3), 294-300. [More Information]\n**2014**\nPerveen, S., Unwin, D., Shetty, A., Byth Wilson, K. (2014). Response to the comments on 'point of care D-dimer testing in the emergency department-A bioequivalence study' and erratum to the results. _Annals of Laboratory Medicine_, 34(1), 66-67. [More Information]\nVaghasiya, M., Murphy, M., O'Flynn, D., Shetty, A. (2014). The emergency department prediction of disposition (EPOD) study. _Australasian Emergency Nursing Journal_, 17(4), 161-166. [More Information]\n**2013**\nRafi, M., Shetty, A., Gunja, N. (2013). Accuracy of computed tomography of the kidneys, ureters and bladder interpretation by emergency physicians. _EMA - Emergency Medicine Australasia_, 25(5), 422-426. [More Information]\nGrewal, H., Varshney, K., Thomas, L., Kok, J., Shetty, A. (2013). Blood pressure cuffs as a vector for transmission of multi-resistant organisms: colonisation rates and effects of disinfection. _EMA - Emergency Medicine Australasia_, 25(3), 222-226. [More Information]\nPerveen, S., Unwin, D., Shetty, A. (2013). Point of Care D-Dimer Testing in the Emergency Department: A Bioequivalence Study. _Annals of Laboratory Medicine_, 33(1), 34-38. [More Information]\n**2012**\nShetty, A., Gunja, N., Byth Wilson, K., Vukasovic, M. (2012). Senior Streaming Assessment Further Evaluation after Triage zone: A novel model of care encompassing various emergency department throughput measures. _EMA - Emergency Medicine Australasia_, 24(4), 374-382. [More Information]\n**2010**\nShetty, A., Lai, K., Byth, K. (2010). The CO2 GAP Project-CO2 GAP as a prognostic tool in emergency departments. _EMA - Emergency Medicine Australasia_, 22(6), 524-531. [More Information]\n** **\n** **\n**Current ongoing research projects**\n· **BLISS 2 trial **– Bacterial load in severe sepsis trial – site lead for this multicentre trial\n· **SMEDSA **(Sydney Multicentre Emergency Department Sepsis Archive) – Project lead/ Chief investigator for development and analysis of patients presenting to ED – multicentre trial – multiple studies\n• **Key big data project evaluations in Sepsis**\n• **Algorithms for screening**\n• **Performance of existing algorithms for screening, severity scores**\n• **Evaluations of bundles of sepsis care and interventions – time to antibiotics. IV fluids**\n• **Age-based cut-off of thresholds**\n• **Sex-based sepsis epidemiology**\n• **Cost of Sepsis in NSW**\n· **Manual CPR, Manual CPR with feedback and Mechanical CPR in simulation **– randomised trial\n· **Alcohol Harm in Emergency Department Study **– Research lead for Westmead hospital for multicentre trial (Australia and New Zealand)\n· **ED/ Hospital in the home costing costing study **– Independent Hospital Pricing Authority led ED level patient care costing study\n· **Motor Traffic Authority **– clinical lead for Westmead hospital – sociodemographic factors in chronic head injury outcomes\n· **Domestic violence in Emergency department **– current practice and future policy impacts\n· **Adolescent presentations to co-located adults and paediatrics hospitals **– qualitative analysis of transitional care.\n· **ED ETP correlation to sepsis, hospital outcomes**\n· **ED ETP correlation to hospital occupancy, access block and ESSU performance**\n· **Impact of SAFE-t zone and trauma pathways on radiology test ordering.**\n· **Developing an retrospective data-based algorithm to predict impacts of different staffing patterns on emergency department waiting times**\n","Slug::Auto":"amith-shetty","recordId":"recDfiHs4NDv9xQhw","Profile Image URL":"https://dl.phage.directory/.attachments/89ee16272884255bcac0d4dff01b3456/ed9fdfd6/CD063_email.jpg","Editable Form Link":{"label":"Form Edit 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I had completed my Bachelor of Science (First Class Honours) in Microbiology at the University of Queensland. During my honours, I studied the harmful effects multidrug resistant Escherichia coli strains cause, particularly in urinary tract infections. \nAfter graduation, I had worked as a Medical Laboratory Technologist for three years in tertiary care public hospitals in Singapore (Singapore General Hospital and Sengkang General Hospital) in the Department of Microbiology (Bacteriology division). Having witnessed the detrimental effects and increasing incidences of multidrug resistant bacterial infections throughout my time there, I became passionate to address multidrug resistance bacterial infections in clinical settings, and this spurred me to start a PhD this that is exploring the potential of bacteriophages to treat antibiotic resistant _Pseudomonas aeruginosa_ lung infections in children with cystic fibrosis.\nI was awarded a number of competitive scholarships to facilitate my studies including the UWA and Graduate Women (WA) Research Scholarship, The CFWA Golf Classic Scholarship, Wesfarmers Centre for Vaccines and Infectious Diseases HDR Scholarship and the Geoffrey Kennedy Convocation Postgraduate Research Travel Award. Since starting my PhD I had presented at numerous international (2), national (4) and state (7) conferences.\nIn my project, I have successfully isolated and purified novel phages (>300 phages) from both environmental and wastewater samples collected from the Perth metropolitan area using a pipeline that I developed and implemented for our group. The phages were assessed and ranked against clinical isolates of _P. aeruginosa_ derived from individuals with CF. The top 30 phages with the broadest activity against all isolates were then selected for whole genome sequencing and genomic characterisation. The phages were also phenotypically characterised according to their stability (both temperature and pH), efficacy and morphology. With the collection information, the phages can be assessed for their feasibility for therapeutic use. Additionally, I am investigating the potential of combination treatment of phages with antibiotic(s) or chemical adjuvant(s) against _P. aeruginosa_ in planktonic and biofilm states. By comparing the efficacy of phage therapy against _P. aeruginosa_ infections on different states, I will be able to gain new insights on the ability of my phages to target both acute and chronic infections. \nThis project will also be the first to establish _P. aeruginosa_ biofilms on CF primary airway epithelial cells cultured at air-liquid interface, mimicking chronic infection of _P. aeruginosa_ in the lungs of children with CF. I will be able to assess the effects of phage treatment on host airway and bacterial load reduction. The results generated will contribute to the knowledge on the inflammatory response and new insights to the potential of phage therapy to optimise treatments. \nMy PhD will be the first to compare the efficacy of phage therapy against clinical-derived isolates of _P. aeruginosa_ from children with CF, and to assess any potential harmful effects on primary airway epithelial cells derived from these individuals. This work aims to explore the feasibility of phage therapy and in so doing develop a screening tool for high throughput phage assessment as well as a novel therapeutic pipeline to eradicate this pathogen in those with CF. \n","Slug::Auto":"renee-ng","recordId":"recsi4k40QDzi4BzP","Profile Image URL":"https://dl.phage.directory/.attachments/cc462155acec2dc7e378962400aa48b8/2ce9bc05/RNg.jpg","Editable Form Link":{"label":"Form Edit 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She then moved to Australia to continue her postdoctoral career under the supervision of Prof. Jonathan Iredell. Since 2018, Alex has been working as a lead phage scientist in the world’s first-in-human clinical trial of intravenous GMP-grade phage therapy (Petrovic-Fabijan et al, 2020 Nature Microbiology), where she studied bacteria-phage interaction and host response in critically ill patients receiving phage therapy. Alex has been recently awarded a 3-year (2022-24) fellowship from Office for Health and Medical Research NSW ($390k) that will support her research on bacterial cell and phage biology, with a special focus on interactions between clinically important bacteria such as L-forms and therapeutic phages. Alex is leading a lab side of Mycobacterium phage therapy at Westmead (Iredell Lab), developing diagnostic methods for therapeutic monitoring of phages and pioneering more accurate and reliable approaches for testing antimicrobial agents in vitro. Her research profile and publications are available at [ResearchGate](https://www.researchgate.net/profile/Aleksandra-Petrovic-Fabijan) and [Google Scholar](https://scholar.google.com/citations?user=byYS_7EAAAAJ&hl=en). \nQualifications: Overseas trained Division 1 Nurse, BSc (Honours), MSc and PhD in Phage Biology.\nAlex is an Executive Board Officer of the [International Society of Viruses of Microbes](http://isvm.org/officers.html) (ISVM) and a member of the organising committee for the ISVM’s conference Viruses of Microbes 2024, Cairns. She is also part of the [ESCMID Study Group for Non-traditional Antibacterial Therapy (ESGNTA)](https://www.escmid.org/research_projects/study_groups/study_groups_g_n/non_traditional_antibacterial_therapy/), where she coordinated the [ESCMID/ESGNTA education course](https://www.escmid.org/fileadmin/src/media/PDFs/1Dates_Events/event_flyers/ESGNTA_Course22_web.pdf) on personalised phage therapy in 2022. 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Her primary research focus is the role of mobile genetic elements (incl. phages) in the evolution of clinically relevant pathogens. Dr Venturini has strong multidisciplinary expertise in lab-based experimental microbiology, animal trials, molecular biology, and microbial genomics (bacterial/phage genomics and metagenomics). In her PhD (2012; UOW, NSW DPI) and early Postdoc (2010-2013; UOW, UQ), Dr Venturini started exploring the relationship between antibiotic resistance, virulence and mobile DNA (plasmid; phage) in multidrug resistant pathogenic bacteria. Later, as part of the Iredell team at the Westmead Institute for Medical Research (2013-2021), she was scientific lead in the investigation of the effects of antibiotics on the ecology of the gut microbiome and related transmissible antimicrobial resistance (AMR) in enteric bacteria, and chief investigator on a project for the rational design of phage therapy protocols from phage isolation to preparation of ad hoc phage mixes against multidrug resistant pathogens, linked to phage therapy trials for compassionate use at Westmead Hospital (since 2018). Joining the Sydney School of Veterinary Sciences in 2021, Dr Venturini is expanding her research to animal settings, consolidating her One Health approach to the investigation of AMR mechanisms and reservoirs and of alternative therapeutic solutions. 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Australia?"]]},"created_time":1654757134675,"last_edited_time":1654848300000,"parent_id":"dd9e3b37-58fb-4173-9a95-79bca8949239","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"ff9a0477-1293-498a-aac7-25fbdc1e6856":{"value":{"id":"ff9a0477-1293-498a-aac7-25fbdc1e6856","version":11,"type":"text","properties":{"title":[["Phage Australia",[["b"],["a","https://www.phageaustralia.org/"]]],[" is a national network (#AusPhageNet) of phage researchers, scientists, and clinicians who aim to professionalise phage therapy as the third major intervention for infectious diseases, after vaccines and antibiotics. While Phage Australia is led by Professor Jon Iredell at Westmead Hospital/Westmead Institute for Medical Research, the network is supported by various collaborative phage research teams across Australia."]]},"created_time":1654757134675,"last_edited_time":1654759860000,"parent_id":"dd9e3b37-58fb-4173-9a95-79bca8949239","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"017ae5ea-bc72-4a85-8568-45f84eaa13b7":{"value":{"id":"017ae5ea-bc72-4a85-8568-45f84eaa13b7","version":8,"type":"text","properties":{"title":[["As the network is dispersed across the country, this study was designed to send a purified "],["Pseudomonas",[["i"]]],[" phage (Pae7) around Australia, to gain information about the shipping process and see how shipment may affect the titre of Pae7! This study demonstrates the beginning of our functional phage exchange network, along with a harmonised data collection system, starting with shipments between research labs within Australia."]]},"created_time":1654757134675,"last_edited_time":1654757400000,"parent_id":"dd9e3b37-58fb-4173-9a95-79bca8949239","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"d4438faf-5348-4030-8d36-1df216e60de8":{"value":{"id":"d4438faf-5348-4030-8d36-1df216e60de8","version":16,"type":"sub_header","properties":{"title":[["What do we know about Pseudomonas phage Pae7?"]]},"created_time":1654757134675,"last_edited_time":1654757880000,"parent_id":"dd9e3b37-58fb-4173-9a95-79bca8949239","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"9c94328b-57d6-4f62-b385-7a35c632c760":{"value":{"id":"9c94328b-57d6-4f62-b385-7a35c632c760","version":8,"type":"text","properties":{"title":[["Pae7 is a Pseudomonas phage that was isolated from sewage by researchers at Westmead Institute for Medical Research, Sydney, Australia (Ali Khalid, Matthew Smith, and Aleksandra Petrovic Fabijan). Confirmed through whole-genome sequencing (WGS), Pae7 is lytic, and belongs to the Myoviridae family, within the order ‘Caudovirales’. On its propagation host, PAO1, phage Pae7 produces medium-sized plaques that display a clear centre surrounded by a hazy ‘halo’ (Figure 1)."]]},"created_time":1654757134675,"last_edited_time":1654757400000,"parent_id":"dd9e3b37-58fb-4173-9a95-79bca8949239","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"2f37272c-7edb-4b4c-b203-71a23037a069":{"value":{"id":"2f37272c-7edb-4b4c-b203-71a23037a069","version":14,"type":"image","properties":{"size":[["442.7KB"]],"title":[["Untitled"]],"source":[["https://s3-us-west-2.amazonaws.com/secure.notion-static.com/cd80d0df-ca58-439a-b64e-cddf683fc728/Untitled.png"]],"caption":[["Figure 1. Characteristics and plaque morphology of Pseudomonas phage, Pae7.",[["i"]]]]},"format":{"block_width":1242,"display_source":"https://s3-us-west-2.amazonaws.com/secure.notion-static.com/cd80d0df-ca58-439a-b64e-cddf683fc728/Untitled.png","block_full_width":false,"block_page_width":true,"block_aspect_ratio":0.5249597423510467,"block_preserve_scale":true},"created_time":1654757640000,"last_edited_time":1654777080000,"parent_id":"dd9e3b37-58fb-4173-9a95-79bca8949239","parent_table":"block","alive":true,"file_ids":["cd80d0df-ca58-439a-b64e-cddf683fc728"],"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"481eec61-05e2-4b60-ba3c-9911ec404fa8":{"value":{"id":"481eec61-05e2-4b60-ba3c-9911ec404fa8","version":15,"type":"text","properties":{"title":[["Pae7 was chosen to be sent across the network as it is the first phage to be purified using our new phage purification protocol, carried out by Ali Khalid and the School of Biotechnology & Biomolecular sciences (BABS) team at the University of New South Wales (UNSW). An overview of the purification process can be found on Twitter "],["here",[["b"],["a","https://twitter.com/PhageAustralia/status/1506024687897219072"]]],[". 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did we go about sending Pae7 across the country?"]]},"created_time":1654757134677,"last_edited_time":1654772220000,"parent_id":"dd9e3b37-58fb-4173-9a95-79bca8949239","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"32da9a27-5ae7-4d43-a540-b967bb6abe34":{"value":{"id":"32da9a27-5ae7-4d43-a540-b967bb6abe34","version":8,"type":"bulleted_list","properties":{"title":[["On Monday (25 April 2022) prior to sending out Pae7, the research team at Westmead checked the titre of Pae7 (2.0 x 10^8 PFU/mL)."]]},"created_time":1654757134677,"last_edited_time":1654757400000,"parent_id":"dd9e3b37-58fb-4173-9a95-79bca8949239","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"60db6300-4cea-430d-8c59-40310e9c9dd9":{"value":{"id":"60db6300-4cea-430d-8c59-40310e9c9dd9","version":11,"type":"bulleted_list","properties":{"title":[["On Tuesday (26 April 2022), Pae7 was shipped using the company "],["World Courier",[["b"],["a","https://worldcourier.com/"]]],[" to the participating teams in a 850 mL bio-bottle screw-top container containing;"]]},"content":["8db48c52-175f-443d-bbd8-b5de0463fc37","0582726c-71a8-4bbe-9e5a-8a019ac5a3c2","8aa0c5b4-0a1e-4720-bdd6-f4b2d7d2adb7"],"created_time":1654757134677,"last_edited_time":1654760460000,"parent_id":"dd9e3b37-58fb-4173-9a95-79bca8949239","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"8db48c52-175f-443d-bbd8-b5de0463fc37":{"value":{"id":"8db48c52-175f-443d-bbd8-b5de0463fc37","version":8,"type":"bulleted_list","properties":{"title":[["1 x frozen ice-pack"]]},"created_time":1654757134677,"last_edited_time":1654757400000,"parent_id":"60db6300-4cea-430d-8c59-40310e9c9dd9","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"0582726c-71a8-4bbe-9e5a-8a019ac5a3c2":{"value":{"id":"0582726c-71a8-4bbe-9e5a-8a019ac5a3c2","version":8,"type":"bulleted_list","properties":{"title":[["2 x 1 mL Pae7 in screw-top cryotubes"]]},"created_time":1654757134677,"last_edited_time":1654757400000,"parent_id":"60db6300-4cea-430d-8c59-40310e9c9dd9","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"8aa0c5b4-0a1e-4720-bdd6-f4b2d7d2adb7":{"value":{"id":"8aa0c5b4-0a1e-4720-bdd6-f4b2d7d2adb7","version":8,"type":"bulleted_list","properties":{"title":[["1 x swab containing PAO1 (bacterial host of Pae7)"]]},"created_time":1654757134677,"last_edited_time":1654757400000,"parent_id":"60db6300-4cea-430d-8c59-40310e9c9dd9","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"468d5d6f-1963-4bb9-9dff-0d46e8ba0f04":{"value":{"id":"468d5d6f-1963-4bb9-9dff-0d46e8ba0f04","version":8,"type":"bulleted_list","properties":{"title":[["Upon receiving the shipment, teams were provided with a protocol to titre Pae7 (as depicted in Figure 2 below)."]]},"created_time":1654757134677,"last_edited_time":1654757400000,"parent_id":"dd9e3b37-58fb-4173-9a95-79bca8949239","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"92da24f1-abf5-47f5-b4c0-a83c99d625f9":{"value":{"id":"92da24f1-abf5-47f5-b4c0-a83c99d625f9","version":8,"type":"bulleted_list","properties":{"title":[["Results from each team were documented and shared through photos of the plates to show the titre of Pae7."]]},"created_time":1654757134677,"last_edited_time":1654757400000,"parent_id":"dd9e3b37-58fb-4173-9a95-79bca8949239","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"df56e7e5-d779-4172-bfba-ffa0d2c3bfa5":{"value":{"id":"df56e7e5-d779-4172-bfba-ffa0d2c3bfa5","version":13,"type":"image","properties":{"size":[["414.7KB"]],"title":[["Untitled"]],"source":[["https://s3-us-west-2.amazonaws.com/secure.notion-static.com/fae581b2-3002-4dc6-9cd8-700f1073cb7f/Untitled.png"]],"caption":[["Figure 2. Workflow of receiving and checking the titre of Pae7. 1) Each team received a bio bottle containing an ice pack, two cryotubes with Pae7 (2.0 x 10^8 PFU/mL) and a swab of PA01 (Pae7 host). 2) The teams were directed to grow PAO1 from the swab onto LB agar and incubate the plate overnight at 37c. 3) With the growth of PAO1 on LB, the teams were directed to create a day culture by inoculating 3 pure colonies into 3 mL LB. 4) Once the culture was at the mid-log phase, 300 uL of the culture was added to 5mL molten overlay (containing 1mM CaCl2) and poured onto a solid LB agar plate. 5) Pae7 was diluted down to 10^-8, spotted onto the set overlay plate and incubated at 37c overnight. 6) Following incubation, the plaques were counted and plugged into a calculation to estimate the titre of Pae7.",[["i"]]]]},"format":{"block_width":1200,"display_source":"https://s3-us-west-2.amazonaws.com/secure.notion-static.com/fae581b2-3002-4dc6-9cd8-700f1073cb7f/Untitled.png","block_full_width":false,"block_page_width":true,"block_aspect_ratio":0.4775,"block_preserve_scale":true},"created_time":1654757700000,"last_edited_time":1654777080000,"parent_id":"dd9e3b37-58fb-4173-9a95-79bca8949239","parent_table":"block","alive":true,"file_ids":["fae581b2-3002-4dc6-9cd8-700f1073cb7f"],"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"e176d93f-1825-44bd-86cc-df3030bd802c":{"value":{"id":"e176d93f-1825-44bd-86cc-df3030bd802c","version":17,"type":"sub_header","properties":{"title":[["So, what did we learn from this?"]]},"created_time":1654757134678,"last_edited_time":1654757820000,"parent_id":"dd9e3b37-58fb-4173-9a95-79bca8949239","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"0885f011-186a-476d-b0ab-6986e953e453":{"value":{"id":"0885f011-186a-476d-b0ab-6986e953e453","version":16,"type":"sub_sub_header","properties":{"title":[["Pae7 took 24 hours to reach the furthest location we shipped to"]]},"created_time":1654757134678,"last_edited_time":1654757820000,"parent_id":"dd9e3b37-58fb-4173-9a95-79bca8949239","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"58bcce41-eb07-4f15-9b90-63e61963a1e9":{"value":{"id":"58bcce41-eb07-4f15-9b90-63e61963a1e9","version":8,"type":"bulleted_list","properties":{"title":[["It took "],["~3 hours",[["b"]]],[" to reach collaborators at the "],["University of Sydney, NSW",[["b"]]],[" (~27 km distance), which was the closest destination (Figure 3)"]]},"created_time":1654757134678,"last_edited_time":1654757400000,"parent_id":"dd9e3b37-58fb-4173-9a95-79bca8949239","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"b143ca05-4584-41bb-b22d-1bf6e1fc9735":{"value":{"id":"b143ca05-4584-41bb-b22d-1bf6e1fc9735","version":8,"type":"bulleted_list","properties":{"title":[["It took "],["~24 hours",[["b"]]],[" to reach "],["Monash University, VIC",[["b"]]],[" (~874 km distance), "],["Flinders University, SA",[["b"]]],[" (~1,359 km distance) & "],["Telethon Kids Institute, WA",[["b"]]],[" (~3,921km distance) (Figure 3)."]]},"created_time":1654757134678,"last_edited_time":1654757400000,"parent_id":"dd9e3b37-58fb-4173-9a95-79bca8949239","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"678990c9-1a14-463d-9688-bd2980104525":{"value":{"id":"678990c9-1a14-463d-9688-bd2980104525","version":13,"type":"image","properties":{"size":[["446.9KB"]],"title":[["Untitled"]],"source":[["https://s3-us-west-2.amazonaws.com/secure.notion-static.com/84a9e82b-bd4d-4c81-89a8-870500a96646/Untitled.png"]],"caption":[["Figure 3. Shipment times of Pae7 to Phage Australia network. The red location pin shows the approximate location of Westmead Institute for Medical Research, NSW, where Pae7 was shipped from. The black location pins show the 4 locations that received Pae7; Location 1: The University of Sydney, NSW, Location 2: Monash University, VIC, Location 3: Flinders University, SA, Location 4: Telethon Kids Institute, WA.",[["i"]]]]},"format":{"block_width":900,"display_source":"https://s3-us-west-2.amazonaws.com/secure.notion-static.com/84a9e82b-bd4d-4c81-89a8-870500a96646/Untitled.png","block_full_width":false,"block_page_width":true,"block_aspect_ratio":0.6022222222222222,"block_preserve_scale":true},"created_time":1654757700000,"last_edited_time":1654777080000,"parent_id":"dd9e3b37-58fb-4173-9a95-79bca8949239","parent_table":"block","alive":true,"file_ids":["84a9e82b-bd4d-4c81-89a8-870500a96646"],"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"7d67587e-29e9-4035-88eb-7903dab01b05":{"value":{"id":"7d67587e-29e9-4035-88eb-7903dab01b05","version":8,"type":"text","properties":{"title":[["The time required for various geographical locations to receive Pae7 was an important finding, as it would allow us to better plan phage shipments in the future. It would also be interesting for us to get clues about whether the titre of Pae7 might be influenced by location/time taken for Pae7 to travel (e.g. would a longer shipping time result in a lower titre of Pae7 on arrival). However, it should be noted that there may have been unforeseen temperature fluctuations even at room temperature shipping that were not controlled for here."]]},"created_time":1654757134678,"last_edited_time":1654757400000,"parent_id":"dd9e3b37-58fb-4173-9a95-79bca8949239","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"b52bb3c3-6466-43aa-9347-7d9cab759a45":{"value":{"id":"b52bb3c3-6466-43aa-9347-7d9cab759a45","version":22,"type":"sub_sub_header","properties":{"title":[["The observed titre of Pae7 spanned a ~1-2 log range"]]},"created_time":1654757134678,"last_edited_time":1654757820000,"parent_id":"dd9e3b37-58fb-4173-9a95-79bca8949239","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"194b24b0-6e4a-4afe-8824-2786abdc069d":{"value":{"id":"194b24b0-6e4a-4afe-8824-2786abdc069d","version":8,"type":"bulleted_list","properties":{"title":[["Researchers that received Pae7 were asked to titre the stock on arrival using the methods outlined in Figure 2."]]},"created_time":1654757134678,"last_edited_time":1654757400000,"parent_id":"dd9e3b37-58fb-4173-9a95-79bca8949239","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"40f8eda6-2b1d-48bf-9f06-77543fe1938c":{"value":{"id":"40f8eda6-2b1d-48bf-9f06-77543fe1938c","version":8,"type":"bulleted_list","properties":{"title":[["When Pae7 was shipped from Westmead Institute, the titre was recorded as 2 x 10^8 PFU/mL (Figure 4a)"]]},"created_time":1654757134678,"last_edited_time":1654757400000,"parent_id":"dd9e3b37-58fb-4173-9a95-79bca8949239","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"48b827d9-36dd-49ef-bdcf-6a74159a6dca":{"value":{"id":"48b827d9-36dd-49ef-bdcf-6a74159a6dca","version":8,"type":"bulleted_list","properties":{"title":[["The first location to receive Pae7 was the University of Sydney, NSW (arrived ~3 hrs after shipping), where researchers recorded a titre of 3.8x10^7 PFU/mL (-0.72 log drop). (Figure 4a)"]]},"created_time":1654757134679,"last_edited_time":1654757400000,"parent_id":"dd9e3b37-58fb-4173-9a95-79bca8949239","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"6d4cb942-5aa5-423a-8d76-f80411c3329b":{"value":{"id":"6d4cb942-5aa5-423a-8d76-f80411c3329b","version":8,"type":"bulleted_list","properties":{"title":[["The next three locations to receive Pae7 were Telethon Kids Institute, WA, Flinders University, SA and Monash University, VIC. Pae7 arrived ~24 hrs after shipping and the researchers recorded a titre of 1.85 x 10^7 PFU/mL (-1.03 log drop) (Telethon Kids, WA), 1.0 x 10^6 PFU/mL (-2.30 log drop) (Flinders University, SA) and 1.2 x 10^7 PFU/mL (-1.22 log drop) (Monash University, VIC). (Figure 4a)"]]},"created_time":1654757134679,"last_edited_time":1654757400000,"parent_id":"dd9e3b37-58fb-4173-9a95-79bca8949239","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"44dad04d-11b6-4be8-881f-163479bb7e46":{"value":{"id":"44dad04d-11b6-4be8-881f-163479bb7e46","version":8,"type":"bulleted_list","properties":{"title":[["We saw an average drop of 1.3 log PFU/mL, and max drop of 2.3 logs (Flinders University)."]]},"created_time":1654757134679,"last_edited_time":1654757400000,"parent_id":"dd9e3b37-58fb-4173-9a95-79bca8949239","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"22f3d8cc-2283-47d0-8d71-5d69ccfb3aa0":{"value":{"id":"22f3d8cc-2283-47d0-8d71-5d69ccfb3aa0","version":8,"type":"bulleted_list","properties":{"title":[["The distance and time taken to receive Pae7 don’t appear to correlate with the magnitude of the drop in titre."]]},"created_time":1654757134679,"last_edited_time":1654757400000,"parent_id":"dd9e3b37-58fb-4173-9a95-79bca8949239","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"521d55b1-2a99-4633-bf76-b9645ef5af4a":{"value":{"id":"521d55b1-2a99-4633-bf76-b9645ef5af4a","version":10,"type":"bulleted_list","properties":{"title":[["Even being transported across the same city led to a 0.72-log drop"]]},"created_time":1654757134679,"last_edited_time":1654757700000,"parent_id":"dd9e3b37-58fb-4173-9a95-79bca8949239","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"232aae91-c7b0-4ece-81f3-d1757e5dcfe0":{"value":{"id":"232aae91-c7b0-4ece-81f3-d1757e5dcfe0","version":13,"type":"image","properties":{"size":[["201.6KB"]],"title":[["Untitled"]],"source":[["https://s3-us-west-2.amazonaws.com/secure.notion-static.com/db8a1430-756e-495c-a7dc-d3ed5b12b548/Untitled.png"]],"caption":[["Figure 4. Titre of Pae7 from various teams across Australia. A) The titre of Pae7 was recorded at Westmead Institute, NSW prior to sending. The titre of Pae7 was recorded upon receiving Pae7. B) Image of the plaque-forming count of Pae7 on PAO1 by Renee Ng, Telethon Kids Institute, WA.",[["i"]]]]},"format":{"block_width":1200,"display_source":"https://s3-us-west-2.amazonaws.com/secure.notion-static.com/db8a1430-756e-495c-a7dc-d3ed5b12b548/Untitled.png","block_full_width":false,"block_page_width":true,"block_aspect_ratio":0.465,"block_preserve_scale":true},"created_time":1654757700000,"last_edited_time":1654777080000,"parent_id":"dd9e3b37-58fb-4173-9a95-79bca8949239","parent_table":"block","alive":true,"file_ids":["db8a1430-756e-495c-a7dc-d3ed5b12b548"],"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"c47f0195-9ac4-42da-a7d1-d25c19a16f5b":{"value":{"id":"c47f0195-9ac4-42da-a7d1-d25c19a16f5b","version":11,"type":"sub_sub_header","properties":{"title":[["Salt concentration in media may influence Pae7 titre, plaque formation, and PAO1 pigmentation"]]},"created_time":1654757134679,"last_edited_time":1654757820000,"parent_id":"dd9e3b37-58fb-4173-9a95-79bca8949239","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"e44ca9f1-c7eb-4229-a5b7-838d647b2fb4":{"value":{"id":"e44ca9f1-c7eb-4229-a5b7-838d647b2fb4","version":8,"type":"text","properties":{"title":[["While we noted that distance traveled or time taken to receive Pae7 didn’t seem to affect the titre of Pae7, a PhD student at Telethon Kids Institute, Renee Ng, took a deep dive into what other factors may affect the titre, plaque morphology and growth of PAO1."]]},"created_time":1654757134679,"last_edited_time":1654757400000,"parent_id":"dd9e3b37-58fb-4173-9a95-79bca8949239","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"f3b6a136-99c0-4838-a3ba-763ce15a77db":{"value":{"id":"f3b6a136-99c0-4838-a3ba-763ce15a77db","version":8,"type":"text","properties":{"title":[["Here is what she found:"]]},"created_time":1654757134679,"last_edited_time":1654757400000,"parent_id":"dd9e3b37-58fb-4173-9a95-79bca8949239","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"9cce6432-4ed0-4cae-b985-bae0e5166ea1":{"value":{"id":"9cce6432-4ed0-4cae-b985-bae0e5166ea1","version":8,"type":"bulleted_list","properties":{"title":[["PAO1 grown in LB overlay with different salt concentrations affects pigmentation slightly: it appears that PAO1 has a yellow-green colouring when grown in LB Miller overlay, compared to showing a green-blue colouring when grown in LB Lennox overlay."]]},"created_time":1654757134679,"last_edited_time":1654757400000,"parent_id":"dd9e3b37-58fb-4173-9a95-79bca8949239","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"49349e12-b79c-45df-bf3c-3a0887d8aba0":{"value":{"id":"49349e12-b79c-45df-bf3c-3a0887d8aba0","version":8,"type":"bulleted_list","properties":{"title":[["The two different LB formulations affected Pae7 titre: Renee noted a ~1-log reduction in Pae7 titre when using LB Miller overlay (10g/L NaCl) compared to LB Lennox (5 g/L NaCl)"]]},"created_time":1654757134679,"last_edited_time":1654757400000,"parent_id":"dd9e3b37-58fb-4173-9a95-79bca8949239","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"0f66fbc1-a997-4d3e-a7dc-b4d3eff01561":{"value":{"id":"0f66fbc1-a997-4d3e-a7dc-b4d3eff01561","version":10,"type":"bulleted_list","properties":{"title":[["It is important to note here that LB Miller and LB Lennox contain the same ingredients: Tryptone, Yeast Extract and Sodium Chloride, however, LB Miller has twice the amount of Sodium Chloride as LB Lennox (10 g/L vs 5 g/L)"]]},"created_time":1654757134679,"last_edited_time":1654757700000,"parent_id":"dd9e3b37-58fb-4173-9a95-79bca8949239","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"132a741d-ede9-4252-a0f1-5f5d788fac66":{"value":{"id":"132a741d-ede9-4252-a0f1-5f5d788fac66","version":13,"type":"image","properties":{"size":[["406.2KB"]],"title":[["Untitled"]],"source":[["https://s3-us-west-2.amazonaws.com/secure.notion-static.com/07f5105e-57d2-45ea-a788-2c37f39cc43b/Untitled.png"]],"caption":[["Figure 5. 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What follows is my perspective on getting myself organized so I can help extend Ali and Helene's work to bridge some of our current gaps."]]},"created_time":1658473440000,"last_edited_time":1658474820000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"c7836a80-a793-4347-acd6-50f7ff0cd8c1":{"value":{"id":"c7836a80-a793-4347-acd6-50f7ff0cd8c1","version":16,"type":"sub_sub_header","properties":{"title":[["Patients are waiting on us"]]},"created_time":1657863795047,"last_edited_time":1658473320000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"357dc494-d7e8-4825-9ee6-1d0fd3b5cc0d":{"value":{"id":"357dc494-d7e8-4825-9ee6-1d0fd3b5cc0d","version":9,"type":"text","properties":{"title":[["First, some context on why we need these phages, since of course, that will drive a lot of our decisions. At Phage Australia, we need phage. Not just any phage, but safe preps of phage we can use in patients. Here in Sydney, we’ve got three patients ready to be treated — they are just waiting for their phages."]]},"created_time":1657863795047,"last_edited_time":1658473320000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"485e6d71-7150-43ea-9f40-891e04d5326f":{"value":{"id":"485e6d71-7150-43ea-9f40-891e04d5326f","version":2,"type":"text","properties":{"title":[["The trouble is, we aren’t fully set up to make phages yet. We are still in the pilot phase of this work, and the funding for our own GMP phage-making setup that we can scale has yet to come in. Sure, we could get phages from other people, but the whole point of Phage Australia is to develop this capacity for ourselves."]]},"created_time":1657863795047,"last_edited_time":1657863780000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"9c30a23c-6380-47c0-b3f8-2f910bc83b50":{"value":{"id":"9c30a23c-6380-47c0-b3f8-2f910bc83b50","version":4,"type":"text","properties":{"title":[["While we wait for the grant (fingers crossed!), we need a system that works now so we can respond to cases that come in, and in the process, prepare to scale up and certify our process once we do get the funding."]]},"created_time":1657863795047,"last_edited_time":1658449320000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"c0bd8874-2bc7-4a50-a675-758424d69ef3":{"value":{"id":"c0bd8874-2bc7-4a50-a675-758424d69ef3","version":7,"type":"sub_sub_header","properties":{"title":[["Making phage is simple, right?"]]},"created_time":1657863795047,"last_edited_time":1657864140000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"3d5e8149-c6d6-40d3-99b5-407ef2169708":{"value":{"id":"3d5e8149-c6d6-40d3-99b5-407ef2169708","version":2,"type":"text","properties":{"title":[["I came into this feeling pretty confident I could make this work. There are tons of ways you can make phages. Tons of papers written about it. Lots of people make phages. You just need a flask, right? So I set out to find a phagemaking protocol. My strategy was to pick a few groups I know are making phages regularly, to roughly the standards we need (US FDA, emergency/compassionate use), check out their most recent papers, and do what they do."]]},"created_time":1657863795048,"last_edited_time":1657863780000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"1ced54a6-7ecc-4144-97ba-8b57f4e11bec":{"value":{"id":"1ced54a6-7ecc-4144-97ba-8b57f4e11bec","version":2,"type":"text","properties":{"title":[["Quickly I realized everyone does things slightly differently. Ok, no problem, I thought, I’ll test a few things and whatever works best, and is easiest, that’s what I’ll do. But what does ‘best’ mean? What does ‘easiest’ mean? Which steps can I skip? Which pitfalls do I want to avoid? I descended down a rabbit hole of things that could matter. It seemed like each paper highlighted why their method was better than the others. And I didn’t have the materials to try everything. Or the time. Suddenly, this did not feel like a simple task. I felt like I had a thousand decisions to make. For instance, how much phage to cell ratio do you use? When do you add phage? How long do you let it incubate? Will more aeration be good for the phage or bad? Should I spin down after 5 hours, or wait until the next day?"]]},"created_time":1657863795048,"last_edited_time":1657863780000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"9a3f3bd8-303c-49a7-b6c6-974e80ed87e7":{"value":{"id":"9a3f3bd8-303c-49a7-b6c6-974e80ed87e7","version":2,"type":"text","properties":{"title":[["And that’s just making the phage. Then there’s purifying it. Some use cesium chloride, while others say that’s an old, crude method that brings in dangerous chemicals. And it’s a pain to set up — careful not to disturb the gradient! Others use organic solvents, or ultrafiltration… Cytiva, Sartorius, Akta Flux, ion exchange, polishing, buffer exchange. So many new words to learn, each with specifications and pore sizes and capacities."]]},"created_time":1657863795048,"last_edited_time":1657863780000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"0f25c5d5-7e40-4bf9-9962-2c7da8608f34":{"value":{"id":"0f25c5d5-7e40-4bf9-9962-2c7da8608f34","version":2,"type":"text","properties":{"title":[["Case in point, I quickly went from ‘this is straightforward’ to option paralysis. What I thought was an opportunity (I get to design this from the ground up! No biases! First principles!) started becoming a dizzying array of options, with no place to start."]]},"created_time":1657863795048,"last_edited_time":1657863780000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"7199a361-8f8e-4328-a116-63ede5cd380f":{"value":{"id":"7199a361-8f8e-4328-a116-63ede5cd380f","version":9,"type":"text","created_time":1657863960000,"last_edited_time":1657863960000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"cdb1b9e3-74a2-4086-a9f9-3a2e6c7f1942":{"value":{"id":"cdb1b9e3-74a2-4086-a9f9-3a2e6c7f1942","version":9,"type":"image","properties":{"size":[["170.0KB"]],"title":[["Whiteboard plan 1 for phage propagation.jpg"]],"source":[["https://s3-us-west-2.amazonaws.com/secure.notion-static.com/231648da-0a41-4041-9f87-3da572735710/Whiteboard_plan_1_for_phage_propagation.jpg"]]},"format":{"block_width":3688,"display_source":"https://s3-us-west-2.amazonaws.com/secure.notion-static.com/231648da-0a41-4041-9f87-3da572735710/Whiteboard_plan_1_for_phage_propagation.jpg","block_full_width":false,"block_page_width":true,"block_aspect_ratio":0.40726681127982645,"block_preserve_scale":true},"created_time":1657864002529,"last_edited_time":1657863960000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"file_ids":["231648da-0a41-4041-9f87-3da572735710"],"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"5879bf9e-9d53-432b-b2e2-191a18bf54d0":{"value":{"id":"5879bf9e-9d53-432b-b2e2-191a18bf54d0","version":8,"type":"text","properties":{"title":[["A snapshot of what my brain was trying to keep track of as I thought about how to get a minimally functional phage-making system up and running.",[["i"]]]]},"created_time":1657863795048,"last_edited_time":1658449320000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"cec27fca-a2a7-46a7-bd3e-ee48e3975684":{"value":{"id":"cec27fca-a2a7-46a7-bd3e-ee48e3975684","version":7,"type":"sub_sub_header","properties":{"title":[["Start with the end in mind (figure out what we're optimizing for)"]]},"created_time":1657863795048,"last_edited_time":1657864140000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"9d3db37f-6df1-416d-bfa8-159d2a88b56d":{"value":{"id":"9d3db37f-6df1-416d-bfa8-159d2a88b56d","version":2,"type":"text","properties":{"title":[["To give myself somewhere to start, I took a breath and thought, ok, what are the actual things we need? What are we optimizing for? What are our constraints?"]]},"created_time":1657863795048,"last_edited_time":1657863780000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"2163a8b8-a3af-4ff3-a244-6e6847742967":{"value":{"id":"2163a8b8-a3af-4ff3-a244-6e6847742967","version":4,"type":"text","properties":{"title":[["To address our imminent patient needs, our needs are actually simple. We need enough phages, and we need them to have low endotoxin to be safe. And right now, we have limited time and materials."]]},"created_time":1657863795048,"last_edited_time":1658449320000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"b8271eb6-6468-4643-9ac2-502f60f8ecb3":{"value":{"id":"b8271eb6-6468-4643-9ac2-502f60f8ecb3","version":2,"type":"text","properties":{"title":[["Our needs"]]},"created_time":1657863795048,"last_edited_time":1657863780000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"260a0c47-f81d-4a99-838f-30417b6eee36":{"value":{"id":"260a0c47-f81d-4a99-838f-30417b6eee36","version":2,"type":"bulleted_list","properties":{"title":[["Enough phages"]]},"created_time":1657863795049,"last_edited_time":1657863780000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"f20a9a58-7feb-4539-a46f-ae69cd274240":{"value":{"id":"f20a9a58-7feb-4539-a46f-ae69cd274240","version":2,"type":"bulleted_list","properties":{"title":[["Safe phages"]]},"created_time":1657863795049,"last_edited_time":1657863780000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"0e08225a-c49c-49f4-8d59-f49a01029aed":{"value":{"id":"0e08225a-c49c-49f4-8d59-f49a01029aed","version":2,"type":"text","properties":{"title":[["Our constraints"]]},"created_time":1657863795049,"last_edited_time":1657863780000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"6985c9ff-b6e2-4052-8a9f-bca6df7d1f40":{"value":{"id":"6985c9ff-b6e2-4052-8a9f-bca6df7d1f40","version":4,"type":"bulleted_list","properties":{"title":[["Limited labour time "]]},"created_time":1657863795049,"last_edited_time":1658474880000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"6f063488-6e20-41cb-a85a-f6eb36d99586":{"value":{"id":"6f063488-6e20-41cb-a85a-f6eb36d99586","version":4,"type":"bulleted_list","properties":{"title":[["Limited ability to order new equipment"]]},"created_time":1657863795049,"last_edited_time":1658449320000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"7446a6a3-45e1-49f8-8ca2-48185061b8fb":{"value":{"id":"7446a6a3-45e1-49f8-8ca2-48185061b8fb","version":9,"type":"sub_sub_header","properties":{"title":[["What is enough? "]]},"created_time":1657863795049,"last_edited_time":1658474880000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"7982524e-2a90-45fd-b592-8bfa13ba10a6":{"value":{"id":"7982524e-2a90-45fd-b592-8bfa13ba10a6","version":18,"type":"text","properties":{"title":[["Phage Australia has a "],["protocol for phage therapy called STAMP",[["a","https://www.phageaustralia.org/approach"]]],[" (recently approved and started recruiting/treating patients earlier this year). In it, dosing is standardized: 10^9 PFU per dose. Minimum 28 courses of that. So we need minimum 2.8 x 10^10 phages for each patient. Let's aim for some wiggle room, and try to get 10^12 phages per patient."]]},"created_time":1657863795050,"last_edited_time":1658474880000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"bd85781d-1f79-43cd-a096-06f15e3d2e1d":{"value":{"id":"bd85781d-1f79-43cd-a096-06f15e3d2e1d","version":7,"type":"sub_sub_header","properties":{"title":[["What is safe?"]]},"created_time":1657863795050,"last_edited_time":1657864080000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"01b35598-d02c-41fd-ba89-9e21a7f7ba29":{"value":{"id":"01b35598-d02c-41fd-ba89-9e21a7f7ba29","version":4,"type":"text","properties":{"title":[["We know how low the endotoxin content needs to be (FDA has guidelines, and Australia will likely follow this: you can only put a max of 5 endotoxin units per kg/h into a patient’s vein). So that means we’re successful if we can get below maximum endotoxin concentration (5 EU/kg/h, meaning for a 70-kg patient, we should aim for below 350 EU per phage dose)."]]},"created_time":1657863795050,"last_edited_time":1658449320000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"ab5e77b9-e53c-44a5-aeae-b046a2a7964b":{"value":{"id":"ab5e77b9-e53c-44a5-aeae-b046a2a7964b","version":7,"type":"sub_sub_header","properties":{"title":[["Limited personnel and equipment"]]},"created_time":1657863795050,"last_edited_time":1657864080000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"ddd1181f-d8e8-4c6b-b56e-fa34cc889b5b":{"value":{"id":"ddd1181f-d8e8-4c6b-b56e-fa34cc889b5b","version":4,"type":"text","properties":{"title":[["We only have two postdocs devoting part of their time to this, so phage-making should be doable in about 20 person-hours or less per week. And since we’re in a relatively isolated country in the middle of a global supply chain crisis, trying to stretch the grant dollars we have until the end of the year, let’s try to limit ourselves to things we have in the lab, and avoid ordering anything new."]]},"created_time":1657863795050,"last_edited_time":1658449320000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"725bbec2-219d-4e5a-b781-aadff320a567":{"value":{"id":"725bbec2-219d-4e5a-b781-aadff320a567","version":9,"type":"header","properties":{"title":[["Decision: let's optimize for making enough safe phages easily, using what we already have."]]},"created_time":1657863795050,"last_edited_time":1658449320000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"5a2aa964-c18a-4679-940d-24d1a9bc05d5":{"value":{"id":"5a2aa964-c18a-4679-940d-24d1a9bc05d5","version":9,"type":"sub_sub_header","properties":{"title":[["Identify the core components of the work"]]},"created_time":1657863795050,"last_edited_time":1657864080000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"40e6eb6e-6dc9-44ee-b635-12899c94e03c":{"value":{"id":"40e6eb6e-6dc9-44ee-b635-12899c94e03c","version":4,"type":"text","properties":{"title":[["At its core, we need to make a bunch of phages, and remove the endotoxin. Next let’s break it down further. What does each step entail? How do we know if it’s successful?"]]},"created_time":1657863795050,"last_edited_time":1658449380000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"9f4e656c-597c-479a-8914-66a8d49ed98b":{"value":{"id":"9f4e656c-597c-479a-8914-66a8d49ed98b","version":23,"type":"sub_sub_header","properties":{"title":[["1. Phage production"]]},"created_time":1657863795050,"last_edited_time":1658449380000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"a10dcade-6550-49cc-b195-06862f2143b0":{"value":{"id":"a10dcade-6550-49cc-b195-06862f2143b0","version":5,"type":"bulleted_list","properties":{"title":[["Grow phage and cells together"]]},"created_time":1657863795050,"last_edited_time":1658449380000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"ae1a0caa-4cf4-424b-8c43-563e86e585e0":{"value":{"id":"ae1a0caa-4cf4-424b-8c43-563e86e585e0","version":5,"type":"bulleted_list","properties":{"title":[["Separate out the phage"]]},"created_time":1657863795050,"last_edited_time":1658449380000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"78a69ad6-3a21-4139-a5b6-5ae6885ebd6d":{"value":{"id":"78a69ad6-3a21-4139-a5b6-5ae6885ebd6d","version":14,"type":"bulleted_list","properties":{"title":[["Successful if",[["b"]]],[": we achieve our minimum per-batch phage amount (10^12 PFU) *"]]},"created_time":1657863795050,"last_edited_time":1658452080000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"7046db37-c067-43b9-b752-49f74cd24880":{"value":{"id":"7046db37-c067-43b9-b752-49f74cd24880","version":11,"type":"sub_sub_header","properties":{"title":[["2. Endotoxin removal"]]},"created_time":1657863795050,"last_edited_time":1658449440000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"df8bb026-88ca-4498-9297-017dcbafbb92":{"value":{"id":"df8bb026-88ca-4498-9297-017dcbafbb92","version":2,"type":"bulleted_list","properties":{"title":[["Concentrate the sample"]]},"created_time":1657863795050,"last_edited_time":1657863780000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"925811c9-1e2d-4711-8b66-fd3f61f14770":{"value":{"id":"925811c9-1e2d-4711-8b66-fd3f61f14770","version":2,"type":"bulleted_list","properties":{"title":[["Remove the endotoxin"]]},"created_time":1657863795050,"last_edited_time":1657863780000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"6027a4ab-2c2f-4708-bbf1-70e932dc84b6":{"value":{"id":"6027a4ab-2c2f-4708-bbf1-70e932dc84b6","version":2,"type":"bulleted_list","properties":{"title":[["Get rid of anything dangerous you added to get rid of the endotoxin"]]},"created_time":1657863795051,"last_edited_time":1657863780000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"4b4d4e4e-6724-455b-92a6-e03708bc6527":{"value":{"id":"4b4d4e4e-6724-455b-92a6-e03708bc6527","version":10,"type":"bulleted_list","properties":{"title":[["Successful if",[["b"]]],[": we get below maximum endotoxin concentration (5 EU/kg/h, ie. 350 EU per 10^9 PFU) *"]]},"created_time":1657863795051,"last_edited_time":1658452080000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"bd769361-64a3-4711-9b83-bd6d322dc72c":{"value":{"id":"bd769361-64a3-4711-9b83-bd6d322dc72c","version":5,"type":"text","created_time":1658449500000,"last_edited_time":1658449500000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"ce9b2667-058e-4a10-bb52-3739148145f1":{"value":{"id":"ce9b2667-058e-4a10-bb52-3739148145f1","version":27,"type":"text","properties":{"title":[["* "],["Note: endotoxin removal is more than just endotoxin removal",[["b"]]]]},"created_time":1657863795051,"last_edited_time":1658449500000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"fc82dd38-2c69-402a-ab8d-0a803805ffc0":{"value":{"id":"fc82dd38-2c69-402a-ab8d-0a803805ffc0","version":4,"type":"text","properties":{"title":[["I have identified at least two shadow steps that come before and after the actual removal of endotoxin: concentrating your sample beforehand, and cleaning it after. Most endotoxin removal steps I’ve looked at require a concentrated phage solution before moving to endotoxin removal. For example, CsCl gradients call for adding ~3 mL phages, meaning no matter how much phage you make, you need it to be concentrated into 3 mL if you want to use CsCl. Another option is octanol — for this step, you’re adding octanol approximately 1:1 to your phage. Unless you want to go through litres of octanol, you’ll want to concentrate your phage ahead of time. Then, after endotoxin removal, you need to remove whatever you added to remove the endotoxin that might be toxic (e.g. cesium, octanol)."]]},"created_time":1657863795051,"last_edited_time":1658449500000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"ab2c79c0-3d4e-4887-8e0d-e1e842d509d1":{"value":{"id":"ab2c79c0-3d4e-4887-8e0d-e1e842d509d1","version":13,"type":"sub_sub_header","properties":{"title":[["Look at our options for each step"]]},"created_time":1657863795051,"last_edited_time":1658449500000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"6be15723-1f06-4e98-bb4a-2e2999154fc1":{"value":{"id":"6be15723-1f06-4e98-bb4a-2e2999154fc1","version":4,"type":"text","properties":{"title":[["For each step, there are many ways you can do it. I found it helpful to list the options/considerations for each. I found ideas by reading a few papers from friends in the phage field I know make phages for compassionate use cases, like TAILOR, IPATH, and the Phage on Tap method, developed by one of our own Phage Australia colleagues."]]},"created_time":1657863795051,"last_edited_time":1658449500000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"5ddca530-86fb-4dca-8b52-eac923d9b4a1":{"value":{"id":"5ddca530-86fb-4dca-8b52-eac923d9b4a1","version":7,"type":"sub_sub_header","properties":{"title":[["Decide what to do at each step, and document why"]]},"created_time":1657863795051,"last_edited_time":1657864020000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"f5c6ea8c-90f5-45c1-9d6a-007d73fe7810":{"value":{"id":"f5c6ea8c-90f5-45c1-9d6a-007d73fe7810","version":6,"type":"text","properties":{"title":[["Next: deciding what to do for each step. To illustrate my thought process and how/why I’m making these decisions, I started laying this out in a table, along with what I’ve tried to date. For each step, I picked one approach (the easiest option available)."]]},"created_time":1657863795051,"last_edited_time":1658456280000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"30917b39-faa2-49f1-bd68-e9c066876729":{"value":{"id":"30917b39-faa2-49f1-bd68-e9c066876729","version":67,"type":"collection_view","view_ids":["5217e3d3-3f39-4f57-b972-4f40eff240fa"],"collection_id":"1162b461-ae6f-49a9-9e95-538c15027043","format":{"collection_pointer":{"id":"1162b461-ae6f-49a9-9e95-538c15027043","table":"collection","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"copied_from_pointer":{"id":"ff0b09aa-646d-417c-aea1-daf3ffec3f0b","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"created_time":1658449936349,"last_edited_time":1658454180000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"copied_from":"ff0b09aa-646d-417c-aea1-daf3ffec3f0b","created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader","collection":{"types":[{"id":"5217e3d3-3f39-4f57-b972-4f40eff240fa","version":14,"type":"table","format":{"table_properties":[{"width":117,"visible":true,"property":"title"},{"width":297,"visible":true,"property":";^Ts"},{"width":166,"visible":true,"property":"wbc]"},{"width":318,"visible":true,"property":"mbo?"},{"width":251,"visible":true,"property":"jvAt"},{"width":652,"visible":true,"property":"`WWh"}]},"parent_id":"30917b39-faa2-49f1-bd68-e9c066876729","parent_table":"block","alive":true,"page_sort":["b61f6002-5594-4079-85a8-794da0d2ec23","3e1e2ffe-0705-4f85-b04c-a7bed39e0133","a0c7b6e9-2844-4750-949d-8de896dcbe70","0d4e0773-a52c-455a-b1ca-935d1d9b64ca","6105904d-bd41-4d5c-b116-477df65b90b1","c68e59e7-a528-4d52-9fda-e424997de4b5","a1b1d1a8-0ac2-4798-9b0a-a7649ef328a9","f647a4a9-5214-45ac-a5c0-19fa7f76ff52","0e36935e-7026-4fc3-91e5-f2622d7c5201","247e7793-b9f9-4753-b7ca-1c87320032e3","4dc041df-12a1-4468-9171-f9ecdb0dbc6f","de5ad531-fb9d-4130-ab8e-0c6b6f0e5ffd","ec411fc0-1041-4bd7-b77e-fecb5cec0193"],"space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}]}},"d3f4cdc7-ea59-430f-ab1a-bcb5028a5645":{"value":{"id":"d3f4cdc7-ea59-430f-ab1a-bcb5028a5645","version":7,"type":"sub_sub_header","properties":{"title":[["Minimize optimization creep!"]]},"created_time":1657863795051,"last_edited_time":1657864020000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"f20c2728-4cf7-4aee-ad90-0a55d0da340f":{"value":{"id":"f20c2728-4cf7-4aee-ad90-0a55d0da340f","version":2,"type":"text","properties":{"title":[["Even though I thought I knew what I was optimizing for, I found that my instinct was to get into the lab and start optimizing everything, setting up little parallel experiments here and there 'just to see'. I found that I was constantly trying to optimize for the highest titre, even though that is NOT what I decided to optimize for. It took me a while to realize this was happening, and I still have to catch myself constantly and resist that urge."]]},"created_time":1657863795051,"last_edited_time":1657863780000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"d989a175-780e-4c08-9328-158b9d403f95":{"value":{"id":"d989a175-780e-4c08-9328-158b9d403f95","version":2,"type":"text","properties":{"title":[["I came to realize that while there's a lot we COULD optimize, we shouldn't try to do this. It would make the task at hand take forever, most likely overwhelm us, and ultimately not help us achieve our goals (patients getting enough safe phages fast!). Hence why I found it helpful to get very clear on what I was optimizing for, then look at all my options through that lens. Given I decided we're going for ‘good enough’, (ie. enough phages, safe enough), that means if a step meets that minimum (ie. we look like we're on track to hit at least 10^12 phages at the end), we move on. Of course, if in the future we use a phage that doesn’t propagate well, or purify well, then that would be grounds to start tweaking the steps prior to that point. Otherwise, we’ll move along."]]},"created_time":1657863795051,"last_edited_time":1657863780000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"2124cc26-caaa-4e42-9868-44d5e85c4162":{"value":{"id":"2124cc26-caaa-4e42-9868-44d5e85c4162","version":2,"type":"text","properties":{"title":[["Of note, most of my work so far has been with two phages, Pae7, a Pseudomonas phage, and Ec134B, an E. coli phage. I fully anticipate things to change with different phages. I’m hoping we can at least find a baseline that works pretty well for lots of phages, then tweak from there when we need to (and only then)."]]},"created_time":1657863795051,"last_edited_time":1657863780000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"541a5004-97be-4374-96a1-fc707983e476":{"value":{"id":"541a5004-97be-4374-96a1-fc707983e476","version":4,"type":"text","created_time":1657863840000,"last_edited_time":1657863840000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"b04d67ba-b4a7-4552-aac1-a5b0fbe9ca1e":{"value":{"id":"b04d67ba-b4a7-4552-aac1-a5b0fbe9ca1e","version":8,"type":"sub_header","properties":{"title":[["A few more notes, learnings, questions"]]},"created_time":1657863795051,"last_edited_time":1657863840000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"71ca8892-2278-4182-8f0e-9b44290b3c84":{"value":{"id":"71ca8892-2278-4182-8f0e-9b44290b3c84","version":9,"type":"sub_sub_header","properties":{"title":[["Getting high enough titres"]]},"created_time":1657863795051,"last_edited_time":1657863900000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"d505de50-44eb-4842-a960-424105c66be4":{"value":{"id":"d505de50-44eb-4842-a960-424105c66be4","version":2,"type":"text","properties":{"title":[["For a while I wanted to achieve higher titres so I could skip or reduce the need for a concentration step prior to endotoxin removal (I’d heard it could be an annoying bottleneck). I played with a bunch of temperature, flask, time and media parameters, which didn’t affect production by much (max about half a log). For now I’ve deemed most these kinds of tweaks to the growth step not worth doing."]]},"created_time":1657863795052,"last_edited_time":1657863780000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"d10b8b73-4e78-49a9-bae9-99aad1b2af72":{"value":{"id":"d10b8b73-4e78-49a9-bae9-99aad1b2af72","version":2,"type":"text","properties":{"title":[["For example, leaving cells+phage together for the weekend at 4C before filtering out the cell debris led to 2-4x more phage, which I felt wasn’t enough of a jump to justify the extra time and unknown effects on the phage that that extra step would bring. Going forward I think we should just focus on choosing a good host strain, letting the phages grow to the titres they get to using standard conditions for that strain, and being ok with having a concentration step."]]},"created_time":1657863795052,"last_edited_time":1657863780000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"25a637e4-1aa0-4ca6-89df-5548848f885f":{"value":{"id":"25a637e4-1aa0-4ca6-89df-5548848f885f","version":2,"type":"text","properties":{"title":[["If phages are finicky, switching to solid media is something I think will help a lot to increase titres (we haven’t gone there so far, since others in our group have seen agar cause problems downstream, but I still think this could be a reasonable tradeoff if the phages won’t propagate well in liquid)."]]},"created_time":1657863795052,"last_edited_time":1657863780000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"82935607-74fa-491f-9c3c-0f36559e931f":{"value":{"id":"82935607-74fa-491f-9c3c-0f36559e931f","version":2,"type":"text","properties":{"title":[["The one thing that worked the best to improve titres was changing out the propagation strain (led to about a log increase). Based on this, I think doing a host range panel to make sure we’re using the best strain we have for that phage would be worth the effort."]]},"created_time":1657863795052,"last_edited_time":1657863780000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"816787c7-9722-4dc9-a6db-4aacf838cb1a":{"value":{"id":"816787c7-9722-4dc9-a6db-4aacf838cb1a","version":9,"type":"sub_sub_header","properties":{"title":[["Getting rid of endotoxin"]]},"created_time":1657863795052,"last_edited_time":1657863900000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"5c2f91df-dae2-4be0-9bc7-830b6635cd3f":{"value":{"id":"5c2f91df-dae2-4be0-9bc7-830b6635cd3f","version":23,"type":"text","properties":{"title":[["So far I’m happy with the amount of effort that octanol required (other than the dialysis step which I’d like to replace, since it was fairly laborious and used litres of ethanol). It will be interesting to see if it’s sufficient to remove endotoxin without removing too much phage. Jonas Van Belleghem and colleagues have done a "],["really nice study contrasting different endotoxin removal methods",[["a","https://www.sciencedirect.com/science/article/abs/pii/S0167701216303414"]]],[", and octanol seems to be a reasonable choice (though it of course depends on the phage). (We have a large amount in the lab right now, and it only took a few mLs to do an extraction, though I’ll need to check how much it is to replace)."]]},"created_time":1657863795052,"last_edited_time":1658449560000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"f2c0b810-ec4b-43d4-9443-61370baf7c39":{"value":{"id":"f2c0b810-ec4b-43d4-9443-61370baf7c39","version":37,"type":"text","properties":{"title":[["Beyond that, I want to try CsCl; first, gradientless (I only recently found out you don’t always have to build a gradient, thanks to Sabrina Green at TAILOR!) (her "],["Youtube video",[["a","https://www.youtube.com/watch?v=-t85C04Ueio&ab_channel=BCMTAILORLabs"]]],[" and "],["protocol",[["a","https://docs.google.com/document/d/1chrbAUFDjwJT2M06RHfI6w3bm7V0u99vk8-mdI8alAg"]]],[" here). The trouble is this method calls for a refractometer to measure density, but we don’t have one. I may try without (I’ve also found "],["this protocol",[["a","https://cpt.tamu.edu/wordpress/wp-content/uploads/2011/12/CsCl-phage-prep-08-17-2011.pdf"]]],[" by the Center for Phage Technology which seems to do this). If that doesn’t work, I’ll do the gradient. Who knows though, we may get our Akta Flux (along with some chromatography columns), before I have the chance or the need to try CsCl."]]},"created_time":1657863795052,"last_edited_time":1658449620000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"ffccdc1e-8c28-49bd-bfbe-ddefad2b6426":{"value":{"id":"ffccdc1e-8c28-49bd-bfbe-ddefad2b6426","version":4,"type":"text","created_time":1657863900000,"last_edited_time":1657863900000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"1c88388a-3425-4abd-b6af-75419ad181f7":{"value":{"id":"1c88388a-3425-4abd-b6af-75419ad181f7","version":9,"type":"sub_sub_header","properties":{"title":[["Concluding thoughts"]]},"created_time":1657863795052,"last_edited_time":1657863900000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"7bac3913-7f14-4371-998b-401c224ad6dd":{"value":{"id":"7bac3913-7f14-4371-998b-401c224ad6dd","version":2,"type":"text","properties":{"title":[["Thanks for reading! I hope you can take away from this that a complex array of options in the lab can be simplified into a path forward. The way I’ve found is helpful is:"]]},"created_time":1657863795052,"last_edited_time":1657863780000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"b7470e80-0157-4faa-aa4b-9ea5b818b0a9":{"value":{"id":"b7470e80-0157-4faa-aa4b-9ea5b818b0a9","version":2,"type":"text","properties":{"title":[["1. Decide what you’re optimizing for (what would success look like?)"]]},"created_time":1657863795052,"last_edited_time":1657863780000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"ecd73fcd-e6ff-4beb-81ce-729e2f5d0757":{"value":{"id":"ecd73fcd-e6ff-4beb-81ce-729e2f5d0757","version":2,"type":"text","properties":{"title":[["2. Break the project into its core components"]]},"created_time":1657863795052,"last_edited_time":1657863780000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"df8a3b9b-05a6-47d1-abb5-a9513c8b8776":{"value":{"id":"df8a3b9b-05a6-47d1-abb5-a9513c8b8776","version":2,"type":"text","properties":{"title":[["3. For each core component, make a list of what your options are"]]},"created_time":1657863795052,"last_edited_time":1657863780000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"6eb4da21-2d40-4728-b524-f13b23252d55":{"value":{"id":"6eb4da21-2d40-4728-b524-f13b23252d55","version":2,"type":"text","properties":{"title":[["4. Filter for materials you have access to"]]},"created_time":1657863795052,"last_edited_time":1657863780000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"8163afb8-250a-4d6f-a2b6-968ea0e9ed95":{"value":{"id":"8163afb8-250a-4d6f-a2b6-968ea0e9ed95","version":2,"type":"text","properties":{"title":[["5. Make a choice of one thing to try first for each step (and document why!)"]]},"created_time":1657863795053,"last_edited_time":1657863780000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"bf09423f-cb69-4289-8aa2-24a8d9c15923":{"value":{"id":"bf09423f-cb69-4289-8aa2-24a8d9c15923","version":4,"type":"text","created_time":1657863900000,"last_edited_time":1657863900000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"329acce8-c42c-44df-a561-f45404ee150d":{"value":{"id":"329acce8-c42c-44df-a561-f45404ee150d","version":2,"type":"text","properties":{"title":[["Ultimately you should have one thing to try for each core component of your process. I decided not to order anything new, then picked what seemed like the easiest thing of the options I had available. I resisted the urge to do everything in parallel and compare based on which gave the highest titre (I was only able to resist this urge once I got clear on what I was optimizing for: hitting a minimum phage titre, the easiest way possible; NOT maximizing phage titre). I found it helped to make a table, then to force myself to list the core function of the step, the options I had available, the decision of what to try first for that step, the outcome, and the next step."]]},"created_time":1657863795053,"last_edited_time":1657863780000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"f743e83e-cc37-44cd-8ad4-21ef9f1dab3e":{"value":{"id":"f743e83e-cc37-44cd-8ad4-21ef9f1dab3e","version":2,"type":"text","properties":{"title":[["What felt before like a dizzying mess now feels like a framework I can build on. As I come across new options, I can look at my table and ask myself, is this new option going to be less laborious or 'better' than what I’m already doing? What evidence do I have for that? Importantly, is it 'better' according to my predefined success metric, or am I starting to optimize additional things I don't need to optimize? (Beware optimization creep!)"]]},"created_time":1657863795053,"last_edited_time":1657863780000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"f6455ab3-96ca-442e-976b-db7af53e87bf":{"value":{"id":"f6455ab3-96ca-442e-976b-db7af53e87bf","version":2,"type":"text","properties":{"title":[["Anyway, I’m happy with this framework for now — I’ll see how it serves me! Would love to hear others’ thoughts, helpful methods you’ve used to manage complexity in the lab and avoid option paralysis, as well as any specifics or magical phage-making tricks I’ve missed here!"]]},"created_time":1657863795053,"last_edited_time":1657863780000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"b0e84574-a58f-41ef-9a2d-89919ef652e0":{"value":{"id":"b0e84574-a58f-41ef-9a2d-89919ef652e0","version":4,"type":"text","created_time":1657863900000,"last_edited_time":1657863900000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"f1afb329-6319-4263-bcb9-e2e63ddb19ec":{"value":{"id":"f1afb329-6319-4263-bcb9-e2e63ddb19ec","version":9,"type":"sub_sub_header","properties":{"title":[["Resources that helped me"]]},"created_time":1657863795053,"last_edited_time":1657863900000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"9e820b12-4331-4430-a7ce-67ad99a96188":{"value":{"id":"9e820b12-4331-4430-a7ce-67ad99a96188","version":25,"type":"bulleted_list","properties":{"title":[["The Barr lab's Phage on Tap method",[["a","https://pubmed.ncbi.nlm.nih.gov/27547567/"]]],[", which was used to make Tom Patterson’s phages"]]},"created_time":1657863795053,"last_edited_time":1658449620000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"03396faf-befa-4464-94f7-956924e1ed6c":{"value":{"id":"03396faf-befa-4464-94f7-956924e1ed6c","version":74,"type":"bulleted_list","properties":{"title":[["A "],["paper by Tiffany Luong et al",[["a","https://pubmed.ncbi.nlm.nih.gov/32709990/"]]],[" at the Roach lab at SDSU, who make phages for IPATH"]]},"created_time":1657863795053,"last_edited_time":1658449680000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"906759aa-6773-4998-8fc6-d08f871ab14a":{"value":{"id":"906759aa-6773-4998-8fc6-d08f871ab14a","version":13,"type":"bulleted_list","properties":{"title":[["A "],["paper by Jonas Van Belleghem",[["a","https://www.sciencedirect.com/science/article/abs/pii/S0167701216303414"]]],[" and colleagues comparing a few endotoxin removal methods side by side"]]},"created_time":1657863795053,"last_edited_time":1658449740000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"5569938c-113b-497d-83cd-b3d728a9bc5b":{"value":{"id":"5569938c-113b-497d-83cd-b3d728a9bc5b","version":21,"type":"bulleted_list","properties":{"title":[["Sabrina Green/TAILOR’s youtube video",[["a","https://www.youtube.com/watch?v=-t85C04Ueio&ab_channel=BCMTAILORLabs"]]],[" showing "],["her protocol",[["a","https://docs.google.com/document/d/1chrbAUFDjwJT2M06RHfI6w3bm7V0u99vk8-mdI8alAg"]]],[" for making phages for Baylor College of Medicine’s phage therapy unit out of Texas"]]},"created_time":1657863795053,"last_edited_time":1658449740000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"e0428bae-6e85-4135-a9fa-e3f0b23a955d":{"value":{"id":"e0428bae-6e85-4135-a9fa-e3f0b23a955d","version":10,"type":"bulleted_list","properties":{"title":[["Center for Phage Technology’s CsCl 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(Especially Rodrigo Ibarra Chávez and Atif Khan who gave great tips!)"]]},"created_time":1657863795054,"last_edited_time":1658449800000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"cdaa4c46-8e0e-4f78-92eb-62e4ff122228":{"value":{"id":"cdaa4c46-8e0e-4f78-92eb-62e4ff122228","version":12,"type":"bulleted_list","properties":{"title":[["Atif Khan's new paper",[["a","https://currentprotocols.onlinelibrary.wiley.com/doi/epdf/10.1002/cpz1.395"]]],[" on increasing phage yield with an extra 4C incubation"]]},"created_time":1657863795054,"last_edited_time":1658449800000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"5a9eb4ca-4713-49ff-a7de-aad5efa2bd4f":{"value":{"id":"5a9eb4ca-4713-49ff-a7de-aad5efa2bd4f","version":16,"type":"text","created_time":1657864020000,"last_edited_time":1657864020000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"2d742373-152f-46e5-b4e3-0706d908e04f":{"value":{"id":"2d742373-152f-46e5-b4e3-0706d908e04f","version":2,"type":"sub_sub_header","properties":{"title":[["Acknowledgments"]]},"created_time":1657863795054,"last_edited_time":1657864020000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"969e409a-53aa-40f5-bac1-a49060fd7eb6":{"value":{"id":"969e409a-53aa-40f5-bac1-a49060fd7eb6","version":2,"type":"bulleted_list","properties":{"title":[["Stephanie Lynch, my co-pilot here in the Iredell lab — we're both closely working on all of this, trying to navigate doing our work as a team rather than as individuals; I could not imagine a better lab co-pilot!"]]},"created_time":1657863795054,"last_edited_time":1657863780000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"82f7dabc-bf89-4406-aada-4eac58f0a21a":{"value":{"id":"82f7dabc-bf89-4406-aada-4eac58f0a21a","version":2,"type":"bulleted_list","properties":{"title":[["Ali Khalid, who’s been working on purification of phage with Phage Australia for the last several months, and has helped me get up to speed on what it can entail. I’ve learned a ton from what he’s done, and he’s helped me get this all straight in my head."]]},"created_time":1657863795054,"last_edited_time":1657863780000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"895fb9ed-61fc-4bed-ac9f-3d081d1d5284":{"value":{"id":"895fb9ed-61fc-4bed-ac9f-3d081d1d5284","version":11,"type":"text","created_time":1657863960000,"last_edited_time":1657863960000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"e3f31cb9-3874-4e51-aa35-96cc75d7c93a":{"value":{"id":"e3f31cb9-3874-4e51-aa35-96cc75d7c93a","version":2,"type":"sub_sub_header","properties":{"title":[["Thanks to you readers for being my virtual labmates!"]]},"created_time":1657863795054,"last_edited_time":1657863960000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"7d2bb8b6-0552-43df-b7be-207d113b76f2":{"value":{"id":"7d2bb8b6-0552-43df-b7be-207d113b76f2","version":2,"type":"text","properties":{"title":[["My dream would be that scientists everywhere would blog about the work they’re doing, the decisions they’re making and why, so we can all learn from each other’s thinking and experience. In my mind there’s no good reason not to. It’s not like one’s blog musings about why they ultracentrifuged at one speed vs. another are going to prevent journals from accepting our papers."]]},"created_time":1657863795054,"last_edited_time":1657863780000,"parent_id":"4b904b6e-8b3d-4453-90ac-bee4c35b1589","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"3d36dd08-264a-479f-8d2e-40611f28c9bc":{"value":{"id":"3d36dd08-264a-479f-8d2e-40611f28c9bc","version":64,"type":"text","properties":{"title":[["If we’re worried about looking stupid, well, I guess that’s the only risk left. I definitely was when we started Capsid & Tail 3.5 years ago. But as I’ve found from putting out the newsletter/blog every week since, and getting told exactly zero times that I’m stupid, I’ve realized it’s probably not that big a risk to say things online, without the shield of peer review and co-authors. You should try it! 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Break the project into its core components"]]},"created_time":1660288314027,"last_edited_time":1660288260000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"d66befff-5397-4650-b8d9-94d8a4db230d":{"value":{"id":"d66befff-5397-4650-b8d9-94d8a4db230d","version":2,"type":"text","properties":{"title":[["3. For each core component, make a list of what my options are"]]},"created_time":1660288314027,"last_edited_time":1660288260000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"d1b03a6b-8c46-4fd9-9f1e-3c3daf807ccb":{"value":{"id":"d1b03a6b-8c46-4fd9-9f1e-3c3daf807ccb","version":2,"type":"text","properties":{"title":[["4. Filter for materials I have access to"]]},"created_time":1660288314027,"last_edited_time":1660288260000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"e98d167d-fc1b-4271-ab43-2fc296545c0e":{"value":{"id":"e98d167d-fc1b-4271-ab43-2fc296545c0e","version":4,"type":"text","properties":{"title":[["5. Make a choice of one thing to try first for each step (and document why!)"]]},"created_time":1660288314027,"last_edited_time":1660623180000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"b8e0a52a-8acc-45e9-887e-94b7cec731a0":{"value":{"id":"b8e0a52a-8acc-45e9-887e-94b7cec731a0","version":4,"type":"text","created_time":1660623180000,"last_edited_time":1660623180000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"4b280a9b-65f6-499d-8478-19650a40f3c0":{"value":{"id":"4b280a9b-65f6-499d-8478-19650a40f3c0","version":8,"type":"sub_sub_header","properties":{"title":[["My success metrics"]]},"created_time":1660288314028,"last_edited_time":1660288380000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"8eeb5f7d-b5b8-4bc8-8977-59adce9765b2":{"value":{"id":"8eeb5f7d-b5b8-4bc8-8977-59adce9765b2","version":2,"type":"bulleted_list","properties":{"title":[["Enough phage (10^12 PFU after all steps)"]]},"created_time":1660288314029,"last_edited_time":1660288260000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"90d188ed-1640-4ca2-99ec-4868001b0766":{"value":{"id":"90d188ed-1640-4ca2-99ec-4868001b0766","version":2,"type":"bulleted_list","properties":{"title":[["Low enough endotoxin (under 350 EU per 10^9 PFU)"]]},"created_time":1660288314030,"last_edited_time":1660288260000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"922c222d-a5da-4ece-8cfa-2f011b7f52f9":{"value":{"id":"922c222d-a5da-4ece-8cfa-2f011b7f52f9","version":5,"type":"text","created_time":1660623180000,"last_edited_time":1660623180000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"ba54d68b-e92e-471f-83e5-2f41a21518e4":{"value":{"id":"ba54d68b-e92e-471f-83e5-2f41a21518e4","version":8,"type":"sub_sub_header","properties":{"title":[["The first set of steps I decided to try"]]},"created_time":1660288314030,"last_edited_time":1660288380000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"4d948e6d-7359-4250-83f8-492ca76b32dc":{"value":{"id":"4d948e6d-7359-4250-83f8-492ca76b32dc","version":2,"type":"text","properties":{"title":[["1. Propagate phages using a single set of growth conditions"]]},"created_time":1660288314030,"last_edited_time":1660288260000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"e1453c14-fe40-41e7-aade-e6dd8d46f5d1":{"value":{"id":"e1453c14-fe40-41e7-aade-e6dd8d46f5d1","version":2,"type":"text","properties":{"title":[["2. Remove bacterial debris using standard centrifugation and filtration"]]},"created_time":1660288314030,"last_edited_time":1660288260000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"17935c25-bbcb-4f88-bd5f-ebb1740c194a":{"value":{"id":"17935c25-bbcb-4f88-bd5f-ebb1740c194a","version":2,"type":"text","properties":{"title":[["3. Concentrate phages using Amicon spin column"]]},"created_time":1660288314030,"last_edited_time":1660288260000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"51bbeab1-87a0-49a5-8dcc-90a5ffb16ad1":{"value":{"id":"51bbeab1-87a0-49a5-8dcc-90a5ffb16ad1","version":2,"type":"text","properties":{"title":[["4. Remove endotoxin using octanol"]]},"created_time":1660288314030,"last_edited_time":1660288260000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"9605c5b6-8296-4648-a33f-c8941fb46be7":{"value":{"id":"9605c5b6-8296-4648-a33f-c8941fb46be7","version":4,"type":"text","properties":{"title":[["5. Remove octanol using 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isolates."]]},"created_time":1660288314031,"last_edited_time":1660288260000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"0adaf009-5032-4b97-9c4d-8a0cbd06081e":{"value":{"id":"0adaf009-5032-4b97-9c4d-8a0cbd06081e","version":5,"type":"text","created_time":1660623120000,"last_edited_time":1660623120000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"1ce59004-f3f0-4b7c-8d57-0360a6f5c39b":{"value":{"id":"1ce59004-f3f0-4b7c-8d57-0360a6f5c39b","version":8,"type":"sub_header","properties":{"title":[["How the process went"]]},"created_time":1660288314031,"last_edited_time":1660288380000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"d208df28-76b1-4ca4-a5c8-4dc87e063ecb":{"value":{"id":"d208df28-76b1-4ca4-a5c8-4dc87e063ecb","version":2,"type":"text","properties":{"title":[["Long story short, the protocol hit my target for low enough endotoxin, and it almost hit my target for enough phage! So we’ll be using this process as our default going forward."]]},"created_time":1660288314032,"last_edited_time":1660288260000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"c88edd8d-67d1-41db-aebf-0ba0a8e39d31":{"value":{"id":"c88edd8d-67d1-41db-aebf-0ba0a8e39d31","version":2,"type":"text","properties":{"title":[["Here’s a run-down of what I did for each step, the titres I got at the different steps, and some commentary on how it felt/anything that was overly laborious:"]]},"created_time":1660288314032,"last_edited_time":1660288260000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"4a096eab-a799-4bd3-bc8c-a9207399cbd3":{"value":{"id":"4a096eab-a799-4bd3-bc8c-a9207399cbd3","version":9,"type":"text","properties":{"title":[["Here’s the slideshow I recently presented to our lab",[["a","https://docs.google.com/presentation/d/1cQfGgCUf4kZ_jNgJeCEnNr2-ruaiQggfxu9MSCjz69Y/edit?usp=sharing"]]],[" to show these results, if anyone is curious."]]},"created_time":1660288314032,"last_edited_time":1660622760000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"0a6babcf-a103-4931-80c2-fee29d6f4028":{"value":{"id":"0a6babcf-a103-4931-80c2-fee29d6f4028","version":4,"type":"text","created_time":1660623120000,"last_edited_time":1660623120000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"2aa178fb-1fe4-4da1-bb12-c021b3d9c887":{"value":{"id":"2aa178fb-1fe4-4da1-bb12-c021b3d9c887","version":8,"type":"sub_sub_header","properties":{"title":[["1. Propagate phage"]]},"created_time":1660288314032,"last_edited_time":1660288380000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"665a2adf-c5b9-4a09-ab7e-7ad8fdd39d94":{"value":{"id":"665a2adf-c5b9-4a09-ab7e-7ad8fdd39d94","version":8,"type":"text","properties":{"title":[["I chose one set of growth conditions to start (150 mL LB + 1mM CaCl2 + 1mM MgCl2, 120 rpm, 30C overnight, inoculated with one 'plaque plug' as done by "],["Luong et al. 2020",[["a","https://pubmed.ncbi.nlm.nih.gov/32709990/"]]],[". It led to about 10^10 phage per mL (x 150 mL = just over 10^12 total PFU!)"]]},"created_time":1660288314032,"last_edited_time":1660622820000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"0438b855-9883-438a-b8dc-e94f2b687671":{"value":{"id":"0438b855-9883-438a-b8dc-e94f2b687671","version":4,"type":"text","created_time":1660288380000,"last_edited_time":1660288380000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"7656702c-5087-4239-be5c-eba882a9d3fc":{"value":{"id":"7656702c-5087-4239-be5c-eba882a9d3fc","version":16,"type":"text","properties":{"title":[["Figure 1",[["a","https://dl.phage.directory/.attachments/e3247cbbb12876834a08e463000a10c6/8e00c9e7/fig1flasks.jpeg"]]]]},"created_time":1660288314032,"last_edited_time":1660622820000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"2de9119a-1dfe-4400-bee5-b1d63b68f580":{"value":{"id":"2de9119a-1dfe-4400-bee5-b1d63b68f580","version":9,"type":"image","properties":{"size":[["228.2KB"]],"title":[["fig 1 flasks.jpeg"]],"source":[["https://s3-us-west-2.amazonaws.com/secure.notion-static.com/8e947bc4-1680-457c-8a78-c2aa163f79a3/fig_1_flasks.jpeg"]]},"format":{"block_width":768,"display_source":"https://s3-us-west-2.amazonaws.com/secure.notion-static.com/8e947bc4-1680-457c-8a78-c2aa163f79a3/fig_1_flasks.jpeg","block_full_width":false,"block_page_width":true,"block_aspect_ratio":1.3333333333333333,"block_preserve_scale":true},"created_time":1660623082929,"last_edited_time":1660623060000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"file_ids":["8e947bc4-1680-457c-8a78-c2aa163f79a3"],"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"7fe49a77-88ac-4040-807b-06cdbb896dd6":{"value":{"id":"7fe49a77-88ac-4040-807b-06cdbb896dd6","version":6,"type":"text","properties":{"title":[["Figure 1. I propagated phage in small (150-mL) liquid cultures in standard glass Erlenmeyers.",[["i"]]]]},"created_time":1660288314032,"last_edited_time":1660622820000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"5217ea57-4e33-426b-a162-1072f27c27a0":{"value":{"id":"5217ea57-4e33-426b-a162-1072f27c27a0","version":4,"type":"text","created_time":1660623120000,"last_edited_time":1660623120000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"c7e5dde4-6ad4-4a92-9a6d-fe61a1ed624a":{"value":{"id":"c7e5dde4-6ad4-4a92-9a6d-fe61a1ed624a","version":8,"type":"sub_sub_header","properties":{"title":[["2. Remove bacterial cells & debris"]]},"created_time":1660288314032,"last_edited_time":1660288440000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"b958152c-a6cf-4b0d-9247-dbfab0d5fa19":{"value":{"id":"b958152c-a6cf-4b0d-9247-dbfab0d5fa19","version":2,"type":"text","properties":{"title":[["This step was easy — nothing special, centrifuged and filtered through 0.22 um filter; worked fine."]]},"created_time":1660288314032,"last_edited_time":1660288260000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"0b790aac-8141-4606-b800-a25a977556db":{"value":{"id":"0b790aac-8141-4606-b800-a25a977556db","version":4,"type":"text","created_time":1660623120000,"last_edited_time":1660623120000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"a52362c2-ccae-4592-95e1-4f68f8990307":{"value":{"id":"a52362c2-ccae-4592-95e1-4f68f8990307","version":8,"type":"sub_sub_header","properties":{"title":[["3. Concentrate the sample"]]},"created_time":1660288314033,"last_edited_time":1660288440000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"fd9822dc-38f4-466a-932d-a7cc6394f7f9":{"value":{"id":"fd9822dc-38f4-466a-932d-a7cc6394f7f9","version":2,"type":"text","properties":{"title":[["I used Amicon spin column (50 kDa) — it worked great! Minimal phage losses. Took hours of 5 min spins though — definitely open to a less laborious method."]]},"created_time":1660288314033,"last_edited_time":1660288260000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"63d5d2f2-c9b0-4f7a-a32f-d28ee22a219e":{"value":{"id":"63d5d2f2-c9b0-4f7a-a32f-d28ee22a219e","version":8,"type":"text","created_time":1660622820000,"last_edited_time":1660622820000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"d91ff14e-a6db-4a02-867e-2df7806dd851":{"value":{"id":"d91ff14e-a6db-4a02-867e-2df7806dd851","version":16,"type":"text","properties":{"title":[["Figure 2",[["a","https://dl.phage.directory/.attachments/d62e717ffbccce9400da39e95e41cb4d/64eb5cb9/fig2amicon.jpeg"]]]]},"created_time":1660288314033,"last_edited_time":1660622820000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"44592b5e-067a-4162-bf2b-7d8e59ba6aca":{"value":{"id":"44592b5e-067a-4162-bf2b-7d8e59ba6aca","version":9,"type":"image","properties":{"size":[["148.5KB"]],"title":[["fig 2 amicon.jpeg"]],"source":[["https://s3-us-west-2.amazonaws.com/secure.notion-static.com/14357959-27d5-46a0-83e5-a9c980000a3d/fig_2_amicon.jpeg"]]},"format":{"block_width":768,"display_source":"https://s3-us-west-2.amazonaws.com/secure.notion-static.com/14357959-27d5-46a0-83e5-a9c980000a3d/fig_2_amicon.jpeg","block_full_width":false,"block_page_width":true,"block_aspect_ratio":1.3333333333333333,"block_preserve_scale":true},"created_time":1660623097783,"last_edited_time":1660623060000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"file_ids":["14357959-27d5-46a0-83e5-a9c980000a3d"],"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"f638f845-5d44-4fa7-8f43-6b491a1c65f7":{"value":{"id":"f638f845-5d44-4fa7-8f43-6b491a1c65f7","version":6,"type":"text","properties":{"title":[["Figure 2. The 50 kDa Amicon spin column worked well. Notice the brownish colour — this picture was taken after I put 100 mL of phage lysate (10-15 mL at a time) through the column.",[["i"]]]]},"created_time":1660288314033,"last_edited_time":1660622820000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"e310c11d-0cef-4660-9cdc-54c8eb851add":{"value":{"id":"e310c11d-0cef-4660-9cdc-54c8eb851add","version":4,"type":"text","created_time":1660623120000,"last_edited_time":1660623120000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"3c6e9ff1-442b-4c53-b405-33a7afb131c1":{"value":{"id":"3c6e9ff1-442b-4c53-b405-33a7afb131c1","version":8,"type":"sub_sub_header","properties":{"title":[["4. Remove the endotoxin"]]},"created_time":1660288314033,"last_edited_time":1660288440000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"60d6aaaf-a38e-48cf-9828-6a1582041fe3":{"value":{"id":"60d6aaaf-a38e-48cf-9828-6a1582041fe3","version":2,"type":"text","properties":{"title":[["I used octanol — also went great! Not laborious really. No real issues here."]]},"created_time":1660288314033,"last_edited_time":1660288260000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"61745914-3b1b-41fb-a8a1-427009b4fac9":{"value":{"id":"61745914-3b1b-41fb-a8a1-427009b4fac9","version":17,"type":"text","created_time":1660622880000,"last_edited_time":1660622880000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"11e4bbc6-41ed-4441-847c-50af83098e72":{"value":{"id":"11e4bbc6-41ed-4441-847c-50af83098e72","version":3,"type":"text","properties":{"title":[["Figure 3",[["a","https://dl.phage.directory/.attachments/f0df75d3e06f67d866c7b0bf3c5a1c6a/12276c18/fig3octanol.jpeg"]]]]},"created_time":1660288314033,"last_edited_time":1660622880000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"63e96e30-f2ee-4467-8628-9fb9ecc2b51f":{"value":{"id":"63e96e30-f2ee-4467-8628-9fb9ecc2b51f","version":9,"type":"image","properties":{"size":[["150.1KB"]],"title":[["fig 3 octanol.jpeg"]],"source":[["https://s3-us-west-2.amazonaws.com/secure.notion-static.com/bb5f2d8b-9e55-4cb4-8b70-38302c61c3c7/fig_3_octanol.jpeg"]]},"format":{"block_width":768,"display_source":"https://s3-us-west-2.amazonaws.com/secure.notion-static.com/bb5f2d8b-9e55-4cb4-8b70-38302c61c3c7/fig_3_octanol.jpeg","block_full_width":false,"block_page_width":true,"block_aspect_ratio":1.3333333333333333,"block_preserve_scale":true},"created_time":1660623105222,"last_edited_time":1660623060000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"file_ids":["bb5f2d8b-9e55-4cb4-8b70-38302c61c3c7"],"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"4bc26180-9dfe-4741-aa00-0ac6da269290":{"value":{"id":"4bc26180-9dfe-4741-aa00-0ac6da269290","version":8,"type":"text","properties":{"title":[["Figure 3. After mixing phage with octanol, two layers form: the bottom (aqueous) layer contains the phage. I extracted this by piercing the tube with an 18 gauge needle attached to a syringe.",[["i"]]]]},"created_time":1660288314033,"last_edited_time":1660622880000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"bd9cc2c1-fd88-43e4-8c67-85628fb679b4":{"value":{"id":"bd9cc2c1-fd88-43e4-8c67-85628fb679b4","version":4,"type":"text","created_time":1660623120000,"last_edited_time":1660623120000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"af37b9be-de01-47e5-bd55-aa0ddf338066":{"value":{"id":"af37b9be-de01-47e5-bd55-aa0ddf338066","version":8,"type":"sub_sub_header","properties":{"title":[["5. Remove the octanol"]]},"created_time":1660288314033,"last_edited_time":1660288440000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"e4e5544f-eba8-4877-826e-85e0f10f11bb":{"value":{"id":"e4e5544f-eba8-4877-826e-85e0f10f11bb","version":2,"type":"text","properties":{"title":[["I used dialysis — this was fairly laborious to set up (but would be easier now that I’ve scavenger-hunted around the lab and have all the materials, and have reminded myself of how to set it up). It took several days, and uses several litres of ethanol to do just one prep (I drained our lab’s supply). So I’d love to replace this method."]]},"created_time":1660288314034,"last_edited_time":1660288260000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"0b375d9d-dd3e-4a61-af6c-292f3d4d5770":{"value":{"id":"0b375d9d-dd3e-4a61-af6c-292f3d4d5770","version":11,"type":"text","properties":{"title":[["I’m also not sure if it worked to get rid of the octanol, because we actually don’t have a way to test it. But it’s been "],["published as being used in patients",[["a","https://journals.asm.org/doi/full/10.1128/AAC.00954-17"]]],[", and octanol is considered fairly safe. Especially when diluted out, which we would do with our phage preps (probably about 100x for this one), it seems that we’ll be okay here. Still, we’re actively looking into getting insight from the pharmacopeia (the big list of rules re: what you can use in a medicinal product) and from chemists we know to see what we should reasonably be doing to cover our bases and make sure we’re not introducing an unsafe component into the patients."]]},"created_time":1660288314034,"last_edited_time":1660622880000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"a575ce8c-f010-447c-8ca0-b6a0b47a3a6d":{"value":{"id":"a575ce8c-f010-447c-8ca0-b6a0b47a3a6d","version":4,"type":"text","created_time":1660623060000,"last_edited_time":1660623060000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"595f54f3-6613-4081-bdf2-1febbeffec73":{"value":{"id":"595f54f3-6613-4081-bdf2-1febbeffec73","version":16,"type":"text","properties":{"title":[["Figure 4",[["a","https://dl.phage.directory/.attachments/80a90f1f24371ec6d92b5772efa5c6dd/87b24a74/fig4dialysis.jpeg"]]]]},"created_time":1660288314034,"last_edited_time":1660622880000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"d0503579-5077-45e2-a740-0325c074c017":{"value":{"id":"d0503579-5077-45e2-a740-0325c074c017","version":9,"type":"image","properties":{"size":[["137.2KB"]],"title":[["fig 4 dialysis.jpeg"]],"source":[["https://s3-us-west-2.amazonaws.com/secure.notion-static.com/0072d08f-dc20-4a92-b2ff-75c00385eb85/fig_4_dialysis.jpeg"]]},"format":{"block_width":768,"display_source":"https://s3-us-west-2.amazonaws.com/secure.notion-static.com/0072d08f-dc20-4a92-b2ff-75c00385eb85/fig_4_dialysis.jpeg","block_full_width":false,"block_page_width":true,"block_aspect_ratio":1.3333333333333333,"block_preserve_scale":true},"created_time":1660623113326,"last_edited_time":1660623060000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"file_ids":["0072d08f-dc20-4a92-b2ff-75c00385eb85"],"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"23647da7-30b4-4bd8-b5ee-730edb88cc80":{"value":{"id":"23647da7-30b4-4bd8-b5ee-730edb88cc80","version":8,"type":"text","properties":{"title":[["Figure 4. My dialysis setup. This is a 2-L beaker.",[["i"]]]]},"created_time":1660288314034,"last_edited_time":1660623120000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"51cca8b7-c160-4188-8c34-b36ea797df1e":{"value":{"id":"51cca8b7-c160-4188-8c34-b36ea797df1e","version":4,"type":"text","created_time":1660623120000,"last_edited_time":1660623120000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"8bbb1021-0f06-4d90-9c48-f880771a6b88":{"value":{"id":"8bbb1021-0f06-4d90-9c48-f880771a6b88","version":14,"type":"sub_header","properties":{"title":[["Looking at the end product: how did it measure up?"]]},"created_time":1660288314034,"last_edited_time":1660622880000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"879881f7-2190-44d7-b771-4318ccd1fd04":{"value":{"id":"879881f7-2190-44d7-b771-4318ccd1fd04","version":19,"type":"sub_sub_header","properties":{"title":[["Success metric 1: Enough phages?"]]},"created_time":1660288314034,"last_edited_time":1660622880000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"0f96cc99-4ddc-41f8-b547-bffa3c580e6f":{"value":{"id":"0f96cc99-4ddc-41f8-b547-bffa3c580e6f","version":8,"type":"text","properties":{"title":[["Successful if: we achieve our min per-batch phage amount (10^12 PFU)",[["b"]]]]},"created_time":1660288314034,"last_edited_time":1660622940000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"3612a3a6-9979-4cae-b6e9-06f635ecfec2":{"value":{"id":"3612a3a6-9979-4cae-b6e9-06f635ecfec2","version":2,"type":"text","properties":{"title":[["After the initial propagation (and filtration to remove cell debris), I had a total phage count of about 2 x 10^12 PFU. After concentrating, I still had pretty much the same amount (2.7 x 10^12). After endotoxin removal, I had 1.1 x 10^12 — still meeting my minimum, which was exciting!"]]},"created_time":1660288314034,"last_edited_time":1660288260000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"e73ccbd1-b100-4f1b-86ee-f52a96743cec":{"value":{"id":"e73ccbd1-b100-4f1b-86ee-f52a96743cec","version":2,"type":"text","properties":{"title":[["The final step I did, filtering that last solution through 0.22 um (a step I added in at the end for good measure, to ensure a sterile prep), seems to be where I lost some phage. It went down to 4.5 x 10^11. I will revisit whether this step is necessary, otherwise I may skip it, or else keep it and consider increasing the input of phage at the beginning."]]},"created_time":1660288314034,"last_edited_time":1660288260000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"a41f5e3e-b3fd-46c3-917c-12d955e0f903":{"value":{"id":"a41f5e3e-b3fd-46c3-917c-12d955e0f903","version":2,"type":"text","properties":{"title":[["Still, even with the losses, my final phage amount was good enough for almost 500 doses, which is still plenty, since I gave myself some wiggle room when setting the success parameters for phage amounts."]]},"created_time":1660288314034,"last_edited_time":1660288260000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"e5abada3-39b3-4e49-8bc4-5e8c4a18a6a8":{"value":{"id":"e5abada3-39b3-4e49-8bc4-5e8c4a18a6a8","version":16,"type":"text","properties":{"title":[["Figure 5",[["a","https://dl.phage.directory/.attachments/2569f6973c843de0fd259b2042b2420d/47865f0e/fig5titrationgraph.png"]]]]},"created_time":1660288314034,"last_edited_time":1660622940000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"bf9a9ace-95ee-415b-86be-7e00083b922a":{"value":{"id":"bf9a9ace-95ee-415b-86be-7e00083b922a","version":9,"type":"image","properties":{"size":[["73.1KB"]],"title":[["fig5 titration graph.png"]],"source":[["https://s3-us-west-2.amazonaws.com/secure.notion-static.com/843f453c-dedb-4183-b3a2-e66e94ff6501/fig5_titration_graph.png"]]},"format":{"block_width":1132,"display_source":"https://s3-us-west-2.amazonaws.com/secure.notion-static.com/843f453c-dedb-4183-b3a2-e66e94ff6501/fig5_titration_graph.png","block_full_width":false,"block_page_width":true,"block_aspect_ratio":0.6113074204946997,"block_preserve_scale":true},"created_time":1660623125885,"last_edited_time":1660623120000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"file_ids":["843f453c-dedb-4183-b3a2-e66e94ff6501"],"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"f3914378-5122-4bc7-8f4e-ccbf9f2e1b5d":{"value":{"id":"f3914378-5122-4bc7-8f4e-ccbf9f2e1b5d","version":11,"type":"text","properties":{"title":[["Figure 5. I used a plaque assay to measure titre at several steps during the process, always checking to see that my 10^12 PFU (total) minimum was being hit.",[["i"]]]]},"created_time":1660288314034,"last_edited_time":1660623120000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"2861ed72-e3ac-4f0a-a95c-5465628ee3f7":{"value":{"id":"2861ed72-e3ac-4f0a-a95c-5465628ee3f7","version":9,"type":"text","created_time":1660622940000,"last_edited_time":1660623120000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"c0906b5e-32e2-48bc-b694-e0dd7d891d86":{"value":{"id":"c0906b5e-32e2-48bc-b694-e0dd7d891d86","version":15,"type":"sub_header","properties":{"title":[["Success metric 2: Safe enough?"]]},"created_time":1660288314034,"last_edited_time":1660622940000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"ce49933e-4447-4669-97e9-88b5d3bd9bbe":{"value":{"id":"ce49933e-4447-4669-97e9-88b5d3bd9bbe","version":8,"type":"text","properties":{"title":[["Successful if: we get below max endotoxin conc. (5 EU/kg/h, ie. 350 EU per dose of 10^9 PFU)",[["b"]]]]},"created_time":1660288314035,"last_edited_time":1660622940000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"eb1efaeb-f387-451b-a95d-0bdd38bc004a":{"value":{"id":"eb1efaeb-f387-451b-a95d-0bdd38bc004a","version":2,"type":"text","properties":{"title":[["This was the big question — after all that, was the endotoxin actually reduced enough? Excitingly, after some difficulties getting the endotoxin kits to work with our spectrophotometer, we got our answer (by switching to a kit made by a different manufacturer [Charles River]— thanks to Ali Khalid for making this happen, and doing the test for me even though he’s mid-thesis writing!)."]]},"created_time":1660288314035,"last_edited_time":1660288260000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"256ff49f-8692-410c-b1b9-09ae5ee1bb58":{"value":{"id":"256ff49f-8692-410c-b1b9-09ae5ee1bb58","version":2,"type":"text","properties":{"title":[["The final value was 618 endotoxin units (EU) per mL, which works out to about 1.35 EU per dose of phage, if a dose is 10^9 PFU/mL). So this means we have about 500 doses of phage with low enough endotoxin to use in patients. Yay! And most importantly, it means we have a process that we can use as a starting point for future phage-making. Double yay!!"]]},"created_time":1660288314035,"last_edited_time":1660288260000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"66d0be3f-d037-4c92-9d7c-8888bfedfc49":{"value":{"id":"66d0be3f-d037-4c92-9d7c-8888bfedfc49","version":4,"type":"text","created_time":1660623120000,"last_edited_time":1660623120000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"9d875332-3687-4879-aedb-a277b78f3302":{"value":{"id":"9d875332-3687-4879-aedb-a277b78f3302","version":8,"type":"sub_header","properties":{"title":[["Looking ahead: how might we turn this into a GMP process?"]]},"created_time":1660288314035,"last_edited_time":1660622940000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"08409cc4-e9ff-4b64-b3f2-811ce3f9c1ad":{"value":{"id":"08409cc4-e9ff-4b64-b3f2-811ce3f9c1ad","version":12,"type":"text","properties":{"title":[["Now that we have a basic minimal working phage-making process, I can start the next step, which I am (nerdily) very excited about: creating a system for documenting everything! This is core to our team’s long term reasons for doing this phage-making method development, which is to set up a "],["GMP (Good Manufacturing Practice)",[["a","https://www.who.int/news-room/questions-and-answers/item/medicines-good-manufacturing-processes#:~:text=What%20is%20GMP%3F,through%20testing%20the%20final%20product"]]],[" facility to support Phage Australia."]]},"created_time":1660288314035,"last_edited_time":1660622940000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"95442ef2-8d14-49e3-8814-5489b17404a3":{"value":{"id":"95442ef2-8d14-49e3-8814-5489b17404a3","version":2,"type":"text","properties":{"title":[["What I’ve been learning is that with GMP, it’s not one special set of things you have to do. GMP means knowing what you do (ie. having a process), and showing that you do it (ie. documenting it all). So that means having detailed Standard Operating Procedures (SOPs) for every step (even, I’m told, things like ‘transporting the material to another room’), and detailed data collection that happens at every step to support that it’s all been done properly."]]},"created_time":1660288314035,"last_edited_time":1660288260000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"83e80102-c7af-4549-98ac-1b71c216b730":{"value":{"id":"83e80102-c7af-4549-98ac-1b71c216b730","version":2,"type":"text","properties":{"title":[["Without SOPs, no GMP. But without a protocol that works, there’s no point meticulously writing out the SOPs. Well, now we have a baseline protocol that works, so it’s time to start writing out the protocols, deciding what to document at each step, and starting to hold ourselves to that. (Because the phages we’re making now are for actual patients, after all)."]]},"created_time":1660288314035,"last_edited_time":1660288260000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"4aa861ea-27b3-4d82-bf5e-b5809dc7a9e2":{"value":{"id":"4aa861ea-27b3-4d82-bf5e-b5809dc7a9e2","version":4,"type":"text","created_time":1660623120000,"last_edited_time":1660623120000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"86069eec-5670-481e-aeca-64269bf80f6e":{"value":{"id":"86069eec-5670-481e-aeca-64269bf80f6e","version":9,"type":"sub_header","properties":{"title":[["Building a ‘master phage-making template’"]]},"created_time":1660288314035,"last_edited_time":1660623000000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"494465eb-0eeb-491e-8d15-cec1b55ed49d":{"value":{"id":"494465eb-0eeb-491e-8d15-cec1b55ed49d","version":2,"type":"text","properties":{"title":[["I’m now working on what I’m calling a ‘master phage-making template’ that we can use to bring ourselves closer to the kind of protocol and documentation practices we'll need if we ever want a process that can meet GMP standards."]]},"created_time":1660288314036,"last_edited_time":1660288260000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"ae174314-22fc-4659-9e94-0a380cf0d3f6":{"value":{"id":"ae174314-22fc-4659-9e94-0a380cf0d3f6","version":2,"type":"text","properties":{"title":[["Why? Because we can’t just be scribbling in the margins of printed-off journal methods sections when we’re making therapeutic phage products for humans, somehow ‘hoping’ we find the time to come back and ‘document everything properly’ later. (I’m sure it’s not just me who has the best of intentions, but constantly wonders why ‘later’ never seems to come). I used to think it was my fault for being lazy, now I believe it’s a flaw in the system as designed."]]},"created_time":1660288314036,"last_edited_time":1660288260000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"a4932aa8-dc82-46d6-989f-2bf0c3ee32cb":{"value":{"id":"a4932aa8-dc82-46d6-989f-2bf0c3ee32cb","version":2,"type":"text","properties":{"title":[["We also can’t rely on paper notebooks alone, which disincentivize detail because it’s so laborious to write out what you did (not to mention: isn’t searchable, isn’t compatible with linking to data sources, images, etc)."]]},"created_time":1660288314036,"last_edited_time":1660288260000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"a0cb55bf-ea02-4122-b7bc-2be2712d5237":{"value":{"id":"a0cb55bf-ea02-4122-b7bc-2be2712d5237","version":2,"type":"text","properties":{"title":[["I’m designing my master phage-making template to hit a bunch of key things: what to do (protocols), a place to write observations at each step (a new copy of each needed protocol, freshly generated and connected to each new use of the template), a place to input results as they’re generated, and ‘decision points’ (prompts to cause reflection / decide whether to proceed based on the results)."]]},"created_time":1660288314036,"last_edited_time":1660288260000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"09066bc3-6bd0-48de-bece-b11f1118aa3b":{"value":{"id":"09066bc3-6bd0-48de-bece-b11f1118aa3b","version":2,"type":"text","properties":{"title":[["I'm envisioning a happy medium between Big Scary GMP Standard Operating Procedures and scrawling in the margins of our dog-eared, always slightly damp copies of journal articles. At this point, I feel like I’m writing the ‘undergrad lab manual version’ I wish I had to do all this work, but for the digital age."]]},"created_time":1660288314036,"last_edited_time":1660288260000,"parent_id":"72f90253-a44e-4da9-b92d-9b70c3d4b723","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"11f9c241-25c8-4db1-8524-00e25ea586df":{"value":{"id":"11f9c241-25c8-4db1-8524-00e25ea586df","version":2,"type":"text","properties":{"title":[["It’s shaping up into something I’m really excited about (my past self would be shocked I’d be unironically excited about something that is essentially ‘documentation’). 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At least for the first phage I tried it with)."]]},"created_time":1663903354422,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"575806e4-934e-4562-a8a4-a3a2dd5f80f9":{"value":{"id":"575806e4-934e-4562-a8a4-a3a2dd5f80f9","version":2,"type":"text","properties":{"title":[["Now that we’ve got a default method of making phage and reducing endotoxin that seems to work, it’s time to decide how we’re going to really show that our phage quality is safe enough to use in a patient. But who makes the rules? How do we meet the standards?"]]},"created_time":1663903354422,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"6cb77cb9-7f58-4e3d-a0fc-45bf19b5fbee":{"value":{"id":"6cb77cb9-7f58-4e3d-a0fc-45bf19b5fbee","version":2,"type":"text","properties":{"title":[["Welcome to post #3, where I will share how I’m thinking about phage quality control these days."]]},"created_time":1663903354422,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"d7959c42-e133-4fa9-8b52-2a4fb42b16c3":{"value":{"id":"d7959c42-e133-4fa9-8b52-2a4fb42b16c3","version":4,"type":"text","created_time":1663903354422,"last_edited_time":1663903560000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"22e29333-f2eb-4793-9a00-df6814381cc4":{"value":{"id":"22e29333-f2eb-4793-9a00-df6814381cc4","version":15,"type":"callout","properties":{"title":[["Note:",[["b"]]],[" what follows is an informal window into my personal journey into learning about phage QC, and a bit about how I'm thinking about it as a beginner trying to make sense of a very complicated web of new concepts. It's also only a snapshot of what will be a constantly evolving process. If you're looking for a comprehensive guide to phage therapy QC, here's an excellent resource: "],["Quality and Safety Requirements for Sustainable Phage Therapy Products",[["a","https://pubmed.ncbi.nlm.nih.gov/25585954/"]]],[" (Pirnay et al. in 2015)"]]},"format":{"page_icon":"⚠️","block_color":"blue_background"},"created_time":1663903354423,"last_edited_time":1663903560000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"c2a8d68f-c7c5-412b-a349-45a3695b4320":{"value":{"id":"c2a8d68f-c7c5-412b-a349-45a3695b4320","version":2,"type":"sub_sub_header","properties":{"title":[["What is safe?"]]},"created_time":1663903354423,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"5da78e56-a47c-45b8-a3f9-c5e01a20c65f":{"value":{"id":"5da78e56-a47c-45b8-a3f9-c5e01a20c65f","version":2,"type":"text","properties":{"title":[["At least in Australia, ‘safe’ is not yet defined for phages. Australia’s federal health regulator, the Therapeutic Goods Administration (TGA), doesn’t have an official position on them. Even if they did, it wouldn’t necessarily apply to the stage we’re currently at. We’re not trying to show a drug product is good enough to test in a clinical trial, we’re just trying to address urgent patient need right now. As with the US FDA, the rules are different when you’re at this stage."]]},"created_time":1663903354423,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"b483cfd2-f413-4575-9559-eb4443a00526":{"value":{"id":"b483cfd2-f413-4575-9559-eb4443a00526","version":2,"type":"sub_sub_header","properties":{"title":[["So we can do whatever we want?"]]},"created_time":1663903354423,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"5b2a894e-3f54-446b-8e79-0618745ad330":{"value":{"id":"5b2a894e-3f54-446b-8e79-0618745ad330","version":2,"type":"text","properties":{"title":[["Not really."]]},"created_time":1663903354423,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"63c54628-1b92-4d71-a940-bb6c60461495":{"value":{"id":"63c54628-1b92-4d71-a940-bb6c60461495","version":2,"type":"text","properties":{"title":[["First, the patient’s doctor needs to justify to the TGA that the patient getting phages qualifies under Australia’s version of compassionate use (it’s called "],["Special Access Scheme Category A",[["a","https://www.tga.gov.au/resources/resource/forms/special-access-scheme"]]],["). (This is similar to how the FDA currently makes this call for phage preparations made by IPATH, TAILOR, Yale, etc)."]]},"created_time":1663903354423,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"76e0b6dc-cd52-45ac-a256-f2485fe2b4e3":{"value":{"id":"76e0b6dc-cd52-45ac-a256-f2485fe2b4e3","version":2,"type":"text","properties":{"title":[["Second, even though there is no official guidance on what safe means, we (the people making the phage) still need to justify to our local drug committee and ethics committee that our product is safe."]]},"created_time":1663903354423,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"0ed5487e-8581-4282-8c48-dcfa1022ea8b":{"value":{"id":"0ed5487e-8581-4282-8c48-dcfa1022ea8b","version":2,"type":"sub_sub_header","properties":{"title":[["So our phages need to be ‘safe’, but no one is going to tell us what ‘safe’ means?"]]},"created_time":1663903354423,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"dec46985-57ae-4f92-9b02-88a6b46d17d4":{"value":{"id":"dec46985-57ae-4f92-9b02-88a6b46d17d4","version":2,"type":"text","properties":{"title":[["Essentially yes. It looks like it’s on us to:"]]},"created_time":1663903354423,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"f4718fac-999e-4f1b-9c35-c8219f09066e":{"value":{"id":"f4718fac-999e-4f1b-9c35-c8219f09066e","version":2,"type":"numbered_list","properties":{"title":[["Decide (and justify) what to test"]]},"created_time":1663903354424,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"f085593b-ca0c-4f1d-bb2e-59063feaf630":{"value":{"id":"f085593b-ca0c-4f1d-bb2e-59063feaf630","version":2,"type":"numbered_list","properties":{"title":[["Figure out how to do the tests"]]},"created_time":1663903354424,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"dc009ed4-cf80-4f2a-87bb-6f2e4d798aa2":{"value":{"id":"dc009ed4-cf80-4f2a-87bb-6f2e4d798aa2","version":2,"type":"numbered_list","properties":{"title":[["Do the tests"]]},"created_time":1663903354424,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"9aa73adb-9e2a-4514-8c28-721a3db678b8":{"value":{"id":"9aa73adb-9e2a-4514-8c28-721a3db678b8","version":2,"type":"numbered_list","properties":{"title":[["Show the results of the tests"]]},"created_time":1663903354425,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"7c09d76d-1ffa-43cd-9825-ff3496ab8097":{"value":{"id":"7c09d76d-1ffa-43cd-9825-ff3496ab8097","version":2,"type":"numbered_list","properties":{"title":[["Show that the tests were done properly"]]},"created_time":1663903354425,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"880745c9-317f-4f13-92cb-db291d3a1e23":{"value":{"id":"880745c9-317f-4f13-92cb-db291d3a1e23","version":2,"type":"sub_sub_header","properties":{"title":[["Can’t we just outsource this?"]]},"created_time":1663903354425,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"3dc662d1-38e9-4fd7-9e18-6a606a345266":{"value":{"id":"3dc662d1-38e9-4fd7-9e18-6a606a345266","version":2,"type":"text","properties":{"title":[["Conveniently, there are companies that you can pay to test the quality of your pharmaceutical products (like Charles River or Eurofins). They presumably have all the right accreditations and know what they’re doing. And of course if we’re the phage makers, anything we do internally is going to be less credible than sending our phage to a third party to give us a clean bill of health for our phage. So outsourcing seems logical."]]},"created_time":1663903354425,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"1d2bd12a-d17f-407c-8dc2-eab1746f9e2a":{"value":{"id":"1d2bd12a-d17f-407c-8dc2-eab1746f9e2a","version":2,"type":"text","properties":{"title":[["Over the last few months, we did reach out to a couple of companies and had some conversations. But what I learned from this experience was — surprise — WE have to be the ones to tell these companies what to test. And we have to know things like ‘what is the volume of final product you’ll have?’, ‘how many aliquots of that will you make?’, ‘is it always going to be made that way?’, and ‘what standards do you want to comply with?’. And every time you give them a new product (ie. a new phage), there is a new ‘validation’ process that needs to be done, which takes extra time and money (understandably, but still). We don’t really have these kinds of answers yet, as we’re anticipating a lot of tweaking with each new phage, having to go up in volume for phages that don’t propagate well, etc."]]},"created_time":1663903354425,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"7a5513f9-60ad-4c68-9205-f3157c94e720":{"value":{"id":"7a5513f9-60ad-4c68-9205-f3157c94e720","version":2,"type":"text","properties":{"title":[["So it doesn’t seem like we’re ready for outsourcing."]]},"created_time":1663903354425,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"f1a78d77-ce71-4ab2-b406-bed9ef11347d":{"value":{"id":"f1a78d77-ce71-4ab2-b406-bed9ef11347d","version":2,"type":"text","properties":{"title":[["Cool… so we’re back to square one? It does seem that way. Once we have a more defined process, we can definitely outsource, but it doesn’t make sense for us right now. For now, let’s get started tackling this on our own, and getting at least a minimal, default phage QC (quality control) pipeline set up."]]},"created_time":1663903354425,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"e73a41a5-e9dd-4080-bb0b-04a7cd476bb3":{"value":{"id":"e73a41a5-e9dd-4080-bb0b-04a7cd476bb3","version":2,"type":"sub_sub_header","properties":{"title":[["What I'll cover today"]]},"created_time":1663903354425,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"4e785ffd-1d96-412c-a577-cbc131f36765":{"value":{"id":"4e785ffd-1d96-412c-a577-cbc131f36765","version":2,"type":"text","properties":{"title":[["In this post, I’ll share a bit about how we made decisions surrounding the first step in my list above:"]]},"created_time":1663903354425,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"a4ace76c-686d-4be4-a6aa-7567a2513e27":{"value":{"id":"a4ace76c-686d-4be4-a6aa-7567a2513e27","version":2,"type":"numbered_list","properties":{"title":[["Decide (and justify) what to test"]]},"created_time":1663903354426,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"2f9a77c2-4278-4d89-85a6-0cdd9ec33b8c":{"value":{"id":"2f9a77c2-4278-4d89-85a6-0cdd9ec33b8c","version":2,"type":"sub_sub_header","properties":{"title":[["What I won't cover today"]]},"created_time":1663903354426,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"44852273-b50c-4b03-854f-1941d064df9a":{"value":{"id":"44852273-b50c-4b03-854f-1941d064df9a","version":2,"type":"text","properties":{"title":[["For now, the rest of the list is still in progress, but I hope to cover it in the future when I know more."]]},"created_time":1663903354426,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"a95c4876-6ff9-43c2-9d02-ec51b1735fcd":{"value":{"id":"a95c4876-6ff9-43c2-9d02-ec51b1735fcd","version":2,"type":"numbered_list","properties":{"title":[["Figure out how to do the tests"]]},"created_time":1663903354426,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"65166720-7034-497c-aae8-b1380494fb9d":{"value":{"id":"65166720-7034-497c-aae8-b1380494fb9d","version":2,"type":"numbered_list","properties":{"title":[["Do the tests\nFor our first two phage preps, I’ve now done endotoxin testing and sterility testing. Will report back on these soon."]]},"created_time":1663903354426,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"1fe3238d-8cf3-466a-b457-0bb24fbe47fb":{"value":{"id":"1fe3238d-8cf3-466a-b457-0bb24fbe47fb","version":2,"type":"numbered_list","properties":{"title":[["Show the results of the tests"]]},"created_time":1663903354426,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"33a63deb-a182-4c12-b1c8-a50fb44510e0":{"value":{"id":"33a63deb-a182-4c12-b1c8-a50fb44510e0","version":2,"type":"numbered_list","properties":{"title":[["Show that the tests were done properly\nThere are controls we’re doing in each test, of course, but beyond that, I’m learning there’s all kinds of tests that can be designed to show that a certain test is valid (’validation protocols’). This is definitely a part that the outsourcing will help us with down the road, but helpful to know about it and think about it now."]]},"created_time":1663903354427,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"545de1f2-8d07-4615-9a78-e0e65d463cc0":{"value":{"id":"545de1f2-8d07-4615-9a78-e0e65d463cc0","version":2,"type":"sub_sub_header","properties":{"title":[["So many things we could test for, so many ways to do each: where to begin?"]]},"created_time":1663903354427,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"30ff366d-ed12-48b2-876b-8ab6c5f663ee":{"value":{"id":"30ff366d-ed12-48b2-876b-8ab6c5f663ee","version":2,"type":"text","properties":{"title":[["There’s a lot of things you could do to demonstrate safety of a phage prep. And lots of ways to measure each one. For instance, we might sequence the phage prep at the end to make sure there’s only that one phage in there, and no trace of the host bacteria or any other contaminating bugs that may have gotten in. We might also culture a sample of the phage prep (a sterility test) so we can be more confident that it’s sterile. And we might measure the pH to make sure it’s close enough to what’s physiological, so it doesn’t shock anyone’s system. But what about toxins or components that don’t come from the phage, but rather from the host?"]]},"created_time":1663903354427,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"94e9110f-c6f3-4c76-9cec-cdbb703d19e7":{"value":{"id":"94e9110f-c6f3-4c76-9cec-cdbb703d19e7","version":2,"type":"text","properties":{"title":[["This sounds like another problem like the one I described in my first post of this series… a dizzying array of things to do, and a multitude of ways to do each. Where to start? I decided to "],["apply the same decision-making framework I used in post #1",[["a","https://www.phageaustralia.org/blog/how-to-start-making-therapeutic-phages"]]],[", where I start by reminding myself what I’m optimizing for, then I break the problem down into components, look at my options for each, filter for materials/expertise I have access to, make a choice of one thing to try first to address each step/component, and document my reasoning. Then I come out with a non-overwhelming starting set of steps I’m happy with that address everything I need to address."]]},"created_time":1663903354427,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"9973ab34-ef4c-47a6-8a66-708ac89a1d72":{"value":{"id":"9973ab34-ef4c-47a6-8a66-708ac89a1d72","version":2,"type":"sub_sub_header","properties":{"title":[["What does success look like? (What are we optimizing for?)"]]},"created_time":1663903354427,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"1df68fb8-30ec-4011-9710-d925f4699a5f":{"value":{"id":"1df68fb8-30ec-4011-9710-d925f4699a5f","version":2,"type":"text","properties":{"title":[["We need phage that is safe enough to satisfy our local drug and ethics committees, and the health regulator (TGA), but for now we don’t exactly know what they would want. But we do know regulators tend to look to other regulators (what are other governments happy with?). So it seems like a reasonable strategy to start with looking at what others do to show their phages are safe, copying them as much as possible, and focusing on documenting it well so decision-makers can make their decisions with confidence."]]},"created_time":1663903354427,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"1c070b79-1ed4-4cf4-bb43-8dc547275cd5":{"value":{"id":"1c070b79-1ed4-4cf4-bb43-8dc547275cd5","version":2,"type":"text","properties":{"title":[["Importantly, we are optimizing for getting our phage product approved for compassionate use, and NOT optimizing for a perfectly safe phage prep (since we are trying to address immediate patient need). We don’t have a lot of time or specialized equipment, and we have a lot of unknowns. And we know the decision-makers are going to factor in the fact that doing nothing, or taking too long to define a perfectly, guaranteed-to-be-safe phage product, will be worse for the patient. So we need to show a good level of safety without taking too long to get there."]]},"created_time":1663903354427,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"58e5b3a1-7679-4347-8bc1-d7761744b306":{"value":{"id":"58e5b3a1-7679-4347-8bc1-d7761744b306","version":2,"type":"sub_sub_header","properties":{"title":[["Making a list of dangerous things we could test for, and how we might test for them"]]},"created_time":1663903354427,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"5c9ef647-32e3-4e9e-bf97-d101ea667481":{"value":{"id":"5c9ef647-32e3-4e9e-bf97-d101ea667481","version":2,"type":"text","properties":{"title":[["Our phage prep is going to contain things that are potentially risky or dangerous. Let’s consider that ‘safe’ means lacking dangerous features. What could be dangerous? (To compile this list I looked at what others seem to be testing for, eg. Sciensano, Belgium’s health authority, which has a phage QC department, and TAILOR labs, who provide phages for US compassionate use cases. I also talked to Jon, my advisor and Phage Australia’s leader, about what might scare him as a clinician.)"]]},"created_time":1663903354427,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"910a5efb-9a67-49d5-87f4-1a49ac9c081e":{"value":{"id":"910a5efb-9a67-49d5-87f4-1a49ac9c081e","version":2,"type":"text","properties":{"title":[["We realized there are three main ‘sources’ of dangerous components: the host, the phage, and the final product (the batch). For each, I’ve listed one or more possible solutions we're considering (and/or some notes on how we’re thinking about it)."]]},"created_time":1663903354427,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"2f4ad9f4-7209-42dc-8411-25781602dce9":{"value":{"id":"2f4ad9f4-7209-42dc-8411-25781602dce9","version":2,"type":"sub_sub_header","properties":{"title":[["Risks from host"]]},"created_time":1663903354427,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"a8ea4796-113e-4a99-9fe6-b6d5337ff0ba":{"value":{"id":"a8ea4796-113e-4a99-9fe6-b6d5337ff0ba","version":2,"type":"text","properties":{"title":[["Problem",[["b"]]],[": Genes from the host bacteria (like prophage genes, AMR genes, virulence genes)\n"],["Solution — Sequence the host",[["b"]]],[": we have access to sequencing and a bioinformatician to analyze the results and come up with a list of ‘red flag’ genes"]]},"created_time":1663903354427,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"36f810c8-2dce-4909-9416-d24716035e34":{"value":{"id":"36f810c8-2dce-4909-9416-d24716035e34","version":2,"type":"sub_sub_header","properties":{"title":[["Risks from phage"]]},"created_time":1663903354427,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"35bdbccc-c85f-4c79-8fa6-fb22f8cc309d":{"value":{"id":"35bdbccc-c85f-4c79-8fa6-fb22f8cc309d","version":2,"type":"text","properties":{"title":[["Problem",[["b"]]],[": Genes from the phage (like lysogeny genes, AMR genes, transduction genes)\n"],["Solution — Sequence the phage",[["b"]]]]},"created_time":1663903354427,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"1afa7c6f-42a5-461b-856d-cb1c69a4fc71":{"value":{"id":"1afa7c6f-42a5-461b-856d-cb1c69a4fc71","version":2,"type":"sub_sub_header","properties":{"title":[["Risks from final product (the batch)"]]},"created_time":1663903354427,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"49b41972-28f3-4b59-b589-b2e66666f3b3":{"value":{"id":"49b41972-28f3-4b59-b589-b2e66666f3b3","version":2,"type":"text","properties":{"title":[["Problem",[["b"]]],[": Bacterial contaminants"]]},"created_time":1663903354428,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"21320f21-c273-41ac-ba8e-af28acc6592f":{"value":{"id":"21320f21-c273-41ac-ba8e-af28acc6592f","version":2,"type":"numbered_list","properties":{"title":[["Solution — Test for sterility:",[["b"]]],[" We are next door to an accredited hospital diagnostics lab, which routinely cultures microbes from patient samples in blood culture bottles; if we inoculate them with our phage preps, they can culture them and let us know if anything grows"]]},"created_time":1663903354428,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"f3a85ec8-ab0b-4ff8-aad0-e789e68f3019":{"value":{"id":"f3a85ec8-ab0b-4ff8-aad0-e789e68f3019","version":2,"type":"numbered_list","properties":{"title":[["Solution — Sequence the batch",[["b"]]]]},"created_time":1663903354428,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"a74d0bb8-12a6-498c-93c5-6ad0d14eac92":{"value":{"id":"a74d0bb8-12a6-498c-93c5-6ad0d14eac92","version":2,"type":"text","properties":{"title":[["Problem",[["b"]]],[": Components from the bacterial lysate during production (like endotoxin, exotoxins)"]]},"created_time":1663903354428,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"8e9f553a-3f59-4ef4-88cd-5fd855bc919d":{"value":{"id":"8e9f553a-3f59-4ef4-88cd-5fd855bc919d","version":2,"type":"numbered_list","properties":{"title":[["Solution — Quantify endotoxin:",[["b"]]],[" we can quantify this using the "],["Charles River LAL (limulus amoebocyte lysate)",[["a","https://www.criver.com/products-services/qc-microbial-solutions/endotoxin-testing/endosafe-cartridge-technology?region=3686"]]],[" system (we have one at our institute)"]]},"created_time":1663903354429,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"8aee5574-cf70-4843-93da-f7199e7a5c4e":{"value":{"id":"8aee5574-cf70-4843-93da-f7199e7a5c4e","version":2,"type":"numbered_list","properties":{"title":[["Solution — Detect known toxin genes by sequencing",[["b"]]],[": Sequencing the host should tell us (at least about known toxins). Also, we’re using fairly benign strains, so this helps reduce this risk too."]]},"created_time":1663903354430,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"806d27b1-ee3f-42f3-8682-4cd9a326800d":{"value":{"id":"806d27b1-ee3f-42f3-8682-4cd9a326800d","version":2,"type":"numbered_list","properties":{"title":[["Solution — Detect unknown harmful factors by cell viability assay",[["b"]]],[": (as done by "],["Luong et al",[["a","https://pubmed.ncbi.nlm.nih.gov/32709990/"]]],[".) Right now we aren’t set up for this but would be good to look into for the future"]]},"created_time":1663903354431,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"4cb728d8-bc72-4a39-8a8d-f6ca8aa9dbd2":{"value":{"id":"4cb728d8-bc72-4a39-8a8d-f6ca8aa9dbd2","version":2,"type":"text","properties":{"title":[["Problem",[["b"]]],[": Overly acidic or overly basic pH of the product\n"],["Solution — Measure pH:",[["b"]]],[" we will check and aim for physiological pH (our phage sample will be diluted 10x-100x or more in standard saline, so presumably this won’t be too big an issue)"]]},"created_time":1663903354431,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"93598666-6c69-4772-9bd7-a01fd9d0c45e":{"value":{"id":"93598666-6c69-4772-9bd7-a01fd9d0c45e","version":2,"type":"text","properties":{"title":[["Problem",[["b"]]],[": Octanol (which we introduced during the production process)\n"],["Solution",[["b"]]],[": We don’t currently have a method to test this, but others ("],["Barr & Rohwer labs",[["a","https://peerj.com/articles/2261/"]]],[", "],["Patterson case",[["a","https://pubmed.ncbi.nlm.nih.gov/28807909/"]]],[") have safely used octanol-purified preps in patients (we will likely submit something similar to the risk assessment they did; many thanks to Jeremy Barr for advising us on this and sharing tips and info!)."]]},"created_time":1663903354431,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"09d6999e-0914-4245-ad69-915f04391269":{"value":{"id":"09d6999e-0914-4245-ad69-915f04391269","version":2,"type":"text","properties":{"title":[["Note: We do know that octanol inhibits the endotoxin test, but we’ve seen that our endotoxin test’s standards work in presence of our phage prep, suggesting octanol levels are low — so this at least suggests that our dialysis step removed most of the octanol, as it should have (see ",[["i"]]],["Phage on Tap protocol",[["i"],["a","https://peerj.com/articles/2261/"]]],[" and ",[["i"]]],["blog post #1",[["i"],["a","https://www.phageaustralia.org/blog/how-to-start-making-therapeutic-phages"]]],[" and ",[["i"]]],["#2",[["i"],["a","https://www.phageaustralia.org/blog/phage-batch-results"]]],[" in this series)",[["i"]]]]},"created_time":1663903354431,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"40547bfe-8b3e-4a5b-ab4c-101ed5fd06d2":{"value":{"id":"40547bfe-8b3e-4a5b-ab4c-101ed5fd06d2","version":2,"type":"text","properties":{"title":[["Problem",[["b"]]],[": Other phages (prophages or contaminating phages)\n"],["Solution — Sequence the batch",[["b"]]]]},"created_time":1663903354431,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"51d5b1c0-1a5e-418e-bd93-cb83f4e46dcc":{"value":{"id":"51d5b1c0-1a5e-418e-bd93-cb83f4e46dcc","version":2,"type":"sub_sub_header","properties":{"title":[["Narrowing the pool and making choices"]]},"created_time":1663903354431,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"359414a3-134a-49a3-a901-03e150cf4be9":{"value":{"id":"359414a3-134a-49a3-a901-03e150cf4be9","version":2,"type":"text","properties":{"title":[["Next, in line with my framework for preventing overwhelm and optimization creep, and to identify gaps in my thinking, I’ve started filling out the table below to document my options, choices, and reasoning:"]]},"created_time":1663903354431,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"de1db32e-3f16-419c-91e4-09dfb7ed464c":{"value":{"id":"de1db32e-3f16-419c-91e4-09dfb7ed464c","version":6,"type":"table","content":["d2a19137-6a5c-4788-918e-62ae2462a238","a1f8a9f3-a79f-4b5a-b7ca-cbcce639313e","c9fad30e-a526-4c73-bda5-9dee39a65ea7","8bb05c2e-bbbc-4a40-ba8c-7e6c63e2a30a","37c93957-a31c-4f4f-8234-e3aacf2c1ec3","9237055d-9ebb-4cd8-b643-ab684c2d6c4a","3c7be754-926a-4149-aab1-3da5fe024760","08021246-3d34-444c-a014-957b50703323","25b66f06-6198-48a8-8ad9-d65dfcb5aa7e","0cb296ff-314a-424d-8f1c-7ab1c834205e"],"format":{"copied_from_pointer":{"id":"41690b45-fe9a-4ec7-b378-b261c3b78e6c","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"table_block_column_order":["@Br]","LR^`","JmuG","gjJ]","H\\SI","PnDq"],"table_block_column_format":{"H\\SI":{"width":290},"JmuG":{"width":179},"LR^`":{"width":203},"PnDq":{"width":143},"gjJ]":{"width":391}}},"created_time":1663903193775,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"copied_from":"41690b45-fe9a-4ec7-b378-b261c3b78e6c","created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"d2a19137-6a5c-4788-918e-62ae2462a238":{"value":{"id":"d2a19137-6a5c-4788-918e-62ae2462a238","version":2,"type":"table_row","properties":{"H\\SI":[["Outcome"]],"JmuG":[["Decision"]],"LR^`":[["Available options"]],"PnDq":[["Next"]],"gjJ]":[["Reason"]]},"format":{"copied_from_pointer":{"id":"1291611b-8c78-4053-b84d-4956ca6668da","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"created_time":1663903193777,"last_edited_time":1663903140000,"parent_id":"de1db32e-3f16-419c-91e4-09dfb7ed464c","parent_table":"block","alive":true,"copied_from":"1291611b-8c78-4053-b84d-4956ca6668da","created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"a1f8a9f3-a79f-4b5a-b7ca-cbcce639313e":{"value":{"id":"a1f8a9f3-a79f-4b5a-b7ca-cbcce639313e","version":2,"type":"table_row","properties":{"@Br]":[["Demonstrate low endotoxin"]],"H\\SI":[["So far so good; first reading was in range and sample ‘passed’ the machine’s internal controls (did not have components that interfered with the reading of the endotoxin standard that was spiked in)"]],"JmuG":[["Use Charles River endotoxin cartridge-based LAL kit in QC lab at WIMR "]],"LR^`":[["Charles River endotoxin cartridge-based LAL kit in QC lab at WIMR \n\nOther endotoxin kits (e.g. Pierce, Biomerieux)"]],"gjJ]":[["Used by Sydney Cell and Gene Therapy labs (downstairs in our building), validated and maintained by QC professionals\n\nTried Biomerieux kit but it was much more laborious and hasn’t been validated"]]},"format":{"copied_from_pointer":{"id":"d0631cd9-980f-417a-a930-1e0e7372b268","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"created_time":1663903193777,"last_edited_time":1663903140000,"parent_id":"de1db32e-3f16-419c-91e4-09dfb7ed464c","parent_table":"block","alive":true,"copied_from":"d0631cd9-980f-417a-a930-1e0e7372b268","created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"c9fad30e-a526-4c73-bda5-9dee39a65ea7":{"value":{"id":"c9fad30e-a526-4c73-bda5-9dee39a65ea7","version":2,"type":"table_row","properties":{"@Br]":[["Demonstrate low exotoxins and other toxic host proteins"]],"H\\SI":[["Waiting on sequencing results"]],"JmuG":[["Analyze propagating strain genome"]],"LR^`":[["Analyze propagating strain genome\n\nMix phage prep with human cells (cell viability assay)"]],"PnDq":[["Analyze sequence data "]],"gjJ]":[["Sequencing should give good enough picture of safety for now; we are using reference "],["E. coli",[["i"]]],[" strains currently so don’t predict this to be an issue; will likely explore cell viability assays in future for more unknown hosts"]]},"format":{"copied_from_pointer":{"id":"4be40654-c2ca-402d-9f4c-b245cdc5631c","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"created_time":1663903193781,"last_edited_time":1663903140000,"parent_id":"de1db32e-3f16-419c-91e4-09dfb7ed464c","parent_table":"block","alive":true,"copied_from":"4be40654-c2ca-402d-9f4c-b245cdc5631c","created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"8bb05c2e-bbbc-4a40-ba8c-7e6c63e2a30a":{"value":{"id":"8bb05c2e-bbbc-4a40-ba8c-7e6c63e2a30a","version":2,"type":"table_row","properties":{"@Br]":[["Demonstrate no bacteria"]],"H\\SI":[["Waiting on results"]],"JmuG":[["Inoculate blood cultures at hospital lab"]],"LR^`":[["Follow how sterility tests are done in the pharmacopeia and implement a version of this in our lab\n\nOutsource the above to contract research org (CRO) (Eurofins or Charles River)\n\nInoculate blood cultures at accredited hospital lab next door"]],"gjJ]":[["Sterility testing according to pharmacopeia via CRO takes over a month; for now we want to get an earlier picture of whether anything grows. Hospital lab’s test should pick up any contaminating microbes and give us a good sense of sterility, and only takes 5-14 days"]]},"format":{"copied_from_pointer":{"id":"c84a9a6b-67bc-4d81-a070-2b55769b06f8","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"created_time":1663903193781,"last_edited_time":1663903140000,"parent_id":"de1db32e-3f16-419c-91e4-09dfb7ed464c","parent_table":"block","alive":true,"copied_from":"c84a9a6b-67bc-4d81-a070-2b55769b06f8","created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"37c93957-a31c-4f4f-8234-e3aacf2c1ec3":{"value":{"id":"37c93957-a31c-4f4f-8234-e3aacf2c1ec3","version":2,"type":"table_row","properties":{"@Br]":[["Demonstrate reasonable pH"]],"H\\SI":[["Have not done yet"]],"JmuG":[["Will test pH of our batches"]],"LR^`":[["pH meter"]],"gjJ]":[["Easy, standard, have equipment"]]},"format":{"copied_from_pointer":{"id":"ecbc030e-e1a8-4417-890b-177cf96ae107","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"created_time":1663903193781,"last_edited_time":1663903140000,"parent_id":"de1db32e-3f16-419c-91e4-09dfb7ed464c","parent_table":"block","alive":true,"copied_from":"ecbc030e-e1a8-4417-890b-177cf96ae107","created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"9237055d-9ebb-4cd8-b643-ab684c2d6c4a":{"value":{"id":"9237055d-9ebb-4cd8-b643-ab684c2d6c4a","version":2,"type":"table_row","properties":{"@Br]":[["Demonstrate no octanol"]],"JmuG":[["For now we will not pursue octanol detection"]],"LR^`":[["Mass spectrometry?"]],"gjJ]":[["We don’t readily have access to a method for doing this, and see it as a small risk to omit this test (Phage on Tap method has used this method in patients without testing for octanol, FDA has allowed use of phage products made with this method without needing to show octanol levels remaining, octanol not considered very hazardous, already in the pharmacopeia as a food additive/flavouring agent)"]]},"format":{"copied_from_pointer":{"id":"ff3686d3-6c18-4085-9421-29137386842b","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"created_time":1663903193782,"last_edited_time":1663903140000,"parent_id":"de1db32e-3f16-419c-91e4-09dfb7ed464c","parent_table":"block","alive":true,"copied_from":"ff3686d3-6c18-4085-9421-29137386842b","created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"3c7be754-926a-4149-aab1-3da5fe024760":{"value":{"id":"3c7be754-926a-4149-aab1-3da5fe024760","version":2,"type":"table_row","properties":{"@Br]":[["Demonstrate no other phages"]],"H\\SI":[["Waiting on results"]],"JmuG":[["Sequence the final prep"]],"LR^`":[["Sequence the final prep (the batch)"]],"gjJ]":[["We have access to sequencing, should provide all the information we need"]]},"format":{"copied_from_pointer":{"id":"c792ab59-8cff-477d-b44d-f3b56db5c3aa","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"created_time":1663903193782,"last_edited_time":1663903140000,"parent_id":"de1db32e-3f16-419c-91e4-09dfb7ed464c","parent_table":"block","alive":true,"copied_from":"c792ab59-8cff-477d-b44d-f3b56db5c3aa","created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"08021246-3d34-444c-a014-957b50703323":{"value":{"id":"08021246-3d34-444c-a014-957b50703323","version":2,"type":"table_row","properties":{"@Br]":[["Demonstrate the tests we choose are the right tests"]],"JmuG":[["Explain that our tests match what other credible orgs use for similar products (e.g Sciensano)"]],"LR^`":[["Explain that our tests match what other credible orgs use for similar products (e.g Sciensano)"]],"gjJ]":[["Since there are not yet defined phage testing standards here in Australia, the only way forward seems to be: propose something based on what others do, supply evidence, let regulator and ethics committee decide "]]},"format":{"copied_from_pointer":{"id":"894c9bb5-9ab0-434f-90d4-52555bde4622","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"created_time":1663903193782,"last_edited_time":1663903140000,"parent_id":"de1db32e-3f16-419c-91e4-09dfb7ed464c","parent_table":"block","alive":true,"copied_from":"894c9bb5-9ab0-434f-90d4-52555bde4622","created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"25b66f06-6198-48a8-8ad9-d65dfcb5aa7e":{"value":{"id":"25b66f06-6198-48a8-8ad9-d65dfcb5aa7e","version":2,"type":"table_row","properties":{"@Br]":[["Demonstrate we’ve done the tests"]],"H\\SI":[["We have created working versions of:\n- Batch Safety Data Sheet \n- Phage Safety Data Sheet\n- Host Safety Data Sheet\n\nHave set meeting with TGA to discuss"]],"JmuG":[["Document what we do, including raw data collection and analysis"]],"LR^`":[["Document what we do, including raw data collection and analysis"]],"PnDq":[["Clean up working versions, get input from colleagues, meet with TGA"]],"gjJ]":[["Very open ended, have to start somewhere"]]},"format":{"copied_from_pointer":{"id":"e008dbae-0c97-433a-a093-6aa06fbc59d6","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"created_time":1663903193782,"last_edited_time":1663903140000,"parent_id":"de1db32e-3f16-419c-91e4-09dfb7ed464c","parent_table":"block","alive":true,"copied_from":"e008dbae-0c97-433a-a093-6aa06fbc59d6","created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"0cb296ff-314a-424d-8f1c-7ab1c834205e":{"value":{"id":"0cb296ff-314a-424d-8f1c-7ab1c834205e","version":2,"type":"table_row","properties":{"@Br]":[["Demonstrate tests are trustworthy"]],"H\\SI":[["Have started conversations with CROs: Eurofins, Charles River; they can help, seem competent"]],"JmuG":[["Do ourselves for now, but work toward third party"]],"LR^`":[["Do the tests ourselves, and document everything\n\nGet third party to do the tests"]],"gjJ]":[["Cheaper/faster to do ourselves for now; third party tests are expensive and require long lead-time, more knowledge about exact volumes we will be generating, etc"]]},"format":{"copied_from_pointer":{"id":"5cca17cd-a160-486c-a94f-e3032f5e0b79","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"created_time":1663903193782,"last_edited_time":1663903140000,"parent_id":"de1db32e-3f16-419c-91e4-09dfb7ed464c","parent_table":"block","alive":true,"copied_from":"5cca17cd-a160-486c-a94f-e3032f5e0b79","created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"ebbf7c37-5621-47a8-89a5-5b9d630f6347":{"value":{"id":"ebbf7c37-5621-47a8-89a5-5b9d630f6347","version":2,"type":"text","properties":{"title":[["Table 1. For each 'dangerous' potential component we've identified could be in a phage batch, I've filled out some options for testing it, decisions we've made, and our reasoning as our team works toward setting up a basic phage quality control pipeline in the lab.",[["i"]]]]},"created_time":1663903354432,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"68f5f376-aa6f-4ce8-aa04-466eab2a54d9":{"value":{"id":"68f5f376-aa6f-4ce8-aa04-466eab2a54d9","version":2,"type":"sub_sub_header","properties":{"title":[["Decisions made: Next, carry them out"]]},"created_time":1663903354433,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"1ea955eb-7361-47c4-88bd-d314be400bd3":{"value":{"id":"1ea955eb-7361-47c4-88bd-d314be400bd3","version":2,"type":"text","properties":{"title":[["For most dangerous components we’ve identified, we’ve decided on a test, and we’ve gotten clear on our reasoning. For now, our ‘minimum viable phage QC pipeline’ looks like:"]]},"created_time":1663903354433,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"d0f61684-4159-4cb1-b682-db6d576996eb":{"value":{"id":"d0f61684-4159-4cb1-b682-db6d576996eb","version":2,"type":"numbered_list","properties":{"title":[["Endotoxin test using LAL assay (Charles River cartridge+machine)"]]},"created_time":1663903354433,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"1b7b7431-3c81-455a-946f-0197027d7176":{"value":{"id":"1b7b7431-3c81-455a-946f-0197027d7176","version":2,"type":"numbered_list","properties":{"title":[["Sterility test using blood culture bottles (hospital lab)"]]},"created_time":1663903354434,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"d67d8bd7-d569-4007-8407-e9cff7081ff7":{"value":{"id":"d67d8bd7-d569-4007-8407-e9cff7081ff7","version":2,"type":"numbered_list","properties":{"title":[["pH test using standard pH meter (our lab)"]]},"created_time":1663903354434,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"b5ccab1d-0301-44cc-8621-711273a61e82":{"value":{"id":"b5ccab1d-0301-44cc-8621-711273a61e82","version":2,"type":"numbered_list","properties":{"title":[["Sequencing the phage, the host and the final batch (sequencing center in our institute)"]]},"created_time":1663903354434,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"f46616e5-bd84-4b29-8fbc-28b296dd1fb9":{"value":{"id":"f46616e5-bd84-4b29-8fbc-28b296dd1fb9","version":2,"type":"numbered_list","properties":{"title":[["Risks we’re not testing for right now: octanol, unknown toxic components (because we believe the risk of the patient having to wait until we can do these tests, which we are not set up for, to be higher than the risk of letting the patient have the prep without these components being tested for, given we believe they are quite low risk)"]]},"created_time":1663903354434,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"a090b661-0f65-4734-8599-e9caf12db505":{"value":{"id":"a090b661-0f65-4734-8599-e9caf12db505","version":2,"type":"numbered_list","properties":{"title":[["Document everything and submit to local drug committee, ethics committee, TGA"]]},"created_time":1663903354435,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"ffc11354-18d1-4766-a124-821681b71be5":{"value":{"id":"ffc11354-18d1-4766-a124-821681b71be5","version":2,"type":"text","properties":{"title":[["I’ve started doing these tests on two phage products I’ve now made (both "],["E. coli",[["i"]]],[" phages), which we’re preparing for a patient at the hospital next door. Once I finish the set of tests we’ve decided on, I’ll be compiling the data and methods, and submitting them to our drug committee and ethics committee (with lots of help from others here who’ve done it before)."]]},"created_time":1663903354435,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"128dc5de-b254-42f4-8b55-0a26a9bf6cf4":{"value":{"id":"128dc5de-b254-42f4-8b55-0a26a9bf6cf4","version":2,"type":"text","properties":{"title":[["In a future post I hope to update you on how these assays went. I will also eventually talk more about the way we’ll be documenting everything, and of course, whether our first preps end up making it through… I am assuming we’ll get feedback and need to make some tweaks, and I’m excited to see what that looks like."]]},"created_time":1663903354435,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"6995aafb-5117-43c5-bab6-f16dd3a7eecc":{"value":{"id":"6995aafb-5117-43c5-bab6-f16dd3a7eecc","version":2,"type":"text","properties":{"title":[["Thanks for reading! As always, I love your comments and emails, please keep sending your thoughts if you feel like it. Especially if there are things I’m missing, or my logic is flawed, or you think there’s an easier way for me to address anything I’m trying to do. Thanks in advance!"]]},"created_time":1663903354435,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"bd3d69b2-c125-42f9-9480-7dd8009cacfa":{"value":{"id":"bd3d69b2-c125-42f9-9480-7dd8009cacfa","version":2,"type":"sub_sub_header","properties":{"title":[["A few meta-reflections as I've delved into this new area"]]},"created_time":1663903354435,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"17a48e75-f206-4131-a749-5bf8e9e459f8":{"value":{"id":"17a48e75-f206-4131-a749-5bf8e9e459f8","version":2,"type":"text","properties":{"title":[["Unexpected source of help: People at my institute that DON'T work on phages",[["b"]]],["\nIn my quest for setting up this minimum viable phage QC pipeline, one of the best things I’ve done is having lots of conversations with others in our institute (Westmead Institute for Medical Research) who are working on everything but phage."]]},"created_time":1663903354435,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"e8597e34-e0ab-4297-a404-150f61e76e1b":{"value":{"id":"e8597e34-e0ab-4297-a404-150f61e76e1b","version":2,"type":"text","properties":{"title":[["For example, there are people upstairs who make CAR-T cells for cancer therapy, and who do things like islet cell transplants for diabetes therapy. There are also people in the neighbouring building who are making viral vectors for gene therapy. All of these end up needing to develop a quality control pipeline that from what I gather, looks a lot like what we need — and they all seem to have started in academic labs, which is encouraging!"]]},"created_time":1663903354435,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"0f00d5c9-119d-40e4-b54d-bada7bcf10a7":{"value":{"id":"0f00d5c9-119d-40e4-b54d-bada7bcf10a7","version":2,"type":"text","properties":{"title":[["So I’m very excited to learn as much as I can from them, and so far it’s been extremely helpful. (e.g. I ask around and set up coffee meetings with T-cell makers and bone marrow researchers and QC managers in my building, etc, and people have been more than happy to help me learn about GMP, QC, and tell me about their process — shoutout to Natasha Barry, Flora Kan and Leighton Clancy especially!)"]]},"created_time":1663903354435,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"5e7e8599-10ea-4123-8590-8d0de8005e2b":{"value":{"id":"5e7e8599-10ea-4123-8590-8d0de8005e2b","version":2,"type":"text","properties":{"title":[["Quality control and manufacturing might actually not be boring",[["b"]]],["\nAs someone who used to think words like ‘GMP’ and ‘manufacturing’ and ‘QC’ were the most boring words possible, I am actually feeling genuinely excited about them these days… I think because I’m starting to see how important it is to get these right, and also how much creativity it actually takes to set these systems up (as opposed to being something that was already solved, or requiring long manuals to read and paperwork to fill out). I’m sure the latter are true, but it’s actually seeming more like a craft than an assembly line, the more I learn about it. And it feels very important to get right. (Now that it feels like if we mess up, a patient could have a bad outcome, I’m hyper focused on documenting things, giving my buffers batch numbers, etc, in a way I never was before)."]]},"created_time":1663903354435,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"55ae1c47-6e14-495b-a389-f52348a58047":{"value":{"id":"55ae1c47-6e14-495b-a389-f52348a58047","version":2,"type":"text","properties":{"title":[["Getting good at this stuff is probably a transferable skill!",[["b"]]],["\nI’m getting the sense that new biological entities are getting turned into therapeutics more and more, and there seems to be a lot of focus on getting GMP production happening in a pseudo-academic setting, rather than waiting until pharma is ready to take the reins… very interesting! Maybe a new in-demand skillset for our future careers?"]]},"created_time":1663903354435,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"876ae145-79aa-4542-be52-942c69086c4a":{"value":{"id":"876ae145-79aa-4542-be52-942c69086c4a","version":2,"type":"sub_sub_header","properties":{"title":[["Resources that have been helpful"]]},"created_time":1663903354435,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"cf3853b6-3bb0-4a0f-902d-cbe78317b218":{"value":{"id":"cf3853b6-3bb0-4a0f-902d-cbe78317b218","version":2,"type":"text","properties":{"title":[["Sciensano, Belgium’s federal health regulator, has put some rules around what constitutes ‘safe’ for phages, and even has a phage QC lab; we are following their lead on what makes sense to test"]]},"created_time":1663903354435,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"b831348e-7721-4433-bfb2-806e6e569b0a":{"value":{"id":"b831348e-7721-4433-bfb2-806e6e569b0a","version":2,"type":"bulleted_list","properties":{"title":[["Magistral phage paper",[["a","https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5850371/"]]],[" (2018), their reference document on how a safe phage should be prepared"]]},"created_time":1663903354436,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"d0fcac20-7320-4201-8f5f-ff4eba16f87a":{"value":{"id":"d0fcac20-7320-4201-8f5f-ff4eba16f87a","version":2,"type":"bulleted_list","properties":{"title":[["Sciensano",[["a","https://www.sciensano.be/en"]]],[" website"]]},"created_time":1663903354436,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"99f51c8e-86c1-44bb-a4a8-c0aea0482256":{"value":{"id":"99f51c8e-86c1-44bb-a4a8-c0aea0482256","version":2,"type":"bulleted_list","properties":{"title":[["Many thanks to Pieter-Jan Ceyssens and Mathieu de Jode at Sciensano for helpful conversations and for sharing your methods!"]]},"created_time":1663903354437,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"9bbcfd4d-f3c8-4e88-8c69-c9415c10ac88":{"value":{"id":"9bbcfd4d-f3c8-4e88-8c69-c9415c10ac88","version":2,"type":"text","properties":{"title":[["TAILOR makes phages to US FDA standards for compassionate use: they create a 'physician desk reference' for their phages and describe how they make/test them:"]]},"created_time":1663903354437,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"8b12178b-4250-4152-828a-43ac983805a6":{"value":{"id":"8b12178b-4250-4152-828a-43ac983805a6","version":2,"type":"bulleted_list","properties":{"title":[["Paper",[["a","https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7327541/"]]],[" by Austen L. Terwilliger et al. 2020"]]},"created_time":1663903354437,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"60301856-a3cc-4342-86d9-864d558457c9":{"value":{"id":"60301856-a3cc-4342-86d9-864d558457c9","version":2,"type":"text","properties":{"title":[["Methods papers we're going back to again and again these days:"]]},"created_time":1663903354437,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"51badda3-4968-491d-8f05-6028164b5d53":{"value":{"id":"51badda3-4968-491d-8f05-6028164b5d53","version":2,"type":"bulleted_list","properties":{"title":[["Phage on Tap",[["a","https://peerj.com/articles/2261/"]]],[" (paper by Bonilla et al. 2016): where we got the octanol method and so much more!"]]},"created_time":1663903354438,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"48266ac6-8a13-4bdc-b724-b4f2b8f5cc35":{"value":{"id":"48266ac6-8a13-4bdc-b724-b4f2b8f5cc35","version":2,"type":"bulleted_list","properties":{"title":[["Luong et al. 2020 paper",[["a","https://pubmed.ncbi.nlm.nih.gov/32709990/"]]],[" (we use lots of their methods for phage production, QC, etc)"]]},"created_time":1663903354438,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"4c41338b-7283-49e7-aca3-50e30ef428a9":{"value":{"id":"4c41338b-7283-49e7-aca3-50e30ef428a9","version":2,"type":"text","properties":{"title":[["A comprehensive look at phage therapy QC and all the factors that should be considered, published by Pirnay et al. in 2015"]]},"created_time":1663903354438,"last_edited_time":1663903320000,"parent_id":"781e4d65-a2c2-408e-b245-09e660a7f8e4","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","last_edited_by_table":"notion_user","last_edited_by_id":"7d750b62-7bbb-4980-9061-0db6317fc6a9","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"22dbcadd-1283-4fd5-9ed6-7338d675efab":{"value":{"id":"22dbcadd-1283-4fd5-9ed6-7338d675efab","version":4,"type":"bulleted_list","properties":{"title":[["Quality and Safety Requirements for Sustainable Phage Therapy 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The System needs to be Auditable",[["b"]]]]},"created_time":1665272843174,"last_edited_time":1665272820000,"parent_id":"5bdf2031-e3bc-46f5-9211-c4b9bf34bd01","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"73539590-9520-419e-b62b-884f4b193d05":{"value":{"id":"73539590-9520-419e-b62b-884f4b193d05","version":2,"type":"text","properties":{"title":[["In order to be auditable, we can borrow concepts from the finance, such as: append-only log (no edits or deletes are allowed; any corrections are "],["added",[["i"]]],["), event-driven architecture (e.g. "],["the available books in a library is a consequence of the number of books previously checked in",[["i"]]],["), and double-entry bookkeeping ("],["every transaction is recorded as a debit and a credit event, and they need match",[["i"]]],[")."]]},"created_time":1665272843175,"last_edited_time":1665272820000,"parent_id":"5bdf2031-e3bc-46f5-9211-c4b9bf34bd01","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"4194135b-9ede-486e-9b19-6438738a5480":{"value":{"id":"4194135b-9ede-486e-9b19-6438738a5480","version":2,"type":"text","properties":{"title":[["The system should also be "],["accountable,",[["i"]]],[" meaning each piece of data should be attributed to a lab member and/or the machine that produced the result. 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Traceable outputs also help us more easily track and fix errors, generate reports for compliance and regulations, cite and reward contributors who provide data, and improve inefficient methods."]]},"created_time":1665272843175,"last_edited_time":1665272820000,"parent_id":"5bdf2031-e3bc-46f5-9211-c4b9bf34bd01","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"8bfce26b-00f5-462b-b134-34676bd02599":{"value":{"id":"8bfce26b-00f5-462b-b134-34676bd02599","version":2,"type":"text","properties":{"title":[["Finally, the data we collect and the reports we generate will build a track record for each phage, which should increase our confidence in the phage’s efficacy and safety profile."]]},"created_time":1665272843175,"last_edited_time":1665272820000,"parent_id":"5bdf2031-e3bc-46f5-9211-c4b9bf34bd01","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"9675f117-a181-4f0b-b358-3ef50842cafe":{"value":{"id":"9675f117-a181-4f0b-b358-3ef50842cafe","version":2,"type":"text","properties":{"title":[["This track record also helps us show authenticity and provenance. A phage provided with an auditable track record should inspire more confidence in its safety and efficacy compared to a phage without any data and questionable provenance."]]},"created_time":1665272843175,"last_edited_time":1665272820000,"parent_id":"5bdf2031-e3bc-46f5-9211-c4b9bf34bd01","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"7db51db5-cba5-465e-ac73-b29d09093da6":{"value":{"id":"7db51db5-cba5-465e-ac73-b29d09093da6","version":2,"type":"text","properties":{"title":[["And with provenance and authenticity systems in place, we can start doing neat things like "],["share the phages with others",[["i"]]],[", and "],["collaboratively generate data.",[["i"]]]]},"created_time":1665272843175,"last_edited_time":1665272820000,"parent_id":"5bdf2031-e3bc-46f5-9211-c4b9bf34bd01","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"847674a3-76e5-42cc-8f08-6ead57eb84b1":{"value":{"id":"847674a3-76e5-42cc-8f08-6ead57eb84b1","version":2,"type":"sub_sub_header","properties":{"title":[["2. The System needs to support Replicability",[["b"]]]]},"created_time":1665272843176,"last_edited_time":1665272820000,"parent_id":"5bdf2031-e3bc-46f5-9211-c4b9bf34bd01","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"c879eb4e-e2b1-40a5-b730-6076b3a70996":{"value":{"id":"c879eb4e-e2b1-40a5-b730-6076b3a70996","version":2,"type":"text","properties":{"title":[["An auditable system is useless if the data isn’t accurate."]]},"created_time":1665272843176,"last_edited_time":1665272820000,"parent_id":"5bdf2031-e3bc-46f5-9211-c4b9bf34bd01","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"517beeb6-48c6-4f2c-adc8-1b9670f6cd38":{"value":{"id":"517beeb6-48c6-4f2c-adc8-1b9670f6cd38","version":2,"type":"text","properties":{"title":[["Our data is only as good as our protocols, methods, and machines. If triplicates are necessary for valid results, then replicates from additional labs should further validate those results."]]},"created_time":1665272843176,"last_edited_time":1665272820000,"parent_id":"5bdf2031-e3bc-46f5-9211-c4b9bf34bd01","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"619d0482-1242-43fa-8833-92bd826f2f13":{"value":{"id":"619d0482-1242-43fa-8833-92bd826f2f13","version":2,"type":"text","properties":{"title":[["The system needs to support adding replicated data from multiple labs working on phages from the same production batch with the same protocols. Pooling the data allows us to get better averages and detect anomalies. Such a “Proof of Data” mechanism would allow multiple labs to separately confirm and validate a phage’s profile in a decentralized way."]]},"created_time":1665272843176,"last_edited_time":1665272820000,"parent_id":"5bdf2031-e3bc-46f5-9211-c4b9bf34bd01","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"bf214aca-2660-4e59-8879-7cceb2b721d5":{"value":{"id":"bf214aca-2660-4e59-8879-7cceb2b721d5","version":2,"type":"text","properties":{"title":[["To support replicability, the system needs to be “federated”. This means that labs will generate and collect their own data, but then elect to consolidate their data into a central registry. As long as the lab follows the protocols and collects data in a way that meets requirements, their data (and even their phages and hosts) can be made available to the wider network."]]},"created_time":1665272843176,"last_edited_time":1665272820000,"parent_id":"5bdf2031-e3bc-46f5-9211-c4b9bf34bd01","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"68758bef-5a00-45d4-ad52-4e5cdb1a6f6c":{"value":{"id":"68758bef-5a00-45d4-ad52-4e5cdb1a6f6c","version":2,"type":"text","properties":{"title":[["With data federation and replicability, multiple labs across the network could create their own specialized phage collections, send those phages to other labs for replication, and trust that if they followed all the protocols, the federated system could generate reports on their phages and make them generally available."]]},"created_time":1665272843176,"last_edited_time":1665272820000,"parent_id":"5bdf2031-e3bc-46f5-9211-c4b9bf34bd01","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"17b2f6bf-22d2-421d-87db-496f155e8288":{"value":{"id":"17b2f6bf-22d2-421d-87db-496f155e8288","version":2,"type":"sub_sub_header","properties":{"title":[["3. 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Robust manufacturing and distribution (including supply chain and biobanking)."]]},"created_time":1665364756675,"last_edited_time":1665365700000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"82576b3f-43d8-48a0-80d6-b7d236c0fba1":{"value":{"id":"82576b3f-43d8-48a0-80d6-b7d236c0fba1","version":17,"type":"text","properties":{"title":[["We collaborate with UNSW Recombinant Products Facility (Chris Marquis, Helene Lebhar, Ali Khalid) for phage purification processes (see Jessica Sacher’s articles [^2]), Citizen Phage Library (Ben Temperton) and Phage Australia network for potential phage supplies, and our own testing on distribution/stability testing of Pae7 phage (see Stephanie Lynch’s article [^3].) We have already produced and distributed a batch of clean home-grown phages to all our partners for testing. I am acutely aware of the effort and investment needed for a biomanufacturing and bioprocessing plant dedicated to phage."]]},"created_time":1665364756676,"last_edited_time":1665365220000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"2533a6da-cd20-4d22-a819-51074dc99ac9":{"value":{"id":"2533a6da-cd20-4d22-a819-51074dc99ac9","version":17,"type":"text","properties":{"title":[["We have demonstrated strong feasibility of networked biobanking at "],["state level",[["b"]]],[" (NSW Govt funding for Pathogen [^4] and Phage [^5] biobanks, WA health department endorsed implementation task force); "],["national level",[["b"]]],[" and "],["international level",[["b"]]],[", i.e., Israel Phage Biobank (Ronen Hazan, Ran Nir-Paz), LysenTech (South Korea, Heejoon Myung), Denmark (Lars Hansen, Nikoline Olsen), Belgium (Jean-Paul Pirnay, Pieter-Jan Ceyssens, Rob Lavigne) etc."]]},"created_time":1665364756676,"last_edited_time":1665365640000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"28420b96-fa73-4eb4-a34e-2abd19fae6b2":{"value":{"id":"28420b96-fa73-4eb4-a34e-2abd19fae6b2","version":20,"type":"text","properties":{"title":[["In the last 12 months we have demonstrated operational logistics in terms of phage exchange at state, national and international level, standardised workflows for sample submission and patient screening, genomics sequencing, patient isolate and phage screening under STAMP [^6] and standardised data curation (see Jan Zheng’s articles [^7]) to produce Australian Phage Passport (to be published soon)."]]},"format":{"copied_from_pointer":{"id":"a41b1ebd-da16-4052-a62d-2f98e7d2fc50","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"created_time":1665365674222,"last_edited_time":1665365760000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"copied_from":"a41b1ebd-da16-4052-a62d-2f98e7d2fc50","created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"73c1941f-029b-465f-bbd6-8dcdd027fe45":{"value":{"id":"73c1941f-029b-465f-bbd6-8dcdd027fe45","version":11,"type":"text","properties":{"title":[["It is important to note that the availability of diverse high-quality phages is facilitated by our bioprospecting programs (Stephen Stick [^8], Anthony Kicic, Trevor Lithgow, Jeremy Barr) and our national and international linkages. The accurate representation of bacterial strains that is our stock-in-trade enables us to identify which phages we need on the shelves and which phages can be lower volumes, as well as which ones can be available in a few days or a week. This sets us apart from all of our competitors and is the power of our national network."]]},"created_time":1665365683169,"last_edited_time":1665365760000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"02938426-36ce-482d-aa28-578cd2508b64":{"value":{"id":"02938426-36ce-482d-aa28-578cd2508b64","version":51,"type":"image","properties":{"source":[["https://lh3.googleusercontent.com/lgkQO95co6MtiRMnEamzPZzmUKVlWpfUpkAbBvAtoMrL-KguOBydJGBCdEy8PUkr9Jn2k0aLA6gjFE6cbguGL3H-UFqO1CpgyZyI-iVw1Z7Y5KUZ4MhNLvMDQJbhDh9znNg24c_PyTpQTXgWOiPVfnPJ1syjHjihgWleEuP7HYri7vwY2q8orGfrG4jG64Cdx0GtCg"]],"caption":[["Fig. 1.",[["b"]]],[" Economies of scale for phage production can be easily achieved. (credit: Jon Iredell)."]]},"format":{"block_width":432,"block_full_width":false,"block_page_width":false},"created_time":1665366711963,"last_edited_time":1665372720000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"6584aabd-d0cc-47bb-948e-b884182c15d9":{"value":{"id":"6584aabd-d0cc-47bb-948e-b884182c15d9","version":11,"type":"text","properties":{"title":[["Here, we present our calculations on phage production [^9]. Phage production is a growth process. We have reconciled with the fact that a small batch costs almost as much as a large batch, and efficiencies of scale are very important. For a ~$60,000 AUD GMP-grade one off batch of ~1,000 doses (~30 courses) means we can produce phages for about the cost of a modestly priced antibiotics. Accounting for a clinical trial with 50% wastage, this is well beyond the inflection point for economies of scale."]]},"created_time":1665365683170,"last_edited_time":1665365760000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"77f13ff9-da54-46af-aac0-7fe0eeadf356":{"value":{"id":"77f13ff9-da54-46af-aac0-7fe0eeadf356","version":4,"type":"text","created_time":1665365760000,"last_edited_time":1665365760000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"4ab1f175-0c07-49b2-91c1-073142a2a6f1":{"value":{"id":"4ab1f175-0c07-49b2-91c1-073142a2a6f1","version":18,"type":"text","properties":{"title":[["[^1]: Phage Biobank: Present Challenges and Future Perspectives. RCY Lin, JC Sacher, PJ Ceyssens, J Zheng, A Khalid, JR Iredell & The Australian Phage Network. Current Opinions in Biotechnology https://doi.org/10.1016/j.copbio.2020.12.018"]]},"created_time":1665364756676,"last_edited_time":1665365460000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"f0f3b16b-e68a-4556-a96e-b2abf9a62539":{"value":{"id":"f0f3b16b-e68a-4556-a96e-b2abf9a62539","version":19,"type":"text","properties":{"title":[["[^2]: "],["https://www.phageaustralia.org/blog/phage-batch-results",[["a","https://www.phageaustralia.org/blog/phage-batch-results"]]],[", https://phage.directory/capsid/phage-making-first-results"]]},"created_time":1665364756677,"last_edited_time":1665365460000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"f3985df4-4158-4981-9737-46be276d7218":{"value":{"id":"f3985df4-4158-4981-9737-46be276d7218","version":16,"type":"text","properties":{"title":[["[^3]: https://phage.directory/capsid/phage-shipping-around-australia"]]},"created_time":1665364756677,"last_edited_time":1665365460000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"78aedaed-52c0-4e9d-a178-9eaed510e00e":{"value":{"id":"78aedaed-52c0-4e9d-a178-9eaed510e00e","version":16,"type":"text","properties":{"title":[["[^4]: NSW Pathogen Biobank, Jon Iredell, Ruby Lin, Tania Sorrell, Dominic Dwyer, Wieland Meyer, Sharon Chen et al. $100k awarded, 2019-2023."]]},"created_time":1665364756677,"last_edited_time":1665365460000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"081ad788-73b1-4923-b840-f5fa9d13b250":{"value":{"id":"081ad788-73b1-4923-b840-f5fa9d13b250","version":16,"type":"text","properties":{"title":[["[^5]: NSW Phage Biobank, Jon Iredell, Ruby Lin. $100k awarded, 2020-4"]]},"created_time":1665364756677,"last_edited_time":1665365460000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"b027ef1d-7a59-444f-a9c1-681d45b606f8":{"value":{"id":"b027ef1d-7a59-444f-a9c1-681d45b606f8","version":6,"type":"text","properties":{"title":[["[^6]: https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=382817&isReview=true"]]},"created_time":1665365779887,"last_edited_time":1665365760000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"3402ce4c-94bc-481e-a22d-c11594ed495e":{"value":{"id":"3402ce4c-94bc-481e-a22d-c11594ed495e","version":6,"type":"text","properties":{"title":[["[^7]: "],["https://phage.directory/capsid/how-to-organize-phage-biobank-data",[["a","https://phage.directory/capsid/how-to-organize-phage-biobank-data"]]],["; "],["https://phage.directory/capsid/how-to-name-a-phage",[["a","https://phage.directory/capsid/how-to-name-a-phage"]]],["; https://phage.directory/capsid/how-to-track-phages"]]},"created_time":1665365779888,"last_edited_time":1665365760000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"fc2a4e50-f96c-4d0a-a130-c7f7c6ea930c":{"value":{"id":"fc2a4e50-f96c-4d0a-a130-c7f7c6ea930c","version":6,"type":"text","properties":{"title":[["[^8]: “On country” bioprospecting, phage naming in language, rapid through-put susceptibility testing; Ng RN, Grey LJ, Vaitekenas A, McLean SA, Rudrum JD, Laucirica DR, "],["et al",[["i"]]],[". Development and validation of a miniaturized bacteriophage host range screening assay against antibiotic resistant Pseudomonas aeruginosa. J Microbiol Methods. 2021;190:106346."]]},"created_time":1665365779888,"last_edited_time":1665365760000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"d095b494-c33a-4de2-ab97-824e77e7a973":{"value":{"id":"d095b494-c33a-4de2-ab97-824e77e7a973","version":6,"type":"text","properties":{"title":[["[^9]: Based on quotes from third party GMP-phage production and hospital statistics."]]},"created_time":1665365779888,"last_edited_time":1665365760000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"45c5195d-9d29-4b00-9055-3ae283dec520":{"value":{"id":"45c5195d-9d29-4b00-9055-3ae283dec520","version":3,"type":"text","created_time":1665365640000,"last_edited_time":1665365640000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"17f7960f-7b55-4195-b758-66aa3bae9188":{"value":{"id":"17f7960f-7b55-4195-b758-66aa3bae9188","version":4,"type":"text","created_time":1665365760000,"last_edited_time":1665365760000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"3b1254b3-75f4-4027-b015-19a5685f1037":{"value":{"id":"3b1254b3-75f4-4027-b015-19a5685f1037","version":15,"type":"sub_header","properties":{"title":[["2. Effective regulatory pathways."]]},"created_time":1665365683170,"last_edited_time":1665447960000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"acc80f66-d2cb-4024-a9d4-ecaeeed0e2d2":{"value":{"id":"acc80f66-d2cb-4024-a9d4-ecaeeed0e2d2","version":2,"type":"text","properties":{"title":[["Facilitated by NSW Health (Tony Penna, Laura Collie, Julia Warning and Sian Hope), we are working with representatives from TGA (Therapeutic Goods Administration) and OGTR (Office of Gene Technology Regulator) to regulate phage therapy in Australia. We will share this in due course."]]},"created_time":1665365683170,"last_edited_time":1665365640000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"03546c5d-5405-4497-8c56-dcd03fc642d4":{"value":{"id":"03546c5d-5405-4497-8c56-dcd03fc642d4","version":7,"type":"text","properties":{"title":[["We have established a clinical network and a nationally approved protocol to regulate phage therapy under the clinical trial framework i.e., Safety and tolerability of Standardised Treatment and Monitoring of Phage therapy (STAMP) in adults and children (Australia and New Zealand Clinical Trial Registry: ACTRN12621001526864 [^10]). This is endorsed by ASID (Australasian Society for Infectious Diseases), ASID paediatric infectious diseases arm (ANZPID), CFA (Cystic Fibrosis Australia) and TSANZ (Thoracic Society of Australia and New Zealand)."]]},"created_time":1665366865167,"last_edited_time":1665366960000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"7b689efd-777d-46e5-9d2a-311dacbaec12":{"value":{"id":"7b689efd-777d-46e5-9d2a-311dacbaec12","version":9,"type":"text","properties":{"title":[["Standardised treatment protocols endorsed by expert groups together with clinicians and nurses, training & education are an integral part of Phage Australia’s value proposition. To note, this will be developed further towards “Phage Therapy for Critical Infection”, similar to the S100-style training i.e., Critical Care Short Courses at both Westmead and the Alfred that have been self- sustainable for over a decade. Furthermore, we have designed a Phage Therapy Education Package for scientists and consumers (Sian Hope, Ruby Lin) that is waiting to be signed off. I will detail the importance of industry participation in training workforce, specifically PhD students [^11], in the next instalment."]]},"created_time":1665366865167,"last_edited_time":1665366960000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"23292831-f606-458d-a5b5-223855a54b62":{"value":{"id":"23292831-f606-458d-a5b5-223855a54b62","version":9,"type":"text","properties":{"title":[["[^10]: https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=382817&isReview=true"]]},"created_time":1665366865167,"last_edited_time":1665366960000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"b736ad57-a341-46c4-a8a6-7e0617ec539b":{"value":{"id":"b736ad57-a341-46c4-a8a6-7e0617ec539b","version":19,"type":"text","properties":{"title":[["[^11]: https://www.science.org/content/article/controversial-plan-brings-ph-d-students-biotech-training"]]},"created_time":1665366865168,"last_edited_time":1665367020000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"4e582e2a-b00d-49e1-8444-8e19f37b299c":{"value":{"id":"4e582e2a-b00d-49e1-8444-8e19f37b299c","version":5,"type":"text","created_time":1665367020000,"last_edited_time":1665367020000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"4ae29f0c-e5e7-4458-9435-735b8719369d":{"value":{"id":"4ae29f0c-e5e7-4458-9435-735b8719369d","version":2,"type":"text","created_time":1665367020000,"last_edited_time":1665367020000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"b8a28811-56a1-4a8f-81fa-f6aa9a0a68d1":{"value":{"id":"b8a28811-56a1-4a8f-81fa-f6aa9a0a68d1","version":41,"type":"sub_header","properties":{"title":[["3. A roadmap for clinical Pathways and the patient journey."]]},"created_time":1665366943955,"last_edited_time":1665379680000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"9385532b-5856-4c2d-9801-3030b0e9dd3b":{"value":{"id":"9385532b-5856-4c2d-9801-3030b0e9dd3b","version":2,"type":"text","properties":{"title":[["In collaboration with NSW Health (Sian Hope, Julia Warning, Laura Collie), we mapped out the patient journey for phage therapy in comparison to patients being treated with antibiotics only at a public hospital, e.g., Westmead Hospital. To note, Jon Iredell and Ameneh Khatami remain the only two clinicians in Australia with phage therapy and therapeutic monitoring experience (see our publications on Phage Australia website), as well as the process of phage-pathogen matching towards production of a purified phage for intravenous administration."]]},"created_time":1665366943955,"last_edited_time":1665366900000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"0840ccaf-ea05-496c-aac7-1dbe5714395e":{"value":{"id":"0840ccaf-ea05-496c-aac7-1dbe5714395e","version":2,"type":"text","properties":{"title":[["A health implementation plan for phage therapy in the clinic (Manisha Yapa) will ensure that the most efficient implementation of this new therapy is understood well in advance of the rollout once it is ‘main streamed’."]]},"created_time":1665366943955,"last_edited_time":1665366900000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"d7f2dff4-5441-4fe1-ad9d-2899be5d416b":{"value":{"id":"d7f2dff4-5441-4fe1-ad9d-2899be5d416b","version":2,"type":"text","properties":{"title":[["Health economics are outlined below, and phage production cost is outlined above."]]},"created_time":1665366943956,"last_edited_time":1665366900000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"fa51d75c-e497-4701-b835-813fcae2d4b4":{"value":{"id":"fa51d75c-e497-4701-b835-813fcae2d4b4","version":4,"type":"text","created_time":1665393780000,"last_edited_time":1665393780000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"73c14399-5321-4615-ae31-99bbf47a7613":{"value":{"id":"73c14399-5321-4615-ae31-99bbf47a7613","version":97,"type":"sub_header","properties":{"title":[["4. Cost-effective payment and reimbursement pathways."]]},"created_time":1665366943956,"last_edited_time":1665379680000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"bbba914f-1c7b-4c60-93a5-16f58b263817":{"value":{"id":"bbba914f-1c7b-4c60-93a5-16f58b263817","version":14,"type":"text","properties":{"title":[["We commissioned HTAnalysts [^12] to map out in the first instance feasibility and impact of phage therapy for AMR (antimicrobial resistance) sepsis [^13] and prosthetic joint infection (PJI)."]]},"created_time":1665366943956,"last_edited_time":1665367080000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"f464ad9f-e684-441c-933c-927b9e590536":{"value":{"id":"f464ad9f-e684-441c-933c-927b9e590536","version":24,"type":"text","properties":{"title":[["Substantial savings are made with phage therapy, i.e., $122.8M over a 6-year window for PJI and $67M for sepsis (over 3 years). See link to the reports. Briefly the findings are outlined here."]]},"created_time":1665366943956,"last_edited_time":1665703080000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"2c950c33-78d6-40f9-b36b-d267adad0c61","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"3230427e-2ef1-4f50-83ae-bb59d20f1019":{"value":{"id":"3230427e-2ef1-4f50-83ae-bb59d20f1019","version":47,"type":"image","properties":{"size":[["467.4KB"]],"title":[["Untitled"]],"source":[["https://s3-us-west-2.amazonaws.com/secure.notion-static.com/3815fd54-c5a5-4dcd-ae12-122fb479dc9d/Untitled.png"]],"caption":[["Fig. 2.",[["b"]]],[" Summarised figure of savings by introducing phage therapy as part of AMR sepsis clinical service. Refer to HTAnalyst report."]]},"format":{"block_width":480,"display_source":"https://s3-us-west-2.amazonaws.com/secure.notion-static.com/3815fd54-c5a5-4dcd-ae12-122fb479dc9d/Untitled.png","block_full_width":false,"block_page_width":false,"block_aspect_ratio":1.1737704918032787,"block_preserve_scale":true},"created_time":1665367200000,"last_edited_time":1665372720000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"file_ids":["3815fd54-c5a5-4dcd-ae12-122fb479dc9d"],"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"ed3da41b-e1a8-497b-8e79-d3f81b19d9be":{"value":{"id":"ed3da41b-e1a8-497b-8e79-d3f81b19d9be","version":17,"type":"text","properties":{"title":[["The key findings for AMR sepsis are (as outlined in the report [^amrsepsis-pdf]):"]]},"created_time":1665367121383,"last_edited_time":1665368040000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"5046cbe1-86bc-4b0b-be36-54a9a8f7985d":{"value":{"id":"5046cbe1-86bc-4b0b-be36-54a9a8f7985d","version":38,"type":"bulleted_list","properties":{"title":[["If all patients across Australia with AMR sepsis (2,461 patients) were treated with bacteriophage therapy, the total savings over 3 years were estimated to be $67.0 million corresponding to an average saving of $27,239 per patient. "]]},"created_time":1665367121384,"last_edited_time":1665367980000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"81c8a323-9148-4649-87cb-94732365a2e6":{"value":{"id":"81c8a323-9148-4649-87cb-94732365a2e6","version":2,"type":"bulleted_list","properties":{"title":[["If all patients across NSW with AMR sepsis (782 patients) were treated with bacteriophage therapy, the total savings over 3 years were estimated to be $21.3 million."]]},"created_time":1665367121385,"last_edited_time":1665367080000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"ff002652-a964-417f-93bc-b04993998131":{"value":{"id":"ff002652-a964-417f-93bc-b04993998131","version":2,"type":"bulleted_list","properties":{"title":[["The total direct savings (healthcare related savings) were $21.8 million, all of which was paid for by the government."]]},"created_time":1665367121385,"last_edited_time":1665367080000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"0b456242-4748-4c5a-9da3-ea5555431975":{"value":{"id":"0b456242-4748-4c5a-9da3-ea5555431975","version":2,"type":"bulleted_list","properties":{"title":[["The total indirect savings (non-healthcare related savings) were $45.2 million, most of which was paid for by patients (63%) followed by employers (20%) and the government (17%)."]]},"created_time":1665367121386,"last_edited_time":1665367080000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"7954fd79-df3b-4d84-a730-f734e4f201c6":{"value":{"id":"7954fd79-df3b-4d84-a730-f734e4f201c6","version":2,"type":"bulleted_list","properties":{"title":[["Length of stay for patients with AMR sepsis is estimated to be reduced by an average of 7.6 days per 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Greater saving per patients were incurred in the first 4 years ($50,846 for year 0-2, $46,153 for year 2-4 and $25,207 for year 4-6)."]]},"created_time":1665367357788,"last_edited_time":1665710280000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"307263b3-eb75-4ccc-869b-5ba10f790adc":{"value":{"id":"307263b3-eb75-4ccc-869b-5ba10f790adc","version":2,"type":"text","properties":{"title":[["These analyses will be repeated using real data in 3 years’ time and we expect this will be the first real-world cost-effectiveness data available for phage therapy."]]},"created_time":1665367357789,"last_edited_time":1665367320000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"b02be1d6-c829-468d-aa88-d3112a40081e":{"value":{"id":"b02be1d6-c829-468d-aa88-d3112a40081e","version":2,"type":"text","properties":{"title":[["Based on these health economics calculations, we can state that phage therapy is an efficient spend of public health dollars right now."]]},"created_time":1665367357789,"last_edited_time":1665367320000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"6f33f950-c403-410f-8c28-46c0851adc38":{"value":{"id":"6f33f950-c403-410f-8c28-46c0851adc38","version":59,"type":"image","properties":{"size":[["127.0KB"]],"title":[["Untitled"]],"source":[["https://s3-us-west-2.amazonaws.com/secure.notion-static.com/11fb8298-cca4-4c5b-b359-0b5c49f1cc85/Untitled.png"]],"caption":[["Fig. 4",[["b"]]],[". 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This graph shows that ICU and bone marrow transplant services are very good value, as are kidney transplants. Coronary bypass grafting (CABG) is over $50,000 AUD. Our externally commissioned modelling showed that phage therapy to be at least as good value as bone marrow transplantation and ICU services. 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The Australian Antimicrobial Resistance Network – AAMRNet – has set out a position statement [^16] around funding of novel antimicrobials in Australia but this remains an open conversation."]]},"created_time":1665367357817,"last_edited_time":1665377940000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"5d9cfe0b-6c8a-4426-857a-904869e8dccf":{"value":{"id":"5d9cfe0b-6c8a-4426-857a-904869e8dccf","version":2,"type":"text","properties":{"title":[["At Phage Australia, we have scheduled for Health Technology Assessment and Market Access Analysis on Phage Therapy, in order to inform PBAC and MSAC."]]},"created_time":1665367406098,"last_edited_time":1665367380000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"60123215-f748-4a14-8478-19bf75c3eb75":{"value":{"id":"60123215-f748-4a14-8478-19bf75c3eb75","version":7,"type":"text","properties":{"title":[["A recent example of experimental therapy being accepted into all aspect of healthcare system is Novartis’ outcome-based healthcare strategy of introducing CAR-T cell therapy into the mainstream market [^17] based on one single-arm data in adults and paediatric patients."]]},"created_time":1665367406098,"last_edited_time":1665377940000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"baf3ecc9-1112-4f6e-b6a8-0a631fc1b081":{"value":{"id":"baf3ecc9-1112-4f6e-b6a8-0a631fc1b081","version":17,"type":"text","properties":{"title":[["[^12]: https://htanalysts.com.au/"]]},"created_time":1665366943956,"last_edited_time":1665368280000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"a5ad3e42-54bf-490e-af0c-13e85007afd4":{"value":{"id":"a5ad3e42-54bf-490e-af0c-13e85007afd4","version":12,"type":"text","properties":{"title":[["[^13]: This included data from our phage therapy clinical trial: Petrovic Fabijan, A., Lin, R.C.Y., Ho, J. et al. 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",[["b"]]],["Overall components of Phage Australia that are attractive to potential investment. 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Such legislation would impact how we (Australia) and other jurisdictions look at funding novel antimicrobials in health services (and broader applications, See One Health Initiative by WHO [^21])."]]},"created_time":1665376390098,"last_edited_time":1665376440000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"589dda39-6ccd-456d-be26-2ab4025e4984":{"value":{"id":"589dda39-6ccd-456d-be26-2ab4025e4984","version":19,"type":"text","properties":{"title":[["[^20]: https://www.novartis.com/research-development/technology-platforms/cell-therapy/car-t-cell-therapy-and-beyond"]]},"created_time":1665376390098,"last_edited_time":1665377940000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"88d630ff-4fde-4468-8fd2-a447d6eaabf2":{"value":{"id":"88d630ff-4fde-4468-8fd2-a447d6eaabf2","version":8,"type":"text","properties":{"title":[["[^21]: https://www.who.int/news-room/questions-and-answers/item/one-health"]]},"created_time":1665376390098,"last_edited_time":1665377940000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"cccc0395-278e-4441-b243-d82b2ab49b9a":{"value":{"id":"cccc0395-278e-4441-b243-d82b2ab49b9a","version":10,"type":"sub_sub_header","properties":{"title":[["Income Stream 2: COST-RECOVERY for BIOBANKING SERVICES"]]},"created_time":1665376475420,"last_edited_time":1665379620000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"babd4cfb-9d41-4172-a178-310840244185":{"value":{"id":"babd4cfb-9d41-4172-a178-310840244185","version":2,"type":"text","properties":{"title":[["We have a collection of phages to screen against representative pathogens. Numerous high value phages can be put forward for therapeutic purposes."]]},"created_time":1665376475420,"last_edited_time":1665376440000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"f2e81375-2393-450b-bd01-dacb249228d4":{"value":{"id":"f2e81375-2393-450b-bd01-dacb249228d4","version":2,"type":"text","properties":{"title":[["A simple cost-recovery system is normal practice amongst well established biobanks e.g., DSMZ ("],["https://www.dsmz.de",[["a","https://www.dsmz.de/"]]],[" German Collection of Microorganisms and Cell Cultures GmbH) and our local Core Facility WIMR biobank (>40 biospecimen collections). For example, WIMR biobank recoups costs by providing DNA and RNA extraction services for the biospecimens held by the facility, requested by researchers."]]},"created_time":1665376475420,"last_edited_time":1665376440000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"8ce2a8f9-038e-435e-b951-d426876ba727":{"value":{"id":"8ce2a8f9-038e-435e-b951-d426876ba727","version":46,"type":"text","properties":{"title":[["Beyond providing phages for clinical trials outlined here (and in the MRFF Frontiers Stage w proposal), this phage collection will be made available to those with any need for bioremediation or biocontrol. Use of phages is well established in the food and agriculture industry (PhageGuard, "],["https://phageguard.com/",[["a","https://phageguard.com/"]]],[" for listeria management), poultry, aquaculture and diary (Proteon Pharmaceuticals, https://www.proteonpharma.com/) etc."]]},"created_time":1665376475420,"last_edited_time":1665702540000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"2c950c33-78d6-40f9-b36b-d267adad0c61","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"85e62754-2b6e-4e04-8ac1-80b22e5df6d8":{"value":{"id":"85e62754-2b6e-4e04-8ac1-80b22e5df6d8","version":2,"type":"text","properties":{"title":[["To note, management and governance of this vast operation will require another discussion piece. Briefly, for Phage Australia, we have adopted a governance model with a national executive committee and an independent strategic advisory committee. In the first instance, terms of reference are signed off by Phage Australia partners, bound by mutual obligations and privileged access to data and biological materials (phages and reference strains). This will evolve in due course."]]},"created_time":1665376475420,"last_edited_time":1665376440000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"5c529f61-2d28-4bea-8d4c-8b8a6b964311":{"value":{"id":"5c529f61-2d28-4bea-8d4c-8b8a6b964311","version":23,"type":"sub_sub_header","properties":{"title":[["Income Stream 3: PACKAGED PHAGE and BACTERIAL PRODUCTS [^22]"]]},"created_time":1665376475421,"last_edited_time":1665376620000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"35d81ab9-6927-4796-acae-f5fe090c46c7":{"value":{"id":"35d81ab9-6927-4796-acae-f5fe090c46c7","version":8,"type":"text","properties":{"title":[["A large holding of phages from worldwide collections broadens the ability to screen and identify high value phages that can be put forward for therapeutic purposes. We have supported several cases in this way, i.e., 2 CF paediatric patients and 1 oncology paediatric patient requiring "],["Mycobacterium abscessus",[["i"]]],[" phages and 1 paediatric patient requiring "],["Pseudomonas",[["i"]]],[" phage [^23]) and could do this as a service, with appropriate recompense to external owners under licensing agreements."]]},"created_time":1665376534047,"last_edited_time":1665376500000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"32072f41-6be1-40d4-a1d1-c6f94fff175f":{"value":{"id":"32072f41-6be1-40d4-a1d1-c6f94fff175f","version":2,"type":"text","properties":{"title":[["In this way, material transfer and licensing agreement should allow the Phage Exchange Program to present a curated collection of phages and bacteria ready for use. This includes;"]]},"created_time":1665376534047,"last_edited_time":1665376500000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"3341259b-8ba5-4c71-a70c-0cbb2388537d":{"value":{"id":"3341259b-8ba5-4c71-a70c-0cbb2388537d","version":2,"type":"bulleted_list","properties":{"title":[[""],["Phages of therapeutic value.",[["i"]]],[" Purified phage can potentially be provided with cost-recovery through the public health system (we have worked out patient journey and are costing this out). This income stream might ideally come from government and hospital contracts as a supplier of certified phages."]]},"created_time":1665376534048,"last_edited_time":1665376500000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"8fe0c161-42e7-4fd3-ac8c-14d4615223f8":{"value":{"id":"8fe0c161-42e7-4fd3-ac8c-14d4615223f8","version":2,"type":"bulleted_list","properties":{"title":[["Phages (single, cocktail, natural, genetically modified or chemically modified) targeting a specific antimicrobial resistant pathogen can be sold to external customers requiring such phages. Customers identified would include research laboratories and industry. Currently there is no service of this nature in the world. A major advantage is our access to a well-curated collection of pathogens (from surveillance programs) and phages. Metadata associated with the host bacteria and phages are systematically processed (SOPs are being established and in the process of harmonising across the network), curated, tested against relevant strains, sequenced and archived."]]},"created_time":1665376534048,"last_edited_time":1665376500000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"9810d395-64f8-465a-9338-b04a3f985392":{"value":{"id":"9810d395-64f8-465a-9338-b04a3f985392","version":2,"type":"bulleted_list","properties":{"title":[["The pathogen collections that enable this screening of phage are also of high value to research laboratories and pharmaceutical companies who wish to test their own new antimicrobial agents."]]},"created_time":1665376534048,"last_edited_time":1665376500000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"830c0bd0-e8bf-49e3-8093-e5304a268a94":{"value":{"id":"830c0bd0-e8bf-49e3-8093-e5304a268a94","version":9,"type":"text","properties":{"title":[["The emergence of COVID-19 in the last 3 years has highlighted global health threat from antimicrobial resistance but at the same time presents an opportunity for the antibiotic resistance market towards growth. The global antimicrobial resistance market was valued at $9.39 billion USD in 2020, and is estimated to reach $13.8 billion USD in 2027, with a compound annual growth rate of 4.68% from 2021-2027 [^24]. WHO recognises that phage therapy offers an alternative approach to combat global AMR threat."]]},"created_time":1665376534048,"last_edited_time":1665377940000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"f94d3f1a-0387-4dae-ab69-26246335c562":{"value":{"id":"f94d3f1a-0387-4dae-ab69-26246335c562","version":12,"type":"text","properties":{"title":[["[^22]: ATCC (https://www.atcc.org/) and Addgene (https://www.addgene.org) both package bacteria and phage products."]]},"created_time":1665376475421,"last_edited_time":1665376560000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"62ff7632-bea8-4225-92e2-08d61514effc":{"value":{"id":"62ff7632-bea8-4225-92e2-08d61514effc","version":9,"type":"text","properties":{"title":[["[^23]: Khatami A, Lin RCY, Petrovic-Fabijan A, Alkalay-Oren S, Almuzam S, Britton PN, Brownstein MJ, Dao Q, Fackler J, Hazan R, Horne B, Nir-Paz R, Iredell JR. Bacterial lysis, autophagy and innate immune responses during adjunctive phage therapy in a child. EMBO Mol Med. 2021 Sep 7;13(9):e13936. doi: 10.15252/emmm.202113936."]]},"created_time":1665376534048,"last_edited_time":1665376560000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"e1d7a475-8b8b-456a-bb40-cda7d93102ac":{"value":{"id":"e1d7a475-8b8b-456a-bb40-cda7d93102ac","version":11,"type":"text","properties":{"title":[["[^24]: https://finance.yahoo.com/news/global-13-8-billion-antimicrobial-110900720.html"]]},"created_time":1665376534048,"last_edited_time":1665376560000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"d10a2678-68c7-4b5b-a5c6-fc640eaabf82":{"value":{"id":"d10a2678-68c7-4b5b-a5c6-fc640eaabf82","version":5,"type":"text","created_time":1665376440000,"last_edited_time":1665376680000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"684b0aff-9ee0-4590-8554-adb3e0566dc4":{"value":{"id":"684b0aff-9ee0-4590-8554-adb3e0566dc4","version":14,"type":"sub_sub_header","properties":{"title":[["Income Stream 4: SYNTHETIC PRODUCTS"]]},"created_time":1665376440000,"last_edited_time":1665379620000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"d93e2430-32f8-473c-81ca-750e5c864fa6":{"value":{"id":"d93e2430-32f8-473c-81ca-750e5c864fa6","version":10,"type":"text","properties":{"title":[["A survey of phage companies [^25] indicated that genetic modification technologies (e.g., CRISPR) have been applied to phages, bacteria and plasmids to generate novel products that are protectable by patent, e.g., Locus Biosciences, BiomX and Eligo Biosciences. Chemically modified phages (e.g., conjugated with antibiotics (Hien Duong) or other valuable molecules and genetically modified phages (e.g., "],["muddy",[["i"]]],[" from Graham Hatfull) will be truly novel and therefore protectable IP of potential high value."]]},"created_time":1665376746096,"last_edited_time":1665379620000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"9abcec9f-90a0-49b7-ab53-19cc749ccc38":{"value":{"id":"9abcec9f-90a0-49b7-ab53-19cc749ccc38","version":2,"type":"text","properties":{"title":[["Manufacturing Bacterial Host Strains.",[["i"]]]]},"created_time":1665376746096,"last_edited_time":1665376740000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"96c9306e-cbd4-4879-a8cb-6a491ddcf637":{"value":{"id":"96c9306e-cbd4-4879-a8cb-6a491ddcf637","version":11,"type":"text","properties":{"title":[["While phage is the end product of a bioprocessing pipeline, the bacterial host strains are key to successful manufacturing. For example, Jon Iredell and Kamal Kamruzzaman have develop a process of curing harmful plasmids from a bacterium that can be applied even to strains with previously uncharacterised systems [^26]. This approach can be applied to ensure that no harmful AMR plasmids are included in the production pipeline, even for phages whose main target is highly AMR strains that are normally full of such plasmids and might be otherwise difficult to produce. Any infectious diseases physicians and clinical microbiologist working at an Australian public hospital would appreciate such an approach."]]},"created_time":1665376746096,"last_edited_time":1665376800000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"9c6740d8-6cc5-4b7b-9d34-5abca3ce2c13":{"value":{"id":"9c6740d8-6cc5-4b7b-9d34-5abca3ce2c13","version":2,"type":"text","properties":{"title":[["A collection of such curated manufacturing bacterial host strains is potentially very valuable (specifically to satisfy regulatory requirement of a therapeutic phage production). Identifying key stakeholders in phage production, marketing and distribution are being mapped out. We believe that such a venture will be the first of its kind and will fill an unique niche in bioprocessing."]]},"created_time":1665376797593,"last_edited_time":1665376740000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"4eab5050-5149-4985-b44f-6817db98b816":{"value":{"id":"4eab5050-5149-4985-b44f-6817db98b816","version":12,"type":"text","properties":{"title":[["[^25]: Phage Directory: Airtable list https://airtable.com/shr8f1wbrK2hvR1an/tblCpqDQJjqyqgtj0/viw01yqq3wEoCCgie"]]},"created_time":1665376746096,"last_edited_time":1665376740000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"d906c7f6-3933-4768-8c10-5010f7ea4f9c":{"value":{"id":"d906c7f6-3933-4768-8c10-5010f7ea4f9c","version":12,"type":"text","properties":{"title":[["[^26]: Kamruzzaman M, Mathers AJ, Iredell JR. A Novel Plasmid Entry Exclusion System in pKPC_UVA01, a Promiscuous Conjugative Plasmid Carrying the blaKPC Carbapenemase Gene. Antimicrob Agents Chemother. 2022 Mar 15;66(3):e0232221. doi: 10.1128/aac.02322-21. Epub 2022 Jan 10. PMID: 35007138; PMCID: PMC8923210."]]},"created_time":1665376797593,"last_edited_time":1665376860000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"4015544a-781f-4e4d-b0f3-b61901119ee0":{"value":{"id":"4015544a-781f-4e4d-b0f3-b61901119ee0","version":5,"type":"text","created_time":1665376800000,"last_edited_time":1665376800000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"2025cd35-63aa-4df1-b2a5-e2d3903faba3":{"value":{"id":"2025cd35-63aa-4df1-b2a5-e2d3903faba3","version":11,"type":"sub_sub_header","properties":{"title":[["Income Stream 5: PERSONALISED PRODUCTS"]]},"created_time":1665376800000,"last_edited_time":1665379620000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"d2458c66-a364-450c-80f6-79c64091813b":{"value":{"id":"d2458c66-a364-450c-80f6-79c64091813b","version":2,"type":"text","properties":{"title":[["Another attractive aspect of personalised production of phages is the "],["Personalised therapy approach ",[["i"]]],["where target selectivity allows a spectrum of antibacterial activity to be tailored for clinical use. Thus, phage combinations or ‘cocktails’ can be designed to be broadly targeted to cover a range of important likely pathogens, or highly microbe-specific phage therapy can be used to leave intact the useful non-target microbiota (‘good’ bacteria) that would normally be damaged by antibiotics."]]},"created_time":1665376854380,"last_edited_time":1665376800000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"3d7d2963-8e3e-4130-b03e-bada9b1bb6b0":{"value":{"id":"3d7d2963-8e3e-4130-b03e-bada9b1bb6b0","version":2,"type":"text","properties":{"title":[["Personalised lifestyle product",[["i"]]],[" (not limited to clinical use) can also be developed. For example, there are phage companies dedicated to cosmetics (acne, https://phylabiotics.com/), animal/pet health (skin infection, gut microbiome) and poultry and dairy industry."]]},"created_time":1665376854380,"last_edited_time":1665376800000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"e963927b-18a0-4360-860e-9c1dc0e9ab6d":{"value":{"id":"e963927b-18a0-4360-860e-9c1dc0e9ab6d","version":28,"type":"text","properties":{"title":[["Management of gut health is part of the lifestyle supplements industry [^27] that generates billions of dollars globally. Despite inherent poor regulation associated with this industry, I cannot help but speculate that phage products can be marketed as a preventative measure for many ailments. Scientifically, restorative effects of supplements that is relevant to gut microbiome and diet [^28] can form part of the intervention strategies in, for example, sport science (e.g., enabling peak performance in elite athletes), cardiovascular diseases that involves the gut (e.g., hypertension), neurodegenerative diseases involving the gut (e.g., Parkinson’s) etc. Use of phages as a prophylaxis on medical devices and medical textile may also be a possibility."]]},"created_time":1665376854381,"last_edited_time":1665702480000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"2c950c33-78d6-40f9-b36b-d267adad0c61","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"0e0c0475-3fe2-47dd-9d18-2eaee5825be6":{"value":{"id":"0e0c0475-3fe2-47dd-9d18-2eaee5825be6","version":2,"type":"text","properties":{"title":[["Current trends in phage therapy involve commercial entities assembling phage cocktails to broaden the spectrum of activities of therapeutic formulations. This presents another set of challenges around the stability of combined phages, phage competition and the problem of routinely injecting high doses of mostly inactive viral particles (since often only one member of a ‘cocktail’ like this will be active against a given strain). An effective mechanism is to quickly screen an isolate against a large bank of phages or even to produce one quickly from bioprospecting. Phage Australia has demonstrated, specifically in the last 12 months that it is feasible to quickly screen (See up-and-coming work from Stephanie Lynch on Patient Screening Workflow) and focusing on bespoke therapy by quickly matching phage to patient isolate may have demand as an alternative service."]]},"created_time":1665376854381,"last_edited_time":1665376800000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"6167869e-9461-4986-9a9d-296ea6c16084":{"value":{"id":"6167869e-9461-4986-9a9d-296ea6c16084","version":5,"type":"text","properties":{"title":[["Agricultural and veterinary applications",[["i"]]],[" are also potentially important. A decade ago, there were only a handful of companies specialising in bacteriophage but by 2022, a fascination with the microbiome and the rise of antibiotic resistance means that bacteriophage research and development is enjoying a renaissance."]]},"created_time":1665376921027,"last_edited_time":1665702240000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"2c950c33-78d6-40f9-b36b-d267adad0c61","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"3e801d5f-f8cc-439f-a594-c3cd35d85a4f":{"value":{"id":"3e801d5f-f8cc-439f-a594-c3cd35d85a4f","version":36,"type":"text","properties":{"title":[["According to Credence Industry Market Research Report (October 2018), the global bacteriophage market held $567.9M USD in 2017 and is expected to grow at compound annual growth rate of 3.9% during the forecast period from 2018 to 2026. A list of phage companies on the market with their value proposition is curated by Phage Directory [^25]."]]},"created_time":1665376921028,"last_edited_time":1665702240000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"2c950c33-78d6-40f9-b36b-d267adad0c61","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"fb09f01d-ebb7-410d-8ef7-1f5d04d1b6cd":{"value":{"id":"fb09f01d-ebb7-410d-8ef7-1f5d04d1b6cd","version":9,"type":"text","properties":{"title":[["[^27]: https://www.gowellnessco.com/gut-health-supplements/"]]},"created_time":1665376854381,"last_edited_time":1665376860000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"ea5843fa-fcca-4eec-b424-5d147c089bab":{"value":{"id":"ea5843fa-fcca-4eec-b424-5d147c089bab","version":16,"type":"text","properties":{"title":[["[^28]: Leigh SJ, Morris MJ. 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As the field moves towards digitalisation [^30] we identified [^31] several enabling features such as centralised governance, standardised protocols, standardised definition (e.g., Data Dictionary used in REDcap to capture STAMP trial data) and good data management that are needed to facilitate contribution of data (clinical and lab data associated with a specific phage) and product (phage and/or bacteria, see Australia Phage Passport) to the Phage Australia biobank and data system."]]},"created_time":1665376992510,"last_edited_time":1665377040000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"9cf7eb6c-696a-48cb-b741-a55e3d864a4a":{"value":{"id":"9cf7eb6c-696a-48cb-b741-a55e3d864a4a","version":13,"type":"text","properties":{"title":[["An integrated platform combining Artificial Intelligence and Distributed Ledger Technology [^32] and internationally standardised quality management system (e.g., ISO9001 accreditation) can ensure seamless audit and quality assurance. This in turn boosts confidence amongst users, stakeholders and investors for a specific product. We are in the process of working out a ledger system for phage product and its companion data to address sample and data provenance. To make it fun, cryptocurrency, e.g., Phage Coin has been discussed but we proceed with caution [^33]."]]},"created_time":1665376992511,"last_edited_time":1665377040000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"f7bccecd-c643-48db-8d1c-caf78c7f7e84":{"value":{"id":"f7bccecd-c643-48db-8d1c-caf78c7f7e84","version":21,"type":"text","properties":{"title":[["The data, data management system and integrated platform we are building at Phage Australia is likely to be attractive to investors. A striking example of success with data utilisation and data linkage is Tempus [^34] - a Chicago-based technology company that offers genetic testing and aggregates clinical information for cancer [^35]. Groupon’s initial investment in 2015 enabled Tempus to be valued at $8.1 billion USD after raising $200 million in equity financing and $250 million in convertible debt by December 2020. Tempus said at the time that their investors included Baillie Gifford, Google, Franklin Templeton, Novo Holdings and funds managed by T. Rowe Price Group Inc. Currently Tempus is a company valued at $3.1 billion USD and its database enables clinicians to diagnose specific cancer type (and the best specific therapy to match) "],["in real time.",[["i"]]],[" There is no such venture in the infectious diseases space. Phage Australia’s effort can fill this gap."]]},"created_time":1665376992511,"last_edited_time":1665377100000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"ce5a9501-219a-4b1c-9a7e-6daad5b2b4ae":{"value":{"id":"ce5a9501-219a-4b1c-9a7e-6daad5b2b4ae","version":26,"type":"text","properties":{"title":[["There are also many examples of co-investment from public and private sectors [^25] to bring different streams of income into an entity by combining a physical collection of samples (e.g., a biobank) integrated with an online collection of data (decentralised databases). Sweden’s national collaboration for genomic medicine [^36] (from sequencing to clinical practice) and Scandinavia’s effort in combining public and private effort to utilise data to innovate [^37] healthcare are good examples."]]},"created_time":1665376992511,"last_edited_time":1665377220000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"f7fdf9cc-6ddd-4d91-a515-2c6d42a5d699":{"value":{"id":"f7fdf9cc-6ddd-4d91-a515-2c6d42a5d699","version":2,"type":"text","properties":{"title":[["Funding from MRFF Frontiers Stage 2, philanthropy and investors can expedite this whole process."]]},"created_time":1665377234279,"last_edited_time":1665377220000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"d95a655c-4d5b-41f2-9658-38b20ac79089":{"value":{"id":"d95a655c-4d5b-41f2-9658-38b20ac79089","version":11,"type":"text","properties":{"title":[["[^30]: https://www.nfx.com/post/biotech-to-techbio"]]},"created_time":1665376992511,"last_edited_time":1665377160000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"ec6d200b-1d1b-4d71-8f4a-9f2d3dc71ecf":{"value":{"id":"ec6d200b-1d1b-4d71-8f4a-9f2d3dc71ecf","version":9,"type":"text","properties":{"title":[["[^31]: Phage Biobank: Present Challenges and Future Perspectives. 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For example, a cost-recovery model was implemented in the first instance to recoup the cost of labour and reagents from a discounted rate to Phage Australia network users for phage, bacteria and metagenome sequencing. All negotiated discounts from Stage 1 were passed on to users. Many genomic sequencing service providers use this model to be self-sustainable without much external funding e.g., Ramaciotti Centre for Genomics at UNSW. We believe this model can be grown but recognise that we are not a genomic service provider."]]},"created_time":1665377295476,"last_edited_time":1665377280000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"4e923bf0-388d-4e00-8fa6-6373738a8e9e":{"value":{"id":"4e923bf0-388d-4e00-8fa6-6373738a8e9e","version":2,"type":"text","properties":{"title":[["Genomic sequencing underpins many essential activities outlined here, in particular, biobanking, phage matching and therapeutic monitoring. Success in making this self-sustainable right at the beginning in stage 1 demonstrates the feasibility of this venture beyond the next 5 years."]]},"created_time":1665377295476,"last_edited_time":1665377280000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"e18277ce-49e2-4322-9420-ddb0cb2d1b0f":{"value":{"id":"e18277ce-49e2-4322-9420-ddb0cb2d1b0f","version":4,"type":"text","created_time":1665376800000,"last_edited_time":1665377280000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"9c650eb5-e996-4833-8afa-98edb073afb5":{"value":{"id":"9c650eb5-e996-4833-8afa-98edb073afb5","version":39,"type":"sub_header","properties":{"title":[["Concluding Remarks"]]},"created_time":1665376800000,"last_edited_time":1665377280000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"6d6f72ee-387f-4b44-bedd-f4fa60a56431":{"value":{"id":"6d6f72ee-387f-4b44-bedd-f4fa60a56431","version":9,"type":"text","properties":{"title":[["Fig. 6. outlines our proposed commercial development pathway, which again, highlights the importance of co-investment of public and private sectors."]]},"created_time":1665377280000,"last_edited_time":1665377400000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"62d01445-fc5c-44b1-978b-eda5045ec25c":{"value":{"id":"62d01445-fc5c-44b1-978b-eda5045ec25c","version":10,"type":"image","properties":{"source":[["https://lh4.googleusercontent.com/ej0G9SPOvalf9bUms4Sb5njgoa5l142sj32qdUhxUFOOUTKcBjSnBHpSE3N2Jvn8_pOdfDQTW9nuyM_TmCV6URQSkraWkmAbYbegJaihK18Q7Ivp3OLXL8W_9XKVdhXhj84qUDT_6zSlwfAJNM7MM4pxTFEIjqFsvK8FwKQMglsXhD6-mYYvVYg5R1bPhzCRDk5sdw"]],"caption":[["Fig. 6.",[["b"]]],[" Commercial development pathway of Phage Australia. X-axis denotes timeline. Dark arrows denote public good funding. Green arrows denote investment. Dotted arrows denote contribution to and from Phage Australia. HTA – health technology assessment. SME – small to medium-sized enterprise. Milestones from Stage 1 has been achieved (COVID permitting). 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From my perspective, the development timeline based on the last 12 months (Fig. 7) can be projected to increase value and de-risk the challenges I have highlighted so far."]]},"created_time":1665377340000,"last_edited_time":1665377340000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"d7371aad-de27-437c-b1f5-eabd0fe5f0b8":{"value":{"id":"d7371aad-de27-437c-b1f5-eabd0fe5f0b8","version":4,"type":"text","created_time":1665702600000,"last_edited_time":1665702600000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"2c950c33-78d6-40f9-b36b-d267adad0c61","last_edited_by_table":"notion_user","last_edited_by_id":"2c950c33-78d6-40f9-b36b-d267adad0c61","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"abeb32de-50c9-409c-afeb-c7b4f2cca96a":{"value":{"id":"abeb32de-50c9-409c-afeb-c7b4f2cca96a","version":6,"type":"text","created_time":1665377400000,"last_edited_time":1665377400000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"3311597b-1f33-4485-b5a9-0563ca772122":{"value":{"id":"3311597b-1f33-4485-b5a9-0563ca772122","version":9,"type":"image","properties":{"source":[["https://lh6.googleusercontent.com/TK1uWP128gC4JeXuLT6d0nhO03qB9VtwwDxEZlcZjDzPYDmKhKbSVJQd7TjsLXq-WubPMvUBcxOg9Wwbc6rP72jynZUgQzx-VRcKOmy-pEp6Qt0YNSkKD5svNyNjGCVDRfW2Xr-N1f4JhKCB2euvY92hdvYfoUVcY7wI4FpEfIqwJ0IoHb_JPcECk1iurhpV559rnw"]],"caption":[["Fig. 7.",[["b"]]],[" Development timeline for phage therapy. 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While it is encouraging to know that there are many new and innovative preclinical pipelines of antibacterial agents [^39] and antibiotics [^40], given the track record of antibiotics leading to AMR, phages pose as an outstanding AMR solution, and demands immediate attention and investment from both the government and venture capital."]]},"created_time":1665377479907,"last_edited_time":1665377520000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"b4efff56-0887-4af8-a052-7bb13f0470d8":{"value":{"id":"b4efff56-0887-4af8-a052-7bb13f0470d8","version":2,"type":"text","properties":{"title":[["So, can phage make money amidst all the challenges I have outlined here?"]]},"created_time":1665377479907,"last_edited_time":1665377460000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"926c30e5-f358-48ab-934c-ae672f1f4b3d":{"value":{"id":"926c30e5-f358-48ab-934c-ae672f1f4b3d","version":2,"type":"text","properties":{"title":[["I would like to quote Stephen Stick and leave you with this thought: “Howard Florey didn’t discover penicillin but he worked out how to use it. His first thought was not “how do we make a buck out of this”? Yet the application of penicillin created a mega industry including discovery, manufacture, formulation and delivery modes.”"]]},"created_time":1665377479908,"last_edited_time":1665377460000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"e90d7472-0ae3-43bf-9654-7a26d57987b0":{"value":{"id":"e90d7472-0ae3-43bf-9654-7a26d57987b0","version":11,"type":"text","properties":{"title":[["[^38]: O'Neill, J. (2016). Tackling Drug-Resistant Infections Globally: final report and recommendations, Wellcome Trust and UK Government."]]},"created_time":1665377479910,"last_edited_time":1665377760000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"95e3f9d0-4f27-4e2e-a3a9-8000d944102a":{"value":{"id":"95e3f9d0-4f27-4e2e-a3a9-8000d944102a","version":11,"type":"text","properties":{"title":[["[^39]: 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on commercialisation of phage and phage therapy: Jon Iredell, Laura Collie, Idalia Dawidowska, Viktor Windeyer, James Jones, Sam Walker, Jan Zheng, Jessica Sacher, Stephen Stick, Trevor Lithgow, Joey Lai, Bill Russell."]]},"created_time":1665377479908,"last_edited_time":1665377460000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"9b9346ff-9f43-46b9-8c93-00a6b66b1220":{"value":{"id":"9b9346ff-9f43-46b9-8c93-00a6b66b1220","version":2,"type":"bulleted_list","properties":{"title":[["Discussion on market sounding analysis of phage therapy, pathogen and phage biobanking, TGA working group and education package on phage therapy: NSW Health i.e., Tony Penna, Laura Collie, Julia Warning, Sian Hope, Patricia Morten, Anne O’Neill, Caitlin Pitt."]]},"created_time":1665377479909,"last_edited_time":1665377460000,"parent_id":"52c76d77-82ef-4f44-ba92-8a8918d6ff40","parent_table":"block","alive":true,"created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"62b128d1-7a88-4c9e-acfb-61b2de65becc":{"value":{"id":"62b128d1-7a88-4c9e-acfb-61b2de65becc","version":2,"type":"bulleted_list","properties":{"title":[["Contribution to HTAnalyst reports: Jon Iredell, Ruby Lin, Ameneh Khatami, Indy Sandaradura, Tim Gilbey, Amit Shetty, Aldo 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resistance",[["a","https://revive.gardp.org/resource/antimicrobial-resistance-amr/?cf=encyclopaedia"]]],[" is still evolving through gene acquisition5 and fundamental adaptations in "],["bacterial",[["a","https://revive.gardp.org/resource/bacteria/?cf=encyclopaedia"]]],[" 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The use of phages to which phage-resistance is more ‘costly’ to the bacterium to develop, the ‘training’ of phages against target pathogens to ensure this, and therapeutic phage diversity are all expected to be important to prevent emergence of phage-insensitive bacterial pathogens.7"]]},"format":{"copied_from_pointer":{"id":"96335a6e-bbe7-4999-b6fe-bcafac8474eb","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"created_time":1673824973601,"last_edited_time":1673824973639,"parent_id":"f2335a6c-209f-46f2-93c0-3ff8d53cf85c","parent_table":"block","alive":true,"copied_from":"96335a6e-bbe7-4999-b6fe-bcafac8474eb","created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"2c006e14-234f-4ea1-8afe-35abdea83cc9":{"value":{"id":"2c006e14-234f-4ea1-8afe-35abdea83cc9","version":3,"type":"header","properties":{"title":[["Precision antimicrobials: a double-edged sword"]]},"format":{"copied_from_pointer":{"id":"31113f0a-92c0-4e60-b332-d8df2bd0c518","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"created_time":1673824973601,"last_edited_time":1673824973639,"parent_id":"f2335a6c-209f-46f2-93c0-3ff8d53cf85c","parent_table":"block","alive":true,"copied_from":"31113f0a-92c0-4e60-b332-d8df2bd0c518","created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"6e27a3ac-dc21-4abc-b70e-2efe98b51f60":{"value":{"id":"6e27a3ac-dc21-4abc-b70e-2efe98b51f60","version":3,"type":"text","properties":{"title":[["A previous writer in this "],["series",[["a","https://revive.gardp.org/rapid-diagnostic-tests-to-support-clinical-trials-of-antibiotics/"]]],["8 pointed to increasing interest in pathogen-specific approaches to multi-drug resistant (MDR) infections.6-11 A precise tool such as a phage is an ideal, pathogen-specific option; neither affected by nor contributing to AMR."]]},"format":{"copied_from_pointer":{"id":"759c328d-287f-41b5-add9-566fe49337a7","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"created_time":1673824973602,"last_edited_time":1673824973639,"parent_id":"f2335a6c-209f-46f2-93c0-3ff8d53cf85c","parent_table":"block","alive":true,"copied_from":"759c328d-287f-41b5-add9-566fe49337a7","created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"5c1059a2-22b3-4b80-990e-68efbb3617fd":{"value":{"id":"5c1059a2-22b3-4b80-990e-68efbb3617fd","version":3,"type":"text","properties":{"title":[["Collateral damage to the human microbiota is minimised by the extreme precision of phage therapy. However, this means that each phage may be used much less than a broad-spectrum antimicrobial and economies of scale may be harder to achieve."]]},"format":{"copied_from_pointer":{"id":"5d360f66-1e74-49cf-9e1b-621f54a059ae","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"created_time":1673824973602,"last_edited_time":1673824973639,"parent_id":"f2335a6c-209f-46f2-93c0-3ff8d53cf85c","parent_table":"block","alive":true,"copied_from":"5d360f66-1e74-49cf-9e1b-621f54a059ae","created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"b4934901-ef2d-495c-80ce-043aacda1def":{"value":{"id":"b4934901-ef2d-495c-80ce-043aacda1def","version":3,"type":"quote","properties":{"title":[["Endpoint QC processes provide flexibility, allowing for phages to be administered safely, even given phage-phage differences. 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Phages are plentiful and ubiquitous; easily modified by forced evolution or bioengineering; and easy to culture and purify. However, production according to traditional "],["Good Manufacturing Practice (GMP)",[["a","https://revive.gardp.org/resource/good-manufacturing-practice-gmp/?cf=encyclopaedia"]]],[" standards9 is infrastructure-intensive and expensive. It is viable only if economies of scale – where average costs per unit produced decrease with an increased magnitude of production – can be achieved."]]},"format":{"copied_from_pointer":{"id":"617d2177-756e-4126-8031-820121ac51d2","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"created_time":1673824973603,"last_edited_time":1673824973639,"parent_id":"f2335a6c-209f-46f2-93c0-3ff8d53cf85c","parent_table":"block","alive":true,"copied_from":"617d2177-756e-4126-8031-820121ac51d2","created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"8dd63603-6a75-4adc-b3c3-dadba9cecfb5":{"value":{"id":"8dd63603-6a75-4adc-b3c3-dadba9cecfb5","version":3,"type":"text","properties":{"title":[["A separate production plant dedicated to each phage is not likely to be economical. Even moving to small-scale GMP-certified facilities for savings in consumables leaves more significant, important, overhead costs in production and quality control (QC) that pertain to each individual batch. Yet we must be responsive to immediate, local needs for highly diverse, safely produced phages. How can we do this?"]]},"format":{"copied_from_pointer":{"id":"cfe7fdea-05b5-4cb4-a76a-642d721493ae","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"created_time":1673824973604,"last_edited_time":1673824973639,"parent_id":"f2335a6c-209f-46f2-93c0-3ff8d53cf85c","parent_table":"block","alive":true,"copied_from":"cfe7fdea-05b5-4cb4-a76a-642d721493ae","created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"bb2db91c-6953-4876-bf09-60e8e3754116":{"value":{"id":"bb2db91c-6953-4876-bf09-60e8e3754116","version":3,"type":"text","properties":{"title":[["One way is to increase the number of patients each phage batch treats. A simple calculation illustrates the need to keep wastage under 90% if possible: i.e., >10% of a batch should be used before the expiry date (Fig. 1), since 5% usage costs 20-fold more than 99.9% usage, 10% costs 10-fold more, 20% 5-fold more, and so on – since batch costs are fixed. Phages can achieve this if they are effective against a sufficiently broad range of commonly encountered bacterial strains, like "],["Staphylococcus aureus",[["i"],["a","https://revive.gardp.org/resource/staphylococcus/?cf=encyclopaedia"]]],[" and "],["Pseudomonas aeruginosa",[["i"],["a","https://revive.gardp.org/resource/pseudomonas/?cf=encyclopaedia"]]],["), are supported by good distribution logistics, and have a good shelf-life."]]},"format":{"copied_from_pointer":{"id":"de525771-8939-487f-be54-55f6e66ad319","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"created_time":1673824973604,"last_edited_time":1673824973639,"parent_id":"f2335a6c-209f-46f2-93c0-3ff8d53cf85c","parent_table":"block","alive":true,"copied_from":"de525771-8939-487f-be54-55f6e66ad319","created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"03aa247a-2d4c-4c41-80e6-7d54b754505d":{"value":{"id":"03aa247a-2d4c-4c41-80e6-7d54b754505d","version":3,"type":"text","properties":{"title":[["For example, if the shelf-life of a phage product is 12 months, a 1,000-dose batch (assuming 30 doses per course) means each batch must treat approximately eight patients a year to place phage acquisition costs in the range of a moderately expensive modern antibiotic."]]},"format":{"copied_from_pointer":{"id":"c114e84f-378d-4159-a31c-cc5a883de0e3","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"created_time":1673824973605,"last_edited_time":1673824973639,"parent_id":"f2335a6c-209f-46f2-93c0-3ff8d53cf85c","parent_table":"block","alive":true,"copied_from":"c114e84f-378d-4159-a31c-cc5a883de0e3","created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"c5e527c4-e60f-477e-b92f-cc7ba03f3cf9":{"value":{"id":"c5e527c4-e60f-477e-b92f-cc7ba03f3cf9","version":3,"type":"image","properties":{"source":[["https://revive.gardp.org/wp-content/uploads/2023/01/Fig1-1024x734.png"]]},"format":{"copied_from_pointer":{"id":"39ae4f3d-6e2f-4da2-b2e9-51f805a1e852","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"created_time":1673824973605,"last_edited_time":1673824973639,"parent_id":"f2335a6c-209f-46f2-93c0-3ff8d53cf85c","parent_table":"block","alive":true,"copied_from":"39ae4f3d-6e2f-4da2-b2e9-51f805a1e852","created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"029bd3f1-ce8a-4f23-b838-0006ebb26f85":{"value":{"id":"029bd3f1-ce8a-4f23-b838-0006ebb26f85","version":3,"type":"text","properties":{"title":[["Figure 1. The relationship between the percentage of batch cost (vertical axis) and batch usage (horizontal axis) indicates an inflection point at ~10% usage."]]},"format":{"copied_from_pointer":{"id":"599bf64b-0fc7-4e6f-bbde-2ec8bb5a885f","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"created_time":1673824973605,"last_edited_time":1673824973639,"parent_id":"f2335a6c-209f-46f2-93c0-3ff8d53cf85c","parent_table":"block","alive":true,"copied_from":"599bf64b-0fc7-4e6f-bbde-2ec8bb5a885f","created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"8e386123-177e-4a49-b893-ff97d0682a5b":{"value":{"id":"8e386123-177e-4a49-b893-ff97d0682a5b","version":3,"type":"text","properties":{"title":[["The simple logic of these economics drives production towards common "],["bacterial targets",[["a","https://revive.gardp.org/resource/bacterial-target/?cf=encyclopaedia"]]],[", often achieved by including multiple phages (the so-called phage ‘cocktail’) in one standardised GMP production line."]]},"format":{"copied_from_pointer":{"id":"cd7a2608-8576-4ea1-9aa0-afaec687f74b","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"created_time":1673824973606,"last_edited_time":1673824973639,"parent_id":"f2335a6c-209f-46f2-93c0-3ff8d53cf85c","parent_table":"block","alive":true,"copied_from":"cd7a2608-8576-4ea1-9aa0-afaec687f74b","created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"7e908446-1640-45ed-9fa9-14f2744afc36":{"value":{"id":"7e908446-1640-45ed-9fa9-14f2744afc36","version":3,"type":"header","properties":{"title":[["Ensuring safety"]]},"format":{"copied_from_pointer":{"id":"59db4a54-cabe-4daf-bb2f-6bb62058528f","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"created_time":1673824973606,"last_edited_time":1673824973639,"parent_id":"f2335a6c-209f-46f2-93c0-3ff8d53cf85c","parent_table":"block","alive":true,"copied_from":"59db4a54-cabe-4daf-bb2f-6bb62058528f","created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"2b547b26-0026-496f-9310-241a2e18c8e7":{"value":{"id":"2b547b26-0026-496f-9310-241a2e18c8e7","version":3,"type":"text","properties":{"title":[["The expensive and time-consuming process of traditional clinical trials for antibiotics is even less suited to highly personalized antimicrobials like phages. Given their inherent safety, phages fit well into an endpoint, quality-control framework, in which the end product’s safety is regulated, similar to the way in which blood products are regulated. 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These data can be presented in a standardised document with evidence that the phage itself has no undesirable biological characteristics. In the absence of comprehensive assays to detect all undesirable characteristics, it is additionally essential to ensure that the phage production strain encodes nothing that may present a risk in the final therapeutic product."]]},"format":{"copied_from_pointer":{"id":"f3c36308-08ab-4e19-8973-7dfc967e000c","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"created_time":1673824973607,"last_edited_time":1673824973639,"parent_id":"f2335a6c-209f-46f2-93c0-3ff8d53cf85c","parent_table":"block","alive":true,"copied_from":"f3c36308-08ab-4e19-8973-7dfc967e000c","created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"21617660-ed6d-456a-835b-19b4375905b1":{"value":{"id":"21617660-ed6d-456a-835b-19b4375905b1","version":3,"type":"text","properties":{"title":[["Endpoint QC processes provide flexibility, allowing for phages to be administered safely, even given phage-phage differences. 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The minimum documents every prescriber needs for phage therapy."]]},"format":{"copied_from_pointer":{"id":"5c64b36e-3d4c-40a3-b43a-f7e7d040d829","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"created_time":1673824973608,"last_edited_time":1673824973639,"parent_id":"f2335a6c-209f-46f2-93c0-3ff8d53cf85c","parent_table":"block","alive":true,"copied_from":"5c64b36e-3d4c-40a3-b43a-f7e7d040d829","created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"1384f2eb-bc57-4947-87b8-8c5938cc7fbe":{"value":{"id":"1384f2eb-bc57-4947-87b8-8c5938cc7fbe","version":3,"type":"text","properties":{"title":[["In the absence of full GMP certification with end-to-end process control, the responsibility for patient safety and the evaluation of risk and potential benefit is often devolved locally to the prescriber and/or the institution with the most direct and explicit duty of care (such as a health care organisation). This is typically handled at the level of a jurisdictional ethics committee, often by delegation to a specialised therapeutics subcommittee (‘drug committee’). The phage, bacterial production strain and manufacturing safety data sheets will be required by the institutional review board/drug safety committee for every bacteriophage considered for use (Fig 2). In our own institution, we provide this in the form of four documents regarding the therapeutic material and provide the therapy within a standardised treatment and monitoring framework. The type of evidence required may vary with jurisdiction to some extent, but some guidelines are published.11,12"]]},"format":{"copied_from_pointer":{"id":"eba24736-12f2-472c-8926-d5cab82b0245","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"created_time":1673824973609,"last_edited_time":1673824973639,"parent_id":"f2335a6c-209f-46f2-93c0-3ff8d53cf85c","parent_table":"block","alive":true,"copied_from":"eba24736-12f2-472c-8926-d5cab82b0245","created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"afcf5d28-0921-4fbb-ad34-fd9963f21090":{"value":{"id":"afcf5d28-0921-4fbb-ad34-fd9963f21090","version":3,"type":"quote","properties":{"title":[["If we can get the economics right and design systems that reflect the critical attributes of phages, phage therapy has the potential to provide a safe, AMR-proof safety net upon which governments and hospitals can rely. This challenge is one that prescribers, regulators and the industry must meet."]]},"format":{"copied_from_pointer":{"id":"d10bcdc7-a804-47fb-8cf7-e0aa90c2a533","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"created_time":1673824973609,"last_edited_time":1673824973639,"parent_id":"f2335a6c-209f-46f2-93c0-3ff8d53cf85c","parent_table":"block","alive":true,"copied_from":"d10bcdc7-a804-47fb-8cf7-e0aa90c2a533","created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"15f5926c-4899-4520-b2d4-b7c0e4291a7e":{"value":{"id":"15f5926c-4899-4520-b2d4-b7c0e4291a7e","version":3,"type":"header","properties":{"title":[["Redesigning how we pay"]]},"format":{"copied_from_pointer":{"id":"ce5db523-12dc-4a18-8ddb-1c97c44df517","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"created_time":1673824973609,"last_edited_time":1673824973639,"parent_id":"f2335a6c-209f-46f2-93c0-3ff8d53cf85c","parent_table":"block","alive":true,"copied_from":"ce5db523-12dc-4a18-8ddb-1c97c44df517","created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"1538d803-529c-448a-bda0-ddba98e31f48":{"value":{"id":"1538d803-529c-448a-bda0-ddba98e31f48","version":3,"type":"text","properties":{"title":[["Just as we need fit-for-purpose regulatory mechanisms, it is essential that payment mechanisms are designed to fit. Volume-based pricing has strangled antibiotic profitability but value-based (outcome-based) models, with payments based on patient outcomes, are an attractive potential solution12 that could work for phages. For example, given the costs of a prosthetic hip joint infection,13 and the estimated efficacy of phages in such settings,14 maintaining an anti-staphylococcal phage service should be a cost-effective use of health resources. Public-private partnerships15 or a subscription model such as recently launched in the UK16 are sensible, potential routes forward."]]},"format":{"copied_from_pointer":{"id":"cbd5e605-3126-4173-81a2-afdcabac5bfa","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"created_time":1673824973610,"last_edited_time":1673824973639,"parent_id":"f2335a6c-209f-46f2-93c0-3ff8d53cf85c","parent_table":"block","alive":true,"copied_from":"cbd5e605-3126-4173-81a2-afdcabac5bfa","created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"dc7b71d8-b9df-4ea0-8cee-ec5ca5089294":{"value":{"id":"dc7b71d8-b9df-4ea0-8cee-ec5ca5089294","version":3,"type":"text","properties":{"title":[["A GMP framework that allows sufficient diversity and caters to sufficient demand means that most needs will be met and that phage production can be cost-effective. 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Nature, 437(7057), 356-361."]]},"format":{"copied_from_pointer":{"id":"8caf6dce-7773-4f4e-a248-e633ce9461ef","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"created_time":1673824973612,"last_edited_time":1673824973639,"parent_id":"f2335a6c-209f-46f2-93c0-3ff8d53cf85c","parent_table":"block","alive":true,"copied_from":"8caf6dce-7773-4f4e-a248-e633ce9461ef","created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"dcd55957-23c9-4463-9011-26fee0d286d8":{"value":{"id":"dcd55957-23c9-4463-9011-26fee0d286d8","version":3,"type":"numbered_list","properties":{"title":[["Brussow H, Hendrix RW (2002). "],["Phage genomics: small is beautiful",[["a","https://www.sciencedirect.com/science/article/pii/S0092867401006377"]]],[". 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improved?"]]},"format":{"copied_from_pointer":{"id":"74fdaae0-e574-42b7-aa83-3c08dfb4146f","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"created_time":1678082148251,"last_edited_time":1678082148352,"parent_id":"5c9a5b23-bada-447e-bcf8-4f05d43d0dca","parent_table":"block","alive":true,"copied_from":"74fdaae0-e574-42b7-aa83-3c08dfb4146f","created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"446edd39-1740-4eba-8a8c-1aca92d09d98":{"value":{"id":"446edd39-1740-4eba-8a8c-1aca92d09d98","version":3,"type":"numbered_list","properties":{"title":[["To what extent is the UK Government ensuring that phage research and development is adequately funded and 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trials are still lacking."]]},"format":{"copied_from_pointer":{"id":"7b12685d-4fce-4f49-9231-d109b7c7ca2b","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"created_time":1678082148253,"last_edited_time":1678153956405,"parent_id":"5c9a5b23-bada-447e-bcf8-4f05d43d0dca","parent_table":"block","alive":true,"copied_from":"7b12685d-4fce-4f49-9231-d109b7c7ca2b","created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"369babfb-cf96-4300-a985-db5c3dbdf42f":{"value":{"id":"369babfb-cf96-4300-a985-db5c3dbdf42f","version":7,"type":"text","properties":{"title":[["The "],["strengths of bacteriophages",[["b"]]],[" are their specificity (thereby avoiding collateral damage to the bacterial ecosystems that protect us), their capacity for "],["in vivo",[["i"]]],[" adaptation to bacterial 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frameworks and finally, their status as ubiquitous naturally occurring viruses that are easily sourced and amplified (which creates questions in regard to IP security). 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This will build important sovereign capacity in health and biotechnology, create smart jobs for the nation, and establish an international leadership position which is unlikely to be challenged in the immediate future as no other governments appear to have taken such as step."]]},"format":{"copied_from_pointer":{"id":"9165bfaa-d83b-4d39-887e-a907248a33c6","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"created_time":1678082148256,"last_edited_time":1678153965529,"parent_id":"5c9a5b23-bada-447e-bcf8-4f05d43d0dca","parent_table":"block","alive":true,"copied_from":"9165bfaa-d83b-4d39-887e-a907248a33c6","created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"3e6f2db5-2180-42be-b582-e32958f80ad4":{"value":{"id":"3e6f2db5-2180-42be-b582-e32958f80ad4","version":3,"type":"text","properties":{"title":[["It is likely that industry will continue to regard the regulatory uncertainties and the other risks outlined above, as poor venture capital investment. 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This does NOT represent the position of the Australian government."]]},"format":{"copied_from_pointer":{"id":"1fbf93a0-9dc0-461d-9b39-fe190ea6a610","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"created_time":1678082148259,"last_edited_time":1678082148352,"parent_id":"5c9a5b23-bada-447e-bcf8-4f05d43d0dca","parent_table":"block","alive":true,"copied_from":"1fbf93a0-9dc0-461d-9b39-fe190ea6a610","created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"90348b8f-0ef0-497e-b167-331cf16c01bc":{"value":{"id":"90348b8f-0ef0-497e-b167-331cf16c01bc","version":25,"type":"sub_header","properties":{"title":[["Clinical training and clinical networks"]]},"format":{"copied_from_pointer":{"id":"d124b3ca-3b8f-4ec2-8cc6-56c540c8c593","table":"block","spaceId":"a8000652-f2c8-4adc-9353-cd51c033cc1f"}},"created_time":1678082148260,"last_edited_time":1678172225787,"parent_id":"5c9a5b23-bada-447e-bcf8-4f05d43d0dca","parent_table":"block","alive":true,"copied_from":"d124b3ca-3b8f-4ec2-8cc6-56c540c8c593","created_by_table":"notion_user","created_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","last_edited_by_table":"notion_user","last_edited_by_id":"5eb42727-2109-44be-b04d-578a4950ef50","space_id":"a8000652-f2c8-4adc-9353-cd51c033cc1f"},"role":"reader"},"f6d659c9-e401-43f8-a35e-6a4e6ef2f9b9":{"value":{"id":"f6d659c9-e401-43f8-a35e-6a4e6ef2f9b9","version":9,"type":"text","properties":{"title":[["In order to ensure that phage therapy is used most appropriately, it may be necessary to weigh the benefits of initially restricting access to phage therapy to an expert sector of clinical prescribers (e.g., Infectious Diseases physicians) in the same way that new anticancer drugs would not be widely available for non-experts to use. 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