A review of the scope of potential genome editing applications, the strategies from the most basic (2012) to the most recent (i.e. No. 11866), the current status of tissue specific delivery, accuracy, precision and safety of genome editing, clinical/therapeutic genome editing, and heritable genome editing. The 115 references to landmarks in the brief history of this science are arranged with bold letter synopsis under each, documenting watershed moments over the previous decade. Doudma concluded her Abstract with, "Genome editing is— or will soon be— in the clinic for several diseases, with more applications under development. The rapid pace of the field demands active efforts to ensure that this breakthrough technology is used responsibly to treat, cure and prevent genetic diseases."

(Thanks to Juan Weiss for this reference and its interpretation.)

Order of authorship in the original publication: Hampton, Watson, Fineran. Summarizes, and documents with 173 references, the extensive research on the multitude of methods that bacteriophages use to disable the CRISPR immune system attacks from their bacteria hosts.

(Thanks to Juan Weiss for this reference and its interpretation.)

Order of authorship in the original publication: Mendoza, Nieweglowska, Govindarajan. The authors showed that the large phage that specifically infects a Pseudomonas bacterium segregates its DNA, which the phage CRISPR would attack and destroy, by building a proteinaceous compartment or wall around its DNA. This protein barrier makes its DNA inaccessible to the CRISPR nuclease attack and destruction. This could be called the operation of natural selection at the molecular level.

(Thanks to Juan Weiss for this reference and its interpretation.)

Order of authorship in the original publication: Al-Shayeb, Sachdeva, Chen.... Doudna.  Open access, available from nature.com at this link.

This paper was a collaboration of about 50 scientists of diverse regions and specialities, assembled to advance knowledge of the bacteriophage evolutionary response and the tools huge phages possess against the onslaught of the bacterial immune system. The authors reconstructed 351 phage sequences and derived metagenomics datasets acquired from human feces, buccal areas, animal fecal samples, freshwater lakes and rivers, marine ecosystems sediments, hot springs soils, deep subsurface habitats, etc., mirroring most aspects of the earth's ecosystems. The main findings of this research were:

1. Many of the genomes of large phages have a length that rivals those of small celled bacteria.

2. These expanded genomes of large phages include diverse and previously undescribed CRISPR-Cas systems, TRNA's, tRNA synthases, tRNA modification enzymes, ribosomal proteins and others.

3. CRISPR-Cas systems of phages have the capacity to silence host transcriptional factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage encoded functions.

4. Some phages may repurpose bacterial CRISPR-Cas systems to eliminate competing phages.

5. The number of huge genome phages was far higher than expected.

6. Some phages that lack genes for interference and spacer integration have similar CRISPR repeats as their hosts and may therefore use the Cas proteins of the host.

(Thanks to Juan Weiss for this reference and its interpretation.)

The definitive reference on Sir William Osler, his life, his times, his friends, and his influence. Osler was voted "the most influential physician in history" in a 2016 survey of North American doctors, but his interests and influence transcend medicine. This is the first comprehensive reference on Osler's personality, character, life, times and thinking about a broad range of issues relevant to the human condition. The nearly 967 page work written by 135 contributors addresses four questions:

What was Osler really like, and what did he do?

What did Osler write, and who influenced his thinking?

How has Osler been assessed during the century since his death in 1919?

Does Osler still matter, and, if so, how?

https://doi.org/10.1016/S1473-3099(20)30120-1

"During the 2019–20 coronavirus pandemic, Gardner recognised that the public, researchers and health authorities needed clear, accessible and up-to-date information.^[8] Working with a team in Australia, Gardner and Ensheng Dong created an interactive dashboard that debuted on January 22, 2020.^[9][10] During March 2020, the platform was accessed 1.2 billion times per day.^[9]" (Wikipedia article on Lauren Gardner (scientist), accessed 3-2020).

https://coronavirus.jhu.edu/map.html

https://systems.jhu.edu/research/public-health/ncov/

Published on March 5, 2020. 

Order of authorship in the original publication: Holshue, DeBolt, Lindquist....Cohn. 

"Summary

"An outbreak of novel coronavirus (2019-nCoV) that began in Wuhan, China, has spread rapidly, with cases now confirmed in multiple countries. We report the first case of 2019-nCoV infection confirmed in the United States and describe the identification, diagnosis, clinical course, and management of the case, including the patient’s initial mild symptoms at presentation with progression to pneumonia on day 9 of illness. This case highlights the importance of close coordination between clinicians and public health authorities at the local, state, and federal levels, as well as the need for rapid dissemination of clinical information related to the care of patients with this emerging infection.

"On December 31, 2019, China reported a cluster of cases of pneumonia in people associated with the Huanan Seafood Wholesale Market in Wuhan, Hubei Province.1On January 7, 2020, Chinese health authorities confirmed that this cluster was associated with a novel coronavirus, 2019-nCoV.2 Although cases were originally reported to be associated with exposure to the seafood market in Wuhan, current epidemiologic data indicate that person-to-person transmission of 2019-nCoV is occurring.3-6 As of January 30, 2020, a total of 9976 cases had been reported in at least 21 countries,7 including the first confirmed case of 2019-nCoV infection in the United States, reported on January 20, 2020. Investigations are under way worldwide to better understand transmission dynamics and the spectrum of clinical illness. This report describes the epidemiologic and clinical features of the first case of 2019-nCoV infection confirmed in the United States."

Digital facsimile from nejm.org at this link.

This article was published in Nature on 3 February 2020. Prior to that a version with a different title and numerous other co-authors was published in bioRxiv on 23 January 2020, as "Discovery of a novel coronavirus associated with a recent pneumonia outbreak in humans and its potential bat origin". The publication date of  23 January 2020 makes this paper the earliest scientific paper  published in a Western language describing the COVID-19 pandemic.

Order of authorship in the original publication: Zhou, Yang, Zheng. 

Abstract of the paper as it appeared in Nature on 3 February 2020:

"Since the outbreak of severe acute respiratory syndrome (SARS) 18 years ago, a large number of SARS-related coronaviruses (SARSr-CoVs) have been discovered in their natural reservoir host, bats 1,2,3,4. Previous studies have shown that some bat SARSr-CoVs have the potential to infect humans 5,6,7. Here we report the identification and characterization of a new coronavirus (2019-nCoV), which caused an epidemic of acute respiratory syndrome in humans in Wuhan, China. The epidemic, which started on 12 December 2019, had caused 2,794 laboratory-confirmed infections including 80 deaths by 26 January 2020. Full-length genome sequences were obtained from five patients at an early stage of the outbreak. The sequences are almost identical and share 79.6% sequence identity to SARS-CoV. Furthermore, we show that 2019-nCoV is 96% identical at the whole-genome level to a bat coronavirus. Pairwise protein sequence analysis of seven conserved non-structural proteins domains show that this virus belongs to the species of SARSr-CoV. In addition, 2019-nCoV virus isolated from the bronchoalveolar lavage fluid of a critically ill patient could be neutralized by sera from several patients. Notably, we confirmed that 2019-nCoV uses the same cell entry receptor—angiotensin converting enzyme II (ACE2)—as SARS-CoV."

Open access from nature.com at this link.

"From online journal clubs to 'tweetorials' to conference updates, social media is changing the dissemination and discussion of biomedicine."

Open access from nature.com at this link.  Reprinted by scientificamerican.com on April 1, 2020 at this link.

This paper was published online on March 26, 2020 and updated periodically.  When I added it to this database on April 2, 2020 it had been updated on March 31, 2020. At that time the paper was available from healthdata.org at this link.

The paper was accompanied by data visualizations entitled COVID-19 US State-by-State Projections.

The interactive versions of these projections, available for the U.S. as a whole, and state by state, were available here:

https://covid19.healthdata.org/projections

Order of authorship in the original publication: Herries, Martin, Leece....Menter.

Summary:

"Understanding the extinction of Australopithecus and origins of Paranthropus and Homo in South Africa has been hampered by the perceived complex geological context of hominin fossils, poor chronological resolution, and a lack of well-preserved early Homo specimens. We describe, date, and contextualize the discovery of two hominin crania from Drimolen Main Quarry in South Africa. At ~2.04 million to 1.95 million years old, DNH 152 represents the earliest definitive occurrence of Paranthropus robustus, and DNH 134 represents the earliest occurrence of a cranium with clear affinities to Homo erectus. These crania also show that Homo, Paranthropus, and Australopithecus were contemporaneous at ~2 million years ago. This high taxonomic diversity is also reflected in non-hominin species and provides evidence of endemic evolution and dispersal during a period of climatic variability."

Available online from science.sciencemag.org at this link.

The Downey cell method for the diagnosis of infectious mononucleosis remains effective and cost-effective nearly 100 years after it was discovered:

"An 18-year-old woman visited her physician because she had a fever, a sore throat, and painful swellings in her neck for the past 5 days. A rapid antigen detection test for streptococcus was negative, and because of exudates on the patient's tonsils and very enlarged cervical lymph nodes, the physician tested for infectious mononucleosis or glandular fever. A rapid point-of-care test for heterophile antibodies—the Monospot test—was negative, a full blood count with autodifferential was normal, and a throat culture for group A streptococcus was negative. Epstein-Barr virus (EBV) antibodies—viral capsid antigen IgM and IgG, and EBV-associated nuclear antigen antibodies—were also negative."

After her visit to the physician the patient's condition deteriorated. When she went to the emergency room a manual differential was done, and it was loaded with with all three types of Downey cells. To confirm the diagnosis of infectious mononucleosis, they tested her plasma for viral DNA with the relatively expensive EBV PCR (Epstein Barr Virus Quantitative Polymerase Chain Reaction test), which gave a positive result. This confirmed the diagnosis.

(Thanks to Juan Weiss for this reference and its interpretation.)

Order of authorship in the original publication: Wu, Zhao...Holmes, Zang. This was the first paper written in China, and published in a Western language, on the first COVID-19 patient admitted to any Wuhan hospital on December 26, 2019. Nature received the paper on January 7, 2020, but did not publish it until February 3, 2020.

Abstract:

"Emerging infectious diseases, such as severe acute respiratory syndrome (SARS) and Zika virus disease, present a major threat to public health1,2,3. Despite intense research efforts, how, when and where new diseases appear are still a source of considerable uncertainty. A severe respiratory disease was recently reported in Wuhan, Hubei province, China. As of 25 January 2020, at least 1,975 cases had been reported since the first patient was hospitalized on 12 December 2019. Epidemiological investigations have suggested that the outbreak was associated with a seafood market in Wuhan. Here we study a single patient who was a worker at the market and who was admitted to the Central Hospital of Wuhan on 26 December 2019 while experiencing a severe respiratory syndrome that included fever, dizziness and a cough. Metagenomic RNA sequencing4 of a sample of bronchoalveolar lavage fluid from the patient identified a new RNA virus strain from the family Coronaviridae, which is designated here ‘WH-Human 1’ coronavirus (and has also been referred to as ‘2019-nCoV’). Phylogenetic analysis of the complete viral genome (29,903 nucleotides) revealed that the virus was most closely related (89.1% nucleotide similarity) to a group of SARS-like coronaviruses (genus Betacoronavirus, subgenus Sarbecovirus) that had previously been found in bats in China5. This outbreak highlights the ongoing ability of viral spill-over from animals to cause severe disease in humans."

Open access from nature.com at this link.

(Thanks to Juan Weiss for this reference and its interpretation.)

https://circulatingnow.nlm.nih.gov/2020/03/26/archiving-web-content-on-the-coronavirus-disease-covid-19/

"The National Library of Medicine is archiving web and social media documenting the Coronavirus (COVID-19) outbreak as part of the Library’s ongoing Global Health Events web archive collection. NLM’s Web Collecting and Archiving Working Group began this effort on January 30 when the World Health Organization declared the outbreak a Public Health Emergency of International Concern (PHEIC), and will continue to develop the collection throughout its duration.  This work follows NLM’s earlier Global Health Events archive collecting related to the 2014 Ebola Outbreak, the 2016 Zika Virus Outbreak, and more.

The Working Group is archiving content documenting the international, federal, state, and local government response to the Coronavirus (COVID-19) outbreak as well as social media communications using popular hashtags.  NLM will continue and expand this effort to document a broad range of perspectives, reactions, and response to the pandemic in support of future research and understanding of this global health event.

This work is supported by the Collection Development Guidelines of the NLM , which considers Web sites, blogs, social media and other web content to play an increasingly important role in documenting the scholarly biomedical record and illustrating a diversity of cultural perspectives in health and medicine. NLM will continue to develop, review, describe, and add content related to the Coronavirus (COVID-19) outbreak to the Global Health Events web archive and welcomes recommendations for additional content to include.  For more information about NLM’s Web collecting efforts, please visit https://www.nlm.nih.gov/webcollecting/."

https://docs.google.com/document/d/1v5tso8spFq6SpW53h2OJULcdRoPEbyI6xpah31kW-H0/edit
[I copied this document into this database on April 9, 2020.]

"Documenting COVID-19

"https://bit.ly/doc-covid19

#doccovid19

This is a collaborative document that lists active documentation projects for the COVID-19. In addition there are sections for guides and tools that can be useful for starting documentation projects of your own. All languages are welcome. The goal is to help build a loose network for sharing practices, resources and expertise. Editing is currently open, but please see the Documenting the Now Code of Conduct for guidance on how to contribute to this document.

Projects

These are active projects to collect materials related to the Coronavirus pandemic. Please list in alphabetical order the name of the project and at least one URL for a page that describes it. If you would like to add more detail please feel free.

• #ArxivemlaCovid19 (#DocumentingCovid19): Society of Catalan Archivist-Records Managers  https://arxivers.com/documentingcovid19-tips-for-citizens-archivists/
• Universität Hamburg, Universität Gießen, Universität Bochum, all Germany:

www.coronarchiv.de an online archive as a public history project (Citizen Science)

• Colorado State University: https://lib.colostate.edu/find/contribute-to-the-covid-19-archive/, https://archive-it.org/collections/13783
• A Journal of the Plague Year: an Archive of CoVid19: https://covid19.omeka.net/
• CoronaDiaries: Documenting the everyday lived experiences of a global pandemic (Dr Michael Ward, Swansea University, UK) 

https://es.britsoc.co.uk/coronadiaries-documenting-the-everyday-lived-experiences-of-a-global-pandemic/ and https://www.swansea.ac.uk/press-office/news-events/news/2020/04/how-your-coronadiary-could-help-us-understand-more-about-living-through-a-pandemic.php 

• COVID-19 Files: Austin Responds to a Pandemic: https://library.austintexas.gov/covid-19-files 
• COVID-19 Oral History Project: https://sites.google.com/iu.edu/covid-19oralhistoryproject/
• CUNY Distance Learning Archive (Documenting the transition to online instruction at CUNY during the 2020 Coronavirus pandemic). https://cdla.commons.gc.cuny.edu/
• DC Public Library Special Collections has around 1 million Twitter records of COVID-19 related material within a 30 mile radius of Washginton, D.C., captured with Social Feed Manager and twarc (https://digdc.dclibrary.org/islandora/object/dcplislandora%3A237558), and the beginnings of a collection in Archive-It, most of which is not yet public  (https://archive-it.org/collections/13803). Contact [email protected]. 
• Digital Justice Lab at Dartmouth (Wernimont and Stevens) has been collecting social media daily since January. More than 10 million records. No public website to date, but open to collab and sharing. Contact [email protected] 
• The Historic New Orleans Collection: https://www.hnoc.org/publications/first-draft/chronicling-coronavirus-our-effort-document-crisis-starts-you 
• International Center for Photography: (https://www.icp.org/news/icpconcerned-a-forum-for-all-to-document-the-covid-19-pandemic)
• International Internet Preservation Consortium. Novel Coronavirus (COVID-19): https://netpreserveblog.wordpress.com/2020/02/13/cdg-collection-novel-coronavirus/ 
• Irvington Historical Society: https://thehudsonindependent.com/irvington-historical-society-requests-personal-stories-during-the-covid-19-crisis/ 
• La Crosse (Wisconsin) Public Library Archives: Documenting Community Voices https://docs.google.com/forms/d/e/1FAIpQLScUqdeEvNtnLWpMlgs8lENQD9bahFY7ukcZqnSwdtG7teoR4Q/viewform
• Manitowoc County (Wisconsin) Historical Society, Telling Your Story: Documenting COVID-19 https://www.manitowoccountyhistory.org/telling-covid19 
• Maryland Historical Society: https://baltimorefishbowl.com/stories/the-maryland-historical-society-wants-to-hear-your-pandemic-story/ 
• Michigan State University: (https://lib.msu.edu/branches/ua/covid19/)
• Monmouth County Historical Association

           https://www.monmouthhistory.org/covid19

• Naper Settlement, Naperville 2020: Pandemic Collecting Initiative https://napersettlement.org/597/Current-Collecting-Initiatives
• National Library of Medicine: Global Health Events Web Archive (Archive-It collection group Coronavirus Disease (COVID-19) Outbreak) NLM blog post: https://circulatingnow.nlm.nih.gov/2020/03/26/archiving-web-content-on-the-coronavirus-disease-covid-19/ . Contact Christie Moffatt ([email protected])
• nCovMemory: https://2019ncovmemory.github.io/nCovMemory/
• Ohio State University (Archive-It): https://archive-it.org/collections/8222?fc=meta_Subject%3ACovid-19 
• Orange County Regional History Center (https://www.orlandosentinel.com/coronavirus/os-ne-health-coronavirus-history-center-collecting-photos-docs-20200320-q3rnuvi52zfh5oasdugtzkl57q-story.html)
• Reddit: Coronavirus Subreddit: http://reddit.com/r/coronavirus 
• Schenectady County Historical Society: http://gremsdoolittlelibrary.blogspot.com/2020/03/covid-19-archive-project.html
• Small Businesses and Coronavirus: https://smallbusinesscovid19.omeka.net/ 
• Society of American Archivists Web Archiving Section: (https://webarchivingrt.wordpress.com/)--contact Nicole Greenhouse ([email protected])
• UNC Charlotte: Contribute Your Stories--COVID-19 Outbreak: https://library.uncc.edu/contribute-your-stories-covid-19-outbreak
• University of Cincinnati web archiving on COVID-19’s impact on campus: https://archive-it.org/collections/13197?fc=websiteGroup%3AUC+COVID-19  
• University of Dayton
• Virgin Mary and COVID-19 web archive (Marian Library): https://archive-it.org/collections/8222?fc=meta_Subject%3ACovid-19 
• The COVID-19 Pandemic and the Church web archive: https://archive-it.org/collections/13703
• Contribute primary sources related to Mary (https://udayton.edu/blogs/imri/2020-03-30-documenting-devotion-to-mary-in-troubled-times.php), and UD community (https://udayton.edu/blogs/libraries/2020-03-31-pandemics.php)
• University of Illinois Archives - What’s Your Story? COVID-19 and the University of Illinois Community: https://archives.library.illinois.edu/about-us/initiatives/covid-19/
• University of San Francisco - USF COVID-19 Response Archive Project: https://twitter.com/usfca_scua/status/1248088840444641280 
• University of Utah - Utah COVID-19 Digital Collection: https://lib.utah.edu/services/digital-library/COVID19_digitalcollection
• University of Virginia Claude Moore Health Sciences Library
• Virginia-focused web archive of COVID-19 --contact Emily Bowden ([email protected]) or Dan Cavanaugh ([email protected]) for more information
• We don’t yet have a public collection link, so I’ll share our Webrecorder how-do documentation instead - geared toward new users: https://docs.google.com/document/d/1IM3IOq94dD1QRXQT8QYZBzt5K0pqTS90W6vAuzKNSO8/edit?usp=sharing
• University of Wisconsin-Milwaukee, COVID-19 MKE: A Milwaukee Coronavirus Digital Archive https://liblamp.uwm.edu/omeka/covid19mke/
• Vermont Folklife Center, Listening in Place https://www.vermontfolklifecenter.org/covid19-updates/listening-in-place
• West Virginia and Regional History Center (WVU Libraries) https://wvrhc.lib.wvu.edu/news-events/wvu-community-covid-19-stories 
• Wisconsin Historical Society, COVID-19 Journal Project
  https://wisconsinhistory.org/records/Article/CS16333
• Wright State University Libraries, Special Collections & Archives: ://www.libraries.wright.edu/community/outofthebox/2020/03/23/coronavirus-covid-19-pandemic-crisis-document-your-story/https
• Twitter harvests with twarc, for libraries and COVID-19 https://github.com/pbinkley/tweets-libraries-covid19, the transition to online teaching https://github.com/pbinkley/tweets-online-classes-covid19, and the National Emergency Library https://github.com/pbinkley/tweets-national-emergency-library 
• Stitching the Curve: knitting a data visualization of COVID-19 cases in Canada https://docs.google.com/document/d/13UtkoPf3wmiRUP9F_sEqBwAPBHnQUiHI5cHlTMLivsk/edit?ts=5e88b3a6
• Lorain Historical Society (Lorain, Ohio) https://www.lorainhistory.org/new-page-5
• Wyner Family Jewish Heritage Center (located in Boston, MA & collecting from Jewish New England communities) https://jewishheritagecenter.org/forthefuture
• BoasBlog, Witnessing Corona: Corona Diaries Project; https://boasblogs.org/witnessingcorona/curare-corona-diaries-project/#disqus_thread

Guides

This is a list of resources & guides that are useful in building a collection. A title and a URL are required, but feel free to add more detail if you think it is useful.

• Society of American Archivists. Documenting in Times of Crisis: A Resource Kit. https://www2.archivists.org/advocacy/documenting-in-times-of-crisis-a-resource-kit 
• Documenting the Now. The Ferguson Principles. https://news.docnow.io/documenting-the-now-ethics-white-paper-43477929ea3e 

ToolsDocNow Tools: https://www.docnow.io/

• Omeka: https://omeka.net 

This list contains tools that you may find useful for creating collections. A name and URL are required, but feel free to add more detail if you think it is useful.

• Social Feed Manager: https://go.gwu.edu/sfm
• Twarc: https://github.com/DocNow/twarc (twitter harvesting)
• Webrecorder: https://webrecorder.io 

Additional Reading

• How Can Photographers Capture Human Connection in the Age of Coronavirus (CNN): https://www.cnn.com/style/article/photographers-human-connection-coronavirus/index.html
• Museums Scramble to Document the Pandemic, Even as it Unfolds (NYT): https://www.nytimes.com/2020/03/31/arts/design/museums-coronavirus-pandemic-artifacts.html "

Chapters relevant to this bibliography include:
 
Zoology by Arnaud Zucker
Botany by Alain Touwaide
Medicine and Pharmacy by Alain Touwaide
Veterinary Medicine by Stavros Lazaris
Byzantine Theories of Vision by Katerina Ierodiakonou.

"Abstract

Order of authorship in the original publication: Radin, Wineinger, Topol, Steinhubl.

"Background

"Acute infections can cause an individual to have an elevated resting heart rate (RHR) and change their routine daily activities due to the physiological response to the inflammatory insult. Consequently, we aimed to evaluate if population trends of seasonal respiratory infections, such as influenza, could be identified through wearable sensors that collect RHR and sleep data.

"Methods

"We obtained de-identified sensor data from 200 000 individuals who used a Fitbit wearable device from March 1, 2016, to March 1, 2018, in the USA. We included users who wore a Fitbit for at least 60 days and used the same wearable throughout the entire period, and focused on the top five states with the most Fitbit users in the dataset: California, Texas, New York, Illinois, and Pennsylvania. Inclusion criteria included having a self-reported birth year between 1930 and 2004, height greater than 1 m, and weight greater than 20 kg. We excluded daily measurements with missing RHR, missing wear time, and wear time less than 1000 min per day. We compared sensor data with weekly estimates of influenza-like illness (ILI) rates at the state level, as reported by the US Centers for Disease Control and Prevention (CDC), by identifying weeks in which Fitbit users displayed elevated RHRs and increased sleep levels. For each state, we modelled ILI case counts with a negative binomial model that included 3-week lagged CDC ILI rate data (null model) and the proportion of weekly Fitbit users with elevated RHR and increased sleep duration above a specified threshold (full model). We also evaluated weekly change in ILI rate by linear regression using change in proportion of elevated Fitbit data. Pearson correlation was used to compare predicted versus CDC reported ILI rates.

"Findings

"We identified 47 249 users in the top five states who wore a Fitbit consistently during the study period, including more than 13·3 million total RHR and sleep measures. We found the Fitbit data significantly improved ILI predictions in all five states, with an average increase in Pearson correlation of 0·12 (SD 0·07) over baseline models, corresponding to an improvement of 6·3–32·9%. Correlations of the final models with the CDC ILI rates ranged from 0·84 to 0·97. Week-to-week changes in the proportion of Fitbit users with abnormal data were associated with week-to-week changes in ILI rates in most cases.

"Interpretation

"Activity and physiological trackers are increasingly used in the USA and globally to monitor individual health. By accessing these data, it could be possible to improve real-time and geographically refined influenza surveillance. This information could be vital to enact timely outbreak response measures to prevent further transmission of influenza cases during outbreaks."

Open access from thelancet.com at this link.

https://covid19.topos.com/

"COVID-19 Compiler aims to display relevant data about the novel coronavirus outbreak in the United States.

"Our goal is to provide a multidimensional view of covid-19’s impact in counties across the US encompassing the mapping of vulnerable populations, state and local policies to reduce transmission, and data on medical / health care resources. The site is updated daily with the latest data available on the outbreak.

The site provides numerous other maps covering different statistics such as political affiliation, income, co-morbidities, etc.

April 1, 2020. https://www.nytimes.com/2020/04/01/world/europe/coronavirus-science-research-cooperation.html

"Using flag-draped memes and military terminology, the Trump administration and its Chinese counterparts have cast coronavirus research as national imperatives, sparking talk of a biotech arms race.

"The world’s scientists, for the most part, have responded with a collective eye roll.

" “Absolutely ridiculous,” said Jonathan Heeney, a Cambridge University researcher working on a coronavirus vaccine.

" “That isn’t how things happen,” said Adrian Hill, the head of the Jenner Institute at Oxford, one of the largest vaccine research centers at an academic institution.

"While political leaders have locked their borders, scientists have been shattering theirs, creating a global collaboration unlike any in history. Never before, researchers say, have so many experts in so many countries focused simultaneously on a single topic and with such urgency. Nearly all other research has ground to a halt.

"Normal imperatives like academic credit have been set aside. Online repositories make studies available months ahead of journals. Researchers have identified and shared hundreds of viral genome sequences. More than 200 clinical trials have been launched, bringing together hospitals and laboratories around the globe.

" “I never hear scientists — true scientists, good quality scientists — speak in terms of nationality,” said Dr. Francesco Perrone, who is leading a coronavirus clinical trial in Italy. “My nation, your nation. My language, your language. My geographic location, your geographic location. This is something that is really distant from true top-level scientists.”.... "



(Thanks to Juan Weiss for this reference.)

(Order of authorship in the original publication: Imachi, Nobu, Nakahara...Takai.) The authors report that after 12 years of research they have cultured a microorganism that may be the transitional species between prokaryotes and eukaryotes. The organism, obtained from deep ocean sediments, they named Prometheoarchaeum syntrophicum. It has a large number of genes that encode eukaryotic signature proteins only found in eurkaryotes. This bacterium has long tentacle-like protrusions emanating from its surface, and its metabolism characteristics prompted the authors to propose a new model for the emergence of the first eukaryotic cell. Instead of the classic phagocytosis concept of one cell eating another, the authors proposed that this host archaeon connected to the metabolic partner using the newly discovered tentacular extracellular structures and simultaneously formed a primitive chromosome surrounding structure that is topologically similar to the nuclear membrane.

"On the basis of the available data obtained from cultivation and genomics, and reasoned interpretations of the existing literature, we propose a hypothetical model for eukaryogenesis, termed the entangle–engulf–endogenize (also known as E³) model." (From the abstract.)

(Thanks to Juan Weiss for this reference and its interpretation.)

Open source from Nature.com at this link.

In addition to the printed version, Brill.com hosts an Open Access version of the text at scholarlyeditions.brill.com/ihom/.

"This volume is the first complete edition and commentary on Mesopotamian medicine from Nineveh dealing with diseases of the eye. This ancient work, languishing in British Museum archives since the 19th century, is preserved on several large cuneiform manuscripts from the royal library of Ashurbanipal, from the 7th century BC. The longest surviving ancient work on diseased eyes, the text predates by several centuries corresponding Hippocratic treatises. The Nineveh series represents a systematic array of eye symptoms and therapies, also showing commonalities with Egyptian and Greco-Roman medicine. Since scholars of Near Eastern civilizations and ancient and general historians of medicine will need to be familiar with this material, the volume makes this aspect of Babylonian medicine fully accessible to both specialists and non-specialists, with all texts being fully translated into English" (publisher).

Researching how the malarial mosquito A. gambiae developed resistance to common pyrethroid insecticides, the authors discovered how natural selection had enabled this insect population to develop resistance. They analyzed the gene-expression profiles of insecticide resistant A. gambiae populations from Burkina Faso and Côte d'Ivoire, finding higher than normal expression of genes that encode a family of chemosensory proteins, called sensory appendage proteins (SAPs). This protein specifically binds to pyrethroids that penetrate the moquito's hard exterior when it lands on a bed net (mosquito net), and thus prevents the insecticide from exerting its toxic effect by sequestering it and preventing its action on the mosquito's nervous system by promoting the breakdown of the pyrethrin. The authors also found that the expression of this protein is enhanced in the legs of the mosquito and mostly at the tips where the legs come in contact with the bed net. (Order of authorship in the original paper: Ingham, Anthousi, Douris, et al.)

(Thanks to Juan Weiss for this reference and its interpretation.)

"This volume contains nine of the most widely disseminated Middle English uroscopies, each of them short enough to be consulted quickly by practitioners and all of them commonly found in English medical miscellanies. Practical in their orientation, they are grounded firmly in Galenic humoralism and derive directly and indirectly from canonical Latin uroscopies, along with the Arabic and Greek antecedents of the Latin tradition. Together they occur in over 120 manuscripts.

"Despite the pervasive incidence of uroscopy in medieval medical manuscripts and medical practice, very few Middle English uroscopies have yet been edited, a gap that this edition seeks to reduce. Three of the texts edited are translated from widely circulated Latin originals; three are translated or adapted from a frequently copied French original (part of the Lettre d'Hippocrate); and three appear to be native English compositions.

"The Apparatus collates each text selectively against four to eight secondary witnesses, chosen primarily to represent different textual families for each item. The edition also contains a detailed Introduction; a Textual Commentary and a Medical Commentary; a detailed Glossary with special attention to medical vocabulary; and images of diagrams that accompany the texts.

'As a group, these texts provide an overview of the best-known elements of English vernacular uroscopy and a precis of western uroscopic knowledge more generally. They also shed light on the day-to-day application of uroscopic diagnosis by ordinary practitioners in the later Middle Ages, and thus on one of the central arenas of healer/patient interaction in the period" (publisher).

"When, why and how was it first believed that the corpse could reveal ‘signs’ useful for understanding the causes of death and eventually identifying those responsible for it? The Body of Evidence. Corpses and Proofs in Early Modern European Medicine, edited by Francesco Paolo de Ceglia, shows how in the late Middle Ages the dead body, which had previously rarely been questioned, became a specific object of investigation by doctors, philosophers, theologians and jurists. The volume sheds new light on the elements of continuity, but also on the effort made to liberate the semantization of the corpse from what were, broadly speaking, necromantic practices, which would eventually merge into forensic medicine" (publisher).

"A preventative medicine physician and staff writer for The Atlantic explains the surprising and unintended effects of our hygiene practices in this informative and entertaining introduction to the new science of skin microbes and probiotics....

"In Clean, doctor and journalist James Hamblin explores how we got here, examining the science and culture of how we care for our skin today. He talks to dermatologists, microbiologists, allergists, immunologists, aestheticians, bar-soap enthusiasts, venture capitalists, Amish people, theologians, and straight-up scam artists, trying to figure out what it really means to be clean. He even experiments with giving up showers entirely, and discovers that he is not alone" (publisher).

Order of authorship in the original paper: Senior, Evans, Jumper. ABSTRACT: "Protein structure prediction can be used to determine the three-dimensional shape of a protein from its amino acid sequence. This problem is of fundamental importance as the structure of a protein largely determines its function; however, protein structures can be difficult to determine experimentally. Considerable progress has recently been made by leveraging genetic information. It is possible to infer which amino acid residues are in contact by analysing covariation in homologous sequences, which aids in the prediction of protein structures. Here we show that we can train a neural network to make accurate predictions of the distances between pairs of residues, which convey more information about the structure than contact predictions. Using this information, we construct a potential of mean force4 that can accurately describe the shape of a protein. We find that the resulting potential can be optimized by a simple gradient descent algorithm to generate structures without complex sampling procedures. The resulting system, named AlphaFold, achieves high accuracy, even for sequences with fewer homologous sequences. In the recent Critical Assessment of Protein Structure Prediction5 (CASP13)—a blind assessment of the state of the field—AlphaFold created high-accuracy structures (with template modelling (TM) scores6 of 0.7 or higher) for 24 out of 43 free modelling domains, whereas the next best method, which used sampling and contact information, achieved such accuracy for only 14 out of 43 domains. AlphaFold represents a considerable advance in protein-structure prediction. We expect this increased accuracy to enable insights into the function and malfunction of proteins, especially in cases for which no structures for homologous proteins have been experimentally determined."

"Hippocrates’ Aphorisms enjoyed great popularity in the ancient and medieval world and, according to Maimonides, it was Hippocrates’ most useful work as it contained aphorisms, which every physician should know by heart. They were translated into Hebrew several times, but it was Maimonides’ Commentary on Hippocrates’ Aphorisms that made the work influential in Jewish circles. For the composition of his commentary, Maimonides consulted the Aphorismsthrough the commentary by Galen, translated by Ḥunayn ibn Isḥāq. This edition of Maimonides’ Arabic commentary and its Hebrew translations, the first with an English translation based on the Arabic text, is part of a project undertaken by Gerrit Bos to critically edit Maimonides’ medical works" (publisher).

"The original Arabic text of Maimonides’ major medical work, Medical Aphorisms, was critically edited and translated into English by Gerrit Bos in the years 2004-2017, and published in earlier volumes of the book series The Medical Works of Moses Maimonides. The present work is a new critical edition of the medieval Hebrew translation by Nathan ha-Meʾati, who was active as a translator of scientific texts in Rome in the late thirteenth century, where his colleague Zeraḥyah Ḥen had completed a translation of the same Maimonidean text in 1277, only a few years earlier. Nathan aimed to provide the general reader with a translation that was easier to understand than Zeraḥyah's translation. The present critical edition of Nathan’s translation is primarily based on MS Paris, BN, héb. 1174, and not on MS Paris, BN, héb. 1173, used by Suessmann Muntner for his edition in 1959, as this copy suffers from many mistakes and corruptions" (publisher).

eBook version available at no cost from play.google.com at this link.

"In early eleventh century Zaragoza, the eminent Jewish scholar Abū l-Walīd Marwān ibn Janāḥ wrote a glossary containing almost 1100 entries, entitled Kitāb al-Talkhīṣ. This important text, considered lost until recently, contains Arabic and foreign-language names of simple drugs, weights, measures, and other medical terms. In the present volume, the Kitāb al-Talkhīṣ is edited and translated for the first time by Gerrit Bos and Fabian Käs. In detailed commentaries, the editors identify the substances mentioned in the Talkhīṣ. They also elaborate on the role of the text in the history of Arabic glossaries concerned with medical nomenclature. Special attention is paid to Ibn Janāḥ’s Ibero-Romance phytonyms, analysed in depth by Mailyn Lübke and Guido Mensching" (publisher).

The authors describe a mechanism for the observed natural viral "immunity" of individuals with spontaneous control of HIV-1. A very few exceptional people have the molecular ability to steer the incoming/infecting cellular virus into the "heterochromatin" areas of their cellular genome where the virus genome is totally segregated, locked in and dormant. Consequentially, over time, most of these patients do not have any detectable virus in the blood. Of the patients reported here, one had no functional HIV viral copies in 1.5 billion cells counted, although a few "non-functional" copies were found. Another had just one functional viral copy of HIV in more than 1 billion blood cells analyzed. Order of authorship in the original paper: Jiang, Lian, Gao....

(Thanks to Juan Weiss for this reference and its interpretation.)

Posted online on February 17, 2020. 2019-nCoV was an interim name for the Novel Coronavirus. These studies, which included the 3D structure of the RBD (receptor binding domain) within the S protein, provided information fundamental to the development of the mRNA vaccines for Covid-19.

From the commentary at the begining of the paper:

Published 15 July 2020. Order of authorship in original publication: Shin, Shukla, Chung....Steinmetz. Probably the first publication on the type of nanotechnology involved in production of the Moderna and Pfizer mRNA vaccines for Covid-19 — vaccines developed within unprecedented short periods of time and manufactured on unprecedented scale.

"Abstract

A very readable and relatively brief, but comprehensive, biography. The appendix provides a complete list of Galen's works with their titles in Latin, also in English translation, correlated to the best editions and translations of each text.

BNT162b2 is synonomous with the Pfizer BioNTech mRNA Covid-19 vaccine. The Pfizer-BioNTech mRNA vaccine was produced from theoretical design to finished product and distribution in less than one year. This was the first published paper on that vaccine. It was posted online on 12-10-2020, with updates on 12-16-2020. It first appeared in print on 12-31-2020.

This paper was also the first appearance in print of a paper describing a vaccine fabricated using the mRNA platform. The vaccine was initially administered under "emergency use authorization" granted by the U.S. FDA until the FDA granted full approval for this vaccine on August 23, 2021.

This vaccine delivers the mRNA needed to code for the membrane anchored S (spike) protein to the inside of the host cell inside an encapsulating hollow lipid nanoparticle. That mRNA then instructs the host cell to produce S protein molecules, which are then ferried out of the host cell, and act as the antigen/immunogen for this vaccine once outside of the cell.

Order of authorship in the original publication: Polack, Thomas, Kitchin.

(Thanks to Juan Weiss for this reference and its interpretation.)

"...includes botanical, chemical, pharmacalogical, and therapeutic details where appropriate, as well as extensive quotations from both contemporary and old, rare books. The text is complemented with the history of obstetrics and gynecology, along with short biographies and illustrations. Additionally, the author presents a unique fund of hard-to-find information in sections devoted to topics such as anesthesia and analgesia, antiseptics, antibiotics and chemotherapy, blood transfusion and Rhesus disease, eclampsia, family planning, menopause, and uterine stimulants" (publisher).

Posted online 1-30-20, updated 2-6-20, and published in print on March 5, 2020. First report of the "asymptomatic transmission" of Covid-19. The authors wrote, “The fact that asymptomatic persons are potential sources of 2019-nCoV infection may warrant a reassessment of transmission dynamics of the current outbreak”. Available from PubMedCentral at this link. (When originally published in print this "letter" was signed by Camilla Rothe, Roman Wölfel, Michael Hoelscher "and Others." "A complete list of authors is available with the full text of this letter at NEJM.org.")

(Thanks to Juan Weiss for this reference and its interpretation.)

Published online 4-7-20; in print in June, 2020. First case report of what became known as Multisystem Inflammatory Syndrome in Children (MIS-C), sometimes present with Kawasaki disease. This is one of the worst complications of Covid-19 infection in children, disproportionately affecting black and hispanic children.

(Thanks to Juan Weiss for this reference and its interpretation.)

The authors, working at Regeneron, showed that a cocktail of two potent neutralizing monoclonal antibodes reduced virus load in the airways and diminshed viral induced pathological sequelae when given both as a prophylatic and/ or as a therapeutic entity. The cocktail also limited evidence of pneumonia in the lungs. One of the antibodies in the cocktail was specifically tailored to safeguard against mutational virus escape. Order of authorship in the original publication: Baum, Ajithdoss...Kyratsous.

(Thanks to Juan Weiss for this reference and its interpretation.)

"Provides a history of the debate about gene editing, a summary of the ethics, and a proposal for moving forward. Re-conceptualizes the historical discussion about gene editing in the context of today's widespread use and potential for unethical applications" (publisher).

Expanding on previous findings by a genome wide association study of severe COVID-19, specifically with respiratory failure which had found that a gene cluster residing on chromosome 3 had a significant association with severe acute respiratory failure post infection, the authors showed that:
1) Chromosome 3 in those patients is specifically populated by a 50,000 DNA nucleotides long segment that entered the human population by gene flow from Neanderthals or Denisovans.
2) This long haplotype entered the Neanderthal population, and was transmitted by Neanderthals to present day humans about 40,000-60,000 years ago.
3) This specific genomic segment is carried by about 50% of people in South Asia, is almost absent in East Asia and is carried by about 16% of European humans overall.
4) The authors posited that this genomic cluster was maintained in the genome most likely as the result of positive natural selection in Neanderthals because it probably contributed to the species chances of survival and reproductive success.

Order of authorship in the original publication: Zeberg, Pääbo. Available from nature.com at this link.

(Thanks to Juan Weiss for this reference and its interpretation.)

"Farmer first visited the Western African Ebola virus epidemic site in July 2014, and much of the book is devoted to his personal experiences. Reviewing the outbreak in 2020, he noted that there were almost no Ebola deaths in the U.S. or Europe. By Farmer's account, the West Africa Ebola death toll arose from the longstanding failure to invest in basic health infrastructure which resulted in a lack of proper medical care. Looking at the history of West Africa, Farmer blames the almost five centuries of European rule that resulted in the "rapacious extraction — of rubber latex, timber, minerals, gold, diamonds and human chattel" for the country's inability to provide adequate health care" (Wikipedia).

The authors located individual atoms with a protein molecule for the first time using cryo-EM. This was the highest resolution imaging of a single protein molecule achieved to date using cryo-EM.

Order of authorship of the original paper: Nakane, Kotech, Sente, et al.

(Thanks to Juan Weiss for this reference and its interpretation.)

Order of authorship in the original publication: Cocquyt, Zhou, Plomp, van Eijck. I

Abstract

"The technique of neutron tomography has, after 350 years, enabled a first look inside the iconic single-lens microscopes of Antoni van Leeuwenhoek. Van Leeuwenhoek’s 17th-century discovery of “animalcules” marks the birth of microbiology. His skillfully self-produced microscope lenses remained unsurpassed for over 150 years. Neutron tomography now enabled us to reveal the lens types Van Leeuwenhoek used. We argue that Van Leeuwenhoek’s instruments incorporate some innovations that testify to an awareness of concurrent developments. In particular, our analysis shows that for making his best-performing microscopes, Van Leeuwenhoek deployed a lens-making procedure popularized in 1678 by Robert Hooke. This is notable, as Hooke always wanted to find the secret of Van Leeuwenhoek’s lenses, but never managed to do so. Therefore, Van Leeuwenhoek was far from the isolated scholar he is often claimed to be; rather, his secrecy about his lenses was motivated by an attempt to conceal his indebtedness to Hooke."

In May 2021 the paper was open access at this link: https://advances.sciencemag.org/content/7/20/eabf2402 .

Documents the power and impact of nearly 200 examples of AIDS posters from around the world and the social activism that continues to bring awareness to a disease without vaccine or a cure. Selected from the 8000 posters concerning AIDS collected by Edward Atwater.

This study demonstrated that "vulnerable infants have a better chance of survival if they start receiving 'kangaroo mother care'--which calls for babies to spend as much time as possible in direct contact with a carefgiver's skin--immediately after birth."

From the abstract:

"Methods
"We conducted a randomized, controlled trial in five hospitals in Ghana, India, Malawi, Nigeria, and Tanzania involving infants with a birth weight between 1.0 and 1.799 kg who were assigned to receive immediate kangaroo mother care (intervention) or conventional care in an incubator or a radiant warmer until their condition stabilized and kangaroo mother care thereafter (control). The primary outcomes were death in the neonatal period (the first 28 days of life) and in the first 72 hours of life.

"Results
"A total of 3211 infants and their mothers were randomly assigned to the intervention group (1609 infants with their mothers) or the control group (1602 infants with their mothers). The median daily duration of skin-to-skin contact in the neonatal intensive care unit was 16.9 hours (interquartile range, 13.0 to 19.7) in the intervention group and 1.5 hours (interquartile range, 0.3 to 3.3) in the control group. Neonatal death occurred in the first 28 days in 191 infants in the intervention group (12.0%) and in 249 infants in the control group (15.7%) (relative risk of death, 0.75; 95% confidence interval [CI], 0.64 to 0.89; P=0.001); neonatal death in the first 72 hours of life occurred in 74 infants in the intervention group (4.6%) and in 92 infants in the control group (5.8%) (relative risk of death, 0.77; 95% CI, 0.58 to 1.04; P=0.09). The trial was stopped early on the recommendation of the data and safety monitoring board owing to the finding of reduced mortality among infants receiving immediate kangaroo mother care.

"Conclusions
"Among infants with a birth weight between 1.0 and 1.799 kg, those who received immediate kangaroo mother care had lower mortality at 28 days than those who received conventional care with kangaroo mother care initiated after stabilization; the between-group difference favoring immediate kangaroo mother care at 72 hours was not significant."

The author manuscript before final editing in the New Engl. J. Med. is available from PubMedCentral at this link.

(Thanks to Juan Weiss for this reference.)

First application of CRISPR gene editing in the successful cure of diseases. Order of authorship in the original publication: Frangoul, Altshuler, Cappellini. 

(Thanks to Juan Weiss for this reference and its interpretation.)

mRNA-1273 is synonymous with the Moderna mRNA Covid-19 vaccine. The Moderna mRNA vaccine was produced from theoretical design to finished product and distribution in less than one year. This was the first published paper on that vaccine. It was first posted online on 12-30-20, updated on 1-15-21, and published in print on 2-4-2021. The vaccine was initially administered under "emergency use authorization" granted by the U.S. FDA.

This vaccine delivers the mRNA needed to code for the pre-fusion stabilized S (spike) protein to the inside of the host cell inside an encapsulating hollow lipid nanoparticle. That mRNA then instructs the host cell to produce S protein molecules which are then ferried out of the host cell and act as the antigen/immunogen for this vaccine once outside of the cell.

(Thanks to Juan Weiss for this reference and its interpretation.)

The authors showed that the Regeneron antibody cocktail has a low incidence of side effects and a profound and rapid effect on viral load, with most reduction occurring within 48 hours, even in patents with the highest viral loads, which would presumably be at higher risk of death. The neutralizing antibody titers in the trial patents were more than 1000 times the titers achievable with convalescent plasma from previously ill patients who had recovered. Order of authorship in the original publication: Weinreich, Sivapalasingam, Norton et al. Available from PubMedCentral at this link.

(Thanks to Juan Weiss for this reference and its interpretation.)

https://encyclopediaofarkansas.net/entries/health-and-medicine-392/

An overview of the history of health and medicine in Arkansas with many cross-references to related articles in the online Encyclopedia of Arkansas.

Concerns only U.S. medical libraries.

"China’s vast and ancient body of documented knowledge about plants includes horticultural manuals and monographs, comprehensive encyclopedias, geographies, and specialized anthologies of verse and prose written by keen observers of nature. Until the late nineteenth century, however, standard practice did not include deploying a set of diagnostic tools using a common terminology and methodology to identify and describe new and unknown species or properties.

"Ordering the Myriad Things relates how traditional knowledge of plants in China gave way to scientific botany between the mid-nineteenth and mid-twentieth centuries, when plants came to be understood in a hierarchy of taxonomic relationships to other plants and within a broader ecological context. This shift not only expanded the universe of plants beyond the familiar to encompass unknown species and geographies but fueled a new knowledge of China itself..." (publisher).

The authors showed how a coronavirus specific protease inhibitor designed in the lab, that could be administered by mouth to humans, achieved excellent plasma concentrations and antiviral potency. This drug, marketed as Pfizer's Paxlovid, was the first successful outpatient medicine for the treatment of COVID-19.
Order of authorship in the original publication: Owen, Allerton, Anderson.

(Thanks to Juan Weiss for this reference and its interpretation.)

Abstract:
"Proteins are essential to life, and understanding their structure can facilitate a mechanistic understanding of their function. Through an enormous experimental effort^1,2,3,4, the structures of around 100,000 unique proteins have been determined⁵, but this represents a small fraction of the billions of known protein sequences^6,7. Structural coverage is bottlenecked by the months to years of painstaking effort required to determine a single protein structure. Accurate computational approaches are needed to address this gap and to enable large-scale structural bioinformatics. Predicting the three-dimensional structure that a protein will adopt based solely on its amino acid sequence—the structure prediction component of the ‘protein folding problem’⁸—has been an important open research problem for more than 50 years⁹. Despite recent progress^{10,11,12,13,14}, existing methods fall far short of atomic accuracy, especially when no homologous structure is available. Here we provide the first computational method that can regularly predict protein structures with atomic accuracy even in cases in which no similar structure is known. We validated an entirely redesigned version of our neural network-based model, AlphaFold, in the challenging 14th Critical Assessment of protein Structure Prediction (CASP14)¹⁵, demonstrating accuracy competitive with experimental structures in a majority of cases and greatly outperforming other methods. Underpinning the latest version of AlphaFold is a novel machine learning approach that incorporates physical and biological knowledge about protein structure, leveraging multi-sequence alignments, into the design of the deep learning algorithm."

In 2024 Demis Hassabis and John Jumper shared the Nobel Prize in Chemistry with David Baker for "revealing protein's secrets through computing and artificial intelligence."

Order of authorship in the original publication: Jumper, Evans...Hassabis.  Open access from Nature at this link.

"During the 1790s and beyond, medicine left the somber halls of universities, hospitals, and learned societies and became profoundly politicized, inspiring a whole panoply of different—often bizarre and shocking—subcultures. Quinlan reconstructs the ethos of the time and its labyrinthine underworld, traversing the intersection between medicine and pornography in the works of the Marquis de Sade, efforts to create a "natural history of women," the proliferation of sex manuals and books on family hygiene, anatomical projects to sculpt antique bodies, the rage for physiognomic self-help books that taught readers to identify social and political "types" in post-revolutionary Paris, the use of physiological medicine as a literary genre, and the "mesmerist renaissance" with its charged debates over animal magnetism and somnambulism.

"In creating this reconstruction, Quinlan argues that the place and authority of medicine evolved, at least in part, out of an attempt to redress the acute sense of dislocation produced by the Revolution. Morbid Undercurrents exposes how medicine then became a subversive, radical, and ideologically charged force in French society" (publisher).

Using the base editor enzyme developed by Liu (GM11865), the authors report that they can “correct the pathogenic HGPS mutation in cultured fibroblasts derived from children with progeria and in a mouse model of HGPS.” Their technique resulted in “87-91% correction of the pathogenic allele, mitigation of the resulting RNA mis-splicing, reduced levels of progerin and correction of the nuclear abnormalities.” Mice treated like this, exhibited “improved vitality and greatly extended median lifespan from 215 to 510 days.” At the end they added that “these findings demonstrate the potential of in vivo base editing as a possible treatment for HGPS and other genetic diseases by directly correcting their root cause.”

Digital facsimile from PubMedCentral at this link. Order of authorship in the original publication: Koblan, Erdos, Wilson....Collins..Liu.

(Thanks to Juan Weiss for this reference and its interpretation.)

Order of authorship in the original publication: Schwartz, Avvad-Portari, Babál, et al....
"Design.—Case-based retrospective clinico-pathological analysis by a multinational group of 44 perinatal specialists from 12 countries of placental and autopsy pathology findings from 64 stillborns and 4 neonatal deaths having placentas testing positive for SARS-CoV-2 following delivery to mothers with COVID-19."

"Conclusions.—The pathology abnormalities composing SARS-CoV-2 placentitis cause widespread and severe placental destruction resulting in placental malperfusion and insufficiency. In these cases, intrauterine and perinatal death likely results directly from placental insufficiency and fetal hypoxic-ischemic injury. There was no evidence that SARS-CoV-2 involvement of the fetus had a role in causing these deaths."

https://doi.org/10.5858/arpa.2022-0029-SA

Chapters by Monique Kornell are: 1. The Illustration of Anatomy,  2. The Living Dead: Animated Anatomy, 3. Arts and Anatomy Books, 4. Anatomy and the Antique, 5. "As Large as Nature": Life Size Anatomical Illustration, 6. Surface Anatomy from the Inside Out. 
Erin Travers contributed Chapter 7, "Restricted Access: The Body, Sex, and Reproduction in Frederk Ruysch's Anatomical Collection and Catalogues."
Thisbe Gensler contributed Chapter 8, "Interior Visions: Representing the Body in Three Dimensions."

The remainder of this elegantly designed, illustrated, and produced book consists of a very extensively annotated catalogue by all the co-authors of 56 exhibited items, followed by an unusually extensive bibliography.

The first sequence of the complete human genome, telomere to telomere, including transcriptional and epigenetic state of the repeat elements, adding 8% novel genome information left unresolved since the 2001 draft sequence. Order of authorship in the original publication: Nurk, Koren, Rhie...Miga. 

(Thanks to Juan Weiss for this reference and its interpretation.)

Abstract:
"The AlphaFold Protein Structure Database (AlphaFold DB, https://alphafold.ebi.ac.uk) is an openly accessible, extensive database of high-accuracy protein-structure predictions. Powered by AlphaFold v2.0 of DeepMind, it has enabled an unprecedented expansion of the structural coverage of the known protein-sequence space. AlphaFold DB provides programmatic access to and interactive visualization of predicted atomic coordinates, per-residue and pairwise model-confidence estimates and predicted aligned errors. The initial release of AlphaFold DB contains over 360,000 predicted structures across 21 model-organism proteomes, which will soon be expanded to cover most of the (over 100 million) representative sequences from the UniRef90 data set."

Open access from academic.oup.com at this link.

1) Using a phylogeographical model of the mammal-virus network, and projections of geographical range shifts, the authors assert that 3,139 mammal species will aggregate in new combinations at high elevations, seeking respite from rising heat.

2) Further they state that most mammalian species will have a range that overlaps with that of at least one previously unfamiliar species, and that more than 300,000 new cross-species encounters will occur globally, especially in tropical Africa and southeast Asia. They project that this will lead to a doubling in the number of cross-species contacts. They add that tropical hotspots of novel viral sharing will broadly coincide with areas of high population density, such as India, Indonesia, eastern China and the Philippines, by 2070.

3) They state that bats will become key drivers of altered virus sharing under climate change. Bats are known for their ability to harbor and transmit emergent pathogens. Furthermore, as winged mammals, bats are well positioned to respond to changing environmental conditions by taking flight and migrating to higher elevations or elsewhere.

4) The authors indicate that these ecological transitions are already underway, and that holding warming under 2 degrees Celsius in the 21^st century will not reduce viral sharing.

5) The authors indicate that birds have the best documented virome after mammals, and account for the majority of non-mammalian reservoirs of zoonotic viruses. Thus changing bird migration patterns in a warming world will have a special impact on transmission.

6) Lastly, they state that climate change could easily become the dominant anthropogenic force in viral cross-species transmission.

Order of authorship in the original publication: Carlson, Albery, Merow....

(Thanks to Juan Weiss for this reference and its interpretation.)

"The substantial collection of Antoine Laurent Lavoisier’s apparatus is not the only surviving collection of eighteenth-century chemical apparatus and instrumentation, but it is without question the most important. The present study provides the first scientific catalogue of Lavoisier’s surviving apparatus. This collection of instruments is remarkable not only for the quality of many of them but, above all, for the number of items that have survived (ca. 600 items). Given such a wealth and variety of instruments, this study also offers the first comprehensive attempt to reconstruct the cultural and social context of Lavoisier’s experimental activities" (publisher).

"The Revolutionary War broke out during a smallpox epidemic, and in response, General George Washington ordered the inoculation of the Continental Army. But Washington did not have to convince fearful colonists to protect themselves against smallpox―they were the ones demanding it. ...Wehrman describes a revolution within a revolution, where the violent insistence for freedom from disease ultimately helped American colonists achieve independence from Great Britain.

"Inoculation, a shocking procedure introduced to America by an enslaved African, became the most sought-after medical procedure of the eighteenth century. The difficulty lay in providing it to all Americans and not just the fortunate few. Across the colonies, poor Americans rioted for equal access to medicine, while cities and towns shut down for quarantines. In Marblehead, Massachusetts, sailors burned down an expensive private hospital just weeks after the Boston Tea Party...." (publisher)

Abstract: "We evaluated the performance of a large language model called ChatGPT on the United States Medical Licensing Exam (USMLE), which consists of three exams: Step 1, Step 2CK, and Step 3. ChatGPT performed at or near the passing threshold for all three exams without any specialized training or reinforcement. Additionally, ChatGPT demonstrated a high level of concordance and insight in its explanations. These results suggest that large language models may have the potential to assist with medical education, and potentially, clinical decision-making."

"In the past three weeks, a new AI model called ChatGPT captured significant attention due to its ability to perform a diverse array of natural language tasks⁹. ChatGPT is a general Large Language Model (LLM) developed recently by OpenAI. While the previous class of AI models have primarily been Deep Learning (DL) models, which are designed to learn and recognize patterns in data, LLMs are a new type of AI algorithm trained to predict the likelihood of a given sequence of words based on the context of the words that come before it. Thus, if LLMs are trained on sufficiently large amounts of text data, they are capable of generating novel sequences of words never observed previously by the model, but that represent plausible sequences based on natural human language. ChatGPT is powered by GPT3.5, an LLM trained on the OpenAI 175B parameter foundation model and a large corpus of text data from the Internet via reinforcement and supervised learning methods. Anecdotal usage indicates that ChatGPT exhibits evidence of deductive reasoning and chain of thought, as well as long-term dependency skills" (from the paper).

https://www.medrxiv.org/content/10.1101/2022.12.19.22283643v2.full-text

Order of authorship: Kung, Cheatham, ChatGPT...Tseng.

Abstract: "Atavisms have attracted people’s attention for a long time. First, atavisms excited their imagination and created fertile ground for myths and superstitions. With the development of science, atavisms became the subject of investigation, which soon provided evidence to support evolutionary theory. However, at the molecular level, the formation of atavisms remained insufficiently understood. Recent progress in comparative genomics and molecular developmental biology has helped in understanding the processes underlying the formation of one of the human atavisms: the vestigial tail."

"Introduction: According Wilhelm Roux, the term “atavism” in biology defines the revival of a biological structure that was lost in ancestors during evolution (Correns et al., 1912). The term “atavism,” coined in 1766 by French botanist Duchenne [i.e. Antoine Nicolas Duchesne] comes from the Latin atavis, which roughly corresponds to the word “precursor” (Hall, 2010; Zanni and Opitz, 2013). We know several atavisms in humans: color blindness, extra nipples, enlarged teeth, an elongated coccyx (“tail”), excess hair, etc. The existence of atavisms is a big problem for creationists challenging evolution. Atavisms are the insurmountable argument of the theory of evolution, which contradicts the basic idea of creationism that animals and plants exist unchanged from the moment of their creation."

The authors stated that “The four genes that are the most likely candidates for the role of genes whose function causes the absence of tail are : 1) TBXT 2) Wnt3a 3) Tbx6 and 4) Msgn1. It is the functional deficiency of these that causes the absence of a tail”.  They also stated that TBXT is the most important of these genes. It is generally stated that mutations in these genes made them non-functional and caused the loss of a tail that resulted eventually in the hominid apes roughly about 18-25 million years ago, Once the tail disappeared, the hominid apes with no tail evolved, such as the Gibbon, Pongo and Gorilla, to a stage reaching the Pan (chimpanzee) species, which has the closest genetic lineage to man.

Open access at https://link.springer.com/article/10.1134/S1062360422030043

(Thanks to Juan Weiss for this reference and its interpretation.)

"In 2018, Linda Villarosa's New York Times Magazine article on maternal and infant mortality among black mothers and babies in America caused an awakening. Hundreds of studies had previously established a link between racial discrimination and the health of Black Americans, with little progress toward solutions. But Villarosa's article exposing that a Black woman with a college education is as likely to die or nearly die in childbirth as a white woman with an eighth grade education made racial disparities in health care impossible to ignore.

"Now, in Under the Skin, Linda Villarosa lays bare the forces in the American health-care system and in American society that cause Black people to "live sicker and die quicker" compared to their white counterparts. Today's medical texts and instruments still carry fallacious slavery-era assumptions that Black bodies are fundamentally different from white bodies. Study after study of medical settings show worse treatment and outcomes for Black patients. Black people live in dirtier, more polluted communities due to environmental racism and neglect from all levels of government. And, most powerfully, Villarosa describes the new understanding that coping with the daily scourge of racism ages Black people prematurely...." (publisher). 

Worobey and colleagues showed:

1) The earliest case of an abnormal pneumonia was first reported to the World Health Organization on Dec. 31, 2019.

2) Using basic epidemiology going back to the now iconic plot maps drawn by John Snow in the 19th century, the authors showed with their 21st century maps that nearly all the reported cases in December 2019 to February of 2020, were reported within a circumferential radius around the Wuhan market, which was defined at about a 13 kilometer radius, but with the greatest group of cases within 8.3 kilometers of the market.

3) They determined that a "lineage B" strain was clustered around a 1.12 km. radius around the market and that a "lineage A" strain was identified beyond a 3.2 kilometer radius. On their maps there is a tight clustering of cases contained within an 8.3 km cluster around the market.

4) They showed that 11 infection susceptible animals were observed and documented at the Huanan market in November 2019, with the raccoon dog being perhaps the most salient. The Wuhan market traded and sold each and all of these raccoon dogs.

5) They suggested that the market was a superspreading event which would be lineage specific. Evidence suggests that lineage A and B likely originated at the market, and then spread from this epicenter into the neighborhoods surrounding the market and beyond.

6) China has not reported the early virological studies done on these animals at the market , so the Chinese are the only ones that know which animals tested positive.

7) Based on their data, the authors posited animal to human viral transmission plausibly from infected live animals at the market. They stated  that “there were probably two viral introductions (A and B), and there was an extensive network of wildlife farms in Wester Hubei Province, including hundreds of thousands of raccoon dogs on farms in Enshi Prefecture, which specifically
supplied the Huanan market."

Order of authorship in the original publication: Worobey, Levy... Lemey....

Digital text from science.org at this link.

(Thanks to Juan Weiss for this reference and its interpretation.)

Abstract: "We analyzed the genomic diversity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) early in the coronavirus disease 2019 (COVID-19) pandemic. We show that SARS-CoV-2 genomic diversity before February 2020 likely comprised only two distinct viral lineages, denoted “A” and “B.” Phylodynamic rooting methods, coupled with epidemic simulations, reveal that these lineages were the result of at least two separate cross-species transmission events into humans. The first zoonotic transmission likely involved lineage B viruses around 18 November 2019 (23 October to 8 December), and the separate introduction of lineage A likely occurred within weeks of this event. These findings indicate that it is unlikely that SARS-CoV-2 circulated widely in humans before November 2019 and define the narrow window between when SARS-CoV-2 first jumped into humans and when the first cases of COVID-19 were reported. As with other coronaviruses, SARS-CoV-2 emergence likely resulted from multiple zoonotic events."

Digital text from science.org at this link.

Thanks to Juan Weiss for this reference.

The authors showed that the complex waggle dance, previously thought to be an inborn trait, is partly learned by young bees as they observe more experienced bees. 

Abstract:

An interpretive exhibition catalogue explaining the relationship of Freud's large collection of antiquities preserved in the Freud Museum to ideas that Freud developed in psychoanalysis.

Published "open access" 11 October 2023. https://www.nature.com/articles/s41586-023-06615-2
"Abstract: "Central nervous system tumours represent one of the most lethal cancer types, particularly among children¹. Primary treatment includes neurosurgical resection of the tumour, in which a delicate balance must be struck between maximizing the extent of resection and minimizing risk of neurological damage and comorbidity. However, surgeons have limited knowledge of the precise tumour type prior to surgery. Current standard practice relies on preoperative imaging and intraoperative histological analysis, but these are not always conclusive and occasionally wrong. Using rapid nanopore sequencing, a sparse methylation profile can be obtained during surgery. Here we developed Sturgeon, a patient-agnostic transfer-learned neural network, to enable molecular subclassification of central nervous system tumours based on such sparse profiles. Sturgeon delivered an accurate diagnosis within 40 minutes after starting sequencing in 45 out of 50 retrospectively sequenced samples (abstaining from diagnosis of the other 5 samples). Furthermore, we demonstrated its applicability in real time during 25 surgeries, achieving a diagnostic turnaround time of less than 90 min. Of these, 18 (72%) diagnoses were correct and 7 did not reach the required confidence threshold. We conclude that machine-learned diagnosis based on low-cost intraoperative sequencing can assist neurosurgical decision-making, potentially preventing neurological comorbidity and avoiding additional surgeries."
Order of authorship in the original publication: Vermeulen, Pagès-Gallego....de Ritter.

The definitive bibliographical catalogue of the historical literature of homeopathy.

https://hmddirectory.nlm.nih.gov/

A world directory of history of medicine libraries edited and published online by NLM. The date this was first published is not stated. I entered it into this database in 2024 and arbitrarily assigned that date to the entry.

Abstract:
"Importance  Interest in artificial intelligence (AI) has reached an all-time high, and health care leaders across the ecosystem are faced with questions about where, when, and how to deploy AI and how to understand its risks, problems, and possibilities.
"Observations  While AI as a concept has existed since the 1950s, all AI is not the same. Capabilities and risks of various kinds of AI differ markedly, and on examination 3 epochs of AI emerge. AI 1.0 includes symbolic AI, which attempts to encode human knowledge into computational rules, as well as probabilistic models. The era of AI 2.0 began with deep learning, in which models learn from examples labeled with ground truth. This era brought about many advances both in people’s daily lives and in health care. Deep learning models are task-specific, meaning they do one thing at a time, and they primarily focus on classification and prediction. AI 3.0 is the era of foundation models and generative AI. Models in AI 3.0 have fundamentally new (and potentially transformative) capabilities, as well as new kinds of risks, such as hallucinations. These models can do many different kinds of tasks without being retrained on a new dataset. For example, a simple text instruction will change the model’s behavior. Prompts such as “Write this note for a specialist consultant” and “Write this note for the patient’s mother” will produce markedly different content.
"Conclusions and Relevance  Foundation models and generative AI represent a major revolution in AI’s capabilities, offering tremendous potential to improve care. Health care leaders are making decisions about AI today. While any heuristic omits details and loses nuance, the framework of AI 1.0, 2.0, and 3.0 may be helpful to decision-makers because each epoch has fundamentally different capabilities and risks."

Order of authorship in the original publication: Howell, Corrado, DeSalvo.