- Dec 2020
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www.nature.com www.nature.com
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endothelial cells
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hepatocytes
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cell populations
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immunohistochemical examinations
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flow cytometry
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gene expression
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hepatic tissue
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cells
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parenchymal
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transcriptional profiles
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single-cell RNA sequencing
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microenvironment
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immune
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human hepatic
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human liver
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human livers
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human liver
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map
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immune
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microenvironment
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human liver
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cells
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immune functions
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metabolic
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body
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solid organ
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liver
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europepmc.org europepmc.org
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community
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code
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healthy
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design
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human disease
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cells
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systematic study
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human tissues
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proofs-of-concept
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open data
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Human Cell Atlas
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cells
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reference map
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map
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morphology
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location
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gene expression
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human cell types
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international
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Human Cell Atlas Project
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human body
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cell types
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scientific community
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single-cell molecular profiling
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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atlas
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cell census
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life span
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human T cell
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lineage commitment
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TCR recombination
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activated dendritic cell
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thymic fibroblast
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CD8αα+ T cell populations
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life span
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T cell receptor (TCR) recombination
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T cell differentiation
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thymic cell types
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T cells
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selection
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differentiation
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human thymus
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human thymus
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thymus
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europepmc.org europepmc.org
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COVID-19 pandemic
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COVID-19 pandemic
Tags
Annotators
URL
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www.nature.com www.nature.com
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Clara
You really should not use "Clara cells." It is a known nazi eponym? https://pubmed.ncbi.nlm.nih.gov/20223917/
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- Nov 2020
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greenelab.github.io greenelab.github.io
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IL-1β is anti-inflammatory
maybe some error here, IL-1beta is considered inflammatory, as far as I know https://en.wikipedia.org/wiki/Interleukin_1_beta
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Figure 5: Mechanism of Action for Potential Therapeutics
this figure is misleading. It looks like compounds like HCQ are in fact effective.
Maybe adding interrogation marks or dashed lines could help to alleviate it,
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This study thus suggests that COVID-19 does not improve recovery from COVID-19, even in otherwise healthy adult patients with mild symptoms.
typo, it should be HCQ/Chloroquine instead of the first COVID-19
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Given
very long paragraph
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The two immunoglobulin classes most pertinent to these goals are immunoglobulin M (IgM), which are the first antibodies produced in response to an infection, and immunoglobulin G (IgG), which are the most abundant antibodies found in the blood. Following SARS infection, IgM and IgG antibodies were detected in the second week post-infection. IgM titers peaked by the first month post-infection, and then declined to undetectable levels after day 180. IgG titers peaked by day 60, and persisted in all donors through the two-year duration of study [307]
It jumps very fast from established knowledge to a study report. Maybe this separation could be clearer.
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Real-Time Polymerase Chain Reaction (RT-PCR
Mistake! RT stands for Reverse transcription, not for real time!
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The Drosten Lab, from Germany, was the first lab to establish and validate a diagnostic test to detect SARS-CoV-2.
That might be neglecting chinese efforts. Such a strong claim of priority might need a stronger source than their original publication.
Also, the paper does real-time RT-PCR, which is the same as qPCR, so it does not make sense that there are 2 sections
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particles on a contaminated surface [???].
many broken references in this session
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S’s S2 domain
confusing
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Like that of SARS-CoV, the entry of SARS-CoV-2 into host cells is mediated by interactions between the viral spike glycoprotein (S) and human angiotensin-converting enzyme 2 (ACE2) [62,65,151,152,153,154,155,156].
Maybe ref https://www.nature.com/articles/s41586-020-2012-7 too? It is the first publication showing need of ACE2 for entry as far as I know
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UniProt, NCBI Genome Database, The Immune Epitope Database and Analysis Resource (IEDB), and The Virus Pathogen Resource (ViPR)
Maybe add citations?
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No comprehensive proteomic analyses of the pathogen or of patients suffering from its infection have yet been reported
Outdated. Ex: Ultra-High-Throughput Clinical Proteomics Reveals Classifiers of COVID-19 Infection
https://www.sciencedirect.com/science/article/pii/S2405471220301976
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SARS-CoV-2 ORF3b gene suppresses IFNB1 promoter activity (IFN-I induction) more efficiently than the SARS-CoV_ORF3b_ gene
SARS-CoV-2 ORF3b and SARS-CoVORF3b gene are diffierentially formated
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This finding suggests that the SARS-CoV-2 antagonist is insufficient for large doses of the virus
This phrase is ambiguous. What is the antagonist, and is it insufficient for which phenomenon?
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Whether SARS-CoV-2 facilitates the positive regulation of its own transmission between host cells is still unclear
For me, it is unclear what "positive regulation of its own transmission" means. Is it supposed to mean upregulation of ACE2?
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CDC has updated its list of symptoms suggestive of COVID-19 to include nausea and vomiting, as well congestion and runny nose [45]
Maybe add when the CDC updated the list. It seems to have been updated May 13, 2020, but maybe they`ll update again some day
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Patients may also experience loss of smell, myalgias (muscle aches), fatigue, or headache.
Maybe citation needed.
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By infecting the epithelium, viruses such as SARS-CoV are known to bypass the physical barriers such as skin and mucus that comprise the immune systems’ first line of defense [68]
"viruses such as SARS-CoV" is precise, but might be misleading. I was under the impression it referred to SARS-CoV-2.
Maybe something like " 2003 SARS-CoV" or SARS-CoV-1 ?
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Neu 5,9 Ac2
Maybe expand acronym to 5-N-acetyl-9-O-acetyl neuraminic acid ? The comma in the middle makes it a bit confusing.
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the virus clusters
Maybe make explicit that it is the virus' genomic sequence that clusters with the ones of other known coronaviruses?
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The current COVID-19 pandemic, caused by the SARS-CoV-2 virus, represents an acute global health crisis where symptoms can range from mild to severe or fatal [45]
Maybe too technical, but symptoms is kind of dangling. There is no mention of the disease in the sentence, only to the pandemic and the health crisis.
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www.nexojornal.com.br www.nexojornal.com.br
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A abertura da matéria já chama atenção: fundo vermelho preenchendo toda a tela. Um gráfico sem marcação de eixos, mas que é imediatamente reconhecido: mortes diárias cumulativas por COVID-19. A palavra "BRASIL" no canto inferior esquerdo delimita o escopo, e no superior direito, o número 100.000 e a cruz cristã. Uma visualização minimalista, sem mostrar nada desnecessário, maximizando o impacto da informação.
Os jornalistas, então, introduzem em 4 parágrafos a série jornalística em si, a pandemia, as particularidades do Brasil e os impactos locais. Os parágrafos, entretanto, são apenas um aperitivo para um gráfico vertical, que progride pelos dias, mostrando a média móvel. Em vez de mostrar somente os pontos ligados por linhas (o "line plot" visto em diversos recursos sobre a pandemia) cada ponto do conjunto de dados é representado por uma linha pontilhada.
A linha pontilhada não é regular, com pontos com "jitter", com espalhamento. Cada observação tem um número de pontos equivalente a seu valor. Desta forma, o gráfico representa explicitamente cada pessoa, cada indivíduo que foi contabilizado, permitindo dimensionar as vidas humanas atrás do gráfico. O gráfico se estende página abaixo, dando espaco digno para as 100.000 mortes.
Ao longo da linha do tempo, os autores adicionam informações e decoram o dado com os recortes importandes, ainda resumindo os dados de forma paupável. "Um trem lotado de mortos a cada dois dias", assim eles descrevem o dado de mortes no Brasil atós o início de agosto.
Para coroar, a matéria ainda mostra as estatísticas demográficas das mortes. Além de usar barras, as porcentagens são mostradas em "barras humanas", mais uma vez humanizando os dados.
A escolha das cores também impacta: a reportagem inteira é em vermelho. Os tons de vermelho transmitem sensação de alerta, e também contribui para dimensão humana. Paletas de cores divergentes trariam destaque para as métricas em si (ex: homem x mulher). Ao usar tons de vermelho, a matéria não permite esquecer que são estatísticas de mortes, mantendo um consistencia interno.
Um trabalho exemplar, tratando dados impactantes de forma impactante, mostrando ao mesmo tempo a figura geral, como permitindo o leitor debruçar sobre detalhes de dados.
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douroucouli.wordpress.com douroucouli.wordpress.com
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Maybe you are lucky to have mad ontology skillz
I literally laughed out loud, thanks for that
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douroucouli.wordpress.com douroucouli.wordpress.com
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It can be tempting to “hack” together an asserted hierarchy as opposed to constructing an ontology in a modular fashion. This is especially true for ontology developers who have not been trained in techniques like modular design.
Another issue that is common to beginner ontologists and software developers.
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- Oct 2020
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www.nature.com www.nature.com
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I wonder how the rank has changed in the past 6 years. Anyone knows if there will be a followup on this article?
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journals.plos.org journals.plos.org
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The semantic web. Ontologies and other formal definitions of data are useful, but in our experience, even simplified things like Dublin Core are rarely encountered in the wild.
This is even more hurtful and even more true.
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Good intentions aside, it always comes down to, "just give me a Word document with tracked changes", or similar
This is hurtfully true.
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Some emerging hybrid systems such as Git Large File Storage (LFS) put textual notes under version control while storing the large data in a remote server,
DVC (Data Version Control) is pretty solid, but might be a bit more advanced than "good enough": https://dvc.org/
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Submit code to a reputable DOI-issuing repository.
Conversely, GitHub users can make releases, that are citable per se, I guess. Not sure if they have DOIs, though.
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Write the manuscript in a plain text format that permits version control.
This is an awesome recommendation!
For GitHub savvy researchers, I specifically recommend Manubot, I love it.
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Ensure that raw data are backed up in more than one location.
I hope the highlights are okay and not too messy. It is mostly a personal selection of the good-enoughest practices
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- Sep 2020
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europepmc.org europepmc.org
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social media post
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