dataesr/scientific-paragraphs-categorization huggingface dataset:
Mouse liver tissue staining analysis Histological analysis. All organs were immediately fixed in a 10% formalin solution after harvesting and subsequently included in paraffin. Liver slices stained with hematoxylin & eosin (H&E) and Sirius Red were obtained for all mice. For immunohistochemistry staining, the following antibodies were used: CD11c (RRID: AB_2800282, #97585, Cell Signaling), CD3 (RRID: AB_1956722, #MA1-90582, Invitrogen), CD4 (RRID: AB_2573008, #14-9766-82, eBioscience), CD8a (RRID: AB_2572861, #14-0808-82, Invitrogen), CLEC4F (RRID: AB_2081339, #AF2784, R&D Systems), Fibronectin-1 (RRID: AB_732380, #ab45688, Abcam), LY6C (RRID: AB_302004, #ab15627, Abcam), MHC II (RRID: AB_10006678, #NBP1-43312, Novus Biologicals), MPO (RRID: AB_307322, #ab9535, Abcam), REL A (RRID: AB_535932, #NB 100-2176, Novus Biologicals), REL B (RRID: AB_632341, #sc-226, Santa Cruz), pP38 (RRID: AB_2139682, #4511, Cell Signaling), HSP70 (RRID: AB_1150514, #IMG-80181, IMGENEX), FAH (RRID: AB_2678806, #HPA044093, Sigma), α-SMA (RRID: AB_476701, #A2547, Sigma).
Staining quantification was performed on entire histological slide or on 5 to 10 consecutive images at 10x or 20x magnification per staining Images were analyzed using ImageJ software v1. 51j8 (Rasband W, National Institutes of Health, USA) or QuPath version 0. 3. 2 (54). For the collagen proportional area quantification in humanized areas, two consecutive liver cuts were stained with FAH and Sirius Red. The corresponding FAH-positive area in the Sirius Red histological slide was selected as region of interest and then the collagen proportional area quantified using ImageJ software  (78). For quantification of other immunostaining in representative humanized area, the humanized areas were selected from the hematoxylin staining based on the phenotype of human hepatocytes showing a brighter cytoplasm and different nucleus and cytoplasm size compared to mouse ones  (21).
RNA extraction from human and murine liver tissue. Liver cells were lysed in TRI- reagent (Molecular Research Center) using GentleMACS Octo Dissociator, and RNA was purified using Direct-zol RNA MiniPrep (Zymo Research) according to the manufacturer's instructions. RNA quantity and quality were assessed using NanoDrop (ThermoScientific). Gene expression profiling was performed using 250-500 ng total RNA. Prognostic liver signature expression analyses. Profiling of the prognostic liver signature (PLS) was performed using Nanostring nCounter assay as described  (80). Induction or suppression of the PLS in gene expression data was determined as previously reported using the Gene Set Enrichment Analysis (GSEA)  (81) , implemented in GenePattern genomic analysis toolkits. False discovery rate (FDR) <0.
25 was regarded as statistically significant  (81). PLS was always determined by using control cells, control animals, or control patient-derived tissues as references. Results are presented as simplified heatmaps showing the classification of PLS global status as poor or good prognosis and the significance of induction/suppression of PLS genes (log10 of FDR values). Global status corresponds to the difference between low-risk and high-risk gene enrichments. ChIPseq and CUT&TAG assay. LX2 cells (RRID: CVCL_5792) were incubated 24h with or without 100 ng/mL TNF-α (Peprotech, #300-01A) and scraped. The CUT&Tag assay against H3K27ac (RRID: AB_2561016, #39133, Active motif) or NF-κB p65 subunit (RRID: AB_10828935, #6956, Cell Signaling Technology) were performed following the manufacturer's instructions (Active motif CUT&Tag-IT Assay Kit, #53165, #53160).
Gene expression data from non-diseased liver tissues (University Strasbourg NASH cohort, table  S1 ) were used as reference controls to verify the induction of the PLS in the studied NASH patients. For non-diseased tissues, the PCLS were cultured in William's E complete medium supplemented with 20% patient serum and were subjected to LPS treatment (100 ng/mL) to induce inflammation and to treatment with control (palivizumab IgG4(  53 )) or CLDN1 mAb (50 µg/mL). After 3 days, the tissues were harvested and proteins extracted to assess effect of the treatment on EGFR and SRC phosphorylation. Genome wide RNA-seq analyses. RNA-Seq libraries were generated from 300 ng of total RNA using TruSeq Stranded mRNA Sample Preparation Kit (Illumina, Part Number RS-122-2101). Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94 °C for 2 min.
RepSox (2 µM, ab142139, Abcam), SML0543 (10 µM, Sigma Aldrich), U0126 (10 µM, Sigma Aldrich) or Wortmannin (10 µM, W3144, Sigma Aldrich) were used as inhibitors of SMAD2/3, p38, ERK and Akt signaling, respectively. The following primary antibodies were used: SMAD 2/3 (RRID: AB_10889933, #8685, Cell Signaling technology), P-SMAD 2/3 (RRID: AB_2631089, #8828, Cell Signaling technology), p38 (RRID: AB_330713, #9212, Cell Signaling technology), P-p38 (RRID: AB_2139682, #4511, Cell PCR of intracellular RNA as described  (86). CLDN1 mAb or control mAb (palivizumab IgG4(  53 )) (10 µg/mL, respectively) were added for 3 days after HCV infection. HBV: HepG2-NTCP cells (RRID: CVCL_JY40) were plated in 12-well plates and infected with HBV purified from patient serum  (87)  in presence of CLDN1 mAb or control mAb (10 µg/mL, respectively).
Phosphosites were selected for subsequent analyses if their signals were statistically significantly different between conditions (by t-test or ANOVA). The signal per phosphosite is the result of the net phosphorylation attributed to the activity of one or more kinases  (89, 90). Instrument operation and imaging were controlled by the EVOLVE 2. 0 software and quantified using BioNavigator 6. 3 (BN6; PamGene International BV). Signal intensities at multiple exposure times were integrated by linear regression (S100), Log2-transformed, and normalized using a Combat correction model for batch correction where the scaling parameters (mean and sd) were estimated using an empirical Bayesian approach. By interpreting kinase activity at multiple phosphosites, an Upstream Kinase Analysis (UKA) was performed.
Exploiting knowledge on specific kinase-to-substrate relationships from publicly available databases, UKA algorithm predicts differential kinase activity in the test condition compared to the control. Kinase statistic represents the change in kinase activity, indicating inhibition if <0 and activation if >0. Mean specificity score represents the specificity of the change in kinase activity, higher scores highlighting a lower chance of observations descending from random set of peptides  (91). The hits of our PamGene assay were then ordered by Median Final Score, a synthetic measure of both target robustness and significance. The 20 top hits were plotted in a heatmap comparing Mean Kinase Statistics of our model vs those of a recently published liver kinome atlas, established with the same technique  (34).
CLDN1 knockout using CRISPR-Cas9 technology. Huh7. 5. 1 stably expressing Cas-9 endonuclease (Huh7. 5. 1-Cas9) were DMSO-differentiated for 7 days (Huh7. 5. 1-Cas9 diff ), and then either co-cultured with LX-2 stellate cells (RRID: CVCL_5792, 20%) and treated with free fatty acids (FFA; 800 µM oleic acid and 400 µM palmitic acid) or infected using HCV Jc1. After 3 (FFA treatment) or 7 days (HCV Jc1 infection), cells were transduced with lentiviruses expressing control single guide RNA (sgRNA) or sgRNA targeting CLDN1 gene expression (sgCLDN1). Expression plasmids were provided by Dr. David Root (Broad Institute of Harvard and MIT, Cambridge, USA). Transduced cells were selected under hygromycin treatment (500 μg/mL) for 3 days and lysed using iScript RT-qPCR sample preparation reagent. The HCV-or FFA-induced PLS was analyzed using nCounter Nanostring technology in cell lysates.
cells in triplicate per condition. PHH and PMH (primary antibody staining): Isolated PHH and PMH were incubated with increasing concentrations of humanized CLDN1 mAb H3L3 or murinized mAb CLDN1 TAR-Rm (0. 01-100 µg/mL), respectively. 293-T cells (primary antibody staining): 293-T cells (RRID: CVCL_4U22) were transfected with plasmids encoding for human or mouse CLDN1 fused with cerulean fluorescent protein or empty plasmid fused with cerulean fluorescent protein (kindly provided by M. Evans, Mount Sinai Hospital, New York). Transfected cells were incubated with increasing concentrations of humanized CLDN1 mAb H3L3, murinized CLDN1 mAb TAR-Rm or the respective isotype control antibodies. Activated hepatic stellate cells (primary antibody staining): Isolated HSCs were differentiated into activated HSCs (aHSCs) within 10 days of culture on plastic (76).
FUNDING Funding was obtained from the following grants:  European Union ERC-AdG -2014 HEPCIR # 671231  (T. F. B. ),  European Union ERC-AdG -2020 FIBCAN # 101021417  (T. F. B. ) , European Union   ERC-PoC-2016 PRELICAN #7555460  (T. F. B. ),  European Union   ERC-PoC-2018 HEPCAN #862551  (T. F. B. ),  European Union ERC  Consolidator grant HepatoMetabopath # 683000  (M. H. ),  European Union   H2020 HEPCAR #667273  (T. F. B. and M. H. ),  Fondation ARC  www. fondation-arc. orgTheraHCC2. 0IHU201901299 (T. F. B. ),  ANRS  Grant  ECTZ103701 CLAUDIN-1  (T. F. B. ),  SATT Conectus, University of Strasbourg (CANCLAU)  (T. F. B. ),  French National Research Agency   LABEX ANR-10-LABX-0028_HEPSYS  (T. F. B. ),  German Research Foundation (DFG)   RO 5983/1-1  (N. R. ),  C1 KU Leuven grant  ( C14/20/097 ) (T.
~1x10 5 5 cells in triplicate per condition. PHH and PMH (primary antibody staining): Isolated PHH and PMH were incubated with increasing concentrations of humanized CLDN1 mAb H3L3 or murinized mAb CLDN1 TAR-Rm (0. 01-100 µg/mL), respectively. 293-T cells (primary antibody staining): 293-T cells (RRID: CVCL_4U22) were transfected with plasmids encoding for human or mouse CLDN1 fused with cerulean fluorescent protein or empty plasmid fused with cerulean fluorescent protein (kindly provided by M. Evans, Mount Sinai Hospital, New York). Transfected cells were incubated with increasing concentrations of humanized CLDN1 mAb H3L3, murinized CLDN1 mAb TAR-Rm or the respective isotype control antibodies. Activated hepatic stellate cells (primary antibody staining): Isolated HSCs were differentiated into activated HSCs (aHSCs) within 10 days of culture on plastic (76).
Acknowledgements We acknowledge support from the  National Natural Science Fund of China  ( 11621404 ,  11561121003 ,  11727812 ,  61775059 ,  12074122 ,  62022033  and  11704123 ),  Shanghai Municipal Science and Technology Major Project  ( 2019SHZDZX01-ZX05 ),  Key Project of Shanghai Education Commission  ( 2017-01-07-00-05-E00021 ),  National Key Laboratory Foundation of China  ( 6142411196307 ),  Shanghai Rising-Star Program and Science and Technology Innovation Program of Basic Science Foundation of Shanghai  ( 18JC1412000 ), the  Agence Nationale de la Recherche  ( ANR-20-CE30-004 ).
This study aimed to determine how leading pharmaceutical companies are engaging with environmental issues, which have made commitments to climate change targets, and what implications these have for pharmaceutical suppliers. Methods: Content analysis was performed of the most recent (2020 or 2021) publicly available company reports of the top 20 pharmaceutical companies, by 2020 prescription revenue  3. Using a pre-formulated data extraction table, data on environmental reporting, climate change targets and sustainability measures were extracted. Proportions of companies that made commitments to net zero emissions, carbon neutrality and GHG emission reductions across their own operations and supply chain were determined. Results: All companies engaged in environmental reporting. Nineteen (95%) of the companies have committed to climate change targets and reducing GHG emissions in their operations, 50% have committed to carbon neutrality and 40% to net zero emissions by a range of target years.
Reach, assessed by social media listening, was broad, but lower for ESMO virtual plenaries than the annual meeting (2147 vs 49,686 total online mentions: primarily Twitter or news stories). Online sentiment for ESMO and ASCO virtual plenaries was positive, with rapid data dissemination cited as a key advantage. Shorter submission to presentation times will likely need to be factored into publication planning. Conclusions: Virtual plenaries appear to be an innovative option for real-time data presentation, allowing for accelerated data dissemination, benefitting the scientific community. For publication planning, virtual plenaries have the potential to amplify discussion around key data releases. Interest in this type of meeting is likely to increase in the future and will warrant further assessment to understand the impact for the scientific community.
Publisher and journal websites were searched for author name change policies. Results: Of 33 unique publishers, 17 (52%) had publicly available name change policies. In all but two of these policies, changes Objective: COVID-19 has mandated remote working across many geographies. We assessed the impact on MedComms work and company culture within one agency network. Results: To date, 44 queries were received from 28 internal publication professionals. The top three query topics included authorship, data disclosure, and copyright. A total of 16 respondents (57%) completed the survey, all of whom indicated the PQIF is easy to use. 81% of respondents had used the PQIF as an FAQ prior to submitting their own question. Most respondents (94%) felt they received a response and resolution to their query in a timely manner and that using the PQIF resulted in a more efficient use of their time.
Conclusions: The PQIF is an innovative, easy-to-use tool that streamlines the publication query process, reducing the number of emails sent and resulting in a more efficient use of time by publication leads and publication advisors. The tool is a resource of FAQ and provides metrics for developing targeted training and informing updates to publication procedural documents. Objective: Podcast articles that undergo a formal peer review and are indexed in literature databases are a novel method to marry the rigor of traditional publications with the convenience of novel delivery systems. We determined best practices for efficient and compliant development of impactful peer-reviewed podcast articles. Methods: We partnered early in the development of a podcast article 1 to ensure a scientifically rigorous and transparent peer review process.
KEYWORDS Best practice; medical/scientific communications; medical writers/writing Measuring the quality of patient engagement in a patient-led and co-authored analysis of the lived experience of a rare disease Objective: ORCID iDs are unique, persistent author identifiers providing disambiguation and transparency in publications. We analysed trends in ORCID iD registration by pharma employees and use in pharma-sponsored publications. Methods: ORCID iD registrations by employees of 14 pharma companies between 01 January 2018 and 07 January 2021 were extracted and pooled using ORCID's application programming interface and organization email domains. Previously, ORCID iD use in publications by six of these companies was assessed using PubMed to search for and extract metadata from their sponsored publications published 01 January 2018-07 January 2019  1.
Results: Each pharma stakeholder group uses a different channel and medium to access content, ranging from PubMed to patient advocacy groups. It is therefore important for pharma to tailor scientific content for each stakeholder and consumption channel being used. Patients and HCPs would like to see more scientific content developed in collaboration with trusted players like patient-advocacy groups and professional societies, respectively. HCPs prefer on-demand self-education via easy-to-find drug information, whereas patients expect HCPs to know and communicate to them all drug information, including side effects and long-term risks. MSLs on the other hand want bite-sized content with more visual elements unifying data from multiple publications. Conclusion: Content personalization may be an effective way for Medical Affairs teams to communicate optimally and enhance trust in pharma.
However, additional studies and data are necessary to confirm these initial conclusions and to identify other factors that may impact article metrics, such as indication, study type, and author renown. Objective: Recent studies suggest that authors "hype" their findings in publications observed more frequently with male authors in high impact factor (IF) (>10) journals  [1] [2] [3] [4] [5]. We examined these gendered differences using a scholarly information platform. Methods: General science and medical journal original research articles (IF >10) in 2002-2021 were assessed using Dimensions, identifying author gender (first and last author) with genderize. io, applying a 90% probability threshold. Hype words 5 were supplemented with similar, handpicked words using GloVe encodings. Results: Across 1,668,863 publications from 311 journals, the percentage of publications with hyped words in abstracts increased over time and male first authors used the most common "hype" words more frequently than their female counterparts (Figure  1 ).
Journals; metrics; medical/scientific communications Objective: This analysis evaluated visibility and content of video abstracts (VAs) in PubMed and select journals. Methods: VAs in PubMed were identified via search string, quantified by journal, and randomly selected for content analysis (n ¼ 40). Journals with dermatologists, gastroenterologists, or infectious disease specialists in the top three audiences of the Journal Selector and Conference Authority database (Anju Software) were analyzed for video visibility within journal sites.
Acknowledgements We thank  Maarten Beekman  ( Medical Impactþ, South Holland, The Netherlands ),  Leigh M. Boehmer  ( Association of Community Cancer Center, Rockville, MD, USA ),  Lily Chu (International Association for Chronic Fatigue Syndrome/Myalgic Encephalomyelitis, Burlingame, CA, USA), and Jessica (Byam) Klein (Ipsen, Boston, MA, USA)  for their inputs on the survey questionnaire.
KEYWORDS Journals; metrics; medical/scientific communications Objective: This analysis evaluated visibility and content of video abstracts (VAs) in PubMed and select journals. Methods: VAs in PubMed were identified via search string, quantified by journal, and randomly selected for content analysis (n ¼ 40). Journals with dermatologists, gastroenterologists, or infectious disease specialists in the top three audiences of the Journal Selector and Conference Authority database (Anju Software) were analyzed for video visibility within journal sites.
Primary and secondary research manuscripts accepted or published between 1 June 2020 and 30 June 2021 were identified in the publication management tool, Datavision. A database of OA status of articles, Unpaywall, was used to characterize the OA status, including type of OA (e. g. Gold) and license (e. g. Creative Commons, CC), for each publication. Medical information consumption and sharing practices in rare diseases -a clinician perspective  ¶ Rosalie Gadiot a , Eline Hanekamp a , Marie Diamonda, Sandra Sirrs b and Tom Rouwette a a Excerpta Medica, Amsterdam, Netherlands; b University of British Columbia, Vancouver, BC, Canada Jacqui Oliver a , Veronica Porkess b , Sarah McSorley a and Dawn Lobban a a Envision Pharma Group, Wilmslow, United Kingdom; b UCB Results: 82 research manuscripts were accepted or published during the 1-year period.
Methods: A survey of industry professionals was commissioned by Cactus Communications, driven by the pharma journal PM360, and distributed via email databases and social media. The survey aimed to assess how respondents define patient cen-tricity, the current state of patient involvement in drug develop-ment and clinical research publication, and the barriers to greater patient involvement. Results: The survey results of 31 pharma and associated industry professionals showed varied definitions of patient centricity: The majority (68%) defined it as "placing the patient's well-being at the core of all initiatives". Interestingly, only 6% of the partici-pants defined it as "including patients as authors, peer reviewers, the pandemic. Conversation drivers primarily focused on vaccines Nicole Parker a , Rajni Parthasarathy a , Ana Costa b , and COVID-19 cases.
According to the French sanitary authorities, samples were PCR screened, among which around 10% were ultra-deeply sequenced (Deepcheck Whole Genome SARS-CoV-2 genotyping V3-V4, ABL SA Group, Metz, France), based on the nCoV-2019 sequencing protocol v3 (LoCost)-ARTIC network  [10]. SARS-CoV-2 temporal genetic variability in general population followed-up at the university hospital was explored on 414 samples according to Pangolin/Nextrain classification at a mutation threshold above 20% to characterize major variants. Potential mixtures of variants of concern (VOCs) Delta and Omicron were also evaluated at a mutation threshold of 5% covering major and minor variants; then variant proportions in each mixture were determined according to covariants, CoV-Spectrum data, Nextclade assignment  [11]  and alignment with Wuhan reference strain (EPI ISL 402124), Delta (EPI ISL 11448607), and Omicron sequences (EPI_ISL_11352845; EPI_ISL_12179603) from GISAID (Global Initiative on Sharing Avian Influenza Data, http://gisaid.
org, assessed on 1 March 2022). Analyses were also performed with the Recombination Detection Program software (RDP v4. 5)  [12]  on the human samples showing SARS-CoV-2 variants mixtures, to investigate for possible viral recombinants by using RDP  [13] , GENECONV  [14] , BootScan  [15] , MaxChi  [16] , Chimaera  [17] , SiScan  [18] , and 3Seq programs  [19]. To explore potential immune modulation that could be generated by SARS-CoV-2 variant mixtures, the hydrophilicity prediction was realized on Delta variant receptor-binding domain, on a putative Delta variant harboring various mutations in receptorbinding domain (RBD), with the Wuhan viral strain as a reference. The SARS-CoV-2 RBD was analyzed for the hydrophilicity correlated with the immunogenicity by using a free epitope database and prediction resource-IEDB (Immune Epitope Database, www.
Wastewater Samples Four wastewater samples (WW) collected in Nancy, France in 2022 (ww1-January 16; ww2-February 16; ww3-March 13; ww4-April 24) were also sequenced for the whole-SARS-CoV-2 genome and the sequences were submitted in GenBank (Table  1 ). Table  1. SARS-CoV-2 genome analysis from patient samples (E1-E10) and WW samples (WW1-WW4). The alignment was carried out with Wuhan reference strain (EPI ISL 402124), Delta (EPI ISL 11448607), and Omicron (EPI_ISL_11352845; EPI_ISL_12179603) from GISAID database. For each sample, the following aspects were mentioned: the main assignation clade (NextClade, Pangolin) and, for the other variants features, the signature mutations, their proportion/percentage in the viral population present in the same sample, their localization in the SARS-CoV-2 genome.
(c) Parker hydrophilicity prediction of Delta RBD, Delta with K417N and E484A mutations RBD and Wuhan reference strain RBD. The X-axis represents the amino acid position on the SARS-CoV-2 RBD and the Y-axis represents the hydrophilicity correlated with the immunogenicity (aa position scale is represented below each X-axis); the yellow surface matches to antigenic residues, the green surface matches to non-antigenic residues (IEDB database).