dataesr/scientific-paragraphs-categorization huggingface dataset:
Data availability The raw sequencing data for all VOGM samples in fastq format generated in this study have been deposited in the NCBI database of Genotypes and Phenotypes as well as AnVIL under accession code phs000744. v5. p2 (https://www. ncbi. nlm. nih. gov/projects/gap/cgibin/study. cgi?study_id=phs000744. v5. p2). Genomic and phenotypic data for 1,798 unaffected siblings of autism cases and unaffected parents from the SSC can be accessed through SFARI Base (https:// base. sfari. org/) with an approved application. The reference genome used in this study is genome assembly GRCh37/hg19 (https://www. ncbi. nlm. nih. gov/datasets/genome/GCF_000001405. 13/). Additionally, the data from the mice used in this study can be found in the Supplementary Information/Source Data file. Source data for this paper are provided herein.
Code availability Software utilized in this study is available at the following web addresses: Samtools v1. 3. 1 (https://github. com/samtools/samtools); GATK HaplotypeCaller v3. 7. 0 (https://github. com/broadinstitute/ gatk/releases); GATK GenotypeGVCFs v3. 7. 0 (https://github. com/ broadinstitute/gatk/releases); GATK VariantRecalibrator v3. 7. 0 (https://github. com/broadinstitute/gatk/releases); TrioDeNovo v0. 6. 0 (http://genome. sph. umich. edu/wiki/Triodenovo); DenovolyzeR v0. 2. 0 (http://denovolyzer. org); Plink v1. 9 (http://pngu. mgh. harvard. edu/ ~purcell/plink); MetaSVM/CADD13/ANNOVAR v4. 2 (http://annovar. openbioinformatics. org); R v3. 5. 0 (https://www. r-project. org/); Python v2. 7 (https://www. python. org/downloads/); EIGENSTRAT v7. 2. 1 (https://github. com/DReichLab/EIG/tree/master/EIGENSTRAT); EnrichR R package v3.
Oral azacitidine (Oral-AZA) is a hypomethylating agent approved for the treatment of adult patients with acute myeloid leukemia (AML) in first remission after intensive chemotherapy (IC). 1, 2 In the phase III, randomized, doubleblind, placebo-controlled QUAZAR AML-001 trial (clinicaltrials gov. identifier: NCT01757535), Oral-AZA significantly prolonged relapse-free survival (RFS) and overall survival (OS) compared with placebo in patients with AML in first complete remission (CR) or CR with incomplete blood count recovery (CRi) after IC (induction ± consolidation) who were not candidates for hematopoietic stem cell transplantation (HSCT). 3 The primary goal of QUAZAR AML-001 was to evaluate the effect of maintenance therapy with Oral-AZA for patients in remission after induction. While there were no protocol-specified criteria regarding prior chemotherapy used before study entry, including the use or number of consolidation cycles received, it is of clinical interest to assess whether the amount of pre-study chemotherapy may have influenced survival outcomes in this trial.
Methods We conducted a retrospective review of the medical records and diving parameters of all consecutive patients over 18 years old who were diagnosed with IPE and admitted to the Hyperbaric Medicine We excluded all patients with a history and clinical evidence of pulmonary barotrauma or decompression sickness from the study. The following data were collected: age, sex, civilian or military status, cardiovascular history (hypertension, diabetes, smoking, history of heart disease or Acute Coronary Syndrome (ACS), history of previous IPE, diving equipment used, gas mixture used, maximum depth reached, surface water temperature (obtained from the nearest meteorological station), total dive time, intense physical exertion during diving (we inquired whether divers perceived the exercise intensity as high, offering only "YES" or "NO" as response options), time from the end of the dive to the onset of symptoms, initial clinical state before and after hospitalization, treatment received during hospitalization, evolution of symptoms after 12 h of treatment, evolution of symptoms after 24 h of treatment, results of pulmonary computed tomography (CT) scan, results of cardiac ultrasound (cUS), elevation of troponin levels, blood gas hypoxemia or desaturation, and time until discharge.
Statistics The data underwent statistical analysis using Prism 6 software (GraphPad Software, La Jolla, California). Continuous variables were reported as means ± SD or medians (25th to 75th percentile), depending on the data distribution determined by the Agostino & Pearson normality test. Categorical variables were presented as absolute values and percentages. Normally distributed continuous variables between both populations were compared using Mann-Whitney's unpaired test. Differences in categorical variables between the two populations were assessed using the Chi-square test with Yates correction or Fisher's exact test for small sample sizes. Statistical significance was defined as p < 0. 05 for all tests.
Limitations It is crucial to take into account the limitations and potential biases when interpreting the findings of this retrospective study. The study was conducted using data from emergency-hospitalized divers treated at the hyperbaric medicine department of military hospital in Toulon (HIA Ste Anne), which attends to a substantial number of injured divers annually, making it one of the highest figures in Europe with around 150 cases per year. However, this hyperbaric medicine department is situated in Toulon, a region with a significant presence of military divers, which could introduce a recruitment bias toward younger subjects. Due to the prominent representation of military divers, particularly those in training, the observed instances of IPE in this study may be more frequent among young subjects compared to regions without a significant military diver presence.
Concerning the extent of ventilatory work, no precise values were measured in our study. Instead, we relied on a cohort of previous scientific studies that examined ventilatory work based on the type of respiratory apparatus used  [21, 39, 44, 46]. While utilizing existing data on ventilatory work can provide useful indications, individual variations and uncertainties may be associated with these estimations. Therefore, direct measurements of ventilatory work in future studies could contribute to a more accurate evaluation of this variable in the context of IPE.
Surgical emergency diseases and correlated clinical scenarios were defined for each of the proposed classes. Surgical diseases that had a CA or CCA < 50% were cancelled from the TACS list; those with a CA or CCA between 50 and 75% were sent to the subsequent voting round and presented with a clearer definition and/ or a different colour-code class, or cancelled according to the comments of the panellists. Subsequent rounds were carried out until a definitive level of consensus was reached. After each round, responses were analysed to modify the questionnaire for the following round. According to the modified Delphi method, the participation was voluntary and the responses of each panellist remain anonymous. Data were collected and stored in an online database protected by a password known only to the principal investigators.
Viruses Clinical HCMV strains, namely HCMV-DB (GenBank KT959235), BL (GenBank MW980585), KM, and FS were isolated from patients that were hospitalized at Besançon University Hospital (France) as described previously  [7, 15]. Cell-free virus stocks and infections were performed as previously detailed  [15]. Careful screening of our viral stocks was conducted to rule out the presence of other oncoviruses  [15]. Infections of HAs and MRC5 cells, quantification of viral replication, and HCMV detection were performed as described previously  [15]  and in "Supplementary Materials and Methods". Primers used are listed in Supplementary Table  1.
ACKNOWLEDGEMENTS This work was supported by grants from the  University of Franche-Comté (UFC)  ( CR3300 ), the  Région Franche-Comté  ( 2021-Y-08292  and  2021-Y-08290 ) and the  Ligue contre le Cancer  ( CR3304 ) to Georges Herbein. REB is a recipient of a doctoral scholarship from  Hariri foundation for sustainable human development. SHA is supported by  ANR (Agence Nationale pour la Recherche)  grant. The funders had no role in the data collection, analysis, patient recruitment, or decision to publish. The authors thank  DImaCell Imaging Ressource Center, University of Bourgogne Franche-Comté, Faculty of Health Sciences, 25000 Besançon, France  for technical support.
Western blot analysis. Proteins were separated using 4-12% gradient poly-acrylamide SDS-PAGE gels (Life Technologies) and electrotransferred to 0. 2 µm nitrocellulose membranes (GE Healthcare, Chicago, IL, USA). After blocking with Tris-Buffered Saline with 0. 1% Tween and 3% bovine serum albumin, membranes were incubated overnight at 4°C under continuous shaking with the appropriate primary antibodies. Primary antibodies were detected using the appropriate secondary antibodies coupled with horseradish peroxidase. Immunoreactive bands were visualized by enhanced chemiluminescence with a Syngene camera. Densitometric analyses of immunoblots were performed using the GeneTools software.
Immunofluorescence analysis. Cells were seeded onto glass slides coated with cell-tak (Corning, Corning, NY, USA), then fixed in 4% paraformaldehyde for 10 min. After PBS washes, cells were incubated in 0. 01% saponin with 3% bovine serum albumin for 30 min and then incubated with anti-LC3B antibody (1/800) for 40 min. Cells were then washed before incubation with secondary antibody (1/800) for 30 min, followed by PBS and distilled H2O washes and mounting in ProLong TM Gold antifade medium with DAPI (4'6-diamidino-2-phenylindole, Invitrogen). Images were acquired using a confocal Zeiss LSM 780. For quantifications, fields were arbitrarily chosen based on DAPI staining, and the number of LC3B dots per cell was determined with Image J software.
Flow cytometry analysis. To determine the number of apoptotic and dead cells, cells were washed and resuspended in 100µl of Annexin-V binding buffer plus 2µl of Annexin-V-FITC and 5µl of Cell Viability Stain. Data were acquired on a Macsquant (Miltenyi Biotec, Bergisch Gladbach, Germany) flow cytometer and analyzed with FlowJo v10 software (Tree Star Inc. , Ashland, OR, USA).
Results Ruxolitinib enhances autophagy in JAK2 V617F cells. Although recent data from the literature indicate that ruxolitinib treatment induces autophagy in cell lines harboring the JAK2 V617F mutation in vitro  (16, 17) , compelling data about the impact of ruxolitinib on autophagy in MPN patients and in vivo are still needed. Therefore, to deeply investigate ruxolitinib effect on autophagy in JAK2 V617F model, we first treated human JAK2 V617F cells from two HEL and SET-2 cell lines and eight primary PV patients with ruxolitinib (1µM) for 2 hours. Bafilomycin (baf) or chloroquine, two autophagy inhibitors were used to monitor the autophagic flux. As expected and as shown in Figure  1A , ruxolitinib reduced STAT5 phosphorylation level in JAK2 cell lines. In addition, in association with bafilomycin, ruxolitinib increased lipidated LC3 (LC3B-II) accumulation, an autophagosomal membrane marker, compared to bafilomycin alone in HEL and SET-2 cell lines.
e. m. ) (C) and the percentage of cell death was determined by Annexin-V labelling and flow cytometry analysis (n=5 ± s. e. m. ) (D). E. CD34+ cells from JAK2 V617F -positive MPN patient samples were plated for colony forming assay in semi-solid medium supplemented or not with ruxolitinib (250nM) and chloroquine (3µM) or SAR405 (3µM). After 14 days, clonogenic potential was assessed by counting the number of BFU-E clones per dish. Data are represented as percentage of control (n=10 ± s. e. m. ). F-G. CD34+ cells from JAK2 WT healthy donor samples treated or not with ruxolitinib (1µM) in the presence or absence of chloroquine (10µM) or SAR405 (3µM). Figure Legends After 2 days, the number of cells was assessed by trypan blue exclusion counting (n=5 ± s. e. m. ) (F) and the percentage of cell death was determined by Annexin-V labelling and flow cytometry analysis (n=5 ± s.
e. m. ) (G). H. CD34+ cells from JAK2 WT healthy donor samples were plated for colony forming assay in semi-solid medium supplemented as indicated. After 14 days, clonogenic potential was assessed by counting the number of BFU-E clones per dish. Data are represented as percent of control (n=6 ± s. e. m. ). After 2 days, the number of cells was assessed by trypan blue exclusion counting (n=5 ± s. e. m. ) (E) and (right panel) the percentage of cell death was determined by Annexin-V labelling and flow cytometry analysis (n=4 ± s. e. m. ) (F). G. CD34+ cells from JAK2 V617F -positive MPN patient samples were plated for colony forming assay in semi-solid medium supplemented or not with ruxolitinib (250nM) and OA (5nM). After 14 days, clonogenic potential was assessed by counting the number of BFU-E clones per dish.
Data are represented as percentage of control (n=10 ± s. e. m. ). H-I CD34+ cells obtained from JAK2 WT healthy donor samples were treated or not with ruxolitinib (1µM) in the presence or absence of OA (5nM). After 2 days, the number of cells was assessed by trypan blue exclusion counting (n=5 ± s. e. m. ) (H) and the percentage of cell death was determined by Annexin-V labelling and flow cytometry analysis (n=5 ± s. e. m. ) (I). J. CD34+ cells from JAK2 WT healthy donor samples were plated for colony forming assay in semi-solid medium supplemented or not with ruxolitinib (250nM) and OA (5nM). After 14 days, clonogenic potential was assessed by counting the number of BFU-E clones per dish. Data are represented as percent of control (n=6 ± s. e. m. ).
Acknowledgements We thank  CREFRE  for mice experimentation. We are grateful to  Manon Farcé  and  Laetitia Ligat  for assistance with flow cytometry and microscopy, respectively. We are very grateful to nurses from the  Hematology service of IUCT-O (Toulouse)  for providing us access to blood samples of MPN patients. We thank  Anne-Marie Bénot  and  Latifa Jarrou  for administrative support. This work is partly supported by labellisation  Ligue Nationale de Lutte  contre le cancer, the  Fondation Toulouse Cancer Santé , and the association GAEL. Charly Courdy is a recipient of la  Ligue Nationale contre le Cancer. Team JE Sarry  is a member of  OPALE Carnot Institute , The Organization for Partnerships in Leukemia.
After 1 h of incubation, the medium which was kept aside was replaced to each well. The 2D cultures were then ready to be imaged using a Spinning Disk Microscope (Nikon) housed at the Institut Pasteur de Lille, Lille, France using the MetaMorph imaging software. We took 1000 images using a 20x (synthetic peptide treatment) or 40x objective (conditioned medium treatment) with 10 ms exposure time and 200 ms intervals, totalizing up to 3 minutes of recording per eld. For each well, up to 5 random elds were chosen, and at least two wells from 3 (for cell conditioned medium) or 4 (for synthetic Aβ) independent culture batches were imaged for each condition.
Analyses of Calcium Transients Time-series data from calcium imaging recordings were at rst converted to. avi format after background subtraction by use of ImageJ software. The videos were subsequently opened on CALciumIMagingAnalyzer (CALIMA) software  [20]. Each video recording of a eld of cells was rst downscaled to 2X in terms of size with a 10X zoom and was checked for the frame average mode. Moreover, in this rst detection stage, pre-set lter parameters were adjusted and applied to enable the detection of the maximum number of uorescent neurons (regions of interest -ROIs) in each eld. During this step, the detected cells were checked several times to ensure that only neurons were selected, based both on cell morphologies and the presence of fast calcium transients. Fluorescence signal noise was ltered using the median of 3 each consecutive images.
For HTO sample, the HTO matrix was normalized using centered log-ratio (CLR) transformation and cells were assigned back to their sample of origin using HTODemux function of the Seurat R Package. Then, normalizations of the gene expression matrix for cellular sequencing depth, mitochondrial percentage and cell cycle phases using the variance stabilizing transformation (vst) based Seurat::SCTransform function were performed. To integrate the experimental replicates of the single cell experiments, the harmony R package (https://github. com/immunogenomics/harmony) was used. In order to integrate the datasets, the SCTransform normalized matrices was merged and PCA was performed using Seurat::RunPCA default parameter. The 50 principal components (dimensions) of the PCA were corrected for batch effect using harmony::RunHarmony function.
We used adjusted p-value < 0. 05 and |log2FC|>0. 25 as cut-offs to de ne differently expressed genes. Functional enrichment analysis was performed using the R package FGSEA (Fast Preranked Gene Set Enrichment Analysis, version 1. 26. 0). To perform fgsea, we utilized a gene set list at adjusted p-value < 0. 05 sorted based on log2FC from three comparisons: APPV717L x Control, APPV717L x APPWT, and APPWT x Control. For the fgseaMultilevel function, the minimum gene set size was set to 15, while the maximum was limited to 400. The signi cance threshold for p-values was de ned as pvalue < 0. 05. To determine the up-or down-regulated terms within the considered ontologies between conditions, we employed the normalized enrichment score (NES). Terms with NES values greater than 0 were classi ed as up-regulated, while those with NES values less than 0 were classi ed as downregulated.
Transcriptional changes in hiNs exposed to elevated concentrations of Aβ peptides We next sought to identify possible changes in gene expression in human-induced astrocytes and neurons elicited by treatment with Aβ. To that, we performed snRNA-seq of mixed hiNs/hiAs cultures treated with conditioned media from CHO-APP V717L or CHO-APP WT and blank Brainphys for 48h (Fig. 1 ). After quality control (Methods), we recovered 7578 nuclei and identi ed 17 different cell types/subtypes using unsupervised clustering based on gene expression (Fig. 3A ). We observed that treatment with conditioned media signi cantly affected the proportion of cells in clusters 1 and 3, but there was no difference between CHO-APP V717L and CHO-APP WT (Fig. 3B ). To annotate main cell types in our dataset, we identi ed the top markers of each cluster (Supplementary Table  1 ) and evaluated the expression of the astrocyte markers SLC1A3 (GLAST), GFAP and TNC; pan-neuronal markers SNAP25, DCX, MAPT; glutamatergic neurons marker SLC17A6 (VGLUT2); GABAergic neurons marker GAD1 and GAD2; and neural progenitor cells (NPCs) markers HES6, CCND2 and CDK6 in different clusters (Fig.
Acknowledgements The authors thank the  BioImaging Center Lille (BICeL ;  US 41 -UMS 2014 ). The authors also thank  Dr. Frédéric Checler  ( Institut de Pharmacologie Moléculaire et Cellulaire ,  UMR6097 CNRS/Université de Nice -Sophia-Antipolis, France ) for kindly providing  CHO-APP V717L  and CHO-APP WT cells.
Funding This work was co-funded by the  European Union  under the  European Regional Development Fund (ERDF)  and by the  Hauts de France Regional Council  (contract no. 18006176 ), the MEL ( contract_2016_ESR_05 ), the  French State  (contract no. 2018-3-CTRL_IPL_Phase2 ), and  Brazilian National Council for Scienti c and Technological Development (CNPq). The  UMR 8199 LIGAN-PM Genomics platform (Lille , France) belongs to the ' Federation de Recherche ' 3508  Labex EGID  ( European Genomics Institute for Diabetes ;  ANR-10-LABX-46 ) and was supported by the  ANR   Equipex 2010 session  ( ANR-10-EQPX-07-01 ; ' LIGAN-PM '). The  LIGAN-PM Genomics platform   (Lille, France ) is also supported by the  FEDER  and the  Region Nord-Pas-de-Calais-Picardie  and is a member of the " France Génomique " consortium ( ANR-10-INBS-009 ).
The surgical procedure was performed under anesthesia by inhalation of 3% isoflurane and maintained with 1. 5%-2% isoflurane mixed with 100% O 2. Assessment of estrous cycle. In gonad-intact female mice, vaginal smears were performed with PBS daily to analyze estrous cyclicity, starting 10 days before vehicle or E4 pellet implantation and for 14 days after. Vaginal cytology was assessed under a Leica DM2500 microscope and LAS X software. Mouse carotid injuries and quantification of reendothelialization. Endovascular injury of the carotid artery was performed on mice as described previously (2), after 2 weeks of estrogenic treatment. Briefly, animals were anesthetized by an intraperitoneal injection of tiletamine/zolazepam (Zoletil, 100 mg/kg) and xylazine (Rompun, 10 mg/kg). The right common carotid artery was exposed and blood flow was locally restricted.
Five minutes before euthanasia, mice were injected retro-orbitally with 50 μL of 4% Evans blue dye (sc-203736, Santa Cruz Biotechnology) diluted in PBS. Mice were perfused with PBS and the right common carotid artery was dissected from the aortic arch to the carotid bifurcation and fixed with 10% phosphate-buffered formalin (Electron Microscopy Sciences) for 20 minutes. Arteries were opened longitudinally and mounted with Kaiser's glycerol gelatin (Merck). Images were acquired and quantified using a Leica DM2500 microscope and LAS X Software. The percentage of reendothelialization was calculated relative to the initial deendothelialized area (day 0). Lentivector construction and production. The cDNA encoding human ERα was subcloned into pENTR1A (Thermo Fisher Scientific) by the transfer of a BamHI/EcoRI fragment from pCR3.
Data were analyzed with Compass software (Protein Simple). Normalization against total proteins in the capillary was achieved using the included Protein Normalization (PN) assay reagent. PLA. The PLA (Duolink, Sigma-Aldrich) was used to detect ERα's interaction with SRC, according to the manufacturer's instructions. Briefly, after treatment, cells were fixed with 4% paraformaldehyde for 10 minutes and then permeabilized in PBS containing 0. 2% Triton X-100 for 10 minutes. Coverslips were incubated with anti-ERα rabbit polyclonal (1:500; Santa Cruz Biotechnology, sc-543) and anti-SRC mouse monoclonal (1:500; Santa Cruz Biotechnology, sc-8056) primary antibodies overnight at 4°C. After washing, cells were incubated with anti-rabbit PLUS and anti-mouse MINUS probes coupled to oligonucleotides (Sigma-Aldrich) for 1 hour at 37°C in a humidity chamber, followed by a ligation step for 30 minutes and a rolling-circle amplification (RCA) reaction in which fluorescently labeled oligonucleotides were hybridized to the RCA product.
Coverslips were then stained for total ERα as described above in the Immunofluorescence section. The cover slides were mounted in Duolink II mounting medium with DAPI (Sigma-Aldrich). Images were obtained with a Zeiss LSM900 confocal microscope at ×63/oil magnification and processed using Zen software. PLA dots were analyzed using ImageJ software (NIH). The plugin "Counter cells" allows analyzing dots and cell numbers. In each condition, red dots were scored in ERα-positive cells from 10 microscopic fields. RNA sequencing and analysis. Total RNA was isolated from uninjured carotid arteries through the phenol-chloroform method using TRIzol (Ambion) reagent. Quality of RNA samples was determined using a Fragment Analyzer Instrument. All selected samples had RNA quality numbers above 7. 2. mRNA.
Acknowledgments The work at  INSERM U1297  was supported by the  National Institute of Health and Medical Research (INSERM) ,  University Hospital Center of Toulouse and University of Toulouse 3, Fondation de France  ( 00133536/WB-2022-44532 ),  Agence Nationale de la Recherche  ( NOSE4 , REGENEV),  Fondation pour la Recherche Médicale  (grant numbers  ECO201806006691  and  FDT202106012979  to MD), and.