dataesr/scientific-paragraphs-categorization huggingface dataset:
Novel insights into function of genes associated with human disease It has been shown that genes causing lethality in the mouse are enriched in disease genes  29, 30. We established orthology between genes in the mouse and human, and used the Human Genome Mutation Database (HGMD) to annotate human disease associations  31, 32. We next compiled an updated list of 3326 essential genes by combining the published data from the Mouse Genome Informatics (MP terms listed in Supplementary Table  7 ) database and 608 genes identified in the IMPC effort as causing lethality and subviability, along with 4919 nonessential genes. With these updated lists, we report an even stronger enrichment of essential genes relative to nonessential for human disease genes catalogued in the HGMD (odds ratio= 2. 00, p-value=6.
Discussion In this study, we describe the systematic characterization of embryonic lethal phenotypes as part the collaborative effort to generate a genome-wide catalogue of gene function. A unique aspect of our pipeline is the incorporation of high-resolution, high-throughput 3D imaging methods, affording detailed morphological information and automated analysis  19. Highresolution datasets are available to the community through a common portal, facilitating additional, in depth analysis by other investigators that will further enrich the phenotype calls reported in the primary screen. These data are provided in real time, without embargo, to create an "open access" environment that allows investigators to rapidly evaluate new models. Importantly, open availability of the mouse models themselves reduces the cost and time lost through duplication of effort.
1N iodine solution (Sigma-Aldrich) for 24 hours. The iodinestained embryo was then embedded in agarose within an 11-mm centrifuge tube and positioned in the micro-CT scanner for imaging. Imaging-3D datasets were acquired for each mouse embryo using a Skyscan 1172 highresolution micro-CT scanner (Bruker, Billerica, MA, USA). With the X-ray source at 100 kVp and 100 µA and the use of a 0. 5 mm aluminum filter, each specimen was rotated 360° around the vertical axis, generating 1200 views in 5 hours. These image projections were reconstructed into digital cross-sections using the Feldkamp algorithm 3 for cone beam CT. The resulting 3D data block contained 2000×1000×1000 voxels of [13. 4 µm] 3 voxel size.
Identification of human orthologs of essential genes and non-lethal genes To investigate the relevance of novel developmental phenotypes uncovered in the IMPC project, we combined the IMPC data with phenotype data for targeted loss-of-function mutant lines reported in the Mouse Genome Informatics database (MGI)  13. Genes annotated with any of 50 Mouse Phenotype (MP) terms including prenatal, perinatal and postnatal lethal phenotypes (Supplementary table 7)  14  were considered to be essential genes (n=3023) (Supplementary table  8 ). The MGI database was also used to select genes with reported targeted loss-of-function phenotypes that are not embryo or pre-weaning lethal (nonessential genes; n=4995). The IMPC effort expanded these lists with 252 essential genes, 101 genes with sub-viable phenotypes and 701 genes with viable mutant phenotypes.
Overlap between cell-essential genes in human haploid cells and human orthologs of essential genes in the mouse We used data from three recent publications on genome-wide screens for cell-essential genes in human cells to address the overlap between essential genes in the human and mouse genome  19, 20, 21. From these papers, we selected 1580 core EGs (genes above essentiality threshold in at least 3 out 5 cell lines in the study) from Hart et al. , 1739 core EGs (genes above essentiality threshold in at least 2 out 4 cell lines in the study) from Wang et al. and 1734 core EGs (genes above essentiality threshold in at least 1 out 2 cell lines in the study) from Blomen et al. We used the combined IMPC-MGI EG list (n=3326, see above) to assess the overlap between human cell-essential genes identified in these three studies and essential genes in the mouse.
Extended Data Extended Data Figure  1. Standard IMPC allele variants and number of alleles for each included in this study. a, Conditional-ready, knockout-first allele (tm1a) design (top) with LacZ reporter, and the Cre converted (tm1b, bottom) version lacking the neo cassette and critical exon. The promoter driven variant is illustrated. b, Schematic of the small number of alleles included where the distal loxP had been lost during targeting (tm1e, top) and the converted (tme. 1) variant with the neo cassette removed. c, Velocigene "definitive null" design (top, tm1) where the LacZ cassette replaces the coding sequence of the target gene, and Cre-excised variant (bottom, tm1. 1). Details of all alleles used are listed in Supplementary Table  2  and 5. Additional details and schematics of all allele variants are available at: http:// www.
Extended Data Figure  3. Multiple GOSlim categories show enrichment for lethal and subviable genes versus viable genes from the IMPC dataset. The analysis was performed for GO Process (a), GO Function (b) and GO Component (c) categories. X-axis is the proportion of genes in each class that are annotated for the GOSlim group for each category. d-f, Novel lethal IMPC genes, previously reported IMPC genes and all MGI genes were subject to the same analysis, showing the large effect analysis and characterization of lethal genes has on GO analysis. Extended Data Figure  4. Schematic of the IMPC embryonic lethal phenotyping pipeline. Lines are defined as lethal if zero homozygous animals are identified after 28+ animals have been genotyped. The KOMP2/IMPC centres begins with a mid-gestation (E12.
(8 Tmem100 +/+ vs. 8 Tmem100 -/-with all 8 showing the defect). (b) LacZ expression in the E12. 5 Tmem100 +/- embryo indicated expression in the heart (arrows), blood vessels and craniofacial regions (blue). d-i, MicroCT imaging revealed a small cochlear volume in E15. 5 Eya4 -/-embryos. E15. 5 Eya4 -/-embryos were registered to an average control dataset of the same age followed by automated analysis to show that mutant embryos had a statistically smaller cochlear volume compared to Eya4 +/+ (WT) embryos. (d) Transverse, coronal, and sagittal sections through the right cochlea are marked with a horizontal and vertical dashed line in the transverse section to indicate the location of the coronal and sagittal sections, respectively. The color corresponds to areas of larger (red) and smaller (blue) volumes in the KO embryos.
Extended Data Figure  7. Coronal sections of Whole Brain MRI revealed many volume changes in the P7 Tox3 -/- (WT) mice. (a) P7 Tox3 -/-(KO) mice brains were registered to an average control dataset of P7 Tox3 +/+ (WT) brains. The color corresponds to areas of larger (red) and smaller (blue) relative volumes in the KO embryos. The color bar minimum corresponds to a false discovery rate (FDR) threshold of 5%. KO mice exhibited altered volumes in multiple brain structures including an enlarged pons, amygdala, and thalamus/hypothalamus and a decreased pontine nucleus when compared to the WT brains (arrows). Most striking was the decrease in the size of the cerebellum of the KO mice (arrows). (8 Tox3 +/+ (WT) vs. 10 Tox3 -/-(KO) with all 10 showing the defects). Histological analysis of Tox3 -/-(KO) mice revealed abnormal development of the cerebellum.
f, Coronal section showing bicuspid aortic valve (av). g, Sagittal section showing fused spinal ganglia (fsg) and additional ganglion material (ag) caudal to the occipital bone (ob) (2/4 embryos). li, liver; lu, lung; lv, left ventricle; e, esophagus; sc, spinal chord; I, 1 st brain ventricle and left telencephalon; II, 2 nd brain ventricle and right telencephalon; c, cusp of semilunar valve; sg, spinal ganglion; dr, dorsal roots of spinal nerve; tongue (to); pulmonary valve (pv). h, Coronal and transverse sections through composites of Cbx4 -/-embryos registered to an average control dataset. Blue = smaller volumes in the mutant; red = larger volumes. The blue clusters in the top panel correspond to the smaller right and left thymic rudiments, the adrenals in the middle panel, and the trigeminal (V) ganglia in the bottom panel (n = 8 mutants).
Acknowledgments The authors would like to thank all of the IMPC members and partners for their contribution to the consortium effort, including this study, and acknowledge the contributions of  Janet Rossant ,  S. Lee Adamson , and  Tania Bubela. This work was supported by  NIH  grants  U42 OD011185  (S. A. M),  U54 HG006332  (R. E. B, K. S),  U54 HG006348-S1  and  OD011174  (A. L. B. ),  HG006364-03S1  and  U42 OD011175 (K. C. K. L. ) ,  U54 HG006370  (P. F. , A-M. M. , H. E. P. , S. D. M. B. ) and additional support provided by the The  Wellcome Trust, Medical Research Council   Strategic Award  (L. T. , S. W. , S. D. M. B. ),  Government of Canada through Genome Canada  and  Ontario Genomics  ( OGI-051 )(C. M. , S. D. M. B. ),  Wellcome Trust Strategic Award "Deciphering the Mechanisms of Developmental Disorders (DMDD) " ( WT100160 ) (D.
A. , T. M. ),  National Centre for Scientific Research (CNRS) , the  French National Institute of Health and Medical Research (INSERM) , the  University of Strasbourg (UDS) , the  "Centre Européen de Recherche en Biologie et en Médecine" , the  "Agence Nationale de la Recherche " under the  frame programme "Investissements d'Avenir"  labelled  ANR-10-IDEX-0002-02 ,  ANR-10-INBS-07 PHENOMIN  to (Y. H. ), The  German Federal Ministry of Education and Research by Infrafrontier  grant  01KX1012  (S. M. , V. G. D. , H. F. , M. HdA. ).
Mass spectrometry. All samples were prepared in a 9:1 v:v MeOH/H2O solution. Triple quadrupole mass spectrometry data were acquired on a Quattro Premier QqQ (Waters Corp. , Milford, MA) equipped with an ESI source employed in the negative ion mode. Collision-induced dissociation (CID) MS/MS spectra were obtained using nitrogen as collision gas in the collision cell and collision energies (Elab) between 5 and 30 eV. Atmospheric pressure photoionization (APPI) experiments were carried out in an Orbitrap XL high resolution instrument (Thermo Scientific). All experimental details are given in the supplementary material. Gas phase acidity calculations. Calculations have been performed using the GAUSSIAN 09 suite of programs. 32 Geometry optimization was carried out with the B3LYP  [33] [34]  functional coupled to the Def2-SVP split valence basis set.
ACKNOWLEDGMENTS Financial support for this research was provided by the  Ile-de-France region through DIM Analytics. This project has been carried out with the support of the  World Anti-Doping Association. Financial support from the  National FT-ICR  network (FR 3624  CNRS ) for conducting this research is gratefully acknowledged. Financial support was also provided by the  National Science Foundation  through  CHE-1058764. We thank  Dr. Etienne Derat  for allowing access to the calculation cluster and for his valuable advice.
INTRODUCTION Atrial fibrillation (AF) is associated with a fivefold increase in stroke risk. 1  Strokes associated with AF have a poorer prognosis compared with non-AF stroke. 2  Evidence-based guidelines for stroke prevention in AF recommend anticoagulant (AC) therapy for patients with additional stroke risk factors,  [3] [4] [5]  but AC therapy is underused in eligible patients. 6 4] [5]  In the present study, the evolving patterns of antithrombotic therapy were investigated using data from a large, prospective, global cohort study of patients with newly diagnosed non-valvular AF in different countries, geographic regions, care settings, and in patients at different levels of stroke and bleeding risks.
Data collection The electronic case report form (eCRF) was designed by Dendrite Clinical Systems Ltd (Henley-on-Thames, UK). Oversight of operations and data management was conducted by the sponsor and coordinating centre (Thrombosis Research Institute-TRI, London, UK), with support from Quintiles (Durham, North Carolina, USA), The University of Birmingham Department of Primary Care Clinical Sciences (Birmingham, UK), Thrombosis Research Group-Brigham and Women's Hospital (Boston, Massachusetts, USA), and AIXIAL (Paris, France). The GARFIELD-AF protocol requires source data verification of 20% of eCRFs, an electronic audit trail for all data modifications, and additional audit of critical variables. 12 Data for the analysis in this report were extracted from the study database on 3 August 2015.
DISCUSSION Data from the GARFIELD-AF cohorts collected over the past 5 years show a pronounced change in the pattern of antithrombotic therapy prescribing in patients with newly diagnosed AF. The use of AC therapy has increased and exceeds 70% in the most recent cohort. This change is predominantly due to increasing use of NOACs. Thromboprophylaxis with AP and VKA therapies alone and in combination has declined. This paradigm shift in prescribing practice has been driven in part by the availability of NOACs, but also the realisation that APs are barely effective compared with ACs. Evaluating the professional society guidelines published over the last 5 years (especially relating to AP therapy),  3 4 18-22  it is notable that the Japanese guidelines, for example, no longer recommend AP for stroke prevention in patients with AF.
This population includes some patients at high thromboembolic risk, with low HAS-BLED scores, for whom anticoagulation would seem to be appropriate. GARFIELD-AF provides a unique picture of prescribing at the end of the VKA-only era, showing the global increase in NOAC prescribing. Our findings are strengthened by protocolmandated source data verification of 20% of eCRFs and central monitoring, ensuring high data quality. A limitation of this study is that only global patterns of antithrombotic therapy were investigated. Regional differences in prescribing trends were not taken into account, nor was the rate of NOAC approvals across each region. Comorbidities were also likely confounders, which were not fully assessed in this analysis.
Independent ethics committee and hospital-based institutional review board approvals were obtained, as necessary, for the registry protocol. The registry is being performed in accordance with the principles of the Declaration of Helsinki, local regulatory requirements, and the International Conference on Harmonisation-Good Pharmacoepidemiological and Clinical Practice guidelines. All patients gave written informed consent to participate. datasets. 16 17 irst-degree interaction between baseline characteristics and time (cohort) or between comorbidities and time (cohort) were tested using likelihood ratio tests. Only significant interactions were included in the final model. Both SAS V. 9. 4 (SAS Institute Inc, Cary, North Carolina, USA) and Stata Statistical Software: Release 14 (StataCorp, College Station, Texas, USA) were used for the data analysis.
Acknowledgements We thank the physicians, nurses, and patients involved in the GARFIELD-AF registry. We would also like to thank the following people who were involved in the preparation of this manuscript:  Bernard J Gersh  ( Mayo Medical School, Rochester, USA ) and  Keith AA Fox  ( University of Edinburgh, Edinburgh, UK ) for their work in the audit of GARFIELD-AF data;  Antonello Ciccarone  ( TRI, London, UK ), SAS programming support;  Claire Aukim-Hastie ,  Emily Chu , and  Rae Hobbs  ( TRI, London, UK ), medical writing support. Competing interests AJC: advisor to Bayer,  Boehringer Ingelheim ,  Pfizer / BMS , and  Daiichi Sankyo. GAm: advisor to  Merck, Menarini , and  Angelini. DA: personal fees from  Bayer Healthcare, BMS/Pfizer ,  Boehringer-Ingelheim , and  MSD. J-PB: personal fees from  Aspen.
Surgery was performed 21-45 days after cycle 8, according to the initial and post-chemotherapy assessment. The clinical response of each patient was evaluated by physicians according to the evolution of the tumour mass by monitoring patients throughout the chemotherapy and after surgery. protein level decrease. In conclusion, our data indicate that successive cycles of chemotherapy in TN patients drive a chronic oxidative stress reaction associated with reduced levels of total H2AX protein, the extent of which could sensitize tumour cells to chemotherapy (Fig  6 ).
Cisplatin IC50 tested on BC cell lines has been recently reported in  (Garnett et al, 2012). Cell cycle distributions were performed on ethanolfixed cells, stained with propidium iodide and analysed by flow cytometry. Flow cytometry data were acquired using CellQuest Pro (Becton Dickinson) software on the FACSCalibur (Becton Dickinson) and were analysed using and ModfitLT (Verity) software. Cell cycle re-entry experiments were performed after 48 h of starvation in 0. 25% FCS-containing medium. All treatments and transfection conditions used for expressing exogenous H2AX-FLAG are described below, # Transfection and Immunoprecipitation (IP).
Animals were chosen in a randomized manner within each subgroup defined according to the genotype and age. For each condition, the sample size calculation was performed using "InvivoStat" software (http://invivostat. co. uk). The number of mice analysed in each experiment is indicated in the corresponding figure legend. Analyses were not performed under blinded conditions. All protocols involving mice and animal housing were in accordance with institutional guidelines as proposed by the French Ethics Committee and have been approved (Agreement number: CEEA-IC #118: 2013-06).
S National Institutes of Health, Bethesda, Maryland,  USA, 1997 USA, -2008)). Quantification of c-H2AX large foci (diameter > 0. 8 lm) was assessed by ImageJ software and further confirmed by visual inspection of images. Briefly, foci were automatically detected by selection of pixel with maximum intensity (Find Maxima macro) in the region of interest defined using DAPI staining. Detected foci had a diameter of at least 0. 8 lm, which corresponds to large foci  (Staaf et al, 2012). The number of foci per cell was evaluated using three independent cell lines for each condition. In average, 50 nuclei per genotype (with a minimum of 30 nuclei) have been used for quantification.
After 16 h of DNA transfection, the cells were treated or not with Cycloheximide at 200 lg/ml (Sigma #CA4859) at various time points. Proteins were extracted as described previously. Western blot analysis of samples were then performed as described above and probed with anti-Flag antibody. For determining the half-life of H2AX-WT and H2AX-K119 proteins, densitometry analysis of Western blots were performed using the ImageJ software  (Schneider et al, 2012). Quantifications were normalized to the untreated time point (t0) and H2AX protein half-life was evaluated from the degradation curve by extrapolating its linear part. Half-life of H2AX was calculated by the formula (0. 5-b)/a, where "b" is the y-intercept and "a" the slope of the regression curve.
Clonogenicity and cell survival assay Clonogenicity experiments and data analysis were performed as described in  (Franken et al, 2006). Right after c-irradiation (2 or 5 Gy, as indicated), cells were seeded at low density (500-5,000 cells). After 7 days of incubation, cells were fixed and stained with 0. 2% crystal violet in 20% ethanol during 20 min. After washing with water, the numbers of colonies containing at least 25 cells were counted. The number of surviving colonies was normalized to nonirradiated samples, with the latter value being set to 100%. This defines the surviving fraction (expressed in % with respect to the untreated samples).
COMET assay COMET assay was performed as described in  (Quanz et al, 2009). Briefly, prior to treatment or after 10 Gy of c-irradiation (t = 0 min, just after irradiation, or at t = 5, 15, 30 or 60 min following c-irradiation), cells were suspended in 0. 5% low-melting-point agarose and transferred onto a microscope slide pre-coated with agarose. Comets were performed in alkaline conditions. The parameters of the comets were quantified using the software Comet Assay 2 (Perceptive Instrument). Duplicate slides were processed for each experimental point. The tail moment was defined as the product of the percentage of DNA in the tail and the displacement between the head and the tail of the comet.
Protein arrays The reverse-phase protein array has been performed at the RPPA Platform of the Institut Curie. Experimental procedures have been performed, as in  Troncale et al (2012). Briefly, serial diluted lysates were deposited onto nitrocellulose-covered slides, probed with primary antibodies and revealed with horseradish peroxidasecoupled secondary antibodies. Arrays were finally probed with Streptavidin-Alexa-647, dried and scanned using a GenePix 4000B microarray scanner (Molecular Devices). Spot intensity was determined with MicroVigene software (VigeneTech Inc). Data were normalized by Sypro Ruby protein stain. The antibodies used are listed here: H2AX (Abcam #ab11175), Phospho-53BP1 (Ser1778) (Cell Signaling Technology #2675), 53BP1 (Cell Signaling Technology #4937), Ape1 (Cell Signaling Technology #4128), ERCC1 (Cell Signaling Technology #3885), Cleaved PARP (Asp214) p25 The cell cycle control/DNA damage phospho-antibody microarray is a high-throughput ELISA based antibody array designed for semi-quantitative protein expression profiling, featuring 238 highly specific and well-characterized site-specific antibodies directed against 95 different proteins (Full Moon BioSystems # PCC238).
Each antibody is printed with six replicates and covalently immobilized on polymer coated glass slides. Experimental procedures have been performed according to the manufacturer's instructions. Briefly, 75 lg of total biotinylated protein lysates extracted from control, junD-and Nfe2l2-deficient fibroblasts were conjugated to the antibody array. We then used Cy3-streptavidin dye for detection followed by GenePix 4000B microarray scanner (Molecular Devices) and MicroVigene software (VigeneTech Inc) for protein quantification.
Minimum sample size required to obtain a power of 80% and a significance level (Type I error probability) of 0. 05 was computed using the R package pwr using the function pwr. t. test. HER2-amplified carcinomas have been defined according to ERBB2 immunostaining using ASCO's guideline. LumA tumours were defined by positive immunostaining for ER (Estrogen receptor) and/or PR (Progesterone receptor). The cut-off used to define hormone receptor positivity was 10% of stained cells. Among invasive ductal carcinomas, the TN immunophenotype was defined as follows: ER À PR À ERBB2 À with the expression of at least one of the following markers: KRT5/6 + , EGF-R + , Kit +. Cohort characteristics have also been previously described in part in  (Marty et al, 2008; Toullec et al, 2010; Maire et al, 2013)  and are summarized in Table  1.
Immunohistochemistry on human breast carcinomas Sections of paraffin-embedded tissue (3 lm) were stained using streptavidin-peroxidase protocol, immunostainer Benchmark, Ventana, Illkirch, France, with specific antibodies recognizing H2AX (1/200, Abcam #ab11175), c-H2AX (1/100, Cell Signaling Technology #2577), actin, alpha2, smooth muscle (SMA) (1/400; Sigma #A2547), Cleaved Caspase 3 (1/150; Cell Signaling technology #9661) and NRF2 (1/100; Santa Cruz #sc-13032). Data were obtained using total sections from 10 LumA, 10 HER2 and 10 TN tumours, hybridized simultaneously. TMA (Tissue Micro-Array) from 33 LumA, 37 HER2 and 47 TN were used to confirm the data on a large set of patients. TMA was composed using three cores of tumours per case (1 mm of diameter each) and hybridized simultaneously.