dataesr/scientific-paragraphs-categorization huggingface dataset:
As already mentioned in the introduction, reproducibility of scientific claims should be enabled by providing the software, the datasets, and the process leading to interpretable results that were used in a particular study. As much as possible, publications should highlight that the code is freely available in, for example, GitHub, together with any other relevant outputs that may have been deposited. In our experience, this openness substantially increases the chances of getting the paper accepted for publication. Journal editors and reviewers receive the opportunity to reproduce findings during the manuscript review process, increasing confidence in the reported results. In addition, once the paper is published, your work can be reproduced by other members of the scientific community, which can increase citations and foster opportunities for further discussion and collaboration.
Rule 9: Promote and Discuss Your Projects: Web Page and More The traditional way to promote scientific software is by publishing an associated paper in the peer-reviewed scientific literature, though, as pointed out by Buckheir and Donoho, this is just advertising  [17]. Additional steps can boost the visibility of an organization. For example, GitHub Pages are simple websites freely hosted by GitHub. Users can create and host blog websites, help pages, manuals, tutorials, and websites related to specific projects. Pages comes with a powerful static site generator called Jekyll that can be integrated with other frameworks such as Bootstrap or platforms such as Disqus to support and moderate comments. In addition, several real-time communication platforms have been integrated with GitHub such as Gitter and Slack.
Real-time communication systems allow the user community, developers, and project collaborators to exchange ideas and issues and to report bugs or get support. For example, Gitter is a GitHub-based chat tool that enables developers and users to share aspects of their work. Gitter inherits the network of social groups operating around GitHub repositories, organizations, and issues. It relies on identities within GitHub creating Internet Relay Chat (IRC)-like chat rooms for public and private projects. Within a Gitter chat, members can reference issues, comments, and pull requests. GitHub also supports wikis (which are version-controlled repositories themselves) for each repository, in which users can create and edit pages for documentation, examples, or general support. A different service is Gist, which represents a unique way to share code snippets, single files, parts of files, or full applications.
Gists can be generated in two different ways: public gists that can be browsed and searched through Discover and secret gists that are hidden from search engines. One of the main features of Gist is the possibility of embedding code snippets in other applications, enabling users to embed gists in any text field that supports JavaScript. Rule 10: Use GitHub to Be Social: Follow and Watch In the same way researchers are following developments in their field, scientific programmers could follow publicly available projects that might benefit their research. GitHub enables this functionality by following other GitHub users (see also  Rule 2)  or watching the activity of projects, which is a common feature in many social media platforms. Take advantage of it as much as possible!.
Conclusions If you are involved in scientific research and have not used Git and GitHub before, we recommend that you explore its potential as soon as possible. As with many tools, a learning curve lays ahead, but several basic yet powerful features are accessible even to the beginner and may be applied to many different use-cases  [6]. We anticipate the reward will be worth your effort. To conclude, we would like to recommend some examples of bioinformatics repositories in GitHub (Table  1 ) and some useful training materials, including workshops, online courses, and manuscripts (Table  2 ).
In agreement with previous studies, we found increased MC density in the cardiac tissue after MI  (Frangogiannis et al. , 1998; Reid et al. , 2011). Nevertheless, we show that, independently of c-Kit signaling, MCs preserve heart function via a mechanism that does not involve changes in cardiac remodeling after MI. Furthermore, we analyzed the recruitment of inflammatory cells and release of their mediators in the Cpa3 cre/+ mice. Our data showed no effects of MCs deficiency in the regulation of local inflammation at the times studied. However, besides the absence of MCs, a reduced basophil compartment has previously been observed in Cpa3 cre/+ animals, and this decrease should be considered when immunological functions are assessed in this model  (Feyerabend et al. , 2011). Depressed cardiac function in response to MC deficiency is mediated by a reduction in cardiomyocyte cell shortening, the kinetics of contraction/relaxation, and Ca 2+ sensitization, as reflected by a right shift on the Ca 2+ -force response curve and an increase in EC 50.
98 mM potassium propionate, 10 mM DTT, and protease and phosphatase inhibitors. All buffers were adjusted to a pH of 7. 0. A complete activation of the myocyte occurred at the beginning and end of the experiment, and the myocyte was discarded if there was <10% rundown. Force-calcium data were fit to the Hill equation: F = F max × C a h /(EC h 50 + Ca h ), yielding F max , calcium sensitivity (Ca 2+ required to achieve 50% maximal force, EC 50 ), and cooperativity (Hill coefficient, h). Organ digestion/cell isolation. Peripheral blood was isolated from the inferior vena cava puncture with heparin solution. Whole blood was lysed after immunofluorescence staining using the FACS lysing solution (BD), and total blood leukocyte numbers were counted using trypan blue (Sigma-Aldrich). BM cells were washed through the femur and the tibia and filtered through a 40-µm nylon mesh (BD).
For detection of cardiac MCs, granulated cells were first gated on SSC/FSC. The total number of cells was normalized to tissue weight. Cells were analyzed using a flow cytometer (LSR II; BD) or were sorted with FAC SAria II (BD). The APC BrdU Flow kit (BD) was used for analysis of proliferation according to the manufacturer's instructions. HSPC isolation was performed as previously described  (Poglio et al. , 2010). In brief, freshly isolated WAT-stromal vascular fraction (SVF) cells were stained in PBS containing FcR Block reagent and CD117 (2B8; BD), Lineage (BD), Sca-1 (E13-161. 7; BD), and CD45. 2 (BD) antibodies. Cells were washed in PBS and sorted with FAC SAria II. Data acquisition and analysis were performed using FAC SDiva software (BD) or FlowJo 7. 5. For detection of inflammatory cells, total cardiac cells were gated on PerCP-conjugated CD45 (BD), and the fol-lowing antibodies were used: DAPI-conjugated anti-CD11b (BD), PE-conjugated anti-Ly6G (1A8; BD), APC-conjugated anti-F4/80 (BioLegend), FITC-conjugated anti-Ly6C (Bio-Legend), APC-conjugated anti-CD8a (BD), PE-conjugated anti-CD45R/B220 (RA3-6B2; eBioscience), PE-Alexa Fluor 700-conjugated anti-CD3 (eBioscience), and FITC-conjugated anti-CD4 (eBioscience).
Streptavidin-PE was added for detection, and flow cytometry was used to differentiate bead populations according to size and fluorescent signature. Analyte concentration was measured using standard curves on the FlowCytomix Pro Software (eBioscience). Data were expressed as picogram of analyte per microgram of cardiac protein homogenate. Quantitative real-time PCR. Quantitative real-time PCR was performed on a Step-One Plus (Applied Biosystems). GAP DH was used to normalize gene expression. The following primer sequences were used: SCF forward, 5′-GGA GAT CTG GAA TCC TGT GA-3′; and reverse, 5′-CCC GGC GAC ATA GTT GAG GGT TAT-3′; mMCP6 forward, 5′-CTG GGG CGA CAT TGA TAA TGA CGA GCC TCT-3′; and reverse, 5′-CCC CCT GAA TCG CCC TGG CAG GAGT-3′; and mMCP4 forward, 5′-CTG GGG CTG GAG CTG AGG AGA TTA-3′; and reverse, 5′-CAA CAC AAA TTG GCG GGT TAT GAG AA-3′.
Acknowledgments The authors would like to thank  Sebastian Amigorena ,  Nicolas Manel  and  Claire Hivroz  for critical reading of the manuscript, Francois-Xavier Gobert for mouse genotyping,  Monique Lafon  ( Institut Pasteur ) for the TLR3 KO mice and  Heinz Wiendl  ( University of Mu ¨nster ) for the PD-L1 KO mice. The authors greatly acknowledge the  Nikon Imaging Center@Institut Curie-CNRS.
Funding: HDM was supported by a fellowship from the  Fondation ARC pour la recherche sur le Cancer. This work has received support under the program «Investissements d'Avenir» launched by the  French Government  and implemented by the  Agence Nationale de la Recherche  with the reference ( ANR-10-IDEX-0001-02 PSL Ã  and  ANR-11-LABX-0043 ),  ANR-09-MIEN-021-01 ,  ANR 15 CE13 0009 01. The work was also supported by  Insitut National du Cancer  ( INCA_9301 ). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
X-ray analyses Experimental details for X-ray data collections of all complexes are given in Table  S1. † Figure graphics were generated using MERCURY 3. 6 supplied by the Cambridge Structural Database; CCDC: Cambridge, U. K. , 2001-2015. Diffraction data were taken using Oxford-Diffraction Xcalibur S or Bruker APEX II CCD kappa geometry diffractometers (Mo-Ka radiation, graphite monochromator, l ¼ 0. 71073 Å). To prevent evaporation of cocrystallized solvent molecules the crystals were coated with light hydrocarbon oil and the data were collected at 150 K or 100 K. The datasets were reduced by CrysAlis 55 or EvalCCD 56 and then corrected for absorption. 57 he structure resolutions were performed with SHELXS or Superip and the structure renement was performed with SHELXL. 58, 59 The crystal structures were rened using fullmatrix least-squares based on F 2 with all non-hydrogen atoms anisotropically dened.
Acknowledgements We would like to thank  Dr Oliver Cooper  for preliminary experiments and  Dr Euro Solari  for elemental analysis. LM is a member of the  Institut Universitaire de France. CAlmip  is acknowledged for the generous grant of computing time. This work was supported by  EPFL , by the  Swiss National Science Foundation  and by funds of the  Joint DFG-ANR  projects ( ANR-14-CE35-0004-01  and  ME1754/7-1 ).
Flow cytometry. To determine cell cycle profile by propidium iodide (PI)-flow cytometry, HCN cells were extracted by Trypsin-EDTA (Sigma T3924), fixed in 2% PFA for 10 min at RT for GFP retention or directly permeabilized in 70% ethanol at 4 °C overnight. Cells were washed in phosphate buffered saline and stained with PI (Sigma P4864) in the presence of RNaseA (Invitrogen 12091) and their DNA content was measured on a FACScalibur flow cytometer (BD Bioscience) with 10,000 events per determination. Cell cycle profile was generated using Flowjo software (Tree Star Inc). Immunocytochemistry. Immunocytochemistry was performed on adherent HCN cells that were washed with phosphate buffered saline and fixed in 4% PFA for 20 min at RT. Cells were blocked and permeabilized (0. 3% Triton X-100 and 3% Normal Donkey Serum in Tris-buffered saline) and stained with proliferation and differentiation markers.
For BrdU studies, HCN cells were also incubated with BrdU (10 mM) for 1 h before fixing in 4% PFA and treated for 30 min in 2 N HCl at 37 °C for 30 min and neutralized with 0. 1 M Borate for 10 min at RT before blocking. For BrdU and IdU, pulse chase pulse experiment, cells were incubated with BrdU (10 uM) for 1 h, replaced with media, and after 24 h cells were pulsed with IdU (10 uM). Then cells were fixed with 4% PFA and treated for 30 min in 2 N HCl at 37 °C for 30 min and neutralized with 0. 1 M Borate for 10 min at RT before blocking. Cells were stained according to previous methods  25. Stained cells were visualized using a Nikon TE2000-U inverted microscope and counted using CellProfiler software. A detailed list of antibodies is available in Supplementary Table1. ChIP-seq/ChIP-qPCR.
Quantitative PCR reactions were performed on Applied Biosystems 7,000 detection system using Biorad iTaq Universal SYBR green supermix (172-5124). Normalization was based on the expression of beta-actin and relative gene expression or relative mRNA level was determined using the deltadelta cycle threshold method. Primers used for quantitative reverse transcription-PCR analysis are available upon request. For RNA-seq, total RNA was isolated from tissue using miRNAeasy (Qiagen 217004) and on column DNAseI digestion was performed (Qiagen 79254). RNA-seq and ChIP-seq data analysis. RNA-seq (N ¼ 2 each for Ctrl electroporation in iQNP and TAP conditions; N ¼ 4 each for REST knock-down electroporation in iQNP and TAP conditions) and ChIP-seq (N ¼ 1 for each, 'homemade' REST antibodies mix and commercial REST antibody for iQNP and TAP conditions; See Supplementary Table  2 ) was performed on the Illumina platform.
Using ngs. plot the input normalized enrichment of binding at these genes was determined and plotted, while UCSC genome browser was used for visualization of RNA-seq and ChIP-seq data of the target genes. BrUTP rRNA synthesis assay. BrUTP assay was used to measure rRNA synthesis following a published protocol specifically developed for monolayer cell culture system. Briefly, adherent HCN cells were pretreated for 2 h with 10 mg ml À 1 alphaamanitin (an inhibitor of extranucleolar RNA) to assay rRNA synthesis (nucleolar RNA) and with 0. 05 mg ml À 1 ActinomycinD as a negative control. The pretreated adherent cells were lipofected with DOTAP-BrUTP (1. 5 mM) complexes prepared in media for 5 min and incubated with adherent cells for 15 min followed by 1 h incubation of the adherent cells in fresh media.
Thereafter, cells were washed and fixed in 4% PFA for 20 min at RT and BrUTP staining was performed by general immunohistochemistry protocol as described above and were visualized using a confocal laser-scanning microscope AIR from Nikon equipped with four laser lines (405, 488, 561 and 633 nm) under 40 Â objective lens. BrUTP punctuate labelling intensity, number and area occupied were quantified using ImageJ software. A detailed list of antibodies is available in Supplementary Table  2. Statistics. All statistical analysis was performed using GraphPad Prism 6. In vitro immunocytochemisty and PI-flow cytometry (TAP versus iQNP, TAP versus TAP', and control EGFP versus REST shRNA-EGFP within iQNP and TAP conditions), qPCR (iQNP versus TAP, and control EGFP versus REST shRNA-EGFP within iQNP and TAP conditions) and ChIP-qPCR (non-RE1 iQNP versus TAP conditions, and RE1 iQNP versus TAP conditions) experiments were analysed for statistical significance using an unpaired, two-tailed Student's t-test with data expressed as mean ±s.
Acknowledgements We thank  Stephen Johnson ,  Ralf Kittler ,  Francois Guillemot ,  Sean Goetsch ,  Bradford Casey ,  Mark Borromeo ,  Derek Smith ,  Tulip Nandu ,  Xin Liu ,  Caelin Potts  and  Benjamin Nelson  for helpful advice on the project,  Jingfei Zhu ,  Mahafuza Aktar ,  Yindi Jiang ,  Zane Lybrand ,  Peiguo Ding , and  Caroline Hsieh  for technical support, and  Michael Buszczak  and  Jane Johnson  for critical reading of the manuscript. We also thank  Jose Cabrera  for graphical support and  Charlene Supnet  for editorial support. This work was supported by  US National Institutes of Health  grants ( R01NS093992 ,  R01NS089770 ,  R01NS081203  and  K02AG041815 ),  American Heart Association   15GRNT25750034 ,  Department of Defense   W81XWH-15-1-0399 , and a grant from the  Texas Institute for Brain Injury and Repair.
Statistics Quantitative variables were described by median and range or mean and standard deviation (SD). For categorical variables, number (N) and percentage (%) were presented for each category. Quantitative parameters were compared by Wilcoxon-Mann-Whitney or Kruskall-Wallis tests. We used exact Fisher test to compare categorical variables. Kaplan-Meier analyses were performed for survival estimates and the log-rank test for comparison of survival functions. All reported p-values were two-sided and were considered significant when <0. 05. SAS Version 9. 3 software was used for statistical analyses. Our analyses and comparisons are exclusively made between groups B and C (only 2 patients in group A).
The use of antiplatelet agents was left at physicians' discretion. Neuromuscular blockade agents were discouraged, except in the first 24 h of refractory hypoxia. The investigators were provided with published guidelines for the management of septic shock. We systematically recorded, on a daily basis during the first week post-randomization, in the case report form, blood glucose levels and dose and duration of insulin, source and pathogens identification and dose and duration of any antibiotic administered to the patients, type and dose of fluid therapy and of vasopressor therapy, score of sedation and delirium and use of any sedation or neuromuscular blocking drug, dose and duration of any anticoagulant, and type, dose and reason for use of any open-labeled corticosteroids. These data will allow careful examination of the adherence of investigators to guidelines for co-interventions.
AP-HP had full access to patients' charts and checked all data recorded onto the electronic case report form (CRF) against original chart. The trial used a Web-based electronic CRF (Telemedecine Technology, France). Data management and statistical analysis were performed independently of the sponsor and of investigators by specialized Biometry unit (Unité de Biométrie, INSERM 1414 Clinical Investigation Centre, Rennes University Hospital, Rennes 1 University, Rennes France). Institutional pharmacists (AGEPS) were responsible for obtaining corticosteroids and their placebos, shipping study drugs to participating sites and getting back unused drugs. They were responsible for accurateness of blinding and pharmaceutical organization of the trial. Vials of lyophilizate for parenteral use of hydrocortisone hemisuccinate 100 mg or placebo and diluent ampoules were obtained from Serb pharmaceutical company.
Study monitoring The Steering committee had monthly conference calls. The study site coordinator (Raymond Poincaré hospital) provided on-demand 24/7 services via phone calls or Fig. 1  Cumulative number of enrolled patients in the trial emails to advise investigators about patients' eligibility or any other issues that may have risen between randomization and 180-day follow-up. There were a total of 28 face-to-face investigators meeting in which trial protocol and procedures were systematically recalled and investigators adherence and compliance to them discussed. A monthly electronic newsletter informed investigators on trial conduct and on any new information from sepsis literature. DSMB met 5 times. DRRC organized data monitoring and quality audits. Baseline characteristics, eligibility criteria, primary outcome and serious adverse events reported in the CRF were systematically checked against original chart for all research participants.
In addition, for one-third of study population, all data reported in CRF were validated against patient's original chart. Serious adverse events and major protocol violations were reported to DRRC, ANSM and CPP. The study coordinator had quarterly face-to-face meeting with DRRC, AP-HP, independent pharmacists to monitor trial conduct according to highest standard for protection of research participants. All randomized patients completed follow-up for the primary outcome and 180-day mortality data.
Lead (Pb) concentration data and/or lead isotope ratios ( 206 Pb/ 207 Pb), obtained by XRF analysis  (Boyle, 2000)  and Quadrapole ICP-MS, were also included in the age models based on the regionally coherent pattern of airborne pollution Pb deposition across Sweden during recent millennia  (Brännvall et al. , 2001; Renberg et al. , 2001). Using the combined data obtained, Bayesian analysis in the OxCal program (v. 4. 1) was used to create age-depth models  (Bronk Ramsey, 2008 , 2009). For Fiolen, the chronological data provided by the different methods were partly inconsistent, making it necessary to select the data points to be used in the final age-depth model  (Fredh et al. , 2013). The preferred age-depth model was based on six terrestrial plant macrofossil samples (three pre-treated), a CRS model (based on nine 210 Pb samples) and four lead pollution markers.
Three macroscopic plant remains and four bulk gyttja samples were dated from Åbodasjön and 2 macroscopic plant remains and three bulk gyttja samples were dated from Lindhultsgöl (Table  3 ). All dates were performed at the Radiocarbon Dating Laboratory, Lund University. For Fiolen, most macroscopic plant remains were identified as terrestrial but a few were difficult to identify (Table  2 ). Only three of the macrofossil samples were larger than 2 mg and pre-treated  (HCl and NaOH). This means that any potential contamination with modern material, for most of the samples, was not removed. For Åbodasjön and Lindhultsgöl, plant remains of terrestrial origin were identified. For all lakes, the OxCal program (v. 4. 1; IntCal09) and the CaliBomb program (Levin's Vermunt and Schauinsland data sets) were used for calibration of 14 C dates based on calibration curves constructed from terrestrial and atmospheric samples  (Bronk Ramsey, 2009; Levin and Kromer, 2004; Levin et al.
Funding This work was funded by the  Swedish Research Council Formas  through grants  2007-1012  (Revealing the dynamics of discontinuous management and biodiversity at different spatial and temporal scales in the traditional cultural landscape),  2006-547  (Brownification of streams, lakes, and coastal waters -an effect of climate change or land-use?), the  Swedish Research Council, Helge Ax:son Johnson Foundation , The  Royal Physiographic Society in Lund , The  Royal Swedish Academy of Sciences  and  The Swedish Foundation for International Cooperation in Research and Higher Education. FM was supported by funding made available by the  French   ANR 2010 JCJC 1804 01 , MODE RESPYR.
Acknowledgements. The  European Union  is acknowledged for its funding through the  Marie-Curie Fellowship   PIEF-GA-2009-251710  and through the project  FP7-ENERGY-2012-1-2STAGE   TRUST  (High-resolution monitoring, real time visualization and reliable modeling of highly controlled, intermediate and upscalable size pilot injection tests of underground storage of CO 2 ). The  ANR  is acknowledged for its funding through its Project  H2MNO4  under the No. ANR-12-MONU-0012-01. Edited by:  A. Guadagnini.
5194/amt-2016 -336, 2016  Manuscript under review for journal Atmos. Meas. Tech. Published: 24 October 2016 c Author(s) 2016. CC-BY 3. 0 License. reflectivity using the oblate spheroid approximation, and the estimation of its accuracy in retrieving CWC in the ice phase part of mesoscale convective systems. The next section of this paper presents the dataset of the first HAIC-HIWC airborne campaign and associated data processing. Subsequently, the cloud radar reflectivity simulation method  (Fontaine et al. (2014) ) also used in this study is briefly reviewed. The CWC values, retrieved from the simulations are then compared to the collocated bulk measurements of CWC. Moreover, the study suggests correction functions for the CWC calculations (based on T-Matrix simulations of the reflectivity factors) as a function of temperature, largest size of hydrometeors in PSD, and ice crystal concentrations in MCS.