dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgements. The authors wish to thank the staff of the Virology Diagnostics Laboratory of CIENI where HIV tests are processed, as well as the administrative and HTC staff of the HIV Testing and Counseling services and the clients who elected to participate. Funding. This study was supported by a scholarship from the Consejo Nacional de Ciencia y Tecnología (Mexico City, Mexico; No. 583962). The study was a requirement toward the first author's master's degree under the adviof the last. The work of the HTC service is supported by the Comisión de Equidad y Género de las legislaturas LX-LXI, and the Comisión de Igualdad de Género de la Legislatura LXII de la H. Cámara de Diputados de la República Mexicana.
Experimental design and statistical analysis Fluorescence photomicrographs were collected with Leica SP5 and Zeiss 710 confocal microscopes. Images of ISHs were collected with Nikon digital camera DXM1200C and a Nikon eclipse 80i microscope. Images were processed using Adobe Photoshop CS2. Unless otherwise stated in figure legends, provided data are the average of three embryos or explants (n) per condition from at least two independent experiments. Cell counting was performed on at least 5 tissue slices per chicken explant. For each tissue slice (60-80 μm), at least 4 optical sections were acquired at 6 μm intervals and cells were counted in each optical section. Quantifications are expressed as the mean number of cells (mean ± s. e. m) in an optical section of hemi-explants. Statistical analyses were performed using the Mann-Whitney U test.
3c , e, g and data not shown). Similarly, electroporation of the dnFGFR expression vector, performed just prior to spinal cord explantation, prevented both ERK1/2 activation and spry1/2 expression while electroporation of a control vector had no effect (Fig. 3h-k ). These results, beyond validating the approach, support the view that FGFRs are indeed responsible for stimulation of MAPK activity and spry1/2 expression in the ventral spinal cord. We next examined OPC generation after FGFR inactivation. In the chicken embryonic spinal cord, coexpression of Olig2 and Nkx2. 2 has been reported to specifically identify OPCs  [3, 4, 20, 28, 78, 83]. Triple immunostaining of Olig2, Nkx2. 2 and O4, also a specific and early marker of OPCs in chicken  [49, 56, 72] , performed on explants cultivated for 2 days allowed identifying the same cell population, i.
Acknowledgements We acknowledge  J. Guimera ,  S. Martinez ,  K. Storey ,  C. Tabin  and  R. Bansal  who kindly provided us with valuable reagents. We are grateful to colleagues in the CBD for help, encouragement and advice. We thank the  Toulouse Regional Imaging Platform (TRI)  for technical assistance in confocal microscopy. We acknowledge the  Developmental Studies Hybridoma Bank , developed under the auspice of  NICHD  and maintained by the  University of Iowa ,  Department of Biological Sciences, Iowa City, IA , for supplying monoclonal antibodies.
Non-isothermal single-phase flow This test case considers a non-isothermal liquid flow with mass density, viscosity, specific internal energy and enthalpy obtained from  [38]. The thermal conductivity is fixed to λ = 2 W. m -1. K -1 and the rock internal energy density is defined by E r (T ) = c r p T with c r p = 16. 10 5 J. m -3. K -1. The gravity is not considered in this test case. The simulation domain is defined by Ω = (0, 2000) 3 in meters. The mesh is a 3D tetrahedral mesh conforming to the fault network and to the wells. It was generated using the implicit framework from the 3D mesh generation package from the Computational Geometry Algorithms Library (CGAL  [39] ). As shown in Figure  9 , there is one injection well (red line) and one multi-branch production well (green line). This mesh contains about 4.
Acknowledgments This work was supported by a joint project between  INRIA  and  BRGM Carnot institutes  ( ANR, INRIA, BRGM ). It was granted access to the  HPC and visualization resources of "Centre de Calcul Interactif " hosted by  University Nice Sophia-Antipolis. The authors would also like to thank the région  PACA  and  BRGM  for co-funding the PhD of  Laurence Beaude  as well as  CEA  for funding the participation of  Thibaud Beltzung  to the project. Writing of this article was supported by the  CHARMS   ANR  project ( ANR-16-CE06-0009 ).
Acknowledgments The study has been developed in the framework of the  Windblown Sand Modeling and Mitigation (WSMM)  joint research, development and consulting group established between  Politecnico di Torino and Optiflow Company. The authors wish to thank  Luigi Preziosi , member of the WSMM group and coinventor of the S4S barrier, for the helpful discussions about the topics of the paper. Computational resources were provided by  HPC@POLITO , a project of  Academic Computing  within the Department of Control and Computer Engineering at the  Politecnico di Torino  (http://www. hpc. polito. it). The S4S patent is funded and managed by the  Technology Transfer and Industrial Liaison Department of Politecnico di Torino.
Acknowledgment We thank  Jean-Michel Morel  for fruitful comments and discussions. Work partly financed by Office of Naval research grant  N00014-17-1-2552 ,  DGA Astrid project "filmer la Terre " n •  ANR-17-ASTR-0013-01 , and  ANRT CIFRE Ph. D. scholarship n •  2014/1323  of the  French Ministry for Higher Studies, Research and Innovation. Image Credits Min H. Kim Jacques Joffre Charles Hessel.
6 (eluent A), running on a Varian Prostar 260 HPLC system. After a 7 mL gradient of 0-10% solution B (100% methanol), disaccharides were eluted over a 35 mL linear gradient of 10-30% solution B at a flow rate of 0. 7 mL/min. Disaccharides were detected by in-line fluorescence (excitation at 428 nm and emission at 525 nm), using a Varian ProStar 363 detector, and data were analysed with the Star software (v6. 43).
Induction and measurement of apoptosis Cell apoptosis was evaluated by measuring phosphatidylserine externalization and caspase-3 activation, essentially as described in  [26]. Briefly, apoptosis was induced in transfected MDA-MB-231 cells (2×10 5 cells per point) by the addition of 100 ng/mL of anti-Fas antibody (Merck Millipore) plus 100 ng/mL TNF-α (PeproTech) for 24 h at 37˚C, or by the addition of 1 μM staurosporin (Merck Millipore) for 4 h at 37˚C. Thereafter, cells were stained with annexin-V and propidium iodide (PI) by using the Annexin-V Apoptosis Detection Kit I (BD Biosciences) and analysed by flow cytometry using a FACSCalibur instrument and the Cell-Quest software (BD Biosciences). This procedure allows assignment of cells in viable (annexin-V -/PI -), early apoptotic (annexin-V + /PI -), late apoptotic (annexin-V + /PI + ) and necrotic (annexin-V -/PI + ) populations.
To differentiate M. bovis from other M. tuberculosis complex subtypes, we used primers flanking specific deletion (RD4) in the genome of M. bovis and obtained the 446 bp DNA pro duct. The spoligotyping subdivided the strains into 3 spoligotypes shared by two to 20 strains. Further molecular investigations of M. bovis strains are needed to characte rize the genetic diversity and population structure of M. bovis strains isolated from cattle in Bulgaria. New information will be added to the global database in the field of molecular epidemiology of the prevalence of M. bovis strains in the cattle population in Bulgaria, which will allow comparative analysis with data from the Balkan region and Europe.
The aim of this multicenter study was to validate and compare different pipelines used for analysis of the Whole Genome Sequencing (WGS) data of Mycobacterium tuberculosis isolates. All 535 M. tuberculosis isolates of culture positive cases in the Netherlands in 2016, were subjected to WGS, in addition to the routine application of VNTR typing. Transmission suggested on basis of identical VNTR profiles of cases in 2016 was further investigated by municipal health services and 41 epi-links were traced. Fastq. gz files of all 535 samples were analysed in four different WGS pipelines to facilitate international comparison: 1) SNP-based method at the RIVM/Bilthoven/ The Netherlands; 2) SNP-based method at Oxford University/UK; 3) SNP-based method and 4) cgMLST at Borstel/Germany. In all pipelines, shorter than 12 SNP distances between the 41 epi-linked cases was observed.
Retrospectively, we have performed an observational study to compare the WGS data to the phenotypic DST to predict the resistance phenotype from the genetic sequence. The study included 877 clinical TB isolates (only one sample per patient was included) received by the Public Health Agency of Sweden between 01. 01. 2016 and 31. 12. 2017. The analysis of the isolates' resistance profiles for the first and second line drugs, obtained from the WGS and Bactec MGIT 960, is ongoing. Simultaneously, we are evaluating the microbroth dilution technique used for the MIC determination of 150 consecutive (MDR) M. tuberculosis together with the corresponding WGS analysis as a part of a collaboration with the CRyPTIC (Comprehensive Resistance Prediction for Tuberculosis: an International Consortium) network.
Varying initial cell density: Culture was prepared as in (1) except culture dilution ranged from 100 to 100,000fold. Cultures were exposed to 0 or 100 µg/mL cefotaxime and time courses were measured by plate reader and the final cell density after 30 hours was recorded. 9. Plate reader data analysis: MATLAB (Version 9. 2. 0. 556344, R2017a) was used to plot and characterize the time courses obtained from the plate reader (i. e. recovery time, growth rate, and change in GFP over time). We assume that the growth rate of cells (g) is limited by s, following the Monod kinetics. We assume the lysis rate (l) can reach a maximum of , depends on a following the Hill kinetics, and g. and   are the natural decay rates of extracellular Bla and antibiotic, respectively. is the rate at which Bla degrades the antibiotic.
When aphid started reproducing, adult aphids were removed and only one nymph was left in each leaf disc and was used as F 1 generation. This procedure was repeated 60 times for control and treatment groups using single aphid as replication. Nymphs were transferred to insecticide free leaf discs every 3 rd day, and when aphid started reproducing, all nymphs were counted and removed on a daily basis until adult died. Biological parameters including development, longevity and fecundity of F 1 generation were recorded daily. Data Analyses. Corrected mortality of melon aphids was determined by using the Abbot's formula  70. The statistical differences among data related to adult longevity, fecundity, duration of instars and duration of immature stage of melon aphids were analyzed by one-way ANOVA followed by the Tukey post hoc test (P < 0.
05) (IBM, SPSS Statistics). Life table data of melon aphid were analyzed according to an age-stage, twosex life table  45, 46  using the TWOSEX-MS Chart computer program  49. The population age-specific survival rate (l x ), age-specific fecundity (m x ), the age specific maturity (l x m x ), the age-stage specific survival rate (s xj ), the age-stage reproductive value (v xj )  71, 72  , the net reproductive rate R 0 (offspring/individual), intrinsic rate of increase r (day -1 ), the finite rate of increase λ (day -1 ) and mean generation time T (day) were calculated according to Chi and Liu  45. Using the TWOSEX-MS Chart computer program, the bootstrap technique  73  was used to calculate the means and standard error. For bootstrap, 100,000 replicates were used  74, 75. Fecundity, survival rate and reproductive value curves were generated using Sigma Plot 12.
During the last decade, the advent of compressed sensing theory led to the emergence of new imager architectures, which include the single-pixel camera (SPC)  [7, 8]. The 2D imaging capabilities of a SPC are due to exploitation of a 2D spatial light modulator (SLM) coupled with a single-point detector. A SPC essentially measures the inner product of the scene and a sequence of SLM patterns. Through the post-processing of the resulting dataset, the image of the scene can be recovered  [9]. Strategies for SPC image recovery include compressed sensing, basis scans, and adaptive basis scans. While compressed sensing theory provides an excellent theoretical framework for single-pixel imaging, it requires a time-consuming image reconstruction step. Basis scans on a predetermined basis (e. g. , Hadamard, Fourier, discrete cosine transform) benefit from rapid inverse transformation for image reconstruction  [10] [11] [12] , but they suffer from long acquisition times.
The spectrometer is composed of a diffraction grating (600 lines/mm) that disperses the light into Λ = 16-channel photomultiplier detectors (PML-16-1; Becker & Hickl GmbH). The 16 spectral channels range from 505 ± 5 nm to 655 ± 5 nm, with a 10-nm step. The TCSPC board (SPC-630; Becker & Hickl GmbH) with 4096 time channels is coupled to the detectors. To adaptively acquire the dataset, the in-house software alternates between two programs: a Matlab program that processes the data and predicts the next DMD patterns to acquire; and a Labview program that controls the set-up acquisition. To increase the signal-to-noise ratio, the TCSPC time channels are binned, so as to have T = 60 time channels that range from 0 ns to 18. 00 ns.
Study design This PASS was designed to collect data on the safety and effectiveness of fluticasone/formoterol prescribed for outpatients with moderate to severe asthma aged ⩾ 12 years over a 12-month period. Participants were under the care of general practitioners or respiratory physicians in primary or secondary care in eight European countries: Czech Republic, Denmark, France, Ireland, Norway, Slovak Republic, Sweden and the United Kingdom. Patients were treated with fluticasone/formoterol according to the licensed indication, with data captured for 1 year from first on-study dose of fluticasone/formoterol. The primary objective was to evaluate the safety of fluticasone/formoterol by collecting data on drug exposure and the frequency of adverse events (AEs) associated with the treatment.
Assessments Demographic information, data on asthma history and the reason for initiation of fluticasone/ formoterol were recorded at the baseline visit. Details of asthma history included prior asthma treatment (in the last 30 days), asthma control status [according to Asthma Control Test (ACT TM ) score], severe asthma exacerbations in the last 12 months and satisfaction with previous treatment. After the baseline visit, physicians' visits, diagnostic procedures and assessments were performed as clinically indicated in the opinion of the treating physician and according to treatment guidelines. Data available at prespecified timepoints of 1, 3, 6, 9 and 12 months postbaseline were collected, including fluticasone/formoterol exposure (including dose change and reason for discontinuation).
Data on AEs were collected via reports from participating patients (either spontaneous report or in response to physicians' open questioning), as well as those detected by diagnostic procedures during routine clinical practice at the physicians' discretion. Asthma control was assessed by means of ACT TM scores (total plus component scores: ability to perform daily activities; shortness of breath; sleep disturbances due to asthma; necessity to use a rescue medication; subject assessment of asthma control). Asthma was defined as 'controlled' if the total ACT TM score was ⩾20, 'somewhat controlled' if the score was 16-19, and 'poorly controlled' if the score was ⩽15. On-study measurements of asthma-related medication use (including rescue medication use, antibiotics, systemic corticosteroids, etc.
Asthma exacerbations treated with courses of corticosteroids separated by 1 week or more were treated as separate exacerbations. Data were also collected on quality of life using the Asthma Quality of Life Questionnaire (AQLQ; total plus component scores: activities limitation; emotional function score; environmental stimuli score; symptoms score), patientand physician-rated satisfaction with treatment, and physicians' estimates of patient adherence. Study data were collated in electronic case report forms by investigator site staff.
Statistical analyses The target study sample size was set at 2500 in order to provide adequate precision in estimating AE rates. Continuous variables were summarized using descriptive statistics; categorical data were summarized as number and percentage of patients with nonmissing data. All analyses were performed on the safety population, which comprised all patients who received at least one dose of study medication during the observational period of the study. For the safety analysis, treatment-emergent AEs, related AEs, severe AEs, AEs leading to death, serious AEs, AEs leading to discontinuation of the study, AEs requiring additional therapy, AEs leading to dose change, and AEs of special interest were summarized. The annual rate of severe exacerbations was calculated for the period of 12 months prior to study enrolment and during the study.
Treatment effectiveness was analysed based on ACT TM scores, AQLQ scores and lung function parameters. For these parameters, data available at each prespecified time point and at end of study, and corresponding changes from baseline, were summarized descriptively [including 95% confidence intervals (CI) for the mean changes]. Changes from baseline were also analysed using the paired t test; given the non-interventional study design, these statistical tests were exploratory. In general, last observation carried forward (LOCF) imputation for missing data was used for the end-of-study analyses of effectiveness parameters. Patient-and physician-rated treatment satisfaction and physicians' estimates of patient adherence at each time point and end of study were summarized by frequency tables.
It is important to note the wider definition for treatment success used in the Salford Lung Study compared with the current study. 29, 30 The mean AQLQ score in the current study increased from 4. 7 at baseline to 5. 6 at end of study; once more, an improvement consistent with that reported in the ffAiRNeSS study (4. 7-5. 6). 28 The pivotal RCTs of fluticasone/formoterol typically featured predose FEV 1 as the primary outcome. In a phase III trial with fluticasone/salmeterol as an active comparator, for example, the least-squares mean (95% CI) change from baseline in predose FEV 1 with fluticasone/formoterol at 12 weeks was 0. 196 l (0. 12, 0. 28). 4 At 3 months in the current study (data for this time point not presented earlier), there was a mean (95% CI) change from baseline in FEV 1 of 0.
For example, the study population contained patients with comorbid conditions such as diabetes mellitus (71 patients, 2. 8%). Whilst not contraindicated, conditions such as diabetes present a need for additional caution when prescribing fluticasone/formoterol. 24  This was relevant to only a very small proportion of the overall study population; nonetheless, documented data on such patients are valuable for informing practice. As a PASS of non-interventional design, this study was inevitably associated with certain limitations. Patient visits and assessments were performed according to local clinical practice or standard of care leading to a high variability in the frequency and schedule of patient visits and the assessments conducted at these visits. Consequently, the availability of data at the prespecified time points varied considerably.
Community -developed standards, such as those for the identification and reporting of data, underpin reproducible and reusable research. The number of community-driven efforts has been on the rise since the early 2000s, their uptake, however, is slow and uneven. Analyzing 70 journals and publishers data policies, we find that these recommend databases and repositories 37 times more often than standards. When a reporting standard is recommended by a publisher, it is more likely to be a minimal reporting guideline than a model, format or ontology even if the latter are the machinereadable standards that underpin the utility of databases and repositories. Here, we evaluate the standards landscape, focusing on those for reporting data and metadata, and their implementation by databases and repositories; we also propose key performance indicators, and highlight the importance of developing open linked data models that instantiate these community standards.
Mapping the landscape Working with and for the producers and consumers of these standards for over 17 years has provided us with invaluable insights into their life cycle along with a network of international collaborators; all essential elements to tackle this challenge. We have developed FAIRsharing (https://fairsharing. org), a curated, informative and educational resource, describing and interlinking standards, databases, repositories, and data policies. Some readers may recognize FAIRsharing by its former name of BioSharing  (6, 7) , launched in 2011 and born from the MIBBI portal released in 2008  (3). As of December 2017, FAIRsharing has over 2175 records mainly relevant to the life, agricultural, environmental, biomedical and health sciences, and is progressively expanding to other disciplines due to community demand.
FAIRsharing brings the producers and consumers of standards closer together and has a growing list of adopters including standardization groups, databases and repositories developers, research data management support initiatives, service providers, curators, data managers, librarians, journal publishers and policy makers (https://fairsharing. org/communities). Using community participation, the FAIRsharing team accurately describes community-driven standards, such as minimum reporting guidelines (or checklists), models/formats and terminologies (such as taxonomies or ontologies) -ranging from generic and multi-disciplinary, to those from specific disciplines; it makes them discoverable and monitors their evolution, implementation in databases and repositories, and recommendation in journal and funder data policies.
Contributing to the FAIR ecosystem There is no better name for a resource that works with and for the community to collect the necessary information to ensure standards, repositories and data policies are Findable (e. g. , by providing functionalities to register, claim, maintain, inter-link, search and discover them), Accessible (e. g. , identifying their level of openness) and encourage they become Interoperable and Reusable, according to the FAIR principles  (9). With the goal of being an interoperable component in the ecosystem of other resources and services, we are in the process of minting Digital Object Identifiers (DOIs) to provide a persistent and unique identifier for referencing our records; also we work with the FAIR Metrics group (http://fairmetrics. org; 10) to develop measurable indicators -which we will implement in the FAIRsharing registry progressively -to guide producers to assess the level of FAIRness of their resources.
We also collaborate with several research and infrastructure programmes, which are generic and across disciplinary, such as the Global and Open (GOFAIR; http://go-fair. org) and the European Open Science Cloud (EOSC; https://eoscpilot. eu), and discipline specific such as ELIXIR (https://www. elixir-europe. org), the US National Institutes of Health (NIH) Big Data to Knowledge Initiative and the FAIR Data Commons (https://commonfund. nih. gov/bd2k/commons). Among others, FAIRsharing features in the upcoming reports by Science Europe (https://www. scienceeurope. org) on "Discipline-specific Research Data Management", and by JISC (https://www. jisc. ac. uk) on "FAIR in practice". To further expand our community engagement work, FAIRsharing also operates as an open working group under two global community initiatives, such as Force11 (https://www.