dataesr/scientific-paragraphs-categorization huggingface dataset:
The e1071 R package was used to train the classifiers and the ROCR package  71  to calculate the ROC area under curve as the main performance metric. We further examined the robustness of the classifiers in presence of two different error models: (i) random error and (ii) uniform noise. Random error. We simulated faulty measurements by replacing a defined fraction of measurements by random numbers drawn from the pool of all measurements of that assay. In this manner, we ensured that the simulated npg © 2016 Nature America, Inc. All rights reserved. nature biotechnology doi:10. 1038/nbt. 3605 erroneous measurements were drawn from the same distribution as the correct measurements without making assumptions about the statistical distribution of the data. Uniform noise. We simulated inaccurate measurements by adding a random number to each measurement.
ACKNOWLEDGMENTS We thank  J. Hadler ,  T. Penz ,  C. Lo Porto ,  B. Schmitt ,  M. Bähr ,  M. Helf ,  O. Mücke ,  N. Mazaleyrat ,  C. V. Wong ,  T. E. Kjeldsen ,  A. Janosch ,  P. Dhami ,  E. Flores  and  H. Gohlke  for technical assistance, and  H. Stunnenberg  as well as the scientific advisory board of BLUEPRINT for their advice and support. This work was performed in the context of the  BLUEPRINT  project (European Union's  Seventh Framework Programme  grant agreement  282510 ), which funded the study logistics and the integrative data analysis. The assay costs were paid by the contributing laboratories using institutional funds and the following grants:  BBSRC BB/G020930/1 ,  BBSRC BB/G020930/1 ,  BMBF 01KU1001A ,  BMBF 01KU1002A ,  BMBF 01KU1216F ,  EU-FP7 282510 ,  FWF I 1575-B19 ,  NHMRC 1063559 ,  NHMRC 1088144  and the  DKFZ Graduate School.
To further evidence differences between success and failure athlete's profiles, Mann-Whitney comparisons were performed for each variable. To examine the relationship between salivary cortisol, sAA, and sCgA concentrations recorded before each race, mood states observed before the competition and sleep parameters observed for the night preceding each race, the Spearman's rank correlation coefficient was used. Results are described as means ± SEM for each assessment. All statistical differences were considered as significant for a p-value < 0. 05. All statistical analysis were performed using Statistica software R v. 10 (Statsoft Inc. , France).
Patients with Q Fever Endocarditis The study of 17 patients with Q fever endocarditis (consisting of six women and eleven men aged between 22 and 79 years old) and their controls was conducted with the approval of the Ethics Committee of Aix-Marseille University (Marseille, France) and with the written consent of each participant. The characteristics of the patients were previously described  (Ka et al. , 2014). Seventeen patients with Q fever endocarditis were included on the basis of the presence of endocarditis, a positive echocardiogram and blood culture, high titers of IgG specific for phase I C. burnetii and data scoring  (Raoult, 2012). Ten age-and sex-matched individuals were included as healthy controls.
After 500,000 events had been completed and debris on the forward/side scatter dot plot and dead cells had been excluded with Aqua-Fluorescent Reactive dye, data were exported and analyzed with FlowJo Software (version 9. 2, Tree Star Ashland)  (Ka et al. , 2014). The proportion of pDCs is expressed as the ratio of living cells expressing the fluorescent marker to the total number of analyzed PBMCs. The phenotypic expression of HLA-DR and PD-1 is expressed as the mean fluorescence intensity (MFI).
The microarray slides were scanned with a pixel size of 5 µm using a DNA Microarray scanner G2505B. The scanned images were analyzed with Feature Extraction Software 10. 5. 1. The data processing and analysis were performed using the R software package (version 2. 15). The raw data were filtered and normalized using the Agi4x44 PreProcess library. Unsupervised and supervised analyses were performed using hierarchical clustering and a principal component analysis. Genes were considered to be differentially expressed if the False Discovery Rate was below 0. 1% and the absolute fold change was above 2. 0  (Gorvel et al. , 2014).
We showed that pDCs were decreased in patients with Q fever endocarditis. We studied patients with Q fever endocarditis and not patients with chronic Q fever since this concept is debated among teams involved in Q fever investigation. In addition, preliminary results showed that patients with primary infection also exhibited decreased amounts of circulating pDCs (data not shown). To our knowledge, this is the first report demonstrating the modulation of the number of circulating pDCs in Q fever. We do not know whether the decrease in circulating pDCs reflects their migration to tissues nor the nature of their role in resistance or susceptibility to C. burnetii. The role of pDCs in the defense against bacteria is only supported by a report in which the depletion of pDCs increases the virulence of C.
Statistical Analysis Data were checked for outliers and missing values and descriptive and univariate analyses were conducted in Statistix 10 (Analytical Software, La Jolla, CA). The observed animal-level prevalence of rumen fluke was calculated for the two age groups (adult vs. calves) and sampling seasons (end of summer vs. end of winter). To determine whether prevalence differed between age groups, seasons and abattoir submissions containing a single age group vs. both age groups, we fitted a generalized linear mixed model including a structural random effect term to account for unmeasured herd level variation, and an individual level random effect term to account for overdispersion. The model assumed a binomial distribution for the number of animals to test positive out of n animals tested (animal-level prevalence) per ith batch, and was fitted using the 'lme4' package in R  [23] : prevalence i ¼ age i þ season i þ submission type i þ ε herd þ i od where age (adult = 1, calf = 0), season (end of summer = 1, end of winter = 0) and submission type (single age group = 1, both age groups = 0) were included as categorical fixed effects, ε herd was a structural random effect at the herd level, and i od was an individual level random effect accounting for overdispersion.
Two-way interactions between main effects were also considered. Significance was declared at P < 0. 05. To further examine the interaction between season and submission type we also fitted a generalized linear mixed model to calf-only and cow-only data using the model structure outlined above but omitting age as independent variable. Batch level presence of rumen fluke (binary response variable: 0,1) was analysed using a generalized linear mixed model with a Bernouilli distribution: presence i ¼ age i þ season i þ submission type i þ ε herd where age (adult = 1, calf = 0), season (end of summer = 1, end of winter = 0) and submission type (single age group = 1, both age groups = 0) were included as categorical fixed effects, and two-way interactions between main effects were also considered.
PCR products were separated on a 1. 2% agarose gel prepared in Tris-acetate-EDTA (TAE) buffer incorporating GelRed (Cambridge Bioscience, UK) and visualised on a UV transilluminator. PCR products of the appropriate size (~500 bp) amplified from individual rumen fluke were purified using QIAquick PCR Purification Kit (QIAGEN, Germany) as specified by the manufacturer. PCR products were eluted using 30μl Elution Buffer and supplied to MWG Eurofins (Germany) at a concentration of 5ng/μl, in 15μl, along with the ITS-2For primer, for direct nucleotide sequencing. The chromatogram files obtained for the forward and reverse sequences were aligned using Lasergene 10 core suite Software SeqMan Pro (DNASTAR, USA) to assess the quality of the sequences and assemble the full-length ITS-2 fragment in order to compare with reference sequences in GenBank using BLASTn at the European Bioinformatics Institute website (http://www.
ebi. ac. uk/). Paramphistomes which were identified as Calicophoron calicophorum were further analysed through amplification of the mitochondrial DNA encoding transfer RNA (tRNA-Thr/Cox1) region using the primers described by Martínez-Ibeas et al (2013)  [25] : tRNA-ThrFor 5'-TGG AGAGTTTGGCGTCTTTTT-3' and tRNA-ThrRev 5'-CCATCTTCCACCTCATCTGG-3'. The 25 μl reaction contained 2μl of DNA template, 20 pmol of each primer, 0. 2 mM of each dNTP, 2. 5 mM MgCl2 and 0. 1U Platinum Taq polymerase in 1× Platinum Taq buffer. The thermocycler was programmed as follows: 92°C for 2 min; 38 cycles of 95°C for 60 secs; 65°C for 30 secs; 72°C for 90 secs; followed by 72°C for 10 min. The amplified product of 885 bp was visualised and sequenced as previously described. Two forward and one reverse sequence for each individual were obtained for alignment using Lasergene 10 core suite software SeqMan Pro (DNASTAR, USA) to provide a consensus.
The tRNA-Thr/Cox1 sequences were aligned by MUSCLE using Alignment Explorer in MEGA6  [26]  and trimmed to equal lengths. A Neighbour-Joining phylogenetic tree was constructed in Tree Explorer to assess the level of heterogeneity. A published Calicophoron daubneyi sequence from the same locus was used as outgroup (Accession number: KJ574046. 1, [18] ). Tree reliability was assessed by the bootstrap method with 1000 pseudoreplicates.
The effect of age was significantly different between submission types and seasons, whilst the effect of submission type was also significantly different seasons (Table  4 ). Inspection of Table  1  suggested that interactions between independent variables might differ between age groups. To explore this, calf and cow data were analysed separately. For animal-level prevalence in calves, the interaction between submission type and season was significant (P = 0. 02), but for cows it was not (P = 0. 10), confirming the complex interaction between independent variables. batch-level, when only main effects were considered, presence of rumen fluke was significantly correlated with age, but not with submission type or season (Table  5 ). As for animallevel data, cows had significantly higher probability of having rumen fluke than calves.
Molecular Characterization Amplification of the ITS-2 region fragments ranging from 350 to 455 bp. For sequence analysis, fragments were trimmed to 344 bp Most fragments contained the entire ITS-2 region (282bp) plus the flanking 5. 8S and 28S sequences. Among 79 fragments that were successfully sequenced, comprising 54 from cattle and 25 from deer, BLAST analysis revealed the presence of C. calicophoron (n = 57), Fischoederius elongatus (n = 12) and Orthocoelium streptocoelium (n = 10). All sequences were between 99. 3-100% homologous to C. calicophoron, F. elongatus and O. streptocoelium sequences (accession numbers: GU133057, GU133062 and GU133058, respectively). All three species were detected in cattle as well as deer, although C. calicophoron dominated in cattle (Table  7 ). Detailed analysis of prevalence within host species is not meaningful because selection of specimens for species identification was not randomized but aimed at maximising phenotypic differences among specimens.
Acknowledgments The authors would like to thank the agents of the  Office de Commercialisation et d'Entreposage Frigorifique  for permission to sample at the abattoir. We would also like to acknowledge financial support from the  Biotechnological and Biological Sciences Research Council   Industrial Partnership Award  ( BBSRC-IPA BB/K015591/1 ; KS) and the  Scottish Government's Rural and Environment Science and Analytical Services Division  (RESAS; GM, PJS and RNZ).
Background: Screening diabetic patients for the presence of asymptomatic coronary artery disease (CAD) may potentially impact therapeutic management and outcome. We performed a systematic review and meta-analysis of randomized trials addressing this question. Methods: We searched the PubMed database for studies reporting a randomized comparison of systematic screening for CAD in diabetic patients versus no systematic screening. The screening protocols were variable with the use of exercise electrocardiogram test, or stress echocardiography, or nuclear test, or coronary computed tomography angiography. Results: The final analysis included 5 randomized studies and 3,314 patients altogether. The screening strategy had no detectable impact on outcome with odds ratios (OR) [95 % confidence interval (CI)] of 1.
Search strategy The PubMed database was searched for eligible studies with no restriction of time in January 2016 by using the terms « (((diabetes) AND coronary) AND screening) AND "randomized controlled trial" [Publication Type] » and the filters « Humans » and « English ». Two investigators (CB and GL) independently checked retrieved titles and abstracts for eligibility and relevant full texts were systematically retrieved for further detailed assessment. The search procedure was repeated in Science Direct and ISI Web of Knowledge (All databases). Major reviews regarding screening for CAD in diabetic patients were also hand-searched. Cross-references and quoted papers were checked to identify other relevant studies. The retrieved studies were examined to exclude overlapping data. Unpublished data and meeting abstracts were not considered for the present analysis because they could not provide adequately detailed data and their results might not be final.
Data extraction The following information was extracted from each study: study name and first author; number of patients; monocentric or multicentric study; geographic area; period of inclusion; duration of follow-up; inclusion criteria; exclusion criteria; screening protocol; treatment plan if screening test was abnormal; baseline characteristics of the patients for the different studies (age, body-mass index, gender, smoking, systolic and diastolic blood pressure, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, triglycerides, type of DM, duration of DM, insulin treatment, levels of glycated hemoglobin, retinopathy, peripheral vascular disease, statin use at baseline, aspirin use at baseline, angiotensin-converting enzyme inhibitor/angiotensin receptor blocker (ACE/ARB) use at baseline); number of patients with all-cause death, cardiovascular death, non-fatal MI, the composite of cardiovascular death or non-fatal MI, in the screening groups versus the control groups at follow-up; number of patients receiving statins, aspirin, ACE/ARB in the screening groups versus the control groups at follow-up; number of patients with abnormal screening; number of patients with protocol-related coronary procedures (coronary angiography, percutaneous coronary intervention (PCI), coronary artery bypass surgery (CABG)) in the screening group.
Data synthesis and statistical analysis Statistical analysis was performed using STATA version 14. 0, StataCorps, College Station, Texas. Odds ratios (ORs) and 95 % confidence intervals (CI) of all-cause death, cardiovascular death, non-fatal MI, cardiovascular death or non-fatal MI, statin use, aspirin use, ACE/ARB use were calculated using the metan command. Overall estimates of effect were calculated with a random-effects model. Between-study statistical heterogeneity was assessed by using the Cochran Q chi-square and the I 2 test. Small-study effect was assessed visually by examining funnel plots of each trial effect size against the standard error.
Population This is a single center cohort study performed at the Montreal Heart Institute, Montreal, Quebec, Canada, a reference center for cardiovascular disease management. From January 2004 to December 2014, all patients aged 90 and older referred to our institution for coronary angiography and PCI were included in our analysis. Data was extracted retrospectively and each angioplasty was reviewed in detail regarding: indications for PCI, vascular access site, fluoroscopic time and total volume of contrast media. Cardiogenic shock was defined as prolonged systolic blood pressure<90 mm Hg, the need for inotropes or use of intra-aortic balloon pump. Vascular complications and 3-month mortality rate data were collected. This study was approved by the local ethics committee.
Limitations This is a single center study and data were collected retrospectively. Therefore, some data regarding medical therapy, left ventricular  ejection fraction and mortality at one year are lacking. The prevalence and outcome of nonagenarian patients admitted for acute coronary syndrome treated medically or by surgery are not available. History of dementia and cerebrovascular events were not reported in our series. Unfortunately, frailty was not evaluated and patients admitted for PCI are probably highly selected. There was no difference in terms of rate of vascular complications between TRA and TFA, probably due to the small sample size.
Flow cytometry SKOV-3 cells were harvested with a cell scraper, suspended in FACS buffer (PBS containing 1% bovine serum albumin and 0. 1% sodium acid) and incubated with anti-human E-cadherin (generated in rabbit; Santa Cruz), and anti-rabbit-IgG FITC was used as secondary antibody. Cells were subjected to flow cytometry (BD LSR II) and analysed with cell quest PRO software. 1x10 4 cells were counted and results are expressed as mean fluorescence intensity.
Neutrophils and neutrophil-derived elastase cause dyshesion of ovarian cancer cell layers The clustering of PMN and ZEB1-positive cells prompted a series of experiments on a possible relationship between PMN and EMT. To this end, effects of PMN on ovarian cancer cell lines were assessed. Cells grown to confluence in chambered slides were co-cultured with isolated PMN having incorporated Calcein-AM, and observed by time-lapse video microscopy. A progressive detachment and dispersion of the tumor cells was seen, accompanied by a drastic shape change, but no apparent cell death (Data for the cell line SKOV-3 are shown in Fig. 2 ; images were extracted from the video after 0 h, 1 h, 3 h, and 6 h). Essentially similar data were obtained with another cell line, OVCAR3 (data not shown). Lysates of PMN also caused dyshesion of cancer cells, suggesting a role for PMN-derived proteases.
Survey distribution Th e survey was developed and hosted online using Sawtooth Soft ware Inc. , MaxDiff SSI Web survey utility. 22 h e survey was launched online in Europe in June 2014 in fi ve languages (English, German, French, Spanish, and Italian) and disseminated by e-mail invitation and social media channels to respondents via bio-based economy associated contacts, networks, and associations, fi rst with innovations in enabling technologies. For this reason many of these existing frameworks may be too simplistic to capture the information required and be reliably deployed in multi-regional and longitudinal analyses of the bio-based economy. Th erefore a systems approach to analysis and interpretation is more appropriate. Innovation Systems (IS) frameworks can be applied to study National (NIS), Regional (RIS), Sectoral (SIS), or Technical (TIS) innovation systems.
Methodology Goal and defi nition of scope Th e primary objective of the survey was to assess the relative merit of a number of proposed policy interventions which have been suggested to support growth in the European bio-based economy. Th e list of interventions was determined through process of elimination based on results of previous consultation studies and dialogue with experts in the fi eld (Table  2 ). 4, 7, 9, 10, 12, 13 Secondary objectives were to assess the degree of consensus and estimate individual-level (MaxDiff ) scores. 25 Further statistical analysis was performed using IBM SPSS statistics V22. Multivariate general linear analyses of variance (MANOVA) were performed to identify signifi cant differences between factors and where appropriate, Student-Newman-Keuls (SNK) post-hoc multiple comparisons were applied (P≤0.
05). Statistical analysis was only performed on the data from France, Germany, Italy, Spain, and the UK where responses were suffi cient in number and balanced between stakeholder groups. A total of 447 credible responses from European regions were given to part 1 of the survey, 331 of which completed within the Climate KIC network in initial survey trials and subsequently broadcast more widely. A database of networks and stakeholders involved in the bio-based economy was prepared by project partners in each region and the link to the questionnaire together with a brief explanation of the project objectives was sent via e-mail in the respective language.
intercomparison projects using the same data structure and organization as the ESM output. This largely facilitates routine evaluation of the ESMs, but to be able to process the data automatically alongside the ESGF, the infrastructure needs to be extended with processing capabilities at the ESGF data nodes where the evaluation tools can be executed on a routine basis. Efforts are already underway to develop community-based evaluation tools, and we encourage experts to provide additional diagnostic codes that would enhance this capability for CMIP. At the same time, we encourage the community to contribute observations and reanalyses for model evaluation to the obs4MIPs and ana4MIPs archives. The intention is to produce through the ESGF a widely accepted quasi-operational evaluation framework for CMIP6 that would routinely execute a series of standardized evaluation tasks.
, 2013). More generally, model evaluation and intercomparison provides a necessary albeit insufficient perspective on the reliability of models and also facilitates the prioritization of research that aims at improving the models. Output from CMIP5 models is archived in a common format and structure and is accessible via a distributed data archive, namely the Earth System Grid Federation (ESGF). 1  The scientific contents of the models and the details of the simulations are further described via the Earth System Documentation (ES-DOC) effort. 2 This has enabled a diverse community of scientists with more than 27 000 registered users  (Williams et al. , 2015)  to readily search, retrieve, and analyse these simulations. Since CMIP5, there has also been a large effort to provide observations and reanalysis products to end users of CMIP results as part of the observations (obs4MIPs;  Teixeira et al.
Given the CMIP6 timeline and the complex and integrated nature of the infrastructure, it is expected that requirements will have to be satisfied by modifications and additions to the current infrastructure, rather than development and deployment of a completely new approach. The proposed infrastructure relies on conventions for data and for recording model and ex-periment documentation that have been developed over the last two decades. Its backbone is the distributed data archive and the delivery system developed by the ESGF, which with CMIP5's success and WCRP's encouragement is increasingly being adopted by the climate research community. We hope the overview presented here inspires additional, focused efforts toward improved and more routine evaluation in CMIP. We emphasize that routine evaluation of the ESMs cannot and is not meant to replace the cutting-edge and in-depth explorative analysis and research that makes use of CMIP output, which will remain essential to close gaps in our scientific understanding.