dataesr/scientific-paragraphs-categorization huggingface dataset:
Details on the key question, search, data synthesis and quality assessment are provided in the online supplementary material. In brief, two authors (CDu and CDe) searched the PubMed, EMBASE and the Cochrane Library databases using Medical Subject Headings (MeSH) terms, full text and truncated words (see online supplementary material for full search strategy) from the inception dates (1946, 1974 and 1993, respectively) to 23 November 2014. The following inclusion criteria were applied: (1) number of patients enrolled ≥20 patients and (2a) full research articles of prospective or retrospective studies on diagnostic accuracy of US in suspected LVV (ie, cranial and extracranial LV-GCA, Takayasu arteritis (TAK) and idiopathic aortitis as these exhibit similar US pathologies) using an appropriate reference standard (ie, clinical diagnosis, published criteria and/or positive temporal artery biopsy) or (2b) cross-sectional studies assessing LVV by US in patients with established GCA, polymyalgia rheumatica (PMR) or TAK.
delphi consensus on definitions of LVV elementary us appearances The group decided to focus the Delphi exercise on US key lesions for GCA only, because of the paucity of US data in TAK and idiopathic aortitis. Based on the results from the SLR, the steering committee (CDu, CDe and WAS) developed a WORD TMbased written questionnaire that included 25 statements. Of these 25 statements, 3 addressed the definitions of the appearances of normal and arteriosclerotic temporal and extracranial large arteries; 15 statements addressed 5 definitions of the 'halo' sign, stenosis (temporal and extracranial large arteries), occlusion, 'compression' sign (temporal arteries) and vessel wall pulsation (temporal arteries) and 7 statements addressed the requirements for diagnosis of vasculitis by US. Twenty-five physicians experienced in US and/or LVV were invited by email to participate.
Four additional videos showed a positive and a negative 'compression' sign of the temporal artery branches in longitudinal and transverse views, respectively. All pathological images and videos originated from patients with active disease who met the expanded ACR classification criteria of GCA, and in whom diagnosis was confirmed either by temporal artery biopsy or on a clinical basis, including US and follow-up. 19 The images and videos were collected by a facilitator of the group (SC) who constructed an electronic database using REDCap (Research Electronic Data Capture; Vanderbilt University, Nashville, Tennessee, USA) hosted by a server from the Italian Society for Rheumatology. 20 rom 550 submitted images and videos, 150 images and videos were selected by the facilitator for the web-based reliability exercise: 20 videos of axillary arteries, 20 still images of axillary arteries, 45 videos of temporal arteries, 45 still images of temporal arteries and 20 videos of the 'compression' sign applied to temporal arteries.
delphi exercise Twenty-four of the 25 invited participants responded to the first Delphi questionnaire (96% response rate). All 24 participants also responded to the second round of the Delphi questionnaire (100% response rate). In round 1, a consensus was achieved on nine definitions on normal temporal and extracranial large arteries, arteriosclerosis, 'halo' sign, stenosis of temporal and extracranial large arteries, occlusion, 'compression' sign (temporal arteries) and US assessment of the 'compression' sign (temporal arteries) (table 1). A definition of the 'halo' sign not including the measurement of the IMT was preferred by the group, because of the high variance of proposed cut-off values for temporal and extracranial large arteries found in the SLR and the lack of validated data at that time.
Images and videos were submitted by participating experts as in previous OMERACT-related US exercises. 14-16 61 Images and videos for the present web-based exercise were taken from patients with newly diagnosed active GCA since US signs in patients with established disease resolve rapidly with treatment. 40 Reliability data for 12 sonographers reading videos from the international multicentre TABUL study have now been published. 2 Videos from that study were randomly chosen from all stored videos of the study, irrespective of their quality, whereas the quality of images and videos in the OMERACT study may have been better as the members submitted material which they deemed representative. Sonographers of the TABUL study were less experienced than sonographers of the present OMERACT study. Kappa values for the intra-rater reliability in the TABUL study were 0.
PCR products were purified by using a QIAquick PCR purification kit and sent for Sanger sequencing at the McGill University nd Genome Quebec Innovation Center. All four bacterial isolates had identical 16S rRNA gene sequences, which best match using BLAST in GenBank was a Pseudomonas poae sequence. The isolates were named as USP1, USP2, USP3, and USP4. The absence of antagonistic interaction between the bacterial isolates was confirmed using the cross-streak method as described by  Hayat et al. (2017).
Questionnaires. Demographic and disease-related data were collected during structured interviews and patients completed the following self-administered questionnaires; The IBS Severity Scoring System (IBS-SSS). IBS-SSS, which includes five items-pain severity, pain frequency, severity of abdominal distension, bowel habit dissatisfaction and daily life interference, was used to assess IBS symptom severity. The scores are combined into an overall IBS score ranging from 0 (no symptoms) to 500 (maximum severity)  44. We used the total score of this questionnaire to analyse the severity of IBS. Visceral sensitivity index (VSI). The VSI was used to assess GI-specific anxiety, i. e. the cognitive, affective, and behavioural responses to the fear of GI sensations and symptoms and in which context these occur.
IBS-quality of life (QoL). The IBSQoL is a disease-specific questionnaire used to evaluate emotional functioning, mental health, physical functioning, energy, sleep, food/diet, social role, physical role, and sexual relations in IBS patients. To facilitate score interpretation, the summed total score is transformed to a 0-100 scale ranging from 0 (poor QoL) to 100 (maximum QoL). The Patient Health Questionnaire (PHQ)-12. The Patient Health Questionnaire (PHQ)-15 asks the subject about the severity of 15 somatic symptoms, each scored from 0 (not bothered at all) to 2 (bothered a lot)  47. In this study the three GI symptoms were excluded and instead PHQ-12 was used, to have a measure specifically for non-GI symptoms  48. Data processing and statistical analysis. Multivariate analysis. Multivariate factor analyses were applied to investigate if fecal protein levels or mucosal mRNA expression of granins (CgA, CgB, SgII and SgIII), fecal and mucosal bacterial genera, immune factors as well as clinical measurements (X variables) discriminated between groups of study subject (Y variables).
As previously described in Tap et al. 23  , co-inertia analysis is an ordination method for coupling 2 (or more) sets of parameters (e. g. , abundance of fecal granins (CgA, CgB, SgII and SgIII) and microbiota OTU proportion) by looking at their linear combinations. In the co-inertia analysis, the co-inertia (the sum of the square of covariance) between the 2 sets is maximized and decomposed. Hence, the co-inertia value, so called RV coefficient, is a global measure of the co-structure between the 2 data sets  51. The co-inertia RV coefficient is high when the 2 sets vary dependently and low when they vary independently. Co-inertia analysis was performed on fecal microbiota beta diversity and the abundance of fecal granins (CgA, CgB, SgII and SgIII). In this study, we used co-inertia analysis based on fecal microbiota composition using JSD distance metric and successively coupled with a principal component analysis computed fecal levels of granins.
Received unrestricted research grants from  Danone, Glycom and Ferring Pharmaceuticals , and served as a Consultant/Advisory Board member for  AstraZeneca ,  Danone, Nestlé, Almirall, Allergan, Albireo, Glycom, Menarini and Shire , and as a speaker for Tillotts,  Menarini ,  Takeda ,  Shire ,  Allergan , and  Almirall. Lena Öhman: Has  received a financial support for research by  Danone Research and AstraZeneca  and served as an advisory board.
Study area and sample selection We carried out a survey in peninsular Spain, i. e. throughout Spanish territory, except for the Balearic Islands, Canary Isles, Ceuta and Melilla. The consumer profile selected was responsible for purchasing at home, consuming any type of meat at least once every two months and aged from 25 to 74 years old. The interview was by telephone and held using CATI (Computer Assisted Telephone Interview) software. Telephone numbers were randomly selected from public telephone listings. The sample size was 800 interviews, for an error of 3. 53% and a confidence level of 95. 5% (2 sigma). The percentages of population with the feature studied (p) and without the feature studied (q) were considered 0. 5. The error was below the desirable limit of 4% indicated by  Cea (2010)  in social research.
Statistical analysis During the telephone interviews, a database was generated with the response codes and transferred to a file compatible with the software used to analyse the results, IBM SPSS Statistics 20  (SPSS, 2011). Depending on the target, a different statistical analysis was used. First, for the positioning analysis, a factorial analysis of correspondences was performed based on the table of selection frequencies for each of the four attributes. If the explanation of the variance for both axes is higher than 60%, the result can be analysed graphically  (Hair et al. , 1999). Second, to describe the image of rabbit meat and the sociodemographic profile of the consumer based on it, basic statistics and cross tabulation of mean values were used. The statistical significance test for differences between mean values was performed by Snedecor's F-test.
In this area a large number of studies were sponsored by CGs with funding from pharmaceutical companies. Our study has limitations. Funding data and role of the sponsors was not always adequately reported. In our study funding data abstraction relied on subjective interpretations of language. To address this limitation, we confirmed doubtful cases with a third author. As our study was limited to breast cancer, it is unclear whether our results could be generalizable to other cancer sites. However, for tumors with a similar incidence the probability to observe similar findings is high. In conclusion, we evaluated the role of CGs in breast cancer and its funding source, identifying a substantial presence of those funded by the pharmaceutical industry, with a decrease in the proportion of those supported by CGs exclusively.
Data extraction Data on the journal and year of publication, total number of study subjects, site locations (number of study countries and number of study centres), type of study drug, phase of the study (II vs. III), the design of the study (randomized vs. single-arm), and intervention arms were recorded. The 2015 journal impact factors (IFs) were obtained from Thomson Reuters Journal Citation Reports and classified as low (IF < 5. 5), intermediate (IF 5. 5-18. 5), or high (IF > 18. 5).
Funding information and outcome assessment We also extracted how funding sources and sponsorship were defined. Funding sources were classified as CGs, industry or government or academic organizations based on the recorded lead sponsor and/or collaborator and/or funding information reported in the disclosure in the published manuscript. "Lead sponsor" was defined as the organization responsible for overseeing the trial and analyzing study data, while "collaborator" was defined as an organization other than the sponsor that provides support for a clinical study, including funding, design, implementation, data analysis, or reporting  [14]. If a CG was listed as a lead sponsor or as a collaborator the trial was considered "CG-sponsored". If industry was the lead sponsor or was listed as a collaborator, the trial was classified as "industry sponsored".
Real-data example In this Section, we consider a sequence of metal corrosion images captured using bright-field transmission electron microscopy. 11 We downsize each image to 308by-308 pixels. There are 23 gray images (frames) in the sequence and 2 frames per second. Hence, this corresponds to 11. 5 seconds from the original video. At some point, a corrosion spot initiates in the image sequence. Sample images from the sequence are illustrated in Fig. 2. The dynamics of the signal model, in terms of the definition in (5. 2), has the following parameters: α t,1 = 1, and α t,s = 0 for s > 1; p(1) = 1 and p(s) = 0 for s > 1; ρ is about 1. 2 × 10 2 and it is estimated from the real-data. In the example, we set the risk tolerance = 0. 1, and let ϑ = 0. 5. To evaluate detection performance, we run 3000 Monte Carlo trials and add zero-mean Gaussian noise (with variance 25) to the images.
* Research was partially supported by  NSF  grants  CAREER CCF-1650913 ,  CCF-1442635 ,  CMMI-1538746 , and a  Georgia Institute of Technology IMat Faculty Fellow (IFF)  Seed Grant. † Research was partially supported by an  FGV grant ,  CNPq  grants  307287/2013-0  and  401371/2014-0 , and  FAPERJ  grant  E-26/201. 599/2014. ‡ Research was supported by the  LabEx PERSYVAL-Lab  ( ANR-11-LABX-0025 ) and  CNPq  grant  401371/2014-0. § Research was supported by  NSF  grants  CCF-1523768 , and  CCF-1415498  and  CNPq  grant  401371/2014-0. 1 imsart-ejs ver.
HRTEM studies of samples before and after in vitro immersion in physiological solution HRTEM, selected area electron diffraction, convergent beam electron diffraction, and energy dispersive X-ray spectroscopy (EDX) were performed on a JEM-2100F High Resolution Transmission Electron Microscope, which was operated at 200 kV with a point-to-point TEM resolution of 0. 23 nm. Fast Fourier transformation (FFT) analysis and inverse FFT analysis were performed using DigitalMicrograph™ software (Gatan Inc. ) to characterize the crystal structural variations in the samples.
Correlation analysis Cross-correlations of residues in the Cas9 protein were computed based on mutual information between all Cα atoms using the generalized correlation analysis approach developed by Lange and Grubmüller  (Lange and Grubmuller, 2006) , which is explained in detail in the SI. The g_correlation module in the Gromacs 3. 3  (Lindahl et al. , 2001)  package has been employed. Based on the computed correlations, the Generalized Correlation score (GCs) has been employed to define quantitatively the inter-dependent couplings established by HNH with the REC lobe. The GCs has been originally introduced by Ricci et al. in the study of the conformational dynamics of the PPARγ-RXRα nuclear receptor complex  (Ricci et al. , 2016) , and used to describe the allosteric effects in CRISPR-Cas9  (Palermo et al.
Acknowledgements. G. P. is supported by the  Swiss National Science Foundation  with the postdoctoral award P300PA_164698. J. S. C. is supported by the  NSF   Graduate Research Fellowship. J. A. M. thanks  NIH, NSF ,  HHMI ,  NBCR , and SDSC grants. Anton-2 computer time was provided by the  Pittsburgh Supercomputing Center  through grant  PSCA16035P  from the  NIH. The Anton-2 machine at PSC was generously made available by D. E. Shaw Research. Computer  time for additional MD has been awarded by  XSEDE  via the grant  TG-MCB160059. G. P. thanks  Dr. Lorenzo Casalino  for useful discussions.
The energy of a jet is corrected to the expected response of the jet at stable-hadron level, using corrections measured in bins of the jet p T and η. These corrections are usually not larger than 10 to 15%. Residual data-to-simulation corrections are applied to the simulated samples. They usually range between sub-percent level at high jet p T in the central part of the detector to a few percent in the forward region. A correction is applied to the direction and magnitude of the p miss T vector based on the differences between the estimates of the hadronic recoil in Z → µµ events in data and simulation. This correction is applied to Z → ττ, W+jets, and signal events, where a well-defined direction and magnitude of genuine p miss T can be defined. The efficiency for genuine and misidentified b jets to pass the Medium working point of the b tagging discriminator is determined from data, using tt events for genuine b jets and Z+jets events for jets predominantly originating from light-flavor quarks.
For associated production with b quarks four-flavor scheme NLO QCD calculations  [104, 105]  and five-flavor scheme NNLO QCD calculations, as implemented in SUSHI based on BBH@NNLO  [106] , are combined using the Santander matching scheme  [107]. The Higgs boson masses and mixing, and the effective Yukawa couplings for the m mod+ h scenario, are calculated using the FEYNHIGGS 2. 10. 2  [87, [108] [109] [110] [111]  code. The branching fraction of the MSSM Higgs bosons to τ leptons is calculated with FEYNHIGGS for the m mod+ h scenario and using the program HDECAY 6. 40  [112]  for the hMSSM scenario. The simulated single neutral Higgs boson signals are combined into a multiresonance signal model for the given values of m A and tan β, taking into account the predictions for the mass, production cross sections, and branching fraction into τ leptons for each of the neutral Higgs bosons.
These results are compatible with the findings of a similar search performed by the ATLAS collaboration, based on an equivalent dataset  [17]. In the low mass region the exclusion contour is similar to the previous CMS publication, while a higher sensitivity might be expected. This can be attributed to three main factors: the choice of single lepton triggers in the eτ h and µτ h final states together with the higher instantaneous luminosity leads to the need for higher p T thresholds at the trigger level and therefore reduced signal acceptance; the change of the discriminating variable from the estimate of the fully reconstructed ττ mass to m tot T provides more sensitivity for high masses, but slightly less sensitivity for lower masses; and finally the prediction of the kinematic distributions of the signal at NLO precision reveals a generally softer p T spectrum for the gluon fusion production mode, which dominates for low values of tan β.
Acknowledgments We thank  Emanuele Bagnaschi  and  Stefan Liebler  for their support in developing the procedure for obtaining the Higgs boson kinematics at NLO plus parton shower precision with POWHEG. This work has been performed in the frame of the  LHC Higgs Cross Section Working Group. We congratulate our colleagues in the CERN accelerator departments for the excellent performance of the LHC and thank the technical and administrative staffs at  CERN  and at other  CMS institutes  for their contributions to the success of the CMS effort. In addition, we gratefully acknowledge the computing centers and personnel of the Worldwide LHC Computing Grid for delivering so effectively the computing infrastructure essential to our analyses. Finally, we acknowledge the enduring support for the construction and operation of the LHC and the CMS detector provided by the following funding agencies:  BMWFW  and  FWF (Austria) ;  FNRS  and  FWO (Belgium) ;  CNPq ,  CAPES ,  FAPERJ , and  FAPESP (Brazil) ;  MES (Bulgaria) ;  CERN ;  CAS, MoST , and  NSFC (China) ;  COLCIENCIAS (Colombia) ;  MSES  and  CSF (Croatia) ;  RPF (Cyprus) ;  SENESCYT (Ecuador) ;  MoER ,  ERC IUT , and  ERDF (Estonia) ;  Academy of Finland ,  MEC , and  HIP (Finland) ;  CEA  and  CNRS/IN2P3  (France);  BMBF ,  DFG , and  HGF (Germany) ;  GSRT (Greece) ;  NKFIA (Hungary) ;  DAE  and  DST (India) ;  IPM (Iran) ;  SFI (Ireland) ;  INFN (Italy) ;  MSIP  and  NRF (Republic of Korea) ;  LAS (Lithuania) ;  MOE  and  UM (Malaysia) ;  BUAP ,  CINVESTAV ,  CONACYT ,  LNS ,  SEP , and  UASLP-FAI (Mexico) ;  MBIE (New Zealand );  PAEC (Pakistan) ;  MSHE  and  NSC (Poland) ;  FCT (Portugal) ;  JINR (Dubna) ;  MON, RosAtom, RAS  and  RFBR (Russia) ;  MESTD (Serbia) ;  SEIDI, CPAN, PCTI  and  FEDER (Spain) ;  Swiss Funding Agencies (Switzerland) ;  MST (Taipei) ; ThEPCenter, IPST, STAR, and  NSTDA (Thailand) ;  TUBITAK  and  TAEK (Turkey) ;  NASU  and  SFFR (Ukraine) ;  STFC  ( United Kingdom );  DOE  and  NSF (USA).
Participating GPs gave written information to their patients regarding the study and asked them to sign an informed consent. This study was conducted by the Sentinelles network, 36 part of the INSERM-Paris Sorbonne University research unit UMR-S 1136. This research group has a standing authorisation from the French independent administrative authority protecting privacy and personal data to conduct research among GPs and their patients (CNIL no 471 393). Measurement of CMDs CMDs were measured using a standardised diagnostic interview: the Mini-International Neuropsychiatric Interview (MINI) that was used as a screening tool. The MINI is, a structured clinical interview that enables the diagnosis of mental disorders based on the Diagnosis and Statistical Manual of Mental Disorders, fourth edition.
05) in a multivariable Poisson regression model excluding occupational factors. Age, gender and occupational grade were included directly in the adjustment variable. Absolute risks among persons who were exposed were computed for each of the studied work dimensions. All analyses were performed using GNU R software V. 3. 1. 1. (lme4 package). 51 52 sults Participation and description of the population Of the 1000 GPs contacted by mail, 185 accepted to participate (response rate=18. 5%) and 121 completed the study (figure  1 ). Participating GPs were more likely to be male (sex ratio=1. 82), and to be 50 years or older; they were disseminated throughout the Nord-Pas-de-Calais region (table  1 ). Participating GPs were representative of those practising in the region in terms of geography, age, type and years of practice.
Acknowledgements The authors thank all the participating GPs of the  Nord-Pas-de-Calais region  and their patients who participated to the Héraclès study. The authors thank the department of general practice of Lille's University and the regional union of health professional of GP's (URPS-ML) of the  Nord-Pas-de-Calais region  for their involvement in the GP recruitment phase. The authors also want to thank the Héraclès study scientific committee members who contributed to the brainstorming and the set-up of this survey. Contributors Study concept and design: MR, NY, MM, AL TB and LP. Data analysis and collection: MR, LFC, MM and LP. Drafting of the manuscript: MR. Critical revision of the manuscript: NY, MM and AL. All authors approved the final manuscript. Funding This work was supported by the  Nord-Pas-de-Calais regional health agency (ARS)  and the  Ile-de-France region-DIM Gestes  ( Mathieu Rivière 's PhD thesis).
Molecular fingerprinting of M. tuberculosis could address this challenge but still awaits versatile, medium-to high-throughput, and cost-effective typing approach that reflects the true transmission picture. IS6110 restriction fragment length polymorphism (IS6110 RFLP), a typing approach based on the polymorphism generated by the insertion sequence IS6110, has proved highly discriminative and has served as the gold standard for the detection and surveillance of outbreaks, notably those involving MDR-TB strains, for many years  [3] [4] [5]. However, as a hybridizationbased approach, IS6110 RFLP is labor-intensive, time-consuming, refractory to automating, and hence not amenable to high-throughput analyses. The method also suffers the major drawback of not being suitable for data banking and inter-laboratory comparisons  [6].