dataesr/scientific-paragraphs-categorization huggingface dataset:
Each trapping session lasted for three consecutive nights: in the rare instances where the same badger was captured twice during the same capture session, data from only the first capture was included in the analysis. Data from all three trapping zones were aggregated into one during each season, since badgers rarely were trapped in more than one zone (between July 2006 and October 2013, eight of 541 trapped individuals (1. 5%) were trapped in more than one zone within a season). Trapping was suspended from February to April inclusive each year to avoid the capture of new-born cubs and their separation from lactating females. Badgers were captured in the immediate vicinity of their setts in peanut-baited cage traps and transported to a sampling facility to be anaesthetised and sampled  26.
Test 3 was culture of all samples except blood for mycobacteria using standard techniques  44. Full details of all tests appear in Drewe et al. 19. The capture history of each badger was summarised from the first to the last capture session as a series of numbers from zero to eight, where zero indicated that it was not captured on that occasion, and values from 1 to 8 corresponded to the eight possible combinations of diagnostic test results (Table  1 ). Multi-event capture-recapture model. A multi-event capture-recapture model  23  was fitted to the whole dataset of capture histories, with infection status as the latent variable. Briefly, it was considered that at first capture, each badger could be in one of two epidemiological states: uninfected [susceptible] or infected. It was further assumed that transition from the uninfected to the infected state could occur between any successive capture sessions.
This was included because the objective of the study was to estimate the probability of an individual being infected at the time of its last (most recent) capture. Model parameters to be estimated are precisely defined in Supplementary Table  S4 , and a multinomial tree diagram of the probability structure of the model is presented in Fig. 5. The likelihood of an individual capture history can be obtained by summing the probability of all possible paths leading to that capture history. The likelihood of a given path can be obtained by multiplying the probabilities appearing along this path. The likelihood of the whole dataset can be obtained by multiplying the probability of all individual capture histories. Parameter estimation was conducted using the maximum likelihood approach implemented in the programme E-SURGE version 1.
In contrast, in 2016, 59,054 ZIKV cases were reported all over Bahia (Fig. 3F , red line) of which only 928 cases originated from Salvador (1. 6%). To see whether the decline of notified cases from Salvador in 2016 could be confirmed by laboratory tests, we tested all specimens for ZIKV RNA and ZIKV IgM. None of the specimens tested positive for ZIKV RNA. In agreement with the high ZIKV seroprevalence from 2015 onwards, IgM-based incidence was detected only in 2015 (2. 2%; CI, 0. 1 to 8. 0%) and 2016 (1. 3%; CI, 0. 6 to 2. 5%) (Fig. 3F, arrows ). Until mid-2017, the number of reported cases remained consistently low from both Salvador and the state of Bahia. This suggests that the outbreak ceased due to the lack of acute cases. Modelling the trajectory of the epidemic in Salvador, Brazil. To test whether population immunity would limit future cases in Salvador, Brazil, we fitted a mathematical model of ZIKV transmission jointly to the independent case notification data from Salvador and the seroprevalence results from our study.
MATERIALS AND METHODS Ethical clearance, sampling sites, and sample storage. Sampling and testing were approved by the Federal University of Bahia (UFBA) research ethics board Climério de Oliveira under protocol 1. 408. 499. HIV patients were sampled at the UFBA teaching hospital. Tuberculosis patients were sampled at the José Silveira Foundation-Brazilian Institute for Investigation of Tuberculosis. Pregnant women were sampled at the time of delivery at the UFBA maternity hospital Climério de Oliveira. All patients attended during the study period accepted participation in the protocol. Microcephaly was diagnosed when the measurement of the cephalic circumference was 2 standard deviations below that of the corresponding gestational age, based on intergrowth charts from the World Health Organization in addition to clinical and imaging data as recommended  (49).
The competitive ELISA using a mutant E protein of ZIKV was conducted according to reference 50 for DENV and is described in detail elsewhere  (56). Briefly, the quadruple mutant E protein from ZIKV (strain H/PF/2013, E-protein amino acid residues 1 to 406, GenBank accession no. KJ776791) bearing the point mutations T76A, Q77G, W101R, and L107R was expressed in Drosophila S2 cells. Serum samples (diluted 1:100 in 100 l blocking solution) were preincubated with 2 g/sample of mutant DENV E proteins (mixture of the four DENV serotypes  [50]  for 1 h to remove DENV antibodies and/or cross-reacting antibodies). Following the preincubations, samples were transferred to 96-well plates coated overnight with ZIKV mutant E protein (150 ng/well), and the assay was completed following standard ELISA procedures.
atlasbrasil. org. br/2013/pt/consulta/) from the United Nations Development Programme (UNDP). HDUs are described by seven different categories: population, demography, housing, labor, education, income, and vulnerability. Maps were generated using ArcGIS 10. 3 (ESRI, Redlands, CA, USA). Statistical analyses. Statistical analyses included 2 and Fisher's exact tests for comparisons of seroprevalence rates (EpiInfo V7. 2; http://www. cdc. gov/epiinfo), two-tailed Mann-Whitney U tests for comparisons of sociodemographic indicators and logistic regression with stepwise backward elimination of variables for multivariate analyses (SPSS V23; IBM, Ehningen, Germany), done on one variable per HDU category, selected according to highest P values in bivariate comparisons. Diagnostic test parameters were calculated using OpenEpi (http://www.
openepi. com). Transmission dynamic modeling. ZIKV outbreak dynamics were analyzed using a susceptibleexposed-infectious-recovered (SEIR) model. The vector population was not explicitly taken into account, but variation in mosquito numbers was modeled through annual seasonal forces acting on the transmission rate. The model was implemented in a Bayesian framework using the LibBi library via the RBi and RBi. helpers packages  (53) (54) (55). The model was jointly fitted to reported ZIKV incidence data from Salvador, Brazil, from the beginning of January 2015 to the end of October 2015 and the proportion of individuals (401/633) who were seropositive to ZIKV in 2016. Incidence was fitted using a Poisson likelihood with overdispersion and approximated with a truncated Gaussian distribution, and seroprevalence was fitted using a binomial likelihood.
ACKNOWLEDGMENTS We thank  Monika Eschbach-Bludau ,  Janett Wieseler ,  Carlo Fischer ,  Victor M. Corman ,  Tobias Bleicker ,  Sebastian Brünink ,  Valdélio de Oliveira Marques ,  María Belen Arriaga Gutierrez ,  Ludy Alexandra Vargas Torres ,  André Pessoa Bonfim Guimarães ,  Katja Steinhagen ,  Jens Miguel Warnecke , and  Erik Lattwein  for their support. This work was supported by the  German Centre for Infection Research (DZIF)  through the  ZIKApath  project to J. F. D. and T. J. , and the  European Union 's  Horizon 2020 research and innovation program  through the  ZIKAlliance  project (grant agreement  734548 ) to J. F. D. , T. J. , B. M. K. , O. J. B. , and X. D. L. The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
MATerIAlS And MeTHodS Patient population This study was performed after approval of the local institutional review board and owing to its retrospective design, informed consent was waived. After a thorough review of the institutional databases from January 2011 to December 2016, all patients who had undergone endovascular re-treatment of a recurrent aneurysm using the WEB device in the two participating centers were identified and included. At both institutions, the treatment indications were discussed in a multidisciplinary neurovascular meeting among neurosurgeons, vascular neurologists, and neuroradiologists. The WEB device was mainly chosen for recurrent aneurysms with a wide neck and an unfavorable configuration for coil occlusion. For each patient and aneurysm, we collected the following data: age; sex; initial aneurysm status (ruptured or unruptured); aneurysm location; size of the initial aneurysm (maximal transverse diameter and height); neck diameter and size of the recurrent aneurysm (maximal transverse diameter and height); dome-to-neck and aspect ratio; number, date, and type of previous treatments; type and size of the WEB device; ancillary treatment methods, such as stents, coils, or remodeling balloons; preoperative clinical status measured on the modified Rankin Scale (mRS).
Hemorrhagic Stroke neck remnant in one category) was described in 79. 3% 8 at 1 year in the French Observatory and in 85. 4% at 6 months in the WEBCAST study. 7 In our study we evaluated aneurysm occlusion by using the three-grade scale previously used in three large prospective multicenter series. 7 8 15 Although other scales have been proposed they are less frequently applied. 16 17 It has been shown that opacification of the WEB's recess is equivalent to complete occlusion, making grade AB in the four-grade WEB Occlusion Scale dispensable. 18 Furthermore, reporting aneurysm occlusion with a three-grade scale may make comparison of the anatomical results using the WEB with historical coiling data more reliable. The choice of the WEB device for re-treatment was mainly based on anatomical considerations-that is, when it was estimated that coiling of the recurrent aneurysm would not be reasonable owing to its configuration.
Data analysis Mean respiratory frequency (f) was computed from the breathing profile measured with OEP in both natural and spirometer breathing, using the same duration (between 30 and 50 s, deleting the first cycles). Ventilation profile measured with spirometer was not analysed in this study. From the force plate data, confidence ellipse (CE) of 95% of the displacement covered by the CoP was computed for each exercise  (Chiari et al. 2002). Three stabilometric parameters were reported: CE ranges along the antero-posterior (AP) and medio-lateral (ML) axis (Figure  1 ) and the mean CoP velocity (MV). AP and ML range were normalized by the subject height in standing position and by top of skull -stool distance in sitting position, NB and SP were compared for all parameters, using a non-parametrical test (Wilcoxon), considering significant difference with a p-value lower than 5%.
Data Availability. Qualified researchers may request access to patient level data and related study documents, from the primary clinical study, including the clinical study report, study protocol with any amendments, blank case report form, statistical analysis plan, and dataset specifications. Patient level data will be anonymized and study documents will be redacted to protect the privacy of trial participants. Further details on Sanofi's data sharing criteria, eligible studies, and process for requesting access can be found at: https://www. clinicalstudydatarequest. com. Thanking Patient Participants. The authors thank all patients for their participation in the LixiLan-L trial. Open Access. This article is distributed under the terms of the Creative Commons Attribution-NonCommercial 4.
ACKNOWLEDGEMENTS Sponsorship for this study, provision of study devices, all study materials, and article processing charges were funded by  Sanofi U. S. (Bridgewater, NJ). All authors had full access to all of the data in this study and take complete responsibility for the integrity of the data and accuracy of the data analysis. All named authors meet the International Committee of Medical Journal Editors (ICMJE) criteria for authorship for this manuscript, take responsibility for the integrity of the work as a whole, and have given final approval to the version to be published. Editorial assistance was provided by  Breanne Landry of Caudex (Oxford, UK) , funded by  Sanofi.
SLC2A1 Molecular Analysis Mutational analysis of all exons and intron-exon boundaries of the SLC2A1 gene were performed on genomic DNA from patients and their parents by direct Sanger sequencing (primer sequences are available upon request). The GenBank [NM_006516] sequence was used as the reference. Pathogenicity was predicted by in silico analysis with Alamut Visual version 2. 7 (Interactive Biosoftware, Rouen, France). When no point mutation was found, a single or multiple exon deletion or duplication was searched by multiple ligation-dependent probe amplification with SALSA MLPA KIT P138 SLC2A1 (MRC-Holland, BV, Amsterdam, Netherlands). 1  Flow Cytometry Analysis of GLUT1 Surface Expression on Circulating RBCs At least 0. 5ml of nonfasted venous blood was collected on ethylenediaminetetraacetic acid (EDTA) tubes and kept at 4 8C for maximum 7 days before analysis.
Whole blood was diluted at 1/3,000 into phosphate-buffered saline (PBS) containing 0. 09% sodium azide, 1mM of EDTA, and 0. 33mg/ml of bovine serum albumin (binding buffer). Approximately 80,000 RBCs per sample were transferred into a 96-well microplate and stained with GLUT1. RBD ligand fused to enhanced green fluorescent protein (eGFP; METAFORA Biosystems, Evry, France) at 37 8C for 20 minutes. 11, 12 RBCs were washed twice with PBS and resuspended in binding buffer. Acquisition was performed on a FACSVerse flow cytometer (BD Biosciences, Franklin Lakes, NJ) equipped with 405-, 488-, and 640-nm lasers. Data analysis was performed using Flowjo software (TreeStar, Inc. , Ashland, OR). Debris and doublets were excluded from the analysis; eGFP signal was collected for each sample, by taking into account geometric mean of gated, GLUT1.
Acknowledgment Part of this work has been realized with the funding support of the  Joshua Hellmann Foundation for Orphan Disease ,  Hong Kong. It has also received funding from the  European Union 's  Horizon 2020 research and innovation program  under Grant Agreement No. 761702  to  Metafora Biosystems. We thank warmly  Drs Benedicte Heron ,  Agathe Roubertie ,  Anne de Saint-Martin ,  Cecile Laroche ,  Elsa Kaphan , and  Claude Cances  for patient referral and fruitful collaboration, as well as  Drs Naomi Taylor  and  Marc Sitbon  for stimulating discussions. We also thank  Karine Bonnet ,  Nadine Litou , and  El eonore Botton from Laboratoire CERBA  for participating in the repeatability and reproducibility study to assess the test's robustness.
USUV infection of human astrocytes elicits a strong anti-viral response Because both USUV and ZIKV efficiently infected primary human astrocytes, we next aimed at analyzing the modulation in the expression of genes involved in anti-viral responses. We used a PCR array consisting in 84 genes that are modulated in the interferon (IFN) response or the cellular pattern recognition receptors (PRR) among other mechanisms  [43]  (S1 Table ). To compare the anti-viral response elicited by flavivirus infection in astrocytes, mRNAs were collected from USUV-and ZIKV -infected astrocytes 4 dpi and subjected to retrotranscription. cDNA relative abundance was then analyzed by qPCR. Under these conditions, we found that 33 genes were significantly upregulated (more than 2 fold) by USUV in astrocytes These data highlight the strong induction of an antiviral response by USUV and suggest substantial differences in the cellular response process against flaviviruses in astrocytes.
Treatments One hour before infection, cells were treated with AXL-blocking antibody or goat IgG control at 10μg/mL and with DC-SIGN at 5μg/mL (R&Dsystems). For apoptotic test cell cultures were incubated with or without zVAD-fmk (100 μM) (Abcam) for 90 min before infection and maintained during all the infection process. ZIKV and USUV strains, production and cellular infection PF-13 ZIKV was produced and provided by the National Reference Center for arboviruses (NRC) and has no more than 5 passages on Vero cells (ATCC). USUV Vienna Austrian strain of USUV (Vienna2001-blackbird, USUV 939/01, GenBank acc: AY453411. 1), was provided from Department of Biotechnology, INIA Madrid and was propagated three times in Vero cells. Viral stocks were prepared by infecting sub confluent Vero cells at the multiplicity of infection (MOI) of 0.
RT-qPCR Astrocytes infected with USUV and ZIKV or mock-treated cells were harvested in RLT buffer (Qiagen). Total RNA was extracted using RNeasy mini-kit (Qiagen). Complementary DNA was synthesized using Omniscript reverse transcriptase (Life Technologies). RT2 Profiler PCR arrays for Human Antiviral Response (96 well format, Qiagen) were used for real-time quantitative PCR analysis, with the use of the LC480 real time PCR instrument (Roche) and the Light Cycler 480 SYBR Green I master Mix (Roche). Volumes of mix, cDNA, RNAse-free water, and cycling conditions were determined according to manufacturer's instructions. Data on gene expression were normalized according to data from the HPRT housekeeping gene. Genes with uninterpretable amplifying curves were excluded from the analysis.
Morphometry and Behavioral Testing The gaps between converging oligodendroglial processes were measured using Openlab software after image acquisition using conventional fluorescence microscopy. The total number of spinal cord oligodendroglia was quantitated in each transverse section, after immunostaining with anti-APC antibody, with ImageJ 1. 47t (NIH) after montage construction (five spinal cord sections per animal, three animals per genotype minimum)  [3]. Statistical analysis was performed with the GraphPad Prism 5. 0c. The grid walking test was performed as described  [20]. Mice were familiarized with the grid apparatus for 5 min of free walking. The following day, each animal was video recorded for 5 min while walking on the mesh, and the number of hindlimb mistakes was counted. G-ratios were measured as described  [36].
Fourteen patients were lost to follow-up. Sixty-five patients with 66 shoulder prostheses were included (64. 1%) with an average follow-up of 25. 6 months (range from 24 to 30. 8 months). There were 24 RSAs and 42 anatomical replacements, including 41 total replacements and 1 hemiarthroplasty. Demographic data are reported in Table  1. The etiologies of anatomic replacements were primary osteoarthritis for 34 cases (80. 9%), instability osteoarthritis for 3 cases (7. 1%), osteonecrosis for 2 cases (4. 8%), posttraumatic osteoarthritis for 2 cases (4. 8%), and rheumatoid arthritis for 1 case (2. 4%). The etiologies of RSA were cuff tear arthropathy for 13 cases (54. 2%), massive rotator cuff tear for 5 cases (20. 8%), primary osteoarthritis with glenoid bone loss for 5 cases (20. 8%), and rheumatoid arthritis for 1 case (4.
Method of Assessment All the patients had a clinical evaluation preoperatively and at minimum a 2-year follow-up using the raw Constant-Murley score (CS), the subjective score value (SSV), and the active range of motion (ROM). Perioperative data (cementation or not, complications) and postoperative complications were reported. Radiological examination used standard radiographs in a strict anteroposterior view, defined by the visualization of the morse taper, and a Lamy profile view. Mechanical complications (implant loosening, disassembly, fracture, instability, and migration) were noted according to clinical and radiographic evaluation. Radiographic reading, measurements, and assessments were realized by a single independent examiner. Radiolucent lines (RLLs) around the stem and the glenoid component in postoperative and last follow-up X-rays were reported as well as their eventual progression.
Next-generation sequencing Virus sequencing from clinical samples was performed directly without virus isolation in cell culture. Viral RNA was extracted from serum using the QiaCube HT device and Cador Pathogen kit (Qiagen). Eight overlapping amplicons spanning the complete genome sequence were produced from the extracted RNA using the SuperScript ® III One-Step RT-PCR System with Platinum ® Taq High Fidelity kit (Thermo Fisher Scientific) and specific primers. PCR products were pooled in equimolar proportions for library building. Sequencing was performed using the PGM Ion torrent technology (Thermo Fisher Scientific) following manufacturer's instructions. Automated read datasets provided by Torrent software suite 5. 0. 2 were trimmed according to quality score (99%) and length (reads shorter than 30bp were removed) using CLC genomics workbench software (CLC bio-Qiagen).
Primers used for RT-PCR were removed using an in-house software package. Reads were mapped on reference (inoculum strain) using CLC. A de novo contig was also produced to ensure that the consensus sequence was not affected by the reference sequence. Substitutions with a frequency higher than 1% (minor variants: variants frequency >1% and <50%) were considered for further analysis. Detailed protocols for extraction, amplification and sequencing are provided in supplemental data. Distribution of variants at synonymous and nonsynonymous sites: The distribution of identified variants at synonymous and non-synonymous sites was compared with an in-house model providing random distribution of the same number of variant sites in EBOV coding regions after 1000 simulation replicates (see supplemental data for details describing the model).
Distribution of major variant sites with reference to GenBank full-genome sequences: We compared the genomic distribution of minor variants identified in infected NHPs, with that of major mutations (frequency !50%) reported in GenBank Ebola Zaire genomic sequences (212 sequences). The number of common variant sites was determined for variants at 1%, 3%, 5% and 10% and compared with the number of common variant sites expected under a regimen of random distribution (see supplemental data for details concerning statistical analysis). Sequencing of the batch inoculum produced in Vero cells (strain EBOV Gabon 2001) was performed by extraction of the RNA from clarified supernatant medium. It was reverse transcribed, amplified, sequenced and analyzed as described above. A complete EBOV genome sequence was obtained after mapping the reads against EBOV Gabon 2002 strain reference (GenBank KC242800, Zaire ebolavirus isolate EBOV/H.
Next-generation sequencing In the absence of previous experimental datasets deciphering the genomic evolution of Ebola virus during the different stages of infection, we attempted to provide answers to the following basic questions: does the genetic diversity observed in blood increase over time and can it be characterized (occurrence of majority and  minor variants) quantified and mapped onto the genome? Is it modified when the virus reaches and propagates in new organs? Is there a clear relationship between the infectious viral challenge dose and virus variability? Are the mutations observed along the genome randomly dispersed or do they appear to arise from genetic selection? For this purpose, complete EBOV genome sequences (except the 5 0 and 3 0 primers, i. e. , 18,871 nucleotides (nt)) were obtained for the viral isolate (EBOV Gabon 2001) used for monkey inoculation, and for all twelve monkeys at days 5, 7 and 9* pi (*day 8 pi for CB821) (except for one monkey with a low viral load at day 5 pi in the 1000ffu group).