dataesr/scientific-paragraphs-categorization huggingface dataset:
Ethics statement Research included in this study was subject to ethical review by the International Review Board of the Pasteur Institute of Tunis and approved as part of a research project submitted in response to a "call" from the National Institutes of Health for funding Tropical Medicine Research Centers. The Pasteur Institute of Tunis, the study sponsor, took out an insurance policy in accordance with the Tunisian law concerning clinical research. All clinical or biological investigations were performed in the Health Centers of each governorate to guarantee the patients' safety, confidentiality and respect. All human samples of Leishmania were isolated from patients after collection of the written informed consent at the time of the clinical examination. Human isolates were anonymized and the associated information coded for privacypreserving data mining.
Microsatellite data analysis The FSTAT Version 2. 9. 3. 2 software  [23]  updated from  [24]  was used to compute estimates and to test the significance of the various population genetic parameters. Genetic polymorphism was measured based on the allelic richness (A) and the Nei's unbiased estimate of genetic diversity within subsamples (Hs)  [25]. The observed heterozygosity (Ho) and expected heterozygosity (He) were also calculated. The Wright's F statistics  [26]  were estimated with the Weir and Cockerham's method  [27] : F IS measures the relative inbreeding of individuals due to the local non-random union of gametes in each subpopulation, and F ST measures the relative inbreeding in subpopulations attributable to the subdivision of the total population into subpopulations of limited size.
Therefore, F ST also measures the genetic differentiation between subpopulations. The significant departure from 0 of these parameters was tested by 10,000 randomization procedures with FSTAT. The genetic differentiation between historical and recent populations, between governorates (Gafsa, Kairouan and Sidi Bouzid) and between the two sub-populations (historical and recent focus) in the Kairouan governorate was explored. The significance of these estimates was confirmed by p-values 0. 05. The gene flow or migration rate between populations was also estimated using FSTAT, as Nm = 1-F ST /4 F ST  [28]. A neighbor-joining tree  [29] , based on the Cavalli-Sforza and Edward's chord distances  [30] , was used to cluster the genotypes. Data were computed using the POPULATION software to build the distance matrix (version 1.
2. 28; CNRS, UPR9034, Langella, O. ) and the tree was generated using FigTree, version 1. 4. 1  [31]. Finally, data were analyzed using a Bayesian model-based approach implemented in STRUCTURE, version 2. 3. 4  [32] , to explore the structure of the L. major populations. STRUC-TURE uses Bayesian Monte-Carlo Markov Chain (MCMC) sampling to identify the optimal number of clusters K for a given multi-locus dataset, without requiring the identification of the population subunits a priori. The parameters used were the admixture model with the length of burn-in period of 200,000 iterations, followed by 200,000 MCMC repeats after burn-in. Based on the multi-locus genotype data, isolates were divided into K subpopulations with K ranging from 1 to 10 and ten independent runs were performed for each value of K.
The K optimal value (i. e. , the optimal number of clusters in the dataset) was calculated using STRUC-TURE HARVESTER, web version  [33]. Two approaches were used to choose K. First, ΔK, which measures the second-order rate of change in the log likelihood of the data between successive values of K, was estimated  [34]. Second, posterior probabilities for the values of K with the highest Ln P(X|K) were compared. STRUCTURE 2. 3. 4 was also used to identify migrants. In this case, prior population information was used in the USEPOPINFO option of STRUC-TURE. Populations defined according to geographic and temporal criteria (GF2008-2012, KR2008-2012 and SBZ2008-2012, SBZ1991-1992, MN2008-2012 and CH2008-2012) were used as prior population information for this test. Run conditions for this analysis were as mentioned above.
Analysis of L. major population structure in the different governorates The data obtained from the ten polymorphic microsatellite markers  [20]  were used to assess and compare the genetic variability of isolates collected from patients in the three Tunisian governorates between 2008 and 2012. The Gafsa isolates (GF2008-2012; n = 66) included 48 genotypes (genotypic diversity = 0. 73), the Kairouan isolates (KR2008-2012; n = 46) 35 genotypes (genotypic diversity = 0. 76) and the Sidi Bouzid isolates (SBZ2008-2012; n = 25) 24 different genotypes (genotypic diversity = 0. 96). This finding shows the high L. major genotypic diversity in these three areas where ZCL is endemic. Unique genotypes and original microsatellite profiles were identified in 18 GF2008-2012 isolates, in four SBZ2008-2012 isolates and in 11 KR2008-2012 samples (S1 Table ).
Conversely, the F ST values were not significantly different between the KR2008-2012 and SBZ2008-2012 populations (Table  3 ). Accordingly, the highest migration rate (Nm) value was between the KR2008-2012 and SBZ2008-2012 populations, whereas the Nm values were much lower between the GF2008-2012 and KR2008-2012 and between the GF2008-2012 and SBZ2008-2012 populations (Table  3 ). The Bayesian model-based clustering analysis implemented in STRUCTURE indicated that our dataset (GF2008-2012, KR2008-2012 and SBZ2008-2012 isolates) could be organized in four (maximum L(K)) or two (maximum ΔK) clusters (K) (Fig 2A  and 2B ). For K = 2, 92% of L. major isolates from Gafsa, 10% from Kairouan and 38% from Sidi Bouzid were included in one of the inferred clusters and the remaining samples in the second one (Fig 2C.
As in all the populations assessed in this study, the mean H o values in the two subpopulations were extremely low compared to the H e values. The heterozygosity deficit (measured by F IS ) was very high in both populations (Table  2 ). The F ST value showed that the genetic divergence in the two foci was very low, but significant (Table  3 ), indicating a genotype flow between populations. Quantification of the migration events in the two districts using F-statistical approaches, revealed 17 migrants per population. The Neighbor joining analysis confirmed that there was no genetic structuring between populations (S2 Fig). The posterior probabilities of belonging to a K cluster and the corresponding ΔK values calculated with the STRUCTURE software showed a peak at K = 2, indicating that two genetic clusters were the best solution for this dataset.
Nevertheless, migration events from other regions cannot be excluded. The calculation of genetic differentiation between L. major population from Sidi Bouzid and those from North Africa  [20] , Central Asia  [20] , Middle East  [20] , Iran  [19]  and Pakistan  [50]  revealed considerable genetic differentiation (>0. 55) with highly significant p-values (0. 05) (S2 Table ). To further understand the L. major temporal/spatial dynamics in Tunisia, we also analyzed recent isolates (2008-2012) from two districts within the Kairouan governorate: Mnara (historical focus) and Chrarda (emerging focus). Considering the long interval (23 years) between the human outbreaks in the two districts, we expected that the more recent focus would show a lower genetic diversity than the historical focus. However, the genetic data showed a slightly higher genetic diversity in the more recent focus (Chrarda), despite the low sample size.
Acknowledgments The authors want thank the  Regional Health Directorates of Sidi Bouzid, Kairouan, and Gafsa (Tunisia) , the " Institut Pasteur Tunis " and the  "Institut de Recherche pour le Développement" (IRD, Montpellier, France) , the  "Centre National de la Recherche Scientifique " ( CNRS, France ) for this cooperative and collaborative project. We acknowledge the field staff of the  Department of Medical Biology, Institut Pasteur Tunis , for strain collections and the cryobank management;  Adel Gharbi  for ensuring strain and patients' data collection in accordance with the current Good Clinical Practice guidelines. Many thanks also to  Dr. Francine Pratlong  and  Patrick Lami  for providing samples from the  French National Reference  Center of Leishmania (CNRL, Montpellier, France) and  Luc Abate  ( IRD, Montpellier, France ) for help with the genotyping analysis.
Acknowledgements The authors would like to thank all participating investigators and laboratories involved in the TEST study; we would also like to thank the staff of IHMA for coordination of TEST. This study was sponsored by  Pfizer Inc. Medical writing support was provided by  Rod Taylor  at  Micron Research Ltd, Ely, UK  and was funded by  Pfizer Inc. Data management services were also provided by  Micron Research Ltd ; these were also funded by  Pfizer Inc.
Population and data analysis The charts of patients referred to our tertiary Otolaryngology and Skull Base Department and operated on by MFA of SCD by the senior author (VD) between 2006 and 2013 were retrospectively assessed and listed in a database (Excel, Microsoft, USA). Inclusion criteria were as follows: a/patients suffering from severe incapacitating balance problems; b/a positive HRCT with an SCD [3 mm in the Po ¨schl plane; c/a decreased threshold (\90 dB) of cVEMPs. Diagnosis of SCD syndrome was made after a thorough search for a history of head trauma, an otoscopic and physical examination, and after obtaining clinical data concerning audiological and vestibular symptoms. We looked for Hennebert's and Halmagyi's signs. Preoperatively, a complete otoneurological work-up was performed, including: • a tone and speech audiogram with search for supranormal BC on low frequencies and calculation of: a/pure tone average (PTA) with air conduction (AC) thresholds according to the American Academy of Otolaryngology-Head and Neck Surgery hearing classification system to describe functional outcome (0.
In cases of bilateral SCD, the most pathological side was operated first. • On HRCT, the position and size of the dehiscence was calculated on the reformatted slices in Po ¨schl's plane. The postoperative course was analyzed by recording the following: • any immediate complications due to the neurosurgical approach (cerebrospinal fluid leak, meningitis, facial paralysis, intracranial hematoma, seizure, wound superinfection) or to acute or delayed labyrinthine suffering, i. e. , sensorineural hearing loss (SNHL), tinnitus, vertigo, nystagmus contralateral to operated side • hospital and intensive care unit (ICU) stay duration • audiometric data obtained at D7 When necessary and possible, patients were managed postoperatively by physiotherapists to accelerate their vestibular compensation. At 1 month postoperative, the following were performed: • a clinical evaluation of audio-vestibular symptoms • a complete audiogram • a cVEMP evaluation If the follow-up was [6 months, we also retained the last recorded audiogram or cVEMPs.
CONCLUSIONS Among patients with HCV genotype 2 or 3 with or without previous treatment, including those with compensated cirrhosis, 12 weeks of treatment with sofosbuvirvelpatasvir resulted in rates of sustained virologic response that were superior to those with standard treatment with sofosbuvir-ribavirin. (Funded by Gilead Sciences; ASTRAL-2 ClinicalTrials. gov number, NCT02220998; and ASTRAL-3, NCT02201953.
Study Assessments For the two trials, screening assessments included measurement of serum HCV RNA levels and IL28B genotyping in addition to standard laboratory and clinical testing. Serum HCV RNA was measured with the use of the COBAS AmpliPrep/ COBAS TaqMan HCV Quantitative Test, version 2. 0 (Roche Molecular Systems), with a lower limit of quantification of 15 IU per milliliter. The HCV genotype and subtype were determined with the use of the VERSANT HCV Genotype 2. 0 Assay (Siemens). For patients for whom genotyping data could not be provided with the VERSANT assay, the TRUGENE HCV 5′NC Genotyping Kit was used. If genotyping with the TRUGENE test was unsuccessful, NS5B sequencing was performed. IL28B genotyping was performed by means of polymerase-chain-reaction amplification and sequencing of the rs12979860 single-nucleotide polymorphism.
Simulation of background and signal events Monte Carlo (MC) simulations of signal and background processes are used to optimize selection criteria, validate analysis performance, determine signal efficiencies, and determine some backgrounds and systematic uncertainties. To simulate these samples, we use the MADGRAPH 5. 1. 3. 30 [34]  leading-order (LO) event generator unless otherwise noted. The PYTHIA 6. 426  [35]  event generator with CTEQ6L1  [36]  parton distribution functions (PDF) and parameters based on measurements from the LHC run at √ s = 7 TeV is used to describe parton showering, hadronization, multiple-parton interactions, and the underlying event for MADGRAPH 5 samples. A full simulation of the CMS detector based on the GEANT4  [37]  package is applied to all samples. Each event is superimposed with a set of simulated minimum bias events to reproduce the effect of pileup.
(6. 1). For definiteness, we assume a normal hierarchy. The running of the neutrino mass matrix up to the triplet mass scale M ∆ is performed using the Mathematica package REAP  [53]. For a hierarchical neutrino spectrum, the only effect of running is to multiply the eigenvalues of the neutrino mass matrix by a common factor r  [54] , which for M ∆ around 10 9 -10 12 GeV lies between 1. 2 and 1. 4. We therefore define the squared mass differences as ∆m 2  21 = r 2 ∆m 2 sun and ∆m 2  31 = r 2 ∆m 2 atm , where ∆m 2 sun and ∆m 2 atm are the parameters extracted from oscillation experiments, and set the lightest eigenvalue m 1 = 10 -3 eV at the scale M ∆ (which corresponds to a lightest neutrino mass in the range (0. 7 -0. 8) × 10 -3 eV). For the oscillations parameters, we take ∆m 2 sun = 7. 59 × 10 -5 eV 2 , ∆m 2 atm = 2.
Acknowledgments We thank  Thomas Hambye  for useful discussions. This work has been supported in part by the  Agence Nationale de la Recherche  under contract  ANR 2010 BLANC 0413 01 , by the  European Research Council (ERC)  Advanced Grant Higgs@LHC, and by the  European Union   FP7 ITN Invisibles (Marie Curie Actions ,  PITN-GA-2011-289442 ).
Acknowledgements D. C. R. , S. A. J. , A. M. , J. deV. , and D. P. O. were supported by the  European Research Council (ERC) Advanced Grant "ACCRETE"  (contract number  290568 ). D. P. O. was also supported by grant  NNX09AE36G  from  NASA 's  Planetary Geology and Geophysics research program. F. N. acknowledges support by  NASA  Origins  NNX11AK60G. We thank  John Hernlund  for discussions and two anonymous reviewers for constructive and helpful criticisms.
8). This allowed the generation of one scaffold with 10 gaps, from 28 bp to 3,271 bp in size. Some gaps were resolved by Sanger sequencing of PCR amplicons. At the end, the genome sequence of D. dianthicola strain RNS04. 9 revealed a circular chromosome consisting of 4,721,506 bp and comprised 7 contigs. No plasmid was detected. The GϩC content was ~56%. Gene prediction using the RAST version 4. 0 automated pipeline  (22, 23)  revealed the presence of 4,351 coding sequences and 97 RNA-assimilated regions. These features are in accordance with other data of the Dickeya spp. genomes and draft genomes that are available in public databases. Nucleotide sequence accession numbers. This draft genome sequence has been deposited at DDBJ/EMBL/GenBank under the accession number APVF00000000. The version described in this paper is the first version, APVF01000000.
ACKNOWLEDGMENTS We thank the  Centre national de la recherche scientifique (CNRS, France) ,  Saclay Plant Sciences LABEX  ( ANR-10-LABX-0040-SPS  and  ANR-11-IDEX-0003-02 ), the  Fédération Nationale des Producteurs de Plants de Pomme de Terre  ( FN3PT/RD3PT ), and the  Association Nationale de la Recherche et de la Technologie  ( ANRT-CIFRE no. 1282/2011 ) for their financial support. Y. R. D. E. also thanks  Yves Le Hingrat  ( FN3PT ) and  Yves Dessaux  ( CNRS ) for editing.
Two-photon imaging and optogenetics Two-photon imaging and electrophysiology recordings were simultaneously performed using a custom-built microscope operated by a custom-written IGOR Pro 6 program (WaveMetrics)  (Wang et al. 2015). To minimize the Ca 2+ signal variances resulting from the different location of synapses and loading time of indicators  (Sabatini and Svoboda 2000; Yasuda et al. 2003) , neighboring expressing and nonexpressing CA1 neuron pairs were broken in simultaneously to load 200 μM green calcium-sensitive indicator Fluo-5F and 20 μM red calcium-insensitive indicator Alexa 594. After ∼15-30 min of loading of indicators, fluorescence of nearby spine pairs of neighboring expressing and nonexpressing CA1 neuron pairs was simultaneously imaged with 500-Hz line scanning that intersected both the spines and their parent dendrites.
Acknowledgments We thank  Dr. Roberto Malinow ,  Dr. Bernardo Sabatini ,  Dr. Karel Svoboda , and  Dr. Robert Wong  for technical advice and invaluable discussions, and members of the  Zhu laboratory  for comments and technical assistance. J. J. Z conceived the project. G. W. , G. B. , Y. C. , K. A. S. , P. Z. , R. L. S. , and J. J. Z. performed the experiments in the  Zhu and Beenhakker laboratories , which are supported in part by  National Institutes of Health  grants  R01NS053570  (to J. J. Z. ) and  R01NS091452  (to J. J. Z. , J. K. , and M. P. B. ). S. J. D. , E. P. -R. , T. P. S. , K. D. , S. M. T. , and J. -H. L. provided reagents, and J. J. Z. supervised the project with input and assistance from A. E. , R. L. S. , S. M. T. , J. K. , and  M. P. B. Additional  support to the project is from a post-doctoral fellowship (no.
Methods This prospective, interventional study was approved by the appropriate Institutional Review Board (Comité de Protection des Personnes Sud-Est VI, Clermont-Ferrand, France; NCT02202720) and conducted in a 16-bed ICU. For each patient, the sevoflurane MAC were increased to 0. 1 MAC every 30 minutes from MAC 0 until MAC 0. 8 then reduced with the same steps. Sevoflurane was administered with the Mirus TM system. RASS was evaluated after 15 min of stability after changing the MAC. Statistical analysis was performed using STATA, p < 0. 05 was considered significant.
Electrophysiological recordings Slices were transferred into a recording chamber mounted on an upright microscope (Axioskop FS, Zeiss, Marly le Roi, France) and perfused with oxygenated ACSF (4 mL/ min) at 30 AE 1°C. Neurons were visualized using a 409 objective and a Hamamatsu "Orca Flash 4. 0" camera. Measurements were performed with an RK 400 amplifier  (BioLogic, Claix, France). The data were acquired with a sampling frequency of 25 kHz on a PC-Pentium D computer using a 12-bit A/D-D/A converter (Digidata 1440A, Axon Instruments, Union City, GA) and PClamp10 software (Axon Instruments). The junction potential was corrected offline. Patch-clamp configurations were achieved with borosilicate pipettes (o. d. : 1. 5 mm; i. d. : 1. 17 mm; Clark Electromedical Instruments, Edenbridge, UK). The recording pipette was filled with the following intracellular solution (131 mmol/L K-gluconate, 10 mmol/L HEPES, 1 mmol/L EGTA, 1 mmol/L MgCl 2 , 2 mmol/L ATP-Na 2 , 0.
Ca 2+ imaging Real-time Ca 2+ imaging was performed on MC soma using an epifluorescence microscope (Zeiss axioscope) with a 409 objective (Zeiss Plan-APOCHROMAT). Ca 2+induced fluorescence was detected with excitation (470/ 40 nm) and emission (dichroic mirror: 495; 525/50 nm) band pass filters (Zeiss filter set 38 HE). The illumination was produced by a white LED (Dual Port OptoLED, CAIRN, Faversham, UK) using the same illumination power for the different samples. Pictures were captured with a digital CCD camera (ORCA Flash 4. 0, Hamamatsu Photonics, Maccy, France). Frames for time-lapse imaging were acquired (every 20 msec) using HCimage software (Hamamatsu Photonics, Massy, France) and analyzed using ImageJ software (NIH, Bethesda, MD). The Ca 2+ probes Fura-2 (200 lmol/L) or Fura2-FF (400 lmol/L) were dissolved in the intracellular medium.
After passing in whole-cell configuration, 10 (Fura2) or 20 min (Fura2-FF) was allowed to pass before image acquisition. The DF/F was calculated as follows: The basal fluorescence (F bas ) was obtained by averaging the neuronal fluorescence intensity of the 500 msec preceding MC intracellular stimulation. The frame fluorescence (F fr ) was the neuronal fluorescence intensity of the frame. Therefore, DF/F = (F fr À F bas )/F fr. The data are expressed as the mean AE SEM.
Data analysis Data analysis was performed using OpenElectrophy (Garcia and Fourcaud-Trocm e 2009), SciPy, and MySql database software (open source licenses). All single-traces were visually inspected to eliminate abrupt Vm modifications contaminating the signal. To reduce the effect produced by the spontaneous modification of the resting Vm on the AHP (i. e. , due to the modification of the driving forces), all the traces for which the Vrest was not in the range from À64 to À62 mV were excluded from the analysis. For the AHP measurements, the baseline, which was calculated as the median of the 5 msec preceding the first step, was subtracted from each trace. Then, the AHPs were aligned on the crossing zero of the AP repolarizing phase and averaged (8-15 traces). The AHP area was calculated as the area between the baseline and the time to which the AHP returned to 10% of the AHP peak.
The different components of the AHP were calculated by offline subtraction of the average signals obtained in the different conditions (control, GBZ, and GBZ+NBQX+APV). The Spike timing analysis was performed by calculating the latency of the action potential peak from the beginning of the current step injected to generate the spike. An average of 8-15 measurements was taken as representative of the latency for each condition. Unless otherwise specified, data are expressed as the average AE SEM. Statistical comparisons were performed using various parametric and nonparametric tests, depending on the normality of value distributions as follows: the Mann-Whitney test for independent samples, the Wilcoxon signed-rank test for paired samples, paired or unpaired Student's t-test and the Friedman test for multiple comparisons.
Objectives: The DIANA project aimed to assess the impact of a course on PEF measurement among primary care physicians in Spain. Methods: A 7-item questionnaire was sent to selected primary care physicians (Phase A). Respondents were then invited to take a web-based course on PEF in asthma diagnosis. Finally, the questionnaire was again sent to all physicians (Phase B). Questionnaires also asked for demographical data such as age, sex, speciality, route of access to speciality, and geographical area. A comparative statistical analysis was performed on the results of both questionnaires. An extended analysis was performed later. Answers were analysed by percentages and using McNemar's test. The planned duration of the project was one year.
Respondents who accessed their specialization through the MIR system answered better (data not shown). When participation in Phases A and B was compared, participants in both phases were younger (median age 47 years) than those who only answered the Phase A questionnaire (median age 50 years) (p<0. 05). There was no difference by gender. In contrast, 87. 8% of participants in both phases were Community and Family Medicine specialists vs. 78. 5% in Phase A (p<0. 05). However, there were no significant differences by age, sex or speciality between those who took the PEF course and those who did not. Changes in answers between Phases A and B were also analysed to establish the impact of PEF course (data not shown). There were some noteworthy findings. In item 3 (usefulness of PEF measurement), 38 respondents (34 of them having taken the course) changed their answer to Maximum.