dataesr/scientific-paragraphs-categorization huggingface dataset:
Cross-validation was insured by use of two independent datasets of 200 frames/se for the development and validation phases, respectively. Establishment of a threshold of bubble abundance for which visualization of the mucosa is significantly impaired is a challenging task. A previous grading system used in three trials was deemed clinically relevant: images with no intraluminal bubble (grade 0) or few gas bubbles (grade 1) were considered as providing no limitation of interpretation  [8, 9, 13]. Based on the figures from these articles and on our clinical experience, we determined that a cutoff of 10 % in terms of bubble abundance on a still frame was adequate. Similarly, the only validated score used to determine the quality of visualization of the mucosa in SB-CE also considers that a visibility over 90 % is optimal  [16, 17].
Conclusion In conclusion, this study showed that a computed algorithm based on the GLCM detector strategy has a perfect reproducibility, a high diagnostic sensitivity (95. 79 %) and specificity (95. 19 %), and is a rapid method of analysis (0. 037 seconds per frame), for assessment of the abundance of bubbles on SB-VCE still frames. It proved to be a powerful tool to differentiate still frames with a low amount of bubbles from those with more than 10 % bubbles. This algorithm could be implemented in SB-CE reading software and used automatically for evaluation of anti-bubble agents. In the future, we aim to develop a computed SB-CE cleaning score with the help of this algorithm. Such a score would be of great interest in the fields of clinical practice and research.
The P values are indicated only when significant (P Ͻ 0. 05). genomes, we identified 4,044 full or partial open reading frames (ORFs) that were classified as var genes using BLAST against a database of classified DBL and CIDR domains (mean number of distinct PfEMP1s per genome ϭ 32 [range: 1 to 60]; mean coverage ϭ 33 reads [range: 8 to 124]) (see Table  S3  in the supplemental material). Of those, 117 genomes contained 1,505 DBL␤ domains with a mean coverage of 35 reads distributed among 1,420 var genes (i. e. , many var genes had multiple DBL␤ domains). For the 8 PNG genomes without DBL␤ domains, 6 had low coverage, resulting in poor sampling of var genes (n ϭ 1 to 6), while 2 isolates had higher coverage and contained 12 and 21 var genes. Among 1,505 PNG DBL␤ sequences (see Table  S3  and Data Set S1 in the supplemental material), 81 contained the ICAM1-binding motif  (21).
4 PFL1955w codon-optimized sequences were synthesized for Escherichia coli expression (GeneArt). The GenBank accession numbers are PF13_0003 (XM_001349704) and PFL1955w (XM_001350761). Sequences were excised from the supplier's vector using BamHI and XhoI and ligated into the pProExHTb expression vector (Invitrogen), which incorporates an N-terminal hexahistidine fusion tag. The vectors were then transformed into E. coli strain BL21(DE3) for expression, as described previously  (37). Briefly, the transformed cultures were grown in superbroth, expression was induced with 1 mm isopropyl 1-thio-␤-D-galactopyranoside, and the cultures were grown for a further 3 h at 37°C. The cells were harvested by centrifugation, lysed by sonication, and processed as either insoluble inclusion bodies (NTS-DBL␣1.
After washing, the samples were resuspended in diluent buffer containing PE (BD Bioscience) and acquired using an LSR Fortessa analyzer (Becton Dickinson, New Jersey, USA). Analysis was performed using FlowJo software, and the median fluorescence intensity (MFI) for each bead (recombinant protein) was calculated. Background (determined from the unconjugated beads with plasma samples and conjugated beads with no plasma samples) was deducted from the mean of each sample. The threshold for a seropositive response was determined using reactivities of 1:100-diluted plasma samples from anonymous malaria-naive Australian adults (n ϭ 12). The mean value among these negative-control plasma samples plus 3 SD was considered seropositive. The analysis was done independently for each antigen. A serial dilution of plasma samples from a pool of hyperimmune PNG adults was included in each plate to determine standard curves, which were later fitted using a 5-parameter logistic regression model  (39)  to transform antibody measured by the two assays into relative antibody units and to correct plate-to-plate variations within an assay.
Statistical analysis. Statistical analyses were performed using STATA version 12. 1 software (Stata Corporation, USA). Differences in median antibody levels by age group and P. falciparum infection status were compared using the Wilcoxon rank sum test. The proportions of children seropositive to different domains were compared using chi-square tests. Correlation coefficients for antibody levels were determined using Pearson's correlation. Analyses of the cohort data showed significant overdispersion in the number of clinical episodes per child  (25) , and as a result, a negative binomial model with generalized estimating equations (GEE) (based on the xtnberg function in STATA) with an exchangeable correlation structure and a semirobust variance estimator was used for the analyses of the association of antibody levels and the incidence of clinical (fever with Ն2,500 parasites/l) and high-density clinical (febrile illness and Ն10,000 parasites/l) episodes during the follow-up period.
Antibody levels were grouped into terciles (low, medium, and high responses), and their association with clinical and high-density clinical episodes was assessed by univariate analyses adjusted for seasonal variation, village of residence, age at the time of enrollment, P. falciparum infection status, and individual exposure, as measured by the mol FOB. The mol FOB is the number of genetically distinct P. falciparum clones (based on msp2 genotyping) each child acquired per year at risk  (26). Sequence analyses. To identify ICAM1-binding DBL␤ domains and corresponding full-length PfEMP1 sequences in the PNG parasite population, we extracted var gene sequences from the genomes of 125 clinical P. falciparum isolates collected from three distinct geographic areas of PNG. These isolates were sequenced as part of the MalariaGEN Community Project (European Nucleotide Archive [ENA] accession numbers are listed in Table  S3  in the supplemental material).
ACKNOWLEDGMENTS We thank all participants in the study and their parents or guardians, and staff involved in the study at the  Papua New Guinea Institute of Medical Research. This research was supported by the  National Health and Medical Research Council of Australia  ( NHMRC grant  numbers  GNT1005653  and  GNT1027109  to A. E. B. ) and the  Danish Council for Independent Research  ( DFF-4004-00624B ). Production of  DBL␤3 PF11_0521  protein was supported by a  U. S. National Institutes of Health  grant  R01AI092120  to A. V. O. I. M. is supported by an  NHMRC   Senior Research Fellowship. The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
3. We will focus on the interpretation of data for MoSe 2 and WS 2 materials, considering them as representatives of 'bright' and 'darkish' family. The CX resonance in WSe 2 monolayer is very weak and broad in our samples, making it difficult to analyze and interpret the data unambiguously. In the absorption process leading to creation of CX, there is a single electron in the initial state, which at low temperature occupies the lower energy conduction band state. In such case, thermal redistribution of the occupation of this individual electronic state leads to polarization of the CX absorption resonance at higher magnetic fields. The rate of the polarization degree increase is directly indicative of the g-factor value corresponding to this individual state. In Boltzmann approximation to Fermi-Dirac statistics, which is valid if the thermal energy is larger than Fermi energy (() ≫ + ), i.
The reflectivity contrast was obtained by measuring the spectra on two locations: on the flake and on the nearby Si/SiO 2 substrate region, then calculated as: ^( ) = ^_`\aZ ( ) -^bcdbY[\YZ ( ) ^_`\aZ ( ) + ^bcdbY[\YZ ( ) The reflectivity spectra were reproduced by using a transfer matrix method including Lorentzian contributions to account for resonances observed in the experimental spectra. The data were fitted with such phenomenological curves to establish the energy and oscillator strength of transitions separately in spectra measured in / polarizations. In the first case, it is assumed that valley and spin terms are the same for MoSe 2 and WS 2 materials. In the second case, the spin term is fixed to the value of the free electron in vacuum (g S = 1). Independently of the approach, the valley term is found to provide a significant contribution to the energy of individual states and its value can be estimated to be g V = 1.
Acknowledgements We kindly thank  J. Marcus  for providing a piece of WSe 2 crystal used and acknowledge helpful discussions with  A. Slobodeniuk  and  D. Basko. The authors acknowledge the support from the  European Research Council  ( MOMB  project No. 320590 ), the  EC Graphene Flagship project  (No. 604391 ) and the  ATOMOPTO  project (TEAM programme of the Foundation for Polish Science cofinanced by the  EU  within the ERDFund). The support of  LNCMI-CNRS , a member of the  European Magnetic Field Laboratory  is also acknowledged. The authors of this manuscript declare no competing financial interest.
Immunohistochemistry. IFP sections In vivo treatments. In vivo ROS imaging. Mice were briefly anaesthetized by inhalation of isoflurane and i. p. injected with 5 mg of luminol (5-amnio-2,3-dihydro-1,4-phtalazinedione, A4685, Sigma Aldrich, Saint Louis, MO, USA) in 100 µl of PBS. The animals' bioluminescence was imaged using an IVIS Spectrum 200 (Caliper Life Science, Hopkinton, MA, USA) for 2 min exposures at different times after luminol injection. Image analyses were performed using LivingImage 3. 0 Software (Caliper Life Science, Hopkinton, MA, USA). The images were colour intensity calibrated from 30 (min) to 330 (max). For each animal, the sham surgery area signal was subtracted from the resected area photon flux. In zebrafish, 2′,7′-dichlorodihydrofluorescein diacetate (H2DCFDA, Calbiochem, San Diego, CA, USA) was used to monitor the accumulation of ROS in adult zebrafish fins.
Fluorescent DCF was formed through ROS oxidation. Zebrafish were incubated with H2DCFDA (50 µM) 2 h prior to confocal imaging. Spinning-disk images were acquired using a 4×/0. 15 N. A. objective on a Nikon Eclipse Ti microscope equipped with a CoolSnap HQ2/CCD camera (Princeton Instruments, Trenton, NJ, USA) and a CSUX1-A1 (Yokogawa) confocal scanner. MetaMorph software (Molecular Devices, Sunnyvale, CA, USA) was used to collect the data. Fluorescence was excited with a 491 nm laser and detected with a 525/39 nm filter. Fluorescence intensity was quantified using ImageJ software. Cell sorting and in vitro ROS quantification. Stromal vascular fraction was prepared from IFP as described by Planat et al. 34  and cells were incubated with 10 µL of anti-CD45 microbeads (Miltenyi Biotec) before magnetic sorting using MACSQuant Tyto (Miltenyi Biotec).
PENK relative gene expression was determined using the ∆∆CT method and normalized to 36B4 level. Primer sequences: Statistical analyses. Studies were not randomized and investigators were blinded to analyses. All results are given as means ± SEM. Data were analysed using an ANOVA test (when there were more than 2 groups) and variance between groups was compared. Statistical differences were measured using an unpaired two-sided Student's-t-test, or a nonparametric test (Mann-Whitney) when variances between groups were different. All statistical analyses were performed in GraphPad Prism 5. 0 software and a two-tailed P value with 95% confidence interval was acquired. Forward primer Reverse primer.
Acknowledgements The authors thank i) the  US006/CREFRE INSERM/UPS  (Toulouse, France), and specifically the animal husbandry facility, for animal care and surgical investigation, and ii) the  Institut des Techniques Avancees du Vivant (ITAV ,  USR3505 ) for tissue imaging. The authors are grateful to  X. Sudre ,  S. Gandarillas  and  Y. Barreira  for animal care,  H. Lulka  for help with luminometer,  C. De Vecchi  for technical assistance,  J. Rouquette  for imaging assistance,  N. Espagnolle  and  A. Varin  for help in cell sorting and  C. Sengenes  for insightful discussions. This work was financially supported through grants from the  EU   FP7  project  DIABAT  ( Health-F2-2011-278373 ), the  Bettencourt Schueller Foundation  and the  Midi-Pyrénées region  ( DESR/12052900  and  DESR/14050455 ).
In addition to that, we shall observe whether the water fraction values of the compartments for the two regions are in confirmation with the pathological knowledge of MS lesions. July 4, 2018 5/14 Patient Data We studied 10 MS patients over a period of 36 months. All patients included in this study had an episode of clinically isolated syndrome (CIS). The patient cohort comprised of an equal number of male and female subjects and their median age was 28 years. All participants of this study gave their written consent. Data was acquired at eight time points over a period of 36 months. An acquisition at the baseline was followed by acquisitions at 3, 6, 9, 12, 18, 24 and 36 months from the baseline. The lesions in patient scans were marked by an expert radiologist on T 2 weighted images at the baseline.
Data collection We identified all articles available up to May 2015 from the Web of Science and Science Direct reporting demographic traits (mortality and reproductive rates) in grey partridge, black grouse, capercaillie and brown hare. These articles were collected through a systematic search that included key-words related to demographic traits (e. g. survival, mortality, reproduction) and names of species. Articles on wild rabbit (Oryctolagus cuniculus), pheasant (Phasianus colchicus), red-legged partridge (Alectoris rufa), hazel grouse (Tetrastes bonasia) and rock ptarmigan (Lagopus muta) were not considered here as they were too rare to allow statistical analyses on the variation of estimates of demographic parameters with time. For a few studies, data were not directly accessible (e.
g. studies in non-English languages) but were available from scientific reviews or comparative studies. Data were not considered when: 1) the estimation value revealed confounding factors (e. g. when estimates of winter mortality from counts showed a 'negative' mortality, meaning that the number of migrants was greater than the number of deaths and emigrants); and 2) data were missing for several factors that we wanted to test (e. g. the year in which rates were estimated) or control for (e. g. the country where the study was performed). Some data sets can be found in several articles (e. g. the Game and Wildlife Conser-vation Trust's Count Scheme in England); these were therefore gathered only once to avoid double counting and were completed when additional information was available from a different article with the same data set.
When data were presented as averages over several years, special attention was paid to using the raw data whenever possible. From all indicators of mortality rates that were used in the literature, we extracted an individual´s probability of dying during the monitoring period considered in the study. Back-transformation from partial estimates (e. g. for data presented in a fragmented format linked to predation) to overall mortality was carried out when possible (i. e. when the total population size was given) (discarded otherwise). Similarly, several reproductive traits were reported in the literature, including clutch and brood size, the proportion of nests in which at least one egg hatched or in which at least one young survived, the proportion of females with a nest or with young, the probability of re-nesting, the number of chicks, young or fledglings per hen, per adult, or per couple.
The estimates of reproductive parameters are presented as rates (e. g. proportion of breeding hens) or real numbers (e. g. brood size, clutch size). We studied the variation in mortality rates and reproduction through the post-hatching brood size, the number of fledglings per hen, and the proportion of hens with fledglings; this provided enough data from the literature to run statistical analyses. Finally, we noted the year and season of the study. For studies exceeding one year and presenting pooled data, the median year was considered. We dealt with the marked heterogeneity in the monitoring periods by considering three classes: (1) one season or less; (2) from one season to less than one year; and (3) one year or more. To control for potentially confounding effects, we also noted the age, sex and origin (reared or wild) of the studied individuals, the monitoring method, and the country of the study, although a detailed presentation of their effects is beyond the scope of this study.
Grey partridge For grey partridge we collected data for mortality rates from 30 papers and data for reproductive traits from 26 papers. The lowest mortality rate was 0. 012 (in a short monitoring period;  Kaiser, 1998)  while the highest rate was 0. 99 (in a long monitoring period;  Buner et al. , 2011). Variation in reproduction with time was analysed using post-hatching brood size, which ranged from 0. 66 to 20. 00  (Rands, 1985; Rymešová et al. , 2013) , and the proportion of hens with fledglings, which ranged from 0. 17 to 0. 66  (Buner et al. , 2011).
, 2013). Both monitoring techniques have a different bias, but radio-collars have mainly been used since the 1980s, implying a possible shift in bias over time  (Barron et al. , 2010; Naef-Daenzer and Grüebler 2014). Miniaturisation in biotelemetry is expected to provide more accurate estimates of demographic traits in future studies that will use lighter transmitters (< 3 % of the bird's weight)  (Casas et al. , 2015). Concerning reproductive traits, the number of fledglings per female is reported heterogeneously across the literature (chicks almost old enough to fly and young), which might also involve a bias. Data on mortality and reproduction in four small game species including wild rabbit, hazel grouse, pheasant and red-legged partridge are rare and thus prevent robust statistical analyses.
Conclusion The present study suggests that data from demographic parameters (mortality and reproductive traits) extracted from published articles might be used to investigate population trends with time. The effects of age, sex, origin of birds, season, country and method on demographic traits should encourage further studies to consider these factors in their experimental design to avoid misleading findings regarding potential patterns. For instance, methodological issues might arise from animal equipment that would affect survival and reproduction rate. Similar comments can be addressed for the effect of the monitoring period, particularly when investigating mortality rates. Although it is not the case in capercaillie and brown hare, our study seems to support the overall decrease that has been reported in grey partridge and black grouse during the last decades.
Funding: This research was funded by  Silesian University of Technology  grant number  BK235/RB6/2017. Acknowledgments: The authors acknowledge the  European Union  for financing the development of intelligent textile sensor (Project  251373 FP7-PEOPLE-2009 - IAPP-Intelligent Systems for Structures Strengthening and Monitoring INSYSM ) and by the  Polish Ministry of Science and Higher Education  (Grant No. BK-235/RB6/2017  and  BK-237/RB6/2018 ). Authors acknowledge also  FISIPE Synthetic Fiber SA, Portugal and S&P Reinforcement Poland  for the supply of carbon fibers.
Statistical analysis The mean, standard deviation, one-way analysis of variance (ANOVA), principal components analysis (PCA) and correlation analysis were calculated using Microsoft Excel and SPSS 21. 0. Over the study, plant growth rate, nutrient removal efficiency, nutrient removal rate and enzyme activity under different hydraulic operating regimes were analyzed by ANOVA for LSD tests. The statistical analysis was considered significant below 0. 05 (p < 0. 05). In the experiment, various parameters could change widely even with similar flow conditions. Hence, in order to understand better the effects of different flow regimes, PCA was used as a multivariate data reduction technique to generate scores representing trends observed between simultaneously-measured indicators  (Turnbull et al.
The park's surface (ca. 270 000 ha) was divided into 100x100m grid pixels. In a pixel, PFG population dynamics are dependent on PFG demographic parameters, their ability to tolerate shade and the pixel's habitat suitability. The amount of shade depends on the size and abundance of PFGs, which can occupy up to 5 vertical strata (see Table A in S3 Appendix) depending on their maximum height. The taller and more abundant a PFG becomes, the more shade it casts on smaller PFGs. Habitat suitability affects seed production and recruitment, and was calculated for each PFG using a species distribution modelling approach (R package biomod2; Thuiller et al. [27] ), with slope, percentage of calcareous soil and five bioclimatic variables as predictors (isothermality, temperature seasonality, temperature annual range, mean temperature of coldest quarter and annual precipitation).
Acknowledgments We thank  Drs. J. Levine  and  F. Jabot  for their useful comments on earlier versions of the manuscript. Research leading to these results received funding from the  European Research Council  ( ERC-2011-StG-281422-TEEMBIO ) and the  French National Research Agency  in the framework of the  Investissements d'avenir program  ( ANR-15-IDEX-02 ,  CDP-Trajectories  project).
Research leading to these results received funding from the  European Research Council  ( ERC-2011-StG-281422-TEEMBIO ) and the  French National Research Agency (Agence Nationale de la Recherche)  in the framework of the  Investissements d'avenir program  ( ANR-15-IDEX-02 ,  CDP-Trajectories  project). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Cells were then infected by exposed viruses and cell impedance, expressed as an arbitrary unit called the cell index (CI), was measured through the electrodes every 15 min. CI decrease due to virus-induced cytopathogenic effect was quantified with the CIT 50 value, which is the necessary time in hours to measure a 50% decrease from the initial CI, always set as the CI value 5 h after infection. CIT 50 values are linearly correlated to the TCID 50 titers of the viral suspensions  (Fang et al. , 2011)  (Supplementary Figure  S4 ). Thus, the increase of the CIT 50 values over time reflects the loss of infectivity. For each exposed viral suspension, CIT 50 values were obtained at different exposure times and plotted to calculate a linear regression slope referred to as the inactivation slope. All data shown on viral persistence have been obtained at different periods and with different viral stock productions.
Statistical Analyses and Software Numerical data were analyzed with Prism software version 6. 07 (Graph Pad Software). If needed, a Grubb's test was performed to identify and remove outliers. ANOVA tests were performed for statistical comparison when variances were equal across samples (Bartlett's test). Otherwise a two-tailed, Wilcoxon-Mann-Whitney test, was used to compare samples distribution. DNA sequence alignments and Sanger sequencing analysis were performed using CLC Main Workbench version 7. 7. 3 (Qiagen). Hemagglutinin structure was visualized using the PyMOL Molecular Graphics system version 1. 8 (Schrodinger, LLC). Microscopy imaging data were processed using LSM software Zen Blue edition version 2. 3 (Zeiss) and flow cytometry data were analyzed with FlowJo (LLC) software. Viruses, Institut Pasteur, Paris) for providing reagents and advices.