dataesr/scientific-paragraphs-categorization huggingface dataset:
Statistical Analyses FVJ consumers were defined as those CCAF participants who listed FVJ at least once in the seven-day diet history. Analyzes of FVJ consumption were conducted separately for children and adults. Additional strata were based on gender (male, female) and socioeconomic status (SES), as assessed by occupation or education of head of household. Data were reported as means and standard errors and/ or medians and percentiles. The statistical significance level was set at p < 0. 05. Differences in dietary nutrient density between FVJ consumers and non-consumers of FVJ were tested using the generalized linear model (PROC GLM). Quartile analysis of NRF scores, based on amounts of FVJ consumption was also carried out. Multiple regression was carried out to explore potential association between amounts of FVJ consumed and NRF9.
The data are presented separately for children and adults. As noted above, percent daily values and NRF scores calculated for each CCAF participant were adjusted for age and gender. FVJ consumers had significantly higher total NRF9. 3 scores than did non-consumers. Nutrient-by-nutrient analyses showed that FVJ consumers had diets that were significantly higher in vitamin C, vitamin E, calcium and potassium compared to non-consumers. Among children, FVJ consumers had diets that were also higher in fiber, vitamin A, and magnesium, as compared to diets of non-consumers. FVJ consumption was not associated with differences in saturated fat but the diets of FVJ consumers were higher in sodium and free sugars. Persons identified as FVJ consumers consumed more total servings of fruit and vegetables per day.
Calculations of the LIM and NRF scores were also performed using added sugars. The data are presented separately for children and adults. As noted above, percent daily values and NRF scores calculated for each CCAF participant were adjusted for age and gender. FVJ consumers had significantly higher total NRF9. 3 scores than did non-consumers. Nutrient-by-nutrient analyses showed that FVJ consumers had diets that were significantly higher in vitamin C, vitamin E, calcium and potassium compared to non-consumers. Among children, FVJ consumers had diets that were also higher in fiber, vitamin A, and magnesium, as compared to diets of non-consumers. FVJ consumption was not associated with differences in saturated fat but the diets of FVJ consumers were higher in sodium and free sugars. Figure  2  shows a positive dose-response relation between quartiles of FVJ intake and NRF values.
Mean FVJ consumption was estimated at only 0. 4 daily servings for children and 0. 3 servings for adults. The data also showed that almost 30% of children and 50% of adults did not consume any FVJ at all. Only one in 10 children and one in 14 adults consumed one glass (200 mL) or more of FVJ per day. These shortfalls in fruit and in FVJ consumption were larger than expected. However, the French data were largely consistent with previously reported results for the US [13], there too, whole fruit provided about 65% of total fruit consumption, while 100% juice provided about 35%. Whereas whole fruit consumption was higher among those with higher incomes or more education, juice was more likely to be consumed by children, minorities and lower-income groups. In both countries, FVJ consumption was well below the recommended norms.
The relation was largely driven by vitamin C, although other NRF index nutrients also contributed. The study had some limitations. First, dietary intake data for younger children in the CCAF were provided by the caregiver. Second, the sample was insufficient to permit detailed analyses of whole fruit and FVJ consumption by age group and SES. Third, data on household SES were provided by self-reports. The study also had strengths. Data of the CCAF study have been collected recently and are representative of current food intakes. The CIQUAL database was supplemented with added or free sugars, obtained from the updated Nutrient database.
Cluster participants were aged from 2 to 40 y and lived in villages located within 30 km from the provincial hospital (SI Appendix, Fig. S2 ). Cluster participants or representative for the participants under 16 y of age provided a written informed consent before enrollment. Exclusion criteria were as follows: (i) pregnancy or breastfeeding; (ii) symptoms inconsistent with dengue and obvious nondengue acute infection (e. g. , otitis media, pneumonia, meningitis); or (iii) known chronic illness. Clinical Data and Blood Collection. DICs and cluster participants were examined during sequential visits as shown in SI Appendix, Figs. S3  and S4. At each visit, data were collected using a standardized questionnaire designed for either hospitalized patients or cluster participants. For hospitalized patients, three blood samples were collected: shortly after hospital admission during the febrile acute phase (visit 1), at the time of defervescence (visit 2), and during the convalescent phase at hospital discharge (visit 3), which in general corresponded to days 3-5 of hospitalization.
The severity of the disease was assessed according to the 1997 World Health Organization (WHO) criteria using clinical, biological, and paraclinical examination data recorded at admission and throughout the entire hospitalization period  (32). To screen cluster participants for DENV infection, home visits were conducted within 24 h after DIC identification [home visit 0 (HV0)] and then again at day 2 (HV2) and day 7 (HV7) during 2012. In 2013, only HV0 and then a visit 4 d later (HV4) were conducted (SI Appendix, Fig. S4 ). Blood samples drawn during visits were sent with ice packs to IPC within 5-10 h for laboratory diagnosis. Blood samples were collected in tubes with EDTA anticoagulant, and volume drawn was adapted according to participant weight: 3. 0 mL for children below 20 kg of weight and 5.
03358976001) at 6,500 rpm for 50 s. Viral load in individual mosquito body parts was measured by qRT-PCR and the results expressed as cDNA copy number per milliliter of legs and wings suspension  (31). Statistical Analyses. All analyses were based on the final cohort of 181 infected human participants including 13 asymptomatic, 42 presymptomatic, and 126 symptomatic people. Analyses of mosquito infection data were performed separately for direct and indirect feeding methods. Detectable plasma viremia levels were log 10 -transformed and analyzed with an analysis of variance. The proportion of infected mosquitoes was analyzed as a function of the covariates using marginal logistic regression models. Dose-response curves and 50% mosquito infectious dose estimates were derived from the logistic regression coefficients.
ACKNOWLEDGMENTS. We express our gratitude to patients who were eagerly willing to participate in the study, particularly in the mosquito transmission experiments. We also acknowledge the staff of  Virology and Epidemiology Units at Institut Pasteur in Cambodia  for their technical support. We thank doctors and nurses of the three hospitals in Kampong Cham Province for their contribution in patients' enrollment, sample collection, and patience. We extend our thanks to our entomology assistants,  Mr. Neung Choueth  and  Mr. Chhin Deth , for their valuable assistance, and to all the team from the  Dengue National Control Program. We thank  A. Fontaine  and  S. Lequime  for assistance with the figures, and three anonymous reviewers for constructive comments that significantly improved the manuscript.
The research leading to these results received funding from the  European Union Seventh Framework Programme  ( FP7/2007/2011 ) under Grant Agreement  282 378. L. L. received funding from the  French Government 's  Investissement d'Avenir Program, Laboratoire d ' Excellence Integrative Biology of Emerging Infectious Diseases  (Grant  ANR-10-LABX-62-IBEID ), and from the  Emergence(s) Program of the City of Paris. T. W. S. was supported by the  Research and Policy for Infectious Disease Dynamics Program of the Science and Technology Directory, Department of Homeland Security , and  Fogarty International Center, National Institutes of Health (NIH). L. L. , K. C. L. , and T. W. S. received support from  NIH  Grant  1P01AI098670-01A1.
The amount of free 125 I is stable over 90 min and represents ~20%-25% of the protein-free plasma fraction of radioactivity and then increases up to ~58% at 180 min, indicating good 125 I-Tyr-MCa stability for 90 min. Single-photon emission computed tomography (SPECT) imaging and biodistribution studies are performed up to 60 min following injection in order to account for the increased deiodination observed thereafter. In this setting, the ~20%-25% of free 125 I detected in the protein-free plasma fraction of radioactivity correspond to ~4% of total blood activity since free 125 I is exclusively located in the protein-free plasma fraction as shown by results from TLC analysis (data not shown). 125 I-Lin-Tyr-MCa is degraded as early as 15 min of incubation with appearance of 11% ˘2% of a first iodinated metabolite ( 125 I-metabolite-1).
A second iodinated metabolite ( 125 I-metabolite-2) appears after 15 min of incubation which proportion increases to 4. 3% ˘1% at 120 min. Finally, a third iodinated metabolite ( 125 I-metabolite-3) appears at 180 min while the presence of 125 I-metabolite-1 and 125 I-metabolite-2 is concomitantly observed. The amount of free 125 I is stable (~30%) and 125 I-Lin-Tyr-MCa decreases to 31. 3% ˘6% after 180 min of incubation. Radioiodinated metabolites of 125 I-Lin-Tyr-MCa evidenced by in vitro experiments can interfere in vivo biodistribution and imaging studies. Accordingly, all subsequent in vivo tracer evaluations are performed using 125 I-Tyr-MCa only. Int. J. Mol. Sci. 2015, 16, page-page 4 correspond to ~4% of total blood activity since free 125 I is exclusively located in the protein-free plasma fraction as shown by results from TLC analysis (data not shown).
4 diameter. The scans were acquired sequentially using Nucline software (Mediso, Budapest, Hungary) at 15, 30, and 60 min post-tracer injection. The SPECT parameters were: 24 projections and 20 sec per projection. The CT was performed between the 30 and 60 min nuclear image acquisition at 45 keV. Reconstruction of scans was carried out using HiSPECT NG (Bioscan, Goettingen, Germany). CT and SPECT acquisitions were reconstructed, fused and quantified using dedicated software (InVivo Scope, Bioscan). SPECT scale, obtained in kBq/voxel, was converted into percentage of injected dose per cm 3 (%ID/cm 3 ) and set to similar levels to allow direct visual comparison. Regions of interest (ROIs) were drawn on the thyroid, liver, kidney, skeletal muscle, stomach, salivary gland, brain, heart, myocardial left ventricle (for blood activity determination) and bladder.
5-1% (v/v) concentration [data from CMGA]-against the MMC-induced genotoxicity in the CBMN assay. Two identical sets of the experiment were conducted for all aforementioned concentrations as well as for positive and negative controls. 24 h after culture initiation the appropriate volumes of chemicals were added and 20 h later Cyt-B was added at final concentration of 6 μg/ml in every culture. According to the scientific literature this concentration of Cyt-B has been proven best in the acquisition of a higher percentage of binucleated (BN) cells and a lower baseline MN frequency  [27]. The incubation of cultures took place in a humidified atmosphere of 5% CO 2 at 37°C. 72 h after the initiation of culture, cells were harvested and collected by centrifugation. 3:1 solution of Ham's medium and milli-q H 2 O was used as a mild hypotonic treatment and cells were left for 3 min at room temperature.
Statistical analysis All results of the CBMN assay are expressed as the mean frequency ± standard error (MF ± se). The G-test for independence on 2x2 tables was used to perform the statistical analysis of the MN data. The chi-square test (χ2 test) was used for the analysis of CBPI among each treatment. Differences at p < 0. 05 were considered significant. The statistical softwares used for data analysis were the Origin 7. 0 (OriginLab Corporation, Northampton, MA, USA), the Minitab statistical software (Minitab Inc. , PA, USA), and the Statistical Package for Social Sciences (SPSS) for Windows, version 17. 0. Statistical analysis of the data derived by the SMART assay was done using the multipledecision procedure  [37, 38]  which is based on the conditional binomial test and the chi-squared test (K.
3, f  and g ). Although no severe thromboembolic complications have been reported so far with oblimersen, side effects include pyrexia, hypotension, and thrombocytopenia. The reported thrombotic events were classified as catheter-related complications  (Advani et al. , 2011) , possibly related to drug dosing. The maximal plasma concentration of oblimersen, measured after 7 mg/kg continuous i. v. infusion, was 0. 84 ± 0. 6 µM  (Marcucci et al. , 2005). Our data show significant effects of ODN2395 in vitro in whole blood assays (Fig. 1 g ), as well as assays in vivo in mice treated to attain an ODN2395 plasma concentration of 1 µM (Fig. 3 a ). Antisense oligonucleotide plasma concentrations vary considerably between patients  (Marcucci et al. , 2005) , implying that plasma concentrations sufficient to cause platelet activation are attainable.
Br ief Definitive Repor t streptavidin-PE was used for samples preincubated with biotinylated ODN2395. After staining, blood samples were lysed with FACS lysing solution (BD), washed twice, and fixed with cell fix. For whole mouse blood experiments, blood was diluted 1:10 in PBS and stained with the appropriate antibodies, and platelets were gated according to size and positive staining for CD41. 10,000 events in the platelet gate were acquired for each sample. Flow cytometry of lysed blood samples was performed on a FACSCanto (BD), and 2,500 CD14 + events were acquired for each sample to evaluate PMA formation. Analysis was performed using CellQuest Pro for FACSCalibur measures and FACSDiva software for data acquired on FACSCanto (BD). Histogram overlays were generated using FlowJo 7. 6. 5 software.
The stimulation index represents the ratio of mean percentage of events within the gate region (M1) of the resting versus the agonist-treated sample. Modeling of potential ODN2395 interactions with GPVI. Poisson-Boltzmann electrostatics were calculated for the extracellular GPVI CBD dimer (PDB ID: 2GI7;  Horii et al. , 2006)  using the APBS Tools 2. 1 plugin for PyMOL v1. 6. 0. 0 (http://www. pymol. org). CRP (PDB ID: 1CAG) was manually docked into the collagen-binding site on D1 of a GPVI monomer using the collagen-binding residues identified from site-directed mutagenesis experiments  (Horii et al. , 2006)  as a guide. The rigid body docking was performed manually within SYBYL-X 2. 1 (Certara, L. P. ). The phosphodiester version of ODN2395 (ODN2395 nonmod) was constructed within SYBYL-X 2.
The sections were counterstained with Mayer's hematoxylin and examined using an Olympus BX50 microscope and image captured with MicroPublisher 3. 3 RTV digital camera (QIMAGING). For quantification, thrombi of 10 transverse cryosections (200 µm apart) of each lobe (left and right superior and right middle) were counted. Statistics. Data are presented as means ± SEM and were analyzed using two-tailed Student's t test or one-way ANOVA with a Tukey post-hoc test. P < 0. 05 was considered statistically significant.
, 2004; Tosca et al. , 2013]. The horizontal resolution of the model is 2. 8°× 2. 8°, with 31 vertical model levels between the surface and 10 hPa. Yearly varying, monthly mean fire emissions of SO 2 , BC, and POM were taken from the Global Fire Emissions Database (GFED3)  [van der Werf et al. , 2010]. The GFED3 emissions are derived using estimates of burnt area, active fire detections, and plant productivity from the Moderate Resolution Imaging Spectroradiometer (MODIS) instrument, combined with estimates of fuel loads and combustion completeness for each monthly time step from the Carnegie-Ames-Stanford-Approach (CASA) biogeochemical model  [van der Werf et al. , 2010]. The injection heights of the fire emissions were distributed in GLOMAP between the surface and 6 km  [Dentener et al. , 2006].
Acknowledgments Data can be made available upon request from the corresponding author. This research was funded by the  Natural Environment Research Council  ( NE/ J004723/1  and  NE/J009822/1 ). Data recorded in French Guiana benefited from an " Investissements d'Avenir " grant managed by  Agence Nationale de la Recherche  ( CEBA ANR-10-LABX-25-01 ). We thank researchers from the  TRENDY multimodel intercomparison  project for access to data and the principal investigators and their staff for establishing and maintaining the AERONET sites used in this study. The Editor thanks two anonymous reviewers for their assistance in evaluating this paper.
Protein Identification Peak lists from the tandem mass spectrometry raw data were generated with the MASCOT DAEMON software (version 2. 3. 2) from Matrix Science using the extract_msn. exe data import filter from the Xcalibur FT package (version 2. 0. 7) proposed by ThermoFisher. Data import filter options were set as follows: at 400 (minimum mass), 5000 (maximum mass), 0 (grouping tolerance), 0 (intermediate scans), and 1000 (threshold). Using the MASCOT search engine (version 2. 3. 02) from Matrix Science, we searched all MS/MS spectra against an in-house polypeptide sequence database containing the sequences of all annotated proteins encoded by the B. cereus ATCC 14579 chromosome (NC_004722) and plasmid, pBClin15 (NC_004721), supplemented with 44 new proteins discovered by a previous proteogenomic analysis (unpublished data).
This database comprises 5299 polypeptide sequences, totaling 1,464,675 amino acids. Searches for tryptic peptides were performed with the following parameters: full trypsin specificity, a mass tolerance of 5 ppm on the parent ion and 0. 6 Da on the MS/MS, static modifications of carboxyamidomethylated Cys (+57. 0215), and dynamic modifications of oxidized Met (+15. 9949). The maximum number of missed cleavages was set at 2. All peptide matches with a peptide score below a p-value of    0. 05 were parsed using the IRMa 1. 28. 0 software  (Dupierris et al. , 2009). A protein was considered to be validated when at least two different peptides were detected in the same sample. The falsepositive rate for protein identification was estimated using the appropriate decoy database as below 0. 1% with these parameters.
Label-free Protein Quantification and Statistical Analysis The number of MS/MS spectra per protein (spectral counts) was extracted for the 27 samples and used for protein quantitation. The normalized spectral abundance factor (NSAF) was calculated by dividing the spectral count for each observed protein by the polypeptide theoretical mass, as described previously  (Christie-Oleza et al. , 2012). Principal component analysis (PCA) was carried out with R version 3. 0. 1 (http://cran. r-project. org/ bin/windows/base/old/3. 0. 1/). The data analyses were performed with "FactoMineR, " a package written in R dedicated to multivariate exploration data analysis  (Lê et al. , 2008). PCA was carried out with biological replicates of each growth phase as individuals and the spectral counts of proteins as quantitative variables.
Functional Insights into the Pan-Exoproteome of B. cereus Figure  3  shows the whole set of exoproteins that were detected for the three growth phases in each growth condition and were classified into six main functional categories. The group ''Others" comprises non-classical secreted proteins (translation, transcription, cell division, rod shape-related proteins), extracellular component of transport systems, proteins that are usually anchored to the bacterial membrane, and proteins with no function yet identified. Remarkably, more than 40% of the identified exoproteins (CDS) were classified in this group. Among these, 27 did not show any significant similarities with any known proteins, as determined by BLAST searches against the NCBInr database. Therefore, these could be considered as lineage-specific proteins for the B.
Principal Component Analysis of B. cereus Exoproteome Dynamics PCA was carried out to simplify the exoproteome time-course data of B. cereus  (Ivosev et al. , 2008; Jayapal et al. , 2008) , following a previous procedure  (Clair et al. , 2013). We chose to exclude from the original datasets (259 proteins, Table  S2  in Supplementary Material) the proteins found in less than two out of the three replicates for each growth phase sample in each condition. Considering the three growth phase-related observations (EE, LE, and S) and the three biological replicates for each observation, datasets for PCA comprised 9 readouts for 88 proteins under low-ORP anaerobiosis, 106 proteins under high-ORP anaerobiosis, and 114 proteins under aerobiosis. These datasets and analytical details are given in Table  S4  in Supplementary Material.
Conclusion We used nanoLC-MS/MS data to analyze global changes in the B. cereus exoproteome during growth in glucose-containing medium under controlled conditions of pH and pO 2. We have shown that PCA can identify groups of exoproteins that are coordinately controlled at the growth phase level. The results indicated that proteins belonging to the toxin-related group define characteristic kinetic profiles correlated with the physiological state of the culture in respiring, as in fermenting, cells. The majority of toxin-related proteins accumulated during the exponential growth phase, whatever the conditions. However, their dynamics differ significantly under aerobiosis and anaerobiosis if we consider how their patterns in terms of metabolism, oxidative stressrelated proteins and the time dynamics of their Met(O) content are interconnected.
Unless otherwise specified, results refer to scenario A as our primary counterfactual scenario, because private land is not usually supported out of conservation budgets. Data were not available to conduct detailed population modeling to quantify probability of extinction in the absence of conservation action. Instead, adapting the approach used by  Butchart et al. (2006) , we used information available to us on population size and trends, knowledge of severity of threats, their scope and intensity, and ongoing conservation interventions to determine as objectively (and conservatively) as possible how the extinction risk of each species would have changed had conservation action ceased in 1996 (see Supporting Information). We used information contained in the accounts for ungulates published on the IUCN Red List website, IUCN action plans (e.
The proportion of ungulates collectively categorized as threatened would have increased from the 46% of non-data deficient species observed in 2008 to 58% (owing to an additional 31 species moving from least concern or near threatened to a threatened category). The estimated rate of decline increased further when the contribution of private land to conservation was factored into our counterfactual (scenario B); 14 species deteriorated by one red-list category per year, demonstrating the under-appreciated biodiversity contribution of private ranch land (Davies-Mostert 2014). For one species, the common wildebeest (Connochaetes taurinus), we estimated that conservation actions prevented a dramatic deterioration from least concern to critically endangered. Indeed, the migratory population of the Serengeti-Mara ecosystem accounts for some 70% of total population  (Estes 2013 ), and we estimated that disruption of migration (e.