dataesr/scientific-paragraphs-categorization huggingface dataset:
Subcellular distribution of sphingomyelin To determine the subcellular distribution of sphingomyelin after treating 3T3-F442A adipocytes with exogenous SM-LA (15 μM), the cells were treated for 2, 4, 8, 24, 32 and 48 h. The viability of the cells was not affected by this treatment (>96%). To ensure that the plasma membrane fraction was not contaminated with nuclear and microsomal membranes, we analyzed the samples for the presence of the nuclear protein Nucleoporin p62 and of the primarily Golgi-localized protein TGN38, respectively. The results (Table  2 ) indicated that the Nucleoprotein p62 and TGN38 proteins levels were 0. 9% and 3. 8% in plasma membrane samples relative to the nuclear and microsomal levels, respectively. The data (Table  3 ) demonstrated that SM accumulates in the PM within 24 h and then in the intracellular space.
Cav-1 and Cav-2 mRNA were enhanced in the presence of exogenous SM-LA (4. 01 and 2. 35 fold) or GSH (5. 37 and 4. 64 fold), respectively (Table  7 ), whereas no changes were observed in PPMPtreated cells. Caveolins mRNA stability were also assessed, as previously described, using the transcription inhibitor actinomycin D. The degradation rate in SM-enriched cells did not significantly differ from that in control cells, suggesting that SM regulates gene expression at the transcriptional level (data not shown). Caveolins were significantly more abundant in the case of SM-LA treatment (Fig  8 ). The increases for Cav-1 and Cav-2 were respectively 2. 1-and 1. 7-fold for mRNA, and 2. 2-and 1. 7-fold for the cellular protein. In total membranes, the increases were: 2. 0-and 1. 8-fold respectively.
Statistical analysis Data were entered by surveyors in a Microsoft Access database created specifically for the study (Microsoft Corporation, Redmond, United States of America). Questionnaires with missing data were included in the analysis. The six Likert's items were combined into two categories: "strongly agree/agree", "very useful/useful" and "always/most of the time" versus the remaining options of the scale unless otherwise stated. Categorical variables were expressed by proportions and their significance was assessed by χ 2 tests or Fisher's exact tests when appropriate. The results of the antibiotic knowledge questions (excluding the two questions about estimations of local antibiotic resistance) were expressed by the values 0 (not correct) or 1 (correct) and a score was calculated for a maximum of 10 points.
Continuous variables were expressed by means and standard deviations (SD) and assessed for statistical significance using either Student's test, the unpaired Wilcoxon's test or the one-way ANOVA test. Statistical analyses were performed using the software STATA SE 11. 1 (StataCorp LP, College station, USA) and 95% confidence interval was calculated. A two-sided P-value of ≤ 0. 05 was considered as significant.
Acknowledgements We thank the surveyors,  Ramarosandratana Albertin ,  Xayavong Bounta ,  Remonja Chitale ,  Avokpaho Euripide ,  Rakotoarimanana Feno ,  Nguyen Thanh Hai ,  Koummalasy Khamphithack ,  Keita Mory ,  Nanthavong Naphavanh ,  Souliyaseng Noy ,  Farambahiny Onimanitra ,  Sitaphone Pathoumphone ,  Xaypadith Sengdavy ,  Phetsouvanh Siriphonexay ,  Somlor Somphavanh ,  Khamphanthong Souphaxay ,  Andriamoria Tatamo ,  Kang Virak  and  Xaymaty Vixay.
Acknowledgments This study was funded by the  ANR  ( 11-PDOC-006-01 ). We would like to thank all children and their parents for participating in this study, the local authorities for their support, as well as all the volunteers for the dual-port olfactometer assays. We are very grateful to the  IRSS  staff in  Burkina Faso  for technical assistance. We thank  Fréderic Simard  and  Karine Mouline  for letting us use their locomotor activity monitor system. We thank the  Laboratoire Mixte International LAMIVECT ,  Bobo Dioulasso ,  Burkina Faso. We are grateful to  A. Wong  and  J. E. Crawford  for their valuable comments.
RESULTS For our study, 487 eligible women met the inclusion and exclusion criteria. From these women, 36 had to be excluded because of sample-handling issues, so data from 451 women were used for the statistical analysis, with the number of women contributed by each site varying between 115 and 17. Their demographic characteristics are given in Table  1. As for the participating women, 92% were Caucasian, their mean age was 32. 8 years (range: 18. 0-44. 0 years), their mean BMI was 24. 3 kg/m 2 (range: 16. 7-52. 7), and 68. 5% were not infertile. Their ages were approximately evenly distributed between groups aged 18-29, 30-34, and 35-39 years, with fewer aged 40-45 years. To minimize interobserver variation, 91% of AFC determinations were performed by 13 clinicians/sonographers. The distribution of AFC and AMH values is shown in Supplemental Table 2 (available online) overall and for each site, together with FSH and E 2 measurements.
These analyses may indicate that AMH measured by this new assay is a more reliable indicator of the ovarian reserve than AFC. The full automation of the AMH assay removes operatorrelated variation; the centralization of hormone analysis  removes a further source of variability, and thus this may not exactly reflect the situation where individual sites perform hormone analysis. The possibility of centralization is an inherent advantage of hormone analysis over ultrasoundbased analysis: recording images and their offline and centralized analysis are possible in principle (  17 ), but they are very time consuming, so one of the key advantages of AFC, its immediacy, is lost. Although AMH and AFC are sometimes regarded as interchangeable, there are emerging data suggesting that AMH is a more reproducible measure of the ovarian response to stimulation.
8  Rivaroxaban is a selective oral direct factor Xa inhibitor anticoagulant approved for multiple clinical indications, including stroke risk reduction in patients with non-valvular AF (NVAF). 9,10 Non-randomized studies suggest that it may be feasible to manage patients undergoing CAwith rivaroxaban. 11 Calls for randomized trials make this study clinically relevant. 12 -14 The objective of this prospective randomized study (NCT01729871) wasto determine whether the number of complications associated with uninterrupted rivaroxaban are similar to those for a VKA in this setting.
The per-protocol analysis set was the pre-specified primary analysis set, including all randomized patients who took at least 1 dose of study drug (safety population) and underwent CA. The safety population was used for the primary safety analysis. The treatment-emergent period spanned the time from administration of the first dose until the last dose of study medication plus 2 days. Statistical analyses were descriptive. All continuous variables were expressed in terms of mean or median and standard deviations. Categorical data were expressed as numbers and percentages. Categorical group comparisons were made using the x 2 -test without continuity correction. Two-sided probability values of ,0. 05 were considered to be statistically significant. The SAS FREQ procedure was used for confidence interval calculation.
54% (MB4). The characteristic global genome stability of M. tuberculosis was also present in these four genomes, while variability appeared to be concentrated in membrane proteins with repetitive sequence motifs, which bear frequent mutations that are probably related to selective pressures imposed by the host immune system. The availability of genomes from field isolates of M. bovis and M. caprae will allow comparative analysis to other mycobacteria species to expand the study of the evolution and host specificity of Mycobacterium spp. and to find correlates with phenotypic variation with implications for TB disease risk assessment and control. Nucleotide sequence accession numbers. The M. bovis MB1, MB3, and MB4 genome sequences were deposited in the European Nucleotide Archive under the accession numbers CDHF01000001 to CDHF01000049, CDHH01000001 to CDHH01000094, and CDHE01000001 to CDHE01000118, respectively.
This research was supported by grant AGL2011-30041 from the Ministerio de Economía y Competitividad, Spain, by the Programa de Tecnologías Avanzadas en Vigilancia Sanitaria (TAVS) from the Comunidad de Madrid (ref. S2013/ABI-2747), the EU H2020 COllaborative Management Platform for detection and Analyses of (Re-) emerging and foodborne outbreaks in Europe (COMPARE) Grant 377/14, and by the EU.
General obesity, as reflected by BMI, is an established risk factor for esophageal adenocarcinoma (EAC), a suspected risk factor for gastric cardia adenocarcinoma (GCC) and appears unrelated to gastric non-cardia adenocarcinoma (GNCC). How abdominal obesity, as commonly measured by waist circumference (WC), relates to these cancers remains largely unexplored. Using measured anthropometric data from 391,456 individuals from the European Prospective Investigation into Cancer and Nutrition (EPIC) study and 11 years of follow-up, we comprehensively assessed the association of anthropometric measures with risk of EAC, GCC and GNCC using multivariable proportional hazards regression. One hundred twenty-four incident EAC, 193 GCC and 224 GNCC were accrued. After mutual adjustment, BMI was unrelated to EAC, while WC showed a strong positive association (highest vs.
Eligible subjects were invited to participate and those who gave informed consent completed questionnaires on diet, lifestyle and medical history. Participants were then invited to a center to have anthropometric measurements taken by trained staff. We excluded 28,268 individuals with prevalent cancer (other than non-melanoma skin cancer) or because they were lost to follow-up (n 5 15). Further exclusions refer to individ-uals for whom data on measured weight and height were missing (n 5 92,440), among them the cohort of Norway (n 5 35,889), 48,616 participants from the French cohorts and 7,935 from the other cohorts. We additionally excluded 1,495 participants with missing questionnaire data and -to reduce the effect of implausible extreme values on the analysis -7,772 individuals who were in the top or bottom 1% of the ratio of energy intake to estimated energy requirement that was calculated from height, weight, gender and age.
Assessment of anthropometric data, diet and lifestyle factors Weight and height were measured according to standardized protocols by trained personnel to the nearest 0. 1 kg and 0. 1 or 0. 5 cm, respectively, with subjects wearing no shoes, as described in detail previously. 17 WC was measured either at the narrowest torso circumference (most centers) or midway between the lower ribs and iliac crest. Hip circumference was measured horizontally at the widest circumference or over the buttocks. In Umeå (Sweden), anthropometric data collection was restricted to measurement of weight and height. Body weight, WC and HC were adjusted for heterogeneity due to protocol differences in clothing worn during measurement. 17 For the "health conscious group" based in Oxford (UK), linear regression models were used to predict sex-and age-specific values from participants with both measured and self-reported body measures as previously described.
Follow-up and ascertainment of endpoints Identification of cancer cases was based on population cancer registries (Denmark, Italy, Netherlands, Spain, Sweden and United Kingdom) or a combination of methods including regional and local cancer registries together with an active follow-up through participants and their next-of-kin (Germany and Naples). Mortality data were also collected from either the cancer registry or mortality registries. Participants were followed up from study entry until cancer incidence, death or end of follow-up, whichever came first. Censoring dates for complete follow-up from cancer registries were between December 2004 and December 2008. For centers with active follow-up, the end of follow-up was considered to be the date of diagnosis, date of the last known contact or date of death, whichever came first.
Mortality data were coded following the rules of the 10th revision of the International Statistical Classification of Diseases, Injuries and Causes of Death (ICD-10) and cancer incidence data following the 2nd revision of the International Classification of Diseases for Oncology (ICD-O-2). Morphology information was used to classify the malignant tumors according to histological type. We included first incident primary adenocarcinomas of the esophagus coded as C15 (n 5 133 before exclusions) and stomach coded as C16 (C16. 0 for cardia and C16. 1-16. 6 for non-cardia, n 5 452 before exclusions); C16. 8 (overlapping tumors) and C16. 9 (not otherwise specified) were not considered. Validation and confirmation of the diagnosis, classification of tumor site and of tumor morphology were performed, for about 50% of the cases, by a panel of pathologists.
Epidemiology Steffen et al. Likewise, we mutually adjusted WC and BMI to estimate whether abdominal obesity is associated with cancer risk beyond the association with general obesity. In sensitivity analyses, we examined associations across strata of smoking status and after exclusion of cases occurring during the first two years of follow-up to exclude reverse causation. All p-values presented are two-tailed and p < 0. 05 was considered statistically significant. Analyses were performed using SAS, version 9. 4 (SAS Institute, Cary, NC).
Data Analysis To evaluate the anatomic results in a homogeneous population with typical indications for WEB-DL, we included patients if their aneurysms met precise criteria: • Located at a bifurcation: ICA, MCA, anterior communicating artery, basilar artery, and PICA • Nonthrombosed • With a wide neck (Ն4 mm) • With a maximum diameter of Յ12 mm. The independent reader, who already analyzed the images (preand postoperative, short-term and midterm follow-up) for the initial series (J. -Y. G. ), reviewed the long-term follow-up images. They were evaluated by using a 3-grade scale: complete occlusion (including complete occlusion with opacification of the proximal recess of the device), neck remnant, and aneurysm remnant. The reader also analyzed the evolution of aneurysm occlusion between mid-and long-term follow-up and classified it as improved, stable, or worsened.
Diffusion imaging analysis All analyses were performed using the Functional MRI of the Brain (FMRIB) software library (FSL v5. 0. 2. 1, http://www. fmrib. ox. ac. uk/fsl)  (Smith et al. , 2004). For each participant, the 32 diffusion-weighted images were all re-aligned (using affine registration) to the b0 image, in order to correct for eddy current distortion and head movements. A brain mask was created from the b0 image ('BET' procedure in FSL) and the mask was applied to all images to remove non-brain tissue. Fitting of the diffusion tensor model in each voxel was performed using the DTIFIT procedure. Images of fractional anisotropy (FA), mean diffusivity (MD), axial diffusivity (AxD) and radial diffusivity (RD) were then derived from eigenvalues of the diffusion tensor, in each participant.
2. 6. 1. Patients with aMCI due to AD vs. controls DTI-derived variables were compared between groups with a whole-brain approach, using the tract-based spatial statistics (TBSS v1. 2) method  (Smith et al. , 2006). Following slight erosion, FA images of each subject were all non-linearly registered to a 1-mm isotropic FA standard-space image ('FMRIB58_FA')  (Rueckert et al. , 1999). The resulting FA images from all participants were then averaged, and a mean white-matter tract skeleton was calculated from the mean FA image (threshold at 0. 2). This skeleton represents the centre of major tracts that would be common to all subjects. For every participant, the nearest tract centre (as determined from the individual spatiallynormalized FA image) was projected onto the mean FA skeleton. Voxel-wise statistics were computed using permutation-based (non parametric) tests, as implemented in the 'randomize' program of FSL.
Acknowledgements This study was supported by a grant from the  'Agence Nationale de la Recherche '  ANR-08-JCJC-0040  ( French National Research Agency ). We thank  Patrice Péran  for his help with image analysis, and  Hélène Gros ,  Lucette Foltier  and  Jean-Pierre Désirat  for their help with participants3 scanning at the  MRI platform of the 'Institut des Sciences Cognitives de Toulouse '.
Acknowledgments We gratefully acknowledge the essential technical assistance and expertise of  Lucien Crobu  in vector construction. We wish to thank  Pierre Travo  and the  RIO Imaging Platform (Montpellier, France)  for assistance in fluorescence microscopy. The monoclonal antibody 12G10 developed by  J. Frankel  and  M. Nelson  was obtained from the  Developmental Studies Hybridoma Bank (IA, USA ) developed under the auspices of the  Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)  and maintained by the  University of Iowa, USA. This study was funded with the assistance of the  Centre National de la Recherche Scientifique (CNRS)  and the  French Ministry of Higher Education and Research for PB's group  and the  Association pour la Recherche sur le Cancer (ARC)  award  N°3140 , the  French National Research Agency (ANR)  awards Nos.
As a control, the purely soluble GRA1 protein  (Sibley et al. , 1995)  was found exclusively in the high-speed supernatant (Figure  1B ). These data were consistent with immunofluorescence analyses of the two antigenic constructs in combination with prototypical markers of the PV membrane (GRA3) and the PV lumen (GRA1). GRA6-HF10 was present both at the PV (D) Upper panel: secretion level of GRA6-HF10 (black line) and SAG1-GRA6-HF10 (gray line) in BMM infected (GFP + ) with the indicated parasite line, for the indicated time and dose, detected with AF647-coupled anti-HF10. Lower panel: secretion level of endogenous GRA6 III in BMM infected (GFP + ) with the indicated parasite line, detected with AF647-coupled anti-HY10. Controls show labelings of GFP À cells from infected cultures (dotted lines) and BMM not mixed with tachyzoites (tinted histogram).
, 2015). Therefore, our data show that rGRA2 association with LUV depends on the domains of its AAH. Next, we evaluated the ability of rGRA2 to deform membranes by analyzing the LUV-protein incubation products by transmission electron microscopy (TEM). Tubules were detected at a lipid:protein ratio of 50:1, only when LUV were incubated with rGRA2 and not with rGRA2 DAAH (Fig-  ures 2C  and 2D  and S2A ). In these conditions, the tubules were, on average, 178 ± 69 nm long, with a diameter of 25-33 nm (Table 1). As HeLa-extruded LUV have a complex lipid composition, we investigated whether the AAH of rGRA2 would exhibit selective affinity for particular membrane lipids. We incubated rGRA2 or rGRA2 DAAH with nitrocellulose membranes spotted with defined synthetic lipids (''fat blots''). Both proteins displayed similar intense reactivity with phosphatidylinositol (4)-monophosphate (PI(4)P), phosphatidylinositol (3,4,5)-trisphosphate (PI(3,4,5)P 3 ), and cardiolipin (CL), as well as similar weak reactivity with phosphatidylserine (PS).
Ex Vivo Analysis of T Cell Response Mice were immunized twice 3 weeks apart with 2 3 10 6 tachyzoites that were previously g-irradiated (120 Gy) and filtered through a 3-mm filter (Millipore). Mice were euthanized 4 days after the second immunization. Peritoneal exudate cells (PEC) were recovered by lavage with 10 ml cold PBS. Spleens were dissociated into single-cell suspensions in complete RPMI medium. Samples were depleted of erythrocytes, and production of IFN-g was measured as described previously  (Feliu et al. , 2013). Samples were run on an FC500 (Beckman-Coulter) or a Fortessa (Becton Dickinson) flow cytometer and analyzed using the FlowJo software.
Immunofluorescence Monolayers of HFF grown on Lab-Tek II chamber slides CC2 (Thermo Scientific Nunc) were infected with T. gondii for 16 to 24 hr. After infection, cells were washed with PBS, fixed for 20 min in 3% paraformaldehyde (Electron Microscopy Sciences) at room temperature (RT), and quenched for 5 min with PBS plus 0. 1 M glycine. Primary antibodies were diluted in permeabilization buffer (PBS, 0. 2% BSA, 0. 05% saponin) and incubated for 1 hr at RT followed by three 5-min washes. Cells were incubated with AF555-coupled anti-rabbit immunoglobulin G (IgG) and AF633-coupled anti-mouse IgG (Invitrogen) for 20 min at RT. z stacks were acquired on a Zeiss LSM710 confocal microscope and analyzed using ImageJ software (NIH). For more details on the quantification of the GRA6 signal, see the Supplemental Experimental Procedures.
ACKNOWLEDGMENTS We thank the following:  D. Soldati-Favre ,  P. Bradley ,  J. Boyle , and  J. Boothroyd  for reagents;  G. van Dooren  and  B. Striepen  for generating the TgRH  GRA6-HF10  parasites;  E. Mare  ´chal for quantification of fatty acid methyl esters; the CPTP flow cytometry and imaging core facilities; the  INSERM UMS006-CREFRE animal care facility ; the  SCME Universitede Montpellier 2 ;  N. A. Guerrero ,  A. Lima-Perez ,  G. Pe  `tre,  L. Travier ,  P. Ruffiot ,  K. Sall ,  M. Jamin ,  E. Gentilhomme , and the N. B. team for help and discussions;  D. Dunia  and  C. Bonnart  for critical reading of the manuscript. This work was supported by the  Agence Nationale de la Recherche  ( ANR-11-BSV3-01002  to N. B. and M. -F. C. -D. ); Region Midi-Pyrenees  (N. B. ); IN-SERM and  Fondation Bettencourt-Schueller  ( Avenir Grant  to N.
B. );  Human Frontier Science Program Organization  ( CDA00047/2011  to N. B. ); a  Marie Curie International Reintegration Grant  (N. B. ); the  PIA Parafrap Consortium  ( ANR-11-LABX0024  to N. B. and M. -F. C. -D. ); PIA Aninfimip equipment  ( ANR-11-EQPX-0003  to N. B. ); a grant from Cluster  10  to  Infectious Diseases-Rhône-Alpes region  ( C. Mercier ); a PhD fellowship from the  Rhône-Alpes region  (A. B. );  Fondation pour la Recherche Medicale  (J. L. );  NIH  grants ( AI091461 ,  AI105593 ,  AI108489 ) (D. J. B. ); and a post-doctoral fellowship from the  ANRS  (G. E. ). We acknowledge support from the platforms of the Grenoble Instruct Center (ISBG;  UMS 3518 CNRS-CEA-UJF-EMBL ) supported by the  French Infrastructure for Integrated Structural Biology Initiative (FRISBI)  ( ANR-10-INSB-05-02 ) and  GRAL  ( ANR-10-LABX-49-01 ) within the  Grenoble Partnership for Structural Biology  (PSB).
Acknowledgements. We would like to thank  Claude Cahier  and  Deborah Crespin  for the animal facilities. Special thanks go to  Christophe Gauthier  for the testosterone assays,  Isabelle Gibert ,  Peggy Jarrier  and  Linda Beauclair  for the genotyping,  Mrs Arlette Gerard  for the FSH and LH assays and  Marie Françoise Pinault  for her help managing the pictures. Florian Guillou  is thanked for providing AMH-Cre line. The English was proofread and corrected by  Helen Lamprell  from  HSB Traductions. This work was funded by two grants from the  Agence Nationale pour la Recherche ('Biodiversité , évolution des écosystemes, écosystemes productifs, agronomie' grant;  2011-2013 ): TimeOfLife2 and EarlyFoll.
Buruli ulcer case data This retrospective study was conducted in the Centre de Diagnostic et de Traitement de l'Ulcere de Buruli in Pobe, Benin. This structure, built in 2004, is one of the four medical centers dedicated to the diagnosis and treatment of Buruli ulcer present in Benin and the closest to the border with Nigeria  [18, 19]. In the Buruli ulcer registry of the medical centre, we identified all patients with PCR-confirmed M. ulcerans infection and Nigerian origin diagnosed in CDTUB of Pobefrom 2004 to 2013. We recorded detailed patient data demographic characteristics, medical history and clinical features. The Nigerian origin was defined as a patient living in Nigeria, ie working in Nigeria for an adult or going to school in Nigeria for a child for at least two years. We considered therefore that the contamination of the patient occurred the most likely in Nigeria.