dataesr/scientific-paragraphs-categorization huggingface dataset:
A good level of knowledge about the transmission modes of HBV was defined as providing a correct response to each of the following four questions: answering "yes" for the three questions worded as "Can transmission occur"…"during sexual relations without a condom?", "when sharing a needle during drug injection?", and "during pregnancy?" and answering "no" to the item "Can transmission occur from a mosquito bite?". Individuals were grouped according to the level of endemicity of HBV in their country of birth  [4]. Having taken drugs intravenously was defined as reporting to have injected drugs at least once during one's lifetime. Analyses were carried out using the Stata® 11. 0 statistical software package (Stata Corporation, College Station, TX).
Acknowledgements Our thanks to the following: To all those who participated in this study. To the agencies and institutes which funded this research. To the IPSOS team for their participation in implementing the survey. To  Jude Sweeney  for the translation of the manuscript. The KABP France group is comprised of  Véronique Doré  for the  ANRS ,  Nathalie Beltzer ,  Isabelle Grémy ,  Gaëlle Pedrono ,  Leïla Saboni ,  Claire Sauvage  and  Cécile Sommen  for the  ORS Île-de-France ,  Cécile Brouard ,  Marie Jauffret-Roustide ,  Guy La Ruche ,  Stéphane Le Vu  and  Caroline Semaille  for the  InVS ,  François Beck ,  Arnaud Gautier ,  Romain Guignard ,  Christine Jestin ,  Nathalie Lydié  and  Jean-Baptiste Richard  for Inpes and  Josiane Warszawski  from  Unité 1018 of Inserm.
Genotyping Genotyping was performed on DNA extracted from leukocytes at baseline  (1999) (2000) (2001)  and kept frozen at -80°C. Centralized facilities for genotyping are provided by the Lille Genopôle. Genotyping of single nucleotide polymorphisms (SNPs) rs1061170 (Complement Factor H, CFH, Y402H) were determined using TaqMan assays (Applied Biosystems, Inc. , [ABI], Foster City, CA), as described by the suppliers. Furthermore, a genome wide scan was performed at the Lille Genopôle  [44]. For the present study, the following genotypes were extracted from the GWAS data: rs10490924 (ARMS2/ HTRA1), rs493258 and rs10468017 (LIPC), rs3764261 (CETP), rs12678919 (LPL) and rs1883025 (ABCA1). Genotypes data for rs10468017 (LIPC), rs3764261 (CETP) and rs12678919 (LPL) were available. For the others SNPs namely rs10490924 (ARMS2/HTRA1), rs493258 (LIPC), rs9621532 and rs1883025 (ABCA1), genotypes were imputed using Markov Chain based haplotyper (MACH v1.
After centrifugation, an aliquot (800 mL) of the clear supernatant fluid was dried under nitrogen at room temperature. The dried residue was quantitatively redissolved in the mobile phase (200 mL n-hexane and acetone; 19%, by vol). The resulting solution was injected (100 mL) into a normal-phase HPLC system equipped with an autosampler (15°C), a column oven (40°C), an HPLC pump, and an ultraviolet-visible detector. Data were analysed with a data acquisition system (Atlas: Thermo Labsystems). The separation was done on a polar column (Lichrosorb, Si60, 5 mm, 250 * 4 mm; Stagroma, Reinach, Switzerland) with a mixture of n-hexane and acetone (19%, by vol) at a flow rate of 1 mL/min. Xanthophylls were detected at a wavelength of 452 nm. To assess the daily and long-term laboratory performance of the HPLC plasma analytics, dedicated control plasma was used.
Associations between plasma lutein and zeaxanthin with LIPC and LPL SNPs were evaluated with linear regression models. Plasma lutein and plasma zeaxanthin were used as the dependent variable and the LIPC and LPL genotypes, age, gender, HDL-cholesterol, LDL-cholesterol, triglycerides and lipid lowering medication as the independent variables. Among the 963 participants, 108 (11. 2%) participants had missing data for plasma lutein and zeaxanthin: 61 (6. 3 %) refused the blood sampling and 47 (4. 9%) had unavailable data for plasma lutein and zeaxanthin. Among the 855 remaining subjects, the LIPC rs493258 genotype was available in 761 subjects, the LIPC rs10468017 in 748 and the LPL rs12678919 genotype in 738 subjects. For AMD variables, eyes with no AMD were the reference. For SNPs genotype, the most frequent polymorphism was used as a reference.
Dot Blot Analysis of CDON Expression in Human Tissues CDON gene expression in human tumor and normal paired tissues was monitored by using the Cancer Profiling Array (CLONTECH) following the manufacturer's suggested procedure. CDON probe was prepared by using Amersham Megaprime DNA Labeling System (GE Healthcare) with human full-length CDON cDNA as template. The following primers were used: 59-GCATCTCGTCCTTATCAAGTGG-39 and 59-TATGGTAT-TCTGCTGGCGATTC-39. The dot blot was quantified by using Quantity one 4. 6. 1 software (Biorad). CDON loss of expression was defined by a fold change (normal versus tumor) greater than 2.
Fluorescence imaging was performed with AxioVision Release 4. 6 software. Antibody for CDON immunohistochemistry was validated after transfection of siRNA silencing CDON expression. Co-immunprecipitations and immunoblots were performed as already described using anti-CDON (1/2,000, R&D Systems), anti-FlagM2 (1/5,000, Sigma), anti-HA (1:7,500, Sigma), anticaspase-9 (1:1,000, Cell Signaling), or anti-b-actin (1:1,000, Chemicon) primary antibodies.
Measurement site The Carbonaceous Aerosol and Radiative Effects Study was a field campaign focusing on the evolution of secondary organic and black carbon (BC) aerosols and their climaterelated properties in the Sacramento urban plume as it was routinely transported into the forested Sierra Nevada foothills area  (Zaveri et al. , 2012). Aerosol measurements were taken from 2 June to 28 June 2010 at the T1 site, which was located about 60 km to the northeast of Sacramento in Cool, CA, a small town situated amidst a forested area rich in biogenic emissions (latitude: 38. 87; longitude: -121. 02; altitude: ∼ 460 m m. s. l. ). The data related to the analysis presented in this paper were available from 10 June to 28 June. Aerosol data included aerosol size distribution, chemical composition, CCN spectrum (as a function of supersaturation), size-resolved CCN spectrum and activated fraction, all of which were taken at the ground level.
Chemical composition The concentrations of submicron non-refractory (NR-PM 1 ) organic and inorganic (nitrate, sulfate, ammonium, chloride) aerosol species were measured using a high-resolution timeof-flight aerosol mass spectrometer (HR-ToF-AMS, Aerodyne Research Inc. , hereinafter AMS for short)  (DeCarlo et al. , 2006). The AMS sampled from an inlet equipped with a PM 1 impactor (Brechtel Manufacturing Inc. , Hayward, CA; model 8003). The ambient air passed through 3 feet (0. 91 m) of stainless steel tube with an inner diameter of 3/4 inch (1. 91 cm), 8 feet (2. 44 m) of copper tube with an inner diameter of 1/4 inch (0. 64 cm), 2 feet (0. 61 m) long temperature-controlled thermodenuder, and a Nafion dryer prior to sampling by the AMS. The resulting data were averaged over 2. 5 min intervals.
03 to 0. 18, compared to nearly a factor of 3 increase when x org was greater than 90 %, and the increase was further reduced to ∼ 40 % (i. e. , the ratio increased from 1. 14 to 1. 52) when 70 % < x org < 80 %. For most of the measurements, the κ org value required for an agreement between calculated and measured N CCN ranged from 0. 03 to 0. 15, in agreement with κ org derived from size-resolved CCN measurements described below. During CARES, aerosols observed at the T1 site were dominated by organics. For the comparison described above, 24 %, 54 %, and 16 % of the data points corresponded to x org > 90 %, 80 % < x org < 90 %, and 70 % < x org < 80 %, respectively. Only 6 % of data points were associated with x org less than 70 %. The decreasing sensitivity of the calculated N CCN to κ org is in agreement with earlier studies (e.
For example, at O : C ratio of 0. 5, κ org derived in above studies ranged from ∼ 0. 1 to ∼ 0. 2. For the results from  Duplissy et al. (2011)  and  Chang et al. (2010) , the differences may be partially due to the uncertainty in derived O : C values. At present, AMS data analysis software only allows derivation of bulk O : C through analysis of high-resolution mass spectral obtained F. Mei et al. : CCN activity of organic aerosols observed downwind of urban emissions during the MS mode operation. This approach was employed by  Massoli et al. (2010)  and  Lambe et al. (2011)  to derive the bulk O : C, which should represent O : C at various CCN sizes in their studies, because no substantial O : C dependence on particle size is expected for organic aerosols formed in the PAM reactor. For this study and  Mei et al.
Study design and population This study incorporated a cross-sectional design and was performed at the Reference Center for inborn metabolic disorders of a French public teaching hospital (La Timone, Marseille, France). The inclusion criteria were as follows: a child with a diagnosis of one of three IEMRD conditions (organic aciduria, urea cycle defect, or MSUD), born between 1993 and 2010, with parents or legal guardians authorizing participation in the study. A medical database allowed the identification of eligible children according to the selection criteria. The study was proposed to consecutive parents and/or patients during a planned routine visit.
Medical records From the medical records, the following data were collected: 1. sociodemographic: age and gender of the child; 2. clinical: nature of IEMRD (organic aciduria, urea cycle defect, or MSUD), feeding modalities at inclusion (exclusively oral, home enteral nutrition), eating disorders at inclusion (presence or absence), current gastrostomy, and previous enteral nutrition; and 3. current clinical complications: neurologic (motor, sensory, or cognitive impairment), renal (based on creatine clearance level), cardiac (based on echocardiography), hepatic (biological markers), and protein-related (based on actual protein intake rate).
Acknowledgements The authors are grateful to all the patients and parents for their participation in the study. The authors thank  Marie-Claude Simeoni  for her expertise related to QoL questionnaires of children,  Jessica Fernandez  for the contribution for the statistical analyses, the  French Society of inborn error of metabolism (Société Française pour l'Etude des Erreurs Innées du Métabolisme, SFEIM) , the  French Group of Reference Centers for inborn metabolic disorders (Groupement des centres de référence et de compétence des Maladies héréditaires du Métabolisme, GMM). This work was supported by institutional grants from the  French 2009 Institut de Recherche en Santé Publique (Concepts, Usages et Déterminants en Qualité de Vie, CUD-QV).
Annihilations on the emulsion surface Direct annihilations on the emulsion surface were also studied with the new gel. One of the microscopes at the LHEP was devoted to AEgIS data analysis. The microscope was equipped with an XY Z computer driven high precision stage, a 1. 3 M-pixels high speed camera and an oil objective lens with a magnification of 50, leading to views of 303 × 242 µm 2 , or to a pixel pitch of 0. 2365 µm. The regions of interest on the emulsion surface were fully digitized by the microscope. Samples of 19'625 views/film were taken, covering surfaces of 3 × 3 cm 2 , and producing files of 1. 1 TB size. The digitizing time was 10 hours, mainly limited by disk access time. The digitized data were displayed on the PC monitor by an event display (the so-called "Virtual Microscope") which can deal with TB data sizes through dynamic data access with multithread programming.
Clearly CHIPS performs much better than FTFP in describing antiproton annihilation at rest. The latter is adequate to describe annihilations at energies above 100 MeV/c  [29]. We should, however, warn the reader that more positive than negative pions are produced by CHIPS, which is surprising since (negatively charged) antiprotons can annihilate on neutrons. Indeed, experimental data show that more negative than positive pions are produced in low energy antiproton annihilations  [30].
Conclusions Emulsion detectors can measure the annihilation vertex of antihydrogen atoms in the AEgIS experiment with very high precision. We have presented here results for emulsion films operating in vacuum at the CERN low energy antiproton decelerator. We have shown data using a promising new emulsion gel with typically a factor of two higher grain density than used before in emulsion detectors. This increases the efficiency for the detection of minimum ionizing particles such as the pions emitted in antiproton annihilations. We have compared our measured particle multiplicites from annihilations in emulsions and aluminium with the Monte Carlo packages CHIPS and FTFP in GEANT4. CHIPS provides a better description of the data than FTFP. We have estimated the resolution and data taking time needed to achieve the AEgIS goals.
Experimental design A rotatable central composite experimental design with three independent factors (a ¼ 1. 68) was used to study the inactivation of B. sporothermodurans spores in distilled water and in skim milk. The factors investigated were pressure, initial temperature in the vessel, and pressure-holding time. Each factor at five coded levels (indicated as À1. 68, À1. 0, 0. 0, þ1. 0, þ1. 68 as shown in Table  1 ) were designed as experimental runs using the software STATGRAPHICS Centurion XV version 15. 2. 06. The real values of the independent variables (X) were coded according to equation: x i ¼ (X i e X 0 )/DX, Where X is the real value of the independent variable; x i is the coded value of the independent variable given by the experimental matrix; X 0 is the real value of the central point, and DX is the step change.
X and x values are shown in Table  1. The experimental response was the number of log cycle reduction of B. sporothermodurans spores (log (N 0 /N)), which was estimated, taking into account the influence of the experimental factors. Three experiments were performed at the center of the experimental domain in order to estimate the residual variance value. An analysis of variance and an estimation of response surface by multiple linear regressions were performed using the software Statgraphics Centurion XV version 15. 2. 06.
Semi-Quantitative Real-Time PCR Total RNA from MACS-selected cell fractions, from GS cells and from seminiferous tubules was employed for Real-Time PCR as previously described  [10]. Briefly, total RNA was purified using TRIzol reagent (Invitrogen) and quantified. One microgram of total RNA/sample was used for cDNA synthesis with random hexamers and Transcriptor Reverse Transcriptase (Roche). In control samples, reverse transcriptase was omitted to monitor genomic DNA contamination. The cDNA was subjected to realtime analysis performed in triplicate for each sample (FluoCy-cleTMII SYBR Green Mix, Euroclone). Reactions were performed on Opticon2 DNA Engine (MJ Research). Primers used to detect target genes were designed and evaluated using the PRIMER3 software (http://frodo. wi. mit. edu/primer3).
Expression profiles of candidate proteins were analyzed by whole-mount immunofluorescence experiments on isolated tubules co-stained with anti-PLZF and anti-GFRA1. This analysis revealed that the actin-binding proteins analyzed showed a broad pattern of expression and were in all germ cells types and somatic cells (data not shown). Surprisingly, the actin-binding protein VASP was highly expressed in PLZF-expressing spermatogonia (Figure  3a, b ). Western blot analysis of proteins extracts from testes at different postnatal ages revealed a doublet of bands at 46-50 kDa. Murine VASP can be phosphorylated on three different residues by protein kinase A and protein kinase G  [23]. Phosphorylation of Ser153 leads to a shift in the apparent molecular mass of VASP, but phosphorylation of Ser235 and Thr274 does not alter VASP mobility in SDS-PAGE  [23].
Afterward, cells were treated for 8 hours with increasing concentrations of GDNF and VASP was analyzed by real-time PCR and western blot in parallel samples. Again, real-time PCR analysis and western blots showed that VASP mRNA and VASP doublets were up-regulated by GDNF in GS cell cultures (Figure  5c, d ). Together, these data show that VASP is possibly regulated by GDNF at both the transcriptional and post-transcriptional level.
Lists of genes The statistical significance of an intersection of gene lists has been calculated using online service List Of Lists Annotated (LOLA) http://www. lola. gwu. edu/ [37]. To standardize the lists of genes extracted from different publications, we have used GenBank GeneIDs as reference points. As the GeneID was not usually provided along with the expression data, we have converted available Affymetrix or Ensembl IDs or Gene names to GeneID by using db2db online tool http://biodbnet. abcc. ncifcrf. gov/ db/db2db. php [38]. In the cases where Gene name was not recognized by the db2db service, we assumed that the authors of the study used a synonym. In these cases, we provide both Gene names: the major one, recognized by db2db service and the synonym from the original publication.
FSHD-related genes List A was created by using supplementary data from  [39] , previously available at www. ucihs. uci. edu/biochem/winokur under 'publications' (Table  S2 ). To our knowledge, at the moment of submission, the data are no longer available for downloading on this server. Genes with fold change >2 and P < 0. 05 were considered as differentially expressed. In total, 527 probes from the two types of microarrays used in the study (HuFL and U95) corresponding to differentially expressed genes were retained by the authors. To standardize this list and make it compatible with the lists originating from other studies, we have transformed probe codes to GeneIDs. Some of probe codes corresponded to multiple genes and some probe codes could not be found in available databases, therefore, the resulting list counted 529 unique gene IDs, 301 up-and 238 down-regulated.
List B was created by using supplementary data from  [40]  previously available at www. ucihs. uci. edu/ biochem/winokur under 'publications'. To our knowledge, at the moment of submission, the data are no longer available for downloading on this server. Using Affymetrix GCS V3. 2 software and undisclosed statistical criteria, the authors attributed an arbitrary value of 1. 1 to transcripts exhibiting an increase (I), 1. 0 -marginal increase (MI), 0. 0 -no change (NC), À1. 0 -marginal decrease (MD) and À1. 1 -decrease (D). We summed these values across all pairwise comparisons and considered transcripts with a sum of >5. 5 as up-regulated and transcripts with a sum of <À5. 5 as down-regulated in FSHD. In total, 236 probes codes corresponding to differentially expressed genes were selected according to these criteria.
After transforming the list of probe codes to a list of GeneIDs, we obtained a list of 297 unique entries (26 up-and 271 down-regulated GeneIDs). Lists Ca, Cb and Cc were created by using supplementary tables A-G from  [41]  available for downloading at http:// gefu. cribi. unipd. it/papers/FSHD/. From these tables, we have retrieved symbols of genes differentially expressed in FSHD biopsies divided into three sublists of genes (a, b and c), corresponding to the groups of patients, containing 194, 164 and 164 gene names respectively. These were converted to three lists of GeneIDs with 207 (112 up-and 95 down-regulated), 177 (118 up-and 59 down-regulated) and 177 (106 up-and 71 down-regulated) unique GeneIDs respectively. List D was created by using data from supplementary table from  [42]  available at http://onlinelibrary.
Acknowledgements The research has been supported by grants from the  Association Franc ßaise contre les Myopathies (AFM)  to YSV and DL. AB was a recipient of the  IRC-SET-Marie Curie International Mobility Fellowships in Science Engineering  and  Technology, Ireland. P. D. was supported by the  Association "Amis FSH"  and the  University Montpellier I. We thank  C ecile Cassan  for critical reading of the manuscript.
In this context, a multi-scale approach is currently ongoing to provide a satisfying predictive modeling of the SiC f /SiC m composites behavior in a reactor. This is carried out by characterizing separately the different components of the composite, i. e. the fibers, the matrix and the interphase. However, only few data are available on the behavior of the last generation of SiC fibers  [7] [8] [9] [10] [11]. As a consequence, it is necessary to improve this database especially under irradiation. Numerous studies have been achieved on the irradiation effects in SiC. Most of them are related to its structural and microstruc-tural evolution under irradiation  [12] [13] [14] [15]. Similarly, the effect of ion beam irradiation on the thermal and mechanical properties of SiC has also been investigated  [16] [17] [18] [19].
Raman spectroscopy characterization Micro-Raman investigations were performed at RT in a backscattering geometry using a Jobin-Yvon T64000 spectrometer coupled with an Olympus microscope which contains an X-Y-Z stage. The 514. 5 nm line of an argon ion laser was focused on a 1 Â 1 lm 2 spot and collected though a 100Â objective with numerical aperture value of 0. 9. The laser output intensity was kept around 30 mW. Preliminary tests were carried to avoid any heating of the sample which could result in defect annealing. To analyze the different Si-Si, Si-C, and C-C related modes, the spectra were recorded in the spectral range between 600 and 1800 cm À1. The fitting module of the Labspec Raman spectroscopy software was used for simulations of spectra  [31].
Data obtained from these images were used to construct isotropic DWI images and apparent diffusion coefficient (ADC) maps. Other imaging included T 1 -weighted imaging with contrast injection (Gadoterate meglumine, Gado dota, DOTAREM; Guerbet Laboratory, Aulnaysous-Bois, France; 0. 1 mmol/kg), and with magnetization transfer contrast (MTC), time-of-flight MR angiography, and perfusion imaging. This MRI protocol was designed to maximize sensitivity to hemorrhage, ischemic stroke, and white matter lesions (that is, leukoencephalopathy). MRI results were categorized as normal or abnormal. In contrast to our previous report, we classified white matter lesions as significant when patchy, confluent, or diffuse. Punctiform white matter lesions were considered not pathologic.
Definition of variables and outcomes Demographic characteristics, known risk factors for cardiovascular disease (that is, smoking, hypertension, coronary artery disease, diabetes, hypercholesterolemia, hypertriglyceridemia, and stroke), estimated prognosis of pre-existing underlying illness (graded as nonfatal, ultimately, and rapidly fatal disease), date and category of admission (medical or surgical) in the ICU, SAPS-II as well as microbiological data were recorded at admission. From admission to the day of MRI, SOFA score, vital signs, type and dose of catecholamine infused, sedatives, analgesics and antibiotics, use of steroids, days of mechanical ventilation, and standard laboratory tests were recorded daily. Hypotension was defined as a mean arterial pressure <60 mm Hg; oxygen desaturation was defined as an SaO 2 <90%.
Statistical analysis STATA software, Version 11. 1 data analysis and statistical software (StataCorp LP, College Station, TX, USA) was used for statistical analysis. Continuous variables are reported as median (10 th and 90 th percentiles) and as number (proportion) for categoric variables. Kruskal-Wallis and χ2 /Fisher Exact tests were used to determine unadjusted association between type of brain lesions and continuous and categoric variables, respectively. Additional multivariable analysis was performed by means of logistic regression to seek adjusted relations between type of brain lesions and ICU mortality and GOS at 6 months. The selection of independent variables for the model was based on statistical significance at univariable testing. Covariates with a value of P < 0. 05 were included in the multivariable analysis.