dataesr/scientific-paragraphs-categorization huggingface dataset:
Study Population and Data Collection Stratall was a 24-month, randomized, open-label trial which enrolled 459 HIV-infected ART-naive adults in 9 rural district hospitals in Cameroon over the period 2006-2010. The protocol was approved by the National Ethics Committee of Cameroon and the institutional Ethics Committee of the French Institut de Recherche pour le Developpement (IRD). The trial was designed to compare the effectiveness of using a laboratory plus clinical (LAB) monitoring approach (six-monthly viral load and CD4 cell count) with clinical (CLIN) monitoring alone, when measuring ART effectiveness. Participants were recruited by hospital healthcare workers during routine HIV care visits. They were eligible if they were 18 years or older, had confirmed HIV-1 group M infection, WHO clinical stage 3 or 4, or WHO clinical stage 2 with a total lymphocyte count of fewer than 1200 cells per mL.
All participants provided written informed consent. They initiated ART at enrolment (month 0 (M0)). Face-to-face interviews were used to collect socio-demographic data and information about disclosure to relatives and friends as well as experience with HIV testing and care. Data regarding patients' reasons for participating in the trial were also collected (e. g. free access to treatment and care, barriers to requesting financial support from relatives and friends associated with disclosure). The schedule of the medical visits and face-to-face interviews is shown in Table  1. Details on the full design and clinical results of the trial are described elsewhere  [2]. Patients with complete data both at enrolment and at least at one follow-up visit were included in the present analysis (n = 385).
05). Since all participants initiated ART at enrolment, ''Time on ART'' was included in the model as a time-varying covariate for the outcome, measured at M3, M6, M12 and M24. Additionally, a mixed Poisson regression model was also used in the univariate analysis to measure the impact of disclosure to one's steady partner on disclosure to relatives and friends. Analyses were performed using Stata version 10. 0 (Stata Corporation, College Station, Texas, USA) and SPSS version 18. 0 (SPSS Inc, Chicago, Illinois, USA).
Participants' Characteristics Among the 385 participants included in the present analysis, 184 and 201 were randomized in the LAB and CLIN groups respectively. Socio-demographic characteristics of the participants are described in Table  2. At enrolment, median [IQR] age was 36 years  [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] , 71. 4% of participants were female, 52. 5% were single, 56. 6% were in active employment and 41% were heads of their household. A minority of participants (16. 5%) were HIVdiagnosed during hospitalization. Clinical data showed that 51% of participants had a CD4 cell count ,200/mm3 and almost all participants were at WHO clinical stage 3 (75. 1%) or 4 (24. 6%). At enrolment, median [IIQ] time since HIV diagnosis was 3  [1] [2] [3] [4] [5] [6] [7] [8] [9]  months.
Fifty five PLWH enrolled in the Stratall trial were not included in the present analysis since they had complete data only at enrolment (M0). Socio-demographic characteristics for these 55 were not significantly different from those of the PLWH who were included, in terms of gender, age, marital status, being the head of their household and CD4 cell count (data not shown). However, a significantly higher proportion of these 55 were unemployed (n = 10 (22. 2%), p,0. 001). Rates of Disclosure Over Time In the study sample, a majority of participants (n = 313, 81. 3%) increased their overall rate of disclosure over time from M0 to M24, irrespective of the six possible relationship categories (father, mother etc. ) assessed in the present analysis. Among the 72 PLWH whose disclosure index remained constant over time, 14 did not reveal their serostatus to anyone (3.
In the present analysis, data were collected from among HIV-positive people initiating ART at study enrolment. The results reported here are complementary to the ones mentioned just above  [17, 18]  and provide an original longitudinal assessment  of this topic within the context of a Sub-Saharan country that has developed a large national program for access to ART based on the decentralization of HIV care. To date, most published studies describing disclosure to family members, friends, partners, colleagues and health workers in Sub-Saharan countries have been based on cross-sectional surveys  [25, 26, 27]. Longitudinal studies of disclosure to different types of relationships are scarce. Some have been carried out in Midwestern USA on men who have sex with men  [28]  and on women  [29] , others have been carried out in general populations in various African countries including South Africa  [14, 30] , Zimbabwe  [31] , and Ethiopia  [32].
Data entry analysis and statistics All data from the TB-DM register were double entered into an electronic database created using EpiData entry software version 3. 1 (EpiData Association, Odense, Denmark), validated for discrepancies and corrected. Additional variables such as age, sex, type of TB and HIV status, were captured in MS Excel ® (Microsoft, Palisade Corp, Newfi eld, NY, USA) and merged into the EpiData database before analysis. The data was analysed using EpiData analysis software (version V2. 2. 2. 180). Statistical differences between patient characteristics among prevalent DM cases and patients with no DM were evaluated using the χ² test or Fisher's exact test, as appropriate. Confi dence intervals of 95% were used; the level of signifi cance was set at ⩽0. 05.
Quantitative Bay of Biscay model A full description of the Bay of Biscay Ecopath implementation, including the diet composition and parameter values, can be found in  Lassalle et al. (2011). For Ecopath results to be meaningful, model parameters need to be based on information specific to the study area. For almost all groups, biomass (B), production/biomass ratio (P/B), consumption/biomass ratio (Q/B), and diet composition (DC) were derived from area and period-specific raw data or stock assessment results. Thirty-two functional groups were included in the model: two seabirds groups, five marine mammal, nine fish, eight invertebrate, three zooplankton, two primary producer, and one bacteria group, as well as discards from commercial fisheries and pelagic detritus. The five main pelagic forage fish species were given their own group, while demersal fish were divided into four multispecies groups based on their diets.
Regarding the main target species, anchovy and sardine were mainly captured by offshore pelagic trawlers and coastal seiners, respectively, hake by offshore netters, sole by netters, and Nephrops by trawlers, both operating from coastal to more offshore waters  (Daures et al. , 2009). Due to these changes in model structure, the model needed re-balancing, i. e. ecotrophic efficiency of piscivorous demersal fish and carnivorous invertebrates' compartments were slightly above 1. Their biomasses were, therefore, increased by 4 and 10%, respectively. For parameterizing the three fishing fleets, for assessed stocks, international landings for Divisions VIIIa and b were obtained from the reports of the relevant ICES Working Groups (see  Lassalle et al. , 2011, for references). For multispecies fish groups, as well as mackerel and horse mackerel, landings were taken from the Eurostat/ICES catch database.
Annual landings were averaged over the period 1998-2003 for all compartments as most of the biomass data were gathered during this interval (Supplementary material 2 in  Lassalle et al. , 2011). Due to the lack of detailed spatial information, landings could not be limited to the central shelf area, so they might be somewhat overestimated. Discards for each fishing fleet were obtained from the OBSMER programme for the year 2010  (Fauconnet et al. , 2011) , stock assessment reports cited above and the scientific literature  (Pierce et al. , 2010). For this, based on expert advice (L. Fauconnet, pers. comm. ) , each fishing gear was uniquely assigned to one of the three modelled fishing fleets (demersal, pelagic, and invertebrates). Due to sparse discard sampling coverage (mostly 2010), observer bias, and non-random trip selection on a voluntary basis, discard estimates included in the present model should be considered as the best estimates available, though they are most likely underestimates.
Bycatch estimates for common dolphin and harbour porpoise were derived from observations of incidental captures of cetaceans and seabirds in European waters (data from national reports on the implementation of regulation 812/2004); they were entered as discards in the model. These recent cetacean bycatch estimates and past scientific publications indicated that pelagic trawls were primarily responsible for common dolphins bycatch and set-nets for harbour porpoises incidental captures (see  Lassalle et al. , 2012, for references). Hence, the estimates were assigned to the pelagic and demersal fleet, respectively.
Acknowledgements This research received financial support from the  EU   FP7  grant  FACTS  ( Forage Fish Interactions ), grant agreement no. 244 966 , and a postdoctoral fellowship from  IFREMER  to  Geraldine Lassalle. It was also funded, in a lesser extent, by the project  DEVOTES (DEVelopment Of innovative Tools for understanding marine biodiversity and assessing good Environmental Status ) funded by the  European Union  under the  7th Framework Programme, "The Ocean for Tomorrow" Theme  (grant agreement no. 308392 ; www. devotes-project. eu). We wish to thank two anonymous referees who provided valuable criticisms and helpful comments in the final stages of the paper.
PARTICIPANTS Five blind subjects and a single normal-sighted individual (3 males; mean age = 34. 3 years, SD = 11. 99) participated in this functional imaging experiment (Table  1 ). All of them were righthanded (Edinburgh handedness inventory) native German speakers without a history of neurological problems or hearing deficits as determined by means of an audiogram. The study design had been approved by the ethics committee of the University of Tübingen. All blind participants received a set of written information (MRI guidelines, data protection, and consent form) as pdf-files by email. Prior to fMRI measurements, the experimenter read, in addition, the materials aloud to each blind individual, and the consent form was signed in the presence of a sighted witness. Since the blind participants were recruited from community organizations, a detailed clinical data bank was not available to the authors and, thus, information on etiology and follow-up of the ophthalmological disorders had to be drawn from personal interviews and previous medical records.
fMRI-DATA ACQUISITION Based upon an event-related design, the set of 180 stimuli of each functional imaging session (30 items at three speaking rates plus the respective backward signals) as well as 40 silent baseline events (scanner noise only) were applied in a randomized order, subdivided into five runs of 44 stimuli each as binaural-symmetric signals to the participants via headphones (Sennheiser HD 570; modified by removal of the permanent magnet, see  Baumgart et al. , 1998). Since these headphones show sufficient dampening of environmental noise, it was not necessary to provide additional earplugs during the experiments. The inter-stimulus interval amounted to 9. 6 s (jitter ± 1. 4 s, steps of 0. 2 s). Since the design did not allow for an explicit control of speech comprehension during the fMRI experiment, behavioral performance was evaluated offline, and during scanning subjects were just instructed to listen carefully to the applied auditory stimuli and to try to understand them.
fMRI-DATA ANALYSES Preprocessing of the data encompassed slice time and motion correction, normalization to the Montreal Neurological Institute (MNI) template space, and smoothing by means of an 8 mm full-width half-maximum Gaussian kernel (SPM5 software package; http://www. fil. ion. ucl. ac. uk/spm). For the sake of statistical analysis, the blood oxygen level-dependent (BOLD) responses were modeled by means of a prototypical hemodynamic function within the context of a general linear model, event durations being specified as 4 s epochs. Any low-frequency temporal drifts were removed using a 128 s high-pass filter. The evaluation of the functional imaging data encompassed the following steps of signal analysis: (1) In order to delineate the brain regions engaged in the processing of moderately fast (=8 syl/s) and ultra-fast (=18 syl/s) verbal utterances before and after the learning interval, pre-and post-training runs were analyzed in a concatenated sequence (1st level SPM analysis).
Architectural Data Analysis The characteristics of trees, axes and root segments were computed in the same way as that described in  [42] , using the AMAPmod software (freely available for Linux and Windows platforms: www. cirad. fr and ftp. cirad. fr/pub/amap/AMAPmod See http://openalea. gforge. inria. fr (Pradal et al. 2008 ))  [43]. Additional computations, statistics and graphs were produced using the R open statistical package (R Core Team 2012. R: A Language and Environment for Statistical Computing}, R Foundation for Statistical Computing, Vienna, Austria, AMAPmod and R functions for root architecture analysis available from the first authors). The allocation to roots was analysed as a ''root partitioning coefficient'' (RPC -see list of abbreviations table  S1 ) or root mass fraction.
Acknowledgments We thank  E. Bertocchi ,  M. Chassagne  and  P. Taris  for technical help. The glasshouse was managed by the  UniteExperimentale de l'Hermitage ,  UE 0570 ,  INRA ,  69  route d'Arcachon, 33612 CESTAS. We also thank the Linux, R and openALEA-AMAP open software community for software and support. AMAP (Botany and Computational Plant Architecture)  is a joint research unit which associates CIRAD ( UMR51 ),  CNRS  ( UMR5120 ),  INRA  ( UMR931 ),  IRD  ( 2M123 ), and  Montpellier 2 University  ( UM27 ). We furthermore thank the anonymous reviewers for helpful comments on an earlier version of the manuscript.
For IC10, in vitro data showed that higher N/P ratios (from N/P of 8 at 10 nmol/l to N/P of 80 at 1 nmol/l) promoted efficient siRNA delivery and gene silencing. It is known that the ratio of lipid to siRNA is one of the key factors that strongly influences the shape, size, and behavior of lipoplexes. 22 The size of the complexes formulated for in vivo use, in 5% glucose solution, with IC10 at various N/P ratios and with jetSI/DOPE at N/P ratio of 6 was evaluated by dynamic light scattering. The size of siRNA/(jetSI/DOPE) complexes was 397. 0 ± 33. 5 nm (mean ± SEM, n = 15). However, complexes were one order of magnitude smaller with a mean size of 32. 1 ± 4. 4 nm (Figure  1c ) when formed with IC10 at N/P 15. The zeta potentials of siRNA/IC10 and siRNA/(jetSi/ DOPE) complexes were +62. 1 ± 3.
Acknowledgments. We thank the IJM imaging platform and  G Levi  for insightful comments. The excellent care provided by  Stéphane Sosinsky ,  Philippe Durand , and  Fabien Uridat  is gratefully acknowledged. This work was supported by the  Centre National de la Recherche Scientifique (CNRS) , the  Museum National d'Histoire Naturelle (MNHN) , the  Association Française contre les Myopathies (AFM)  "[grant number  MNM1 2012-14685 ],"  European Union contracts "Crescendo"  "[grant number  LSHM-CT-2005-018652 ], " Switchbox " [grant number  FP7-Health-2010 n° 259772]," and the French ANR "Thrast"  "[grant number  11BSV2 019 02 ]. "A. L. -J. received a PhD grant from the  Association national de la Recherche et technologie (ANRT)  and Polyplus-transfection S. A. under CIFRE convention "[grant number  251/2007 ].
Longitudinal and Transverse Ultrasonic Velocities. The ultrasonic setup is composed of a pulse generator and receiver Sofranel model 5800 PR, two piezoelectric transducers of longitudinal waves and two piezoelectric transducers of transverse waves, a computer for data acquisition and data processing with a card oscilloscope/digitizer of 20 MHz sampling frequency, and a program of acquisition and signal processing developed under LabView environment.
, 1988). The reaction was started by adding 10 mM MgATP in a stirred microcuvette containing 50 l of vesicles and 20 M AO, equilibrated at 32°C. The reaction was stopped after 15-20 min by adding 50 mM (NH 4 ) 2 SO 4 to dissipate the proton gradient across the vesicular membrane and release AO from the vesicular lumen. Changes of fluorescence were analyzed using a Photon Technology International spectrofluorimeter (excitation, 490 nm; emission, 530 nm). The acidification kinetics were analyzed using Felix32 software (Photon Technology International) for acquisition of AO fluorescence and Prism4 (Graph-Pad Software) for kinetics and statistical analysis. Traces were normalized to the fluorescence at t ϭ 0 and corrected for baseline shifts induced by volume changes associated with the additions.
Statistical Analyses Experimental data are expressed as means 6 SEM. One-way ANOVA (Dunnett's multiple-comparison test) and two-way ANOVA (Bonferroni's post-test) were performed using Graph-Pad Prism (version 5. 01). Differences were considered statistically significant as follows: * p#0. 05, **p#0. 01, and ***p#0. 005 versus buffer or the appropriate diluent. Densitometric analyses were performed using AlphaEaseFC (FluorChem HD2).
S100A8 and S100A9 Induce Inflammatory Cytokine Secretion The effect of S100A8 and S100A9 on the production of cytokines/chemokines was first screened using an antibody array. As illustrated in Figure  1A  and 1B, S100A8 and S100A9 induced the secretion of several pro-inflammatory cytokines in PBMCs (Fig. 1A  and 1B ). Among these, the cytokines IL-6, IL-1b, TNFa and the chemokines IL-8, growth-regulated oncogene alpha (Gro-a), MIP-1a, and MIP-1b were the most secreted. The secretion of IL-6 and IL-8 in PBMCs was also confirmed by ELISA (Fig. 1C ). The concentrations of these cytokines were comparable to those observed in the supernatants of cells stimulated with LPS. Isolation of monocytes, CD4+ T cells, CD8+ T cells, and B cells revealed that monocytes were the only cell type responsible for cytokine production (data not shown).
Statistical analysis Associations between groups and specific classes of allele, as well as genotypes were analyzed by the two-tailed Fisher's exact test. Odds ratios (OR) and the associated 95% confidence interval (CI) were calculated to assess the relative risk conferred by a particular allele or genotype. We also performed logistic regression analysis including the hemophilia-causing mutations, using the SAS software for Windows, version 9. 3. In the logistic regression analysis, patients with inversions in intron 1 or intron 22 were pooled in the same group to reach a sufficient number of cases. 29 tatistical significance was accepted at P<0. 05.
Acknowledgments We thank  Robert Calvora  ( Baxter, Maurepas, France ) for his trust and support. We also thank  Ludivine Launay  for statistical analyses. The research leading to these results was conducted as part of the  ABIRISK consortium (Anti-Biopharmaceutical Immunization : prediction and analysis of clinical relevance to minimize the risk). For further information please refer to www. abirisk. eu.
Funding This work was supported by the  Institut National de la Santé et de la Recherche Médicale ,  Centre National de la Recherche Scientifique, Université Pierre et Marie Curie -Paris 6 ,  Agence Nationale de la Recherche  ( ANR-07-MRAR-028-01 ), and the  Innovative Medicines Initiative Joint Undertaking  under grant agreement n. 115303, with resources from the  European Union 's  Seventh Framework Programme  ( FP7/2007-2013 ) and EFPIA companies' in kind contribution. JDD and SD were recipients of fellowships from the  Fondation de la Recherche Médicale  ( FRM, Paris ). IP was the recipient of a fellowship from the  Ministère de la Recherche (France).
Protein electrophoresis and Western blotting Cells were harvested by scraping, homogenized, and analyzed by SDS-PAGE followed by Western blotting using the indicated antibodies. Quantification was performed using ImageJ software (National Institutes of Health). The mean intensity of each individual band of interest was calculated after background value subtraction. Values were normalized to the mean intensity of the loading control band for each sample. To quantify phosphorylated GFP-MyoVI, the mean intensity of the phospho-GFP-MyoVI band was normalized to the total immunoprecipitated GFP-MyoVI. SGs and cytosol purification from bovine adrenal medulla Bovine adrenal medullas were fractionated as previously described  (Simon et al. , 1988; Meunier et al. , 2005; Wen et al. , 2011). In brief, isolated medullas were homogenized in 0.
Myosin VI knockdown For transient myosin VI knockdown, PC12 cells were transfected twice at 24-h intervals using Lipofectamine LTX (Invitrogen) and shRNA constructs against rat myosin VI (XM_236444; obtained from the NCBI Nucleotide database) target sequences: clone 2 (sh2-RNA), 5-AGATGACCTTC-GAGTCAGTTT-3; clone 3 (sh3-RNA), 5-AAGCGACTCGATAAGTTCAAT-3; and scrambled RNA (control), 5-GGAATCTCATTCGATGCATAC-3 (SABiosciences). Each shRNA vector expressed GFP under a separate promoter. To generate stable myosin VI knockdown PC12 cells, puromycinresistant sh2-RNA (SABiosciences) was used. Transfected cells were selected using 3 µg/ml puromycin for 3 wk and subsequently maintained in 2. 5 µg/ml puromycin. For TIRF experiments, PC12 cells were transfected twice at 24-h intervals, with NPY-mCherry and control, sh2-RNA, or sh3-RNA plasmids as in this paragraph, and the cells were sorted using a cell sorter (Influx; BD).
The sample was spotted 1:2 with diluted -cyano-4-hydroxycinnamic acid (CHCA; Bruker). The diluted matrix was prepared by 1:10 dilution of saturated CHCA in acetone (Sigma-Aldrich) into 6:3:1 ethanol (Sigma-Aldrich)/acetone/0. 1% TFA. The peptide calibration mixture (Bruker) was manually spotted onto the appropriate calibration positions. Targets were allowed to air dry for 30 min before loading into the ion source of the MALDI-time of flight (TOF)/TOF (Ultraflex III; Bruker). Automated data acquisition was performed using the Compass 1. 3 suite of the software  (FlexControl, FlexAnalysis, WarpLC, and BioTools; Bruker). MALDI-TOF-MS was performed in positive ion reflector mode with digitizing at 1 GHz to allow acquisition with a laser rate of 200 Hz over the mass/charge (m/z) range of 900-3,500.
All LIFT was acquired at 200 Hz using a 1-GHz digitizer rate. Data processing. Each sample was separated twice by HPLC, and each target was analyzed twice by MALDI-TOF/TOF (LC-MALDI) for a total of four LC-MALDI datasets per sample. The four BTDX. xml files generated by WarpLC and BioTools, containing parent and fragment ion mass and intensity data for each run, were combined using an in-house algorithm to generate an averaged Mascot (Matrix Science) generic file (MGF) representative of the total peptides present in all four runs. The Mascot generic files of averaged data were used to perform an in-house Mascot search of the International Protein Index bovine database and SwissProt database (all taxa) using the following parameters: enzyme containing semitrypsin with two missed cleavages, fixed modifications of carbamidomethylcysteine, variable modifications of deamidated NQ and oxidized M, peptide tolerance of 50 ppm, and MS/MS tolerance of 0.