dataesr/scientific-paragraphs-categorization huggingface dataset:
Participants and data collection A case report form (CRF) was used to collect at the baseline and at different visits. This included data on the family environment (socio-demographic and economic characteristics of the family, information on parents), monitoring of pregnancy and childbirth (anthropometric parameters at birth, data concerning the PMTCT, clinical features of the infant) information on the anthropometric parameters of the children (weight, height, cranial and brachial perimeter). Weight was measure with the child supine and the crown of the head touching a vertical headboard using scale and flexible measuring tape respectively. For those aged 2 to 5 years, they step onto scale with one foot on each side. For the length, the child stands against the stadiometer on the board facing the practitioner Clinical status (clinical events since the last protocol visit), family environment, data related to ARV treatments received since the last visit (including adherence to treatment) was collected longitudinally.
Main outcome definition and covariables The main outcome was growth retardation including underweight, stunting or wasting defined at each visit using anthropometric indices as weight-for-age (WAZ) <-2, weight-forlength (WLZ) <-2, and length-for-age (LAZ) <-2 Z-scores respectively (7, 14). Z-score was calculated using the 2006 WHO growth standard  [19]. Prior to the data analysis, a number of variables were recoded. Thus, the mother's marital status was recoded in married, cohabitation and single/divorced/widow; the level of household income in <100,000 CFA francs and �100,000; the level of CD4 in <25% and � 25%. The hemoglobin level was recoded according to the 2011 WHO criteria  [20]  as follows: not anemia (� 11 g / dl in children aged 0-24 months and � 10 g / dl in in children aged 24-60 months), mild or moderate anemia (7 to 10.
[29]. This method was chosen because its capacity to account for biases generated by missing data on the growth indices (dependent variables). Due to the participants' behavior concerning LTFU, we hypothesize that the mechanism of the missing data was informative, placing us in the context of Missing Not At Random according to the missing data typology proposed by Rubin et al. [30]. In the first stage, a GEE probit model was used to identify factors associated with missing data at any visit of the scheduled follow-up, taking into account both the variables observed at baseline and time-dependent variables. The residuals of this model were used to compute the inverse mills ratio (IMR), representing the effect of all unobserved variables that can influence the missingness process. In the second stage, a GEE identity was used to model the marginal expectation of anthropometric indices.
05 or when the confidence interval of the associated estimate did not contain the value 0. Due to the moderate proportion of missing around 10% accounting for all variables, we first imputed values using multiple imputations by conditional approach under the Missing At Random hypothesis. All variables (except anthropometric parameters) with missing data were included in the imputation model. This strategy for handling missing data was chosen because it allows both problems of bias and precision that could induce an inappropriate method to be resolved, especially when the imputation is done correctly  [32]. We considered 10 multiple imputations with 10 iterations. All analyzes were carried out using WHO Anthro (for the estimation of Z-scrores during follow-up) and R software, with the packages mice and mitools for multiple imputation, msm for multi-state model, geepack and BSagri for GEE.
The multi-state models of the Markovian type used allowed us to study the dynamics evolution of the growth retardation taking into account the censorship interval observed on the occurrence of the growth retardation. Available studies are mostly based on Cox proportional hazard models that consider right censorship of deaths and first occurrence of growth retardation. Another interesting aspect of this study was the missing data consideration using the most well-known methods for minimizing induced biases based on the hypothesis of the nonresponse process: multiple imputation and Heckman methods. Three common growth indicators encountered during the first five years of live in the literature were used: weight-for-age, weight for length, and length-for-age Z-score. One of the perspectives of this work would be to define, using these 3 indices, a single indicator for the growth retardation.
Acknowledgments We would like to thank all those who contributed to this study, especially the parents who agreed the inclusion of their children in this study. We thank the coordination team and all the staff involved in the ANRS-PEDIACAM study. We gratefully acknowledge very helpful and constructive comments and suggestions from the academic editor and the anonymous referee, which lead to significant improvements of this manuscript. The  ANRS-Pediacam Study Team  is as follows: Primary investigators:  Prof Albert Faye  ( Hopital Robert Debre/ Univ. Paris 7, France ) and  Dr Mathurin Cyrille Tejiokem  ( Centre Pasteur du Cameroun, Yaounde ). Co-investigators:  Prof Francoise Barre-Sinoussi  and  Dr Daniel Scott  ( Unitede Regulations des Infections Retrovirales, Institut Pasteur de Paris, France ),  Dr Frederic Tangy (Unitede Genomique virale et Vaccinantion ,  Institut Pasteur de Paris, France) ,  Dr Josiane Warszawski  (Equipe 4 (VIH et  IST)-INSERM U1018 (CESP)/Univ.
Apart from this single rainwater sample, ICP-MS based Se speciation data for rainwater are not available. Although long-range atmospheric transport of marinederived I and Se has been suggested,  14, 15, 21, 41, [55] [56] [57]  studies that directly link I and Se in rainfall to the origin of moisture sources are scarce. To study potential long-range transport and contributions of marine versus continental moisture sources, we investigated time series of I and Se concentrations and speciation in wet deposition at two high altitude sites, i. e. , Jungfraujoch (Alps, Switzerland) and Pic du Midi (Pyrenees, France). Apart from I and Se, we determined bromine (Br) and sulfur (S) concentrations and speciation. Br and S share chemical properties and environmental pathways with I and Se; however, they generally have higher environmental concentrations than I and Se, e.
Furthermore, this study presents the first quantitative and qualitative data on I and Se in precipitation at high-altitude sites and time series for speciation of I, Se, Br, and S in precipitation. These sites are particularly suitable to investigate long-range transport as they are often exposed to free tropospheric air. 66, 67 t both sites, bulk precipitation was collected with an open sampler (JFJ bulk/PDM bulk) with a collection area of 0. 04 m 2. In addition to the bulk sampler at PDM, wet-only precipitation (referred to as "PDM wet-only", collection only during rain events) was collected with a sampler from Eigenbrodt (NSA181/E HD-PE), especially designed for high altitudes. The precipitation at JFJ (JFJ bulk) was collected weekly from July 2015 to September 2016 (28/07/15-27/09/ 16).
The concentrations were determined using calibration series with mixed standards of stock solutions of selenite (SeO 3 2-, SeIV), selenate (SeO 4 2-, SeVI) (Spectracer), sulfate (SO 4 2-, Fluka), MSA (Sigma-Aldrich), and sodium and potassium salts of bromide (Br -), bromate (BrO 3 -) (Sigma-Aldrich), iodate (IO 3 -), and iodide (I -) (Sigma-Aldrich). All chromatographic peaks could be unambiguously identified (Figure  S5 ). ICP-QQQ and LC-ICP-QQQ data collection and processing were performed using MassHunter software. Anion Quantification with IC and Calculated Sulfate Fractions. 3] [74]  A detailed description of methods can be found in the SI. Statistical calculations were performed using SPSS, RStudio, and Origin 7. 0. Correlations were performed as Spearman rank correlations (correlation coefficient indicated by ρ) and partial correlations restricted by precipitation volume (Pearson correlations, correlation coefficient indicated by r) and were all based on significance p < 0.
05. Trajectory-Based Moisture Source and Loss Analysis. Air parcel backward trajectories were calculated using the 3D wind fields from two different atmospheric model data sets. 75, 76 On a global scale 6-hourly data from the ERA-Interim reanalyses  77  of the European Centre for Medium-Range Weather Forecasts (ECMWF) were used on a regular horizontal grid of 1°resolution with 60 vertical levels. On the regional European scale the higher spatial and temporal resolution analysis data of the limited-area model COSMO  78, 79  was chosen to obtain a more realistic representation of the European orography and the coastal regions. Hourly COSMO data are provided operationally by MeteoSwiss with 7 km horizontal grid spacing and 60 vertical levels. The two trajectory data sets served as a basis to identify evaporative moisture sources of precipitation at the two sites JFJ and PDM following a Lagrangian procedure.
80 For more information on the two atmospheric analysis data sets used, the trajectory calculation and the moisture source diagnostics see SI and Figures  S1, S2,  and S3. From the air parcel trajectories and the moisture source information several characteristic quantities of atmospheric moisture cycling were derived: 1. Moisture source contributions from different regions: in particular, the share of continental vs marine moisture sources were calculated. For this, the gridded moisture uptakes as obtained from the moisture source diagnostics  80  (see also SI Figures  S1  and S2 ) were integrated over marine and continental areas respectively by using the land-sea mask of the ERA-Interim data set. The global ERA-Interim data set was used for this analysis because it covers the whole North Atlantic, which can represent a large share of the moisture sources at the two sites in particular in winter.
However, at JFJ rainfall data was only obtained using a bulk sampler (same type as used at PDM). Therefore, for PDM only precipitation data derived from the bulk sampler are discussed, to enable a comparison between the two sites. In contrast to JFJ, for PDM no data are available for winter and only limited data for autumn. Total concentrations of Se, I, S, and Br over the whole sampling period ranged from 0. 16 to 2. 33 nM (0. 62 ± 0. 41, VWM 0. 65 nM), 0. 4-26. 8 nM (9. 4 ± 5. 1 nM, VWM 10. 1 nM), 2. 2-44. 3 μM (11. 4 ± 8. 3, VWM 1. 1 μM), and 14. 9-98. 8 nM (44. 0 ± 19. 2 nM, 41. 7 nM), respectively (Table  1 , S5). When the same seasons are compared (see Figures  S6  and S7 ), it can be seen that concentrations of these elements are generally higher in rainfall at PDM than at JFJ. These differences are likely not only explained by the difference in elevation as very low concentrations were also found at lower altitude stations in Switzerland (see Table  1 , S5).
Contamination of fresh water bodies by human enteric viruses from wastewater discharge is a well-established phenomenon. Here we propose a model of viral contamination of rivers based on acute gastroenteritis epidemiology and assess how well it can simulate in situ experimental monitoring. Noroviruses, rotaviruses, enteroviruses, adenoviruses and hepatitis A viruses were quantified by molecular methods after water concentration. Water flows were obtained from the Hydro databank and wastewater treatment plant (WWTP) data. Acute gastroenteritis cases based on medical prescriptions were recorded by the French public health agency. We estimated the total number of daily viral acute gastroenteritis cases and modeled virus shedding and fate in WWTPs and rivers. Simulated virus concentrations were compared to the weighted sum of measured concentrations.
8 to 10 +4. 0 for RV-A, 10 +0. 8 to 10 +2. 4 for EV, and 10 +2. 8 to 10 +6. 0 for AdV (Fig. 4c ). These orders of magnitude were in agreement with published data  (D'Ugo et al. , 2016; Prevost et al. , 2015; Sinclair et al. , 2009) , and with the seasonal variations in quantity  (Iaconelli et al. , 2016; Vieira et al. , 2016). Virus infectivity is only assayed by cultivation. Most enteric viruses are not easily cultivable in vitro, so that molecular techniques have become very common for virus detection, even though the detection of viral nucleic acids does not consistently imply infectious risk. Virus integrity assay based on particle pretreatment with monoazides (EMA, PMA, PMAxx) was suggested for a better estimation of infectious risk associated to genome detection. Nevertheless, in a previous study, we did not find any significant difference of virus quantification in environmental waters based on total genome detection (RT-qPCR) or integrity assay using monoazide dyes  (Prevost et al.
From September 2015 to August 2016, cumulated rainfall was 564 mm, and mean temperature was 12. 3 °C at the Clermont-Ferrand airport weather station. Additional data concerning the Artière River flow upstream of wastewater discharge (45. 77 N, 3. 14 E) was obtained from the Hydro databank run by the French Ministry for Ecology, Energy and Sustainable Development (Ministère de l'Ecologie, du Développement Durable et de l'Energie,.
Acknowledgments This work was supported by the  French State  through the  French National Research Agency  under the " Investments for the Future"  under reference  ANR-10-LABX-001-01   Labex Agro  (project headed "Fate of human enteric viruses after the discharge or reuse of treated wastewater"). It was also partly supported by the  Bourgogne -Franche Comté Regional Council  and the  "Fonds Européen de DEveloppement Régional" (FEDER). The authors thank the  Provence-Alpes-Côte-d'Azur Regional Council  and the  French National Institute of Agronomic Research (INRA)  for support through  V. Tesson 's PhD grant. We also thank all the stakeholders who helped us for this work:  Clermont-Auvergne-Métropole  and Veolia operating the 'Trois Rivières' WWTP during the experimental sampling period, the  French health agency Santé publique France  and the French health insurance system, the ' ASA Limagne Noire ' farmers association reusing the treated wastewater and other farmers who gave us access to vegetable gardens or wells to the alluvial aquifers of Artière and Allier rivers, SOMIVAL Engineering and  Consultancy, Eiffage , the  Sucrerie de Bourdon of Cristal Union agroindustrial cooperative group , and the  Auvergne-Rhône-Alpes INRA Research Centre in Clermont-Ferrand.
Curcumin binds iron Spectroscopic shift techniques have shown that iron binds to curcumin in solution  54, 63. Figure  1  illustrates the capability of curcumin to chelate divalent cations, i. e. , iron (Fe 2+ ). We used an alternative metal affinity chromatography method with handmade Fe-NTA columns. Figure  2a  shows the loading efficiency of curcumin from solution to the Fe-NTA-agarose column. Curcumin binding was rapid and efficient, reaching 90-95% after incubation for 10 min on the iron-containing resin. It is well known that the diketone groups of curcumin likely interact with the Fe-NTA-resin in a similar fashion to the phosphate oxygens of phosphopeptides, for which this iron affinity chromatography resin was developed  64. The data extracted from Fig. 2  gave an affinity estimation around μM, in agreement with the high-affinity iron binding site of curcumin reported by Baum et al.
Finally, the fluorescence spectra were recorded after spectrograph dispersion, in the 380-630 nm region on a 1024 diode-intensified optical multichannel analyzer (Princeton Instruments, Inc. , Princeton, NJ) with a resolution of 0. 25 nm/diode. Each fluorescence emission spectrum was collected from 1 to 10 s. Data were stored and processed on an 80286 IBM PS/2 microcomputer using the Jobin-Yvon "Enhanced Prism" software. It should be noted that, in order to avoid any possible fluorescence from a plastic or glass support during analysis with near-UV excitation, cells were grown on quartz plates that were then placed on the microscope stage in 50-mm thermostated Petri dishes, filled with 5 mL of phosphate buffered saline (PBS). A uranyl glass bar was used as a fluorescence standard to control laser power and instrumental response and to enable quantitative comparison between spectra recorded on different days.
Statistical analysis Results are given as mean ± standard error (SEM). Differences between dietary groups were analyzed in statistical software R (R Development Core  Team, 2008)  or SigmaStat 3 (SPSS, Chicago, IL, USA) using one-way ANOVA. Tocopherol data were analyzed using two-way ANOVA to compare data from oocytes with data at swim-up fry stage. All data were tested for normal distribution and homogeneity and only in case the assumptions were not respected, the ANOVA was performed instead on ranks. The binary spawning data were analyzed pairwise using χ 2 test. Percentages were arc-sin transformed before analysis. A Newman-Keuls post-hoc test was used to compare means, when a significant difference (P < 0. 05) was found.
Acknowledgements The authors have no conflict of interest to declare for this work that was labelled by the  "Institut Carnot France Futur Elevage  ( IC-F2E )". This present study was supported by I-site  E2S  from the  University of Pau and Pays de l'Adour  ( P. W. , PhD  fellowship) and  IMR  (P. A. J. P. , ParSel Project no. 15329 ). The authors wish to thank  P. Maunas  and  N. Turonnet  for the care of fish and  F. Terrier ,  F. Sandres  and  A. Lanuque  for the preparation of diets. The authors are also very grateful to  L. Larroquet ,  V. Véron  and  C. Héraud  for technical assistance in lipid, enzyme activity and tocopherol analysis. The help of M. Sérusier and M. Cluzeaud in sampling and training was also greatly appreciated.
Acknowledgements Two anonymous reviewers are thanked for many important comments, especially about the statistically validity of the results. We thank the  CNRS  via a grant of the mission pour les initiatives transverses et interdisciplinaires ( MITI) Defi ISOTOP (grant MAMI ) and the  Université Sorbonne Paris Cité  for a Chaire d'Excellence. Parts of this work were supported by  IPGP  multidisciplinary program PARI, and by  Region île-de-France SESAME  Grant No. 12015908.
All animal procedures were conducted in compliance with and approved by the IACUC of the Saban Research Institute of the Children's Hospital of Los Angeles. Images were then acquired using a Zeiss LSM 710 confocal system. Sections of five different regions of interest (100 × 100 µm) spaced at 100, 200, 300, 400, and 500 µm extending radially from the edge of the ARH explants were acquired with a 10X objective. The image analysis was performed using ImageJ analysis software (NIH), as previously described  (13, 21). Briefly, each image plane was binarized to isolate labeled fibers from the background and to compensate for differences in fluorescence intensity. The integrated intensity, which reflects the total number of pixels in the binarized image, was then calculated for each image. This procedure was conducted for each image plane in the stack, and the values for all of the image planes in a stack were summed.
The relative infectivity values were obtained from survival time bioassays in reporter tg338 mice. Specific infectivity values of (c) LA21K fast scrapie strain classified as fast strain (mean survival times of 56 days in tg338 mice), (d) LA19K (133 days), (e) Nor98 (186 days) and (f) sheep BSE (135 days), as slow strains. The amount of PrP Sc assemblies in terms of object (red line) has been estimated by dividing the sedimentogram expressed in the equivalent of monomeric PrP by the theoretical fraction-molecular weight correspondence after calibration of the gradient for molecular weight  [25]. The guanidine hydrochloride denaturation values of each strain are indicated ([Gdn] 1/2 values in mol/L ± SEM, data from  [23] ). The PrP solubilization conditions play an important role in the interpretation of PrP Sc quaternary structure studies and PrP assemblies density estimation.
Lung histology Twenty eight-to 31-week-old mice were euthanized and the lungs and heart were dissected en bloc. The lungs were inflated with 4% PFA fixative administration through the trachea and immediately separated, the right lobe immersed in PFA for histology and the left lobes immersed in glutaraldehyde 2. 5% for transmission electron microscopy (TEM) (see supplemental Methods). For histology, paraffin-embedded lung tissue was sectioned (5-mm-thick sections) and stained with either Masson trichrome or hematoxylin and eosin staining. Alveolar space and multilamellar bodies were quantified using ImageJ software. Flow cytometry for measurement of integrin aIIbb3 activation, P-selectin, and LAMP1 exposure and mepacrine loading capacity Washed platelets (5 3 10 7 /mL) were stimulated with thrombin and subsequently blocked with hirudin (100 U/mL), colabeled with anti-GPIbb antibody and JonA-PE (1/50, recognizing activated aIIbb3) or P-selectin (5 mg/mL) or LAMP1 (1/100).
RAB32 and RAB38 are required for dense granule formation We next investigated whether the absence of DG contents was the result of the absence of DG compartments or reflected only their defective storage capacity. As seen on TEM images, DG formation in DKO mouse platelets was strongly impaired, with only a few granules being observed. Furthermore, these DGs presented an abnormal dense core having a very small, linear, or poorly condensed appearance (Figure  4A , right), in contrast to normal DGs having a typical "bull's-eye" morphology  35  (Figure  4A , left). No morphological defect in platelet DGs was observed in single knockout or in [Rab32 1/2 ;Rab38 2/2 ] or [Rab32 2/2 ;Rab38 1/2 ] mice (data not shown). Because empty or immature granules may not be identified by TEM, mepacrine uptake was quantified as a measure of DG amount.
36, 37 Mepacrine uptake was decreased by 45% in resting DKO platelets compared with WT (Figure  4B ). As a control, we observed that thrombin preactivated platelets incorporated minor amount of mepacrine, irrespective of their genotype (Figure  4B ). Altogether, these data indicate that DKO platelets combine a decreased DG number and an impaired granule content. We then used focused ion beam (FIB)/scanning electron microscopy analysis and 3-dimensional (3D) reconstruction  38  to determine the exact number of DGs per platelet, even if empty. We counted 17. 6 6 1. 4 DG (mean 6 SEM) in WT platelets, consistent with our previous observations of a higher number of DGs in mouse than in human platelets (A. E. , personal observations). A 70% decrease in the total number of DGs in DKO platelets (5.
Severely impaired hemostasis and thrombosis in Rab32/Rab38-deficient mice The main function of the secretion of DG content is to recruit other circulating platelets to the site of injury and amplify platelet activation. As patients with DG deficiencies have a compromised hemostatic capacity,  1, 7, 39  we evaluated hemostasis and thrombosis. Hemostasis evaluated in a tail bleeding assay appeared unaffected in Rab32 or Rab38 single knockout mice, in accordance with data in cht mouse. 21 In contrast, a marked increase in bleeding time was recorded in DKO animals with no cessation after 30 minutes (Figure  5A ). No intermediate phenotype was observed in [Rab32 2/2 ;Rab38 1/2 ] or [Rab32 1/2 ;Rab38 2/2 ] mice, indicating that their partial 5-HT and ADP content was sufficient to prevent excessive bleeding.
1%/192 mM; pH 8. 8,  Laemmli, 1970). These stainfree gels contain trihalogen compounds that allow reactions with tryptophan residues of proteins that can be detected by fluorescence emission after UV excitation. After electrophoresis (200 volts, 75 mA for 30-40 min), gels were placed on a stainfree tray for the detection of protein bands by fluorescence using the Gel DocTM EZ system 2. The level of seed protein abundance was determined by image analysis using Image Lab Software (Bio-Rad 3  ). The mean value of relative abundance for the SSPs at 12 (napin) and 30 kDa (cruciferin) was calculated for each treatment (Supplementary Figure  S1 ).