dataesr/scientific-paragraphs-categorization huggingface dataset:
Food composition Food composition data was retrieved from the Open Food Facts project database (http://world. openfoodfacts. org/). Open Food Facts is a collaborative web project gathering food composition data based on labeling from all over the world. Data is collected by volunteer contributors and includes information about ingredients and nutrition facts from food products purchased in stores. The collected data is available freely as an open data source and can be downloaded for research purposes. As the items in the database are collected from stores, foods and beverages included are exclusively manufactured pre-packaged foods. The open Food Facts database contains data from national brands, store brands and discount brands. Some products may have multiple entries if they are sold in various amounts (e.
g. Nutella® can be purchased in packs of 200, 440, 630, 780 or 1 kg, each appearing in the Open Food Facts database as a separate item), leading in some cases to multiple data lines. The Open Food Facts database therefore reads as supermarket referencing. Data was retrieved from the Open Food Facts database on December 2nd, 2014. Only products marketed in France were used for the analysis. Products with complete available data for the computation of the FSA score were retained for the analyses (n = 7777).
Additionally, the results observed in our study are consistent with those investigating the consistency of the FSA score, using nutritional composition data from a database used for scientific purpose, confirming the stability of results using two different sources of data  [13]. Front-of-pack labels currently in use in Europe include nutrient-specific labels, either factual (e. g. Guidelines Daily Amounts (GDAs), displaying the relative contribution for a portion size in energy, fat, saturated fat, sugar and sodium of a given product  [16] ) or with a color- coding (e. g. 'Traffic lights' , displaying 'green' 'amber' or 'red' dots for content per 100 g in the same nutrients  [17] ) and single indicators of nutritional quality, using nutrient profiling systems (the Danish green 'Keyhole'  [18]  or the Dutch 'Choices'  [19] ).
Our results tend to show that the use of a modified FSA score associated with the 5-CNL, while being 'across-the-board' from most food items, responds to these imperative and would support both 'displacement' and 'substitution'  Data are n(raw %) Foods with a a have a modified distribution from the original score strategies, as nutritional quality across food groups, but also within food groups is consistently discriminated. Our study is subject to some limitations. First, though the Open Food Facts database collects data from products currently on the market, we were not able to analyze the representativeness of the sample of foods retrieved, either in terms of number of products or market share. However, our purpose was not to be exhaustive, but rather to test the performance of the 5-CNL in reallife situations, for which the Open Food Facts database is sufficiently large to give a consistent evaluation.
In the dry grain, the outer layers have a protective role and with the endosperm-derived aleurone layer they constitute the bran. These outer layers are composed of different tissues: the pericarp, which is divided into the outer pericarp and inner pericarp, the testa or seed coat and the nucellar epidermis  (Gassner 1973; Xiong et al. , 2013). The composition of cell walls in wheat grain outer layers has been revealed in several studies using neutral sugar and phenolics analyses, which have revealed that cell wall composition varies considerably between the different layers  (Antoine et al. , 2003; Beaugrand et al. , 2004; Parker et al. , 2005; Barron et al. , 2007). The metabolism of cell wall polysaccharides requires the intervention of numerous enzymes. Enzymes acting on carbohydrates are listed and classified on the basis of their sequence similarities and activities in the CAZy database (http://www.
Analysis of peptides by mass spectrometry Extracted proteins were briefly separated on 12% SDS-PAGE. Each lane was then systematically cut into 15-20 slices. In-gel digestion was performed after reduction and alkylation according to  Larré et al. (2010). Nanoscale LC-MS/MS analyses of the digested proteins were performed using an Ultimate 3000 RSLC system (Dionex) coupled with an LTQ-Orbitrap VELOS mass spectrometer (Thermo Fisher). Chromatographic separation was conducted on a reverse-phase capillary column (Acclaim Pepmap C18 2 µm 100A, 75 µm i. d. ×15 cm length; Dionex) at a flow rate of 300 nl min -1 as described in  Suliman et al. (2013). Mass data acquisitions were performed using Xcalibur 2. 1 software. Full MS scans were acquired at high resolution (FWMH 30 000) in the Orbitrap analyser [mass-to-charge ratio (m/z)=400-2000], while collision-induced dissociation (CID) spectra were recorded on the five most intense ions in the linear LTQ traps.
Database search and interpretation Raw data collected during LC-MS/MS analyses were processed into mgf format files and further searched against databanks using X!Tandem Spectrum Modeler. Protein identification was achieved by querying mass data (MS and MS/MS spectra) against UniProt Knowledgebase (http://www. uniprot. org/) restricted to Poaceae (version 2014-12) and a contaminant database including keratins and trypsin. A database search was performed with XTandem Sledgehammer 2013. 09. 01. 1 (http://www. thegpm. org/TANDEM/) via the X!tandem pipeline available at http://pappso. inra. fr/bioinfo/xtandempipeline/. Enzymatic cleavage was declared as a trypsin digestion with one possible miscleavage event. Fixed modifications of cysteine residues by iodoacetamide as well as oxidized methionins were considered.
Precursor mass and fragment mass tolerance were set at 5 ppm and 0. 8 Da, respectively. Identified proteins were filtered according to the following specifications: at least two peptides in the same band with an E value below 0. 01 and a protein E value below 10 -4. Two sets of data were generated, one for the outer pericarp obtained by combining the results from the three sequential protein extracts, and one for the intermediate layers obtained by combining the results from three enriched Golgi fractions. To take redundancy into account, in each set, proteins with at least one peptide in common were grouped. The number of identified proteins given in this report corresponds to the number of protein groups. In some groups, sub-groups of proteins were defined. The proteins in these subgroups shared some peptides with the other proteins of the group but were distinguished by at least one specific peptide.
Proteins (groups) potentially involved in lignin and cutin metabolism were identified through their annotation. Identification of enzymes acting on carbohydrates was performed by blasting one protein per sub-group against the entire non-redundant sequences of the CAZy database using protein domains (Pfam) association rules in CAZymes Analysis Toolkit  (Park et al. , 2010). CAZy hits (e-value<0. 01) were gathered with their annotation. The annotation of proteins belonging to families implicated in cell wall metabolism was subsequently checked using tBLASTN  (Altschul et al. , 1997)  against NCBI nr restricted to Viridiplantae. When the proposed activity had no association with cell wall metabolism, the protein was not retained. For the enzymes of interest, all the protein hits were compared between pericarp and intermediate layers.
Subcellular proteomics revealed cell wall-related protein families While the sequencing of the hexaploid wheat genome is still underway, the genome of several related Poaceae species has been sequenced, annotated and published recently  (Initiative IB, 2010; Brenchley et al. , 2012; Mayer et al. , 2012; Jia et al. , 2013; Ling et al. , 2013). To identify proteins, the UniProt database was restricted to Poacae and interrogated. First, a global analysis of all spectra generated from the pericarp microsomal fraction and from Golgi-enriched fractions from intermediate layers was performed. A total of 822 and 1304 proteins were identified respectively in the pericarp microsomal fraction and in the Golgi-enriched fractions from intermediate layers (Supplementary Table  S2 ). In order to identify all putative GTs, which were the primary targets, a BLAST search was run against the entire non-redundant sequences of the CAZy database.
The interrogations resulted in many hits in CAZy in different families of GTs, GHs, proteins with carbohydrate binding modules (CBMs), carbohydrate esterases (CEs), proteins with auxilliary activities (AAs). Several CAZy families have been implicated in cell wall metabolism and/or were localized in Golgi or in cell walls  (Nikolovski et al. , 2012; Pellny et al. , 2012; Douché et al. , 2013). The CAZy families implicated in cell wall metabolism were manually examined. Additional cell wall-related proteins were identified in Supplementary Table  wall-related proteins were examined and completed if required with a tBLASTN analysis. Protein hits with confirmed relations with cell walls are reported in Supplementary Table  S3  together with their proposed target polymer. A short list is given in Table  1.
Correlations between polysaccharide distribution and identified proteins in the grain outer layers The presence in the cell walls of the developing wheat grain at 250°D of several polysaccharides is documented in the literature  (Beaugrand et al. , 2004; Philippe et al. , 2006; Pellny et al. , 2012; Chateigner-Boutin et al. , 2014). Table  2  presents a summary of published immunodetections with data available for the grain outer layers. Immunolabellings were performed on sections of grains harvested at 250°D with several well established antibodies to complete the cell wall analysis. The aim was to detect the product/substrate of the different GT, GH and CE activities. The micrographs are shown in Supplementary Fig. S3. CAZy families implicated in the synthesis of AX have been identified in this paper.
Moreover the identification criteria of one single specific peptide may not be stringent enough, especially in protein families highly represented in databases. Protein families implicated in cell wall metabolism were identified and several could be ascribed to cell wall components that are reported to be present in the cell walls of the different grain tissues. Xylans are a class of polysaccharides that contain a backbone constituted of β(1-4) xylose residues. Xylans can be decorated with many other residues  (Saulnier et al. , 2012). The precise distribution of the different structures of xylans in wheat cell layers is not fully established. Here specific antibodies targeting xylan substituted with either arabinose or (methyl)glucuronic acid revealed a differential distribution of the two forms of xylans.
Acknowledgements This research was supported by  INRA-CEPIA AIC  and post-doctoral fundings. We thank  INRA-Rennes  for growing the wheat,  G. Deshayes  for assistance with proteomics,  M. Pavlovic  and  A. Geairon  for assistance in mass spectrometry. Mass spectrometry and TEM were performed at Biopolymers,  Structural Biology platform (BIBS ,  UR1268   BIA, INRA Angers-Nantes ). The authors would like to acknowledge the assistance of  I. Kolotueva  ( Microscopy Imaging Center Rennes ) in sample preparation for high pressure freezing. We also thank  Gaétan Guillaume  and  Yann Le Borgne , and our lab colleagues who kindly helped us dissect the grains.
Suspected Cholera Case and Water Supply Data Daily admissions to the CTC during the period of January 1, 2009, to April 30, 2014, were extracted from the database held by the district health office since 2009, which is updated weekly from the paper register used by clinical staff at the CTC. Patients admitted at the CTC are recorded along with their neighbourhood of residence, and patients residing outside of Uvira municipality were excluded from the analysis. In order to conform to the WHO suspected cholera case definition in endemic areas, patients aged 5 y or under were excluded  [9]. Daily volume of water supplied for the same time period was collected from the register held at the Regideso water treatment plant in Uvira, in which river water drawn upstream of town is treated by sedimentation/flocculation and chlorination before being fed to a single 1,600 m 3 reservoir supplying the town gravity distribution system.
Based on actual tap metering, this estimate accounts for the large variability between taps in use (shared or private) and water availability that is dependent on the tap location on the distribution network. Daily precipitation rates in mm/h estimates averaged for Uvira area at a 0. 25 degree by 0. 25 degree spatial resolution were obtained from NASA Tropical Rainfall Measuring Mission (TRMM) 3B42-v7, through the Giovanni online data system, developed and maintained by the NASA Goddard Earth Sciences Data and Information Services Center (NASA GES DISC). Daily variations of temperature are small in Uvira, and no complete daily temperature record for the region was identified. Temperature was therefore not included as a confounder in the analysis.
Study Design and Ethics Local authorities and international non-governmental organisations (NGO) involved in cholera control activities in Uvira observed that major cholera epidemics often seemed to follow water supply interruptions. In order to investigate this possible association, the authors retrospectively collected relevant data from the local water agency Regideso and from Uvira CTC, and the reliability, size, and completeness of the dataset was deemed sufficient to perform a time-regression analysis. No formal prospective analysis plan was submitted. This study was approved by the Observational Committee of the London School of Hygiene & Tropical Medicine Research Ethics committee (reference 7745). The Committee waived informed consent from participants as the data were anonymously collected and analysed.
Oomycetes are microorganisms that are distantly related to true fungi and many members of this phylum are major plant pathogens. Oomycetes express proteins that are able to interact with plant cell wall polysaccharides, such as cellulose. This interaction is thought to be mediated by carbohydrate-binding modules that are classified into CBM family 1 in the CAZy database. In this study, the two CBMs (1-1 and 1-2) that form part of the cell wall glycoprotein, CBEL, from Phytophthora parasitica have been submitted to detailed characterization, first to better quantify their interaction with cellulose and second to determine whether these CBMs can be useful for biotechnological applications, such as biomass hydrolysis. A variety of biophysical techniques were used to study the interaction of the CBMs with various substrates and the data obtained indicate that CBEL's CBM1-1 exhibits much greater cellulose binding ability than CBM1-2.
Within the Carbohydrate Active enzyme database (http://www. cazy. org/), CBMs are classified into 71 families (as of July 2015) based on amino acid sequence similarity  [3]. Among the reported targets of CBMs, several have been shown to bind to crystalline cellulose, while others bind to amorphous cellulose, chitin, β-1,3-glucans, xylan, mannan, galactan or starch, with association constants ranging from 10 3 M -1 to 10 6 M -1  [4, 5]. In this context, the main proposed role for CBMs is to bind to polysaccharides, thus increasing effective enzyme concentration and enhancing enzyme activity  [6, 7]. Furthermore, it was also demonstrated that CBMs can potentiate enzyme activity by targeting polymers other than the substrate of the catalytic domain  [8]. This study suggests that the possession of a CBM would confer an advantage for polysaccharide degrading enzymes in the context of complex substrate (e.
Heterologous expression of proteins in E. coli Cloning of TvXynB in E. coli. XynB from Talaromyces versatilis (GenBank AJ489605. 1) was cloned into pET28a between NdeI and HindIII (generating pET-TvXynB), using PCR to amplify the two exons of the XynB gene, exon1 primers E1fo 5'-ATACTTCATATGGCTGAGG CGATCAACTACAACC-3' and E1re 5'-CTGTAGGTGATGGGTTAGCATCACCTGGTTGCCA ACC-3', and exon 2 primers were E2fo 5'-GGCAACCAGGTGATGCTAACCCCATCACCTAC AGCGGC-3' and E2re 5'-ATTCAAAGCTTCTTGGCACTGGCTGTAGTAAGCG-3'. Using the previously prepared construction as template DNA, TvXynBΔCBM was obtained by PCR, amplifying only the xylanase-encoding sequence (nucleotides 1 to 693) of the previously cloned XynB sequence using primers E1fo and E2SSCBM: 5'-ATTCAAAGCTTCAGCAGCACCGGTG CCTCC-3' and cloned into pET28 (generating pET-TvXynBΔCBM).
The sequence encoding the first copy of CBM1 (designated CBM1-1) from the Phytophthora parasitica CBEL (amino acids 23 to 55) was amplified by PCR using the CBEL cDNA  [27]  as the template. The amplicon was cloned into pET28a-TvXynBΔCBM using HindIII and XhoI, thus creating a new cassette encoding the fusion protein TvXynB-CBM1-1. Protein expression in E. coli. CBEL from Phytophthora parasitica (GenBank ID: X97205) and variants thereof (CBEL Y52A_Y188A , CBEL Y52A , CBEL Y188A ) were expressed in E. coli strain BL21 DE3 as previously described  [27]. Briefly, protein expression was induced by adding isopropylthio-β-D-1-thiogalactopyranoside (500 μM final) to a bacterial culture (incubated at 37°C with shaking) when an absorbance (600nm) reading of 0. 5 (approximately 3 h after inoculation) was achieved.
The binding parameters (K D and B max ) were calculated by fitting the data to a single-site Langmuir isotherm using Sigma-plot software (version 12. 0). Each experiment was performed in triplicate. Fluorescence spectroscopy experiments. Fluorescence spectra were acquired at 25°C using a Cary Eclipse Agilent technology spectrofluorimeter and 5 mm × 5 mm quartz cuvettes. The excitation and emission wavelengths were 295 and 300-500 (scan) nm respectively and slit widths were 5 nm. To perform the experiments, a buffered protein solution 7 μM protein (final concentration) in 50 mM HEPES, pH 7. 5 was placed in a cuvette with 0, 0. 05, 0. 1, 0. 5, 1 and 1. 5% w/v of final concentration of a suspension of cellulose nanocrystals. Spectra were recorded at 2 nm intervals until no further spectral changes were detected.
At this point it was assumed that binding was complete. All titrations were performed in triplicate. When a wavelength shift of intensity E max was observed, the barycentric mean wavelength of the integral between 300 to 500 nm was calculated as previously described  [32]. The dissociation constant K D and B max were calculated from the curve by fitting the data to a one site binding (hyperbola) model contained in the Sigma-plot software suite (version 12. 0). Isothermal titration calorimetry (ITC). Isothermal titration calorimetry (ITC) experiments were conducted at 25°C in 50 mM HEPES, pH 7. 4 using a Microcal ITC200 instrument (GE Healthcare, Little Chalfont, UK). To ensure minimal buffer mismatch, prior to the experiment the proteins were dialyzed against the buffer and the ligand molecules were directly solubilized in it.
Experiments consisted of a series of 20 x 2 μl injections of cellohexaose (1. 6 to 3 mM) into a protein solution (CBEL or CBEL Y52A_Y188A at 80 to 110 μM) contained in the thermostatic cell (initial delay of 60 s, duration of 4 s and spacing of 100 s). ITC experiments were systematically performed in duplicate. A titration of the ligand in the sample cell containing only buffer was subtracted from the actual binding experiment before data analysis. The corrected binding isotherms were fitted to a two sequential binding sites model using non-linear least squares analysis to obtain the value of the equilibrium binding constant (K A ), and enthalpy changes (ΔH) associated with ligand binding. Measurement of xylanase activity. All enzyme activity measurements were performed in triplicate by monitoring the release of reducing sugars, which were quantified using the standard DNS method.
0). To measure activities, the DNS method was employed and reactions were performed as described in the xylanase activity section unless stated otherwise. Activities were expressed in units, where 1 unit is defined as the quantity of enzyme required to release 1 μmole of reducing xylose equivalent per minute. Once the optimal conditions for TvXynB were determined, enzyme kinetics were studied by performing reactions in 50 mM citrate-phosphate buffer, pH 3. 0 at 40°C using eight different concentrations of BWX in the range 0. 5-25 g. l -1. Reactions were monitored using the DNS and initial velocities were plotted as a function of substrate concentration using SigmaPlot Ver12. 0 enzyme kinetics package. Data were processed using the non-linear regression algorithm and values of k cat and apparent K m were obtained.
Fluorescence spectroscopic analysis of CBM-ligand interactions. To further investigate the binding properties of the CBEL variants, the interaction of these with cellulose nanocrystals was studied using fluorescence spectrophotometry. The advantage of using cellulose nanocrystals was that these are water soluble and mimic the cellulose surface  [34, 35]. In these experiments, the calculated value for K D was 2. 5 g. L -1 for CBEL, but binding was not detected in the case of CBEL Y52A_Y188A , a result that is once again consistent with the other data reported in this study (Table  2 ). Likewise, as before the binding ability of the single mutant CBEL Y52A was found to be severely reduced with the K D value being increased approximately 40-fold, while that of CBEL Y188A was only increased 6-fold (Table  2 ).
Acknowledgments The authors would like to thank  Dr. P. Roblin  ( Soleil-Synchroton, Saclay, France ) for scientific discussions and  M. Maestracci  and  O. Guais  for kindly providing the TvXynB gene. The equipment used for isothermal titration calorimetry is part of the  Integrated Screening Platform of Toulouse (PICT, IBiSA ). Dr. V. Gervais  is gratefully acknowledged for assistance with the ITC experiment.
Statistics All statistical analyses were performed with the R software (R Development Core Team, 2004, http://www. R-project. org/; version 2. 13. 2). The homogeneity and normality of data were tested using the Bartlett test and the Kolmogorov-Smirnov test, respectively. Since the data were not normally distributed, non-parametric tests were used for all statistical analyses. The Mann-Whitney U test was used to compare i) Cd accumulation in eggs for each solution (i. e. , control versus 5 mg/L, 5 mg/L versus 10 mg/L, etc. ) and ii) qRT-PCR results in control and Cd-exposed samples at 6 and 12 days. Kruskal-Wallis test was used to compare i) levels of Cd measured in eggs at each date for the same concentration of exposure (i. e. , at 1, 6 and 12 days for 5 mg/L exposure), and ii) differences between the 3 MT gene transcript values of controls (comparisons of CdMT, CuMT and Cd/CuMT values at 6 and 12 days in control).
Peptide Analysis by Nano-LC-ESI-MS/MS The purified enzyme (58 kDa) was excised from the SDS-PAGE and analyzed by ESI, as described previously  [32, 33]. Analysis of the triptych peptides showed similarities to β-glucosidase 24-like in Cucumis sativus (cucumber: XP_004154617. 1), which possesses a calculated molecular mass of 58. 142 kDa. Searches performed by the BLAST program found seven peptides with relative masses ranging from 874. 3643 to 1587. 8297 (protein score 62), covering 10% of the sequence for glycosyl hydrolase, GH I (Table  2 ). The analysis of triptych peptides in the 58 kDa subunit from β-glucosidase in S. edule exhibited little similarity in the amino acid sequences, relative to other β-glucosidases existing in the data bases. In this study, low homology was found in the β-glucosidase in cucumber (Cucumis sativus) and the seven peptides in S.