dataesr/scientific-paragraphs-categorization huggingface dataset:
We also excluded 258 outliers. These were defined based on the WHO standards with recommended flag limits: WHZ-5, +5; HAZ-6, +6 (source: http:// www. who. int/nutgrowthdb/software/Differences_NCHS_-WHO. pdf?ua=1). For SSRZ, as no reference population exists, we used the flag limits -3 SD, +3SD of the study population. Therefore, the final dataset included 14,409 children. Dependent variables were defined as either WHZ -2 or MUAC 125. Independent variables were dichotomized to correspond to categories usually used in field nutrition programs: young age (age < 24 months vs. age ≥ 24 months), stunting (HAZ<-2SD vs. HAZ≥-2SD of the reference population), sex (male vs. female). We also created the variable 'longer legs' by dichotomizing SSRZ (SSRZ in the lower tertile vs. SSRZ in the 2 upper tertiles of the study population).
A recent meta-analysis showed a dramatic increase in mortality risk in children combining low WHZ and stunting  [21]. A similar analysis is needed for MUAC. Our study is the first one to document the concomitant influences of age, sex, HAZ and 'longer legs' on the diagnosis of acute malnutrition by either MUAC 125 or WHZ -2. However, it is not without limitations. First, we used routine data collected in a growth monitoring program or data collected in field surveys conditions, which may have an impact on the accuracy of measurements. However, assessors received a training or a refresher session prior to the data collection, and outliers were few. Second, the analysis was based on crosssectional assessments of anthropometric indicators alone with no possibility to assess the functional outcomes of the various malnutrition indicators.
Cells that contained successfully constructed plasmids were obtained using an X-Gal screening test. The plasmids were obtained using EZ-10 Spin Column Plasmid DNA Minipreps Kit (BBI, Shanghai, China) according to the recommended protocol and then sequenced at BGI (Beijing, China). The partial-length 16S rDNA gene sequences were directly compared with corresponding sequences in the 16s ribosomal RNA sequences (Bacteria and Archaea) databank via National Center for Biotechnology Information using BLASTN.
karger. com/ProdukteDB/produkte. asp?doi=380889 )). The quantitative results were normalized by contrasting to the total intestinal microbiota. The dilutions were added to a final volume of 25 μl. Amplification and detection of DNA by RT-PCR was performed with ABI PRISM 7900 HT (Applied Biosystems, Foster City, CA, USA) using 384-well plates. Duplicate sample analysis was routinely performed in a total volume of 25 μl using SYBR ® Premix Ex TaqTM II (TAKARA, Dalian, China). Data from duplicate samples were analyzed using the ABI 7900 SDS software (version 2. 3; Applied Biosystems).
Statistical Analyses Principal component analysis (PCA) was done based on peak density value of bands using PC-ORD program, and the results were obtained using the princomp program of SAS 9. 2 (SAS Institute Inc. , Cary, NC, USA). The data are expressed as means ± SEM. Differences between groups were assessed by ANOVA. Statistical analyses were performed with SAS 9. 2. The differences were considered as statistically significant for p < 0. 05.
MSG and Dietary Fat Promoted Fat Deposition in Muscle in Growing Pigs MSG and dietary fat had no obvious effects on average daily gain and food intake of pigs. The parameters used to evaluate carcass segmentation, containing slaughter yield, back fat thickness, lion-eye area, total fat and total skeletal muscle, were also not effected by dietary supplementation of MSG and dietary fat (data not shown). The result of longissimus dorsi composition analysis was shown in figure  1. Both dietary supplementation of MSG and fat had no effect on crude protein and dry matter. Surprisingly, MSG and fat promote fat deposition in longissimus dorsi , and an obviously synergistic effect was found when the two nutrients were given in one diet.
During the rest period that followed stimulation, myocytes were repetitively scanned along the entire length of the cell at 1. 5-ms intervals, for a maximum of 6 s. The laser intensity was reduced to 5% maximum to decrease cell damage and dye bleaching. Line scan diagrams were constructed by stacking emission lines, corresponding to excitation scans, in temporal order. An average of the Ca 2 þ sparks was determined by the intensity of each sequential scan line and plotting the mean intensity as a function of time. The SparkMaster plug-in for ImageJ software was used to detect and analyze Ca 2 þ sparks.
Acknowledgments A part of this work was financially supported by the  Université de Montpellier  (Grants  BQR-2008  and  2011 ), the  Centre National de la Recherche Scientifique (CNRS)  for  PEPII INSB-INC , and the  Fondation pour la Recherche Médicale (FRM)  ( DCM20111223047 ). We are grateful to  Valérie Bultel-Poncé  and  Alexandre Guy  for their assistance in synthesizing the 4(RS)-4-F 4t -NeuroP and to  Valérie Scheuerman  and  Patrice Bideaux  for performing biochemistry and preparing the PMI mice, respectively.
Another aspect that needs to be considered is the impact of nutrient and organic matter concentrations and quality in determining FIB survival. At present none of the models take these factors into account and this is true for temperate systems where extensive datasets exist as well as in tropical environments where it is even more critical. Given that FIB may well be able to proliferate in tropical systems, it is clear that this must be taken into account in any model that wishes to simulate FIB dissemination or proliferation. The compilation of a comprehensive data base of epidemiological parameters will also provide a new avenue for testing the role of climate in the dispersion of FIB and the impacts of contaminated waters on public health in developing countries. More research is needed in these areas if we are to meet the Millennium Development goals as regards clean water access and the prevention of water borne diseases in these often poor, rural tropical areas.
Acknowledgments This work was funded by the  French ANR " Teciteasy " ( ANR-13-AGRO-0007 ),  French Institut de Recherche pour le Développement (IRD) , the  UMR iEES-Paris  and the  UMR GET. The  MSEC (Multi-Scale Environmental Changes , http://web2. obs-mip. fr/msec/)network is also thanked. This work forms part of the PhD thesis requirements of NTMH who benefited from a thesis research grant from  IRD (ARTS).
Clinical signs of malnutrition, such as symmetrical edema, skin lesions, and dry, thin and depigmented hair, were assessed. Anthropometric measurements included weight (kilogram), length (centimeter), cephalic, thoracic, and abdominal circumferences (centimeter) as well as triceps and subscapular skinfold thickness (millimeter). They were performed according to standard WHO procedures  (8). Z scores for weight for age (WAZ), weight for height (WHZ), and height for age (HAZ) were calculated using the Anthropometric calculator module of WHO Anthro software (version 3. 2. 2, January 2011) (based on The 2006 WHO child growth standards)  (9). After calculation of WAZ, WHZ, and (HAZ), the studied groups were classified into normal nutritional status and malnutrition (moderate or severe). The WHO global database on child growth and malnutrition (under-nutrition) recommends a cut-off Z score of ≤-2 to classify low WAZ (underweight), low HAZ (stunting), and low WHZ (wasting) as moderate malnutrition, and a Z score of ≤-3 SD to define severe malnutrition  (9).
Results A total of 100 children with symptomatic CHD were included in the study. Details of demographic characteristics, anthropometric measurements, and biochemical markers are given in Table  1. There were no significant differences between patients and controls regarding the demographic data except for birth weight, which was higher in the control group. Further, the poor nutritional history is significantly different in the patient cohort. All anthropometric measurements were significantly lower in the patients group than in the control group, as well as hemoglobin, serum iron, ferritin, and albumin levels. Table  2  shows the distribution of cardiovascular defects in the patient group. Ventricular septal defect (VSD) was the most common cardiac lesion, whereas tetralogy of Fallot (TOF) was the most common cardiac lesion among cyanotic CHD.
Background: Necrotizing enterocolitis (NEC) is the most frequent life-threatening gastrointestinal disease experienced by premature infants in neonatal intensive care units. The challenge for neonatologists is to detect early clinical manifestations of NEC. One strategy would be to identify specific markers that could be used as early diagnostic tools to identify preterm infants most at risk of developing NEC or in the event of a diagnostic dilemma of suspected disease. As a first step in this direction, we sought to determine the specific gene expression profile of NEC. Methods: Deep sequencing (RNA-Seq) was used to establish the gene expression profiles in ileal samples obtained from preterm infants diagnosed with NEC and non-NEC conditions. Data were analyzed with Ingenuity Pathway Analysis and ToppCluster softwares.
The prepared libraries were then sequenced using Illumina's HiSeq 2000 to obtain 50-bp single-end reads using four lanes (4 samples per lane). Sequence data quality check was performed using FastQC (v1. 0. 0). [27]  The RNA-Seq data were mapped to the hg19 reference genome using TopHat for Illumina (v1. 5) using default options. Assembly of transcripts and estimation of their abundance (FPKM: fragments per kilobase of exon per million fragments mapped) were calculated using Cufflinks software (v0. 0. 6)  [27]. We used the program Cuffdiff (v0. 0. 7)  [27]  to test for differential transcript expression between CTRL and NEC (p < 0. 05).
RNA-Seq analysis and identification of differentially expressed genes (DEGs) RNA-Seq analysis of intestinal samples generated 2231 × 10 6 base pairs (bp) from NEC and 1589 × 10 6 bp from CTRL. Mapping resulted in 44. 63 × 10 6 (±8. 7 × 10 6 ) reads in NEC and 31. 79 × 10 6 (± 0. 12 × 10 6 ) in CTRL. In total, 24346 genes were identified in both preterm intestinal samples. The data have been deposited in the National Center for Biotechnology Information's Gene Expression Omnibus and are accessible through GEO Series accession number GSE64801. We used the Illumina HiSeq2000 to investigate the gene expression profiles of the ileum of preterm infants with NEC vs without NEC (CTRL). In total, 804 DEGs (p < 0. 05) were identified, 383 up-regulated and 421 down-regulated genes (See Additional file 2 for the gene list with fold changes).
Acknowledgements The authors thank  Aline Simoneau  for technical assistance,  Elizabeth Herring  for reviewing the manuscript and  Dr. Marie-Pierre Garand  of the  Biostatistics Facility of the Centre de Recherche du CHUS  for assistance in the statistical analyses. This work was supported by a  Canadian Institutes of Health   Research grant  ( MOP 136991 ) and the  Canada Research Chair in Intestinal Physiopathology (JFB) , the  Canada Research Chair in Immune-Mediated Gastrointestinal Disorders (EGS)  and the J. A. DeSeve Research Chair in Nutrition (EL).
Acknowledgements. Ideas discussed here are based in part on a presentation of the author at the 12th Euro Fed Lipid Congress. This work as supported by  ATIP grant  from the  "Centre National de la Recherche Scientifique" (CNRS)  and by the  "Agence Nationale de la Recherche " ( ANR -09-BLAN-0267-02  and  ANR 11 BSV1 021 01 ).
Subjects We recruited (n = 165) male and female adolescents from Constantine district in Algeria. All the participants belonged to Arab-Berber ethnicity. The study was conducted on a young population (Table  1 ). The exclusion criteria for participants were any history of a chronic pathology such as cardiovascular disease, diabetes, liver, or kidney disease. The smokers were also excluded from the study. A written consent was obtained from all participants and their parents, and they were assured about the confidentiality of the study. All personal data, such as names and dates of birth, were erased from the database.
Statistical Analysis Statistical analysis was conducted by Statistica 14 software (Statsoft, Tulsa, OK, USA). One-way ANOVA was used to compare the difference between parameters in the study groups. For correlation between various parameters, Spearman rank correlation was performed. Hardy-Weinberg equilibrium (HWE) was assessed by chi-square (χ 2 ) test. For the comparison of allelic and genotype frequencies between obese and control, Fisher exact test was used. All data in the tables and figures are presented as means ˘SEM, and p < 0. 05 was considered as statistically significant.
ACKNOWLEDGMENTS AF and MJS were supported by the doctoral school ABIES; MAA was supported by a grant from the  Syrian government  and by  ANR DESIRABLE ; AM was supported by a  Marie-Curie International Incoming Fellowship  PIIF-GA-2012-330101 Acronym: TASTEVOL; AY was supported by a  JSPS  grant; FMP was supported by  ANR DESIRABLE.
Literature data confirmed the presence of EPA and DHA in different parts of the scallops i. e. muscle, gonad, digestive gland  (Kraffe, Soudant, & Marty, 2004; Palacios et al. , 2005; Zhou et al. , 2010)  and also in the different lipid species  (Kraffe et al. , 2004). It is worth noting that to our knowledge, only one study in literature reported on supercritical extraction of scallops. Extraction of scallop viscera was carried out with pure CO 2 at 50 C and 28 MPa aiming at recovering lipids and specially EPA and DHA  (Zhou et al. , 2010)  but the specific recovery of phospholipids was not foreseen. The objective of this work was to investigate the selective extraction of phospholipids from scallop wastes. After a deoiling step performed by CO 2 at 45 C and 30 MPa, the PL extractions were carried out by CO 2 :EtOH mixture, varying temperature (27 Ce60 C) and fluid composition (15:85 to 50:50 w:w) as operational parameters.
Typical acquisition parameters were as follow: 50 kHz spectral width, 90 pulse width of 14 ms, 5 s relaxation delay, 32 K data points, number of scans between 64 and 1000 per spectrum depending of samples, temperature of 25 C. Data were processed using Topspin software version 2. 1, exponential noise filtering with a width of 10 Hz was applied prior Fourier transformation. Analyzed samples were prepared as follow: a known amount of dried extract (obtained by the gentle evaporation of ethanol by nitrogen flux and zeodrated during 12 h) was dissolved in 400 mL of a chloroform:methanol mixture (2:1 in volume, deuterated solvents) and placed in tube of 5 mm diameter. For quantification, appropriate amount of internal standard, e. g. 0. 24 mg of pyrophosphate (purity of 99%, Sigma Aldrich, Saint-Quentin Fallavier, France) have been exactly weighted and dissolved in 60 mL of deuterated water.
Acknowledgements Financial support from  Region Aquitaine  (Grant 20081102011) is greatly appreciated. The technical Center for Agro Ressources (A. G. I. R. , 33600 Pessac, France) and  E. Diehl  ( Spectral Service GmbH , www. spectralservice. de)are greatly thanked for the scallop preparation and the high resolution NMR analysis, respectively.
Loose cell-attached recordings (15-100 M⍀ seal resistance) were made with pipettes filled with ACSF and used several times on different neurons. Bundles of OSN axons projecting inside a given glomerulus were stimulated using a theta pipette filled with ACSF as described previously  (Najac et al. , 2011). The electrical stimulus (100 s) was delivered using an isolator-11 Stimulus Isolation Unit (Molecular Devices). Recordings were acquired with a multiclamp 700A amplifier (Molecular Devices), low-passed filtered at 2-4 kHz, and digitized at 10 kHz using Clampex 9 software (Molecular Devices). In current-clamp recordings, a constant hyperpolarizing current was injected to maintain the cell at a potential of Ϫ60/Ϫ70 mV. In voltage-clamp recordings, access resistance (R a Ͻ 10 M⍀ for mitral, R a Ͻ 20 M⍀ for tufted and ET cells, R a Ͻ 30 M⍀ for PG cells) were not compensated.
For recordings, we followed the two-photon targeted patching approach  (Margrie et al. , 2003)  using regular patch pipettes (ϳ4 -8 M⍀) containing Alexa Fluor 594 (10 -20 M). The dyefilled patch pipette and EYFP ϩ neurons were imaged simultaneously with two detection channels using an excitation wavelength of 900 nm. The pipettes were filled with (in mM) 130 K-gluconate, 4 MgCl 2 , 4 Na-ATP, 0. 5 Na-GTP, 10 HEPES, and 10 phosphocreatinine, pH 7. 3 (ϳ280 Osm/L) for the experiments shown in Figure  6A  or with the Cs-MeSO 3based internal solution used in slices for the experiments shown in Figure  6B. Data were acquired the same way as in slices using an Axopatch 200B amplifier (Molecular Devices). Access resistances (25-40 M⍀) were not compensated. Analysis. Voltage-clamp data were digitally low-passed filtered offline at 1-2 kHz when necessary and analyzed using Axograph X (Axograph Scientific) and Igor Pro (WaveMetrics).
neuromatic. thinkrandom. com/) by a y-threshold level detector for values on a positive slope deflection. Reliability of mitral cell spiking responses (see Fig. 8 ) was analyzed using MATLAB (MathWorks). For the ensemble analysis of mitral cell responses to the stimulation of OSNs (see Fig. 8G ), we constructed a nineneuron ensemble by pooling the nine recorded mitral cells, each of them having at least 14 trials for each condition, with and without GBZ. By random non-redundant combination of nine trials of 9 ϫ 14, we created 14 artificial trials of the activity of an ensemble of nine mitral cells. Unless indicated otherwise, we used the unpaired t test to compare two sets of data acquired from different populations. Results are expressed as mean Ϯ SD. Immunohistochemistry. Adult mice (1-3 months old) were deeply anesthetized with an intraperitoneal injection of xylazine (16 mg/kg) and ketamine (100 mg/kg) and perfused with 4% paraformaldehyde in which the brains were kept overnight.
Program Organisation Grant  RGP0089/2009-C ,  National Agency for Research Grants   ANR-12-JSV4-006-01  (D. D. S. J. ) and  ANR-R11036KK  (S. C. ), the  Foundation for Medical Research , the  National Institute of Health and Medical Research , the  National Center of Scientific Research , and the  Ministry of Higher Education and Research. We thank  Thomas Kno  ¨pfel for the kind gift of the Kv3. 1-EYFP transgenic mouse and  Hannah Monyer  for the kind gift of the CR-EGFP transgenic mouse. We also thank  Gwenae ¨lle Bouchery and Andrea Virolle  for technical assistance and members of the laboratory for constructive comments throughout the project.
mansoni (Fig. 3b , p-value <0. 0001). The relative divergence time of SGTP3 and SGTP4 suggested that these phylogenetic events coincide in time, and they are recently evolved glucose transporters compared to SGTP2 and SGTP1. The phylogenetic position of SGTP3 and SGTP4 (Fig. 2 ), Fig. 2  Phylogeny of the trehalose and glucose transporter family. The figure shows a phylogenetic tree of trehalose and glucose transporters from vertebrates, trematodes and insects. The topologies obtained with ML, MP and NJ methods were similar, and thus only ML is displayed. Numbers on internal branches are the bootstrap values (only >80 % are shown); the statistical support obtained with approximate likelihood ratio test (aLRT) was similar. Sequences are labeled with data collected from GenBank as name of species (four first letters), type of transporters (T: trehalose, G: glucose), number (if reported) of the sugar transporter and accession numbers.
However, these sequence modifications have no effect on the core glucose transporter structure. The transcript sequence was submitted to GenBank [GenBank: KT895372]. The schistosome genome sequence and the derived exon/intron structure shown in Fig. 4  and Table  1  are aligned with published transcript sequences of SGTP1 and SGTP4, the transcript sequence of SGTP2 predicted from the genome, and the predicted transcript sequence of SGTP3. We analyzed the gene structure of human glut1, and collected that of glut4 from the literature  [24] , for comparison, since our phylogenetic analyses placed the human GLUT1 and GLUT4 within the same clade as SGTP2 and SGTP3. The analysis shows that the gene structures of sgtp1 and sgtp4 are similar to each other, but different from those of sgtp2 and sgtp3, which are also similar to each other.
e. , the initial conformation). Glucose association (i. e. , conformation of XylE) and disassociation (i. e. , conformation of GLUT1) trigger the migration of glucose towards an environment with a lower concentrationi. e. , the intracellular compartment  [12]. The final conformation, glucose-free As proof of principle for our simulations, we submitted the modelled S. mansoni glucose transporters to the DALI server  [39]  to find homologous crystal structures with the best matching conformation. The crystal structures GLUT1 of H. sapiens [PDB: 4PYP] and XylE of E. coli [PDB: 4GBZ] were among the top candidates. This provided two opportunities to control our simulations since, (i) glucose is not the substrate of XylE, it is a competitive inhibitor and (ii) XylE and GLUT1 are the two sequential intermediate structural conformations during glucose binding and diffusion, respectively  [12].
The conformational changes during binding occur mainly in TM α-helices 1, 4, 7 and 10 that cause the occlusion by the intracellular α-helices to open, thereby permitting diffusion  [12]. Root mean square deviation (RMSD) is frequently used in structural bioinformatics to measure the average distances between atoms from two or more protein structures. The superposition in Fig. 6a  graphically shows these overall structural differencesthe RMSD between XylE [PDB: 4GBZ] and GLUT1 [PDB: 4PYP] is 3. 2 Å. Figure  6b  shows the predicted tertiary structures of S. mansoni glucose transporters SGTP1-SGTP4 and their structural similarity to GLUT1 and XylE. Both SGTP1 (RMSD 1. 0 Å) and SGTP4 (RMSD 1. 3 Å) are structurally homologous to XylE. SGTP2 (RMSD 2. 3 Å) and SGTP3 (RMSD 0. 6 Å) are structurally homologous to GLUT1.
For example, using the S. mansoni glucose transporter structures, the aglycone could be altered to computationally test for stability and affinity of the designed glucoside(s). The top glucoside candidate(s) could then be experimentally analyzed for effectiveness. Since glucosides are non-transportable  [43]  they could "trap" themselves in the active site to maintain the structural conformation similar to SGTP1 in Fig. 8  i. e. , the glucose-bound, occluded conformation of XylE. One of the caveats of the PELE algorithm is that it cannot perform large protein conformational changes, as those described by Deng et al. [12]. Such simulations to rationally design drugs will benefit from other molecular dynamics software such as Desmond  [44].
The ratios of relative expression were calculated using the 2 -ΔΔCt ratio  [46]  with S. mansoni α-tubulin as the endogenous control gene  [47]. The statistical significance between groups was evaluated using the unpaired non-parametric Mann Whitney's test in the GraphPad 6 Prism program (GraphPad Software Inc. ). Differences were considered significant when p-value <0. 05.
Phylogenetic analyses Sequences were collected from GenBank for phylogenetic analyses of sugar transporter proteins from mammals (3 species), fish (teleosts, 7 species), insects (8 species), cestodes (6 species) and flukes (4 species). A Drosophila melanogaster sucrose transporter was introduced as an outgroup. The species, sugar specificity and accession numbers of each sequence is provided in Fig. 2. Glucose transporter amino acid sequences were aligned using MUSCLE (v3. 7) configured for highest accuracy  [48]  and non-aligned regions were removed with Gblocks (v 0. 91b)  [49]. Thus, the final alignment contained 333 gap-free amino acid positions. The best-fit model of the sequence evolution was selected based on Akaike Information Criterion (AIC), Corrected Akaike Information Criterion (cAIC) and Bayesian Information Criterion (BIC) implemented in Datamonkey  [50].