dataesr/scientific-paragraphs-categorization huggingface dataset:
Principal component analysis (PCA) was applied on stacks of images using Mantis software and the number of principal components (PC) was determined based on the recommendations for STXM analyses. 25 Cluster analyses (CA) and non-negative matrix approximation (NNMA) routines were conducted using Mantis default settings and using the PC number previously determined. For NNMA, the initial spectra were the cluster spectra found in the CA. Quantitative component images were produced using the singular value decomposition linear regression procedure with starch, zeins and lipids as reference spectra. RGB images were plotted using Fiji software. 26.
Methods: The HPN-QOL questionnaire was modified to suit a paediatric HPN population. Data on demographics, aetiology of intestinal failure and duration of HPN were collected from a departmental database. Quality-of-Life grading of functional and symptom scales, HPN specific items and overall QOL Numerical Rating Scales were determined. Results: Fourteen out of 17 families returned the completed questionnaires. QOL was significantly impaired by increased dependency regarding items of daily living such as eating, dressing, washing, and mobility, but was not affected in the domains of school attendance, general fatigue, pain and body image. There were no significant differences in QOL when patients with and without enterostomy were compared. Patients felt well supported by the hospital nutrition team in managing logistics related to HPN.
Quality of life measure and data collection procedure The HPN-QOL © questionnaire was developed as a treatment specific instrument for the assessment of QOL in patients treated with HPN. It has been translated into Danish, Dutch, French, German, Italian, Polish and Spanish, using forward-backward methodology  (16). The French translation was adapted for use in Belgium and French-speaking Canada and the English version adapted for use in the US and Canada. Psychometric small-sample validation of the English version confirmed the scale structure of the questionnaire  (17). The questionnaire contains 7 multi-item functional scales and 1 single-item functional scale, as well as 6 multi-item and 3 single-item symptom scale  (17). The functional scales include General Health (GH), Ability to Holiday or Travel (HT), Coping (CO), Physical Function (PF), Ability to Eat and Drink (ED), Employment (EM), Sexual Function (SX), and Emotional Function (EF); for these scales, a high score indicates a high level of functioning.
The questionnaire was self completed by the patients, either at a scheduled outpatient visit or at home after mail delivery. Socio-demographic and clinical data including age, gender, educational level, marital and employment status, underlying disease, reason for HPN (life prolonging, quality of life improving or maintaining), duration of HPN, characteristics of the HPN program (day of infusion per week and hours of individual infusion) and functional status, were collected by the treating clinicians.
Statistical analysis The HPN-QOL © was scored according to scoring rules previously reported  (17). When more than 50% of items in a scale or for the whole questionnaire were missing, the scale score or the questionnaire were dropped from analysis on a patient basis; when the number of missed items was ≤ 50% for a single scale, the mean of the completed items was used for simple imputation. Scores were rescaled to range from 0 to 100 and, to further improve readability, made uniform inasmuch as high scores indicate "good condition" in all scales (i. e. high function/good status as well as low symptom or problem intensity). Psychometric analyses (Aim 1 of the study) evaluated the following aspects: data completeness, convergent /discriminant validity and internal-consistency reliability. Data completeness was measured by the percentages of missing scale scores.
All participants signed informed consent. The study was approved by the French Ethical Committee located in Toulouse (CPP SOOM II). The trial was registered at a publicly accessible database under the registration number NCT00672685. Participants were recruited in 13 memory clinics in France and Monaco between 30 May 2008 and 24 February 2011. Participants were randomly assigned (1:1:1:1) using a computer-generated randomization procedure to one of the four following groups: (I) ω3-PUFA alone (two capsules a day, providing a total daily dose of 800 mg DHA and 225 mg EPA), (II) ω3-PUFA plus the multidomain intervention (43 group sessions integrating advice for physical activity (PA), nutrition, cognitive training, and three preventive consultations), (III) the multidomain intervention plus placebo, or (IV) placebo alone.
For each outcome, two subgroup analyses were performed according to baseline red blood cell DHA and EPA concentrations (participants with low (DHA+EPA) erythrocyte level at baseline (lowest quartile, ≤4. 83%) were compared with others quartiles) and according to the level of adherence to the multidomain intervention and ω3-PUFA supplementation during the 36 months follow-up (participants with adherence ≥75% for both intervention were compared with others). All p values are presented before and after adjustment for multiple comparisons with the Hochberg procedure to take into account that three intervention groups were compared with the placebo group in each model  [19]. All analyses were performed using SAS software version 9. 4 (SAS Institute Inc. , Cary, NC, USA).
Acknowledgments: The MAPT study was supported by grants from the  Gérontopôle of Toulouse , the  French Ministry of Health  ( PHRC 2008(PHRC , 2009) ), the  Pierre Fabre Research Institute  (manufacturer of the polyunsaturated fatty acid supplement),  Exhonit Therapeutics , and  Avid Radiopharmaceuticals. The promotion of this study was supported by the  University Hospital Center of Toulouse. We are indebted to the investigators from  CHU de Toulouse ,  Centre Hospitalier Lyon-Sud, Hôpital de Tarbes, Hôpital de Foix, Hôpital de Castres, CHU de Limoges, CHU de Bordeaux, Hôpital de Lavaur, CHU de Montpellier, Hôpital Princesse Grace, Hôpital de Montauban ,  CHU de Nice , and  CHU de Dijon  for their participation in this study. Members of the  MAPT Study Group Bruno Vellas ,  Sophie Guyonnet ,  Isabelle Carrié ,  Lauréane Brigitte ,  Catherine Faisant ,  Françoise Lala ,  Julien Delrieu ,  Hélène Villars ,  Emeline Combrouze ,  Carole Badufle ,  Audrey Zueras ,  Sandrine Andrieu ,  Christelle Cantet ,  Christophe Morin ,  Gabor Abellan Van Kan ,  Charlotte Dupuy ,  Yves Rolland ,  Céline Caillaud ,  Pierre-Jean Ousset ,  Bertrand Fougère ,  Sherry Willis ,  Sylvie Belleville ,  Brigitte Gilbert ,  Francine Fontaine ,  Jean-François Dartigues ,  Isabelle Marcet ,  Fleur Delva ,  Alexandra Foubert ,  Sandrine Cerda ,  Marie-Noëlle-Cuffi ,  Corinne Costes ,  Olivier Rouaud ,  Patrick Manckoundia ,  Valérie Quipourt ,  Sophie Marilier ,  Evelyne Franon ,  Lawrence Bories ,  Marie-Laure Pader ,  Marie-France Basset ,  Bruno Lapoujade ,  Valérie Faure ,  Michael Li Yung Tong ,  Christine Malick-Loiseau ,  Evelyne Cazaban-Campistron ,  Françoise Desclaux ,  Colette Blatge ,  Thierry Dantoine ,  Cécile Laubarie-Mouret ,  Isabelle Saulnier ,  Jean-Pierre Clément ,  Marie-Agnès Picat ,  Laurence Bernard-Bourzeix ,  Stéphanie Willebois ,  Iléana Désormais ,  Noëlle Cardinaud ,  Marc Bonnefoy ,  Pierre Livet ,  Pascale Rebaudet ,  Claire Gédéon ,  Catherine Burdet ,  Flavien Terracol ,  Alain Pesce ,  Stéphanie Roth ,  Sylvie Chaillou ,  Sandrine Louchart ,  Kristel Sudres ,  Nicolas Lebrun ,  Nadège Barro-Belaygues ,  Jacques Touchon ,  Karim Bennys ,  Audrey Gabelle ,  Aurélia Romano ,  Lynda Touati ,  Cécilia Marelli ,  Cécile Pays ,  Philippe Robert ,  Franck Le Duff ,  Claire Gervais ,  Sébastien Gonfrier ,  Yannick Gasnier ,  Serge Bordes ,  Danièle Begorre ,  Christian Carpuat ,  Khaled Khales ,  Jean-François Lefebvre ,  Samira Misbah El Idrissi ,  Pierre Skolil ,  Jean-Pierre Salles ,  Carole Dufouil ,  Stéphane Lehéricy ,  Marie Chupin ,  Jean-François Mangin ,  Ali Bouhayia ,  Michèle Allard ,  Frédéric Ricolfi ,  Dominique Dubois ,  Marie Paule Bonceour Martel ,  François Cotton ,  Alain Bonafé ,  Stéphane Chanalet ,  Françoise Hugon ,  Fabrice Bonneville ,  Christophe Cognard ,  François Chollet ,  Pierre Payoux ,  Thierry Voisin ,  Sophie Peiffer ,  Anne Hitzel ,  Michèle Allard ,  Michel Zanca ,  Jacques Monteil ,  Jacques Darcourt ,  Laurent Molinier ,  Hélène Derumeaux ,  Nadège Costa ,  Christian Vincent ,  Bertrand Perret ,  Claire Vinel ,  Pascale Olivier-Abbal.
Dose was applied as increments in GI or GL intakes. For quantitative DRM, T2D-GI and GL risk relations were expressed as RR per 10 units GI and 80 g/d GL adjusted to a 2000 kcal (8400 kJ) diet, respectively. These rates corresponded approximately to an increment in the RR per average dose increment from the 10th to the 90th percentiles of population intakes for eligible studies (CORR > 0. 55). This was the principal method used throughout this review. Extreme quantile meta-analysis (EQM) was used where quantitative information on GI or GL was not available, which was the case for BMI subgroups at the study level in the original prospective cohort studies. All statistical analyses were undertaken in Stata software (release 11. 2 SE, 2009; StataCorp LP College Station, TX, USA) using the "mais" installation  [53].
Acknowledgments: The authors are indebted especially to those researchers having published prospective cohort studies relating GI and GL to T2D and particularly to those having corresponded to provide confirmatory and/or Supplementary Materials. Canada Foundation for Innovation (CFI) , and the  Ontario Research Fund (ORF). He has received in-kind supplies for trials as research support from the  Almond Board of California, Walnut Council of California, American Peanut Council, Barilla, Unilever, Unico, Primo, Loblaw Companies, Quaker (Pepsico) ,  Pristine Gourmet ,  Bunge Limited ,  Kellogg Canada ,  WhiteWave Foods. He  has been on the speaker's panel, served on the scientific advisory board, and/or received travel support and/or honoraria from the  Almond Board of California, Canadian Agriculture Policy Institute, Loblaw Companies Ltd.
were funded by  Independent Nutrition Logic Ltd. , which in turn came from  BENEO GmbH (DE). J. LS. was funded by a  PSI Graham Farquharson Knowledge Translation Fellowship, Diabetes Canada Clinician Scientist Award , and  Banting & Best Diabetes Centre (BBDC)   Sun Life Financial New Investigator Award for Diabetes Research. DJAJ was funded by the  Government of Canada  through the  Canada Research Chair Endowment. The funding sources, other industries or commercial enterprises other than the author affiliations had no role in the initiation, conception, execution, interpretation, including commenting, editing, choice of journal and submission of the manuscript for publication.
MUAC is furthermore a more recommendable measure to use in clinical practice for assessing poor nutritional status  [4] , and a better predictor of mortality  [5]. Cut-offs values have been internationally defined  [6]. Lastly, differently from BMI, MUAC can be used also for pregnant women  [7]. The sample size calculation was done using EpiInfo® (version 7. 2. 2. 6. ) for a matched case-control study. We think some differences in sample size calculation can be observed depending on the software and/or the test used. Our sample size allowed to detect risk factors with an OR of 3 and a prevalence of 80% among controls. However, the OR can be lower if the prevalence among controls is lower. We clearly stated in out article that "Resources allowed to increase the sample size to 411, including 137 cases and 274 controls.
Large confidence intervals might be due to this sparse data bias, and not due to low number of cases. Gupta et al. suggested to use a p-value of 0. 2 rather than 0. 05 for the stepwise selection procedure. This would be true for a forward elimination, but we used a backward elimination. We first put all variables in the model and keep, as recommended, only those with a p-value < 0. 05 in the final model. Gupta et al. did understand that cases were interviewed at the hospital, leading to a differential recall bias. However, only morbidity data was collected at the hospital -anthropometric measures were extracted from the hospital register. As we started in our article, "data on health and nutritional status of caretaker, household WASH (water, sanitation and hygiene) conditions, socio-economic and demographic data were collected on the following day during the household visit through face-to-face interview", for both groups.
Analysis of the heterokont genomes reveals candidate genes encoding ␤-(133)-D-glucan phosphorylases Ochromonas ␤-(133)-glucan phosphorylases were expected to share residual sequence similarity to genes encoding these enzymes in the GH94 and GH149 families. To investigate this hypothesis, the translated transcriptome of Ochromonas sp. BG-1 from the Marine Microbial Eukaryote Transcriptome (MMET) database was interrogated using BLASTP with GH94 (21 sequences) and GH149 EgP1 sequences as queries. Three sequences were recovered (CAMPEP_0173148212, CAM-PEP_0173133844, and CAMPEP_0173155066), with 21% identity to a GH94 laminaribiose phosphorylase (LBP) sequence from Halorhadus tiamatea and 24% to EgP1 sequence (Table  1 ). These three sequences were found to be 99% identical, and therefore CAMPEP_0173155066 was taken forward as a representative, designated OcP1 (see supporting information for the full sequence).
Interrogation of the NCBI nonredundant protein database and the MMET database using PSI-BLAST with OcP1 as a query uncovered several hundred orthologs (File S1). Of these, 69 sequences (with 32-58% sequence identity to OcP1; File S2) originated from eukaryotes in the phyla Bacillariophyta, Ochrophyta, Haptophyta, and Miozoa, all of which belong to infrakingdom Heterokonta (collectively termed heterokonts) (Fig. 2 , orange). One sequence, GenBank TM accession number BAU78234. 1 (identity ϭ 58%, E-value ϭ 0), was identified from Ochromonas danica. The remaining 332 sequences identified that share 31-41% sequence identity to OcP1 (File S2) were from Gram-positive bacteria in the phylum Firmicutes (Fig. 2 , cyan; 229 sequences), 85 of which were from Paenibacillus spp. To establish the relationship between OcP1 orthologs and GH families containing ␤-(133)-D-glucan phosphorylases (GH94 and GH149), phylogenetic relationships were recon- New enzyme family containing ␤-(133)-glucan phosphorylases structed using amino acid sequences.
New enzyme family containing ␤-(133)-glucan phosphorylases A GH161 sequence from Paenibacillus polymyxa ATCC 842 (GenBank TM accession number WP_019688419. 1, 37% identity to OcP1), designated PapP, was chosen as a target for recombinant protein expression and in vitro biochemical characterization. The coding sequence (gene locus: PPT_ RS0121460) was amplified and cloned into a pOPINF vector  (36) , which installs a fused N-terminal His 6 tag, and expressed in E. coli (Rosetta PLysS). The recombinant PapP protein was purified by immobilized metal affinity chromatography (IMAC) (Fig. S1, A  and B ) and subsequently by gel filtration (Fig. S1C ). Protein with an approximate molecular mass of 120 kDa, based on SDS-PAGE analysis, was recovered (Fig. S1D ). Gel filtration analysis of PapP against protein standards revealed that PapP formed a dimer in solution under nondenaturing conditions, with an estimated molecular mass of 241 kDa.
5  and Fig. S3 ). The relaxed acceptor regioselectivity observed in PapP suggested that this function might also be a property of GH149 enzymes. To investigate this hypothesis, Pro_7066 was assayed in the glycan synthetic reactions in the presence of Glc-Glc disaccharides with varying glycosidic linkages, which also showed glycan synthetic activity toward isomeric ␤-linked acceptors in the same manner as for PapP (Figs. S4  and S5 ). During bioinformatics analyses of GH161 sequences in the NCBI database, we came across sequence from the Gram-negative thermophilic bacterium Thermosipho africanus TCF52B (TaCDP, GenBank TM number ACJ76363. 1) that had recently been reported as a cellodextrin (␤-(134)-glucan) phosphorylase, operating on Glc and cello-oligosaccharides  (37). This was at odds with our expectations and warranted further investigation, given that TaCDP phosphorolytic activity on ␤-(133)gluco-oligosaccharide substrates had not been assessed and the glucan products for ␤-(134)-glucan extension had not been subjected to linkage analysis.
To confirm the substrate specificity of TaCDP enzyme, the TaCDP gene sequence (GenBank TM number CP001185. 1, locus 1948177-1951236) was codon-optimized for E. coli expression, and the synthetic gene was amplified by PCR and subsequently cloned into a pOPINF vector. The gene was expressed in E. coli BL21 (DE3), and the resulting recombinant protein was purified by IMAC. To establish the substrate specificity of TaCDP, we assayed the enzyme in the phosphorolytic reaction against laminaribiose, cellotriose, and laminaritriose in the same manner as described for PapP. This showed that TaCDP was active exclusively on laminaritriose, with no detectable activity on either laminaribiose or cellotriose (Fig. 6, A  and B ). The enzyme also showed weak activity on Glc as an acceptor in the presence of Glc1P, producing an insol-uble product after 4 days of incubation at 37 °C (Fig.
Bioinformatic analysis and phylogeny Orthologous sequences to OcP1 were obtained from the nonredundant protein sequence database and the MMET Sequencing Project, using BLASTP or tBLASTn with an E-value score of 0. 0001 or better. Multiple-sequence alignments of amino acid sequences were performed using Clustal Omega (53) (www. clustal. org/omega, 5 version 1. 2. 2) with the default settings and edited with trimAl version 1. 2 using a heuristic automated method  (54). The alignments were visualized by Jalview (version 14. 6. 4) (55). Phylogenetic trees were reconstructed from a matrix of 306 unambiguously aligned amino acids using PhyML version 3. 0  (56)  with the best fit model as inferred by a smart model selection (SMS). Bootstrap values were determined from a population of 100 replicates.
Acquisition of Visible/Near Infrared Spectra In 2016, after homogenizing the samples, the ground frozen and barn-stored forages were placed in a 50 mm-diameter ring cup and scanned in reflectance mode at 2-nm intervals from 400 to 2500 nm using a Foss NIRSystems model 6500 scanning VIS/NIR spectrometer (Foss NIRSystems, Silver Spring, MD, USA). Spectra and reference values were recorded using ISIscan version 2. 21 software (Infrasoft International, State College, PA, USA). Each spectrum was averaged from 32 scans. A reference scan (using the internal ceramic reference tile) was taken before each sample. The reflectance (R) values were converted into absorbance (A) values using the formula A = log (1/R). The raw NIR spectroscopy data were pre-processed using the standard normal variate and de-trending scatter correction procedure  [23].
Statistical Analyses Data on the forage chemical composition and PCDMD were tested by ANOVA using the mixed procedure of the SAS statistical package  [24]. The model used the included storage method and sample as its factors. The storage method was considered to be a repeated measure and the sample to be a random variable. The effect of the storage method after 29 years (frozen vs. barn temperature) was studied for all determinations, whereas the effect of time was only tested for ash, TSC, starch, and PCDMD because the methods of analysis performed in 1987 differed from those performed in 2016 for all other determinations. The levels of both effects were compared by orthogonal contrasts.
Background: Water is recommended as the main beverage for daily fluid intake. Previous systematic reviews have studied the consumption of sugar-sweetened beverages (SSBs) among children, but none have focused on water consumption. Insight into factors that are associated with children's water intake is needed to inform the development of interventions aimed at the promotion of water consumption. The objective of this review was therefore to summarize the current evidence on factors associated with water consumption among children aged 2 to 12 years. Methods: A systematic literature search in seven electronic databases was conducted in May, 2018 and retrieved 17,850 unique records. Two additional studies were identified by hand-searching references of included articles. Studies were selected if they had a cross-sectional or longitudinal study design, focused on children aged 2-12 years and published in an English language peer-reviewed journal.
Search strategy A systematic literature search was conducted in May, 2018, using the following electronic databases: Embase, Medline Ovid, Web of Science, Cochrane, PsychINFO Ovid, CINAHL EBSCOhost, and Google Scholar. A combination of the following key words were included in the search: (water or beverage* or drink* or related key words) and (child* or infant* or toddler* or related key words) and (determinant* or factor* or life-style* or diet* or parental attitude* or related key words). The search strategy was adapted to each database. The complete search strategies used are presented in Additional file 1. In addition to database searching, the references of relevant articles were screened for other potentially relevant studies. We registered the systematic review protocol for this study in the PROSPERO registry under registration number CRD42018093362 on May 22, 2018.
Data extraction A standardized data extraction form was developed after discussion and consensus among the study team. This standardized form was used to extract data from the included studies by a researcher (CF or LW) and all data entered in the form was checked by one of the researchers (CF). Extracted information included: year and author of study, country, study design, population and characteristics, outcome, measurement instruments used, type and level (individual, interpersonal, environmental) of factor studied, and the association between correlate/determinant and outcome. For each factor, we qualitatively described the association between correlate/ determinant and water consumption (positive; negative; or no significant positive/negative association), see Additional file 3: Table  S1.
Study selection The process of inclusion and exclusion of articles at each stage is described using the preferred reporting items of systematic reviews and meta-analyses (PRISMA)  [46]  flow chart (Fig. 1 ). A total of 33,410 records were identified after searching the seven databases. After removal of duplicates, 17,850 records remained. After all rounds of screening, 61 articles were identified. Two additional studies were identified by hand-searching the references of the included articles, resulting in a total of 63 articles that met the inclusion criteria and were included in the analysis.
Strengths and limitations To our knowledge, this was the first systematic review to investigate factors associated with water consumption in children. Previous reviews have focused on factors associated with SSB consumption in children and intervention studies aiming to reduce SSB intake  [35, 116]. We performed an extended literature search in seven databases and followed a rigorous procedure for the selection of studies  [117]. In addition, the references of included studies were hand-searched, which resulted in the inclusion of two additional studies. Some limitations of our review must also be acknowledged. Because we only included published studies, there is a possibility of publication bias in the findings of this review  [118]. Furthermore, we only studied articles published in English and thus might have missed studies that were published in other languages.