dataesr/scientific-paragraphs-categorization huggingface dataset:
4, and 150 mM NaCl. Spectra acquisition was performed at 25 °C using a spectropolarimeter (J-815, Jasco) in the far UV (200 -260 nm) with the following parameters: 1 nm step, 2 nm bandwidth, and scan speed 200 nm/min. The optical path length was 1 mm. Model Building-The three-dimensional model was generated using Chimera and Modeler version 9. 10. The sequence of At4g14030 was aligned with sequences from the Protein Data Bank using Blast and Blosum62 as the alignment matrix. The structure of the hypothetical selenium-binding protein from Sulfolobus tokodaii (PDB entry 2ECE) was the closest homologue and used to generate a three-dimensional model with the program Modeler (E-value of 7e-86; 40% sequence identity). The model of At4g14030 with the lowest discrete optimized protein energy score was selected.
Unfortunately, arterial puncture is an invasive procedure, and is associated with technical problems that complicate the use of this marker. In addition, interpretation of the data requires that blood flow is measured simultaneously. Alternatively, plasma phenylalanine can be measured as a marker of protein turnover. Some authors have suggested measuring the phenylalanine:tyrosine ratio for this purpose It has been shown  [80]  that plasma phenylalanine correlates well with nitrogen balance in burn patients. At present, there are insufficient data available to recommend the use of plasma phenylalanine or of the phenylalanine:tyrosine ratio as a reliable marker of protein turnover.
This work was supported by grants from the  Burgundy Region council , the  Fond Europeen de Developpement Economique , and the  ANR-2010-JCJC-1410-1   MEMOLAP  to GC and TTD. SR was funded by the  French Ministry of Higher Education and Research. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Data collection and follow-up At the time of inclusion, the following baseline characteristics are recorded: age, sex, date of ICU admission, height, body weight, BMI, primary diagnosis, McCabe score, Knaus score and preexisting comorbidities (including chronic renal failure, liver failure, pulmonary disease and heart failure; malignant disease; and immunosuppression). Use of sedatives, insulin, proton pump inhibitors, dialysis, neuromuscular blockers and gastric prokinetic agents before inclusion are also recorded. The Simplified Acute Physiology Score II is computed 24 hours after ICU admission  [69]. The information listed below is recorded daily until extubation or until day 28 during intubation, whichever occurs first.
Coordination and conduct of the trial Before the start of patient recruitment procedures, all physicians and other health-care workers in the 44 participating ICUs attended formal training sessions on the study protocol and data collection in the electronic case report form (eCRF). All documents required for the study are available in each ICU. The eCRF is a secure, interactive, web response system available at each study center, provided and managed by the biometrical unit of the Tours University Hospital (CIC INSERM 1415, Tours, France). In each participating ICU, the physicians and a clinical research nurse and/or clinical research assistant are in charge of daily patient screening and inclusion, ensuring compliance with the study protocol and collecting the study data in the eCRFs. The Clinical Research Unit of the La Roche-sur-Yon Hospital will review the screening forms and clinical data at regular intervals.
The principal investigators will meet with the ICU teams to discuss any problems with data collection and protocol compliance and to evaluate study progress. According to French law, the eCRF and database organization have been approved by the appropriate committees (CCTIRS: Comité Consultatif sur le Traitement de l'Information en matière de Recherche dans le domaine de la Santé; and CNIL: Commission Nationale de l'Informatique et des Libertés).
For descriptive bacteriological data (organisms recovered with their resistance profiles for each nosocomial infection), only descriptive analyses will be performed. For the proportion of patients with at least one episode of vomiting or regurgitation, diarrhea, constipation, documented acute colonic pseudo-obstruction (Ogilvie syndrome), documented bowel ischemia, mechanical complication of CVC insertion and liver dysfunction, the method used will be the same as that employed for the nosocomial infections. Changes over time in calories delivered daily by the enteral and parenteral routes and changes over time in enteral and parenteral feed volumes delivered daily will be compared between the two groups using a mixed linear model, after data transformation if necessary. The proportions of patients who achieved their daily calorie target will be compared between the two groups using a logistic random-effects model.
Acknowledgments We are indebted to  Antoinette Wolfe, MD , for assistance in preparing and reviewing the manuscript;  Carine Coffre  for managing the database; and  Prof. Veronique Sebille  ( EA 4275, Biostatistics, Pharmacoepidemiology and Subjective Measures in Health Sciences, University of Nantes, Nantes, France ),  Prof. Jean Chastre  ( Medical ICU, La Pitié-Salpêtrière Hospital, Paris, France ) and  Prof. Laurent Papazian  ( Medical ICU, Détresses respiratoires et infections sévères, Hopital Nord, Marseille, France ) for constituting the independent data safety and monitoring board. Funding NUTRIREA-2 is supported by a grant from the  French Ministry of Health  ( Programme Hospitalier de Recherche Clinique 2012 ,  PHRC-12-0184 ).
Acknowledgements. The author thanks the support of  Philippe Guesnet  and  Fabienne Aujard  in the achievement of the studies of ω3 fatty acids in the Grey mouse lemur. This work was financially supported by the  Groupe Lipides et Nutrition  (part of the  Association Française pour l'Étude des Corps Gras) , the  Centre National de la Recherche Scientifique/Muséum National d'Histoire Naturelle , and the  Institut National de la Recherche Agronomique.
Acknowledgments We thank  Drs Christian Halaszovich  and  Sandeep Dembla  for critically reading the manuscript. Supported by grants from  SFB 593  (to J. O. ) and  National Institutes of Health  ( HD058577  and  ES01678 ; to K. K. ). Open Access This article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution, and reproduction in any medium, provided the original author(s) and the source are credited.
statistical analysis Statistical Package for the Social Sciences version 13. 0 software (SPSS Inc. , Chicago, IL, USA) was used for calculation of statistical data, which were expressed as the mean ± standard deviation and assessed for statistical significance. We used the Student's t-test to compare skin surface hydration, TEWL, and CPT. We used Pearson's correlation coefficient and conducted a linear regression analysis to determine correlations between skin surface hydration and CPT. For most of the tests, a value of P0. 05 was considered to be statistically significant (a value of P0. 10 was considered to be statistically significant for CPT).
Dovepress Clinical Interventions in Aging is an international, peer-reviewed journal focusing on evidence-based reports on the value or lack thereof of treatments intended to prevent or delay the onset of maladaptive correlates of aging in human beings. This journal is indexed on PubMed Central, MedLine, CAS, Scopus and the Elsevier Bibliographic databases. The manuscript management system is completely online and includes a very quick and fair peer-review system, which is all easy to use. Visit http://www. dovepress. com/testimonials. php to read real quotes from published authors.
All mothers were offered at least five home visits, the first occurred in the third trimester of pregnancy. Qualitative descriptions of the intervention are given elsewhere  [23] [24] [25]. Sample size calculation was done for EBF and diarrhea prevalence  [18]. Those intending to breastfeed and planning to stay in the selected cluster in the forthcoming year were included, further details on recruitment, inclusion and exclusion are given in the Additional file 1. The analysis included 2,579 singleton live children. The trial profile is given in Figure  1. Data were collected between 2006 and 2008 using a recruitment interview late in pregnancy, and further interviews targeted at weeks 3, 6, 12 and 24 after birth. Structured questionnaires were developed and adapted from the literature  [26, 27]  and informed by prior work in the participating countries  [28] [29] [30].
The first recruitment interview focused mainly on socio-demographic and socio-economic characteristics. The follow-up contact points captured mother-reported feeding practices and infant illness, and the children's length and weight were recorded. Interviews were regarded as 'timely' if they were done within the following time periods: 1. 5-4. 5 (3); 4. 5-9 (6); 9-18  (12) ; and 18-28  (24)  weeks. Timely measurements provided data for the undernutrition prevalence estimates. The trial profile reflects number of 'timely' out of 'total' interviews per scheduled visit (Figure  1 ). The trial profile also reflects the number of anthropometric measurements, all measurements went into the longitudinal modelling of the anthropometric data. Length was measured to the nearest 0. 1 cm using 'Shorr Height-Length Measuring Board' (Maryland, USA) provided as 'Baby/infant/adult Length-height measuring system SET 2' from UNICEF in Uganda, and 'Seca 210 mobile measuring mats for babies and toddlers, ' with 0.
5 cm precision, in Burkina Faso and TALC's roller mat infantometer (Oxford, UK) in South Africa. Infant weight was recorded to the nearest 0. 1 kg using the 'Infant scale spring type, 25 kg, 100 g' from UNICEF in Uganda, the 'SECA 872 scale with mother-infant children's' function' in Burkina Faso and 'Mascott electronic bucket' in South Africa. The measurement procedures followed standard WHO guidelines  [31]. All data collectors underwent training in content, questionnaire techniques and measurements and were kept uninformed about cluster allocation. For the weight and length measurements, reproducibility and validity exercises were conducted. Re-training and evaluation were done at least semi-annually during the data collection period. The acceptable technical error of measurement (TEM) for a data collector  [32]  was a value less than two times that of the data collector supervisor, a clinical specialist.
Data handling and analysis Descriptive statistics included means with 95% confidence intervals, medians and ranges for continuous variables and prevalence estimates with 95% confidence intervals for categorical variables. The data were analysed using STATA SE11. 0 (Stata Corp LP, College Station, TX, USA) and SAS V9. 2 (SAS Institute Inc. , Cary, NC, USA). Missed visits, the fact that some mothers did not consent to measurements at all visits, and the data cleaning process resulted in some missing anthropometric data. A detailed description of data cleaning and handling of missing anthropometric information is presented in the Additional file 1. An inverse-probability weighted method (IPW) was used instead of a plain available-subject-analysis to adjust for potential differences in follow-up between groups (Additional file 1).
Ethical approval Approval for the trial (ClinicalTrials. gov: NCT00397150) was obtained from the following bodies: 1) Burkina Faso: the Institutional Review board of Centre Muraz (No 013/2005/CE-CM) and from the Ministry of Health at national and regional level; 2) Uganda: Makerere University Faculty of Medicine Research and Ethics Committee, and the Uganda National Council for Science and Technology; 3) South Africa: Ethics Committee of the Medical Research Council South Africa; and 4) Norway: Regional Committees for Medical and Health Research Ethics (REK VEST), 8 Sept 2005, issue number 05/8197. Women provided verbal informed consent for participation in the peer-counselling programme, which was regarded as a service. Written informed consent for participation in the study was signed or thumb-printed by each caretaker.
Financial support The study was funded by:  EU  6 th Framework INCO DEV, contract no  INCO-CT 2004-003660 ;  Research Council of Norway, Swedish International development cooperation agency (Sida) ; The  Norwegian Programme for Development, Research and Education (NUFU) ;  Rockefeller Brothers Foundation ; and the  South African National Research Foundation (NRF). Funding The study was funded by:  EU  6 th Framework INCO DEV, contract no  INCO-CT 2004-003660 ;  Research Council of Norway; Swedish International development cooperation agency (Sida) ; The  Norwegian Programme for Development, Research and Education (NUFU) ;  Rockefeller Brothers Foundation ; and the  South African National Research Foundation (NRF). List of members for the  PROMISE-EBF study group Steering Committee :  Thorkild Tylleskär ,  Philippe Van de Perre ,  Eva-Charlotte Ekström ,  Nicolas Meda ,  James K.
Objective: to examine the clinical evidence reporting the prevalence of sarcopenia and the effect of nutrition and exercise interventions from studies using the consensus definition of sarcopenia proposed by the European Working Group on Sarcopenia in Older People (EWGSOP). Methods: PubMed and Dialog databases were searched ( January 2000-October 2013) using pre-defined search terms. Prevalence studies and intervention studies investigating muscle mass plus strength or function outcome measures using the EWGSOP definition of sarcopenia, in well-defined populations of adults aged ≥50 years were selected. Results: prevalence of sarcopenia was, with regional and age-related variations, 1-29% in community-dwelling populations, 14-33% in long-term care populations and 10% in the only acute hospital-care population examined.
Search strategy PubMed and Dialog databases were searched from January 2000 to May 2013 using the pre-defined search terms sarcopenia and muscle mass: additional pre-defined search terms were applied (see Supplementary data available in Age and Ageing online, Appendix S1) for each of the three areas of interest: prevalence of sarcopenia, nutrition interventions for sarcopenia and exercise interventions for sarcopenia (Figure  1 ). An additional short search of PubMed and Dialog databases using the terms 'sarcopenia', 'elderly', 'intervention', 'prevalence' and 'treatment' was conducted to cover articles published in the period May-October 2013 (Figure  1 ). The reference lists of systematic review articles and meta-analyses were scanned for any additional references missed from the PubMed and Dialog searches.
Other criteria used to exclude studies in each of the three categories are provided in Supplementary data available in Age and Ageing online, Appendix S2. Observational studies were included in the prevalence category, but for the exercise and nutrition intervention categories, only randomised controlled trials were selected. The ISI group was divided into three subgroups (prevalence, exercise and nutrition). Final papers selected for inclusion in each of the three categories were agreed upon by each subgroup consensus.
Data synthesis Data tables were compiled independently for each topic. For the prevalence of sarcopenia category, data were recorded on demographics (country, gender and age), assessment method used for each domain (muscle mass, muscle strength and physical performance) and sarcopenia prevalence. For the interventional categories, data were collected on population, numbers studied (by gender), age, intervention, control group, duration of intervention, outcomes measured and the main results. The methodological quality of each randomised, controlled trial was assessed using the 11-point Physiotherapy Evidence Database (PEDro) scale. Each item on the scale that the trial satisfied (except for item 1, which assesses external validity and is not included in the total score) contributed one point to the total PEDro score, with 0 representing the lowest score and 10 the highest [4].
Results Overall, 4810 publications were identified (Figure  1 ). Of these, 3909 were excluded, leaving 901 publications for potential inclusion ( prevalence: 252; exercise: 175; nutrition: 474). In addition, 11 papers were identified as suitable for inclusion as a result of a short search of PubMed and Dialog databases to identify articles published in the period May-October 2013. Eighteen prevalence, 7 exercise and 12 nutrition papers were finally chosen by the working group members for inclusion within this review (Figure  1 ).
5418 A ˚) with a MarRearch 345 image-plate detector at School of Life Sciences, University of Science and Technology of China (USTC, Hefei, China) and were processed with the program MOSFLM 7. 0. 4 [29]. The apo-SCO4226 structure was determined by single wavelength anomalous dispersion (SAD) method  [30]. The Ni-SCO4226 structure was determined by the molecular replacement method using the structure of apo-SCO4226 as a search model with the program MOLREP  [31]  in CCP4i  [32]. The initial models were refined by using the maximum likelihood method with the program REFMAC5  [33]  and rebuilt interactively with the programs PHENIX  [34]  and COOT  [35]  until the free R-factor converged. The occupancy refinement with PHENIX was used to refine the individual occupancies of nickel ions and group occupancies of citrate in Ni-SCO4226.
Isothermal titration calorimetry The chemical NiSO 4 was bought from Sangon, China. The titrations of Ni 2+ into the SCO4226 protein solution were performed at 28uC using VP-ITC Isothermal Titration Calorimeter (ITC, MicroCal Inc. ). Before each ITC experiment, the pH values were adjusted to the same, and the protein solution was degassed for 2-5 min to eliminate air bubbles. In each individual titration, the 40 mL NiSO 4 solution of varying concentrations (200-500 mM) was injected into the SCO4226 protein solution (10-20 mM) in the same buffer containing 20 mM Tris-HCl, pH 7. 0, 100 mM NaCl. A 180 sec interval between injections was used for complete equilibrium. Titration of Ni 2+ into the buffer alone under the same conditions was used as the control. The data were fitted using a non-linear least squares minimization algorithm to a theoretical titration curve, using the MicroCal Origin software.
UV/visible spectroscopy The chemical NiSO 4 and Ethylene Diamine Tetraacetic Acid (EDTA) were bought from Sangon, China. The turbidity of the protein solution towards NiSO 4 was measured at 28uC by monitoring the change in absorbance at 340 nm in 30 min or more with the interval of 15 sec, using a DU800 spectrophotometer (Beckman Coulter, Fullerton, CA, USA). Titrations of NiSO 4 (0-2 mM) against 10-50 mM SCO4226 were performed in the buffer of 0. 1 M Tris-HCl, pH 7. 5, 100 mM NaCl. Then EDTA was added to a final concentration of 5 mM in the turbidity solution. The data were recorded by the program Origin 7. 5. The assays were performed in triplicates.
Overall Structure The structures of SCO4226 in both apo-and nickel-bound forms (termed apo-and Ni-SCO4226, respectively) have been solved at 1. 30 and 2. 04 A ˚resolution, respectively (PDB IDs: 4OI3 and 4OI6). The two structures are quite similar to each other with a root-mean-square deviation (RMSD) of 0. 48 A ˚over all the 162 Ca atoms. Each asymmetric unit contains a dimer of SCO4226, with a buried interface area of about 1100 A ˚2 on each subunit. The two subunits of the dimer are almost identical, with an RMSD of 0. 14 A ˚for apo-SCO4226, and 0. 29 A ˚for Ni-SCO4226. Size-exclusion chromatography in our previous study also indicated that SCO4226 exists as a dimer in solution  [26]. The overall structure of SCO4226 adopts a ferredoxin-like fold  [38]  with an a+b structure: five b-strands (b1-5) packing against two a-helices (a1-2) (Figure  1A-1B ).
Structural comparison Structural similarity search using DALI server (http://ekhidna. biocenter. helsinki. fi/dali_server/) [39]  gave 266 hits of 58 unique proteins with a Z-score of $6. 0. The top hits include DNA transposase ISHp608 from Helicobacter pylori (PDB: 2A6M, Zscore 7. 7, RMSD 2. 6 A ˚for 76 Ca atoms), the nickel-dependent transcription factor NikR from H. pylori (PDB: 3QSI, Z-score 7. 3, RMSD 2. 9 A ˚for 71 Ca atoms), and the metallochaperone protein Hah1 from Homo sapiens (PDB: 1FE4, Z-score 6. 0, RMSD 2. 4 A for 63 Ca atoms). Superposition of subunit A of the apo-SCO4226 structure against the ferredoxin-like fold domain of these structures revealed that the overall structures could be superimposed, except for the extension of b5 at the C-terminus of SCO4226 (Figure  1C ). Nevertheless, significant structural variations were found between SCO4226 and these proteins.
RNA Isolation and qPCR Total RNA was isolated from whole lung homogenates using the RNeasy Mini Kit (Qiagen, Valencia, CA) and reverse transcribed using the iScript kit (BioRad, Hercules, CA). miRNA was isolated using the miRNeasy Mini kit with on-column DNase digestion (Qiagen, Valencia, CA) and reverse transcribed using the Taqman MicroRNA Reverse Transcription Kit (Life Technologies, Grand Island, NY). Quantitative PCR was performed on a StepOnePlus Real Time PCR System (Applied Biosystems, Foster City, CA). Data for RNA analysis were normalized to 18 s and data for miRNA analysis were normalized to snoRNA202.
Microarray Analysis Total lung RNA was isolated from Scap D/D , Insig1/2 D/D , and respective control littermates at E17. 5, E18. 5 and PN1 using RNeasy Mini Kit (Qiagen, Valencia, CA). The cRNA was then hybridized to the Mouse Gene 1. 0 ST Array (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol. Three biological replicates were used for each condition. The RNA quality and quantity assessment, probe preparation, labeling, hybridization, and image scan were carried out in the Cincinnati Children's Hospital Medical Center Affymetrix Core using standard procedure. Data were further analyzed using Gene-Spring GX 11. 5 (Agilent Technologies, Santa Clara, CA). Differentially expressed genes in Scap D/D vs. control mice at different developmental time points were identified using two-way ANOVA (genotype and time dependent gene changes).
Genes altered in Insig1/2 D/D vs. control were identified using Student's ttest with the threshold of corrected P#0. 01 and fold change $1. 5. Benjamini-Hochberg false discovery rate (FDR) was applied for multiple testing correction. The probe sets were pre-filtered by their expression range within 35-100 percentiles for at least 66% of samples to remove probes with extremely low expression signals in both mutant and control samples. The complete dataset has been submitted to the Gene Expression Omnibus (GEO) database with the accession number of GSE53397. miRNA Analysis miRNA expression profile was determined by using GeneChip miRNA 3. 0 Array (www. affymetrix. com). This array platform provides complete coverage of miRBase v17, snoRNA and scaRNA probes on the same array, and covers 153 organisms including human, mouse and rat.
Lung samples from Scap D/D and control littermates at E18. 5 (n = 3 per genotype) were used to isolate RNA using miRNeasy kit with on column DNase digestion (Qiagen, Valencia, CA). The Expression Console software (Affymetrix, Inc. ) was used for data summarization, normalization, and quality control. The miRNAs with P,0. 01 and fold changes. 1. 3 was defined as differentially expressed using BRB-Array-Tools Version: 4. 2. 1 (http://linus. nci. nih. gov/BRB-ArrayTools. html). miRNA target prediction and filtering were performed using miRNA Target Filter tool in IPA. miRNA and mRNA targets showing inverse expression patterns in response to Scap deletion at E18. 5 were selected for further analysis (i. e. miRNA up, mRNA down OR miRNA down, mRNA up). Differentially expressed genes at different lung maturation stages (i.