dataesr/scientific-paragraphs-categorization huggingface dataset:
First, the ITR does not collect detailed perioperative data on donor selection criteria; specific surgical techniques; nutritional management; protocols to detect rejection; and protocols to prevent viral, bacterial and fungal infections  (3, 14, 42, (60) (61) (62) (63). Second, the data provided to the ITR have not been audited or independently verified. Third, some data elements are incomplete. On the other hand, as discussed above, the ITR's ability to examine long-term, global outcomes in a large number of patients is a major strength. In summary, IT and the ITR continue to evolve. Current graft survival rates are comparable with the results of other solid organ transplants. The main challenge now is to improve our understanding of the reasons for late graft failure and to develop treatment protocols that will provide durable, longterm intestine graft function  (33, 54).
Acknowledgments The contributing authors participated fully in the data analysis, reporting and preparation of the manuscript. The time and effort invested by all of the programs that contributed to the ITR is greatly appreciated. The authors are particularly grateful for the manuscript review and advice provided by  O. Goulet , and  M. Marquez  who is the ITR Manager since 2009. Charles Victor performed the statistical analyses. Support for the ITR was provided by unrestricted educational funds provided by  Astellas Canada  ( 1999-2011 ) and  University Hospital, London ,  Ontario  ( 1987 )(1988)(1989)(1990)(1991)(1992)(1993)(1994)(1995)(1996)(1997)(1998)(1999).
Static light scattering (SLS) Static light scattering kinetic experiments were performed with a homemade device using a 407-nm laser beam. Lightscattered signals were recorded at a 112°angle. Signals were processed with a homemade MatLab program. This technique was coupled with size-exclusion chromatography, to estimate the absolute molecular weight of AChE (oligomeric state) using the relationship between the intensity of light scattered by the molecule and its molecular weight and concentration, as described by the Rayleigh theory. A 60 × 0. 78 cm TSK4000SW column (Tosoh Bioscience, Worcestershire, UK) was used with 20 mM Mes pH 6. 0 as elution buffer. The temperature of the column was maintained at 18°C. Carbonic anhydrase was used as standard protein for calibration purposes.
Fibril annealing and PK digestion assay PrP fibrils in the presence or absence of AChE were treated as described previously  [43]. Samples were heated in denaturing sample buffer (60 mM Tris-HCl, 2% SDS, 5% β-mercaptoethanol, 2. 25 M urea) at 95°C for 15 min and separated on 12% Criterion™ XT Bis-Tris Precast Gels (Bio-Rad) followed by silver staining. Quantification of protein-band intensities was performed by densitometric analysis using NIH ImageJ software (National Institutes of Health, Bethesda, MD).
, Suffolk, UK). Digital images were captured from 10 random fields for each sample (≈3500 cells total) using an Axiovert 200 M Zeiss inverted microscope (Carl Zeiss S. A. S. , Marly le Roi, France). Neuronal cell death was determined by counting the bright neurons and expressed as the percentage of the total cell number compared with control cultures. Data were analyzed by one-way analysis of variance and a Tukey test was carried out on the results of four independent experiments. Inhibition of AChE enzymatic activity 7. 3 nM AChE was mixed with PrP fibrils (concentration ranging from 8 to 25 μM) or 25 μM monomeric PrP at 37°C in 100 mM sodium phosphate buffer pH 7. 4 containing 0. 33 mg/mL BSA. The residual activity contained in a 10-μL aliquot was monitored at 25°C and pH 7. 4, according to the Ellman's method, using 1 mM acetylthiocholine and 0.
AChE detection in brain and spleen 200 mg of total proteins were separated on 7. 5% Criter-ion™ TGX™ Gels (Bio-Rad) in reducing conditions, and then transferred to nitrocellulose membranes. Blots were blocked in Tris-buffered saline (TBS) with 0. 5% Tween 20 (TBS-T) containing 5% nonfat dried milk at 4°C overnight before incubation with a rabbit anti-AChE antibody  [41] , (1:2000 in the same TBS-T buffer) at 4°C overnight. Blots were then incubated with peroxidaseconjugated anti-rabbit IgG antibodies (1:10,000; Abliance SAS, Compiègne, France) at room temperature for 30 min, washed extensively and exposed to the chemiluminescent substrate ECL Plus (GE Healthcare). The amount of AChE present in each tissue was determined with the GeneTools software after acquisition of the chemiluminescent signals with a GeneGnome digital imager (Syngene, Frederick, Maryland, USA).
Acknowledgments We are grateful to the staff of the  Animalerie Rongeurs (INRA, Jouy-en-Josas, France)  for excellent animal care. We also thank  Prof. P. Taylor  ( Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, USA ) for the gift of the anti-AChE antibody. We thank  Veronique Perrier  ( Inserm, Montpellier, France ) for helpful discussion. Joan Torrent  (research scientist at  Inserm ) is grateful to  Inserm  for institutional support. Alba Vilchez-Acosta  thanks  Erasmus Programme  for a mobility grant.
In each country, a ministry of health focal point or a national consultant was also identified to coordinate the study activities. These teams served as technical working groups to support deliberations on the introduction of new vaccines by National Immunization Technical Advisory Groups (NITAGs), where these exist. IWG partners provided ongoing technical support throughout the study, with in-country visits to initiate and support the study and a final visit to review databases, address any methodological challenges, and assist in interpreting the results for decision-making purposes. CDC partners led technical reviews and provided recommendations regarding epidemiological data on rotavirus and pneumococcal disease. After data collection, multidisciplinary country teams critically assessed the data and conducted the analyses.
Acknowledgements We thank  Claire Cherbuy ,  Muriel Mercier-Bonin ,  Françoise Rul , and  Joanna Radziwiłł-Bieńkowska  for fruitful discussions. SM and RM received funding from the  FPARIS collaborative project , which was selected and supported by the  Vitagora Competitive Cluster  and funded by the  French FUI (Fond Unique Interministériel ;  FUI: n°F1010012D ), the  FEDER  ( Fonds Européen de Développement Régional ; Bourgogne:  34606 ), the  Burgundy Region , the  Conseil Général 21 , and the  Grand Dijon.
Data Analysis and Statistics All electrophysiological results were analyzed using PatchMaster (HEKA Electronik, Germany) software. Dose-response curves were constructed by fitting values obtained at different concentrations, after normalization. The responses to glycine concentration were fitted using the non-linear fitting routine of the Origin 7. 5 software (OriginLabs, USA) with the Hill equation: I = 1/(1 + (EC 50 /[A]) nH ), where I is the normalized current amplitude induced by the agonist at concentration  [A] , n H is the Hill coefficient and EC 50 is the concentration at which a half-maximum response was induced. Paired and unpaired Student's t-tests were used for statistical analysis. The data are expressed as the means ± SEM.
Drugs Ginkgolic acid (C15:1, HWI Analytic GmbH, Germany) was initially dissolved in pure DMSO and then diluted with control medium to the maximal final concentration of DMSO 0. 016% in experiments with using 25 μM ginkgolic acid. In test experiments, DMSO itself had no effects on the I gly (data not shown; see also  Mascia et al. , 1996; Hall et al. , 2004). Other drugs were obtained from Tocris or Sigma-Aldrich (France).
Low-dose RUTF protocol Buthidaung towns) from July 2009 to January 2010. Available data from the OTP records were collected weekly using standard methods. Age was recorded to the nearest month, estimated through an interview with the caregiver, using dental charts and a seasonal calendar. Children were weighed to the nearest 0. 1 kg in minimal clothing on a portable hanging spring balance 25 kg scale. Recumbent length (for children <87 cm) and standing height (for those ≥87 cm) were recorded to the nearest 0. 1 cm using a locally manufactured wooden height board. MUAC was measured on the left arm, midway between shoulder and elbow, to the nearest millimetre using numbered MUAC measuring tapes. Presence of bilateral oedema was assessed by applying thumb pressure on both feet and assessing whether any indentations remained after 3 second.
Those who were discharged by the clinics but whose discharge measurements were not complete were reclassified as 'missing discharge criteria'. 2006) , data from children with heightfor-age z-score (HAZ) below -6 or above +6, weightfor-age z-score (WAZ) below -6 or above +5, or WHZ below -5 or above +5 were excluded from analysis (Fig. 1 ). The total length of stay was calculated in days for all children included in the programme as the period between the date of discharge and admission. Weight gain (g kg -1 day -1 ) was calculated as the difference between discharge and admission weight, in grams, over the admission weight, in kilograms, divided by the number of days of stay in the programme.
Ethical approval All the data were collected as part of routine nutritional care and programme monitoring activities. No specific consent was sought for data extraction and analysis. No personal identifiers were entered in the dataset. Ethical approval for analysis was provided by the MSc Research Ethics Committee of the London School of Hygiene & Tropical Medicine on 22 June 2010 (Ref. 009/487). This was a retrospective analysis of historical data and therefore pre-study approval was waived by the Ethics Committee. ACF analysed the data every month in real time to monitor the quality of recovery and to provide the basis for a decision to stop the implementation of the low-dose RUTF protocol had it not performed to standards.
Results Data from 3083 children treated under the low-dose RUTF protocol were available for analysis. Median (IQR) age at admission was 30 months  [18; 46] ; median  MUAC 118 mm [114; 122] , median ] and median HAZ -3. 2 [-4. 2; -2. 2]. As shown in Table  1 , 2782 (90. 2%) children recovered under the low-dose RUTF protocol, 62 (2. 0%) defaulted from the programme, 28 (0. 9%) were classified as non-responders, 2 (0. 07%) were transferred to the hospital for medical reasons, and 33 (1. 1%) were classified as unconfirmed defaulter. No death was recorded during the studied period. For 141 (4. 6%), the outcome recorded in their clinical records could not be verified with their clinical data, and were labelled as 'unconfirmed recovered'. Thirty-five children (1. 1%) had missing discharge criteria and were classified as such.
This may have contributed to the good results observed in this project. In order to reduce the misclassification that is frequent in secondary data from real-life programmes like this, we recalculated the anthropometric indicators at discharge for all children. This resulted in a number of recovered children who were reclassified as 'unconfirmed recovered' and others who were reclassified as 'missing discharge criteria'. Additionally, some defaulters who were not found during a subsequent home visit were considered as 'unconfirmed defaulters' and analysed separately, since they could have represented children who had died. Although this uncertainty around some of the treatment outcomes may have affected our conclusions, we think that this may not be the case: Even if all the 'unconfirmed defaulters' (1.
The data are expressed as mean ± SE. Differences between quantitative data measured at D0 and changes from D0 to D84 were evaluated by the Mann-Whitney U test or Student t test to determine whether or not the individual values were normally distributed. The differences in time courses (from D0 to D84), type of yogurts and interactions between time course and type of yogurts for serum 25(OH)D, PTH, CTX and TRAP5b were evaluated by repeated-measure analysis of variance (ANOVA) with adjustment by the Tukey's test. Statistical analysis of the data was conducted by using SAS V9. 2 (SAS Institut Inc, Cary, NC, USA) and STATA software version 9. 2 (StataCorp LP, College Station TX, USA). In addition, chi-square tests were used  (20)  to compare the proportion of FY vs CY, with serum values of 25(OH)D ≥ 50 nmol/L (the IOM sufficiency threshold (  14 )), and of PTH ≤ 46 ng/L (the normal range limit) after 84 days of intervention.
The study responds to the concept of comparative effectiveness research, since the fortified yogurts were compared to identical but non-fortified dairy products. Another strength is the intention-to-treat analysis supporting the results with the demonstration of the vitamin D status improvement associated with the reduction of both secondary hyperparathyroidism and bone resorption markers in women at moderate risk of fragility fractures. The good compliance to the consumption of the two compared food products during three months can also be considered as an asset in this clinical trial. A limitation was the uncomplete data related to the dietary survey. Indeed, the 3-day dietary diaries to assess the spontaneous calcium and macronutrient intakes at baseline and during the intervention were not reliably completed by all of the enrolled participants.
Acknowledgments: J. P. B, V. B. and S. A. designed the study; S. A. supervised the practical carrying out of the clinical trial; J. P. B. , V. B. and S. W. analyzed the data; J. P. B and V. B. wrote the manuscript; J. P. B. had the primary responsibility for final content. All authors read and approved the final manuscript. Funding source:  Yoplait France , 150  Rue Galliéni , 92641  Boulogne Cedex , France. Disclosure summary: J. P. B. is clinical consultant for Yoplait France; V. B. is a scientific collaborator of Yoplait France; S. A. and S. W. have nothing to disclose.
The other PUL-XylL SusD-like protein, BACOVA_03429, could not be expressed in a recombinant form. In addition to the SusD-like proteins, PULs often encode surface-located glycan binding proteins (SGBPs), which are functionally analogous to SusE and F from the prototypic starch utilization system  [17] [18] [19] 31. The capacity of three non-catalytic  lipoproteins encoded by the xylan PULs (candidate SGBPs) to bind xylans and undecorated xylooligosaccharides was thus also explored. The data show that BACOVA_04391, from PUL-XylS, bound xylans and xylooligosaccharides with affinity increasing with chain length (Supplementary Table  3 ). The SGBP displayed similar specificity to the PUL-XylS SusD-like protein, albeit with higher affinity for all ligands. The crystal structure of BACOVA_04391 (PDB accession code 3ORJ) revealed a protein that contains three b-sandwich domains that are aligned in a linear orientation with respect to each other (Supplementary Fig.
Cq values were calculated using LightCycler 480 SW 1. 5. Data were normalized to 16 S rRNA transcript levels, and change in expression level calculated as fold-change compared with minimal media, glucose cultures. Cell localization studies. Potential surface-located enzymes (containing either a predicted lipoprotein signal sequence or uncleaved TM anchor) encoded by the B. ovatus xylan PULs were initially identified using the LipoP 1. 0 (http://www. cbs. dtu. dk/services/LipoP/) and SigP 4. 1 (http://www. cbs. dtu. dk/services/SignalP/) servers. Note, the database N-term methionine for BACOVA_03425 GH43 is mis-annotated; the correct N-terminus actually starts 24aa downstream at the sequence MKN. Proteinase K treatment. Cultures of B. ovatus (50 ml) were grown in minimal media on WAX (0. 5% w/v) as a sole carbon source, to mid-exponential growth phase (OD 600 B0.
HTCS ¼ hybrid two component system (light or dark blue). MFS ¼ transporter of the major facilitator superfamily (pink). Grey ¼ unknown function (note, there is a structure of BACOVA_03430, PDB accession code 3N91). SusC-like (yellow) and SusD-like (light tan) proteins are a defining feature of PULs and are responsible for import of complex glycans across the outer membrane 18. SusC-like proteins are TonB-dependent transporters, while SusD-like proteins are surface lipoproteins that likely function to deliver the target glycan to their partner SusC. (c) Cells were grown on minimal media with polysaccharide as the sole carbon source, and levels of different susC transcripts (locus tags shown; used as a proxy for expression of the whole PUL) from each PUL were quantified by qRT-PCR. The y-axis shows the Log fold-change relative to a minimal media-glucose reference; x-axis labels indicate the xylans used.
ovatus GH95. The active site pocket that houses b-L-Gal product is boxed. (f) Side chains of the active site residues of BACOVA_03438 (magenta carbons) and the GH95 a-L-fucosidase (blue carbons; PDB: 2EAE) from Bifidobacterium bifidum, bound to L-Gal (green carbons) and L-Fuc (orange carbons), respectively. Predicted hydrogen bonds between the amino-acid side chains and carbohydrates are shown as yellow dotted lines, except for the H-bond between the Og of BACOVA_03438 Thr370 and O6 of L-Gal, which is shown as a red dotted line. (g) Overlay of the active site residues displayed in panel (f) with the side-chains of the Thr/His polymorphism that may play a role in specificity for L-Gal over L-Fuc labelled. A stereo image of a portion of the electron density map is shown in Supplementary Fig.
Although not shown on the CX model, the PUL-XylS apparatus will be present, albeit at low levels (see Fig. 2c). A schematic of the crystal structures, colour-ramped from blue (N-terminus) to red (C-terminus), of two of the xylan degrading enzymes, determined in this study (BACOVA_03438 GH95; PDB accession code 4UFC) and in a recent report 37 (BACOVA_03449 GH115; PDB accession code 4C91) are shown. The red arrow heads indicate glycan transport between cellular locations, while the yellow arrow heads show the ligand (or potential ligand in case of the question mark) that binds and activates the hybrid two component system (HTCS) encoded by PUL-XylS (BACOVA_04394, light blue HTCS; activating ligand xylotetraose 4 ) or PUL-XylL (BACOVA_03437, dark blue HTCS; activating ligand likely an arabino-xylooligosaccharide).
MFS is a member of the Major Facilitator Superfamily of transport proteins, and SGBP signifies the two surface xylan binding proteins encoded by the xylan PULs, BACOVA_03431 (inactive GH10, PUL-XylL) and BACOVA_04391 (PUL-XylS). A schematic of the crystal structure of BACOVA_04391 (PDB accession code 3ORJ), colour-ramped from blue (N-terminus) to red (C-terminus), is shown. Note only one of the two SusC/D pairs from PUL-XylL is shown for clarity.
(e) Solvent exposed surface representation of B. ovatus GH95. The active site pocket that houses b-L-Gal product is boxed. (f) Side chains of the active site residues of BACOVA_03438 (magenta carbons) and the GH95 a-L-fucosidase (blue carbons; PDB: 2EAE) from Bifidobacterium bifidum, bound to L-Gal (green carbons) and L-Fuc (orange carbons), respectively. Predicted hydrogen bonds between the amino-acid side chains and carbohydrates are shown as yellow dotted lines, except for the H-bond between the Og of BACOVA_03438 Thr370 and O6 of L-Gal, which is shown as a red dotted line. (g) Overlay of the active site residues displayed in panel (f) with the side-chains of the Thr/His polymorphism that may play a role in specificity for L-Gal over L-Fuc labelled. A stereo image of a portion of the electron density map is shown in Supplementary Fig.
Light, polarized light and differential interference contrast images were obtained. Suspensions of the starch were prepared in the same way as the samples analysed by µDSC. The appropriate amount of IL, water (when required) and starch were weighed. These mixtures were stirred for 1 h and then heated in an oil bath (Ministat 240, Huber, Offenburg, Germany) at 1 °C min -1 until the corresponding temperature was reached. Samples were then removed from the oil bath and cooled in an ice bath. The samples were immediately observed under the microscope. 2. 2. 5. Statistical analysis. The data obtained were statistically treated by variance analysis, while means were compared by the Fisher LSD test at a significance level of 0. 05 (INFOSTAT statistical software, Facultad de Ciencias Agropecuarias, Universidad Nacional de Cordoba, Argentina).
Improvements in the water-supply infrastructure were here found to increase the time that women allocate to income-generating activities (although no magnitudes are given). Ilahi and Grimard did not study impacts on children's school enrollment. Lokshin and Yemtsov (2005)  used community-level data from Georgia to assess the welfare impact of infrastructure rehabilitation projects (school rehabilitation, improvements in road infrastructure, and water system rehabilitation projects) in rural areas between 1998 and 2000. Using propensity score-matching and difference-in-difference methods, they measured the impact of water projects (including installing new or repairing existing communal water tanks, installing water treatment equipment, fitting new pumps, repairing or installing pipes, and rehabilitating wastewater management networks) on various outcomes including female wage employment and incidence of water-borne diseases.
The dataset We use data collected during four rounds of the DHS in  Ghana: 1993 Ghana: -94 (5,822 households surveyed), 1998 Ghana: -99 (6,003 households), 2003 Ghana: (6,251 households), 2008 (11,778 households) (11,778 households). 6 The four rounds include data for each household on the main source of drinking water and the time it takes to walk to this source, fetch water, and return. It is thus a perround-trip measure. The number of trips, by each household per day, to collect water is not available in the data. Characteristics of all household members are also available, in particular age, sex and whether each member is or is not in school. The information available for each household however differs somewhat from one round to the other. Each household belongs to a unique cluster which is spatially identified by GPS coordinates data.
Statistical analyses The results are presented as means and standard deviations. Variables were assessed for normality of distribution using the Shapiro-Wilk test. If the normality assumption was rejected, a log transformation of the data was performed. The incremental AUC between 0 and 120 min (AUC 0-120 min ) for blood glucose and insulin concentrations was computed following the FAO recommendation  (12). AUC 0-120 min and maximum concentration (C max ) for glucose and insulin were analysed using a mixedmodel ANCOVA with 'product' as fixed effect, 'subject' as random effect and glucose or insulin baseline value as covariate. A statistical analysis was conducted on the modified intention-to-treat (mITT) population and on the per protocol (PP) population using SAS ® software version 9. 1. 3 (SAS Institute Inc.
Acknowledgements The authors would like to thank  Marjorie Lejeune ,  Laurence Baron ,  Anne Ehret ,  Xavier Coustenoble ,  Coralie Berthier  and  Nathalie Frisicale  for their support to this study. We also thank  Tereos Syral  and  Beghin Meiji  for the financial support of this research study and for kind contribution of the foods for the study. A. W. and F. R. are employees of Tereos. The remaining authors declare no conflict of interest.
Study design and Intervention The design (see Figure )  Measures. The parent participating in the research completed a fluid-specific dietary record on the intake of all fluids for children and themselves, over 7 consecutive days  [21]  in each of six "waves" (see Figure ); here we focus on baseline (wave 1) and final results (wave 6). For in-depth analysis and methodological control a subsample of five mothers recorded two full days of interaction with their child using wearable miniature video-cameras, and participated in "replay interviews"  [22]  on those recordings. Data Analysis. We analysed volumes of water intake, using ANOVA carried out on SPSS (18. 0) software.