dataesr/scientific-paragraphs-categorization huggingface dataset:
Two other residues stabilize the sucrose ligand in the active site and help to maintain a productive conformation. The first one is the residue Q2394 that forms a hydrogen bond with the O6 of the glucosyl. The second one is the nucleophile residue D2210 which shows an interesting behaviour, i. e. one oxygen atom of the carboxyl group forms a hydrogen bond with the O1 of the fructose moiety, whereas the second one is oriented toward the C1 of the glucosyl, favouring thus the nucleophilic attack. Comparison of the two X-ray structures of ΔN 123 -GBD-CD2 (unbound and bound enzyme: glycerol) revealed that subdomain H1-H2 (residues 2324-2368) displays the highest structural divergence (S7 Fig). Furthermore, the corresponding motif in DSR-M undergoes a similar shift when comparing free enzyme (pdb entry: 5LFC) and sucrose-inactive mutant complex (pdb entry: 5O8L)  [20].
Similarly, the structure of GTF-180-ΔN in complex with sucrose (pdb entry: 3HZ3) shows a shift of this subdomain. In overall, analysis of the different available Xray structures suggests that the shift of the H1-H2 subdomain in direction of the catalytic pocket is only observed when sucrose (3HZ3 and 5O8L) or glycerol (3TTQ, 3KLK) molecules is bound to the catalytic site. The examination of subdomain H1-H2 conformations shown in  Fig 8,  provides that this subdomain undergoes in MD simulations the same shift observed in X-ray structures when enzyme is bound to sucrose. These results strongly suggest the implication of the subdomain H1-H2 dynamics in the recognition of sucrose and its stabilisation in the active site. Effect of sucrose binding on the global dynamics of ΔN 123 -GBD-CD2. As described in the previous section, the first principal component presents a shift in the kernel density center when comparing the free enzyme and the enzyme: sucrose complex simulations, moreover its distribution appears more harmonic in the complex system.
3D-model construction The three-dimensional modelling of ΔN123-GBD-CD2 was based on the 1. 8Å resolved crystallographic structure of ΔN123-GBD-CD2 (pdb entry: 3ttq  [7] ) for which the missing loop 1839-1849 was rebuilt using the FREAD server  [68]. The enzyme:sucrose complex was constructed by extracting sucrose molecule from the X-ray structure of homologous GTF180 in complex with sucrose (pdb entry 3hz3  [22] ). The H++ webserver  [69]  was used to determine the protonation state of ionisable residues at pH 5. 4 at which ΔN123-GBD-CD2 exhibits the optimum of activity  [70]. The heptacoordinated calcium and sodium ions located at the interface of domains A and B or domains V and IV, respectively, were considered in MD simulations.
Molecular dynamics simulations MD simulations were performed using the AMBER ff14SB force-field  [71]  for enzymes and GLYCAM_06j-1  [72]  for sucrose ligand. The NAMD program  [73]  was used for simulations with the free enzyme whereas pmemd. CUDA  [74]  which supports the mixed scaling of 1-4 non-bonded electrostatic and van der Waals terms  [75]  in amino acids and sugars was used for simulations on enzyme:sucrose complex. MD simulations were carried out at constant temperature (303K) and pressure (1bar) using the Berendsen algorithm  [76]. The integration time-step was 2fs and covalent bonds involving hydrogens were constrained using SHAKE  [77]. The non-bonded pair-list was updated heuristically. Long-range electrostatic interactions were treated using the Particle Mesh Ewald (PME) approach  [78].
Normal mode analysis. The initial enzyme coordinates were taken from the crystal structure of ΔN123-GBD-CD2 (pdb entry: 3ttq). Hydrogen atoms were added, and system topology was generated using the CHARMM-GUI web-based graphical interface  [81]. The energy was minimized by the conjugate gradient method using the CHARMM36 program  [82]  with CHARMM36 force field  [83]. Harmonic constraints were applied to heavy atoms to allow smooth minimization without abrupt deviation from the crystallographic structure for the first 1000 steps. The positional restraints were gradually decreased over 100 steps, the constant forces were 250, 100, 50, 25, 10 and 5 kcal/mol/Å 2 , followed by 20 000 steps of a non-constrained minimization. The DIMB method  [84, 85]  was used to compute low-frequency normal modes in the Cartesian space (ϖ < 10 cm -1 , 26 modes), with a convergence of 0.
Analysis of normal modes, essential dynamics trajectories and X-ray structure was performed in terms of covariance matrix c ij and Dynamical Cross-Correlation Matrices (DCCM)  [88]. All coordinates were translated and rotated by means of a least-square-fitting procedure using heavy atoms of backbone and side chains to align the equilibrated starting conformation of simulated data or X-ray structure (pdb entry: 3TTQ). The covariance matrix c ij for the position vectors of two residues i and j in the fitted structure is calculated as: c ij ¼ hðr i À hr i iÞðr j À hr j i Þi ¼ hr i r j i À hr i ihr j i The cross-correlation matrix elements C ij are defined by the following equation: C ij ¼ c ij ffiffiffiffi c ii p ffiffiffiffi c jj p ¼ hr i r j i À hr i ihr j i ffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffi ffi ½ðhr 2 i i À hr i i 2 Þðhr 2 j i À hr j i 2 Þ q Cross-correlation coefficients range from a value of -1 (completely anti-correlated motions) to a value of +1 (completely correlated motions).
Wavelet analysis. In our study, we used the new implementation of wavelet analysis  [49]  in CPPTRAJ 2017 software to perform the wavelet analysis using Fast Fourier Transform (FFT) algorithm  [89]  on MD simulation trajectory. Translational and rotational motions were removed as described above. Wavelet analysis contains two main steps which perform Continuous Wavelet Transform (CWT) and statistical significance testing as described by Torrence and Compo  [90]. For each heavy atom, Morelet CWT  [91]  is calculated over a given scale ranging from 0. 2 to 25 ns and by multiplying with a correction value of 1. 01. All wavelet analyses were done using χ 2 = 1. 6094 which is the minimum acceptable value for running a significance test at 99% confidence level. Free-energy landscape. The free-energy landscape of a macromolecule can be obtained using a MD simulation sampling method that allows to explore the conformations near the native state structure  [67].
Acknowledgments This work was supported by the  French National Research Agency  ( ANR  Project  CARBUNI-VAX ,  ANR-15-CE07-0019-01 ). This work was granted access to the HPC resources on the  TGCC-Curie supercomputer  under the allocations x2016077709,  A0030707709  and the  Computing mesocenter of Region Midi-Pyrenees (CALMIP, Toulouse, France)  under allocation  P16008.
Patients and Methods A single time point multi-centre cross-sectional survey was conducted by contacting all paediatric ITx centres to identify patients who were alive, with a functional intestinal graft for 10 years after ITx, on January 31 st , 2015. A case report form (supplementary file 1) was completed by the referring physician from each centre. The following data were recorded at time of ITx and on long term follow up (FU) after 10 years: age, indication, type of ITx with/without inclusion of graft colon, growth parameters, immunosuppression, graft function, health care status, frequency of hospital admissions, education and psychosocial status. The median level of tacrolimus of the last 3 determinations was recorded for each patients for the analysis. Nutritional status was evaluated throughout: height, weight, BMI (expressed in Z-score), need for either parenteral or enteral nutrition based on dietician records.
Discussion This report is the first European multicentre survey describing long-term survival in patients after intestinal transplantation in childhood. The longest survivor was 27 years after ITx. This snapshot is highly representative of the European experience before 2005 because we could enrol 87% of transplanted children and over 90% of long survivors after paediatric intestinal transplantation. Missing patients had been transplanted in centers no longer active. Our poor patient survival rate (47%) is identical to data shown in the most recent Intestinal Transplant Registry report; however we found a slightly lower rate of graft survival (31%)  (1). This difference could be related to very late graft losses (more than 10 year) and study design. Patients enrolled included the very first intestinal transplanted patients with a median FU well over the 10 years cut-off (14 years).
Fourier Transform Infrared (FTIR) Spectroscopy of Purified EPS. The structural characterization of the purified EPS was studied using Fourier transform infrared (FTIR) spectroscopy in order to determine their functional groups distribution. The translucent pellets (5mmØ) were made by mixing and pressing the freeze-dried polysaccharides samples with KBr powder (5:100 w/w). The FTIR spectra were recorded in transmittance mode at a spectral range of 4000 and 400 cm -1 with an accumulation of 15 scans and a resolution was 4 cm -1 , using a spectrophotometer type Perkin Elmer Spectrum BX5, equipped with a He-Ne laser and a detector MCT type broadband and high sensitivity  [33]. The spectra acquisition was performed via spectrum v5. 3. 1 software. The bands identification was accomplished according to the data cited by Wiercigroch et al.
Randomization and Blinding Thirty villages (clusters) (village population: 1000-2000) with CHWs in each country were randomly selected from all eligible clusters. Distance from the center of each village to the nearest health facility was calculated and used to group the clusters into 3 distance categories. Randomization was performed using computer-based randomization (Stata software, StataCorp, College Station, Texas) and was stratified by the 3 distance categories.
Statistical Analysis It was assumed that the intervention would decrease placental malaria from 15% to 10. 5%, with a coefficient of variation of 0. 15. Within each country, 15 clusters, each with 60 pregnant women per arm, would be able to detect a significant difference with 80% power and at the 5% significance level. Thus, 90 clusters with a total of 5400 women were required. All data were double entered using OpenClinica databases. The primary endpoint (prevalence of placental malaria) was examined with logistic regression. Random effects for trial cluster were used to account for intracluster correlation. An analysis of the primary endpoint adjusted for season, gravidity, and number of SP and AL doses was carried out. All other binary endpoints were examined with random effects logistic regression.
Samples Selected for the Analysis From January 1999 to December 2015, water samples were collected in 66 cities and urban municipalities, out of which only the most complete series of data over the 16-year period were retained for analysis. Some sets were removed, such as the data from the year 2009, which was marked by a political crisis. Sites with one year or two consecutive quarters of missing data were also removed. The city of Antananarivo provided more than half of the total samples but was also excluded from the study in order to conduct a separate analysis. Overall, 32 out of 66 public water supplies were selected for the analysis, providing data on 12,495 drinking water samples (described in Table  S1 ). Seven major cities (Toamasina, Mahajanga, Toliara, Fianarantsoa, Antsirabe, Antsiranana, and Tolagnaro) provided 6855 samples (55% of the total).
Parameters Selected for the Description of the Water Supply Systems Climate and temperate data were extracted from https://fr. climate-data. org [21]  based on the Köppen-Geiger classification (Cwa, Cwb, Cfa, Aw, Am, Af, Bwh, and Bsh)  [22]. The daily rainfall in each city from 2007 to 2015 (no previous complete data for all concerned cities) was obtained from the International Institute for Research on Climate and Society (IRI). The climate in Madagascar is mainly tropical (type A, Köppen-Geiger) along the coast, arid in the south (type B), and temperate inland (Type C)  [21, 22]. The average annual rainfall is around 1500 mm, but with large regional variation from 3000 mm in the east littoral area to less than 400 mm in the extreme south. The whole country experiences a rainy season from November to March and a dry season from April to October.
Statistical Analysis The frequency of microbial contamination of samples was calculated for the monthly, seasonal, yearly, and 16-year periods as the ratio of the number of positive samples to the total number of samples in the period considered (in percent). Each specific measure of contamination (SSRC, IE, EC, TC, or FIB) was expressed as the ratio of the number of positive samples to the total number of samples. The rainfall data were summarized as the cumulative precipitation per season (quarterly starting in December) for each site and an average for relevant group of sites was calculated. The statistical analysis was done in XLSTAT (Addinsoft: New York, NY, USA, 2016), with a significance level set at 0. 05. A non-parametric Kruskal-Wallis test was used to analyse differences between populations  [25].
Main Factors Influencing Water Quality (Environmental Clustering) According to environmental parameters the whole set of water systems, six main component factors were obtained, explaining more than 80% of the total variance of the dataset. The first axis (component) compares the variables "surface water" plus "classic treatment type" to "groundwater" plus "classic + neutralization treatment type" (Figure  7a ). This axis also correlates with the environmental threat "population growth". The second axis had a large positive association with "unconventional treatment type" (45% of the variability of dataset).
Main Factors Influencing Water Quality (Environmental Clustering) According to environmental parameters the whole set of water systems, six main component factors were obtained, explaining more than 80% of the total variance of the dataset. The first axis (component) compares the variables "surface water" plus "classic treatment type" to "groundwater" plus "classic + neutralization treatment type" (Figure  7a ). This axis also correlates with the environmental threat "population growth". The second axis had a large positive association with "unconventional treatment type" (45% of the variability of dataset). Using these main component factors, four groups of systems can be observed on the observations plot (Figure  7b ). Group 1 represents water systems that are supplied by water from conventionally treated surface water with a final neutralization step (Ambatolampy, Antsirabe, Farafangana, Nosy-Be, Port Berge, and Tsiroanomandidy).
Antioxidant activity The results for antioxidant activities measured by DPPH method of the cultivars studied are presented in Fig. 3. The DPPH radical scavenging assay is usually applied to determine the capacity of antioxidant to scavenge free radicals and the scavenging potentials of the antioxidant extract were measured according to the degree of discoloration of mixture. In this current work, the variation of antioxidant capacity between the juices was statistically significant and the data were among 31. 16% and 66. 82% for local cultivars and for foreign cultivars among 45. 65% and 76. 3%. When the value is high, the total antioxidant capacity is high  (Hmid et al. , 2013). However, for measuring the EC50, reaction between DPPH free  radical and antioxidant of juices achieved the steady state in 1 h.
1 g)  (Martinez et al. , 2012). The data of the physical aspect of the fruits in this study showed that eighteen cultivars are different in all investigated analysis except two parameters : seed weight and aril length. However, the local cultivars 'Chioukhi' (L3), 'Bzou' (L8), and 'Sefri 2' (L10) seem the most interesting, combined more aril percentage, least skin percentage, and least seed percentage that was a highly desirable characteristic by consumer. The foreign cultivars are also very promising such as 'Gordo de Jativa' (F1), 'Ruby' (F4), 'Mollar Osin Hueso' (F6) and Wonderful cultivars (F3) which having a high percentage Arils. All cultivars are evaluated under the same climatic conditions and agricultural practices; therefore, the observed variability in terms of TP was due to genetic variability.
Neurotransmitter Assays Glutamate and gamma aminobutyric acid (GABA) concentrations were measured by high-pressure liquid chromatography (HPLC). In brief, 200 µL of brain homogenates was subjected to a deproteinization step using 30% sulfosalicylic acid solution (Sigma). Then, supernatants were diluted with Jeol sampling buffer (JEOL) containing 0. 2 µmol/mL of aminoethylcysteine and glucosaminic acid (internal standards; Sigma). Supernatants (50 µL) were then injected into an automated amino acid analyzer (JEOL Aminotac 500; Tokyo, Japan) and eluted with lithium citrate buffers. Glutamate and GABA were detected at 570 nm. Data acquisition and calculations were performed using the JEOL Workstations software. Serotonin concentrations were measured by HPLC with fluorescence detection (Waters).
8 ± 1. 6% vs. 73. 5 ± 2. 1%, p < 0. 01; Figure  2E ). However, unlike alpha-TTP-deficient mice in which the systemic and complete alpha-tocopherol deficient trait led to abnormal motor performance and severe ataxia in addition to anxiety  (Yokota et al. , 2001) , PLTP -/-mice showed no evidence of disorders in activity and neuromotor coordination  (Desrumaux et al. , 2005). We next measured anxiety levels in 6 months old PLTP -/- mice born from vitamin E-supplemented parents and fed a vitamin E-enriched diet from weaning. Interestingly, anxiety levels in these mice were comparable to those measured in WT mice (73. 1 ± 5. 6% entries in closed arms compared to 71. 5 ± 5. 6% in WT mice; data not shown). To distinguish the impact of early vitamin E supplementation from that of late supplementation, we compared anxiety levels in ''E'' PLTP -/- mice, in ''L'' PLTP -/-mice, and in WT mice.
FUNDING This study was supported by the  Agence Nationale de la Recherche (ANR)  under the  program ''Investissements d'Avenir'' with reference   ANR-11-LABX-0021-LipSTIC , the  University of Bourgogne-Franche-Comté , the  Conseil Régional de Bourgogne and FEDER, INSERM, EPHE  and the  University of Montpellier.
Associations have been sought between breast milk lipids and growth and development of the child. Several studies concern term infants  (47, 48)  but the development of preterm infants has also been studied. Mead acid (C20:3 n-9, an omega-9 fatty acid) in early breast milk is associated with general movement's score at 40 weeks of gestational age suggesting that increased concentration in mead acid influenced this score negatively  (49). Similarly arachidonic acid was also negatively correlated with some behavioral assessment scores. These relatively simple associations reflect likely a more complex reality such as a shortage of fatty acids ω6 and ω3 or an imbalance between ω3 and ω6 fatty acids. To better understand the role of different families of breast milk lipids, in a context of prematurity, we conducted a pilot study, on 2 groups of 11 mothers of infants born premature, and selected in the LACTACOL cohort (NCT01493063), on the basis of growth (rather good [difference between discharge and birthweight Z-score during neonatal hospitalization of -0.
Questionnaire This study relied on data obtained using a clinical questionnaire that was filled out upon admission to the phlebotomy program. As previously described  [22] , this questionnaire, which was completed by a referral physician, collected information on socio-demographic characteristics (gender, age at diagnosis, etc. ), lifestyle factors (height, weight, alcohol intake, etc. ) and biological parameters (including transferrin saturation and serum ferritin). It also recorded data on reproductive functions, on the presence (and number if any) of pregnancies prior to the beginning of the treatment (excluding miscarriages and abortions occurring in the first trimester), as well as on the menopausal status at admission to the phlebotomy program. Patients were also asked if they were regular blood donors, if they had chronic bleedings (including gastrointestinal bleedings, chronic hematuria, bleedings due to parasitic infections) and if they received blood transfusions (and how many if any), all this prior to admission to the phlebotomy program.
At the end of the depletion stage, treatment-related data (i. e. the number and average volume of the phlebotomies) were recorded. These data enable estimation of the amount of iron removed (AIR; in grams) to normalise patient's iron stores (i. e. to reach SF < 100 μg/L). This calculation was performed assuming that 1 L of blood contains 0. 5 g of iron  [23].
Baseline characteristics of the study population During the study period, 140 p. Cys282Tyr homozygous hemochromatosis women were enrolled into a phlebotomy program at the blood centre of Brest. The "pregnancy" variable was documented for 137 (97. 9%) women and 127 of them (92. 7%) completed the depletion phase during the study. The baseline characteristics of the women included in the study and for whom data on pregnancies was available are presented in Table  1. These women were diagnosed in mean at the age of 52. 5 years (± 14. 0). Among them, 29. 8% were overweight (BMI ≥ 25 kg/m 2 ) and 4. 5% declared having excessive alcohol consumption. More than 60% of the women were menopausal at entry into the phlebotomy program, with a mean age at menopause of 49. 2 y. (± 4. 3).
Therefore, a new strategy based on small scale processing for various traditional productions and, if relevant,related innovations needs to be developed. Such an approach has to start with a deeper understanding of the physical, biochemical and technological foundations of quality for these traditional food products and of the diversity of renewable resources required to produce them. Detailed analytical data must be obtained about texture, flavor, health-related compounds, potential safety issues, etc. in order to gain a firm understanding of the diversity of products and their unique character. This understanding would serve to develop a sound system for defining labels and setting standards in order to protect these local products and support policy actions for their development. For processing, the understanding of physical and molecular changes at nano, micro and meso scales during transformation of heterogeneous agro resources will serve the design and development of appropriate downsized technologies.