dataesr/scientific-paragraphs-categorization huggingface dataset:
The dry residue was immediately dissolved in 0. 2 ml of methanol, and reaction product was analyzed by liquid chromatography-mass spectrometry. The LC-APCI/MS/MS used was a 6120 Quadrupole LC/MS with an atmospheric pressure chemical ionization (APCI) interface and a LCMS Chemstation software from Agilent Technologies (Palo Alto, CA, USA). Chromatographic separation was performed using a XTerra MS C18 column (2. 1 mm × 50 mm, 2. 5 μm; Waters, Milford, MA, USA) with a mobile phase of methanol, 0. 1% acetic acid (96:4) in isocratic condition. The column temperature was 48°C. The flow rate in the LC column was 0. 4 ml/min. The injection volume was 20 μl. The temperature of the auto sampler tray was set to 5°C, and the samples were protected from the daylight. Detection was by MS with APCI source in positive mode.
tive departments, indicated by their respective administrative number in Figure 3. Sampling was performed in 65 different locations. Species identification for each sample was based on mitochondrial cytochrome b sequence. For all the samples, amplified sequences presented more than 98% of homology with published sequences of M. musculus domesticus cytochrome b. To identify mutations in the Vkorc1 gene of the 266 mice, the coding sequences and splice junctions of Vkorc1 gene were amplified and sequenced. Obtained sequences were subsequently compared to published Vkorc1 sequences for M. musculus domesticus (GenBank accession number GQ905715) and for Mus spretus (GenBank accession number GQ905711). Only 73 samples presented no missense mutation in the coding sequences of Vkorc1 gene (i. e. , 27.
Strain Marseille-P3084 T was first isolated after direct inoculation of the samples on Colombia agar with 5% of sheep's blood (COS; bioMérieux, Marcy l'Etoile, France) and a 3-day incubation in an anaerobic atmosphere (anaeroGen Compact; Oxoid, Thermo Scientific, Dardilly, France) at 37°C. Colonies were white and punctiform. Cells were Gram-negative bacilli with a length of 1. 2 μm and a width of 0. 5 μm. Strain Marseille-P3084 T did not exhibit catalase or oxidase activities. This strain was motile and non-endospore forming. Strain Marseille-P3084 T had a 92. 1% sequence similarity  [4]  with Alistipes putredinis type strain ATCC 29800 T (GenBank accession no. L16497), the phylogenetically closest species with standing in nomenclature (Fig. 1 ), which was first isolated from human sources in 2003  [5].
This is in good agreement with recently published data for the thermostability of TDP-43 fragment 1-256 a. a. monitored by circular dichroism  30. Progressive increase of zinc ion concentrations from 20 to 625 μM resulted in the decrease of RRM12 thermostability, as shown by the gradual shift of the denaturation peak to lower temperatures down to 40. 0 ± 0. 2 °C (Fig. 3 ). Interestingly while most divalent ions binding to proteins generally increases their thermostability  31, 32   zinc ions often decrease protein thermostability  33, 34. As a negative control of unspecific influence of divalent ions on RRM12 thermostability, calcium ions were used. The presence of Ca 2+ did not impact RRM12 thermostability in a large range of concentrations (data not shown). To estimate the zinc binding constant, we used experimental values of denaturation temperature T m at different concentrations of zinc ions.
Using the equation linking the shift in melting temperature to the binding constant  35  , we fitted the experimental data (Fig. 3 , insert) and obtained a value for the constant of zinc binding to RRM12 of 1. 0 ± 0. 5 × 10 6 M -1. To further characterize the thermodynamics of this interaction isothermal titration calorimetry (ITC) was used. Thermodynamics of RRM12/zinc interaction. No significant heat exchange was detected at 10, 25 and 37 °C upon RRM12 titration by zinc (data not shown), indicating that enthalpy of binding ΔH is close to zero. Thus, to increase the ΔH we conducted ITC experiments at 42 °C (Fig. 4 , black curve). Indeed at 42 °C, as we showed by DSF, the binding of zinc leads to RRM12 unfolding. The ΔH is thus apparent since it comprises the heat of unfolding of RRM12 upon zinc binding.
of the dilution was measured by injecting the ligand (ZnCl 2 ) into the buffer solution; the values obtained were subtracted from the heat of the reaction to obtain the effective heat of binding. Data were analyzed using the MicroCal Origin software and were fitted with a "one set of sites" model that led to the determination of affinity constants (K a ), stoichiometry (zinc to protein ratio, N) and enthalpy of binding (ΔH). Consequently, the entropy variations (ΔS) were calculated according to the standard equations. All experiments were repeated at least three times. Differential Scanning Fluorimetry. The protein thermostability was measured in the presence of different concentrations of divalent ions in 50 mM Tris, 1 mM TCEP at pH 7. 3 using a label-free fluorimetric analysis with a Prometheus NT.
Plex instrument (NanoTemper Technologies). NanoDSF grade capillaries were filled with a 25 µM solution of RRM12. Concentration of zinc or calcium ions varied from 19. 5 to 625 µM. Capillaries were loaded into the Prometheus NT. Plex and heated from 25 °C to 70 °C with a 1 K/min heating rate at low detector sensitivity with an excitation power of 10%. Unfolding transition points (T m ) were determined from the first derivative of the changes in the emission wavelengths of tryptophan fluorescence at 330 nm, which were automatically identified by the Prometheus NT. Plex control software  52. Dynamic Light Scattering. Dynamic light scattering (DLS) experiments were carried out using a Zetasizer Nano S (Malvern Instruments) at 25 °C. Three measurements were performed; each one consisting in 10-15 runs of 10 seconds.
Images were recorded using a 4 k × 4 k slow-scan CCD camera (Gatan, Inc. Pleasanton, USA). TDP43 structure analysis. Coordinates for RNA-TDP43 complex NMR derived structure (PDBID: 4BS2)  36  was obtained from the PDB data bank. The python PMX module was used to parse the atom coordinates  53. For atoms ND1, NE2 and SG in HIS and CYS residues neighboring atoms with names ND1, NE2, SG, OE1 and OD1 were searched with distances less than 6 Å. False positive contacts for ASN and GLN were filtered and results were ranged on base of neighbors count and printed. Top two were chosen for further discussion. All operations were done with Python program language.
Acknowledgements The authors thank  Peter J Lukavsky  for providing plasmid of TDP-43 fragment  102-269. Part of this work was performed in the frame of project supported by the grant of  Russian Science Foundation  #  14-23-00160P. Microcalorimetry and DSF experiments were performed in  Timone Microcalorimetry Platform, Marseille, France. We thank  Patrick Bron  from the  Centre de Biochimie Structurale  ( CBS, Montpellier, France ) for his help in electron microcopy. The CBS is a member of the  France-BioImaging (FBI)  and the  French Infrastructure for Integrated Structural Biology (FRISBI) , 2 national infrastructures supported by the  French National Research Agency ,  ANR-10-INBS-04-01  and  ANR-10-INBS-05  respectively. Prometheus NT. Plex instrument was acquired with the financial support of  Région PACA  ( APR-EX 2016 Neuro-Plasma ).
Cloning and sequence analyses of SmILK, SmPINCH and SmNck2 In eukaryotic systems integrin-GFR cooperation can be accomplished by ILK, PINCH, and Nck2. As cytoplasmic molecules they bind to the intracellular parts of integrin (ILK) or GFR (Nck2), or simultaneously to both receptors with PINCH as bridging molecule connecting ILK and Nck2  [32, 33]. To investigate the possibility of such an interaction in S. mansoni, we first searched for orthologs in the schistosome database  [34, 35]. Based on comparisons to orthologs from human, potential candidate genes were identified and analyzed in silico. Deletion clones, including those potentially originating from alternative splicing events, were excluded from further analyses. Finally, full-length cDNAs of the longest variants of SmILK (Smp_079760), SmPINCH (Smp_020540.
5 μl of 2x PerfeCTa SYBR Green super mix (Quanta). No template controls (NTC) were included in each run. RNAi-mediated knockdown of gene expression was analysed by absolute quantification. Therefore, a standard curve on diluted gel eluate was included in each run  [65]. For qPCR analyses to study transcript profiles of SmBAK (Smp_095190), SmBAX (Smp_072180), SmmTor (Smp_122910), and SmSod (Smp_056440) several genes were tested for their suitability as reference. Based on transcriptome data  [53]  the gene Smp_008900 (annotated as eukaryotic translation initiation factor 4 gamma) fulfilled this criterion and was further tested under various condition using an absolute quantification approach. To this end, the Smp_008900 amplicon was cloned into pDrive (Qiagen) and served as template in dilution series.
Results Characterization of the oat accessions by their origin. The accessions included in this study come from five countries: four of them from the Mediterranean area (Spain, Greece, Italy, and Tunisia) and the fifth, the USA. The overall mean of the evaluated parameters of all these lines as well as the means of the subsets according to their origin are shown in Table  1  (raw data can be found in Supplementary Table  S1 ). When the mean values of each group were compared with that of the whole set, the group of lines from Greece presented more differences than any other, since that group was significantly earlier and with lower plant height, and the composition of the flour also significantly differed for all parameters except protein content. The group from Tunisia was also earlier, while the USA group was the second most deviating from the average, with lower and higher levels of starch and protein, respectively, in flour.
Subsequently, the tissue was incubated with primary antibody diluted in BS for 2 h at RT in a humid chamber. After washing 3x with PBS for 5 min, the tissue was incubated with secondary antibody, diluted in BS, for 1 h in a humid chamber, followed by a wash step with PBS for 5 min. The tissue was counterstained with DAPI (4′ ,6-Diamidin-2-phenylindol). Fluorescence images were obtained using an upright Axioscope microscope equipped with a Zeiss CCD camera (16 bits; 1280 × 1024 ppi) using Axiovision software (Zeiss) and analyses of signal intensities of the tissue sections were performed with ImageJ 1. 48r. Cell lysis and RNA preparation. Cells were harvested and resuspended in 600 μ l RIPA buffer, and kept for qRT-PCR. cDNA synthesis of pooled RNAs was performed with the iScript TM cDNA Synthesis Kit (Bio-Rad) according to the manufacturer's protocol in a total reaction volume of 20 μ l and a maximum of 1 μ g RNA/reaction.
Quantitative real-time-PCR was performed using the SSoAdvanced Universal SYBR ® Green Supermix (Bio-Rad) and customized PrimePCR plates in 96 well format with immobilized primers (Bio-Rad) according to the manufacturer's protocol with a final reaction volume of 20 μ l and 2 ng cDNA/well. Resulting data was analyzed using the hydroxymethylbilane synthase (HMBS) or Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) gene as an internal standard to normalize transcript levels. Cycle threshold (ct) values were calculated by CFX Manager (version 3. 1). All quantitative real-time PCR reactions were run in technical duplicates for each of the 2 patient and control cell lines and mean ct-values for each reaction were taken into account for calculations. Alternatively, first strand synthesis and quantitative real-time-PCR amplification were performed in a one-step, single-tube format using the QuantiFast TM SYBR_Green RT-PCR kit from Qiagen according to the manufacturer's protocol in a total volume of 20 μ l.
Thermal cycling and fluorescent detection were performed using the Rotor-Gene Q real-time PCR machine (model 2-Plex HRM) (Qiagen). The SYBR Green I reporter dye signal was measured. Resulting data were analyzed using the HMBS gene as an internal standard to normalize transcript levels. Cycle threshold (ct) values were calculated by the Rotor-Gene Q Software (version 2. 0. 2). All quantitative real-time PCR reactions were run in technical triplicates for each of the 2 patient and control cell lines and mean ct-values for each reaction were taken into account for calculations. Protein biochemistry. To obtain homogenate from GI tissue, small intestinal epithelium was isolated from mesenchyme following a protocol after Nik and Carlsson  70. In brief, small intestine was cut into 4-5 cm long pieces.
Statistic. Statistical analysis was performed using Graph Pad Prism 5 and tested for significance using t tests (all values were normally distributed). Two-Way ANOVA with Bonferroni correction was used to identify treatment (Zn depletion/supplementation) or genotype effects, or interaction between the two factors using SPSS version 20. Statistical tests were two tailed with a significance level of α ≤ 0. 05. Significances are stated with p values < 0. 05*; < 0. 01**; < 0. 001***. An observed trend (p between 0. 05 and 0. 1) is indicated with "#" and the p value stated in the figures. qRT PCR quantification. Relative quantification is based on internal reference genes to determine virtual mRNA levels of target genes. Cycle threshold (ct) values were calculated by the Rotor-Gene Q Software (version 2.
Acknowledgements We thank the  Phelan-McDermid-Gesellschaft e. V. for support in hair sample collection as well as  Michael Schoen  from the  Institute for Anatomy and Cell Biology, Ulm University  and  Andrea Ludolph  from the  Department of Child and Adolescent Psychiatry, Ulm University. TMB has received support from the  Innovative Medicines Initiative Joint Undertaking  under grant agreement n°  115300 , resources of which are composed of financial contribution from the  European Union 's  Seventh Framework Programme  ( FP7/2007-2013 ) and EFPIA companies' in kind contribution. Furthermore by the  Helmholtz Gesellschaft ("RNA Dysmetabolism in ALS  and FTD" to TMB) and the  Deutsche Forschungsgemeinschaft  ( DFG SBF1149  to TMB). AMG was supported by the  Else-Kröner-Fresenius Stiftung  ( 214_A251 ).
After receiving a thorough explanation of the possible risks and discomforts associated with the experimental procedures, each participant provided their written informed consent to take part in the experiment. The study was conducted according to the Declaration of Helsinki. The protocol and the consent form were fully approved (identification code: 8/16) by the review board "Local committee of the Laboratory of Biochemistry, CHU Habib Bourguiba, Sfax, Tunisia" before the commencement of the assessments. Additionally, all ongoing and related trials for this intervention are registered in Clinical Trials. gov (identification code: NCT02697903).
Statistical Analyses All statistical analyses were performed using STATISTICA 10. 0 Software (StatSoft, Maisons-Alfort, France). Normality of the data distribution was confirmed using the Shapiro-Wilks-W-test. To analyze the effect of POMj supplementation on the biological responses during training sessions (pre-post values), a two-way analysis of variance ANOVA (2 levels (supplementation (PLA and POMj)) × 2 levels (training-session (Pre and Post)) with repeated measures) was employed. To analyze the effect of POMj supplementation on the recovery kinetics of the selected parameters, a one-way ANOVA was utilized. When significant main effects were observed, Tukey's honest-significance-difference (HSD) post-hoc tests were conducted. Effect sizes were calculated as partial eta-squared (ηp 2 ) for the ANOVA analysis to assess the potential practical significance of the findings.
Study design This is a secondary analysis of a cross-sectional retrospective study conducted in 2011 to measure the effect of a UNICEF-led pilot program of behavior change communication (BCC) program promoting child health care  [17]. The program began initially in 2008 in two regions of Niger, Maradi and Zinder. The original datasets are derived from three surveys: individual women's survey, household survey and community survey. These were merged for this secondary analysis.
Sampling method and study population This evaluation study is based on a non-randomized purposive sample of 50 villages selected for piloting BCC program activities. In addition to these villages, we added another 25 villages that were not covered by the program at the time of data collection to constitute two groups: exposed and unexposed in a retrospective manner. Within each village purposively selected, 15 households and women were selected based on a two-stage stratified random sampling with no probability proportional to size. The study population for the secondary analysis was extracted from the original dataset of the survey and included all female household members aged 15-49 years who have at least one child below 24 months, currently pregnant or not. The total number of the study population of this secondary analysis is 1026.
Data analysis Chi-square tests, bivariate and multivariate logistic regression were used to calculate unadjusted and adjusted odds ratio with STATA SE/13. 1 using 95% confidence interval for each independent variable. First, a descriptive analysis depicts each selected variable per program exposure. Second, we measured odds of early initiation of breastfeeding based on the entire study sample adjusted for the program exposure and confounding variables associated with early breastfeeding.
Yet we deemed it important to use the available datasets of program evaluation surveys, which are often conducted in forms of observational studies and are not correctly interpreted despite considerable time and the funds invested. Nevertheless, these findings could provide some clues to understand what could inhibit early initiation of breastfeeding. Highly significant association with social and economic vulnerability clearly indicates that early breastfeeding is impaired by poverty. They are characterized by poverty income, limited access to health facility and disintegration from family support and social network that compromises support from family, community and health professionals. Besides, autonomy of mothers able to take part in decision making about household budget distribution and to manage expenditure for their child's health care positively influenced early initiation of breastfeeding.
These findings allow the BCC program to revisit its strategy and focus their actions on the most deprived populations prevented from financial and technical support for improved environmental and maternal and child health. The dataset includes unique sets of variables to address mothers' behavior in family and community settings. At first sight, there is a significant difference in socioeconomic and demographic characteristics of mothers between the two groups: exposed and unexposed to the program (Table  1 ). When comparing healthcare services related variables between the two groups, the chance of accessing health services within the village of residence is significantly greater in the intervention group. This is due to the non-randomization of the program intervention when selecting villages to start pilot BCC activities.
The reasons why there is a discrepancy between the current study and the original article with regard to significance of the program impact on early breastfeeding could be explained by the following: The original article used a study sample in four regions (n = 2091)  [17] , whereas we conducted a secondary analysis of the same database using the sample in two regions (n = 1026) that were initially targeted by the program at the time of data collection. It is clear that the gap in the total number of study populations has led to a different result and, that with a smaller sample the program impact on early breastfeeding turned out to be no longer statistically significant.
RACE PCR of the 5′ and 3′ UTR of the Cd/Cu-MT The coding region of the Cd/CuMT gene was sequenced by us previously and is already available in GenBank as two allelic variants (V1 and V2) under the accession numbers GU111728 (V1) and GU111729 (V2). To obtain the full length cDNA of the Cd/CuMT isoform gene, the SMARTer™ Race cDNA Amplification Kit (Clontech, Canada) was applied. Total RNA (300-700 ng) from three adult Roman snails was used for generation of RACE-Ready cDNA according to the manufacturer's instructions. For the rapid amplification of the 5′ and the 3'UTRs, gene specific primers were employed as follows: GSP1, 5′-ATG TGG CAA GAT TCC TGT GCG GCT GTG G-3′; and GSP2, 5′-AAC AGC AA C CCC TGC AGC TGC GGC GAC G-3′. PCR was carried out according to manufacturer's instructions under the following conditions: 5 cycles at 95 °C for 30 s and 72 °C for 3 min, 5 cycles at 94 °C for 30 s, 70 °C for 30 s and 72 °C for 3 min, and 20 cycles at 94 °C for 30 s, 68 °C for 30 s and 72 °C for 3 min.
(2009). For the Cd/CuMT gene, suitable primers were designed with the Primer Express 3. 0 software (Applied Biosystems, Foster City, CA, USA). Optimal primer concentrations were estimated by performing a dissociation curve (as described in  Palacios et al. , 2011). To assess the Δct value, a calibration curve (y = -3. 4372 × + 33. 419) from the PCR product was established. The working concentrations and sequences of all applied gene-specific primers of the three different MT isoforms are shown in Table  1. The estimated PCR efficiency for the Cd and the CuMT isoform genes was 100% whereas for the Cd/CuMT gene the PCR efficiency was 95%. To compare the transcription levels of the three different MT isoforms genes, the PCR efficiency of the Cd/CuMT gene was adopted to 100% as described in  Pérez et al.
Data analyses and statistics All data derived from qRT PCR were analysed using the software package Sigma Plot 12. 5. Data were proofed for homoscedasticity and normal distribution. Significant outliers (Grubb's test; P ≤0. 05) were removed from the dataset. To compare the treatments with the controls a t-test for normal distributed data and a Mann-Whitney Rank Sum test for non-normal distributed data were applied. Significance level was set at P ≤ 0. 05. To analyse the MT expression of all three MT isoforms over developmental time, an ANOVA on ranks was used due to non-normal data distribution. For sequence editing and analysis the software CLC Main workbench 6. 9 and the online alignment tool Clustal omega (http://www. ebi. ac. uk/Tools/msa/clustalo/) were utilized. For characterization of the untranslated regions the online tools Scan for Motifs (http://bioanalysis.
otago. ac. nz/sfm/sfm_main. pl) (Biswas and Brown, 2014)  and RBPDB database v1. 3. 1 (http://rbpdb. ccbr. utoronto. ca/) (Cook et al. , 2011)  were adopted. Also, the miRBase (http://www. mirbase. org/) (Kozomara and Griffiths-Jones, 2014)  was utilized to screen for potential miRNA binding sites applying the datasets from the taxons Ecdysozoa and Lophotrochozoa.
WHO and UNICEF recommend to define severe acute malnutrition (SAM) in infants using of weight for height indicators with the cutoff of below À3 standard deviations and a MUAC cut-off point of 115 mm to define SAM with MUAC  [5, 31]. In infants aged from birth to 6 months, minimal data exists as to a reliable MUAC for diagnosing SAM. One small study from Indian suggests a lower range of 110 mm for infants 1-6 months of age  [32]. The International Classification of Diseases (ICD-10) defines Failure to thrive as the lack of expected normal physiological development and defines Malnutrition as ''The degree of malnutrition is usually measured in terms of weight, expressed in standard deviations from the mean of the relevant reference population. When one or more previous measurements are available, lack of weight gain in children, or evidence of weight loss in children or adults, is usually indicative of malnutrition.