dataesr/scientific-paragraphs-categorization huggingface dataset:
About 10 images per experiment were captured for each condition. Data were obtained from 3 independent experiments and presented as means (% of cell viability) ± SD. Fluorescence resonance energy transfer (FRET) FRET microscopy was performed to assess physical binding between DVL2 and NXN proteins. FRET was measured with the sensitized emission method  [41]  using TCS SP2 AOBS confocal microscope as previously described  [26] , and the parameter settings were kept constant throughout all experiments. Different set of cell specimens were prepared to get the fully corrected FRET signal  [42] : a FRET specimen consisting in a cell sample labeled with both the donor (Alexa Fluor 488-labeling DVL2) and the acceptor (Alexa Fluor 594-labeling NXN), and from which the FRET signal can be detected; and reference specimens labeled with the donor only and the acceptor only to obtain calibration coefficients required for adequate corrections of direct acceptor excitation and donor emission bleed-through.
2b ): FRET eff Fig. 6  AA treatment stimulates the expression of the WNT/β-catenin signaling target gene MYC. MYC mRNA levels (fold change) were evaluated by quantitative real-time PCR at 0, 24 and 48 h after the differentiation was induced. Data for untreated cells were compared with cells treated with 15 mM LiCl, 200 μM AA (short treatment) or 0. 5 μM RuR. Values are mean ± SD of three independent experiments. *P ≤ 0. 05 compared with untreated differentiating cells at t = 0 h; # P ≤ 0. 05 between each treatment condition at t = 48 h; ns, non-significant started to decrease at 1 h when ROS levels significantly increased, and the strongest reduction of the FRET eff value happened at 3 h when the highest levels of ROS were reached and maintained in a plateau. Though ROS levels returned at baseline at 4 h, FRET eff still remained at its lowest value indicating that both proteins do not reassociate anymore; the cells do no longer maintain high ROS metabolism for promoting DVL2 release as the protein complexes were already fully dissociated  [26].
Identification of genes Nineteen P. kudriavzevii genes involved in folate biosynthesis were identified in a draft genome of P. kudriavzevii (GeneBank #ALNQ00000000. 1,  [Chan et al. , 2012] ). The genes were identified on different contigs by aligning with Blast Program  (Altschul et al. , 1997)  the protein sequences retrieved from both SGD and CGD databases, against the whole genome shotgun contigs (wgs) of P. kudriavzevii. For FOL3, FOL2, FOL1, ABZ1, ABZ2, DRF1 and CDC21 genes, responsible for the conversion of folate precursor (GTP) into tetrahydrofolate (THF), specific primers were designed by Primer 3 (version 4. 0. 0) (http://primer3. ut. ee/). Primers sequences are shown in Table  1.
DNA extraction and PCR conditions DNA of each strain was extracted from the pellet obtained from 1 mL of 24 h YPD pure culture and centrifuged at 14 000g for 10 min, 4 C. The pellet of cells was subjected to DNA extraction according to the procedure described by  Cocolin et al. (2000). DNA was quantified using the Nanodrop Instrument (Spectrophotometer ND-1000, Thermo Fisher Scientific, Milan, Italy) and diluted to a concentration of 100 ng mL À1. The PCR temperature profile was as follow: 5 min at 95 C followed by 35 cycles of 1 min at 95 C, 1 min at 55 C and 2 min at 72 C. At the end, 10 min at 72 C were performed. Amplicons were analyzed by visualization on 1. 2% agarose gel electrophoresis in 1X TAE (80 V, 25 min) after staining with ethidium bromide (10 mg mL À1 ). Amplified sequences were sent for sequencing (MWG Biotech, Ebersberg, Germany) and results aligned in GenBank using the Blast Program  (Altschul et al.
Acknowledgements The authors would like to thank  Prof. D. J. Hounhouigan  and  Dr. Wilfrid Padonou  at the  Universit e d'Abomey-Calavi (Cotonou, Benin)  for the assistance during the isolation of the strains used in this study and  Dr. Youna M. Hemery  at  IRD (Montpellier, France ) for her important inputs and assistance during folate quantification. Fabien Saubade  acknowledges a PhD grant from the  French Ministry of Education and Research. A part of this work was included into the  FolEA  project (ERAfrica  ERAFRICA_IC-027 ,  FP-226154 ).
Methods General procedures. Reagents and solvents for the synthesis were anhydrous (purchased or self-dried) to ensure good product yield. Solvents used for separations were ACS chemical grade, purchased from commercial sources and used upon arrival. NH 4 Cl was sublimed in our lab for Birch reduction. Reactions for light sensitive Reactions for non-UV active compounds were visualized on TLC by 5% phosphomolybdic acid in ethanol. All NMR data were collected on a Bruker Avance III 400 MHz NMR or a Varian Inova 500 MHz NMR. Samples were dissolved in 0. 5 mL CDCl 3 , methanol-d 4 , DMSO-d 6 or actone-d 6 , and NMR data were collected at r. t. Mass spectra of compounds were acquired using a Bruker LC-IT-MS system with an ESI source. High-resolution MS spectra and extracted ion chromatogram (EIC) were obtained using a Waters ACQUITY UPLC I-Class System equipped with a Xevo G2-S QTof mass spectrometer based on our previously reported conditions  26, 27.
Crystals were obtained in 50 mM Bis-Tris pH 6. 5, 1. 6 M lithium sulfate and 50 mM magnesium sulfate. Protein crystals were mounted in a fiber loop and flash-cooled under a nitrogen flux after cryo-protection with 20% glycerol. Data collection from a single frozen crystal was performed at 100 K on the ID23-1 beamline at ESRF (France). The raw data were processed and scaled with the HKL2000 program suite  29. The crystals belong to the space group P6 5 22, with one LBD complex per asymmetric unit. The structure was solved and refined using BUSTER  30  , Phenix  31  and iterative model building using COOT  32. Crystallographic refinement statistics are presented in Supplementary Table  S9. All structural figures were prepared using PyMOL (www. pymol. org/). Biosynthesis of 1,20S(OH) 2 D 3. Enzymatic synthesis of 1,20S(OH) 2 D 3 involved the 20S-hydroxylation of 1α(OH)D 3 by recombinant bovine CYP11A1 and was carried out as described in detail before  7.
The forward reverse primers for VDR, CYP24A1, TRPV6 and CYP27B1 genes were designed based on the rat and mouse sequences using Primer Quest software (Integrated Device Technology, San Jose, CA, USA). Reactions (n = 3) were performed at 50 °C for 2 min, 95 °C for 10 min and then 40 cycles of 95 °C for 15 s, 60 °C for 30 s and 72 °C for 30 s. Data were collected and analyzed on a Roche Light Cycler 480. Using a comparative Ct method  25  , the amount of the final amplified product was normalized to the amount of β-actin as a housekeeping gene.
Acknowledgements This work was supported by  NIH  grants  1R21AR063242  (W. L. , D. D. M. ),  1S10OD010678  (W. L. ),  1S10RR026377  (W. L. ),  R21AR066505  (A. S. ) and  1R01AR056666  (A. S. ),  ANR  grant  ANR-13-BSV8-0024-01  (N. R. ), and institutional funds (N. R. ) from Instruct which is part of the  European Strategy Forum on Research Infrastructures (ESFRI). We thank  Dr. Dejian Ma  in UTHSC,  Dr. Stephen W. White   in St. Jude Children's Research Hospital , and the staff of the ID23-1 beamline at  ESRF  synchrotron for the experimental assistance. Z. L. thanks the support from the pre-doctoral Alma and  Hal Reagan Fellowship  from  UTHSC , and a national scholarship award from  China Scholarship Council. The content is solely the responsibility of the authors and does not necessarily represent the official views of the  NIH.
ACKNOWLEDGMENTS Authors are thankful to  S. Grall  and  C. Fenech  ( CSGA, Dijon, France ) for their technical help in the cell culture preparation and to  A. Lefranc ,  L. Decocq , and  A. Mathou  ( CSGA, Dijon, France ) for animal care taking. This work was supported by grants from  Marie Curie Foundation (CIG NeuROSenS   PCIG09-GA-2011-293738 , XF),  Société Francophone du Diabète (XF). CC was supported by a salary award from the  Institut National de la Recherche Agronomique (INRA).
Study design The Lipinflox study was approved by the French Ethics Committee of Lyon Sud-Est-II and AFSSAPS (French National Agency for Medicines and Health Products Safety) and registered at Clinical Trials (#NCT01249378). The primary outcome about the effect of fat structure on postprandial dietary fatty acid handling and metabolism was previously published in a companion paper  [6]. Of note, results about the impact of fat amount on postprandial LPS handling were also reported previously  [3]. Here we report secondary outcomes of the Lipinflox study on the modulation of postprandial endotoxemia by fat structure. In a crossover randomized controlled design, subjects performed 2 days of metabolic testing separated by at least 3 weeks. After a standardized dinner evening before and an overnight fast, subjects came to the Human Nutrition Research Center Rhône-Alpes (Lyon, France) and consumed one of the 2 test breakfasts containing 40 g of milk fat, 50 g of bread and 160 mL of skimmed milk and providing 251 kcal.
Statistical analysis Data were analyzed using GraphPad Prism software (GraphPad version 5). We calculated that eight subjects per group would provide an 80% power at P < 0. 05 to detect a 60% difference in endotoxemia according to the emulsified vs. unemulsified structure taking into account a coefficient of variation of 60% according to our previous data in rats  [4]. Data normality was checked using the Kolmogorov-Smirnov test. Endotoxemia and chylomicron data followed a normal distribution. The incremental areas under the curve (iAUC; area above baseline fasting value) were calculated by the conventional trapezoid rule from data during the different postprandial periods. Intra-comparisons between test meals were performed using paired Student's t-test and intercomparisons between subject groups with unpaired Student's t-test.
Acknowledgements We thank the volunteers for their involvement in the clinical trial. The clinical team of the  CRNH Rhône-Alpes  ( C Maitrepierre ,  J Peyrat ,  N Torche ;  M Sothier ;  Dr. S Lambert-Porcheron ,  Dr. N Feugier ) is acknowledged for the assistance in the trial set up and process. A Faure ,  M Cervantes ,  C Norbert  and  S Gonin  are acknowledged for their help in the management of lipid analyses.
data collection Baseline and anthropometric data On the day before the start of the trial, potential participants will be assessed for eligibility at the test-feeding site, using an exclusion form, and through the collection of baseline data, including demographic, anthropometric, morbidity and dietary data (breastfeeding, food frequency and dietary diversity). Anthropometric measures include weight to the nearest 0. 1 kg (with SECA scale), recumbent length to the nearest 0. 1 cm (with wooden UNICEF height boards) and MUAC to the nearest 1 mm (with a UNICEF flexible insertion tape).
Substudy 1: acceptability to children On the 12 days of substudy 1, data will be collected daily including time of arrival and of last feeding or breast feeding, and morbidity data pertaining to the previous 24 hours. Caregivers will be asked to bring their child to their designated test-feeding site. They will be asked not to feed their child for the preceding hour, if possible. The same food will be given 3 days in a row, to allow averaging of results and reduce the effect of chance findings. Children will receive the four foods, namely the RUSF snack, RUSF added to borbor, CSB++ porridge and Sprinkles added to borbor, for 3 days each over 12 days. Children in each group will taste each food in a different sequence (to balance for carryover effects), as in figure  1  below. A woman from each of the four sites will be hired and trained to prepare an appropriate quantity of the food each day, under the study team's supervision.
17 he bowl with remaining food, spoon and napkins will be weighed after the child has finished eating. Children will not be separated from their caregivers at any point. Children will not be forced to eat the foods. If they become excessively distressed, they will be given the option of taking a break or withdrawing. After eating the food for 3 days, each caregiver will be asked to assess how he or she thinks the child liked the food, taking into account the amount eaten and the child's reactions and emotional state during feeding. Responses will be recorded by staff on a data collection form, using a five-point hedonic scale (1=disliked a lot, 2=disliked a little, 3=neither liked nor disliked, 4=liked a little and 5=liked a lot). The hedonic scale is a standard tool for measuring food acceptability, that is, how much a consumer likes or dislikes a product.
18 bstudy 2: acceptability to caregivers On the 13th day, caregivers will be asked to come to the test-feeding site, alone if possible. Baseline data will be collected from caregivers, including their pregnancy status, and morbidity data pertaining to the previous 3 days. First, in a sensory test, the foods will be presented to caregivers one at a time. No weighing is necessary, and caregivers will not be expected to eat a whole bowl. Between foods, the caregiver will be asked to rinse his/ her mouth out with water. Caregivers will rate them with respect to colour, consistency, smell, taste and their overall opinion. Responses will be recorded by staff on a data collection form, using the five-point hedonic scale (1=very bad, 2=bad, 3=neither bad nor good, 4=good and 5=very good). A score of 3=neither bad nor good will be considered the threshold for acceptance of the food.
Then the foods will be presented at the same time, and caregivers will be asked to rank them. Responses will be recorded by staff on a data collection form (1=best, 2=second best, 3=third best and 4=least good or worst). Finally, a smaller number of caregivers  [8] [9] [10] [11] [12]  will be asked to stay for a focus group discussion related to infant feeding practices and more detailed reasons for preference ranking. Caregivers will be asked if they would use or buy the novel RUSF and their reasons for doing so, including the perceived benefits and value (monetary) of using such a product. The discussion will be led in the Khmer language by facilitator. A notetaker will be responsible for electronic recording, as well as taking notes, especially about non-verbal communication. The recording will be transcribed and translated into English.
19  third outcome is caregivers' ranked preference for the food, as preference of the caregiver also determines in large part whether a new food will be used or not. 19 21 hese outcomes indicate how well accepted the food is by children and caregivers and how likely they would be to eat the food or feed it to their children if it were provided in the context of programming for the prevention of malnutrition. statistical analysis All data will be double-entered in Excel and will be analysed in the statistical software STATA V. 13. 1. Since repeated measures are being taken, the assumption of independence is not satisfied, and all statistical tests will be for dependent samples. For all tests, significance levels will be considered p<0. 05.
Enrolment data Enrolment data describing the characteristics of the recruited children (eg, sex, age, anthropometric measures, morbidity and breastfeeding status) and caregivers (eg, age, morbidity and breastfeeding status) will be reported as means±SD for continuous measures. Anthropometric indices will be calculated using WHO 2006 standards (ANTHRO V. 3. 2. 2, January 2011) and expressed as z-scores for weight-for-height (WHZ), weight-for-age (WAZ) and height-for-age (HAZ). Any missing data will be treated as 'missing at random' and accounted for using mixed model and multiple imputation. However, the immediate nature of data collection, on-site presence of a supervisor and follow-up methods should limit protocol non-adherence and missing data.
First-Meal Pattern analysis At 160 days of age, rats (8-12 animals/group) were individually housed (22 ± 2°C, 12:12-h light/dark cycle, lights on at 7:30) for 3 days in plexiglas Phecomb cages (Bioseb, Vitrol, France) equipped to monitor meal pattern by continuous and automatic weighing of food. Phecomb system weights the food tray for each second. It allows precisely quantifying the food consumption and identifying feeding events. Artifacts as large vibrations when the rat enters in contact with the tray but without eating are taken into account by filters on the hardware and the software (Phecomb system monitoring software Compulse). A percentage of reliability of the quality signal was calculated by the software and only experiments with a percentage >80% have been used. A meal was defined with a minimal size of 0.
5 g and a minimum inter-meal interval of 20 min. A meal is composed of several bouts. Meal parameters extracted from Compulse software included latency to eat, meal size, duration of the meal, inter-meal interval, and satiety ratio. After 48 h of fasting and 24 h of acclimatization to the cage, data were recorded from the beginning of the second day (8:00 a. m. ) each 5 s over a 24-h period. This prolonged caloric restriction of 48 h was chosen on the basis of previous reports showing that 24-48 h duration of fasting triggers VAN to switch from anorectic to orexigenic phenotype  (16, 25, 26). Other previous studies used this duration of fasting to promote feeding in adult rats weighting more than 500 g (6, 7).
Band intensities were quantified by infrared scanning densitometry (Odyssey Imaging Systems, LI-COR, Germany). Data are expressed as the ratio of phosphorylated protein relative to total protein. Protein load was controlled with anti-actin mouse monoclonal antibody (diluted 1/2,000, Sigma). immunohistochemistry Cryostat sections (7 µm) of fixed nodose ganglia in 4% paraformaldehyde were mounted on SuperFrost Plus Gold slides (Thermo Scientific; Braunschweig, Germany). Sections were stained with a rabbit polyclonal antibody raised against CCK-1R diluted at 1/200 (Santa Cruz Biotechnology, CA, USA). The secondary antibody used at appropriate dilution (1/1,000) was a goat biotinylated antirabbit polyclonal antibody (Vector Laboratories, Clinisciences, Nanterre, France) followed by Alexa Fluor ® 488-conjugated streptavidin antibody (Molecular Probes, Life Technologies).
Nuclei were counterstained with DAPI. Tissues sections were mounted in Prolong Gold antifading medium (Molecular Probes, Thermo Scientific, Courtaboeuf, France). Three to five sections of nodose ganglia per rat were analyzed by fluorescence microscopy (Zeiss Axiovert 200M, Carl Zeiss, France). Fluorescence was quantified on image mosaic representing the total surface of each longitudinal nodose ganglia section using Volocity software (Volocity 6. 2. 1, Perkin Elmer, France).
statistical analysis All statistical analyses were carried out using GraphPad Prism 6 (GraphPad Software, Inc. , San Diego, CA, USA) software. Comparisons between control and LP groups were performed with an unpaired, two-tailed, Mann-Whitney test. When measures were repeated (dose-response), Friedman test was applied following Wilcoxon signed rank test. A P value ≤ 0. 05 was considered statistically significant.
Vagal neurochemical Phenotype and ccK-1r signaling Since short-term regulation of FI by CCK acts primarily via vagal nerve, the expression of CCK-1R was measured in nodose ganglia. The basal expression of vagal CCK-1R measured by immunofluorescence (P < 0. 01) was lower in LP rats as compared to control rats and could contribute to the loss of sensitivity to CCK-induced satiety in LP rats (Figures  5A, B ). No effect of refeeding on vagal CCK-1R expression was observed (data not shown) in the present experiment as previously reported  (32). The neurochemical switch operated by CCK on VAN determines an anorexigenic vs orexigenic phenotype that mediates an appropriate response at the brain stem and hypothalamic levels to regulate FI  (14, 15). Anorexigenic peptides (CART) and receptors (Y2-R) as well as orexigenic NPY were analyzed in nodose ganglia in response to refeeding in both groups.
Previous data showing CCK-induced phosphorylation of ERK in NTS reported that the effect occurred very quickly, as soon as 6 min following injection  (21). Here, we measured CCK signaling 20 min after stimulation, this may have contributed, in combination with the low dose used, to the absence of phosphorylation signal in nodose ganglia. An analysis on a shorter time needs to be further performed and CCK signaling measured at the afferent endings in the NTS may provide a better comprehension of the underlying mechanism. Concerning calcium signaling, we showed that LP lowered TRPV2 expression in nodose ganglia. This observation could be put in relation with the attenuated level of CaMKII and pCaMKII measured in this model as compared to normal birth-weight rats. Such a reduced expression of CaMKII has been previously reported in the frontal cortex in young adult LP rats  (46).
Our model includes calcium transport, water flow and ambient humidity. The regulatory interplay between the epidermal barrier and these transport processes allows the in silico epidermis to self-organize into stratified layers displaying calcium and water gradients comparable to in vivo data. To allow a dynamic cell shape, we developed a 3D off-lattice cell-centre-based biomechanical model (BM), thus extending the BM portfolio of the modelling and simulation platform EPISIM  18, 22. This platform uniquely allows creating agent-based models intuitively through a graphical modelling language, enabling less computer-savvy users to create complex cell behavioural models (CBM). The new BM yields a SC with realistic flattened corneocyte morphology. In our new CBM, cells in the SG and SC flatten and produce tight junctions and lipids that impede diffusion, thus generating an epidermal barrier.
Methods EPISIM multiscale multicellular modelling and simulation platform. We previously introduced the EPISIM platform for graphical multi-scale modelling and cell-based simulation of multicellular systems  18, 22. The EPISIM platform consists of two ready-to-use software tools: (i. ) EPISIM Modeller (graphical modelling system) and (ii. ) EPISIM Simulator (agent-based simulation environment). Each EPISIM-based model is composed of at least a cell behavioural and a biomechanical model (CBM and BM). The BM covers all spatial and biophysical cell properties; the EPISIM simulation environment offers a multitude of different BMs (e. g. lattice and off-lattice). In this work, we extend the portfolio of available BMs by introducing a novel off-lattice cell-centre-based cell morphology model with a more realistic representation of biomechanical forces.
Results A total of 179 febrile children aged less than 5 years old were recruited in the clinical study in Bertoua in 2003. The mean age (±standard deviation) was 29 ± 17 months (range 6-58 months old). The sex ratio was 0. 97 (88 boys and 91 girls). The minimum required parasitaemia for inclusion was 2000 asexual parasites/µl of blood. Parasitaemia ranged from 2000 to 250,000 asexual parasites/ µl of blood. The clinical and parasitological outcome was published elsewhere  [5, 6]. Among 101 participants of the survey conducted in Messok in 2012, data on age and gender were available for 96 and 95 individuals, respectively. The median age at inclusion was 36 years (interquartile range, 25-55 years old). There were 38 men and 57 women. Microscopic examination of blood smears for malaria detection was not performed.