dataesr/scientific-paragraphs-categorization huggingface dataset:
and S2 Fig). Cluster 9 is the only cluster (Fig 7 and S2 Fig), which can lead to type III PKS, which might be responsible for the production of chalcone and stilbene synthase as the key enzyme shows 70% identities with homologous gene in the Colletotrichum higginsianum (GenBank, ID CCF34076. 1). We also identified three genes encoding aristolochene synthase (g9860. t1), geranylgeranyl diphosphate synthase (g13546. t1) squalene synthase (g5738. t1) forming two clusters (Fig 7 and S2 Fig) on the scaffolds scaf-fold440 and scaffold446.
Acknowledgments The research of the project MARINE FUNGI leading to these results has received funding from the  European Union   Seventh Framework Program  ( FP7/2007-2013  under grant agreement number  265926 ). We thank  Hanna Schmidt  for DNA and RNA isolation and  Linda Paun  for providing strain M26, respectively. We also thank  Genotypic Technology  ( Bangalore, India ) for providing Ion-torrent based genome sequencing as a gift. We also thank  Chandan Goswami  for editing final version of this MS.
Nuclei were stained with 0. 5 lg/ml DNA intercalant Hoechst #33258 (Life Technologies). Sections were mounted using Prolong Gold Antifading reagent (Life Technologies). Omission of primary antibodies was used as negative controls of immunostaining. Tissues were observed under LSM 700 confocal or Axiovert inverted microscopes (Zeiss, Jena, Germany). Images were analyzed using the Axiovision (Zeiss), Photoshop and ImageJ (NIH) softwares. The number of plaques was blindly scored in two brain sections per animal by three investigators at bregma -1. 9 and -2. 9 and normalized by the surface of the brain region analyzed. Densitometric analysis of immunostained sections was performed using ImageJ software and binarization methods, applying the same threshold of immunofluorescence across experimental groups.
Blots were developed using appropriate horseradish peroxidase-conjugated secondary IgG antibodies (anti-mouse/anti-rabbit, Promega Corp. , Madison, WI, USA; anti-rat, Santa Cruz Biotechnology Inc. , Dallas, TX, USA) and the ECL chemiluminescence system (GE Healthcare). Quantification of sAPPa and sAPPb bands was carried out using Fuji Las-4000 software (Fuji Film inc. , Minato, Tokyo, Japan). Levels of PS1, Aph1, Pen2 and nicastrin were analyzed in solubilized cell membranes as reported previously  [23]. Briefly, intact cell pellets were resuspended in 10 mM Tris-HCl buffer, pH 7. 5 with proteinases inhibitors (Sigma-Aldrich), subjected to repeated passages through a 25 G needle and first centrifuged at 8009g for 10 min at 4 °C. The resulting supernatants were subjected to an additional 20,0009g centrifugation for 1 h at 4 °C.
ELISA assay for Ab and IL-1b quantifications For detection of soluble Ab38, Ab40 and Ab42 species in the DEA fractions, we used the MSD Ab Triplex sandwich immunoassay (MesoScale Discovery, Rockville, MD, USA)  [21]. MSD C-terminal-specific antibodies were prespotted into each well. For detection, a ruthenylated 4G8 antibody was used. The concentrations of Ab peptides were normalized to protein content and calculated using the MSD Discovery Workbench software. For detection of IL-1b in the soluble fraction, we used the murine IL-1b ELISA Development Kit (PeproTech, Neuilly-sur-Seine, France), loading 5 lg of protein per well, according to the manufacturer's recommendations.
Test frequency to evoke fEPSPs was 0. 066 Hz. Slices that displayed epileptic-like activity were discarded. Data storage and analysis were performed with MC Rack software (Multi Channel Systems). Changes in synaptic transmission were assessed by measuring peak amplitudes of fEPSPs, which were modified in a way similar to fEPSP slopes, as previously reported by others using MEAs  [33]. Applying a single train of stimulation at 100 Hz for 1 s triggered LTP.
Statistics Significant differences between groups were determined using the Kaleida Graph software. We used a one-way ANOVA followed by post hoc Fisher's LSD or Kruskal-Wallis tests for multiple comparisons. Two-tailed unpaired Student's t test was used to compare two experimental groups. Values represent the mean ± SEM of the indicated number of independent experiments/animals, and the level of significance was set for p \ 0. 05.
Acknowledgments This work was supported by funding from the  CNRS  and  Aix-Marseille Universite , and by grants from the  French National Agency for Research (ANR)  to SR, MK and MV (TIMPAD, PREVENTAD and ADHOC, respectively) within the frame of the  French ''Fondation Plan Alzheimer ''. The work was also supported by LECMA grants to SR, FC and MK, by grants to SR and  MK from ''Fonds Europeen de Developpement Regional '' FEDER in PACA, by  BMBF KNDD, SyNergy (DFG)  and the  Verum Foundation  to SFL, by the  Bavarian-French University Center  to SR and SFL, by '' Fondation pour la Recherche Medicale '' and by the '' Conseil General des Alpes Maritimes '' to FC. This work was also supported through the  LABEX (excellence laboratory, program  investment for the future)  DISTALZ (Development of Innovative Strategies  for a Transdisciplinary Approach to Alzheimer's disease).
Twenty-three pairs of primers were designed between contigs using the Primer3 software  (5). The endpoint PCRs were conducted on a Veriti Applied Biosystems thermocycler (Life Technologies, Carlsbad, CA). Twenty-two gaps were closed, and the resulting assembly consisted of 2 chromosomal contigs (1,275,359 bp and 1,956,412 bp). The total genome length is 3,231,771 bp. The GϩC content is 44. 49%, which is consistent with the results reported for other L. plantarum genomes (44. 5 to 44. 7%). Annotation was performed using the RAST annotation server  (6). A total of 3,165 protein-coding sequences (CDSs) were identified; defined biological functions were assigned to 2,424 CDSs. Six hundred seventy-five CDSs were homologous to sequences encoding hypothetical proteins in other organisms, and 66 CDSs did not have a database match.
ACKNOWLEDGMENTS The Illumina sequencing was conducted by ProfileXpert:  Génomique & Microgénomique , Lyon, France. The work was funded by an  ERC  starting grant (FP7/2007-2013-no. 309704 ). The lab of F. L. is sponsored by the  EMBO YIP program , the  ATIP/AVENIR program , the  Fondation FINOVI , and the  Fondation Schlumberger pour l'Education et la Recherche.
Classification systems and cutoff values The three classification systems under study are all based on the LMS method  [9, 25]. This method consists in grouping together data from three specific curves as a function of age: the M (mu) curves correspond to the median BMI; the S (sigma) curves correspond to the coefficient of variation; and the L curves (lambda) correspond to the dissymmetry  [25]. Each percentile value of the BMI curve corresponds to one or more standard deviations from the median curve (50th percentile), commonly called the Z-score. Z-scores are calculated using the formula: Z = [(BMI/M) L À 1]/[L Â S].
IOTF references The BMI values in the study sample were introduced into the free access software developed by Dr. Tim Cole -LMS Growth software (http://www. healthforallchildren. com). Z-scores were calculated using the formula associating the international LMS parameters by age as defined by the considered international population (Brazil, Great Britain, Hong Kong, Singapore, United States, The Netherlands)  [9]. Each child's weight status was determined according to the cutoff values associated with the percentile curves: obesity: percentile curve passing through BMI = 30 kg/m 2 at age 18; overweight: percentile curve passing though BMI = 25 kg/m 2 at age 18; ''normal'' weight: percentile curve passing through BMI = 18. 5 kg/m 2 at age 18.
WHO References AnthroPlus (http://www. who. int/growthref/tools/en/) is a free-access software published by the WHO. AntrhoPlus was used to calculate the BMI Z-scores of the study sample and determine the weight status of each child according to the following cutoffs defined by the WHO in 2007  [22] : for children aged < 5 years: obesity: BMI Z-score > 3, overweight: 2 < BMI Z-score 3, ''normal'' weight À3 < BMI Z-score 2; for children aged ! 5 years: obesity: BMI Z-score > 2, overweight: BMI Z-score 2, ''normal'' weight À2 < BMI Z-score 1.
The kappa coefficient (k) was used to assess the degree of agreement of the three classification systems: French, IOTF, WHO. The systems were considered to be in: disagreement to weak agreement (k = 0. 00-0. 40); moderate to strong agreement (k = 0. 41-0. 80); nearly perfect agreement (k = 0. 81-1. 00); perfect agreement (k = 1. 00)  [21]. The level of significance was set at P < 0. 05 for all comparisons. SPSS Statistics 17. 0 was used for the statistical analysis.
Acknowledgements The authors are indebted to children and parents for participation in this study. We extend our gratefulness to the  City council of Maubeuge , the  Nursing training school IFSI Maubeuge , and the  Academic District of Avesnes-Maubeuge  for their commitment in this project. Finally, many thanks to  Dr. Marie-Francoise Rolland-Cachera  for providing us with the reference data of the French pediatric population.
MATERIALS AND METHODS A systematic search of the literature was undertaken to identify studies in humans and animals that assessed the effects of consumption of LES on EI and/or BW and/or body mass index (BMI). LES were defined as ingredients contributing negligible energy to products to achieve a sweetness similar in comparison with caloric sweeteners. Thus LES include intense sweeteners and non-metabolized sugars but exclude most sugar alcohols (see Supplementary Information for full definition and examples). We use 'sugars' to refer to caloric sweeteners, usually sucrose. The databases of MEDLINE and EMBASE via OVID interface and Web of Science were searched from their inception to 01 February 2015, using a combination of MeSH terms and key word terms to identify research addressing the relevant combinations of exposures (sweetener types) and outcomes (describing food or EI, anthropometric measures or changes in these).
ANIMAL STUDIES Study selection and data extraction We identified 62 articles reporting a total of 90 eligible studies testing the effects of repeated consumption of LES on BW and/or EI in non-human animals (rats or mice). These studies were divided into three sets based on their primary purpose. The first set investigated effects of long-term compulsory consumption of LES on BW and EI often from primarily a toxicological perspective. The second set included a contrast of voluntary LES consumption usually as a sweetness-control in studies of effects of sugar on behaviour. The third set explored the hypothesis that LES can uncouple the predictive relationship between sweetness and EI ('learning studies').
OBSERVATIONAL (PROSPECTIVE COHORT) STUDIES IN HUMANS Study selection and data extraction Studies of over 500 participants that reported on prospective analyses with more than 1 year of follow-up were included. These studies had to report on LES beverages or LES intake as an exposure and BW or relative adiposity as an outcome. Studies that reported on LES consumption and metabolic syndrome but did not report separate associations for an anthropometric component of metabolic syndrome were excluded. Only one report of the results from each prospective study was included. Where there were several reports of the same study we included either the most detailed report of the results or the report with the longest follow-up. We did not include studies published only as an abstract. Our methods for data extraction are described in the Supplementary Information.
SHORT-TERM (⩽1 DAY) INTERVENTION STUDIES/RCTs Study selection and data extraction and analysis Eligibility criteria for short-term intervention studies were: LES exposure of ⩽ 24 h and EI measured in an ad libitum meal (test meal) after consumption of the LES (preload) compared with a 'control' condition. We extracted data for test meal EI after the LES preload and comparison preload(s), and for the energy content of the preloads. We also noted the preload-to-test meal interval, and the number of participants and their gender, and where available their age, BW and/or BMI, dieting and/or dietary restraint status. We categorized the extracted data into five types of comparisons: LES versus sugar, LES versus unsweetened products, LES versus water, LES versus nothing and LES in capsules versus placebo capsules.
ACKNOWLEDGEMENTS This work was conducted by an expert group of the European branch of the  International Life Science Institute (ILSI Europe). The expert group received funding from the  ILSI Europe Eating Behaviour and Energy Balance Task Force. Industry members of this task force are listed on the ILSI Europe website at www. ilsi. eu. For further information about ILSI Europe, please e-mail: info@ilsieurope. beor call  +32 2 771 00 14. The opinions expressed herein and the conclusions of this publication are those of the authors and do not necessarily represent the views of ILSI Europe, nor those of its member companies and the authors affiliations. Part of the research leading to this review received funding from the  European Union Seventh Framework Programme  for research, technological development and demonstration under grant agreement no.
Apoptosis assays Apoptosis was quantified by Annexin V-fluorescein isothiocyante/7-Aminoactinomycin D staining (Beckman Coulter, Milan, Italy) followed by flow cytometry analysis according to the manufacturer's instructions using FC500 (Beckman Coulter). Experiments are duplicated. IC 50 was determined by constructing a dose-response curve and by analyzing the results with the GraphPad Prism5 software.
3. 1. (Oar_v3. 1) using STAR aligner (v. 2. 3. 1y)  12. The alignments were sorted with Samtools  13. The data were also tested for contamination using BWA  14  on the Escherichia coli genome. To compare expression between genes within the same sample, gene expression was estimated using Cuffquant and Cuffnorm packages from Cufflinks  15. Gene abundances were normalized by library and gene length by calculating Fragments Per Kilobase Of Exon Per Million Fragments Mapped (FPKM) using the Ensembl annotated genes (Oar_v3. 1) as a reference. Assembly and differential expression analysis. The aim of the assembly was producing a new annotation reference including novel genes and transcripts, to be used in the downstream analysis. The Samtools package was used to remove the duplicated reads and to merge the alignments.
The Cufflinks and Cuffmerge tools from the Cufflinks package  15  were used to create a "transcripts. gtf " file to be used as reference in our assembly. The Cufflinks option "-g" followed by the available gtf file from the Oar_v3. 1 reference sequence was used to guide the assembly but not excluding new genes. Cuffmerge was used to filter genes with low or no expression from our reference gtf file. Cuffcompare was used to compare the reference gtf file obtained with Cuffmerge with the reference annotation file downloaded from Ensembl (http://www. ensembl. org/Ovis_aries/Info/Index) to estimate the abundance of transcripts classified in different Cufflinks class codes. To compare the expression levels of genes across samples, raw counts for the genes and transcripts were obtained using SigCufflinks (available at http://www.
sigenae. org). SigCufflinks is a modified version of the cufflinks code that provides raw read counts per gene and transcript, by using the sorted bam file from the alignment and the reference gtf file created in the assembly. The "-G" option of sigcufflinks was used to guide the alignment but excluding new genes. To evaluate the differentially expressed genes (DEGs) from the RNA-seq data, two different R packages, DESeq2  16  and edgeR  17  , were used. The DESeq2 package performs independent filtering. In general, genes that have very low counts are not likely to see significant differences due to high dispersion. The edgeR package has no function for independent filtering. To choose a cut-off to eliminate the lowest expressed genes, we plotted a histogram on R with the log 10 (effmax + 1), thereby maintaining those genes for which the distribution becomes normal and eliminating the genes with less than 15 counts.
RNA-Seq read counts were modeled by a generalized linear model considering the experimental design, with two breed groups (Churra and Assaf) and four lactation time points per group (D10, D50, D120 and D150). The model for both programs includes breed and day factors and the interaction day x breed. After discarding a possible interaction between these two factors, we performed the following analyses with edgeR and DESeq2. First, with the aim of providing a dynamic expression profile of the mammary gland across lactation, differential expression analyses were performed for all the possible time point pairs, considering the Churra and Assaf datasets jointly. Second, to assess the impact of the breed factor on the global expression pattern of sheep lactation, a differential expression analysis between Churra and Assaf, was performed.
1 assembly. For both breeds, the lactation time point with the highest number of expressed genes was D50 (17,386 genes in Assaf and 17,192 genes in Churra). From a global view, the transcriptome results revealed that the majority of the genes had low expression (FPKM < 10) across lactation for both breeds (Table  1 ). The average gene expression levels reported here for sheep MSCs are in agreement with previous reports on the mammary gland transcriptome of other ruminant species  2, 20. A total of 107,877 transcripts were assembled by Cufflinks using the 30 analyzed milk samples. According to the Cuffcompare results (Table  2 ), 23. 95% of the transcripts matched exactly with annotated exons, and a total of 12,057 (11. 18%) potentially novel isoforms were predicted. A high percentage, 61. 87% (66,739) of transcripts, were annotated as intergenic transcripts, which is in agreement with the results reported from the RNA-Seq analysis of the ovine muscle transcriptome in which the proportion of intergenic fragments ranged between 55.
The genes with the highest FPKM values for both breeds and at the four studied lactation time points are CSN2 (β -casein), CSN3 (κ -casein), ENSOARG00000005099 (LGB, β -lactoglobulin), CSN1S2 (casein-α -S2), CSN1S1 (α -S1-casein) and LALBA (α -lactoalbumin). These highly expressed genes encode four caseins and two whey proteins, principal components of milk. Caseins and whey proteins encompass the 5. 5% of total milk composition in sheep, a higher percentage than in bovine milk (3. 2%)  23. Caseins and whey protein expression remained constant for Churra along lactation. As shown in Fig. 1 , these six genes were slightly more abundant in Churra sheep at the first two sampling time points (D10 and D50) than in Assaf sheep. In contrast, the expression of caseins and whey proteins in the Assaf breed underwent an increase at the last two time points studied (D120 and D150).
Twenty terms were significantly enriched in relation to the "biological processes" category. The most significantly enriched GO terms within this dataset were immune response (GO: 0006955), and immune system process (GO:0002376), which were associated to upregulated genes in the Assaf breed. In the "cellular component" GO term category, 11 terms were significantly enriched; the most significant ones were related to extracellular region (GO: 0005576) and extracellular region part (GO:0044421) also associated to Assaf upregulated genes. The rest of significantly enriched terms (11) belonged to the "molecular function" category, and, the most significant ones were receptor binding (GO:0005102) related to Assaf DEGs, and three terms related to serine hydrolase (GO:0017171) and endopeptidase activities (GO:0008236, GO:0004252), the three of them related to Churra DEGs.
By contrast, the enzymes are nearly inactive against arginine and creatine substrates, as previously shown for SmTK  (40). We report herein a comprehensive structural and biochemical study of the SmTK contiguous dimer. We solved the crystal structure of the substrate-free form at 2. 2 Å resolution. The structural bases of the catalytic mechanism were investigated by determining the crystal structures of SmTK in complex with TSA components at 2. 3 Å resolution (SmTK-TSA) and in complex with L-arginine at 1. 9 Å resolution (SmTK-Arg). Small angle x-ray scattering (SAXS) data were collected for the free and substrate-bound enzymes to characterize structural rearrangements in solution. Enzymatic and isothermal titration calorimetry (ITC) experiments were performed on the wild-type enzyme and invariant cysteine mutants to investigate a cooperative mechanism in the duplicated structure.
The syringe contained the ADP usually at a concentration of 0. 3-0. 4 mM as determined by UV light absorbance using the 260-nm ADP molar extinction coefficient of 1. 54 ϫ 10 4 M Ϫ1 ⅐cm Ϫ1. The injection syringe was supplemented with taurocyamine and ion cofactors according to the type of experiment performed. The enzyme solution used for ITC measurements was concentrated with an ultrafiltration device (cutoff 30 kDa). The ultrafiltrate solution was used to prepare the ligand solution in order to minimize heats of dilution. Blank titrations were done in the absence of enzyme to record the heat of dilution. The data corrected for the heat of dilution were best fitted to a single set of identical independent binding sites model with the Origin version 7. 0 software to obtain the binding parameters K a (association constant) from which the K D (dissociation constant, 1/K a ) was obtained, ⌬H (enthalpy), and n (stoichiometry).
Finally, the structure of the SmTK-TSA complex with a closed active site was obtained from a crystal soaked for 5 min in the optimized crystallization solution supplemented with 100 mM taurocyamine, 20 mM ADP, 50 mM Mg(NO 3 ) 2 , and 1% (v/v) DMSO to improve ligand solubility. This soaking resulted in the doubling of the a unit cell dimension (see Table  1 ). X-ray Diffraction Experiments and Structure Determination-Synchrotron data were collected at 100 K on the MX beamlines at the European Synchrotron Radiation Facility in Grenoble, France, and on the PXIII beamline at the Swiss Light Source in Villigen, Switzerland. The XDS and XSCALE programs were used for data reduction and scaling  (46). Five percent of the randomly selected reflections were kept apart for cross-validation, and the phasing problem was solved by molecular replacement as described previously  (38).
The substratefree structure was further refined by several cycles of rigid body in PHENIX  (47)  followed by positional and B-factor refinement. The model was manually improved during the course of the crystallographic refinement using the graphic program COOT  (48). The SmTK-Arg structure was refined using a similar protocol. The SmTK-TSA structure was solved by molecular replacement using the program PHASER (49) and substratefree SmTK as a search model. Because the taurocyamine structure is absent from the Protein Data Bank (PDB), a model was generated with the program eLBOW  (50). All bound ligands were positioned in F o Ϫ F c difference maps with COOT. The flexible loop at 671-680 was rarely observed in electron density maps and was not included in the final models of SmTK chain A, SmTK-Arg chain A, and SmTK-TSA chain B.