dataesr/scientific-paragraphs-categorization huggingface dataset:
Dietary Data Throughout the entire SU. VI. MAX study trial phase (1994-2002), participants were asked to provide a 24-hour dietary record every 2 months, for a total of 6 records per year covering all days of the week and all seasons of the year. For these analyses, mean dietary intakes were calculated across all available, valid 24-hour dietary records obtained during the first 2 years of follow-up, in order to obtain a proxy for habitual dietary intakes. Participants with <3 valid records during this period were excluded from analyses. Dietary records were considered invalid if energy intake was <100 or >6000 kcal/ day. Additionally, men reporting <800 kcal/day and women reporting <500 kcal/day across one third or more of records were excluded to account for energy underreporting. An instruction manual including validated photographs of generic foods and portion sizes was provided to facilitate coding food portions.
22 A food composition table was used to estimate nutrient intake. 23 We used the DII to determine the "inflammatory potential" of the diet. This index relies on information contained in 1943 published studies reporting association between nutritional factors and inflammatory markers. 17 riefly, points were assigned to every food parameter on the basis of relevant articles found in the literature, according to whether each food parameter increased (+1), decreased (À1), or had no (0) effect on 6 inflammatory biomarkers: interleukin-1b, interleukin-4, interleukin-6, interleukin-10, tumor necrosis factor-a, and C-reactive protein. The DII computed from the 24-hour records in this study includes data on 36 of the 45 food parameters comprising the DII: carbohydrate, protein, total fat, energy, alcohol, fiber, cholesterol, saturated fatty acids, monounsaturated fatty acids, polyunsaturated fatty acids, omega 3, omega 6, niacin, thiamin, riboflavin, vitamin B6, vitamin B12, iron, magnesium, vitamin A, vitamin C, vitamin D, vitamin E, folic acid, bcarotene, anthocyanidins, flavan-3-ol, flavonols, flavonones, flavones, isoflavones, garlic, ginger, pepper, onion, and tea.
Dietary intakes for these parameters were first standardized using a "world" mean and SD, derived from nutritional databases from 11 populations around the world, then transformed to percentiles and multiplied by literature-derived inflammatory points for each food parameter, then summed up. Thus, lower DII scores indicate a lower inflammatory potential of the diet. DII scores were computed on the basis of participant-specific mean nutrient and food intakes, which were obtained by averaging intakes across all available dietary records, as explained in the first paragraph of the Dietary Data section (ie, DII scores were not first calculated per day and then averaged). More details on the score computation can be found elsewhere. 17.
Case Ascertainment Information about health was self-reported via a monthly questionnaire during the follow-up. Other sources of information regarding outcome included yearly clinical examinations. In case of no contact with a participant for a long period, or nonattendance at the yearly visit, an investigation was launched to determine the reasons. In case of a suspected event, investigations were conducted to obtain relevant medical data (clinical, biochemical, histological, and radiological reports) from participants, physicians, and/or hospitals. All cardiovascular events were reviewed and validated by an independent expert committee, unaware of the supplementation group assignment, and then classified using the International Classification of Diseases, 10th Revision, Clinical Modification (codes I20-I24, I64).
In order to verify the robustness of our findings, we performed a set of sensitivity analyses. First, we reanalyzed our data after removing participants who developed a cardiovascular event during the first 2 years of follow-up. Second, we selected only participants with at least six 24hour records during the first 2 years of follow-up in order to improve the accuracy of nutritional estimates. Finally, we repeated our analyses with a DII score in which dietary intakes for all parameters were first adjusted for overall energy intake, using the energy density method ([crude intakes/total energy intake]91000), named "DII 2". All tests were 2-sided and P<0. 05 was considered statistically significant, except for interaction tests for which statistical power is often weak in observational studies.
Strengths of the present study include its large sample size and its prospective design, allowing us to assess the association between baseline inflammatory potential of the diet and CVD risk through a long follow-up period of 13 years. In addition, our clinical and dietary data exhibited a high level of accuracy, with a mean of nine 24-hour dietary records per participant. Finally, we used an index that was specifically designed to measure the inflammatory potential of any diet: The DII was based on peer-reviewed literature focusing specifically on inflammation; furthermore, this index can be adapted to virtually any dietary assessment method that provides estimates of nutrient intake; and it is standardized to dietary intakes from representative populations around the world, thus facilitating easy quantitative comparisons across studies.
Acknowledgments We thank  Younes Esseddik ,  Gwena€ el Monot ,  Paul Flanzy ,  Mohand A€ ıt Oufella ,  Yasmina Chelghoum , and  Than Duong Van  (computer scientists),  Rachida Mehroug  (logistic assistant), and  Nathalie Arnault ,  V eronique Gourlet ,  Fabien Szabo ,  Laurent Bourhis , and  Stephen Besseau  (statisticians) for their technical contribution to the SU. VI. MAX study.
Sources of Funding This work was supported by grants from the  Fondation Coeur et Art eres , the  French National Research Agency (Agence Nationale de Recherche, ANR)  (grant no. ANR-05-PNRA-010 ) and the  French Ministry of Health (Direction G en erale de Sant e, DGS). Assmann was supported by a doctoral fellowship from the  Ecole Doctorale Galil ee, University of Paris 13, Sorbonne Paris Cit e. Drs Shivappa ,  H ebert , and Wirth were supported by the  United States National Institute for Diabetes, Digestive and Kidney Diseases  (grant no. R44DK103377 ).
FTIR microspectroscopy FT-IR data were used to localize and determine the chemical nature of the pathological deposits in the skin biopsies. As discussed in previous reports  [20, 23] , skin biopsies were deposited on low-e microscope slides (MirrIR, Kevley Technologies, Tienta Sciences, Indianapolis). All the FT-IR hyperspectral images were recorded with a Spectrum Spotlight 400 FT-IR imaging system (Perkin Elmer Life Sciences, France), with a spatial resolution of 6. 25 mm and a spectral resolution of 8 cm À1. Each spectral image, covering a substantial part of the biopsy, consisted of about 30,000 spectra. All biopsies presumed to contain crystal deposits were analyzed with the Spotlight 400 FTIR imaging System in the mid     infrared (4000e700 cm À1 ) spectral range to obtain infrared maps of tissue slides at high spatial resolution, down to 10 microns.
Surgery and Mifepristone Treatment. For pellets implantation, the skin was lifted on the back side of the C57BL6/J male mice and an incision was made. A pocket was formed with a pair of forceps about 2 cm beyond the incision site. Finally, mifepristone or placebo pellets were implanted into the pocket with forceps. Mifepristone pellets released continuously 20 mg/kg/day for 21 days (Innovative Research of America (IRA)). Innocuousness of the compound at this dose and time has been revealed by measuring body weight change and locomotor activity (data not shown). After 21 days of treatment, open-field and social interaction tests were performed as described below. (see Figure  3 (a) for the timeline).
As our previous study, which has examined the effects of nutritional omega-3 deficiency and stress on this neuronal class within the mPFC, has found selective effects on the apical dendrites, as opposed to the basal dendrites, analysis was restricted to the apical dendritic tree. Three to 5 neurons per mouse and per region were reconstructed by a trained experimenter blind to the conditions using a Zeiss microscope Axio Imager 2 (×100) and analysed using the Neurolucida software. Sholl analysis was performed, in which the centre of the soma was used as a reference point and dendritic length was quantified both as a total measure per cell and as a function of radial distance from the soma in 10 m increments.
Acknowledgments This research was financially supported by  INRA ,  FRM ,  ANR MoodFood , and the  Region Aquitaine. Thomas Larrieu  was the recipient of a postdoctoral fellowship from the " Société Francaise de Nutrition " and the  Labex BRAIN. The authors thank  C. Tridon ,  M. Cadet , and  C. Testa  of the animal facility and  Dr N. Abrous  and  M. Koehl  for the Neurolucida software. The authors also thank the " Biochemistry Platform " of the Neurocampus funded by the  Labex BRAIN.
Moreover, the approaches usually used show poor fit because of non-negative data and the excess of zero values, generally termed 'sparse data'  (32). Lee & Seung  (33)  proposed a new latent-variable-based method, the negative matrix factorisation (NMF) method, specifically adapted to sparse and non-negative data. This method has already been proven to be effective in food risk assessment to identify dietary patterns or chemical mixtures  (23, 34, 35). The major aim of this study was thus to identify the main dietary patterns in the French adult population using the NMF approach and the food consumption data of a nationally representative survey (the second French national cross-sectional dietary survey (INCA2)). Next, we determined their main demographic and socio-economic characteristics and assessed their nutritional and environmental profiles in order to highlight their specific features.
The low variability of the weighting factor for adults (mean of 1 and a SD of 0•7) demonstrated the good representativeness of the INCA2 adult sample compared with the French general adult population. Only adults were considered in this study. As recommended by the European Food Safety Authority, under-reporting subjects (i. e. those who, voluntarily or not, under-reported amounts consumed; 26•9 % of adult sample) were identified and included in the statistical analyses  (40). Besides, twentyfour subjects (0•9 % of the adult sample) with an extremely low total energy intake (TEI) were excluded from the final sample (estimated from the following formula: log ðTEIÞ < mean log ðTEI ð ÞÀ3 SD log ðTEIÞ ð Þ Þ  (41). The INCA2 survey was approved by the French Data Protection Authority (Commission Nationale de l'Informatique et des Libertés) and the French National Council for Statistical Information (Conseil National de l'Information Statistique).
Data Collection of data on food consumption. Dietary intake was assessed using a 7-d food record. A trained and certified investigator delivered at home the food record with a selfadministered questionnaire and explained to the subjects how to complete them. The investigator returned to the home immediately after the week to check the accuracy of the information reported in both documents. Each day of the food record was divided into three main meals (breakfast, lunch and dinner) and three between-meal snacks. The subjects were asked to describe as precisely as possible the nature and the amount of all foods and beverages consumed during the survey week. Consumed quantities were estimated using the SU. VI. MAX (SUpplémentation en VItamines et en MInéraux AntioXydants) photographic booklet  (42)  or expressed directly in weight or in household measures (e.
Nutritional intake was estimated by matching the French Food Composition database for the year 2008  (48, 49)  to the individual food consumption data. The individual average daily intake of macronutrients (i. e. total energy content, total carbohydrates, simple carbohydrates, total fats, SFA, proteins, alcohol, fibres and salt), minerals (i. e. Ca, Fe, Na, Mg, K) and vitamins (i. e. vitamins A, C, E, B 1 , B 6 , B 9 ) was thus determined. Food contamination data. Food contamination data were provided by the Second French Total Diet Study (TDS2). The TDS2 was conducted between 2006 and 2010 to evaluate the exposure of the French population to various substances that are likely to be found in foods 'as consumed'. This study collected 20 000 food products, representing 212 types of food, for which 445 substances of interest were investigated.
Food sampling was based on the data from the INCA2 survey, covering about 90 % of dietary consumption in the adult and child populations  (50). The 212 foods selected were linked to the INCA2 nomenclature. Of the 445 substances analysed, ten chemical substances, for which toxicological risk could not be excluded, were considered in this study  (50)  : trace elements (i. e. Pb, Al, Cd, inorganic As, organic Hg), acrylamide, one mycotoxin (i. e. deoxynivalenol (DON) and its acetylated derivatives), polychlorinated biphenyls (PCB)/dioxins (i. e. non-dioxin-like polychlorinated biphenyls (NDL-PCB), polychlorinated dibenzo-p-dioxins and dibenzofurans and dioxinlike polychlorinated biphenyl) and one additive (sulphites). The individual average daily exposure levels to the ten substances were estimated by combining individual food consumption data and contamination data from the food sample analysis, considering the same hypotheses as those described in the TDS2 report  (51, 52).
The CS k with significant and positive V tests were used to describe dietary patterns. Characterisation of the dietary patterns. Demographic and socio-economic characteristics of each dietary pattern were investigated using binomial logistic regression. Each tested model identified the main demographic and socio-economic determinants of each dietary pattern independently of the others, by comparing with the overall population. Variables considered were age, level of education, wealth index, household size, household composition, occupational status, region, food insecurity and municipality size. These factors were selected because of their significant associations with the dietary patterns in univariate analysis (data not shown), as well as the consistent associations between dietary intake and these demographic and socio-economic determinants  (57) (58) (59) (60) (61).
All analyses were performed among men and women separately in order to take into account the significant interaction observed between sex and other factors (data not shown). The mean nutrient intake was calculated for each dietary pattern. The association between nutritional intake and dietary patterns was assessed using ANOVA, and specific nutrient intake was identified by comparing the mean of each dietary pattern with the overall mean. All models were controlled for age, sex, season, TEI, level of education, wealth index, occupational status, household size, food insecurity, household composition, municipality size and region. As previously mentioned, these covariates were selected on preliminary analyses and previous studies  (57) (58) (59) (60) (61). Diet quality indices can evaluate the overall diet of an individual based on the following: (i) nutrient indicators, which reflect the adequacy to nutritional requirements; and (ii) foods to assess the variety of food intake  (62, 63).
The mean of quality scores of each dietary pattern was thus compared with the overall mean. Finally, mean contaminant exposure levels were calculated for each dietary pattern. Associations between dietary patterns and exposure levels were assessed using ANOVA-adjusted covariates described above. On the basis of the ANOVA model, specific exposure levels were identified by comparing the mean contaminant levels of each dietary pattern with the overall mean. All values were survey-weighted means. A P value of 0•05 was used as the threshold of significance. All analyses were implemented in the software R version 3. 0. 2. The LS-NMF algorithm was implemented using the R package 'NMF'  (78). The package 'Factominer' was used to run the clustering  (55). The package 'Survey' was used to account for the complex INCA2 sampling frame design  (79).
These findings provide new information on the diversity of food consumption in France and give an overview of the nutritional quality of the different food consumption behaviours. From a public health perspective, our results provide interesting insights for developing behaviourally targeted policies. In addition, because of contradictory results for a given dietary pattern between high-quality nutritional intake and high contaminant exposure levels (and vice versa), this study also demonstrates the necessity to analyse the risks and the benefits of food consumption behaviours, particularly in a public health context. Finally, the food consumption data were collected several years ago (i. e. 2006-2007) and the third INCA survey is currently underway, potentially providing the opportunity to assess the trends in dietary patterns at the national level.
Acknowledgements The authors wish to thank the  CIQUAL  for providing the national food composition tables, the  Institut de Sondage Lavialle (ISL)  team for the collection of data, and all the families for their cooperation. This research received institutional support from the  French agency  for food, environmental and occupational health safety (ANSES). R. G. designed the study, analysed and interpreted the data, wrote the manuscript and had primary responsibility for final content. C. B. and S. H. contributed to the analytical approach, the interpretation of the results and revised each draft. S. H. , P. D. -P. , C. D. , V. S. and A. C. contributed to the design of the surveys ( INCA2  and  EAT2 ), to the data collection and help to write the paper. The authors have no financial or personal conflicts of interest to declare.
They consist of defense systems against plasmid and phage invasions that are classified into three major groups (types I, II, and III)  (21). Whereas in L. bulgaricus, only type II or III seems to be present, if any  (22) , interestingly, CFL1 appeared to possess both of these CRISPR-Cas system types simultaneously. The availability of the genome sequence and annotation of L. bulgaricus CFL1 will allow a deeper insight into its stress response mechanisms, thus making it possible to identify potential preservation issues and to better understand cell damages following production and end-use processes, especially through transcriptomic and proteomic approaches. Nucleotide sequence accession numbers. The draft genome sequences of L. bulgaricus CFL1 have been deposited at the EMBL database under accession numbers CZPS01000001 to CZPS01000044.
ACKNOWLEDGMENTS We thank the  INRA GeT-PlaGE platform  (http://get. genotoul. fr)for sequencing the genome, the  INRA MIGALE bioinformatics platform  (http: //migale. jouy. inra. fr)for providing computational resources and support, and the  IMG E/R pipeline  for generating annotations. crossmark Genome Announcements March/April 2016 Volume 4 Issue 2 e00052-16 genomea. asm. org 1.
The observations from studies elaborating on the perception of the umami flavour  [51]   together with evidences of visual stimuli activating gustatory responses  [52]  indicate the synergism of primary senses in the formation of flavour preferences. Thus, it appears that early plant-diet exposure in trout may mediate feed acceptance of the same diet at a later life stage by affecting pathways regulating Fig. 3  Summary of functional gene ontological analyses significantly enriched based on early nutritional history in the brain. The biological significance of the 1112 up-regulated mRNA probes and 675 down-regulated mRNA probes in the brain of trout based on nutritional history was ascertained by performing gene ontology (GO) analysis using the functional annotation cluster and chart tools from the DAVID (Database for Annotation, Visualization and Integrated Discovery) bioinformatics resource  [137, 138].
The resulting data was used as input in the DAVID Enrichment Map plugin from the Bader Lab  [139, 140]  in the Cytoscape network visualization tool (version 2. 8. 3)  [141] [142] [143]. The nodes (circles) represent individual GO terms and the lines represent the relationship between the genes assigned to respective GO terms. Blue and green lines represent up-regulated and down-regulated mRNA probes in the brain respectively Fig. 4  Summary of functional gene ontological analyses significantly enriched based on early nutritional history in the liver. The biological significance of the 573 up-regulated mRNA probes and 351 down-regulated mRNA probes in the liver of trout based on nutritional history was ascertained by performing gene ontology (GO) analysis using the functional annotation cluster and chart tools from the DAVID (Database for Annotation, Visualization and Integrated Discovery) bioinformatics resource  [137, 138].
Confirmation of selected microarray expressed targets by real-time PCR Real time PCR analysis (Additional file 7) was performed on selected genes that represent the different pathways (see Additional files 1, 5 and 6) enriched by nutritional history in the brain or liver in order to confirm the significance of differential mRNA expression pattern observed in the microarray data. For all genes tested, despite some differences in the scale of differential expression, the expression pattern between microarray data and real time PCR data was congruent (Additional file 7).
A follow-up proteomic analysis could be interesting, especially in the liver, to have a better overview of the functional changes in hepatic metabolic processes due to nutritional programming. In this respect, it is encouraging that our results on cholesterol and carbohydrate metabolism compare favourably with proteome data from a previous study in trout  [9]. Additionally, candidate enzymatic studies, as in the case of protease regulation and xenobiotic metabolism, in both the 3-week fry and in the juvenile trout liver could help clarify the role of these enzymes in fish fed plant-ingredient rich feed. Overall, the present molecular dataset, complementary to our previous data on the positive effect of prior plantdiet feeding on its later acceptance (feed intake and feed utilisation efficiency) in trout  [34] , fortifies the notion that the period of transition from reliance on yolk to exogenous feeding is a critical window for nutritional programming in rainbow trout, and possibly in other teleosts.
Microarray hybridization, data acquisition and analysis Distinct RNA samples from trout swim-up fry exposed to diet M (n = 4 fry) or diet V (n = 3 fry) for 3 weeks, and whole brain (n = 4 samples) and whole liver (n = 4 samples) of juvenile trout with nutritional history of diet M or diet V after the 25 day V-challenge were used for labelling and hybridisation. For each sample, 150 ng of total RNA was amplified and labelled using Cy3-CTP according to the manufacturer's instructions (Agilent). Briefly, RNA was first reverse transcribed, using a polyDT T7 primer, Cy3 was then incorporated by a T7 polymerase mediated transcription and excess dye was removed using a RNeasy kit (Qiagen). The level of dye incorporation was evaluated using a spectrophotometer (Nanodrop ND1000, Lab-Tech). Yield (>0.
825 μg cRNA) and specific activity (>6pmol of Cy3 per μg of cRNA) of the Cy3-cRNA produced were checked with the Nanodrop ND1000 (LabTech). 600 ng of Cy3-cRNA was then fragmented in the appropriate buffer (Agilent) for 30 min at 60 °C and hybridized on a sub-array. Hybridisation was performed in a microarray hybridization oven (Agilent) for 17 h at 65 °C. The slides were then rinsed in gene expression wash buffers 1 and 2 (Agilent) and scanned with an Agilent scanner (Agilent DNA Microarray Scanner, Agilent Technologies, Massy, France) using the standard parameters for a gene expression 8x60K oligoarray (3 μm and 20 bits). Data were then obtained with the Agilent Feature Extraction software (10. 7. 1. 1) according to the appropriate GE protocol (GE1_107_Sep09). Arrays were normalised using scale normalization with GeneSpring software (version 12.