dataesr/scientific-paragraphs-categorization huggingface dataset:
Dietary and ruminal factors modify the ruminal biohydrogenation (RBH) of polyunsaturated fatty acids (FA), with duodenal FA flows being quantitatively and qualitatively different from FA intake. Using a meta-analysis approach from a database on duodenal flows of FA in ruminants, this study aimed to determine predictive equations for duodenal and absorbed flows of saturated FA, C18:1, C18:2 and C18:3 isomers, odd-and branched-chain FA (OBCFA), C20:5n-3, C22:5n-3 and C22:6n-3 and to quantify the effects of dietary and digestive factors on those equations. The database was divided into four subsets: forage, seed, vegetable oils or animal fats (oil/fat), and fish products (fish) subsets. Models of duodenal and absorbed FA flows were obtained through variance-covariance analysis. Effects of potential interfering factors (conservation mode and botanical families of forages, lipid source, technological processing of lipid supplements, diet composition and animal characteristics) were analysed.
Selection of publications The AGRum database (IDDN. FR. 001. 510032. 000. R. C. 2011. 000. 10300) has been previously described  (Glasser et al. , 2008; Schmidely et al. , 2008). Its update was performed with trials published between 2008 and 2014. The PRISMA diagram  (Moher et al. , 2009)  described the selection process of the peer-reviewed papers considered in this study (Supplementary Figure  S1 ). Publications were taken from the Web of Knowledge and Science Direct research platforms, using the keywords: ruminant, cow, ewe, goat, sheep, biohydrogenation, duodenal FA and digestion. Data with ruminal or postruminal infusion of nutrients were excluded. The database was then composed of 104 publications (Supplementary Material S1) reporting 167 experiments (N exp ) with a total of 437 treatments (N trt ).
The animal species are divided between bovine (N trt = 358) and ovine (N trt = 79). Dairy cows are the most studied animals among bovines (N trt = 202) followed by beef cattle (N trt = 156). The feedstuffs from the database were characterised according to the INRA (2010) feed tables based on their reported chemical composition on a dry matter (DM) basis for CP, NDF, starch, total FA and FA profile (Baumont et al. , 2007; Maxin et al. , 2013).
Coding Codes were assigned to each study according to the experimental factors studied and then four database subsets were created: forage, seed, vegetable oils or animal fats (oil/fat) and fish products (fish) subsets. In the forage subset, botanical families and their conservation mode (fresh or pasture, silage and hay) were coded as experimental factors, with all diets based only on one or several forages called forage diets (Supplementary Table  S1 ). In the seed and oil/fat subsets, the lipid source and their technological processing were coded as experimental factors, with two codes designated to each treatment according to lipid source and technological process. The fish subset was created for studies including fish products (oil and meal), with the lipid percentage in the diet (no lipid supplement v.
Duodenal OBCFA  (Fievez et al. , 2012)  flows that arise mainly from microbial synthesis in the rumen and isomers of C18:1, C18:2 and C18:3 flows were regressed against dietary data (e. g. concentrate, dietary starch and CP contents) or digestive parameters which may reflect or affect ruminal microbial activities, for example, rumen protein balance (RPB), CP microbial synthesis, efficiency of microbial protein synthesis (EMPS), organic matter truly digested in the rumen (OMDr), using the INRA model of feed and diet nutritive values  (Sauvant and Nozière, 2013)  implemented within the Sytool. fr. application  (Chapoutot et al. , 2015)  and ruminal pH and acetate/propionate (A/P) ratio measured in publications. Absorbed flow was calculated as the difference between duodenal flow and faecal flow or as the difference between ileal flow and faecal flow.
The models in equations (  1 ) and (2) were used to describe the relationships between duodenal FA (FA duo , g/kg DMI) and FA intake (FA int , g/kg DMI) and those between absorbed FA (FA abs , g/kg DMI) and FA duo. For absorbed FA models, the analysis included all experiments from the database without taking into account the separation into different subsets: FA duo;ij = β 0 + S i + β 1 + β i ð ÞÁFA int;ij + ε ij (1) FA abs;ij = β 0 + S i + β 1 + β i ð ÞÁFA duo;ij + ε ij (2) where i = experiment index and j = treatment index. β 0 is the overall intercept, S i the fixed effect of experiment i, β 1 the overall regression slope, β i the fixed effect of experiment i on the slope and ε ij the unexplained residual error. 3 )) was used for quantitative factors. For the forage subset, in addition of the previous approach, a global linear regression was performed including two variables, mode of conservation and forage families, and their interactions with the FA intake for duodenal FA flows prediction (equation (  4 )).
To study the pure effect of forage families, treatments consisting of a blend of legumes and grasses were not taken into account. The following model was used: yÀŷ ð Þ duo;j = β 0 + β 1 Á factor j + ε j (3) FA duo;j = β 0 + β 1 + FAM j + CM j À Á Á FA int;j + FAM j + CM j + ε j (4) where FAM and CM are forage families (Gramineae and Leguminosae) and conservation mode (fresh or pasture, silage and hay), respectively. β 0 is the overall intercept, β 1 the regression coefficient and ε ij the random residual error. All statistical analyses were performed with the software Minitab ® (version 17; State College, PA, USA). We considered P < 0. 05 to be statistically significant and P < 0. 10 to represent a trend. Model assessments. To evaluate the models, the coefficients of linear regressions between observed and predicted values were tested using a F-test in which the intercept was compared with 0 and the slope was compared with unity.
Discussion The separation of the database into different subsets was essential to highlight the FA digestion according to the nature of lipid supplements or forages. For the seed, oil/fat and fish subsets, the intra-experiment relationships were close to the  Predicting duodenal fatty acid flows from diets global ones, indicating that the prediction of these flows was probably not biased. For the forage subset, these relationships were sometimes different, probably because the conservation mode and forage families, were confounded with c9c12c15-C18:3 and c9c12-C18:2 intakes, respectively. Previous metaanalysis  (Glasser et al. , 2008; Schmidely et al. , 2008)  were compared with the present models for total FA, total C18:2, total C18:3 and c9c12-C18:2. Overall, the independent variables are the same between the previous models and those proposed in this study, with the exception of c9c12c15-C18:3 which was not calculated by  Glasser et al.
Acknowledgements The authors are grateful to  C. Gérard  and  B. Delord  that funded this meta-analysis study through Neovia and Limagrain brands, respectively, which are greatly acknowledged for their financial support to  Lucas de Ofeu Aguiar Prado CIFRE  scholarship. In addition, the authors would like to thank  Patrick Chapoutot  from  INRA-UMR0791 Mosar team  for granting us permission to work on the Systool model and its help on feedstuff characterisation.
Acknowledgments The authors are grateful to all the people who gave assistance in operating traps on several nights and surveys of hosts around the trapping sites. This study was partially funded by  EU  grant  FP7-613996  Vmerge and is catalogued by the  VMERGE Steering Committee as Vmerge027  (http://www. vmerge. eu). The contents of this publication are the sole responsibility of the authors and don't necessarily reflect the views of the  European Commission.
RNA sequencing analyses RNA sequencing (RNAseq) data were collected from the following databases: NCBI gene expression omnibus GSE99655 for data from Medicago, chives, and Nicotiana benthamiana as well as laser microdissected ARBs and IRM; extraradical mycelium (ERM) and germinating spores from DDBJ database DRA002591; Lotus japonicus and tomato from DDBJ database DRA005187. RNAseq data were analysed as described by  Zeng et al. (2018). Quantification was done using default setting in CLC GENOMICS WORKBENCH 10. 0. 1.
Data availability Genomic or coding sequences of AM-secreted LysM (SLM) proteins mentioned in this research can be retrieved in Genbank under the following accession nos. : RiSLM, XM_025315479; RcSLM, KU305772; RiSLM_A1, MN520639; RiSLM-1_A4, MN520643; RiSLM-2_A4, MN520642; RiSLM-3_A4, MN520 641; RiSLM-4_A4, MN520640; RiSLM_C2, MN520636; RiSLM_B3, MN520637; GmSLM, MN520644; GrSLM, MN520645.
Acknowledgements The authors declare no conflict of interest. We would like to thank  Natalia Requena  for providing the pYST-02 vector. TB and EL were supported by the  European Research Council  ( ERC-2011-AdG294790 ). SF and SC acknowledge the technical support of the MS and nuclear magnetic resonance facilities of ICMG (FR2607). JJB acknowledge the  F ed eration de Recherche Agrobiosciences ,  Interactions et Biodiversit e (FR 3450 ),  CNRS ,  Universit e de Toulouse, UPS, Castanet-Tolosan, France ,  INRA SPE Department , and the  IDEX 'UNITI' Universit e de Toulouse  ( GO-AHEAD  project) for their contributions to the funding of the Nanotemper Monolith NT. 115.
Statistical analyses The mortality results from the concentration-mortality bioassays were subjected to probit analyses using the software PoloPlus 2. 0  (LeOra software, 2006)  to allow the assessment of the imidacloprid toxicity to each aphid species, which also allowed the estimates of the LC5 and LC50 ' s. The toxicity curves were considered as significantly different when the confidence limits (95%) at their LC5 and LC50 values did not overlap  (Prabhaker et al. , 2011). The instantaneous rate of population growth (ri), a strong surrogate estimator of the intrinsic rate of population growth (rm)  (Stark and Banks 2003) , was calculated using the formula ri= [Ln(Nj /Ni )]/Dt, where Nj and Ni are the final and initial number of live insects (in each cage), respectively, and Dt is the duration of the experiment (i.
e. , 7 days). The following statistical analyses were performed using R version 3. 3. 3. After checking the assumptions of normality and homoscedasciticy, three-way analyses of variance using generalized linear model were carried out to test the impact of the initial aphid density (intra and interspecific competition) and the presence of insecticide on the final insect population and on the instantaneous rate of population growth (ri). The results of interspecific competition were subjected to regression analyses with initial insect density of both aphid species as independent variables and their final density and rate of population growth as dependent variables. The regressions models were obtained using the curve-fitting procedure of the software TableCurve 3D (Systat, San Jose, CA, USA).
Acknowledgements This study was financially supported by the  Modern Agro-industry Technology Research System  ( CARS-05 ). wheat. Pest Management Science. 2: 1141-1149. Zhao X. ,  Reitz S. R. , Yuan H. , Lei Z. ,  Paini D. R. , and Gao Y. (2017). Pesticide-mediated interspecific competition between local and invasive thrips pests. Sci. Rep. 7:  40512. DOI: 10. 1038/srep40512. Zhu Y. C. Yao J. ,  Adamczyk J. , and  Luttrell R. , (2017). Feeding toxicity and impact of imidacloprid formulation and mixtures with six representative pesticides at residue concentrations on honey bee physiology (Apis mellifera). PLoS ONE. 12: e0178421.
Currently, PADI-web collects disease information from Google News because of its international and multiple language coverage. We implemented machine learning techniques to identify the relevant disease information in texts (i. e. , location and date of an outbreak, affected hosts, their numbers and clinical signs). In order to train the model for Information Extraction (IE) from news articles, a corpus in English has been manually labeled by domain experts. This labeled corpus  (Rabatel et al. , 2017)  is presented in this data paper.
Subject area Epidemiological surveillance in agriculture More specific subject area Text-mining approaches for animal health surveillance In Natural Language Processing (NLP) domain: Disambiguation of locations based on spatial infor- mation (i. e. spatial coordinates). In Information Retrieval (IR) domain: As each document is labeled as relevant, related, or irrelevant, this dataset can be used for evaluating classification and/or clustering methods. In visualization domain: spatio-temporal visualization of data. In epidemiology domain: analysis of spatio-temporal information of exotic animal infectious diseases.
Experimental design, materials and methods The dataset was constructed by collecting all notification reports sent to the World Organization for Animal Health (OIE) from 2014 to 2015 and available on their web page. Each report has been automatically processed to get the name of the disease, the country, the date of the outbreak and the date of the notification. For each report, a query has been built on Google News, to retrieve news articles which were published between the reported outbreak's starting date and the date of notification, and such that the title contained both the disease and the country name. For each query, the top ten news articles have been collected (or all articles when the query returned less than ten results). The queries resulted in 532 distinct news articles (HTML web pages) and were processed with Readability [https://www.
Each candidate entity from a relevant article has been manually labeled (i. e. , correct/partial/incorrect) by two experts in epidemiology and health informatics (the first authors of this data paper). The labeled dataset was finally used to build a Support Vector Machine model in order to predict the relevance of each candidate in new documents. This model has been integrated into the PADI-web system. This dataset is an enriched version of the data that were used in PADI-web (the main difference being that partial candidate labels in PADI-web were all considered as correct) to obtain F-measure scores of 80% for locations, 83% for dates, 95% for diseases, 95% for hosts, and 85% for case numbers  [2].
Acknowledgements This work was funded by the  French Directorate General for Food (DGAL) , the  French Agricultural Research Centre for International Development (CIRAD) , and the  SONGES  project ( FEDER and Occitanie -France ). We thank  R. Lancelot  and  B. Dufour  for their expertise in epidemiological surveillance, and  S. Falala ,  A. Mercier ,  S. Valentin ,  J. de Goër de Hervé ,  D. Chavernac ,  B. Belot ,  C. Hemeury ,  M. Devaud , and  T. Filiol  for their contribution in the development of PADI-web. We also thank the members of the  French Epidemic Intelligence Team for International Monitoring of Animal Health (VSI team)  for their constructive comments during the development of PADI-web.
c PSII quantum yield (Φ PSII = (F M '-F S )/F M ') at increasing light intensities, whiskers and box plot shows the minimum, first quartile, median, average, third quartile and maximum of each dataset. d Non-photochemical quenching (NPQ = (F M -F M ')/F M ') after 1 min of exposure at different light intensities. These measures were performed with a Fluorcam (MF800 -PSI) with blue light LEDs (470 nm). Each value represents the average of a pot containing 2-3 plants. Error bars indicate ± SD (n = 3 biologically independent samples). Data points for the items b-d are available in Supplementary data 1 Loss of PGR6 affects the photoactive PQ pool. To address whether the defects in protein phosphorylation and state transitions are linked to a decrease in PQ availability, we compared the photosynthetic behaviour of pgr6 to that of sps2 (solanesyl phosphate synthase 2 mutant).
d The oxidised and reduced PQ amount was measured in leaf discs exposed either to 2min far-red light (5. 5μmol m -2 s -1 ) to fully oxidise the photoactive PQ pool or to 15 s saturating flash (2000μmol m -2 s -1 ) to fully reduce the photoactive PQ. The total photoactive PQ pool was calculated from the difference between these two conditions. Average values are reported as PQ nmoles cm into the ETC. It thus provides quantitative data on all the ETC electron acceptors, including the PSII internal electron acceptors (Q A and Pheophytin), the plastocyanin downstream of the cytochrome b 6 f complex and the PQ connected to PSII (the photochemically active pool). Using this approach, we found that the ETC electron capacity is not different between pgr6 and wild type when plants were grown under moderate light.
Statistics and reproducibility. The sample size was determined empirically for each experiment (minimum of three independent organism and two experimental replicates), on the basis of experience with similar assays and from sample sizes generally used by other investigators. No data were excluded from the analysis. The experiment were replicated at least two times, the results were reproducible when the plants were not stressed before the experiment. When testing light condition, the position of the plants of different genotypes was changed randomly in order to reduce any possible positioning effect. The data were compared for statistical difference by a two-tailed, heteroscedastic Student's t test (Excel 2016). Reporting Summary. Further information on research design is available in the Nature Research Reporting Summary linked to this article.
Acknowledgements This work was supported by the  Swiss National Science Foundation (SNSF)  grants  31003A_156998  and  31003A_176191. G. F. acknowledges funding by the  HFSP   RGP0052  project and the  INRA AAP  project  PURIST funds form the GRAL  ( ANR-10-LABX-49-01 ) labex. We thank  Prof. Goldschmidt-Clermont  for his helpful discussion and support during the project.
Western Blotting Total protein concentration in cell lysates was determined by Bradford Coomassie brilliant blue assay (Sigma-Aldrich). Equal amounts of cellular proteins were resolved in SDS polyacrylamide gel electrophoresis (SDS-PAGE) and transferred to a PVDF membrane (GE Healthcare). Membranes were first saturated in TBS solution containing 5% non-fat milk and 0. 1% Tween20, and then incubated with specific primary and secondary antibodies. Anti-β-tubulin was used as loading control. Bound antibodies were revealed using ECL prime western blotting detection reagent (GE Healthcare), according to the manufacturer's instructions. Densitometry analysis of western blot protein bands was performed using the GelQuant. NET software provided by http://biochemlabsolutions. com.
The luciferase activity was restored by the rescue of TRAF3 expression in transfected TRAF3-KO  FIGURE 1 | Continued (C) HEK293T (WT) and TRAF3-KO cells were lysed and immunoblot analysis was performed to compare the levels of endogenous IκB. The amount of IκB was measured relative to the amount of β-tubulin. (D) HEK293T (WT) and TRAF3-KO cells were stained with anti-p65 (green signal) primary antibody. Nuclei were stained with DAPI (blue signal). Scalebar, 10 µm. Total cells and nuclei of cells (n = 10) indicated by a number from 1 to 10 in white were delineated using ImageJ software, and the mean brightness ratio of the nuclear RelA/p65 staining was calculated and presented as box-plot. (E) Immunoblot analysis of p100/p52 proteins expression levels in HEK293T (WT) and TRAF3-KO cells. (F) HEK293T (WT) and TRAF3-KO cells were transfected with phRG-TK renilla vector, NF-κB-luciferase reporter and p65, Tax-1, Tax-2, or TRAF3 expression plasmids.
Cell lysates were collected and luciferase levels were measured. Immunoblot analysis was performed to detect of TRAF3, p65, Tax-1 and Tax-2 (N. S. = not significant). (G) RNA from HEK293T (WT) and TRAF3-KO cells were analyzed by qRT-PCR for NF-κB-related transcripts. The values were normalized to RPLP0 and the results were expressed as relative fold change of expression levels. (H) HEK293T (WT) and TRAF3-KO cells were transfected with Tax-1 encoding vector and stained with anti-p65 (green signal) and anti-Tax-1 (red signal) primary antibody. Nuclei were stained with DAPI (blue signal). Total cells and nuclei were delineated using ImageJ software, and the mean brightness ratio of the nuclear p65 staining was calculated (right panel). Scalebar, 10 µm. P < 0. 05 ( * ) and P < 0. 01 ( * * ). cells (Figure  1B ).
(E,F) HEK293T cells were transfected with p65 or p52, Flag-APH-2, or Flag-HBZ expression vectors. Tagged proteins were immunoprecipitated with an anti-Flag antibody and the presence of the p65 or p52 proteins was examined by western blot. (G) Jurkat cells were transfected with VSV-APH-2 and Tax-2 expression vectors. Samples were stained with anti-VSV, anti-Tax-2 and anti-p65 primary antibodies to detect APH-2 (green signal), Tax-2 (red signal), and endogenous p65 (magenta signal), respectively. Total cells and nuclei were delineated using ImageJ software, and the mean brightness ratio of the nuclear p65 staining was calculated (right panel). Values obtained in non-transfected cells were then subtracted from those for APH-2, Tax or APH-2+Tax-expressing cells. Scalebar, 10 µm. (H) TNF-α expression was analyzed by qRT-PCR from RNA of HEK293T cells transfected with VSV-APH-2 and Tax-2.
The study was conducted as part of a research grant awarded by the German Research Foundation (DFG; www. dfg. de) to ASG (grant identifier: GO 1107/4-1). The DFG's board of ethics passed the research proposal that underlies the present study. Additional approval by other ethics committees (e. g. , from universities) are not required by projects funded by DFG. After reading the short description of the purpose of the study (see Section 2. 2. ) all participants gave their written informed consent on line, in accordance with DFG's board of ethics. The investigation was carried out in accordance with the latest version of the Declaration of Helsinki  [23].
Acknowledgements We thank  Nikolay Ouzounov  and  Zemer Gitai  for strains  NO34 ,  NO53 ,  Natasha Ruiz  for strain  NR693 ,  Suckjoon Jun  for plasmid pDB192,  Richard Wheeler  and  Ivo Boneca  for help with measuring mDAP incorporation,  Waldemar Vollmer  for the suggestion to digest sacculi with lysozyme, and  Piernicola Spinicelli  for technical support on phase microscopy. This work was supported by the  European Research Council (ERC)  under the Europe Union's  Horizon 2020 research and innovation program  [Grant Agreement No. (679980)], the  French Government 's  Investissement d'Avenir program Laboratoire d'Excellence "Integrative Biology of Emerging Infectious Diseases"  ( ANR-10-LABX-62-IBEID ), the  Mairie de Paris "Emergence(s) "  program , and the  Volkswagen Foundation.
Discussion The fruticose lichen U. taylorii (Parmeliaceae), found in nutrient-poor environments, was expected to be increasingly grazed by the snail N. hookeri, after acetone rinsing. Indeed,  Gauslaa (2005)  evidenced that acetone-rinsed lichens belonging to Parmeliaceae, rich in specialised metabolites, were more palatable to generalist land snails. Contrary to our expectation snails were equally distributed between rinsed and intact thalli in the four arms of the feeding choice arenas. Most of the snails were counted on the rocks in the two other arms, suggesting that U. taylorii could not be a resting place after feeding. Although information about lichen choice was lost because 68% of the snails preferred the rocks, simulations made from the real data set confirmed that absence of difference was not a bias due to a very low power of the test (Table  S2 ).