dataesr/scientific-paragraphs-categorization huggingface dataset:
Data sources and searches A systematic search of three bibliographic databases [MEDLINE (http://www. ncbi. nlm. nih. gov/pubmed), Cochrane Central Register of Controlled Trials and Cochrane Database of Systematic Reviews (http://www. thecochranelibrary. com)] was performed covering the period from January 1 st 1993 to March 4 th 2015, by using the following search strategy: whole grainrelated key words [e. g. , "whole(-)cereal(s)" OR "whole(-)grains" OR individual cereal names such as "wheat" OR "rye"] were combined with key words related to the health outcomes of interest, namely, overall mortality, obesity, cardiovascular diseases, T2D and associated risk factors [e. g. , "overall mortality" OR "obesity" OR "body weight" OR "cardio(-)vascular" OR "blood cholesterol" OR "diabetes" OR "insulin sensitivity"] (see S1 Fig).
Data extraction Data were extracted by three PhD (ACR, AM and VB) by using a predefined data template. Disagreements were resolved through discussion. Extracted data were as shown in column headings of Table  1. Furthermore, the following data were extracted, when available, for each category of whole grain intake: daily intake of whole grains (median, range or mean), number of subjects, occurrence of T2D (number of cases), number of person-years (total cumulative follow up), age (mean), sex (% males). The three reviewers independently evaluated the individual studies regarding the appropriateness of the sample size, of the description of inclusion and exclusion criteria and of baseline characteristics of the subjects, and of the methods used to address potential sources of bias and to adjust for the effects of potential confounding variables.
Information on declaration of conflict of interest or identification of funding sources was also collected for individual studies. For the meta-analysis, all data on whole grain intakes were standardized in g/d of whole grain ingredients. Therefore, whole grain intakes which were given in amounts of whole grain foods in original publications were computed by assuming that one serving of whole grain foods was equivalent to 30 g, and that whole grain foods contained on average 51% of whole grain ingredients. The latter assumption was based on the FDA whole grain claim  [11]. We were conscious that this assumption might be seen as a minimalist approach as many of the most consumed whole grain foods may contain more than 51% of whole grain ingredients  [13]. However, regarding our ultimate objective of deriving a quantitative recommendation of whole grain intake for the population, we were concerned that it would be preferable to slightly underestimate the amount of whole grain which is associated to a beneficial health effect, leading to a slight overestimation of a possible recommendation, rather than the opposite, which may lead to abusively promote whole grain amounts which might be too low to elicit favorable health effects.
Such recommendations should be complemented with data on the quantitative relationship between whole grain intakes and other health outcomes, such as the risk of cardiovascular diseases, obesity or overall mortality, for which similar analyses are ongoing. Finally, in setting up a quantitative recommendation for whole grain consumption, stakeholders should also provide consumers with clear labeling of whole grain foods and, more generally, with effective means of following recommendations. effect-size for each study and by computing the Kendall's rank correlation test statistic (Kendall's tau) between the standardized effect size and the standard errors of these effects. (PPTX) S1 Protocol. Protocol of the systematic review as published on the PROSPERO register. (PDF) S1 Table. List of the 210 articles selected for full text evaluation.
Eosinophil isolation First, granulocytes were isolated by density-gradient centrifugation over Histopaque 1077 and Histopaque 1119 (Sigma Aldrich). Residual erythrocytes were lysed by Versalyse (Beckman Coulter). The granulocyte suspension was stained with anti-CD45-PC7, CD24-PE and CD16-PC5 (Beckman Coulter). Eosinophils were sorted from the granulocyte suspension by FACSAria (BD Biosciences) based on FSC and SSC characteristics, CD45 and CD24 expression and lack of CD16 expression. All steps were performed on ice. Eosinophil viability after FACS sorting was assessed by trypan blue exclusion (>90%) and purity (>99%) was assessed by FACS (data not shown) and cytospin (Fig  1B ). Cells were stored in the lysis buffer (see below) at -80°C until batch RNA extraction.
Raw. tiff images were then extracted using Agilent "Feature Extraction, version 10. 10. 1. 1" following "GE2_1010_Sep10" protocol. Median raw expression values were further normalized by quantile method  [14]. Differentially expressed (DE) genes were selected using the fold change (FC) based method proposed by Dembélé et al  [15]. This method proceeds as follows: using pair of samples from two biological conditions, FCs are computed for all the genes. These FCs are sorted in increasing order and their ranks are associated to genes. This is repeated with all the pair of samples in the dataset. An average rank is computed and used as statistic leading to p-values for genes. Finally a threshold (0. 01) is used to select significant genes. Importantly, there is no multiple comparison issue(s) with this method.
After an initial denaturation step at 96°C for 10 min, the cycling conditions were 95°C for 10 s/60°C for 30 s, using a Rotor-Gene™ 6000 real-time PCR machine (Corbett Life Science). Amplification products were detected as an increased fluorescent signal of SYBR 1 Green during the amplification cycles. Results were obtained using Rotor-Gene 6000 Series Software and evaluated using Excel (Microsoft). Melting-curve analysis was performed to assess the specificity of PCR products. Results were normalized to β-actin levels. The RT-qPCR results are presented as means and standard error of the mean (SEM). Differences in the expression of mRNA were determined by using a two-tailed non parametric Mann-Whitney test with the GraphPad Prism 6 software. P values <0. 05 were considered as significant.
To get a broader view of these differentially expressed genes, gene ontology analysis was performed using the DAVID database (Database for Annotation, Visualization and Integrated Discovery)  [22]. The statistically significant (p<0. 01) functional categories (filtered to exhibit at least 10% concordance), which were enriched, are predominantly related to response to stimuli (i. e. , external, organic, biotic, chemical), homeostatic processes, response to wounding and inflammatory responses (Table  3 ). Incidentally, this analysis also reveals a linkage between this set of genes and asthma (p = 0. 006) among few other diseases in this list (Table  3 ). The above described microarray observations were validated by quantitative RT-PCR (RT-qPCR) for 8 of the 47 differentially expressed genes.
Acknowledgments We thank  Violaine Alunni  ( IGBMC, Plateforme «Biopuces et Séquençage» ) for her expertise in microarray experiments and  Drs. Philippe Kastner  and  Antoine Magnan  for critical reading of this manuscript. This work was funded by institutional grants from the  Institut National pour la Santé et de la Recherche Médicale (INSERM).
Design and study population Cross-sectional surveys were identified from 13 different countries to summarize country-specific TFI of participants aged 4-18 years. The surveys (whose aim was to systematically obtain a complete set of data from fluid intake) were conducted during one period of the year in Latin America (Mexico, Brazil, Argentina, Uruguay), Europe (Spain, France, Belgium, UK, Poland, Turkey) and Asia (Iran, China, Indonesia) by private research organizations, the Université libre de Bruxelles/the Club Européen des Diététiciens de l'Enfance (CEDE), the Iranian National Nutrition & Food Technology Research Institute (NNFTRI) and the Chinese Center for Disease Control (CDC). The individual surveys took place between 2008 and 2014 (Online Resource 1). The protocol of the published surveys was described in detail elsewhere  [13, 14, 25] , but will again briefly be described.
The parents of the recruited school children were informed via meetings, written information sheets or phone calls. The surveys performed in the 10 other countries randomly recruited participants using a quota-based method with quotas set for age, gender, region of the country, habitat and/or socio-economic characteristics. The parents of the children were contacted via a database of individuals volunteering for population surveys or via a systematic doorto-door approach, with an invitation for their child to participate. Having a parent working in advertising, marketing, market research, media or manufacture, distribution and sale of beverages (in order to have participants that were not specifically aware of their fluid intake) and being incapable of completing the questionnaire in the language presented were exclusion criteria.
Assessment of body composition and socio-economical level Body mass index (BMI) serves as a proxy for both low physical activity and poor health status, two key determinants of water requirements. Height in metres (m) and weight in kilograms (kg) were self-reported in the surveys in Spain, France, UK and Turkey and measured by the investigator in the surveys in Belgium, Poland, Iran and China. No anthropometric data were collected in Mexico, Brazil, Uruguay, Argentina and Indonesia. Body mass index (BMI) was calculated (kg/m 2 ) and categorized using the International Obesity Task Force cutoff points  [8, 9]. These cut-off points were established according to thinness, sex and age (i. e. male, 8 years, BMI 14. 14 kg/m 2 or lower = underweight; male, 8 years, BMI = 14. 15-18. 43 kg/m 2 = normal weight; male, 8 years, BMI = 18.
To estimate the strength of the association, odds ratios and 95 % confidence intervals (CI) were assessed using age-or gender-stratified forest plots. The models were adjusted for gender, BMI and SEL. Males were considered as reference in the first model (Fig. 2 ). Indonesia, Mexico, Argentina, Brazil and Uruguay were excluded from the logistic regression analysis due to the lack of data for some covariates. Analyses were performed using SPSS software version 20. 0 (SPSS Inc, Chicago, IL). All statistical tests were twotailed, and the significance level was set at p < 0. 05.
Sample description The general characteristics of both male and female subjects are presented by country in Tables  1  and 2. A total of 5766 males (11. 2 ± 3. 3 years) and 6333 females (11. 4 ± 3. 3 years) were included in this study. In only 8 out of 13 countries, anthropometric data were obtained, and consequently the BMI of only 3934 males and 4498 females was calculated, and 64. 5 % males and 67. 8 % females of these were classified as normal weight. Medium socio-economic class was the most common SEL (44. 0 % males and 47. 0 % females). China contributed the highest number of males to the total male study sample (Table  1 ) (n = 2705, 47 % of total male study sample) and the lowest Turkey (n = 67, 1 % of total male sample). The youngest females were from France (8. 9 ± 3. 4 years) and the oldest were from Iran (13.
Uruguay (<20 %) and Brazil (<40 %) had the lowest percentages of non-adherents to EFSA AIs for fluids. Together with Argentina, Turkey and Indonesia, Uruguay had the highest mean fluid intakes, similar to the values observed in a previous study in Brazil  [18]. One of the plausible explanations for this finding could be the high humidity and temperatures in these countries, which result in people drinking more  [30]. This raises one of the limitations of present analysis of cross-sectional surveys. The fact that the surveys were performed in the same period of the year, and therefore the impact of the seasons on TFI was neglected. Nevertheless, the data collection was performed during the spring or autumn, periods expected to have a mild climate. The impact of climate on TFI should be investigated by recording the temperature and humidity in future surveys and considered in analyses.
Acknowledgments Data collection was performed by the  Center of Disease Control in China ; the  National Nutrition and Food Technology Research Institute in Iran ; the  School of Public Health, Université Libre de Bruxelles  and the  Club Européen des Diététiciens de l'Enfance in Belgium. We acknowledge  Christine Jean , Market Research & Consumer  Intelligence Danone Waters  and the entire  MRCI Team  to raise the methodology of fluid intake surveys to the current standard and to guide  IPSOS in Mexico, UK  and  Turkey ;  TNS in Argentina, France, Germany ,  Poland  and  Spain ;  Nielsen in Indonesia ; and  GFK in Brazil  and Uruguay, with the preparation of the survey.
The revelation was processed with the Vector Red Alkaline Phosphatase Substrate Kit (SK-5100, Vector), and nuclei were counterstained with hematoxylin. To analyze matrix accumulation, a Masson trichrome stain using hematoxylin (nuclear staining), ponceau fuchsin (cytoplasm staining) and anyline blue (collagen staining) was performed on lungs sections. The infiltration of macrophages was evaluated by immunostaining using a mouse monoclonal anti-CD68 antibody (MCA341R, AbDserotec, Colmar, France) revealed by a 594-Alexa fluor anti-mouse secondary antibody. Smooth muscle fibers were stained with a mouse monoclonal anti-α-Smooth Muscle Actin (SMA) FITC conjugated antibody (F3777, Sigma-Aldrich). Nuclei were stained with DAPI. At the end of the procedure, all stainings were analyzed with an epifluorescence microscope and NiS element software (Nikon 80i, Japan).
PA-SMCs apoptosis detection Apoptosis of PA-SMCs was evaluated by immunostaining with TUNEL (TdT-mediated dUTP Nick-End Labeling) assays. Briefly, paraformaldehyde-fixed cells grown on coverslips were incubated with TUNEL reaction mixture in a humidified atmosphere for 1 hour at 37°C in the dark according to the manufacturer's instructions (DeadEnd TUNEL System, Promega, Madison, USA). Cells on coverslips were then counterstained with DAPI and examined with an epifluorescence microscope and NiS element software (Nikon 80i, Japan). Quantification of TUNEL positives cells were performed with 4 images per coverslips.
Statistics Statistics were performed on GraphPad Prism 5 software and data are expressed as means ± SEM. Gaussian distributions of values were tested with adequate normality tests. Data that followed Gaussian distribution were analyzed with parametric tests, such as ANOVA associated with Dunnett post-tests to compare three or more groups to the control group and ttests to compare two groups. Tukey post-tests were performed for statistical comparisons of the three treated groups in the study evaluating the effect of PFT on rat PH development. Matched ANOVA or paired t-tests were used when values are paired. Data that did not follow Gaussian distribution were analyzed with non parametric tests (Mann-Whitney tests).
This work was supported by grants from the  Agence National de la Recherche  ( ANR-08-GENOPAT-004  to S. E. , A. L. -V. and M. H. ),  Leg Poix  ( Chancellerie de Paris ) and  CORDDIM (Domaine d'Intérêt Majeur: Cardiovasculaire Obésité Rein Diabète ,  Region Ile de France). The " Telomeres and Cancer" laboratory is a team labeled  " Ligue Contre le Cancer ". The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Method Design and data analysis An A-B design  (Barlow & Hersen, 1984)  with follow-up was implemented. During the baseline period, two therapists 1 (AH and CB) met the client once in order to administer and collect the baseline measurements. Following the baseline, the same two therapists delivered the mindfulness training over an eight-week period. After the treatment, outcomes were assessed. Finally, the client returned to the clinical center six-month after the final training session for follow-up assessment. The statistical recommendations for singlecase design of Crawford, Garthwaite, and Porter (2010) were followed. A statistical Bayesian approach was used. There has been an explosion of interest in Bayesian statistical methods over the last decades (e. g. ,  Heeren, Maurage, & Philippot, 2013).
It estimates the probability that, according to a random selection, any individual of the 15 normative control participants would exhibit a larger difference than the single case, in either direction. Second, the Bayesian point estimate and 95% confidence interval for the abnormality of the case's score are reported. The point estimate of the abnormality of the case's score is the Bayesian estimated percentage of the normative sample that would obtain a score lower/higher than the case and the interval estimate quantifies the uncertainty over this percentage  (Crawford, Garthwaite, & Howell, 2009). Data analyses were performed using SingleBayes_ES. exe (Crawford et al. , 2010). This program implements Bayesian methods for comparison of a single case's score to scores obtained in a normative sample.
Similar structures are widely used for SERS and SPR biosensors, and the HLP mode can help to increase the sensitivity of such detection systems. Other modes, such as the BM, can prove to be useful to confine the electromagnetic field at nanometric scales around metallic nanoparticles. Thus, the proposed analytical model can help to optimize such structures for various applications. Acknowledgements. This work is supported by the IDI 2012 project funded by the IDEX Paris-Saclay (ANR-11-IDEX-003-02), ANR P2N (ANR-12-NANO-0016), CNANO IDF as well as LUMAT for partial funding of the project. IOGS/CNRS is also part of the European Network of Excellence in BioPhotonics: Photonics for Life (P4L).
The in-house code developed in Matlab for this work, calculates the S-matrix (or related matrices that relates the electromagnetic fields at different slices along z-axis as shown in Figure  1 ) using FEM for the nanostructured section of the geometry. Then, using the matrix formulation of FMM, we can relate the fields calculated around the nano-structures, to the far-field transmission (T) and reflection (R) of the complete array. The absorption (A) of the system was also calculated as a function of incident frequency (ω) and in-plane wave-vector (k x ). This hybrid method can give accurate results, which have been verified by experiments here and in our recent publications. Nanostructure fabrication. The gold nanocylinder array was fabricated by electron beam lithography to assure homogeneity, and have stable control of the size and shape of nanostructures over a large area (500 × 500 µm 2 ).
This observation confirms the enrichment of LDs in the floating fraction. Anti-GFP antibodies reacted against both purified LD proteins and the total protein extract, confirming the presence of GFP-Ypt7p on LDs. Mass-spectrometry analysis of purified LDs from the GFP-YPT7/ERG6-RFP strain identified 151 associated proteins (Table  2  for a sub-set of the proteins identified based on their involvement in LD dynamics (lipid metabolism, trafficking proteins) and ion transport, and supplementary material Table  S1  for the complete list) classified into ten groups based on function using the Saccharomyces Genome Database SGB (http://www. yeastgenome. org/) (Fig. 3C ). We identified many proteins (19%) involved in lipid anabolism as previously described  (Goodman, 2009). This suggests that LDs function as a cellular site for lipid synthesis or are involved in lipid mobilization, in addition to lipid storage  (Athenstaedt et al.
Control of the experiment was done by epifluorescence analysis of the cells incubated with BCECF-AM 490/455, a vacuole marker, before ConA or DMSO treatment. Error bars: mean/s. d. and "kiss-and-run"-like mechanism. These recent results obtained in mammals on the role of Rab7 in LD multiple fusion processes reinforce the data we obtained on the role of Ypt7 on LD dynamics in yeast. Proteomic analysis showed that three subunits from the peripheral V1 domain of the V-ATPase were associated to LDs. Moreover, Vma13p, the H subunit of the peripheral V1 domain of the V-ATPase, was identified by Co-IP experiments as a potential Ypt7p partner on LDs. These results lead us to focus on the V-ATPase. Functional validation through biochemical and microscopic studies of a vma13Δ mutant demonstrated that the deletion of VMA13 gene modifies the total FA content and the number of LDs.
Transmission electron microscopy Cells (∼10 A 600 nm U or 5 mg dry weight) were treated as previously described  (Froissard et al. , 2009). Thin sections (70 nm) were cut, stained with lead citrate and examined in a Zeiss EM902 TEM at 80 kV. TEM observations were made with a Zeiss EM902 transmission electron microscope, micrographs were acquired using a MegaView III CCD camera and analyzed with ITEM software (Eloise SARL, France).
Sub-set of the proteins identified in the S. cerevisiae LD proteome associated with LD dynamics and ion transport (the complete list of proteins is shown in supplementary material TableS1)LDs were isolated from cells grown in Low C/N YNB medium and collected at the exponential phase. Proteins were identified by at least two different peptides. Database used: Saccharomyces Genome Database (SGB) (http://www. yeastgenome. org/). ACT, actin cortical patch; Cm, cytoplasm; Ct, cytosol; E, endosome; ER, endoplasmic reticulum; G, golgi; IntM, integral to membrane; LD, lipid body or Lipid Droplet; M, mitochondria; N, nucleus; P, peroxysome; PM, plasma membrane; V, vacuole; Ve, vesicule. Only the major functions and localizations are described for each protein.
Acknowledgements We are grateful to  C. Ungermann  ( University of Osnabruck, Department of Biology/Chemistry, Osnabruck, Germany ) for the kind gift of the GFP-MYC-YPT7 strain,  H. Riezman  ( University of Geneva, Geneva, Switzerland ) for the kind gift of Gas1 antibodies and  R. Haguenauer Tsapis  ( Institut Jacques Monod, Paris, France ) for the kind gift of p416ADH-GFP plasmid. We thank  C. Longin  and  S. Chat  ( Plateau de microscopie eĺectronique MIMA2, INRA, Jouy-en-Josas, France ) for electron microscopy,  O. Grandjean  ( Observatoire du Veǵetal, IJPB, INRA, Versailles, France ) for confocal microscopy,  C. Boulard  for proteomics data and  P. Jolivet  for fruitful scientific discussions.
To calculate the spin and orbital angular momentum for specific k-points, we used the LCPAO coefficients of local atoms. 1120296), and the Office of Naval Research (Grant No. N00014-12-1-0791). PDCK acknowledges support from the Royal Society through a University Research Fellowship. HIW acknowledges support from the NSF IGERT program (DGE-0903653) and the National Science Foundation Graduate Research Fellowship under Grant no. DGE-1144153. We acknowledge SOLEIL for provision of synchrotron radiation facilities (CASSIOPEE beamlime) and also thank Diamond Light Source for access to beamline I05 (proposal number SI9427) that contributed to the results presented here. We thus assign all eight Fermi crossings as arising from two-dimensional subband states formed within a near-surface quantum well arising from the downward band bending potential at the Te-terminated surface.
ACKNOWLEDGEMENTS We acknowledge  M. S. Bahramy  for useful discussions. This work was supported by the  Engineering and Physical Sciences Research Council, UK  (Grant Nos. EP/I031014/1 ,  EP/M023427/1  and  EP/G03673X/1 ), the  Ministry of Science and Technology in Taiwan  (project number  MOST-102-2119-M-002 -004 ),  TRF-SUT  Grant  RSA5680052 , the  National Science Foundation  (Grant Nos. DMR-0847385  and DMR-.