dataesr/scientific-paragraphs-categorization huggingface dataset:
Electrophoresis, immunoblotting and quantification Samples were analysed by SDS-PAGE using 12% gels according to Laemmli, except that the sample buffer contained 10 mM EDTA. Gels were stained, destained and processed for fluorography as previously described  [20]. Immunoblotting was as described in Le Parc et al. [15]. The intensity of the ECL signal for relevant protein bands or the amounts of [ 3 H]leucine-labelled caseins were quantified from X-ray film scans (300 dpi) using the ImageJ software (Wayne Rasband, NIH, USA, http://rsb. info. nih. gov/ij/). The background noise was estimated in the proximal area of the film and subtracted from the integrated density of the protein band. For PDI and ERLIN2, ECL signal was digitalised using ImageQuant LAS 4000 from GE Healthcare Life Sciences.
Electron microscopy Tissues were fixed with 2% glutaraldehyde in 0. 1 M Na cacodylate buffer pH 7. 2, for 3 hours at room temperature. Samples were then postfixed with 1% osmium tetroxide containing 1. 5% potassium cyanoferrate, gradually dehydrated in ethanol (30% to 100%) and embedded in Epon (Delta Microscopy, Labege, France). Thin sections (70 nm) were collected onto 200 mesh cooper paladium grids, and counterstained with lead citrate before examination with a Zeiss EM 902 transmission electron microscope at 80 KV (MIMA2 -UR 1196 Genomique et Physiologie de la Lactation, INRA, plateau de Microscopie Electronique, 78352 Jouy-en-Josas, France). Microphotographies were acquired using MegaView III CCD camera and analysed with the ITEM software (Eloi ¨se SARL, Roissy CDG, France).
Acknowledgments We are indebted to  P. Dahirel  ( Nutrition et Regulation Lipidique des Fonctions Cerebrales, INRA, Jouy-en-Josas, France ) for supervision of rat care. We greatly acknowledge the  INRA MIMA2 core facility  for expertise and help in electron microscopy analysis. We are grateful to  Dr. F. Le Provost  ( INRA, Jouy-en-Josas, France ) for critical reading of the manuscript.
Fig. S5  shows that strings do not coalign with microtubules and are impervious to short-term action of nocodazole or cytochalasin Videos 1-4 display time-lapse microscopy of PrP Sc strings and of PrP C on the surface of live GT1 and ScGT1 cells. Online supplemental material is available at http://www. jcb. org/cgi/content/full/jcb. 201308028/DC1. Additional data are available in the JCB DataViewer at http://dx. doi. org/10. 1083/jcb. 201308028. dv. Tissue and cell processing for cryosectioning Animals and preparation of tissue. Prion-infected and control brain tissues were provided by H. Wille and S. B. Prusiner (University of California, San Francisco, San Francisco, CA). Wild-type FVB mice were injected intracerebrally with 30 µl of 1% brain homogenate from mice infected with RML prions or from normal mice as controls.
The blocks were then allowed to cool slowly (20 min) and rinsed with PBS before transfer into sucrose solution. Immunofluorescence labeling of cryosections. Cryosections were rinsed twice with PBS and five times for 3 min with PBSG. Non-specific Ab binding was then blocked with PBSG containing 0. 5% cold fish gelatin and 0. 1% BSA (gel + BSA) for 15 min. Sections were incubated with 1 µg/ml SAF32 in PBS containing gel + BSA for 1 h at RT. Slides were rinsed five times for 3 min with PBSG before incubating for 30 min with Alexa 488-conjugated goat anti-mouse IgG (Invitrogen) in PBS containing gel + BSA. Sections were washed five times for 3 min with PBSG and then mounted in Vectashield (Vector Laboratories) containing 2 µg/ml DAPI. Images were made using an AxioObserver Z1 inverted microscope (Carl Zeiss), equipped with an ORCA AF Black and White CCD camera (Hamamatsu Photonics) and axiovision software (Carl Zeiss), which adds false colors to the images.
Feinstein-Rotkopf  ( Core facility ,  Faculty of Medicine, HUJI ) for their help with the TEM and confocal microscopy. This work was supported in part by a  USAID American Schools and Hospitals Abroad  grant for the procurement of an LSM710 confocal microscope at the  Faculty of Medicine (HUJI). This study was supported by grants from the  Israel Science Foundation  (to A. Taraboulos), the  US-Israel Binational Science Foundation  (to  G. A. Carlson  and  A. Taraboulos) ,  European Commision FP7  project No. 222887   PRIORITY  (to  C. Korth ,  P. J. Peters ,  K. Kristensson , and  A. Taraboulos ), and the  Horwitz Foundation  (to A. Taraboulos). S. Karniely was supported by a  Valazzi-Pikovski Fellowship  for postdoctoral researchers. C. Korth was supported by the  Joint Programme for Neurodegenerative Disease Research DEMTEST  ( BMBF 01ED1201B ).
ACKNOWLEDGMENTS We thank  R. L ührmann  for the gift of HeLa cell extracts and antibodies,  C. H. Hagedorn  for the pGST-eIF4E plasmid,  A. Schweigert  for technical assistance,  E. Westhof  for invaluable input and constant support,  P. Carbon  and  G. Eriani  for helpful discussions and critical reading of the manuscript and  J. Steitz  for useful comments and critical reading of the manuscript. Authors contributions: L. W, A. S. G. B. , C. V. , A. K. , E. B. and C. A. designed research. A. S. G. B. , L. W. , C. V. , M. L. , A. T. , S. B. , F. M. and C. A. performed research. L. W. , A. S. G. B. , C. V. , F. M. , A. K. , E. B. and C. A. analyzed data. C. A. wrote the paper.
FUNDING Centre national de la recherche scientifique (CNRS);  Agence Nationale de la Recherche  [ BLAN06-2 134682 ,  ANR-2011-svse8 02501  to F. M. ]. French Ministry of Research and the National Research Fund, Luxembourg  [to L. W. ]; Contract Doctoral of the  University of Strasbourg  [A. S. G. ]. Funding for open access charge: CNRS.
Sequences were compared with those available in GenBank database using basic local alignment search tool (BLAST). Seven of 35 (20%) pairs yielded a PCR product with the stool specimen as did control A. castellanii DNA. The analysis of 348 clones identified 28 eukaryotic species consisting of 17 (61%) Viridiplantae species, eight (29%) fungi S. cerevisiae, P. solitum, C. bruhnei, C. capitatum, Sclerotium sp. , M. pachydermatis, M. restricta and M. globosa; two metazoa M. trossulus and M. galloprovincialis and one protozoan Tetratrichomonas spp. (Table  2 ). Original sequences here reported have been deposited in GenBank database with accession numbers from JX132667 to JX133078. In addition, one gram of stool was diluted in 9 mL sterile phosphate-buffered saline and then spread in duplicate on potato dextrose agar (PDA) (Sigma-Aldrich, Saint-Quentin Fallavier, France), Czapeck dox agar (Sigma-Aldrich) supplemented with 0.
Discussion Mycological data were certified since negative controls introduced in both PCR-and culture-based observations remained negative. Moreover, four fungi were detected by culture as well as by PCR-sequencing. Combining two methods, a total of ten different fungal species were detected, including S. cerevisiae, A. flavus, M. pachydermatis, M. globosa and M. restricta previously detected in the stools of healthy individuals and patients; as well as C. capitatum and Sclerotium sp. previously detected in intestinal biopsy from inflammatory bowel disease  [1]. A. ruber, P. solitum, C. bruhnei and Tetratrichomonas sp. have not been previously detected in human stool, although Tetratrichomonas sp. has been previously found in the oral cavity and respiratory tract. These organisms have no known pathogenicity in the human gut.
1% Tween ® 20 and 1% skim milk (Ctr1, ATP7A, ATP7B, SOD1, and TH) or 1% casein (Atox1) at the following concentrations: Ctr1 (1:200), Atox1 (1:250), ATP7A (1:750), ATP7B (1:1500), SOD1 (1:10,000), and TH (1:5000) overnight at 4 °C. Following incubation with horseradish peroxidase-conjugated mouse anti-goat IgG (1:10,000), goat anti-mouse IgG (1:2,000), donkey anti-sheep/goat IgG (1:2,000), or donkey anti-rabbit IgG (1:5000), protein inserm-00968923, version 1 -1 Apr 2014 signals were obtained using an ECL Western blotting detection system (Bio-Rad) as per the manufacturer's instructions, and developed using the Chemi-Doc XRS (Bio-Rad). Signal intensities were quantified by densitometry using Quantity One® software (Bio-Rad) and normalized to -actin (1:10,000) levels. TH levels in the SN were quantified by Western blot to provide an indication of dopaminergic cell loss.
Acknowledgements Tissues were received from the  New South Wales Tissue Resource Centre at the University of Sydney , supported by the  National Health and Medical Research Council of Australia ,  Schizophrenia Research Institute  and the  National Institute of Alcohol Abuse and Alcoholism (NIH (NIAAA)   R24AA012725 ), and from the  Sydney Brain Bank , which is supported by  Neuroscience Research Australia , the  University of New South Wales  and the  National Health and Medical Research Council of Australia. The  European Synchrotron Radiation Facility  is acknowledged for provision of synchrotron radiation beam time (exp MD-304,  MD-258 ). The synchrotron Diamond is acknowledged for provision of beam time (exp. SP7238). The authors are grateful to  AIFIRA facility  for granted access to nuclear microprobe end-station.
This work was supported by research grants from the  Partenariats Hubert Curien (PHC)-FAST , the  Australian Department of Innovation, Industry, Science and Research International Science Linkage FAST programs , the  National Health and Medical Research Council of Australia  (project grant to KLD and JFBM),  Parkinson's New South Wales  (seed grant to KLD), the 36th District of Quota International, AMP, and a donation from Greg Connolly on behalf of the  AMP Foundation and Charter Financial Planning. KMD was a recipient of an  Australian Postgraduate Award  and a  Research Excellence Award  form the  University of New South Wales. DJH was a recipient of a  Research Fellowship  from the  Australian Research Council , and KLD and GMH were recipients of Research Fellowships from the  National Health and Medical Research Council of Australia.
In this context, it must be recognised that the use of functional foods enriched with plant sterols/stanols is currently not advised for children under 6 years. There is, however, a substantial database showing consistent LDL-C lowering efficacy in children. In controlled clinical trials in children Fig. 3. Schematic summarising the three main steps (indicated by the numbers in red circles) involved in the intestinal handling of cholesterol and non-cholesterol sterols. In the first step within the intestinal lumen, sterols are incorporated into mixed micelles  (1). At the brush border membrane, sterols are released from the micelles and transported into the cell via the Niemann-Pick C1-Like1 transporter (NPC1L1)  (2). Once internalised, these sterols can be handled in different ways  (3). For the bulk of the internalised noncholesterol sterols, efflux back into the lumen occurs via ABCG5/ABCG8 (ATP binding cassette transporters G5 and G8).
The genomes of several L. lactis strains have thus been determined, including strains of L. lactis subsp. lactis, such as IL1403 (8), KF147  (9) , and CV56  (10) , as well as strains of L. lactis subsp. cremoris, such as MG1363  (11)  and SK11  (12). We report here the genome of L. lactis subsp. lactis TOMSC161, a strain isolated from the dairy environment and more specifically from a scaled nonscalded curd pressed cheese, and presenting very interesting technological properties (acidifying, proteolytic, and texturing activities). Sequencing was performed by Imagif (CNRS, Gif-sur-Yvette, France) using HiSeq paired-end sequencing. A total of 20,391,131 reads were used for assembly by using the Velvet and VelvetOptimiser softwares, leading to an average coverage of 730ϫ. A total of 56 large contigs ranging from 1,013 to 431,322 bp in size were generated and annotated using AGMIAL, an integrated bacterial genome annotation platform  (13).
lactis TOMSC161 still contains genes involved in the utilization of certain plant sugars (mannose, mannitol, arabinose, ribose, and xylose) related to the original habitat of L. lactis. Furthermore, the analysis showed the presence of genes involved in exopolysaccharide and bacteriocin (e. g. , lactococcin) production, which are interesting technological features. The availability of the genome sequence of L. lactis TOMSC161 will allow the powerful application of transcriptomics and proteomics to investigate the metabolic responses and thus the physiological processes involved in the adaptation to different environmental conditions. Nucleotide sequence accession numbers. The genome sequence and annotation of L. lactis subsp. lactis TOMSC161 have been deposited in the EMBL database under accession numbers CBUJ010000001 to CBUJ010000062.
Interestingly, the fluorescence detection method also is comparably sensitive to enzyme enhancement techniques and relatively quick with a low hands-on time. In this study 7 French ovine field TSE cases were investigated by the triplex-WB technique. 38 These cases were previously detected in France as deviating in conventional Western blots from the usual migration pattern of PrP res of classical scrapie, and were categorized as CH1641-like in our bead-based methodology. 37 By using a set of samples as reference for classical scrapie, CH1641 and BSE, the new triplex-WB data support the idea that especially in some of those deviant field cases variable levels of a second PrP res population (also having a different N-terminal susceptibility to proteolytic cleavage) occur. The implications of the data indicate that biochemical diagnosis in brain homogenates alone is not always straightforward and that therefore other methods such as rodent bioassays for small ruminant scrapie typing remain essential.
All lanes presented were scanned at 532 nm excitation wavelength, except lane 24 at 633 nm. Molecular mass references: lane 1 rec-ovPrP, lanes 2 and 24 blue molecular mass markers that yield a strong signal at excitation wavelength 633 nm (in kDa). TE applied per lane: 0. 25 mg in lanes 4, 18-20, and 0. 5 mg in lanes 3, 5-17, 21-23. (B) Dotplot of the 2 methods of dual population estimation. Vertical axis, the ratio between SAF84/L42 fraction of the 24kDa band in the PrP res triplet (see Fig. 1 ). Horizontal axis, the band 2 versus band 1 ratio estimated in blots of the 54 cases as exemplified in panel a. For all samples analyzed a linear regression correlation curve is presented together with the mathematical curve data and regression value R 2. estimated. Bovine H-type BSE and ovine CH1641 did show presence of a dual PrP res population but they differed in the relative content of the 12B2 N-terminus epitope being amply present in H-type, but close to zero in CH1641.
Molecular masses of triplet PrP res bands detected with L42 were calculated using GelPro software (GeL-Pro analyzer; Media Cybernetics) and with InvitroGen SeeBlue Ò prestained molecular mass markers (Life Sciences) as applied in 2 lanes per gel; these standards have a high fluorescence yield in the 488 nm channel. In all runs rec-ovPrP ARQ was included as a correction reference for signal level differences between emission light intensities in the 3 different Typhoon Trio laser light channels. As a further correction to quantify the relative N-terminal 93-97 epitope presence in 12B2/L42 ratio estimations, the average 12B2/ L42 value for all scrapie samples in an experiment (usually n D 32) was considered to be 1, 39 therefore each individual 12B2 x / L42 x outcome was multiplied with 1/(12B2 scr /L42 scr ) where the 12B2 scr /L42 scr ratio is representing the average 12B2/L42 value of all 3two classical scrapie cases in the experiment.
Acknowledgments We thank  Dr. Jim Foster  from  Roslin institutes (UEDIN, Edinburgh, UK ) for supply of CH1641 challenge material used for generating the different experimental CH1641 tissues at  CVI  and  AHVLA. Dr. Jacques Grassi  ( CEA, Saclay, France ) and  Dr. Martin Groschup  ( FLI, Riems-Greifswald, Germany ) provided kindly an initial batch of respectively antibodies  SAF84  and  L42. We thank  Dr. Human Rezaei  ( INRA, Jouy-en-Jozas, France ) for kind gift of rec-ovine PrP ARQ.
Vitamin K UPLC-MS Analysis Analyses were performed by ultraperformance liquid chromatography using an ACQUITY system (Waters Corp. , Milford, MA) linked simultaneously to a diode array detector (UPLC DAD, Waters Corp. ) and interfaced with a Bruker Daltonics HCT Ultra Ion Trap mass spectrometer via an atmospheric pressure chemical ionization source operated in positive ion mode (UPLC DAD/APCI-MS). Compass TM software (Bruker Daltonics, Bremen, Germany) was used for mass spectrometric instrument control and data processing. UPLC conditions were modified from Song et al. (27). Separation was carried out using an ACQUITY UPLC BEH C18 column (50 mm ϫ 2. 1 mm, inner diameter 1. 7 m; Waters). The column temperature was 35 °C, the flow rate was 0. 45 ml min Ϫ1 , and 10 l was injected. Analysis was achieved using a gradient of Milli-Q water/2-propanol (80:20, v/v) containing 0.
Statistical Analysis Results are expressed as means Ϯ S. E. Differences between more than two groups of unpaired data were analyzed using the non-parametric Kruskal-Wallis test. The non-parametric Mann-Whitney test was used as a post hoc test when the Kruskal-Wallis test showed significant differences between groups. Differences between only two groups of unpaired data were tested via Mann-Whitney U test. Values of p Ͻ 0. 05 were considered significant. All statistical analyses were performed using Statview software, version 5. 0 (SAS Institute, Cary, NC). Relationships between two variables were examined by regression analysis using KaleidaGraph version 3. 6 software (Synergy Software, Reading, PA).
An image of each sector was acquired. A total of 384 images were obtained and in total more than 3900 glomeruli were quantified. The mean densitometric value of GLUT4 labeling was first compared between the zones, then between the sectors. In order to better represent GLUT4 intensity of labeling according to the zones, sectors and feeding states, a colored image plot was constructed using MySql database software and Python script. The glomerular GLUT4 densitometric values were ranked in descending order and were coded with a color scale which illustrates intensities of immunostaining (dark red corresponds to the highest value, blue corresponds to the lowest one). For each sector, a matrix was built with the highest densitometric value placed in the center, and values decreasing in magnitude from the center to the edge of the matrix in a spiral shape, so that the smallest values were located in the most peripheral part of the matrix.
Preparation of electrochemical sensors The glucose biosensor uses glucose oxidase and amperometric detection of hydrogen peroxide  (Vasylieva et al. , 2011). The tip of the probe was coated with glucose oxidase that metabolizes glucose in the extracellular fluid. An oxidation current is thus generated and measured using Neurolabscope software. Each biosensor was connected to a potentiostat, which sends readings of the current generated by glucose in extracellular fluid to a computer. Glucose biosensors have been shown previously to have a range of 0-10 mM with in vitro sensitivity of 1. 6 ± 0. 4 nA/mM (mean ± s. e. m. ). To confirm the accuracy of the biosensors, prior to implantation and immediately following testing, we placed each biosensor probe in 0. 1 M PBS, connected to the potentiostat, and readings were allowed to stabilize (generally stable within 15-30 min).
STATISTICAL ANALYSIS Data are shown as mean values ± s. e. m. Physiological parameters (glycemia, plasma and OB insulin level) were analyzed using a non-parametric Mann-Whitney test, or Wilcoxon test when data were paired (Statview Software). For Western Blot data, quantification of glomerular GLUT4 immunostaining, and extracellular glucose measurements, statistical analysis were performed by either a Student's t-test or one-or Two-Way repeated-measures ANOVA depending on the data set. A Student-Newman-Keuls (SNK) post-hoc test was used to complete the analysis when appropriate (Statview software). In all cases, P < 0. 05 was considered statistically significant.
PHYSIOLOGICAL HALLMARKS OF SATIATED AND FASTED RATS Body weight was regularly measured to monitor the influence of restricted access to food on the physiological and nutritional status of rats. Rats started to gain weight only 3 days after the restrictive 2-h access to food had started (data not shown). Glycemia and insulin levels in the blood and the OB were significantly different between satiety and fasting (Table  1 , P < 0. 01, Mann-Whitney test).
12, Figure  3B ). Thus, chronic restricted feeding up-regulates GLUT4 expression in the OB but not in the somatosensory cortex. SGLT1 positive control performed by using rat kidney tissue extract revealed that SGLT1 antibodies bound to a polypeptide band at about 75 KDa (data not shown). Conversely to GLUT4, there was no interaction between brain areas and feeding states for SGLT1. SGLT1 expression was however, significantly different between the two brain areas [F (1, 8) = 19. 03, P < 0. 005], but independent from the feeding state. A post-hoc test (SNK) showed further that SGLT1 expression was higher in the OB (Figure  3B ). Regionalization of GLUT4 in the glomeruli of adult fasted and satiated rats was studied by two different immunohistochemistry procedures: (i) using a rabbit anti-GLUT4 primary antibody, and (ii) omitting the primary antibody.
ACKNOWLEDGMENTS This work was supported by the  Centre National de la Recherche (CNRS) , the  Claude Bernard University of Lyon  ( University Lyon1 ) and a grant from  Institut Fédératif des Neurosciences de Lyon  (Projet structurant IFNL 2008). We would like to thank the staff of the plateforme technologique Neurochem, ( Université Claude-Bernard-Lyon I, 69373 Lyon Cedex 08, France ),  Anne Meiller  and  Stephane Marinesco  for the engineering of the glucose biosensors. We would like to thank  Jen Kennedy  in the.
It could also be argued that a threshold may exist and a low intake of R-TFA may even have beneficial effects. Hansen et al. (17)  recently demonstrated an inverse association between lower intakes of R-TFA and change in body weight. To achieve a more exhaustive estimation of the effects of R-TFA intake, we first performed a systematic review. We then analysed the data from thirteen randomised clinical trials to quantify the relationship between the dose of R-TFA and the change in the ratios of TC:HDL-C and LDL-C:HDL-C in healthy adults.
Study selection A systematic literature search was conducted on studies published between January 1975 and December 2011, using the following search terms on the PubMed and Scopus databases, respectively: (('Fatty Acids/blood' OR 'Cholesterol/ blood' OR 'Lipoproteins/blood') AND ('Dairy Products' OR 'Trans Fatty Acids' OR 'Linoleic Acids, Conjugated')) and: (('fatty acids') OR cholesterol OR lipoproteins) AND (('dairy products') OR ('trans fatty acids') OR ('linoleic acids, conjugated')) AND ((clinical trial) OR (controlled study)). An updated secondary search was conducted on studies published up until December 2013. The search strategy had language (English) and study design (clinical trial, randomised controlled trial) restrictions. We also limited our search to studies conducted in adults.
Data extraction and classification From each study, we extracted quantitative data that were adjusted according to the measurement unit, and all the relevant information on (1) study characteristics such as first author, year of publication, study design and country of origin, (2) subject characteristics such as name of the group (group name), sample size (n), sex, age and BMI, (3) lipid and lipoprotein blood concentrations at baseline and at the end of the intervention period such as TC, LDL-C, HDL-C, TAG in mmol/l, and (4) diet characteristics including total energy intake (EI) in MJ, daily energy from carbohydrate (CARB), protein (PROT) and fat (FAT) in percentage of EI, fatty acid composition of experimental diets in percentage of EI, such as SFA, MUFA, PUFA, total R-TFA, total R-trans-18 : 1 (total R-18 : 1t), vaccenic acid (trans-11 18 : 1), rumenic acid (cis-9, trans-11 18 : 2) and total CLA.