dataesr/scientific-paragraphs-categorization huggingface dataset:
Results Myoscape localizes to sarcolemmal t-tubules. On the basis of the notion that proteins specifically expressed in the heart are likely to play a role in cardiac pathophysiology  23  , we systematically screened the expressed sequence tag (EST) databases for sequences predominantly found in cardiac complementary DNA (cDNA) libraries  24. Data extraction relied on the T-STAG (Tissue-Specific Transcripts and Genes; http:// tstag. molgen. mpg. de/) and the Unigene (National Center for Biotechnology; http://www. ncbi. nlm. nih. gov/unigene) databases. Several of the identified ESTs corresponded to the human Unigene cluster Hs. 489988 or the Mus musculus Unigene cluster Mm. 56097. ESTs in these clusters were significantly enriched in the heart compared with other tissues (Supplementary Fig.
9a ). The absence of Myoscape led to 'super-induction' of the fetal gene program member ANF, which was not seen under unchallenged conditions (Fig. 4j  and Supplementary Fig. 9b  and c ). Likewise, we observed an additional increase of cardiomyocyte cell size (592 mm 2 ± 6. 3 s. e. m. versus 519 mm 2 ± 5. 1 s. e. m. ; Po0. 05 (ANOVA); Fig. 4l, m ) in response to TAC. Cardiomyocyte hypertrophy was accompanied by a strong induction of RCAN1. 4 mRNA (Fig. 4k ) and protein (Supplementary Fig. 9d ) expression, indicating excessive activation of calcineurin/NFAT signalling in Myoscape KO hearts in response to increased biomechanical stress  32. Consistently, Myoscape KO mice showed enhanced fibrosis after aortic constriction, as shown by sirius red stainings of heart sections (Supplementary Fig.
5% PAA-Gel and transferred on a PVDF-Membrane. The membrane was probed as indicated with a polyclonal anti-Myoscape antibody generated in rabbit (Eurogentech; Peptide EPO70153 as immunogen) or an anti-human FAM40B antibody (HPA019657 Sigma) at a dilution of 1:200 according to the manufacturer's protocol followed by ECL detection (GE Healthcare RPN2106). For mouse LTCC western blots an Anti-Cav1. 2 calcium channel, NeuroMab clone L57/46 antibody was used (1:200). For rat heart material, we used the Anti-CACNA 1 C Antibody from Novus Biologicals (NBP1-42820 (1:250)). The monoclonal anti-alpha-actinin 2 antibody was purchased from SIGMA and was used in a dilution of 1:1,000. Immunofluorescence microscopy. The subcellular localization of Myoscape was determined in ARVCMs and in cryosections of mouse and rat cardiac tissue using indirect immunofluorescence.
Measurements were carried out using an inverse Olympus microscope (IX70) with a UV filter connected to a monochromator (Polychrome II, T. I. L. L. Photonics GmbH, Germany). Cells were electrically stimulated with a biphasic pulse to contract at 37 °C at 2 Hz and excited at 340/380 nm. Epifluorescence emission was detected at 510 nm, digitized, and analysed off-line with T. I. L. L. VISION software (v. 3. 3). Baseline data from 10 consecutive steadystate transients after 15 min of electrical stimulation were averaged for analysis of transient amplitudes. Isoproterenol (10-9-10-7M) was superfused through a gravity-fed perfusion system and Ca 2 þ transients were recorded 5 min after AR stimulation. Cardiomyocyte contractility. Contractile parameters in isolated ARVCM's were obtained by a blinded observer, 24 h after plating and adenoviral infection by video edge detection following a previously published protocol  [57] [58].
Briefly, contraction amplitudes were assessed in HEPES-modified medium 199. Analysis of steady-state twitches at 2 Hz field stimulation, 37 °C and 2 mM extracellular calcium concentration was performed by custom designed software written in LabView (version 5. 0, National Instruments). Data from five consecutive steady-state twitches were averaged for analysis of fractional cellular shortening of ARVCM. L-type calcium current recordings. L-type calcium currents (ICa) were recorded in single cardiomyocytes with the whole-cell patch clamp configuration of the Multi Clamp 700 amplifier (Molecular Devices, Sunnyvale, CA, USA) as described below. Cardiomyocytes were incubated in external solution containing (mM): TEA-Br 140, CaCl2 2, Mg-acetate 1, Hepes 10, 4-amino-pyridine (4-AP) 5, CsBr 5, TTX 0.
B. Calcium-dependent inactivation was measured using the IV protocol. After adjusting the baseline, peak amplitude was normalized. Time constant was calculated after fitting the data sets with two exponential functions. For measuring steady-state inactivation CMs were stimulated by a twin-pulse protocol (C). Fractions of current (I 2 /I 1 ) were plotted against the prepulse voltage. E 0. 5 was calculated after fitting the data sets with a Boltzmann equation.
Acknowledgements We thank  Christin Tannert ,  Linda Ko ¨hler ,  Gabriele Brunke ,  Philipp Doldi ,  Susann Werkmeister ,  Jutta Krebs  and  Sabine Marquart  for their excellent technical assistance, as well as  Prof. Dr. med. Renate Lu ¨llmann-Rauch  and  Hiltraud Hosser  for performing EM ultrastructural analyses. We are grateful to  Prof. Dr. Stefan Wiemann  for providing the human qPCR analysis. This work has been supported by the  Landesstiftung Baden-Wu ¨rttemberg , by a grant of the  Bundesministerium fu ¨r Bildung und Forschung, Germany (INSIGHT-DCM consortium) , to N. F. ( 01KU0901B ), the  GSF  grant of the  Bundesministerium fu ¨r Bildung und Forschung, Germany , to N. F. (FKZ:  01GR0430 ), and the  German Center for Cardiovascular Research (DZHK)  to N. F. and B. M.
Since our aim was to identify differential pathways associated with the absolute tumour burden, we wanted to have a bottom 20% group with absolute low numbers of substitutions. Samples were thus ranked according to mutational burden independent of ER-status to obtain the bottom and top 20% groups. In ER-positive cases, this gave a group of n ¼ 15 in the top 20% versus n ¼ 52 in the bottom 20%. In ER-negative cases there were only two samples in the bottom 20%, precluding a meaningful analysis. Pathway analysis were performed using the R-package 'global test'  39  using Biocarta (www. biocarta. com) and KEGG (ref. 40) as annotation databases. All P values were corrected for multiple testing (Bonferroni-Holm) and checked by re-sampling 1,000 times to ascertain the number of times an equally sized, randomly chosen group of genes is at least as significant as the true set of genes belonging to a pathway.
Pathways were considered of interest if the P value of the global test after correcting for multiple testing and the re-sampling P value were both below 0. 05. Second, pathways were considered relevant pathways if these consistently showed multiple genes higher expressed in the cases with high numbers of a signature. Neo-antigen prediction and hydrophobicity of amino acids. To ascertain which of the amino acid changing substitutions potentially contain a neo-epitope, all unique, non-silent, non-terminating amino acid substitutions were selected (n ¼ 26,475) and we focused our analyses on CD8 T-cell epitopes. FASTA files of the wild-type sequences were obtained via the consensus coding sequence database (http://www. ncbi. nlm. nih. gov/CCDS/CcdsBrowse. cgi) and custom Perl scripts were used to mutate the wild-type sequence according to the identified substitution in our cohort.
Changes in electric charge were evaluated by assigning Aspartic acid and Glutamic acid as negatively charged and Lysine, Arginine and Histidine as positive. Next, base substitutions were evaluated if a resulting amino acid change led to a change in electrical charge. Since all substitutions are assigned to a mutational signature, the total number of charge changing (and hydrophobicity changing) substitutions per signature was established. Independent validation set. In-house and publicly available gene expression data of lymph-node negative primary breast cancer patients, who were not treated (neo)adjuvantly with hormonal/chemotherapy and available metastasis-free survival data were used, leading to a cohort of 867 patients (n ¼ 625 ER-positive). This selection enables a pure study on prognosis.
Data were gathered from Gene Expression Omnibus (http://www. ncbi. nlm. nih. gov/geo/) entries GSE2034, GSE5327, GSE2990, GSE7390 and GSE11121, with all data available on Affymetrix U133A chip. Raw. cel files were processed using fRMA (ref. 42) parameters (median polish), after which batch effects were corrected using ComBat (ref. 43). The average expression of TIL genes  22  and MCC genes (Gene Ontology:0000278) were calculated of each sample, and the samples in the top quartile for TIL and the top quartile for MCC were used to group the patients in three groups; those with high TIL/low MCC, those with low TIL/high MCC and the remaining patients. Statistics. Associations between gene expression levels and gene-status (mutant, amplification and so on) were analysed using MWU, or KW when more than two categories were evaluated.
Acknowledgements This work has been funded through the  ICGC Breast Cancer Working group  by the  Breast Cancer Somatic Genetics Study  (a European research project funded by the  European Community 's  Seventh Framework Programme  ( FP7/2010-2014 ) under the grant agreement number  242006 ); the  Triple Negative  project funded by the  Wellcome Trust  (grant reference  077012/Z/05/Z ). Personally funded by grants: FGR-G, SM, KR, SM were funded by  BASIS. JAF was funded through an  ERC Advanced Grant  ( ERC-2012-AdG-322737 ). SN-Z is a  Wellcome Beit Fellow  and personally funded by a  Wellcome Trust   Intermediate Fellowship  ( WT100183MA ). ALR is partially supported by the  Dana-Farber/Harvard Cancer Center SPORE in Breast Cancer  ( NIH/NCI 5 P50 CA168504-02 ). AS was supported by  Cancer Genomics Netherlands  (CGC.
nl) through a grant from the  Netherlands Organisation of Scientific research (NWO). MS was supported by the  EU-FP7 -DDR response project. CD was supported by a grant from the  Breast Cancer Research Foundation. EB was funded by  EMBL. JE was funded by The  Icelandic Centre for Research (RANNIS). For technical or administrative support:  Lira Mamanova  from the  Wellcome Trust Sanger Institute  is thanked for her expertise in RNA library preparation. We thank contributors  Luc Dirix  ( Antwerp, Belgium ) and  Suet-Feung Chin (Cambridge, UK) ,  Jon G Jonasson  ( University of Iceland ), The Icelandic Cancer Registry and from  Nijmegen  (The Netherlands):  Margrete Schlooz-Vries ,  Jolien Tol ,  Hanneke van Laarhoven ,  Fred Sweep  and  Peter Bult. Benita Kiat Tee Tan  from the  National Cancer Centre Singapore and Singapore General Hospital  is thanked for contributing patient samples for this study as are OSBREAC, the  Oslo Breast Cancer Research Consortium, Norway  (http://ous-research.
Data availability. WGS, RNA-seq and methylation data that support the findings in this study are available at the European-Genome Phenome Archive (https:// www. ebi. ac. uk/ega) under the accession code EGAS00001001178. For the validation data, in-house GSE2034 and GSE5327, and otherwise public data GSE2990, GSE7390 and GSE11121 are available at the Gene Expression Omnibus website (http://www. ncbi. nlm. nih. gov/geo/). All other data are contained within the Article and its Supplementary files or available from the authors on request.
Study population The InCHIANTI (Invecchiare nel Chianti) is a prospective population-based study aimed at investigating the factors contributing to the decline of mobility in older subjects living in two municipalities located in Tuscany (Italy). A description of the study rationale, design and methods is provided in detail elsewhere  (14). The study population comprised 1,155 participants aged 65-102 years, who were randomly selected from the residents' registry with the use of a multistage stratified sampling method. The response rate was 91. 6%. Data collected at baseline  (1998) (1999) (2000)  and during the nine-year follow-up assessment  (2007) (2008) (2009)  were used for the current analyses. Participants with missing data at baseline on TUP (n=346, individuals without 24-h urine sample), SPPB at baseline (n=30) or SPPB at nine-year follow-up (n=408, of whom 126 had no physical performance assessment, 225 died, 42 refused and 15 emigrated before the nine-year visit) were excluded.
Total polyphenol exposure At baseline, 24-h urine samples were obtained from participants. Urine samples were immediately aliquoted and stored at -80 °C until analysis. Samples were thawed on ice and analysed using the Folin-Ciocalteau (F-C) assay after a solidphase extraction, which allows the elimination of interfering substances that could react with the F-C assay, as described previously  (13). TUP concentrations were expressed as mg of gallic acid equivalents (GAE) per 24-h urine. A validated Italian version of food frequency questionnaire was self-administered to assess the intake of 236 food items (g/d) consumed in the preceding year  (16). TDP intake was estimated using a food composition database on polyphenols  (17)  based on three USDA databases  (18) (19) (20)  and the Phenol-Explorer database  (21).
There was no evidence of collinearity. In the sensitivity analysis, we excluded participants if they had an extreme energy intake (participant in the top or the bottom 1% of the distribution of the reported total energy intake) in models for TDP. In a second sensitivity analysis, participants with an extreme change in SPPB score, considered as a change of ≥9 points in the SPPB score over the 9 years of follow-up, were excluded in TUP and TDP models. All analyses were performed using the SPSS package program version 20. 0 (SPSS, Chicago, IL). Two-tailed P<0. 05 was considered statistically significant.
Second, TUP was measured only once at baseline. Although there was a decrease in the polyphenol intake during the follow-up as in other studies with aging (48), we were interested in the long-term predicting ability of total polyphenol exposure in the physical performance decline. Third, the TDP intake may be underestimated, although the dietary intake was assessed using a validated country-specific FFQ (  16 ) and a comprehensive database on polyphenols  (17, (34) (35). In conclusion, the current longitudinal study shows that higher concentrations of TUP, a nutritional biomarker of polyphenol-rich exposure, were associated with a lower risk of substantial decline in physical performance in older subjects living in a community. A polyphenol-rich diet seems to play an important preventive role against physical performance decline, and therefore in the delay of the onset of disability.
Acknowledgments The authors are grateful for support granted by  Spanish government  grants from the  Ministry of Economy and Competitiveness (MINECO)  and cofounded by the  FEDER (Fondo Europeo de Desarrollo Regional) : the  AGL2009-13906-C02-01 , the  CONSOLIDER-INGENIO 2010 program ,  FUN-C-FOOD  ( CSD2007-063 ), and the  JPI HDHL FOODBALL  ( PCIN-2014-133 ). We also thank the award of  2014SGR1566  from the  Generalitat de Catalunya's Agency AGAUR. In the framework of the  COST Action POSITIVE FA1403. Partially funded by the  International Nut and Dried Fruit Council Foundation (INC)  in collaboration with the  Bosch i Gimpera Foundation  ( FBG307906 ). The InCHIANTI study was supported in part by the  Italian Ministry of Health  and by the  U. S. National Institute on Aging (NIA). M. U.
Methods Human muscle sampling. Data and samples from men aged between 34 and 53 years with varying degree of BMI and insulin sensitivity were available from a prior study (n = 33)  39. Of these, 11 were normal weight sedentary controls, 11 were obese sedentary and 11 were normal weight endurance-trained individuals. The overall study design and subject testing have been partly described in  39. The study was performed according to the latest version of the Declaration of Helsinki and the Current International Conference on Harmonization (ICH) guidelines. The research protocol was approved by the Université Laval ethics committee and all subjects provided written informed consent. Samples of vastus lateralis (~40 mg) were obtained, blotted free of blood, cleaned to remove fat and connective tissue and snap-frozen in liquid nitrogen for Western blot analyses.
The amplification reaction was performed in duplicate on 10ng of cDNA in 96-well reaction plates on a StepOnePlus TM system (Applied Biosystems). All expression data were normalized by the 2 (ΔCt) method using 18 S as internal control. Western blot analysis. Muscle tissues and cell extracts were homogenized in a buffer containing 50 mM HEPES, pH 7. 4, 2 mM EDTA, 150 mM NaCl, 30 mM NaPPO 4 , 10 mM NaF, 1% Triton X-100, 1. 5 mg/ml benzamidine HCl and 10 μ l/ml of each: protease inhibitor, phosphatase I inhibitor and phosphatase II inhibitor (Sigma-Aldrich). Tissue homogenates were centrifuged for 25 min at 15,000 g and supernatants were stored at -80 °C. A total of 30 μ g of solubilized proteins from muscle tissue and myotubes were run on a 4-12% SDS-PAGE (Biorad), transferred onto nitrocellulose membrane (Hybond ECL, Amersham Biosciences), and blotted with the following primary antibodies: PLIN5 (#GP31, Progen), ATGL (#2138, Cell Signaling Technology Inc.
), Akt (#4691, Cell Signaling Technology Inc. ), pAkt S473 (#4060, Cell Signaling Technology Inc. ), pAkt T308 (#2965, Cell Signaling Technology Inc. ). Subsequently, immunoreactive proteins were blotted with secondary HRP-coupled antibodies (Cell Signaling Technology Inc. ) and revealed by enhanced chemiluminescence reagent (SuperSignal West Femto, Thermo Scientific), visualized using the ChemiDoc MP Imaging System and data analyzed using the ImageLab 4. 2 version software (Bio-Rad Laboratories, Hercules, USA). GAPDH (#2118, Cell Signaling Technology Inc. ) was used as an internal control. Determination of glucose metabolism. Cells were pre-incubated with a glucose-and serum-free medium for 90 min, then exposed to DMEM supplemented with D[U-14 C] glucose (1 μ Ci/ml; PerkinElmer, Boston, MA).
For electrical pulse stimulation experiments, cells were chased for 24 h in DMEM containing 1 mM glucose, 0. 5% FA-free BSA and 10 μ M triacsin C while electrically stimulated by 2 ms pulses at a frequency of 0. 1 Hz. TAG-derived FA oxidation was measured by the sum of 14 CO 2 and 14 C-ASM (acid soluble metabolites) in absence of triacsin C as previously described  40. Myotubes were harvested in 0. 2 ml SDS 0. 1% at the end of the pulse and of the chase period to determine oleate incorporation into TAG and protein content. The lipid extract was separated by TLC using heptane-isopropylether-acetic acid (60:40:4, v/v/v) as developing solvent. All assays were performed in duplicates, and data were normalized to cell protein content. Palmitate oxidation rate was measured as previously described  43.
Statistical analyses. All statistical analyses were performed using GraphPad Prism 5. 0 for Windows (GraphPad Software Inc. , San Diego, CA). Normal distribution and homogeneity of variance of the data were tested using Shapiro-Wilk and F tests, respectively. One-way ANOVA followed by Tukey's post hoc tests and Student's t-tests were performed to determine differences between treatments. Two-way ANOVA and Bonferroni's post hoc tests were used when appropriate. All values in figures and tables are presented as mean ± SEM. Statistical significance was set at p < 0. 05.
Acknowledgements The authors thank  Justine Bertrand-Michel ,  Fabien Riols  and  Aurélie Batut  ( Lipidomic Core Facility, INSERM ,  UMR 1048  [part of  Toulouse Metatoul Platform ] for lipidomic analysis, advice and technical assistance. We also thank  Cédric Baudelin  and  Xavier Sudre  from the  Animal Care Facility. Special thanks for all the participants for their time and invaluable cooperation. The authors would also like to thank  Josée St-Onge ,  Marie-Eve Riou ,  Etienne Pigeon ,  Erick Couillard ,  Guy Fournier ,  Jean Doré ,  Marc Brunet ,  Linda Drolet ,  Nancy Parent ,  Marie Tremblay ,  Rollande Couture ,  Valérie-Eve Julien ,  Rachelle Duchesne  and  Ginette Lapierre  for their expert technical assistance in the LIME study. This work was supported by grants from the  National Research Agency   ANR-12-JSV1-0010-01  (CM),  Société Francophone du Diabète (CM) ,  Canadian Institutes of Health Research  grant  CIHR MOP-68846  (DRJ) and a  Pfizer /CIHR research Chair on the pathogenesis of insulin resistance and cardiovascular diseases (AM).
Western blot analysis To determine the cellular amounts of SibA, Phg1 and Talin, we resuspended cell pellets in sample buffer and separated the proteins on a polyacrylamide gel (7% for SibA and Talin and 10% for Phg1), after which they were transferred to a nitrocellulose membrane (Invitrogen, Carlsbad, CA). The membranes were incubated with a polyclonal anti-SibA antibody (SibA)  [12] , the YC1 rabbit antipeptide antiserum to a Phg1 peptide  [5] , or the anti-talin 169. 477. 5  [16] , a kind gift from Prof. G. Gerisch (Martinsried, Germany). Binding of antibodies was revealed by ECL using a secondary HRP-coupled antibody (Amersham Biosciences). The signal intensity was evaluated using Quantity One software (Bio-Rad).
Acknowledgements The authors wish to acknowledge the support of  Princeton University and INED. The  MAFE  project is coordinated by  INED (C. Beauchemin)  in partnership with the  Université catholique de Louvain (B. Schoumaker) ,  Maastricht University  (V. Mazzucato), the  Université Cheikh Anta Diop (P. Sakho) , the  Université de Kinshasa (J. Mangalu) , the  University of Ghana (P. Quartey) , the  Universitat Pompeu Fabra (P. Baizan) , the  Consejo Superior de Investigaciones Científicas  ( A. González-Ferrer ), the  Forum Internazionale ed Europeo di Ricerche sull'Immigrazione (E. Castagnone) , and the.
Sequencing Analysis Written informed consent was obtained from her parents. Genomic DNA was extracted from the patient peripheral blood leukocytes using QIAamp DNA blood midi kit (QIA-GEN). We screened all the 23 coding exons of LRP5 for the case and for her parents. The PCR products were sequenced on both strands with ABI Prism 3130 Genetic Analyzer (Life Technologies, Saint-Aubin, France). Sequences were analyzed using SeqScape 4. 0 software (Life Technologies) and compared with the genomic reference sequence (NG 015835. 1) for LRP5. Mutation nomenclature was based on HGVS nomenclature guidelines [http://www. hgvs. org/mutnomen/] and exonic numbering was based on genomic reference (Figure  3 ). Reference F R Q V L V W R D L D N P R G G A G C C C A A C A G G T T C A G G G A A G T G T G C T C C T G A A G G C C C T T G G A G C C C A A C A G G T T C A G G A G G T G T G C T C C T G A A G G C C T T.
Study population This retrospective study included all consecutive patients followed in our Reference Centre for Rare Diseases, with a diagnosis of NF1 according to the National Institute of Health (NIH) criteria  [28] , and with clinical manifestations that were suspected to undergo malignant transformation into MPNST (pain, neurological deficit, tumour growth). All patients underwent imaging in accordance with current national regulations (verbal informed consent was obtained and reported in patient medical records). Collection and analysis of data were retrospective and performed after de-identification. This non-interventional study was approved by our IRB on March 3, 2014 (Comité de Protection des Personnes Ile-de-France VI), and written consent was waived.
Quantitative metabolic parameters Our approach was to characterize global metabolic tumour burden by different PET-derived parameters. First, SUV max of each hypermetabolic NF1 tumour was identified visually on the attenuation-corrected. Then, a spherical, cylindrical or cubical bounding volume-of-interest was drawn around each target lesion by a nuclear medicine physician (SDA); shape and size of the volumes-of-interest were adjusted to ensure that they neither included areas of high physiological uptake (bladder, myocardium) nor exceeded the anatomical tumour boundaries seen on CT in case of low tumour/background contrast. Metabolic tumour volume (MTV) was computed within each volume-of-interest by summing all voxels above a 41% SUV max threshold using a semiautomatic software (Imagys1; Keosys, Saint-Herblain, France)  [29].