dataesr/scientific-paragraphs-categorization huggingface dataset:
Future research will build on these observations to further investigate the mechanisms that may underlie the pathological role of the Ryk-ICD/FOXO3a pathway in HD. Besides testing whether Ryk cytotoxicity might be modulated by mammalian Wnt ligands or Ryk inhibitory antibodies  [33]  and studying whether an excess of the Ryk-ICD fragment might tether b-catenin away from FOXO, it will be interesting to identify the FOXO3a transcriptional targets that may be deregulated by Ryk in mutant polyQ neurons and understand how this may impact brain longevity mechanisms as the pathogenic process develops in HD. The type and activity of FOXO target genes may greatly depend on the cellular context in which FOXO operates  [4, 44] , which may also be true in HD, as suggested by the study of context dependence in FOXO interaction networks across mouse and human datasets  [25].
Interestingly, the transcriptomic signature of 128Q nematode touch receptor cells contains 84 genes that were previously identified as putative daf-16/FOXO targets in C. elegans, including 31 genes that are highly conserved in mice (Table  S7 ), suggesting that FOXO target genes may be altered by mutant polyQ expression. The deregulation status of most of these 31 genes appeared to be greatly context-dependent, as evaluated by using entropy-based feature selection across 14 HD-associated conditions including murine striatum and human (postmortem brains, blood samples, induced pluripotent stem cells) datasets (Table  S7 )  [5] , which emphasizes the importance of context (e. g. , cell type, time requirement) in future analyses of the physiological impact of abnormal Ryk signaling on FOXO activity in HD.
The expression of LIN-18 ICD cDNA was confirmed by RT-PCR for all of the arrays generated. EV, empty vector overexpression. Data are means 6 SEM (more than 200 animals tested). *p,0. 001 compared to 19Q animals. ns, not significant. Significance was tested using one-way ANOVA, with correction for multiple testing by Tukey's Multiple Comparison Test. (TIF) Compared with age-matched control specimens (a-d), Ryk immunofluorescence was increased within astroglia from human caudate nucleus Grade 4 HD patients (e-f), but not on a one-toone basis. Several Ryk immunofluorescence signals were observed in the GFAP-negative area (white arrows), and there are multiple glial figures without co-localized Ryk. Ryk immunofluorescence was assessed using the same Ryk antibody as in Figure  S8. Scale bar, 20 mm.
(B) Expression of LIN-18 ICD cDNA (4 ng/ml) in touch receptor neurons using the mec-3 promoter is also sufficient to abolish the protective activity of lin-18 LOF on axonal swelling in the PLM neurons of 128Q nematodes as tested in two independent extrachromosomal arrays (Lin-18 ICD: A1 is ID1333, A2 is ID1334; Lin-18: A1 is ID1325, A2 is ID1326). The expression of LIN-18 ICD cDNA was confirmed by RT-PCR for all of the arrays generated. Expression of empty vector (4 ng/ml) showed no effect as tested in two independent extrachromosomal arrays (A1 is ID1339, A2 is ID1340). Data are mean 6 SEM (more than 200 animals tested). *p,0. 001 compared to 128Q animals, **p,0. 001 compared to 128Q;lin-18 animals. ns, not significant. Significance was tested using one-way ANOVA, with correction for multiple testing by Tukey's Multiple Comparison Test.
Acknowledgments We thank  Cheryl Wellington  and  Michael Hayden  ( University of British Columbia, Canada ) for providing constructs encoding HTT with 128 Glns;  Elena Cattaneo  ( University of Milano, Italy ) for cell lines derived from HdhQ111 mice;  Marie-Francoise Chesselet ,  Nick Franish , and  Vincent Lemesre  ( University of California, Los Angeles ) for 140CAG mouse brain extracts;  Lisa Ellerby  ( Buck Institute, CA ) for the construct encoding FOXO3a;  Anne Brunet  ( Stanford University, CA ) for the FOXO3a antibody NFL;  Karine Merienne  ( IGBMC, Illkirch, France ) for the Pol2 antibody 7C2;  Stephane Le Crom  and the  Plateforme Transcriptome 's team of  ENS (Paris, France ) for microarray analysis;  Jean-Francois Gilles  and the Cell Imaging and  Flow Cytometry  facility of the  IFR 83 (Paris, France)  for precious help in microscopy and image analysis;  Celine Lefebvre  ( Institut Gustave Roussy, Villejuif, France ) for advice on bioinformatics; and  Aurelie Darbois  and  Cedric Bicep  for technical assistance.
This work was supported by  Inserm  and  Associated International Laboratory 'Neuronal longevity'  (http://www. inserm. fr/), AP-HP  (http://www. aphp. fr/),'' Equipe FRM Ile-de-France'' program  of the  Fondation pour la Recherche Medicale  (http://www. frm. org/)Grant  DEQ20061107955 , the  Agence Nationale de la Recherche  (http://www. agence-nationale-recherche. fr/)Grants  ANR-08-MNPS-024-01  and  ANR-12-BSV4-0023-01  and the  Association Francaise contre les Myopathies  (http://www. afm-telethon. fr/), Paris, France , and the  Hereditary Disease Foundation  (http://www. hdfoundation. org/home. php)and  CHDI Foundation  (http://chdifoundation. org/),  USA. C. T. is supported by  AP-HP  under the  University Hospital Department  ' Fight Aging and Stress' program. J. A. P. was supported by a  Young Researcher Award  from  Inserm.
Replicationbased mechanisms, such as Fork Stalling and Template Switching (FoSTeS) or microhomology-mediated breakinduced replication (MMBIR), have also been proposed for germline and somatic complex rearrangements including amplifications  (17) (18) (19). Using fluorescent in situ hybridization (FISH) and whole genome sequencing approaches, we analysed at nucleotide resolution the organization of co-amplified sequences from the EGFR and MYC loci at successive passages of a xenografted human oligodendroglioma. Dmins were present at the early passages and an hsr was observed later. Our data support a mechanism of formation of the dmins and of their transformation into hsr driven by multiple rearrangements of the initial sequence resulting in the fusion of fragments of various lengths, some of them only a few tens of base pairs (bp) long.
Characterization of the amplified regions: whole genome sequencing Amplifications of the EGFR and MYC genes in ODA14 were established by screening a series of glioma using quantitative polymerase chain reaction (PCR) (not shown). The Affymetrix Genome-Wide Human SNP Array 6. 0 was first used to determine the extent of the amplifications. To delve deeper into the characterization of the amplified regions, whole genome sequencing was used. The libraries were prepared using Illumina TrueSeq sample preparation. The two samples were sequenced on an Illumina HiSeq 2000 in paired end mode with a read length of 100 bases. The sequencing resulted in about 100 million raw paired reads per sample corresponding to a coverage of ×10. Sequence data were recorded in the Sequence Read Archive database (Accession: ODA14p4, SRS476246; ODA14p2, SRS476247).
For cluster generation we used the Illumina TruSeq PE Cluster Kit V3 and for sequencing the Illumina TruSeq SBS V3 Kit. The base calling, filtering of the data, index sorting and the adapter trimming were performed automatically by CASAVA Pipeline version 1. 8. 0. We first mapped the reads against human genome assembly hg19, using BWA v0. 5. 9-r16  (21). We then selected discordant reads using samtools v0. 1. 17 (22)  and bedTools v2. 14. 2  (23). Discordant reads were aligned using novoalign v2. 08. 01 (Novoalign, www. novocraft. com), in two passes, once with the option '-r Random' and once with the option '-r Ex' in order to align missed concordant pairs in the first step. The remaining discordant mappings were processed with hydra-sv v0. 5. 3  (24). Finally, only breakpoints with more than two sequencing reads and falling into the amplified regions determined using Single-nucleotide polymorphism (SNP) data were selected.
The final structure was confirmed by PCR using primers designed in sequences localized at both ends of the contig. PCR products were sequenced by the conventional Sanger capillary sequencing method and compared with the reference genome to determine the exact position of the junctions. Sequence data used in this work refer to the human genome sequence (hg19 released February 2009) available at the University of California Santa Cruz (UCSC) Genome Bioinformatics site (http://genome. ucsc. edu/) (25). Sequence comparisons were performed using BLAT software. Repeated sequences (low-copy repeats, segmental duplications and repetitive elements) were identified using the human genome sequence data.
In ODA14, no small deletions were localized in the 50-bp sequences both sides of the junctions and we identified only five transition or transversion events (G to A or G to C) at five junctions (2, 5, 18, 19 and 82; Supplementary Fig-  ure S1 ). None of these nucleotide variations was present in the dbSNP data base, suggesting that they do not represent common polymorphisms. This lack of a high rate of mutations in the vicinity of the junction was not in favour of the involvement of a replication-based mechanism in their formation. Finally, no significant differences in the junction characteristics were found between chromosomes or passages (Supplementary Figure  S2 ).
The prp16 mutants display only very mild splicing defects for several intron-containing genes Typically, prp16 mutations cause a second step splicing defect  (35). However, initial RT-qPCR analysis of the prp16-D473E, prp16-Q685H and prp16-R686I mutants detected only very low levels of either lariat or pre-mRNA accumulation for ACT1 at 25 or 35 • C (data not shown). As the most striking effect on growth was seen on combining the brr2-R1889G and prp16-Q685H mutations, we analyzed splicing of several intron-containing transcripts by RT-qPCR in the single and double mutant strains as well as in the well characterized prp16-2 mutant. Figure  3  shows the levels of pre-mRNA, excised lariat/lariat-exon2, mRNA and exon2 for the ACT1 intron-containing gene in cultures grown at 25.
ACKNOWLEDGMENTS We thank  Patrizia Fabrizio  for the Prp16p E. coli expression vector,  Beate Schwer  for Prp22p E. coli expression vector,  Vladimir Pena  for the Brr2p Sec63-2p E. coli expression vector,  Alain Jacquier  for guidance with the genetic interaction screen and  Laurence Decourty ,  Antonia Doyen ,  Emmanuel Frachon  and  Christophe Malabat  for help with the screen. We are grateful to  Josette Banroques  and  David Tollervey  for critical reading of the manuscript. Author contributions: CS performed the GIM screen. RDA,  J. D. Barrass  and A. G. performed RNA analyses. DH and OC contributed equally to the other experimental work. JDB and OC designed the project, which was led by OC. JDB, DH and OC wrote the manuscript.
FUNDING Wellcome Trust  [ 087551  to  J. D. Beggs ,  092076  core funding grant];  Darwin Trust of Edinburgh  [studentships to D. H. and A. G. ];  French 'Agence Nationale de la Recherche ' [ ANR-08-JCJC-0019-01  to C. S. ];  Royal Society  [ Darwin Trust Research Professorship  to  J. D. Beggs]. Funding  for open access charge:  Wellcome Trust.
Statistical analysis Muscle fibre type distribution and cross-sectional areas were expressed as means and standard deviation. Statistical significance of the differences between means for the different combinations of antibodies was assessed by analysis of variance (ANOVA) using the GLM procedure of SAS Software (Statistical Analysis System, Cary, NC, USA). A Student's t-test was performed to compare the fibre type distributions obtained with the immunohistochemical method to those obtained with the electrophoresis method. A probability of less than 5% was considered statistically significant.
Characterisation of fibres by image analysis Fibre type composition was determined in 8 mice with the two selected combinations of antibodies using semi-automatic image analysis as described by Meunier et al. 16  The mean percentages of each fibre type were in agreement with the data presented in Tables  3  and 4 , and with data from the literature. In the TA, we revealed a predominance of type IIB (57%). A low percentage of hybrid IIA-X fibres (3%) was observed (Table  5 ). No hybrid IIX/IIB fibres were observed. This result was confirmed using anti RTD9 antibody (data not shown). The SOL consisted mainly of type IIA and I fibres (respectively 46% and 43%, Table  5 ). We did not observe any hybrid fibres in this muscle. We estimated the total number of fibres on the whole muscle section area in both SOL (muscle area 2 mm 2 ) and TA (mus-cle area <12 mm 2 ) muscles (Figure  3 ).
Relationships between immunohistochemical classification of fibres and electrophoretic separation of MyHCs isoforms In order to validate our classification we compared the immunohistochemical data with the proportion of each MyHC determined by electrophoresis for both muscles. We separated the four MyHC isoforms: fast (IIa, IIx, IIb) and slow (I) isoforms (Figure  4 ). The relative abundances of the MyHC isoforms separated by electrophoresis (Table  5 ) was compared to the classification of fibres obtained with the immunohistochemical technique for both muscles (Figure  5 A, B ). They showed not significant differences. Electrophoresis detected the presence of MyHC IIb in the SOL which was not revealed by immunohistochemistry.
Funding: The i-Select chips was funded by the French National Foundation on Alzheimer's disease and related disorders. The French National Fondation on Alzheimer's disease and related disorders supported several I-GAP meetings and communications. Data management involved the Centre National de Genotypage,and was supported by the Institut Pasteur de Lille, Inserm, FRC (fondation pour la recherche sur le cerveau) and Rotary. This work has been developed and supported by the LABEX (laboratory of excellence program investment for the future) DISTALZ grant (Development of Innovative Strategies for a Transdisciplinary approach to ALZheimer's disease) and by the LABEX GENMED grant (Medical Genomics). The French National Foundation on Alzheimer's disease and related disorders and the Alzheimer's Association (Chicago, Illinois) grant supported IGAP in-person meetings, communication and the Alzheimer's Association (Chicago, Illinois) grant provided some funds to each consortium for analyses.
EADI The authors thank Dr. Anne Boland (CNG) for her technical help in preparing the DNA samples for analyses. This work was supported by the National Foundation for Alzheimer's disease and related disorders, the Institut Pasteur de Lille and the Centre National de Genotypage. The Three-City Study was performed as part of a collaboration between the Institut National de la Santeet de la Recherche Medicale (Inserm), the Victor Segalen Bordeaux II University and Sanofi-Synthelabo. The Fondation pour la Recherche Medicale funded the preparation and initiation of the study. The 3C Study was also funded by the Caisse Nationale Maladie des Travailleurs Salaries, Direction Generale de la Sante, MGEN, Institut de la Longevite, Agence Francaise de SecuriteSanitaire des Produits de Sante, the Aquitaine and Bourgogne Regional Councils, Agence Nationale de la Recherche, ANR supported the COGINUT and COVADIS projects.
Thus the first aim of this study is to test for gene-wide association with AD, using a powerful mega-meta analysis of genome-wide datasets as part of the International Genomics of Alzheimer's Project (IGAP) Consortium comprising four AD genetic consortia (see the full list of consortia members in Materials S1): Genetic and Environmental Risk in Alzheimer's Disease (GERAD), European Alzheimer's Disease Initiative (EADI), Cohorts for Heart and Aging in Genomic Epidemiology (CHARGE) and Alzheimer's Disease Genetics Consortium (ADGC) (see full IGAP datasets description in Materials S2). A two stage study was undertaken. In Stage 1 the combined sample included 17,008 AD cases and 37,154 controls. In Stage 2 loci with p-values (combined over all SNPs at the locus) less than 10 24 were selected for replication for 8,572 AD cases and 11,312 controls of European ancestry.
med. miami. edu/myers/LFuN/data%20ajhg. html. Comparing 137 AD vs 176 controls with temporal or frontal cortex expression values by t-test, t showed significantly higher TP53INP1 expression in cases compared to controls (p = 0. 0128). Further examination in the BRAINEAC database  [22]  (www. braineac. org) from the UK Brain Expression Consortium showed TP53INP1 to have a best cis-eQTL p-value of 6. 8610 26 (for rs4582532 SNP, which is about 7. 6 kb upstream of the gene). The three SNPs with association p#10 24 mentioned above (rs4735333, rs1713669, rs896855) had significant cis-eQTL pvalues of 8. 2610 26 , 7. 8610 25 and 1. 1610 25 respectively in BRAINEAC brain expression data. The r 2 between the cis-eQTL and the three associated SNPs were 0. 80, 0. 65, and 0. 81, respectively). Further analysis of additional independent brain expression and methylation datasets (see Methods S1) indicated significant cis eQTLs and meQTLs for TP53INP1 (Tables  S10  and S11 ).
The probe for the meQTL is in a CpG island region that corresponds well with ENCODE DNAse/ChIP-seq/Histone marks and is located upstream (,1. 5 kb) of the TP53INP1 Table  1. Overrepresentation of replication of significant genes/loci available at Stage 2, excluding all loci of 0. 5 Mb around genes previously reported  [4] [5] [6] [7] [8]  and Stage 1 IGAP genes  [9, 19]  containing genome-wide significant SNPs. transcription start site. In combination these results suggest a possible epigenetic mechanism whereby the associated variants in the region influence TP53INP1 expression in several brain regions. These expression data provide further evidence supporting the functional relevance of TP53INP1 to AD susceptibility. The IGHV1-67 gene was not found in those databases. In addition we detected two genome-wide significant loci 1) ZNF3 (chr7: 99,661,653-99,679,371; p = 8.
Stage 1 data The main dataset was reported by the IGAP consortium  [9, 19]  and consists in total of 17,008 cases and 37,154 controls. This sample of AD cases and controls comprises 4 data sets taken from genome-wide association studies performed by GERAD, EADI, CHARGE and ADGC (see primary IGAP manuscript  [9, 19]  for more details). The full details of the samples and methods for conduct of the GWA studies are provided in the respective manuscripts  [4] [5] [6] [7] [8]. Each of these datasets was imputed with Impute2  [38]  or MACH  [39]  software using the 1000 genomes data (release Dec2010) as a reference panel. In total 11,863,202 SNPs were included in the SNPs allelic association result file. To make our analysis as conservative as possible, we only included autosomal SNPs which passed stringent quality control criteria, i.
e. we included only SNPs with minor allele frequencies (MAF) $0. 01 and imputation quality score greater than or equal to 0. 3 in each individual study, resulting in 7,055,881 SNPs which are present in at least 40% of the AD cases and 40% of the controls in the analysis. The summary statistics across datasets were combined using fixed-effects inverse variance-weighted meta-analysis. We corrected all individual SNPs p-values for genomic control (GC) l = 1. 087. These SNPs are well imputed on a large proportion of the sample, which increases confidence in the accuracy of the association analysis upon which gene-wide analysis is based.
Assignment of SNPs to genes SNPs were assigned to genes if they were located within the genomic sequence lying between the start of the first and the end of the last exon of any transcript corresponding to that gene. The chromosome and location for all currently known human SNPs were taken from the dbSNP132 database, as was their assignment to genes (using build 37. 1). In total, we retained 2,804,431 (39. 7% of the total) SNPs which annotated 28,636 unique genes with 1-16,514 SNPs per gene. For the gene-wide analysis we have excluded genes which contain only one SNP in the IGAP Stage 1 analysis, leaving a total of 25,310 genes. If a SNP belongs to more than one gene, it was assigned to each of these genes. In order to account for possible signals which are correlated with those in a gene, gene-wide analysis was also performed using a 10 kb window around genes to assign SNPs to genes.
Test for excess of associated SNPs/loci The effective number N of independent SNPs in the whole genome (excluding genes with SNPs that are genome-wide significant in the Stage 1 IGAP dataset 6 0. 5 Mb was estimated by the method described in  [43]  taking LD into account, as were the observed number of independent SNPs significant at each pvalue criterion (adjusting individual SNP p-values for genomic control l = 1. 087 before hand). LD was computed from the 1000 Genomes database (http://www. 1000genomes. org/). In the absence of excess association, the expected number of independent SNPs significant at significance level a is a normally distributed random variable whose mean and standard deviation (SD) can be calculated as aN and !Na(1-a) (mean and SD for a binomial distribution). The number of independent SNPs (and thus statistical tests) in the whole genome were estimated as ,3.
Karolien Bettens is a postdoctoral fellow of the FWO. The Antwerp site authors thank the personnel of the VIB Genetic Service Facility, the Biobank of the Institute Born-Bunge and the Departments of Neurology and Memory Clinics at the Hospital Network Antwerp and the University Hospitals Leuven. Finish sample collection: Financial support for this project was provided by the Health Research Council of the Academy of Finland, EVO grant 5772708 of Kuopio University Hospital, and the Nordic Centre of Excellence in Neurodegeneration. Italian sample collections: the Bologna site (FL) obtained funds from the Italian Ministry of research and University as well as Carimonte Foundation. The Florence site was supported by grant RF-2010-2319722, grant from the the Cassa di Risparmio di Pistoia e Pescia (Grant 2012) and the Cassa di Risparmio di Firenze (Grant 2012).
«fondazione Monzino». The authors thank the expert contribution of  Mr. Carmelo Romano. The Roma site received financial support from  Italian Ministry of Health , Grant  RF07-08  and  RC08-09-10-11-12. The Pisa site is grateful to  Dr. Annalisa LoGerfo  for her technical assistance in the DNA purification studies. Spanish sample collection: the Madrid site (MB) was supported by grants of the  Ministerio de Educacion y Ciencia  and the  Ministerio de Sanidad y Consumo (Instituto de Salud Carlos III) , and an institutional grant of the  Fundacion Ramon Areces  to the CBMSO. The authors thank  I. Sastre  and  Dr. A. Martı  ´nez-Garcı ´a for the preparation and control of the DNA collection, and  Drs. P. Gil  and  P. Coria  for their cooperation in the cases/controls recruitment. The authors are grateful to the  Asociacion de Familiares de Alzheimer de Madrid (AFAL)  for continuous encouragement and help.
A full list of CHS investigators and institutions can be found at http://www. chs-nhlbi. org/pi. The provision of genotyping data was supported in part by the  National Center for Advancing Translational Sciences, CTSI  grant  UL1TR000124 , and the  National Institute of Diabetes and Digestive and Kidney Disease Diabetes Research Center (DRC)  grant  DK063491  to the  Southern California Diabetes Endocrinology Research Center. Framingham Heart Study (FHS) : This work was supported by the  National Heart, Lung and Blood Institute's Framingham Heart Study  (Contract No. N01-HC-25195 ) and its contract with  A_ymetrix, Inc  for genotyping services (Contract No. N02-HL-6-4278 ). A portion of this research utilized the Linux Cluster for Genetic Analysis (LinGA-II) funded by the  Robert Dawson Evans Endowment  of the  Department of Medicine at Boston University School of Medicine and Boston Medical Center.