dataesr/scientific-paragraphs-categorization huggingface dataset:
stoloniferum, S. fendleri and S. polytrichon are phylogenetically related. This is consistent with the study of Jacobs et al. ,  [31]  which considered these three taxa as a single species. Our RanGAP2 dataset also confirms a lack of phylogenetic structure in Solanum section Petota partly attributed to numerous interspecific hybridizations at both the diploid and polyploid levels  [28]. This can explain how three pairs of species (S. tuberosum ssp andigena/S. phureja, S. tuberosum ssp tuberosum/S. vernei and S. vernei/S. spegazzinii) have one RanGAP2 haplotype in common. Positive selection hallmarks in RanGAP2 were searched using the Tajima's D statistic. Though negative values were mostly obtained for the species investigated, none appear significantly different from neutral expectations.
Positive values of the Tajima's D statistic were observed in  S. cardiophyllum (genome BB) and its sister derived species S. stoloniferum (genome AABB). It is tempting to speculate that the traces of balancing selection can be linked to the BB genome. However calculation of the values of the Tajima's D statistic was hampered in most of the other species corresponding to the BB genome by the lack of at least four different alleles. We also took advantage of the sequencing of RanGAP2 in multiple species to investigate the evolutionary constraints acting on this gene based on dN/dS ratios. Using a reduced dataset made of one consensus sequence per species in order to consider only inter-specific sequences as is recommended  [33] [34] [35] , RanGAP2 does not appear to be under positive selection and appears rather to be under strong evolutionary constraints as previously suggested by its low diversity and as also confirmed by the numerous (at least 38) sites under purifying selection identified by both SLAC and FEL analysis.
However, using the complete sequence dataset we were able to identify two key (aa position 106 and 237) that are predicted by at least two different methods to be under positive selection. One possible explanation of this pattern is that alleles displaying these two amino acid changes, also found in linkage disequilibrium, have passed through the different Solanum species as an advantageous combination. In a similar way, key residues under positive selection were detected in the translation factor eIF4E, which is also involved in resistance to potyviruses in pepper, using a data set comprising both intra-and inter-specific sequences  [36, 37]. Similarly to eIF4E, the two key positions identified in RanGAP2 using the whole RanGAP2 dataset could be linked to its role in the incompatible resistance interaction between CP and Rx or Gp-RBP-1 and GPA2.
Diversity at position 106 could thus affect the three-dimensional conformation of the entire GPA2/RanGAP2/GP-RBP-1 complex Theoretical combinations of proline (P) and serine (S) at position 106 with phenylalaline (F) and leucine (L) were calculated using the frequency of each amino acid in the total dataset and assuming that the nature of an amino acid at position 106 is not linked to the nature of an amino acid at position 237. These theoretical combinations were compared to the observed combinations in the dataset (A). Linkage disequilibrium between residues at positions 106 and 237 was evaluated using the D' value, the significance of which was tested with Fisher and Chi-square tests (B). and thus contribute to the initiation of defense mechanisms by facilitating transition from an auto-inhibited to an active form of the NB-LRR protein  [5].
Methods Plant materials, DNA isolation, amplification and cloning Nicotiana benthamiana seeds were germinated and plants were grown for 5 weeks in a Conviron growth cabinet (Conviron, http://www. conviron. com), where conditions were as follow: 21°C/21°C day/night, 16-h day, 60% relative humidity, and light intensity of 100 μmol m -2 s -1. Fifty five diploid and tetraploid accessions from 18 Solanum species belonging to the plastid DNA clade 2 and 4 of section Petota  [29]  were examined (Table  5 ). Total DNA from each accession was isolated using the protocol described by Fulton et al. [49]. A Genbank RanGAP2 S. tuberosum sequence (http://www. ncbi. nlm. nih. gov/nuccore/AM411448) was used to design primers in the 5' and 3' ends of the 1662pb intronless gene. PCR reactions were carried out in a final volume of 25 μL using 30 ng of template genomic DNA, 0.
5 unit of Taq polymerase (Takara Ex Taq™) and 6μL of the 10× Ex Taq Buffer. The PCR protocol was 5 min at 98°C, followed by 35 cycles of 10 sec at 98°C, 30 sec at 55°C, 2 min 30s at 72°C and a final step of 10 min at 72°C. PCR products were sequenced by Genoscreen using the following three primers: RanGap2JC695-R reverse primer (5' CTAACTCCCTTCTCACCCAGA 3') for the 3'end sequence, RanGap2JC435-F forward primer (5' GCCATTAAAAGAGCCTGGAA 3') for the 5' end sequence and RanGap2JC1015-F forward primer (5' GGTCCAGAAGTTGGTCTTGTGT 3') as an internal sequencing primer. All the sequences have been deposited to GenBank/EMBL databases under the following accession numbers HE681572 to HE681718. For each RanGAP2 allele, the EMBL number accession is reported in Additional file 1: Table  S1.
Sequence alignments and evolutionary analyses Previously obtained sequences were assembled using the cap contig assembly program of Bioedit  [50]. This same module was used to construct the consensus sequence of RanGAP2 for each species. When possible, Mega5 software was used to manually correct ambiguous nucleotides based on the chromatograms  [51]. RanGAP2 sequences were aligned using Mega5  [51]  and the ClustalW (1. 6) DNA weight matrix. Mega5  [51]  was also used to find the best DNA substitution model fitting our dataset. Phylogenetic analyses on RanGAP2 sequences were carried out using, maximum likelihood and maximum parsimony methods and minimum evolution algorithms with the Tamura 3-parameter model  [52]  and a Gamma parameter of 0. 163. This model was the best model fitting our dataset and available in Mega5 software  [51].
The robustness of the minimum evolution trees was evaluated by bootstrapping with 1000 repetitions. Motifs were detected in translated DNA sequences using SMART (Simple Modular Architecture Research Tool)  [53]. The pi indicator (average number of nucleotide differences per site between two sequences), haplotype diversity was computed using DnaSP v5 software  [54]. To examine whether RanGAP2 has evolved under positive selection we used the ratio of non-synonymous to synonymous substitution rates per site (ω=dN/dS) estimated by site specific models implemented in the PAML package v 3. 14  [55]. The tree used in PAML analysis was first obtained after running M0 in PAML (model = 0 and NS sites = 0. The CODEML program of PAML assigns a likelihood score to models for selection. A likelihood score for a model incorporating positive selection (M2 or M8) that is higher than that for a null model without positive selection (M1 or M7) is evidence for positive selection.
To identify the sites under positive selection we used several different methods including the Bayes Empirical Bayes implemented in CODEML, which calculates the posterior probabilities that each site fell into a different ω class, the Single-Likelihood Ancestor Counting (SLAC)  [56]  and the Fixed-Effects Likelihood (FEL)  [56] , both available through the DataMonkey web interface  [57]. Linkage disequilibrium values between sites of interest were evaluated by calculating the " D' " value associated with its Fisher and Chi-square statistical tests, using DnaSP v5 software  [54]. The intra-and inter-species /genotype variabilities were evaluated by AMOVA using Arlequin 3. 1 software  [58].
Detailed informations on the Solanum species analyzed in this study (Continued)The species and country of origin of the 55 accessions used in this study are detailed in the table. The genotype code used in this study is indicated with the corresponding accession number of the considered genotype. G. pallida and PVX resistance (Rce) information is also included for each genotype. Resistance to G. pallida may have been evaluated only for pathotype 3 (*) or pathotype 2 (**). These informations were obtained from either the Sturgeon Bay collection, Braunschweig Institute or INRA. The amino acid at position 106 and 237 for each RanGAP2 sequences obtained are also indicated in the table.
Acknowledgements We thank the  genetic resource centre BrACySol (INRA Ploudaniel)  for providing the Solanum accessions. We are grateful to  Florence Esnault  for critical reading of the manuscript. JC is supported by the  Région de Bretagne  through a three year PhD grant (nb  08005871 ). We thank the  INRA departments "Génétique et Amélioration des Plantes" and "Santé des Plantes et Environnement"  for their financial support. We also thank the  Université Européenne de Bretagne  for providing a grant to  Jean Carpentier  to visit the  Université de Sherbrooke  and all members of the  Moffett lab  for their support and input during this three month period. The Moffett lab is supported by funds from the  National Sciences and Engineering Research Council of Canada.
11; finally, we searched the DECIPHER database for previously identified 16p13. 11 copy number variants. In the clinical referral series, we identified 46 cases with CNVs of variable size at 16p13. 11, including 28 duplications and 18 deletions. Patients were referred for various phenotypes, including developmental delay, autism, speech delay, learning difficulties, behavioural problems, epilepsy, microcephaly and physical dysmorphisms. CNVs at 16p13. 11 were also present in 17 controls. Association analysis revealed an excess of CNVs in cases compared with controls (OR = 2. 59; p = 0. 0005), and a sex-biased effect, with a significant enrichment of CNVs only in the male subgroup of cases (OR = 5. 62; p = 0. 0002), but not in females (OR = 1. 19, p = 0. 673). The same pattern of results was also observed in the DECIPHER sample.
Array CGH Analysis Testing was carried out at a cytogenetics CPA accredited laboratory. DNA samples were analyzed by array comparative genomic hybridisation (aCGH), using a 60 K Agilent array (designs 028469 and 017457), with a total imbalance detection rate of 24%. Array CGH analysis was performed as described previously  [30]. In brief, DNA extracted from blood samples (1 mg) was labelled using CGH Labelling Kit for Oligo Arrays (Enzo Life Sciences, USA), then applied to a 60 K oligonucleotide array (Agilent, USA). Image quantification, array quality control and aberration detection were performed using Feature Extraction and DNA Analytics software packages (Agilent, USA) for oligo arrays, according to the manufacturer's instructions. All copy number variations in the 16p13. 11 region  (46/46)  were confirmed either by a second CGH array with a different comparison sample or by a multiplex ligation-dependent probe amplification assay (MLPA kits P064, P245 and custom probes; MRC-Holland, Netherlands)  [30, 31].
Genomic data and referral phenotype information was recorded in a clinical database, which at the time of analysis contained 10,397 clinical referrals (63. 4% males; October 2012), including approximately 1,400 patients referred for ASD, 26% of whom were female. The overall ethnic distribution (self-reported data) was 70% Caucasians, 15% Africans and 15% other/mixed ancestry. Copy number variants in this population are available in the Brain and Body Genetic Resource Exchange database (BB-GRE; http://bbgre. org).
DNA samples were derived from immortalised cell lines (58 BC cohort) and venous blood (screened controls and NBS cohort). Screened control samples were genotyped on the Illumina HumanHap 610-Quad beadchip, whereas WTCCC2 samples were genotyped on a modified Illumina 1 M beadchip. To ensure comparable CNV detection from different array types, control CNVs were identified using a consensus marker set between the 610 K and 1 M chips, which mimics the Illumina HumanHap 550 beadchip (detailed description of data analysis and quality control criteria can be found in the Methods S1 and in Rucker et al. [34] ). Additionally, we used control data from two previously published studies by Shaikh et al. and Cooper et al. [35, 36]. The Shaikh control sample consists of 2,026 healthy children (1,104 female, 922 male) recruited within the Children's Hospital of Philadelphia (CHOP) health care network, uniformly genotyped using the Illumina HumanHap 550 beadchip, with DNA samples obtained from whole blood, (overall precision.
96% in identifying CNVs represented by. 10 probes) (http://cnv. chop. edu) [35]. The Cooper control sample originally consisted of 8,329 individuals, but we used genomic information only for the subset of 3,173 subjects (2,148 female, 1,025 male) for which gender data were available. DNA was obtained from cell lines (HGDP, n = 984), and blood samples (London, n = 760; FHCRC, n = 1,429), and genotyping was performed using the Illumina HumanHap 550 K, 650 Y and 610-Quad beadchips, with an overall precision. 89% in identifying CNVs. 100 kbp (dbVar, nstd54)  [36]. Ethnic distribution in the total control population (n = 11,277) was 77% Caucasians, 8. 5% Africans and 14. 5% other/mixed ancestry. Although the control sample was slightly enriched in Caucasians (77% vs 70%) and had slightly fewer African individuals (8.
DECIPHER Database Search We performed a search in the DECIPHER database (https:// decipher. sanger. ac. uk), in order to identify additional cases with CNVs in the 16p13. 11 region. DECIPHER (Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources) is an interactive web-based database that collects clinical phenotype information and copy number change data from a sample of. 18,000 patients suffering from developmental disorders, enabling clinical scientists worldwide to maintain records for their patients and to share this information with the clinical research community  [41]. At the time of analysis (October 2012), the DECIPHER database contained 18,451 clinical referrals, 54% of whom were male.
500 kpb in size (comparable sensitivity and specificity between aCGH and SNP arrays) (Table  S1 , Table  S2 ). This additional analysis confirmed all the results described above, both overall (OR = 2. 64; p = 0. 0013), and in the male (OR = 6. 35; p = 0. 00048) and female subgroups (OR = 1. 13; p = 0. 794). In an attempt to further confirm our findings, we next tested for a sex-biased prevalence of the variations also in the DECIPHER sample. The DECIPHER database search identified 101 patients with NAHR-mediated CNVs at the 16p13. 11 locus, including 61 duplications and 40 deletions, with nine distinct CNV categories (Figure  S2 , Table  S3 , Table  S4 ). Overall, we observed a significant enrichment of CNVs in the cases compared with controls (OR = 3. 35; p = 9. 8610 27 ), with the effect coming from both deletions (OR = 5.
16p13. 11 CNVs in DECIPHER Performing a search in the DECIPHER database (https:// decipher. sanger. ac. uk)  [41] , we identified 101 subjects with NAHR-mediated CNVs at the 16p13. 11 locus, including 61 duplications and 40 deletions (Figure  S2 , Table  S4 ). Phenotypic information was available for 78 of the 101 patients (49 duplication carriers and 29 deletion carriers), and between them, seven cases (patients 250947, 250061, 1230, 249225, 993, 4598, 250436) were not diagnosed with a neurodevelopmental disorder, but were referred for physical dysmorphism and congenital anomalies. Information about the inheritance pattern of the variations was available for seventy-one family trios. Five duplications (3 males, 1 female, and 1 unknown sex) and seven deletions (6 males and 1 female) arose de novo, whereas fifty-nine variations were inherited from a parent, including forty duplications (24 maternal, 11 paternal, and 5 unknown sex) and nineteen deletions (8 paternal, 6 maternal, and 5 unknown sex).
Twentyseven of the 101 patients (19 duplication carriers and 8 deletion carriers) harboured one or more additional genomic imbalances, either clinically significant (37%) or of uncertain clinical significance (63%) (Table  S4 ). Notably, the DECIPHER database search also identified two patients (250140 and 265264) carrying non-NAHR mediated 23 kbp microdeletions encompassing the NTAN1 gene (chr16:15,131,723-15,154,746) identical to those we found in two cases of the referral series (Figure  S1 ). Phenotypes of the patients and inheritance pattern of the variations were unknown, and both probands harboured a second genomic imbalance of uncertain significance (dupl 2q13 and del 12q13. 3) (Table  S4 ). Patients with duplications mostly presented with developmental delay (43/49) and physical dysmorphism (n = 24).
Association analysis showed a significant enrichment of NAHRmediated CNVs in the cases compared with controls, with the strongest overrepresentation coming from deletions. In line with our preliminary hypothesis, we observed a sex-biased effect, with a significant enrichment of CNVs only in the male subgroup of cases, also confirmed in the DECIPHER sample. All the findings also held after excluding from the analysis cases and controls with rare second-hit CNVs. 500 kpb in size. Assuming an equal incidence of the 16p13. 11 imbalances in males and females, our data clearly suggest a male bias in the penetrance of the neurodevelopmental phenotypes at the 16p13. 11 locus. Importantly, in re-examining the data reported in the literature, we found a trend toward a male-specific prevalence of 16p13.
Acknowledgments We would like to thank  Prof Evan Eichler ,  Dr Bradley Coe  and the  CHOP CNV team  for the kind cooperation and for sharing the gender data for controls. We thank  Dr Aoife McLysaght  and  Dr Takashi Makino  for providing the ohnologs data. We also thank  Drs J. Swaminathan ,  E. Bijlsma ,  B. Dallapiccola ,  A. Destre  ´e,  H. Goel ,  J. Graakjaer ,  S. Kjaergaard ,  C. Le Caignec ,  F. Mari ,  M. Mucciolo ,  A. Novelli ,  A. Renieri ,  C. Rosenberg ,  J. Shelagh ,  M. Splitt ,  Z. Tu ¨mer  and  O. Vanakker  for providing additional data on the DECIPHER families. This study makes use of data generated by the  DECIPHER Consortium. A full list of centres who contributed to the generation of the DECIPHER data is available from http://decipher. sanger. ac. uk and via email from ; decipher@sanger.
This project and the  BBGRE database (BBGRE. org)was funded through a strategic partnership of the  South London and Maudsley Trust NIHR specialist Biomedical Research Centre  and the  Guys and St Thomas Trust NIHR comprehensive Biomedical Research Centre. DAC is funded by the  European Commission Seventh Framework project PsychCNVs  (http://www. psych-cnv. eu/;Grant agreement number  HEALTH-2007-2. 2. 1-10-223423 ). This work was supported by the  Wellcome Trust  ( Wellcome Trust  Case control consortium; WTCCC2) (DAC). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Methods: We constituted a cohort of women over 65 receiving a first AI therapy for breast cancer between 2006 and 2008, and followed them until June 2011. Women were selected in the population-based French National Health Insurance databases, and data was collected on the basis of pharmacy refills, medical records and face-to-face interviews. Nonpersistence to treatment was defined as the first treatment discontinuation lasting more than 3 consecutive months. Time to treatment discontinuation was studied using survival analysis techniques. Results: Overall among the 382 selected women, non-persistence to treatment went from 8. 7% (95%CI: 6. 2-12. 1) at 1 year, to 15. 6% (95%CI: 12. 2-19. 8) at 2 years, 20. 8% (95%CI: 16. 7-25. 6) at 3 years, and 24. 7% (95%CI: 19. 5-31. 0) at 4 years. In the multivariate analysis on a sub-sample of 233 women with available data, women using complementary or alternative medicine (CAM) (HR = 3.
Introduction In the field of oncology, the use of oral therapy is on the rise, and treatment adherence is under increasing scrutiny  [1, 2]. Oral adjuvant hormonal therapy in hormone-responsive early breast cancer (BC) reduces the risk of recurrence and increases survival rates  [3]. Aromatase Inhibitors (AIs) were shown to improve disease-free survival as compared to tamoxifen in post-menopausal women  [4, 5, 6, 7, 8]. They therefore constitute an alternative to adjuvant treatment of early BC  [9, 10]. Non-adherence and early discontinuation of hormonal treatment are likely to affect treatment efficacy in BC patients  [3, 11, 12, 13]. In a recently published meta-analysis on 29 observational studies, discontinuation rates for AIs ranged from 31 to 73% over the treatment period  [14, 15]. These heterogeneous results are derived either from pharmacy databases or from samples of limited size using self-reported measures of adherence.
Studies on the determinants of non-adherence are therefore limited either by self-reported measures of adherence -known to largely overestimate adherence -or by access to a restricted number of covariates in available pharmacy databases. While most database studies in pharmacoepidemiology use high quality pharmacy and medical data, they only rarely link these with medical records or with patient questionnaires. Combining data sources is necessary to improve our understanding of medication consumption patterns in conjunction with the patients' broader environment  [16]. Our objective was to combine multiple sources of data to obtain a description of adherence and persistence with AI treatment (along with their determinants) in a population-based cohort of post-menopausal women with primary BC.
Primary data source The primary data source for patient selection was provided by The French National Health Insurance System (NHIS). The NHIS delivers universal health coverage; hence its database is population-based, i. e. it covers all segments of the population. Data was obtained from the NHIS which provides health insurance to 98% of the French population. The study area comprised 3 French administrative districts (Alpes-Maritimes, Bouches-du-Rhone, Var), which correspond to a population of approximately 4 million inhabitants. In France, hormonal therapy treatment is available only in pharmacy by medical prescription. Level of reimbursement varies according to drug and patient characteristics. BC patients are reported to the NHIS by their physician and receive all treatment free of charge.
Study Population The ELIPPSE 65 cohort was constituted in order to document the medium and long-term psychosocial impact of BC on women over 65. Eligible participants were women with a biopsy-proven diagnosis of primary BC who had been registered in the NHIS database between October 2006 and December 2008. Women were excluded if they had a previous history of BC; if they suffered from severe cognitive impairment, deafness or acute mental disorder; or if they were unable to answer a questionnaire. Followup was interrupted in June 2011. We restricted the analysis to cohort members who received at least one supply of AI treatment for BC, as registered in the NHIS medication database.
Data Collection Patient Data. In the month following BC diagnosis, all eligible women registered in the NHIS database were sent an explanatory letter about the survey by the NHIS medical advisory board and invited to return their written consent. Women who agreed to participate in the ELIPPSE 65 cohort were then sent a short self-administered questionnaire by mail, which included questions on patient characteristics and the circumstances of patient diagnosis. The follow-up comprised an in-home, face-toface interview at 10 months. These interviews provided data on socio-demographic and psychosocial characteristics, drug use, complementary and alternative medicine (CAM) use, medical follow-up, and a geriatric assessment conducted as part of this study. The geriatric assessment focused on independent living skills with the Activities of Daily Living scale (ADL)  [18] , the Instrumental Activities of Daily Living scale (IADL)  [19] , and cognitive functions by the Mini-Cog  [20].