dataesr/scientific-paragraphs-categorization huggingface dataset:
To better evaluate the evolutionary history between C. robusta and C. intestinalis populations, we used a population graph approach implemented in the TREEMIX program  (Pickrell & Pritchard 2012) , which infers patterns of splitting and migration between populations. By using the matrix of allele frequency covariance between pair of populations, this method generates maximum likelihood population trees under the hypothesis of an absence of migration or the alternative hypothesis of migration event(s) (that are sequentially added). By comparison with other methods commonly used to make demographic inferences or to picture population relationships over time (e. g. Beaumont et al. 2002; Gutenkunst et al. 2009; Hey & Nielsen 2001) , TREEMIX has the advantage to be applicable to a large number of populations by using a tree-construction based approach and, at once, testing for gene flow between populations  (Pickrell & Pritchard 2012).
To avoid noises due to small sample sizes and intra-specific migration (i. e. infra-specific admixture), we pooled populations according to the region of sampling (i. e. no. 4a and 4b for C. intestinalis; no. 5 and 6 and no. 7 to 12 for each species). Using the total dataset (i. e. 310 loci), we search for the best tree to fit the data testing for a range of migration events from 0 to 8 (reaching an asymptotic value, Figure  S3 ). Based on these inferences, we used a block-jackknife procedure with blocks of 10 SNPs to determine which migration events significantly improved the model fit. A complementary analysis based on f3-statistic test, developed by  Reich et al. (2009) , was done to test the null hypothesis that the evolutionary history of Ciona populations was consistent with the absence of migration events between populations.
Diversity of the SNP panel Overall, 451 individuals (including the two F1-hybrids from experimental crosses) were genotyped successfully at 310 SNPs defined from a transcriptome dataset of Ciona robusta and C. intestinalis  (Roux et al. 2013). Following this genotyping, the distribution of SNPs across the categories, defined from a small sample of 10 specimens for each species, was modified, as shown in Table  S1. The most substantial change was a decrease of the sf and sxA categories (i. e. a decrease of 31% and 22%, respectively) and a concomitant increase of the sxB and ss categories (17% and 22%, respectively). We considered these new categories in the analyses below.
Low hybrid index disregarding the regional category and population status A total of 105 loci, showing a FST strictly superior to 0. 9, were used with the R package INTROGRESS to examine the patterns of shared polymorphism between the two species in the contact zone and in allopatric populations. At the species level (i. e. across all individuals for each species), values of h were very low, with an average value across individuals of 0. 0029 for C. robusta and 0. 0055 for C. intestinalis. Table  1  is providing the average values of the hybrid index (h) for each population of C. robusta and C. intestinalis. A noticeable result was the presence of one individual in this latter population with an h value of 0. 5. When removing this individual from the h estimation, the value in Camaret dropped to 0.
006, a value close to the average values for C. intestinalis populations. This individual was assigned with a probability of 1 to a 'F1 hybrid' with NEWHYBRIDS (Table  1 ) with the 105 SNPs dataset; a result confirmed with the full (310 SNPs) and the random (58 SNPs) dataset. The two F1hybrids obtained experimentally were also assigned with a probability of 1 to the 'F1-hybrid' category which ascertains the robustness of NEWHYBRIDS for detecting individuals derived from recent crosses. It is noteworthy that all the other study individuals were assigned to their respective parental 'species' categories (Table  1 ). We also examined the relationship between h-value and the heterozygosity rate across the 105 loci used with INTROGRESS, by using a triangle plot displayed in Figure  2 : all except one individual displayed extreme h-values (closed to 0 or 1) and an extremely low proportion of heterozygote loci for C.
Heterogeneous polymorphism rates at the genome level The subset of 105 SNPs used for examining the patterns of shared polymorphism between the two species (i. e. showing FST values higher than 0. 9) showed the following patterns over the whole dataset: 65 were differentially fixed (i. e. sf loci), 39 with private polymorphisms (i. e. sxA or sxB; 8 polymorphic in C. robusta and 31 in C. intestinalis) and only one locus showing shared polymorphism (i. e. ss locus) between populations of the two species (snp18 on the chromosome 1). The 40 loci showing shared and private polymorphisms were distributed randomly along the genome of the two species (Fig. 4a ), as previously observed in  Roux et al. (2013). Among the 105 SNPs, some were found in two introgression hotspots defined by  Roux et al. (2013).
Using a large number of informative loci with a large sample, we found that with the exception of a single individual all the other occurrence of shared polymorphism are the likely consequence of a low level of past introgression, i. e. ancient gene flow between the two species, rather than contemporary hybridization. At a given locus some individuals can be found heterozygotes at quasi diagnostic loci, but averaging at many such loci shows every individual have the same hybrid index value. The only contemporary hybrid was a F1, as supported by both NEWHYBRIDS (whatever the dataset used) and INTROGRESS analyses (Table  1 , Fig. 2  and 4a ). The mtDNA type of this individual is typical of C. intestinalis which corresponds in many studies to crosses easily produced in laboratory experiments  (Bouchemousse et al.
2016; Harris & Nielsen 2016). None of the loci identified matched with genes coding for a known phenotypic or physiological trait (Table  S4 ). It    Terminal nodes are labelled by locality number (Table  1 ). Note that we pooled populations according to regions of sampling (i. e. no. 4a and 4b for C. intestinalis; no. 5 and 6 and no. 7 to 12 for each species) to avoid noises by intra-specific admixture events. Admixture arrows are colored according to the migration weight. The two admixture events significantly improved the model as compared to a situation without migration (P < 0. 001). Results of the STRUCTURE analysis on additional dataset. STRUCTURE analyses were carried out for K = 2 using a subset of 1) 58 SNPs randomly selected, 2) 105 SNPs used in the INTROGRESS analysis (i. e. highly differentiated loci with FST > 0.
9, see Fig. S2 ), 3) 245 SNPs: all except the SNPs that were differentially fixed between the two species, and 4) 42 SNPs polymorphic in the two species. Using different subset of markers do not influence the admixture patterns (see also Fig. 3b  in the main text for the same analysis carried out on the full dataset). The F1-hybrid found in the Camaret (no. 11) population and the F1-Hybrids experimentally produced (Exp F1) are well recovered by the analysis, including with the 42 SNP panels which is composed only of loci polymorphic in the two species, a property that is prone to false identification. Terminal nodes are labelled by locality number (Table  1  in the main text). Note that the single F1-hybrid sampled in natural populations (no. 11) was removed of the analysis. Table  S1. Number of SNPs per categories defined according to their polymorphism patterns: 1) sf: loci differentially fixed between the two species; 2) sxA: loci polymorphic in Ciona robusta only; 3) sxB: loci polymorphic in C.
Acknowledgment The authors are very grateful to  C. Roux  and  N. Galtier  for making available RNA sequences from the  Pophyl  Project,  K. Belkhir  of the  Montpellier Bioinformatics Biodiversity computing platform  for his precious help to the optimization of loci selection and the  ADN id society (Montpellier)  for the genotyping of SNPs. We are also grateful to all our colleagues who contributed to the collection of samples: the divers of the  Marine Operations department (Service Mer & Observation) at the Roscoff Biological Station ,  J. D. D. Bishop ,  S. Krueger-Hadfield ,  B. Lundve ,  J. Pechenik. The authors kindly acknowledge  C. Roux  and  C. Fraisse  for help and advices on R packages and scripts and three anonymous reviewers for their helpful comments and advices on the manuscript.
An exponential fit, f (t) = A 0 exp(-ln 2 T t) + B is performed to extract the lifetimes and the number of detected isomers for this multiplicity range. The fit parameters are reported in Table  1. According to the fit results, the peaks located at 762 keV and 1. 1 MeV are associated with isomers with lifetimes of T 1/2 = 35. 0 ± 0. 9 ns and T 1/2 = 10. 8 ± 0. 5 ns, respectively. In the nuclear table from  [15] , these two isomers are identified as the J π = 5/2 -, T 1/2 = 32. 8 ± 2. 4 ns level located at 761. 7 keV and the J π = 15/2 + , T 1/2 = 11. 1 ± 1. 0 nslevel located at 1356. 9 keV respectively. In this database, the T 1/2 = 11. 1 ns isomer is fed by another isomer located at 1437. 9 keV whose lifetime is not accurately known: T 1/2 < 13 ns. As we have not succeeded in fitting the decay curve of Fig.
P<0. 05 was considered to indicate a statistically significant difference. Statistical analysis was performed using by MedCalc v12. 5 (MedCalc Software bvba, Ostend, Belgium). Tumor characteristics. The characteristics of all tumors are presented in Table  I. The tumors were grade 1, 2 and 3 in 16. 3, 53. 3 and 30. 4% of patients, respectively. In addition, 32. 6, 30. 4, 21. 7 and 15. 2% of patients were N0, N1, N2 and N3, respectively, and tumor size was T1, T2 and T3 in 20. 7, 69. 6 and 9. 8% of patients, respectively. ER was positive in 82. 6% of patients and negative in 17. 4%, while PgR was positive in 81. 5% of patients and negative in 18. 5%. The IQR M estrogen and progesterone Allred scores were 6. 2 and 5, respectively. HER-2 expression was classified as 0, 1, 2 and 3 in 44. 6, 16.
Therefore, the X-linked SNPs outside of the PARs that were reported as heterozygous in males were excluded. To control whether other SNPs, including autosomal SNPs, could map on the Y chromosome and bias our results, we performed a systematic sequence similarity search using  BLAST (Altschup et al. 1990 ) of their flanking sequences (±30 bp around the SNP) against the Y chromosome sequence (using the hg18 human genome assembly). Any SNP whose flanking sequences had a perfect match with Y-linked sequences was removed (36 SNPs; supplementary table S2, Supplementary Material online). After quality control, the mean number of SNPs per population was 1,122,087 SNPs. We focused most of our analyses on genic SNPs. The positions of all genes known to date were downloaded from the UCSC database (build NCBI36/hg18;  Karolchik et al.
Investigating a Sex-Specific Population Structure We first evaluated the level of sex-specific stratification in each of the 11 populations from HapMap. We calculated the allele sharing distance (ASD)  (Bowcock et al. 1994 ) between individuals using the software asd (http://szpiech. com/software. html, last accessed May 2, 2016) developed by Zachary Szpiech and performed a multidimensional scaling (MDS) analysis on these genetic distances. Because missing data result in skewed ASD values, we only included individuals harboring less than 0. 5% of missing data. Additionally, we LDpruned (linkage disequilibrium) the data to keep only independent SNPs using the "-indep-pairwise" option in PLINK  (Purcell et al. 2007 ) with an r 2 threshold of 0. 25 within a window of 50 SNPs and a step of 10 SNPs.
Concordance between the 1000 Genomes Project and the HapMap Data Set We compared the allelic frequencies of the SD SNPs (genic and genome-wide) between data sets obtained with different molecular technologies: HapMap III. 3  (Altshuler et al. 2010 ), a genotyping data set, versus the 1000 Genomes (1000 Genome Project Consortium 2010), a resequencing data set. For this comparison, we used the 1000 Genomes Phase 1 SNP calls data set, which contains the genotype of 1,092 individuals for 14 populations, including 8 populations shared with the HapMap data set. This allowed us to detect genotypes with discordant allelic frequencies between the two molecular technologies which therefore are likely to present technical issues. To assess significance, two Fisher's exact tests were performed, respectively comparing the allelic frequencies of males and females.
Functional Enrichment Analysis A gene was defined as SD if it contained at least one genic SD SNP in one population within ±5 kb of its coordinates. Each SD gene was associated with the lowest P-value of its genic SD SNPs. For this analysis, we did not use the list of LD-pruned genic SD SNPs because this would result in randomly removing one of the linked SNPs and therefore excluding SNPs with potential functional significance. We detected 5,705 SD genes, by pooling all populations and all chromosomes. We performed a genome-wide functional enrichment analysis on the SD gene list using the DAVID functional annotation chart tool  (Huang et al. 2009). A subset of the Gene Ontology database, the GO FAT set, was used to calculate the functional enrichment, allowing a better readability of the results by keeping only specific terms.
2004 ). However, recurrent sex-specific admixture events, with constant migrations biased toward one sex, would affect allelic frequencies both on the autosomes and the X chromosome. To assess whether such structures exist in our data set, we performed an MDS analysis on each of the 11 HapMap populations and tested whether the genetic distance between males and females was significant. The MDS analyses were based on pairwise ASDs among individuals, computed either for the autosomes or for the X chromosome (supplementary figs. S3 and S4, Supplementary Material online). On the autosomes (supplementary table S5, Supplementary Material online), the LWK population (Luhya from Webuye, Kenya) showed a significant mean genetic distance between males and females (P = 0. 03) and was therefore removed from the study.
Therefore, differences in LD between chromosomes do not lead to a bias of significant SNPs in favor of the X chromosome. Noteworthy, chromosome 19, which tends to show higher proportions of genic SD SNPs compared with the other autosomes, is known to have a high gene density compared with the other chromosomes  (Grimwood et al. 2004 ). To evaluate whether genotyping errors in the HapMap data set could lead to an excess of genic SD SNPs on the X chromosome, notably because of genotyping quality issues owing to male hemizygosity, we also performed our analysis exclusively on SNPs that had concordant allelic frequencies between the genotyping data set used here (HapMap III) and a resequencing data set-the 1000 Genomes project (1000 Genome Project Consortium 2010). Even though four autosomes that were previously significantly different from the X chromosome did not reach significance in this analysis (supplementary fig.
In our data, the mean F ST observed for genic SD SNPs after LD-pruning in the nonadmixed HapMap populations is of 0. 092 on the X chromosome, while it is of 0. 067 on autosomes. Considering our simulation results before resampling, these F ST values would require extreme selection coefficients, higher than 0. 5, which are exceedingly unrealistic. However, when we take into account the sampling effect, we show that such F ST values can be observed for selection coefficients as low as s = 0. 1. Given the high variance, it is difficult to assess the selection coefficients necessary to produce the observed F ST , and the study of a data set with larger sample sizes will be necessary to estimate the strength of SA selection on viability acting on human populations.
Pseudoautosomal Regions Another region of particular interest to study SA polymorphism would be the PARs, which have recently been the subject of several theoretical and empirical studies  (Qiu et al. 2013; Charlesworth et al. 2014; Kirkpatrick and Guerrero 2014). Indeed, they are the only regions of the sex chromosomes to exhibit autosomal features for recombination and inheritance, but their evolutionary dynamics are also influenced by their sex linkage. Under some conditions, it has been theoretically shown that the maintenance of SA polymorphisms on PARs is facilitated compared with sex-specific regions of the X chromosome and to the autosomes  (Otto et al. 2011). The genotyping of the PARs in the HapMap data set is currently not of high enough quality to be further studied. It would however be interesting to investigate in the future signatures for SA selection in these regions, for example, with resequencing data sets.
Acknowledgments We thank  Mark Kirkpatrick ,  Paul Verdu ,  Frederic Austerlitz ,  Patricia Balaresque  and two anonymous reviewers for useful comments and suggestions. E. A. L. was financed by a PhD grant from the  French Ministry of Higher Education and Research. Part of this work used the high performance computing resources " Calcul Intensif et Algorithmique" (PCIA)  from the  Museum National d'Histoire Naturelle (MNHN).
Varietal Diversity: Past and Current State for Yams in Guadeloupe We examined variety reports with a list of 20 varieties of D. alata and other species (D. rotundata-cayenensis complex, D. trifida, and D. esculenta) cultivated in Guadeloupe. We then ranked them from most frequent to rare based on past cultivation (excluding variation from previous year), and contrasted past cultivation frequencies to current cultivation frequencies. We further assessed variety censuses from previous unpublished studies from 2005 and 2010, to investigate the impact of sample size on our frequency estimates and assessed for sampling bias in our data set (Defèche, Voisin, personal communications, N = 69 and 37, respectively). We tested for variety and other yams species differences between current and past variety numbers using 'Welch unequal variances t-test' with R software  (R Core Team, 2012)  in order to account for greater dispersion around means with regard to varieties cultivated in the past.
, 2009). This method has numerous advantages: it is not affected by variance differentials compared to classical parametric analyses; it is generally not strongly affected by outliers; without the need to transform or edit the dataset beyond fixing typographs; it can deal with missing data and accommodates mixed data (for example binary, categorical, quantitative) and high dimension datasets. Last, exploratory tree models are graphically easy to interpret  (De'ath and Fabricius, 2000). Disadvantages for regression trees are mostly concerns about the univariate nature of splitting decisions, where an early split may lead to suboptimal later splits. Most recent procedures are built upon model predictive ability and are either based on data resampling approaches (bootstrap) or model averaging (bagging, random forests)  (Leathwick et al.
, 2006; Cutler et al. , 2007; De'Ath, 2007; Elith et al. , 2008). Our approach was descriptive rather than predictive, and we therefore opted for simple tree models which are easier to interpret  (De'ath and Fabricius, 2000; Olden et al. , 2008). We thus followed classical procedure of growing trees and pruning via assessing complexity parameter 'cp' and chose the tree with lowest complexity within the threshold of 1 standard error of null model in order to avoid overfitting data  (De'ath and Fabricius, 2000; De'Ath, 2002). We illustrated both full model tree and consequently pruned tree models. We used the rpart package from R software (R Core Team, 2012) for all regression tree analyses, see  Olden et al. (2008)  for a general overview of these procedures. All the analyses produced trees that described varietal dynamics stratification to the exception of dynamics of species other than D.
Some varieties had important variations in cultivation frequency, while other did not. The varietal pool under study exhibited the following trends: popular varieties from the past had the greatest rate of decline, and the observed decline attenuated for varieties less cultivated in the past. Two varieties strongly departed from this trend: "Boutou" had a strong decline, and "Goana" had a strong growth compared to past cultivation frequency. The observed trend was supported by comparing with variety census datasets from 2005 and 2009, with the exception of a few cases all belonged to species other than D. alata (namely "Pas Possible", "Adon", "Igname Poule Jaune", "Igname Poule Blanc", "Cousse-Couche") mostly from the long tail of rank distribution. These species were subjected to either sampling bias variation or greater yearly variance in cultivation due to casual diversification opportunities for producers (data not shown, marginal effect).
8 n addition, Vietnam is witnessing a change in HIV transmission patterns with increasing numbers of heterosexually transmitted HIV Tuberculosis HIV co-infection Vietnam disease control epidemiology A B S T R A C T Tuberculosis (TB) and human immunodeficiency virus (HIV) infection are leading causes of disease and death in Vietnam, but TB/HIV disease trends and the profile of co-infected patients are poorly described. Methods: We examined national TB and HIV notification data to provide a geographic overview and describe relevant disease trends within Vietnam. We also compared the demographic and clinical profiles of TB patients with and without HIV infection. Results: During the past 10 years (2005-2014) cumulative HIV case numbers and deaths increased to 298,151 and 71,332 respectively, but access to antiretroviral therapy (ART) improved and new infections and deaths declined.
Methods The cumulative number of HIV-infected cases, number of patients on ART and IPT, as well as the number of newly diagnosed HIV-infections and deaths over a 10-year period (2005-2014) were reviewed using HIV program data. In addition, we analysed routine notification data collected by the national TB program in Vietnam over a 4-year period (2011-2014). We assessed geographic patterns of disease in 2014, by mapping the TB incidence, HIV prevalence and total number of TB/HIV co-infected patients notified in each province. We compared the profiles of TB patients with and without HIV infection by combining more detailed HIV and TB programmatic data from the 2011-2014 period. Descriptive and comparative statistics was performed using Stata v. 13 (Stata Corporation, Texas, USA). Odds ratios and 95% confidence intervals (CI) were calculated using Chi2 test and StatCalc function in Epi Info 7 (wwwn.
If indicated, membranes were incubated with the primary antibodies against phosphoERK (pERK), phosphoAkt (pAkt), phosphoMEK (pMEK), Akt (clones D13. 14. 4, 193H12, 41G9, and 11E7, respectively, with 1:500 dilution; Cell Signaling Technology, Danvers, MA) and actin (1:1000 dilution; Santa Cruz Biotechnology, Dallas, TX), followed by appropriate peroxidase-conjugated secondary antibodies (1:10 000 dilution; antimouse and antirabbit secondary antibodies from Santa Cruz Biotechnology and Cell Signaling Technology, respectively) and analyzed with ECL prime reagent (GE Healthcare Life Sciences) and LAS-3000 (Fujifilm, Tokyo, Japan). Image analysis and blot quantification was performed with Multigauge software (Fujifilm).