dataesr/scientific-paragraphs-categorization huggingface dataset:
Simulation Experiments All our experiments were conducted on a lattice of dimension 50650, which had reflecting boundaries, and genes were initialised to random values. There were two parts to our simulation experiments. First, we ran a large set of simulations to establish how predator dispersal evolves across a broad range of prey dynamics. These simulations were run both for the case where only emigration rate is allowed to evolve and for the extended model where emigration rate evolves jointly with the stopping rule. We systematically varied reproductive rate of prey r from 0. 5 to 4. 0 in increments of 0. 25 and c from 0. 01 to 0. 05 in increments of 0. 01, plus 0. 10 and 0. 20, and, for each combination, ran 5 independent simulations. We allowed the model to run for 1000 generations and then collected data on the population mean and inter-individual variation in predator dispersal strategies.
Treatment outcomes at this ART service were recorded in a weekly multidisciplinary meeting and these data were entered in a prospectively maintained ART cohort database on a weekly basis. Patients were classified as alive and on treatment, dead, transferred out or LTFU. 'Transfer-out' was the term used to refer to patients who were attending the clinic and whose care was transferred to another clinic by giving the patient a referral letter. A decision to transfer care usually arose as a result of either a new ART service being opened closer to the patient's home, to relocation of the patient to another area  [7]  or upon the patient's request. Clinic-and field-based counsellors supported the ART service. The counsellors provided educational support, home visits and liaised with the clinical team.
Basic descriptive statistics were used in the analyses of the most recent characteristics prior to transfer. These analyses were restricted to patients who transferred out after at least 1 year of follow-up on ART at this service. A sub-analysis was performed comparing the most recent viral load among ART-naı ¨ve patients transferring out with that at a comparable time point among ART-naı ¨ve patients not transferring out. A folder review was also conducted to determine the reason why some ART-naı ¨ve patients transferred out with a viral load $1000 copies/mL. Wald confidence limits were used for all multivariate models. All statistical tests were 2-sided at alpha of 0. 05. Stata statistical software, version 10. 0 was used for analyses (Stata Corporation, College Station, TX).
The strengths of the study include the study of a very well characterized cohort with careful patient follow-up, including 4monthly CD4 cell count and viral load measurements. The patient within this township cohort are typical of large public sector ART cohorts throughout Cape Town, South Africa. Study limitations include selection bias due to missing information in multivariate analysis may exist although this is likely to be minimal in view of the completeness of the data collected and that the few missing observations were random. This was an observational study that used data collected from routine program evaluation which are limited by operational constraints. The contribution of socioeconomic status of ART patients on transfer out rates could not be ascertained from our data. However, the community in which the clinic operated has a high unemployment rate in general and therefore serves mainly low-income ART patients.
MDN is supported as an operational research fellow by the  International Union Against Tuberculosis and Lung Disease, Paris, France. SDL is funded by the  Wellcome Trust, London UK. RW is funded in part by the  Cost-Effectiveness of Preventing AIDS Complications (CEPAC)  funded by the  National Institutes of Health (NIH ,  5 R01AI058736-02 ); International Epidemiologic Database to  Evaluate Aids  with a grant from the  National Institute of Allergy and Infectious Diseases (NIAID :  5U01AI069924-02 );  USAID Right to Care  ( CA 674 A 00 08 0000 700 ) and the  South African Centre for Epidemiological Modelling and Analysis (SACEMA). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Isolation and identification of new compounds 1-11 The hydroalcoolic extracts of Gypsophila trichotoma roots were purified by multiple chromatographic steps over Silicagel, Reversed phase C8, Reversed phase C18 and finally purified by semi-preparative HPLC over C18, yielding eleven new saponins (1-11, Fig 1 ) with a known saponin (12), the 3OβDxylopyranosyl(13)[βDgalactopyranosyl(12)] βDglucuronopyranosylgypsogenin28OβDxylopyranosyl(14)[βDglucopyran osyl(13)]αLrhamnopyranosyl(12)βD4Oacetylfucopyranoside already reported in the seeds of Agrostemma githago L. var. githago  (Siepmann et al. , 1998). Among them, saponins 9 and 11 were obtained in a poor quantity to obtained 13 C NMR data. Acid hydrolysis of crude saponin mixture afforded an aglycone identified, after purification, as gypsogenin from 1 H and 13 C NMR spectra referring to the reported data  (Mahato and Kundo, 1994)  and a prosaponin identified as 3-O-β-D-6-O-methylglucuronopyranosylgypsogenin (13), previously isolated after hydrolysis of Momordica saponin  (Iwamoto et al.
HPLC system II HPLC was performed on a Dionex apparatus equipped with an ASI-100 automated sample injector, a STH 585 column oven, a P580 pump, a diode array detector UVD 340S and the Chromeleon ® software. Prepacked C18 reversed phase columns 201SPTM, 4. 6 x 250 mm, 5 µm (Dionex, vydac, France) or a Luna 5u C18, 4. 6 x 250 mm, 5 m, 90 Å (Phenomenex, France) were used for analytical HPLC with a binary gradient elution (solvent A: H2O -TFA, 0. 025 %, solvent B: MeCN) and a flow rate of 1 ml. min -1. The semi-preparative HPLC were performed with a binary gradient elution (solvent A: H2O -TFA 0. 0025%, solvent B: MeCN) on prepacked C18 reversed phase columns 201SP510, 10 x 250 mm, 5 µm, 90 Å (Dionex, vydac, France) (system II-A) or a Luna 5u C18, 10 x 250mm, 5 m, 90 Å (Phenomenex, France) (system II-B) with a flow rate of 4 ml.
Briefly, after 24 h incubation with the plant extract, MTT-solution (10 mg/ml in PBS) was added (10 l/well) to tissue culture medium and cells were further incubated for 3. 5 h at 37°C. Formed formazan crystals were dissolved by adding 110 l/well of 0. 04 N HCl in isopropanol. Absorption was measured by an ELISA reader (Labexim LMR1) at 540 nm. The reference filter was set on 690 nm. For each concentration, at least 8 wells were used. RPMI-1640 medium (100 µM) with 10 l MTT stock-solution and 110 l 0. 04 N HCl in 2-propanol was used as blank solution. Data obtained were presented as percentage of untreated control (% of untreated control = E (extinction of viable cells in treated samples) x 100/ E0 (extinction of viable cells in untreated control)).
Numerous studies have indicated an increased risk of vascular disease among migraineurs. Alterations in endothelial and arterial function, which predispose to atherosclerosis and cardiovascular diseases, have been suggested as an important link between migraine and vascular disease. However, the available evidence is inconsistent. We aimed to review and summarize the published evidence about the peripheral vascular dysfunction of migraineurs. We systematically searched in BIOSIS, the Cochrane database, Embase, Google scholar, ISI Web of Science, and Medline to identify articles, published up to April 2013, evaluating the endothelial and arterial function of migraineurs. Several lines of evidence for vascular dysfunction were reported in migraineurs. Findings regarding endothelial function are particularly controversial since studies variously indicated the presence of endothelial dysfunction in migraineurs, the absence of any difference in endothelial function between migraineurs and non-migraineurs, and even an enhanced endothelial function in migraineurs.
Search strategy and selection criteria Data for this review were obtained through searches in BIOSIS, the Cochrane database, Embase, Google scholar, ISI Web of Science, and Medline from their first availability up to April 2013. The search terms included "migraine" OR "headache" AND ("endothelial function", "endothelial injury", "arterial stiffness", "arterial distensibility", "vascular resistance", "vascular reactivity", "flow-mediated dilation", "forearm blood flow", "arterial pulse wave velocity", "augmentation index"). We also searched reference lists of identified articles and papers quoting identified articles. We reviewed only studies published in English.
METHODS Patients. Patients whose stool samples were sent routinely to the diagnostic microbiology laboratory of the Royal Infirmary of Edinburgh from August 2010 to July 2011 and which tested positive for C. difficile toxin by two-step glutamate dehydrogenase (GDH) and toxin A/B ELISA (see later) were prospectively followed up for 1 year after the first stool sample tested positive. Relevant ethical approval was obtained for the study. Data collection. Initial patient demographics, clinical features and co-morbidity data were collected at the start of each episode of CDI, at 10 days and at 1 year. For outpatients, the same data were collected by telephone contact with the requesting doctor. Recovery, recurrence, treatment, and mortality were recorded. The Charlson comorbidity index (CCI) was calculated using a macro enabled Excel tool available online  (Hall et al.
, 2004). Haematological and biochemical data (white cell count, creatinine, lactate) were obtained from the local laboratory information system. Mortality data were obtained from the NHS Lothian Public Health Department. Cause of death was determined by reviewing the ICD codes on the death certificates. ICD10 codes A04. 7, A09, A41. 4, A49. 8 were included in analysis  (Anonymous, 2006). Stool samples were tested using a two-step algorithm for C. difficile toxin EIA (A and/or B) (Tox A/BII, Techlab) and GDH (C. DIFF CHEK-60, Techlab). GDH-negative stools were excluded from the study. The stools positive for both GDH and toxin EIA were cultured on cefoxitin-cycloserine-egg yolk (CCEY) medium  (Brazier, 1993). All isolates were later subjected to toxin A and toxin B PCR  (Persson et al. , 2011).
However, since the initial reactions for ribotyping were rather weak, the cycle for ribotyping was later increased to 27 cycles. After PCR, the products of the ribotyping and toxin gene multiplex were mixed as follows. First dilution: 18 ml nuclease-free water and 10 ml ribotyping PCR products and 2 ml toxin gene PCR product. This was mixed well by pipetting. Final dilution, 1 ml of the diluted products were mixed with 9 ml of HiDi formamide mix. Capillary gel electrophoresis (ABI 3730) was used for PCR product analysis and ribotypes were assigned by comparing with a set of known strains on GeneMarker 1 software version 1. 95 (Softgenetics). Known strains of ribotypes 001, 106 and 027 were included with each run of ribotyping and toxin multiplex PCR for quality control. The toxin gene images were compared against the PaLoc indicator panel (kindly provided by Dr Derek Fairley).
Thirty day all-cause mortality (n563) was also compared to those who were alive at 30 days (n5264). For recurrent infections, patients who had a documented episode in the past before the commencement of this study (n535) were removed from analysis. In addition, to exclude those patients who die before they get a chance to develop recurrence, all patients who died within 30 days of development of CDI (n553) were also removed from this analysis. Hence, a total of 247 patients were included in the statistical analysis of this section (56 patients who developed more than one episode and 191 patients who had only one documented episode). Statistical analysis was performed using Minitab statistical software version 15. 1. 0. 0. Fisher's exact test and the chi-square test were used for categorical variables and the two-sample t-test for numerical variables.
We conducted a replicated burning experiment in fire-prone natural grasslands of South Brazil where besides the description of spider communities we collected information on the functional traits of the plant communities as a surrogate of habitat structure characterization. We aim at (1) assessing the resilience of spider communities to fire (e. g. the time needed by spider communities to recover after fire);  (2)  detecting relationships between spider and vegetation communities from a functional perspective in burned and unburned sites, and (3) exploring spider trait-convergence and trait-divergence on gradients of plant biomass and plant functional diversity generated by fire. For this we used trait data collected on spider individuals, which enabled us to consider the entire trait variability between individuals  [36] , including variability related to phenology and sex, both within and between experimental treatments.
Vegetation sampling The experimental plots were sampled before fire to test initial vegetation homogeneity between paired plots. We sampled the vegetation again in all experimental plots approximately nine months after fire (late winter/early spring) to examine spider community responses to fire through changes in plant community functional structure. We used this last data set for comparison with the post-fire winter spider data. In both occasions we calculated the mean cover (%) of each plant species and bare soil that were visually estimated in five 1 m 2 quadrats randomly distributed in each plot at each date. Plant aboveground biomass was assessed in each quadrat by cutting and weighting fresh biomass. An aliquot from total biomass was oven-dried (60uC for 72 h) and weighed for total dried biomass estimation.
The sampling quadrats within plots were randomly located at the beginning of the experiment and were non-overlapping. For the data analysis we used the average species composition and biomass of each experimental plot and period. Plant species were described by traits that could affect structural features of the habitat offered to spiders, that is, plant life-form (graminoid, forb or rosette), and other morphological traits (plant height, leaf area, leaf width and length; Table  1 ). The traits were Table  1. Description of spider and plant traits used in the study. recorded for the most dominant and most frequent species, that is, those with a minimum cover of 10% in at least one of the quadrats and those occurring in at least 30 among the 140 evaluated quadrats. In this way, traits for 52 species, corresponding to 46% of the total species pool (114 species), comprising up to 88% of total plant cover were recorded.
Data Analysis In data analysis, we (1) tested for effects of fire on the spider and plant communities described by taxon identities and by their traits, (2) examined the relationships between spider traits and vegetation traits, and (3) identified spider assembly patterns related to vegetation gradients. Data matrices. For the analysis, we organized the spider and vegetation data collected at each sampling period in the following matrices: matrix B S of spider individuals by traits, binary matrix W S of experimental plots (in rows) described by the presence of the spider individuals, which was standardized to unit total within experimental plot and period, and matrix F S with the same plots described by the abundance of individuals classified in spider families. Similarly, the vegetation data was arranged in matrix B P of plant species by traits, matrix W P of experimental plots by the cover of plant species (also standardized to unit total within experimental plot and period), and matrices E PB and E FD (actually vectors) respectively with aboveground plant biomass and calculated plant functional diversity (see below) in the experimental plots.
T S in this case was based on the spider individuals collected between six to seven months after fire, and T P on the plant species composition recorded nine months after fire, in both burned and control plots. Firstly we performed PCA of the two matrices and selected for each of them the principal axis to reduce their dimensionality. Secondly, the concordance between the two data sets was maximized by the rotation of the multidimensional space, generating new axes  [65]. Finally, the significance of these associations was tested by permutation. To interpret the relationships between specific traits of spiders and plants in the treatments we also plotted their CWM traits in two separated PCAs. For interpretation, we only considered those traits with statistically significant responses to burning (see previously described ANOVA).
After this procedure we evaluated the significance of r(TE) and r(XE. T) obtained with the optimal trait subsets related to each gradient. After identifying significant sets of optimal traits for TCAP, we plotted CWM of each trait of the optimal subset and the ecological gradient. Also, matrix X defined by the optimal trait subset maximizing r(XE. T) was analyzed by Principal Coordinates Analysis (PCoA). PCoA was performed with Euclidean distances between sampling units, bi-plotting traits (CWM) and the related environmental variable (E). All analyses but trait-assembly pattern analysis were performed with R 2. 15. 1  [69]. For trait-assembly pattern analysis in ecological gradients we used the software SYNCSA (available in http://ecoqua. ecologia. ufrgs. br), but also available in the package SYNCSA for R.
Relationships between spider traits and plant traits in burned and control plots Co-inertia analysis of the simplified dimensional data of spider traits6plots (PCA, five eigenvectors, 92. 91%) and plant traits6 plots (PCA, four eigenvectors, 96. 83%) showed marginally positive association between these two datasets (RV = 0. 40; p = 0. 068; Figure  1A ). The first and second axes of the co-inertia biplot clearly reflected the fire treatment, and represented 68. 3% and 22. 9% of the co-structure respectively, with unburned control plots in the bottom right corner of the ordination and burned plots in the top left corner The blocked design of the fire experiment was reflected by closeness of the paired plots (burned and control) in the ordination space. Figures  1B  and 1C  show the contribution of the functional traits of the two trophic levels to the canonical space.
The project was supported by grants from  CNPq, Brazil, to Valerio Pillar  ( 479083/2008-8  and  306573/2009-1 ). Luciana Podgaiski  and  Fernando Joner  received PhD Scholarships from  CAPES, Brazil. The project benefitted from travel funding provided to  Luciana Podgaiski  and Valerio Pillar by the  Dimensions of Biodiversity Distributed Graduate Seminar (NSF, USA , grant  1050680  coordinated by  Sandy Andelman  and  Julia Parrish. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
ACKNOWLEDGEMENTS This work was supported by  FAPESP (Fundação de Amparo a Pesquisa do Estado de São Paulo, São Paulo, Brazil). LFC, RLS and JM are recipients of fellowships from  CNPq  ( Conselho Nacional de Desenvolvimento Científico e Tecnológico, Brasília, Brazil). Work in the RLS lab is supported by  CNPq  and  FAPEMIG (Fundação de Amparo a Pesquisa do Estado de Minas Gerais, Belo Horizonte, Brazil). Work in the JM lab is supported by  CNPq  and  FAPESP. RLS is currently a fellow of the  John Simon Guggenheim Memorial Foundation.
For each exposure predictor, we also considered the other contaminants as potential confounders. A parsimonious and stable regression model was obtained, by the use of a data-dependent procedure based on backward variable elimination (PROC GLMSELECT) in multiple bootstrap samples  [35, 36]. Variables were retained if they were selected in at least 30% of the 1000 bootstrap samples with a = 0. 05. All analyses were carried out with SAS software version 9. 3 (SAS Institute, Inc. , Cary, NC, USA). All tests were two-tailed, and p values#0. 05 were considered statistically significant.
We excluded obese subjects and those with acute or chronic pathological conditions thought to have a strong impact on hormone metabolism. We also collected extensive data for adjustment on the basis of factors associated with changes in blood steroid hormone levels and to reduce the bias of the estimates. Our cross-sectional study also presents several limitations. Given the years during which DDT and PCBs were used worldwide, the study population had been exposed to these chemicals or their metabolites throughout much of their lifetimes. For chlordecone, the exposure period began in 1973, at a median age of 30 years. Single blood determinations to estimate exposure to these contaminants may not adequately reflect past exposure. However, unlike women, men are not subject to the mobilization of fatsoluble pollutants during pregnancy or breastfeeding that can significantly alter the pollutant load of the whole body.
Acknowledgments Manolo Carta is supported by grants from the  MJFF ,  Regione Autonoma della Sardegna ,  Fondazione Banco di Sardegna ,  Italian Ministry of Education  ( PRIN 2011 ). Elisabetta Tronci  is supported by  Regione Autonoma della Sardegna  ( Project Master  and  Back , code  PRR-MAB-A2011-19237 ). This study was supported by a grant from the  Michael J Fox Foundation.
Acknowledgments The authors wish to thank  Dr. Chih-Pin Liu  ( Department of Immunology, Beckman Research Institute, City of Hope, Duarte, USA ) for the gift of MHC class II tetramers carrying a BDC2. 5 T cell-specific mimotope (tetAg7/p79) and  JA Bluestone  ( UCSF, San Francisco, California ) for the gift of the cell line producing the 145 2C11 F(ab9) 2. We also thank  Jasper Dingemanse  ( Actelion Pharmaceuticals Ltd ) for his critical review of the manuscript.
Fly Culture and Morphological Analyses Males and females were obtained from laboratory cultures of the nine species of the melanogaster subgroup (Table  1 ) and reared on standard Drosophila medium at 21uC. Cultures were kindly provided by Jean R. David (CNRS, Gif-sur-Yvette) and we confirmed the identification of each species based on speciesspecific male genitalia traits  [32] [33] [34] [35] [36] [37] [38]. Genitalia of at least 10 individuals per sex and per species were dissected, mounted on microscopic slides in DMHF mounting medium (Entomopraxis A9001) and photographed under a Keyence VHX-2000 light microscope. Outlines of male epandrial posterior lobes and female oviscapt pouches were drawn manually on the light microscope images and their areas were estimated with the ImageJ software package  [39].
yakuba and D. teissieri. Furthermore, we detected sclerifications on internal walls of the vagina, that we named vaginal shields, in three species. Those of D. orena were previously described by Tsacas and David  [35]. We provide below a detailed account of these female structures. To identify the male parts that contact these female structures during copulation, we examined the anatomy of copulating pairs. Based on previous reports for seven D. melanogaster subgroup species  [21, 22, 25, 26, 30, 31]  and our observations for two species for which no data were available, we identified male organs that contact each female structure during copulation. Phylogenetic correlation analysis revealed significant correlated evolution of these interacting male and female genitalia structures in the D.
Acknowledgments We thank  Jean David  for providing strains and for mounting mating pairs, Leonidas  Tsacas  ( National Museum of Natural History, Paris ) for sharing SEM images,  David Montero  and the  Scanning Electron Microscopy platform of the ITODYS laboratory in UniversiteParis 7 Diderot  for their help in SEM preparation and observation. We also thank two anonymous referees for their constructive criticisms on an earlier version of this manuscript.