dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgements. We are grateful to  S Szuplewski ,  S Gaumer  and  F Peronnet  for their critical reading of the manuscript. We thank  B Hay  for a generous gift of dIAP1 antibody. Confocal microscopy was performed on CYMAGES imaging facility. qPCR experiments were done in the  UMR 1198  ' Biologie du Developpement et Reproduction' (INRA, Jouy-en-Josas ). This work was supported by the  'Universitede Versailles Saint-Quentin-en-Yvelines' (UVSQ)  and by grants from the  'Ligue Nationale Contre le Cancer'. Amandine Clavier  was the recipient of a doctoral contract from  UVSQ. Adrienne Baillet  was supported by the  UVSQ  and the  Ecole Pratique des Hautes Etudes.
Saturation was not allowed to drop below 70% to minimize stress effects  (Peck & Prothero-Thomas 2002). Control chambers (without urchins) were run simultaneously, and all calculated rates of oxygen consumption were corrected for controls. Chamber volumes were corrected for animal volumes prior to calculating oxygen consumed. Animal volume, whole animal wet mass (g AE 0Á01) and test diameter (mm AE 0Á1) were recorded for each urchin. The second group was allocated for destructive sampling to obtain ash free dry masses (AFDM) for each treatment at each sampling time point (n = 8). Within each treatment, live wet volumes vs. urchin diameter regressions were used to relate oxygen consumption measurements to animal AFDM. adult data collectiongrowth, calcification and gonad index Animal volume, whole animal wet and dry mass (AE0Á01 g), test diameter and thickness (measured at mid-test height from interambulacral plates) (AE0Á01 mm), gonad wet and dry tissue mass (AE0Á01 g), AFDM (AE0Á01 g), sex and gonad index were recorded for each animal used in the destructive sampling analyses.
statistical analyses and data accessibility Each treatment (temperature and pH) was analysed as an independent factor nesting tank or replicate for oxygen uptake, test diameter, whole animal wet mass (balanced from random removal of unbalanced data), egg size and larval post-oral arm data. Data were analysed in Minitab (Statistical Software version 15, Coventry, UK) using either Nested ANOVA via a general linear model (GLM) (larval data) or one-way ANOVA (adult data) after assessing normality using Anderson-Darling (P > 0Á05) and homogeneity of variance using Levene's test. After significant ANOVA results, Tukey's or Bonferroni's pairwise comparisons were used to determine treatment differences. Nonparametric Kruskal-Wallis tests were carried out where data consisted of ranks or heterogeneous residual variability remained after transforming data following  Sokal & Rohlf (1995).
Proportional data were arcsin transformed prior to analysis  (Kelly et al. 2000). Adult growth was assessed for normality (Anderson-Darling), and relationships with time were determined using correlation and regression analyses. Multiple comparisons of treatment slopes were assessed with a GLM of interacting treatments with time and using time as a covariant. Results were accepted after homogeneity of residuals was met. Growth and standard error of slopes were quantified from the GLM's resulting coefficient terms. Due to multiple testing, P-values were adjusted for larval morphometrics, development stages and abnormalities using the method of  Benjamini & Hochberg (1995). Data are available via the Polar Data Centre  (Suckling et al. 2014).
Acknowledgements Coleen Suckling was supported by a  NERC  studentship ( NE/G523539/1 ) and partly by a  Scottish Association for Marine Science Research Bursary. The authors would like to thank all members of the  Rothera Dive Team  for providing samples. Overall diving support was provided by the  NERC National Facility for Scientific Diving at Oban. Thanks also to BAS aquarium technical staff for support of the experiment and four anonymous reviewers for their very useful constructive comments.
Albeit an ever growing number of sequences in GenBank and research work using hsp70 gene expression as a molecular marker in nematodes  (Guisbert et al. 2013) , lumbricides  (Chen et al. 2011) , slugs and snails  (Köhler et al. 1998; Reuner et al. 2008) , and collembolans  (Bahrndorff et al. 2009; Waagner et al. 2012 ) information about stress genes of the soil fauna is still relatively scarce. The premise to any quantitative stress gene expression study is the availability of at least a partial hsp70 sequence. Accordingly, the objective of this study was to characterize the nucleotide sequence of a highly conserved region of the 70 kDa heat shock protein in the diplopod species Tachypodoiulus niger (Leach 1815) (Julidae). The approach employs degenerate primers targeting a conserved region of the hsp70 family genes  (Bahrndorff et al.
1 ). DNA sequencing revealed (1) two genomic sequences of 701 and 549 bp that subsequent BLAST searches suggested as being the hsc70 gene for the longer sequence and as hsp70 for the shorter one; (2) a short cDNA sequence with high similarity to the 70 kDa heat shock cognate and (3) another short cDNA sequence identified as the gene coding for glucose regulated protein grp78 (Table  1 ). The respective DNA sequences can be retrieved from EMBL/GenBank (accession numbers are provided in Table  1 ). On the one hand, these results confirm the universal applicability of these degenerate oligonucleotides (see also  Schill et al. 2004; Reuner et al. 2008). Particularly, the targeted, highly conserved consensus region codes for the N-terminal nucleotide-binding domain of the hsp70 proteins (Conserved Domain Database, http://www.
ncbi. nlm. nih. gov/Structure/ cdd/cdd. shtml; (Marcheler-Bauer et al. 2011) , which regulates chaperone activity by ATP hydrolysis  (Wisniewska et al. 2010 ). This domain is considered to be less variable than the also well-conserved peptide-binding domain  (Reddy et al. 2010). On the other hand, the degenerate primers amplify various isoforms, and thus, primers specific to the different isoforms need to be designed on the basis of the sequences obtained with degenerate primers (e. g. as in  Bahrndorff et al. 2009). The deduced amino acid sequences of the T. niger hsp70s (Fig. 2 ) were aligned to hsp70 sequences from 18 other species retrieved from GenBank (Fig. 3 ). The network obtained with a neighbour joining analysis illustrates the basic split into two major groups of sequences (Fig.
5 min at 72 °C followed by a final 10 min at 72 °C) were adopted from Köhler et al. (Köhler et al. 1998 ) and slightly modified when necessary. PCR products were purified by agarose gel electrophoresis and subsequently cloned into the pCR4-TOPOvector (Invitrogen, Groningen, The Netherlands). The plasmid DNA was isolated from positive clones with the E. Z. N. A. plasmid miniprep kit II (Peqlab). A custom sequencing was carried out in both directions and confirmed twice by Seqlab, Sequencing Laboratories (Göttingen, Germany). The BLAST searches  (Altschul et al. 1990 ) were used for sequence identification. Alignments of the hsp70 sequences were carried out using ALIGN program  (Smith and Waterman 1981 ). 1999; Daugaard et al. 2007 ). However, the number and distribution of introns reported in the literature is highly variable as is the inducibility of the respective genes.
Background: Mindfulness Based Stress Reduction (MBSR) is a secular form of meditation training. The vast majority of the extant literature investigating the health effects of mindfulness interventions relies on wait-list control comparisons. Previous studies have found that meditation training over several months is associated with improvements in cognitive control and attention. Methodology/Principal Findings: We used a visual continuous performance task (CPT) to test the effects of eight weeks of mindfulness training on sustained attention by comparing MBSR to the Health Enhancement Program (HEP), a structurally equivalent, active control condition in a randomized, longitudinal design (ClinicalTrials. gov, NCT01301105) focusing on a non-clinical population typical of MBSR participants. Researchers were blind to group assignment.
Our sample size was comparable to other MBSR studies and power analyses based on effect sizes reported in the literature. Participants were masked to research questions and researchers were masked to intervention assignment throughout data collection. As part of our effort to maximize the potential effectiveness of both interventions, our inclusion/ exclusion criteria (see Table  1 ) included elements important for both MBSR and HEP. For example, just as we required inexperience in meditation practice prior to participating in MBSR, we required relative inexperience in HEP components as well (e. g. , excluding participants with ''Engagement in moderate sport and recreational activities more than 5 times a week. ''). Data were collected and analyzed at UW-Madison. All analyses reported are based on participants who started and completed their intervention.
Both groups were assessed pre, mid, and post a 3-month retreat (retreat 1). When this was complete, the wait-list group was assessed again pre, mid, and post their 3-month retreat (retreat 2). Participants in our study were tested in a quiet, darkened room using Presentation software (Neurobehavioral Systems, available from http://www. neurobs. com) and a Windows laptop computer. At each assessment, participants completed a threshold procedure (,10 min) followed by a 24-min CPT (although this was 8 min shorter than the task used by MacLean et al, the analysis in MacLean et al focused on training-related improvements in vigilance that were evident within the first 16 min of task performance). In both tasks, participants saw a single vertical line appear at the center of the screen. This line was either a frequent (90%) long non-target or a rare (10%) short target.
One participant was removed as an extreme outlier for Time 1 A9. Another was removed as the only participant with outlier A9 data for both halves at Time 2. Finally, two participants were removed from analyses who had extreme outlier scores on target threshold at any time point. Thus, there were 29 MBSR participants and 25 HEP participants for analyses. All analyses are conducted with participants' originally assigned interventions. We also collected diary reports of both minutes and sessions of class-related home practice during the intervention (between T1 and T2) and from the of the intervention to the four-month follow-up (between T2 and T3). By summing these data, we created variables indicating practice minutes and sessions from T1 to T2 and the same variables extending from T1 to T3.
Source of material Old World accessions of A. barbata were donated by Agriculture Canada's Plant Genome Resources of Canada (PGRC) germplasm station in Saskatoon, Saskatchewan, Canada, and the USDA National Small Grains Collection (NSGC) in Aberdeen, Idaho, USA. We attempted to obtain accessions from across A. barbata's range in the Old World, but with particular emphasis on the Iberian Peninsula (Spain and Portugal) as this is thought to be the origin of Californian A. barbata  (Jain & Marshall, 1967; Garcia et al. , 1989; Minnich, 2008). Official repository accession names, our own sample code names, GenBank accession numbers along with sampling locations and other information are given in Supplemental Information 1A. In May 2010, we carried out an extensive geographic survey of A. barbata sites in California, USA.
Ploidy assessment Forty-eight accessions from the Old World, and 24 Californian individuals were assayed for ploidy via flow cytometry. Flow cytometry was performed with a BD FACSCalibur flow cytometer at the University of Guelph, Ontario, Canada with CellQuest Pro software (BD Biosciences, San José, USA). All assays came from fresh leaf tissue harvested from young plants (10-20 cms in height) from the greenhouse at Dalhousie University and were shipped to Guelph in moist paper towels. Sample preparation was modified slightly from a previous protocol  (Doležel, Greilhuber & Suda, 2007). The DNA content standard used was Vicia faba (26. 90 pg/2C)  (Doležel, Cíhalíková & Lucretti, 1992). Approximately 0. 5 cm 2 of V. faba and 1. 2 cm 2 of A. barbata were chopped with a razor blade, and was placed in cold extraction buffer for staining (100 µg/ml propidium iodide and 50 µg/ml RNAse-in this study LB01 buffer was used  (Doležel, Greilhuber & Suda, 2007) ).
Chloroplast DNA variation To create the phylogeny, we obtained cpDNA sequences from 49 Old World and 32 Californian accessions, which included two Mesic and two Xeric standards (the parents of the mapping population described in  Latta et al. (2004) ). We chose California sites that formed North-South and East-West transects by choosing at least one accession from sites previously sampled by  Clegg (1972)  and  Hutchinson (1982). DNA extraction was carried out from leaf tissue following a slightly modified protocol of plant DNA extraction  (Dellaporta, Wood & Hicks, 1983) ; we also employed an expedient protocol optimized for seeds  (Ivanova, Fazekas & Hebert, 2008)  for 10 samples. Table  1  Summary of intergenic cpDNA loci used. Intergenic locus region target, the primer pair (as given in reference), the number of variable characters for each locus, and the length of the fragment uploaded to GenBank.
Bayes v. 3. 2. Chloroplast trace files were blasted and annotated using the web server tool CpGAVAS  (Liu et al. , 2012)  and uploaded to NCBI using the web server tool-BankIt. For the Californian accessions assayed with SSCPs, we modeled the relative frequency of chloroplast haplotype at a site with respect to latitude using a generalized linear binomial model using the R package 'lme4'  (Bates, Maechler & Dai, 2008). For this approach, any samples in the same population were treated as non-independent observations. Within California we estimated the overall F ST for individuals at geographic sites assayed with SSCPs (n = 204).
ACKNOWLEDGEMENTS We thank  Dr. Harold Bockelman  from the  USDA Small Grains Collection  and  Dr. Dallas Kessler  from  Agriculture Canada at Plant Genome Resources Canada (PGRC ) for supplying the Old World germplasm. We are grateful to the  Marine Gene Probe Laboratory at Dalhousie University  for help with SSCPs analysis. We are indebted to  Dr. Brian Husband  and  Paul Kron  for help with flow cytometry. We also thank two anonymous reviewers from  Axios Review  for helpful comments.
The methods performance in predicting the pattern of prevalence in a number of countries (Cote d'Ivoire, Ghana, Kenya, Malawi, Tanzania and Uganda) was assessed using both internal (leave-one-out cross validation and partitioned data hold-back) and external validation approaches. Results of the validation exercise will be published on HIV Modelling Group website; comparison with data from the previous available survey. In the medium term, it was recommended to develop a complex Bayesian model allowing estimates, as well as measures of the inherent uncertainty, to be inferred from the data. The urgent need for countries to understand subnational variations in HIVepidemiology was noted. In the short term, it was suggested to use the prevR  [4]  approach to generate subnational estimates for timelimited use by countries.
In surveys released since 2009, the displacement is also restricted to the country's second administrative level where possible. We selected all surveys whose data are available on http:// www. dhsprogram. com, with HIV testing and survey clusters geolocation, conducted in 2008 or later (they were all released in 2009 or later). For countries with two or more selected surveys, we only kept the most recent one (see Table  1 ). Survey clusters with missing geolocation, individuals with an indeterminate result or not aged 15-49 years were excluded. Various researchers used kernel estimators for spatial epidemiology  [6] , such as the estimation of a surface of relative risks  [7] [8] [9]. A surface of prevalence is the ratio between two intensity surfaces (number of cases per surface unit), while a surface of relative risks corresponds to the ratio between the density surface (whose integral has been reduced to one) of positive cases and the density surface of control cases (population exposed to the risk).
With fixed bandwidths, some researchers  [7, 9]  suggest using the same constant to estimate both density surfaces (positive cases and control cases). However, the research  [7, 8, 10]  suggests that the use of adaptive bandwidths is more relevant to health-related matters in order to get a closer match of the spatial distribution of the population and thus reduce the smoothing of information. The prevR approach was explained in details elsewhere  [4]  and implemented in a package for the statistical software R  [11]. It is a kernel density estimation using adaptive bandwidths based on a minimal number of observations (N parameter). Figure  1  summarizes the prevR approach. For each cluster, a circle is drawn such that the number of persons surveyed within it is at least equal to a fixed minimum (N parameter).
A surface is computed using a Gaussian kernel with a bandwidth depending on that circle and a height proportional to the weighted number of tested individuals in that cluster, that is the sum of the individual sampling weights. These sampling weights are provided in DHSs datasets and are adjustment factors to adjust for differences in probability of selection  [12]. All clusters are summed to compute the intensity surface of observed individuals. The same approach is used to compute the intensity surface of HIV-positive individuals. The prevalence surface is the ratio of the intensity surface of the number who tested positive to the surface of the total number tested. This method is an adaptation from the nearest neighbour technique (described by Silverman  [13]  and Altman  [14]  among others, and tested by Bithell  [7] ) to the difficulty of computing the ratio of two intensity surfaces.
LandScan data were rescaled to national DemProj estimates to produce a surface of the 15-49 year-olds population ( pop 15-49 ) and a surface of 50 and more year-old population ( pop 50þ ). DemProj is the demographic projection module from the Spectrum/Estimation and Projection Package (EPP) software used by UNAIDS to estimate prevalence and incidence trends  [17]  at a national level. Using prevR and DHS's sampling weights, we produced a surface of unadjusted HIV prevalence of 15-49 year-olds ( prev un. 15-49 ) at the same resolution than the LandScan grid. An unadjusted surface of 15-49 year-old people living with HIV (PLWHIV) is obtained as prev un. 15-49 Â pop 15-49. This surface is then proportionally rescaled to make the total number of 15-49 PLWHIV equal to the national estimates obtained with Spectrum/ EPP, generating an adjusted surface of 15-49 PLWHIV ( plwhiv a.
15-49 ). The same approach was used to calculate an adjusted 50þ PLWHIV surface, considering that the spatial distribution of 50þ PLWHIV was similar to the spatial distribution of 15-49 PLWHIV. Finally, the adjusted 15-49 HIV prevalence surface is equal to plwhiv a. 15-49 /pop 15-49. UNAIDS estimates are mid-year estimates. For countries with a DHS conducted during a single year, the estimates are adjusted to the same year. For countries with DHS conducted between 2 years, estimates are adjusted to UNAIDS estimates for the second year of the survey. GADM is a spatial database of the location of administrative areas or administrative boundaries worldwide  [18]. Administrative division is country-specific. In Table  1 , we featured the type of administrative units retained for each country. Boundaries were obtained from GADM, except for Rwanda (boundaries were provided by the National Institute of Statistics of Rwanda [19]), Gabon (Ministry of Health of Gabon/Department of Cartography) and Uganda (Global Administrative Unit Layers was used  [20] ).
In a recent and influential paper published in this journal, Chandrasekaran et al. [21]  present a number of analyses about the ''natural statistics of audiovisual speech'', based on various databases in different languages (British and American English, and French), with four major results: firstly, there is a robust correlation in time between variations of mouth opening and variations of the acoustic envelope; secondly, focusing the acoustic envelope to narrow regions in the acoustic spectrum, correlation is maximum in two regions, one around 300-800 Hz, typically where is situated the first vocal tract resonance (formant) F1, and the other around 3000 Hz interpreted by the authors as corresponding to the second and third resonances F2 and F3; thirdly, temporal comodulations of the mouth and acoustic envelope appear in the 2-7 Hz frequency range, typically corresponding to the syllabic rhythm; last but not least in the context of the present paper, ''the timing of mouth movements relative to the onset of the voice is consistently between 100 and 300 ms'' (penultimate sentence of the paper abstract).
We recorded a small database of 6 repetitions of 8 syllables /pa ta ka ba da ga ma na/ uttered by a French speaker either in isolation /Ca/ or in sequence /aCa/. The syllables were produced in a fixed order at a relatively slow rhythm (around 800 ms per syllable). In the ''isolated syllables'' condition, syllables were embedded in silence: /pa#ta#ka#ba#da#ga#ma#na/ where /#/ means a silence (typically 500 ms silence between two consecutive syllables). In the ''chained syllables'' condition, they were produced in the same order though with no silence between syllables: /apatakabadagamana/. The recording was done with a PAL camera at 50 Hz. The recording set up was based on the classical paradigm we use in Grenoble since years  [26, 27]  with blue make up applied on the lips. For each image, we extracted automatically and precisely the lip contours by applying a Chroma Key process extracting blue areas on the face.
Analysis Detection of auditory and visual events. Then on each CV utterance of this database we labeled auditory and visual events. The acoustic analysis was done with Praat  [28]. The first formant was extracted after a Linear Predictive Coding (LPC) analysis. A typical display of the synchronized acoustic signal with its time-frequency analysis (including intensity and formants) and lip trajectory (one measure every 20 ms) is presented on Figure  3a  for an isolated /pa/ and Figure  3b  for a /pa/ chained in a sequence (with a zoom around the consonant /p/ in /apa/). On such kinds of displays we detected auditory and visual events corresponding to the onset of opening or closing gestures, with criteria based on given ranges of energy decrease/increase -1 dB -, formant decrease/increase -60 Hz -or lip height decrease/increase -0.
Viability and cell cycle assays. Cell viability was evaluated by MTT assay. Cells (2 Â 10 4 cells in 100 ml) were seeded for 6 days in 96-well plates and treated with 100 nM VD3 and 1 mM Len either alone or in combination. Cell death was assessed using an Annexin V staining kit (Beckman Coulter, Marseille, France). The cell cycle stage was assessed using propidium iodide (PI) staining (Beckman Coulter). Flow cytometric analysis was performed on a FACSCalibur flow cytometer (Becton Dickinson, San Jose, CA, USA) using Cell Quest software. Western blotting. The analysis of protein expression was conducted by western blotting, as previously described. 20 The following primary antibodies were used: Mcl-1 (S19, Santa Cruz Biotechnology, Santa Cruz, CA, USA), Bik (FL160, Santa Cruz Biotechnology), Puma (Calbiochem, Merck, Darmstack, Germany), Bcl-x L , Bad, Bid, Bak (BD Biosciences, Le Pont de Claix, France), Bcl-2, caspase 9, (Cell Signalling, Saint Quentin en Yvelines, France), actin (Millipore Bioscience Research Reagents, Merck, Saint-Quentin en Yvelines, France), Noxa (Alexis, Paris, France) and Bax (Enzo Life Sciences, Villeurbanne, France).