dataesr/scientific-paragraphs-categorization huggingface dataset:
Although susceptibility to viruses shows a strong phylogenetic correlation, susceptible hosts can occasionally be grouped into phylogenetically distant groups, allowing parasites to jump great phylogenetic distances  [49]. Our data possibly show a further trend that can be added to the aforementioned ones -colonizing species that disperse across different geographic regions have increased HTT rates. It is noteworthy that of the 12 Jockey families in which HTT events were validated, in five (Jockey-F39, Jockey-F43, Jockey-F44, Jockey-F58, and Jockey-F62), the transfers occurred between two distantly related groups of species (the melanogaster group and Zaprionus) that migrated from the Eastern region to Africa. In addition, in three other families (Jockey-F36, Jockey-F53, and Jockey-F65), the transfer involved D.
Extraction of jockey sequences from genome assemblies Genome assemblies for 48 species were downloaded from public databases (Additional file 1: Table  S1 ): The European Nucleotide Archive (ENA, https://www. ebi. ac. uk/ena) for 31 of the 48, Ensembl Metazoa for the 12 first sequenced genomes  [56] , http://popoolation. at/ for D. lowei and D. mauritiana and https://www. diark. org/ diark/species_list/Drosophila for D. malerkotliana pallens. We also used draft genomes of the three Zaprionus species (Z. africanus, Z. indianus, and Z. gabonicus), for which we provide RepeatMasker outputs, but the genome assemblies are not yet available (Haudry, pers. com. ). On each assembly, RepeatMasker was run using the complete Repbase library to detect all elements in each genome and their closest match, using the Drosophila model.
We then used the program OneCodeTo-FindThemAll  [57]  to parse RepeatMasker outputs, identify copies with respect to the 80-80-80 rule (using the "strict" option) and export sequences in FASTA format. From each set containing all 80-80-80 copies of the genome, a manually curated Repbase library, 111 Jockey families of Drosophila containing sequences of transcriptase reverses [Additional file 4: Data S1] was blasted to select Jockey copies with RT, with the option of evalue <1e-5 and a percentage of identity > 80%. Finally, a custom script was run to select the sequences corresponding to the three best hits (based on the bitscore criteria) per Jockey family in FASTA format. All Jockey sequences extracted from the genomes were submitted to the NCBI's Conserved Domains Database  [58]  for identification of the RT domain region, and sequences that presented a minimum extension of 300 nt for this domain were selected for the analyses.
The phylogeny of the drosophilid species involved in this study was reconstructed based on 48 sequences of the nuclear gene Amyrel, which was obtained from Gen-Bank for most of the species (Additional file 1: Table  S4 ). For Z. gabonicus and Z. africanus, the sequences were retrieved from the genomes using the Z. indianus sequence (EF458322. 1) as a query. Bayesian inference was performed with BEAST v16. 1  [61]  using General Time Reversible (plus Gamma distribution and invariable sites) as the substitution model and an a posteriori phylogenetic support test, using sampling of 100,000 trees and a burn-in of 10%. The evolutionary model of substitution that best fit the data was determined by the Find Best DNA Model in MEGA7  [63].
Inference of HTT The inference of HTT was initially carried out by the classical criteria: sequence similarity and phylogenetic incongruence. When the necessary data were available, these inferences were validated by the application of VHICA (vertical and horizontal inheritance consistence analysis) methodology, which provides statistical support for corroboration of the inferences of HTT  [18]. The method is based on discrepancies between the rate of evolution at synonymous sites (dS) and the ENC between pairs of TE sequences and vertically transferred orthologous genes. ENC is used to estimate selection due to codon usage bias (CUB) at synonymous sites. The use of dS and CUB together provides robustness in the HTT inferences because being dS and CUB correlated, a low dS does not necessarily indicates HTT if associated with a high CUB, but low dS associated with low CUB is inconsistent with VT  [18].
Gene and TE sequences used in the VHICA analysis For the candidates of HTT among species (Fig. 1 ), we performed de novo gene prediction using Augustus  [64] , with "fly" as the training species, except for D. erecta, for which annotated CDSs were retrieved from the file "Drosophila_erecta. dere_caf1. cds. all. fa" available from the NCBI (https://www. ncbi. nlm. nih. gov/). A custom nucleotide database was created for each species that contained all the predicted/annotated (for D. erecta) coding sequences using makeblastdb and then used for a blastn search against the sequences of 50 single copy D. melanogaster genes from a set of 50 Drosophila single copy orthologous genes  [18] , using the following command: blastn -db $species. codingseq -query dmel_vhica_genes. fas -outfmt 6| sort -k1,1 -k12,12nr -k11,11n | sort -u -k1,1 --merge >best_sin-gle_hits.
Funding This research was funded by the  Brazilian agency FAPESP -Fundação de Amparo à Pesquisa do Estado de São Paulo  to CMAC (grant number  2016/ 19271-2 ). APEGE CNRS DynET and BQR Université Lyon1 EC grants awarded to AH. CNPq-Conselho Nacional de Desenvolvimento Científico e Tecnológico awarded fellowship  to CMAC (grant number  303455/2017-9 ) and to ILT (grant number:  158389/2017-4 ).
While these MON levels are the most relevant from a toxicological point of view, they are higher than the levels identified from the occurrence database in the EFSA Opinion on MON (EFSA, 2018). It cannot be excluded however, that such high levels would occur in practice, given the fact that these levels were reached in the animal feeds in the reported studies using experimental cultures of toxigenic Fusarium strains such as F. verticillioides producing FB 1 and F. fujikuroi producing MON. A rigorous assessment of the interactive toxicity of a mixture is complex; there is overall a methodological gap between the in vitro and in vivo studies exploring the combined toxicity of mycotoxins  (Groten et al. , 1998; Lei et al. , 2013). The classical testing for a possible interaction requires the comparison of the actual effect of the mixture to a theoretically expected no-interaction effect, the socalled additive effect  (Alassane-Kpembi et al.
The contamination was confirmed by additional chemical investigations using Pyrolysis Gas Chromatography coupled with Mass Spectrometry (Py-GC/MS). They revealed the presence of a silicone-based contaminant in the Salkhit bone probably used to make the endocast (Fig. 4 )  7. The hydrolysis of the collagen and isolation of the amino acid hydroxyproline obviated this problem. DNA extraction and mtDNA enrichment. DNA was extracted from 30. 9, 27. 0 and 33. 1 mg of powder removed from the sampling spots B, C and D, respectively (Fig. 2 )  26. Aliquots of the extracts were converted to single-stranded libraries  27  and enriched for human mtDNA fragments using a present-day human mtDNA probe set  28. The enriched library molecules were sequenced from both ends. Overlapping paired-end reads were merged to reconstruct full-length molecules sequences, which were then mapped to the revised Cambridge reference sequence of the human mitochondrial genome (rCRS, GenBank acc.
Adapter sequences were trimmed and overlapping paired-end reads merged using leeHom  44  before mapping the sequences to the revised Cambridge Reference mitochondrial genome (rCRS, NC_0120920) using the Burrows-Wheeler Aligner (BWA)  45  with parameters « -n 0. 01 -o 2 -l 16500 »  46. Mapped sequences with identical alignment start and end coordinates were collapsed using bam-rmdup (https://bitbucket. org/ ustenzel/biohazard). Only overlap-merged sequences of at least 35 base pairs in length were retained for subsequent analyses. After masking terminal C to T substitutions, a perl script was used to call the consensus mtDNA sequence (based on the «mpileup» command of SAMtools  47  ) requiring a minimum coverage of 5 and a consensus support of at least 80% at each position. Phylogenetic analyses.
The Salkhit mtDNA haplogroup was assigned using Haplogrep  31  and mtPhyl5 (https://sites. google. com/site/mtphyl/home) based on the Phylotree database (mtDNA tree Build 17)  32. The number of mutations that occurred in the Salkhit mtDNA since its divergence from the root of haplogroup N was inferred by maximum parsimony analysis using mtPhyl. A multiple sequence alignment of the Salkhit mtDNA sequence to 115 complete mtDNAs of modern humans  18, 34, 36  and one Neandertal mtDNA  48  was generated H 3 C CH 3 H 3 C H 3 C H 3 C H 3 C C H 3 O O O O O O Si Si Si Si Si H 3 C H 3 C CH 3 CH 3 CH 3 CH 3 CH 3 Si Si Si Si Si O O O O O H 3 C H 3 C H 3 C Si Si O Fig. 4  Py-GC/MS characterization. Blue profile-Pyrogram obtained on 450 µg of the Salkhit bone; Black profile-Pyrogram obtained on 220 µg of an uncontaminated bone (Latton, UK) used as a standard at the ORAU.
The main compounds identified in both profiles are pyrolytic products of collagen  51, 52. The profile of the Salkhit sample also shows the presence of 3 compounds with siloxane structure (red arrows) that are reported as pyrolysis products of silicone  53  leading to assess the residual presence of such material within the bone matrix using MAFFT  49. We then estimated the molecular age of the Salkhit mtDNA based on its branch length in a Bayesian statistical framework  38  as implemented in BEAST2 50 using the dataset above. We used tip dates of zero for present-day mtDNA sequences and individual fossil dates intervals as priors for the ancient mtDNA sequences (Supplementary Table  3 ). As determined by jModelTest2, we performed the analyses using a GTR +I+G model for nucleotide substitution with a gamma distributed rates among sites.
A strict clock and an uncorrelated lognormal-distributed relaxed clock, both under a constant size population and a Bayesian skyline coalescent tree prior, were tested. To estimate the posterior distribution of each model, we performed two runs of the Markov Chain Monte Carlo (MCMC) algorithm implemented in the Beast software. Each MCMC run was performed with 50,000,000 iterations and sampled every 10,000 generations. After discarding 10% of the sampled iterations as burn-in, the output was analyzed with Tracer v1. 5. 0 (http://tree. bio. ed. ac. uk/software/tracer/). The effective sample sizes estimate supported the strict clock model over the relaxed clock model, while neither the constant size nor the Bayesian skyline coalescent models were rejected. The age of the Salkhit mtDNA was therefore estimated based on a strict clock model and a Bayesian skyline coalescent model.
Acknowledgements Funding was provided by the  Max Planck Society  and the  European Research Council  under the European Union's  Seventh Framework Programme  (FP7/2007-2013);  ERC  grant  324139 PalaeoChron  awarded to  Professor Tom Higham  and  ERC  grant  694707-100 100  Archaic Genomes awarded to  Professor Svante Pääbo. We thank the staff of the  Oxford Radiocarbon Accelerator Unit at the University of Oxford  for support in the lab,  Cosimo Posth  at the  Max Planck Institute for the Science of Human History (Jena) ,  Martin Sikora  and  Ashot Margaryan  at the  Centre for GeoGenetics, University of Copenhagen  and  Mateja Hajdinjak ,  Alexandre Huebner ,  Stéphane Peyrégne ,  Viviane Slon  and  Mark Stoneking  at the  Max Planck Institute for Evolutionary Anthropology, Leipzig  for helpful discussions.
Statistical analysis All analysis were performed using SAS software (version, SAS Institute, Inc. , NC, USA). Descriptive statistics are given as medians (with interquartile range) because the distribution of continuous variables was not normal according to the Shapiro-Wilk test. Numbers (with percentages) are given for categorical variables. The Wilcoxon test was used to compare the longitudinal change of visual acuity. The Mann-Whitney test was used to compare continuous variables between groups. The chi-square test or the Fisher exact test were used to compare categorial variables between groups. The tests were two-tailed and P-values of less than 0. 05 were considered statistically significant.
Ethics and dissemination Ethical approval: McGill university Health Centre committee number MP-37-2016-2456. Canadian Canadian Institutes of Health Research/ Canadian HIV Trials Network (CTN) protocol CTNPT027. Results will be made available through publication in peerreviewed journals and through the CTN website. trial registration number NCT02659306 IntroduCtIon HIV persistence during antiretroviral therapy Antiretroviral therapy (ART) decreases HIV plasma viral load below the limit of detection of clinical assays, leading to major improvements in the health of people living with HIV (PLWH). However, these individuals on prolonged ART develop significant metabolic complications that contribute to an increased risk of inflammatory non-AIDS events. 1  Such clinical events are associated with persistent immune activation, and occur more often when ART initiation is delayed.
and in table 1). A total of 22 HIV-infected participants will be recruited; it is estimated that there will be a 10% lost to follow-up/ study non-completion. Based on our prior studies, it is expected that approximately 50% of participants will consent to participate in the optional substudy examining the effect of metformin on the composition of the gut immune environment in gut mucosa samples obtained by colonoscopy. 50 51  A convenient sample of 22 participants was chosen without formal power calculations. The data that will be obtained in this study should suffice for calculations for future studies. Participants will be recruited by clinicians at the Chronic Viral Illness Service at the McGill University Health Centre (Montréal, QC, Canada) and the Immunodeficiency Clinic of the Ottawa Hospital (Ottawa, ON, Canada); each of these clinics provides care to 1300-2300 PLWH.
Acknowledgements The authors would like to thank  Michael Pollak ,  Rafick Sékaly  and  Jean-François Yale  for their contributions to the study hypothesis and design,  Gina M Graziani  for her help writing the manuscript,  Angie Massicotte ,  Josee Girouard ,  Guillaume Theriault  and  Cynthia Dion  for their help with coordination. The authors thank  John Lin  for manuscript improvement. Collaborators Group Authorship/Collaborating Author Names: J-PR, SI, VM, MO, NC, PA, RP, DP, FPD and JBA for the  Lilac Study Group. Contributors J-PR, VM, MO, NC, PA and JBA designed the study. J-PR, SI and VM wrote the manuscript. RP, DP, FPD and SI will participate in data collection and analysis. All authors critically reviewed the manuscript and approved the final version. Funding This study was funded by the  Canadian Institutes of Health Research (CIHR) Canadian HIV trials Network (CTN)  ( CTN PT027  grant to JPR),  CIHR  ( IBC-154053  grant to PA) and by the  Canadian HIV Cure Enterprise (CanCURE)  (Team Grant  HIG-133050  to JPR), awarded by the  CIHR  in partnership with the  Canadian Foundation for AIDS Research (CANFAR)  and with the  International AIDS Society (IAS).
Intra-specific robustness to maternal gradient concentration We used the AC/DC2 model to assess the effect of changing the maternal Bcd and Cad gradients on the position of the bifurcation boundary (cf. Figure  4 ). In the region between 47 and 61% A-P position, Bcd spans a range of concentration from 24 to 7 arbitrary units in our data (Figure  4B ). For each nucleus in this region, we fixed Cad levels to their values during early C14A (time point T1), while varying Bcd levels in steps of 0. 01 from to 30 arbitrary units. We then calculated the phase portraits of AC/ DC2 for each combination of maternal input concentrations (see 'Materials and methods'). The resulting dynamical regimes are shown in the phase diagram displayed in Figure  4B. There is a threshold response at a Bcd concentration of approximately 15 arbitrary units: above this threshold, the system is bistable; below, it is monostable.
Acknowledgements We would like to thank  Anton Crombach  for insightful discussions, comments on the manuscript, and for providing the fitted full model used in this analysis. Other members of the  Jaeger Lab in Barcelona , as well as fellows and visitors at the  KLI Klosterneuburg , provided inspiring and motivating feedback on the project. We thank  Erik Clark  and  Ruben Perez-Carrasco  for countless discussions and for their thoughtful comments on the manuscript. We thank  Ovidiu Radulescu  for initial discussions about the dynamical behaviour of the full circuit. The authors thankfully acknowledge the computer resources, technical expertise and assistance provided by the  Barcelona Supercomputing Center-Centro Nacional de Supercomputacion. We conclude that the dynamical repertoire of the AC/DC circuit contains at least six different monostable and multistable regimes, three of which correspond to behaviour observed in insect segmentation.
Data availability Gap gene expression data used to solve and fit the full model are available as supplementary information (S1_Data. ods; https://doi. org/10. 1371/journal. pbio. 2003174. s009) in Verd et al. (2018, PLoS  Biology). They were published previously in Ashyraliev et al. (2009, PLoS Comp Biol 5: e1000548). Optimizaton and simulation code is available freely online at: https://subversion. assembla. com/svn/ flysa (https://github. com/BVerd/flysa-Revision-14/tree/flysa and https://github. com/BVerd/flysa-Revision-14/tree/flyssm).
Important research questions arising from these issues are: • Deep-water formation is mainly driven by brine rejection in the Weddell Sea shelf region, a process that is sensitive to the temperature and salinity balance that affects the equilibrium concentration of dissolved carbon dioxide. How will the system respond to accelerated warming and an intensified freshwater cycle? © 2019 American Geophysical Union. All rights reserved. • A significant unknown is the response of biota in the face of warming and acidifying surface waters, and decreasing carbonate ion availability -how will this affect carbon drawdown driven by biological production that leads to surface CO2 undersaturation and thus uptake of anthropogenic CO2 from the atmosphere sensu Hauck and Völker (2015)? There is thus great scope to improve our comprehension of the carbon cycle in the WG, with important questions remaining and large gaps existing in available datasets; poor spatial and temporal resolution in observations (Figure  13 ) is currently the limiting factor for advancing understanding and projecting changes in CO2 throughout the water column and its physical and biological drivers.
The cause was suggested to be enhanced upwelling. Nutrients thus appear to be useful indicators of changes occurring in the WG system. Nutrient measurements along this Weddell Sea section and possibly other sections should be continued to monitor future changes in upwelling. Helpful to this cause is the current availability of certified reference materials for nutrient analysis in seawater  (Aoyama et al. , 2012) , which will cater for consistent data among different laboratories. There is no understanding whether the upwelling rate will continue to intensify. Teleconnections like the Southern Annular Mode may play a role in nutrient changes in the WG, which requires more investigation. For example, a wind-driven increase in deep upwelling might enhance nutrient and micronutrient supply to the surface, but observations are scarce and more investigations are needed to confirm the actual role of this mechanism.
How to address the challenges in biology? Climate models and long-term datasets indicate that polar waters will be particularly prone to global change. As in the entire Southern Ocean, expected changes in the WG for the coming century include warming, decline in sea-ice cover and concurrent freshening of surface waters as well as a shoaling of the upper mixed layer, despite increasing westerly winds which may increase coastal upwelling  (Pörtner et al. , 2014; Sallée et al. , 2013; Stammerjohn et al. , 2012). © 2019 American Geophysical Union. All rights reserved. Shallow mixed layers and increased stratification may reduce the input of nutrients such as Fe from deeper water, while increasing average irradiance levels experienced by phytoplankton. However, the recent increase in macronutrient concentrations in surface waters of the WG suggests increased upwelling within the WG  (Hoppema et al.
All rights reserved. Water. Black stippled lines mark two repeat sections along the Prime Meridian and across the Weddell Sea. (Hellmer et al. , 2016, Open Access). © 2019 American Geophysical Union. All rights reserved. © 2019 American Geophysical Union. All rights reserved. © 2019 American Geophysical Union. All rights reserved. © 2019 American Geophysical Union. All rights reserved. reference. Data computed from sea ice concentration data provided by NSIDC  (Cavalieri et al. , 1996). Note different y-axis scales. Right: Regional ice concentration trends in 1979 -2018. Carbon data (left) and for winter only (May-Oct, right) as available from the GLODAPv2 dataset  (Olsen et al. , 2016). Bottom: All surface fCO2 data (left) and for winter only (May-Oct, right) as available from the SOCATv3 dataset  (Bakker et al.
46 Left atrial emboli causing ischaemic stroke were described a decade later. 47 In the Framingham Heart Study, AF was associated with a five-fold longterm increased risk of stroke. 48, 49 Prospective randomized studies from the late 1980s reported a dramatic and highly significant reduction in stroke in patients with AF treated with warfarin. The randomized AFASAK,  50  SPAF,  51  and BAATAF  52  studies were among the first to demonstrate that dose-adjusted warfarin prevented strokes effectively in patients with AF, confirmed in a later metaanalysis. 53 9] [60]  Atrial fibrillation stroke risk prediction models have, in general, not included AF type  [61] [62] [63] [64]  perhaps because of absence of AF pattern information in hospitalization/discharge databases that were used for their derivation and validation.
PCR bands were ligated to pGEM-T vector (Promega, Madison, WI, USA) and used to transform competent Escherichia coli JM-109 cells (Promega). Plasmid minipreps were conducted (QIAprep Spin Miniprep Kit), and the clones were sequenced with the aid of an ABI Prism 3100 Automated Sequencer (LANGEBIO, CINVESTAV-Irapuato, Mexico). Sequencing was unidirectional and conducted using the T7 primer. The Glomeromycotina origin of the sequences was confirmed by BLAST-N comparison with sequences deposited in GenBank (NCBI) and Glomeromycotina dedicated database MaarjAM  (Öpik et al. 2010). Multiple alignment was performed using MUSCLE  (Edgar 2004) , and the alignment was manually optimized with Jalview software  (Waterhouse et al. 2009 ). The evolutionary history was inferred by using the Maximum Likelihood method based on the Kimura 2-parameter model  (Kimura 1980 ).
The tree with the highest log likelihood (-3,947. 04) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches. The tree was drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 54 nucleotide sequences. All positions with less than 95 % site coverage were eliminated. That is, fewer than 5 % alignment gaps, missing data, and ambiguous bases were allowed at any position. There was a total of 453 positions in the final dataset. Evolutionary analyses were conducted in MEGA7  (Kumar et al. 2016). Statistical analyses. Data were checked for normal distribution with the Shapiro-Wilk test. One-way analysis of variance (ANOVA) at a significance level of 0. 05 was performed on fungal colonization variables.