dataesr/scientific-paragraphs-categorization huggingface dataset:
Differential expression analysis Reads were strand-specifically mapped to tORFs and conserved genes using the coverageBed command from the BEDTools package version 2. 26. 0  (Quinlan and Hall 2010) , with parameter -s. We examined significant tORF expression changes using DESeq2  (Love et al. 2014 ) using a 5% FDR and minimum of twofold change. We identified lineage-specific expression increases when the expression of the tORFs in the considered lineage was significantly more expressed than for the other strains in all pairwise comparisons. For SpB-SpC increases, we selected tORFs when SpB and SpC strains were both more expressed than YPS128 and SpA, and S. paradoxus increases when all S. paradoxus lineages were more expressed than YPS128. For the visualization of tORF sequence coverage (Fig.
All strains were then transferred to DMSO (control) and MTX DHFR PCA media (0. 67% yeast nitrogen base without amino acids and without ammonium sulfate, 2% glucose, 2. 5% noble agar, drop-out without adenine, methionine, and lysine, and 200 µg/mL MTX diluted in DMSO [or only DMSO in the control medium]). Plates were incubated for 4 d at 30°C, after which a second round of MTX selection was performed to decrease noise. Plates were incubated for another 4 d at 30°C. Images were taken with an EOS Rebel T5i camera (Canon) every 2 h during the entire course of the experiment. Incubation and imaging were performed in a spImager custom platform (S&P Robotics). Data from the second round of MTX selection were used for the downstream analysis. Images were processed using the gitter. batch function in the R package Gitter  (Wagih, Parts 2014, version 1.
Acknowledgments We thank  G. Charron  and the IBIS sequencing platform ( B. Boyle ) for technical help and  A. R. Carvunis ,  R. Dandage , and the Turnover of translated de novo ORFs in wild yeast Genome Research 941 www. genome. orgreviewers for comments on the manuscript. This work was supported by a  Natural Sciences and Engineering Research Council of Canada (NSERC)   Discovery grant  and a  Fonds de recherche Nature et Technologies Quebec (FRQNT)   Team Grant  ( 2015-PR-181807 ) to C. R. L. C. R. L. holds the  Canada Research Chair in Evolutionary Cell and Systems Biology.
Data access High-throughput sequencing data generated in this study have been submitted to the NCBI BioProject database (https:// www. ncbi. nlm. nih. gov/bioproject) under accession number PRJNA400476 (Sequence Read Archive [SRA; https://www. ncbi. nlm. nih. gov/sra] accession numbers SRR5996796-SRR5996803 for ribosome profiling and SRR6022778-SRR6022785 for total mRNA experiments). New assemblies, annotation files, and custom analysis scripts are available as Supplemental Data and Supplemental Code.
Purpose: Controversy exists regarding the outcomes following ventral hernia repair with polypropylene (PP) or polyester (PET) mesh. Monofilament PP less frequently requires extraction in the setting of contamination compared to multifilament PET mesh. The purpose of this systematic review and meta-analysis was to analyze the clinical outcomes of ventral hernia repair with PP and PET mesh. Patients and methods: A comprehensive literature search was performed using the Ovid search platform. Criteria included ventral hernia repair publications using either PP or PET mesh with a minimum follow-up duration of one year. Included studies were subject to data extraction including mesh position, weight, recurrence rates, infection, and complications. Random effect meta-analysis was run to provide pooled event rate and 95% CI.
Search criteria A comprehensive literature search was performed using the Ovid search platform. This platform encompassed 12 Databases were searched using the keywords "ventral AND hernia AND mesh AND recurrence AND (placement OR overlap OR position)" and "Ventral hernia mesh repair. " The literature was searched for articles discussing polyethylene terephthalate (PET) or polypropylene (PP) mesh used in ventral, incisional, or parastomal hernia procedures. Both generic PET/PP mesh terms and specific product terms were included in the search. No date filter was applied to this search.
Data extraction For comparative studies, each arm was assessed individually and inclusion/exclusion criteria were implemented for each arm. When prospective or retrospective papers reported different kinds of meshes, the subgroups were included only if the results were detailed enough to be able to assign the complications to different meshes with certainty and if each subgroup met inclusion criteria. When mesh weight was not described in the paper, but either the brand or the mesh was identified with certainty, mesh weight was obtained from the company website, brochures, or publications. The extracted data included the following: First author, year of publication, mesh studied, mesh weight, material, manufacturer, surgical approach, number of patients, hernia type, Oxford classification, methodology, mesh positioning, fascial closure, number of hernias treated, mean follow-up, previous ventral repair, number of recurrences, number of mesh-related recurrences, number of non-mesh-related recurrences, number of unknown recurrences, patient comorbidities, and patient preoperative medical history.
Statistical analysis Primary and secondary outcomes were measured using incidence rate reported in individual groups from each single-arm study. Pooled estimation of risk was calculated using random effect model, as data come from literature review from heterogeneous and mainly nonrandomized studies, using different methods and designs on various populations. An overlap between event rate confidence intervals from different groups suggests that there was no apparent trend in the results in favor of one group or the other. Sub-group analyses were performed on the basis of surgical approach (laparoscopic or open) and mesh weight (light or heavy). Summary of effect size and the associated forest plots were generated using Comprehensive Meta-Analysis software version 2. 2 (Biostat, Inc. ; Englewood, NJ, USA).
Results One-hundred and nine articles were identified of which 81 articles satisfied all inclusion criteria. A total of 10,022 patients operated for ventral hernia repairs were included in the analysis. Table  S1  provides a descriptive summary of the included studies. Studies containing separate data on multiple subset populations are segregated in the appendix and treated as separate studies. In total, 81 studies resulted in 97 individual study data sets. Analyses were performed to evaluate the pooled recurrence rate in ventral PET and PP hernia repair. Studies were separated based on mesh material (ie, PET or PP), approach (ie, open or laparoscopic), and mesh weight (ie, LW or HW). Due to insufficient papers and data, we were unable to report results on the following categories: recurrence rate in laparoscopic procedures using LW PET or PP meshes, recurrence rate using HW PP mesh, and seroma formation for both PET and PP mesh.
DovePress undermining skin flaps or subcutaneous mesh placement, which has been associated with poor outcomes, could not be addressed. 17 Additional known risk factors for hernia recurrence and complications including smoking status, history of COPD, diabetes, and BMI were unable to be addressed in this review due to inconsistent reporting. Finally, the literature review was quality controlled, and some manuscripts were excluded from using the same data. However, the analysis datasets may contain some patient data in duplicate though the authors believe this would only be in a very limited number of patients.
Acknowledgments Medical writing and editorial support was provided by  Nicholas Paquette, PhD  of Medtronic based on content and conclusions determined by the authors. The abstract of this paper was presented at the American Hernia Society 2016 and 36th Annual Meeting of the  Surgical Infection Society  conferences as poster presentations. The posters' abstracts were published in the 18th Annual Hernia Repair and Program and Abstracts 36th Annual Meeting of the  Surgical Infection Society Palm Beach , Florida, May 18-21, 2016.
Nocturnal PSG An overnight PSG was performed in the sleep center. Infants were systematically studied in the SP then in the PP for a minimum of 2 sleep cycles for each condition; if the SP was not tolerated, the infant was excluded from this study. Raw PSG data were analyzed by a single reviewer (L. C. ) who was blinded as to sleep position during the overnight sleep study. The nocturnal PSG was performed in the presence of the child's father/mother or guardian, without tilting of the mattress, and using a Morpheus recorder (Micromed, Mogliano Veneto, Italy). Sleep and respiratory events were scored using sleepRT software (OSG, Rumst, Belgium). The PSG recording employed frontal, central, and occipital leads (FP1, FP2, C3, C4, O1, O2, A1, and A2), video, 2 electrooculograms, 1 chin electromyogram, and 1 electrocardiogram, inductance plethysmography of chest and abdominal respiratory movements, as well as a nasal cannula, oronasal thermistor and saturation values.
Patient characteristics PSG recordings were performed in 21 infants with PRS (11 girls, ten boys) aged (median [IQR]) 44 days [27-70]; 3 children were excluded because they did not tolerate sleep in the SP (OAHI = 15/h in the PP). In total, PSG data were available for both SP and PP positions for 18 infants. Among these, 12 infants (67%) presented an isolated PRS and 6 (33%) an associated or syndromic PRS, (syndromic: Franceschetti n=2/6, Rubinstein-Taybi n=1/6, del22q11 n=1/6; associated: n=2/6). The mean ± SD age at the time of PSG was 44 ± 26 days. A total of 12 (67%) infants had respiratory symptoms at the time of the recording (snoring or noisy breathing or apneas or apparent life-threatening events or frequent arousals because of respiratory effort or desaturation or stridor). There were 15 (83%) infants who did not have respiratory support; before PSG, the PP was used for 14 infants, and the SP was used for 4 infants (1 in ambient air and 3 with respiratory support).
Discussion The present study found that although PP improved breathing quality and sleep quality for two-thirds of infants, it was sufficient to decrease the OSA index below the severe level only for 3 of the 18 patients studied. Interestingly, it was also found that among infants with PRS, a third did not present OSA clinical manifestations although all of them had a severe OSAS (OAHI > 10/h) as assessed by PSG and three-quarters had a very severe OSA (OHAI > 25/h). This is in accordance with a previous study that has published data on the incidence of OSAS in PRS; Daniel et al. report 75% of severe OSA in a cohort of 33 PRS infantsthe slightly lower incidence may be explained by the age of the patients (mean: 12 months)  14. It appears from the present study that clinical evaluation alone underestimates both the frequency and the severity of OSAS in PRS.
Briefly, the 16S V3-V4 variable region  (Fadrosh et al. , 2014)  [341/785 primers, with barcode on the forward primer  (Herlemann et al. , 2011) ] was amplified in a 28-cycle PCR using the HotStarTaq Plus Master Mix Kit (Qiagen, United States) under the following conditions: 94 • C for 3 min, followed by 28 cycles of 94 • C for 30 s, 53 • C for 40 s and 72 • C for 1 min, after which a final elongation step was performed at 72 • C for 5 min. PCR products were then purified using calibrated Ampure XP beads and used to prepare a DNA library following the Illumina TruSeq DNA library preparation protocol. Blank DNA extraction controls were sequenced to verify there was no contamination, which was confirmed as these gave no amplification. Prokaryotic 16S rRNA paired-end reads were merged using USEARCH  (Edgar and Flyvbjerg, 2015)  after q25 trimming of the ends.
The resulting 16S reads were processed using FROGS, implemented on the Galaxy platform  (Escudié et al. , 2018) , multifasta files were parsed, checked for quality, and trimmed by length (expected value of 455b ± 35b). Sequences were then clustered with SWARM  (Mahé et al. , 2014)  using a distance threshold of three, chimeras were removed using the UCHIME algorithm  (Edgar et al. , 2011)  implemented in VSEARCH  (Rognes et al. , 2016) , and taxonomic affiliation was performed for each OTU by NCBI Blast+  (Camacho et al. , 2009)  using the Silva 132 16S gene database  (Quast et al. , 2013). Additional filtering on abundance at the threshold of 0. 005%  (Bokulich et al. , 2013)  and on BLAST at 95% minimum coverage and 80% minimum identity was also performed to remove non-biologically relevant OTU sequences.
Statistical Analysis Alpha diversity within the 40 samples was estimated with OTU number and Inverse Simpson index  (Simpson, 1949). Difference in the alpha diversity indexes among body structure and vent field categories were tested using Mann-Whitney tests and the difference between developmental stages, by Kruskal-Wallis followed by pairwise Wilcox tests; p < 0. 05 was considered the threshold of significance for a difference between samples. For further statistical analysis, the sequence dataset was normalized by cumulative sum scaling to minimize the effect of different sequence numbers obtained with each sample  (Paulson et al. , 2013). Beta diversity was analyzed by hierarchical clustering using the complete method based on Bray-Curtis dissimilarity matrices. The homogeneity between categories was tested with the betadisper function of the Vegan R package, and significant differences between categories were tested for by Permutational Analysis of Variance (PERMANOVA, 9999 permutations) with the adonis function of the same package  (Oksanen et al.
, 2008). Multilevel comparisons for the developmental stage condition were also performed with the pairwise adonis function  (Arbizu, 2017). Taxonomic composition and diversity results were visualized using the R package Phyloseq v. 1. 14. 0 (McMurdie and Holmes, 2013). The linear discriminant analysis (LDA) effect size (LefSE) method  (Segata et al. , 2011)  was used to characterize and highlight microorganisms specific to each of the different conditions. Results were shown both with a plot of LDA score for each bacterial group and with a cladogram, each concentric circle representing a taxonomic level, the innermost being the phylum and the outermost the genus.
052; Supplementary Figure  S3D ). No significant differences were found between TAG and Snake Pit samples for eggs or pleopods (Supplementary Figures  S3B, C ). Regardless of the vent site, egg, and pleopod communities were significantly different from each other (PERMANOVA R 2 = 0. 233, p < 0. 001, Supplementary Table  S3 ). Body surface (egg vs. pleopod) was also the main factor structuring our dataset, followed by vent site effect (R 2 = 0. 195) and developmental stage effect (R 2 = 0. 148, Supplementary Table  S3 ). Taken separately, both egg and pleopod surfaces, showed a strong vent site effect on bacterial community composition, with significant differences between TAG and Snake Pit assemblages (PERMANOVA R 2 0. 291 and 0. 316 p < 0. 001 for both eggs and pleopods). In addition, significant variations in bacterial communities were detected through the egg development stages (PERMANOVA R 2 0.
Microbial Taxonomic Comparison Based on rDNA 16S sequence affiliation according to the Silva 132 database, nine phyla could be identified in our samples, with just four phyla accounting for more than 99% of the sequences obtained (Figure  3 ). The most abundant taxa were Epsilonbacteraeota, representing in 39% of the total dataset in relative abundance, followed by Proteobacteria (36%), Patescibacteria (13%), and Bacteroidetes (11%). Among Proteobacteria, three major classes were present with a clear dominance of Gammaproteobacteria (63. 7%), followed by Zetaproteobacteria and Alphaproteobacteria (17. 7% each). Sequences affiliated to Rothia sp. from the Actinobacteria phylum (0. 007%), Streptococcus sp. , and Enterococcus sp. from the Firmicutes phylum (0. 013%) were only present in a few samples and most likely correspond to potential contaminants.
In addition the absence of these two groups in either TAG or Snake Pit samples could also be related to an insufficient sequencing depth since they were present in low abundance in our dataset. A striking case supporting the major influence of vent fluid chemistry is that of Zetaproteobacteria, a group of iron-oxidizing bacteria that were significantly more abundant in TAG than in Snake Pit samples, both on egg and pleopod surfaces. Vent fluids from TAG are described as having much higher concentrations of Fe, Cu, and Mn than Snake Pit, which are richer in Cd and Pb  (Jean-Baptiste et al. , 1991; Tivey et al. , 1995; Fouquet et al. , 2010). Thus, a higher relative abundance of Zetaproteobacteria on both surfaces at TAG could result from a higher concentration of the energy source that fuels their metabolism.
ACKNOWLEDGMENTS We would like to thank the chief scientists of the BICOSE 2014 (http://dx. doi. org/10. 17600/14000100 )and BICOSE 2 (http://dx. doi. org/10. 17600/18000004 )cruises (M-AC-B), the captains and crews of the R/V Pourquoi pas?, the ROV Victor 6000 and Nautile submersible teams for their efficiency. We would like to thank  G. Hamel  for his implication in the design of the pressurizedrecovery device. We would like to thank  P. Elies  and the  PIMM platform of Université de Bretagne Occidentale  for the use of the ultramicrotome for thin sectioning used for FISH experiments. We would like to thank  Dr. S. Laming  for his help and knowledge about microscopy, from sectioning to image capturing for FISH experiments. We would also like to thank  H. Mc Combie-Boudry  of the  Bureau de Traduction of Université de Bretagne Occidentale  for English edition.
FUNDING This work was supported by the  Ifremer REMIMA program. Pressure equipments used in this study were funded by the  European Community programs EXOCET/D  ( FP6-GOCE- CT-2003-505342 ), and  MIDAS  ( FP7/2007-2013-603418 ) and by the  CNRS  project " Defi Instrumentation aux limites " (2016).
relaxation  (Wertheim et al. 2015). We used the program RELAX as a second method to refine our analysis. RELAX allows more subtle estimation of x variations by considering different categories of sequence sites that can evolve under different selective constraints  (Wertheim et al. 2015). For PAML analysis, four nested models allowing the calculation of different x values for some subsets of branches were defined: M0, the null model with one x for the whole tree; M1, which allowed x to differ between outgroups (x 0 ) and Neottieae (x N ); M2, same as M1 but allowing a different x for Palmorchis (x p ) and the remaining Neottieae (x N* ; below noted as Neottieae* ¼ Neottieae without Palmorchis); M3, same as M2 but allowing x to differ between autotrophic (x Na ) and mixotrophic Neottieae* (x Nx , see fig.
2004 ). The LCBs obtained were individually aligned a second time using the MAFFT online service  (Katoh et al. 2017)  with automatic selection of alignment strategy, gap opening penalty set to 3. 0, offset value set to 0. 1 and other parameters left as default. The resulting alignments were then concatenated. Model selection was done with the ModelFinder algorithm  (Kalyaanamoorthy et al. 2017 ) implemented in the IQ-TREE program  (Nguyen et al. 2015). The model with lowest Bayesian information criterion score was used for ML analysis with IQ-TREE  (Nguyen et al. 2015). The first model with the lowest Bayesian information criterion compatible with MrBayes v3. 2 parameters  (Ronquist et al. 2012)  was chosen for Bayesian inference with this program. A complementary analysis using the nuclear marker ITS, including ITS1-5.
Selective Regime Analyses All CDS were extracted from the same set of plastomes used for phylogeny reconstruction, except the six mycoheterotrophic species. Except for NDH complex, genes that were lost or pseudogenized in at least one of the remaining species were discarded from subsequent analyses (see table 2 for the remaining genes). For NDH, because some species had lost all the genes, we rather only kept for subsequent analysis only the 15 species, which retained the 11 NDH genes (table  2 ). CDS were aligned based on their amino acid sequences with subsequent backtranslation using the AlignTranslation function  (Wright 2015)  of the DECIPHER package  (Wright 2016)  in the R environment for statistical computing (R Development Core Team 2007). Functional gene groups were built by concatenating CDS for photosynthesis, NDH, ATP-synthase, PEP, and housekeeping genes (table 2).
ycf1 and ycf2 were combined and analyzed independently because of their specific evolutionary rates  (Barrett et al. 2014 ). In addition, some genes were analyzed individually when long enough for confident parameter estimation: ccsA, psaA, psaB, psbA, psbB, psbC, psbD, rbcL, accD, and matK (see supplementary table  S2 , Supplementary Material online). x, the ratio of nonsynonymous substitutions per nonsynonymous site (d N ) to synonymous substitutions per synonymous site (d S ), was used to estimate selective pressure for different sets of genes. The codeml program implemented in PAML version 4. 9  (Yang 2007 ) was used to compute x values, with the branch model and the tree shown in figure  1B. The codon frequency parameter was set to F3X4. Four nested models allowing the calculation of different x values for some subsets of branches were defined: M0, the null model with a unique x for the whole tree; M1, which allowed x to differ between outgroups (x 0 ) and Neottieae (x N ); M2, same as M1 but allowing a different x for Palmorchis (x p ) and the remaining Neottieae (x N* ); M3, same as M2 but allowing x to differ between autotrophic (x Na ) and mixotrophic Neottieae* (x Nx , see fig.
1B  for species considered as mixotrophic). Models were compared by likelihood ratio tests following this scheme: M1 versus M0, M2 versus M1, and M3 versus M2. The statistic of the test (K) was calculated as two times the difference in model likelihood and compared with a chi-squared distribution with degrees of freedom equaling the difference in parameters number between the two models. P values were obtained using the function pchisq of the R stats package. We completed the PAML analysis with a specific test dedicated to the detection of changes in selective pressure (relaxation or intensification). This was carried out with the program RELAX, available at the Datamonkey webserver http://datamonkey. org/relax; last accessed March 6, 2019. RELAX allows more subtle estimation of x variations by considering different categories of sequence sites that can evolve under different selective constraints  (Wertheim et al.
2015). x distributions are estimated for a test (T) and a reference (R) subset of branches and a selection intensity parameter k such that x T ¼ x k R is introduced. The program then compares the goodness of fit of the data to a branch-site evolutionary model with k ¼ 1 (null model) or k being a free parameter (alternative model). When the alternative model shows a better fit following a likelihood ratio test, k < 1(resp. k > 1) indicates a relaxation (resp. an intensification) of selective constraints in the test group. Three different tests were done with three different designs of test versus reference groups, copying what has been done with the PAML nested analysis (see supplementary fig. S2 , Supplementary Material online, for group designs).