dataesr/scientific-paragraphs-categorization huggingface dataset:
To rule out any effect of Tet on the parasites proliferation at the elevated temperature, WT cells in the presence of Tet were included as an additional control. After different times, the cells were counted and the cultures diluted to the starting density of 5 x 10 5 cells/ml, if necessary. For the cKO cells, the data represent the mean ± SD from three cell lines. In the case of WT cells, a representative analysis of three repetitions is depicted. A paired t-test was used to evaluate significant differences between the 5S-Trx2 cKO cells grown in the absence of Tet at 27˚C and 37˚C, respectively ( � = p<0. 05 and �� = p<0. 01). https://doi. org/10. 1371/journal. ppat. 1008065. g004 about 4-fold within the first 24 h, and 2-3-fold within the next 24 h. After 48 h exposure to 37˚C, proliferation of the cells stopped until the experiment was terminated after 120 h.
AndreSchneider, Bern. Recombinant T. brucei Tpx  [69] , rabbit antibodies against T. brucei lipoamide dehydrogenase  [27]  and guinea pig antibodies against mitochondrial peroxiredoxin (mPrx; TriTrypDB: Tb927. 8. 1990)  [12]  were obtained previously. Guinea pig antibodies against T. brucei Trx2 (TriTrypDB: Tb427. 03. 4240) were generated by Eurogentec, Seraing, Belgium. Mouse anti-c-myc and HRP-conjugated goat antibodies against mouse IgGs were from Santa Cruz Biotechnology. HRP-conjugated goat antibodies against rabbit IgGs were purchased from ThermoFisher. HRP-conjugated donkey antibodies against guinea pig IgGs were from Merck.
Immunofluorescence microscopy Immunofluorescence microscopy was conducted as described previously  [7]. Approximately 2 x 10 6 BS and PC cells inducibly expressing myc-tagged versions of Trx2 grown in the presence of Tet were harvested, washed with PBS, and stained with MitoTracker Red CMXRos (Life Technologies). Afterwards, the cells were fixed, permeabilized and treated with anti-c-myc antibodies (1:200 in 0. 5% gelatin in PBS) for 1 h at room temperature followed by goat antimouse antibodies coupled to Alexa Fluor 488 (1:1,000 in 0. 5% gelatin in PBS, Molecular Probes). The nucleus and kinetoplast were visualized by DAPI staining. Cells were examined under a Carl Zeiss Axiovert 200 M microscope equipped with an AxioCam MRm digital camera using the AxioVision program (Zeiss, Jena).
Size-exclusion chromatography with multi-angle light scattering (SEC-MALS) SEC-MALS was performed to determine the absolute molecular mass of 5S-Trx2. Typically 100 μl of 80 μM recombinant 5S-Trx2 was injected into a Superdex 200 10/300 column connected to an A ¨KTA Purifier. This system was coupled to a light scattering detector (DAWN8+ HELEOS, Wyatt Technology) and a refractometer (Optilab tREX, Wyatt Technology) to measure the absolute refractive index of the solution. Runs were carried out at 4˚C and a flow rate of 0. 4 ml/min. Data were analyzed using the manufacturer supplied software (ASTRA 6. 1, Wyatt Technology). The Rayleigh ratio and differential refractive index were plotted against the elution volume.
(S1B Fig). Structural modeling of T. brucei Trx2 (https://swissmodel. expasy. org/interactive) revealed that the protein may adopt a Trx-fold with a long central insertion (see the alignment in S1A Fig) and with the CXXC motif correctly placed at the N-terminus of an α-helix. A Blast-P search with T. brucei Trx2 against all nonredundant GenBank CDS translations retrieved exclusively Trx-like proteins but no glutaredoxins or tryparedoxins. The top hits belonged to Kinetoplastid Trx2-homologues (S1C Fig).
The data depicted are representative for three independent experiments conducted with three 5S-Trx2 clones. (B) 5S-Trx2 cKO cells were pre-cultured in Tet-free medium until they demonstrated a proliferation defect, usually observed around six days after Tet removal (see Fig 3D). WT parasites and cKO cells expressing WT-Trx2 or 5S-Trx2 as well as 5S-Trx2 cKO cells kept in Tet-free medium were either continuously grown under standard conditions (control) or transferred to 37˚C. To rule out any effect of Tet on the parasites proliferation at the elevated temperature, WT cells in the presence of Tet were included as an additional control. After different times, the cells were counted and the cultures diluted to the starting density of 5 x 10 5 cells/ml, if necessary. For the cKO cells, the data represent the mean ± SD from three cell lines.
Acknowledgments Dr. Irmgard Sinning ,  BZH, Heidelberg , is kindly acknowledged for her support with the SEC-MALS measurements. We thank  Drs Andre  ´Schneider, Bern,  Keith Matthews ,  Edinburgh , and  Christine Clayton ,  Heidelberg , and  Gunter Stier, Heidelberg , for their kind gifts of antibodies and/or plasmids and  Dr. Marta Bogacz, Heidelberg , for her help with the oxidative stress experiments. M. A. C. acknowledges the technical assistance of  Ana Paula Arevalo (Transgenic and Experimental Animal Unit, Institut Pasteur de Montevideo ).
The work of L. K. S. was funded by the  Deutsche Forschungsgemeinschaft (DFG)   Priority Program SPP 1710  ( KR1242/6-2 ) and  KR 1242/8-1. K. U. and U. J. thank the  DFG Priority Program SPP 1710  ( Schw823/3-2 ) for supporting their work. M. A. C. acknowledges the support of  ICGEB  grant  CRP/URU14-01. A. E. L. obtained a postdoctoral fellowship from the  Peter und Traudel T. perspective regarding the physiological function of thioredoxintype proteins in trypanosomes. Engelhorn-Stiftungwas  supported for protein mass spectrometry by the  Centre for Chemical Microscopy (ProVIS) at the Helmholtz Centre for Environmental Research , which is supported by  European regional development funds (EFRE-Europe Funds Saxony)  and the  Helmholtz Association. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Bryophytes have been proposed as ideal indicators of ecosystem change, because they are important components of forest integrity, and considerable research indicates that some groups are sensitive to the changes associated with specific human disturbances. Bryophyte richness and abundance have been found to vary predictably along elevational gradients, but the role of human impacts on these distribution patterns remains unclear. The aim of this study is to explore the impact of human disturbance on the elevational patterns of bryophyte diversity, along an elevational gradient. Along the gradient we collected three datasets in the following sites: preserved (P), forest track roadsides (R) and disturbed by agriculture/silviculture practices (D). Two survey plots of 100 m 2 were established at every 200 m elevational step for each sites P, R, D, and in each plot bryophytes were sampled in a stratified manner.
All samples are deposited in the herbarium TFC-Bry of La Laguna University (Tenerife, Canary Islands). Nomenclature follows Losada-Lima et al, 2010  [36]. As a result of this stratified sampling, we sampled a total of 68 microplots along the elevational gradient (P sites: 24 microplots; R and D: each 22 microplots), and within these a total of 194 subplots (P: 70 subplots, R: 65, D: 59). The number of subplots sampled in the different transects varied because bryophytes were not always present on every substrate or the particular substrate was absent. For analyses, data from microplots on each substrate were pooled to the level of these subplots by averaging mean cover values for each species. At each plot, we took a detailed description of the vegetation, recording all vascular species present, their relative cover and whether they were herbs, shrubs or trees.
Data analysis Bryophytes were assigned to categories reflecting their life-history strategy (Table  2 ). Life strategy classification followed Du ¨ring (1979)  [37]. For the analyses, specimens of the division Anthocerotophyta were included together with Marchantiophyta, due to their low number of species and occurrence along the gradient. Total number of species was calculated for sites P, R and D. For analyses, microplot data for each substrate was pooled within subplots by averaging mean cover values for each species. We calculated number and percentage cover of mosses, liverworts (with regarding of families) in P, R and D sites and also percentage of life forms in each site type. To highlight elevational trends of species richness, we applied non-parametric locally weighted scatterplot smoothing by using function lowess in R (gplots package).
To analyse elevational range distributions of colonist and perennial species, we took the minimum and maximum elevational range of the respective species, and used the median as the range centre to account for accidental outliers. In order to assess vegetation similarity and heterogeneity between plots and gradients, we performed ordination techniques (Detrended Correspondence Analysis) based on Bray-Curtis similarity index, with subplots as cases and mean cover of species as a variable. Cover of each species at each microplot was pooled together to obtain the mean value for subplot, for species in every substrate. In order to reduce noise in the dataset, we downweighted rare species. Environmental characteristics recorded in the sampling sites (see methods section) were fitted to the ordination result in order to assess their possible contribution to community assemblage patterns.
Acknowledgments We are especially grateful to  Julio Leal Perez , for his inestimable help in setting up the plots and during fieldwork, and  Nicholas Wilding  for reviewing the English of this manuscript. We thank  Servicio de Medio Ambiente  del  Cabildo Insular de La Palma  for their help and for providing authorization for the fieldwork, especially Felix  Manuel Medina Hijazo  and  Rafael Pedro Rodrı ´guez de Paz. We also thank  Alejandro Barrera de Paz  and  Amalia Martı ´n Barrera  for their help during fieldwork. This research benefited from the support of the  Agence Nationale de la recherche, Conseil Regional de La Reunion ,  Conseil Regional de Guadeloupe, Government of Azores, Government of Canarias , under the framework of the  Net-Biome transnational first call  ( Moveclim  project).
Primary antibodies for immunofluorescence were anti-HNF4α (Cell signalling 3113S), anti-5hmC (Active Motif 39769). After secondary antibodies, coverslips were washed and mounted on a slide with a mounting medium containing DAPI (Vectashield). Fluorescence was visualized with an Olympus Inverted Microscope model IX71 and images captured with Evolution/QImaging Digital Camera (Cybernetics). Data analysis was performed using ImageJ (National Institutes of Heatlh).
Bioinformatic Analyses Raw expression and methylation data were imported and processed using R/Bioconductor packages for Illumina bead arrays  [Du et al. , 2008]. Data quality was inspected using boxplots for the distribution of expression signals, and inter-sample relationship using multidimensional scaling plots and unsupervised clustering. For methylation data, we removed low quality probes with a detection P value > 0. 01 in more than 10% of the samples. Following swan (Subsetquantile Within Array) normalization  [Maksimovic et al. , 2012]  implemented in the minfi package  [Aryee et al. , 2014] , 5hmC "peaks" were identified by subtracting the signal of oxidative bisulfite from the signal of conventional bisulfite. Next, we performed Maximum Likelihood Estimate (MLE) of 5mC and 5hmC (oxBS.
MLE) with the ENmix package  [Xu et al. , 2016]. Using a binomial model at each CpG locus in each sample, oxBS. MLE outputs a matrix of MLEs of 5mC levels and a matrix of MLEs of 5hmC levels, setting as NA any negative value. To define differentially expressed genes (DEGs), differentially methylated positions (DMPs) and differentially hydroxymethylated positions (DhMPs), we modelled experimental conditions as categorical variables in a linear regression using an empirical Bayesian approach  [Smyth, 2004]. Differentially methylated and hydroxymethylated regions (DMRs and DhMRs, respectively) were identified with the DMRcate package using the recommended proximity-based criteria  [Peters et al. , 2015]. Comparisons with an FDR-adjusted P value below 0. 05 were considered statistically significant.
In addition, only DhMPs with at least 10% change in 5hmC were considered as significant for any given comparison, as this has been suggested as a threshold for the sensitivity of this technique  [Skvortsova et al. , 2017]. DEGs, DMPs, and DMRs were further analyzed to determine functional pathways and ontology enrichment using EnrichR  [Chen et al. , 2013]. Genomic context annotations, including chromatin states (ChromHMM) were performed with the ChIPseeker  [Yu et al. , 2015]  and Annotatr  [Cavalcante and Sartor, 2017]  packages. EnrichedHeatmap package  [Gu et al. , 2018]  was used for summary heatmaps of genomic context. All expression and methylation data will be deposited to the Gene Expression Omnibus repository.
Acknowledgements The authors thank  Cyrille Cuenin  ( Epigenetics Group, IARC, Lyon ) and  Severine Croze  ( Claude Bernard, University Lyon 1 ) for their help with the HT-12 array and MethylEPIC assays. The authors also thank  Florence Le Calvez-Kelm  and  Geoffroy Durand  ( Genetic Cancer Susceptibility Group, IARC, Lyon ) for Covaris Sonicator supply,  Zdenko Herceg  ( Epigenetics Group, IARC, Lyon ) for facilitating the infrastructure to realize hMeDIP experiments,  Ramón González García-Conde  ( Research Center on Cellular Dynamics, UAEM, Mexico ) for HepaRG cell line donation for preliminary assays,  Emilio-Rojas del Castillo  ( Department of Genomic Medicine and Environmental Toxicology, IIB-UNAM, Mexico ) for his advice during JRRA PhD studies,  Pedro Valencia Mayoral (Planning Direction, Hospital Infantil de México "Federico Gómez ") for training JRRA on liver histopathology during PhD Studies,  Athena Sklias  and  Andrea Halaburkova  ( Epigenetics Group, IARC, Lyon ) for their enriching discussions during laboratory work, and  Aurelie Salle  ( Epigenetics Group, IARC, Lyon ),  Georgina Guerrero-Avendaño  and  Rosario Pérez-Molina  ( Department of Molecular Genetics, IFC-UNAM, Mexico ) for their technical assistance.
Statistical analysis Statistical analysis was accomplished by the help of MedCalc (MEDCALC Software, Acacialaan 22 8400 Ostend, Belgium). Analysis of the clinical and basic parameters were done by independent samples t test, chi-square test, and One-Way ANOVA followed by post hoc tukey test. Hardy-Weinberg was calculated with the help of Arlequin V3. 0. Genotype analysis was done by using chi-square test and Fisher exact test. For statistical power calculation, OSSE online tool (http://osse. bii. astar. edu. sg/calculation2. php) was used both in IDCM subjects and healthy controls. P values <. 05 reflecting a statistically significant results.
Acknowledgments Authors are thankful to the  Higher Education Commission  ( SRGP 21-523 ), and  COMSATS University Islamabad  ( CRGP 792 ),  Islamabad, Pakistan , for funding contribution and to all blood donors for their voluntary participation in the study. We also acknowledged the guidance of  Dr. Noor ul Ain , Associate Professor COMSATS and  Dr. Humayoon Shafique Satti ,  Bone Marrow  transplant center,  Rawalpindi. Also , would like to thank  Maahil Arshad  of  Victoria Park CI, Toronto, Canada , for correcting the grammar and revising the English.
(e) Measurement of mitochondrial properties Because only two samples could be run simultaneously to measure mitochondrial properties, liver samples of the two individuals in a processing batch were first homogenized as in  [15, 16]  and assessed for mitochondrial function, while the subsample of white muscle was preserved in respirometry buffer on ice for the subsequent run. Oxygen and magnesium green fluorescence signals were detected simultaneously using two respirometry chambers equipped with fluorescent sensors and recorded using DATLAB software (Oroboros Instruments, Innsbruck Austria). Tissue homogenate from each fish was added to one of the two measurement chambers immediately following preparation. Mitochondrial efficiency was measured as in Salin et al. [31]. Briefly, we used a protocol for estimating the ATP/O ratio that simultaneously measures both oxygen consumption and ATP production on the same sample.
Material and Methods This study included all 1021 autologous FET in one French academic fertility center from January 2013 to December 2016. The embryos were derived either from conventional in vitro fertilization (IVF) or intracytoplasmic sperm injection (ICSI) cycles. The Ethical committee gave its unrestricted approval for the study and all patients had previously given their informed consent for the use of their data (Comité de l'évaluation de l'ethique des recherches biomédicales Paris Nord », IRB 00006467: ID 2018-013). All the data were collected from the Medifirst® software, which meets recognized medical and ethical specifications according to the French information protection commission (ID 2068638).
X-ray crystallography Crystallization screening was carried out by the sitting-drop vapor-diffusion method with a Mosquito ® (TTP Labtech) automated crystallization system. All crystals were grown at 18°C using the hanging-drop vapor-diffusion method. Crystals of 15-20 mg/ml LtgA were grown at 18°C and appeared within 2-3 days. LtgA was crystallized in a 1:1 (v/v) ratio against a well solution of 33% (w/v) PEG 6000 and 100 mM HEPES, pH 7. 5. Crystals were rectangular in shape and grew to approximately 200-300 μm in length. The data set was collected at the Soleil Synchrotron (Beamline Proxima-1) (Supplementary Table  3 ). Phasing by molecular replacement was performed using Phenix  62. Building was performed using Coot  63  , and restrained refinement was carried out using a combination of Phenix and the ccp4 software suite  62, 64.
Data analysis was performed with MaxQuant (version 1. 6. 3. 4) 73 using the Andromeda search engine with the default search settings, including a false discovery rate of 1% at both the peptide and protein levels. Spectra were searched against a database of 2204 proteins from N. meningitidis strain 8013 (taxid 604162, downloaded from http://www. ncbi. nlm. nih. gov/). The mass tolerance for precursor and fragment ions was set to 4. 5 and 20 ppm, respectively, during the main search. Enzyme specificity was set as C-terminal to arginine and lysine, also allowing cleavage at proline bonds, with a maximum of two missed cleavages. Variable modifications were set to oxidation of methionine residues. Only proteins with at least one unique or razor peptide were retained, leading to the identification of 879 Neisseria proteins.
Proteins were quantified by the MaxLFQ algorithm integrated in MaxQuant software  74. A minimum ratio count of two unique or razor peptides was required for quantification. Further data analysis was performed with Perseus software (version 1. 5. 2. 4) after loading the protein group file from MaxQuant LFQ intensity values were log2 transformed and replicate samples of the three strains were grouped. Proteins with less than three valid values in at least one group were removed, and missing values were imputed from a normal distribution around the detection limit. Then, t-tests were performed (FDR=0. 05 and S0=1) for pairwise comparisons of ltgA ltgA with ΔltgA and ltgA ltgAΔ30 with ΔltgA. The results of these t-tests are listed in Supplementary Table  2.
Acknowledgments We would like to acknowledge the beamline staff (PROXIMA-1 at SOLEIL and X06DA at  SLS ) for their assistance. We are extremely grateful to  Frederick Saul ,  Patrick Weber  and  Marco Bellinzoni  for their constant helpful guidance, advice and assistance. We thank  Dr. Antoine. CC-BY 4. 0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted April 12, 2019. ; https://doi. org/10. 1101/607697doi: bioRxiv preprint.
Subsequently, researchers met with the school board and the class directors to explain the goal of the study and how the data would be collected. After this meeting, a leaflet was distributed by all students, requiring the parents to authorize their students to participate in the study. After collecting the signed authorizations, the questionnaires were applied to the students who agreed to participate in the study. Data were collected via paper-and-pencil, during May and June 2018, by a trained researcher. The anonymity of the participants was ensured. The questionnaire took approximately 20 min to complete.
Data analyses Various data analyses were conducted, such as descriptive statistics, confirmatory factor analysis (CFA), reliability, analyses of variance (ANOVAs), Pearson product-moment correlations, and hierarchical multiple regressions. CFA was performed to assess the adequacy of the unidimensional model for the SWFLS. Regarding CFA diverse goodness-of-fit statistics, the goodness of fit index (GFI), comparative fit index (CFI), standardized root mean square residual (SRMR), and root mean square error of approximation (RMSEA) were evaluated. Cronbach's alpha was used to analyze the reliability of the scales. ANOVAs were used to evidence potential sociodemographic effects. To test for convergent and discriminant validity, bivariate Pearson's correlations between the SWFLS and various measures of wellbeing and psychological functioning were evaluated.
Convergent and discriminant validity In order to estimate the convergent validity of the SWFLS, one tool was also chosen to obtain a measure of family satisfaction. The selected instrument was the FSAS  (Barraca et al. , 2000). A significant correlation was found between the two instruments (r = 0. 64, p < 0. 001). An additional method used to obtain data about the validity was to estimate the relationships between the SWFLS scores and wellbeing and interpersonal functioning measures. As expected, there were strong significant positive correlations between the scores of the SWFLS, and life satisfaction (r = 0. 65, p < 0. 001) and family support (r = 0. 65, p < 0. 001). These findings support the convergent validity of the SWFLS. Validity was also tested by conducting hierarchical multiple regression to explore whether the SWFLS adds incremental validity to the FSAS.
Whole genome sequencing WGS was performed systematically on all invasive cultured isolates received at the NRCMHi. Genomic DNA was extracted with the MagNA Pure 96 system (Roche Molecular System, Pleasanton, USA). Library preparation were performed with the Nextera ® XT DNA library Preparation Kit (Illumina, San Diego, USA) and whole genome sequencing was processed with Illumina technology (NextSeq 500, Illumina) with paired-end strands of 150 bp and a sequencing depth of 50X. All de novo assemblies were generated using SPAdes 3. 10 (CAB, St. Petersburg State University, Russia). Sequences are available through the PubMLST https://pubmlst. org/hinfluenzae/ database  (16). WGS data were used to infer sequence types (ST) according to the Multilocus Sequence Typing (MLST) scheme  (17)  WGS data were also analysed using a "gene-by-gene" approach using the annotated reference strain (Rd KW20) on the Bacterial Isolate Genome Sequence Database (BIGSdb) platform on PubMLST  (18).
SplitsTree4 (version 4. 14. 6) was used to visualise the resulting distance matrices as Neighbour-net networks. (19)  GrapeTree was also drawn on the basis of comparisons of allelic profiles for the isolates with complete MLST data  (20). IDs of all these isolates are given in the supplementary Table  2  to allow retrieving of WGS sequences in FASTA formats as well as the ENA accession numbers (project accession N° PRJEB28646).