dataesr/scientific-paragraphs-categorization huggingface dataset:
Growth rate () and length of the lag phase (hours) were determined from the mean growth curves generated using the GroFit package in R software  (51). Antibiotic susceptibility assay. Phenotypic changes in HEPB-adapted B. vietnamiensis strain G4 derivatives were characterized by antibiotic susceptibility profiling using Etest strips (bioMérieux, UK) according to manufacturers' guidelines. Eight antibiotics with various modes of action were examined: amikacin (AMK), azithromycin (AZM), ceftazidime (CAZ), chloramphenicol (CHL), ciprofloxacin (CIP), imipenem (IPM), piperacillin (PIP), and trimethoprim-sulfamethoxazole (SXT).
GCA_000016205. 1). Bioinformatic analysis was carried out using a virtual machine, hosted by the Cloud Infrastructure for Microbial Bioinformatics (CLIMB)  (53). Coding sequence features were extracted (https://github. com/ aleimba/bac-genomics-scripts/tree/master/cds_extractor), and a Basic Local Alignment Search Tool (BLAST) algorithm was used to compare nucleotide queries. Additional analysis was performed using the Burkholderia Genome Database  (54). Twenty mutants from across the mutant bank were selected for validation of single random chromosomal integration of the transposon and sufficient coverage of the multireplicon G4 chromosome. Mutants were confirmed as B. vietnamiensis strain G4 by RAPD analysis  (50). HEPB susceptibility screening of G4 mutants. B. vietnamiensis mutants with altered HEPB susceptibility were identified by agar or broth dilution MIC assays and growth curve analysis as described above.
Bioinformatic analysis was carried out as described by Green et al. (55)  with the following modifications. Quality control and adaptor trimming of the paired-end sequencing data were conducted using Trim Galore software v0. 4. 4  (56). As an additional enrichment step for mRNA sequence data, Artemis software (v16. 0) (57) was used to obtain the 16S-to-23S rRNA gene region sequence data from the complete B. vietnamiensis strain G4 genome sequence (obtained from NCBI). The RNA-seq reads were first aligned to the 16S-23S rRNA gene region via a Burrows-Wheeler Aligner transformation (BWA) with the BWA-MEM algorithm (v0. 7. 13-r1126)  (58). The aligned sequence reads were removed from the data set using the SAM Tools toolkit (v1. 3) (59). The rRNA-clean sequence reads were then aligned to the complete B.
vietnamiensis strain G4 genome sequence via a BWA using the BWA-MEM algorithm. Sequence Alignment/Map (SAM) files of the aligned sequence reads were then sorted into BAM files using the SAM Tools toolkit. The aligned reads that mapped to annotated gene features of the B. vietnamiensis strain G4 genome were counted using the Python program HTSeq-count (v0. 6. 0) (60). Differential gene expression was determined using the R Bioconductor program DESeq2 (v1. 14. 1)  (61)  and was defined as exhibiting a log 2 fold change of Ͼ1. 5 as previously described  (2, 33, 55). Identifying genomic alterations in HEPB-adapted B. vietnamiensis G4. Genomic DNA of the wild-type and HEPB-adapted derivatives (T2s, T2L, and T3) was extracted using the Maxwell 16 tissue DNA purification kit according to manufacturer's guidelines.
DNA library preparations and sequencing on an Illumina NextSeq 500 system were carried out in cooperation with the Genomics Research Hub at Cardiff School of Biosciences. The resulting reads were trimmed using Trim Galore software v0. 0. 4 and assembled using Unicycler (v0. 4. 7)  (62). Annotation of the assembled draft genomes was conducted using Prokka (v1. 12)  (63). DNA polymorphisms between the sequence reads of the wild-type genome and the HEPB-adapted derivatives genomes were identified using Snippy (v4. 1. 0) (64) , with default parameters of a minimum base quality of 20, minimum read coverage of 10ϫ, and 90% read concordance at each locus. Statistical analysis. All experiments were performed as 3 biological replicates except for RNA sequencing, which was performed in quadruplicate for each condition.
ACKNOWLEDGMENTS We acknowledge the services of the  Genome Technology Hub at Cardiff School of Biosciences  for RNA sequence analysis and whole-genome sequencing and the  Bioimaging Hub at Cardiff University  for confocal microscopy. Bioinformatic analysis used the CLIMB consortium funded by the  MRC  (grant number  MR/L015080/1 ). We acknowledge assistance by members of the  Microbiomes, Microbes and Informatics Group at Cardiff University  who provided guidance in bioinformatic analysis:  Rebecca Weiser ,  Matthew Bull ,  Alex Mullins , and  Edward Cunningham-Oakes. Jason Gillespie  at  Cardiff University  offered assistance on chemistry. We also acknowledge technical and financial support from  Olivier Da Cruz ,  Patricio Guerreiro , and  Maria Dalko. Conceptualization: E. M. , J. -Y. M.
Data availability. RNA sequence reads are available in the ArrayExpress database (http://www. ebi. ac. uk/arrayexpress) under accession number E-MTAB-7906. The whole-genome sequence reads of B. vietnamiensis strain G4 (wild-type) and HEPB-adapted derivatives T2L, T2s, and T3 are available at the European Nucleotide Archive (accession numbers ERS4125347, ERS4125348, ERS4125349, and ERS4125350, respectively). Gene numbers and nomenclature correlate with those shown on www. burkholderia. com for the B. vietnamiensis G4 genome.
ID G4 DNA flanking transposon insertion site (20 bp) Gene ID Replicon Mutated gene and putative function a COG category b 9:G3 ACCCATCACCATGCCCACA 4698 chr2 ilvD; dihydroxy-acid dehydratase Amino acid transport and metabolism 44:B9 CGTTCCGGCGCGGCGCTGCC 6500 chr3 Cellulose synthase domain-containing protein Carbohydrate transport and metabolism 42:E3 AAGTAAGACAGGTCACGAAC 1471 chr1 RND efflux system outer membrane lipoprotein Cell wall/membrane/envelope biogenesis 14:C2 AGCAGTTCATCGCGCTGGC 0037 chr1 Type III restriction enzyme, res subunit Defense mechanisms 9:D8 ATCGCTGACCACCCGCGCT 0174 chr1 Hypothetical protein (putative restriction endonuclease) Defense mechanisms 5:D5 CGGCTAGGCGGCCAGATCT 3088 chr1 puuB; gamma-glutamylputrescine oxidoreductase Energy production and conversion 43:B11 AGGAGAAAGGCCCCGTCATC 3033 chr1 2-Oxoacid ferredoxin oxidoreductase Energy production and conversion 6:F3 AGGCGGCCAGATCTGATCA 7566 pBVIE04 Hypothetical protein Function unknown 9:D7 CCCCCCCGTACTAGTCGAC 3807 chr2 Amine oxidase Function unknown 19:E4 CGCTGGCGGCCAGATCTGA 1415 chr1 Hypothetical protein Function unknown 44:E6 GTCAACGCGTGGCCAAATCG 6803 pBVI01 Hypothetical protein Function unknown 29:B7 c CGGCTAGGCGGCCAGATCT 2890 chr1 kefC; glutathione-regulated potassium-efflux system Inorganic ion transport and metabolism protein 27:G3 CCCCCGCCGTACTAGTCGA 5515 chr3 msrA; peptide methionine sulfoxide reductase Posttranslational modification, protein turnover, chaperones 19:D4 CTGCTCCGGCACGACGTCCA 0426 chr1 DNA primase TraC Replication, recombination and repair 42:B11 ATAATAGTCAAGGCGTGGCC 6093 chr3 Transposase Tn3 family protein Replication, recombination and repair 7:G7 TGAGTTTAATGTCTTCGCT 6805 pBVIE01 Putative signal transduction protein Signal transduction mechanisms 19:H7 CCGACGCGCGCCGGCAGCG 2370 chr1 kdpD; sensor protein Signal transduction mechanisms 35:G5 CGTGACCAGGTGCTCGCGA 3929 chr2 Integral membrane sensor hybrid histidine kinase Signal transduction mechanisms 8:D10 GGCAGGCCAGATCTGATCA 7553 pBVIE04 Helicase domain-containing protein Transcription 6:F4 CGTGACGACCGAGTCGAAG 3650 chr2 Chromosome replication initiation inhibitor protein Transcription 43:G1 CGCTCACTGCCGGCCGGCAA 4632 chr2 LysR-family transcriptional regulator Transcription 20:G12 c TACGACCAGTCTGCGAATCG 3794 chr2 noc; nucleoid occlusion (parB-like) protein Transcription 22:E11 c TCAGCTAGGCGGCCAGATCT 0918 chr1 spoT; bifunctional (p)ppGpp synthase/hydrolase Transcription, signal transduction mechanisms (65)tative function of poorly characterized proteins based on predicted protein-protein interactions networks in the STRING database(17).
Peptides were resuspended in 17 μl of 5% acetonitrile, 0. 05% TFA. 5 μl of each sample were loaded onto a C-18 precolumn (300 μm inner diameter x 5 mm, Dionex) at 20 μl/min in 5% acetonitrile, 0. 05% TFA. After 5 min of desalting, the precolumn was switched online with the analytical C-18 column (75 μm inner diameter × 50 cm; in-house packed with Reprosil C18) equilibrated in 95% solvent A (5% acetonitrile, 0. 2% formic acid) and 5% solvent B (80% acetonitrile, 0. 2% formic acid). The peptides were eluted using a 5% to 50% gradient of solvent B at 300 nl/min flow rate for 160 min. The mass spectrometer was operated in data-dependent acquisition mode with the XCalibur software. Survey MS scans were acquired in the Orbitrap on the 400-1500 m/z range with a resolution of 120,000 (m/z 400). The most intense ions per survey scan were selected for higher-energy collisional dissociation fragmentation (time between Master scans: 3 s), the resulting fragments were analysed at a resolution of 30,000 in the Orbitrap.
Data analysis For protein identification, raw data was converted to mzXML using Proteowizard. Peptide and protein identification as well as the after statistical validation were performed in Trans Proteomics Pipeline version 5. 1. 0 using included software pipeline: X! Tandem Jackhammer TPP (2013. 06. 15. 1-LabKey, Insilicos, ISB) search engine, PeptideProphet and ProteinProphet. The parameters were set as follows: parent mass error of 10 ppm, fragment mass error of 0. 04 Da, carbamidomethyl (Cys) and oxidation (Met) as fixed and variable modifications respectively. All results were filtered for FDR threshold of 1% as well as a minimum of two peptides per protein. Data extraction and table generation was done using R version 3. 4. 4. In order to select for specific MGL-binding proteins, we further filtered for proteins that were identified with peptide at least in one of the technical replicate LC-MS/MS runs from one MGL pull-down and at least in two out of the three biological replicate MGL pull-downs.
Moreover, the selection required that the protein was never found in the corresponding pull-downs with the mutant-MGL (negative controls). From the final list of MGL-binding proteins, we subsequently selected the cell surface proteins based on Gene Ontology (GO) subcellular location, selecting for "cell surface", "plasma membrane", "integral component" and/or "external side". For the identification of glycopeptides, MS/MS spectra containing the specific HexNAc oxonium ions at m/z 204. 087 (HexNAc, [C8H14NO5] + ) and 186. 076 (HexNAc-H2O, [C8H12NO4] + ) were selected from the raw data and written to a. mgf file (in house software). The selected spectra were searched for N-and O-glycopeptides using Byonic version 2. 13. 2 (proteinmetrics. com), with default settings. Carbamidomethyl (Cys) was set as fixed modification, whereas oxidation (Met) as variable one.
"N-glycan 309 mammalian no sodium" or "O-glycans 78 mammalian" databases were used for glycosylation annotation. A Byonic score higher than 200 was considered stringent for further glycopeptides selection. All glycopeptide MS/MS spectra carrying potential MGL-binding glycan epitopes were manually validated using Xcalibur (Thermo) for the spectrum visualization and Protein Prospector (prospector. ucsf. edu) for the calculation of theoretical peptide fragment masses.
LacdiNAc and Tn antigens are carried by cell surface MGL ligands in CRC cell lines To obtain information on the glycan structures that were present on the cell surface proteins captured by MGL (Table  S2 ), and whether these could explain the binding to MGL, we performed additional MGL-Fc pull-down experiments with HCT116 and HT29 cells. To identify intact tryptic glycopeptides, we used a glycoproteomics data acquisition and analysis workflow that we recently optimized for this purpose  [22]. Briefly, additional MS/MS experiments were performed once the characteristic HexNAc oxonium ion at m/z 204. 087 was found in an MS/MS spectrum. For these acquisitions, different HCD collision energies were used. Moreover, an ion trap CID spectrum was recorded. All this helped for the confident identification of glycopeptides.
Acknowledgements We thank  Gabi W. van Pelt  for providing the human CRC cells and the availability to use the cell culture facility from the  Department of Surgery, LUMC. We acknowledge the  Flow Cytometry Facility (FCF) of the LUMC  for providing courses, equipment and support for flow cytometry experiments. This project was supported by the  European Commissions Horizon   2020 programme "GlyCoCan" project , grant number  676421 , and by the  research programme Investment Grant NWO Medium  with project number  91116004 , which is (partially) financed by  ZonMw. This work was also supported in part by the  Région Occitanie  and the  French Ministry of Research  with the program " Investissement d'Avenir, Infrastructures Nationales en Biologie et Santé" (Proteomics French Infrastructure ,  ProFI , project  ANR 10-INBS-08 ).
In this study, the likely contribution of VviUCC1 to the phenotypic variation obtained for cluster compactness and a series of rachis architecture traits in a grapevine collection of diverse wine, table, and multi-purpose grape cultivars has been explored. Based on next-generation sequencing data, the VviUCC1 gene and promoter nucleotide diversity have been characterized, evaluating the degree of linkage disequilibrium (LD) between the polymorphisms detected. In addition, a reduced number of haplotype blocks with little evidence of historic genetic recombination events have been inferred. Finally, a series of association mapping analyses were also performed between the VviUCC1 gene polymorphisms and the variation observed for cluster compactness and seven rachis architecture traits, considering the phenotypic data of three consecutive seasons and the best linear unbiased prediction (BLUP) values obtained after data modeling.
Plant Material and Phenotyping A grapevine collection of 114 varieties (including wine, table, and multi-purpose grape cultivars) held at the Grapevine Germplasm Collection of the Instituto de Ciencias de la Vid y del Vino (ICVV, FAO institute code: ESP217) were analyzed (see Table  S1  for further details). This dataset includes 111 Vitis vinifera L. genotypes and three Vitis spp. interspecific crossings grown as hybrid direct producers. Genotypes are maintained as previously detailed  [22, 44]  in two separate plots, "Finca Valdegón" and "Finca La Grajera", separated by ca. 30 km. These varieties were phenotyped in three consecutive seasons (2011 and 2012 in "Finca Valdegón" and 2013 in "Finca La Grajera") for a series of traits  [8]  including cluster compactness (COMP, following the visual O.
22. 0 (IBM, Chicago, USA). For these five traits, the BLUP values were estimated through the lmer function of the lme4 package  [46]  for R v. 3. 6. 2 to fit a linear mixed-effects model to the experimental data. To this aim, genotypes were used as random variables, and the season (2011, 2012, and 2013) and plot ("Finca Valdegón" and "Finca La Grajera") values as the covariates. Phenotypic distributions were explored for seasonal data using the ggplot2 R package, and correlation analyses were performed by means of the cor function of the corrplot R package using Pearson correlation coefficients (p < 0. 05).
Genotypic Data and Sequence Analyses Young and fresh leaves were sampled for each grapevine genotype and frozen at -80 • C. DNA was extracted as previously detailed  [22, 44]. DNA quality and concentration were assessed by visual comparison with lambda DNA on ethidium bromide-stained agarose gels (0. 8%), and by means of a NanoDrop spectrophotometer (Thermo Scientific, Wilmington, USA). Grapevines were genotyped using 25 nuclear SSR loci (VMC1B11, VMC4F31, VVIB01, VVIH54, VVIN16, VVIN73, VVIP31, VVIP60, VVIQ52, VVIV37, VVIV67, VVMD21, VVMD24, VVMD25, VVMD32, VVMD7, ssrVrZAG67, VVMD27, VVMD5, ssrVrZAG29, ssrVrZAG62, ssrVrZAG112, VVS2, ssrVrZAG83, and VVMD28)  [47] [48] [49] , which were used for structure and kinship matrices estimation, as detailed below. In addition, these markers were used for cultivar identification by means of pairwise comparisons with the grapevine genotypes stored in the ICVV database.
The VviUCC1 gene (Vitvi12g00555 in the VCost. v3 gene annotation version [50], corresponding to VIT_12s0059g02640 in the previous V1 version) was sequenced including 1000 bp in the promoter region according to grapevine 12X V1 gene predictions. Thus, a region of 1971 bp (chr12: 7355541:7357512) was targeted for next-generation sequencing (NGS), performed as previously detailed  [44]. Briefly, paired-end libraries with an insert size of ca. 350 bp were sequenced by the Beijing Genomics Institute (BGI, Shenzhen, People's Republic of China) in an Illumina HiSeq 2000 platform. Resulting reads (90 nucleotides in average) were aligned to the 12X V1 Vitis vinifera PN40024 reference genome with Bowtie 2  [51]. Sequence variations (SNPs and insertion/deletions (INDELs)) were detected as previously detailed  [22, 44] , and then filtered to generate a consensus genotype per variety by means of an ad hoc Perl script  [44].
Polymorphisms were verified using the Integrative Genomics Viewer (IGV) software [52], and named according to Tello et al. [44]. The likely effect of SNPs and INDELs was predicted with SnpEff v. 4. 0  [53] , and the effect of single amino acid substitution on protein function was predicted by means of SNAP  [54]  and PROVEAN  [55]. The effect of these substitutions on the protein secondary and tertiary structure was explored using the intensive modeling mode of the Phyre2 web portal  [56]. The likely effect of the polymorphisms located in the promoter region was evaluated through the in silico detection of putative cis-acting regulatory elements, as implemented in PlantCARE  [57]. VviUCC1 haplotypes were inferred using the Partition-Ligation-Expectation-Maximization (PLEM) algorithm implemented in PHASE v.
2. 1 using default settings  [58]. These were tested for recombination using the three alternative algorithms (MaxChi, Chimaera, and 3Seq) available in RDP4 v. 4. 46  [59]. The software DnaSP v. 5. 10 [60]  was used to estimate the diversity parameters (π and Watterson's θ) and to run two tests of selective neutrality (Tajima's D and Fu and Li's D* tests), considering all the haplotypes detected by PHASE. Linkage disequilibrium (LD) was calculated considering those polymorphisms with a frequency of the minor allele (MAF) higher than 5%. Thus, standardized disequilibrium coefficients (D') and squared correlations of allele frequencies (r 2 ) were calculated for each pair of polymorphisms by means of Haploview v. 4. 2  [61]. LD blocks (haploblocks) were estimated using the solid spine of the LD algorithm implemented in Haploview with a critical D' value of 0.
VviUCC1 Sequence Analysis A region of 1971 bp, corresponding to the VviUCC1 gene sequence and 1000 bp of the promoter region, was sequenced in a collection of 114 wine, table, and multi-purpose grape varieties. A 100% of coverage of the targeted sequence was achieved in all varieties after alignment with the PN40024 reference genome, with an average coverage depth of 94. 1 ± 14. 3 reads/nucleotide. BAM files are available at the National Center for Biotechnology Information's Sequence Read Archive (Accession PRJNA625274). Previous RNAseq analyses  [31]  confirmed the VviUCC1 gene structure annotated for the reference PN40024 genome (VCost. v3), consisting of a 5 -UTR (17 bp), two exons (145 and 539 bp) separated by an intron (146 bp), and a 3 -UTR (125 bp) (Figure  1  and Table  S2 ). Thus, the VviUCC1 gene consists of a coding region of 684 nucleotides that codes for a 228 amino acid protein.
SNPs Y-984 and Y-231/K-88 were additionally associated with RM1LE in 2011 and 2013, and SNPs Y-984, Y-231/K-88, Y158 and K217 were also associated with RM2LE, RM3LE, and RM4LE in 2013. No significant associations were found for RALE, PDULE, or PDILE. The whole list of significant associations is shown in Table  S5 , and those markers associated with seasonal data and BLUP values are shown in Table  4. Considering the association tests performed with BLUP values, 16 significant associations involving ten SNPs were obtained. Y-984 and Y-231/K-88 were found to be associated with three traits (COMP, RM1LE, and RM2LE), Y158 and K217 with COMP, W-497 and R10 (in perfect LD, D' = 1; r 2 = 1), W-207, Y271, and S407 (in perfect LD, D' = 1; r 2 = 1) with PDULE. SNPs associated with COMP, RM1LE, and RM2LE explained between 12.
Acknowledgments: The authors acknowledge  H. Zinelabidine  for genetic structure data,  R. Aguirrezábal ,  S. Hernáiz ,  B. Larreina ,  M. I. Montemayor , and  E. Vaquero  for technical assistance, and  J. L. Pérez-Sotés  and the  SIVV (Gobierno de La Rioja ) for plant material maintenance.
Similar amounts of bacteria were found on mouse skin after treatment, showing that this effect was not due to a difference in levels of colonization by the mutant strains of bacteria (Figure  S5 ). The abundance of gDNA for these cysteine proteases was increased in NS subjects with elevated S. aureus abundance in the metagenomic dataset (Figure  4C ). In parallel with these findings, both scpA and scpB showed significantly increased abundance of mRNA on lesional NS skin compared with non-lesional and healthy controls and correlated with the absolute abundance of S. aureus found on NS subjects (Figures  4D  and 4E ). These findings show that S. aureus cysteine proteases staphopain A and B can also contribute to skin barrier damage on subjects with NS.
epidermidis, were predominant on NS subjects. Genomic and functional analysis identified specific gene products from these bacteria that altered the proteolytic activity of the epidermis and therefore were relevant to subjects with loss of SPINK5. This human disease demonstrates how products of the human and microbial genomes can interact and illustrates the functional consequences of loss of homeostasis driven by a defect in this system. The epidermal ecosystem is multidimensional, and our findings show how several bacterial genes from different species can contribute to a disease phenotype. Overall we provide an important model of how communication with commensal microbes influences human health. This study presents one of the most deeply sequenced skin microbiome datasets to date, which has allowed metagenomic co-assembly.
Before indexing, the quality and fragment-size of the libraries were checked using High Sensitivity D1000 ScreenTape according to manufacturer's instructions (Agilent Technologies). Finally, HiSeq 2500 150bp paired-end sequencing (Illumina) was performed. 17 samples in total (12 NS lesional (n = 6) and non-lesional (n = 6) and 5 healthy controls) were selected for metagenomic sequencing based upon < 98% human DNA contamination. Cumulatively, the total number of reads across all samples was 2. 6x10 8 reads (with an average of 1. 5x10 7 reads per sample. Quality control, host removal and metagenomic co-assembly-Raw metagenomic reads were trimmed for quality by removing low quality reads, followed by removal of reads that mapped to the human genome (assembly19) using KneadData (version 0. 5. 4) with default parameters.
Taxonomic composition using species and strain level profiling-Species level taxonomic profiling was performed on the post-processed reads in order to examine the community composition using MIDAS (version 1. 3. 0) by leveraging approximately 30,000 bacterial reference genomes, clustered into 5,952 species groups. Relative taxonomic abundances were estimated for each of the bacterial species groups, or strains, across 30 universal single copy marker genes included in the marker_genes reference database by mapping reads to gene-specific, species-level mapping thresholds (94. 5%-98% nucleotide identity). Hierarchical clustering was performed for the top 40 most prevalent species were visualized for the entire cohort using "dplyr" to filter the data frame and "heatmap3" with the "average" linkage method for generating the heatmap in R (version 3.