cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.j315n.2/2.2
title: VinVoile.VQSR.HighQualitybiall.vcf

description: Compressed (tgz) Vcf file containing a subset of high quality biallelic variant filtered out from the genotyping output file  VQSR.vcf  produced by GATK, when filtering for only variants corresponding to the best genotyping scored (Indicated with PASS).  Population analysis measures (Dxy and Da) are performed on a second subset of this file after filtering  genotypes according to allelic depth and genotyping quality with vcftools, with  parameters: --minGQ 30 --minDP 10 --maf 0.001 . This filtered data set is used for figure 2C, and Figure S7.
DOI: 10.5061/dryad.j315n.2/4.2
title: Evaluation of variant impact on protein functions according to SIFT(4G)_ High quality biallelic variant set

description: Compressed file  containing the impact of each variant  on each annotated transcript, inferred with SIFT4G, for the file including all variant (VinVoile.VQSR.HighQualitybiall.vcf).
DOI: 10.5061/dryad.mf02n/1
title: Shrubs locations

description: Spatial coordinates corresponding to 7865 individuals belonging to 48 species of perennial shrubs and grasses.
DOI: 10.5061/dryad.mt048/1
title: Eaton_PineBarrens
DOI: 10.5061/dryad.n82r2/1
title: BLKI Data_forDRYAD

description: This file contains all the data used in the paper: physiological, morphological, and molecular data for Black-legged Kittiwake chicks in 2009 and 2011 from Middleton Island, Alaska.  It includes chicks in supplementally fed nests and non-fed nests, chicks in experimentally enlarged nests (including fosters), and chicks in control nests of 2 natural chicks.
DOI: 10.5061/dryad.nd58h/1
title: Nodularia and phage counts from 4 day experiment
DOI: 10.5061/dryad.nd58h/2
title: Phytoplankton cell counts from filtrate experiment
DOI: 10.5061/dryad.nd58h/3
title: Filament length data for phage susceptible and phage resistant Nodularia isolates
DOI: 10.5061/dryad.qn42t/1
title: S1

description: Figure S1. Mtb infection enhances the dissemination of bacteria in T2DM. Control and  T2DM mice were infected with 50-100 CFU of aerosolized Mtb H37Rv A & B. Bacterial burden in the spleen and liver six months post-infection. C & D. Random blood glucose levels and body weight were measured at monthly intervals for up to 6 months.
DOI: 10.5061/dryad.qn42t/2
title: S2

description: Figure S2. Type 2 diabetes enhances pro- and anti-inflammatory responses during Mtb infection. Control and  T2DM mice were infected with 50-100 CFU of aerosolized Mtb H37Rv. One and six months p.i., lung homogenates were collected from uninfected control and diabetic mice and from Mtb-infected control and diabetic mice and subjected to multiplex ELISA to determine the various cytokines and chemokines. Mean values, p-values and SEs are shown. *P &lt; 0.05, **P &lt; 0.01, ***P &lt; 0.001.
DOI: 10.5061/dryad.qn42t/3
title: S3

description: Figure S3. Type 2 diabetes enhances pro- and anti-inflammatory responses during Mtb infection. Control and T2DM mice were infected with 50-100 CFU of aerosolized Mtb H37Rv. A to M. Six months p.i., lung cytokine mRNA expression was determined by real-time PCR. Mean values, p-values and SEs are shown. *P &lt; 0.05, **P &lt; 0.01, ***P &lt; 0.001.
DOI: 10.5061/dryad.qn42t/4
title: S4

description: Figure S4. CD11c+ dendritic cells are the major source of IL-6 in Mtb-infected type 2 diabetic mice. Control and T2DM mice were infected with 50-100 CFU of aerosolized Mtb H37Rv. A. Six months p.i., pooled CD4+, CD8+, DX5+ and CD11c+ cells from the lung, spleen and lymph nodes were isolated by magnetic selection. IL-6 mRNA expression was determined by real-time PCR. The results of three independent experiments are shown. B & C. Splenic DX5+ and CD11C+ cells were isolated by magnetic selection and cultured (1 NK cell and 4 dendritic cells) with or without g-irradiated Mtb (10 µg/ml). Some of the g-irradiated Mtb H37Rv cultured cells were cultured in the presence of neutralizing antibodies (10 µg/ml) against DNAM-1 or rat IgG2a, κ (the isotype control antibody for the anti-DNAM-1 antibody) or against NKG2D or rat IgG1, κ (the isotype control antibody for the anti-NKG2D antibody). After 18 hours, cell-free culture supernatants were collected and IL-6 levels were measured by ELISA. Mean values, p-values and SEs are shown. *P ≤ 0.05, **P ≤0.01, ***P ≤ 0.001.
DOI: 10.5061/dryad.qn42t/5
title: S5

description: Figure S5 Natural killer and dendritic cell interaction enhanced IL-6 production in Mtb-infected type 2 diabetic mice. Control and T2DM mice were infected with 50-100 CFU of aerosolized Mtb H37Rv. Six months p.i., lungs from Mtb-infected control and T2DM mice were isolated and formalin-fixed. Paraffin-embedded tissue sections were prepared and confocal microscopy analysis was performed to determine NK (pink), IL-6+ (green) and dendritic (red) cell co-localization. Scale bar: 20 µm (yellow bar) and 5 µm (white bar). Representative images of staining pattern of three independent experiments, each with three per group were shown.
DOI: 10.5061/dryad.qn42t/6
title: S6

description: Figure S6. IL-6 is responsible for the increased pro-inflammatory cytokine production in type 2 diabetic patients with pulmonary tuberculosis. Blood from 20 pulmonary tuberculosis patients with T2DM and 20 pulmonary tuberculosis patients without diabetes was obtained. Whole blood was cultured with 10 µg/ml of purified protein derivative (PPD) as indicated in the methods section. A representative flow cytometric contour plot showing the frequency of cells expressing IFN-, TNF-, IL-17 and IL-2 is shown.
DOI: 10.5061/dryad.rp4d6/1
title: ESM Table S1
DOI: 10.5061/dryad.s20g8/1
title: CHC analysis R-script

description: Script used in the program R to estimate heritability values for individual cuticular hydrocarbon compounds, as well as composite PCA axes. It uses a Bayesian animal model approach (based on the MCMCglmm package), parent-offspring regression, as well as paternal half-sib analysis.
DOI: 10.5061/dryad.s20g8/2
title: CHC data

description: For each sampled individual, its age (adult or nymph), gender (female or male), strain (Rennes or Dijon), mother (grandmothers and mothers of the F2 generation), and raw cuticular hydrocarbon peak areas (25 CHCs commonly found on the cuticle of Blattella germanica).
DOI: 10.5061/dryad.s20g8/3
title: Pedigree

description: Pedigree (P, F1, and F2) used in the animal model approach to estimate heritabilities of cuticular hydrocarbons of Blattella germanica.
DOI: 10.5061/dryad.s20g8/4
title: CHC data FS HS

description: For each sampled individual that had both full siblings (FS) and half-siblings (HS), its age (adult or nymph), gender (female or male), strain (Rennes or Dijon), mother (grandmothers and mothers of the F2 generation), and raw cuticular hydrocarbon peak areas (25 CHCs commonly found on the cuticle of Blattella germanica).
DOI: 10.5061/dryad.t8016/1
title: Supplementary Material

description: Supplementary Figures and Tables
DOI: 10.5061/dryad.t8016/2
title: PHRAPL tutorial

description: A tutorial for running PHRAPL
DOI: 10.5061/dryad.t8016/3
title: Sequences for Homo sapiens

description: Sequences used from Homo sapiens
DOI: 10.5061/dryad.t8016/4
title: Scincella lateralis sequences

description: Sequences used from Scincella lateralis
DOI: 10.5061/dryad.tg01f/1
title: JAPPL-2016-00582.R2 data

description: This file contains the data on species richness and tree regeneration used in the analysis for this paper. Further notes on interpreting table embedded in the spreadsheet.
DOI: 10.5061/dryad.v84c2/14
title: BrIP seq genomic reads

description: BrdU incorporated genomic strand reads
DOI: 10.5061/dryad.v84c2/15
title: BrIP seq WT reads

description: BrdU incorporated nascent strand reads in WT cells
DOI: 10.5061/dryad.v84c2/16
title: BrIP seq ORC1B14 reads

description: BrdU incorporated nascent strand reads in ORC1B14 cells
DOI: 10.5061/dryad.v84c2/17
title: BrIP seq ORC2B2 reads

description: BrdU incorporated nascent strand reads in ORC2B2 cells
DOI: 10.5061/dryad.vh610/1
title: Sartor_F_RD_Data_2016
DOI: 10.5061/dryad.017v9/5
title: Summarized False Positive Data
DOI: 10.5061/dryad.052q5.1
title: Data from: Global terrestrial Human Footprint maps for 1993 and 2009
DOI: 10.5061/dryad.0sn63/1
title: EXP1BMR- basal metabolic rate

description: File contains data relevant to the comparison of BMRs between birds eating different diets
DOI: 10.5061/dryad.0sn63/2
title: EXP1PMR

description: Contains data to compare metabolic rates during exercise in a hop/hover wheel
DOI: 10.5061/dryad.0sn63/3
title: EXP1metabs

description: Contains data on plasma metabolites in various fasting, fed, and exercise states
DOI: 10.5061/dryad.0sn63/4
title: EXP2comp

description: Contains body composition of birds eating 3 diets
DOI: 10.5061/dryad.0sn63/5
title: EXP2flight

description: Contains data on energetics and fuel use of birds during flight
DOI: 10.5061/dryad.15g78/1
title: NIL-F2 for QTL mapping
DOI: 10.5061/dryad.1900s/1
title: Data_Quailbrain

description: Brain data from Japanese quail artificially selected for high or low maternal investment.
DOI: 10.5061/dryad.1v074/1
title: Zebrafish_KATP_Emfinger_et_al_RSOS_Data

description: This is the data for the paper: Expression and function of ATP-dependent potassium channels in zebrafish islet β-cells
Christopher H. Emfinger, Alecia Welscher, Zihan Yan, Yixi Wang, Hannah Conway, Jennifer B. Moss, Larry G. Moss, Maria S. Remedi, and Colin G. Nichols
These data are organized into sub-folders which include PCRs for the sorted cells (cf Figure 3), the whole islets (cf Figure 3), the electrophysiological records (cf Figures 2 and 4; raw and data-reduced, with subfolders for the ATP sensitivity, ADP activation, and pharmacology (Diazoxide and Pinacidil activation and glibenclamide and tolbutamide inhibition), as well as the injection studies (cf figure 1). These are uploaded as a single zip file for download. The raw electrophysiological traces are in pClamp-compatible file formats. The PCR gels are in PDFs. The data for injections are in an excel file with processing in a GraphPad prism.
DOI: 10.5061/dryad.1vh64/1
title: Malagasy Camponotus  grandidieri and niveosetosus species groups measurements

description: Basic measurements of individual specimens of the Malagasy Camponotus grandidieri and niveosetosus species groups arranged by species code, collection code, and specimen code (unique identification number). See text for abbreviations
DOI: 10.5061/dryad.25h9d/1
title: Lohman_Code_Stats

description: R code for simulations and plotting. Full statistics from empirical data analysis.
DOI: 10.5061/dryad.2m1k2/1
title: Adventdalen_mesic_2014_community

description: Data was collected at mesic meadow site in Adventdalen valley (78.19ºN, 15.93ºE) of Svalbard in July 2014. A warming treatment by Open Top Chambers (OTCs) was initiated on the site in 2003. Every year between 2003 and 2014, OTCs were placed at the site in late spring and removed each autumn. Within each block, plots were also randomly distributed between three levels of a grazing treatment by captive Barnacle Geese in 2003-2005: no grazing (UG), intermediate (low) grazing (LG), and high grazing, (HG). Grazing treatments were discontinued after 2005. Site setup and treatments are further described in Cooper et al 2004, 2006. For details of community and species-specific measurements taken in 2014, see ReadMe file.
DOI: 10.5061/dryad.55p06/1
title: data_nex

description: This zip package includes data matrices used in this study.
DOI: 10.5061/dryad.55p06/2
title: DataBase_1470candidates

description: The database containing a total of 1470 NPC marker candidates for beetle phylogenety, including nucleotide and protein alignments,and summary information of the marker candidates.
DOI: 10.5061/dryad.55p06/3
title: python_scripts

description: Automation Python scripts used in the analysis, including some genome mining procedures (Filter_long_single_copy_seqs,Auto_filter_alignments) and Auto_exclusion_introns. All scripts call module of Biopython. Please install Biopython before use.
DOI: 10.5061/dryad.55p06/4
title: Supplemental_Tables

description: Supplemental Tables in this study.
DOI: 10.5061/dryad.6jk98/1
title: Fichier Dryad
DOI: 10.5061/dryad.79hb8/1
title: Repeated-measures abundance of protists species

description: This data file contains the abundances of the three protist species we used in the experiment described in the paper (Colpidium, Paramecium, and Dinidium). Rows are sampling units (Petri dishes). Columns are disturbance treatments (no, intermediate, and high), resource (seed, no_seed), and week measured. Column headings should be self explanatory. Missing values appear as blank spaces.
DOI: 10.5061/dryad.79hb8/2
title: Protist species occupancy

description: Repeated-measures abundance and occupancy of protist species manipulated in the experiment per disturbance treatment. Measurements start at week 2.
DOI: 10.5061/dryad.79hb8/3
title: XY coordinates for spatial modelling

description: This file is just an arbitrary x-y coordinate coding to designate each Petri dish. It was used for the spatial modelling.
DOI: 10.5061/dryad.79hb8/4
title: Ecosystem functioning

description: This file contains the two ecosystem properties we measured (NH4 and Chlorophyll) in weeks 4, 5, and 6 of the experiment, along with the respective Paramecium abundance. Figure S2 can be made using these data.
DOI: 10.5061/dryad.79hb8/5
title: Spatial point pattern

description: This is the data we used for calculating the Kcross statistics in the spatial point pattern section of the paper.
DOI: 10.5061/dryad.8qp7s/1
title: Acceptance_Cohorts_a-i

description: Acceptance_Cohorts_a-i.csv
This dataset includes acceptance data (eggs laid per day) on three different host plants (BaDay=Barbarea vulgaris, ArDay=Armoracia rusticana, and BrDay=Brassica napus). Columns include also the Cohort (a-i), the butterfly ID number, the site of the experiment (Stockholm/Uppsala), the generation (direct developing/diapausing), the total number of eggs laid in the acceptance experiment, the discal cell length (right forewing), the eggs left in abdomen and the total number of eggs (laid+unlaid).
DOI: 10.5061/dryad.8qp7s/2
title: Acceptance_Size_cohorts_a,b.csv

description: This dataset links the acceptance data (eggs laid/ day) on the three host plants to the size of the female and the size of her mating partner. Columns include also female ID, female size group, male size group, size combination and size combination
DOI: 10.5061/dryad.8qp7s/3
title: Comp_Acc-Pref_Cohorts_a,b.csv

description: This dataset compares the acceptance data (eggs laid/ day) on three different host plants (BaDay=Barbarea vulgaris, ArDay=Armoracia rusticana, and BrDay=Brassica napus) with preference data (eggs laid/day) on the same three hosts. The columns include also female ID, cohort, and test type (choice test of preference, no-choice test of acceptance).
DOI: 10.5061/dryad.8qp7s/4
title: Sample_Effect__Cohorts_a.csv

description: This dataset underlies the analysis of effect size vs. sample size, and reports the Cohort, the mean number of eggs laid by each cohort on each of the three host plants (Barbarea vulgaris, Armoracia rusticana, and Brassica napus), the mean total number of eggs laid, the sample size (n), and the effect size (mean number of eggs laid on Barbarea vulgaris minus the mean number of eggs laid on Armoracia rusticana, mean number of eggs laid on Barbarea vulgaris minus the mean number of eggs laid on Brassica napus, and mean number of eggs laid on Armoracia rusticana minus the mean number of eggs laid on Brassica napus, respectively).
DOI: 10.5061/dryad.8qp7s/5
title: Cohort_j.csv

description: This dataset reports the number of eggs laid and the number of eggs left in the abdomen in a set of P. napi females that were allowed to oviposit on Brassica napus during their entire post-mating life.
DOI: 10.5061/dryad.b0h4h/1
title: repeatability data eady

description: treat: 1 = same male same female, 2 = diff male diff female. Femaleid = individual female identity, maleid = individual male identity, matenumber = mating sequence (1, 2, 3, 4), starttokick = raw data, starttokicks = time from start of copula to the female kicking phase (seconds), normstok = normalised start to kick time, ktoends = duration of kick to end phase (seconds), totals = total cop duration (seconds), normtotal = normalised total duration, femelytra = female elytra length (mm), maleelytra = male elytra length (mm).
DOI: 10.5061/dryad.ch7kk/1
title: respondent_information

description: Demographic information, detailed best-worst scaling responses, and write-in questions from survey participants.
DOI: 10.5061/dryad.ch7kk/2
title: unscaled_ranks

description: Raw scores from Hierarchical Bayesian analysis of survey respondents’ ranking of 25 ocean research questions.
DOI: 10.5061/dryad.ch7kk/3
title: ocean_priorities_survey

description: Example of the ocean priorities survey format
DOI: 10.5061/dryad.f7tp6/2
title: Mosites_Microbiome_Sharing_Kenya_20170119

description: Questionnaire and microbiome data for Microbiome Sharing Between Children, Livestock and Household Surfaces in Western Kenya., Mosites, Emily, et al.
DOI: 10.5061/dryad.fn921/1
title: Wolowski_etal_JournalofEcology_data

description: Raw data used for analyses of phylogenetic and functional structure of hummingbird-plant communities and phylogenetic generalized least squares regression.
DOI: 10.5061/dryad.h6v7g.2
title: Data from: Macroevolution of specificity in cyanolichens of the genus Peltigera section Polydactylon (Lecanoromycetes, Ascomycota)
DOI: 10.5061/dryad.h6v7g.2/1.2
title: SupplementaryFigureS1NN

description: Supplementary figure S1.
DOI: 10.5061/dryad.h6v7g.2/2.2
title: Supplementary Figure S2
DOI: 10.5061/dryad.h6v7g.2/3.2
title: Supplementary Figure S3
DOI: 10.5061/dryad.h6v7g.2/4.2
title: Supplementary Figure S4
DOI: 10.5061/dryad.h6v7g.2/5.2
title: Supplementary Figure S5
DOI: 10.5061/dryad.h6v7g.2/6.2
title: SupplementaryText_jm+FL

description: Supplementary text
DOI: 10.5061/dryad.hh375/27
title: 14-MI12026-10M

description: Magnetic resonance imaging data of animal 14-MI12026-10M, acquired with a Bruker 7 T magnet, with ParaVision 5.1 software. Each subfolder contains a ParaVisions study. The name of the subfolder refers to the date of data acquisition. An overview of all animals is provided in 'animal_overview.xlsx'.
DOI: 10.5061/dryad.hh375/28
title: 14-MI12026-11M

description: Magnetic resonance imaging data of animal 14-MI12026-11M, acquired with a Bruker 7 T magnet, with ParaVision 5.1 software. Each subfolder contains a ParaVisions study. The name of the subfolder refers to the date of data acquisition. An overview of all animals is provided in 'animal_overview.xlsx'.
DOI: 10.5061/dryad.hh375/29
title: 14-MI12026-12M

description: Magnetic resonance imaging data of animal 14-MI12026-12M, acquired with a Bruker 7 T magnet, with ParaVision 5.1 software. Each subfolder contains a ParaVisions study. The name of the subfolder refers to the date of data acquisition. An overview of all animals is provided in 'animal_overview.xlsx'.
DOI: 10.5061/dryad.hh375/30
title: 15-MI10230-01M

description: Magnetic resonance imaging data of animal 15-MI10230-01M, acquired with a Bruker 7 T magnet, with ParaVision 5.1 software. Each subfolder contains a ParaVisions study. The name of the subfolder refers to the date of data acquisition. An overview of all animals is provided in 'animal_overview.xlsx'.
DOI: 10.5061/dryad.hh375/31
title: 15-MI10230-02M

description: Magnetic resonance imaging data of animal 15-MI10230-02M, acquired with a Bruker 7 T magnet, with ParaVision 5.1 software. Each subfolder contains a ParaVisions study. The name of the subfolder refers to the date of data acquisition. An overview of all animals is provided in 'animal_overview.xlsx'.
DOI: 10.5061/dryad.hh375/32
title: 15-MI10230-03M

description: Magnetic resonance imaging data of animal 15-MI10230-03M, acquired with a Bruker 7 T magnet, with ParaVision 5.1 software. Each subfolder contains a ParaVisions study. The name of the subfolder refers to the date of data acquisition. An overview of all animals is provided in 'animal_overview.xlsx'.
DOI: 10.5061/dryad.hh375/33
title: 15-MI10230-04M

description: Magnetic resonance imaging data of animal 15-MI10230-04M, acquired with a Bruker 7 T magnet, with ParaVision 5.1 software. Each subfolder contains a ParaVisions study. The name of the subfolder refers to the date of data acquisition. An overview of all animals is provided in 'animal_overview.xlsx'.
DOI: 10.5061/dryad.j059v/9
title: Description of the files deposited in Dryad Vera et al

description: Description of the files deposited in Dryad Vera et al for the mansucript "Genomic survey provides insights on the evolutionary changes during invasive European expansion of the mosquitofish (Gambusia holbrooki)"
DOI: 10.5061/dryad.j315n.1
title: Data from: Genomic signatures of adaptation to wine biological aging conditions in biofilm-forming flor yeasts
DOI: 10.5061/dryad.j315n.2/15.2
title: Data XPCLR of Wine and Spain Italy Flor strain

description: XPCLR selection test: Data for XPCLR of Wine and Spain and Italy Flor strain recombination rate 403 M. Window= 0.1 cM, window 1kb
DOI: 10.5061/dryad.j315n.2/16.2
title: Data XPCLR of Wine and France and Hungary Flor strain

description: XPCLR selection test: Data for XPCLR of Wine and French (Jura) and Hungarian Flor strain recombination rate 403 M. Window= 0.1 cM, window 1kb
DOI: 10.5061/dryad.j315n.2/17.2
title: Combined set of SNPS including wine and flor strains and strains from other origins(Allyeast-set)

description: Data for Phylogeny and population structure (Figure 1, Figure2A and B). Compressed Vcf file containing a set of biallelic variant with less than 20 % missing position among all strains, obtained from the genotyping  of 20 flor and wine strains  compared to 82 strains with available genome sequences (obtained from Saccharomyces genome database (http://www.yeastgenome.org/), of from the SGRP project (http://www.sanger.ac.uk/research/projects/genomeinformatics/sgrp.html) (Liti et al. 2009, Population genomics of domestic and wild yeasts. Nature, 458, 337–41)
DOI: 10.5061/dryad.j315n.2/19.2
title: Data for differentiation based method PCA, Dxy, Da

description: - plink format files  AssembliesGenowine.raw and .map for PCA performed with adegenet   - Vcf phased data files for each chromosome of flor and wine population - R script utilising on PopGenome performing all analysis of Theta, pi, Dxy (Da = Dxy – (Piwine+piflor)/2 ) on each chromosome datafile).
DOI: 10.5061/dryad.j315n.2/20.2
title: DT FineStructure Flor Wine Champagne

description: These are the data files used for the FineStructure analysis for the hybrid nature of strains of the Champagne group (Figure S1)
DOI: 10.5061/dryad.j315n.2/21.2
title: Data for Linkage desequilibrium analysis (figureS3)

description: ped and map files  for Flor  and wine populations. Files are prepared from phased vcf file . Data used with plink  with options --ld-window 1000
  --ld-window-kb 50
  --ld-window-r2 0
  --r2
DOI: 10.5061/dryad.j315n.2/22.2
title: Data for Estimation of recombination rates  (Figure S4)

description: This data has been used for the genome scan of recombination rate (Figure S4) using a model with hotspot as inplemented in the "INTERVAL" module of LDHAT package. A global estimate of recombination rate has also been estimated for flor strain using PAIRWISE  with the module "PAIRWISE"  of the same package.
DOI: 10.5061/dryad.j315n.2/23.2
title: Data of figure4: Biofilm images used for the evaluation of the impact of each wine and flor allele on biofilm formation

description: The compressed archive contains the photos and the notice indicating for image its organization.
DOI: 10.5061/dryad.j315n.2/24.2
title: de-novo draft assemblies

description: This is a gzip/tar compressed data archive containing the draft contig de-novo assemblies generated in this study.  This data is used for  phylogenic trees and genes sequence alignments (Figures S2, S6, S8).
DOI: 10.5061/dryad.k7c40/1
title: MakeNemoInputs_NormalDisp

description: R script to generate Nemo input files for simulations with Gaussian dispersal kernels.