cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4gt8g/2
title: codes

description: Details about what each code does for paper "Markovian language model of the DNA and its information content", Author: Srivastava, S. and Baptista, M.Upload the genomic sequence to be used by using fastaread command from matlab.genomenomode.m - Use this file for creating Fig. 1. and Fig. 2(a) and 2(c). The code calculates Correlation.MIR.m - Use this file for Fig. 2(b). calculates MIR. Needs additional file powerthres.m.thresholdgreater.m -  Use this file for creating Fig. 3 and Fig. 4. The code applies threshold and the network can be created for selected thresholds.one_dim_gene.m - This code is needed for calculating the specificity and sensitivity in separated genes. It converts all the values into one dimension. 		This codes reads data generated by file gene_separated_genomenomod.mROC_gene.m -  Use this file for creating Fig. 5. and calculating the sensitivity and specificity values for genes at different thresholds.
DOI: 10.5061/dryad.57t89/2
title: Genotype data for multi-locus heterozygosity estimates

description: This file contains the microsatellite genotype data required for the analyses of standardized multi-locus heterozygosity (sMLH) estimates between blind and non-blind individuals. sMLH was estimated using the program Genhet (Coulon 2010).
DOI: 10.5061/dryad.794d4/1
title: Walsh et al. 2016 ProcB data
DOI: 10.5061/dryad.89j5k/1
title: Table_S4

description: Call variables average values per species.
DOI: 10.5061/dryad.9nt37/1
title: dryad_10.1111oik.02884

description: Excel file with 6 sheets. The sheet entitled "read_me" contains descriptions of all sheets (databases) and their parameters
DOI: 10.5061/dryad.9pn24/1
title: villain_dataset_RSOS_villain_beggingcalls_ZF_dryad
DOI: 10.5061/dryad.b54gp/18
title: FTD4Files

description: Matlab Struct array of data for subject FTD4. Contains raweyedata which is of the form [time pupilrecognition xposition(pix) yposition(pix)] , xdat which is the value associated with the image and trial which gives the trial letter for the given data.
DOI: 10.5061/dryad.b54gp/19
title: FTD5Files

description: Matlab Struct array of data for subject FTD5. Contains raweyedata which is of the form [time pupilrecognition xposition(pix) yposition(pix)] , xdat which is the value associated with the image and trial which gives the trial letter for the given data.
DOI: 10.5061/dryad.b54gp/20
title: PSP1Files

description: Matlab Struct array of data for subject PSP1. Contains raweyedata which is of the form [time pupilrecognition xposition(pix) yposition(pix)] , xdat which is the value associated with the image and trial which gives the trial letter for the given data.
DOI: 10.5061/dryad.b54gp/21
title: AD1Files

description: Matlab Struct array of data for subject AD1. Contains raweyedata which is of the form [time pupilrecognition xposition(pix) yposition(pix)] , xdat which is the value associated with the image and trial which gives the trial letter for the given data.
DOI: 10.5061/dryad.bm8nv/1
title: Optical quality and intraocular scattering measurement in children
DOI: 10.5061/dryad.c867b.2
title: Data from: Temporal variation in antibiotic environments slows down resistance evolution in pathogenic Pseudomonas aeruginosa
DOI: 10.5061/dryad.c867b.2/1.2
title: Data for dose response curves

description: This file contains the data for the dose-response curves as shown in supplementary Fig. S2 of the paper. The columns indicate the following:$date: the data was collected on two days; $treatment: specifies antibiotic treatment; $ID: a number from "0" to "10" that serves as ID for the ascending antibiotic concentrations; $conc_ng_ml: concentration of antibiotic in ng/ml; $replicate: name of technical replicate; $od_600: optical density at 600 nm read after 12h of incubation at 37°C.
DOI: 10.5061/dryad.c867b.2/2.2
title: Data for both evolution experiments

description: This file contains the data from the two evolution experiments, as summarized in Figs. 1,2,3,5,S3,S5, and S6 of the paper. The columns show the following:$well: position of population in 96-well plate;$season: number of transfers within the evolution experiment;  $time: time point of od measurement in hours; od was measured in 15 min intervals; $od_600: optical density at 600 nm;  $ID: a number from "1" to "10" that serves as ID for treatment groups as specified in the paper plus "11" for the evolving nodrug references; $treatment: treatment type, including monotherapy (mono), regular changes of antibiotics (regular), and random changes of antibiotics (random); $drug: antibiotic used; $exp: number of evolution experiment.
DOI: 10.5061/dryad.c867b.2/3.2
title: Data for cross-resistance test

description: This file contains the data for the cross-resistance test (Fig. 4).$evoexp: number of evolution experiment or the ancestral population$evoexp_season: season of the evolution experiment after which populations were streaked on agar plates for characterization$evoexp_drug: antibiotic present in $evoexp_season and on the agar plates$evoexp_well: position of population in 96-well plate during evolution experiment$clone_id: name of the five cfus that were isolated from each $evoexp_well$test_drug: antibiotic present in the cross-resistance test$ic: the inhibitory concentration aimed for with the applied concentration; if the value is "E" these are wells with antibiotic but without the bacteria$concentration_ng_ml: concentration of the antibiotic in the cross-resistance test in ng/ml$od_600: optical density at 600 nm after 12h of incubation at 37°C
DOI: 10.5061/dryad.cj432/1
title: Phenotypes for QTL mapping

description: Growth rate (mm day-1), temperature sensitivity and yeast/hyphae dimorphism phenotypes for the quality filtered retained progeny used in the QTL analysis for each of the two crosses.
DOI: 10.5061/dryad.d4p98/1
title: Amphibians Inv threatened

description: Excel list of amphibian species threatened by IAS
DOI: 10.5061/dryad.d4p98/2
title: Birds Inv Threatened

description: Excel list of bird species threatened by IAS
DOI: 10.5061/dryad.d4p98/3
title: Mammals Inv threatened

description: Excel list of mammal species threatened by IAS
DOI: 10.5061/dryad.d4p98/4
title: Reptiles Inv threatened

description: Excel list of reptile species threatened by IAS
DOI: 10.5061/dryad.d4p98/5
title: Amphibians_invasive_sumCRENVU

description: raster of amphibian species threatened by IAS
DOI: 10.5061/dryad.d4p98/6
title: birds_invasive_sumCRENVU

description: raster of bird species threatened by IAS
DOI: 10.5061/dryad.d4p98/7
title: Mammals Inv threatened

description: raster of mammal species threatened by IAS
DOI: 10.5061/dryad.d4p98/8
title: reptiles_invasive_sumCRENVU

description: raster of reptiles threatened by IAS
DOI: 10.5061/dryad.db017/1
title: Ant species occurrence records from East Asia

description: Ant species checklists representing local species pools across 159 islands and areas in East Asia were compiled, including Japan, South Korea, North Korea, China and Russia (Far East). The records represent nominal valid species and are based on 1093 publications from 1874-2014. This .txt file consists of two columns, listing species and area names. The preceding letters before the area names separated by an underscore abbreviate countries or island archipelagoes where the areas belong to (C China, DT Daito Islands, IZ Izu Islands, J Japan, JM Japanese main islands, NK North Korea, OG Ogasawara Islands, R Russia, RC Ryukyu Islands - central, RFE Russia Far East, RN Ryukyu Islands - north, RS Ryukyu Islands south, SK South Korea, SKM South Korea mainland, SN Senkaku Islands).
DOI: 10.5061/dryad.dc30t/1
title: MorosinottoEtal_JAB2016_Dataset

description: The data set is composed of one excel file with several data sheets. There is one sheet per experiment/study; 3 predator studies: Pygmy owl, Tengmalm's owl, weasel and "Suppl feeding" for food supplementation study. In addition there is one separate sheet with the data on progesterone concentration in the pygmy owl study in 2009, we have no data on the concentration for this hormone in previous years so it was analyzed separately. Finally, there are three sheets for the data on female condition: Female_pygmySites, Female_Tengmalm'sSites and Female_FeedingSites. The variables listed are: location (Forest patch and Nest Box in the predators files and Nest ID in the supplementary feeding experiment), year, predator (PO pygmy owl, TO Tengmalm's owl, W weasel), Treatment (there is a comment on the file itself explaining what we mean case by case, generally 0 correspond to control/unfed/low risk site and 1 correspond to treatment/fed/high risk site), Laying date, Clutch size, Yolk mass, Egg mass, Tngg (testosterone concentration), Anngg (A4 concentration), P4ngg (progesterone concentration). In addition, in the supplementary feeding file there are also the column "ExactEggOrder" (actual order in which each egg was laid) and "Laying order" (this is the variable used in the analyses, there is a comment on the file itself explaining what we mean case by case). In the female condition files mass, wing and female hematocrit are also presented.
DOI: 10.5061/dryad.f6g68/1
title: Frequency of the ruby-throated phenotype

description: Frequency of the ruby-throated phenotype assayed in different combinations of host and parasite lines. "Pairing" indicates the specific pairing of host and parasite lines being made. "Host" and "Parasite" columns provide additional details. In these columns, Ancestor and Ancestor-sm2170 refer to the ancestral populations of host and parasite, respectively, used to initiate experimental evolution. Similarly, control, singly, and co-passaged refer to the products of 20 generations of experimental selection under the Control, Singly-passaged, and Co-passaged treatments, respectively. "Line" indicates the replicate lineage being tested, and "Replicate" indicates the replicate assay plate within each replicate lineage. "Frequency" indicates the proportion of adult hermaphrodites displaying the ruby-throated phenotype in the assay population.
DOI: 10.5061/dryad.f6g68/2
title: Fecundity of ruby-throated hermaphrodites

description: Fecundity of ruby-throated hermaphrodites, resulting from different combinations of host and parasite lines. "Pairing" indicates the specific pairing of host and parasite lines being made. "Host" and "Parasite" columns provide additional details. "Line" indicates the replicate lineage being tested, and "Replicate" indicates the replicate assay plate within each replicate lineage. For each replicate assay plate, 10 hermaphrodites were observed - column "Hermaphrodite." The number of offspring produced by each hermaphrodite is reported in the column "Offspring."
DOI: 10.5061/dryad.f6g68/3
title: Fecundity of healthy hermaphrodites

description: Fecundity of healthy hermaphrodites, assayed in otherwise the same way as fecundity of ruby-throated hermaphrodites. "Host" indicates the host experimental evolution treatment being assayed, and "Line" the replicate lineage. Fifteen hermaphrodites were sampled per replicate lineage, identified under "Hermaphrodite." The number of offspring produced by each hermaphrodite is reported in column "Offspring."
DOI: 10.5061/dryad.f6g68/4
title: Mortality rate

description: Mortality rate induced by parasite populations following experimental evolution. All parasite populations were evaluated against the ancestral host lineage of matching number. “Parasite” indicates the parasite experimental evolution treatment being assaying, and “Line” the replicate lineage. “Replicate” indicates the replicate assay plate. “Mortality_Rate” gives the proportion of hosts found to be dead or morbid following 24 hours of exposure to the parasite population.
DOI: 10.5061/dryad.h8fp2/1
title: Microsatellite genotypes

description: Genotype information from 11 microsatellite loci (Hefo1, Hefo4, Hefo10, Hefo2, Hefo11, Hefo13, Hefo9, Hefo8, Hefo7, Hefo3, Hefo5) for individual Helleborus foetidus plants sampled
DOI: 10.5061/dryad.kg4mq/10
title: A.lugubris_StarBEAST_5gene

description: StarBEAST tree utilizing the nuclear genes CXCR4, KIAA2013, RAG2, SVEP1, and ZEB1
DOI: 10.5061/dryad.kg4mq/11
title: A.lugubris_StarBEAST_7gene

description: StarBEAST tree utilizing the mitochondrial ND4 and cytb genes, and the nuclear genes CXCR4, KIAA2013, RAG2, SVEP1, and ZEB1
DOI: 10.5061/dryad.kg4mq/7
title: A.lugubris_SVEP1_unphased

description: SVEP1 alignment
DOI: 10.5061/dryad.kg4mq/8
title: A.lugubris_ZEB1_unphased

description: ZEB1 alignment
DOI: 10.5061/dryad.kg4mq/9
title: A.lugubris_StarBEAST_4gene

description: StarBEAST tree utilizing the ND4, cytb, CXCR4, and KIAA2013 genes
DOI: 10.5061/dryad.kj275/1
title: Dryad_metab_stress_15

description: Data used in the study "Work stress and metabolic syndrome in police officers. A prospective study".Legends: followup	concluded follow-up (0=no, 1=yes)	eta	age, years	fumo	smoke, 0=no, 1=yes	sonno	sleep disorders, 0=no, 1=yes	col0	cholesterol, baseline	hdlcol0	hdl-cholesterol, baseline	tg0	triglycerides, baseline	gluc0	blood glucose, baseline	obe0	obesity, baseline	hipres0	high blood pressure	hitg0	high triglycerides	lowhdl0	low HDL-C	higluc0	hi blood glucose	metcomp0	MetS components, number	MetS0	MetS at baseline	hdlcol	HDL-C value at follow-up	trigl	follow-up	vakueglic	follow-up	valueobes	follow-up	obesityhipres	follow-up	hypertensionhitry	follow-up	hypertriglyceridemialowhdl	follow-up	low HDL-Cmetcomp	follow-up	metabolic componentshigluc	follow-up	diabetesMetS	follow-up	MetS prevalenceincidMetS	follow-up	 incident cases of MetSstrestot	stress, rank 	x_dem	mean demand	x_contr	mean control	x_supp	mean support	x_eff	mean effort	x_rew	mean reward	x_over	mean overcommitment	x_dcr	mean job strain	x_eri	mean ERI	hi_x_dcr	DCR&gt;1	hi_x_eri	ERI&gt;1	hi_x_stres	stress level: 0:&lt;1; 1: exceeding 1 in one model; 2: &gt;1 with both models
DOI: 10.5061/dryad.n3s7d/1
title: Data and scripts - Master file

description: The raw imaging data (Leica SP5) and MatLab analysis scripts reproducing all data-dependent figures in the paper (Fig. 4 and Supplementary Figures S1, S2 and S3). Archive split into volumes to keep file size under 1Gb. Download all files, unzip, then run "RUN_ME.m" in Matlab to process the data and generate all the figures. Data acquired by Shawn C. Little, analysis scripts by Mikhail Tikhonov.
DOI: 10.5061/dryad.q2b49/1
title: M_tanosi_1

description: Two pairs of gzip-compressed fastq files with paired-end GBS sequence data from Microcebus tanosi.
DOI: 10.5061/dryad.q2b49/2
title: M_tanosi_2

description: Two pairs of gzip-compressed fastq files with paired-end GBS sequence data from Microcebus tanosi.
DOI: 10.5061/dryad.q2b49/3
title: M_tanosi_3

description: Two pairs of gzip-compressed fastq files with paired-end GBS sequence data from Microcebus tanosi.
DOI: 10.5061/dryad.q2b49/4
title: M_tanosi_4

description: Two pairs of gzip-compressed fastq files with paired-end GBS sequence data from Microcebus tanosi.
DOI: 10.5061/dryad.q2b49/5
title: M_tanosi_5

description: Three pairs of gzip-compressed fastq files with paired-end GBS sequence data from Microcebus tanosi.
DOI: 10.5061/dryad.q2b49/6
title: M_tanosi_6

description: Two pairs of gzip-compressed fastq files with paired-end GBS sequence data from Microcebus tanosi.
DOI: 10.5061/dryad.r55m2/1
title: Houle_etal_Scripts

description: Matlab code for the simulation model. The main model file is food_mul.m
DOI: 10.5061/dryad.rb921/1
title: BehavData

description: Behavioral performance data of all subjects for all sessions.
DOI: 10.5061/dryad.sq227/1
title: Raw data for Proceedings

description: This file contains raw LabChart files documenting changes ventilation and metabolism during an acute hypoxic exposure in naked mole rats acclimated to 8-10 day of either chronic sustained normoxia or chronic sustained hypoxia
DOI: 10.5061/dryad.th15b/1
title: Data for constraint-MA

description: Data for conducting the constraint-MA investigating the effects of OS on growth.  Hedges' g values (the response variable denoting whether groups of the same species that had been found to differ in OS levels also had significantly different growth rates) and their variances are given, as well as moderator details and sample size.
DOI: 10.5061/dryad.th15b/2
title: Data for cost-MA

description: Data for conducting the cost-MA investigating the effects of growth on OS.  Hedges' g values (the response variable indicating if there was a significant difference in OS between two groups of the same species that had been found to differ phenotypically in growth rate) and their variances are given, as well as moderator details and sample size.
DOI: 10.5061/dryad.0f8q1/1
title: F0L_coverage_MethLevels

description: MethPipe input data father liver with coverage, raw methylation levels. Columns: scaffold, starting position, strand, CpG, methylation level, coverage
DOI: 10.5061/dryad.0f8q1/2
title: F1L_coverage_MethLevels

description: MethPipe input files sons liver with coverage, raw methylation levels. Columns: scaffold, starting position, strand, CpG, methylation level, coverage
DOI: 10.5061/dryad.16q70/1
title: Putman et al. Supplemental Tables - BL

description: Supplemental TablesDescription of Supplemental Excel Tables (names are different tabs within the Excel Workbook)Table S1. Connectivity. Table listing hatchling abundance, by species, for each nesting area and connectivity between those areas and the spill site. Percentage of particles backtracked from the spill site arriving from each of the nesting areas of green, loggerhead, and Kemp’s ridley turtles within a given year, scaled relative to the number of particles that encountered any nesting area during that same period. Table S2. Literature-Survival. Table of data used for estimating clutch size (number of eggs per nest), clutch survival, and oceanic survival.Table S3. Green (number). The number of each age class of surface-pelagic green turtles from each of the twenty-four nesting areas estimated to be at the spill site based on median, maximum, and minimum estimates of oceanic survival.Table S4. Loggerhead (number). The number of each age class of surface-pelagic loggerhead turtles from each of the eight nesting areas estimated to be at the spill site based on median, maximum, and minimum estimates oceanic survival.Table S5. Kemp’s ridley (number). The number of each age class of surface-pelagic Kemp’s ridley turtles from each of the four nesting areas estimated to be at the spill site based on median, maximum, and minimum estimates of oceanic survival. Table includes results for passive drift “retentive behavior” simulations.Table S6. Green (percent). The percentage of survivors of each age class of oceanic-stage green turtles from each nesting area estimated to be at the spill site.Table S7. Loggerhead (percent). The percentage of survivors of each age class of oceanic-stage loggerhead turtles from each nesting area estimated to be at the spill.Table S8. Kemp’s ridley (percent). The percentage of the total survivors of each age class of surface-pelagic Kemp’s ridley turtles from each nesting area estimated to be at the spill site. Table includes results for passive drift “retentive behavior” simulations.
DOI: 10.5061/dryad.2d4m9/1
title: Model 1 datasets (island model), full datasets

description: This zipped file contains 50 datasets simulated under an island model with 10 subpopulations and 200 individuals per subpopulation. The files, in Fstat format, were created by the EASYPOP program.
DOI: 10.5061/dryad.2d4m9/2
title: Model 1 datasets (island model), sampling strategy No. 1

description: This zipped file contains 50 datasets simulated under an island model, with 10 subpopulations evenly sampled and a total of 620 individuals (sampling strategy no. 1; cf. Table 1). The files, in Fstat format, were simulated in the EASYPOP program and sampled in R via a custom written script.
DOI: 10.5061/dryad.2d4m9/3
title: Model 1 datasets (island model), sampling strategy No. 2.1

description: This zipped file contains 50 datasets simulated under an island model, with 10 subpopulations unevenly sampled and a total of 620 individuals (sampling strategy no. 2; cf. Table 1). The files, in Fstat format, were simulated in the EASYPOP program and sampled in R via a custom written script.
DOI: 10.5061/dryad.2d4m9/4
title: Model 1 datasets (island model), sampling strategy No. 2.2

description: This zipped file contains 50 datasets simulated under an island model, with 10 subpopulations sampled (20 individuals sampled in eight subpopulations and 10 in the remaining two), and a total of 180 individuals (cf. 'Sub-Sampling' section in M&M). The files, in Fstat format, were simulated in the EASYPOP program and sampled in R via a custom written script.
DOI: 10.5061/dryad.2d4m9/5
title: Model 1 datasets (island model), sampling strategy No. 3

description: This zipped file contains 50 datasets simulated under an island model, with 6 subpopulations evenly sampled (4 subpopulations not sampled) and a total of 150 individuals (sampling strategy no. 3; cf. Table 1). The files, in Fstat format, were simulated in the EASYPOP program and sampled in R via a custom written script.
DOI: 10.5061/dryad.2d4m9/6
title: Model 1 datasets (island model), sampling strategy No. 4

description: This zipped file contains 50 datasets simulated under an island model, with 6 subpopulations unevenly sampled (4 subpopulations not sampled) and a total of 150 individuals (sampling strategy no. 4; cf. Table 1). The files, in Fstat format, were simulated in the EASYPOP program and sampled in R via a custom written script.
DOI: 10.5061/dryad.2d4m9/7
title: Model 2 datasets (hierarchical island model), full datasets

description: This zipped file contains 50 datasets simulated under a hierarchical  island model with 10 subpopulations and 200 individuals per subpopulation. The files, in Fstat format, were created by the EASYPOP program.
DOI: 10.5061/dryad.2v2m1/1
title: Data - Broly et al. 2015

description: Raw data used for the figures
DOI: 10.5061/dryad.35hq4/10
title: data_subject10

description: data subject 10
DOI: 10.5061/dryad.35hq4/5
title: data_subject5

description: data subject 5
DOI: 10.5061/dryad.35hq4/6
title: data_subject6

description: data subject 6
DOI: 10.5061/dryad.35hq4/7
title: data_subject7

description: data subject 7
DOI: 10.5061/dryad.35hq4/8
title: data_subject8

description: data subject 8
DOI: 10.5061/dryad.35hq4/9
title: data_subject9

description: data subject 9
DOI: 10.5061/dryad.44p35/1
title: Consensus sequences of Babesia, Borrelia, C. Neoehrlichia, Plasmodium, and Trypanosoma

description: This data file contains consensus sequences of ribosomal and mitochondrial genes for Babesia, Borrelia, C. Neoehrlichia, Plasmodium, and Trypansosoma identified in lemur blood samples from Madagascar.
DOI: 10.5061/dryad.5145k/1
title: Original data obtained from the choice experiment
DOI: 10.5061/dryad.5145k/2
title: Transformed data for the analysis of STATA
DOI: 10.5061/dryad.5n72m/1
title: Table 1. Collecting Sites

description: Collecting sites analyzed in the study
DOI: 10.5061/dryad.5n72m/2
title: Table 2. Microsatellite Loci Details

description: List of microsatellites genotyped in the study and oligonucleotide primer pairs (forward and reverse) used to PCR amplify loci.
DOI: 10.5061/dryad.5n72m/3
title: Table 3. Microsatellite allele frequencies for Utetes canaliculatus

description: Microsatellite allele frequencies for U. canaliculatus attacking different Rhagoletis hosts (hawthorn, apple, snowberry, and flowering dogwood flies) at nine sites designated 1-9 in the eastern U.S.
DOI: 10.5061/dryad.71f99/1
title: Final GBS vcf dataset 4274 SNPs

description: Final GBS dataset used for population genetic inferences (.vcf) and its associated information for each sample used (X/Y, Country, cluster assignation, ID).
DOI: 10.5061/dryad.71f99/2
title: Input ADMIXTURE files

description: ADMIXTURE input files used to infer popuation genetic structure using the 4274 SNPs