cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.mk471/5
title: Ovary_Angio_GSEA_Results

description: Results from GSEA Analysis in Angiogenic subtype of ovarian cancer
DOI: 10.5061/dryad.mk471/8
title: Ovary_Global_GSEA_Results

description: Results from GSEA Analysis in Global ovarian cancer analysis
DOI: 10.5061/dryad.mt5sj/2
title: R scripts

description: R scripts used in data analyses and making of figures
DOI: 10.5061/dryad.pd658/17
title: Figure10F

description: Confocal image stack
DOI: 10.5061/dryad.r606d128/10
title: Lemmon-etal2012_Phylogenetics_BEST_Amniote_treeDist
DOI: 10.5061/dryad.r606d128/2
title: Lemmon-etal2012_SupplementalTables

description: This Excel file contains all of the supplemental tables and table captions.
DOI: 10.5061/dryad.r606d128/4
title: Lemmon-etal2012_Contigs
DOI: 10.5061/dryad.s4s2b/2
title: Weights of aphids reared with and without ants

description: The file contains data related to the (wet) weights of the aphids in the different cages at the time of collection (end of a generation), over the generations of the main experiment of the study.
DOI: 10.5061/dryad.s4s2b/3
title: Weight differences between unattended and ant-attended aphids

description: The file contains differences of values of variables (from the data file aphid_weight_data.txt) between the two cylinders in a pair, for GenRel going from 0 to 4 (where 1 is the first ant attended generation in a trial). The differences are formed as the value for the ant attended cylinder in a pair minus the value for the unattended cylinder.
DOI: 10.5061/dryad.tm093/1
title: All_ENMpoints

description: This file contains latitude and longitude coordinates for localities used to construct species distribution models.
DOI: 10.5061/dryad.tm093/2
title: Structure infile

description: Input file for Structure analysis.
DOI: 10.5061/dryad.14214/5
title: Cymbidium_IR region
DOI: 10.5061/dryad.14214/6
title: Cymbidium_LSC
DOI: 10.5061/dryad.1qf3s/4
title: Worker_Mortality

description: Script for worker mortality analysis
DOI: 10.5061/dryad.1v0tb/4
title: Script containing R-based analysis, data matrixes and plotting code

description: This archive contains the main analysis and plotting functions, and the data matrixes used in the analysis.
DOI: 10.5061/dryad.23td2/1
title: Doubly-labelled water data and energetics comparison used to generate figures

description: Includes several worksheets: (1) "Background" are the background deuterium and oxygen-18 measuremetns from thick-billed mures in 2006. (2) "DEE calculations" provides the raw ppm data and calculations made to estimate daily enegy expenditure in thick-billed murres. Each band number (ID) can be cross-referenced with the time-activity file. (3) "Activity costs" represents the average body mass, mass loss and activity budgets and total energy expenditure (from Part (2)) used to calculate activity-specific costs. (4) "Interspecies comparison" data used to generate figures in the paper. (5) "Morphological comparison" database used to generate the figures in the paper. (6) "PECO ppm and DEE": Pelagic cormorant ppm data and calculations used to estimate daily energy expenditure. (7) "PECOactivity": Pelagic cormorant activity budgets (derived from accelerometer files) and daily energy expenditure (from 6), along with mass and mass loss (from 6).
DOI: 10.5061/dryad.23td2/2
title: Thick-billed murre text data files used to generate activity budgets

description: Dive data files from Lotek 1100 time-depth recorders recorded at 3 second intervals. Each file name has the five- or eight-digit band number that corresponds to the doubly-labelled water measurements, except for those birds that were not banded and only identified by colour marked on their chest. One recorder was also attached to the top of the blind to record ambient temperature and pressure. Each text file has, after, a pre-amble, the date-time, depth (in psi; multiply by 0.71 to approximate depth in m) and temperature (in degrees Celsius).
DOI: 10.5061/dryad.23td2/3
title: CEFAS G6A pelagic cormorant files (Part 1a)

description: Text files downloaded from the accelerometers attached to pelagic cormorants (first of five folders). Each folder refers to one individual bird (cross-referenced with doubly-labelled water data). The file name within each folder refers to the CSV file created by the CEFAS program and has the logger ID and the date the file was created (downloaded). The data file provides date/time, depth (pressure in dbars which is generally equivalent to depth in m) and acceleration in three dimensions at 25 Hz (in g), after a preamble generated by the logger that includes the daylog. Note that data is partitioned into two sections. The first section has data every 1 s, the second section has data at 25 Hz in the "fast log"; for five files, the fine-scale (25 Hz) data was only recorded when the bird was diving. The CEFAS G6A manual is here: https://www.cefastechnology.co.uk/downloads/file.aspx?file=33.
DOI: 10.5061/dryad.23td2/4
title: CEFAS G6A pelagic cormorant files (Part 2)

description: Text files downloaded from the accelerometers attached to pelagic cormorants (first of five folders). Each folder refers to one individual bird (cross-referenced with doubly-labelled water data). The file name within each folder refers to the CSV file created by the CEFAS program and has the logger ID and the date the file was created (downloaded). The data file provides date/time, depth (pressure in dbars which is generally equivalent to depth in m) and acceleration in three dimensions at 25 Hz (in g), after a preamble generated by the logger that includes the daylog. Note that data is partitioned into two sections. The first section has data every 1 s, the second section has data at 25 Hz in the "fast log"; for five files, the fine-scale (25 Hz) data was only recorded when the bird was diving. The CEFAS G6A manual is here: https://www.cefastechnology.co.uk/downloads/file.aspx?file=33.
DOI: 10.5061/dryad.23td2/5
title: CEFAS G6A pelagic cormorant files (Part 3)

description: Text files downloaded from the accelerometers attached to pelagic cormorants (first of five folders). Each folder refers to one individual bird (cross-referenced with doubly-labelled water data). The file name within each folder refers to the CSV file created by the CEFAS program and has the logger ID and the date the file was created (downloaded). The data file provides date/time, depth (pressure in dbars which is generally equivalent to depth in m) and acceleration in three dimensions at 25 Hz (in g), after a preamble generated by the logger that includes the daylog. Note that data is partitioned into two sections. The first section has data every 1 s, the second section has data at 25 Hz in the "fast log"; for five files, the fine-scale (25 Hz) data was only recorded when the bird was diving. The CEFAS G6A manual is here: https://www.cefastechnology.co.uk/downloads/file.aspx?file=33.
DOI: 10.5061/dryad.23td2/6
title: CEFAS G6A pelagic cormorant files (Part 4)

description: Text files downloaded from the accelerometers attached to pelagic cormorants (first of five folders). Each folder refers to one individual bird (cross-referenced with doubly-labelled water data). The file name within each folder refers to the CSV file created by the CEFAS program and has the logger ID and the date the file was created (downloaded). The data file provides date/time, depth (pressure in dbars which is generally equivalent to depth in m) and acceleration in three dimensions at 25 Hz (in g), after a preamble generated by the logger that includes the daylog. Note that data is partitioned into two sections. The first section has data every 1 s, the second section has data at 25 Hz in the "fast log"; for five files, the fine-scale (25 Hz) data was only recorded when the bird was diving. The CEFAS G6A manual is here: https://www.cefastechnology.co.uk/downloads/file.aspx?file=33.
DOI: 10.5061/dryad.27vh0/1
title: Brain measurements of nine-spined sticklebacks

description: Brain measurements together with population, habitat, sex and treatment information.
DOI: 10.5061/dryad.2rg92p5v/2
title: Supplementary Figure 2: Strict consensus tree of four most parsimonious trees from complete European dataset of Agabini diving-beetles

description: Parsimony analysis done in TNT with driven search strategy using tree-fusing and sectorial searches.
DOI: 10.5061/dryad.3ft19/5
title: Appendix5

description: tests setups
DOI: 10.5061/dryad.3ft19/6
title: Appendix6

description: This graph presents the results of the performance tests we ran on IKey+, the blue bars represent the time necessary for each test to complete, and the red curve represents the number of queries rejected by IKey+ for each test (IKey+ rejects any query received when the CPU load of the host server is greater than 80%).
These results clearly show that, among the parameters available to the end-user, only the score method parameter has a significant influence on the time needed to complete the test (tests 2d & 2e)
The results of tests 4a to 4c show that increasing the number of simultaneous threads querying IKey+ increases the number of rejected queries.
On the other hand, the test 4d shows that adding a random delay (0-1000 ms) at the start of each thread decreases the number of rejected queries dramatically, even with a large number of simultaneous threads (100 in test 4d). This is encouraging, since we consider this setup to be the closest to a production environment.
DOI: 10.5061/dryad.3ft19/7
title: Appendix7

description: Usability test results
DOI: 10.5061/dryad.3g57k/4
title: all result trees

description: All result trees from analysis including: summary files of all trees, and R-out files from each analysis.
DOI: 10.5061/dryad.3q332/1
title: Raw Data Klepsatel et al

description: We followed the life histories of a large number of individual females, derived from three recently caught, geographically distinct wild populations from Austria, Zambia and South Africa over their lifetime. We measured ovariole number, fecundity (daily number of eggs), hatchability (of the offspring of the experimental females) as a function of maternal age, and lifespan (age at death) of experimental females under optimal laboratory conditions. Here we present the demographic raw data for these traits/measurements; each line represents an individual female fly. Fom these raw data, we then estimated individual lifetime fecundity, total lifetime production of viable eggs, and the length of the reproductive and post-reproductive period (these estimates are not shown here but can be found in our publication). For details see our paper, Klepsatel et al. (2013) in Journal of Evolutionary Biology. For additional, more specific (sub-)datasets based on the raw data presented here (e.g., data for survival analysis based on the distribution of age at death), which we have used for particular statistical analyses, or for statistical analyses outputs please contact the corresponding author, Thomas Flatt at thomas.flatt@unil.ch
DOI: 10.5061/dryad.4jj8r/1
title: Supplementary Table 2

description: The courtship values and statistics for the four genotypes tested (simulans/deficiency, simulans/ Balancer, melanogaster/Deficiency, melanogaster/Balancer).
DOI: 10.5061/dryad.4s6g0/1
title: Langos et al

description: Data collected in the field transferred into R (Program) further information see ReadMe file.
DOI: 10.5061/dryad.5b9b0/1
title: Dryad Dataset

description: Behavioural results for positive and negative self-resemblance experiment. Codes are as follows: id = participant number; yoke_id = number of the participant who also evaluated the focal participant's stimuli (yoked participant); sex = participant sex; ts_self = focal participant's trust preference score for focal participant's positively resembling images; ts_yoke = yoked participant's trust preference score for focal participant's positively resembling images; ls_self = focal participant's long-term attractiveness preference score for focal participant's positively resembling images; ls_yoke = yoked participant's long-term attractiveness preference score for focal participant's positively resembling images; ss_self = focal participant's short-term attractiveness preference score for focal participant's positively resembling images; ss_yoke = yoked participant's short-term attractiveness preference score for focal participant's positively resembling images; ta_self = focal participant's trust preference score for focal participant's negatively resembling images; ta_yoke = yoked participant's trust preference score for focal participant's negatively resembling images; la_self = focal participant's long-term attractiveness preference score for focal participant's negatively resembling images; la_yoke = yoked participant's long-term attractiveness preference score for focal participant's negatively resembling images; sa_self = focal participant's short-term attractiveness preference score for focal participant's negatively resembling images; sa_yoke = yoked participant's short-term attractiveness preference score for focal participant's negatively resembling images.
DOI: 10.5061/dryad.63fr7/4
title: Germination

description: This file contains two measures of germination success, as well as tree genotype class: germination success and number of abnormal germinants.
DOI: 10.5061/dryad.63fr7/5
title: Disease Susceptibility

description: This file contains the results of the controlled inoculation of trees with three fungal diseases: Melampsora larici-populina, M. medusae f.sp. deltoidae, and M. occidentalis.  Susceptibility was measured by number of uredia by unit area.
DOI: 10.5061/dryad.63fr7/6
title: Structure file for genotype assignment

description: This file contains the recoded SNP data for input into Structure to estimate admixture in each individual.
DOI: 10.5061/dryad.63fr7/7
title: New Hybrid data file

description: The file contains the recoded genotype data for each tree for analysis in New Hybrids.
DOI: 10.5061/dryad.67r45/1
title: Genotype_Morphology_ B. japonicus
DOI: 10.5061/dryad.6vk6f/1
title: R code for fitness trait analyses

description: This file contains the commented R code for all the fitness trait analyses performed in the manuscript.
DOI: 10.5061/dryad.6vk6f/2
title: Tree characteristics

description: This file contains the tree genotype, age, height, and diameter at breast height.
DOI: 10.5061/dryad.6vk6f/3
title: Biomass and yield fitness traits

description: This file contains the biomass and yield traits measured for trees in this study. The biomass traits are: total catkin biomass, total seed biomass, 100 seed biomass, capsule biomass, stem biomass, and cotton biomass.
DOI: 10.5061/dryad.6vk6f/4
title: Germination

description: This file contains germination fitness data measured for each tree: germination success and number of abnormal germinants.
DOI: 10.5061/dryad.6vk6f/5
title: Disease Susceptibility

description: This file contains the results from controlled inoculations of three Melampsora species on poplars of known genotypes. Fitness was measured as the number of uredia per square centimeter.
DOI: 10.5061/dryad.7m6kg/13
title: Fig. 3b: Bioturbation in Nectocaris ?pteryx from Chengjiang

description: HKMF-50001 — Magnification of head region
DOI: 10.5061/dryad.82201/1
title: ExpressionGI

description: qPCR results for gene PaGI
DOI: 10.5061/dryad.82201/3
title: ExpressionFTL2

description: qPCR results for gene PaFTL2
DOI: 10.5061/dryad.82201/5
title: ExpressionPRR7

description: qPCR results for gene PaPRR7
DOI: 10.5061/dryad.82201/6
title: genotype_pabies445

description: Illumina GoldenGate genotyping results for 18 populations with a latitude range from 47 to 68 N.
DOI: 10.5061/dryad.84m54/4
title: Volumetric data from a micro-CT scan of the anterior end of Hermodice carunculata
DOI: 10.5061/dryad.b70pn/2
title: dataArchive_26Apr2012

description: Site level variables measured in experiment.
DOI: 10.5061/dryad.d7639/1
title: Supplemental Material

description: Supplemental material associated with the Systematic Biology article, "A Gateway for Phylogenetic Analysis Powered by Grid Computing Featuring GARLI 2.0".
DOI: 10.5061/dryad.d7639/2
title: Supplemental Table 1

description: A snapshot of information associated with The Lattice Project grid resources. The resources are shown sorted by composite throughput rating.
DOI: 10.5061/dryad.d7639/3
title: Supplemental Figure 1

description: The file repository belonging to an example registered user. Registered users may select from among the files found in their repository when specifying input files for a GARLI analysis, in addition to being able to upload new files.
DOI: 10.5061/dryad.d7639/4
title: Supplemental Figure 2

description: The create job page found at molecularevolution.org, as viewed by a registered user.
DOI: 10.5061/dryad.d7639/5
title: Supplemental Figure 3

description: The job status page found at molecularevolution.org, as viewed by a registered user.
DOI: 10.5061/dryad.d7639/6
title: Supplemental Figure 4

description: The job details page found at molecularevolution.org, as viewed by a registered user.
DOI: 10.5061/dryad.d7639/7
title: Supplemental Figure 5

description: The partitioned analysis portion of the create job page, currently showing a guided mode specification of two character sets and two data subsets.
DOI: 10.5061/dryad.f058c/16
title: Pop13

description: Standard Flowgram Format (sff) file that contains NGS reads for 16S and Cyt b amplicons from population-pool 13. Individuals that belong to population-pool 13 are listed in Table 1.
DOI: 10.5061/dryad.hm796/4
title: Naso data

description: An XL spreadsheet of sampling data for each recruit. Includes date, location, length and weight of each individual.
DOI: 10.5061/dryad.jj0fg/1
title: Schindler et al. data

description: Observations of bears and gulls taken throughout the Wood River system of SW Alaska. Bear observations are expressed as the total number of years observed per day by camera trap. Gull data are expressed as the total number of gulls observed at sites when surveys occurred.
DOI: 10.5061/dryad.mk471/15
title: molsigdb.v3.0.entrezForR.txt

description: molsigdb.v3.0.entrezForR contains the molsigdb, downloaded from the Broad Institute. The file is used to read the molsigdb.v3.0 gene sets into R.
DOI: 10.5061/dryad.mk471/16
title: BreastOutput_TradScaled

description: BreastOutput_TradScaled.RData is an R-workspace contains the objects: allPs, allPs.adj, sumTable. These were generated from applying the SAPS method to the breast cancer meta-data set scaled by transforming each feature into its Z score across all patients in a data-set prior to merging across data-sets.
DOI: 10.5061/dryad.mk471/17
title: BreastOutput_SubScaled

description: BreastOutput_SubScaled.RData is an R-workspace contains the objects: allPs, allPs.adj, sumTable. These were generated from applying the SAPS method to the breast cancer meta-data set scaled by transforming each feature into its Z score across all patients within a breast cancer subtype data-set prior to merging across data-sets.
DOI: 10.5061/dryad.mk471/18
title: BreastSubtypeSpecScaleRankDir

description: BreastSubtypeSpecScaleRankDir contains the ranked gene lists of concordance indices used to perform the GSEA in breast cancer.
DOI: 10.5061/dryad.mk471/19
title: OvaryOutput_TradScaled

description: OvaryOutput_TradScaled.RData contains the objects: allPs, allPs.adj, sumTable.BreastOutput_TradScaled.RData. These were generated from applying the SAPS method to the ovarian cancer meta-data set scaled by transforming each feature into its Z score across all patients in a data-set prior to merging across data-sets.
DOI: 10.5061/dryad.mk471/20
title: OvaryOutput_SubScaled

description: OvaryOutput_SubScaled.RData is an R-workspace contains the objects: allPs, allPs.adj, sumTable. These were generated from applying the SAPS method to the ovarian cancer meta-data set scaled by transforming each feature into its Z score across all patients within a ovarian cancer subtype data-set prior to merging across data-sets.
DOI: 10.5061/dryad.mk471/22
title: BreastOvary_HCv2

description: BreastOvary_HCv2.zip – This zip directory contains files to generate Figure 10 (Hierarchical clustering of breast and ovarian cancer subtypes based on SAPS scores) using JavaTreeView (http://jtreeview.sourceforge.net/)
DOI: 10.5061/dryad.s4s2b/4
title: Aphid embryo size distribution

description: The file contains data on the distribution of aphid embryos over size categories, for a number of dissected adult aphids that were sampled from the main experiment of the study, including unattended and ant-attended aphids. Each row of the data file corresponds to one dissected aphid.
DOI: 10.5061/dryad.td237/2
title: Gen_data

description: The file 'Gen_data' consists of information used in population genetic analysis and includes: sampling site, sampling year, cohort and loci information.
DOI: 10.5061/dryad.tm093/3
title: CCSA_conductance_infile

description: Conductance grid obtained from ENMs (LGM, CCSA3) used as input data in CIRCUITSCAPE to generate spatial resistance distances among populations.
DOI: 10.5061/dryad.tm093/4
title: MIROC_conductance_infile

description: Conductance grid obtained from ENMs (LGM, MIROC) used as input data in CIRCUITSCAPE to generate spatial resistance distances among populations.
DOI: 10.5061/dryad.tm093/5
title: 2050_conductance_infile

description: Conductance grid obtained from ENMs (Future, 2050) used as input data in CIRCUITSCAPE to generate spatial resistance distances among populations.
DOI: 10.5061/dryad.tm093/6
title: Present_conductance_infile

description: Conductance grid obtained from ENMs (Present time) used as input data in CIRCUITSCAPE to generate spatial resistance distances among populations.
DOI: 10.5061/dryad.tm093/7
title: Landcover_conductance_infile

description: Conductance grid obtained from ENMs (Land cover) used as input data in CIRCUITSCAPE to generate spatial resistance distances among populations.
DOI: 10.5061/dryad.tm093/8
title: Topography_conductance_infile

description: Conductance grid obtained from ENMs (Topography) used as input data in CIRCUITSCAPE to generate spatial resistance distances among populations.
DOI: 10.5061/dryad.vj4f7/1
title: Khanshour et al_SupMat_Figure S1

description: Comparisons among 15 microsatellite markers and the number of populations out of 14 for which any pair of markers shows significant LD at p&lt;0.05
DOI: 10.5061/dryad.14214/7
title: Cymbidium_SSC
DOI: 10.5061/dryad.20r9k/20
title: Myotis_lucifugus_genomicORs

description: Genomic ORs mined from little brown bat genome
DOI: 10.5061/dryad.23td2/10
title: CEFAS G6A pelagic cormorant files (Part 5b)

description: Text files downloaded from the accelerometers attached to pelagic cormorants (first of five folders). Each folder refers to one individual bird (cross-referenced with doubly-labelled water data). The file name within each folder refers to the CSV file created by the CEFAS program and has the logger ID and the date the file was created (downloaded). The data file provides date/time, depth (pressure in dbars which is generally equivalent to depth in m) and acceleration in three dimensions at 25 Hz (in g), after a preamble generated by the logger that includes the daylog. Note that data is partitioned into two sections. The first section has data every 1 s, the second section has data at 25 Hz in the "fast log"; for five files, the fine-scale (25 Hz) data was only recorded when the bird was diving. The CEFAS G6A manual is here: https://www.cefastechnology.co.uk/downloads/file.aspx?file=33.