cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.34pb0/1
title: Network responses and training sets for Dawson/Gupta paper

description: The directories included in the zip file provide the training files and the results for the PLOS ONE manuscript “Probability matching in perceptrons: Effects of conditional dependence and linear nonseparability” by Michael Dawson and Maya Gupta. 
The responses of the various networks in the two simulations that are reported are given in the two Excel spreadsheets. Each spreadsheet provides details about the training patterns, the likelihood of each pattern type being rewarded in a training set, and the responses of networks to patterns after training in separate worksheets. Comments are provided on each worksheet to explain the numbers that it contains.
The other two directories provide the raw training sets used in each simulation; there are 5 for Simulation 1 and there are 20 for Simulation 2. To be run with the software they need the .net extension; however they are all simply text files.

The simulations were conducted using the Rosenblatt program, which implements gradient descent training of perceptrons. Detailed descriptions of the mathematics of this program, and accounts of using the software, have been previously published (Dawson, 2004, 2005). The program itself is available as freeware from this location:
http://www.bcp.psych.ualberta.ca/~mike/Software/Rosenblatt/index.html 
References
Dawson, M. R. W. (2004). Minds And Machines: Connectionism And Psychological Modeling. Malden, MA: Blackwell Pub.
Dawson, M. R. W. (2005). Connectionism : A Hands-on Approach (1st ed.). Oxford, UK ; Malden, MA: Blackwell Pub.
DOI: 10.5061/dryad.7t7ph/1
title: Population_size_data

description: Population size data over seven generations
DOI: 10.5061/dryad.81r20/1
title: LarvalTrait-AssociationPGi_Data2007

description: excel file,  larval data from individuals collected in the Fall 2006
DOI: 10.5061/dryad.81r20/2
title: Oviposition-ALOLSAUP-2010

description: Oviposition data from cage experiment that took place in Summer 2010, individuals collected in the Fall 2009
DOI: 10.5061/dryad.81r20/3
title: Life-Histories_ALOLSAUP_2010

description: Life-history traits, including larval traits and adult traits, of individuals collected in the fall 2009 that were adult in the Summer 2010
DOI: 10.5061/dryad.8fh3g/1
title: MHC I peptide elutions from TAPBPR-WT and TAPBPR-C94A expressing cells
DOI: 10.5061/dryad.95h17/1
title: Molluscan RNA data

description: This dataset is obtained from http://www.rna.icmb.utexas.edu/SIM/4D/Mollusk/alignment.gb. This dataset in nexus format is converted from the original dataset in GenBank format using EMBOSS. The dataset in fasta format used in the data analysis section of the paper can be obtained directly from https://github.com/yzhai220/geopip together with the source code.
DOI: 10.5061/dryad.g7h7n/40
title: Elison_Lake_July_17_2007-July 16 2011 thermistor

description: Elison Lake thermistor data from July 17 2007 to July 16 2011
DOI: 10.5061/dryad.g7h7n/41
title: Grouping rationale

description: Additional summary of field notes providing support for grouping rationale.
DOI: 10.5061/dryad.g7h7n/42
title: High Lake activity

description: High Lake 210Pb activity from gamma-dating
DOI: 10.5061/dryad.g7h7n/43
title: Moraine activity

description: Moraine Pond 210Pb activity from gamma-dating
DOI: 10.5061/dryad.g7h7n/44
title: Paradise activity

description: Paradise Pond 210Pb activity from gamma-dating
DOI: 10.5061/dryad.g7h7n/45
title: Plateau Pond2 activity

description: Plateau Pond 2 210Pb activity from gamma-dating
DOI: 10.5061/dryad.g7h7n/46
title: Proteus activity

description: Protease Lake 210Pb activity from gamma-dating
DOI: 10.5061/dryad.g7h7n/47
title: SV Pond 5 activity

description: SV Pond 5 210Pb activity from gamma-dating
DOI: 10.5061/dryad.g7h7n/48
title: SV Pond 8 activity

description: SV Pond 8 210Pb activity from gamma-dating
DOI: 10.5061/dryad.g8t00/1
title: Rueda et al. 2017_Ecography-Appendix 1_Trait values

description: Species list and trait values for 85 gymnosperms and 219 woody angiosperms of North America. Imputed missing values for each trait are highlighted in bold.
DOI: 10.5061/dryad.j4567/1
title: Contributions of local speech encoding and functional connectivity to audio-visual speech perception

description: See README.pdf
DOI: 10.5061/dryad.jg660/1
title: DATA FOR JEcol-2017-0111.R1
DOI: 10.5061/dryad.jv351/1
title: Insectivorous bat data

description: Acoustic data collected using anabats. Species scientific names given in supplementary materials of paper.
DOI: 10.5061/dryad.jv351/3
title: Exotic bird data

description: Data from timed area searches for birds. Species exotic to Australia are included. Species scientific names given in supplementary materials of paper.
DOI: 10.5061/dryad.jv351/4
title: Native bird data

description: Data from timed area searches. Only species native to Australia are included. Species scientific names given in supplementary materials of paper.
DOI: 10.5061/dryad.jv351/5
title: Coleopteran data

description: Beetle data collected using light traps. Family scientific names given in supplementary materials of paper.
DOI: 10.5061/dryad.kj3km/1
title: Scots pine and European beech BAI and iWUE 1980-2013

description: These data series describe the values for BAI and iWUE for Scots pine and European beech trees in the period 1980-2013 growing in the southwestern Pyrenees.
DOI: 10.5061/dryad.mn65t/1
title: SDE_3islands

description: This is the simulation code written in C.
DOI: 10.5061/dryad.nj0v4/1
title: Alcyonium digitatum microsatellite data

description: Alcyonium digitatum microsatellite data. Excel file. Data for 8 loci in 2 column format, 648 individuals, 20 sites.
DOI: 10.5061/dryad.nj0v4/2
title: Eunicella verrucosa microsatellite data

description: Eunicella verrucosa microsatellite data. Excel file. Data for 13 loci in 2 column format, 905 individuals, 27 sites.
DOI: 10.5061/dryad.p8f6n/1
title: Symbiodinium ITS2 sequences from the Umm al Quwain lagoon

description: ITS2 sequences for corals in the UAQ lagoon across two sampling periods.
DOI: 10.5061/dryad.ph826/1
title: Caterpillar Models

description: Data from experiment using aluminum operative temperature models of caterpillars
DOI: 10.5061/dryad.ph826/2
title: Spectra of models and caterpillars

description: Reflectance spectra of painted aluminum models and live caterpillars
DOI: 10.5061/dryad.ph826/3
title: Effect of behavior and color on survival

description: Data from experiment on the effects of behavior and color on survival using live caterpillars
DOI: 10.5061/dryad.ph826/4
title: Calibration of models with caterpillars

description: Data for comparison of temperatures of different colored caterpillars with the corresponding aluminum models.
DOI: 10.5061/dryad.ph826/5
title: Effect of color on behavior

description: Data from field experiment on the effect of color on refuge-seeking behavior using live caterpillars
DOI: 10.5061/dryad.pp0jp/5
title: CDBird_CommunityComposition_Data
DOI: 10.5061/dryad.pp0jp/6
title: CD_Mammal_CommunityComposition_Data
DOI: 10.5061/dryad.pt240/1
title: crossing locations info

description: This file contains information on the places where spider monkeys crossed the road (given in X and Y coordinates, UTM zone 16N, datum WGS 84) and other info about the crossing (e.g. road width and gap).
DOI: 10.5061/dryad.pt240/2
title: spider monkeys locations

description: This file contains the locations of spider monkeys subgroups separated by 30min intervals from 2005 to 2008. The x and y coordinates are given in UTM format 16N zone, WGS84 datum.
DOI: 10.5061/dryad.pt240/3
title: Habitat types_ZIP

description: This is a compressed RASTER file (tiff and corresponding reference files) for ArcGIS containing 4 habitat types: 1) primary forest, 2) secondary forest, 3) young secondary forest, 4) no forest.  UTM format 16N, WGS 84.
DOI: 10.5061/dryad.pt240/4
title: roads_shapefile ZIP

description: This is a compressed shapefile (ArcGIS) of the paved and dirt roads covering the study area. UTM format 16N, WGS 84.
DOI: 10.5061/dryad.s29j7/2
title: Supplementary+Data+2

description: Slices from XMT scan of one enrolled specimen of Parabailella languedocensis (C-12).
DOI: 10.5061/dryad.s29j7/3
title: Supplementary+Model+1

description: Interactive 3-D reconstruction of Bailiaspis? glabrata (MPZ2017/310) in VAXML format.
DOI: 10.5061/dryad.s29j7/4
title: Supplementary+Model+2

description: Interactive 3-D reconstruction of Bailiaspis? glabrata (MPZ2017/311) in VAXML format.
DOI: 10.5061/dryad.s29j7/5
title: Supplementary+Model+3

description: Interactive 3-D reconstruction of Parabailella languedocensis (C-12) in VAXML format.
DOI: 10.5061/dryad.s29j7/7
title: Supplementary+Movie+2

description: 3-D model of Bailiaspis? glabrata showing the enrolment procedure.
DOI: 10.5061/dryad.tc722/1
title: Blackbird_Blood_Transcriptome

description: Multifasta file containing the sequences of the blackbird transcriptome. The assembly was generated de novo using the program Trinity v20140717 (Grabherr et al. 2011) with the default k-mer size of 25 and a minimum contig length of 200 bp. To identify transcripts corresponding to coding genes, the obtained assembly was subjected to sequence similarity searches against a custom database containing the available bird proteins (chicken, duck, flycatcher, turkey and zebra finch; source: Ensembl release 77) and the well-annotated human and mouse protein datasets (Ensembl release 77).
DOI: 10.5061/dryad.tc722/2
title: Blackbird_genotypes

description: Filtered individuals’ genotypes stored in a VCF file generated by the Bayesian genetic variant detector FreeBayes v1.0.2 (Garrison & Marth), run with default parameters.
DOI: 10.5061/dryad.tq381/1
title: Shanks et al. Ecol Mono

description: Data are a combination of field-collected data on barnacle populations at stations from San Diego, California to La Push, Washington. Stations names are in column A and they were cataloged (column B) as either rocky shores (1, continuous rocks intertidal for at least 50 m) or rocks within beaches (2, rocky shore &lt;50 m). The latitude and longitude (columns D and E) are precise locations using the ‘place’ tool in Google Earth. Columns F and G are alongshore wind stress (a proxy for upwelling/downwelling) and average wave height calculated for each station latitude. See Shanks et al (in press) for descriptions of the methods. Daily solar radiation (column H) is from the National Solar Radiation Data Base (http://rredc.nrel.gov/solar/old_data/nsrdb/). Average surfzone width (Column I) was determined from Google Earth images (See Shanks et al, in press for methods). Intertidal width and beach angle (columns J and K) were measured in the field at the time the stations were sampled and methods are described in Shanks et al. (in press). Barnacle data (columns L-W) are from photographs taken in the field at each sample site. ImageJ was used to analyze the photographs and methods are describe in Shanks et al. (in press).
DOI: 10.5061/dryad.tq381/2
title: Daily Barncle settlement in 2011

description: Daily barnacle settlement data for 2011. Data are daily settlement to bare rock surface quadrats. There were three replicates at Pack Trail, Bastendorff, Carmel North, and Carmel South. Blanks in the matrix indicate missing data. See Shanks et al. (in press) for a description of the methods and the latitude and longitude of the sample sites.
DOI: 10.5061/dryad.tq381/3
title: Weekly barnacle recruitment in 2010

description: Weekly barnacle recruitment data to bare rock quadrats in 2010. The latitude and longitude of each sample site is in Shanks et al. (in press) as well as a detailed description of the sample methods.
DOI: 10.5061/dryad.tq381/4
title: Barnacle Size frequency data for 26 samples stations

description: Size frequency distributions (percent) for barnacles in a latitudinal study of populations along the west coast of North America. Size bins are in mm. Station locations can be found in Shanks et al. (in press).
DOI: 10.5061/dryad.vh396/3
title: teis_CI_natural_backgrounds

description: Data related to analysis of CI in D. teissieri with Wolbachia in their natural host backgrounds.
DOI: 10.5061/dryad.vh396/4
title: teissieri_F1_CI

description: Data related to analysis of CI in D. teissieri with Wolbachia in F1 backgrounds.
DOI: 10.5061/dryad.vh396/5
title: teis_backcross

description: Data related to analysis of CI in D. teissieri with Wolbachia backcrossed into different host backgrounds.
DOI: 10.5061/dryad.vh396/6
title: teis_CI_ixi

description: Data related to analysis of female protection from CI in D. teissieri.
DOI: 10.5061/dryad.vh396/7
title: prop_mated

description: Data related to analysis of Wolbachia effects on intraspecific and interspecific mating in all three host species.
DOI: 10.5061/dryad.vh396/8
title: eggs_laid_and_viability

description: Data related to analysis of Wolbachia effects on intraspecific and interspecific fecundity and egg to adult viability in all three host species.
DOI: 10.5061/dryad.vh396/9
title: infection_status

description: Data related to analysis of Wolbachia infection frequencies in all three host species, in Bioko and Sao Tome.
DOI: 10.5061/dryad.00b1d/1
title: Microbial community data

description: Archaea, bacteria, and fungi identification, abundance, and diversity across smooth brome invaded and uninvaded plots, including environmental data.
DOI: 10.5061/dryad.1vr54/1
title: Ladybeetle captures at Kellogg Biological Station, 1989-2012

description: Counts of 13 ladybeetle species collected from yellow sticky cards at sampling stations in the Main Cropping System Experiment at Kellogg biological station in southwestern Michigan
DOI: 10.5061/dryad.31dj3/1
title: Channelrhodopsin Cell 1: 121025 C2
DOI: 10.5061/dryad.31dj3/2
title: Channelrhodopsin Cell 2: 120906 C1
DOI: 10.5061/dryad.31dj3/3
title: Channelrhodopsin Cell 3, 4, 5: 120823 C1, C2 and 4
DOI: 10.5061/dryad.31dj3/4
title: Channelrhodopsin Cell 6 and 7: 120627 C1 and 2
DOI: 10.5061/dryad.31dj3/5
title: Channelrhodopsin Cell 8 en 9: 121019 C1 and 2
DOI: 10.5061/dryad.31dj3/6
title: Channelrhodopsin Cell 10: 121018 C2
DOI: 10.5061/dryad.31dj3/7
title: Channelrhodopsin Cell 11: 120903 C1
DOI: 10.5061/dryad.31dj3/8
title: Channelrhodopsin Cell 12 and13: 121015 C1 and 5
DOI: 10.5061/dryad.32j7r/1
title: Raclariu et al_2017_FASTQ Raw
DOI: 10.5061/dryad.35fh0/1
title: Deforestation model dataset

description: Data used to model satellite-derived Normalized Difference Vegetation Index (NDVI) in response to precipitation
in deforested and non-deforested areas of the Brazilian semi-arid Caatinga biome.

Variables:
cell_id - Numeric ID of the pixel included in the analysis
ndvi - Montlhy Normalized Difference Vegetation Index (NDVI) score of the pixel
prec - Monhtly precipitation value of the pixel
long - Longitude of the pixel centroid
lat - Latitude of the pixel centroid
deforestation - Catogrical variable indicating existance (YES or NO) of deforestation in the pixel
DOI: 10.5061/dryad.35fh0/2
title: Land protection model dataset

description: Data used to model satellite-derived Normalized Difference Vegetation Index (NDVI) in response to precipitation
on areas of the Brazilian semi-arid Caatinga biome under different protection levels.

Variables:
cell_id - Numeric ID of the pixel included in the analysis
ndvi - Montlhy Normalized Difference Vegetation Index (NDVI) score of the pixel
prec - Monhtly precipitation value of the pixel
long - Longitude of the pixel centroid
lat - Latitude of the pixel centroid
protection_type - Catogrical variable indicating the level of land protection in the pixel, including no protection,
		  sustainable use or full protection status.
DOI: 10.5061/dryad.4p30k/1
title: MATLAB Code - Autocorrelation and the costs of plasticity

description: Matlab code for simulation and plotting selected degree of plasticity in a continuously changing environment.
DOI: 10.5061/dryad.4p30k/2
title: Plasticity_Fixed

description: Matlab code for simulation and plotting of selected plasticity and environmental specialisation in an environment with fixed environmental states
DOI: 10.5061/dryad.5dk27/1
title: Matrix_data_and_code

description: Zip containing the full data set for each matrix at each time point, the randomised data sets (separated by modularity and nestedness) and the r code used to analyse data.
DOI: 10.5061/dryad.65vs3/1
title: PME_JEcol_main_data

description: All data, except mycorrhizal colonisation data, collected for the analyses presented in this paper. All plant materials were field-collected along the Jurien Bay dune chronosequence in Western Australia in 2013. Data in this file include: root phosphomonoesterase (PME) activity (dry and fresh weight basis), leaf [N], leaf [P], leaf N:P, leaf δ15N and %Ndfa. This PME_JEcol_main_data.csv file was created using Microsoft Excel 2013. See readme file for descriptions of (abbreviated) column headings.
DOI: 10.5061/dryad.755jp/1
title: juvenile data

description: Data on juvenile body size (PC), feather quality (PC), and juvenile survival. Observe that the ring and territory identity does not match other datasets.
DOI: 10.5061/dryad.755jp/2
title: Number of fledglings

description: Number of fledglings. Observe that the territory identifier does not match other datasets.
DOI: 10.5061/dryad.755jp/3
title: number of eggs

description: Number of eggs. Observe that the territory identity does not match other datasets.
DOI: 10.5061/dryad.755jp/4
title: female survival

description: Female survival. Observe that the territory identity does not match other datasets.
DOI: 10.5061/dryad.7pt2m/1
title: GBS-SNPs

description: SNP genotypes generated using genotyping by sequencing approaches. SNPs were used to characterize genomic diversity of captive Peromyscus leucopus populations. See readme for additional information.
DOI: 10.5061/dryad.7pt2m/2
title: genome annotation

description: Annotation associated with genome sequencing of Peromyscus leucopus. Additional details are provided in the readme file, and raw reads are available via genbank.
DOI: 10.5061/dryad.7pt2m/3
title: Peromyscus leucopus genome assembly

description: Genome assembly that utilized 2 lanes of illumina 150bp, paired end reads (available at NCBI genbank accession number PRJNA375113).
DOI: 10.5061/dryad.7t7ph/2
title: Mortality_data

description: Mortality data at Ph3 selected generations 3 and 6
DOI: 10.5061/dryad.7t7ph/3
title: Unselected_genotype_data

description: Unselelected populations genotype data
DOI: 10.5061/dryad.7t7ph/4
title: Selected_genotype_data

description: Selected populations genotype data
DOI: 10.5061/dryad.8125b/1
title: Burton_etal_TraitData

description: Whole plant, leaf, stem and root trait data for 57 forest understory species from western Oregon, USA. Growth forms are: F = fern, G = graminoid (grasses, sedges and rushes), H = herbaceous forbs, LS = low clonal shrubs, TS = tall shrubs. GLI = gap light index (%). Total_pct_cover = total cover of understory vegetation surrounding specimen; soil__n = total soil nitrogen (%); CMD = climatic moisture deficit (mm); DELTA15N = Δ15N = δ15Nleaf - δ15Nsoil; iWUE = intrinsic water use efficiency (A/g); SLA = specific leaf area (mm2/mg); LNC = leaf nitrogen content (mg/g); Narea = leaf nitrogen per area (g/m2); LDMC = leaf dry matter content; leaf size (cm2); SSD = stem specific density (mg/mm3); SRL = specific root length (m/g).
DOI: 10.5061/dryad.8qp4n/1
title: BIGSdb gene-by-gene alignment, xmfa format

description: This is an extended fasta (xmfa) format gene-by-gene alignment of all the genomes included in the study to all loci in the H. pylori reference genome 26695.
DOI: 10.5061/dryad.8qp4n/3
title: BIGSdb gene-by-gene alignment, fasta format

description: This is a fasta format gene-by-gene alignment of all the genomes included in the study to all loci in the H. pylori reference genome 26695. The loci are subsequently concatenated into one entry per genome.
DOI: 10.5061/dryad.dh250/1
title: Mamet et al, 2017 - Toxicological Sciences - 05 25 17 -Supplemental protocol information

description: Supplemental protocol information
DOI: 10.5061/dryad.dh250/2
title: Mamet et al, 2017 - Toxicological Sciences - 05 25 17  -Supplemental Table 1

description: Stability of AYX1: calcium formulation with sodium phosphate or Tris buffers at 2 weeks
DOI: 10.5061/dryad.dh250/3
title: Mamet et al, 2017 - Toxicological Sciences - 05 25 17  -Supplemental Table 2

description: Stability of the AYX1: calcium formulation with Tris buffer at 3 months
DOI: 10.5061/dryad.g7h7n/49
title: Water chem additional parameters all sites

description: Additional water chemistry parameters for all sites
DOI: 10.5061/dryad.g7h7n/50
title: West activity

description: West Lake 210Pb activity from gamma-dating
DOI: 10.5061/dryad.g7h7n/51
title: High Lake dates

description: High Lake 210Pb dates using CRS dating method
DOI: 10.5061/dryad.g7h7n/52
title: Moraine Pond Dates

description: Moraine Pond 210Pb dates using CRS dating method
DOI: 10.5061/dryad.g7h7n/53
title: Paradise dates

description: Paradise Pond 210Pb dates using CRS dating method
DOI: 10.5061/dryad.g7h7n/54
title: Plateau Pond2 dates

description: Plateau Pond 2 210Pb dates using CRS dating method
DOI: 10.5061/dryad.g7h7n/55
title: Proteus dates

description: Proteus Lake 210Pb dates using CRS dating method
DOI: 10.5061/dryad.g7h7n/56
title: SV Pond 5 dates

description: SV Pond 5 210Pb dates using CRS dating method
DOI: 10.5061/dryad.js5k0/1
title: MatingTiming_LazarusCode_Replace

description: We are submitting the code for individual based model simulations, written in Lazarus 1.6.
DOI: 10.5061/dryad.jv351/2
title: Bee data

description: Data on bees, collected using sweep net and coloured pan traps. Species scientific names given in supplementary materials of paper.
DOI: 10.5061/dryad.jv351/6
title: Heteropteran bug data

description: Bug data collected using sweep net. Species scientific names given in supplementary materials of paper.
DOI: 10.5061/dryad.jv351/7
title: Environmental co-variates

description: Site specific co-variates per green space
DOI: 10.5061/dryad.jv351/8
title: Appendix B R/Stan code
DOI: 10.5061/dryad.k6916/1
title: Colour and behavioural data, Activity level survey data, and predation experiments data file
DOI: 10.5061/dryad.mn65t/2
title: SDE_3islands_result example

description: A simulated result of three-island SDE.
DOI: 10.5061/dryad.pp127/4
title: Efficacy_clothianidin_treated_maize
DOI: 10.5061/dryad.pp127/5
title: BeeHeads_Feb16
DOI: 10.5061/dryad.q1j50/1
title: Supplementary Movie 1. Invadopodia formation in CTRL SUM159 cells in response to PDBu.

description: SUM159 cells expressing a CTRL shRNA were infected with mCherry-cortactin adenovirus and plated on glass-bottom coverslips 24 h after infection. Cells were imaged at 37°C in a CO2 and humidity controlled environment. At indicated times cells were stimulated to form invadopodia with PDBu. Images were captured at 15 sec intervals for the duration of the movie.
DOI: 10.5061/dryad.q1j50/2
title: Supplementary Movie 2. Invadopodia formation in Rac1 KO cells.

description: Rac1 KO SUM159 cells were infected with adenovirus encoding mCherry-cortactin as in Supp Movie 1. At indicated times cells were stimulated to form invadopodia with PDBu. Images were captured at 15 sec intervals for the duration of the movie.
DOI: 10.5061/dryad.q1j50/3
title: Supplementary Movie 3. Invadopodia formation in Rac1 KO/rescue cells.

description: Rac1 KO SUM159 cells were co-infected with adenovirus encoding mCherry-cortactin and mycRac1. At indicated times cells were stimulated to form invadopodia with PDBu. Images were captured at 15 sec intervals for the duration of the movie.
DOI: 10.5061/dryad.q1j50/4
title: Supplementary Movie 4. Invadopodia in RhoG KD SUM159 cells.

description: SUM159 cells stably expressing a RhoG targeting shRNA were infected with mCherry-cortactin adenovirus as in Supp Movie 1. At indicated times cells were stimulated to form invadopodia with PDBu. Images were captured at 15 sec intervals for the duration of the movie.