cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2m85h/4
title: Simulation data - submission 2

description: binary/asymm/dist_Kin_scale: data on E-I network of Ginzburg neurons for Fig. 1C. binary/asymm/mcculloch_pitts: data on binary E-I network with population-specific connection probability for Fig. 3. binary/symm: data on binary E-I network with population-independent connection probability, scaled to preserve zero-lag covariances, for Fig. 6.spiking/E_I_LIF_network: data on scaling of network of leaky integrate-and-fire neurons with population-independent connection probability, preserving correlations, for Fig. 7. spiking/inhibitory_LIF_network: data on single-population network of inhibitory leaky integrate-and-fire neurons, for Fig. 2.spiking/LIF_network_rate_comparison: data on E-I network of leaky integrate-and-fire neurons with different firing rates, for Fig. 5.spiking/microcircuit: data on scaling of microcircuit model of Potjans & Diesmann (Cereb Cortex, 2014), for Fig. 4.
DOI: 10.5061/dryad.2m85h/5
title: Python scripts for analysis and plotting - submission 2

description: fig1.py, fig2.py, fig3.py, fig4.py, fig5.py, fig6.py, fig7.py: reproduce the figures of the paper using the data and additional figure files in this repository. binary_network_asymm.py, binary_network_symm.py, g_gamma_K_scaling.py, ginzburg_network_dist_Kin_scale.py, inhibitory_LIF_network.py, LIF_network_rate_comparison.py: NEST simulation scripts for random recurrent networks. parameters_binary_asymm.py, parameters_binary_symm.py, parameters_g_gamma_K_scaling.py, parameters_ginzburg.py, parameters_inhibitory_LIF_network.py, parameters_LIF_network_rate_comparison.py: corresponding parameter files.hambach_run_g_gamma_K_scaling.py, hambach_run_inhibitory_LIF_network.py, hambach_run_LIF_network_rate_comparison.py, hambach_run_sim_dist_Kin_scale.py: scripts for running the corresponding simulations on a cluster.h5py_wrapper.py: for storing and loading h5 files.plotfuncs.py, plot_utils.py, ps_manip.py: general plotting scripts.corr_hawkes_like.py, ginzburg_theory.py, ginzburg_theory_distKin.py, hawkesnet.py, siegert.py: contain functions for computing covariances and related quantities. microcircuit: folder containing NEST simulation scripts for the Potjans and Diesmann microcircuit model.
DOI: 10.5061/dryad.2m85h/6
title: Accessory figure files - submission 2

description: fig_scaling_framework.json: configuration file for Fig. 1.relevant_scales.eps, why_scaling.eps, scaling_as_subsampling.eps: diagrams included in Fig. 1.redistributing_synapes.eps: diagram included in Fig. 6.spiking_network_scaling_diagram.eps: diagram included in Fig. 7.
DOI: 10.5061/dryad.4g40g/1
title: Test for specificity of antimicrobial activity in eggs of Tenebrio molitor

description: For the two data files provided, data were collected from 2 experiments which tested specificity of antimicrobial activity in eggs of Tenebrio molitor females after being immune challenged with inactivated bacteria (PPATHOGENS-D-15-00414_bacteria.csv) or fungi (PPATHOGENS-D-15-00414_fungi.csv). Females were immune challenged (female.treatment) with different inactivated microorganisms (Ag: Arthrobacter globiformis; Bt: Bacillus thuringiensis; Ec: Escherichia coli; Se: Serratia entomophila;Ca: Candida albicans; Ma: Metarizhium anisopliae) and antimicrobial activity of their eggs (egg.assay) were assayed on the same microbes used for the maternal challenge and other bacteria (Bs: Bacillus subtillis; Sm: Serratia marcescens). Presence of antimicrobial activity using a zone of inhibition assay was recorded as presence/absence (binary) and as the diameter of the zone inhibition they produced in millimeter (size.ZI).
DOI: 10.5061/dryad.60p5d/1
title: Bioclimatic data C. diffusa experimental populations

description: Geographic and climatic information for 14 sampled populations of native and invasive Centaurea diffusa (diffuse knapweed). Also, first three principal components from an analysis of this data.
DOI: 10.5061/dryad.60p5d/2
title: Planting information C. diffusa experimental plants

description: Planting information for experimental Centaurea diffusa plants
DOI: 10.5061/dryad.60p5d/3
title: Occurrence records C. diffusa

description: Records of Centaurea diffusa in Europe and North America, from GBIF.org, downloaded January 9, 2015
DOI: 10.5061/dryad.60p5d/4
title: Location information for collected C. diffusa populations

description: Location and collection information for populations of native and invasive Centaurea diffusa (diffuse knapweed) used in the experimental PCA and occurrence PCA.
DOI: 10.5061/dryad.60p5d/5
title: Adjusted location information for collected C. diffusa populations

description: Adjusted location and collection information for populations of native and invasive Centaurea diffusa (diffuse knapweed) used in the experimental PCA and occurrence PCA.
DOI: 10.5061/dryad.60p5d/6
title: Bioclimatic data for C. diffusa occurrences

description: Bioclimatic data and PCA values for occurrence records of Centaurea diffusaGeographic and climatic information for 662 occurrence records of native and invasive Centaurea diffusa (diffuse knapweed) from North America and Europe. Occurrence records include records from GBIF.org as well as collected populations.
DOI: 10.5061/dryad.60p5d/7
title: Trait data at harvest, from C. diffusa common garden

description: Trait data for experimental populations of Centaurea diffusa, measured at harvest.Trait values measured in common field experiment in Montpellier, France, 2011. File also include the first three principal components from the experimental PCA of the bioclimatic data for these populations.
DOI: 10.5061/dryad.60p5d/8
title: Phenological trait data, from C. diffusa common garden

description: Phenological trait data for experimental populations of Centaurea diffusa, measured throughout experimentTrait values measured in common field experiment in Montpellier, France, 2011. File also include the first three principal components from the experimental PCA of the bioclimatic data for these populations.
DOI: 10.5061/dryad.63n3f/1
title: European Starling Provisioning Data

description: Nest visit rates, individual identifying bands,environmental data and reproductive success in European starlings.  See ReadMe file for further description.
DOI: 10.5061/dryad.87jb3/1
title: Data: determinants of laying date at the population level

description: Data used for the analysis of the determinants of laying date at the population level, where each line represented a farm within a year. Columns included year (YEAR), farm identity (FARM), mean laying date (MEAN.LD), (DENSITY; % of occupied nest boxes), distance to St-Laurent River (FSL; kilometers); longitude and latitude (LONG, LAT; decimal degrees), altitude (ALT; meters),  rainfall (PREC; milimeters) and temperature (TEMP; Celcius degrees).
DOI: 10.5061/dryad.87jb3/2
title: Data: change between 2 consecutive years

description: Data used for the first individual plasticity  analysis (change between 2 consecutive years), where each line represented a female. Columns included female identity (ID), for the second-year (SY) dataset the change in laying date (SY.dLD), in density (SY.dDENSITY) and in temperature (SY.dTEMP),  for the after second-year (ASY) dataset the change in laying date (ASY.dLD), in density (ASY.dDENSITY) and in temperature (ASY.dTEMP), for the total (TOTAL) dataset the change in laying date (TOTAL.dLD), in density (TOTAL.dDENSITY) and in temperature (TOTAL.dTEMP).
DOI: 10.5061/dryad.976qm/1
title: Data Exp I - III

description: All data in Matlab format. A data description file is included in the zipped archive.
DOI: 10.5061/dryad.g3jc1/7
title: Structure_input_file
DOI: 10.5061/dryad.hm5k9/23
title: Bighorn #22 prefire BBMM
DOI: 10.5061/dryad.hm5k9/24
title: Bighorn #22 postfire BBMM
DOI: 10.5061/dryad.hm5k9/25
title: Bighorn #25 prefire BBMM
DOI: 10.5061/dryad.hm5k9/26
title: Bighorn #25 postfire BBMM
DOI: 10.5061/dryad.hm5k9/27
title: Bighorn #26 prefire BBMM
DOI: 10.5061/dryad.hm5k9/28
title: Bighorn #26 postfire BBMM
DOI: 10.5061/dryad.hm5k9/29
title: Bighorn #27 prefire BBMM
DOI: 10.5061/dryad.hm5k9/30
title: Bighorn #27 postfire BBMM
DOI: 10.5061/dryad.hs2g9/1
title: Genomic reads of 6 Hawaiian Drosophila species mapped to the D. grimshawi genome

description: File is in standard BAM format. Species names are identified by read groups IDs.
DOI: 10.5061/dryad.hs2g9/2
title: RAD-tag reads mapped to reference ant genomes

description: The archive contains 6 BAM files with genomic reads from three species of ants mapped to their respective reference genomes.
DOI: 10.5061/dryad.n64kk/1
title: Data_salt_tolerance_angiosperms_Moray_et_al_BMC_Evo_Bio

description: Please see ReadMe file.
DOI: 10.5061/dryad.pc537/1
title: Dataset of QQ group social network

description: Participation in social groups are important but the collective behaviors of human as a group are difficult to analyze due to the difficulties to quantify ordinary social relation, group membership, and to collect a comprehensive dataset. Such difficulties can be circumvented by analyzing online social networks.In this paper, we analyze a comprehensive dataset obtained from Tencent QQ, an instant messenger with the highest market share in China. Specifically, we analyze three derivative networks involving groups and their members { the hypergraph of groups, the network of groups and the user network { to reveal social interactions at microscopic and mesoscopic level. Our results uncover interesting behaviors on the growth of user groups, the interactions between groups, and their relationship with member age and gender. These  findings lead to insights which are difficult to obtain in social networks based on personal contacts.
DOI: 10.5061/dryad.r2b26/1
title: Kruuk BiolLetters Gambusia

description: Please see ReadMe file.
DOI: 10.5061/dryad.s01kf/25
title: DatasetP_n38

description: Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
DOI: 10.5061/dryad.s01kf/26
title: DatasetQ_n38

description: Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
DOI: 10.5061/dryad.s01kf/27
title: DatasetR_n84

description: Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
DOI: 10.5061/dryad.s01kf/28
title: DatasetS_n16

description: Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
DOI: 10.5061/dryad.s01kf/29
title: DatasetT_n16

description: Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
DOI: 10.5061/dryad.s01kf/30
title: DatasetU_n16

description: Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
DOI: 10.5061/dryad.t3v71.1
title: Data from: Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding
DOI: 10.5061/dryad.t3v71.2/7.2
title: Danum Valley dataset:  all fna and qual files

description: see Readme file: dryad metadata.txt
DOI: 10.5061/dryad.t3v71.2/8.2
title: Thetford dataset:  all fna and qual files

description: see Readme file: dryad metadata.txt
DOI: 10.5061/dryad.t3v71.2/9.2
title: arthropods.txt

description: Example input file for the R script, containing species X site data.
DOI: 10.5061/dryad.038q8/1
title: raw plot data from globally distributed sites
DOI: 10.5061/dryad.15237/1
title: TableS1

description: Table S1. Standardized volumes of the 563 spots common to all experiments for all treatments. Highlighted in green, spots which proteins have been identified (see Tables 2,3). RT: room temperature treatment (control). Biological replicas: r1, 2, 3.
DOI: 10.5061/dryad.15237/3
title: 6569_documents_from_Agabus_454

description: Fasta file with the contigs of the whole transcriptome of combined specimens of Agabus ramblae (Coleoptera, Dytiscidae) after being subjected for 12h to three temperature treatments: 4ºC, control (room temperature) and 27ºC.
DOI: 10.5061/dryad.35nn0/1
title: Sequential aphid population census data

description: Tab-delimited file containing aphid census data on 20 plant genotypes. Each replicate plant is identified by a unique numeric code ('ID') to indicate repeated measures. 'Chamber' refers to one of two growth chambers. 'Census' refers to the five sequential censuses, while 'Growth.days' is the number of days since aphid introduction. Aphid numbers are given as 'Juvenile', 'Apterous' (unwinged adult), 'Alate' (winged adult), and the summed total.
DOI: 10.5061/dryad.35nn0/2
title: Sequential plant size data

description: Tab-delimited file containing repeated plant size measurements of 20 plant genotypes. Each replicate plant is identified by a unique numeric code ('ID') to indicate repeated measures. 'Chamber' refers to one of two growth chambers. 'Census' refers to the five sequential censuses, while 'Age' is the number of days since planting. 'Age.aph.int' is the plant age at time of aphid introduction (variation is due to some differences in day of planting). Plant size is given by the number of leaves, the number of stem nodes, and the plant height [cm].
DOI: 10.5061/dryad.35nn0/3
title: Chemistry data

description: Tab-delimited file containing chemistry data of plant (Sample.type = Pl), aphid (Sample.type = Aph), and honeydew (Sample.type = Hd) samples. 'Chamber' refers to one of two growth chambers. For a subset of plant samples, the foliar C:N ratio is given in column 'C.N'. All columns headed with cX.X are individual cardenolide compounds [ng/mg sample], with X.X referring to their HPLC retention time.
DOI: 10.5061/dryad.35nn0/4
title: Honeydew exudation data

description: Tab-delimited file containing honeydew weights on all 20 plant genotypes and number of aphids present during time of collection. 'Aphid.start' and 'Aphid.end' are actual numbers of aphids present at the beginning and end of honeydew collection, while 'Exposure.time' indicates the duration of collection in days. Columns headed 'day1' through 'day5' are predicted aphid numbers based on linearly integrating start and end censuses, and 'Cumulative.aphids' is the sum of predicted aphids present throughout honeydew collection.
DOI: 10.5061/dryad.35nn0/5
title: Genotype trait means

description: Tab-delimited file containing trait means for all 20 plant genotypes and aphid growth on these plants (RGR.an = A. nerii, RGR.mp = M.persicae, RGR.ma = M. asclepiadis). Plant traits include C:N ratio (C.N), absolute growth rate at time of aphid introduction (Plant.AGR) and total (Card.tot) cardenolide concentration [ng/mg]. In addition, the average sum of the four most polar (Card.pol) or six most apolar (Card.apo) cardenolides is given.
DOI: 10.5061/dryad.35rt2/1
title: Nest architecture measures and recruitment speed

description: Each nest site (column B) has network and volume measures (columns D-H). Column C contains the average recruitment speed of the colony whose ID is in column A while it occupied the nest site in column B.
DOI: 10.5061/dryad.364mb/1
title: Appendix 4: Dynamic factor analysis code

description: R script containing code to run dynamic factor analysis. See the ReadMe file for full description.
DOI: 10.5061/dryad.364mb/2
title: Appendix 5: Bayesian linear model code

description: R script containing code to run Bayesian linear model. See the ReadMe file for full description.
DOI: 10.5061/dryad.60p5d/9
title: Repeated measures of traits, from C. diffusa common garden

description: Trait data for experimental populations of Centaurea diffusa, repeated measures.Trait values measured in common field experiment in Montpellier, France, 2011. File also include the first three principal components from the experimental PCA of the bioclimatic data for these populations.
DOI: 10.5061/dryad.63r07/1
title: Dataset of individual values of self-evaluation of quality of life, resilience, WHPQOL-BREF and DREEM

description: Individual values of a random sample of 1,350 medical students from 22 medical schools in Brazil. Values are from self-evaluation of quality of life in general and quality of life in medical school, all domains of quality of life questionnaire (WHOQOL-BREF) and all domains of questionnaire of educational environment perception (DREEM).
DOI: 10.5061/dryad.72kd2/1
title: Haplotype List

description: Haplotypes of 841 P. vivax isolates typed with 11 microsatellite markers
DOI: 10.5061/dryad.87jb3/3
title: Data: random regression analysis with the within-individual centring technique

description: Data used for the second plasticity analysis (random regression analysis with the within-individual centring technique), where each line represented an individual observation within a year for all females observed at least in two years. Columns included year (YEAR), female identity (ID)  and its age (AGE; SY=second-year, ASY=after second-year), farm identity (FARM), laying date (LD; julian days), temperature (TEMPs; std), density (DENSITYs; std) and latitude (LATs; std), between-individual component of temperature (M.TEMP; within individual mean of TEMPs) and density (M.DENSITY; within individual mean of DENSITYs), within-individual component of temperature (TEMP.PLAST; deviation from the individual mean) and density (DENSITY.TEMP; deviation from the individual mean).
DOI: 10.5061/dryad.8k823/1
title: Data from: Fixational eye movements predict visual sensitivity

description: Data for 7 subjects and a file describing the data [MATLAB necessary for .mat and .m files]
DOI: 10.5061/dryad.8sn65/1
title: COI alignment

description: Alignment of 579 COI sequences used for the analyses.
DOI: 10.5061/dryad.8sn65/2
title: Figure F1

description: Neighbor-Joining tree based on K2P distances of 579 COI sequences from North Sea molluscs.
DOI: 10.5061/dryad.9j7j0/1
title: Input files for the different analyses

description: The compressed folder includes the input files used for the following analyses: a) gene trees, b) species tree, c) Structure, d) Isolation with migration model analyses, e) the phased sequence data for all loci and f) a spreadsheet to make the link between the acronyms used in the analyses input files and the Tissue number/localities/subspecies
DOI: 10.5061/dryad.bb5hr/1
title: Grb10 sequence data

description: This file contains Grb10 exomic sequences from tumors described in the manuscript.
DOI: 10.5061/dryad.d8f84/1
title: ASD-lncRNA

description: Expression profile of lncRNAs in ASD peripheral bloods
DOI: 10.5061/dryad.h5s2q/1
title: satfind

description: Satfind has been designed to find satellites that contain patterns (the seed) of length L (&lt;15)  that appear at least n times in a DNA subsequence of length  N. Once a satellite is found the search is continued until no more seeds are found in N bases, then the search may continue beyond the original length N. Each seed defines a possible repeat that ends at the start of the next seed. The satellite is accepted if we are able to select a percentage p of  possible repeats (selected repeats) with the same length and, in this case,  these selected repeats become the repeats of the satellite. The first one is chosen  as the representative repeat of the satellite.
DOI: 10.5061/dryad.h5s2q/2
title: malig: DNA multialignment software

description: Malig has been implemented in C. Just untar malig.tar  and run the make file utility. Malig has been designed to global align DNA sequences with similar length using the progressive multialignment method whose pairwise alignment uses the dynamic programming algorithm designed by Needlema and Wunsch, both with the affine gap penalty function.As a progressive multialignment method malig first computes the similarity score between all pairs of sequences. This computation is made under the following criteria:	Normalized score: the idea is that a multialignment of identical sequences has to be scored one. 	Reverse sequences: the input file is increased by adding the reverse sequences.	Cycle permutations:  to compute the score between two sequences, we choose the cycle permutation of the second one with the greatest score, and this cycle is applied when the multialignment is built.Then the progressive multialignment is started. Recall that in a classic multialignment algorithm this process finishes when all sequences are aligned. In our case the process finish when the score is smaller than a similarity threshold (input parameter).
DOI: 10.5061/dryad.hm5k9/31
title: Bighorn #33 prefire BBMM
DOI: 10.5061/dryad.hm5k9/32
title: Bighorn #33 postfire BBMM
DOI: 10.5061/dryad.hm5k9/33
title: Bighorn #34 prefire BBMM
DOI: 10.5061/dryad.hm5k9/34
title: Bighorn #34 postfire BBMM
DOI: 10.5061/dryad.j4103/1
title: Matrix AFLPs Canarina canariensis

description: Original Matrix of Canarina canariensis AFLPs
DOI: 10.5061/dryad.j4103/2
title: cpDNA_Canarina_canariensis

description: NEXUS files for the concatenated cpDNA dataset of Canarina canariensis
DOI: 10.5061/dryad.p2c0b/1
title: Microsatellite and Phenological Data for Lobelia inflata

description: This dataset contains five spreadsheets. The first shows the growth conditions, initial size and phenological characters for the 811 S1 offspring of the field-sourced P1 generation of experimental plants. This data was analyzed using the GLM and GLMM models shown in the paper. The second shows the pairwise comparisons between the eleven genetic lineages for each locus. When two lineages share the same allele at a given locus, this is listed as “1”, and if they differ, this is listed as “0”. The total (overall) pairwise similarity between lineages is shown at the bottom of the spreadsheet. The third shows summary data reporting the pairwise similarity data for all lineages. The fourth reports the environmental data used to plot Figures S1-S3. The fifth shows the genotypic data for each of the original P1 individuals as analyzed by GENEPOP 4.2.
DOI: 10.5061/dryad.r78vn/1
title: DMRT3 genotypes and performance data for Finnhorses

description: DMRT3 genotypes and phenotype information for Finnhorses. The riding performance data was collected via questionnaires and the harness racing performance data was provided by The Finnish trotting and breeding association (Hippos). The harness racing performance data shows the total number of starts and placings for each horse.
DOI: 10.5061/dryad.rg70p/1
title: Alignment_complete_rbcL_Eunotia

description: Alignment of complete rbcL sequences of the Eunotia bilunaris/flexuosa complex used for phylogeny reconstruction (Fig. S1).
DOI: 10.5061/dryad.s9n91/1
title: Coordinates of sample locations and genotype data for two species : Lycopus europeus and Oenanthe aquatica

description: Coordinates (decimal degrees) and nuclear genetic data (microsatellite loci genotypes) for Oenanthe aquatica and Lycopus europeus species.
DOI: 10.5061/dryad.sp418/1
title: THE ORNATE SPINY LOBSTER P. ORNATUS IN THE SOUTH-EAST ASIAN ARCHIPELAGO
DOI: 10.5061/dryad.sp418/2
title: Table S1

description: Spatial distribution of control region haplotypes among Panulirus ornatus from six localities in the South-East Asian archipelago.
DOI: 10.5061/dryad.sp418/3
title: Table S2

description: Null allele frequencies in original dataset and after correction calculated by using FreeNA 3.0.  Values above 10% are in bold.
DOI: 10.5061/dryad.sp418/4
title: Table S3

description: Summary table of analysis of molecular variance (AMOVA) describing the partitioning of genetic variation for six Panulirus ornatus populations in original dataset and after correction based on 10 microsatellite loci.
DOI: 10.5061/dryad.sp418/5
title: Table S4

description: Genetic differentiation between Panulirus ornatus from collection locations using pairwise FST  for microsatellite loci in original dataset (lower value) and after correction (upper value). No significant value was found after correction using FDR.
DOI: 10.5061/dryad.sp418/6
title: Table S5

description: Migration rate (and standard errors) in each population that are migrants derived from other populations per generation.
DOI: 10.5061/dryad.038q8/2
title: R script for Table_1_analyses_FigS1
DOI: 10.5061/dryad.038q8/3
title: R script for within_site_GLMs_Fig2A_TableS2