cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.qh53f/17
title: Fig4F

description: This data file is associated with Fig4F of the accompanied publication.  Flow cytometry of splenic CD4+PD-1+CXCR5+ cell populations was analyzed.  CD4+PD-1+CXCR5+ cell populations are indicative of T-follicular helper (Tfh) cells.  Any relevant information for this figure, including experimental conditions and setup are included in the methods, results, or discussion section of the accompanied publication.
DOI: 10.5061/dryad.qh53f/18
title: Fig4G

description: This data file is associated with Fig4G of the accompanied publication. Flow cytometry of B220+ B cells was analyzed.  High B cell counts following transplantation are indicative of improved immune reconstitution and reduced GVHD pathogenesis.  Any relevant information for this figure, including experimental conditions and setup are included in the methods, results, or discussion section of the accompanied publication.
DOI: 10.5061/dryad.qh53f/19
title: Fig4H

description: This data file is associated with Fig4H of the accompanied publication.  Column and row labels are self-explanatory. Any relevant information for this figure, including experimental conditions and setup are included in the methods, results, or discussion section of the accompanied publication.
DOI: 10.5061/dryad.qh53f/20
title: Fig5A

description: This data file is associated with Fig5A of the accompanied publication.  Survival of mice given 1-2 x 10^6 whole splenocytes.  Column A is the mouse identification number.  Column B is the time-point at which either a survival ("0") or non-survival ("1") event occurred.  Other column and row titles should be self-explanatory.  Mouse #482 was excluded from the results due to a non-GVHD related death confirmed by a DLAR veterinarian.   Any relevant information for this figure, including experimental conditions and setup are included in the methods, results, or discussion section of the accompanied publication.
DOI: 10.5061/dryad.qh53f/21
title: Fig5B

description: This data file is associated with Fig5B of the accompanied publication.  Clinical score of recipients given 1-2 x 10^6 whole splenocytes was monitored once per week following transplantation.  Column A indicates time-point at which the clinical score was measured.  Additional column and row titles are self-explanatory. Any relevant information for this figure, including experimental conditions and setup are included in the methods, results, or discussion section of the accompanied publication.
DOI: 10.5061/dryad.qh53f/22
title: Fig6A

description: This data file is associated with Fig6A of the accompanied publication.  Survival of mice receiving 0.5-0.75 x 10^6 purified T cells. Column A indicates mouse identification number, Column B indicates time at which a non-survival ("1") or survival ("0") even occurred.  Other columns and rows are self-explanatory.  Any relevant information for this figure, including experimental conditions and setup are included in the methods, results, or discussion section of the accompanied publication.
DOI: 10.5061/dryad.s01kf/10
title: vcf_de-novo_Andalalani

description: Directory containing the GATK output .vcf file from denovo-assembled reads of A. ndalalani. Directory contains 1 .vcf file and 1 index file.
DOI: 10.5061/dryad.s01kf/11
title: vcf_de-novo_Oamphimelas

description: Directory containing the GATK output .vcf file from denovo-assembled reads of O. amphimelas. Directory contains 1 .vcf file and 1 index file.
DOI: 10.5061/dryad.s01kf/12
title: DatasetA_n92

description: Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'.
DOI: 10.5061/dryad.s01kf/13
title: DatasetB_n25

description: Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
DOI: 10.5061/dryad.s01kf/14
title: DatasetC_n92

description: Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
DOI: 10.5061/dryad.s01kf/15
title: DatasetD_n92

description: Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
DOI: 10.5061/dryad.s01kf/7
title: vcf_de-novo_Aalcalica

description: Directory containing the GATK output .vcf file from denovo-assembled reads of A. alcalica. Directory contains 1 .vcf file and 1 index file.
DOI: 10.5061/dryad.s01kf/8
title: vcf_de-novo_Agrahami

description: Directory containing the GATK output .vcf file from denovo-assembled reads of A. grahami. Directory contains 1 .vcf file and 1 index file.
DOI: 10.5061/dryad.s01kf/9
title: vcf_de-novo_Alatilabris

description: Directory containing the GATK output .vcf file from denovo-assembled reads of A. latilabris. Directory contains 1 .vcf file and 1 index file.
DOI: 10.5061/dryad.vq2tn/1
title: KRL data

description: Time to hemolysis for 50% of red blood cells in the KRL assay.  File is tab-delimited text file with 11 variables (columns). The first row is the headers for each column and there are 39 subsequent rows of data.Variables names are:Band No
Breed Experience (Experienced = known prior breeding experience; inexperienced = no known prior breeding experience on the main study area; blanks indicate unknown because the bird was captured off the main study area)
Time to 50% hemolysis (the response variable)
Jdate for KRL (date blood was sampled for KRL assay; 1=1 May)
Tarsus (tarsus length of bird, mm)
Mass (total body mass of bird, g)
Mask (facial mask size of bird, mm^2)
bib size (size of yellow throat patch, mm^2)
Yellow brightness (see Methods)
Ccar (see Methods)
N replicates (number of different assays performed; see Methods)
DOI: 10.5061/dryad.vq2tn/2
title: OxidativeStress & GSH data

description: Tab delimited file with 14 columns (variables) and 52 rows (top row contains the variable names). Variables are: Band Number (band number of individual bird [4 digit prefix and 5 digit suffix, after the decimal point])Capture Date(1=1May)Breed Experience (see KRL file for description)Exper Group  (see KRL file for description)Mask  (see KRL file for description)bib size (see KRL file for description)Yellow Brightness  (see KRL file for description)Ccar  (see KRL file for description)Tarsus (mm)Weight pre (g, prior to bird being put in an aviary, if part of the LPS experiment)GSH pre (see Methods for GSH; "pre" refers to estimate prior to LPS experiment)ROMs/TAC_pre  (see Methods; "pre" refers to estimate prior to LPS experiment)GSH post-pre  (see Methods; "pre" refers to estimate prior to LPS experiment)ROMs/TAC post-pre  (see Methods; "pre" refers to estimate prior to LPS experiment)
DOI: 10.5061/dryad.39jv1/3
title: TatooshTrophic

description: Text file containing a matrix indicating absence (0), prey (1) or consumer (-1) trophic effects of one species (across columns of the matrix) on another species (down rows of the matrix) from the middle intertidal (mussel-dominated) zone of Tatoosh Island, Washington, USA. Species names and order corresponding to matrix columns/rows are found in file TatooshSpeciesNames.txt and Tatoosh-Taxonomy.csv
DOI: 10.5061/dryad.39jv1/4
title: Tatoosh Interaction Web

description: Interaction web (trophic and non-trophic) for the middle intertidal, mussel dominated community of Tatoosh Island, Washington, provided as a matrix of positive (1), negative (-1) or no (0) interaction.  Taxon identity and order are contained in Tatoosh-Taxonomy.csv
DOI: 10.5061/dryad.bq872/2
title: Mec-15-0566 Archiving Data

description: This is a compressed file folder which includes five files. Of which three files contain sequences of 16 mtDNA haplotypes in Fasta format,and 33 nrDNA ribotypes in both Fasta and Mega format. The fourth file (table 1) contains the information of geographic locality, coordinates and collector for each sampling population. The fifth file (Table 2) indicates the geographic distribution of each mtDNA haplotype and nrDNA ribotypes in every sampling locality.
DOI: 10.5061/dryad.bq872/3
title: Mec-15-0566 Archiving Tree files

description: This compressed package contains mtDNA Cox1 and nrDNA ITS1+2 sequences with Fasta format, using for underlying phylogenetic construction.
DOI: 10.5061/dryad.bq872/4
title: Mec-15-0566 Arching Data for each sample's mtDNA Cox1 and nuclear ITS1+2

description: This is a compressed file which contains 452 aligned mitochondrial Cox1 sequences and 370 aligned nuclear ITS1+2 sequences for the red alga Chondrus ocellatus. For each sequence, we provide the identification information with sampling code (e.g. KJ) + specimen number + the name of marker.
DOI: 10.5061/dryad.c6688/1
title: OTUS pyrosequencing

description: Excel table with the AOA OTUs abundance obtained from pyrosequencing. Sheet 1: forward sequenced, Sheet 2: reverse sequenced. Label indicates the name of the sample. Region and depth are also indicated
DOI: 10.5061/dryad.c6688/2
title: GPS coordinates

description: Excel table with the Cruise number, Station number during the cruise, cast, code for the station, sampling date, GPS coordinates, and final station number through the transect
DOI: 10.5061/dryad.c6688/3
title: T-RFLP data
DOI: 10.5061/dryad.dh3st/4
title: Tree

description: The file contains the tree used to calculate the phylogenetic diversity.
DOI: 10.5061/dryad.fh592/1
title: Data from Uribe-Convers et al - A targeted subgenomic approach for phylogenomics based on microfluidic PCR and high throughput sequencing
DOI: 10.5061/dryad.fm4mk/1
title: Dataset_S1_Killer_Whale_SNP_genotypes

description: O. orca SNP genotypes for 91 SNPs, 128 samples. Alleles have been re-coded for programs that only accept numerical alleles. G = 1, A =2 , C = 3, T = 4.  Missing data are represented by 0.
DOI: 10.5061/dryad.fm4mk/2
title: Dataset_S2_Beast_in_158mtGen_partitioned

description: Input xml file for phylogenetic analysis in the program BEAST 1.8, containing partitioned mitochondrial sequence data and phylogenetic analysis parameters as described in the methods.
DOI: 10.5061/dryad.fm4mk/3
title: Dataset_S3_Beast_out_158mtGen_partitioned_consant

description: Tree file output from BEAST v1.8 phylogenetic analysis of the data from Dataset S2.
DOI: 10.5061/dryad.fm4mk/4
title: Dataset_S4_SNAPPinput_AS7_42SNP_113indiv

description: Input xml file for analysis of SNP data in the program SNAPP, within the BEAST v2.0 package.
DOI: 10.5061/dryad.fm4mk/5
title: Dataset_S5_SNAPPoutput_AS7_42SNP_113indiv

description: Output phylogenetic tree file from the program SNAPP, based on data and parameters in the input file Dataset_S4.
DOI: 10.5061/dryad.fm4mk/6
title: Dataset_S6_Delphinidae

description: XML file of aligned Delphinidae mitochondrial genome sequences with partitions and parameters used for time-calibrated phylogenetic analysis in BEAST.
DOI: 10.5061/dryad.fm4mk/7
title: Dataset_S7_Delphinidae

description: Maximum clade credibility tree file of Delphinidae mitochondrial phylogeny from BEAST analysis of Dataset_S6.
DOI: 10.5061/dryad.g3jc1/3
title: A_glutinosa_haplotypes_alignment
DOI: 10.5061/dryad.g3jc1/4
title: A_glutinosa_haplotypes_TreeMB
DOI: 10.5061/dryad.g3jc1/5
title: A_glutinosa_haplotypes_TreeMP
DOI: 10.5061/dryad.g3jc1/6
title: microsatellite_genotypes
DOI: 10.5061/dryad.hm5k9/14
title: Bighorn #10 postfire BBMM
DOI: 10.5061/dryad.hm5k9/15
title: Bighorn #12 prefire BBMM
DOI: 10.5061/dryad.hm5k9/16
title: Bighorn #12 postfire BBMM
DOI: 10.5061/dryad.hm5k9/17
title: Bighorn #14 prefire BBMM
DOI: 10.5061/dryad.hm5k9/18
title: Bighorn #14 postfire BBMM
DOI: 10.5061/dryad.hm5k9/19
title: Bighorn #18 prefire BBMM
DOI: 10.5061/dryad.hm5k9/20
title: Bighorn #18 postfire BBMM
DOI: 10.5061/dryad.hm5k9/21
title: Bighorn #19 prefire BBMM
DOI: 10.5061/dryad.hm5k9/22
title: Bighorn #19 postfire BBMM
DOI: 10.5061/dryad.p1529/1
title: Assessment of disability among the elderly in Xiamen of China a representative sample survey sample of 14,292 older adults
DOI: 10.5061/dryad.qh53f/23
title: Fig6B

description: This data file is associated with Fig6B of the accompanied publication.  Column A indicates time-point at which the clinical score was measured. Additional column and row titles are self-explanatory.  Any relevant information for this figure, including experimental conditions and setup are included in the methods, results, or discussion section of the accompanied publication.
DOI: 10.5061/dryad.qh53f/24
title: Supplementary Information

description: This data file is associated with all supplementary figures and information of the accompanied publication.  This archive includes data files for S1_Fig, S2_Fig, S3_Fig, S4_Fig, S5_Fig.  Individual data files of graphs or data within each supplementary figure (e.g., A in S1_Fig) are also included.  Any relevant information for these figures, including experimental conditions and setup are included in the methods, results, or discussion section of the accompanied publication.
DOI: 10.5061/dryad.rd71s/1
title: Infection_success_data

description: Spreadsheet "Infection_success" summarizes the results of our attempts to introduce Hamiltonella strains from multiple donors into two recipient genotypes of Sitobion avenae.Rows represent different host genotype - symbiont strain combinations. Columns are as follows:***Recipient_genotype - aphid clonal genotype into which a symbiont was introduced;***Donor_genotype - aphid clonal genotype whose symbiont-containing haemolymph was injected into the recipient;***Donor_species - donor species, abbreviated as Siave (Sitobion avenae), Sifra (S. fragariae), Acpis (Acyrthosiphon pisum), Utsp1 (Utamphorophora sp.), Apfab (Aphis fabae);***Intraspecific - denotes whether a particular symbiont transfer was made between clones of a single host species (S. avenae), or between different species***Injected - the numbers of recipient aphids injected with haemolymph from the donor clone***Surviving - the number of injected aphids which produced offspring after the 14th day from injection***Infected - the number of injected aphids that after the 14th day from injection produced at least one infected offspring***Stable - denotes whether after symbiont establishment in the first generation we observed cases of symbiont loss in subsequent generations***COI_dist - p-distance (the proportion of nucleotide sites at which two sequences differ) between the recipient genotype and the donor genotype, calculated using a 641bp alignment of COI gene***Hami_dist - p-distance between the symbiont strain infecting the donor genotype and the strain that had originally infected the recipient genotype (but was removed with antibiotics prior to the experiment) calculated using concatenation of six household genes, accD, gyrB, hrpA, murE, recJ and rpoS, of the total length of 3905bp.
DOI: 10.5061/dryad.rd71s/2
title: Fecundity_data

description: Spreadsheet "Fecundity" contains the results of the fecundity assay. We counted the number of offspring produced by isolated winged aphids, representing one of two Sitobion avenae genotypes and either facultative endosymbiont-free or hosting one of Hamiltonella or Regiella strains, during consecutive three-day intervals. In the spreadsheet, rows represent individual experimental aphids. Columns are as follows: ***Host_genotype - either Co23 or Co26; ***Symbiont_presence - 0 (no symbiont), Hami (Hamiltonella) or Reg (Regiella); ***Symbiont_genotype; ***Fecundity_16_days-from_birth - number of offspring produced by a given female within 16 days from birth.
DOI: 10.5061/dryad.rd71s/3
title: Parasitoid_susceptibility_data

description: Spreadsheet "Parasitoid_susceptibility" contains the results of the parasitoid susceptibility assay. We exposed groups of 30 aphids, representing one of two Sitobion avenae genotypes and either facultative endosymbiont-free or hosting one of Hamiltonella or Regiella strains, to females of the parasitoid wasp Aphidius ervi. After fifteen days, all aphids were checked for survival, and whether the parasitoid pupated within those aphids that died. In the spreadsheet, each row represents a replicate of approx. 30 aphids. Columns are as follows: ***Host_genotype - either Co23 or Co26; ***Symbiont_presence - 0 (no symbiont), Hami (Hamiltonella) or Reg (Regiella); ***Symbiont_genotype; ***Block - numbers denote unique experimental blocks; ***Alive - the number of aphids in a replicate that were alive at the time of the final census; ***Mummified - the number of exposed aphids which died, and within which the parasitoid pupated; ***Dead_not_mummified - the number of aphids which died over the course of the experiment, and within which the pathogen did not pupate; ***Total - the total number of aphids scored
DOI: 10.5061/dryad.rd71s/4
title: Pathogen_susceptibility_data

description: Spreadsheet "Pathogen_susceptibility" contains the results of the pathogen susceptibility assay. We exposed groups of  approx. 20 aphids, representing one of two Sitobion avenae genotypes and either facultative endosymbiont-free or hosting one of Hamiltonella or Regiella strains, to spores of the pathogenic fungus Pandora neoaphidis. After eight days all aphids were checked for survival, and whether the the pathogen did sporulate within those aphids that died. In the spreadsheet, each row represents a replicate of approx. 20 aphids. Columns are as follows: ***Host_genotype - either Co23 or Co26; ***Symbiont_presence - 0 (no symbiont), Hami (Hamiltonella) or Reg (Regiella); ***Symbiont_genotype; ***Treatment - aphids in most replicates were exposed to pathogen spores (treatment "Pathogen_exposure"), but we also provide data for a small number of control replicates (treatment "Control_no_pathogen"), not exposed to spores and still suffering high mortality under the experimental conditions; ***Block - dates denote unique experimental blocks; ***Alive - the number of aphids in a replicate that were alive eight days after exposure; ***Fungus_sporulated - the number of exposed aphids which died, and within which the pathogen sporulated ***Dead_not_fungus - the number of aphids which died during the course of the experiment, but which did not sporulate; ***Total - the total number of aphids scored
DOI: 10.5061/dryad.s01kf/16
title: DatasetE_n92

description: Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
DOI: 10.5061/dryad.s01kf/17
title: DatasetF_n48

description: Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
DOI: 10.5061/dryad.s01kf/18
title: DatasetG_n91

description: Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
DOI: 10.5061/dryad.s01kf/19
title: DatasetH_n91

description: Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
DOI: 10.5061/dryad.s01kf/20
title: DatasetJ_n91

description: Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
DOI: 10.5061/dryad.s01kf/21
title: DatasetK_n91

description: Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
DOI: 10.5061/dryad.s01kf/22
title: DatasetL_n91

description: Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
DOI: 10.5061/dryad.s01kf/23
title: DatasetM_n84

description: Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
DOI: 10.5061/dryad.s01kf/24
title: DatasetN_n84

description: Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
DOI: 10.5061/dryad.t3v71.2
title: Data from: Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding
DOI: 10.5061/dryad.t3v71.2/1.2
title: Example_R_script

description: Example R script for running the analyses used in the paper.
DOI: 10.5061/dryad.t3v71.2/2.2
title: arthropods.env.txt

description: Input file (environmental information) for use with the example R script
DOI: 10.5061/dryad.t3v71.2/3.2
title: MBCarthropods.txt

description: Example input file for the R script, containing species X site data.
DOI: 10.5061/dryad.t3v71.2/4.2
title: RSW2_Test.R

description: R script for a Monte Carlo test to compare whether metabarcode and standard data select similar sets of sites for conservation, given a budget.
DOI: 10.5061/dryad.t3v71.2/5.2
title: RSW2SoftwareResults.txt

description: Input dataset for RSW2_Test.R (output from the RSW2 software package)
DOI: 10.5061/dryad.t3v71.2/6.2
title: Ailaoshan dataset:  all fna and qual files

description: see Readme file: dryad metadata.txt
DOI: 10.5061/dryad.1257p/1
title: Horowitz and Patton 2015 Intent Despite Intermittent Disturbance

description: Data for each of eight human subjects is in a MATLAB structure array by trial. Fieldnames are descriptive. Experiment consists of targeted reaching with intermittent disturbance by large pulses of force or Gaussian noise.
DOI: 10.5061/dryad.2m85h/1
title: Simulation data

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. 5. 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/microcircuit_param_scan: data on scaling of microcircuit model of Potjans & Diesmann (Cereb Cortex, 2014) with and without regard for covariances, for Figs. 3 and 4.
DOI: 10.5061/dryad.2m85h/2
title: Python scripts for analysis and plotting

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: NEST simulation scripts for random recurrent networks. parameters_binary_asymm.py, parameters_binary_symm.py, parameters_ginzburg.py, parameters_inhibitory_LIF_network.py: corresponding parameter files. hambach_run_g_gamma_K_scaling.py, hambach_run_inhibitory_LIF_network.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. ginzburg_theory.py, ginzburg_theory_distKin.py, hawkesnet.py, siegert.py: contain functions for computing covariances and related quantities. microcircuit_analysis.py: functions for loading and analyzing data from simulations of the Potjans and Diesmann (Cereb Cortex, 2014) microcircuit model. microcircuit: folder containing NEST simulation scripts for the Potjans and Diesmann microcircuit model.
DOI: 10.5061/dryad.2m85h/3
title: Accessory figure files

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.