cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.s43c7/4
title: Table S4. List of genes differentially regulated by NAA+NF compared to control conditions

description: List of genes differently expressed in the NF+NAA treatment compared to control conditions. The first column corresponds to the NimbleGen probe ID, the second to the equivalent Mt4 coding sequence reference when available. Affy ID corresponds to the more accurate medicago affymetrix probe. LFC: Log2 fold change. CT=control condition.  NAA= 10-6M NAA; NF=10-7M NF; NAA+NF=10-6M NAA + 10-7M NF. All treatments are for 10h.
DOI: 10.5061/dryad.s43c7/5
title: Table S5. List of genes from the first synergistic group

description: List of genes in the first synergistic group. The first column corresponds to the NimbleGen probe ID, the second to the equivalent Mt4 coding sequence reference when available. Affy ID corresponds to the more accurate medicago affymetrix probe, "other affy ID" to some related affymetrix probes. LFC: Log2 fold change.pval BH= p-value obtained using a Benjamini Hochberg FDR test. CT=control condition.  NAA= 10-6M NAA; NF=10-7M NF; NAA+NF=10-6M NAA + 10-7M NF. All treatments are for 10h.
DOI: 10.5061/dryad.s43c7/6
title: Table S6. List of genes differentially regulated by NAA+NF compared to NAA

description: List of genes differently expressed in the NF+NAA treatment compared to NAA condition. The first column corresponds to the NimbleGen probe ID, the second to the equivalent Mt4 coding sequence reference when available. Affy ID corresponds to the more accurate medicago affymetrix probe. pval BH= p-value obtained using a Benjamini Hochberg FDR test.  LFC: Log2 fold change. CT=control condition.  NAA= 10-6M NAA; NF=10-7M NF; NAA+NF=10-6M NAA + 10-7M NF. All treatments are for 10h.
DOI: 10.5061/dryad.st6sc.1
title: Data from: Defensive traits exhibit an evolutionary trade-off and drive diversification in ants
DOI: 10.5061/dryad.st6sc.2
title: Data from: Defensive traits exhibit an evolutionary trade-off and drive diversification in ants
DOI: 10.5061/dryad.st6sc.2/1.2
title: Trait Database of Morphological & Ecological Traits for All Ant Genera

description: Trait database including various morphological and ecological traits for every described ant genus (as of June 2015). Data collected from the primary literature as well as online databases (primarily AntWeb and AntWiki). Traits were binned into discrete categories that are described in the header of each column for each trait.
DOI: 10.5061/dryad.st6sc.2/2.2
title: MCC Tree of the Ants with Data Matrix

description: Nexus file including the Maximum Clade Credibility (MCC) genus-tree of the ants and associated aligned matrix of nine concatenated nuclear and mitochondrial genes.
DOI: 10.5061/dryad.tk41q/1
title: Prevalence of blood parasites in Eleonora's falcon

description: Data on infection status by Plasmodium and Haemoproteus of adult Eleonora’s falcons (Falco eleonorae) from the Canary Islands. The first column (Recaptures) indicates birds that were recaptured in successive years. The year of capture, sex, color morph, body condition and the ring number (ID) of each bird are provided.
DOI: 10.5061/dryad.vf8d2/1
title: FE-2016-00613-sup-Data

description: Gross (GEP) and net (NEE) ecosystem photosynthesis, ecosystem respiration (ER), evapotranspiration (ET),carbon (CUE) and water (WUE) use efficiency, related abiotic and biotic factors under five precipitation levels in a semiarid steppe from 2012 to 2014.
DOI: 10.5061/dryad.vk7rd/1
title: Subjective Memory Complaints in Elderly with Previous Depression

description: A cross-sectional study was carried out in people aged 60 or over with previous major depression. Subjective memory complaint was defined on the basis of a score ≧4 on the subscale of Geriatric Mental State schedule, a maximum score of 8. Older people aged equal or over 60 without any psychiatric diagnosis were enrolled as healthy controls. Cognitive function was evaluated using a series of cognitive tests assessing verbal memory, attention/speed, visuospatial function, verbal fluency, and cognitive flexibility in all participants. This data was registered by SPSS.
DOI: 10.5061/dryad.13vk0/1
title: Detections

description: Detections by location, time, and body mass
DOI: 10.5061/dryad.208b1/1
title: Results

description: An R file containing all the results for the analysis of tetrapod data, including different timescaling methods and different length timeslices. Corresponds to plots shown in main manuscript and supplementary figures.
DOI: 10.5061/dryad.2fn1k/1
title: Data Archive Copy  Dryad repository
DOI: 10.5061/dryad.39n4g/1
title: readme

description: instructions for using code and simulation data here
DOI: 10.5061/dryad.39n4g/2
title: files_plotfigures

description: Contains Matlab code (.m files) for plotting the figures.
DOI: 10.5061/dryad.39n4g/3
title: files_calc_matingfunctions

description: Contains Matlab code (.m files) for calculating the mating functions used in model simulations, and the corresponding data files (matfiles).
DOI: 10.5061/dryad.4478b/1
title: Genotype file WTAL_DRYAD

description: This is normal excel genotype file of WTAL Bengal tiger
DOI: 10.5061/dryad.50584/1
title: All data

description: All the data are put in this file
DOI: 10.5061/dryad.55gb7/2
title: Species codes

description: 02 - Species codes.File name: 02_species_codes.xlsx.This file contains correspondence between the species codes and the species latin names.A unique coding was used for cored individuals among sites.“Non-cored” individuals received another coding depending on the site.
DOI: 10.5061/dryad.55gb7/5
title: Tree size

description: 05 - Tree size on each site.File names in the 05_DBH folder: dbhABI.csv, dbhBIC.csv, dbhD1823.csv, dbhD1847.csv, dbhSUT.csv.These files contain the diameter at breast height (mm) of all living trees.Trees ID are coded with their species code followed by a number.
DOI: 10.5061/dryad.55gb7/6
title: Tree ring data

description: 06 -  Tree ring data.20 files in the 06_TRD folder. File names are coded with species initials followed by the name of the site.These files contain ring width measurement for all trees kept for the analyses.Trees ID are coded with a site code (1: D1823, 2: D1847, 3: ABI, 4:BIC, 5: SUT) followed by their species code, followed by a number.
DOI: 10.5061/dryad.5bn81/1
title: Morris_Letnic_Data_1_Fauna

description: Data on dingo and kangaroo counts collected in the field.
DOI: 10.5061/dryad.5bn81/2
title: Morris_Letnic_Data_2_Diet

description: Data on content of dingo scats collected in the field.
DOI: 10.5061/dryad.5bn81/3
title: Morris_Letnic_Data_3_Vegetation

description: Data on vegetation cover collected in the field.
DOI: 10.5061/dryad.5bn81/4
title: Morris_Letnic_Data_4_Soil

description: Data on soil nutrients collected in the field and analysed at the Southern Cross University, Environmental Analysis Laboratory.
DOI: 10.5061/dryad.5bn81/5
title: Morris_Letnic_Rcode

description: R code used for data preparation, graphing and statistical analysis.
DOI: 10.5061/dryad.71tv1/1
title: BEAST_files

description: BEAST files, including input .xml and final maximum clade credibility tree.
DOI: 10.5061/dryad.71tv1/2
title: RAxML_files

description: RAxML files, including input alignment & partition file and final tree
DOI: 10.5061/dryad.71tv1/3
title: PartitionFinder_files

description: Input & output from PartitionFinder analyses.
DOI: 10.5061/dryad.71tv1/4
title: 12Files_Platygonus_compressus_SeqData_Filtered_Collapsed.fastq

description: FASTQ files containing filtered, de-mulitplexed, and collapsed HiSeq (Illumina) sequencing reads corresponding to the 12 Platygonus compressus enriched genomic libraries. See main publication for full details on data processing.
DOI: 10.5061/dryad.71tv1/5
title: 3Files_Pecari_tajacu_SeqData_Filtered_Collapsed.fastq

description: FASTQ files containing filtered, de-mulitplexed, and collapsed HiSeq (Illumina) sequencing reads corresponding to the 3 Pecari tajacu enriched genomic libraries. See main publication for full details on data processing.
DOI: 10.5061/dryad.71tv1/6
title: Catagonus_wagneri_KY987545_SeqData_Filtered_Collapsed.fastq

description: FASTQ file containing filtered, de-mulitplexed, and collapsed HiSeq (Illumina) sequencing reads corresponding to the Catagonus wagneri enriched genomic library. See main publication for full details on data processing.
DOI: 10.5061/dryad.71tv1/7
title: Tayassu_pecari_KY987556_SeqData_Filtered_Collapsed.fastq

description: FASTQ file containing filtered, de-mulitplexed, and collapsed HiSeq (Illumina) sequencing reads corresponding to the Tayassu pecari enriched genomic library. See main publication for full details on data processing.
DOI: 10.5061/dryad.80c1f/1
title: Read me2

description: Description of all the datafiles
DOI: 10.5061/dryad.80c1f/2
title: CSmanual

description: manual analysis CS songs
DOI: 10.5061/dryad.80c1f/3
title: perLmanual

description: manual analysis of perL songs
DOI: 10.5061/dryad.80c1f/4
title: first25CSsongs

description: Manual analysis of first 24 CS songs plus cong CS71
DOI: 10.5061/dryad.80c1f/5
title: CS&perLplus5s

description: Binned analysis of CS and perL songs 5s out of phase
DOI: 10.5061/dryad.80c1f/6
title: TullyCS

description: Manual analysis of CSTully songs from Arthur et al 2013
DOI: 10.5061/dryad.80c1f/7
title: interobserver

description: results on inter-observer analyses of 3 songs
DOI: 10.5061/dryad.8ff46/1
title: Lynx genetic data

description: This file contains genetic scores at 14 neutral microsatellites and the dinucleotide repeat within the promoter region of the IGF-1 gene in Canada lynx sampled from eastern Canada (Quebec, Labrador, New Brunswick and the islands of Newfoundland and Cape Breton Island).
DOI: 10.5061/dryad.8m2t5/2
title: Cormorant Bayesian Phylogram

description: Phylogram generated using Mrbayes
DOI: 10.5061/dryad.8m2t5/3
title: DCHS1 alignment

description: DCHS1 alignment  (fasta format) for PAML positive selection analysis
DOI: 10.5061/dryad.8m2t5/4
title: DVL1 alignment

description: DVL1 alignment  (fasta format) for PAML positive selection analysis
DOI: 10.5061/dryad.8m2t5/5
title: DYNC2H1 alignment

description: DYNC2H1 alignment  (fasta format) for PAML positive selection analysis
DOI: 10.5061/dryad.8m2t5/6
title: EVC alignment

description: EVC alignment (Fasta format) for PAML positive selection analysis
DOI: 10.5061/dryad.8m2t5/7
title: FAT1 alignment

description: FAT1 alignment (Fasta format) for PAML positive selection analysis
DOI: 10.5061/dryad.8m2t5/9
title: GLI3 alignment

description: GLI3 alignment (Fasta format) for PAML positive selection analysis
DOI: 10.5061/dryad.cm603/1
title: Fig. S1. Limb reconstruction on uniform clock phylogeny

description: Fig. S1. Ancestral state reconstructions from MultiState in BayesTraits showing the probability of fully-developed hind limbs (blue), reduced limbs (yellow), and completely lost limbs (red) for each node as well as the states coded for terminal taxa on the uniform clock phylogeny. As in Fig. 4, white areas of pies at internal nodes indicate the posterior probability that a node does not exist.
DOI: 10.5061/dryad.cm603/2
title: Fig. S2. Macrostomatan phenotype reconstruction on uniform clock phylogeny

description: Fig. S2. Ancestral state reconstructions from MultiState in BayesTraits showing the probability of the non-macrostomatan phenotype (blue) and macrostomatan phenotype (yellow) for each node as well as the states coded for terminal taxa on the uniform clock phylogeny. As in Fig. 4, white areas of pies at internal nodes indicate the posterior probability that a node does not exist.
DOI: 10.5061/dryad.cm603/3
title: Fig. S3. Limb reconstruction on constrained, fossil tip FBD phylogeny

description: Fig. S3. Ancestral state reconstructions from MultiState in BayesTraits showing the probability of fully-developed hind limbs (blue), reduced limbs (yellow), and completely lost limbs (red) for each node as well as the states coded for terminal taxa on the constrained, fossil tip FBD phylogeny. As in Fig. 4, white areas of pies at internal nodes indicate the posterior probability that a node does not exist.
DOI: 10.5061/dryad.cm603/4
title: Fig. S4. Macrostomatan phenotype reconstruction on constrained, fossil tip FBD phylogeny

description: Fig. S4. Ancestral state reconstructions from MultiState in BayesTraits showing the probability of the non-macrostomatan phenotype (blue) and macrostomatan phenotype (yellow) for each node as well as the states coded for terminal taxa on the constrained, fossil tip FBD phylogeny. As in Fig. 4, white areas of pies at internal nodes indicate the posterior probability that a node does not exist.
DOI: 10.5061/dryad.cm603/5
title: Fig. S5. Limb reconstruction on constrained, diversified FBD Tetrapodophis excluded phylogeny.

description: Fig. S5. Ancestral state reconstructions from MultiState in BayesTraits showing the probability of fully-developed hind limbs (blue), reduced limbs (yellow), and completely lost limbs (red) for each node as well as the states coded for terminal taxa on the constrained, diversified FBD Tetrapodophis excluded phylogeny. As in Fig. 4, white areas of pies at internal nodes indicate the posterior probability that a node does not exist. The phylogeny is plotted without Diablophis or Portugalophis because of issues visualizing branch lengths when these taxa were included, but they were included in the trees used for ancestral state reconstruction.
DOI: 10.5061/dryad.cm603/6
title: Fig. S6. Macrostomatan phenotype reconstruction on constrained, diversified FBD Tetrapodophis excluded phylogeny

description: Fig. S6. Ancestral state reconstructions from MultiState in BayesTraits showing the probability of the non-macrostomatan phenotype (blue) and macrostomatan phenotype (yellow) for each node as well as the states coded for terminal taxa on the constrained, diversified FBD Tetrapodophis excluded phylogeny. As in Fig. 4, white areas of pies at internal nodes indicate the posterior probability that a node does not exist. The phylogeny is plotted without Diablophis or Portugalophis because of issues visualizing branch lengths when these taxa were included, but they were included in the trees used for ancestral state reconstruction.
DOI: 10.5061/dryad.cm603/7
title: Fig. S7. Limb reconstruction on constrained, diversified FBD Tetrapodophis and Caldwell et al. (2015) fossils excluded phylogeny

description: Fig. S7. Ancestral state reconstructions from MultiState in BayesTraits showing the probability of fully-developed hind limbs (blue), reduced limbs (yellow), and completely lost limbs (red) for each node as well as the states coded for terminal taxa on the constrained, diversified FBD Tetrapodophis and Caldwell et al. (2015) fossils excluded phylogeny. As in Fig. 4, white areas of pies at internal nodes indicate the posterior probability that a node does not exist.
DOI: 10.5061/dryad.f09rh.1/10.1
title: Ctenochaetus_striatus_batch_1_filtered.vcf

description: Filtered RAD reads in .vcf format for Ctenochaetus striatus.
DOI: 10.5061/dryad.f09rh.1/6.1
title: Chaetodon_paucifasciatus_batch_1_filtered.vcf

description: Filtered RAD reads in .vcf format for Chaetodon paucifasciatus.
DOI: 10.5061/dryad.f09rh.1/7.1
title: Chaetodon_pictus_batch_1_filtered.vcf

description: Filtered RAD reads in .vcf format for Chaetodon pictus.
DOI: 10.5061/dryad.f09rh.1/8.1
title: Chaetodon_semilarvatus_batch_1_filtered.vcf

description: Filtered RAD reads in .vcf format for Chaetodon semilarvatus.
DOI: 10.5061/dryad.f09rh.1/9.1
title: Chaetodon_trifascialis_batch_1_filtered.vcf

description: Filtered RAD reads in .vcf format for Chaetodon trifascialis.
DOI: 10.5061/dryad.f5qk7.1
title: Data from: Targeted capture of complete coding regions across divergent species
DOI: 10.5061/dryad.f5qk7.1/1.1
title: Supplementary File 2 - Probe Design and Sequences

description: Complete set of probes used for cross-species targeted capture and associated data
DOI: 10.5061/dryad.f5qk7.1/2.1
title: Supplementary File 3 - Assembly and Analysis Pipelines and Scripts

description: Custom pipelines and scripts for the assembly and analysis of cross-species  targeted capture data
DOI: 10.5061/dryad.f5qk7.1/3.1
title: Supplementary File 4 - Anolis Reference

description: Reference file used for assembly
DOI: 10.5061/dryad.f5qk7.1/4.1
title: Supplementary File 5 - Snake Reference

description: Reference file used for assembly
DOI: 10.5061/dryad.f5qk7.1/5.1
title: Supplementary File 6 - Gekko Reference

description: Reference file used for assembly
DOI: 10.5061/dryad.f5qk7.2/3.2
title: Supplementary File 4 - Anolis Reference

description: Reference file used for assembly
DOI: 10.5061/dryad.f5qk7.2/4.2
title: Supplementary File 5 - Snake Reference

description: Reference file used for assembly
DOI: 10.5061/dryad.f5qk7.2/5.2
title: Supplementary File 6 - Gekko Reference

description: Reference file used for assembly
DOI: 10.5061/dryad.hg785/6
title: Stegodyphus sarasinorum .alleles file
DOI: 10.5061/dryad.hg785/7
title: Stegodyphus tentoriicola .alleles file
DOI: 10.5061/dryad.m2dk7/1
title: Multiple sequence alignment files

description: This submission contains multiple sequence alignment files used for phylogenetic reconstructions. 
Sequences reconstructed from sediments are denominated by the site and layer of origin. 
The comparative data (identical in all files) is identified by the name of the individual and the accession code of its mtDNA sequence.
DOI: 10.5061/dryad.qb70g/1
title: Quercus phenology data

description: These data were obtained from the USA National Phenology Network (USA-NPN) database, accessible at www.usanpn.org/results/data. Data were collected by citizen and professional scientists through the Nature's Notebook monitoring program (www.naturesnotebook.org). This dataset was selected from the "Individual Phenometrics" data type available from the USA-NPN Phenology Observation Portal which delivers derived estimates of phenophase onset and end for individual plants. This dataset was customized by selecting all available data for four species of Quercus: Q. alba, Q. agrifolia, Q. lobata, and Q. rubra from 2009-2014 on two phenophases, "breaking leaf buds" and "flowers and flower buds".  The dataset was filtered to only include onset dates that were detected within 7 days of a negative observation record. This data files includes one tab with estimated onset and end dates for phenophase activity and one tab with data field descriptions. For additional information on USA-NPN protocols and phenophase definitions visit www.usanpn.org/data.
DOI: 10.5061/dryad.r14ch/1
title: Data for Cettiidae song evolution study

description: Raw song measurements as well as the ecology traits data (i. e. breeding latitude, migration and morphology) for 30 species in Cettiidae are provided.
DOI: 10.5061/dryad.s43c7/7
title: Table S7. List of genes from the second synergistic group

description: List of genes in the second synergistic group. The first column corresponds to the NimbleGen probe ID, the second to the equivalent Mt4 coding sequence reference when available. Affy ID corresponds to the more accurate medicago affymetrix probe, "other affy ID" to some related affymetrix probes. LFC: Log2 fold change.pval BH= p-value obtained using a Benjamini Hochberg FDR test. CT=control condition.  NAA= 10-6M NAA; NF=10-7M NF; NAA+NF=10-6M NAA + 10-7M NF. All treatments are for 10h.
DOI: 10.5061/dryad.s43c7/8
title: Table S8. List of genes with a potential hormonal or LRF function

description: List of differentially expressed genes with a potential hormonal function. The first column corresponds to the NimbleGen probe ID, the second to the equivalent Mt4 coding sequence reference when available. Affy ID corresponds to the more accurate medicago affymetrix probe. All genes had a significant adjusted pvalue in at least one of the conditions tested.  LFC: Log2 fold change. CT=control condition.  NAA= 10-6M NAA; NF=10-7M NF; NAA+NF=10-6M NAA + 10-7M NF. All treatments are for 10h.
DOI: 10.5061/dryad.s43c7/9
title: Table S9. List of genes from the third synergistic group

description: List of genes in the third synergistic group. The first column corresponds to the NimbleGen probe ID, the second to the equivalent Mt4 coding sequence reference when available. Affy ID corresponds to the more accurate medicago affymetrix probe, "other affy ID" to some related affymetrix probes. LFC: Log2 fold change.pval BH= p-value obtained using a Benjamini Hochberg FDR test. CT=control condition.  NAA= 10-6M NAA; NF=10-7M NF; NAA+NF=10-6M NAA + 10-7M NF. All treatments are for 10h.
DOI: 10.5061/dryad.vt5n0/1
title: The association between exposure to environmental bisphenol A and gonadotropic hormone levels among men

description: The data describe the information of males in a district of China. The information contains the males' characteristics, habits, and history of chemical substance contact. Besides this, the BPA levels in urine sample and hormone levels in blood samples are also included.
DOI: 10.17632/37gp2djcst.1
title: Supplemental Table S2: Orthologous gene groups in Stentor

description: A list of all predicted Stentor genes and the ortholog groups they were sorted into, as well as the phyletic distributions of genes in each ortholog group.
DOI: 10.17632/dgxfv4s5vt.1
title: Generalized possibilistic fuzzy c-means with novel cluster validity indices for clustering noisy data

description: Dear Researcher, Thank you for using this code and datasets. I explain how GPFCM code related to my paper "Generalized possibilistic fuzzy c-means with novel cluster validity indices for clustering noisy data" published in Applied Soft Computing, works. The main datasets mentioned in the paper together with GPFCM code are included. If there is any question, feel free to contact me at: bas_salaraskari@yahoo.com s_askari@aut.ac.ir Regards, S. Askari Guidelines for GPFCM algorithm: 1. Open the file "GPFCM-Code" using MATLAB. 2. DATA1 to DATA6 are the data sets we used in the paper. Each data set contains the data "yd", optimal value of ρ "ruopt" and number of clusters "C". 3. In line 13 of the code, change the number in "DATA1" to the number of the desired data set. For example, to load DATA3, change "load DATA1" to "load DATA3". 4. Click somewhere on the file "GPFCM-Code" and then Press "Ctrl+Enter" to run the code. 5. VFCM, VPFCM, and VGPFCM which appear on the command window are cluster centers computed by each of the algorithms FCM, PFCM, and GPFCM, respectively. You can find all of them in the "Workspace" of MATLAB as well. 6. Sometimes, PFCM may yield two or more coincident clusters for DATA4 or any other data. Then GPFCM will also give two or more coincident clusters because it starts with PFCM. You may run the algorithm again to get probably all cluster centers accurately. Generally, if you use GFCM rather than GPFCM, you'll get better results with no coincident clusters. Settings of the code for GFCM are mentioned in item 14. 7. Since the algorithm starts randomly, order of the cluster centers may be different in various runs but numerical values of the cluster centers will not change. For example, if is obtained as the third cluster center in one run which is the third column of the matrix VGPFCM, it may move to the fifth row of the matrix in another run (if ). But its value would not considerably change and is very close to . This is just because of random initializations of the algorithm. Since FCM (by which GPFCM is initialized) is randomly initialized, sometimes it is sensitive to initialization (depending on the data) and there may be negligible differences between cluster centers obtained in different runs. For example, consider DATA3 with 6 clusters. In one run we get: VGPFCM1 = -4.9960 -1.0169 -4.9708 1.9575 1.0521 -2.0271 -1.9853 -5.0464 5.9470 0.0031 6.0183 1.9896 And in another run we have: VGPFCM2 = -4.9960 -1.0169 1.9575 1.0521 -2.0271 -4.9708 -1.9853 -5.0464 0.0031 6.0183 1.9896 5.9470 It is observed that cluster centers are the same as those of the first run but their positions in the matrix VGPFCM is changed. 8. Line 46 computes Covariance norm matrix. If you "uncomment" line 47, then the program uses Identity norm matrix (Euclidean distance).