cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/w9k8hxd34t.3
title: Data for: Phase-Space Wavepacket Dynamics of Internal Conversion via Conical Intersection: Multi-State Quantum Fokker-Planck Equation Approach

description: Detailed derivation of equations in "Phase-Space Wavepacket Dynamics of Internal Conversion via Conical Intersection: Multi-State Quantum Fokker-Planck Equation Approach"
DOI: 10.5061/dryad.10m4k6q/1
title: Gene expressions mapped with probes in GSE76427

description: A combined 3 sets of differentially expressed genes, a total of 3315 genes, of which 1573 were upregulated, were regarded as hepatocellular carcinoma related differentially expressed genes for analysis. Among them, 1568 gene expressions mapped to probes in GSE76427 (S1 Table), which contained pre-processed raw data used for WGCNA in our research.
DOI: 10.5061/dryad.10m4k6q/2
title: External clinical traits of GSE76427

description: External clinical traits of GSE76427, used for WGCNA in our research.
DOI: 10.5061/dryad.10m4k6q/3
title: Gene significance and module membership based on WGCNA

description: Based on gene significance and module membership, the top 50 core genes in the Green module were regarded as hub genes.
DOI: 10.5061/dryad.248g184/1
title: Shoot_NxTime_genePlots

description: Gene expression plots for all N-responsive genes in shoots.
DOI: 10.5061/dryad.248g184/2
title: Root_NxTime_genePlots

description: Gene expression plots of all N-responsive genes in Roots
DOI: 10.5061/dryad.2hd320d/1
title: Waring&Powers_ERL_for Dryad
DOI: 10.5061/dryad.6j58m7g/3
title: Compressed cordy2_R1_.fastq

description: Compressed ddRAD library
DOI: 10.5061/dryad.6j58m7g/4
title: Compressed cordy2_R2_.fastq

description: Compressed ddRAD library
DOI: 10.5061/dryad.6j58m7g/5
title: Compressed RSA1Library_S2_L001_R1_001.fastq

description: Compressed ddRAD library
DOI: 10.5061/dryad.6j58m7g/6
title: Compressed RSA1Library_S2_L001_R2_001.fastq

description: Compressed ddRAD library
DOI: 10.5061/dryad.6j58m7g/7
title: Accession barcodes

description: List of barcodes file for all accessions included in this study as well as some accessions not used but included on the same sequencing lane.
DOI: 10.5061/dryad.6tb1702/1
title: gene expression data

description: This file contains data of gene expression data from qRT-PCR. This file was made with Microsoft excel 2010.
DOI: 10.5061/dryad.6tb1702/2
title: Supplementary excel 1

description: This file contains all the difference expression genes from RNA-seq analysis. This file was made with excel 2010
DOI: 10.5061/dryad.6tb1702/3
title: Supplementary excel 2

description: This file contains GO results which enriched by DEGs of RNA-seq. This file was made with Microsoft excel 2010
DOI: 10.5061/dryad.6tb1702/4
title: Supplementary excel 3

description: This file contains KEGG pathway results which enriched by DEGs of RNA-seq. This file was made with Microsoft excel 2010
DOI: 10.5061/dryad.7k78dg0/1
title: plant_biomass

description: Plant biomass data from each of the three field sites (Montana, Kansas, Texas).  These data are from surveys at each site, not the experiment.
DOI: 10.5061/dryad.7k78dg0/2
title: plant_richness

description: Plant species richness for each of the three study sites (Montana, Kansas, Texas).  Data are for surveys at each site, not the experiment.
DOI: 10.5061/dryad.7k78dg0/3
title: orthoptera_density

description: Survey data from each site (Montana, Kansas, Texas) measuring grasshopper density.
DOI: 10.5061/dryad.7k78dg0/4
title: orthoptera_richness

description: Grasshopper community composition data for each site (Montana, Kansas, Texas).  Data were collected from sweep net samples.  Each Orthopteran species collected is listed, as well as the number of each species caught.
DOI: 10.5061/dryad.7k78dg0/5
title: experimental_data

description: Plant biomass data from the experiment, examining how Orthopteran species richness and functional richness affect plant biomass in three grasslands located in Montana, Kansas, and Texas.
DOI: 10.5061/dryad.7k78dg0/6
title: README_Laws_etal_grasshoppers_prairie

description: Readme file for: Effects of grasshoppers on prairies: herbivore composition matters more than richness in three grassland ecosystems, Laws, Angela, Prather, Chelse, Branson, David, Pennings, Steven
DOI: 10.5061/dryad.7r5d56c/1
title: plant and rodent data during first peak for Microtus oeconomus

description: Microtus oeconomus numbers and related plant functional group biomass during small rodent population peak 2006-2007.
DOI: 10.5061/dryad.7r5d56c/2
title: plant and rodent data during first peak for Myodes rufocanus

description: Myodes rufocanus numbers and related plant functional group biomass during small rodent population peak 2006-2007.
DOI: 10.5061/dryad.7r5d56c/3
title: plant and rodent data during first peak for Lemmus lemmus

description: Lemmus lemmus numbers and related plant functional group biomass during small rodent population peak 2006-2007.
DOI: 10.5061/dryad.84g0s87/1
title: Dryad_TRES Settlement 2016

description: Data collected from a tree swallow population in Davis, CA during the 2016 breeding season. Explanations of variables provided on sheet 2.
DOI: 10.5061/dryad.9046k0r/1
title: Capture-recapture data

description: Data description

The capture-recapture data used in Cayuela et al. (2018, J. Appl. Ecol) were collected in a spatially structured population of Bombina variegata in France, over an 9-years period (2000-2008). Several capture sessions were performed per year (detailed in Supplementary material S1 of the paper). The individuals are in raws and the capture occasion on column (labelled “H:”). The column “S:” specifies the end of the capture history. The column labeled “$COV:sex” is the sex coded as a group effect (1 = male, 2 = female).

The capture-recapture histories are coded with the following events. For an individual captured at t and t–1, we attributed a code of 1 if it had not dispersed and occupied a patch destroyed at t+1 or a code of 4 if the patch was still available; we attributed a code of 2 if an individual had dispersed and occupied a patch destroyed at t+1 or a code of 5 if the patch was still available. For an individual not captured at t–1 but captured at t, a code of 3 or 6 was attributed respectively if it occurred in a patch destroyed at t+1 or not. An individual was coded 0 if it was not captured at t. 

The txt file is compatible with E-SURGE program.
Code to enter in the GEMACO in E-SURGE program to run the most general model.
For Initial State: IS - Step 1 - (1): to 
 For Transition: Survival - Step 1 - (5): from(1:6, 7:12).t(6 10 14 19 20 23 26).g+[t(6 10 14 19 20 23 26)+t(1 2 3 4 5 7 8 9 11 12 13 15 16 17 18 21 22 24 25 27 28)] 
 For Transition: Dispersal - Step 2 - (5): from(1:3, 4:6).t(1 2 3 4 5 7 8 9 11 12 13 15 16 17 18 21 22 24 25 27 28, 6 10 14 19 20 23 26)+g 
 For Transition: Site dynamics - Step 3 - (8): t(1 2 3 4 5 7 8 9 11 12 13 15 16 17 18 21 22 24 25 27 28, 6, 10, 14, 19, 20, 23, 26) 
 For Transition: Recapture - Step 4 - (11): from(1:6, 7:12)+t(1 2 3 4 5 6, 7 8 9 10, 11 12 13 14, 15 16 17 18, 19, 20, 21 22 23, 24 25 26, 27 28 29)+g 
 For Event: Events - Step 1 - (0): firste+nexte
DOI: 10.5061/dryad.bb85640/1
title: Link-Perez_and_Laffan_2018_distribution-data_EPSG-4326

description: Geographic coordinates (rounded to 0.001 decimal degrees) for the 32,012 georeferenced occurrence records used in the study. Data are provided in the original WGS84 (EPSG:4326) reference coordinate system.
DOI: 10.5061/dryad.cr6dm10/1
title: Report from improved cook stove tests in Bangalore slums
DOI: 10.5061/dryad.f5g2482/1
title: phylogenetic_data
DOI: 10.5061/dryad.h78n6s3/2
title: Anthesis

description: Growth and morphological parameters of wheat recorded at anthesis (DC65).
DOI: 10.5061/dryad.h78n6s3/3
title: Maturity

description: Growth, yield and morphological parameters of wheat recorded at maturity (DC90).
DOI: 10.5061/dryad.h78n6s3/4
title: Leaf gas exchange

description: Net photosynthetic assimilation rate and stomatal conductance of the flag leaf of wheat were recorded weekly using an open path infrared gas analyser (IRGA, Li-6400, Li-Cor, Lincoln, NE, USA).
DOI: 10.5061/dryad.h78n6s3/5
title: Soil water content

description: Soil water content measured in the top (0-30cm) and bottom (31-60cm) soil layers of the column used for growing wheat.
DOI: 10.5061/dryad.k6gf1tf/11
title: ARC_readmap linking trimmed reads and samples

description: The readmap shows read count for each of the two PCR replicates per sample. The readmap is constructed using USEARCH software.
DOI: 10.5061/dryad.k6gf1tf/12
title: Zeale_readmap linking trimmed reads and samples

description: The readmap shows read count for each of the two PCR replicates per sample. The readmap is constructed using USEARCH software.
DOI: 10.5061/dryad.k6gf1tf/13
title: ARC final readmap

description: This readmap contains the final read counts for each sample.
DOI: 10.5061/dryad.k6gf1tf/14
title: Zeale final readmap

description: This readmap contains the final read counts for each sample.
DOI: 10.5061/dryad.k6gf1tf/15
title: Raw sequences of ARC and Zeale fragments

description: DNA extracted from individual Pardosa glacialis; two PCR replicates per ARC and Zeale primer respectively; sequenced using Illumina MiSeq.
DOI: 10.5061/dryad.k6gf1tf/9
title: ARC_ZOTUS_Sequences

description: Clustered to zero-radius OTUs (ZOTUs) using USEARCH algorithm.
DOI: 10.5061/dryad.pc5gc05/7
title: Tail Shape Means_Goodeidae

description: Caudal region (means) for all 2-Dimensional landmark data in Goodeidae trunk analyses.
DOI: 10.5061/dryad.pp0q255/1
title: Genotypes (microsatellites)

description: Microsatellite genotype data are provided in the GenAlEx software format.
DOI: 10.5061/dryad.t153690/28
title: Fig_5a_100Ind_SwitchBack_Strategy_iii_1stPhase

description: The microscopy images of the data in Fig. 5a for the following condition: 2 hours of CRISPRi induction (100% induction level) followed by inducers removal and the addition of 60 nM of AHL in the new medium. There are 61 microscopy stage positions with three channels each: phase-contrast bright field, mVenus, mRFP. The images were binned (2x2).
DOI: 10.5061/dryad.t153690/29
title: Fig_5a_100Ind_SwitchBack_Strategy_iii_2ndPhase_1

description: The microscopy images of the data in Fig. 5a for the following condition: 2 hours of CRISPRi induction (100% induction level) followed by inducers removal and the addition of 60 nM of AHL in the new medium. There are 61 microscopy stage positions with three channels each: phase-contrast bright field, mVenus, mRFP. The images were binned (2x2).
DOI: 10.5061/dryad.t153690/30
title: Fig_5a_100Ind_SwitchBack_Strategy_iii_2ndPhase_2

description: The microscopy images of the data in Fig. 5a for the following condition: 2 hours of CRISPRi induction (100% induction level) followed by inducers removal and the addition of 60 nM of AHL in the new medium. There are 61 microscopy stage positions with three channels each: phase-contrast bright field, mVenus, mRFP. The images were binned (2x2).
DOI: 10.5061/dryad.t153690/31
title: Fig_S9_S10_SwitchBack_Microfluidics

description: This file contains the microscopy images of the data in Fig. S9 and S10 for the following condition: 2 hours of CRISPRi induction (43% induction level) followed by inducers removal and the addition of 60 nM of AHL in the new medium. There are 29 microscopy stage positions with three channels each: phase-contrast bright field, mVenus, mRFP. The images were binned (2x2).
DOI: 10.5061/dryad.t153690/32
title: readme_Mueckl_et_al

description: This file includes a list of the data files within this repository and a short description of their content.
DOI: 10.5061/dryad.tf56fm1/1
title: Community raw data

description: Excel file containing the raw read numbers, as well as dubious sample information.
DOI: 10.5061/dryad.tf56fm1/2
title: Analytical scripts

description: A compressed folder including the scripts, as well as final datasets for HMSC models.
DOI: 10.5061/dryad.tf56fm1/3
title: README

description: Readme for contents of this Dryad package.
DOI: 10.5061/dryad.tf56fm1/4
title: CO1 taxonomy

description: The taxonomy matrix used to identify taxa in CO1 analyses of the article.
DOI: 10.5061/dryad.tf56fm1/5
title: 16S taxonomy

description: The 16S (bacterial) taxonomy and OTU names used in the article.
DOI: 10.5061/dryad.tf56fm1/6
title: ITS taxonomy

description: The ITS (fungal) taxonomy and OTU names used in the article.
DOI: 10.5061/dryad.vv34p8h/1
title: minchin_rawls_2018_dryad_upload

description: Nile Red images saved as .tif files for the mutant and food restricted cohorts. Image# corresponds to Fish# in Supplemental Table 1, and DRYAD# in Supplemental Table 2.
DOI: 10.5061/dryad.vv36g/4
title: Raw images - NEKO

description: Raw image (JPEG) files for photographs captured in NEKO Harbour (NEKO). There are 6 folders in total (images are separated by camera and year). Date, time, moon phase and temperature are shown within each image. Image names are in the following format: SITExYEARx_imagenumber.JPG. Please see the associated paper for more information.
DOI: 10.5061/dryad.vv36g/5
title: Raw images - PETE.1

description: Raw images (JPEG) files for photographs captured on Petermann Island (PETE). There are 2 folders in total (images are separated by year); additional PETE images can be found in 'PETE.2'. Date, time, moon phase and temperature are shown within each image. Image names are in the following format: SITExYEARx_imagenumber.JPG. Please see the associated paper for more information.
DOI: 10.5061/dryad.vv36g/6
title: Raw images - PETE.2

description: Raw image (JPEG) files for photographs captured on Petermann Island (PETE). There are 2 folders in total (images are separated by camera and year); additional PETE images can be found in 'PETE.1'. Date, time, moon phase and temperature are shown within each image. Image names are in the following format: SITExYEARx_imagenumber.JPG. Please see the associated paper for more information.
DOI: 10.5061/dryad.vv36g/7
title: Raw images - SPIG

description: Raw image (JPEG) files for photographs captured on Spigot Peak (SPIG). There are 3 folders in total (images are separated by year). Date, time, moon phase and temperature are shown within each image. Image names are in the following format: SITExYEARx_imagenumber.JPG. Please see the associated paper for more information.
DOI: 10.5061/dryad.vv36g/8
title: PW Anonymised Raw Classifications and Metadata

description: This folder contains 32 csv files, each providing the metadata (including - but not limited to - 'user_name' (anonymised), 'subject_zooniverse_id', 'temperature_f', 'timestamp', and raw 'x' and 'y' coordinates for volunteer clicks) associated with each of the 63,070 Penguin Watch subjects (photographs) provided in this repository. Please see the associated paper for further information and an explanation of terms. The metadata are divided by camera/year, although some are subdivided for clarity and consistency with the 'PW Consensus Click Data' files. For information on how to filter the raw coordinates prior to performing a cluster analysis, please see the 'Clustering Algorithm' section of the accompanying 'Data Descriptor'. Please note that any missing information is absent because it could not be obtained from the cameras, or was missing from the Penguin Watch database - all available metadata have been uploaded to the repository.
DOI: 10.5061/dryad.vv36g/9
title: PW Consensus Click Data

description: This folder comprises 32 csv files, each containing 'consensus click' data relating to the 63,070 Penguin Watch subjects (photographs) also published in this repository. These data are produced via a clustering algorithm (see the 'Methods' section of the associated paper for more information), the code for which can be found on GitHub at the following address: https://github.com/zooniverse/aggregation/blob/master/penguins/aggregate.py (a static version is also archived on Figshare at: https://doi.org/10.6084/m9.figshare.5472544.v1). Please also see the associated paper for an explanation of terms. Please note that the data for some cameras have been subdivided into multiple files - this is to increase clarity, and for consistency with respect to the 'Anonymised Raw Classifications and Metadata' files.
DOI: 10.17632/2dcycpz4k9.1
title: Data for: SNP-haplotypes: an accurate approach for parentage and relatedness inference in gilthead sea bream (Sparus aurata)

description: SNP positions included in our gilthead sea bream final panel. SNP positions are represented on the gene sequences by the letter N.
DOI: 10.17632/2dcycpz4k9.2
title: Data for: SNP-haplotypes: an accurate approach for parentage and relatedness inference in gilthead sea bream (Sparus aurata)

description: SNP positions included in our gilthead sea bream final panel. SNP positions are represented on the gene sequences by the letter N.
DOI: 10.17632/4cs6y4m59z.1
title: Data for: SNP-haplotypes: an accurate approach for parentage and relatedness inference in gilthead sea bream (Sparus aurata)

description: SNP positions included in our gilthead sea bream final panel. SNP positions are represented on the gene sequences by the letter N.
DOI: 10.17632/4cs6y4m59z.2
title: Data for: SNP-haplotypes: an accurate approach for parentage and relatedness inference in gilthead sea bream (Sparus aurata)

description: SNP positions included in our gilthead sea bream final panel. SNP positions are represented on the gene sequences by the letter N.
DOI: 10.17632/8jg3bwzg9y.1
title: Data for: Live imaging of collagen deposition during skin development and repair in a collagen I – GFP fusion transgenic zebrafish line

description: ImageJ plugin for fibre orthogonality analysis
DOI: 10.17632/gk38b5vcw7.1
title: Data for: Accurate interatomic force field for molecular dynamics simulation by hybridizing classical and machine learning potentials

description: The multisclae pair (pair_multiscale.h, pair_multiscale.cpp) has been implemented in LAMMPS. Compile: cp pair_multiscale.h pair_multiscale.cpp ~/lammps-31Mar17/src make ubuntu Usage: Example: pair_style multiscale pair_coeff * * Al.eam.alloy Al.agni Al Al Al 10 100 5 6 1 1 2 3 4 5 6 7 8 9 10 10 coefficients: 1: filename and path for EAM-FS potential 2: filename and path for AGNI potential 3-5: element name 6: Nevery, the CS parameter is computed every Nevery timesteps 7: Nfreq, the CS parameters are averaged every Nfreq timesteps based on the calculated CS parameter in the preceding portion of the simulation every Nevery timesteps. 8: Threshold value, the atoms in simulation are divided into two sub-regions based on the comparison between averaged CS parameters and the threshold value option-coeff: 9: The thickness of the transition region 10: Whether to dump the atomic sub-regions to atomic types. For more questions, please feel free to contect wangp@shu.edu.cn.
DOI: 10.17632/wv4zk4bhys.1
title: Data for: Electrochemical Control of the Thermal Stability of Atomically Thin Ag Films on Au(111)

description: This document describes the materials and methods used for our Electrochemical Scanning Tunneling Microscopy (EC-STM) study of Ag deposition on Au(111).
DOI: 10.5061/dryad.248g184/3
title: DE_Spline

description: R script for identifying differential gene expression in response to N-supply.
DOI: 10.5061/dryad.248g184/4
title: ShootRawCounts

description: Raw counts of total RNA-Seq reads aligned to each gene model in the Arabidopsis thaliana genome (TAIR10 version). These counts are from the RNA-Seq libraries constructed from shoot samples.
DOI: 10.5061/dryad.248g184/5
title: RootRawCounts

description: Raw counts of total RNA-Seq reads aligned to each gene model in the Arabidopsis thaliana genome (TAIR10 version). These counts are from the RNA-Seq libraries constructed from root samples.
DOI: 10.5061/dryad.248g184/7
title: Plotting DEgenes

description: R script to create gene expression plots from the normalized counts.
DOI: 10.5061/dryad.248g184/8
title: Plot Data

description: Data files needed to generate the gene expression plots.
DOI: 10.5061/dryad.2pb6901/1
title: data files on colony census, melanisation, head width, mortality
DOI: 10.5061/dryad.2ts54jj/1
title: GC_defoliation_compiled

description: This dataset contains percent live canopy of Tamarix for Grand County, Utah. Live canopy is a site average for point intercept data collected along transects. There are 4 years of canopy data included. The dataset also includes values for environmental variables measured in 2014.
DOI: 10.5061/dryad.34hp52d/1
title: geospatial_tb_south_africa_tab-delim

description: Tab-delimited text file containing: Location, City, Age, Sex, Year.first.tested, Latitude, Longitude, ID RIF.test INH.test.
DOI: 10.5061/dryad.3rh2043/1
title: CBB_presence_infestation_dryad_JAPPL_2017_01146.R2

description: Data set of the total number of coffee berries, number of bored berries, and ant activity. Used to test CBB presence and CBB infestation.
DOI: 10.5061/dryad.426658h/1
title: Fuzzy-coded longevity

description: Fuzzy-coded longevity for all taxa in the database, in four longevity classes (&lt;1, 1-3, 3-10, and &gt;10 years).
DOI: 10.5061/dryad.426658h/2
title: Comparative trawl studies data

description: Data extracted in a systematic review of comparative bottom trawl studies The readme file gives a more detailed description of the headers.
DOI: 10.5061/dryad.4b3j2bj/4
title: Supplemental figures

description: The supplemental figures referred to in the paper (Figures S1-S40).
DOI: 10.5061/dryad.4b3j2bj/6
title: Gecko sample data

description: A tab-delimited text file containing the data for all the geckos that were analyzed in the paper. The field numbers in the table correspond to the data in the NCBI BioProject PRJNA486413.
DOI: 10.5061/dryad.4s3t2p3/1
title: Wood duck input
DOI: 10.5061/dryad.61g8620/1
title: code_and_data

description: This file provides codes and data for analyzing the simulation results.
DOI: 10.5061/dryad.63nm407/1
title: Stacks and Plink Commands

description: GBS pipeline commands for SNP discrovery including Stacks and post-filtering with populations and Plink
DOI: 10.5061/dryad.69k0b3r/1
title: Differential expression and ASE data
DOI: 10.5061/dryad.6tv5ct1/1
title: Rowsey et al. 2018 Data Files

description: Archive containing necessary files to conduct diversification analyses described in the study.
DOI: 10.5061/dryad.7f1h767/1
title: Dryad_CA_neonates

description: Crawl speed and DIV genotypic data for California neonate snakes
DOI: 10.5061/dryad.7f1h767/2
title: Dryad_PNW_neonates

description: Crawl speed and DIV genotypic data for Pacific Northwest neonate snakes
DOI: 10.5061/dryad.7f1h767/3
title: Ts1.4_cl1.1_Illinois_FI

description: Fast inactivation data for Nav1.4 Illinois clone
DOI: 10.5061/dryad.7f1h767/4
title: Ts1.4_cl1.1_Illinois_IV

description: Activation data for Nav1.4 Illinois clone
DOI: 10.5061/dryad.7f1h767/5
title: TTXcalc_Ts1.4_IL_Cl-1.1_UDB

description: TTX data for Nav1.4 Illinois clone
DOI: 10.5061/dryad.7f1h767/6
title: Ts1.4_cl2_LVNV_FI

description: Fast inactivation data for Nav1.4 LVNV clone
DOI: 10.5061/dryad.7f1h767/7
title: Ts1.4_cl2_LVNV_IV

description: Activation data for Nav1.4 LVNV clone
DOI: 10.5061/dryad.7f1h767/8
title: TTXcalc_Ts1.4_LVNV_cl2_UDB

description: TTX data for Nav1.4 LVNV clone
DOI: 10.5061/dryad.7r5d56c/4
title: plant and rodent data during second peak for Microtus oeconomus

description: Microtus oeconomus numbers and related plant functional group biomass during small rodent population peak 2010-2011.
DOI: 10.5061/dryad.7r5d56c/5
title: plant and rodent data during second peak for Myodes rufocanus

description: Myodes rufocanus numbers and related plant functional group biomass during small rodent population peak 2010-2011.
DOI: 10.5061/dryad.7r5d56c/6
title: plant and rodent data during second peak for Lemmus lemmus

description: Lemms lemmus numbers and related plant functional group biomass during small rodent population peak 2010-2011.
DOI: 10.5061/dryad.7r5d56c/7
title: rodent data both peaks and seasons Microtus oeconomus

description: Microtus oeconomus numbers during both peaks and seasons.