cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5383948.v2
title: Dataset 1: Information on the 276 SNPs genotyped in 177 genes in P. falciparum parasite populations from The Gambia, Kilifi and Rachuonyo South

description: <b>Dataset 1:</b> <b>Information on the 276 SNPs genotyped in
177 genes in <i>P. falciparum </i>parasite
populations from The Gambia, Kilifi and Rachuonyo South. </b>The columns
contain the following information: study_location, site of sample collection;
sample_id, unique sample identifier; gene_symbol, gene name (if available);
chr_valid, chromosome; coord_valid= base position of SNP on chromosome;
sequence_code, SNP name; assay_code, name of assay; rsnumber, unique SNP
identifier in dbSNP; reference_allele, 3D7 reference allele,
alternative_allele, alternative allele; single letter code, IUPAC code for
SNPs; result, genotype call after processing; allele1, IUPAC code for allele 1;
allele2, IUPAC code for allele 2; allele_ratio1, proportion of allele 1;
allele_ratio2, proportion of allele 2; pass_fail, coding of SNP based on
availability of valid genotype (pass) or lack of a valid genotype (fail).
Geospatial data for homestead location is considered sensitive data and
therefore cannot be made open access. However, it can be accessed through a
request to our data governance committee, using the email address
mmunene@uat/newsite.
DOI: 10.5281/zenodo.250156
title: Sequence Data For The Article "Whole Transcriptome Analysis Of Thousands Of Facs-Sorted Single Cells With The Single Cell Nanocage Protocol" - Protocol Optimization

description: Sequence data (Illumina MiSeq runs) for the article "Whole transcriptome analysis of thousands of FACS-sorted single cells with the single cell nanoCAGE protocol". Optimization of the protocol. Files names indicate unique run identifiers. In the manuscript, the link between unique run identifiers, cells and purpose of the experiment is found in the Supplemental Table 1.
DOI: 10.5281/zenodo.251550
title: Sequence Data For The Article "Whole Transcriptome Analysis Of Thousands Of Facs-Sorted Single Cells With The Single Cell Nanocage Protocol" - Single Cells Dataset

description: Sequence data (Illumina MiSeq runs) for the article "Whole transcriptome analysis of thousands of FACS-sorted single cells with the single cell nanoCAGE protocol". dataset of 2300 single cells. File names indicate unique sequencing runs. In the manuscripts, the informations about cell lines are found in the Supplemental Table 1.
DOI: 10.5281/zenodo.60229
title: X-Ray Reflection Table Models

description: Xspec Table Models of Monte Carlo X-ray reflection simulations from Giant Molecular Clouds.

See, http://arxiv.org/abs/1609.00175, for description of the models.

The number on the end of each file name represents the iron abundance relative to solar.
DOI: 10.5281/zenodo.61308
title: Spinning Test-Body Orbiting Around Schwarzschild Black Hole:   Circular Dynamics And Gravitational-Wave Fluxes

description: We release gravitational wave fluxes at null-infinity from a spinning test-body in circular equatorial orbits around a Schwarzschild black hole. Four different prescriptions are used for the dynamics:  the Mathisson-Papapetrou formalism under the Tulczyjew (TUL) spin-supplementary-condition (SSC), the Pirani (PIR) SSC and the Ohashi-Kyrian-Semerak (OKS) SSC, and the spinning particle limit of the effective-one-body Hamiltonian (HAM) of [Phys.~Rev.~D.90,~044018(2014)]. For more details see xxxx .

The multipolar fluxes are given for l=2,3 m=1,2,3 at the Boyer-Lindquist radii

  r =  4 5 6 7 8 10 12 15 20 30   ,

in cases they were not computed the data contains a "42". Note that the fluxes in these data files are assumed to contain both the +m and -m contributions, since they are identical for equatorial orbits and aligned spins. <br>
Additionally, the data files contain the key numbers describing the circular dynamics (see paper).

Units <em>c</em>=<em>G</em>=1.
description: {"references": ["Spinning test-body orbiting around Schwarzschild black hole: circular dynamics and gravitational-wave fluxes,", "Enno Harms, Georgios Lukes-Gerakopoulos, Sebastiano Bernuzzi, Alessandro Nagar,", "xxxxx"]}
DOI: 10.5281/zenodo.61438
title: Influence Of Volatile Anesthesia On The Release Of Glutamate And Other Amino Acids In The Nucleus Accumbens Of Alcohol-Withdrawn Rats

description: An alcohol withdrawal syndrome is a potentially life-threatening condition, which may occur when patients with alcohol use disorders have to undergo general anesthesia. Excitatory amino acids, such as glutamate, act as neurotransmitters and play a key role in alcohol withdrawal. We investigated the influence of isoflurane, sevoflurane, and desflurane anesthesia on the profile of excitatory and inhibitory amino acids in the Nucleus accumbens (NAcc) of alcohol-withdrawn rats (AWR).

80 Wistar rats were randomized into two groups of 40, pair-fed with alcoholic or non-alcoholic nutrition. Nutrition was withdrawn and microdialysis trials were performed to measure the activity of amino acids in the NAcc. The withdrawal onset time was determined in a first trial with 20 rats. 60 rats then received isoflurane, sevoflurane, or desflurane anesthesia for three hours during withdrawal period, followed by one hour of elimination. Amino acid concentrations were obtained by chromatography. Quantification was done by integration and analysis of the area under the curve (AUC).
DOI: 10.5281/zenodo.61523
title: Research Data For Doi:10.1016/J.Talanta.2016.05.023

description: Research data for the paper doi:10.1016/j.talanta.2016.05.023. This zip file contains ASCI files with data for each curve showed in Figure 3,4, and 5.
DOI: 10.22021/bbldntz201705
title: The Linked Open British National Bibliography – Books. 1950/2017-05 – N-Triples
DOI: 10.22021/bbldrdfz201705
title: The Linked Open British National Bibliography – Books. 1950/2017-05 – RDF/XML
DOI: 10.5281/zenodo.1171755
title: Cancermine

description: Results from tool executed using PubRunner on MEDLINE corpus.
DOI: 10.5281/zenodo.61572
title: Drosophila Simulans Ld Results From Plink For Chromosome 2L

description: <strong>Abstract</strong>: Heritable phenotypic variation in natural populations exceeds the levels predicted under mutation-selection balance where purifying selection removes variation. Balancing selection, inefficient or weak selection, polygenic adaptation, and non-equilibrium populations are all possible explanations for excess variation. Yet, available genomic data indicate an abundance of directional selection. One potential explanation is that fleeting directional selection drives beneficial mutations to high frequency in rapid waves resulting in many intermediate frequency haplotypes. This hypothesis is supported by the genomic data from a panel of 170 D. simulans genotypes established from a single stable population which show evidence for an abundance of incomplete soft sweeps. Demography, admixture, and balancing selection cannot entirely explain the patterns in these data, while transient selective sweeps can account for all the patterns of variation observed in this population. One interpretation is that constant environmental shifts rapidly change the optimal phenotype within Drosophila populations, leaving a signature of adaptive responses.

<strong>Material type</strong>: Text files of pairwise linkage disequilibrium (LD) calculations from Plink (v). 

<strong>Larger Body of Work</strong>: Pervasive incomplete selective sweeps in D. simulans account for excess variation.

<strong>Related publications and datasets</strong>: Drosophila simulans VCF, LD results from chromosomes 2R, 3L, 3R, 4, and X.
description: LD calculated for all possible pairwise combinations of SNPs. Performed for each chromosome separately. This file contains only data for chromosome 2L.
DOI: 10.5281/zenodo.61573
title: Drosophila Simulans Ld Results From Plink For Chromosome 2R

description: <strong>Abstract</strong>: Heritable phenotypic variation in natural populations exceeds the levels predicted under mutation-selection balance where purifying selection removes variation. Balancing selection, inefficient or weak selection, polygenic adaptation, and non-equilibrium populations are all possible explanations for excess variation. Yet, available genomic data indicate an abundance of directional selection. One potential explanation is that fleeting directional selection drives beneficial mutations to high frequency in rapid waves resulting in many intermediate frequency haplotypes. This hypothesis is supported by the genomic data from a panel of 170 D. simulans genotypes established from a single stable population which show evidence for an abundance of incomplete soft sweeps. Demography, admixture, and balancing selection cannot entirely explain the patterns in these data, while transient selective sweeps can account for all the patterns of variation observed in this population. One interpretation is that constant environmental shifts rapidly change the optimal phenotype within Drosophila populations, leaving a signature of adaptive responses.

<strong>Material type</strong>: Text files of pairwise linkage disequilibrium (LD) calculations from Plink (v). 

<strong>Larger Body of Wor</strong>k: Pervasive incomplete selective sweeps in D. simulans account for excess variation.

<strong>Related publications and datasets</strong>: Drosophila simulans VCF, LD results from chromosomes 2L, 3L, 3R, 4, and X.
description: LD calculated for all possible pairwise combinations of SNPs. Performed for each chromosome separately. This file contains only data for chromosome 2R.
DOI: 10.5281/zenodo.61574
title: Drosophila Simulans Ld Results From Plink For Chromosome 3L

description: <strong>Abstract</strong>: Heritable phenotypic variation in natural populations exceeds the levels predicted under mutation-selection balance where purifying selection removes variation. Balancing selection, inefficient or weak selection, polygenic adaptation, and non-equilibrium populations are all possible explanations for excess variation. Yet, available genomic data indicate an abundance of directional selection. One potential explanation is that fleeting directional selection drives beneficial mutations to high frequency in rapid waves resulting in many intermediate frequency haplotypes. This hypothesis is supported by the genomic data from a panel of 170 D. simulans genotypes established from a single stable population which show evidence for an abundance of incomplete soft sweeps. Demography, admixture, and balancing selection cannot entirely explain the patterns in these data, while transient selective sweeps can account for all the patterns of variation observed in this population. One interpretation is that constant environmental shifts rapidly change the optimal phenotype within Drosophila populations, leaving a signature of adaptive responses.

<strong>Material type</strong>: Text files of pairwise linkage disequilibrium (LD) calculations from Plink (v). 

<strong>Larger Body of Work</strong>: Pervasive incomplete selective sweeps in D. simulans account for excess variation.

<strong>Related publications and datasets</strong>: Drosophila simulans VCF, LD results from chromosomes 2L, 2R,  3R, 4, and X
description: LD calculated for all possible pairwise combinations of SNPs. Performed for each chromosome separately. This file contains only data for chromosome 3L.
DOI: 10.5281/zenodo.61576
title: Drosophila Simulans Ld Results From Plink For Chromosome 3R

description: <strong>Abstract</strong>: Heritable phenotypic variation in natural populations exceeds the levels predicted under mutation-selection balance where purifying selection removes variation. Balancing selection, inefficient or weak selection, polygenic adaptation, and non-equilibrium populations are all possible explanations for excess variation. Yet, available genomic data indicate an abundance of directional selection. One potential explanation is that fleeting directional selection drives beneficial mutations to high frequency in rapid waves resulting in many intermediate frequency haplotypes. This hypothesis is supported by the genomic data from a panel of 170 D. simulans genotypes established from a single stable population which show evidence for an abundance of incomplete soft sweeps. Demography, admixture, and balancing selection cannot entirely explain the patterns in these data, while transient selective sweeps can account for all the patterns of variation observed in this population. One interpretation is that constant environmental shifts rapidly change the optimal phenotype within Drosophila populations, leaving a signature of adaptive responses.

<strong>Material type</strong>: Text files of pairwise linkage disequilibrium (LD) calculations from Plink (v). 

<strong>Larger Body of Work</strong>: Pervasive incomplete selective sweeps in D. simulans account for excess variation.

<strong>Related publications and datasets</strong>: Drosophila simulans VCF, LD results from chromosomes 2L, 2R,  3L, 4, and X.
description: LD calculated for all possible pairwise combinations of SNPs. Performed for each chromosome separately. This file contains only data for chromosome 3R.
DOI: 10.5281/zenodo.61577
title: Drosophila Simulans Ld Results From Plink For Chromosome 4

description: <strong>Abstract</strong>: Heritable phenotypic variation in natural populations exceeds the levels predicted under mutation-selection balance where purifying selection removes variation. Balancing selection, inefficient or weak selection, polygenic adaptation, and non-equilibrium populations are all possible explanations for excess variation. Yet, available genomic data indicate an abundance of directional selection. One potential explanation is that fleeting directional selection drives beneficial mutations to high frequency in rapid waves resulting in many intermediate frequency haplotypes. This hypothesis is supported by the genomic data from a panel of 170 D. simulans genotypes established from a single stable population which show evidence for an abundance of incomplete soft sweeps. Demography, admixture, and balancing selection cannot entirely explain the patterns in these data, while transient selective sweeps can account for all the patterns of variation observed in this population. One interpretation is that constant environmental shifts rapidly change the optimal phenotype within Drosophila populations, leaving a signature of adaptive responses.

<strong>Material type</strong>: Text files of pairwise linkage disequilibrium (LD) calculations from Plink (v). 

<strong>Larger Body of Wor</strong>k: Pervasive incomplete selective sweeps in D. simulans account for excess variation.

<strong>Related publications and datasets</strong>: Drosophila simulans VCF, LD results from chromosomes 2L, 2R,  3R, 3L, and X.
description: LD calculated for all possible pairwise combinations of SNPs. Performed for each chromosome separately. This file contains only data for chromosome 4.
DOI: 10.5281/zenodo.61579
title: Drosophila Simulans Ld Results From Plink For Chromosome X

description: <strong>Abstract</strong>: Heritable phenotypic variation in natural populations exceeds the levels predicted under mutation-selection balance where purifying selection removes variation. Balancing selection, inefficient or weak selection, polygenic adaptation, and non-equilibrium populations are all possible explanations for excess variation. Yet, available genomic data indicate an abundance of directional selection. One potential explanation is that fleeting directional selection drives beneficial mutations to high frequency in rapid waves resulting in many intermediate frequency haplotypes. This hypothesis is supported by the genomic data from a panel of 170 D. simulans genotypes established from a single stable population which show evidence for an abundance of incomplete soft sweeps. Demography, admixture, and balancing selection cannot entirely explain the patterns in these data, while transient selective sweeps can account for all the patterns of variation observed in this population. One interpretation is that constant environmental shifts rapidly change the optimal phenotype within Drosophila populations, leaving a signature of adaptive responses.

<strong>Material type</strong>: Text files of pairwise linkage disequilibrium (LD) calculations from Plink (v). 

<strong>Larger Body of Work</strong>: Pervasive incomplete selective sweeps in D. simulans account for excess variation.

<strong>Related publications and dataset</strong>s: Drosophila simulans VCF, LD results from chromosomes 2L, 2R,  3R, 3L, and 4.
description: LD calculated for all possible pairwise combinations of SNPs. Performed for each chromosome separately. This file contains only data for chromosome X.
DOI: 10.22021/bcldntz201705
title: The Linked Open British National Bibliography – Forthcoming Books. 2017-05 – N-Triples
DOI: 10.22021/bcldrdfz201705
title: The Linked Open British National Bibliography – Forthcoming Books. 2017-05 – RDF/XML
DOI: 10.22021/bsldntz201705
title: The Linked Open British National Bibliography – Serials. 1950/2017-05 – N-Triples
DOI: 10.22021/bsldrdfz201705
title: The Linked Open British National Bibliography – Serials. 1950/2017-05 – RDF/XML
DOI: 10.5281/zenodo.1171754
title: Cancermine

description: Results from tool executed using PubRunner on MEDLINE corpus.
DOI: 10.5281/zenodo.61631
title: Nexus And Data Files For Pokemon Evolutionary Phylogeny

description: Data files associated with the following publication:

Matan Shelomi, Andrew Richards, Ivana Li, Yukinari Okido. (2012) “A Phylogeny and Evolutionary History of the Pokémon.” Annals of Improbable Research, 18(4): 15-17.

Free to use for educators and researchers hoping to use the Pokémon to teach evolution, phylogenetics, etc. Cite in publications as you see fit.<br>
These datasets contain Pokémon up to the 5th generation. Researchers are welcome to produce new, updated datasets so long as they cite our original work, either this dataset and/or the Annals of Improbable Research paper.
description: {"references": ["Matan Shelomi, Andrew Richards, Ivana Li, Yukinari Okido. (2012) \u201cA Phylogeny and Evolutionary History of the Pok\u00e9mon.\u201d Annals of Improbable Research, 18(4): 15-17."]}
DOI: 10.5281/zenodo.61649
title: Popc With 0, 10, 20, And 30 Mol-% Of Cholesterol At 310 K. Charmm36 Force Field. *Obsolete*

description: A POPC bilayer consisting of 200 lipids (100 per leaflet) <br>
is simulated in the presence of 0% (0 molecules), 10 %<br>
(22 molecules), 20 % (50 molecules), or 30 % (86 molecules)<br>
of cholesterol. The Charmm36 model [1] is employed for lipids and the Charmm-compatible variant of the tip3p model for water.

The Charmm36 force field parameters were obtained from CHARMM-GUI [2] at http://www.charmm-gui.org

 

*** IMPORTANT ***

These simulations were performed using an erroneous charmm36.itp file provided by version 1.7 of CHARMM-GUI, as stated in  http://www.charmm-gui.org/?doc=log : "The multiplicity (of dihedral parameters) issue in GROMACS inputs; this issue affects the systems generated from August 21<sup>th</sup> 2015 to December 9<sup>th</sup> 2015." Due to the bad .itp, the deuterium order parameters of C2, as well as the glycerol group, show strange behavior. The systems simulated with the correct itp file can be accessed at: DOI: 10.5281/zenodo.159759.

––––––––––––––––––––––––––––––––––––––––––––––––––––––

The files are in GROMACS format. Trajectory (.xtc) is 100 ns long with data saved every 100 ps. Additionally, the initial structure (.gro), topology (.top), index file (.ndx), simulation paremeter file (.mdp), binary run input file for GROMACS v. 5.0–&gt; (.tpr) and the energy output file (.edr) are provided. 

––––––––––––––––––––––––––––––––––––––––––––––––––––––

[1] Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types

Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites,  Joseph W. O’Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez, Igor Vorobyov, Alexander D. MacKerell, Jr., and Richard W. Pastor

The Journal of Physical Chemistry B 2010 114 (23), 7830-7843

DOI: 10.1021/jp101759q

 

[2] CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

Jumin Lee, Xi Cheng, Jason M. Swails, Min Sun Yeom, Peter K. Eastman, Justin A. Lemkul, Shuai Wei, Joshua Buckner, Jong Cheol Jeong, Yifei Qi, Sunhwan Jo, Vijay S. Pande, David A. Case, Charles L. Brooks, III, Alexander D. MacKerell, Jr., Jeffery B. Klauda, and Wonpil Im

Journal of Chemical Theory and Computation 2016 12 (1), 405-413

DOI: 10.1021/acs.jctc.5b00935
DOI: 10.5281/zenodo.61660
title: Qtl Script And Vcf Files - Genetic Architecture Of Flowering-Time Variation In Brachypodium Distachyon

description: Supplemental data for the article:

GENETIC ARCHITECTURE OF FLOWERING-TIME VARIATION IN BRACHYPODIUM DISTACHYON (Woods et al., 2016).

Supplemental data includes:


	
	A folder named “Data”, which contains:

	
		
		<strong>Raw genotypic data</strong>. Data showing the parental genotype in a RIL population (F7; Bd21 X Bd1-1)
		
		
		<strong>Raw phenotypic data</strong>. Flowering time (leaves and days to flowering) of the RIL population in different growth environments.
		
		
		<strong>The genetic map </strong>(see material and methods section of Woods et al., 2016 for additional information).
		
		
		<strong>Gene positions.</strong> A file containing the position of annotated genes on the Brachypodium distachyon genome V2.1. Data from Phytozome (https://phytozome.jgi.doe.gov/pz/portal.html).
		
	
	
	
	The<strong> R script</strong> used for the QTL analysis (Final_script.R).
	
	
	<strong>VCF files of the loci of interest</strong>. A folder called “VCF” includes the VCF files of the genes presented in Fig. 6  (VRN1, PHYC, VRN2, and FD).
DOI: 10.5281/zenodo.61664
title: Spatial Tournament Data On A Cyclic Tournament Size 50 - Msc Dissertation

description: A data set that contains the results of 1000 spatial games, for the iterated prisoner's dilemma.  The spatial topology used is a cyclic network, and the tournament size set is 50.
DOI: 10.5281/zenodo.61665
title: Spatial Tournament Data On A Periodic Lattice Tournament Size 5 - Msc  Dissertation

description: A data set that contains the results of 1000 spatial games, for the iterated prisoner's dilemma.  The spatial topology used is a periodic lattice network, and the tournament size set is 5.
DOI: 10.5281/zenodo.61666
title: Spatial Tournament Data On A Periodic Lattice Tournament Size 50 - Msc Dissertation

description: A data set that contains the results of 1000 spatial games, for the iterated prisoner's dilemma.  The spatial topology used is a periodic lattice network, and the tournament size set is 50.
DOI: 10.5281/zenodo.61667
title: Round Robin Tournament Size 5 - Msc Dissertation

description: A data set that contains the results of 100 tournaments, for the iterated prisoner's dilemma.  The topology is of a round robin, and the tournament size set is 5.
DOI: 10.5281/zenodo.61668
title: Round Robin Tournament Size 50 - Msc Dissertation

description: A data set that contains the results of 100 tournaments, for the iterated prisoner's dilemma.  The topology is of a round robin, and the tournament size set is 50.
DOI: 10.5281/zenodo.61669
title: Spatial Tournament Data For Complex Networks Non Deterministic Size - Msc Dissertation

description: A data set that contains the results of various spatial tournaments, for the iterated prisoner's dilemma.  Three different types of complex networks have been used as topology for the spatial tournaments. Small world, random and complete networks.
DOI: 10.5281/zenodo.61672
title: Spatial Evolve Algorithm Results For Random Topology Median Normalized Rank - Msc Dissertation

description: A data set containing the results of the spatial evolve lookup algorithm. The topologies used for the spatial tournaments has been random between, small world, random and complete. The objective function taken into account has been the median normalized rank. Three files are contained here based on the list of strategies,deterministic and non, and on the sample size.