cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.11134
title: Data From "Corset: Enabling Differential Gene Expression Analysis For De Novo Assembled Transcriptomes"

description: This dataset contains de novo transcriptome assemblies for three publicly available RNA-seq dataset (SRA055442, SRR453566-SRR453571 and GSE37704 ). For each assembly we also provide a table with the read counts per contig, the output from corset (clusters and counts), and the results from a genome-based analysis. This dataset was used to assess the performance of the corset software. More detail is provided in the paper: Nadia M Davidson and Alicia Oshlack,<strong> </strong>Corset: enabling differential gene expression analysis for de novo assembled transcriptomes, <em>Genome Biology</em> 2014, <strong>15</strong>:410. http://genomebiology.com/2014/15/7/410/abstract
DOI: 10.5281/zenodo.32794
title: Data Sets For Sar Progression Analysis

description: Four compound data sets assembled from ChEMBL are provided that have been subjected to SAR progression analysis, to be published in Journal of Medicinal Chemistry.
DOI: 10.5281/zenodo.32805
title: Learning The Structure Of Biomedical Relationships From Unstructured Text (Part Ii)

description: These files contain the seed sets and corresponding test sets of drug-gene pairs reflecting pharmacogenomic (PGx) and drug-target relationships that were used to evaluate EBC in the PLoS Comp Bio paper. Unfortunately, they didn't make it into the first upload for this paper. There are four zipped directories in this upload:

data-drug-gene (PGx relationships, dense matrix)

data-drug-target (drug-target relationships, dense matrix)

data-drug-gene-fullmatrix (PGx relationships, sparse matrix)

data-drug-target-fullmatrix (drug-target relationships, sparse matrix)
DOI: 10.5281/zenodo.32813
title: Dataset For Figures In Paper Doi:/10.1016/J.Cattod.2015.09.031

description: Datasets for figures in the publication "

Facile synthesis of palladium phosphide electrocatalysts and their activity for the hydrogen oxidation, hydrogen evolutions, oxygen reduction and formic acid oxidation reactions"

Anthony R.J. Kucernak†, K. Fahy, V. N. Naranammalpuram Sundaram

Department of Chemistry, Imperial College London, London SW7 2AZ, United Kingdom

 

† Corresponding author, a.kucernak@imperial.ac.uk, Phone: +44 20 75945831, Fax: +44 20 75945804

Published in Catalysts Today, 2015.

Please cite this paper DOI:/10.1016/j.cattod.2015.09.031 when referencing this data
DOI: 10.5281/zenodo.32886
title: An Example Of Ecmwf Deterministic Model Analysis Data For Dynamo

description: The full dataset is hosted by Earth Observing Laboratory at the National Center for Atmospheric Research. This is only one example used to compute momentum budget associated with the Madden-Julian Oscillation during DYNAMO.
DOI: 10.5281/zenodo.32889
title: Research Methodology Examples

description: Αρχεία εργασίας για το βιβλίο μεθοδολογία έρευνάς
DOI: 10.5281/zenodo.11225
title: Weight Data For Ceramic Finds From The Byzantine Quarter In Gortys, Crete

description: This dataset consists of one table in CSV format.

Each record corresponds to a single ceramic sherd for which weight in grams was measured and recorded together with the stratigraphical context of provenance and a broad category label. All contexts are from the excavation in the Byzantine Quarter near the temple of Apollo Pythios in Gortys, Crete, and are dated to the Late Roman and Early Byzantine period (4th-8th century).

A total of 25 contexts is included in the dataset, recorded in the years 2012-2014 during fieldwork seasons.

Column descriptions:


	Weight: weight in grams, recorded with a common electronic kitchen scale capable of measuring 7000±1 g and a minimum of 2 g;
	Category: a generic label describing the category of ceramic find ‒ most should be self-explaining apart from “Sovradipinta”, a semi-fine painted ware locally produced in Gortys, basically identical to the plain wares. For some records the “Category” field is empty (for reasons of time constraints in the fieldwork season) and should be treated as NA;
	Context: a numeric identifier for the stratigraphic context of provenance.
	Measured by: initials of operator who performed the weighing (Stefano Costa, Elisa Triolo, Enrico Zanini, Andrea Bellotti);
	Notes: notes.
DOI: 10.5281/zenodo.11388
title: Données De Base De L'Étude "Les Femmes Politiques Dans La Presse: Mythèmes, Biographèmes Et Archétype"

description: L'auteure a recensé et archivé toutes les désignations, informations biographiques et néologismes contenus dans la presse de référence française et allemande (8 organes de presse français et 8 allemands, soit 12.600 articles en tout) à propos d'Angela Merkel en 2005 et de Ségolène Royal en 2006-2007. Ces données forment le corpus de base de l'étude "Les femmes politiques dans la presse: mythèmes, biographèmes et archétype. Les représentations genrées de Ségolène Royal et Angela Merkel dans la presse française et allemande pendant leurs campagnes électorales" (2014, éd. König & Neumann).

Die Autorin hat alle Bezeichnungen, biographische Informationen und neue Wortschöpfungen, die in der Referenzpresse Frankreichs und Deutschlands für Angela Merkel 2005 und Ségolène Royal 2006-2007 verwendet wurden, erfasst und archiviert (8 französische Presseorgane und 8 deutsche, insgesamt 12.600 Artikel). Diese Daten bilden den Grundkorpus der Studie "Politikerinnen in der Presse: Mytheme, Biographeme und Archetyp. Die gender-betonte Darstellung von Ségolène Royal und Angela Merkel in der französischen und deutschen Presse während ihrer Wahlkampagnen." (2014, Verlag König & Neumann)

The author has recorded and archived all the designations, biographic information and neologisms applied to Angela Merkel in 2005 and Ségolène Royal in 2006-2007 in the press of reference in France and Germany (8 French and 8 German papers, 12,600 press reports altogether). Those data form the basic body of the study "Women politicians in the press: mythems, biographems and archetype: the gender-related representation of Ségolène Royal and Angela Merkel in the French and German press during their election campaigns". (2014, ed. König & Neumann)
DOI: 10.5281/zenodo.11455
title: Vcf File Of Variants In A Wide Onion Cross Segregating For Bolting

description: VCF (variant call format) file of variants from bulked segregant RNA PoolSeq (BSR-seq) of F2 progeny pools of a wide onion cross segregating for bolting (precocious flowering). The reference assembly is GBGJ00000000.1 http://www.ncbi.nlm.nih.gov/nuccore/656904698

The pools were taken from materials sampled for validation of the <em>AcBlt1</em> locus as described in http://www.ncbi.nlm.nih.gov/pubmed/24247236

Pools were from bolting or non-bolting plants homozygous at the most closely linked marker to <em>AcBlt1  </em>either for the bolt-associated genotype (AA) or the non-bolt genotype (BB).
DOI: 10.5281/zenodo.11481
title: A Comparative Usability Analysis Of Eye-Tracking And Mouse Click Data Taken From Digital Libraries

description: This dataset is the result of a study, in which we analyzed parallels and differences between clicks as well as eye movements on two different digital library homepages. For this analysis we used diverse tracking tools for mouse clicks and eye tracking data that where further studied with respect to specific areas of interest (AOI).  

The dataset contains two screenshots indicating the areas of interest (AOIs; entitled “AreasOfInterest_Kartenportal.jpg and AreasOfInterest_Webportal.jpg), which separate the homepages into analyzable parts. It also contains eight screenshots of the homepages containing the total amount of collected clicks (each name starting with “clicks”) and two screenshots with the eye tracking heat maps (starting with “Heatmap”). The screenshots have directly been extracted from the click and eye tracking tools and matched with the before mentioned AOIs in order to gain the total count of clicks and views as well as the view duration the concerned area.

All data are synthesized in a document containing three sheets with different tables: a first one with the initial data compilation for all AOIs of the two analyzed homepages (entitled “Data”), a second one with a more visual compiled data analysis for both homepages and all AOIs (entitled “Data2) and last one with the duration of the view as well as the duration of the fixation and the compiled click data (entitled « Eye tracking study data »).
DOI: 10.5281/zenodo.11573
title: Kinase Inhibitors And Scaffolds

description: On the basis of the assessment of compound and scaffold coverage of human kinome, sets of kinase inhibitors and scaffolds with high-confidence activity data assembled from ChEMBL release 18 are provided. In addition, sets of scaffolds involving in different types of structural relationships, having varying degrees of promiscuity and representing highly potent inhibitors are made available. A documentation file (i.e., README.txt) is given.
DOI: 10.5281/zenodo.11576
title: Drug Activity Data

description: Three sets of approved drugs with associated activity data at varying confidence levels are provided. Approved drugs are taken from DrugBank. Each drug in each set is associated with ChEMBL activity records for individual time intervals.
DOI: 10.5281/zenodo.32864
title: Dataset Case-Control Study: Risk Factors For Sporadic Non-Pregnancy Related Listeriosis In Germany, 2012-2013

description: The dataset contains data of a nationwide age-frequency matched case-control study in Germany, 2012-2013, which was performed to identify underlying conditions and foods asscociated with sporadic listeriosis. It covers anonymous sociodemografic information, information on underlying conditions, and &gt;60 food items. Data for control subjects were obtained from a population-based random telephone sample, which was generated according to the method by Gabler and Häder and considered telephone numbers not registered in telephone books.
DOI: 10.5281/zenodo.32993
title: Modeling Sympathetic Cooling Of Molecules By Ultracold Atoms: Supporting Data

description: Data used in preparation of the paper "Modeling sympathetic cooling of molecules by ultracold atoms", authored by Jongseok Lim, Matthew D. Frye, Jeremy M. Hutson and M. R. Tarbutt.

There are four different types of data:

(1) Tables of total cross sections versus collision energy for collisions of CaF with Li and Rb for various values of s-wave scattering length (see figure 1)

(2) Tables of differential cross sections versus energy for collisions of CaF with Li and Rb for various values of s-wave scattering length. The differential cross sections are given as cumulative distribution functions.

(3) Simulated kinetic energy distributions at 1s intervals for sympathetic cooling of CaF with Li and Rb for various values of s-wave scattering length (see figures 5 and 6).

(4) Simulated kinetic energy distributions at 1s intervals for sympathetic cooling of CaF with Rb with various evaporative cooling ramps applied to the Rb (see figure 13).
DOI: 10.5281/zenodo.33055
title: Dopc Lipid Bilayer Simulation Trajectory And Files From Franova Et Al. Bba 1838 (2014) 1406–1411

description: Simulation files for pure DOPC (no pyrene present) simulation from "Can pyrene probes be used to measure lateral pressure profiles of lipid membranes? Perspective through atomistic simulations" Franova et al. Biochimica et Biophysica Acta 1838 (2014) 1406–1411
description: {"references": ["Franova et al. Biochimica et Biophysica Acta 1838 (2014) 1406\u20131411"]}
DOI: 10.5281/zenodo.11654
title: Eeg And Fmri_Plos One

description: subject and data information

5_subjects

sampling frequency: 1000 Hz

256 channels
DOI: 10.5281/zenodo.11667
title: Deeg And Fmri_Plos One

description: subject and data information

5_subjects

self-paced motor movement task

sampling frequency: 1000 Hz

256 channels

After processing files
DOI: 10.5281/zenodo.11675
title: Students Responses Per School For The Research Project "Perspectives On Learning Technologies"

description: A Microsoft Excel dataset that includes students' responses for a research project entitled "Perspectives on learning Technologies" conducted in year 2014. Students from three Schools (Psychology, Electrical Engineering Electronics and Computer Science-EEE & CS and Law) of the University of Liverpool participated in it.
DOI: 10.5281/zenodo.11676
title: Teachers' Responses Per School For The Research Project "Perspectives On Learning Technologies"

description: A Microsoft Excel dataset that includes teachers' responses for a research project entitled "Perspectives on learning Technologies" conducted in year 2014. Teachers from three Schools (Psychology, Electrical Engineering Electronics and Computer Science-EEE & CS and Law) of the University of Liverpool participated in it.
DOI: 10.5281/zenodo.11771
title: Accession Numbers In Supplementary Files

description: This dataset contains database accession numbers which are automatically extracted from the supplementary files linked to open access full text biomedical articles.
DOI: 10.5281/zenodo.14653
title: Powertac 2014-04 Qualifying 271-280

description: Log and boot files of games 271 - 281
DOI: 10.5281/zenodo.17299
title: Grid Based Global Carbon Edge Regression Coefficents

description: Grid cell based regression coefficients for predicting global biomass in the pantropics.

To better account for the variability within a continent, we constructed 100-km grid cells throughout the pantropics. In grid cells where the majority of pixels were from forest biomes, we consider three candidate regression models to represent the relationship between biomass density and distance to forest edge.  In particular, we consider:


	Asymptotic: \(\mathrm{Biomass} = \theta_1-\theta_2\cdot\exp(-\theta_3\cdot\mathrm{Distance})\),
	Logarithmic: \(\mathrm{Biomass}=\beta_0+\beta_1\ln\cdot(\mathrm{Distance})\) , or
	Linear: \(\mathrm{Biomass}=\eta_0+\eta_1\cdot Distance\)


Then, for each grid cell, the candidate with the highest R<sup>2</sup> is used to best represent the relationship between density and distance to forest edge.  Models (2) and (3) were deemed as suitable (and more simplistic) alternatives in cells where higher distances were generally not observed and as a result the forest core was not firmly established. We also note that in the vast majority of grid cells, model (1) was optimal. For each cell the magnitude and distance of the edge effect were again estimated.  In cells using models (2) or (3) the forest core (\(\theta_1\)) was estimated as the average biomass density at the largest observed distance in the cell.
DOI: 10.5281/zenodo.33204
title: Lapedo: Hybrid Skeletons For Programming Heterogeneous Multicore Machines In Erlang

description: We describe Lapedo, a novel library of hybrid parallel skeletons for programming heterogeneous multi-core/many-core CPU/GPU sys- tems in Erlang. Lapedo’s hybrid skeletons comprise a mixture of CPU and GPU components, allowing skeletons to be flexibly and dynamically mapped to available resources. We also describe a model for deriving near-optimal division of work between CPUs and GPUs, ensuring load balancing between resources. Finally, we evaluate the effectiveness of Lapedo on three realistic use cases from different domains, demonstrat- ing significant speedups compared to executing the same application on only CPU cores or a GPU
DOI: 10.5281/zenodo.33223
title: Dynamic Re-Calibration Of Perceived Size In Fovea And Periphery Through Predictable Size Changes

description: Dataset relative to the following publication:

Valsecchi, M. & Gegenfurtner, K.R (2016). Dynamic re-calibration of perceived size in fovea and periphery through predictable size changes. Current Biology, 26, 59-63.

Each folder contains the data relative to one experiment and the script that was used to generate them. 

Each data folder contains a description of the data format which should be sufficient to replicate the analyses as performed in the paper. 

Additional info can be deducted fromt he experimental scripts.
DOI: 10.5281/zenodo.33331
title: Dopc Lipid Bilayer With Pyr8 Simulation Trajectory And Files From Franova Et Al. Bba 1838 (2014) 1406–1411

description: Simulation files for DOPC with PYR8 simulation from "Can pyrene probes be used to measure lateral pressure profiles of lipid membranes? Perspective through atomistic simulations" Franova et al. Biochimica et Biophysica Acta 1838 (2014) 1406–1411
description: {"references": ["Franova et al. Biochimica et Biophysica Acta 1838 (2014) 1406\u20131411"]}
DOI: 10.5281/zenodo.33353
title: Dopc Lipid Bilayer With Pyr4 Simulation Trajectory And Files From Franova Et Al. Bba 1838 (2014) 1406–1411

description: Simulation files for DOPC with PYR4 simulation from "Can pyrene probes be used to measure lateral pressure profiles of lipid membranes? Perspective through atomistic simulations" Franova et al. Biochimica et Biophysica Acta 1838 (2014) 1406–1411
description: {"references": ["Franova et al. Biochimica et Biophysica Acta 1838 (2014) 1406\u20131411"]}
DOI: 10.5281/zenodo.33382
title: Dopc Lipid Bilayer With Pyr6 Simulation Trajectory And Files From Franova Et Al. Bba 1838 (2014) 1406–1411

description: Simulation files for DOPC with PYR6 simulation from "Can pyrene probes be used to measure lateral pressure profiles of lipid membranes? Perspective through atomistic simulations" Franova et al. Biochimica et Biophysica Acta 1838 (2014) 1406–1411
description: {"references": ["Franova et al. Biochimica et Biophysica Acta 1838 (2014) 1406\u20131411"]}
DOI: 10.5281/zenodo.33394
title: Dopc Lipid Bilayer With Pyr10 Simulation Trajectory And Files From Franova Et Al. Bba 1838 (2014) 1406–1411

description: Simulation files for DOPC with PYR10 simulation from "Can pyrene probes be used to measure lateral pressure profiles of lipid membranes? Perspective through atomistic simulations" Franova et al. Biochimica et Biophysica Acta 1838 (2014) 1406–1411
description: {"references": ["Franova et al. Biochimica et Biophysica Acta 1838 (2014) 1406\u20131411"]}
DOI: 10.5281/zenodo.11896
title: Values Of The Reference Prior For The Poi(S+B) Model From Jinst 7 (2012) P01012

description: Plain text table with the values of the reference prior π(s) for the Poi(s+b) model used in the statistical inference about counting experiments, as explained in JINST 7 (2012) P01012, doi:10.1088/1748-0221/7/01/P01012, http://arxiv.org/abs/1108.4270.  The values are useful to find approximate expressions which are quicker to compute than the original prior, as explained in http://arxiv.org/abs/1407.5893 (where this dataset is referred to).

Each line is a sequence of spaces-separated values, and the file can be considered a table.  The first line starts with two strings "shape" and "rate" which represent the titles of the corresponding columns in the data table.  They refer to the shape and rate parameters defining the background prior.  Next, N signal values starting from s=0 to s=70 are reported.  They are the values at which π(s) is computed for any subsequent line.

Starting from the second line, the format is always the same.  The first two values are the shape and rate parameters defining the background prior used to compute π(s) in this line.  Next, the N values π(s=0), ..., π(s=70) are reported.  As π(0) = 1, the third column is constant (it might be useful to debug the data reading).

As explained in http://arxiv.org/abs/1108.4270, simple functional forms may be used to fit the N points (s, π(s)).  As the shape and rate parameters from the user's application may be different from those reported in this table, the following procedure shall give a very good approximation to π(s).  In the (log(shape), log(rate)) parameters space, locate the neighboring points to the user's background parameter values (in log-log scale).  Then interpolate each of the π(s) values to obtain a set of N values (a linear interpolation in log-log scale shall be sufficient).  Finally, fit these interpolated values to find the reference prior for the user's application.
description: {"references": ["10.1088/1748-0221/7/01/P01012"]}
DOI: 10.5281/zenodo.33413
title: Wds-Rda Publishing Data Workflows Working Group Analysis Sheet Final

description: <strong>NB: This dataset is superseded by:</strong>

Murphy, Fiona et al.. (2015). WDS-RDA-F11 Publishing Data Workflows WG Synthesis FINAL CORRECTED. Zenodo. 10.5281/zenodo.33899

Data Publishing Workflows collected and analysed between 1 February - 30 June 2015. Fields were populated using a combination of consultation and desk research. This is a refined version of the previous spreadsheet also lodged in Zenodo: 

Murphy, Fiona et al.. (2015). WDS-RDA Publishing Data Workflows Working Group Analysis sheet. Zenodo. 10.5281/zenodo.19107

Publication date: 29 June 2015

Keyword(s): <strong>data publishing, workflows, journals, repositories, research data</strong>
description: This is a previous version of Zenodo. 10.5281/zenodo.33899

 and a developed version of Zenodo. 10.5281/zenodo.19107
DOI: 10.5281/zenodo.33491
title: Model Systems With Gpcrs Embedded In Multicomponent Membranes

description: Files required to run coarse-grained simulations on various lipid membranes with embedded adenosine A_2A and dopamine D_2 receptors. These simulations were performed to study the effect of the presence of polyunsaturated fatty acid on GPCR oligomerization. The detailed description of the aims, methodologies and results of this study are explained in the research paper [1]. The composition and purpose of each simulated system will also be explained in this paper [1].

The Martini force field [2,3] was employed in the study, and the simulations were performed with version 4.5.x of the GROMACS package [4].

For each system the following (in GROMACS compatible format) is provided:

1) Initial structure (*Start.gro)

2) Topology file (*.top)

3) Index file (*.ndx)

In addition, for systems other than those containing only one protein, the final structure is given (*End.gro).

Other files required to run the simulations, which are common for all the systems, are also provided:

4) Simulation parameter file (.mdp)

5) Force field parameters (.itp)

 

<strong>References:</strong>

 

[1] Guixà-González et al., Membrane omega-3 fatty acids modulate the oligomerisation kinetics of adenosine A2A and dopamine D2 receptors. <em>Scientific Reports</em> <strong>6</strong>, Article number: 19839 (2016) <strong>DOI:</strong>10.1038/srep19839​

[2] Marrink et al., The MARTINI Force Field:  Coarse Grained Model for Biomolecular Simulations.<em> Journal of Physical Chemistry B </em><strong>111</strong>, 7812–7824 (2007), <strong>DOI:</strong>10.1021/jp071097f

[3] Monticelli et al., The MARTINI Coarse-Grained Force Field: Extension to Proteins.   <em>Journal of Chemical Theory and Computation </em><strong>4</strong>, 819–834 (2008), <strong>DOI:</strong>10.1021/ct700324x

[4] Pronk et al., GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. <em>Bioinformatics </em><strong>29</strong>  845-854 (2013), <strong>DOI:</strong>10.1093/bioinformatics/btt055
DOI: 10.5281/zenodo.33497
title: Bioactive Compounds With No Structural Analogs (High-Confidence Activity Data)

description: A set of 52,815 unique bioactive compounds (human targets, high-confidence activity data) with no structural analogs with high-confidence activity data was extracted from ChEMBL. For each compound the ChEMBL compound ID (CHEMBLID_Compound) and high-confidence target annotation(s) (CHEMBLID_Targets) are provided. The data set was generated as a part of an analysis to be published in 'Medicinal Chemistry Communications'.
DOI: 10.5281/zenodo.17602
title: Tapir Detection Histories (Tapirus Bairdii) From Rio Indio, Nicaragua

description: Camera trap detection histories from June-August 2014.
DOI: 10.5281/zenodo.17627
title: Update To Dartmouth Isochrones Triangulation

description: This file supersedes older dartmouth.tri uploads; for use with the "isochrones" python package, which should download this automatically.