cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.940987
title: ERCB-Nephromine-EuRenOmics Database

description: The main goal of WP7 is to develop a multiscalar view of rare renal diseases by integrating diverse large-scale data sources. Data generated in WP 2-6 as well as data from cooperating consortia and publically available datasets will be implemented in the EURenOmics platform. The European Renal cDNA Bank (ERCB) hosts over 2600 renal biopsies with anonymized clinical parameters. In this consortium more than 550 genome-wide Affymetrix-based datasets from glomerular and tubulointerstitial specimen from 289 patients have been generated. Out of these, a dataset comprising of 369 samples (183 glomerular, 186 tubulointerstitial) and their basic clinical data has been selected to be integrated in the EURenOmics database. These include data from patients with minimal change disease (n=24), focal segmental glomerulosclerosis (n=47), membranous nephropathy (n=39), but also data from patients with diabetic nephropathy (n=11), hypertensive nephropathy (n=35), IgA nephropathy (n=52) and lupus nephritis (n=64). Pretransplant biopsies from living donors were used as controls (n=84). Another resource for transcriptomic data is Nephromine (http://nephromine.org). It is a web-based kidney specific systems biology search engine that provides data from 20 publically available gene expression datasets from 1757 samples (murine and human), incorporates clinical data and allows various analyses (differential gene expression, coexpression, outlier analysis and concept association). A basic database concept has been defined and a web-based functional data repository allowing a smooth up-and download as well as sharing data amongst partners has been generated. Uploaded data will be used to establish a multilevel analysis domain (EuRenOmics Database), which allows the integration of data from different –omics platforms as well as the implementation of clinical information. The interactive platform provides standardized and harmonized datasets and uses existing architectures from Genomatix’s GePS and ElDorado databases. This search engine will provide a central bioinformatics platform which allows addressing mechanistic, diagnostic and therapeutic challenges at the systems biology level.
DOI: 10.6084/m9.figshare.940993.v1
title: Hydrogen diffusion around a Si(001)/Si(110) corner

description: Coordinate files and XYZ files for hydrogen diffusion around a corner on nanopillar on Si(001). Paper available at: http://arxiv.org/abs/1404.1769 Accepted in J. Phys.:Condens. Matter
DOI: 10.6084/m9.figshare.940973
title: Data of ventricular mechanistic measurements evaluation

description: Data 1 control: Circumferential strain in one healthy control<br>Data show the circumferential strain in the left ventricular wall in one healthy control during systole (columns: sectors 1-160, rows: time 0-620 ms). Data 1 patient: Circumferential strain in one patient<br>Data show the circumferential strain in the left ventricular wall in one patient during systole (columns: sectors 1-160, rows: time 0-620 ms). Data 2 controls: Global strains of healthy controls<br>Data show the global strains of all healthy controls during systole (columns: subject 1-9, rows: time 0-580 ms). Data 2 patients: Global strains of patients<br>Data show the global strains of all patients during systole (columns: subject 1-10, rows: time 0-580 ms)
DOI: 10.6084/m9.figshare.940973.v1
title: Data of ventricular mechanistic measurements evaluation

description: Data 1 control: Circumferential strain in one healthy control<br>Data show the circumferential strain in the left ventricular wall in one healthy control during systole (columns: sectors 1-160, rows: time 0-620 ms). Data 1 patient: Circumferential strain in one patient<br>Data show the circumferential strain in the left ventricular wall in one patient during systole (columns: sectors 1-160, rows: time 0-620 ms). Data 2 controls: Global strains of healthy controls<br>Data show the global strains of all healthy controls during systole (columns: subject 1-9, rows: time 0-580 ms). Data 2 patients: Global strains of patients<br>Data show the global strains of all patients during systole (columns: subject 1-10, rows: time 0-580 ms)
DOI: 10.6084/m9.figshare.939455
title: Structures of microhydrated calcium oxalate clusters

description: These are the structures reported in: Rosas-García, Victor M., Isabel del Carmen Sáenz-Tavera, Verónica Janeth Rodríguez-Herrera, y Benjamín Raymundo Garza-Campos. «Microsolvation and Hydration Enthalpies of CaC2O4(H2O) N (n = 0-16) and C2O4 2-(H2O) N (n = 0-14): An Ab Initio Study». Journal of Molecular Modeling 19, n.o 4 (1 de abril de 2013): 1459-1471. doi:10.1007/s00894-012-1707-6
DOI: 10.6084/m9.figshare.939420
title: Original 1200 dpi plates for Wilf et al. 2014 Agathis zamunerae paper in American Journal of Botany.

description: Original resolution, 1200 dpi versions of figures published in: Wilf P, IH Escapa, NR Cúneo, RM Kooyman, KR Johnson, A Iglesias. 2014. First South American <em>Agathis</em> (Araucariaceae), Eocene of Patagonia. American Journal of Botany, v. 101, p. 156-179. doi:10.3732/ajb.1300327
DOI: 10.6084/m9.figshare.939455.v1
title: Structures of microhydrated calcium oxalate clusters

description: These are the structures reported in: Rosas-García, Victor M., Isabel del Carmen Sáenz-Tavera, Verónica Janeth Rodríguez-Herrera, y Benjamín Raymundo Garza-Campos. «Microsolvation and Hydration Enthalpies of CaC2O4(H2O) N (n = 0-16) and C2O4 2-(H2O) N (n = 0-14): An Ab Initio Study». Journal of Molecular Modeling 19, n.o 4 (1 de abril de 2013): 1459-1471. doi:10.1007/s00894-012-1707-6
DOI: 10.6084/m9.figshare.939405
title: Gaussian Job Archive for C15H20FeGeN2O4

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.939405.v1
title: Gaussian Job Archive for C15H20FeGeN2O4

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.939420.v1
title: Original 1200 dpi plates for Wilf et al. 2014 Agathis zamunerae paper in American Journal of Botany.

description: Original resolution, 1200 dpi versions of figures published in: Wilf P, IH Escapa, NR Cúneo, RM Kooyman, KR Johnson, A Iglesias. 2014. First South American <em>Agathis</em> (Araucariaceae), Eocene of Patagonia. American Journal of Botany, v. 101, p. 156-179. doi:10.3732/ajb.1300327
DOI: 10.6084/m9.figshare.939420.v2
title: Original 1200 dpi plates for Wilf et al. 2014 Agathis zamunerae paper in American Journal of Botany.

description: Original resolution, 1200 dpi versions of figures published in: Wilf P, IH Escapa, NR Cúneo, RM Kooyman, KR Johnson, A Iglesias. 2014. First South American <em>Agathis</em> (Araucariaceae), Eocene of Patagonia. American Journal of Botany, v. 101, p. 156-179. doi:10.3732/ajb.1300327
DOI: 10.6084/m9.figshare.939420.v3
title: Original 1200 dpi plates for Wilf et al. 2014 Agathis zamunerae paper in American Journal of Botany.

description: Original resolution, 1200 dpi versions of figures published in: Wilf P, IH Escapa, NR Cúneo, RM Kooyman, KR Johnson, A Iglesias. 2014. First South American <em>Agathis</em> (Araucariaceae), Eocene of Patagonia. American Journal of Botany, v. 101, p. 156-179. doi:10.3732/ajb.1300327
DOI: 10.6084/m9.figshare.939374
title: Gaussian Job Archive for C30H40Fe2Ge2N4O8

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.939375
title: Gaussian Job Archive for C30H40Fe2Ge2N4O8

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.939372
title: Mutations in ANKS6 cause a Nephronophthisis‐Like Phenotype with End Stage Renal Disease

description: Nephronophthisis (NPHP) is one of the most common genetic causes of chronic kidney disease (CKD); however the underlying genetic abnormalities have been established in less than 50% of cases. We performed genome-wide analysis followed by targeted re-sequencing in a Turkish consanguineous multiplex family and identified a canonic splice site mutation in ANKS6 as the cause of an NPHP-like phenotype. Furthermore, we identified 4 additional ANKS6 variants in a cohort of 56 unrelated patients diagnosed with CKD due to nephronophthisis, chronic glomerulonephritis, interstitial nephritis or unknown etiology. We demonstrated expression of ANKS6 in human embryonic kidneys and showed that both total and active β-catenin were increased in pre-cystic tubuli in Cy/+ rats, indicating strong activation of the Wnt pathway
DOI: 10.6084/m9.figshare.939373
title: IDL routine to compute BANYAN II field contamination probabilities

description: Computes the probability that a given candidate member to a nearby, young moving association (NYA) originates from the field distribution, according to the Monte Carlo analysis presented in Gagné et al. (2014). Please cite this reference when using this routine. All required IDL Data files (.sav format) are also included here.
DOI: 10.6084/m9.figshare.939374.v1
title: Gaussian Job Archive for C30H40Fe2Ge2N4O8

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.939420.v5
title: Original 1200 dpi plates for Wilf et al. 2014 Agathis zamunerae paper in American Journal of Botany.

description: Original resolution, 1200 dpi versions of figures published in: Wilf P, IH Escapa, NR Cúneo, RM Kooyman, KR Johnson, A Iglesias. 2014. First South American <em>Agathis</em> (Araucariaceae), Eocene of Patagonia. American Journal of Botany, v. 101, p. 156-179. doi:10.3732/ajb.1300327
DOI: 10.6084/m9.figshare.939375.v1
title: Gaussian Job Archive for C30H40Fe2Ge2N4O8

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.939371
title: PartitionFinder source code version 1.1.0

description: This is source code for PartitionFinder version 1.1.0. The .tar.gz file contains a copy of the entire GitHub repository at the time that this version was created. This file can also be found on GitHub, assuming that the repo still exists, here: <br><br>https://github.com/brettc/partitionfinder/archive/v1.1.0.tar.gz#<br><br>And the latest version of the source code for PartitionFinder can be found here: https://github.com/brettc/partitionfinder/
DOI: 10.6084/m9.figshare.939372.v1
title: Mutations in ANKS6 cause a Nephronophthisis‐Like Phenotype with End Stage Renal Disease

description: Nephronophthisis (NPHP) is one of the most common genetic causes of chronic kidney disease (CKD); however the underlying genetic abnormalities have been established in less than 50% of cases. We performed genome-wide analysis followed by targeted re-sequencing in a Turkish consanguineous multiplex family and identified a canonic splice site mutation in ANKS6 as the cause of an NPHP-like phenotype. Furthermore, we identified 4 additional ANKS6 variants in a cohort of 56 unrelated patients diagnosed with CKD due to nephronophthisis, chronic glomerulonephritis, interstitial nephritis or unknown etiology. We demonstrated expression of ANKS6 in human embryonic kidneys and showed that both total and active β-catenin were increased in pre-cystic tubuli in Cy/+ rats, indicating strong activation of the Wnt pathway
DOI: 10.6084/m9.figshare.939420.v4
title: Original 1200 dpi plates for Wilf et al. 2014 Agathis zamunerae paper in American Journal of Botany.

description: Original resolution, 1200 dpi versions of figures published in: Wilf P, IH Escapa, NR Cúneo, RM Kooyman, KR Johnson, A Iglesias. 2014. First South American <em>Agathis</em> (Araucariaceae), Eocene of Patagonia. American Journal of Botany, v. 101, p. 156-179. doi:10.3732/ajb.1300327
DOI: 10.6084/m9.figshare.938920
title: Data From: Selecting optimal partitioning schemes for phylogenomic datasets.

description: This collection includes all of the input files, results, and scripts to generate the figures found in this paper: Selecting optimal partitioning schemes for phylogenomic datasets. Robert Lanfear, Brett Calcott, David Kainer, Christoph Mayer, Alexandros Statmatakis Which is accepted at BMC Evolutionary Biology
DOI: 10.6084/m9.figshare.938920.v1
title: Data From: Selecting optimal partitioning schemes for phylogenomic datasets.

description: This collection includes all of the input files, results, and scripts to generate the figures found in this paper: Selecting optimal partitioning schemes for phylogenomic datasets. Robert Lanfear, Brett Calcott, David Kainer, Christoph Mayer, Alexandros Statmatakis Which is accepted at BMC Evolutionary Biology
DOI: 10.6084/m9.figshare.939373.v1
title: IDL routine to compute BANYAN II field contamination probabilities

description: Computes the probability that a given candidate member to a nearby, young moving association (NYA) originates from the field distribution, according to the Monte Carlo analysis presented in Gagné et al. (2014). Please cite this reference when using this routine. All required IDL Data files (.sav format) are also included here.
DOI: 10.6084/m9.figshare.938242
title: Wynton-Anglim Booking Task (The WAB Task)

description: The Wynton-Anglim Booking Task is a task for studying skill acquisition. Additional information about the task will be made available at a later point.The version posted is the same version used in Anglim and Wynton (2015). If you use the task, please cite:Anglim, J., & Wynton, S. K. (2015). Hierarchical Bayesian models of subtask learning. <i>Journal of experimental psychology: learning, memory, and cognition</i>, <i>41</i>(4), 957-974. doi:10.1037/xlm0000103 Licence: MIT Designed by: Sarah K. A. Wynton and Jeromy Anglim Programmed by: Simon A. Wynton<br><br>
DOI: 10.6084/m9.figshare.938243.v1
title: Analysis for "Hierarchical Bayesian Models of Subtask Learning Consistency on a Simulated Booking Task"

description: This is a place holder file that will eventually be replaced with the data and analysis code for the manuscript: "Hierarchical Bayesian Models of Subtask Learning Consistency on a Simulated Booking Task".
DOI: 10.6084/m9.figshare.939373.v2
title: IDL routine to compute BANYAN II field contamination probabilities

description: Computes the probability that a given candidate member to a nearby, young moving association (NYA) originates from the field distribution, according to the Monte Carlo analysis presented in Gagné et al. (2014). Please cite this reference when using this routine. All required IDL Data files (.sav format) are also included here.
DOI: 10.6084/m9.figshare.938242.v1
title: Wynton-Anglim Booking Task

description: The Wynton-Anglim Booking Task is a task for studying skill acquisition. Additional information about the task will be made available at a later point.
DOI: 10.6084/m9.figshare.938230
title: Connecting diagnostic labs: Cafe Variome and DNA sequencing software

description: During the FP7 project GEN2PHEN (http://www.gen2phen.org/) we developed the concept of sharing pointers to diagnostics data to facilitate the public exchange of the existence of information, avoiding the problem of directly exchanging diagnostics information. A minimal set of data was defined to point to variant/mutation information generated by diagnostics laboratories: required data are exact genomic positions of the detected variants and the source (which lab or user generated the data, or publication or public data base), optional information may include the amino acid or protein change, phenotype information, or an anonymised patient identifier. The project also developed a standard to exchange the information: VarioML (http://varioml.org/). We present Café Variome, which has been implemented as a federated market place for these pointers: a public instance has been created (http://www.cafevariome.org/) and populated with public data (such as dbSNP, 1000 Genomes…) or pointers to data (HGMD, LSDBs…). Users can either chose to submit directly to this public instance, or setup a local instance to share detailed data with selected collaborators (such as a national network or a disease-specific collaboration) and connect this instance to the public instance, sharing only pointers. The system has comprehensive management tools for fine-grained user control as well as data sharing control. Because manual data submission is error prone as well as a major barrier to usage, we implemented public APIs to allow both the submission and automated query automatically of data via secure internet connection. We will present two examples of this automatic transmission of pointer information: Gensearch for capillary DNA sequencing and GensearchNGS for NGS DNA sequencing.
DOI: 10.6084/m9.figshare.938243.v2
title: Analysis for "Hierarchical Bayesian Models of Subtask Learning Consistency on a Simulated Booking Task"

description: This is a place holder file that will eventually be replaced with the data and analysis code for the manuscript: "Hierarchical Bayesian Models of Subtask Learning Consistency on a Simulated Booking Task".
DOI: 10.6084/m9.figshare.938235
title: Soaring migratory birds avoid wind farm

description: Supporting data set
DOI: 10.6084/m9.figshare.938242.v2
title: Wynton-Anglim Booking Task

description: The Wynton-Anglim Booking Task is a task for studying skill acquisition. Additional information about the task will be made available at a later point.
DOI: 10.6084/m9.figshare.938235.v1
title: Soaring migratory birds avoid wind farm

description: Supporting data set
DOI: 10.6084/m9.figshare.938242.v4
title: Wynton-Anglim Booking Task (The WAB Task)

description: The Wynton-Anglim Booking Task is a task for studying skill acquisition. Additional information about the task will be made available at a later point.The version posted is the same version used in Anglim and Wynton (2015). If you use the task, please cite:Anglim, J., & Wynton, S. K. (2015). Hierarchical Bayesian models of subtask learning. <i>Journal of experimental psychology: learning, memory, and cognition</i>, <i>41</i>(4), 957-974. doi:10.1037/xlm0000103 Licence: MIT Designed by: Sarah K. A. Wynton and Jeromy Anglim Programmed by: Simon A. Wynton<br><br>
DOI: 10.6084/m9.figshare.938243.v3
title: Analysis for "Hierarchical Bayesian Models of Subtask Learning Consistency on a Simulated Booking Task"

description: This is a place holder file that will eventually be replaced with the data and analysis code for the manuscript: "Hierarchical Bayesian Models of Subtask Learning Consistency on a Simulated Booking Task".
DOI: 10.6084/m9.figshare.938218
title: Alignment investigation script

description: A simple script in Python which can be used to display alignments from BLAST xml results. Allows identification of specific proteins from large searches.
DOI: 10.6084/m9.figshare.938219
title: Translation Script

description: A python script which allows multiple sequences to be translated in to 6 frames.
DOI: 10.6084/m9.figshare.938242.v3
title: Wynton-Anglim Booking Task

description: The Wynton-Anglim Booking Task is a task for studying skill acquisition. Additional information about the task will be made available at a later point. Licence: MIT Designed by: Sarah K. A. Wynton and Jeromy Anglim Programmed by: Simon A. Wynton
DOI: 10.6084/m9.figshare.938243.v4
title: Analysis for "Hierarchical Bayesian Models of Subtask Learning"

description: This is a place holder file that will eventually be replaced with the data and analysis code for the manuscript: "Hierarchical Bayesian Models of Subtask Learning" following acceptance for publication.
DOI: 10.6084/m9.figshare.938217
title: BLAST Query Script

description: Python script which allows multiple files and sequences to be queried against any of the local blast databases, and return the results in xml file format.
DOI: 10.6084/m9.figshare.938219.v1
title: Translation Script

description: A python script which allows multiple sequences to be translated in to 6 frames.
DOI: 10.6084/m9.figshare.938216
title: Online Blast Script

description: Python script which allows queries to be made against the online version of the BLAST database, and results returned in xml format.
DOI: 10.6084/m9.figshare.938217.v1
title: BLAST Query Script

description: Python script which allows multiple files and sequences to be queried against any of the local blast databases, and return the results in xml file format.
DOI: 10.6084/m9.figshare.938207
title: Influence of Population Structure on Variance Decomposition

description: Variance decomposition of 'startle response' in <em>Drosophila melongaster</em> and 'mastitis 1.2' in Danish Holstein dairy cattle. Variance is partitioned by sets of randomly sampled genes. Files: <strong>'results.pdf' is the main report of results; compiled from following script.</strong> 'results.Rnw' is a knitr script to produce final report and figures for paper. 'results_partitioning.txt' contain results from analysis on startle response. Remaining data files contain results from multiple complex traits in dairy cattle, evaluations on reduced models and statistics from AI-REML algorithm.
DOI: 10.6084/m9.figshare.938214
title: JIT Requirements Quality Framework

description: Until now quality assessment of requirements has focused on traditional up-front requirements. Just-in-time (JIT) requirements are by definition incomplete, not specific and might be ambiguous when initially specified, indicating a different notion of ‘correctness’. We analyze how assessment of JIT requirements quality should be performed, based on literature of traditional and JIT requirements. We have designed a quality framework for JIT requirements and instantiated it for feature requests in open source projects. We have translated the framework into a checklist with a scoring algorithm to evaluate feature requests. We have performed an initial qualitative validation of our checklist for feature requests with eight practitioners from the Dutch agile community, receiving overall positive feedback. Then we conducted an experiment with over 80 software engineers to apply the checklist on three open source projects. This resulted in quantitative data from over 550 feature requests, together with some qualitative feedback. We use the same data to present a summarized view of the feature request quality for the three open source projects. The data sets, check list, questionnaire and interview questions (in Dutch) can be found on-line for reference.
DOI: 10.6084/m9.figshare.938243.v5
title: Analysis for "Hierarchical Bayesian Models of Subtask Learning"

description: This is a place holder file that will eventually be replaced with the data and analysis code for the manuscript: "Hierarchical Bayesian Models of Subtask Learning" following acceptance for publication.
DOI: 10.6084/m9.figshare.938193
title: Data of paraflocculus cochlear trauma and modulation of gene expression.

description: Cochlear threshold data<br>Spreadsheet showing animal number (column A), treatment of each animal (column B) and cochlear threshold data. Cochlear threshold data are supplied as compound action potential (CAP) threshold values for frequency range 4 to 24 kHz in dB SPL determined ipsilaterally before treatment (Columns A-K), immediately after treatment (Columns L-V) and 2 weeks after treatment (Columns W-AG) as well as contralaterally 2 weeks after treatment (Columns AJ-AT). RT-PCR Data<br>Spreadsheet showing animal number (column A), treatment of each animal (column B) and replicate Ct values for gene of interest and for housekeeping genes ribosomal protein S16 (RPS16) and beta-2-microglobulin (B2M) (column E), from samples from left and right paraflocculus (PF). Columns C-H data for GABA-A receptor subunit alpha 1 (GABRA1); columns I-N data for glutamate decarboxylase 1 (GAD1); columns O-T data for glutamate receptor NMDA subunit 1 (GRIN1); columns U-Z data for a member of RAB family of small GTPase (RAB3A).