cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1344670.v1
title: Gaussian Job Archive for BrH5O6

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1344669.v1
title: Gaussian Job Archive for ClH5O6

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1344765.v3
title: SamSrf toolbox for pRF mapping

description: Our Matlab toolbox for pRF mapping analysis. Uses SPM and FreeSurfer functionality for preprocessing. Also requires Statistics Toolbox, Optimization Toolbox, and Curve Fitting Toolbox (not strictly necessary) for Matlab.<br><br>An extensive documentation "cookbook" is included. Please contact Sam (sampendu.wordpress.com) for any questions but please be advised that we are not able to provide tech support for people we don't collaborate with.<br><br>Current version: 5.49 (02-04-2015)
DOI: 10.6084/m9.figshare.1344765.v4
title: SamSrf toolbox for pRF mapping

description: Our Matlab toolbox for pRF mapping analysis. Uses SPM and FreeSurfer functionality for preprocessing. Also requires Statistics Toolbox, Optimization Toolbox, and Curve Fitting Toolbox (not strictly necessary) for Matlab.<br><br>An extensive documentation "cookbook" is included. Please contact Sam (sampendu.wordpress.com) for any questions but please be advised that we are not able to provide tech support for people we don't collaborate with.<br><br>Current version: 5.49 (02-04-2015)
DOI: 10.6084/m9.figshare.1344567
title: Gaussian Job Archive for ClH7O7

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1344570
title: Gaussian Job Archive for ClH5O6

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1344765.v5
title: SamSrf toolbox for pRF mapping

description: Our Matlab toolbox for pRF mapping analysis. Uses SPM and FreeSurfer functionality for preprocessing. Also requires Statistics Toolbox, Optimization Toolbox, and Curve Fitting Toolbox (not strictly necessary) for Matlab.<br><br>An extensive documentation "cookbook" is included. Please contact Sam (sampendu.wordpress.com) for any questions but please be advised that we are not able to provide tech support for people we don't collaborate with.<br><br>Current version: 5.49 (02-04-2015)
DOI: 10.6084/m9.figshare.1344542
title: international forest law

description: builds on http://figshare.com/articles/forest_governance_participation_dataset/1334120 with data about which countries are party to which instruments of international forest law
DOI: 10.6084/m9.figshare.1344544
title: Generation times data in Blastocystis by qPCR and by microscopy

description: Generation time (Tg) data of Blastocystis cultures in Barret’s and in Pavlova’s media during 48 h., from IBS patients and from asymptomatic carriers, measured by microscopy and by quantitative PCR are shown in present table. The generation times of Blastocystis isolates, were calculated according to Zhang et al. [17], with the following equation: Tg=(T2-T1)/(log2(n2/n1)), where Tg denotes the generation time, n1 represents the number of cultured parasitic organisms at the initial time (T1), and n2 represents the number of parasitic cells at subsequent time (T2). Thus, (T2-T1) = 48 hours of in vitro culture. Besides, for to absolute quantification by qPCR, it was necessary to consider i) the size of the Blastocystis genome ~ 18.8Mbp[36]; ii) 1pg of DNA ~ 978Mbp[37] and iii) the concentration of DNA control was 160ng/µL; thus, by cross multiplications, the number of copies of the genetic marker amplified were estimated.
DOI: 10.6084/m9.figshare.1344567.v1
title: Gaussian Job Archive for ClH7O7

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1344542.v2
title: international forest law

description: builds on http://figshare.com/articles/forest_governance_participation_dataset/1334120 with data about which countries are party to which instruments of international forest law
DOI: 10.6084/m9.figshare.1344765.v6
title: SamSrf toolbox for pRF mapping

description: Our Matlab toolbox for pRF mapping analysis. Uses SPM and FreeSurfer functionality for preprocessing. Also requires Statistics Toolbox, Optimization Toolbox, and Curve Fitting Toolbox (not strictly necessary) for Matlab.<br><br>An extensive documentation "cookbook" is included. Please contact Sam (sampendu.wordpress.com) for any questions but please be advised that we are not able to provide tech support for people we don't collaborate with.<br><br>Current version: 5.49 (02-04-2015)
DOI: 10.6084/m9.figshare.1344541
title: Gene expression analysis of Pacific oysters (Crassostrea gigas) subjected to accute heat stress

description: Gene expression changes, in response to heat shock, were compared between the pre- and post-heat shocked oysters. The RNA-seq analysis was performed using the Tuxedo suite. The Tuxedo suite was used to align the raw sequencing reads to the published Crassostrea gigas genome (ENSEMBL 1.24), quantify, and calculate differential gene expression between the two sample groups. This project for the Univ. of Washington class, FISH546 Winter 2015, contains the data products generated during the analysis, as well the Jupyter (IPython) notebook used for the analysis. The Jupyter notebook is included to encourage reproducibility and can be used to re-run the analysis in a semi-autonomous fashion. README.md Products/: This directory contains all products generated from the analysis of this project. The products within are described in detail in the data_records.md file. Reproducibility/: This directory contains the Jupyter (IPython) notebook and the sub-directories used by the notebook in order to reproduce the products in this project. background.md: Provides a brief summary of the underlying experiment and goals of this project. methods.md: Describes the means by which the data for this project was analyzed. data_records.md: Describes the various products generated by RNAseq_TopHat_Cufflinks_Workflow.ipynb, including describing the IPython notebook itself.
DOI: 10.6084/m9.figshare.1344544.v1
title: Generation times data in Blastocystis by qPCR and by microscopy

description: Generation time (Tg) data of Blastocystis cultures in Barret’s and in Pavlova’s media during 48 h., from IBS patients and from asymptomatic carriers, measured by microscopy and by quantitative PCR are shown in present table. The generation times of Blastocystis isolates, were calculated according to Zhang et al. [17], with the following equation: Tg=(T2-T1)/(log2(n2/n1)), where Tg denotes the generation time, n1 represents the number of cultured parasitic organisms at the initial time (T1), and n2 represents the number of parasitic cells at subsequent time (T2). Thus, (T2-T1) = 48 hours of in vitro culture. Besides, for to absolute quantification by qPCR, it was necessary to consider i) the size of the Blastocystis genome ~ 18.8Mbp[36]; ii) 1pg of DNA ~ 978Mbp[37] and iii) the concentration of DNA control was 160ng/µL; thus, by cross multiplications, the number of copies of the genetic marker amplified were estimated.
DOI: 10.6084/m9.figshare.1344570.v1
title: Gaussian Job Archive for ClH5O6

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1343279
title: Numerical simulation of abandoned gob methane drainage through surface vertical wells

description: Vertical displacements, reynolds number, and static pressureon on the survey line.
DOI: 10.6084/m9.figshare.1344542.v1
title: international forest law signatories

description: builds on http://figshare.com/articles/forest_governance_participation_dataset/1334120 with
DOI: 10.6084/m9.figshare.1343101
title: List of programs, by country, that promotes the return of Science, Technology, Engineering, and Mathematics (STEM) talent back to their home country.

description: Table 1. List of programs, by country, that promotes the return of Science, Technology, Engineering, and Mathematics (STEM) talent back to their home country. doi:10.1371/journal.pone.0118183.t001
DOI: 10.6084/m9.figshare.1344541.v1
title: Gene expression analysis of Pacific oysters (Crassostrea gigas) subjected to accute heat stress

description: Gene expression changes, in response to heat shock, were compared between the pre- and post-heat shocked oysters. The RNA-seq analysis was performed using the Tuxedo suite. The Tuxedo suite was used to align the raw sequencing reads to the published Crassostrea gigas genome (ENSEMBL 1.24), quantify, and calculate differential gene expression between the two sample groups. This project for the Univ. of Washington class, FISH546 Winter 2015, contains the data products generated during the analysis, as well the Jupyter (IPython) notebook used for the analysis. The Jupyter notebook is included to encourage reproducibility and can be used to re-run the analysis in a semi-autonomous fashion. README.md Products/: This directory contains all products generated from the analysis of this project. The products within are described in detail in the data_records.md file. Reproducibility/: This directory contains the Jupyter (IPython) notebook and the sub-directories used by the notebook in order to reproduce the products in this project. background.md: Provides a brief summary of the underlying experiment and goals of this project. methods.md: Describes the means by which the data for this project was analyzed. data_records.md: Describes the various products generated by RNAseq_TopHat_Cufflinks_Workflow.ipynb, including describing the IPython notebook itself.
DOI: 10.6084/m9.figshare.1344765.v7
title: SamSrf toolbox for pRF mapping

description: Our Matlab toolbox for pRF mapping analysis. Uses SPM and FreeSurfer functionality for preprocessing. Also requires Statistics Toolbox, Optimization Toolbox, and Curve Fitting Toolbox (not strictly necessary) for Matlab.<br><br>An extensive documentation "cookbook" is included. Please contact Sam (sampendu.wordpress.com) for any questions but please be advised that we are not able to provide tech support for people we don't collaborate with.<br><br>Current version: 5.49 (02-04-2015)
DOI: 10.6084/m9.figshare.1342823
title: TopoSWAT Source

description: Topography exerts critical control on many hydrologic, geomorphologic, and environmental biophysical processes. In order to properly model such dynamics in the Soil and Water Assessment Tool (SWAT), we explicitly integrate topography into the initialization procedure with a purpose-built extension. This ArcMap® toolbox (TopoSWAT) interfaces directly with ArcSWAT, to create multiple SWAT data layers, update the SWAT databases and generate the lookup tables required by the model. User defined data layers are processed in a single-step toolbox and include, aspect, elevation, and topographic index (TI), which are then intersected with the vector FAO Global Soils dataset. The toolbox then builds a soil raster layer at the resolution of the project’s base Digital Elevation Model and creates the ArcSWAT required ‘usersoil’ database table along with the corresponding soil lookup table required to map the specific raster soil values to the soil parameters in the ‘usersoil’ database table. This toolbox effectively creates a new soil dataset that incorporates topographic features. This standardized method and toolset allows SWAT modelers to easily incorporate topographic features they believe are important for their catchments without requiring any changes to the current ArcSWAT initialization system. Some of the topographic features may be necessary for process-based routines that one may want to incorporate into SWAT, e.g., energy-budget snowmelt modeling. However, such routines will need to be added to the SWAT model source code. This SWAT toolbox adds flexibility to SWAT modeling with little extra effort on the part of modelers.
DOI: 10.6084/m9.figshare.1342817
title: Germline DNA methylation in five coral transcriptomes

description: This directory comprises Jay Dimond's final project for FISH 546 - Winter 2015. This is a graduate course at the University of Washington taught by Dr. Steven Roberts. The project is an analysis of germline DNA methylation in five reef coral species. Further information on the project background, methods, and results can be found in the Background, Methods, and Data Records sections, respectively.
DOI: 10.6084/m9.figshare.1342816
title: Apertium LMF-RDF conversion scripts

description: To create the RDF version of an Apertium in LMF, 1. The LMF data has to be preprocessed with the lldtools.jar java program 2. In Open refine, three projects have to be created: two for the lexicons and one for the translation set. In each of the proyects, the corresponding json transformations have to be imported for 2.1 Data cleaning 2.2 RDF generation
DOI: 10.6084/m9.figshare.1342823.v1
title: TopoSWAT Source

description: Topography exerts critical control on many hydrologic, geomorphologic, and environmental biophysical processes. In order to properly model such dynamics in the Soil and Water Assessment Tool (SWAT), we explicitly integrate topography into the initialization procedure with a purpose-built extension. This ArcMap® toolbox (TopoSWAT) interfaces directly with ArcSWAT, to create multiple SWAT data layers, update the SWAT databases and generate the lookup tables required by the model. User defined data layers are processed in a single-step toolbox and include, aspect, elevation, and topographic index (TI), which are then intersected with the vector FAO Global Soils dataset. The toolbox then builds a soil raster layer at the resolution of the project’s base Digital Elevation Model and creates the ArcSWAT required ‘usersoil’ database table along with the corresponding soil lookup table required to map the specific raster soil values to the soil parameters in the ‘usersoil’ database table. This toolbox effectively creates a new soil dataset that incorporates topographic features. This standardized method and toolset allows SWAT modelers to easily incorporate topographic features they believe are important for their catchments without requiring any changes to the current ArcSWAT initialization system. Some of the topographic features may be necessary for process-based routines that one may want to incorporate into SWAT, e.g., energy-budget snowmelt modeling. However, such routines will need to be added to the SWAT model source code. This SWAT toolbox adds flexibility to SWAT modeling with little extra effort on the part of modelers.
DOI: 10.6084/m9.figshare.1344765.v8
title: SamSrf toolbox for pRF mapping

description: Our Matlab toolbox for pRF mapping analysis. Uses SPM and FreeSurfer functionality for preprocessing. Also requires Statistics Toolbox, Optimization Toolbox, and Curve Fitting Toolbox (not strictly necessary) for Matlab.<br><br>An extensive documentation "cookbook" is included. Please contact Sam (sampendu.wordpress.com) for any questions but please be advised that we are not able to provide tech support for people we don't collaborate with.<br><br>Current version: 5.6 (17-11-2015)
DOI: 10.6084/m9.figshare.1342816.v1
title: Apertium RDF Gold Standard for EN-CA, ES-CA, EN-ES translations

description: Gold stadard translations for the EN-CA, ES-CA, EN-ES language pairs, extracted from the Apertium RDF bilingual dictionaries (See http://linguistic.linkeddata.es/apertium/). This dataset is intended for testing indirect translations inferred from the Apertium RDF graph (eg., EN-ES-CA).
DOI: 10.6084/m9.figshare.1342817.v1
title: Germline methylation of five coral transcriptomes

description: This directory comprises Jay Dimond's final project for FISH 546 - Winter 2015. This is a graduate course at the University of Washington taught by Dr. Steven Roberts. The project is an analysis of germline DNA methylation in five coral species. Further information on the project background, methods, and results can be found in the Background, Methods, and Data Records sections, respectively.
DOI: 10.6084/m9.figshare.1344765.v9
title: SamSrf toolbox for pRF mapping

description: Our Matlab toolbox for pRF mapping analysis. Uses SPM and FreeSurfer functionality for preprocessing. Also requires Statistics Toolbox, Optimization Toolbox, and Curve Fitting Toolbox (not strictly necessary) for Matlab.<br><br>An extensive documentation "cookbook" is included. Please contact Sam (sampendu.wordpress.com) for any questions but please be advised that we are not able to provide tech support for people we don't collaborate with.<br><br>Current version: 5.61 (18-11-2015)
DOI: 10.6084/m9.figshare.1342816.v3
title: Apertium LMF-RDF conversion scripts

description: To create the RDF version of an Apertium in LMF, 1. The LMF data has to be preprocessed with the lldtools.jar java program 2. In Open refine, three projects have to be created: two for the lexicons and one for the translation set. In each of the proyects, the corresponding json transformations have to be imported for 2.1 Data cleaning 2.2 RDF generation
DOI: 10.6084/m9.figshare.1342823.v2
title: TopoSWAT Source

description: Topography exerts critical control on many hydrologic, geomorphologic, and environmental biophysical processes. In order to properly model such dynamics in the Soil and Water Assessment Tool (SWAT), we explicitly integrate topography into the initialization procedure with a purpose-built extension. This ArcMap® toolbox (TopoSWAT) interfaces directly with ArcSWAT, to create multiple SWAT data layers, update the SWAT databases and generate the lookup tables required by the model. User defined data layers are processed in a single-step toolbox and include, aspect, elevation, and topographic index (TI), which are then intersected with the vector FAO Global Soils dataset. The toolbox then builds a soil raster layer at the resolution of the project’s base Digital Elevation Model and creates the ArcSWAT required ‘usersoil’ database table along with the corresponding soil lookup table required to map the specific raster soil values to the soil parameters in the ‘usersoil’ database table. This toolbox effectively creates a new soil dataset that incorporates topographic features. This standardized method and toolset allows SWAT modelers to easily incorporate topographic features they believe are important for their catchments without requiring any changes to the current ArcSWAT initialization system. Some of the topographic features may be necessary for process-based routines that one may want to incorporate into SWAT, e.g., energy-budget snowmelt modeling. However, such routines will need to be added to the SWAT model source code. This SWAT toolbox adds flexibility to SWAT modeling with little extra effort on the part of modelers.
DOI: 10.6084/m9.figshare.1342816.v2
title: Apertium LMF-RDF conversion scripts

description: TO BE COMPLETED
DOI: 10.6084/m9.figshare.1342798
title: Bootstrapped evidence toolbox

description: Bootstrapped evidence toolbox for using the methods described in my article "Non-dichotomous inference using bootstrapped evidence" (currently unpublished)
DOI: 10.6084/m9.figshare.1342817.v2
title: Germline methylation of five coral transcriptomes

description: This directory comprises Jay Dimond's final project for FISH 546 - Winter 2015. This is a graduate course at the University of Washington taught by Dr. Steven Roberts. The project is an analysis of germline DNA methylation in five coral species. Further information on the project background, methods, and results can be found in the Background, Methods, and Data Records sections, respectively.
DOI: 10.6084/m9.figshare.1344765.v10
title: SamSrf toolbox for pRF mapping

description: Our Matlab toolbox for pRF mapping analysis. Uses SPM and FreeSurfer functionality for preprocessing. Also requires Statistics Toolbox, Optimization Toolbox, and Curve Fitting Toolbox (not strictly necessary) for Matlab.<br><br>An extensive documentation "cookbook" is included. Please contact Sam (sampendu.wordpress.com) for any questions but please be advised that we are not able to provide tech support for people we don't collaborate with.<br><br>Current version: 5.62 (26-11-2015)
DOI: 10.6084/m9.figshare.1342817.v4
title: Germline DNA methylation in five coral transcriptomes

description: This directory comprises Jay Dimond's final project for FISH 546 - Winter 2015. This is a graduate course at the University of Washington taught by Dr. Steven Roberts. The project is an analysis of germline DNA methylation in five reef coral species. Further information on the project background, methods, and results can be found in the Background, Methods, and Data Records sections, respectively.
DOI: 10.6084/m9.figshare.1342817.v3
title: Germline methylation of five coral transcriptomes

description: This directory comprises Jay Dimond's final project for FISH 546 - Winter 2015. This is a graduate course at the University of Washington taught by Dr. Steven Roberts. The project is an analysis of germline DNA methylation in five coral species. Further information on the project background, methods, and results can be found in the Background, Methods, and Data Records sections, respectively.
DOI: 10.6084/m9.figshare.1344765.v12
title: SamSrf toolbox for pRF mapping

description: Current version: 5.63 (15-12-2015)Our Matlab toolbox for pRF mapping analysis. Uses SPM8 (12 should also be okay) and FreeSurfer functionality for preprocessing. Also requires Statistics Toolbox, Optimization Toolbox, and Curve Fitting Toolbox (not strictly necessary) for Matlab.<br><br>An extensive documentation "cookbook" is included. Please contact Sam (sampendu.wordpress.com) for any questions but please be advised that we are not able to provide tech support for people we don't collaborate with.As of version 5.63, we included a new tutorial explaining how to delineate visual areas using the DelineationTool in MatLab and giving advice on what to do with tricky retinotopic maps.<br>
DOI: 10.6084/m9.figshare.1342795
title: Evolution of the perlecan/HSPG2 gene and its activation in regenerating Nematostella vectensis

description: In situ images, sequence data and phylogeny from our paper concerning the evolution of the perlecan/HSPG2 gene and its activation during regeneration of Nematostella vectensis.
DOI: 10.6084/m9.figshare.1342796
title: Discordance in Recovery Between Altered Locomotion and Muscle Atrophy Induced by Simulated Microgravity in Rats

description: ABSTRACTExposure to a microgravity environment leads to adverse effects in motion and musculoskeletal properties. However, few studies have investigated the recovery of altered locomotion and muscle atrophy simultaneously. The authors investigated altered locomotion in rats submitted to simulated microgravity by hindlimb unloading for 2 weeks. Motion deficits were characterized by hyperextension of the knees and ankle joints and forward-shifted limb motion. Furthermore, these locomotor deficits did not revert to their original form after a 2-week recovery period, although muscle atrophy in the hindlimbs had recovered, implying discordance in recovery between altered locomotion and muscle atrophy, and that other factors such as neural drives might control behavioral adaptations to microgravity.
DOI: 10.6084/m9.figshare.1342798.v1
title: Bootstrapped evidence toolbox - Version 1.00

description: Bootstrapped evidence toolbox for using the methods described in my article "Non-dichotomous inference using bootstrapped evidence" (currently unpublished)