cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.799692
title: Convergence of PyGBE with Kirkwood sphere

description: This file bundle includes data, figures and plotting scripts of convergence results for PyGBe and APBS using a spherical molecule of radius 4 Armstrong with a centered charge of –1e. The errors were calculated with respect to the corresponding extrapolated values (obtained from Richardson extrapolation). This result is part of the paper: —"A biomolecular electrostatics solver using Python, GPUs and boundary elements that can handle solvent-filled cavities and Stern layers", Christopher D. Cooper, Jaydeep P. Bardhan, L. A. Barba. <em>Comput. Phys. Comm.</em>, <strong>185</strong>(3):720–729 (March 2014). 10.1016/j.cpc.2013.10.028 // Preprint arXiv:1309.4018 PyGBe solves biomolecular electrostatics problems using an implicit-solvent model (Poisson-Boltzmann) and it uses GPU hardware for fast execution. It is written in Python, PyCUDA and CUDA and is open-source under MIT license. More information about the PyGBe code in: —<em>Validation of the PyGBe code for Poisson-Boltzmann equation with boundary element methods.</em> Christopher Cooper, Lorena A. Barba. figshare.<br>http://dx.doi.org/10.6084/m9.figshare.154331 <strong>Acknowledgement:</strong><br>This research is made possible by support from the Office of Naval Research, Applied Computational Analysis Program, N00014-11-1-0356. LAB also acknowledges support from NSF CAREER award OCI-1149784.
DOI: 10.6084/m9.figshare.799702
title: Convergence and time to solution of PyGBe with lysozyme molecule

description: This file bundle includes data, figures and plotting scripts of convergence and time-to-solution versus error for PyGBe and APBS using a lysozyme molecule. The errors were calculated with respect to the corresponding extrapolated values (obtained from Richardson extrapolation). This result is part of the paper: —"A biomolecular electrostatics solver using Python, GPUs and boundary elements that can handle solvent-filled cavities and Stern layers", Christopher D. Cooper, Jaydeep P. Bardhan, L. A. Barba. <em>Comput. Phys. Comm.</em>, <strong>185</strong>(3):720–729 (March 2014). 10.1016/j.cpc.2013.10.028 // Preprint arXiv:1309.4018 PyGBe solves biomolecular electrostatics problems using an implicit-solvent model (Poisson-Boltzmann) and it uses GPU hardware for fast execution. It is written in Python, PyCUDA and CUDA. More information about the PyGBe code in: <em>—Validation of the PyGBe code for Poisson-Boltzmann equation with boundary element methods</em>. Christopher Cooper, Lorena A. Barba. figshare.<br>http://dx.doi.org/10.6084/m9.figshare.154331 <strong>Acknowledgement:</strong><br>This research is made possible by support from the Office of Naval Research, Applied Computational Analysis Program, N00014-11-1-0356. LAB also acknowledges support from NSF CAREER award OCI-1149784.
DOI: 10.6084/m9.figshare.799711.v1
title: new fileset

description: R markdown code used in the preparation of the presentation at workshop section of academic week of forestry - CAV/UDESC Codigo de R markdown utilizado na preparação da apresentação realizada na seção de minicurso da semana academica em engenharia florestal - CAV/UDESC
DOI: 10.6084/m9.figshare.799681
title: Gaussian Job Archive for F4S2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.799680
title: Gaussian Job Archive for F4S2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.799681.v1
title: Gaussian Job Archive for F4S2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.799711.v2
title: R: Noções Básicas Aplicadas à Engenharia Florestal

description: R markdown code used in the preparation of the presentation at workshop section of academic week of forestry - CAV/UDESC Codigo de R markdown utilizado na preparação da apresentação realizada na seção de minicurso da semana academica em engenharia florestal - CAV/UDESC
DOI: 10.6084/m9.figshare.799678
title: Gaussian Job Archive for F6P2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.799679
title: Gaussian Job Archive for Cl2F2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.799680.v1
title: Gaussian Job Archive for F4S2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.799678.v1
title: Gaussian Job Archive for F6P2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.799679.v1
title: Gaussian Job Archive for Cl2F2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.799711.v3
title: Minicurso sobre noções básicas do R: Noções Básicas Aplicadas à Engenharia Florestal

description: R markdown code used in the preparation of the presentation at workshop section of academic week of forestry - CAV/UDESC Codigo de R markdown utilizado na preparação da apresentação realizada na seção de minicurso da semana academica em engenharia florestal - CAV/UDESC
DOI: 10.6084/m9.figshare.799711.v5
title: Minicurso: Noções Básicas Sobre o R Aplicadas à Engenharia Florestal

description: R markdown code used in the preparation of the presentation at workshop section of academic week of forestry - CAV/UDESC Codigo de R markdown utilizado na preparação da apresentação realizada na seção de minicurso da semana academica em engenharia florestal - CAV/UDESC
DOI: 10.6084/m9.figshare.798854
title: Neostromboceros albicomus (Konow, 1900), Lygodium sawfly

description: <strong><em>Neostromboceros albicomus</em> </strong>(Konow, 1900) (Hymenoptera, Tenthredinidae, Selandriinae) 39 specimens of <em>Neostromboceros albicomus</em> were examined from Thailand, Chiang Mai Province, collected by Saowapa Sonthichai with Malaise traps. According to the labels, the detailed data are as follows: 1–10 August 1997: 18.692°N 98.816°E, 270 m. Pa Huay Thong: Thambon Nam Bo Luang. Amphur Sampatong (7 ♀). 10–20 August 1997: 18.542°N 98.954°E, 250 m. Pa Huay Thong: Thambon Nam Bo Luang. Amphur Sampatong, in field at edge of mixed deciduous forest (2 ♀). 1–10 September 1997: Rim Pa Huay Tong, 18°48.07' N, 98°57.27' E, 270 m. Thambon Bo Luang. Amphur Sampatong, at edge of deciduous forest (11 ♀, 2♂ ). 10–20 September 1997: Rim Pa Huay Tong, 18°48.07' N, 98°57.27' E, 270 m. Thambon Bo Luang. Amphur Sampatong, at edge of deciduous forest (12 ♀, 2 ♂). 20–30 September 1997: Rim Pa Huay Tong, 18.801°N 98.938°E, 250 m. Thambon Nam Bo Luang. Amphur Sampatong, in mixed deciduous forest (3 ♀). Several specimens are figured to show the variability of this species. <strong>Taxonomy:</strong> Smith clarified the synonymy of the species, and synonymized the type species of <em>Neostromboceros, Stromboceros (Neostromboceros) metallica</em> Rohwer, 1912, with <em>N. albicomus</em>. Hitherto, the species is known from Malyasia, Philippines, Singapore, Thailand, Vietnam (Smith et al. 2002). <em>Stromboceros albicomus</em> KONOW, 1900. Type locality: Malaysia: Perak (4.100°N 101.016°E). Synonyms: <em>Stromboceros cenchralis</em> KONOW, 1908. Type locality: Philippines: Palawan Island (9.600°N 118.600°E) <em>Stromboceros (Neostromboceros) metallica</em> ROHWER, 1912. Type locality: Singapore, Malay Peninsula. One female collected February 25, 1909 (1.366°N 103.800°E). Konow, F. W. 1900: Neue Chalastogastra-Arten (Hym.). - Természetrajzi Füzetek, Budapest 24[1901]: 57-72 (preprint) Konow, F. W. 1908: Neue mittel- und südamerikanische Tenthrediniden. (Hym.). - Zeitschrift für systematische Hymenopterologie und Dipterologie, Teschendorf bei Stargard i. Mecklenburg 8(3): 144-163 Rohwer, S. A. 1912: Notes on sawflies, with descriptions of new species. - Proceedings of the United States National Museum, Washington 43: 205-251 Smith, D. R.; Wright, A. D.; Winotal, A.; Desmier de Chenon, R. 2002: Studies on <em>Neostromboceros albicomus</em> (Konow) (Hymenoptera: Tenthredinidae), a Potential Biological Control Agent for the Old World Climbing Fern, with Notes on Two Other Species of <em>Neostromboceros</em>. - Journal of Hymenoptera Research, Washington 11(1): 142-151.
DOI: 10.6084/m9.figshare.799711.v4
title: Minicurso sobre noções básicas do Aplicadas à Engenharia Florestal

description: R markdown code used in the preparation of the presentation at workshop section of academic week of forestry - CAV/UDESC Codigo de R markdown utilizado na preparação da apresentação realizada na seção de minicurso da semana academica em engenharia florestal - CAV/UDESC
DOI: 10.6084/m9.figshare.798854.v1
title: Neostromboceros albicomus (Konow, 1900), Lygodium sawfly

description: <strong><em>Neostromboceros albicomus</em> </strong>(Konow, 1900) (Hymenoptera, Tenthredinidae, Selandriinae) 39 specimens of <em>Neostromboceros albicomus</em> were examined from Thailand, Chiang Mai Province, collected by Saowapa Sonthichai with Malaise traps. According to the labels, the detailed data are as follows: 1–10 August 1997: 18.692°N 98.816°E, 270 m. Pa Huay Thong: Thambon Nam Bo Luang. Amphur Sampatong (7 ♀). 10–20 August 1997: 18.542°N 98.954°E, 250 m. Pa Huay Thong: Thambon Nam Bo Luang. Amphur Sampatong, in field at edge of mixed deciduous forest (2 ♀). 1–10 September 1997: Rim Pa Huay Tong, 18°48.07' N, 98°57.27' E, 270 m. Thambon Bo Luang. Amphur Sampatong, at edge of deciduous forest (11 ♀, 2♂ ). 10–20 September 1997: Rim Pa Huay Tong, 18°48.07' N, 98°57.27' E, 270 m. Thambon Bo Luang. Amphur Sampatong, at edge of deciduous forest (12 ♀, 2 ♂). 20–30 September 1997: Rim Pa Huay Tong, 18.801°N 98.938°E, 250 m. Thambon Nam Bo Luang. Amphur Sampatong, in mixed deciduous forest (3 ♀). Several specimens are figured to show the variability of this species. <strong>Taxonomy:</strong> Smith clarified the synonymy of the species, and synonymized the type species of <em>Neostromboceros, Stromboceros (Neostromboceros) metallica</em> Rohwer, 1912, with <em>N. albicomus</em>. Hitherto, the species is known from Malyasia, Philippines, Singapore, Thailand, Vietnam (Smith et al. 2002). <em>Stromboceros albicomus</em> KONOW, 1900. Type locality: Malaysia: Perak (4.100°N 101.016°E). Synonyms: <em>Stromboceros cenchralis</em> KONOW, 1908. Type locality: Philippines: Palawan Island (9.600°N 118.600°E) <em>Stromboceros (Neostromboceros) metallica</em> ROHWER, 1912. Type locality: Singapore, Malay Peninsula. One female collected February 25, 1909 (1.366°N 103.800°E). Konow, F. W. 1900: Neue Chalastogastra-Arten (Hym.). - Természetrajzi Füzetek, Budapest 24[1901]: 57-72 (preprint) Konow, F. W. 1908: Neue mittel- und südamerikanische Tenthrediniden. (Hym.). - Zeitschrift für systematische Hymenopterologie und Dipterologie, Teschendorf bei Stargard i. Mecklenburg 8(3): 144-163 Rohwer, S. A. 1912: Notes on sawflies, with descriptions of new species. - Proceedings of the United States National Museum, Washington 43: 205-251 Smith, D. R.; Wright, A. D.; Winotal, A.; Desmier de Chenon, R. 2002: Studies on <em>Neostromboceros albicomus</em> (Konow) (Hymenoptera: Tenthredinidae), a Potential Biological Control Agent for the Old World Climbing Fern, with Notes on Two Other Species of <em>Neostromboceros</em>. - Journal of Hymenoptera Research, Washington 11(1): 142-151.
DOI: 10.6084/m9.figshare.798826
title: Mouse responsivity and discrimination threshold data to rat kairomones

description: Dose responsiveness file:<br>Dose responsiveness of mice (n=10) to differing volumes (ul) of rat urine (kairomone) or control (PBS). Time was measured in seconds; total time in the enclosure was 600 seconds. Mice were exposed to concentrations in ascending order, with a 24 hour gap between tests. Data corresponds to Fig 1 in the main manuscript. Single dose responsiveness file: Responsiveness of mice (n=5) to a single volume (ul) of rat urine (kairomone) or control (PBS) over 5 days. Time was measured in seconds; total time in the enclosure was 600 seconds. Mice were exposed to concentrations in ascending order, with a 24 hour gap between tests. Detection threshold: Discrimination threshold of mice (n=15) when exposed to two different volumes (ul) of rat urine (kairomone): a specific volume vs. either a 20% or a 30% increase in this volume. Time was measured in seconds; total time in the enclosure was 600 seconds. Mice were exposed to concentrations in ascending order, with a 24 hour gap between tests. Data corresponds to Fig 2 in the main manuscript.
DOI: 10.6084/m9.figshare.798828
title: Annotation Comparison of 80 Million Human DNA Variants from a Whole-Genome Sequencing Study

description: These data are supplementary to the paper: McCarthy, DJ et al. Choice of transcripts and software has a large effect on variant annotation. Genome Medicine. 2014, 6:26. doi:10.1186/gm543 http://genomemedicine.com/content/6/3/26/abstract Variant annotation is a fundamental step in the analysis of genome sequence data. However, annotation results can vary widely depending on the transcript sets and software tools used to obtain annotations. This dataset was designed to investigate the extent of difference in annotations due to use of different transcript sets and different software tools. We recommend starting with the README.md file, which describes the contents of the two large data files. The archive source_code_for_mccarthy_et_al_2014_gm_anno_comparison.tar contains that the source code that was used to produce the results presented in the paper cited above. The two large files are gzipped, tab-delimited files containing details of annotations for 80 million DNA variants from a whole-genome sequencing study. The file union_rfs_ens_comparison_with_tx.tab.gz contains annotions using the RefSeq (version 57) and Ensembl (version 69) transcript sets obtained with the annotation package Annovar (version of Feb 2013). This dataset can be used to investigate the differences in annotation that arise when using these two transcript sets. The file ANV_VEP_ens_comparison_best_annos.tab.gz contains annotations using the Ensembl (version 69) transcript set, but different software tools: Annovar (version of Feb 2013) and Ensembl's Variant Effect Predictor (VEP; version 2.7). This dataset can be used to assess the differences in annotations due to different software tools even when they start with the same transcript set for the basis of variant annotation. Please consult the README.md file, the paper cited above and its supplementary material for more details on the data and results obtained from it.
DOI: 10.6084/m9.figshare.798826.v1
title: Mouse responsivity and discrimination threshold data to rat kairomones

description: Dose responsiveness file:<br>Dose responsiveness of mice (n=10) to differing volumes (ul) of rat urine (kairomone) or control (PBS). Time was measured in seconds; total time in the enclosure was 600 seconds. Mice were exposed to concentrations in ascending order, with a 24 hour gap between tests. Data corresponds to Fig 1 in the main manuscript. Single dose responsiveness file: Responsiveness of mice (n=5) to a single volume (ul) of rat urine (kairomone) or control (PBS) over 5 days. Time was measured in seconds; total time in the enclosure was 600 seconds. Mice were exposed to concentrations in ascending order, with a 24 hour gap between tests. Detection threshold: Discrimination threshold of mice (n=15) when exposed to two different volumes (ul) of rat urine (kairomone): a specific volume vs. either a 20% or a 30% increase in this volume. Time was measured in seconds; total time in the enclosure was 600 seconds. Mice were exposed to concentrations in ascending order, with a 24 hour gap between tests. Data corresponds to Fig 2 in the main manuscript.
DOI: 10.6084/m9.figshare.798828.v4
title: Annotation Comparison of 80 Million Human DNA Variants from a Whole-Genome Sequencing Study

description: These data are supplementary to the paper: McCarthy, DJ et al. Choice of transcripts and software has a large effect on variant annotation. Genome Medicine. 2014, 6:26. doi:10.1186/gm543 http://genomemedicine.com/content/6/3/26/abstract Variant annotation is a fundamental step in the analysis of genome sequence data. However, annotation results can vary widely depending on the transcript sets and software tools used to obtain annotations. This dataset was designed to investigate the extent of difference in annotations due to use of different transcript sets and different software tools. We recommend starting with the README.md file, which describes the contents of the two large data files. The archive source_code_for_mccarthy_et_al_2014_gm_anno_comparison.tar contains that the source code that was used to produce the results presented in the paper cited above. The two large files are gzipped, tab-delimited files containing details of annotations for 80 million DNA variants from a whole-genome sequencing study. The file union_rfs_ens_comparison_with_tx.tab.gz contains annotions using the RefSeq (version 57) and Ensembl (version 69) transcript sets obtained with the annotation package Annovar (version of Feb 2013). This dataset can be used to investigate the differences in annotation that arise when using these two transcript sets. The file ANV_VEP_ens_comparison_best_annos.tab.gz contains annotations using the Ensembl (version 69) transcript set, but different software tools: Annovar (version of Feb 2013) and Ensembl's Variant Effect Predictor (VEP; version 2.7). This dataset can be used to assess the differences in annotations due to different software tools even when they start with the same transcript set for the basis of variant annotation. Please consult the README.md file, the paper cited above and its supplementary material for more details on the data and results obtained from it.
DOI: 10.6084/m9.figshare.798819
title: Gaussian Job Archive for C153H153(1-)

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.798820
title: Gaussian Job Archive for C144H146

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.798824.v1
title: Gaussian Job Archive for F4S2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.798828.v3
title: Annotation Comparison

description: These data are supplementary to the paper: McCarthy, DJ et al. Choice of transcripts and software has a large effect on variant annotation. Genome Medicine. 2014, 6:26. doi:10.1186/gm543 http://genomemedicine.com/content/6/3/26/abstract Variant annotation is a fundamental step in the analysis of genome sequence data. However, annotation results can vary widely depending on the transcript sets and software tools used to obtain annotations. This dataset was designed to investigate the extent of difference in annotations due to use of different transcript sets and different software tools. We recommend starting with the README.md file, which describes the contents of the two large data files. The archive source_code_for_mccarthy_et_al_2014_gm_anno_comparison.tar contains that the source code that was used to produce the results presented in the paper cited above. The two large files are gzipped, tab-delimited files containing details of annotations for 80 million DNA variants from a whole-genome sequencing study. The file union_rfs_ens_comparison_with_tx.tab.gz contains annotions using the RefSeq (version 57) and Ensembl (version 69) transcript sets obtained with the annotation package Annovar (version of Feb 2013). This dataset can be used to investigate the differences in annotation that arise when using these two transcript sets. The file ANV_VEP_ens_comparison_best_annos.tab.gz contains annotations using the Ensembl (version 69) transcript set, but different software tools: Annovar (version of Feb 2013) and Ensembl's Variant Effect Predictor (VEP; version 2.7). This dataset can be used to assess the differences in annotations due to different software tools even when they start with the same transcript set for the basis of variant annotation. Please consult the README.md file, the paper cited above and its supplementary material for more details on the data and results obtained from it.
DOI: 10.6084/m9.figshare.798818
title: The Mediteranean Diet: Proximity to a Traditional Hunter Gater Diet

description: The Mediterranean “diet” has gained overwhelming popularity in recent health news because of its many proclaimed health benefits. As more adhering dieters start adapting the Med Diet into their lifestyle we can see how food intake habits and patterns directly affect human health. Aspects of the diet including plant-fat, high fiber foods, low glycemic foods, and seasonal fruits and vegetables making it comparable to a traditional hunter gather diet seperating it from a typical Western diet.
DOI: 10.6084/m9.figshare.798819.v1
title: Gaussian Job Archive for C153H153(1-)

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.798820.v1
title: Gaussian Job Archive for C144H146

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.797523
title: The Publishing Delay in Scholarly Peer-Reviewed Journals

description: The data describe was the basis for an article titled “The publishing delay in scholarly peer-reviewed journals” published in Journal of Informetrics doi:10.1016/j.joi.2013.09.00. This is the CSV file a codebook is also available
DOI: 10.6084/m9.figshare.797524
title: The Publishing Delay in Scholarly Peer-Reviewed Journals

description: The data described was the basis for an article titled “The publishing delay in scholarly peer-reviewed journals” published in Journal of Informetrics doi:10.1016/j.joi.2013.09.00. The methods section is included below followed by a codebook for the data contained in a CSV file.
DOI: 10.6084/m9.figshare.798818.v1
title: The Mediteranean Diet: Proximity to a Traditional Hunter Gater Diet

description: The Mediterranean “diet” has gained overwhelming popularity in recent health news because of its many proclaimed health benefits. As more adhering dieters start adapting the Med Diet into their lifestyle we can see how food intake habits and patterns directly affect human health. Aspects of the diet including plant-fat, high fiber foods, low glycemic foods, and seasonal fruits and vegetables making it comparable to a traditional hunter gather diet seperating it from a typical Western diet.