cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.92425
title: Weak scaling of parallel FMM vs. FFT up to 4096 processes

description: This figure shows the weak scaling of a parallel FMM-based fluid solver on GPUs, from 1 to 4096 processes. The FMM (fast multipole method) is used as the numerical engine in a vortex method fluid solver, simulating decaying isotropic turbulence. The reference method for this application is the pseudo-spectral method, which uses FFT as the numerical engine. Given the communication pattern of FFT, only 14% parallel efficiency is obtained with the spectral method on 4096 processes (no GPU acceleration). The parallel efficiency of the FMM-based solver is 74% going from one to 4096 processes (one GPU per MPI process, 3 GPUs per node). It is important to note that the results correspond to the full-application codes, not just the FMM and FFT algorithms. The spectral method calculations were done using the 'hit3d' code (see link below). The size of the largest problem corresponds to a 4096^3 mesh, i.e., almost 69 billion points (about 17 million points per process). These calculations were run on the TSUBAME 2.0 system of the Tokyo Institute of Technology, thanks to guest access, during October 2011. We include here the dataset (ASCII files in 1003.zip), the Matlab plotting script (readTimes1003.m) and the figure file (weakGPU.pdf) that is being included in the following paper: “Petascale turbulence simulation using a highly parallel fast multipole method”, Rio Yokota, L A Barba, Tetsu Narumi, Kenji Yasuoka. Comput. Phys. Comm. (online 13 Sept. 2012) doi:10.1016/j.cpc.2012.09.011<br>Preprint arXiv:1106.5273 [cs.NA] The figure is here shared under CC-BY 3.0. Please use the handle and doi above for citation if you use it.
DOI: 10.6084/m9.figshare.92425.v1
title: Weak scaling of parallel FMM vs. FFT up to 4096 processes

description: This figure shows the weak scaling of a parallel FMM-based fluid solver on GPUs, from 1 to 4096 processes. The FMM (fast multipole method) is used as the numerical engine in a vortex method fluid solver, simulating decaying isotropic turbulence. The reference method for this application is the pseudo-spectral method, which uses FFT as the numerical engine. Given the communication pattern of FFT, only 14% parallel efficiency is obtained with the spectral method on 4096 processes (no GPU acceleration). The parallel efficiency of the FMM-based solver is 74% at 4096 processes (one GPU per MPI process, 3 GPUs per node). It is important to note that the results correspond to the full-application codes, not just the FMM and FFT algorithms. The spectral method calculations were done using the 'hit3d' code (see link below). The size of the largest problem corresponds to a 4096^3 mesh, i.e., almost 69 billion points (about 17 million points per process). These calculations were run on the TSUBAME 2.0 system of the Tokyo Institute of Technology, thanks to guest access, during Fall 2011. The figure is here shared under CC-BY. Please use the handle and doi above for citation if you use it.
DOI: 10.6084/m9.figshare.92424.v1
title: Magnitude of the bubble effect on transfer velocity for CO2 vs DMS using the Woolf (1997) bubble model

description: to follow
DOI: 10.6084/m9.figshare.92426.v1
title: ExaFMM: An open source library for Fast Multipole Methods

description: This is a trifold brochure, prepared to accompany our poster on the exaFMM code, presented at the Supercomputing Conference, November 2011, Seattle. <strong>What's new? An open source FMM</strong>—The fast multipole method (FMM) is a numerical engine used in many applications, from acoustics, electrostatics, fluid simulations, wave scattering, and more. Despite its importance, there is a lack of open community code, which arguably has affected its wider adoption. It is also a difficult algorithm to understand and to program, making availability of open-source implementations even more desirable. Items in the brochure: - Method: multiople-based, hierarchical - Features - Performance: Strong and weak scaling - GPU relevance: Compute-bound - Applications: Electrostatics, Turbulence Simulation It folds like a trifold brochure! Instructions: http://autobodyconsultinggrp.wordpress.com/2011/01/17/tri-fold_brochure/
DOI: 10.6084/m9.figshare.92425.v2
title: Weak scaling of parallel FMM vs. FFT up to 4096 processes

description: This figure shows the weak scaling of a parallel FMM-based fluid solver on GPUs, from 1 to 4096 processes. The FMM (fast multipole method) is used as the numerical engine in a vortex method fluid solver, simulating decaying isotropic turbulence. The reference method for this application is the pseudo-spectral method, which uses FFT as the numerical engine. Given the communication pattern of FFT, only 14% parallel efficiency is obtained with the spectral method on 4096 processes (no GPU acceleration). The parallel efficiency of the FMM-based solver is 74% going from one to 4096 processes (one GPU per MPI process, 3 GPUs per node). It is important to note that the results correspond to the full-application codes, not just the FMM and FFT algorithms. The spectral method calculations were done using the 'hit3d' code (see link below). The size of the largest problem corresponds to a 4096^3 mesh, i.e., almost 69 billion points (about 17 million points per process). These calculations were run on the TSUBAME 2.0 system of the Tokyo Institute of Technology, thanks to guest access, during October 2011. We include here the dataset (ASCII files in 1003.zip), the Matlab plotting script (readTimes1003.m) and the figure file (weakGPU.pdf) that is being included in the following paper: Petascale turbulence simulation using a highly parallel fast multipole method on GPUs, R. Yokota , L. A. Barba, T. Narumi, K. Yasuoka. To appear in <em>Computer Physics Communications</em>. Preprint arXiv:1106.5273v2 [cs.NA] The figure is here shared under CC-BY 3.0. Please use the handle and doi above for citation if you use it.
DOI: 10.6084/m9.figshare.92419
title: 3 figures summarising field data on ocean-atmosphere gas transfer velocity

description: Plots (and code and data to generate plots) demonstrating our current understanding and field data on air-sea gas transfer velocity. If you want to re-plot then download all the files in this fileset into a directory and 'source' kw_plots.R (you'll need R installed). Note, code released under CC_BY-SA licence (share-alike). Plots CC-BY (just attribution required) Readme file and further details to follow.
DOI: 10.6084/m9.figshare.92411
title: Data for "Fish lateral line innovation: insights into the evolutionary genomic dynamics of a unique mechanosensory organ"

description: This zip file "Fish_lateral_line_comparative_genomics_data" contains two folders and two text files. The data contained in them pretains to the manuscript: Siby Philip, João Paulo Machado, Emanuel Maldonado, Vítor Vasconcelos, Stephen J O’Brien, Warren E Johnson, and Agostinho Antunes. Fish lateral line innovation: insights into the evolutionary genomic dynamics of a unique mechanosensory organ. Mol Biol Evol first published online July 27, 2012 doi:10.1093/molbev/mss194 The first folder "nexus_sequence_and_tree_file" contain "nexus" format files for all the 34 genes used in the study, the GBlocks filtered alignment followed by the corresponding phylogenetic tree. This file was used to carry out the HYPHY compartmentalization analysis (see the manuscript for details). The phylogenetic trees were built using PHYML and the best fit nucleotide substitution model was found using MrAIC, which is presented in the text file "MrAIC_AICc_models.txt". The second folder contains the phylogenetic trees used for the PAML analysis of the Postduplication branches, thus there are only 15 trees as specified in the manuscript. The text files contain the MrAIC chosen best fit substitution model (file 1) and the PyCogent Ensembl query script used (file 2; this same script is available in the PyCogent cookbook). any further request for data or detailed results should be addressed to Siby Philip (sibyphilips at gmail dot com).
DOI: 10.6084/m9.figshare.92419.v1
title: 3 figures summarising field data on ocean-atmosphere gas transfer velocity

description: Plots (and code and data to generate plots) demonstrating our current understanding and field data on air-sea gas transfer velocity. code to plot figures is in kw_plots.R Note, code released under CC_BY-SA licence (share-alike). Plots CC-BY (just attribution required) Readme file and further details to follow.
DOI: 10.6084/m9.figshare.92404
title: Aligner-specific VCF files containing the mutations called for each set of reads in single and paired-end modes

description: VCF files describing the mutations detected in the sixty-seven groups of BRCA1 reads when testing each alignment program in paired-end and single-end mode.
DOI: 10.6084/m9.figshare.92411.v2
title: Data for "Fish lateral line innovation: insights into the evolutionary dynamics of a unique mechanosensory organ"

description: This zip file "Fish_lateral_line_comparative_genomics_data" contains two folders and two text files. The data contained in them pretains to the manuscript "Fish lateral line innovation: insights into the evolutionary dynamics of a unique mechanosensory organ" Siby Philip, João Paulo Machado1, Emanuel Maldonado, Vítor Vasconcelos, Stephen J O'Brien, Warren E Johnson and Agostinho Antunes The first folder "nexus_sequence_and_tree_file" contains "nexus" format files for all the 34 genes used in this study, the GBlocks filtered alignment followed by the corresponding phylogenetic tree. This file was used to carry out the HYPHY compartmentalization analysis (see the manuscript for details). The phylogenetic trees were built using PHYML and the best fit nucleotide substitution model was found using MrAIC, which is presented in the text file "MrAIC_AICc_models.txt". The second folder contains the phylogenetic trees used for the PAML analysis of the Postduplication branches, thus there are only 15 trees as specified in the manuscript. The text files contain the MrAIC chosen best fit substitution model (file 1) and the PyCogent Ensembl query script used (file 2; this same script is available in the PyCogent cookbook). ny further request for data or detailed results should be addressed to Siby Philip (philipsiby at gmail dot com).
DOI: 10.6084/m9.figshare.92411.v3
title: Data for "Fish lateral line innovation: insights into the evolutionary genomic dynamics of a unique mechanosensory organ"

description: This zip file "Fish_lateral_line_comparative_genomics_data" contains two folders and two text files. The data contained in them pretains to the manuscript: Siby Philip, João Paulo Machado, Emanuel Maldonado, Vítor Vasconcelos, Stephen J O’Brien, Warren E Johnson, and Agostinho Antunes. Fish lateral line innovation: insights into the evolutionary genomic dynamics of a unique mechanosensory organ. Mol Biol Evol first published online July 27, 2012 doi:10.1093/molbev/mss194 The first folder "nexus_sequence_and_tree_file" contain "nexus" format files for all the 34 genes used in the study, the GBlocks filtered alignment followed by the corresponding phylogenetic tree. This file was used to carry out the HYPHY compartmentalization analysis (see the manuscript for details). The phylogenetic trees were built using PHYML and the best fit nucleotide substitution model was found using MrAIC, which is presented in the text file "MrAIC_AICc_models.txt". The second folder contains the phylogenetic trees used for the PAML analysis of the Postduplication branches, thus there are only 15 trees as specified in the manuscript. The text files contain the MrAIC chosen best fit substitution model (file 1) and the PyCogent Ensembl query script used (file 2; this same script is available in the PyCogent cookbook). any further request for data or detailed results should be addressed to Siby Philip (sibyphilips at gmail dot com).
DOI: 10.6084/m9.figshare.92419.v2
title: 3 figures summarising field data on ocean-atmosphere gas transfer velocity

description: Plots (and code and data to generate plots) demonstrating our current understanding and field data on air-sea gas transfer velocity. code to plot figures is in kw_plots.R Note, code released under CC_BY-SA licence (share-alike). Plots CC-BY (just attribution required) Readme file and further details to follow.
DOI: 10.6084/m9.figshare.92401
title: VCF files describing the known mutations in each read file

description: VCF files describing the mutations contained in the sixty-seven groups of BRCA1 reads. These were selected from a test set of 2211 (1299 unique) known BRCA1 variants containing 1340 SNPs, 320 insertions and 551 deletions.
DOI: 10.6084/m9.figshare.92393
title: Gaussian Job Archive for B2(2-)

description: Gaussian Job Archive
DOI: 10.6084/m9.figshare.92372
title: List of interactive public display systems

description: List of publications about interactive public display systems, used in the analysis about interactive controls.
DOI: 10.6084/m9.figshare.92372.v3
title: List of interactive public display systems

description: List of publications about interactive public display systems, used in the analysis about interactive controls.
DOI: 10.6084/m9.figshare.92393.v2
title: Gaussian Job Archive for B2(2-)

description: Gaussian Job Archive
DOI: 10.6084/m9.figshare.92372.v2
title: Uncovering interactive controls for public displays

description: Poster presented at the International Symposium on Pervasive Displays (June 2012) in Porto, Portugal.
DOI: 10.6084/m9.figshare.92393.v1
title: Gaussian Job Archive for B2(2-)

description: Gaussian Job Archive
DOI: 10.6084/m9.figshare.92338
title: Simulated Illumina BRCA1 reads in FASTQ format

description: Sixty-seven groups of 200,000 90bp paired-end FASTQ Illumina reads from the human BRCA1 gene (hg19). Each sequence grouping was mutated in-silico to introduce a combination of 20 SNPs and 13 INDELs.
DOI: 10.6084/m9.figshare.92338.v1
title: Simulated Illumina BRCA1 reads in FASTQ format

description: Sixty-seven groups of 200,000 90bp paired-end FASTQ Illumina reads from the human BRCA1 gene (hg19). Each sequence grouping was mutated in-silico to introduce a combination of 20 SNPs and 13 INDELs.
DOI: 10.6084/m9.figshare.92324.v1
title: Movie S5 - orange, light blue, green, purple, blue.mov

description: <strong>Movie S5.</strong> High diversity. In this scenario, five type survive the bottleneck: <em>CNp</em> (orange), <em>Cnp</em> (light blue), <em>cNp</em> (green), <em>cnP</em> (purple), and <em>cnp</em> (blue). This scenario includes the mutualistic interactions between single-enzyme producers as in Movie S2, the asymmetric coalition between <em>CNp</em> and <em>cnP</em> in Movie S4, and competition from cheaters, leading to a complex set of interactions. <em>CNp</em> is able to grow much faster than other types because it is more independent and catalyzes its own growth. This community is stable to invasion by other types due to mutation and represents the highest diversity outcome of this scenario.
DOI: 10.6084/m9.figshare.92320
title: Should children with ADHD be given fish oil tablets instead of the drug Ritalin?

description: A report including various studies on whether or not Ritalin is beneficial to children with ADHD and if fish oils would be an appropriate subsitute.
DOI: 10.6084/m9.figshare.92320.v1
title: Should children with ADHD be given fish oil tablets instead of the drug Ritalin?

description: A report including various studies on whether or not Ritalin is beneficial to children with ADHD and if fish oils would be an appropriate subsitute.
DOI: 10.6084/m9.figshare.92314
title: Visual Search experiment (Vogel)

description: Vogel experiment data and results
DOI: 10.6084/m9.figshare.92315
title: Stimulus appraisal and cardiac reactivity

description: Data and results from study published in: Mocaiber, I., Perakakis, P., Pereira, M., Machado-Pinheiro, W., Volchan, E., de Oliveira, L., Vila, J. (2011). Stimulus appraisal modulates cardiac reactivity to briefly presented mutilation pictures. International Journal of Psychophysi- ology. 81, pp. 299–304
DOI: 10.6084/m9.figshare.92314.v1
title: Visual Search experiment (Vogel)

description: Vogel experiment data and results
DOI: 10.6084/m9.figshare.92315.v1
title: Stimulus appraisal and cardiac reactivity

description: Data and results from study published in: Mocaiber, I., Perakakis, P., Pereira, M., Machado-Pinheiro, W., Volchan, E., de Oliveira, L., Vila, J. (2011). Stimulus appraisal modulates cardiac reactivity to briefly presented mutilation pictures. International Journal of Psychophysi- ology. 81, pp. 299–304
DOI: 10.6084/m9.figshare.92280
title: Data file from Wicherts and Bakker (2012)

description: Data file from: Wicherts, J. M. & Bakker, M. (2012). Publish (your data) or (let the data) perish! Why not publish your data too? <em>Intelligence, 40,</em> 73-76.
DOI: 10.6084/m9.figshare.92280.v1
title: Data file from Wicherts and Bakker (2012)

description: Data file from: Wicherts, J. M. & Bakker, M. (2012). Publish (your data) or (let the data) perish! Why not publish your data too? <em>Intelligence, 40,</em> 73-76.
DOI: 10.6084/m9.figshare.92258
title: Lipid droplet census, ctd.

description: We observe diversity of lipid droplet morphology in yeast cells treated with the SSRI antidepressant sertraline/Zoloft, including lipid droplet fusion, fisson and assimllation into organelles involved in vesicle transport. For context, please see a link to the Perlstein lab's recent PLoS ONE paper, which shows that sertraline induces lipid droplet formation in mutants with altered clathrin function.
DOI: 10.6084/m9.figshare.92258.v1
title: Lipid droplet census, ctd.

description: We observe diversity of lipid droplet morphology in yeast cells treated with the SSRI antidepressant sertraline/Zoloft, including lipid droplet fusion, fisson and assimllation into organelles involved in vesicle transport. For context, please see a link to the Perlstein lab's recent PLoS ONE paper, which shows that sertraline induces lipid droplet formation in mutants with altered clathrin function.
DOI: 10.6084/m9.figshare.92221
title: Lipid droplet census

description: Lipid droplet intermediates have recently been described in the fission yeast <em>Schizosaccharomyces pombe</em> (please see link below). These intermediates arise from fission and fusion events, and presumably occur during lipid droplet biogenesis, degradation or interaction with other organelles. Here we show similar and novel lipid droplet intermediates in the budding yeast <em>Saccharomyces cerevisiae</em>.
DOI: 10.6084/m9.figshare.92221.v1
title: Lipid droplet census

description: Lipid droplet intermediates have recently been described in the fission yeast <em>Schizosaccharomyces pombe</em> (please see link below). These intermediates arise from fission and fusion events, and presumably occur during lipid droplet biogenesis, degradation or interaction with other organelles. Here we show similar and novel lipid droplet intermediates in the budding yeast <em>Saccharomyces cerevisiae</em>.
DOI: 10.6084/m9.figshare.92221.v3
title: Lipid droplet census

description: Lipid droplet intermediates have recently been described in the fission yeast <em>Schizosaccharomyces pombe</em> (please see link below). These intermediates arise from fission and fusion events, and presumably occur during lipid droplet biogenesis, degradation or interaction with other organelles. Here we show similar and novel lipid droplet intermediates in the budding yeast <em>Saccharomyces cerevisiae</em>.
DOI: 10.6084/m9.figshare.92186.v1
title: social network analysis of biomedical research in the philippines

description: Third best paper, poster category, presented at the National Medical Students' Conference 2011 (April 2011) in Manila, Philippines.
DOI: 10.6084/m9.figshare.92221.v2
title: Lipid droplet census

description: Lipid droplet intermediates have recently been described in the fission yeast <em>Schizosaccharomyces pombe</em> (please see link below). These intermediates arise from fission and fusion events, and presumably occur during lipid droplet biogenesis, degradation or interaction with other organelles. Here we show similar and novel lipid droplet intermediates in the budding yeast <em>Saccharomyces cerevisiae</em>.
DOI: 10.6084/m9.figshare.92201.v1
title: Virological Survey of Surface Waters in Norway

description: Poster submitted to the 3rd Food and Environmental Virology Conference, held in Lisbon, Portugal, 7-10 October 2012.
DOI: 10.6084/m9.figshare.92168
title: Is this bilayer expansion?

description: A clathrin heavy chain (chc1) mutant that is resistant to the SSRI antidepressant sertraline/Zoloft exhibits what appears to be bilayer expansion under both steady state and sertraline-treated conditions. It is also possible that the expansion of electron lucent (that is, white) material is occurring inside the lumen of amphisomes (aka autophagolysosomes). What do you think? Please annotate in the comment thread below.
DOI: 10.6084/m9.figshare.12922036.v1
title: Additional file 11 of Annual dialysis data report for 2018, JSDT Renal Data Registry: survey methods, facility data, incidence, prevalence, and mortality

description: Additional file 11. Trends in major causes of death for 1983-2018
DOI: 10.6084/m9.figshare.12922039
title: Additional file 12 of Annual dialysis data report for 2018, JSDT Renal Data Registry: survey methods, facility data, incidence, prevalence, and mortality

description: Additional file 12. Trend in annual crude death rate for 1983-2018
DOI: 10.6084/m9.figshare.12922033.v1
title: Additional file 10 of Annual dialysis data report for 2018, JSDT Renal Data Registry: survey methods, facility data, incidence, prevalence, and mortality

description: Additional file 10. Deceased dialysis patient distribution by cause of death and sex for 2018
DOI: 10.6084/m9.figshare.12922045.v1
title: Additional file 14 of Annual dialysis data report for 2018, JSDT Renal Data Registry: survey methods, facility data, incidence, prevalence, and mortality

description: Additional file 14. Trend in average age of incident dialysis patients for 1983-2018
DOI: 10.6084/m9.figshare.12922048
title: Additional file 15 of Annual dialysis data report for 2018, JSDT Renal Data Registry: survey methods, facility data, incidence, prevalence, and mortality

description: Additional file 15. Incident dialysis patient distribution by primary disease and sex for 2018
DOI: 10.6084/m9.figshare.12922057.v1
title: Additional file 18 of Annual dialysis data report for 2018, JSDT Renal Data Registry: survey methods, facility data, incidence, prevalence, and mortality

description: Additional file 18. Trends in major causes of death during the incident year for 1990-2018
DOI: 10.6084/m9.figshare.12922042
title: Additional file 13 of Annual dialysis data report for 2018, JSDT Renal Data Registry: survey methods, facility data, incidence, prevalence, and mortality

description: Additional file 13. Incident dialysis patient distribution by age and sex for 2018
DOI: 10.6084/m9.figshare.12922051.v1
title: Additional file 16 of Annual dialysis data report for 2018, JSDT Renal Data Registry: survey methods, facility data, incidence, prevalence, and mortality

description: Additional file 16. Trends in major primary diseases of incident dialysis patients for 1983-2018
DOI: 10.6084/m9.figshare.12922057
title: Additional file 18 of Annual dialysis data report for 2018, JSDT Renal Data Registry: survey methods, facility data, incidence, prevalence, and mortality

description: Additional file 18. Trends in major causes of death during the incident year for 1990-2018
DOI: 10.6084/m9.figshare.12922033
title: Additional file 10 of Annual dialysis data report for 2018, JSDT Renal Data Registry: survey methods, facility data, incidence, prevalence, and mortality

description: Additional file 10. Deceased dialysis patient distribution by cause of death and sex for 2018