cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24701392
title: Data_and_Code.zip from Applying collective motion models to study discordant individual behaviours within a school of fish

description: Computational models of collective motion successfully reproduce the most common behaviours of a school of fish, using only a few elementary interactions between individuals. However, their ability to also reproduce individual behaviours that are discordant from those of the group has not yet been adequately investigated. In this paper, a self-propelled particle model using three interaction zones is considered in relation to the counter-rotation of an individual: a phenomenon observable in real schools of fish milling in a torus, when an individual moves in the same torus but in the opposite direction for a certain period of time. This study shows that the interactions of repulsion, orientation and attraction between individuals moving at constant speed in a three-dimensional space, with asynchronous updating, can generate temporary counter-rotations. The analysis of such events sheds light on the mechanisms that start the counter-rotation and those that end it. Although the contribution of the repulsion interaction is often significant to start and terminate the counter-rotation, it does not prove to be decisive. Indeed, it is observed that even when interactions between individuals are limited to attraction alone, temporary counter-rotations of individuals occur, provided the fish density along the circumference is not uniform. Some of these conclusions, deduced from the simulations performed, are visually consistent with what is observed in some underwater video recordings of milling schools of fish.
DOI: 10.6084/m9.figshare.24701392.v1
title: Data_and_Code.zip from Applying collective motion models to study discordant individual behaviours within a school of fish

description: Computational models of collective motion successfully reproduce the most common behaviours of a school of fish, using only a few elementary interactions between individuals. However, their ability to also reproduce individual behaviours that are discordant from those of the group has not yet been adequately investigated. In this paper, a self-propelled particle model using three interaction zones is considered in relation to the counter-rotation of an individual: a phenomenon observable in real schools of fish milling in a torus, when an individual moves in the same torus but in the opposite direction for a certain period of time. This study shows that the interactions of repulsion, orientation and attraction between individuals moving at constant speed in a three-dimensional space, with asynchronous updating, can generate temporary counter-rotations. The analysis of such events sheds light on the mechanisms that start the counter-rotation and those that end it. Although the contribution of the repulsion interaction is often significant to start and terminate the counter-rotation, it does not prove to be decisive. Indeed, it is observed that even when interactions between individuals are limited to attraction alone, temporary counter-rotations of individuals occur, provided the fish density along the circumference is not uniform. Some of these conclusions, deduced from the simulations performed, are visually consistent with what is observed in some underwater video recordings of milling schools of fish.
DOI: 10.48567/sr1e-t053
title:  Palmer Station climatology summary data, 1989-present (ongoing).
DOI: 10.48567/cerh-x235
title: Palmer Station CLIMAT surface observational data, 2007-present (ongoing).
DOI: 10.6084/m9.figshare.24701992
title: Supplementary Material - Tables from Gene expression patterns of <i>Salpa thompsoni</i> reveal remarkable differences in metabolism and reproduction near the Antarctic Polar Front

description: <i>Salpa thompsoni</i> is an important grazer in the Southern Ocean and most abundant in the Antarctic Polar Front (APF) region. During recent decades, their distribution expanded southwards. However, it is unclear whether salps can maintain their populations in the high Antarctic regions throughout the year due to a poor understanding of their physiological responses to changing environmental conditions. We examined gene expression signatures of salps collected in two geographically close regions south of the APF that differed in water mass composition and productivity. The observed differences in the expression of genes related to reproductive, cellular and metabolic processes reflect variations in water temperature and food supply between the two regions studied here. Our study contributes to a better understanding of the physiological responses of <i>S. thompsoni</i> to changing environmental conditions, and how the species may adapt to a changing environment through potential geographical population shifts under future climate change scenarios.
DOI: 10.6084/m9.figshare.24701992.v1
title: Supplementary Material - Tables from Gene expression patterns of <i>Salpa thompsoni</i> reveal remarkable differences in metabolism and reproduction near the Antarctic Polar Front

description: <i>Salpa thompsoni</i> is an important grazer in the Southern Ocean and most abundant in the Antarctic Polar Front (APF) region. During recent decades, their distribution expanded southwards. However, it is unclear whether salps can maintain their populations in the high Antarctic regions throughout the year due to a poor understanding of their physiological responses to changing environmental conditions. We examined gene expression signatures of salps collected in two geographically close regions south of the APF that differed in water mass composition and productivity. The observed differences in the expression of genes related to reproductive, cellular and metabolic processes reflect variations in water temperature and food supply between the two regions studied here. Our study contributes to a better understanding of the physiological responses of <i>S. thompsoni</i> to changing environmental conditions, and how the species may adapt to a changing environment through potential geographical population shifts under future climate change scenarios.
DOI: 10.48567/0fzs-fy93
title: Palmer Station Automated Weather Data System observational data, 2001-present (ongoing).
DOI: 10.6084/m9.figshare.22720711
title: Supplemental Table S1. Means, standard deviations, and correlation coefficients for cardiorespiratory fitness with summary sleep variables

description: Supplemental material for Cardiorespiratory Fitness and Circadian Rhythms in Adolescents: A Pilot Study.
DOI: 10.6084/m9.figshare.22720708
title: Supplemental Table S2. Means, standard deviations, and correlation coefficients for cardiorespiratory fitness with physical activity and circadian rhythm variables of the sample with participants without morning sport commitments (N=16).

description: Supplemental material for Cardiorespiratory Fitness and Circadian Rhythms in Adolescents: A Pilot Study.
DOI: 10.6084/m9.figshare.24270766
title: Supplemental Table S3. Means, standard deviations, and correlation coefficients for cardiorespiratory fitness with circadian rhythm variables of the entire sample, stratified by sex (N=18).

description: Supplemental material for Cardiorespiratory Fitness and Circadian Rhythms in Adolescents: A Pilot Study.
DOI: 10.6084/m9.figshare.24270775
title: Supplemental Table S4. Means, standard deviations, and correlation coefficients for cardiorespiratory fitness with circadian rhythm variables of the entire sample, stratified by pubertal status (N=18).

description: Supplemental material for Cardiorespiratory Fitness and Circadian Rhythms in Adolescents: A Pilot Study.
DOI: 10.6084/m9.figshare.24702282.v1
title: Brugia malayi ATAC-seq metagenome assembly binned contigs

description: We performed ATAC-seq on <i>Brugia malayi</i> adult female samples containing the endosymbiotic bacterium <i>Wolbachia</i>. The reads were randomly downsampled to 10 million reads. Metagenome assembly was performed using metaSpades. Here, we provide the output of the metaSpades assembly after binning by sequencing depth (1000 avg reads), removing all contigs mapping to <i>Brugia</i>, and removing contigs less than 500 bps in length.
DOI: 10.6084/m9.figshare.24702858
title: Brugia malayi gDNA metagenome assembly all contigs

description: We performed gDNA sequencing on <i>Brugia malayi</i> adult female samples containing the endosymbiotic bacterium <i>Wolbachia</i>. The reads were randomly downsampled to 10 million reads. Metagenome assembly was performed using metaSpades. Here, we provide the output of the metaSpades assembly with all contigs present.
DOI: 10.6084/m9.figshare.24701145
title: Brugia malayi ATAC-seq metagenome assembly all contigs

description: We performed ATAC-seq on <i>Brugia malayi</i> adult female samples containing the endosymbiotic bacterium <i>Wolbachia</i>. The reads were randomly downsampled to 10 million reads. Metagenome assembly was performed using metaSpades. Here, we provide the output of the metaSpades assembly with all contigs present.
DOI: 10.6084/m9.figshare.24701145.v1
title: Brugia malayi ATAC-seq metagenome assembly all contigs

description: We performed ATAC-seq on <i>Brugia malayi</i> adult female samples containing the endosymbiotic bacterium <i>Wolbachia</i>. The reads were randomly downsampled to 10 million reads. Metagenome assembly was performed using metaSpades. Here, we provide the output of the metaSpades assembly with all contigs present.
DOI: 10.6084/m9.figshare.24702282
title: Brugia malayi ATAC-seq metagenome assembly binned contigs

description: We performed ATAC-seq on <i>Brugia malayi</i> adult female samples containing the endosymbiotic bacterium <i>Wolbachia</i>. The reads were randomly downsampled to 10 million reads. Metagenome assembly was performed using metaSpades. Here, we provide the output of the metaSpades assembly after binning by sequencing depth (1000 avg reads), removing all contigs mapping to <i>Brugia</i>, and removing contigs less than 500 bps in length.
DOI: 10.6084/m9.figshare.24702858.v1
title: Brugia malayi gDNA metagenome assembly all contigs

description: We performed gDNA sequencing on <i>Brugia malayi</i> adult female samples containing the endosymbiotic bacterium <i>Wolbachia</i>. The reads were randomly downsampled to 10 million reads. Metagenome assembly was performed using metaSpades. Here, we provide the output of the metaSpades assembly with all contigs present.
DOI: 10.57967/hf/1411
title: 8chan
DOI: 10.6084/m9.figshare.24703149
title: Brugia malayi gDNA metagenome assembly binned contigs

description: We performed gDNA sequencing on <i>Brugia malayi</i> adult female samples containing the endosymbiotic bacterium <i>Wolbachia</i>. The reads were randomly downsampled to 10 million reads. Metagenome assembly was performed using metaSpades. Here, we provide the output of the metaSpades assembly with the binned contigs. Contigs were binned by BLASTN results, keeping all contigs that map to bacterial sequences in the NT database. All contigs with a length less than 500 bps were removed.
DOI: 10.6084/m9.figshare.24703149.v1
title: Brugia malayi gDNA metagenome assembly binned contigs

description: We performed gDNA sequencing on <i>Brugia malayi</i> adult female samples containing the endosymbiotic bacterium <i>Wolbachia</i>. The reads were randomly downsampled to 10 million reads. Metagenome assembly was performed using metaSpades. Here, we provide the output of the metaSpades assembly with the binned contigs. Contigs were binned by BLASTN results, keeping all contigs that map to bacterial sequences in the NT database. All contigs with a length less than 500 bps were removed.
DOI: 10.5281/zenodo.7696185
title: A transnational newspaper dataset covering Spenceanism

description: To analyse the media legacy of English radical thinker Thomas Spence (1750–1814), his revolutionary "Plan", and his disciples (the "Spencean Philanthropists") in global press circuits, a dataset consisting of 275 Spencean-related articles in newspapers from Ireland (106 articles), the British West Indies (35), British India (29), the Australian colonies (4), Canada (1), and the United States (100) was created. The corpus consists of either the full text of each article or relevant extracts, as well as additional metadata such as source, date, title (if applicable), keyword, and region. In particular, the following databases have been relied upon: the Irish Newspaper Archives for Ireland, the Caribbean Newspapers: Digital Library of the Caribbean and Caribbean Newspapers 1718–1876 for the British West Indies, Newspapers & Gazettes – Trove for Australia, America's Historical Newspapers and Chronicling America: Historic American Newspapers for the US, Newspapers.com by Ancestry for Canada, Ireland, and the US, and the British Newspaper Archive for British India, Ireland, and the Caribbean. These databases were searched using the following keywords: "Thomas Spence" [1750–1814], "Spence's Plan", "Spencean" / "Spenceans", and "Spenceanism"; "swinish multitude", "people's farm", and "pigs' meat" were also used. All databases checked for Australia, the Caribbean, India, and Canada have been exhausted, and many Irish and US-American articles have also been grabbed. Due to the low scan quality of databases, most articles needed to be copied and corrected manually. The 275 articles of the corpus consist of 167,515 tokens. In addition, 157 articles on Spence and the Spenceans from British newspapers have been downloaded, too, and were added to this dataset for qualitative analysis and comparative purposes. Overall, the dataset made available here thus consists of 432 articles. The results from analysing this corpus are shown and discussed in a paper entitled "Transnational Echoes of Spenceanism: A Text Mining Exploration in English-Language Newspapers (1790–1850)", which is accepted for publication in the International Review of Social History (IRSH).
DOI: 10.5281/zenodo.7696184
title: A transnational newspaper dataset covering Spenceanism

description: To analyse the media legacy of English radical thinker Thomas Spence (1750–1814), his revolutionary "Plan", and his disciples (the "Spencean Philanthropists") in global press circuits, a dataset consisting of 275 Spencean-related articles in newspapers from Ireland (106 articles), the British West Indies (35), British India (29), the Australian colonies (4), Canada (1), and the United States (100) was created. The corpus consists of either the full text of each article or relevant extracts, as well as additional metadata such as source, date, title (if applicable), keyword, and region. In particular, the following databases have been relied upon: the Irish Newspaper Archives for Ireland, the Caribbean Newspapers: Digital Library of the Caribbean and Caribbean Newspapers 1718–1876 for the British West Indies, Newspapers & Gazettes – Trove for Australia, America's Historical Newspapers and Chronicling America: Historic American Newspapers for the US, Newspapers.com by Ancestry for Canada, Ireland, and the US, and the British Newspaper Archive for British India, Ireland, and the Caribbean. These databases were searched using the following keywords: "Thomas Spence" [1750–1814], "Spence's Plan", "Spencean" / "Spenceans", and "Spenceanism"; "swinish multitude", "people's farm", and "pigs' meat" were also used. All databases checked for Australia, the Caribbean, India, and Canada have been exhausted, and many Irish and US-American articles have also been grabbed. Due to the low scan quality of databases, most articles needed to be copied and corrected manually. The 275 articles of the corpus consist of 167,515 tokens. In addition, 157 articles on Spence and the Spenceans from British newspapers have been downloaded, too, and were added to this dataset for qualitative analysis and comparative purposes. Overall, the dataset made available here thus consists of 432 articles. The results from analysing this corpus are shown and discussed in a paper entitled "Transnational Echoes of Spenceanism: A Text Mining Exploration in English-Language Newspapers (1790–1850)", which is accepted for publication in the International Review of Social History (IRSH).
DOI: 10.15787/vtt1/0pnr4u
title: E-Scooter Safety Assessment and Campus Deployment Planning (VTTI-00-023)

description: Project Description:. VTTI and Spin deployed a fleet of e-scooters on the Virginia Tech campus through an exclusive, controlled research program from September 2019 through May 2022. Through on-scooter data acquisition systems, fixed infrastructure cameras, anecdotal injury reports, and surveys, data was collected to assess safety impact as well as to understand beneficial and problematic user behaviors and patterns for subsequent countermeasure development and deployment recommendations. The resulting naturalistic dataset includes over 9,000 miles of riding data. This dataset includes the annotated crash data and baseline data from VTTI’s data acquisition system. Data Scope: The dataset includes categorical and text data for 789 baseline events and 154 safety critical events from phase 1 and phase 2 of the project. Data Specification: Please see the Data Dictionary document below for details.
DOI: 10.5281/zenodo.10233349
title: Phased VCF outputs for "HiPhase: Jointly phasing small, structural, and tandem repeat variants from HiFi sequencing"

description: The collection of raw and processed VCF files for the paper titled: "HiPhase: Jointly phasing small, structural, and tandem repeat variants from HiFi sequencing".
Raw VCF files from DeepVariant, pbsv, and TRGT are included in the unphased subfolder. Outputs from WhatsHap and HiPhase are in their own subfolders. Three replicates of HG002 are included in all subfolders. Layout is as follows:

hiphase_vcfs
├── all_vcfs.md5
├── hiphase
│   ├── HG002-rep1.GRCh38.deepvariant.hiphase.vcf.gz
│   ├── HG002-rep1.GRCh38.deepvariant.hiphase.vcf.gz.tbi
│   ├── HG002-rep1.GRCh38.pbsv.hiphase.vcf.gz
│   ├── HG002-rep1.GRCh38.pbsv.hiphase.vcf.gz.tbi
│   ├── HG002-rep1.GRCh38.trgt.hiphase.vcf.gz
│   ├── HG002-rep1.GRCh38.trgt.hiphase.vcf.gz.tbi
│   ├── HG002-rep2.GRCh38.deepvariant.hiphase.vcf.gz
│   ├── HG002-rep2.GRCh38.deepvariant.hiphase.vcf.gz.tbi
│   ├── HG002-rep2.GRCh38.pbsv.hiphase.vcf.gz
│   ├── HG002-rep2.GRCh38.pbsv.hiphase.vcf.gz.tbi
│   ├── HG002-rep2.GRCh38.trgt.hiphase.vcf.gz
│   ├── HG002-rep2.GRCh38.trgt.hiphase.vcf.gz.tbi
│   ├── HG002-rep3.GRCh38.deepvariant.hiphase.vcf.gz
│   ├── HG002-rep3.GRCh38.deepvariant.hiphase.vcf.gz.tbi
│   ├── HG002-rep3.GRCh38.pbsv.hiphase.vcf.gz
│   ├── HG002-rep3.GRCh38.pbsv.hiphase.vcf.gz.tbi
│   ├── HG002-rep3.GRCh38.trgt.hiphase.vcf.gz
│   └── HG002-rep3.GRCh38.trgt.hiphase.vcf.gz.tbi
├── unphased
│   ├── HG002-rep1.GRCh38.deepvariant.vcf.gz
│   ├── HG002-rep1.GRCh38.deepvariant.vcf.gz.tbi
│   ├── HG002-rep1.GRCh38.pbsv.vcf.gz
│   ├── HG002-rep1.GRCh38.pbsv.vcf.gz.tbi
│   ├── HG002-rep1.GRCh38.trgt.vcf.gz
│   ├── HG002-rep1.GRCh38.trgt.vcf.gz.tbi
│   ├── HG002-rep2.GRCh38.deepvariant.vcf.gz
│   ├── HG002-rep2.GRCh38.deepvariant.vcf.gz.tbi
│   ├── HG002-rep2.GRCh38.pbsv.vcf.gz
│   ├── HG002-rep2.GRCh38.pbsv.vcf.gz.tbi
│   ├── HG002-rep2.GRCh38.trgt.vcf.gz
│   ├── HG002-rep2.GRCh38.trgt.vcf.gz.tbi
│   ├── HG002-rep3.GRCh38.deepvariant.vcf.gz
│   ├── HG002-rep3.GRCh38.deepvariant.vcf.gz.tbi
│   ├── HG002-rep3.GRCh38.pbsv.vcf.gz
│   ├── HG002-rep3.GRCh38.pbsv.vcf.gz.tbi
│   ├── HG002-rep3.GRCh38.trgt.vcf.gz
│   └── HG002-rep3.GRCh38.trgt.vcf.gz.tbi
└── whatshap
    ├── HG002-rep1.GRCh38.deepvariant.whatshap.vcf.gz
    ├── HG002-rep1.GRCh38.deepvariant.whatshap.vcf.gz.tbi
    ├── HG002-rep2.GRCh38.deepvariant.whatshap.vcf.gz
    ├── HG002-rep2.GRCh38.deepvariant.whatshap.vcf.gz.tbi
    ├── HG002-rep3.GRCh38.deepvariant.whatshap.vcf.gz
    └── HG002-rep3.GRCh38.deepvariant.whatshap.vcf.gz.tbi
3 directories, 43 files
DOI: 10.5281/zenodo.10233350
title: Phased VCF outputs for "HiPhase: Jointly phasing small, structural, and tandem repeat variants from HiFi sequencing"

description: The collection of raw and processed VCF files for the paper titled: "HiPhase: Jointly phasing small, structural, and tandem repeat variants from HiFi sequencing".
Raw VCF files from DeepVariant, pbsv, and TRGT are included in the unphased subfolder. Outputs from WhatsHap and HiPhase are in their own subfolders. Three replicates of HG002 are included in all subfolders. Layout is as follows:

hiphase_vcfs
├── all_vcfs.md5
├── hiphase
│   ├── HG002-rep1.GRCh38.deepvariant.hiphase.vcf.gz
│   ├── HG002-rep1.GRCh38.deepvariant.hiphase.vcf.gz.tbi
│   ├── HG002-rep1.GRCh38.pbsv.hiphase.vcf.gz
│   ├── HG002-rep1.GRCh38.pbsv.hiphase.vcf.gz.tbi
│   ├── HG002-rep1.GRCh38.trgt.hiphase.vcf.gz
│   ├── HG002-rep1.GRCh38.trgt.hiphase.vcf.gz.tbi
│   ├── HG002-rep2.GRCh38.deepvariant.hiphase.vcf.gz
│   ├── HG002-rep2.GRCh38.deepvariant.hiphase.vcf.gz.tbi
│   ├── HG002-rep2.GRCh38.pbsv.hiphase.vcf.gz
│   ├── HG002-rep2.GRCh38.pbsv.hiphase.vcf.gz.tbi
│   ├── HG002-rep2.GRCh38.trgt.hiphase.vcf.gz
│   ├── HG002-rep2.GRCh38.trgt.hiphase.vcf.gz.tbi
│   ├── HG002-rep3.GRCh38.deepvariant.hiphase.vcf.gz
│   ├── HG002-rep3.GRCh38.deepvariant.hiphase.vcf.gz.tbi
│   ├── HG002-rep3.GRCh38.pbsv.hiphase.vcf.gz
│   ├── HG002-rep3.GRCh38.pbsv.hiphase.vcf.gz.tbi
│   ├── HG002-rep3.GRCh38.trgt.hiphase.vcf.gz
│   └── HG002-rep3.GRCh38.trgt.hiphase.vcf.gz.tbi
├── unphased
│   ├── HG002-rep1.GRCh38.deepvariant.vcf.gz
│   ├── HG002-rep1.GRCh38.deepvariant.vcf.gz.tbi
│   ├── HG002-rep1.GRCh38.pbsv.vcf.gz
│   ├── HG002-rep1.GRCh38.pbsv.vcf.gz.tbi
│   ├── HG002-rep1.GRCh38.trgt.vcf.gz
│   ├── HG002-rep1.GRCh38.trgt.vcf.gz.tbi
│   ├── HG002-rep2.GRCh38.deepvariant.vcf.gz
│   ├── HG002-rep2.GRCh38.deepvariant.vcf.gz.tbi
│   ├── HG002-rep2.GRCh38.pbsv.vcf.gz
│   ├── HG002-rep2.GRCh38.pbsv.vcf.gz.tbi
│   ├── HG002-rep2.GRCh38.trgt.vcf.gz
│   ├── HG002-rep2.GRCh38.trgt.vcf.gz.tbi
│   ├── HG002-rep3.GRCh38.deepvariant.vcf.gz
│   ├── HG002-rep3.GRCh38.deepvariant.vcf.gz.tbi
│   ├── HG002-rep3.GRCh38.pbsv.vcf.gz
│   ├── HG002-rep3.GRCh38.pbsv.vcf.gz.tbi
│   ├── HG002-rep3.GRCh38.trgt.vcf.gz
│   └── HG002-rep3.GRCh38.trgt.vcf.gz.tbi
└── whatshap
    ├── HG002-rep1.GRCh38.deepvariant.whatshap.vcf.gz
    ├── HG002-rep1.GRCh38.deepvariant.whatshap.vcf.gz.tbi
    ├── HG002-rep2.GRCh38.deepvariant.whatshap.vcf.gz
    ├── HG002-rep2.GRCh38.deepvariant.whatshap.vcf.gz.tbi
    ├── HG002-rep3.GRCh38.deepvariant.whatshap.vcf.gz
    └── HG002-rep3.GRCh38.deepvariant.whatshap.vcf.gz.tbi
3 directories, 43 files
DOI: 10.48567/ks86-6r29
title: Palmer Station Automated Tide Data System, 1993-present (ongoing).
DOI: 10.34740/kaggle/dsv/7093779
title: consumer_venezuela
DOI: 10.5066/p9n8gv23
title: KdPAR and surface water-quality data collected in the Sacramento-San Joaquin River Delta in 2013 and 2014

description: Data release provides diffuse light attenuation coefficient of photosynthetically active radiation (KdPAR) derived from in-situ light measurements, along with surface water-quality and atmospheric data collected in the Sacramento-San Joaquin Rive Delta in California between January 2013 and May 2014. These associated surface level water-quality and atmospheric data, and categorical variables (for example season, region, etc.) were used to develop a KdPAR model using in situ light profile data collected in tandem, which we derived KdPAR from.
DOI: 10.34740/kaggle/dsv/7093828
title: Country Data