cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20383014.v4
title: Complete assembly, annotation of virulence genes and CRISPR editing of the genome of Leishmania amazonensis PH8 strain

description: <em>Leishmania amazonensis</em> is one of the etiological agents of tegumentary and visceral leishmaniasis. Genome studies focusing on genes encoding virulence factors that play crucial roles in the establishment of the infection constitute an essential step towards the molecular characterization of a protozoan parasite that is being increasingly recognized as a significant human pathogen. Here, we report the sequencing and assembly of the <em>L</em><em>. amazonensis </em>PH8 strain combining data from long PacBio reads, short Illumina reads and synteny with the <em>Leishmania mexicana</em> genome. The final assembly, composed of 34 chromosomes, represents a genome of ~32 Mb with 8317 annotated genes. Several multigene families encoding virulence factors, such as A2, amastins, metalloproteins GP63 and cysteine proteases, were identified and compared to their annotation in the genomes of other <em>Leishmania</em> species. The <em>L. amazonensis </em>PH8 strain genome has 27 genes encoding all four sub-classes of amastins (α, β, γ and δ), 5 genes encoding A2 antigens, 9 genes encoding the metalloprotease GP63 and 76 genes encoding cysteine proteases. For all gene families analysed, we identified a larger number of copies and presented a more complete gene repertoire associated with <em>L. amazonensis </em>virulence factors, compared to previously published genomes. As they have been recently recognized as virulence factors essential for disease establishment and progression of the infection, we have also identified 14 genes encoding proteins involved in the parasite iron and heme metabolism and compared them to this gene repertoire in other Trypanosomatids. To follow these studies with a genetic approach that would allow us to directly address the role of these virulence factors, we tested two CRISPR-Cas9 protocols to generate <em>L. amazonensis</em> knockout cell lines. Using the Miltefosine Transporter (MT) gene as a proof of concept, we transfected promastigotes expressing the <em>Streptococcus pyogenes</em> Cas9 with <em>in vitro</em> transcribed sgRNA targeting this gene. As an alternative protocol, promastigotes were transfected with recombinant <em>Staphylococcus aureus </em>Cas9 complexed with sgRNAs. With both strategies, we were able to disrupt the MT gene with high efficiency, as shown by PCR and restriction digestion analysis as well as the development of miltefosine-resistant parasites.
DOI: 10.5281/zenodo.6883467
title: NuclearGazeAuth

description: Eye and head movement dataset from Random Dot viewing, 360 image viewing, and a 360 nuclear reactor training procedure collected in VR. This dataset is referenced in the following paper: LaRubbio, K., Wright, J., David-John, B., Enqvist, A., & Jain, E. (2022). Who do you look like? Gaze-based authentication for workers in VR. IEEE Conference on Virtual Reality and 3D User Interfaces Abstracts and Workshops (IEEE VRW) 2022. Please use our reference spreadsheet for cross-referencing img_idx and ImageViewing block # with the images from the code repo for NuclearGazeAuth.
DOI: 10.5281/zenodo.6883466
title: NuclearGazeAuth

description: Eye and head movement dataset from Random Dot viewing, 360 image viewing, and a 360 nuclear reactor training procedure collected in VR. This dataset is referenced in the following paper: LaRubbio, K., Wright, J., David-John, B., Enqvist, A., & Jain, E. (2022). Who do you look like? Gaze-based authentication for workers in VR. IEEE Conference on Virtual Reality and 3D User Interfaces Abstracts and Workshops (IEEE VRW) 2022. Please use our reference spreadsheet for cross-referencing img_idx and ImageViewing block # with the images from the code repo for NuclearGazeAuth.
DOI: 10.5281/zenodo.4642612
title: ET-DK2 Dataset

description: Eye and head movement dataset from 360 image viewing on a subset of the Salient360! dataset and 360 degree images of construction sites near the University of Florida. This dataset is referenced in the following two papers: David-John, B., Hosfelt, D., Butler, K., & Jain, E. (2021). A privacy-preserving approach to streaming eye-tracking data. <strong> </strong>IEEE Transaction on Visualization and Computer Graphics (TVCG) Special Issue on IEEE Virtual Reality and 3D User Interfaces (IEEE VR) 2021 John, B., Raiturkar, P., Le Meur, O., & Jain, E. (2018, December). A Benchmark of Four Methods for Generating 360° Saliency Maps from Eye Tracking Data. In 2018 IEEE International Conference on Artificial Intelligence and Virtual Reality (AIVR) (pp. 136-139). IEEE.
DOI: 10.5281/zenodo.4642566
title: ET-DK2 Dataset

description: Eye and head movement dataset from 360 image viewing on a subset of the Salient360! dataset and 360 degree images of construction sites near the University of Florida. This dataset is referenced in the following two papers: David-John, B., Hosfelt, D., Butler, K., & Jain, E. (2021). A privacy-preserving approach to streaming eye-tracking data. <strong> </strong>IEEE Transaction on Visualization and Computer Graphics (TVCG) Special Issue on IEEE Virtual Reality and 3D User Interfaces (IEEE VR) 2021 John, B., Raiturkar, P., Le Meur, O., & Jain, E. (2018, December). A Benchmark of Four Methods for Generating 360° Saliency Maps from Eye Tracking Data. In 2018 IEEE International Conference on Artificial Intelligence and Virtual Reality (AIVR) (pp. 136-139). IEEE.
DOI: 10.7284/103005
title: Anemometer data collected during research cruise CH0709 using a RMYoung 05103 instrument system onboard the platform RV Cape Hatteras

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/103015
title: Anemometer data collected during research cruise CH0709 using a RMYoung 05103 instrument system onboard the platform RV Cape Hatteras

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/102462
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise CH0709 using a SeaBird SBE-911+ instrument system onboard the platform RV Cape Hatteras

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/102875
title: Fluorometer data collected during research cruise CH0709 using a Turner 10-AU instrument system onboard the platform RV Cape Hatteras

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/102885
title: Gyrocompass data collected during research cruise CH0709 using a Sperry MK-37 instrument system onboard the platform RV Cape Hatteras

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/103233
title: Meteorological Station data collected during research cruise CH0709 using a RMYoung 26700 instrument system onboard the platform RV Cape Hatteras

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/102524
title: Singlebeam Echosounder data collected during research cruise CH0709 using a Furuno FCV-292 instrument system onboard the platform RV Cape Hatteras

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.20383014.v5
title: Complete assembly, annotation of virulence genes and CRISPR editing of the genome of Leishmania amazonensis PH8 strain

description: <em>Leishmania amazonensis</em> is one of the etiological agents of tegumentary and visceral leishmaniasis. Genome studies focusing on genes encoding virulence factors that play crucial roles in the establishment of the infection constitute an essential step towards the molecular characterization of a protozoan parasite that is being increasingly recognized as a significant human pathogen. Here, we report the sequencing and assembly of the <em>L</em><em>. amazonensis </em>PH8 strain combining data from long PacBio reads, short Illumina reads and synteny with the <em>Leishmania mexicana</em> genome. The final assembly, composed of 34 chromosomes, represents a genome of ~32 Mb with 8317 annotated genes. Several multigene families encoding virulence factors, such as A2, amastins, metalloproteins GP63 and cysteine proteases, were identified and compared to their annotation in the genomes of other <em>Leishmania</em> species. The <em>L. amazonensis </em>PH8 strain genome has 27 genes encoding all four sub-classes of amastins (α, β, γ and δ), 5 genes encoding A2 antigens, 9 genes encoding the metalloprotease GP63 and 76 genes encoding cysteine proteases. For all gene families analysed, we identified a larger number of copies and presented a more complete gene repertoire associated with <em>L. amazonensis </em>virulence factors, compared to previously published genomes. As they have been recently recognized as virulence factors essential for disease establishment and progression of the infection, we have also identified 14 genes encoding proteins involved in the parasite iron and heme metabolism and compared them to this gene repertoire in other Trypanosomatids. To follow these studies with a genetic approach that would allow us to directly address the role of these virulence factors, we tested two CRISPR-Cas9 protocols to generate <em>L. amazonensis</em> knockout cell lines. Using the Miltefosine Transporter (MT) gene as a proof of concept, we transfected promastigotes expressing the <em>Streptococcus pyogenes</em> Cas9 with <em>in vitro</em> transcribed sgRNA targeting this gene. As an alternative protocol, promastigotes were transfected with recombinant <em>Staphylococcus aureus </em>Cas9 complexed with sgRNAs. With both strategies, we were able to disrupt the MT gene with high efficiency, as shown by PCR and restriction digestion analysis as well as the development of miltefosine-resistant parasites.
DOI: 10.25828/v71j-3b55
title: Timing of Referral to Antiretroviral Clubs Study 2017-2018
DOI: 10.17632/4rkrhngzm4.1
title: Appendix A Metadata for the selected articles (AR instruction K-12)

description: The key metadata information for the 129 selected articles for the systematic review.
DOI: 10.17632/m3p9m9vc4g.4
title: ExAgBov: a public database of annotated variations from hundreds of bovine whole-exome sequencing samples

description: ExAgBov: A public database of annotated variations from hundreds of bovine whole-exome sequencing samples

Rotem Raz1,2, Zvi Roth2 and Moran Gershoni1*

1.	Department of Ruminant Science, Institute of Animal Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion 7505101, Israel
2.	Department of Animal Sciences, Robert H. Smith Faculty of Agriculture, Food and Environment, the Hebrew University, Rehovot 76100, Israel.

*Corresponding author: Moran Gershoni (gmoran@volcani.agri.gov.il)

Cite this database:
Raz, R., Roth, Z. & Gershoni, M. ExAgBov: A public database of annotated variations from hundreds of bovine whole-exome sequencing samples. Sci Data 9, 469 (2022). https://doi.org/10.1038/s41597-022-01597-8


Abstract
Large reference datasets of annotated genetic variations from genome-scale sequencing are essential for interpreting identified variants, their functional impact, and their possible contribution to diseases and traits. However, to date, no such database of annotated variation from broad cattle populations is publicly available. To overcome this gap and advance bovine NGS-driven variant discovery and interpretation, we obtained and analyzed raw data deposited in the SRA public repository. Short reads from 262 whole-exome sequencing samples of Bos Taurus were mapped to the Bos Taurus ARS-UCD1.2 reference genome. The GATK best practice workflow was applied for variant calling. Comprehensive annotation of all recorded variants was done using the Ensembl Variant Effect Predictor (VEP). An in-depth analysis of the population structure revealed the breeds comprising the database. The Exomes Aggregate of Bovine- ExAgBov is a comprehensively annotated dataset of more than 20 million short variants, of which ~2% are located within open reading frames, splice regions, and UTRs, and more than 60,000 variants are predicted to be deleterious. 


The following files are available:
1. BovExAg.DB.TSV+DP.filtered = The filtered database file. includes variants that pass the quality filtration for the read quality and depth of coverage (see Raz R. et al.)
2. ExAgBov.DB.TSV.gz = The database file with all the annotated variants and the supporting information
3. ExAgBov.DP.all-var.csv.gz = The depth of coverage of all variants in all samples
4. SRA.ID+breed.csv = The SRA ID of the ExAgBov WES samples including the sample breed whenever available in the metadata
5. ExAgBov.SRA.metadata.txt = The complete metadata file of all the WES samples included in the ExAgBov database
DOI: 10.5281/zenodo.6891712
title: PRJNA860062 Assigned Taxonomy and QIIME2 Pipeline

description: <strong>PRJNA860062 Assigned Taxonomy:</strong> This upload comprises two datasets with the assigned taxonomy for sequence variants of BioProject PRNJA860062. PRJNA860062_ASVCounts_NCBItaxonomy.txt PRJNA860062_ASVCounts_SILVAtaxonomy.txt BioProject PRNJN860062 compares bacterial profiles of zebrafish larvae microbiota resulting from two different microbial colonization methods. The full description and sequence data for this project can be obtained from the Sequence Read Archive (https://www.ncbi.nlm.nih.gov/bioproject). The dataset with the SILVA taxonomy can directly be obtained using the QIIME2 script included in this upload ('PRJNA860062_QIIME2Script.txt'). As previously noted by Lesack and Birol (2018), SILVA species annotations include nomenclature errors (DOI: 10.1101/441576). Therefore, the dataset with the NCBI taxonomy comprises a manually corrected taxonomy for BioProject PRNJA860062, based on the family to phylum level nomenclature of the NCBI taxonomy browser (https://www.ncbi.nlm.nih.gov/taxonomy). Both files are tab-delimited text files, include the domain to species level taxonomy in the first 7 columns, and include the number of assigned sequence variants (ASVs) per taxon in the final 6 colums, corresponding to BioSample SAMN29820940, SAMN29820941, SAMN29820942, SAMN29820943, SAMN29820944, and SAMN29820945. <strong>QIIME 2 Pipeline:</strong> The QIIME2 script that was used to obtain the assigned SILVA taxonomy BioProject PRNJA860062 is uploaded as: PRJNA860062_QIIME2Script.txt Input files that are required to run this script, including a manifest text file, sample metadata, and the reference sequences and taxonomy from the SILVA 138 small subunit (16S/18S) rRNA database Ref NR 99, are uploaded in the zipped file: PRJNA860062_InputFiles.zip FASTQ sequence data for BioSample SAMN29820940, SAMN29820941, SAMN29820942, SAMN29820943, SAMN29820944, and SAMN29820945, can be obtained from the Sequence Read Archive under BioProject PRNJA860062 (https://www.ncbi.nlm.nih.gov/bioproject). All output files are uploaded in the zipped file: PRJNA860062_OutputFiles.zip Data provenance, including the versions of python (3.6.7) and python packages, can be acquired by dragging QIIME2 Visualizations (.qzv output files) into the QIIME2 viewing interface (http://view.qiime2.org).
DOI: 10.5281/zenodo.6891711
title: PRJNA860062 Assigned Taxonomy and QIIME2 Pipeline

description: <strong>PRJNA860062 Assigned Taxonomy:</strong> This upload comprises two datasets with the assigned taxonomy for sequence variants of BioProject PRNJA860062. PRJNA860062_ASVCounts_NCBItaxonomy.txt PRJNA860062_ASVCounts_SILVAtaxonomy.txt BioProject PRNJN860062 compares bacterial profiles of zebrafish larvae microbiota resulting from two different microbial colonization methods. The full description and sequence data for this project can be obtained from the Sequence Read Archive (https://www.ncbi.nlm.nih.gov/bioproject). The dataset with the SILVA taxonomy can directly be obtained using the QIIME2 script included in this upload ('PRJNA860062_QIIME2Script.txt'). As previously noted by Lesack and Birol (2018), SILVA species annotations include nomenclature errors (DOI: 10.1101/441576). Therefore, the dataset with the NCBI taxonomy comprises a manually corrected taxonomy for BioProject PRNJA860062, based on the family to phylum level nomenclature of the NCBI taxonomy browser (https://www.ncbi.nlm.nih.gov/taxonomy). Both files are tab-delimited text files, include the domain to species level taxonomy in the first 7 columns, and include the number of assigned sequence variants (ASVs) per taxon in the final 6 colums, corresponding to BioSample SAMN29820940, SAMN29820941, SAMN29820942, SAMN29820943, SAMN29820944, and SAMN29820945. <strong>QIIME 2 Pipeline:</strong> The QIIME2 script that was used to obtain the assigned SILVA taxonomy BioProject PRNJA860062 is uploaded as: PRJNA860062_QIIME2Script.txt Input files that are required to run this script, including a manifest text file, sample metadata, and the reference sequences and taxonomy from the SILVA 138 small subunit (16S/18S) rRNA database Ref NR 99, are uploaded in the zipped file: PRJNA860062_InputFiles.zip FASTQ sequence data for BioSample SAMN29820940, SAMN29820941, SAMN29820942, SAMN29820943, SAMN29820944, and SAMN29820945, can be obtained from the Sequence Read Archive under BioProject PRNJA860062 (https://www.ncbi.nlm.nih.gov/bioproject). All output files are uploaded in the zipped file: PRJNA860062_OutputFiles.zip Data provenance, including the versions of python (3.6.7) and python packages, can be acquired by dragging QIIME2 Visualizations (.qzv output files) into the QIIME2 viewing interface (http://view.qiime2.org).
DOI: 10.6084/m9.figshare.20422128
title: The legacy of forest logging on organic matter inputs and storage in tropical streams

description: Data of litterfall to the forest, and litter inputs and accumulation (storage) in streams at two reference and two clear-cut logged sites collected at monthly intervals for two years in the Cerrado biome.
DOI: 10.6084/m9.figshare.20422128.v1
title: The legacy of forest logging on organic matter inputs and storage in tropical streams

description: Data of litterfall to the forest, and litter inputs and accumulation (storage) in streams at two reference and two clear-cut logged sites collected at monthly intervals for two years in the Cerrado biome.
DOI: 10.7284/111797
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise PE09-29 using a SeaBird SBE-911+ instrument system onboard the platform RV Pelican

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/111809
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise PE09-40 using a SeaBird SBE-911+ instrument system onboard the platform RV Pelican

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.5281/zenodo.6954593
title: Global Positioning System Based on Optical Flow and Convolutional Neural Network

description: Two datasets used in the paper Global Positioning System Based on Optical Flow and Convolutional Neural Network, to evaluate the proposed CNN model to the task of position estimation. The datasets cover 2 different modes of motion of a drone, and were captured using Google API.
DOI: 10.5281/zenodo.6954592
title: Global Positioning System Based on Optical Flow and Convolutional Neural Network

description: Two datasets used in the paper Global Positioning System Based on Optical Flow and Convolutional Neural Network, to evaluate the proposed CNN model to the task of position estimation. The datasets cover 2 different modes of motion of a drone, and were captured using Google API.
DOI: 10.7284/111822
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise PE10-07 using a SeaBird SBE-911+ instrument system onboard the platform RV Pelican

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.3761562.v2298
title: Online Labour Index: Measuring the Online Gig Economy for Policy and Research

description: Data repository for the data underlying the Online Labour Index. See http://ilabour.oii.ox.ac.uk online-labour-index/ for details.
DOI: 10.7284/111827
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise PE10-10 using a SeaBird SBE-911+ instrument system onboard the platform RV Pelican

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/111833
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise PE10-19 using a SeaBird SBE-911+ instrument system onboard the platform RV Pelican

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/111842
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise PE10-29 using a SeaBird SBE-911+ instrument system onboard the platform RV Pelican

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/111849
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise PE10-36 using a SeaBird SBE-911+ instrument system onboard the platform RV Pelican

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.3886/e148541v1-124580
title: Code for: Human Trafficking and Regulating Prostitution

description: Code accompanying article with the following abstract: Certain markets are illicit because part of the supply is coerced, but little is known about the optimal regulation of such markets. We model a prostitution market with voluntary and coerced prostitutes and askwhat regulation can restore the benchmark outcome that would arise under laissez-faire absent coercion. Whereas current policies -- decriminalization, criminalization of the buy or sell sides, and licensing -- are ineffective against trafficking or harm voluntary suppliers, we show that an alternative policy can restore the benchmark outcome. Our results are relevant to the ongoing debate about decriminalizing prostitution and provide guidance for empirical work on prostitution regulation.<br>
DOI: 10.7284/109807
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise PS0915 using a SeaBird SBE-911+ instrument system onboard the platform RV Point Sur

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/109893
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise RR0907 using a SeaBird SBE-911+ instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/109751
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise RR0908 using a SeaBird SBE-911+ instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/109750
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise RR0909 using a SeaBird SBE-911+ instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.12789383
title: Tetraploid vcf

description: In total 380 potato clones were genotyped. Library construction and genotyping by genotyping by sequencing (GBS) was outsourced to the Genomics Facility at Cornell University in 2015. The DNA was digested with EcoT221 restriction enzyme and the libraries were 48x multiplexed for sequencing. For polyploid calling the raw FASTQ files were processed with Stacks (Catchen et al., 2013) to remove the barcodes and with TrimGalore https://github.com/FelixKrueger/TrimGalore to trim the ends of reads. The reads were aligned to the reference genome version <i>S. tuberosum_448_v4.03</i> (Sharma et al., 2013) using BWA (Li and Durbin, 2009) and the resulting SAM files were converted to BAM files using Samtools (Li et al., 2009). The variants were called using GATK HaplotypeCaller option (Poplin et al., 2017), disabling the duplicate read filter (this is recommended for GBS data) and joint genotyping using the -ERC GVCF mode.