cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/fh47g3dp6t.1
title: Processed unique sort BAM files of High Risk HPV types 16, 18, 45 and 68b transcripts

description: RNAseq raw data of RNA extracted from five cervical cancer cell lines were mapped to HPV16 (NC_001526.2 or NC_001526.4), HPV18 (NC_001357.1), HPV68b (FR751039.1) and HPV45 (X74479.1). The processed BAM files were further analysed using The Hisat2 v2.1.0 aligner, Cufflinks v. 2.2.1, Cuffmerge and Cuffdiff. The processed sort BAM files containing sequences of viral transcripts were shown as ‘sort BAM files’. The HPV16 transcripts data and their expression levels reported as FPKM can be visualized using IGV software. The number of total reads and viral reads after mapping to viral references were shown in ‘HR-HPV genes and isoforms FPKM tracking file’, the spliced transcripts were named as CUFF. The integration sites of four high risk HPV types were analysed and shown in ‘fusion file’. According to IGV visualization, the splicing junctions of all four HPV types were found within E6 and E1 regions. For E6 region, one splicing donor (SD) at the 5′ end and different splicing acceptor (SA) positions at the 3′ end were found as follow; three splicing junctions were found in HPV16 positive cervical cancer cell lines, CaSki and SiHa, SD226^SA409(E6*I), SD226^SA526(E6*II) and SD226^SA742(E6*X). Two splicing junctions were found in HPV18 (HeLa), SD233^SA416(E6*I), SD233^SA635, HPV45(MS751); SD230^SA412(E6*I), SD230^SA640 and HPV68b (ME180); SD129^SA311(E6*I), SD129^SA406. Splicing junctions within E1 region found in CaSki and SiHa were SD880^SA3358, SD880^SA3361, SD880^SA3391, SD880^SA1726, SD880^SA2405, SD880^SA2582(E1C), SD880^SA2709(E2*), SD880^SA3020, SD880^SA3078, SD880^SA3329, SD577^SA6810, SD898^SA1725, SD1302^SA2709, SD1302^SA3358(E2C), SD1760^SA3391, SD1263^SA3391, SD2309^SA3461 and the other forms were SD96^SA1063, SD226^SA2709 (E6*IV), SD226^SA3329, SD226^SA3358(E6*III), SD226^SA3361, SD226^SA3391 and SD579^SA6809. Splicing junctions within E1 region in HPV18(HeLa) were SD929^SA2779, SD977^SA1836, SD1342^SA1436, SD1987^SA2047 and one splicing event within E7 region, SD599^SA619. HPV68b(ME180) were SD839^SA2586, SD683^SA2586, SD839^SA2586 and no E1 splicing junctions were found in HPV45(MS751).
DOI: 10.6084/m9.figshare.7205873
title: Alabama Gulf Coast State-Wide Wave Exposure Map

description: <pre>This raster was originally created to visualize the distribution of wave exposure across the Gulf coastline of Alabama, USA in an effort to improve sea turtle nest relocation decisions. Sea turtle nests are relocated if they are deemed at-risk of wave exposure but misinterpretation of the current criterion (i.e, proximity to the daily high tide line) has resulted in a large percentage of unnecessary relocations. This wave exposure raster can be used as a decision tool to better identify at-risk locations for sea turtles as well as other beach-dwelling species. The underlying methodology used to produce it can be applied to any sandy coastline as a real-time, hindcast, or forecast tool.</pre><pre>Inundation events caused by wave wash-over and groundwater inundation can be fatal to developing sea turtle eggs and other beach-dwelling organisms. Wave runup models have been applied in the past to assess flooding risk during storm, model sediment transport, and design coastal construction. However, their use in coastal species management has not been evaluated. This wave runup map was developed using a time-averaged digital elevation model (based on 12 LiDAR surveys from 1998 to 2016) and offshore wave data (from the Orange Beach, AL NOAA buoy during the 2009 to 2016 nesting seasons). The extent of the raster represents the maximum available extent of sea turtle nesting habitat, stretching from mean low water to the dune line/back-beach construction.</pre>
DOI: 10.6084/m9.figshare.7205873.v1
title: Alabama Gulf Coast State-Wide Wave Exposure Map

description: <pre>This raster was originally created to visualize the distribution of wave exposure across the Gulf coastline of Alabama, USA in an effort to improve sea turtle nest relocation decisions. Sea turtle nests are relocated if they are deemed at-risk of wave exposure but misinterpretation of the current criterion (i.e, proximity to the daily high tide line) has resulted in a large percentage of unnecessary relocations. This wave exposure raster can be used as a decision tool to better identify at-risk locations for sea turtles as well as other beach-dwelling species. The underlying methodology used to produce it can be applied to any sandy coastline as a real-time, hindcast, or forecast tool.</pre><pre>Inundation events caused by wave wash-over and groundwater inundation can be fatal to developing sea turtle eggs and other beach-dwelling organisms. Wave runup models have been applied in the past to assess flooding risk during storm, model sediment transport, and design coastal construction. However, their use in coastal species management has not been evaluated. This wave runup map was developed using a time-averaged digital elevation model (based on 12 LiDAR surveys from 1998 to 2016) and offshore wave data (from the Orange Beach, AL NOAA buoy during the 2009 to 2016 nesting seasons). The extent of the raster represents the maximum available extent of sea turtle nesting habitat, stretching from mean low water to the dune line/back-beach construction.</pre>
DOI: 10.6084/m9.figshare.7205882.v2
title: Dataset for Internet-delivered cognitive-behavioural therapy for perfectionism: targeting dysmorphic concern

description: Cleaned up dataset
DOI: 10.7284/131921
title: Winch data collected during research cruise SR1711 using a Markey CAST-6-125 instrument system onboard the platform RV Sally Ride

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7205858
title: Motion-related correlations between torque and posture of trunk in a computational fluid dynamics model of zebrafish larva swimming

description: Original data of the figures in the paper entitled "Motion-related correlations between torque and posture of trunk in a computational fluid dynamics model of zebrafish larva swimming." The file names correspond to the figure numbers.
DOI: 10.6084/m9.figshare.7205882.v1
title: Dataset for Internet-delivered cognitive-behavioural therapy for perfectionism to target symptoms of subclinical body dysmorphic disorder

description: Cleaned up dataset
DOI: 10.6084/m9.figshare.7205858.v1
title: Motion-related correlations between torque and posture of trunk in a computational fluid dynamics model of zebrafish larva swimming

description: Original data of the figures in the paper entitled "Motion-related correlations between torque and posture of trunk in a computational fluid dynamics model of zebrafish larva swimming." The file names correspond to the figure numbers.
DOI: 10.7284/128348
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise SR1713 using a Hawaii UHDAS instrument system onboard the platform RV Sally Ride

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.17632/mvcy7y3fyr.1
title: SUPPLEMENTARY MATERIAL: Blue and grey urban water footprints through citizens’ perception and time series analysis of Brazilian dynamics

description: This document provides the data and information that supported the study reported in the manuscript “Blue and grey urban water footprints through citizens’ perception and time series analysis of Brazilian dynamics”, submitted to the Hydrological Sciences Journal. For further details, contact Felipe Souza at felipeaas@usp.br.
DOI: 10.7284/128354
title: Expendable Probe data collected during research cruise SR1713 using a Turo Quoll instrument system onboard the platform RV Sally Ride

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/128357
title: GNSS (Global Navigation Satellite System) data collected during research cruise SR1713 using a Trimble BD982 instrument system onboard the platform RV Sally Ride

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.17632/243kvmtzt3.1
title: Nature's Law and Water Treaties: Dataset and Code

description: This folder contains the code and the dataset to reproduce the paper "Nature's Law and Water Treaties" of Fabien Candau and Tchapo Gbandi, that analyzes how climate change, economic and political factors have affected the implementation of Water Treaties.
DOI: 10.6084/m9.figshare.7205801
title: Comparable nutrient uptake across diel cycles from three distinct algal communities

description: Three algal communities cultured from inocula sourced from geographically distinct locations within the continental United States were maintained under identical sequencing-batch growth conditions in photobioreactors and sampled over 82 days. Eukaryotic communities were sequenced via both V4 and V8-V9 18S rRNA gene sequencing. Prokaryotic communities were sequenced via V1-V3 16S rRNA gene sequencing. Mothur and R were used to analyze sequencing data and to describe and compare community dynamics within and between communities. This project includes both mothur and R script files used to analyze the data.
DOI: 10.6084/m9.figshare.7205831
title: Quantified play dataset

description: Links for video and text analysed for paper 'Quantified play: Self-tracking in videogames'
DOI: 10.6084/m9.figshare.7205831.v1
title: Quantified play dataset

description: Links for video and text analysed for paper 'Quantified play: Self-tracking in videogames'
DOI: 10.6084/m9.figshare.7205798
title: Untitled ItemComparable nutrient uptake across diel cycles from three distinct algal communities

description: Three algal communities cultured from inocula sourced from geographically distinct locations within the continental United States were maintained under identical sequencing-batch growth conditions in photobioreactors and sampled over 82 days. Eukaryotic communities were sequenced via both V4 and V8-V9 18S rRNA gene sequencing and prokaryotic communities were sequenced via V1-V3 16S rRNA gene sequencing. Mothur and R were used to analyze sequencing data and to describe and compare community dynamics within and between communities. This project includes both mothur and R script files used to analyze the data.
DOI: 10.6084/m9.figshare.7205801.v1
title: Comparable nutrient uptake across diel cycles from three distinct algal communities

description: Three algal communities cultured from inocula sourced from geographically distinct locations within the continental United States were maintained under identical sequencing-batch growth conditions in photobioreactors and sampled over 82 days. Eukaryotic communities were sequenced via both V4 and V8-V9 18S rRNA gene sequencing. Prokaryotic communities were sequenced via V1-V3 16S rRNA gene sequencing. Mothur and R were used to analyze sequencing data and to describe and compare community dynamics within and between communities. This project includes both mothur and R script files used to analyze the data.
DOI: 10.7284/128359
title: INS (Inertial Navigation System) data collected during research cruise SR1713 using a Kongsberg Seapath 330+ instrument system onboard the platform RV Sally Ride

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7205798.v1
title: Untitled ItemComparable nutrient uptake across diel cycles from three distinct algal communities

description: Three algal communities cultured from inocula sourced from geographically distinct locations within the continental United States were maintained under identical sequencing-batch growth conditions in photobioreactors and sampled over 82 days. Eukaryotic communities were sequenced via both V4 and V8-V9 18S rRNA gene sequencing and prokaryotic communities were sequenced via V1-V3 16S rRNA gene sequencing. Mothur and R were used to analyze sequencing data and to describe and compare community dynamics within and between communities. This project includes both mothur and R script files used to analyze the data.
DOI: 10.7284/131928
title: INS (Inertial Navigation System) data collected during research cruise SR1713 using a Kongsberg Seapath 330+ instrument system onboard the platform RV Sally Ride

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.17632/t3dzny838v.1
title: Expressão ABH Primatas do Novo Mundo

description: Tabela de descrição expresão tecidos
DOI: 10.7284/131929
title: INS (Inertial Navigation System) data collected during research cruise SR1713 using a iXSea Hydrins instrument system onboard the platform RV Sally Ride

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7205702
title: “The genomic architecture of fowl typhoid resistance in commercial layers”

description: Uploaded are the raw genotypes of commercial layers from a natural disease outbreak of fowl typhoid in Northern Ireland in 2012. The birds are genotyped with the 600K SNP array Affymetrix. These are the raw genotypes before any quality control. All the animals have been genotyped using four 96 well plates. The uploaded files contain: 1) the raw genotypes for plate 1 and plate 4, plate 2 and plate 3; 2) an excel containing the continuous phenotypes of Salmonella load measured in the liver of these birds; 3) an excel connected the sample ids with the ones found in the genotyping plates; 4)a READ_ME file with more details for these files<br><br>
DOI: 10.6084/m9.figshare.7205696
title: Tara Akshar Research Project

description: This zip file contains the data instruments and data of the Tara Akshar Research Project (2013-2018). A comprehensiveoverview of this project can be found on:https://sites.google.com/site/taraaksharresearchproject/home<br>A short description of the data is also included in the attached World Development paper. <br><br>
DOI: 10.6084/m9.figshare.7205684
title: Occurences Dataset of Heteroblasty in African Restionaceae

description: This is the Occurence dataset (embargoed until October 2019) of the publictation, included in the dataset published here: https://doi.org/10.6084/m9.figshare.6668936.v1<br>"Ecophysiological strategy switch through development in heteroblastic species of mediterranean ecosystems – an example in the African Restionaceae" <br><br>by <br>Merten Ehmig, Mario Coiro, H. Peter Linder.<br>published 2018 in Annals of Botany<br><br>If you have any questions regarding scripts or data please address Merten Ehmig via mail: merten.ehmig@systbot.uzh.ch, or cropbird@ymail.com<br><br><br>if you use this script or data, pleas cite the Annals of Botany Paper
DOI: 10.6084/m9.figshare.7205687
title: example IFC file generated by Homemaker

description: This is an example of a generated building in IFC format. The exporter is not complete, in particular stairs and columns/posts are missing<br>
DOI: 10.7284/128349
title: Meteorological Station data collected during research cruise SR1713 using a SIO MET-System instrument system onboard the platform RV Sally Ride

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7205684.v1
title: Occurences Dataset of Heteroblasty in African Restionaceae

description: This is the Occurence dataset (embargoed until October 2019) of the publictation, included in the dataset published here: https://doi.org/10.6084/m9.figshare.6668936.v1<br>"Ecophysiological strategy switch through development in heteroblastic species of mediterranean ecosystems – an example in the African Restionaceae" <br><br>by <br>Merten Ehmig, Mario Coiro, H. Peter Linder.<br>published 2018 in Annals of Botany<br><br>If you have any questions regarding scripts or data please address Merten Ehmig via mail: merten.ehmig@systbot.uzh.ch, or cropbird@ymail.com<br><br><br>if you use this script or data, pleas cite the Annals of Botany Paper
DOI: 10.17632/6gpc32dyy7.2
title: Raw data from Anti-androgens may protect against severe COVID-19 outcomes: results from a prospective cohort study of 77 hospitalized men

description: Raw data. Prospective cohort of patients admitted for COVID-19 in Madrid.
DOI: 10.6084/m9.figshare.7205666
title: STRique repeat detection data

description: Fast5 raw data for enrichment, BAC and plasmid data generated in "Analysis of short tandem repeat expansions and their methylation state with nanopore sequencing"<br>## 24-5-2.tar.gz:Enrichment data from patient 24-5-2<br>## sc105.tar.gzEnrichment data from patient sc105 iPS6/iPS7<br>## 20170626_FAE22321_FLO-MIN106_SQK-RAD002_BAC_c9orf72.tar.gzBAC data from c9orf72 locus with up to 800 repeats<br>## 20171116_FAH31667_FLO-MIN106_SQK-LSK108_plasmid_c9orf72.tar.gzPlasmid data with following repeat lengths:NB07 : 8 G4C2NB08 : 32 G4C2NB09 : 50 G4C2NB10 : 56 G4C2NB11 : 76 G4C2NB12 : 76 G4C2 + M.SssI<br>## 20190514_FAK69132_FLO-MIN106_SQK-LSK108_plasmid_FMR1.tar.gzPlasmid with 99 CGG repeats:NB01 : 99 CGG + M.SssINB02 : 99 CGG + M.SssINB03 : 99 CGGNB04 : 99 CGG
DOI: 10.6084/m9.figshare.7205681
title: Adaptive finite element–discrete element analysis for the multistage supercritical CO2 fracturing

description: This file includes the original images, tables, and figures that underlie the conclusions of our paper.
DOI: 10.7284/128351
title: Multibeam Echosounder data collected during research cruise SR1713 using a Kongsberg EM712 instrument system onboard the platform RV Sally Ride

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7205681.v1
title: Adaptive finite element–discrete element analysis for the multistage supercritical CO2 fracturing

description: This file includes the original images, tables, and figures that underlie the conclusions of our paper.
DOI: 10.7284/128353
title: Multibeam Echosounder data collected during research cruise SR1713 using a Kongsberg EM122 instrument system onboard the platform RV Sally Ride

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7205666.v1
title: STRique repeat detection data

description: Fast5 raw data for enrichment, BAC and plasmid data generated in "Analysis of short tandem repeat expansions and their methylation state with nanopore sequencing"<br>## 24-5-2.tar.gz:Enrichment data from patient 24-5-2<br>## sc105.tar.gzEnrichment data from patient sc105 iPS6/iPS7<br>## 20170626_FAE22321_FLO-MIN106_SQK-RAD002_BAC_c9orf72.tar.gzBAC data from c9orf72 locus with up to 800 repeats<br>## 20171116_FAH31667_FLO-MIN106_SQK-LSK108_plasmid_c9orf72.tar.gzPlasmid data with following repeat lengths:NB07 : 8 G4C2NB08 : 32 G4C2NB09 : 50 G4C2NB10 : 56 G4C2NB11 : 76 G4C2NB12 : 76 G4C2 + M.SssI<br>## 20190514_FAK69132_FLO-MIN106_SQK-LSK108_plasmid_FMR1.tar.gzPlasmid with 99 CGG repeats:NB01 : 99 CGG + M.SssINB02 : 99 CGG + M.SssINB03 : 99 CGGNB04 : 99 CGG
DOI: 10.7284/128352
title: Singlebeam Echosounder data collected during research cruise SR1713 using a Knudsen 3260 instrument system onboard the platform RV Sally Ride

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/128358
title: Splitbeam Echosounder data collected during research cruise SR1713 using a Kongsberg EK80 instrument system onboard the platform RV Sally Ride

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.17632/mmsfb8pzdz.1
title: SUPPLEMENTARY MATERIAL: Blue and grey water footprints through citizens’ perception scenarios and short time series analysis of Brazilian local scale dynamics

description: This document provides the data and information that supported the study reported in the manuscript “Blue and grey water footprints through citizens’ perception scenarios and short time series analysis of Brazilian local scale dynamics”, submitted to the Hydrological Sciences Journal.
DOI: 10.7284/131925
title: Winch data collected during research cruise SR1713 using a Markey DETW-9-11 instrument system onboard the platform RV Sally Ride

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/131926
title: Winch data collected during research cruise SR1713 using a Markey CAST-6-125 instrument system onboard the platform RV Sally Ride

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/131927
title: Winch data collected during research cruise SR1713 using a Markey CAST-6-125 instrument system onboard the platform RV Sally Ride

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.17632/h87crtj49c.3
title: Evolution in aviculture: genetic diversity and divergence head-colour morph frequencies in the domesticated Gouldian finch

description: ABSTRACT: Aviculturists are enthusiastic to be included in conservation efforts by providing expertise or genetic stock to support captive-breeding or reintroduction programs, but little work has explored these possibilities. Bringing organisms into captivity can have rapid and profound effects on behaviour, physiology and population genetic diversity, which can have important consequences for viability of reintroduction and the extrapolation captive experiments to wild counterparts. The Gouldian finch (Erythrura gouldiae) is a popular avicultural species that is endangered in the wild, and potential flagship for such reintroduction efforts. Here we used microsatellite and mitochondrial markers to characterise genetic diversity within and among avicultural populations in the broader population of domesticated Gouldian finches in Australia, and with respect to natural head-colour morphs and artificially selected plumage variation. Domesticated Gouldian finches have 32-48% lower genetic diversity compared to current wild populations, increased inbreeding, and genetic structure among aviculturists. Indeed, regardless of collection size no aviculturist approached the total diversity held among all breeders. Head-colour genotype frequencies were substantially different from the wild, and showed evidence of selection, or non-random mating. Given the previously established relationship between head-colour and functional traits, and possible adaptation to captivity, we suggest caution before introducing domesticated stock into the wild. Indeed, the status quo of relatively closed populations is potentially susceptible to inbreeding depression and further loss of genetic diversity, and we recommend a nationwide genetics-aware approach to any reintroduction programs.
DOI: 10.7284/128327
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise SR1714 using a Hawaii UHDAS instrument system onboard the platform RV Sally Ride

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7205393
title: Long-term effects of straw and straw-derived biochar on soil aggregation and fungal community in a rice-wheat rotation system

description: Straw and straw-derived biochar would affect the aggregation and fungi community structure in different aggregates. Therefore, Illumina Miseq sequeneing analysis was performed to determine the relationship between fertilization and fungi composition.<br>
DOI: 10.7284/128333
title: Expendable Probe data collected during research cruise SR1714 using a Turo Quoll instrument system onboard the platform RV Sally Ride

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.17632/pc795c8w4p.2
title: Concentration of elements in diets from a mining area

description: This data was collected in a toxicovigilance effort to enable the baselining of exposures, risks and nutritional adequacy of elements in diets from the Western regions of Ghana, where gold mining prevalent. The data shows the communities and diet groups for antimony, arsenic, barium, cadmium, cobalt, lead, manganese, mercury, molybdenum, silver, strontium, tin, tungsten, uranium, vanadium, zirconium, calcium, copper, iron, potassium, selenium and zinc. The elemental concentrations in mg/kg were determined using XRF analyzer (Niton XL 3T 900 Model, Thermo Scientific, UK) after the diets were freeze dried.