cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5053369.v1
title: Data file containing workspace for different hand dtesigns

description: This data file contains the workspace corresponding to different hand designs as well as for different contact location on the object.
DOI: 10.5519/qd.b0arsj99
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (10 records)
DOI: 10.5281/zenodo.3878527
title: CellMAPtracer TIFF files

description: These are accompanying files to the CellMAPtracer software (https://doi.org/10.5281/zenodo.3878087) and manuscript (under review).
DOI: 10.6084/m9.figshare.5053306
title: Annotated Sugarcane PacBio Iso-Seq Transcriptome

description: Sugarcane transcriptome, sequenced by PacBio Isoform sequencing, the SUGIT. Annotated by Blast2GO.<b>Publication: Hoang, N. V., Furtado, A., Mason P. J., Marquardt, A., Kasirajan, L., Thirugnanasambandam, P. P., Botha, F. C., & Henry, R. J. (2017). A survey of the complex transcriptome from the highly polyploid sugarcane genome using PacBio full-length isoform sequencing compared with <i>de novo</i> assembly from Illumina RNA sequencing. <i>BMC </i><i>Genomics, </i>18(1): 395. doi : 10.1186/s12864-017-3757-8.</b>
DOI: 10.5281/zenodo.3878526
title: CellMAPtracer TIFF files

description: These are accompanying files to the CellMAPtracer software (https://doi.org/10.5281/zenodo.3878087) and manuscript (under review).
DOI: 10.6084/m9.figshare.5053291
title: SelfBlastFilter.py

description: Created on Jan 21, 2011this is designed to run in a folder with a single fasta file and blast txt file that has been run blasting that fasta file against itself, with the number of descriptions &gt; the number of times a given ID is hit.<br>ex. script:nohup pb blastn -dbnuc InputFasta_length_added.fas -query InputFasta_length_added.fas -out InputFasta_length_added75.txt -num_descriptions 75 -evalue 0.00001 -outfmt 10&<br>note that the fasta headers for the file being used CCDS are unique <br>Note that the input fasta file needs to be screened to make sure the is only onegene ID for each entry. I do this by adding their length to their end, but there are stillsome replicates, but these are OK since they are the same.
DOI: 10.6084/m9.figshare.5053204
title: WP2: MGEP Experimental Data

description: Milling process experimetnal Results
DOI: 10.6084/m9.figshare.5053306.v1
title: Annotated Sugarcane PacBio Iso-Seq Transcriptome

description: Sugarcane transcriptome, sequenced by PacBio Isoform sequencing, the SUGIT. Annotated by Blast2GO.<b>Publication: Hoang, N. V., Furtado, A., Mason P. J., Marquardt, A., Kasirajan, L., Thirugnanasambandam, P. P., Botha, F. C., & Henry, R. J. (2017). A survey of the complex transcriptome from the highly polyploid sugarcane genome using PacBio full-length isoform sequencing compared with <i>de novo</i> assembly from Illumina RNA sequencing. <i>BMC </i><i>Genomics, </i>18(1): 395. doi : 10.1186/s12864-017-3757-8.</b>
DOI: 10.6084/m9.figshare.5053291.v1
title: SelfBlastFilter.py

description: Created on Jan 21, 2011this is designed to run in a folder with a single fasta file and blast txt file that has been run blasting that fasta file against itself, with the number of descriptions &gt; the number of times a given ID is hit.<br>ex. script:nohup pb blastn -dbnuc InputFasta_length_added.fas -query InputFasta_length_added.fas -out InputFasta_length_added75.txt -num_descriptions 75 -evalue 0.00001 -outfmt 10&<br>note that the fasta headers for the file being used CCDS are unique <br>Note that the input fasta file needs to be screened to make sure the is only onegene ID for each entry. I do this by adding their length to their end, but there are stillsome replicates, but these are OK since they are the same.
DOI: 10.6084/m9.figshare.5053204.v2
title: WP2: MGEP Experimental Data

description: Milling process experimetnal Results
DOI: 10.6084/m9.figshare.5053204.v1
title: WP2: MGEP Experimental Data

description: Milling process experimetnal Results
DOI: 10.5519/qd.r1uei9xa
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (32 records)
DOI: 10.5519/qd.c7zrs0hw
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (195 records)
DOI: 10.6084/m9.figshare.12906104.v2
title: Test-retest reliability_RMS.xlsx

description: Reliability of pulmonary function among Type 2 diabetes mellitus
DOI: 10.6084/m9.figshare.12906104
title: Test-retest reliability_RMS.xlsx

description: Reliability of pulmonary function among Type 2 diabetes mellitus
DOI: 10.6084/m9.figshare.12906104.v1
title: Test-retest reliability_RMS.xlsx

description: Reliability of pulmonary function among Type 2 diabetes mellitus
DOI: 10.6084/m9.figshare.12812081
title: the complete mitochondrial genome ogf pronghorn spiny lobster Panulirus penicillatus (Olivier, 1791) sequencing cleandata

description: the complete mitochondrial genome ogf pronghorn spiny lobster Panulirus penicillatus (Olivier, 1791) sequencing cleandata
DOI: 10.6084/m9.figshare.12812081.v1
title: the complete mitochondrial genome ogf pronghorn spiny lobster Panulirus penicillatus (Olivier, 1791) sequencing cleandata

description: the complete mitochondrial genome ogf pronghorn spiny lobster Panulirus penicillatus (Olivier, 1791) sequencing cleandata
DOI: 10.6084/m9.figshare.5051956
title: Supplemental Figure 13

description: Material-dependent maintenance of hESC pluripotency.
DOI: 10.6084/m9.figshare.5051959
title: Supplemental Figure 14

description: NMR quantification of peptide conjugation to PEG molecules.
DOI: 10.6084/m9.figshare.5051953
title: Supplemental Figure 12

description: Shear modulus of synthetic hydrogels used in hESC culture
DOI: 10.6084/m9.figshare.5051947
title: Supplemental Figure 5

description: Aortic explant sprouting assays in Matrigel and synthetic hydrogels.
DOI: 10.6084/m9.figshare.5051953.v1
title: Supplemental Figure 12

description: Shear modulus of synthetic hydrogels used in hESC culture
DOI: 10.6084/m9.figshare.5051956.v1
title: Supplemental Figure 13

description: Material-dependent maintenance of hESC pluripotency.
DOI: 10.6084/m9.figshare.5051959.v1
title: Supplemental Figure 14

description: NMR quantification of peptide conjugation to PEG molecules.
DOI: 10.6084/m9.figshare.5051941
title: Supplemental Figure 3

description: Characterization of synthetic hydrogel stability and non-crosslinked components.
DOI: 10.6084/m9.figshare.5051944
title: Supplemental Figure 4

description: Characterization of synthetic hydrogel swelling over time.
DOI: 10.6084/m9.figshare.5051950
title: Supplemental Figure 6

description: Synthetic PEG hydrogels optimized for use in 96-well angiogenesis plates.
DOI: 10.6084/m9.figshare.5051938
title: Supplemental Figure 2

description: Thin-hydrogelscreening system to identify HUVEC network-forming conditions which incorporated a VEGF binding peptide (VBP)into the formulation. VEGF sequestration by PEG hydrogels containing VBP.
DOI: 10.6084/m9.figshare.5051941.v1
title: Supplemental Figure 3

description: Characterization of synthetic hydrogel stability and non-crosslinked components.
DOI: 10.6084/m9.figshare.5051947.v1
title: Supplemental Figure 5

description: Aortic explant sprouting assays in Matrigel and synthetic hydrogels.
DOI: 10.6084/m9.figshare.5051950.v1
title: Supplemental Figure 6

description: Synthetic PEG hydrogels optimized for use in 96-well angiogenesis plates.
DOI: 10.6084/m9.figshare.5051932
title: Supplemental Figure 1

description: Shear modulus of synthetic hydrogels with varying PEG concentration and VBP presencein precursor solutions, vascular network disruption when exposed to 20 μM Sunitinib®.
DOI: 10.6084/m9.figshare.5051935
title: Figure 1

description: Qualitative scoring system for HUVEC networkformation
DOI: 10.6084/m9.figshare.5051938.v1
title: Supplemental Figure 2

description: Thin-hydrogelscreening system to identify HUVEC network-forming conditions which incorporated a VEGF binding peptide (VBP)into the formulation. VEGF sequestration by PEG hydrogels containing VBP.
DOI: 10.6084/m9.figshare.5051944.v1
title: Supplemental Figure 4

description: Characterization of synthetic hydrogel swelling over time.
DOI: 10.6084/m9.figshare.5051935.v1
title: Figure 1

description: Qualitative scoring system for HUVEC networkformation
DOI: 10.6084/m9.figshare.5051923
title: Figures 3 and 4

description: Concentration-dependent inhibition of endothelial-network formation by the vascular inhibitors Vatalanib (PTK787), Semaxinib (SU5416)sFlt-1, anti-VEGF, Prinomastat hydrochloride andSutent, measured as percent change in network area compared with vehicle controls.
DOI: 10.6084/m9.figshare.5051926
title: Figure 5

description: Identification of vascular inhibitors from a subset of candidatechemical compounds from the ToxCast library with the use of synthetichydrogel versus Matrigel systems
DOI: 10.6084/m9.figshare.5051929
title: Figure 6

description: Material-dependent maintenance of hESC pluripotency
DOI: 10.6084/m9.figshare.5051932.v1
title: Supplemental Figure 1

description: Shear modulus of synthetic hydrogels with varying PEG concentration and VBP presencein precursor solutions, vascular network disruption when exposed to 20 μM Sunitinib®.
DOI: 10.6084/m9.figshare.5051920
title: Figure 2

description: Endothelial-network formation in synthetic hydrogel and Matrigel systems is quantified andsubjected to the Z′ test to verify their efficacy as toxicity screening systems
DOI: 10.6084/m9.figshare.5051929.v1
title: Figure 6

description: Material-dependent maintenance of hESC pluripotency
DOI: 10.6084/m9.figshare.5051923.v1
title: Figures 3 and 4

description: Concentration-dependent inhibition of endothelial-network formation by the vascular inhibitors Vatalanib (PTK787), Semaxinib (SU5416)sFlt-1, anti-VEGF, Prinomastat hydrochloride andSutent, measured as percent change in network area compared with vehicle controls.
DOI: 10.6084/m9.figshare.5051926.v1
title: Figure 5

description: Identification of vascular inhibitors from a subset of candidatechemical compounds from the ToxCast library with the use of synthetichydrogel versus Matrigel systems
DOI: 10.6084/m9.figshare.5051869
title: Water You Doing UCLA?: An Inventory of Public Water Use

description: This project served to quantify public water fixtures on UCLA's campus and approximate their use and efficiency in hopes of developing a better inventory for the University. Data_Collection1 holds the inventory data of fixtures per building and their individual use, Data_Collection2 holds info on their total use and building-specific characteristics (i.e square footage and building age). Read the README_GCURSP file for more specific information.
DOI: 10.6084/m9.figshare.5051872
title: Evaluating a Conversion to Solar Street Lamps in North Village, Westwood, California

description: This research consists of producing a report card for the streets in North Village by UCLA in Westwood. The streets were analyzed on the conditions they provided to support solar street lamps. Measurements were taken by already existing lampposts so as to minimize infrastructure changes and the streets were also analyzed through a satellite image. The criteria for each grade on the report card was then defined and each street received a grade based on how well they met the criteria.
DOI: 10.6084/m9.figshare.5051920.v1
title: Figure 2

description: Endothelial-network formation in synthetic hydrogel and Matrigel systems is quantified andsubjected to the Z′ test to verify their efficacy as toxicity screening systems
DOI: 10.6084/m9.figshare.5051869.v1
title: Water You Doing UCLA?: An Inventory of Public Water Use

description: This project served to quantify public water fixtures on UCLA's campus and approximate their use and efficiency in hopes of developing a better inventory for the University. Data_Collection1 holds the inventory data of fixtures per building and their individual use, Data_Collection2 holds info on their total use and building-specific characteristics (i.e square footage and building age). Read the README_GCURSP file for more specific information.
DOI: 10.6084/m9.figshare.5051872.v2
title: Evaluating a Conversion to Solar Street Lamps in North Village, Westwood, California

description: This research consists of producing a report card for the streets in North Village by UCLA in Westwood. The streets were analyzed on the conditions they provided to support solar street lamps. Measurements were taken by already existing lampposts so as to minimize infrastructure changes and the streets were also analyzed through a satellite image. The criteria for each grade on the report card was then defined and each street received a grade based on how well they met the criteria.
DOI: 10.6084/m9.figshare.5051872.v1
title: Evaluating Streets in North Village Based on Conditions Required for Solar Street Lamp Efficiency

description: This research consists of producing a report card for the streets in North Village by UCLA in Westwood. The streets were analyzed on the conditions they provided to support solar street lamps. Measurements were taken by already existing lampposts so as to minimize infrastructure changes and the streets were also analyzed through a satellite image. The criteria for each grade on the report card was then defined and each street received a grade based on how well they met the criteria.
DOI: 10.6084/m9.figshare.5051836
title: VirusData.csv

description: This dataset can be used to replicate the analysis we describe in "Transmissibility of emerging viral zoonoses."
DOI: 10.6084/m9.figshare.5051839
title: Species list and identification reference

description: An excel spreadsheet which provided following information: list of species, references for the species identification, occurrence of each species on every island and species richness of each island.
DOI: 10.6084/m9.figshare.5051821
title: Input data for salp_anon_to_sfon

description: Contains files necessary to run the following github repo:https://github.com/bensutherland/salp_anon_to_sfon<br>
DOI: 10.6084/m9.figshare.5051815
title: Single copy orthologs in the Drosophila validation work

description: 1) dmel_70_100_80cov.fa – Contains the single copy orthologs from <i>Drosophila melanogaster</i> that had atleast 80% coverage and 70% identity in a reciprocal best blast search with single copy orthologs from <i>Drosophila virilis</i>. 2) dviri_70_100_80cov.fa – Contains the single copy orthologs from <i>Drosophila</i> <i>virilis </i>that had atleast 80% coverage and 70% identity in a reciprocal best blast search with single copy orthologs from <i>Drosophila melanogaster</i>.
DOI: 10.6084/m9.figshare.5051836.v1
title: VirusData.csv

description: This dataset can be used to replicate the analysis we describe in "Transmissibility of emerging viral zoonoses."
DOI: 10.6084/m9.figshare.5051821.v2
title: Input data for salp_anon_to_sfon

description: Contains files necessary to run the following github repo:https://github.com/bensutherland/salp_anon_to_sfon<br>
DOI: 10.6084/m9.figshare.5051749
title: Supplementary_Table_3_RNA_viruses.docx

description: Table S3. List of RNA phage genomes analyzed. CRISPR spacers from all published genomes were tested for similarity to RNA phage genomes listed here.
DOI: 10.6084/m9.figshare.5051755
title: Supplementary_Table_4_RT_loci_spacer_hits.xlsx

description: Table S4. Spacer matches for CRISPR arrays encoded in RT-Cas1 loci in NR database. CRISPR spacers from all RT-containing loci were tested for similarity to all non-redundant protein records. The few observed matches are listed here.
DOI: 10.6084/m9.figshare.5051821.v1
title: Input data for salp_anon_to_sfon

description: Contains files necessary to run the following github repo:https://github.com/bensutherland/salp_anon_to_sfon<br>
DOI: 10.6084/m9.figshare.5051749.v1
title: Supplementary_Table_3_RNA_viruses.docx

description: Table S3. List of RNA phage genomes analyzed. CRISPR spacers from all published genomes were tested for similarity to RNA phage genomes listed here.
DOI: 10.6084/m9.figshare.5051755.v1
title: Supplementary_Table_4_RT_loci_spacer_hits.xlsx

description: Table S4. Spacer matches for CRISPR arrays encoded in RT-Cas1 loci in NR database. CRISPR spacers from all RT-containing loci were tested for similarity to all non-redundant protein records. The few observed matches are listed here.
DOI: 10.6084/m9.figshare.5051743
title: Supplementary_Table_2_Curated_Spirulina_hits.txt

description: Table S2. Details of Spirulina spacers with identified metagenomic sources. Each record (separated by ***) contains BLASTx results for a metagenomic sequence or assembly identified as related to a known ORF, followed by BLASTn results depicting the best mapping of a Spirulina spacer to the metagenomic read or assembly. Other, weaker spacer matches to the same metagenomic target are also summarized. The only type III-B spacer match is indicated at the beginning of the relevant record.
DOI: 10.6084/m9.figshare.5051743.v1
title: Supplementary_Table_2_Curated_Spirulina_hits.txt

description: Table S2. Details of Spirulina spacers with identified metagenomic sources. Each record (separated by ***) contains BLASTx results for a metagenomic sequence or assembly identified as related to a known ORF, followed by BLASTn results depicting the best mapping of a Spirulina spacer to the metagenomic read or assembly. Other, weaker spacer matches to the same metagenomic target are also summarized. The only type III-B spacer match is indicated at the beginning of the relevant record.
DOI: 10.6084/m9.figshare.5051725
title: Stern_et_al_2017_Applied_Env_Microbiology(1of2)

description: Raw (joined, paired-end Illumina MiSeq) 16S sequences and Mapping files for data in experiments CF1 and DCF from: <br>Stern, N., Ginder-Vogel, M., Stegen, J.C., Arntzen, B., Kennedy, W.K., Larget, B.R., Roden, E.R. (2017). Colonization habitat controls biomass, composition, and metabolic activity of attached microbial communities in the Columbia River hyporheic corridor. Applied Environmental Microbiology. Accepted March 2017(Under Revision).<br>Unassembled reads are listed in un1 (forward) and un2 (reverse).<br>
DOI: 10.6084/m9.figshare.5051623
title: DCF_MappingFile

description: Mapping file for DCF experiment.
DOI: 10.6084/m9.figshare.5051638
title: Epifauna and infauna datasets

description: These are the epifaunal and infaunal data of a Before-After-Control-Impact experiment conducted in Cardigan Bay in the UK in 2014. The epifaunal animals were collected with a 2mm mesh size 2m beam trawl. The infaunal animals were collected with a Hamon grab of 0.1m2.
DOI: 10.6084/m9.figshare.5051725.v1
title: CF1_andDCF_fastqjoin.join

description: Raw joined Illumina MiSeq 16S sequences for experiments CF1 and DCF. File is compressed due to large size, must be unzipped for data analysis. Associated mapping files found in main project folder at the following link:<br>https://figshare.com/projects/Stern_et_al_2017_Applied_Environmental_Microbiology/22213<br><br>Data from: Stern, N., Ginder-Vogel, M., Stegen, J.C., Arntzen, B., Kennedy, W.K., Larget, B.R., Roden, E.R. (2017). Colonization habitat controls biomass, composition, and metabolic activity of attached microbial communities in the Columbia River hyporheic corridor. Applied Environmental Microbiology. Accepted March 2017(Under Revision).<br>
DOI: 10.6084/m9.figshare.5051719
title: Supplementary_Table_1_RT_cas_loci_details.xlsx

description: <b>Table S1. Comprehensive survey of RT-containing CRISPR-Cas loci. Genomic co-ordinates, Genbank IDs, and annotations are provided for genes in the vicinity of CRISPR-associated RTs.</b>
DOI: 10.6084/m9.figshare.5051617
title: CF2_MappingFile

description: Mapping file for CF2 experiment.
DOI: 10.6084/m9.figshare.5051623.v1
title: DCF_MappingFile

description: Mapping file for DCF experiment.
DOI: 10.6084/m9.figshare.5051638.v1
title: Epifauna and infauna datasets

description: These are the epifaunal and infaunal data of a Before-After-Control-Impact experiment conducted in Cardigan Bay in the UK in 2014. The epifaunal animals were collected with a 2mm mesh size 2m beam trawl. The infaunal animals were collected with a Hamon grab of 0.1m2.
DOI: 10.6084/m9.figshare.5051719.v1
title: Supplementary_Table_1_RT_cas_loci_details.xlsx

description: <b>Table S1. Comprehensive survey of RT-containing CRISPR-Cas loci. Genomic co-ordinates, Genbank IDs, and annotations are provided for genes in the vicinity of CRISPR-associated RTs.</b>
DOI: 10.6084/m9.figshare.5051617.v1
title: CF2_MappingFile

description: Mapping file for CF2 experiment.
DOI: 10.6084/m9.figshare.5051596
title: Short-term EEG dynamics and neural generators evoked by navigational images

description: Data from the paper entitled: "Short-term EEG dynamics and neural generators evoked by navigational images"<br>Files structure is as stated in: filestructure.txt<br>Raw data from subjects.All recordings were unipolar against the left earlobe electrode Vertical eye movements (EOG) were recorded unipolarly against the common reference and horizontal EOG was recorded bipolarly. All electrode impedances were maintained below 5 kΩ. Scalp potentials were amplified by ANT DC-amplifiers (ANT, the Netherlands) and digitized with a rate of 2.048 Hz, a resolution of 16 bit (range 11 mV). A band pass from DC to 256 Hz and a notch filter (47.5-52.5 Hz) were also applied.
DOI: 10.6084/m9.figshare.5051608
title: Stern_et_al_2017_Applied_Env_Microbiology(2of2)

description: Raw (joined, paired-end Illumina MiSeq) 16S sequences and Mapping file for data in experiment CF2 from: <br>Stern, N., Ginder-Vogel, M., Stegen, J.C., Arntzen, B., Kennedy, W.K., Larget, B.R., Roden, E.R. (2017). Colonization habitat controls biomass, composition, and metabolic activity of attached microbial communities in the Columbia River hyporheic corridor. Applied Environmental Microbiology. Accepted March 2017(Under Revision).<br>Unassembled reads are listed in un1 (forward) and un2 (reverse).<br>
DOI: 10.6084/m9.figshare.5051611
title: CF1_MappingFile

description: Mapping file for CF1 experiment.
DOI: 10.6084/m9.figshare.5051725.v2
title: CF1_andDCF_fastqjoin.join

description: Raw joined Illumina MiSeq 16S sequences for experiments CF1 and DCF. File is compressed due to large size, must be unzipped for data analysis. Associated mapping files found in main project folder at the following link:<br>https://figshare.com/projects/Stern_et_al_2017_Applied_Environmental_Microbiology/22213<br><br>Data from: Stern, N., Ginder-Vogel, M., Stegen, J.C., Arntzen, B., Kennedy, W.K., Larget, B.R., Roden, E.R. (2017). Colonization habitat controls biomass, composition, and metabolic activity of attached microbial communities in the Columbia River hyporheic corridor. Applied Environmental Microbiology. Accepted March 2017(Under Revision).<br>
DOI: 10.6084/m9.figshare.5051593
title: P3HT and PCBM atomistic force fields

description: GROMOS 53A6 based atomistic force field for the conjugated polymer P3HT, the fullerene derivative PCBM and chlorobenzene.<br>The provided files are in GROMACS format (see GROMACS manual and tutorial in case of need). A pre-equilibrated system containing a P3HT chain (24 repeat units) and a PCBM molecule solvated in chlorobenzene is provided. The associated top(ology) file (and files included therein) is provided, along with run parameter files for an energy minimization (em.mdp), NVT equilibration (shortNVT.mdp), NPT equilibration (shortNPT.mdp), and production run (prodNPT.mdp).<br>NOTE! The archive "p3ht_gromos_v_2017RA-JACS.ff.zip" needs to be unzipped first (command: unzip p3ht_gromos_v_2017RA-JACS.ff.zip).<br> For details on the atomistic force fields, see the associated publication (and please cite it if you find the files useful for your work):<br><b>Bulk Heterojunction Morphologies with Atomistic Resolution from Coarse-Grain Solvent Evaporation Simulations</b>Riccardo Alessandri, Jaakko J. Uusitalo, Alex H. de Vries, Remco W. A. Havenith, and Siewert J. Marrink<i>J. Am. Chem. Soc.</i>, <b>2017</b>, 139 (10), pp 3697–3705<br>