cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12645458
title: Gene database of Shewanella putrefaciens CN-32

description: <i>Shewanella putrefaciens</i> is a Gram-negative, facultative anaerobic bacterium whose natural habitat is the marine environment. Capable of using manganese and iron as terminal electron acceptors in the electron transport chain, the bacterium has been tapped for biotechnology purposes such as production of nanoparticles through surface mediated reactions on the cell membrane. More recently, <i>S. putrefaciens</i> is exploited for use in bioelectrochemical reactions to power a bioeconomy. This work sought to provide fundamental information of the genetic repertoire of <i>S. putrefaciens</i> CN-32 through parsing the annotated genome sequence of the bacterium available on Genbank. The resulting gene database comprise gene name, gene function, and gene sequence, and should find use in guiding molecular cloning work to exploit the genetic endowment of <i>S. putrefaciens</i> for applications in other microbial chassis. At the same time, the gene database is also useful for informing genome editing workflow to construct loss of function mutants needed in functional elucidation of genes in this emerging biotechnology workhorse.
DOI: 10.6084/m9.figshare.12645455
title: original data.xlsx

description: Raw data from the article " Skeletal muscle dysregulation in rheumatoid arthritis: metabolic and molecular markers in a rodent model and patients" published at Journal PlosONE.https://doi.org/10.1371/journal.pone.0235702<br>
DOI: 10.6084/m9.figshare.12645455.v1
title: original data.xlsx

description: Raw data from the article " Skeletal muscle dysregulation in rheumatoid arthritis: metabolic and molecular markers in a rodent model and patients" published at Journal PlosONE.https://doi.org/10.1371/journal.pone.0235702<br>
DOI: 10.6084/m9.figshare.12645371
title: citeseer acknowledgments data

description: Acknowledgments data from CiteSeer. These data were analyzed in: https://www.pnas.org/content/101/51/17599
DOI: 10.6084/m9.figshare.12645371.v1
title: citeseer acknowledgments data

description: Acknowledgments data from CiteSeer. These data were analyzed in: https://www.pnas.org/content/101/51/17599
DOI: 10.6084/m9.figshare.12645326
title: Datasets_for_analyzing_Tara_V9_amplicon_datasets

description: Data used for looking for my Chaetoceros isolate in the tara datasets.<br>The scrips used to analyze these data are found in:Scripts_for_analyzing_Tara_V9_amplicon_datasets<br>"TARA_stations_coords.txt" - Lat and Long for each station sampled as part of the Tara oceans project."formatted_Polarsample_sheet.txt" - Tara polar sample data including all NCBI accessions."Global_ASV.fa" - Representative sequences for ASVs recovered from the Tara Global dataset (as analyzed in Callahan et al., 2017)<br>Citations:Callahan BJ, McMurdie PJ, Holmes SP. Exact sequence variants should replace operational taxonomic units in marker-gene data analysis. The ISME journal. 2017 Dec;11(12):2639-43.<br><br><br><br>
DOI: 10.6084/m9.figshare.12645341
title: Light_stress_test

description: Data and scripts for analyzing the growth response to a lethal light dose.
DOI: 10.6084/m9.figshare.12645326.v1
title: Datasets_for_analyzing_Tara_V9_amplicon_datasets

description: Data used for looking for my Chaetoceros isolate in the tara datasets.<br>The scrips used to analyze these data are found in:Scripts_for_analyzing_Tara_V9_amplicon_datasets<br>"TARA_stations_coords.txt" - Lat and Long for each station sampled as part of the Tara oceans project."formatted_Polarsample_sheet.txt" - Tara polar sample data including all NCBI accessions."Global_ASV.fa" - Representative sequences for ASVs recovered from the Tara Global dataset (as analyzed in Callahan et al., 2017)<br>Citations:Callahan BJ, McMurdie PJ, Holmes SP. Exact sequence variants should replace operational taxonomic units in marker-gene data analysis. The ISME journal. 2017 Dec;11(12):2639-43.<br><br><br><br>
DOI: 10.6084/m9.figshare.12645341.v1
title: Light_stress_test

description: Data and scripts for analyzing the growth response to a lethal light dose.
DOI: 10.6084/m9.figshare.12645299
title: Fig. 3

description: Matlab files for generating graphs in Fig. 3
DOI: 10.6084/m9.figshare.12645299.v1
title: Fig. 3

description: Matlab files for generating graphs in Fig. 3
DOI: 10.6084/m9.figshare.12645311
title: Datasets_for_Narragansett_Bay_18S_analysis

description: Environmental data from Narragansett Bay compiled from Rynearson et al., 2020, Narragansett Bay time series website (https://web.uri.edu/gso/research/plankton/data/), National Data Buoy Centers station QPTR1 – 8454049 at nearby Quonset Point (https://www.ndbc.noaa.gov/station_page.php?station=qptr1), and the National Research Reserve System’s Central Data Management Office website (https://cdmo.baruch.sc.edu/dges/) for station NARPCMET.<br>Analysis of the sequence data can be found in: Scripts_for_Narragansett_Bay_18S_analysis<br>"metadata.csv" - Metadata given in Rynearson et al., 2020."NARPCMET.csv" - Irradiance data downloaded from NERRS"easy_name_NB_count.csv" - Count data from denoised amplicons with row names changed to asv#"rep_asv.fasta" - Representative sequences for each ASV output from DADA2."chl_a_raw.csv" - Chlorophyll a data from NERRS<br>citation for Rynearson et al., 2020:Rynearson TA, Flickinger SA, Fontaine DN. Metabarcoding Reveals Temporal Patterns of Community Composition and Realized Thermal Niches of Thalassiosira Spp.(Bacillariophyceae) from the Narragansett Bay Long-Term Plankton Time Series. Biology. 2020 Jan;9(1):19.<br><br><br>
DOI: 10.6084/m9.figshare.12645275
title: Shahab et al. (2020) Supplementary file II. Environmental Conditions on Each Testing Day for F-v-P testing

description: Table with enviromental information on the two days of testing
DOI: 10.6084/m9.figshare.12645311.v2
title: Datasets_for_Narragansett_Bay_18S_analysis

description: Environmental data from Narragansett Bay compiled from Rynearson et al., 2020, Narragansett Bay time series website (https://web.uri.edu/gso/research/plankton/data/), National Data Buoy Centers station QPTR1 – 8454049 at nearby Quonset Point (https://www.ndbc.noaa.gov/station_page.php?station=qptr1), and the National Research Reserve System’s Central Data Management Office website (https://cdmo.baruch.sc.edu/dges/) for station NARPCMET.<br>Analysis of the sequence data can be found in: Scripts_for_Narragansett_Bay_18S_analysis<br>"metadata.csv" - Metadata given in Rynearson et al., 2020."NARPCMET.csv" - Irradiance data downloaded from NERRS"easy_name_NB_count.csv" - Count data from denoised amplicons with row names changed to asv#"rep_asv.fasta" - Representative sequences for each ASV output from DADA2."chl_a_raw.csv" - Chlorophyll a data from NERRS<br>citation for Rynearson et al., 2020:Rynearson TA, Flickinger SA, Fontaine DN. Metabarcoding Reveals Temporal Patterns of Community Composition and Realized Thermal Niches of Thalassiosira Spp.(Bacillariophyceae) from the Narragansett Bay Long-Term Plankton Time Series. Biology. 2020 Jan;9(1):19.<br><br><br>
DOI: 10.6084/m9.figshare.12645311.v1
title: Datasets_for_Narragansett_Bay_18S_analysis

description: Environmental data from Narragansett Bay compiled from Rynearson et al., 2020, Narragansett Bay time series website (https://web.uri.edu/gso/research/plankton/data/), National Data Buoy Centers station QPTR1 – 8454049 at nearby Quonset Point (https://www.ndbc.noaa.gov/station_page.php?station=qptr1), and the National Research Reserve System’s Central Data Management Office website (https://cdmo.baruch.sc.edu/dges/) for station NARPCMET.<br>Analysis of the sequence data can be found in: Scripts_for_Narragansett_Bay_18S_analysis<br>"metadata.csv" - Metadata given in Rynearson et al., 2020."NARPCMET.csv" - Irradiance data downloaded from NERRS"easy_name_NB_count.csv" - Count data from denoised amplicons with row names changed to asv#"chl_a_raw.csv" - Chlorophyll a data from NERRS<br>citation for Rynearson et al., 2020:Rynearson TA, Flickinger SA, Fontaine DN. Metabarcoding Reveals Temporal Patterns of Community Composition and Realized Thermal Niches of Thalassiosira Spp.(Bacillariophyceae) from the Narragansett Bay Long-Term Plankton Time Series. Biology. 2020 Jan;9(1):19.<br><br><br>
DOI: 10.6084/m9.figshare.12645275.v1
title: Shahab et al. (2020) Supplementary file II. Environmental Conditions on Each Testing Day for F-v-P testing

description: Table with enviromental information on the two days of testing
DOI: 10.6084/m9.figshare.12645206
title: Human-Made Very-Low-Frequency Transmitters Bifurcate Energetic Electron Belt in Near-Earth Space

description: This is the dataset used to produce figures for the paper under review with the title of "Human-Made Very-Low-Frequency Transmitters Bifurcate Energetic Electron Belt in Near-Earth Space".
DOI: 10.6084/m9.figshare.12645206.v1
title: Human-Made Very-Low-Frequency Transmitters Bifurcate Energetic Electron Belt in Near-Earth Space

description: This is the dataset used to produce figures for the paper under review with the title of "Human-Made Very-Low-Frequency Transmitters Bifurcate Energetic Electron Belt in Near-Earth Space".
DOI: 10.6084/m9.figshare.12645206.v2
title: Human-Made Very-Low-Frequency Transmitters Bifurcate Energetic Electron Belt in Near-Earth Space

description: This is the dataset used to produce figures for the paper under review with the title of "Human-Made Very-Low-Frequency Transmitters Bifurcate Energetic Electron Belt in Near-Earth Space".
DOI: 10.6084/m9.figshare.12645167
title: PituitaryAdenomaOCT_Analysis20200712.xlsx

description: The data are retinal indices derived from spectral-domain optical coherence tomography (SD-OCT) scans for the quantitative analysis of the retinal light reflection characteristic in pituitary adenoma.
DOI: 10.6084/m9.figshare.12645167.v1
title: PituitaryAdenomaOCT_Analysis20200712.xlsx

description: The data are retinal indices derived from spectral-domain optical coherence tomography (SD-OCT) scans for the quantitative analysis of the retinal light reflection characteristic in pituitary adenoma.
DOI: 10.6084/m9.figshare.12644981
title: Singular Spectrum Analysis of monthly stroke deaths and mean monthly sunspot numbers

description: An excel with Two sheets <br>1st sheet: raw data (columns A-B) and processing of stroke death events 1985-1989 (rest of columns)2nd sheet: raw data (columns A-B) and processing of sunspot numbers 12/1944-12/2004 (rest of columns)<br><br>
DOI: 10.6084/m9.figshare.12644930
title: Use of a mutation-specific genotyping method to assess for HIV-1 drug resistance in antiretroviral-naïve HIV-1 Subtype C-infected patients in Botswana

description: PANDAA Cq values. Age, CD4 count and viral load for each patient
DOI: 10.6084/m9.figshare.12644930.v1
title: Use of a mutation-specific genotyping method to assess for HIV-1 drug resistance in antiretroviral-naïve HIV-1 Subtype C-infected patients in Botswana

description: PANDAA Cq values. Age, CD4 count and viral load for each patient
DOI: 10.6084/m9.figshare.12644921
title: A Comparative Study of Test Code Clones and Production Code Clones - Replication Package

description: The dataset of our work "A Comparative Study of Test Code Clones and Production Code Clones". It contains the dataset, the classified code clones, and all python scripts used during the postprocessing step of our evaluation.
DOI: 10.6084/m9.figshare.12644915
title: NIR Session - 1. Extracted the iris region after iris detection

description: Records in 2019.
DOI: 10.6084/m9.figshare.12644918
title: NIR Session - 2. The Zero padding on extraced iris images

description: Records in 2019.
DOI: 10.6084/m9.figshare.12644981.v1
title: Principal Components Analysis of monthly stroke deaths and mean monthly sunspot numbers

description: An excel with Two sheets <br>1st sheet: raw data (columns A-B) and processing of stroke death events 1985-1989 (rest of columns)2nd sheet: raw data (columns A-B) and processing of sunspot numbers 12/1944-12/2004 (rest of columns)<br><br>
DOI: 10.6084/m9.figshare.12644912
title: NIR Session - 1. Extracted the iris region after iris detection

description: Records in 2019.
DOI: 10.6084/m9.figshare.12644903
title: VW Session - 2. The Zero padding on extraced iris images

description: Records in 2019.
DOI: 10.6084/m9.figshare.12644900
title: VW Session - 1. Extracted the iris region after iris detection

description: Records in 2019.
DOI: 10.6084/m9.figshare.12644852
title: Species-Area Relationship: A Mesocosm Experiment with Annual Plants

description: 1. The increase in species richness with increased island area is one of the most widely documented patterns in ecology and biogeography but its mechanisms are still under debate. Disentangling these mechanisms in natural systems is challenging due to various kinds of confounding effects. 2. Here we use a novel mesocosm experiment focusing on annual plants to disentangle the effects of two mechanisms that may lead to higher richness on large islands: increasing population sizes and increasing opportunities for within-island dispersal. Theoretical studies show that both mechanisms may contribute to higher richness on large islands, but no previous study has attempted to separate their effects. We also test an alternative, 'null' hypothesis, according to which the only mechanism underlying the increase in richness with increased area is a pure sampling effect (the 'passive sampling hypothesis'). 3. As expected, increasing area had a strong positive effect on species richness. However, the main mechanism underlying the difference in richness between small and large islands was passive sampling. Moreover, our results indicate that dispersal had a negative rather than positive effect on island richness. 4. Synthesis: Our results corroborate previous observational studies that failed to reject the passive sampling hypothesis. However, in contrast to previous studies, our findings are based on experimental manipulations of island area, under controlled uniform conditions, at small spatial scales that facilitate within-island dispersal, and in three independent systems that differed in resource availability and disturbance. These findings emphasize the need for a careful examination of sampling effects in future research of the species-area relationship.
DOI: 10.6084/m9.figshare.12644816
title: JVASP-13824 to JVASP-14728

description: JARVIS-DFT
DOI: 10.6084/m9.figshare.12644819
title: JVASP-14729 to JVASP-15277

description: JARVIS-DFT
DOI: 10.6084/m9.figshare.12644819.v1
title: JVASP-14729 to JVASP-15277

description: JARVIS-DFT
DOI: 10.6084/m9.figshare.12644813
title: JVASP-12636 to JVASP-13822

description: JARVIS-DFT
DOI: 10.6084/m9.figshare.12644813.v1
title: JVASP-12636 to JVASP-13822

description: JARVIS-DFT
DOI: 10.6084/m9.figshare.12644727
title: Additional file 5 of Last Glacial Maximum led to community-wide population expansion in a montane songbird radiation in highland Papua New Guinea

description: Additional file 5 Table S1. Details of samples used in this study along with the number of cleaned reads obtained from Illumina sequencing and details on COI gene amplification. Museum abbreviation: BMNHC = Burke Museum of Natural History and Culture, Seattle, USA.
DOI: 10.6084/m9.figshare.12644730
title: Additional file 6 of Last Glacial Maximum led to community-wide population expansion in a montane songbird radiation in highland Papua New Guinea

description: Additional file 6 Table S2. Genetic pairwise COI distances (p distances) between various scrubwren species are shown below the diagonal and standard error estimates are shown above the diagonal.
DOI: 10.6084/m9.figshare.12644730.v1
title: Additional file 6 of Last Glacial Maximum led to community-wide population expansion in a montane songbird radiation in highland Papua New Guinea

description: Additional file 6 Table S2. Genetic pairwise COI distances (p distances) between various scrubwren species are shown below the diagonal and standard error estimates are shown above the diagonal.
DOI: 10.6084/m9.figshare.12644727.v1
title: Additional file 5 of Last Glacial Maximum led to community-wide population expansion in a montane songbird radiation in highland Papua New Guinea

description: Additional file 5 Table S1. Details of samples used in this study along with the number of cleaned reads obtained from Illumina sequencing and details on COI gene amplification. Museum abbreviation: BMNHC = Burke Museum of Natural History and Culture, Seattle, USA.
DOI: 10.6084/m9.figshare.12644682
title: Additional file 4 of LINE-1 ORF1p does not determine substrate preference for human/orangutan SVA and gibbon LAVA

description: Additional file 4: VNTR structure of orangutan SVAPA_7 elements. Ten orangutan SVAPA_7 in ponAbe3 were selected at random and their VNTR subunit structure was determined based on the code developed in Lupan et al. (2015). CONSENSUS ponAbe2 - consensus VNTR structure of the SVAPA_7 elements identifiable in ponAbe2. The VNTR structure of the two elements tested (OU3, OU4) is given for comparison.
DOI: 10.6084/m9.figshare.12644679
title: Additional file 3 of LINE-1 ORF1p does not determine substrate preference for human/orangutan SVA and gibbon LAVA

description: Additional file 3: Subgroups of human SVA_E elements containing both fixed and polymorphic elements. SVA_E3: VNTR subunit structure of SVA_E subgroup E3 containing four fixed and four polymorphic elements. Based on divergence from subgroup consensus (div; Alu-like region and SINE-R) and VNTR structure the two fixed elements on chromosome 1 would be candidates to test for activity. AF - allele frequency as provided in Stewart C, Kural D, Strömberg MP, Walker JA, Konkel MK, et al. (2011) A Comprehensive Map of Mobile Element Insertion Polymorphisms in Humans. PLoS Genet 7(8): e1002236. Arrays of VNTR subunits are boxed. Polymorphic elements are highlighted in yellow. SVA_E4: VNTR subunit structure of SVA_E subgroup E4 containing eight fixed and three polymorphic elements. Candidates to test for activity based on divergence from subgroup consensus (div; Alu-like region and SINE-R) and VNTR structure are indicated. AF - allele frequency; Sources: chr1:112,834,947–112,837,733–1000 Genomes Phase 3 Integrated Variant Calls track of the UCSC genome browser; chr2:223760192–223,762,683 - Stewart C, Kural D, Strömberg MP, Walker JA, Konkel MK, et al. (2011) A Comprehensive Map of Mobile Element Insertion Polymorphisms in Humans. PLoS Genet 7(8): e1002236; chr5:43,086,412-43,089,307 - dbRIP. Arrays of VNTR subunits are boxed. Polymorphic elements are highlighted in yellow.
DOI: 10.6084/m9.figshare.12644682.v1
title: Additional file 4 of LINE-1 ORF1p does not determine substrate preference for human/orangutan SVA and gibbon LAVA

description: Additional file 4: VNTR structure of orangutan SVAPA_7 elements. Ten orangutan SVAPA_7 in ponAbe3 were selected at random and their VNTR subunit structure was determined based on the code developed in Lupan et al. (2015). CONSENSUS ponAbe2 - consensus VNTR structure of the SVAPA_7 elements identifiable in ponAbe2. The VNTR structure of the two elements tested (OU3, OU4) is given for comparison.
DOI: 10.6084/m9.figshare.12644673
title: Additional file 1 of LINE-1 ORF1p does not determine substrate preference for human/orangutan SVA and gibbon LAVA

description: Additional file 1: Human and orangutan SVAs referred to in the study. Human SVA_E1: Human SVA_E elements displaying a 6 bp insertion in the SINE-R. Genomic positions, target site duplications (TSD), polymorphic status and the VNTR subunit structure are shown. Arrays of VNTR subunits are boxed. Boxes highlighted in red indicate VNTR subunits providing splice acceptors for splicing to the mneoI cassette. Orangutan SVAs: Orangutan SVAs genotyped and amplified. Buschi, Babu, Dunja, Kiki and Elsi are P. abelii individuals for which short read archives are available. Numbers (011 etc) refer to individuals genotyped on genomic DNA. Positional information refers to the primary amplicon. Fields highlighted in yellow indicate the animals from which the respective element was amplified. TSD - Target site duplication; TD – transduction. Orangutan SVA VNTR: VNTR subunit structure of the orangutan SVAs tested for their retrotranspositional activity. Arrays of VNTR subunits are boxed.
DOI: 10.6084/m9.figshare.12644679.v1
title: Additional file 3 of LINE-1 ORF1p does not determine substrate preference for human/orangutan SVA and gibbon LAVA

description: Additional file 3: Subgroups of human SVA_E elements containing both fixed and polymorphic elements. SVA_E3: VNTR subunit structure of SVA_E subgroup E3 containing four fixed and four polymorphic elements. Based on divergence from subgroup consensus (div; Alu-like region and SINE-R) and VNTR structure the two fixed elements on chromosome 1 would be candidates to test for activity. AF - allele frequency as provided in Stewart C, Kural D, Strömberg MP, Walker JA, Konkel MK, et al. (2011) A Comprehensive Map of Mobile Element Insertion Polymorphisms in Humans. PLoS Genet 7(8): e1002236. Arrays of VNTR subunits are boxed. Polymorphic elements are highlighted in yellow. SVA_E4: VNTR subunit structure of SVA_E subgroup E4 containing eight fixed and three polymorphic elements. Candidates to test for activity based on divergence from subgroup consensus (div; Alu-like region and SINE-R) and VNTR structure are indicated. AF - allele frequency; Sources: chr1:112,834,947–112,837,733–1000 Genomes Phase 3 Integrated Variant Calls track of the UCSC genome browser; chr2:223760192–223,762,683 - Stewart C, Kural D, Strömberg MP, Walker JA, Konkel MK, et al. (2011) A Comprehensive Map of Mobile Element Insertion Polymorphisms in Humans. PLoS Genet 7(8): e1002236; chr5:43,086,412-43,089,307 - dbRIP. Arrays of VNTR subunits are boxed. Polymorphic elements are highlighted in yellow.
DOI: 10.6084/m9.figshare.12644673.v1
title: Additional file 1 of LINE-1 ORF1p does not determine substrate preference for human/orangutan SVA and gibbon LAVA

description: Additional file 1: Human and orangutan SVAs referred to in the study. Human SVA_E1: Human SVA_E elements displaying a 6 bp insertion in the SINE-R. Genomic positions, target site duplications (TSD), polymorphic status and the VNTR subunit structure are shown. Arrays of VNTR subunits are boxed. Boxes highlighted in red indicate VNTR subunits providing splice acceptors for splicing to the mneoI cassette. Orangutan SVAs: Orangutan SVAs genotyped and amplified. Buschi, Babu, Dunja, Kiki and Elsi are P. abelii individuals for which short read archives are available. Numbers (011 etc) refer to individuals genotyped on genomic DNA. Positional information refers to the primary amplicon. Fields highlighted in yellow indicate the animals from which the respective element was amplified. TSD - Target site duplication; TD – transduction. Orangutan SVA VNTR: VNTR subunit structure of the orangutan SVAs tested for their retrotranspositional activity. Arrays of VNTR subunits are boxed.
DOI: 10.6084/m9.figshare.12644656
title: Additional file 5 of Gut microbiota maturation during early human life induces enterocyte proliferation via microbial metabolites

description: Additional file 5: Supplemental Table 5. Enriched pre-term metabolic pathways mapped to Homo sapiens. A list of human metabolic pathways enriched in pre-term stool samples compared to term stool samples as determined by KEGG orthologs.
DOI: 10.6084/m9.figshare.12644656.v1
title: Additional file 5 of Gut microbiota maturation during early human life induces enterocyte proliferation via microbial metabolites

description: Additional file 5: Supplemental Table 5. Enriched pre-term metabolic pathways mapped to Homo sapiens. A list of human metabolic pathways enriched in pre-term stool samples compared to term stool samples as determined by KEGG orthologs.