cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6073/pasta/7b4756b1dd0fe6b72a02b0462c5e3ba3
title: Total biomass of two native and one nonnative Eugenia congeners from growth chamber experiment with site, soil microbe, and temperature treatments to test biotic interaction effects of range expansion.

description: To assess the potential for invasive plants to shift ranges more readily than native plant species, a growth chamber experiment was set up to monitor changes in biomass under different site, temperature, and soil biota treatments. Total biomass (above and belowground) of three Eugenia congeners was assessed by site, soil microbe, and temperature treatments. Of the three congeneric shrub species, two are native to southern and central Florida (Eugenia foetida and E. axillaris,), and one is a non-native invasive from south America (E. uniflora). We measured total biomass for these plant species in growth chambers grown under live and sterile soils from two sites within their current range, and one site in their expected range, simulating current (2010) and predicted future (2050) spring growing season temperatures in the new range. The experiments took place from 2012 - 2013 in University of Central Florida growth chambers.
DOI: 10.6084/m9.figshare.12890867
title: Plateosaurus skulls from Trossingen and Halberstadt

description: Collection photographs of skulls of the basal sauropodomorph Plateosaurus from Trossingen and Halberstadt, Germany.<br>Supplementary information for:Lallensack et al., submitted<br>
DOI: 10.6084/m9.figshare.6713153
title: Theoretical ribosomal protein mass fingerprint of Staphylococcus epidermidis

description: This is a dataset containing the theoretical molecular mass of various ribosomal proteins in the large and small ribosome subunit of <i>Staphylococcus epidermidis.</i><br><br>
DOI: 10.6084/m9.figshare.6713153.v1
title: Theoretical ribosomal protein mass fingerprint of Staphylococcus epidermidis

description: This is a dataset containing the theoretical molecular mass of various ribosomal proteins in the large and small ribosome subunit of <i>Staphylococcus epidermidis.</i><br><br>
DOI: 10.6084/m9.figshare.6713147
title: Clean Drinking Water Data (Analysis)

description: This dataset relates to the analysis of the mechanical properties, the fibre structural properties and the mathematical models. <br>The analyses were computed using four MS Excel spreadsheets:ANALYSIS Mech Prop ...xls: analysis of mechanical properties from each specimenANALYSIS Fibre Diam...xls: analysis of fibre diameterANALYSIS Pore Diam...xls: analysis of pore sizeanalysis_dib...xls: analysis of the mathematical models used in this paper to predict stiffness (E), fracture strength (sU) and water flux
DOI: 10.6084/m9.figshare.6713147.v2
title: Clean Drinking Water Data (Analysis)

description: This dataset relates to the analysis of the mechanical properties, the fibre structural properties and the mathematical models. <br>The analyses were computed using four MS Excel spreadsheets:ANALYSIS Mech Prop ...xls: analysis of mechanical properties from each specimenANALYSIS Fibre Diam...xls: analysis of fibre diameterANALYSIS Pore Diam...xls: analysis of pore sizeanalysis_dib...xls: analysis of the mathematical models used in this paper to predict stiffness (E), fracture strength (sU) and water flux
DOI: 10.6084/m9.figshare.6713147.v1
title: Clean Drinking Water Data (Analysis)

description: This dataset relates to the analysis of the mechanical properties, the fibre structural properties and the mathematical models. <br>The analyses were computed using four MS Excel spreadsheets:ANALYSIS Mech Prop ...xls: analysis of mechanical properties from each specimenANALYSIS Fibre Diam...xls: analysis of fibre diameterANALYSIS Pore Diam...xls: analysis of pore sizeANALYSIS E sU Flux...xls: analysis of the mathematical models used in this paper to predict stiffness (E), fracture strength (sU) and water flux
DOI: 10.6084/m9.figshare.6713132
title: Intermediate results reproduced from "A Comprehensive Analysis of Primer IDs to Study Heterogeneous HIV-1 Populations"

description: The study "A Comprehensive Analysis of Primer IDs to Study Heterogeneous HIV-1 Populations" includes Illumina sequencing data deposited in the Sequence Read Archive and code for performing alignments and calling Primer ID consensus sequences, available from github. We have recomputed these intermediate alignment and consensus sequence results for use in other studies of HIV plasmid sequences.<br>
DOI: 10.6084/m9.figshare.6713132.v1
title: Intermediate results reproduced from "A Comprehensive Analysis of Primer IDs to Study Heterogeneous HIV-1 Populations"

description: The study "A Comprehensive Analysis of Primer IDs to Study Heterogeneous HIV-1 Populations" includes Illumina sequencing data deposited in the Sequence Read Archive and code for performing alignments and calling Primer ID consensus sequences, available from github. We have recomputed these intermediate alignment and consensus sequence results for use in other studies of HIV plasmid sequences.<br>
DOI: 10.6084/m9.figshare.6713129
title: Theoretical ribosomal protein mass fingerprint of Staphylococcus aureus

description: This is a dataset containing the theoretical molecular mass of various ribosomal proteins in the large and small ribosome subunit of <i>Staphylococcus aureus</i>.<br><br>
DOI: 10.6084/m9.figshare.6713129.v1
title: Theoretical ribosomal protein mass fingerprint of Staphylococcus aureus

description: This is a dataset containing the theoretical molecular mass of various ribosomal proteins in the large and small ribosome subunit of <i>Staphylococcus aureus</i>.<br><br>
DOI: 10.6084/m9.figshare.6713126
title: Theoretical ribosomal protein mass fingerprint of Shewanella putrefaciens

description: This is a dataset containing the theoretical molecular mass of various ribosomal proteins in the large and small ribosome subunit of <i>Shewanella putrefaciens.</i>
DOI: 10.6084/m9.figshare.6713126.v1
title: Theoretical ribosomal protein mass fingerprint of Shewanella putrefaciens

description: This is a dataset containing the theoretical molecular mass of various ribosomal proteins in the large and small ribosome subunit of <i>Shewanella putrefaciens.</i>
DOI: 10.6084/m9.figshare.6713123
title: Training Rmd file

description: A short Rmd file based on Data Carpentry lesson
DOI: 10.6084/m9.figshare.6713123.v1
title: Training Rmd file

description: A short Rmd file based on Data Carpentry lesson
DOI: 10.6084/m9.figshare.6713063
title: Distributional data for Dysanellus bruchi, D. transverserugosus, Torobus laetipes and T. purpurascens

description: Raw data for Torobus laetipes, Torobus purpurascens, Dysanellus bruchi and Dysanellus transverserugosus
DOI: 10.6084/m9.figshare.6713063.v1
title: Distributional data for Dysanellus bruchi, D. transverserugosus, Torobus laetipes and T. purpurascens

description: Raw data for Torobus laetipes, Torobus purpurascens, Dysanellus bruchi and Dysanellus transverserugosus
DOI: 10.6084/m9.figshare.6713033
title: EMAPA Enrichment - Discard

description: EMAPA Enrichment results based on differentially expressed gene lists for the Discard set.<br>see README.md for more details.
DOI: 10.6084/m9.figshare.6713021
title: EMAPA Enrichment - No Delay

description: EMAPA Enrichment results based on differentially expressed gene lists for the No Delay set.<br>see README.md for more details.
DOI: 10.6084/m9.figshare.6713021.v1
title: EMAPA Enrichment - No Delay

description: EMAPA Enrichment results based on differentially expressed gene lists for the No Delay set.<br>see README.md for more details.
DOI: 10.6084/m9.figshare.6713018
title: EMAPA Enrichment - Delay

description: EMAPA Enrichment results based on differentially expressed gene lists for the Delay set.<br>see README.md for more details.
DOI: 10.6084/m9.figshare.6713018.v1
title: EMAPA Enrichment - Delay

description: EMAPA Enrichment results based on differentially expressed gene lists for the Delay set.<br>see README.md for more details.
DOI: 10.6084/m9.figshare.6713015
title: EMAPA Enrichment - Mutant Response

description: EMAPA Enrichment results based on differentially expressed gene lists for the Mutant Response set.<br>see README.md for more details.
DOI: 10.6084/m9.figshare.6713015.v1
title: EMAPA Enrichment - Mutant Response

description: EMAPA Enrichment results based on differentially expressed gene lists for the Mutant Response set.<br>see README.md for more details.
DOI: 10.6084/m9.figshare.6712823
title: Mechanical Drawings

description: Mechanical drawings of spectrometer components
DOI: 10.6084/m9.figshare.6712820
title: Model Data for comparisons

description: case data to reconstruct figures from Van Roekel et al 2018<br>
DOI: 10.6084/m9.figshare.6712820.v1
title: Model Data for comparisons

description: case data to reconstruct figures from Van Roekel et al 2018<br>
DOI: 10.15468/tdpvtu
title: First record of Longosomatidae (Annelida: Polychaeta) from Iceland with a worldwide review of diagnostic characters of the family

description: This dataset contains the digitized treatments in Plazi based on the original journal article Parapar, Julio, Aguirrezabalaga, Florencio, Moreira, Juan (2014): First record of Longosomatidae (Annelida: Polychaeta) from Iceland with a worldwide review of diagnostic characters of the family. Journal of Natural History 48 (17): 983-998, DOI: 10.1080/00222933.2013.859316
DOI: 10.15468/3k4nup
title: New eriophyoid mites (Acari: Prostigmata: Eriophyoidea) from cultivated plants from northeastern Brazil, including the second taxon in the Prothricinae

description: This dataset contains the digitized treatments in Plazi based on the original journal article Reis, Aleuny Coutinho, Jr, Manoel Guedes Corrêa Gondim, Flechtmann, Carlos Holger Wenzel, Navia, Denise (2014): New eriophyoid mites (Acari: Prostigmata: Eriophyoidea) from cultivated plants from northeastern Brazil, including the second taxon in the Prothricinae. Journal of Natural History 48 (19): 1135-1152, DOI: 10.1080/00222933.2013.862574
DOI: 10.15468/4uwfnk
title: Taxonomy of the genus Oriverutus Siddiqi, 1971 (Nematoda: Dorylaimida: Nordiidae)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Peña-Santiago, Reyes, Liébanas, Gracia, Ahmad, Wasim (2014): Taxonomy of the genus Oriverutus Siddiqi, 1971 (Nematoda: Dorylaimida: Nordiidae). Journal of Natural History 48 (21): 1253-1278, DOI: 10.1080/00222933.2013.861942
DOI: 10.5281/zenodo.4006999
title: PatternScout Evaluation Data

description: This folder contains the data that was used to evaluate accuracy of PatternScout query generation. It is structured as follows: Data related to each pattern category is segregated as <br> 1. Creational<br> 2. Structural<br> 3. Behavioral Within each category, there is a seperate directory for the patterns evaluated in that category. Each pattern has the follwing subdirectories: 1. uml_images - PNG images of UML diagrams of each variant considered<br> 2. uml_xmi - XMI version of the UML diagram for each variant<br> 3. queries - SPARQL queries generated by PatternScout in .rq format<br> 4. model_fragments - .mfj files of each UML diagram for importing into tools like StarUML if any new variant needs to be created by extending or updating these diagrams<br>
DOI: 10.6084/m9.figshare.12890900
title: supporting_information.pdf

description: Supporting information of Nguyen et al. (2020)<br>
DOI: 10.6084/m9.figshare.12890900.v1
title: supporting_information.pdf

description: Supporting information of Nguyen et al. (2020)<br>
DOI: 10.6084/m9.figshare.6710087
title: Carini relic DNA temporal data.zip

description: Associated sequencing and soil characteristics files for the manuscript titled "Unraveling the effects of spatial variability and relic DNA on the temporal dynamics of soil microbial communities" by Carini, et al.<br>There are five files in the .zip archive:1) Demultiplexed forward sequencing reads for 16S rRNA gene amplicons2) Demultiplexed reverse sequencing reads for 16S rRNA gene amplicons3) Demultiplexed forward sequencing reads for fungal internal transcribed spacer (ITS) gene region amplicons4) Demultiplexed reverse sequencing reads for fungal internal transcribed spacer (ITS) gene region amplicons5) Map file for the sequencing reads that includes data on sampling time, sub-plot number (Rep), treatment (PMA or not) measured soil and environmental characteristics<br>
DOI: 10.6084/m9.figshare.6710087.v1
title: Cross-domain temporal seq files.zip

description: Associated sequencing and soil characteristics files for the manuscript titled "Cross-domain temporal dynamics in soil microbial communities" by Carini, et al. <br>There are five files in the .zip archive:1) Demultiplexed forward sequencing reads for 16S rRNA gene amplicons2) Demultiplexed reverse sequencing reads for 16S rRNA gene amplicons3) Demultiplexed forward sequencing reads for fungal internal transcribed spacer (ITS) gene region amplicons4) Demultiplexed reverse sequencing reads for fungal internal transcribed spacer (ITS) gene region amplicons5) Map file for the sequencing reads that includes data on sampling time, sub-plot number, treatment (PMA or not) measured soil and environmental characteristics<br>
DOI: 10.6084/m9.figshare.6710087.v2
title: Cross-domain temporal seq files.zip

description: Associated sequencing and soil characteristics files for the manuscript titled "Unraveling the effects of spatial variability and relic DNA on the temporal dynamics of soil microbial communities" by Carini, et al.<br>There are five files in the .zip archive:1) Demultiplexed forward sequencing reads for 16S rRNA gene amplicons2) Demultiplexed reverse sequencing reads for 16S rRNA gene amplicons3) Demultiplexed forward sequencing reads for fungal internal transcribed spacer (ITS) gene region amplicons4) Demultiplexed reverse sequencing reads for fungal internal transcribed spacer (ITS) gene region amplicons5) Map file for the sequencing reads that includes data on sampling time, sub-plot number (Rep), treatment (PMA or not) measured soil and environmental characteristics<br>
DOI: 10.6084/m9.figshare.6709490
title: STOTEN27464

description: This dataset is the supplementary data source for the manuscript "Seasonal patterns of canopy photosynthesis captured by remotely sensed sun-induced fluorescence and vegetation indexes in mid-to-high latitude forests: a cross-platform comparison" accepted for publication in Science of the Total Environment.The time series of all parameters presented in the manuscript is recorded in the Excel file of each site.Since the data policy of Fluxnet and European Data Flux Cluster prevents us from redistributing their data, We are unable to share with you the EC_GPP of each site.‘SIF’here in every Excel refers to GOME-2 SIF.If you have any questions regarding this data set, do not hesitate to contact Xinchen Lu (Stevenlvrs@foxmail.com)
DOI: 10.6084/m9.figshare.6709490.v2
title: STOTEN27464

description: This dataset is the supplementary data source for the manuscript "Seasonal patterns of canopy photosynthesis captured by remotely sensed sun-induced fluorescence and vegetation indexes in mid-to-high latitude forests: a cross-platform comparison" accepted for publication in Science of the Total Environment.The time series of all parameters presented in the manuscript is recorded in the Excel file of each site.Since the data policy of Fluxnet and European Data Flux Cluster prevents us from redistributing their data, We are unable to share with you the EC_GPP of each site.‘SIF’here in every Excel refers to GOME-2 SIF.If you have any questions regarding this data set, do not hesitate to contact Xinchen Lu (Stevenlvrs@foxmail.com)
DOI: 10.6084/m9.figshare.6709490.v1
title: STOTEN27464

description: This dataset is the supplementary data source for the manuscript "Seasonal patterns of canopy photosynthesis captured by remotely sensed sun-induced fluorescence and vegetation indexes in mid-to-high latitude forests: a cross-platform comparison" accepted for publication in Science of the Total Environment.The time series of all parameters presented in the manuscript is recorded in the Excel file of each site.Since the data policy of Fluxnet and European Data Flux Cluster prevents us from redistributing their data, We are unable to share with you the EC_GPP of each site.‘SIF’here in every Excel refers to GOME-2 SIF.If you have any questions regarding this data set, do not hesitate to contact Xinchen Lu (Stevenlvrs@foxmail.com)
DOI: 10.15468/x54ywb
title: The soil mite family Galumnidae of Iran (Acari: Oribatida)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Bayartogtokh, Badamdorj, Akrami, Mohammad Ali (2014): The soil mite family Galumnidae of Iran (Acari: Oribatida). Journal of Natural History 48 (15): 881-917, DOI: 10.1080/00222933.2013.840397
DOI: 10.6084/m9.figshare.6709322
title: Identification and characterization of the VAX2 p.Leu139Arg variant: possible involvement of VAX2 in cone dystrophy

description: <b>Objective</b>: This study was undertaken with the objective to investigate the potential involvement of VAX2 in retinal degeneration. <b>Methods</b>: A cohort of macular and cone dystrophy patients (<i>n</i> = 70) was screened for variant identification. Polymerase chain reaction (PCR) products were purified using ExoSAP-IT. Direct sequencing of PCR products was performed using BigDye 3.1 on the ABI 3730 DNA Analyzer and analyzed using DNASTAR software tool. Search for known variant was performed using the following platforms: 1000 Genomes Project, Ensembl, UCSC, ExAc, and dbSNP. The <i>VAX2</i> mutants were generated using the GeneArt® Site-Directed Mutagenesis kit. <i>In vitro</i> analysis was performed in hTERTRPE-1 (RPE-1) cell line. Cells were photographed using a Zeiss AXIOVERT S100 microscope. Images were analyzed using Photoshop CS4 software. <b>Results</b>: Here, we report the identification of a heterozygous non-synonymous variant (c.416T&gt;G; p.Leu139Arg) in one cone dystrophy proband. Functional characterization of this variant <i>in vitro</i> revealed an aberrant phenotype seen as protein mislocalization to cytoplasm/nucleus and aggregates undergoing degradation or forming aggresomes. The cellular phenotype suggests protein loss-of-function. Analysis of the <i>VAX2</i> p.Leu139Met, a variant present in the normal population, showed a phenotype similar to the wild-type, further supporting the hypothesis for the Leucine 139 to Arginine change to be damaging. <b>Conclusions</b>: This study raises the interesting possibility for evaluating <i>VAX2</i> as a candidate gene for cone dystrophy.
DOI: 10.6084/m9.figshare.6709322.v1
title: Identification and characterization of the VAX2 p.Leu139Arg variant: possible involvement of VAX2 in cone dystrophy

description: <b>Objective</b>: This study was undertaken with the objective to investigate the potential involvement of VAX2 in retinal degeneration. <b>Methods</b>: A cohort of macular and cone dystrophy patients (<i>n</i> = 70) was screened for variant identification. Polymerase chain reaction (PCR) products were purified using ExoSAP-IT. Direct sequencing of PCR products was performed using BigDye 3.1 on the ABI 3730 DNA Analyzer and analyzed using DNASTAR software tool. Search for known variant was performed using the following platforms: 1000 Genomes Project, Ensembl, UCSC, ExAc, and dbSNP. The <i>VAX2</i> mutants were generated using the GeneArt® Site-Directed Mutagenesis kit. <i>In vitro</i> analysis was performed in hTERTRPE-1 (RPE-1) cell line. Cells were photographed using a Zeiss AXIOVERT S100 microscope. Images were analyzed using Photoshop CS4 software. <b>Results</b>: Here, we report the identification of a heterozygous non-synonymous variant (c.416T&gt;G; p.Leu139Arg) in one cone dystrophy proband. Functional characterization of this variant <i>in vitro</i> revealed an aberrant phenotype seen as protein mislocalization to cytoplasm/nucleus and aggregates undergoing degradation or forming aggresomes. The cellular phenotype suggests protein loss-of-function. Analysis of the <i>VAX2</i> p.Leu139Met, a variant present in the normal population, showed a phenotype similar to the wild-type, further supporting the hypothesis for the Leucine 139 to Arginine change to be damaging. <b>Conclusions</b>: This study raises the interesting possibility for evaluating <i>VAX2</i> as a candidate gene for cone dystrophy.
DOI: 10.6084/m9.figshare.6709247
title: TAI-Volta data

description: This dataset contain crop production and area for the Volta basin (Burkina Faso and Ghana) at the second level administrative unit for the period 1993-2012. Additionally a number of variables that matches some of Ostrom's SES framework are included. This repo contains the data analysed in "Mapping Social-Ecological Systems Archetypes" available as preprint at: https://www.biorxiv.org/content/early/2018/04/13/299693<br>
DOI: 10.6084/m9.figshare.6709184
title: Supplementary Material for: PKD Phosphorylation as Novel Pathway of K<sub>V</sub>11.1 Regulation

description: <b><i>Background/Aims:</i></b> The voltage-gated potassium channel K<sub>V</sub>11.1 has been originally cloned from the brain and is expressed in a variety of tissues. The role of phosphorylation for channel function is a matter of debate. In this study, we aimed to elucidate the extent and role of protein kinase D mediated phosphorylation. <b><i>Methods:</i></b> We employed mass spectrometry, whole-cell patch clamp electrophysiology, confocal microscopy, site-directed mutagenesis, and western blotting. <b><i>Results:</i></b> Using brain tissue from rat and mouse, we mapped several phosphorylated K<sub>V</sub>11.1 residues by LC-MS mass spectrometry and identified protein kinase D (PKD1) as possible regulatory kinase. Co-expression of K<sub>V</sub>11.1 with PKD1 reduced current amplitudes without altering protein levels or surface expression of the channel. Based on LC-MS results from <i>in vivo</i> and HEK293 cell experiments we chose four K<sub>V</sub>11.1 mutant candidates for further functional analysis. Ablation of the putative PKD phosphorylation site in the mutant S284A increased the maximal current indicating S284 as a main PKD target in K<sub>V</sub>11.1. <b><i>Conclusions:</i></b> Our data might help mitigating a long-standing controversy in the field regarding PKC regulation of K<sub>V</sub>11.1. We propose that PKD1 mediates the PKC effects on K<sub>V</sub>11.1 and we found that PKD targets S284 in the N-terminus of the channel.
DOI: 10.5281/zenodo.4007008
title: Evaluation Data

description: This folder contains the data that was used to evaluate accuracy of PatternScout query generation. It is structured as follows: Data related to each pattern category is segregated as <br> 1. Creational<br> 2. Structural<br> 3. Behavioral Within each category, there is a seperate directory for the patterns evaluated in that category. Each pattern has the follwing subdirectories: 1. uml_images - PNG images of UML diagrams of each variant considered<br> 2. uml_xmi - XMI version of the UML diagram for each variant<br> 3. queries - SPARQL queries generated by PatternScout in .rq format<br> 4. model_fragments - .mfj files of each UML diagram for importing into tools like StarUML if any new variant needs to be created by extending or updating these diagrams<br>
DOI: 10.5281/zenodo.4006998
title: Evaluation Data

description: This folder contains the data that was used to evaluate accuracy of PatternScout query generation. It is structured as follows: Data related to each pattern category is segregated as <br> 1. Creational<br> 2. Structural<br> 3. Behavioral Within each category, there is a seperate directory for the patterns evaluated in that category. Each pattern has the follwing subdirectories: 1. uml_images - PNG images of UML diagrams of each variant considered<br> 2. uml_xmi - XMI version of the UML diagram for each variant<br> 3. queries - SPARQL queries generated by PatternScout in .rq format<br> 4. model_fragments - .mfj files of each UML diagram for importing into tools like StarUML if any new variant needs to be created by extending or updating these diagrams<br>