cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.3401476
title: Human-specific tandem repeat expansion and differential gene expression during primate evolution

description: THIS DATASET IS PART OF THE FOLLOWING STUDY:<br> https://www.pnas.org/content/early/2019/10/22/1912175116 THE RAW SEQUENCING 10x GENOMICS READS CAN BE DOWNLOADED FROM SRA:<br> https://www.ncbi.nlm.nih.gov/bioproject/PRJNA593056 <br> ORIGINAL UPLOAD: 09/06/2019 UPDATES: 10/28/2019; 01/27/2020 DESCRIPTION: Contigs were assembled using Phased-SV (Chaisson et al, Nature Communications 2019) on six human haplotypes (i.e., H0 and H1 in NA19240, HG00514, and HG00733), and six nonhuman haplotypes (this study, H0 and H1 in Clint the chimpanzee, Kamilah the gorilla, and Susie the orangutan). The long read data (PacBio CLR) from NHPs were phased into haplotypes H0 and H1 using linked reads from 10X Genomics prior to assembly, whenever possible. If not possible (e.g., in the case of long runs of homozygosity regions), long reads from both haplotypes were used to generate a "squished assembly". Using human haplotype data, we identified 21,442 polymorphic STRs/VNTRs, followed by a targetted phasing of these regions in the three NHPs. All of the human and nonhuman primate contigs were padded by 2 kbp both upstream and downstream, followed by mapping against the human reference (GRCh38). We did the same for "squished assemblies" from a Yoruban individual, CHM13, and three NHPs as described in Kronenberg et al, Science 2018. The BAM and BAI files in this dataset contain the alignment of all these contigs against GRCh38.
description: These BAM files contain all ~20,000 STR/VNTR contigs used in the study "Human-specific tandem repeat expansion and differential gene expression during primate evolution". Each locus is flanked by ~2 kbp of unique sequence to facilitate their anchoring in GRCh38.p12.
DOI: 10.5281/zenodo.3401477
title: Human-specific tandem repeat expansion and differential gene expression during primate evolution

description: THIS DATASET IS PART OF THE FOLLOWING STUDY:<br> https://www.pnas.org/content/early/2019/10/22/1912175116 THE RAW SEQUENCING 10x GENOMICS READS CAN BE DOWNLOADED FROM SRA:<br> https://www.ncbi.nlm.nih.gov/bioproject/PRJNA593056 <br> ORIGINAL UPLOAD: 09/06/2019 UPDATES: 10/28/2019; 01/27/2020 DESCRIPTION: Contigs were assembled using Phased-SV (Chaisson et al, Nature Communications 2019) on six human haplotypes (i.e., H0 and H1 in NA19240, HG00514, and HG00733), and six nonhuman haplotypes (this study, H0 and H1 in Clint the chimpanzee, Kamilah the gorilla, and Susie the orangutan). The long read data (PacBio CLR) from NHPs were phased into haplotypes H0 and H1 using linked reads from 10X Genomics prior to assembly, whenever possible. If not possible (e.g., in the case of long runs of homozygosity regions), long reads from both haplotypes were used to generate a "squished assembly". Using human haplotype data, we identified 21,442 polymorphic STRs/VNTRs, followed by a targetted phasing of these regions in the three NHPs. All of the human and nonhuman primate contigs were padded by 2 kbp both upstream and downstream, followed by mapping against the human reference (GRCh38). We did the same for "squished assemblies" from a Yoruban individual, CHM13, and three NHPs as described in Kronenberg et al, Science 2018. The BAM and BAI files in this dataset contain the alignment of all these contigs against GRCh38.
description: These BAM files contain all ~20,000 STR/VNTR contigs used in the study "Human-specific tandem repeat expansion and differential gene expression during primate evolution". Each locus is flanked by ~2 kbp of unique sequence to facilitate their anchoring in GRCh38.p12.
DOI: 10.25345/c5bt0w
title: MassIVE MSV000084324 - Hspg2C1532YNeo DBA Distal Humeral Cartilage Proteomic Comparison Dataset
title: Murine cartilage was dissected from the distal humerus, physically disrupted in 4M GuHCl, then protein was extracted and digested into peptides. Mass spectra were obtained by LC-MS/MS and analyzed in silico using MaxQuant to compare relative protein abundance as a function of development and perlecan knockdown.
DOI: 10.25345/c5gh2s
title: MassIVE MSV000084323 - A Novel Mechanism For NF-kB-Activation via IkB-Aggregation
title: Proteins which co-localize with IkBa in insoluble aggregates known as Mallory-Denk bodies where characterized by AP-MS, Biotinylation by antibody recognition (BAR), and LCMS analysis of detergent solubalized aggregates.
DOI: 10.5061/dryad.qr5s6b8/1
title: Dryad Item 10.5061/DRYAD.QR5S6B8/1

description: (:tba)
DOI: 10.5061/dryad.d39b44r/1
title: Dryad Item 10.5061/DRYAD.D39B44R/1

description: (:tba)
DOI: 10.5258/soton/d1071
title: Dataset for: Efficient State Retention in Transiently Powered Computing Systems

description: Modelled and experimental data obtained throughout the duration of the PhD on "Efficient State Retention in Transiently Powered Computing Systems". Experimental data mainly obtained from two experimental boards: MSP430FR5739 and LPC-Xpresso 810. Modelled data are an output of ModelSim and Design Compiler.
DOI: 10.5281/zenodo.3407724
title: Underlying data of the project "A survey exploring biomedical editors' perceptions of editorial interventions to improve adherence to reporting guidelines"

description: <em><strong>Survey dataset.xlsx</strong></em> contains the anonymised responses to the survey.
DOI: 10.5281/zenodo.3407725
title: Underlying data of the project "A survey exploring biomedical editors' perceptions of editorial interventions to improve adherence to reporting guidelines"

description: <em><strong>Survey dataset.xlsx</strong></em> contains the anonymised responses to the survey.
DOI: 10.5519/qd.lw1jdw8l
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (8919 records)
DOI: 10.5061/dryad.d39b44r/2
title: Dryad Item 10.5061/DRYAD.D39B44R/2

description: (:tba)
DOI: 10.5061/dryad.ng94td0/1
title: Dryad Item 10.5061/DRYAD.NG94TD0/1

description: (:tba)
DOI: 10.5258/soton/d1074
title: Data set for "Acoustic focussing for sedimentation-free high-throughput imaging of microalgae"

description: Data relating to paper: "Acoustic focussing for sedimentation-free high-throughput imaging of microalgae" in Applied Phycology.
DOI: 10.5281/zenodo.3407716
title: Data for paper "Low Resource Technique for Measurement of H+ and O+ in the Terrestrial Magnetosphere"

description: Data set for paper "Low Resource Technique for Measurement of H+ and O+ in the Terrestrial Magnetosphere" to be published in Journal of Geophysical Research: Space Physics (Technical Methods). Data set is a single Microsoft Excel file containing Data Set S1, Data Set S2, Data Set S3.
description: This document is approved for public release and assigned document number LA-UR-19-26266.
DOI: 10.5281/zenodo.3407717
title: Data for paper "Low Resource Technique for Measurement of H+ and O+ in the Terrestrial Magnetosphere"

description: Data set for paper "Low Resource Technique for Measurement of H+ and O+ in the Terrestrial Magnetosphere" to be published in Journal of Geophysical Research: Space Physics (Technical Methods). Data set is a single Microsoft Excel file containing Data Set S1, Data Set S2, Data Set S3.
description: This document is approved for public release and assigned document number LA-UR-19-26266.
DOI: 10.5281/zenodo.3379428
title: Microclimate predicts frost-hardiness of alpine Arabidopsis thaliana populations better than elevation

description: In mountain regions, topological differences on the micro-scale can strongly affect microclimate and may counteract the average effects of elevation, such as decreasing temperatures. While these interactions are well understood, their effect on plant adaptation is understudied. We investigated winter frost hardiness of Arabidopsis thaliana accessions originating from 13 sites along altitudinal gradients in the Southern Alps during three winters on an experimental field station on the Swabian Jura and compared levels of frost damage with the observed number of frost days and the lowest temperature in eight collection sites. We found that frost-hardiness increased with elevation in a log-linear fashion. This is consistent with adaptation to a higher frequency of frost conditions, but also indicates a decreasing rate of change in frost hardiness with increasing elevation. Moreover, the number of frost days measured with temperature loggers at the collection sites correlated much better with frost-hardiness than the elevation of collection sites, suggesting that populations were adapted to their local microclimate. Notably, the variance in frost days across sites increased exponentially with elevation. Together, our results suggest that strong microclimate heterogeneity of high alpine environments can preserve functional genetic diversity among small populations. Synthesis. Here we tested how plant populations differed in their adaptation to frost exposure along an elevation gradient and whether microsite temperatures improve the prediction of frost hardiness. We found that local temperatures, particularly the number of frost days, is a better predictor of the frost hardiness of plants than elevation. This reflects a substantial variance in frost frequency between sites at similar high elevations. We conclude that high mountain regions harbor microsites that differ in their local microclimate and thereby can preserve a high functional genetic diversity among them. Therefore, high mountain regions have the potential to function as a refugium in times of global change.
DOI: 10.5281/zenodo.3379429
title: Microclimate predicts frost-hardiness of alpine Arabidopsis thaliana populations better than elevation

description: In mountain regions, topological differences on the micro-scale can strongly affect microclimate and may counteract the average effects of elevation, such as decreasing temperatures. While these interactions are well understood, their effect on plant adaptation is understudied. We investigated winter frost hardiness of Arabidopsis thaliana accessions originating from 13 sites along altitudinal gradients in the Southern Alps during three winters on an experimental field station on the Swabian Jura and compared levels of frost damage with the observed number of frost days and the lowest temperature in eight collection sites. We found that frost-hardiness increased with elevation in a log-linear fashion. This is consistent with adaptation to a higher frequency of frost conditions, but also indicates a decreasing rate of change in frost hardiness with increasing elevation. Moreover, the number of frost days measured with temperature loggers at the collection sites correlated much better with frost-hardiness than the elevation of collection sites, suggesting that populations were adapted to their local microclimate. Notably, the variance in frost days across sites increased exponentially with elevation. Together, our results suggest that strong microclimate heterogeneity of high alpine environments can preserve functional genetic diversity among small populations. Synthesis. Here we tested how plant populations differed in their adaptation to frost exposure along an elevation gradient and whether microsite temperatures improve the prediction of frost hardiness. We found that local temperatures, particularly the number of frost days, is a better predictor of the frost hardiness of plants than elevation. This reflects a substantial variance in frost frequency between sites at similar high elevations. We conclude that high mountain regions harbor microsites that differ in their local microclimate and thereby can preserve a high functional genetic diversity among them. Therefore, high mountain regions have the potential to function as a refugium in times of global change.
DOI: 10.21227/y5vr-4c54
title: Development of a Model for Forecasting LTE Network Performance during Rainy Seasons

description: Abstract— In this research, a model for LTE network performance forecast during the rainy season was developed. During the rainy season, cellular network performance is greatly affected. optimization Engineers find it difficult to ascertain cellular (LTE) network parameters that negatively influences the network performance and make a performance prediction during the rainy season. In achieving this, an experimental approach was used to study network samples collected over the LTE network of MTTN in Lagos during the rainy season for a period of 48weeks. Network parameters that are greatly affected by rainfall were identified and a model was developed for predicting and forecasting the network performance during rainy seasons. From the experimental result, Signal quality parameters such as the Referenced Signal Received Quality (RSRQ) and Signal-to-Interference Noise Ratio (SINR) become bad and negatively affect the network performance during rainy seasons. Optimization activities by cellular network operators should be geared towards improving the signal quality parameters during rainy seasons.Abstract— In this research, a model for LTE network performance forecast during the rainy season was developed. During the rainy season, cellular network performance is greatly affected. optimization Engineers find it difficult to ascertain cellular (LTE) network parameters that negatively influences the network performance and make a performance prediction during the rainy season. In achieving this, an experimental approach was used to study network samples collected over the LTE network of MTTN in Lagos during the rainy season for a period of 48weeks. Network parameters that are greatly affected by rainfall were identified and a model was developed for predicting and forecasting the network performance during rainy seasons. From the experimental result, Signal quality parameters such as the Referenced Signal Received Quality (RSRQ) and Signal-to-Interference Noise Ratio (SINR) become bad and negatively affect the network performance during rainy seasons. Optimization activities by cellular network operators should be geared towards improving the signal quality parameters during rainy seasons.
DOI: 10.3886/e111841v1
title: IPV and WPV against female garment workers

description: This data comes from a project entitled "Evaluation of HERrespect intervention addressing intimate partner and workplace violence against female garment workers". There are two separate data sets for workers and management staff.
DOI: 10.5066/f7ns0stq
title: Data and Shapefiles for the Potentiometric Surface of the South Coast Aquifer and Hydrologic Conditions in the Santa Isabel area, Puerto Rico, March-April 2014

description: A groundwater-level survey and reconnaissance of the hydrologic conditions in the coastal alluvial plain of southern Puerto Rico was conducted by the U.S. Geological Survey, in cooperation with the Puerto Rico Department of Natural and Environmental Resources. The objective of the field survey was to delineate the potentiometric surface of the coastal alluvial aquifer between the Rio Descalabrado to the west and the Rio Jueyes to the east of the town of Santa isabel. The field survey took place from March 31 to April 17, 2014, and included measuring groundwater levels at 55 wells, groundwater specific conductance at 8 wells, estimating groundwater withdrawal rates at 34 active production wells, and measuring instantaneous streamflow at 15 locations in streams and irrigation canals. instantaneous streamflow measurements were made at selected sites along the Rio Coamo, Rio Descalabrado, Rio Canas, and the Canal de Juana Diaz to evaluate ground and surface-water interactions during the synoptic survey. A potentiometric surface map of the coastal alluvial aquifer was created from the survey data to indicate the directions of groundwater flow in the aquifer. The potentiometric contours were drawn using water-level data collected at wells during the dry season, from March 31 to April 17. Measured values of the potentiometric surface ranged from -22.8 to 185.4 feet above mean sea level in the alluvial deposits of the south coastal plain. The total rate of groundwater withdrawal for public supply was 5.74 million gallons per day and was calculated using meter readings of instantaneous discharge from 10 production well. During the survey, groundwater withdrawals for irrigation totaled 5.59 million gallons per day; these withdrawal rates were estimated using data obtained from 24 active wells in the study area. Groundwater specific conductance values measured during the study at observation wells ranged from 411 to 1,332 microsiemens per centimeter at 25 degrees Celsius. Results of the study indicate a cone of depression has formed in the coastal alluvial aquifer near the center of the study area, where the potentiometric surface is below mean sea level. in the long-term, this feature could result in saline-water intrusion and an increase in concentrations of total dissolved solids.
DOI: 10.3886/e111841
title: IPV and WPV against female garment workers

description: This data comes from a project entitled "Evaluation of HERrespect intervention addressing intimate partner and workplace violence against female garment workers". There are two separate data sets for workers and management staff.
DOI: 10.5281/zenodo.3407342
title: Soil moisture for Har Ha`Negev

description: Pixel values represent the surface soil moisture content (in m3m-3*100) of, approximately, the top 5 cm of soil. The retrieval was based on Sentinel-1 time-series and a Support Vector Machine based approach. L. Pasolli, C. Notarnicola, G. Bertoldi, L. Bruzzone, R. Remelgado, F. Greifeneder, G. Niedrist, S. Della Chiesa, U. Tappeiner, and M. Zebisch, “Estimation of Soil Moisture in Mountain Areas Using SVR Technique Applied to Multiscale Active Radar Images at C-Band,” Sel. Top. Appl. Earth Obs. Remote Sens., vol. 8, no. 1, pp. 262–283, 2015.
DOI: 10.5281/zenodo.3407343
title: Soil moisture for Har Ha`Negev

description: Pixel values represent the surface soil moisture content (in m3m-3*100) of, approximately, the top 5 cm of soil. The retrieval was based on Sentinel-1 time-series and a Support Vector Machine based approach. L. Pasolli, C. Notarnicola, G. Bertoldi, L. Bruzzone, R. Remelgado, F. Greifeneder, G. Niedrist, S. Della Chiesa, U. Tappeiner, and M. Zebisch, “Estimation of Soil Moisture in Mountain Areas Using SVR Technique Applied to Multiscale Active Radar Images at C-Band,” Sel. Top. Appl. Earth Obs. Remote Sens., vol. 8, no. 1, pp. 262–283, 2015.
DOI: 10.5281/zenodo.3407352
title: The pan-genome of Saccharomyces cerevisiae

description: These datasets are related to 'The pan-genome of <em>Saccharomyces cerevisiae</em>' (Li G., Ji B., and Nielsen J.). This deposition contains following datasets: (1) Genomes.tar.gz: a compressed file containing 1392 <em>Saccharomyces cerevisiae </em>genome assembles analyzed (2) genome_information_2.0.tsv: a tab-separated text file that contains the basic information of above genomes, including genomeSize, contigNums, N50, busco_C(%), busco_S(%), busco_D(%), busco_F(%), busco_M(%), busco_n, number_of_genes, number_of_partial_genes, download_from, Eco_Source, Ploidy, Aneuploidies. (3) ClusterFasta.tar.gz: a compressed file that contains a list of fasta files. Each fasta file contains protein sequences in a cluster. The name of the fasta file is the name of the representative sequence of that cluster. (4) sc_gene_cluster_info_0.7_v4.tsv: a tab-separated text file that contains the properties of gene clusters. (5) gene_presence_absence_v4.tsv: a tab-separated text file that contains the gene-presence/absence information. Each columns is a gene cluster. Each row is a genome. Y/N is used to present presence/absence. (6) gene_num_in_clusters_of_each_strain_v4.tsv: a tab-sparated text file that contains the gene number of each genome in each cluster (copy number). Each columns is a gene cluster. Each row is a genome. (7) feature_importances_cv5_pa_cnv.tsv: a tab-separated file that contains the feature importance from a random forest classifier in a 5-fold cross-validation approach. The classifier was trained on gene presence/absence table (PA) or copy number table (CNV). The columns 'pa_x' indicate the feature importance in each fold of cross-validation on PA dataset. The columns 'cnv_x' indicate the feature importance in each fold of cross-validation on CNV dataset.
DOI: 10.5281/zenodo.3407363
title: Soil moisture for Gran Paradiso

description: Pixel values represent the surface soil moisture content (in m3m-3*100) of, approximately, the top 5 cm of soil. The retrieval was based on Sentinel-1 time-series and a Support Vector Machine based approach. L. Pasolli, C. Notarnicola, G. Bertoldi, L. Bruzzone, R. Remelgado, F. Greifeneder, G. Niedrist, S. Della Chiesa, U. Tappeiner, and M. Zebisch, “Estimation of Soil Moisture in Mountain Areas Using SVR Technique Applied to Multiscale Active Radar Images at C-Band,” Sel. Top. Appl. Earth Obs. Remote Sens., vol. 8, no. 1, pp. 262–283, 2015.
DOI: 10.5281/zenodo.3407364
title: Soil moisture for Gran Paradiso

description: Pixel values represent the surface soil moisture content (in m3m-3*100) of, approximately, the top 5 cm of soil. The retrieval was based on Sentinel-1 time-series and a Support Vector Machine based approach. L. Pasolli, C. Notarnicola, G. Bertoldi, L. Bruzzone, R. Remelgado, F. Greifeneder, G. Niedrist, S. Della Chiesa, U. Tappeiner, and M. Zebisch, “Estimation of Soil Moisture in Mountain Areas Using SVR Technique Applied to Multiscale Active Radar Images at C-Band,” Sel. Top. Appl. Earth Obs. Remote Sens., vol. 8, no. 1, pp. 262–283, 2015.
DOI: 10.25606/surf.578c6039-01f73394
title: The Cosmogrid Simulation: Statistical Properties of Small Dark Matter Halos (2048-666)

description: We present the results of the "Cosmogrid" cosmological N-body simulation suites based on the concordance LCDM model. The Cosmogrid simulation was performed in a 30 Mpc box with 2048³ particles. The mass of each particle is 1.28x10^5 Msun, which is sufficient to resolve ultra-faint dwarfs. We found that the halo mass function shows good agreement with the Sheth & Tormen fitting function down to ~10^7 Msun. We have analyzed the spherically averaged density profiles of the three most massive halos which are of galaxy group size and contain at least 170 million particles. The slopes of these density profiles become shallower than -1 at the inner most radius. We also find a clear correlation of halo concentration with mass. The mass dependence of the concentration parameter cannot be expressed by a single power law, however a simple model based on the Press-Schechter theory proposed by Navarro et al. gives reasonable agreement with this dependence. The spin parameter does not show a correlation with the halo mass. The probability distribution functions for both concentration and spin are well fitted by the log-normal distribution for halos with the masses larger than ~10^8 Msun. The subhalo abundance depends on the halo mass. Galaxy-sized halos have 50% more subhalos than ~10^11 Msun halos have. This is snapshot 666 of the 2048³ resolution collection.
DOI: 10.5519/qd.0txj2o0u
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (9 records)
DOI: 10.17632/9dmrydy7x8.1
title: Data for: EFFECT OF MICROSTRUCTURE ON HYDRIC STRAIN IN CLAY ROCK: A QUANTITATIVE COMPARISON
DOI: 10.17632/cm84nbrp9d.1
title: Data for: Underspecification in Toddlers' and Adults' Lexical Representations

description: The data uploaded include five datasets with each data for one of the experiments conducted in the present study.
DOI: 10.17632/mmd7c449f7.1
title: Data for: Evaluation of an Enhanced Treatment Media and Permeable Pavement Base to Remove Stormwater Nitrogen, Phosphorus, and Metals under Simulated Rainfall

description: Raw data from rainfall simulations on a novel permeable pavement base material and stormwater treatment media.