cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.34740/kaggle/dsv/1443994
title: YouTube Trending Video Dataset (updated daily)
DOI: 10.6084/m9.figshare.9808451.v1
title: Supplementary Data 2

description: This file contains the benign variants used in our study with selected dbNSFP annotations (as described in Methods: Benign variants).<br>
DOI: 10.6084/m9.figshare.9808454.v1
title: Supplementary Data 3

description: This file contains the GTEx gene expression data used in our study (as described in Methods: Gene expression data).<br>
DOI: 10.6084/m9.figshare.9808445.v1
title: Supplementary Data 1

description: This file contains a R list of ClinVar pathogenic variants for the 1,879 HPO terms considered in our study (as described in Methods: Pathogenic variants).<br>
DOI: 10.6084/m9.figshare.9808385
title: Dataset for: Nonlinear reaction-diffusion process models improve inference for population dynamics

description: Partial differential equations (PDEs) are a useful tool for modeling spatio-temporal dynamics of ecological processes. However, as an ecological process evolves, we need statistical models that can adapt to changing dynamics as new data are collected. We developed a model that combines an ecological diffusion equation and logistic growth to characterize colonization processes of a population that establishes long-term equilibrium over a heterogeneous environment. We also developed a homogenization strategy to statistically upscale the PDE for faster computation, and adopted a hierarchical framework to accommodate multiple data sources collected at different spatial scales. We highlighted advantages of using a logistic reaction component instead of a Malthusian component when population growth demonstrates asymptotic behavior. As a case study, we demonstrated that our model improves spatio-temporal abundance forecasts of sea otters in Glacier Bay, Alaska. Further, we predicted spatially-varying local equilibrium abundances as a result of environmentally-driven diffusion and density-regulated growth, and integrating equilibrium abundances over the study area in our application enabled us to infer the overall carrying capacity of sea otters in Glacier Bay, Alaska.
DOI: 10.6084/m9.figshare.9808412
title: Dataset for: Covariate-Adjusted Region-Referenced Generalized Functional Linear Model for EEG Data

description: Electroencephalography (EEG) studies produce region-referenced functional data in the form of EEG signals recorded across electrodes on the scalp. It is of clinical interest to relate the highly structured EEG data to scalar outcomes such as diagnostic status. In our motivating study, resting state EEG is collected on both typically developing (TD) children and children with Autism Spectrum Disorder (ASD) aged two to twelve years old. The peak alpha frequency (PAF), defined as the location of a prominent peak in the alpha frequency band of the spectral density, is an important biomarker linked to neurodevelopment and is known to shift from lower to higher frequencies as children age. To retain the most amount of information from the data, we consider the oscillations in the spectral density within the alpha band, rather than just the peak location, as a functional predictor of diagnostic status (TD vs. ASD), adjusted for chronological age. A covariate-adjusted region-referenced generalized functional linear model (CARR-GFLM) is proposed for modeling scalar outcomes from region-referenced functional predictors, which utilizes a tensor basis formed from one-dimensional discrete and continuous bases to estimate functional effects across a discrete regional domain while simultaneously adjusting for additional non-functional covariates, such as age. The proposed methodology provides novel insights into differences in neural development of TD and ASD children. The efficacy of the proposed methodology is investigated through extensive simulation studies.
DOI: 10.6084/m9.figshare.9808385.v1
title: Dataset for: Nonlinear reaction-diffusion process models improve inference for population dynamics

description: Partial differential equations (PDEs) are a useful tool for modeling spatio-temporal dynamics of ecological processes. However, as an ecological process evolves, we need statistical models that can adapt to changing dynamics as new data are collected. We developed a model that combines an ecological diffusion equation and logistic growth to characterize colonization processes of a population that establishes long-term equilibrium over a heterogeneous environment. We also developed a homogenization strategy to statistically upscale the PDE for faster computation, and adopted a hierarchical framework to accommodate multiple data sources collected at different spatial scales. We highlighted advantages of using a logistic reaction component instead of a Malthusian component when population growth demonstrates asymptotic behavior. As a case study, we demonstrated that our model improves spatio-temporal abundance forecasts of sea otters in Glacier Bay, Alaska. Further, we predicted spatially-varying local equilibrium abundances as a result of environmentally-driven diffusion and density-regulated growth, and integrating equilibrium abundances over the study area in our application enabled us to infer the overall carrying capacity of sea otters in Glacier Bay, Alaska.
DOI: 10.6084/m9.figshare.9808412.v1
title: Dataset for: Covariate-Adjusted Region-Referenced Generalized Functional Linear Model for EEG Data

description: Electroencephalography (EEG) studies produce region-referenced functional data in the form of EEG signals recorded across electrodes on the scalp. It is of clinical interest to relate the highly structured EEG data to scalar outcomes such as diagnostic status. In our motivating study, resting state EEG is collected on both typically developing (TD) children and children with Autism Spectrum Disorder (ASD) aged two to twelve years old. The peak alpha frequency (PAF), defined as the location of a prominent peak in the alpha frequency band of the spectral density, is an important biomarker linked to neurodevelopment and is known to shift from lower to higher frequencies as children age. To retain the most amount of information from the data, we consider the oscillations in the spectral density within the alpha band, rather than just the peak location, as a functional predictor of diagnostic status (TD vs. ASD), adjusted for chronological age. A covariate-adjusted region-referenced generalized functional linear model (CARR-GFLM) is proposed for modeling scalar outcomes from region-referenced functional predictors, which utilizes a tensor basis formed from one-dimensional discrete and continuous bases to estimate functional effects across a discrete regional domain while simultaneously adjusting for additional non-functional covariates, such as age. The proposed methodology provides novel insights into differences in neural development of TD and ASD children. The efficacy of the proposed methodology is investigated through extensive simulation studies.
DOI: 10.17633/rd.brunel.9807953
title: Towards industrial Al-Nb-B master alloys dataset

description: Measured grain size data as a function of Nb and B levels<br><br>Format of data: xls
DOI: 10.6084/m9.figshare.9808028
title: 3250 Lab 1 Materials Ari, Luke, Saman, Max

description: A dataset displaying the type of data that will be collected during our field work. The experiment tests whether there is a relationship between species richness and distance from an area with a high disturbance regime. <br>Also included is a diagram of the study area and a flow chart.<br>
DOI: 10.6084/m9.figshare.9808127
title: Factors Influencing Stakeholder Participation Dynamics in Research for Development Interventions with Multi-Stakeholder Platforms; A metric approach to studying stakeholder participation

description: The data represents the participation of stakeholders to 411 different events organized by an research for development intervention; Humidtropics, innovation platforms in Uganda between 2013 and 2016.
DOI: 10.17633/rd.brunel.9807953.v1
title: Towards industrial Al-Nb-B master alloys dataset

description: Measured grain size data as a function of Nb and B levels<br><br>Format of data: xls
DOI: 10.6084/m9.figshare.9808127.v1
title: Factors Influencing Stakeholder Participation Dynamics in Research for Development Interventions with Multi-Stakeholder Platforms; A metric approach to studying stakeholder participation

description: The data represents the participation of stakeholders to 411 different events organized by an research for development intervention; Humidtropics, innovation platforms in Uganda between 2013 and 2016.
DOI: 10.6084/m9.figshare.9808028.v1
title: 3250 Lab 1 Materials Ari, Luke, Saman, Max

description: A dataset displaying the type of data that will be collected during our field work. The experiment tests whether there is a relationship between species richness and distance from an area with a high disturbance regime. <br>Also included is a diagram of the study area and a flow chart.<br>
DOI: 10.6084/m9.figshare.9807860
title: Detecting interspecific hybridization with Illumina SNP BeadChips: A case study based on the Spanish ibex

description: Single nucleotide polymorphism (SNP) arrays allowing to characterize the genome-wide diversity of domestic species have been developed in the last decade. Herewith, we aim to assess the applicability of the Goat SNP50 BeadChip to detect the introgression of Iberian wild goats (<i>Capra pyrenaica</i>) with domestic goats (<i>Capra hircus</i>). By genotyping 118 Iberian wild goats, we have found that as much as 21,621 caprine SNPs (40.54% of all SNPs contained in the goat chip) segregate in the Iberian wild goat population (MAF &gt; 0.01). This extensive sharing of polymorphic markers was due to the presence of eight Iberian wild goats from Tortosa-Beceite showing signs of domestic goat introgression. Information provided by the chip made possible to demonstrate that genomic segments containing introgressed SNPs were enriched in genes related with the immune and neuronal systems. Moreover, we have surveyed the genetic variation of Iberian wild goats by sequencing. This experiment yielded a data set of 5.08 million SNPs that can be accessed at Figshare database. Only 4.69% of these SNPs were also present in a SNP data set generated from 40 domestic goat whole-genome sequences. The main conclusion that can be derived from our study is that massive SNP arrays are an excellent tool to survey, at a large-scale and with a modest economic cost, the introgression of wild species with their domestic counterparts. The application of this tool to the study of Iberian wild goat diversity has demonstrated that introgression with domestic goats is not widespread. <br>
DOI: 10.6084/m9.figshare.9807758
title: EEG data of experiment in paper (manuscript), titled Event-related potentials reveal limited readiness to access phonetic details during word processing in dogs; Authors: Magyari, L., Huszár, Zs., Turzó, A., Andics, A

description: Recorded EEG data of each participants (dogs).
DOI: 10.6084/m9.figshare.9807860.v1
title: Detecting interspecific hybridization with Illumina SNP BeadChips: A case study based on the Spanish ibex

description: <b>Background</b> The Spanish ibex (<i>Capra pyrenaica</i>) is a wild goat species distributed in the Iberian Peninsula. Four subspecies have been defined: <i>C. p. hispanica</i> (CPH, south and east of the Iberian Peninsula), <i>C. p. victoriae</i> (CPV, center and northwest of the Iberian Peninsula), <i>C. p. lusitanica</i> (CPL, Galicia and north of Portugal) and <i>C. p. pyrenaica</i> (CPP, Pyrenees mountains). Hunting, epidemics and habitat loss caused the extinction of CPL (disappeared in the 19<sup>th</sup> century) and CPP (extinct in the year 2000) as well as severe population bottlenecks decreasing the diversity of CPV and CPH. There are evidences that the coexistence of Spanish ibex populations with domestic goats raised in mountainous areas might have favoured the occurrence of hybridization events between both species. In the current work, we wanted to investigate these putative hybridization events by using genome-wide diversity data. We also wanted to evaluate whether the population bottleneck experienced by CPP resulted in the accumulation of deleterious mutations with harmful effects on viability and reproductive success. <b>Findings</b> By using a high throughput genotyping approach, we have identified the presence of Spanish ibexes introgressed with domestic goats in Tortosa-Beceite. Individual sequencing of one of the last CPP representatives (16× coverage) and Pool-sequencing (39× coverage) of 30 CPH and 23 CPV individuals revealed an extensive sharing of SNPs (74%) between the CPP individual and the extant CPV and CPH subspecies, Sequencing experiments also revealed that the genome of one of the last CPP representatives contains stop-gained mutations, with heterozygous genotypes, in the <i>WASF2</i>, <i>RBM17</i> and <i>SERPINB10</i> genes. The inactivation of WASF2 and RBM17 causes embryonic lethality, while SERPINB10 belongs to a family of serin proteases with key roles in immunity and other biological processes. <b>Conclusions</b> We have demonstrated that interspecific hybridization with domestic goats has been an important source of novel variability for Spanish ibexes living in Tortosa-Beceite. The presence of stop-gained mutations with highly harmful effects in the genome of one of the last representatives of the CPP subspecies suggests that its extinction might be partly explained by the progressive accumulation of mutations with adverse consequences on fitness and reproductive success.
DOI: 10.6084/m9.figshare.9807860.v3
title: Detecting interspecific hybridization with Illumina SNP BeadChips: A case study based on the Spanish ibex

description: Single nucleotide polymorphism (SNP) arrays allowing to characterize the genome-wide diversity of domestic species have been developed in the last decade. Herewith, we aim to assess the applicability of the Goat SNP50 BeadChip to detect the introgression of Iberian wild goats (<i>Capra pyrenaica</i>) with domestic goats (<i>Capra hircus</i>). By genotyping 118 Iberian wild goats, we have found that as much as 21,621 caprine SNPs (40.54% of all SNPs contained in the goat chip) segregate in the Iberian wild goat population (MAF &gt; 0.01). This extensive sharing of polymorphic markers was due to the presence of eight Iberian wild goats from Tortosa-Beceite showing signs of domestic goat introgression. Information provided by the chip made possible to demonstrate that genomic segments containing introgressed SNPs were enriched in genes related with the immune and neuronal systems. Moreover, we have surveyed the genetic variation of Iberian wild goats by sequencing. This experiment yielded a data set of 5.08 million SNPs that can be accessed at Figshare database. Only 4.69% of these SNPs were also present in a SNP data set generated from 40 domestic goat whole-genome sequences. The main conclusion that can be derived from our study is that massive SNP arrays are an excellent tool to survey, at a large-scale and with a modest economic cost, the introgression of wild species with their domestic counterparts. The application of this tool to the study of Iberian wild goat diversity has demonstrated that introgression with domestic goats is not widespread. <br>
DOI: 10.6084/m9.figshare.9807860.v2
title: Detecting interspecific hybridization with Illumina SNP BeadChips: A case study based on the Spanish ibex

description: <b>Background</b> The Spanish ibex (<i>Capra pyrenaica</i>) is a wild goat species distributed in the Iberian Peninsula. Four subspecies have been defined: <i>C. p. hispanica</i> (CPH, south and east of the Iberian Peninsula), <i>C. p. victoriae</i> (CPV, center and northwest of the Iberian Peninsula), <i>C. p. lusitanica</i> (CPL, Galicia and north of Portugal) and <i>C. p. pyrenaica</i> (CPP, Pyrenees mountains). Hunting, epidemics and habitat loss caused the extinction of CPL (disappeared in the 19<sup>th</sup> century) and CPP (extinct in the year 2000) as well as severe population bottlenecks decreasing the diversity of CPV and CPH. There are evidences that the coexistence of Spanish ibex populations with domestic goats raised in mountainous areas might have favoured the occurrence of hybridization events between both species. In the current work, we wanted to investigate these putative hybridization events by using genome-wide diversity data. We also wanted to evaluate whether the population bottleneck experienced by CPP resulted in the accumulation of deleterious mutations with harmful effects on viability and reproductive success. <b>Findings</b> By using a high throughput genotyping approach, we have identified the presence of Spanish ibexes introgressed with domestic goats in Tortosa-Beceite. Individual sequencing of one of the last CPP representatives (16× coverage) and Pool-sequencing (39× coverage) of 30 CPH and 23 CPV individuals revealed an extensive sharing of SNPs (74%) between the CPP individual and the extant CPV and CPH subspecies, Sequencing experiments also revealed that the genome of one of the last CPP representatives contains stop-gained mutations, with heterozygous genotypes, in the <i>WASF2</i>, <i>RBM17</i> and <i>SERPINB10</i> genes. The inactivation of WASF2 and RBM17 causes embryonic lethality, while SERPINB10 belongs to a family of serin proteases with key roles in immunity and other biological processes. <b>Conclusions</b> We have demonstrated that interspecific hybridization with domestic goats has been an important source of novel variability for Spanish ibexes living in Tortosa-Beceite. The presence of stop-gained mutations with highly harmful effects in the genome of one of the last representatives of the CPP subspecies suggests that its extinction might be partly explained by the progressive accumulation of mutations with adverse consequences on fitness and reproductive success.
DOI: 10.6084/m9.figshare.9805388
title: US-NC4 soil respiration data

description: Site info: Alligator River National Wildlife RefugeEcosystem type: Mixed hardwood swamp forest (forested wetland)Data info: Continuous soil respiration data - 30 min and daily mean<br>
DOI: 10.6084/m9.figshare.9805388.v1
title: US-NC4 soil respiration data

description: Site info: Alligator River National Wildlife RefugeEcosystem type: Mixed hardwood swamp forest (forested wetland)Data info: Continuous soil respiration data - 30 min and daily mean<br>
DOI: 10.6084/m9.figshare.9805394.v1
title: Predicting the Emergence of Community Smells using Socio-Technical Metrics

description: Online appendix of the paper titled: "Predicting the Emergence of Community Smells using Socio-Technical Metrics"
DOI: 10.6084/m9.figshare.9805325
title: Raw Data DO NOT USE

description: Unformatted data
DOI: 10.6084/m9.figshare.9805319
title: Current insights into the mechanism of mammalian immunoglobulin class switch recombination

description: Immunoglobulin (Ig) class switch recombination (CSR) is the gene rearrangement process by which B lymphocytes change the Ig heavy chain constant region to permit a switch of Ig isotype from IgM to IgG, IgA, or IgE. At the DNA level, CSR occurs via generation and joining of DNA double strand breaks (DSBs) at intronic switch regions located just upstream of each of the heavy chain constant regions. Activation-induced deaminase (AID), a B cell specific enzyme, catalyzes cytosine deaminations (converting cytosines to uracils) as the initial DNA lesions that eventually lead to DSBs and CSR. Progress on AID structure integrates very well with knowledge about Ig class switch region nucleic acid structures that are supported by functional studies. It is an ideal time to review what is known about the mechanism of Ig CSR and its relation to somatic hypermutation. There have been many comprehensive reviews on various aspects of the CSR reaction and regulation of AID expression and activity. This review is focused on the relation between AID and switch region nucleic acid structures, with a particular emphasis on R-loops.
DOI: 10.6084/m9.figshare.9805325.v2
title: Raw Data DO NOT USE

description: Unformatted data
DOI: 10.6084/m9.figshare.9805319.v1
title: Current insights into the mechanism of mammalian immunoglobulin class switch recombination

description: Immunoglobulin (Ig) class switch recombination (CSR) is the gene rearrangement process by which B lymphocytes change the Ig heavy chain constant region to permit a switch of Ig isotype from IgM to IgG, IgA, or IgE. At the DNA level, CSR occurs via generation and joining of DNA double strand breaks (DSBs) at intronic switch regions located just upstream of each of the heavy chain constant regions. Activation-induced deaminase (AID), a B cell specific enzyme, catalyzes cytosine deaminations (converting cytosines to uracils) as the initial DNA lesions that eventually lead to DSBs and CSR. Progress on AID structure integrates very well with knowledge about Ig class switch region nucleic acid structures that are supported by functional studies. It is an ideal time to review what is known about the mechanism of Ig CSR and its relation to somatic hypermutation. There have been many comprehensive reviews on various aspects of the CSR reaction and regulation of AID expression and activity. This review is focused on the relation between AID and switch region nucleic acid structures, with a particular emphasis on R-loops.
DOI: 10.6084/m9.figshare.9805325.v1
title: Meta_Data

description: Meta Data of Sites in Nepal, Biome Health Project
DOI: 10.6084/m9.figshare.9805274
title: An Assimilation of TRIZ in Dissecting the Statistical Outcomes of Tactile Sensitivity, Pinch Force and Endurance among Elderly People

description: This data is an experiment which measures elderlies finger pinch endurance time and force with reduced and increased tactile sensation.
DOI: 10.6084/m9.figshare.9805262
title: Supplementary Material for: Mindfulness-Based Therapy Regulates Brain Connectivity in Major Depression

description: Medicine
DOI: 10.6084/m9.figshare.9805274.v1
title: An Assimilation of TRIZ in Dissecting the Statistical Outcomes of Tactile Sensitivity, Pinch Force and Endurance among Elderly People

description: This data is an experiment which measures elderlies finger pinch endurance time and force with reduced and increased tactile sensation.
DOI: 10.6084/m9.figshare.9805286.v1
title: The rational SPDE approach for Gaussian random fields with general smoothness

description: A popular approach for modeling and inference in spatial statistics is to represent Gaussian random fields as solutions to stochastic partial differential equations (SPDEs) of the form Lβu=W, where W is Gaussian white noise, <i>L</i> is a second-order differential operator, and β&gt;0 is a parameter that determines the smoothness of <i>u</i>. However, this approach has been limited to the case 2β∈N, which excludes several important models and makes it necessary to keep <i>β</i> fixed during inference. We propose a new method, the rational SPDE approach, which in spatial dimension d∈N is applicable for any β&gt;d/4, and thus remedies the mentioned limitation. The presented scheme combines a finite element discretization with a rational approximation of the function x−β to approximate <i>u</i>. For the resulting approximation, an explicit rate of convergence to <i>u</i> in mean-square sense is derived. Furthermore, we show that our method has the same computational benefits as in the restricted case 2β∈N. Several numerical experiments and a statistical application are used to illustrate the accuracy of the method, and to show that it facilitates likelihood-based inference for all model parameters including <i>β</i>. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.12867401
title: multiTimeline.csv

description: Lorem ipsum test data entered here