cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5280256
title: Olfactory Bulb Cells: Summary Table of Electrical Behaviors

description: A list of electrical membrane behaviors that have been experimentally observed in olfactory bulb cells.<br>
DOI: 10.6084/m9.figshare.5280265.v1
title: Dataset for: SpinDynamica: Symbolic and numerical magnetic resonance in a <i>Mathematica</i> environment

description: <i>SpinDynamica</i> is a set of <i>Mathematica</i> packages for performing numerical and symbolic analysis of a wide range of magnetic resonance experiments and phenomena. An overview of the <i>SpinDynamica</i> architecture and functionality is given, with some simple representative examples.
DOI: 10.6084/m9.figshare.5280229
title: SQLite database of variants in Collaborative Cross founder mouse strains

description: A SQLite database with two tables: "description" and "variants". The description table includes URLs for the source files. The "variants" table contains the data, including the fields snp_id, chr (1-19, X, Y, MT), pos (in basepairs, GRCm38/mm10 build), alleles (major and minor alleles), sdp (strain distribution pattern, used by R/qtl2), ensembl_gene, consequence, the 8 founders' genotypes (as numeric codes with 1 = major allele), and type (snp/indel/SV). The ensembl_gene field may contain multiple comma-separated values. The consequence field may also contain multiple comma-separated values, and each has the form "gene:consequence".<br><br>The script used to create it is at GitHub.<br>
DOI: 10.6084/m9.figshare.5280238.v1
title: SQLite database with mouse gene annotations from Mouse Genome Informatics (MGI) at The Jackson Laboratory

description: A SQLite database with two tables: "description" and "genes". The description table includes the URL for the source file. The "genes" table contains the data, with 14 fields including chr (1-19, X, Y, MT), start and stop (in basepairs, GRCm38/mm10 build), source, strand, Name, and type.
DOI: 10.6084/m9.figshare.5280229.v1
title: SQLite database of variants in Collaborative Cross founder mouse strains

description: A SQLite database with two tables: "description" and "variants". The description table includes URLs for the source files. The "variants" table contains the data, including the fields snp_id, chr (1-19, X, Y, MT), pos (in basepairs, GRCm38/mm10 build), alleles (major and minor alleles), sdp (strain distribution pattern, used by R/qtl2) ensembl_gene, consequence, the 8 founders' genotypes (as numeric codes with 1 = major allele), and type (snp/indel/SV).
DOI: 10.17028/rd.lboro.5280082
title: Emblem and Kit History of Leicester City Football Club

description: It is difficult to trace why the blue colour has been decided for the identity of the Leicester City Football Team. However the club's home colours of royal blue shirts, white shorts, and royal blue socks have been used for the team's kits throughout most of its history. Until now the official Leicester City Home kits for the 2017/18 season still continue to feature the club's traditional shade of blue alongside fox tonal gold badges half sleeve graphic, specifically designed as identity of the club.<br><br>Apart from the uniform, the club emblems are also associated blue colour throughout the long history of the club. In 1948, an image of a fox was first time incorporated into the club crest, as Leicestershire is known for foxes and fox hunting. This is the origin of the nickname ‘The Foxes’ of the club. For the transformation of the badges in the club’s history, it consists using blue as main themed colour for the club. That is why in local terms, the club is also known as ‘The blues’.
DOI: 10.6084/m9.figshare.5280193.v1
title: Competing Place Meanings in Complex Landscapes: A Social–Ecological Approach to Unpacking Community Conservation Outcomes on the Wild Coast, South Africa

description: Despite a general awareness of the social–ecological complexities within which conservation interventions are embedded, approaches to understanding a diversity of local perspectives of heterogeneous landscapes and how they matter for the outcomes of these interventions are seldom demonstrated. We apply a social–ecological approach to exploring the multiple place meanings related to key landscape elements around a proposed community conservation intervention on the Wild Coast, South Africa, by identifying and analyzing three narratives about this impending change. These narratives mobilize competing meanings of the landscape to argue for or against the conservation project. By linking place meanings to locally defined landscape units (ecotopes), we engage multiple interpretations of the heterogeneous and changing landscape to gain a holistic and more inclusive picture of social–ecological landscape processes such as increasing woodlands and field abandonment. The obstruction of this particular intervention indicates the importance of engaging with multiple cultural values of nature.
DOI: 10.6084/m9.figshare.5280238.v2
title: SQLite database with mouse gene annotations from Mouse Genome Informatics (MGI) at The Jackson Laboratory

description: A SQLite database with two tables: "description" and "genes". The description table includes the URL for the source file. The "genes" table contains the data, with 15 fields including chr (1-19, X, Y, MT), start and stop (in basepairs, GRCm38/mm10 build), source, strand, Name, and type.
DOI: 10.17028/rd.lboro.5280082.v1
title: Emblem and Kit History of Leicester City Football Club

description: It is difficult to trace why the blue colour has been decided for the identity of the Leicester City Football Team. However the club's home colours of royal blue shirts, white shorts, and royal blue socks have been used for the team's kits throughout most of its history. Until now the official Leicester City Home kits for the 2017/18 season still continue to feature the club's traditional shade of blue alongside fox tonal gold badges half sleeve graphic, specifically designed as identity of the club.<br><br>Apart from the uniform, the club emblems are also associated blue colour throughout the long history of the club. In 1948, an image of a fox was first time incorporated into the club crest, as Leicestershire is known for foxes and fox hunting. This is the origin of the nickname ‘The Foxes’ of the club. For the transformation of the badges in the club’s history, it consists using blue as main themed colour for the club. That is why in local terms, the club is also known as ‘The blues’.
DOI: 10.6084/m9.figshare.5280070.v1
title: Efficient estimation of the nonparametric mean and covariance functions for longitudinal and sparse functional data

description: We consider the estimation of mean and covariance functions for longitudinal and sparse functional data by using the full quasi-likelihood coupling a modification of the local kernel smoothing method. The proposed estimators are shown to be consistent, asymptotically normal, and semiparametrically <i>efficient</i> in terms of their linear functionals. Their superiority to the competitors is further illustrated numerically through simulation studies. The method is applied to analyze AIDS study and atmospheric study.
DOI: 10.6084/m9.figshare.5280238.v4
title: SQLite database with mouse gene annotations from Mouse Genome Informatics (MGI) at The Jackson Laboratory

description: A SQLite database with two tables: "description" and "genes". The description table includes the URL for the source file. The "genes" table contains the data, with 15 fields including chr (1-19, X, Y, MT), start and stop (in basepairs, GRCm38/mm10 build), source, strand, Name, and type.
DOI: 10.6084/m9.figshare.5280052
title: Reconciling Curvature and Importance Sampling Based Procedures for Summarizing Case Influence in Bayesian Models

description: Methods for summarizing case influence in Bayesian models take essentially two forms: (1) use common divergence measures for calculating distances between the full-data posterior and the case-deleted posterior, and (2) measure the impact of infinitesimal perturbations to the likelihood to study local case influence. Methods based on approach (1) lead naturally to considering the behavior of case-deletion importance sampling weights (the weights used to approximate samples from the case-deleted posterior using samples from the full posterior). Methods based on approach (2) lead naturally to considering the local curvature of the Kullback–Leibler divergence of the full posterior from a geometrically perturbed quasi-posterior. By examining the connections between the two approaches, we establish a rationale for employing low-dimensional summaries of case influence obtained entirely via the variance–covariance matrix of the log importance sampling weights. We illustrate the use of the proposed diagnostics using real and simulated data. Supplementary materials are available online.
DOI: 10.6084/m9.figshare.5280238.v5
title: SQLite database with mouse gene annotations from Mouse Genome Informatics (MGI) at The Jackson Laboratory

description: A SQLite database with two tables: "description" and "genes". The description table includes the URL for the source file. The "genes" table contains the data, with 15 fields including chr (1-19, X, Y, MT), start and stop (in basepairs, GRCm38/mm10 build), source, strand, Name, and type.
DOI: 10.6084/m9.figshare.5280052.v1
title: Reconciling Curvature and Importance Sampling Based Procedures for Summarizing Case Influence in Bayesian Models

description: Methods for summarizing case influence in Bayesian models take essentially two forms: (1) use common divergence measures for calculating distances between the full-data posterior and the case-deleted posterior, and (2) measure the impact of infinitesimal perturbations to the likelihood to study local case influence. Methods based on approach (1) lead naturally to considering the behavior of case-deletion importance sampling weights (the weights used to approximate samples from the case-deleted posterior using samples from the full posterior). Methods based on approach (2) lead naturally to considering the local curvature of the Kullback–Leibler divergence of the full posterior from a geometrically perturbed quasi-posterior. By examining the connections between the two approaches, we establish a rationale for employing low-dimensional summaries of case influence obtained entirely via the variance–covariance matrix of the log importance sampling weights. We illustrate the use of the proposed diagnostics using real and simulated data. Supplementary materials are available online.
DOI: 10.6084/m9.figshare.5280010
title: Linear Hypothesis Testing in Dense High-Dimensional Linear Models

description: We propose a methodology for testing linear hypothesis in high-dimensional linear models. The proposed test does not impose any restriction on the size of the model, that is, model sparsity or the loading vector representing the hypothesis. Providing asymptotically valid methods for testing general linear functions of the regression parameters in high-dimensions is extremely challenging—especially without making restrictive or unverifiable assumptions on the number of nonzero elements. We propose to test the moment conditions related to the newly designed restructured regression, where the inputs are transformed and augmented features. These new features incorporate the structure of the null hypothesis directly. The test statistics are constructed in such a way that lack of sparsity in the original model parameter does not present a problem for the theoretical justification of our procedures. We establish asymptotically exact control on Type I error without imposing any sparsity assumptions on model parameter or the vector representing the linear hypothesis. Our method is also shown to achieve certain optimality in detecting deviations from the null hypothesis. We demonstrate the favorable finite-sample performance of the proposed methods, via a number of numerical and a real data example. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5280019
title: A Unified Framework for Fitting Bayesian Semiparametric Models to Arbitrarily Censored Survival Data, Including Spatially Referenced Data

description: A comprehensive, unified approach to modeling arbitrarily censored spatial survival data is presented for the three most commonly used semiparametric models: proportional hazards, proportional odds, and accelerated failure time. Unlike many other approaches, all manner of censored survival times are simultaneously accommodated including uncensored, interval censored, current-status, left and right censored, and mixtures of these. Left-truncated data are also accommodated leading to models for time-dependent covariates. Both georeferenced (location exactly observed) and areally observed (location known up to a geographic unit such as a county) spatial locations are handled; formal variable selection makes model selection especially easy. Model fit is assessed with conditional Cox–Snell residual plots, and model choice is carried out via log pseudo marginal likelihood (LPML) and deviance information criterion (DIC). Baseline survival is modeled with a novel transformed Bernstein polynomial prior. All models are fit via a new function which calls efficient compiled C++ in the R package spBayesSurv. The methodology is broadly illustrated with simulations and real data applications. An important finding is that proportional odds and accelerated failure time models often fit significantly better than the commonly used proportional hazards model. Supplementary materials for this article, including a standardized description of the materials available for reproducing the work, are available as an online supplement.
DOI: 10.6084/m9.figshare.5280010.v1
title: Linear Hypothesis Testing in Dense High-Dimensional Linear Models

description: We propose a methodology for testing linear hypothesis in high-dimensional linear models. The proposed test does not impose any restriction on the size of the model, that is, model sparsity or the loading vector representing the hypothesis. Providing asymptotically valid methods for testing general linear functions of the regression parameters in high-dimensions is extremely challenging—especially without making restrictive or unverifiable assumptions on the number of nonzero elements. We propose to test the moment conditions related to the newly designed restructured regression, where the inputs are transformed and augmented features. These new features incorporate the structure of the null hypothesis directly. The test statistics are constructed in such a way that lack of sparsity in the original model parameter does not present a problem for the theoretical justification of our procedures. We establish asymptotically exact control on Type I error without imposing any sparsity assumptions on model parameter or the vector representing the linear hypothesis. Our method is also shown to achieve certain optimality in detecting deviations from the null hypothesis. We demonstrate the favorable finite-sample performance of the proposed methods, via a number of numerical and a real data example. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5280019.v2
title: A Unified Framework for Fitting Bayesian Semiparametric Models to Arbitrarily Censored Survival Data, Including Spatially Referenced Data

description: A comprehensive, unified approach to modeling arbitrarily censored spatial survival data is presented for the three most commonly used semiparametric models: proportional hazards, proportional odds, and accelerated failure time. Unlike many other approaches, all manner of censored survival times are simultaneously accommodated including uncensored, interval censored, current-status, left and right censored, and mixtures of these. Left-truncated data are also accommodated leading to models for time-dependent covariates. Both georeferenced (location exactly observed) and areally observed (location known up to a geographic unit such as a county) spatial locations are handled; formal variable selection makes model selection especially easy. Model fit is assessed with conditional Cox–Snell residual plots, and model choice is carried out via log pseudo marginal likelihood (LPML) and deviance information criterion (DIC). Baseline survival is modeled with a novel transformed Bernstein polynomial prior. All models are fit via a new function which calls efficient compiled C++ in the R package spBayesSurv. The methodology is broadly illustrated with simulations and real data applications. An important finding is that proportional odds and accelerated failure time models often fit significantly better than the commonly used proportional hazards model. Supplementary materials for this article, including a standardized description of the materials available for reproducing the work, are available as an online supplement.
DOI: 10.6084/m9.figshare.5280004
title: Statistical Methods for Standard Membrane-Feeding Assays to Measure Transmission Blocking or Reducing Activity in Malaria

description: Transmission blocking vaccines for malaria are not designed to directly protect vaccinated people from malaria disease, but to reduce the probability of infecting other people by interfering with the growth of the malaria parasite in mosquitoes. Standard membrane-feeding assays compare the growth of parasites in mosquitoes from a test sample (using antibodies from a vaccinated person) compared to a control sample. There is debate about whether to estimate the transmission reducing activity (TRA) which compares the mean number of parasites between test and control samples, or transmission blocking activity (TBA) which compares the proportion of infected mosquitoes. TBA appears biologically more important since each mosquito with any parasites is potentially infective; however, TBA is less reproducible and may be an overly strict criterion for screening vaccine candidates. Through a statistical model, we show that the TBA estimand depends on μ<sub><i>c</i></sub>, the mean number of parasites in the control mosquitoes, a parameter not easily experimentally controlled. We develop a standardized TBA estimator based on the model and a given target value for μ<sub><i>c</i></sub> which has better mean squared error than alternative methods. We discuss types of statistical inference needed for using these assays for vaccine development. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5280019.v1
title: A unified framework for fitting Bayesian semiparametric models to arbitrarily censored survival data, including spatially-referenced data

description: A comprehensive, unified approach to modeling arbitrarily censored spatial survival data is presented for the three most commonly-used semiparametric models: proportional hazards, proportional odds, and accelerated failure time. Unlike many other approaches, all manner of censored survival times are simultaneously accommodated including uncensored, interval censored, current-status, left and right censored, and mixtures of these. Left-truncated data are also accommodated leading to models for time-dependent covariates. Both georeferenced (location exactly observed) and areally observed (location known up to a geographic unit such as a county) spatial locations are handled; formal variable selection makes model selection especially easy. Model fit is assessed with conditional Cox-Snell residual plots, and model choice is carried out via LPML and DIC. Baseline survival is modeled with a novel transformed Bernstein polynomial prior. All models are fit via a new function which calls efficient compiled C++ in the R package spBayesSurv. The methodology is broadly illustrated with simulations and real data applications. An important finding is that proportional odds and accelerated failure time models often fit significantly better than the commonly-used proportional hazards model. Supplementary materials are available online.
DOI: 10.6084/m9.figshare.5280004.v1
title: Statistical Methods for Standard Membrane-Feeding Assays to Measure Transmission Blocking or Reducing Activity in Malaria

description: Transmission blocking vaccines for malaria are not designed to directly protect vaccinated people from malaria disease, but to reduce the probability of infecting other people by interfering with the growth of the malaria parasite in mosquitoes. Standard membrane-feeding assays compare the growth of parasites in mosquitoes from a test sample (using antibodies from a vaccinated person) compared to a control sample. There is debate about whether to estimate the transmission reducing activity (TRA) which compares the mean number of parasites between test and control samples, or transmission blocking activity (TBA) which compares the proportion of infected mosquitoes. TBA appears biologically more important since each mosquito with any parasites is potentially infective; however, TBA is less reproducible and may be an overly strict criterion for screening vaccine candidates. Through a statistical model, we show that the TBA estimand depends on μ<sub><i>c</i></sub>, the mean number of parasites in the control mosquitoes, a parameter not easily experimentally controlled. We develop a standardized TBA estimator based on the model and a given target value for μ<sub><i>c</i></sub> which has better mean squared error than alternative methods. We discuss types of statistical inference needed for using these assays for vaccine development. Supplementary materials for this article are available online.
DOI: 10.34760/5f479939a6d4b
title: Skeleton 2341
DOI: 10.6084/m9.figshare.5278297
title: Mendenhall 2014

description: Sequences, mapping file, taxa relative abundances
DOI: 10.6084/m9.figshare.5278264
title: Data_files

description: This is the data set of simulations. Always rename the parameters.in file before running.
DOI: 10.6084/m9.figshare.5278297.v1
title: Mendenhall 2014

description: Sequences, mapping file, taxa relative abundances
DOI: 10.6084/m9.figshare.5278264.v1
title: Data_files

description: This is the data set of simulations. Always rename the parameters.in file before running.
DOI: 10.6084/m9.figshare.5278213
title: Calamita Immune Response

description: Followup of immune response to PHA in Epidalea calamita toads<br>
DOI: 10.6084/m9.figshare.5278234
title: Data for Sunday et al., 2017

description: This is the data for <br>Sunday, M.A., Donnelly, E., Gauthier, I. (2017). Individual differences in perceptual abilities in medical imaging: The Vanderbilt Chest Radiograph Test. <i>Cognitive Research: Principles and Implications</i>
DOI: 10.6084/m9.figshare.5278213.v1
title: Calamita Immune Response

description: Followup of immune response to PHA in Epidalea calamita toads<br>
DOI: 10.6084/m9.figshare.5278102
title: MacMillan.et.al.2017.Sci.Rep.Supplementary.Datasets.zip

description: This .zip file contains supplementary data and images accompanying MacMillan et al. (2017) <b>Thermal acclimation mitigates paracellular leak from the <i>Drosophila</i> gut. </b>Published in Scientific Reports.<br>For detailed descriptions of methods and analyses performed please see the main manuscript.<br><b>This archive contains:</b>1) An excel file containing supplementary datasets that is organized into tabs by experiment.2) A set of TEM images.3) A set of immunoblot images.4) A set of tissue damage images (Live/Dead cell staining).
DOI: 10.6084/m9.figshare.5278111
title: MiSeq Analysis of on-target editing in vivo and in vitro

description: Next-generation sequencing (NGS; MiSeq) analysis of on-target editing evaluating deletions and insertions (indels) in the CRISPR-HTT group in vitro and in vivo.The files give for each read, the CIGAR string and whether indels were detected closed to expected cleavage site or not.