cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.987100
title: An Approximation Method for Improving Dynamic Network Model Fitting

description: There has been a great deal of interest recently in the modeling and simulation of dynamic networks, that is, networks that change over time. One promising model is the separable temporal exponential-family random graph model (ERGM) of Krivitsky and Handcock, which treats the formation and dissolution of ties in parallel at each time step as independent ERGMs. However, the computational cost of fitting these models can be substantial, particularly for large, sparse networks. Fitting cross-sectional models for observations of a network at a single point in time, while still a nonnegligible computational burden, is much easier. This article examines model fitting when the available data consist of independent measures of cross-sectional network structure and the duration of relationships under the assumption of stationarity. We introduce a simple approximation to the dynamic parameters for sparse networks with relationships of moderate or long duration and show that the approximation method works best in precisely those cases where parameter estimation is most likely to fail—networks with very little change at each time step. We consider a variety of cases: Bernoulli formation and dissolution of ties, independent-tie formation and Bernoulli dissolution, independent-tie formation and dissolution, and dependent-tie formation models.
DOI: 10.6084/m9.figshare.987111.v1
title: Agilent Barley Gene Expression Microarray Reannotation

description: An attempt was made to reannotate as many sequences as possible in the Agilent Barley Gene Expression Microarray, 4x44K, based on the UniProt plant protein collection and the Gramene rice genome annotation. After downloading the full sequences of the array oligos from the Core and EST sections of the NCBI Nucleotide Archive, the TIGR Plant Transcript Assembly and the DFCI Gene Indices collection, which were not provided with the array annotation, a search was made for possible homologs in the 2 February 2011 UniProt Knowledgebase Plant section and the Gramene rice genome assembly, version MSU6. A BLAST search was run with default parameters, the only modification being the use of the query sequence filtering for low complexity regions. After the BLAST search, the results were filtered, choosing the one with the best score, but requiring an e-value lower than 1e-30 and an overall fraction of iden- tical positions across the hit and query alignment of at least 50%. The description and GeneOntology (GO) associations were reannotated for all array oligos where a suitable homolog was found either in UniProt or in the Gramene database. The file contains the full sequence collection from which the array probes were derived, the Molecular function, Biological process and Cellular compartment Gene Ontology annotations in BiNGO (http://apps.cytoscape.org/apps/bingo) format and the annotation table with the UniProt and Gramene hits in a tab delimited file.
DOI: 10.6084/m9.figshare.987098
title: Functional Additive Mixed Models

description: We propose an extensive framework for additive regression models for correlated functional responses, allowing for multiple partially nested or crossed functional random effects with flexible correlation structures for, for example, spatial, temporal, or longitudinal functional data. Additionally, our framework includes linear and nonlinear effects of functional and scalar covariates that may vary smoothly over the index of the functional response. It accommodates densely or sparsely observed functional responses and predictors which may be observed with additional error and includes both spline-based and functional principal component-based terms. Estimation and inference in this framework is based on standard additive mixed models, allowing us to take advantage of established methods and robust, flexible algorithms. We provide easy-to-use open source software in the pffr() function for the R package refund. Simulations show that the proposed method recovers relevant effects reliably, handles small sample sizes well, and also scales to larger datasets. Applications with spatially and longitudinally observed functional data demonstrate the flexibility in modeling and interpretability of results of our approach.
DOI: 10.6084/m9.figshare.987100.v2
title: An Approximation Method for Improving Dynamic Network Model Fitting

description: There has been a great deal of interest recently in the modeling and simulation of dynamic networks, that is, networks that change over time. One promising model is the separable temporal exponential-family random graph model (ERGM) of Krivitsky and Handcock, which treats the formation and dissolution of ties in parallel at each time step as independent ERGMs. However, the computational cost of fitting these models can be substantial, particularly for large, sparse networks. Fitting cross-sectional models for observations of a network at a single point in time, while still a nonnegligible computational burden, is much easier. This article examines model fitting when the available data consist of independent measures of cross-sectional network structure and the duration of relationships under the assumption of stationarity. We introduce a simple approximation to the dynamic parameters for sparse networks with relationships of moderate or long duration and show that the approximation method works best in precisely those cases where parameter estimation is most likely to fail—networks with very little change at each time step. We consider a variety of cases: Bernoulli formation and dissolution of ties, independent-tie formation and Bernoulli dissolution, independent-tie formation and dissolution, and dependent-tie formation models.
DOI: 10.6084/m9.figshare.987100.v1
title: An approximation method for improving dynamic network model fitting

description: There has been a great deal of interest recently in the modeling and simulation of dynamic networks, i.e., networks that change over time. One promising model is the separable temporal exponential-family random graph model (ERGM) of Krivitsky and Handcock, which treats the formation and dissolution of ties in parallel at each time step as independent ERGMs. However, the computational cost of fitting these models can be substantial, particularly for large, sparse networks. Fitting cross-sectional models for observations of a network at a single point in time, while still a non-negligible computational burden, is much easier. This paper examines model fitting when the available data consist of independent measures of cross-sectional network structure and the duration of relationships under the assumption of stationarity. We introduce a simple approximation to the dynamic parameters for sparse networks with relationships of moderate or long duration and show that the approximation method works best in precisely those cases where parameter estimation is most likely to fail—networks with very little change at each time step. We consider a variety of cases: Bernoulli formation and dissolution of ties, independent-tie formation and Bernoulli dissolution, independent-tie formation and dissolution, and dependent-tie formation models.
DOI: 10.6084/m9.figshare.988687.v16
title: Data, code, and figures from Dunnette et al. 2014, Biogeochemical impacts of wildfires over four millennia in a Rocky Mountain subalpine watershed. New Phytologist. In Press (doi: 10.1111/nph.12828)

description: SEE README.pdf OR README.md This archive includes data and scripts needed to reproduce the analyses in Dunnette et al. 2014; it includes 49 files and is 23 MB when downloaded as a .zip archive. After extracting the .zip archive, sort by file type. Most data files are in .csv format, while some are in .xls format. Scripts and functions are written for MATLAB software (*.m file type; www.mathworks.com), and each is file fully commented, including dependencies. For some scripts or functions, the MATLAB statistics or curve fitting toolbox is required; all other functions required are provided in this archive. Dunnette, P.V., P.E. Higuera, K.K. McLauchlan, K.M. Derr, C.E. Briles, and M.H. Keefe. 2014. Biogeochemical impacts of wildfires over four millennia in a Rocky Mountain<br>subalpine watershed. New Phytologist In Press doi: 10.1111/nph.12828
DOI: 10.6084/m9.figshare.987098.v2
title: Functional Additive Mixed Models

description: We propose an extensive framework for additive regression models for correlated functional responses, allowing for multiple partially nested or crossed functional random effects with flexible correlation structures for, for example, spatial, temporal, or longitudinal functional data. Additionally, our framework includes linear and nonlinear effects of functional and scalar covariates that may vary smoothly over the index of the functional response. It accommodates densely or sparsely observed functional responses and predictors which may be observed with additional error and includes both spline-based and functional principal component-based terms. Estimation and inference in this framework is based on standard additive mixed models, allowing us to take advantage of established methods and robust, flexible algorithms. We provide easy-to-use open source software in the pffr() function for the R package refund. Simulations show that the proposed method recovers relevant effects reliably, handles small sample sizes well, and also scales to larger datasets. Applications with spatially and longitudinally observed functional data demonstrate the flexibility in modeling and interpretability of results of our approach.
DOI: 10.6084/m9.figshare.987097
title: A Localized Implementation of the Iterative Proportional Scaling Procedure for Gaussian Graphical Models

description: In this article, we propose localized implementations of the iterative proportional scaling (IPS) procedure by the strategy of partitioning cliques for computing maximum likelihood estimations in large Gaussian graphical models. We first divide the set of cliques into several nonoverlapping and nonempty blocks, and then adjust clique marginals in each block locally. Thus, high-order matrix operations can be avoided and the IPS procedure is accelerated. We modify the Swendsen–Wang Algorithm and apply the simulated annealing algorithm to find an approximation to the optimal partition which leads to the least complexity. This strategy of partitioning cliques can also speed up the existing IIPS and IHT procedures. Numerical experiments are presented to demonstrate the competitive performance of our new implementations and strategies.
DOI: 10.6084/m9.figshare.988687.v17
title: Data, code, and figures from Dunnette et al. 2014, Biogeochemical impacts of wildfires over four millennia in a Rocky Mountain subalpine watershed. New Phytologist. In Press (doi: 10.1111/nph.12828)

description: SEE README.pdf OR README.md This archive includes data and scripts needed to reproduce the analyses in Dunnette et al. 2014; it includes 49 files and is 23 MB when downloaded as a .zip archive. After extracting the .zip archive, sort by file type. Most data files are in .csv format, while some are in .xls format. Scripts and functions are written for MATLAB software (*.m file type; www.mathworks.com), and each is file fully commented, including dependencies. For some scripts or functions, the MATLAB statistics or curve fitting toolbox is required; all other functions required are provided in this archive. Dunnette, P.V., P.E. Higuera, K.K. McLauchlan, K.M. Derr, C.E. Briles, and M.H. Keefe. 2014. Biogeochemical impacts of wildfires over four millennia in a Rocky Mountain<br>subalpine watershed. New Phytologist In Press doi: 10.1111/nph.12828
DOI: 10.6084/m9.figshare.987098.v1
title: Functional Additive Mixed Models

description: We propose an extensive framework for additive regression models for correlated functional responses, allowing for multiple partially nested or crossed functional random effects with flexible correlation structures for, e.g., spatial, temporal, or longitudinal functional data. Additionally, our framework includes linear and nonlinear effects of functional and scalar covariates that may vary smoothly over the index of the functional response. It accommodates densely or sparsely observed functional responses and predictors which may be observed with additional error and includes both spline-based and functional principal component-based terms. Estimation and inference in this framework is based on standard additive mixed models, allowing us to take advantage of established methods and robust, flexible algorithms. We provide easy-to-use open source software in the pffr() function for the R-package refund. Simulations show that the proposed method recovers relevant effects reliably, handles small sample sizes well and also scales to larger data sets. Applications with spatially and longitudinally observed functional data demonstrate the flexibility in modeling and interpretability of results of our approach.
DOI: 10.6084/m9.figshare.987096
title: A simple measure of the strength of convergent evolution

description: Datafiles from the empirical example using Anolis lizards.
DOI: 10.6084/m9.figshare.988687.v19
title: Data, code, and figures from Dunnette et al. 2014, Biogeochemical impacts of wildfires over four millennia in a Rocky Mountain subalpine watershed. New Phytologist. 203: 900-912 (doi: 10.1111/nph.12828)

description: SEE README.pdf OR README.md This archive includes data and scripts needed to reproduce the analyses in Dunnette et al. 2014; it includes 49 files and is 23 MB when downloaded as a .zip archive. After extracting the .zip archive, sort by file type. Most data files are in .csv format, while some are in .xls format. Scripts and functions are written for MATLAB software (*.m file type; www.mathworks.com), and each file is fully commented, including dependencies. For some scripts or functions, the MATLAB statistics or curve fitting toolbox is required; all other functions required are provided in this archive. Dunnette, P.V., P.E. Higuera, K.K. McLauchlan, K.M. Derr, C.E. Briles, and M.H. Keefe. 2014. Biogeochemical impacts of wildfires over four millennia in a Rocky Mountain<br>subalpine watershed. New Phytologist In Press doi: 10.1111/nph.12828
DOI: 10.6084/m9.figshare.987095
title: Supplementary files

description: Supplementary files of "Blanco Bercial L, Cornils A, Copley N, Bucklin A. DNA barcoding of marine copepods: assessment of analytical approaches to species identification. PLOS Currents Tree of Life. 2014 Apr 4. Edition 1. "
DOI: 10.6084/m9.figshare.988687.v18
title: Data, code, and figures from Dunnette et al. 2014, Biogeochemical impacts of wildfires over four millennia in a Rocky Mountain subalpine watershed. New Phytologist. In Press (doi: 10.1111/nph.12828)

description: SEE README.pdf OR README.md This archive includes data and scripts needed to reproduce the analyses in Dunnette et al. 2014; it includes 49 files and is 23 MB when downloaded as a .zip archive. After extracting the .zip archive, sort by file type. Most data files are in .csv format, while some are in .xls format. Scripts and functions are written for MATLAB software (*.m file type; www.mathworks.com), and each is file fully commented, including dependencies. For some scripts or functions, the MATLAB statistics or curve fitting toolbox is required; all other functions required are provided in this archive. Dunnette, P.V., P.E. Higuera, K.K. McLauchlan, K.M. Derr, C.E. Briles, and M.H. Keefe. 2014. Biogeochemical impacts of wildfires over four millennia in a Rocky Mountain<br>subalpine watershed. New Phytologist In Press doi: 10.1111/nph.12828
DOI: 10.6084/m9.figshare.987092
title: S1.Alignment

description: Fasta file
DOI: 10.6084/m9.figshare.987097.v1
title: A Localized Implementation of the Iterative Proportional Scaling Procedure For Gaussian Graphical Models

description: In this paper, we propose localized implementations of the iterative proportional scaling (IPS) procedure by the strategy of partitioning cliques for computing maximum likelihood estimations in large Gaussian graphical models. We first divide the set of cliques into several non-overlapping and non-empty blocks, and then adjust clique marginals in each block locally. Thus, high order matrix operations can be avoided and the IPS procedure is accelerated. We modify the Swendsen-Wang Algorithm and apply the simulated annealing algorithm to find an approximation to the optimal partition which leads to the least complexity. This strategy of partitioning cliques can also speed up the existing IIPS and IHT procedures. Numerical experiments are presented to demonstrate the competitive performance of our new implementations and strategies.
DOI: 10.6084/m9.figshare.987092.v1
title: S1.Alignment

description: Fasta file
DOI: 10.6084/m9.figshare.987095.v2
title: Supplementary files

description: Supplementary files of "Blanco Bercial L, Cornils A, Copley N, Bucklin A. DNA barcoding of marine copepods: assessment of analytical approaches to species identification. PLOS Currents Tree of Life. 2014 Apr 4. Edition 1. "
DOI: 10.6084/m9.figshare.987097.v3
title: A Localized Implementation of the Iterative Proportional Scaling Procedure for Gaussian Graphical Models

description: In this article, we propose localized implementations of the iterative proportional scaling (IPS) procedure by the strategy of partitioning cliques for computing maximum likelihood estimations in large Gaussian graphical models. We first divide the set of cliques into several nonoverlapping and nonempty blocks, and then adjust clique marginals in each block locally. Thus, high-order matrix operations can be avoided and the IPS procedure is accelerated. We modify the Swendsen–Wang Algorithm and apply the simulated annealing algorithm to find an approximation to the optimal partition which leads to the least complexity. This strategy of partitioning cliques can also speed up the existing IIPS and IHT procedures. Numerical experiments are presented to demonstrate the competitive performance of our new implementations and strategies.
DOI: 10.6084/m9.figshare.987095.v1
title: Supplementary files

description: Supplementary files of "Blanco Bercial L, Cornils A, Copley N, Bucklin A. DNA barcoding of marine copepods: assessment of analytical approaches to species identification. PLOS Currents Tree of Life. 2014 Apr 4. Edition 1. "
DOI: 10.6084/m9.figshare.987087
title: Data for synaptic proteins expression levels and pathological scores in prefrontal cortex, anterior cingulate gyrus and parietal cortex

description: Dataset1: The dataset includes the values of Dynamin1 and phospho-/total CaMKII measured in the prefrontal cortex, used for the statistic analysis. The first three columns report the semi-quantitative scoring of AD and Lewy Body pathology in this brain region. Dataset2: The dataset includes the values of Dynamin1 and phospho-/total CaMKII measured in the anterior cingulated gyrus, used for the statistic analysis. The first three columns report the semi-quantitative scoring of AD and Lewy Body pathology in this brain region. Dataset3: The dataset includes the values of Dynamin1 and phospho-/total CaMKII measured in the parietal cortex, used for the statistic analysis. The first three columns report the semi-quantitative scoring of AD and Lewy Body pathology in this brain region.
DOI: 10.6084/m9.figshare.987097.v2
title: A Localized Implementation of the Iterative Proportional Scaling Procedure for Gaussian Graphical Models

description: In this article, we propose localized implementations of the iterative proportional scaling (IPS) procedure by the strategy of partitioning cliques for computing maximum likelihood estimations in large Gaussian graphical models. We first divide the set of cliques into several nonoverlapping and nonempty blocks, and then adjust clique marginals in each block locally. Thus, high-order matrix operations can be avoided and the IPS procedure is accelerated. We modify the Swendsen–Wang Algorithm and apply the simulated annealing algorithm to find an approximation to the optimal partition which leads to the least complexity. This strategy of partitioning cliques can also speed up the existing IIPS and IHT procedures. Numerical experiments are presented to demonstrate the competitive performance of our new implementations and strategies.
DOI: 10.6084/m9.figshare.987085
title: BJET KEy issues survey 2013

description: Approximately every two years, BJET carries out a short survey short survey with members of the BJET Reviewer Panel and other learning technologists across the world. The aim is to get a view on the key issues facing learning technology at that time. The previous seminars were carried out in 2009 and 2011. The results allow some comparisons to be made between the issues that are judged to be important now and in the past.
DOI: 10.6084/m9.figshare.987086
title: Data sets for UK Pulmonary Rehabilitation Programmes in real-life clinical settings

description: The data-sheet shows demographics and outcomes of patients who participated in two UK Pulmonary Rehabilitation Programmes. Hospital 1 offered 3 sessions per week over 6 weeks (Group 1) and Hospital 2 offered 2 sessions per week over 9 weeks (group 2). Data have been anonymised.
DOI: 10.6084/m9.figshare.987087.v1
title: Data for synaptic proteins expression levels and pathological scores in prefrontal cortex, anterior cingulate gyrus and parietal cortex

description: Dataset1: The dataset includes the values of Dynamin1 and phospho-/total CaMKII measured in the prefrontal cortex, used for the statistic analysis. The first three columns report the semi-quantitative scoring of AD and Lewy Body pathology in this brain region. Dataset2: The dataset includes the values of Dynamin1 and phospho-/total CaMKII measured in the anterior cingulated gyrus, used for the statistic analysis. The first three columns report the semi-quantitative scoring of AD and Lewy Body pathology in this brain region. Dataset3: The dataset includes the values of Dynamin1 and phospho-/total CaMKII measured in the parietal cortex, used for the statistic analysis. The first three columns report the semi-quantitative scoring of AD and Lewy Body pathology in this brain region.
DOI: 10.6084/m9.figshare.987080
title: Suppl. Fig. - Lipidomic analysis of lipid droplets from murine hepatocytes reveals distinct signatures for nutritional stress

description: Supplementary Figures
DOI: 10.6084/m9.figshare.987081
title: Suppl. Table - A comprehensive method for lipid profiling by liquid chromatography-ion cyclotron resonance mass spectrometry

description: Supplemental table
DOI: 10.6084/m9.figshare.987085.v1
title: BJET KEy issues survey 2013

description: Approximately every two years, BJET carries out a short survey short survey with members of the BJET Reviewer Panel and other learning technologists across the world. The aim is to get a view on the key issues facing learning technology at that time. The previous seminars were carried out in 2009 and 2011. The results allow some comparisons to be made between the issues that are judged to be important now and in the past.
DOI: 10.6084/m9.figshare.987078
title: Suppl. Fig. - The impact of genetic stress by ATGL deficiency on the lipidome of lipid droplets from murine hepatocytes

description: Supplementary Figures
DOI: 10.6084/m9.figshare.987079
title: Suppl. Table - Lipidomic analysis of lipid droplets from murine hepatocytes reveals distinct signatures for nutritional stress

description: Supplementary tables
DOI: 10.6084/m9.figshare.987080.v1
title: Suppl. Fig. - Lipidomic analysis of lipid droplets from murine hepatocytes reveals distinct signatures for nutritional stress

description: Supplementary Figures
DOI: 10.6084/m9.figshare.987081.v1
title: Suppl. Table - A comprehensive method for lipid profiling by liquid chromatography-ion cyclotron resonance mass spectrometry

description: Supplemental table