cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5387140.v1
title: simulated_head_sinograms.mat

description: Mats Persson and Jonas Adler<br>Current version: 2017-09-07<br><br>These are simulated basis materials sinograms used for the proceedings paper <br>M. Persson* and J. Adler*, “Spectral CT reconstruction with anti-correlated noise model and joint prior”, in Proceedings of The 14th International Meeting on Fully Three-Dimensional Image Reconstruction in Radiology and Nuclear Medicine, 2017, pp. 580–585.<br><br>This is meant as an example dataset for the reconstruction code belonging to this paper, which is available online at https://github.com/adler-j/spectral_ct_examples<br><br>Contents of the .mat file:<br>multiPhantom (600x600x2)<br>This contains the two basis images for the FORBILD head phantom: multiPhantom(:,:,1) is the soft tissue image and multiPhantom(:,:,2) is the bone image.<br><br>decomposedbasisProjectionsmm (853x360x2)<br>This matrix contains the basis sinograms (soft tissue and bone in that order) estimated from measured data using basis material decomposition. The values are given as projected path lengths in mm. The first index is the detector element number, the second index is view angle and the third image is the basis material.<br><br>CRLB (853x360x2x2)<br>This is the Cramer-Rao lower bound on basis image variance estimated from the noisy projection data for each projection line. The first two indices are detector element number and view angle. CRLB(i,j,:,:) is the lower bound (and in practice also an accurate estimate) of the covariance matrix of the estimated projected thicknesses of soft tissue and bone in ray (i,j). So CRLB(i,j,1,1) is the soft tissue image variance and CRLB(i,j,2,2) is the bone variance, CRLB(i,j,1,2)=CRLB(i,j,2,1) is the covariance. <br>The unit is mm^2.
DOI: 10.6084/m9.figshare.5387029
title: birthDefects.xlsx

description: Data for Figure 1. Average birth defects consistent with congenital Zika syndrome per month, with corresponding average daily temperatures and rainfall during presumed maternal month of infection.<br>
DOI: 10.6084/m9.figshare.5387038.v1
title: COI Disclosures

description: List of relationships between physicians who author gastroenterology clinical practice guidelines and the specific companies and products payments were associated with.
DOI: 10.6084/m9.figshare.5387008
title: F_H33NLALXX_L3_1.clean.fq.gz

description: fastq1
DOI: 10.6084/m9.figshare.5387029.v1
title: birthDefects.xlsx

description: Data for Figure 1. Average birth defects consistent with congenital Zika syndrome per month, with corresponding average daily temperatures and rainfall during presumed maternal month of infection.<br>
DOI: 10.6084/m9.figshare.5387008.v1
title: F_H33NLALXX_L3_1.clean.fq.gz

description: fastq1
DOI: 10.6084/m9.figshare.5387035.v1
title: OpenPayments Data

description: Survey of payments received by physicians who authors CPGs. Correlation with products and their relevance to guideline authorship.
DOI: 10.6084/m9.figshare.5386993
title: A Lattice-Based Smoother for Regions with Irregular Boundaries and Holes

description: We consider the problem of estimating a smooth function over a spatial region that is delineated by an irregular boundary and potentially contains holes within the boundary. Methods commonly used for spatial function estimation are well-known to suffer from bias along such boundaries. The estimator we propose is a kernel regression estimator where the kernel is an approximation to a two-dimensional diffusion process contained within the region of interest. The diffusion process is approximated by the distribution of length-<i>k</i> random walks originating from each observation location and constrained to stay within the domain boundaries. We propose using a cross-validation criterion to find the optimal walk length <i>k</i>, which controls the smoothness of the resulting estimate. Simulations show that the method outperforms the soap film smoother of Wood et al. (2008) in many realistic scenarios, when data are noisy and borders are highly irregular. We illustrate the practical use of the estimator using measurements of soil manganese concentration around Port Moller, Alaska.
DOI: 10.6084/m9.figshare.5386999
title: Degradation in Common Dynamic Environments

description: Degradation studies are often used to assess reliability of products subject to degradation-induced soft failures. Because of limited test resources, several test subjects may have to share a test rig and have their degradation measured by the same operator. The common environments experienced by subjects in the same group introduce significant interindividual correlations in their degradation, which is known as the block effect. In the present article, the Wiener process is used to model product degradation, and the group-specific random environments are captured using a stochastic time scale. Both semiparametric and parametric estimation procedures are developed for the model. Maximum likelihood estimations of the model parameters for both the semiparametric and parametric models are obtained with the help of the EM algorithm. Performance of the maximum likelihood estimators is validated through large sample asymptotics and small sample simulations. The proposed models are illustrated by an application to lumen maintenance data of blue light-emitting diodes. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5386996
title: Hierarchical Decompositions for the Computation of High-Dimensional Multivariate Normal Probabilities

description: We present a hierarchical decomposition scheme for computing the <i>n</i>-dimensional integral of multivariate normal probabilities that appear frequently in statistics. The scheme exploits the fact that the formally dense covariance matrix can be approximated by a matrix with a hierarchical low-rank structure. It allows the reduction of the computational complexity per Monte Carlo sample from O(n2) to O(mn+knlog(n/m)), where <i>k</i> is the numerical rank of off-diagonal matrix blocks and <i>m</i> is the size of small diagonal blocks in the matrix that are not well-approximated by low-rank factorizations and treated as dense submatrices. This hierarchical decomposition leads to substantial efficiencies in multivariate normal probability computations and allows integrations in thousands of dimensions to be practical on modern workstations. Supplementary material for this article is available online.
DOI: 10.6084/m9.figshare.5386999.v1
title: Degradation in Common Dynamic Environments

description: Degradation studies are often used to assess reliability of products subject to degradation-induced soft failures. Because of limited test resources, several test subjects may have to share a test rig and have their degradation measured by the same operator. The common environments experienced by subjects in the same group introduce significant interindividual correlations in their degradation, which is known as the block effect. In the present article, the Wiener process is used to model product degradation, and the group-specific random environments are captured using a stochastic time scale. Both semiparametric and parametric estimation procedures are developed for the model. Maximum likelihood estimations of the model parameters for both the semiparametric and parametric models are obtained with the help of the EM algorithm. Performance of the maximum likelihood estimators is validated through large sample asymptotics and small sample simulations. The proposed models are illustrated by an application to lumen maintenance data of blue light-emitting diodes. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5386993.v1
title: A Lattice-Based Smoother for Regions with Irregular Boundaries and Holes

description: We consider the problem of estimating a smooth function over a spatial region that is delineated by an irregular boundary and potentially contains holes within the boundary. Methods commonly used for spatial function estimation are well-known to suffer from bias along such boundaries. The estimator we propose is a kernel regression estimator where the kernel is an approximation to a two-dimensional diffusion process contained within the region of interest. The diffusion process is approximated by the distribution of length-<i>k</i> random walks originating from each observation location and constrained to stay within the domain boundaries. We propose using a cross-validation criterion to find the optimal walk length <i>k</i>, which controls the smoothness of the resulting estimate. Simulations show that the method outperforms the soap film smoother of Wood et al. (2008) in many realistic scenarios, when data are noisy and borders are highly irregular. We illustrate the practical use of the estimator using measurements of soil manganese concentration around Port Moller, Alaska.
DOI: 10.6084/m9.figshare.5386996.v1
title: Hierarchical Decompositions for the Computation of High-Dimensional Multivariate Normal Probabilities

description: We present a hierarchical decomposition scheme for computing the <i>n</i>-dimensional integral of multivariate normal probabilities that appear frequently in statistics. The scheme exploits the fact that the formally dense covariance matrix can be approximated by a matrix with a hierarchical low-rank structure. It allows the reduction of the computational complexity per Monte Carlo sample from O(n2) to O(mn+knlog(n/m)), where <i>k</i> is the numerical rank of off-diagonal matrix blocks and <i>m</i> is the size of small diagonal blocks in the matrix that are not well-approximated by low-rank factorizations and treated as dense submatrices. This hierarchical decomposition leads to substantial efficiencies in multivariate normal probability computations and allows integrations in thousands of dimensions to be practical on modern workstations. Supplementary material for this article is available online.
DOI: 10.6084/m9.figshare.5386966
title: Dataset for: A review of tensor-based methods and their application to hospital care data

description: In many situations, a researcher is interested in the analysis of the scores of a set of observation units on a set of variables. However, in medicine, it is very frequent that the information is replicated at different occasions. The occasions can be time-varying or refer to different conditions. In such cases the data can be stored in a three-way array or tensor. The Candecomp/Parafac and Tucker3 methods represent the most common methods for analyzing three-way tensors. In this work a review of these methods is provided and then this class of methods is applied to a three-way data set concerning hospital care data for a hospital in Rome (Italy) during fifteen years distinguished in three groups of consecutive years (1892-1896, 1940-1944, 1968-1972). The analysis reveals some peculiar aspects about the use of health services and its evolution along the time.
DOI: 10.6084/m9.figshare.5386966.v1
title: Dataset for: A review of tensor-based methods and their application to hospital care data

description: In many situations, a researcher is interested in the analysis of the scores of a set of observation units on a set of variables. However, in medicine, it is very frequent that the information is replicated at different occasions. The occasions can be time-varying or refer to different conditions. In such cases the data can be stored in a three-way array or tensor. The Candecomp/Parafac and Tucker3 methods represent the most common methods for analyzing three-way tensors. In this work a review of these methods is provided and then this class of methods is applied to a three-way data set concerning hospital care data for a hospital in Rome (Italy) during fifteen years distinguished in three groups of consecutive years (1892-1896, 1940-1944, 1968-1972). The analysis reveals some peculiar aspects about the use of health services and its evolution along the time.
DOI: 10.6084/m9.figshare.5386882
title: Data for "Warm northern river temperatures increase post-exercise fatigue in an Arctic migratory salmonid but not in a temperate relative"

description: Data for the article titled "Warm northern river temperatures increase post-exercise fatigue in an Arctic migratory salmonid but not in a temperate relative" in Functional Ecology, 2017<br> <br>
DOI: 10.6084/m9.figshare.5386846
title: Lack of knowledge in Arabian Gulf Mangroves

description: The number of papers published on mangroves in WOS and Scopus was 16697 and 16301, respectively. However, the refined search for “Arabian/ Persian Gulf mangroves” yielded 134 and 107 for WOS and Scopus, respectively, representing only 0.7 to 0.8% out of the total global publications on mangroves, see supplementary for information’s and search query.
DOI: 10.6084/m9.figshare.5386882.v1
title: Data for "Warm northern river temperatures increase post-exercise fatigue in an Arctic migratory salmonid but not in a temperate relative"

description: Data for the article titled "Warm northern river temperatures increase post-exercise fatigue in an Arctic migratory salmonid but not in a temperate relative" in Functional Ecology, 2017<br> <br>
DOI: 10.6084/m9.figshare.5386789
title: Second portion of depth stream data from human grasp dataset

description: File containing second portion of depth data acquired during grasping experiments
DOI: 10.6084/m9.figshare.5386789.v1
title: Second portion of depth stream data from human grasp dataset

description: File containing second portion of depth data acquired during grasping experiments
DOI: 10.6084/m9.figshare.5386678
title: Codon adaptation to tRNAs with Inosine modification at position 34 is widespread among Eukaryotes and present in two Bacterial phyla

description: The modification of adenosine to inosine at position 34 of tRNA anticodons has a profound impact upon codon-anticodon recognition. In bacteria, I34 is thought to exist only in tRNA<sup>Arg</sup>, while in eukaryotes the modification is present in eight different tRNAs. In eukaryotes, the widespread use of I34 strongly influenced the evolution of genomes in terms of tRNA gene abundance and codon usage. In humans, codon usage indicates that I34 modified tRNAs are preferred for the translation of highly repetitive coding sequences, suggesting that I34 is an important modification for the synthesis of proteins of highly skewed amino acid composition. Here we extend the analysis of distribution of codons that are recognized by I34 containing tRNAs to all phyla known to use this modification. We find that the preference for codons recognized by such tRNAs in genes with highly biased codon compositions is universal among eukaryotes, and we report that, unexpectedly, some bacterial phyla show a similar preference. We demonstrate that the genomes of these bacterial species contain previously undescribed tRNA genes that are potential substrates for deamination at position 34.
DOI: 10.6084/m9.figshare.5386666
title: Resin monoterpene defenses decline within three widespread species of pine (Pinus) along a 1530-m elevational gradient

description: This is a data set regarding defensive resin chemistry across a large climatic gradient in three species of pines: <i>Pinus contorta</i>, <i>Pinus ponderosa</i>, and <i>Pinus flexilis</i>. The data were collected in the Front Range of the Rocky Mountains, Boulder County, Colorado, USA. <br>The data are reported in:Ferrenberg et al. (in press) Resin monoterpene defenses decline within three widespread species of pine (Pinus) along a 1530-m elevational gradient. Ecosphere. <br>Resin chemistry is characterized by the presence/absence and concentrations of 10 individually identified monoterpenes and the pooled concentration of unidentified monoterpenes (Other Monoterpenes). <br>The total concentration, diversity (calculated as Shannon H') and dissimilarity (calculated as Bray-Curtis Dissimilarity) of monoterpenes for each individual tree are included. <br>Individual trees of each species are also characterized by their elevation of occurrence, age, diameter at breast height (DBH), radial growth of the last 5 years, and basal area increment represented by this growth.
DOI: 10.6084/m9.figshare.5386678.v2
title: Codon adaptation to tRNAs with Inosine modification at position 34 is widespread among Eukaryotes and present in two Bacterial phyla

description: The modification of adenosine to inosine at position 34 of tRNA anticodons has a profound impact upon codon-anticodon recognition. In bacteria, I34 is thought to exist only in tRNA<sup>Arg</sup>, while in eukaryotes the modification is present in eight different tRNAs. In eukaryotes, the widespread use of I34 strongly influenced the evolution of genomes in terms of tRNA gene abundance and codon usage. In humans, codon usage indicates that I34 modified tRNAs are preferred for the translation of highly repetitive coding sequences, suggesting that I34 is an important modification for the synthesis of proteins of highly skewed amino acid composition. Here we extend the analysis of distribution of codons that are recognized by I34 containing tRNAs to all phyla known to use this modification. We find that the preference for codons recognized by such tRNAs in genes with highly biased codon compositions is universal among eukaryotes, and we report that, unexpectedly, some bacterial phyla show a similar preference. We demonstrate that the genomes of these bacterial species contain previously undescribed tRNA genes that are potential substrates for deamination at position 34.
DOI: 10.6084/m9.figshare.5386666.v1
title: Resin monoterpene defenses decline within three widespread species of pine (Pinus) along a 1530-m elevational gradient

description: This is a data set regarding defensive resin chemistry across a large climatic gradient in three species of pines: <i>Pinus contorta</i>, <i>Pinus ponderosa</i>, and <i>Pinus flexilis</i>. The data were collected in the Front Range of the Rocky Mountains, Boulder County, Colorado, USA. <br>The data are reported in:Ferrenberg et al. (in press) Resin monoterpene defenses decline within three widespread species of pine (Pinus) along a 1530-m elevational gradient. Ecosphere. <br>Resin chemistry is characterized by the presence/absence and concentrations of 10 individually identified monoterpenes and the pooled concentration of unidentified monoterpenes (Other Monoterpenes). <br>The total concentration, diversity (calculated as Shannon H') and dissimilarity (calculated as Bray-Curtis Dissimilarity) of monoterpenes for each individual tree are included. <br>Individual trees of each species are also characterized by their elevation of occurrence, age, diameter at breast height (DBH), radial growth of the last 5 years, and basal area increment represented by this growth.
DOI: 10.15131/shef.data.5384275
title: Bookshelf data

description: This is the data and models associated with the paper "A comparison of validation techniques for a nonlinear bifurcating system"a guide to the data is contained in the word document "data guide"
DOI: 10.6084/m9.figshare.5384203
title: Acute myeloid leukemia disrupts endogenous myelo-erythropoiesis by compromising the adipocyte bone marrow niche

description: Additional experimental repeats related to Figure 5g. <br>Representative images corresponding to Supplementary Fig. 3c.<br>Representative images corresponding to Supplementary Fig. 3e.<br><br>
DOI: 10.6084/m9.figshare.5384203.v1
title: Acute myeloid leukemia disrupts endogenous myelo-erythropoiesis by compromising the adipocyte bone marrow niche

description: Additional experimental repeats related to Figure 5g. <br>Representative images corresponding to Supplementary Fig. 3c.<br>Representative images corresponding to Supplementary Fig. 3e.<br><br>
DOI: 10.6084/m9.figshare.5384089
title: Dataset 1: Spiroplasma prevalence in Anopheles gambiae s.l. field populations

description: The prevalence of Spiroplasma insolitum in wild caught Anopheles gambiae sl mosquitos from several sites in Kenya.
DOI: 10.6084/m9.figshare.5384101
title: Dataset 2: Spiroplasma transmission and effects on survival and fecundity

description: Samples used to determine the effects of Spiroplasma on the fecundity and egg to adult survival of Anopheles mosquitoes.
DOI: 10.6084/m9.figshare.5384101.v1
title: Dataset2 Fecundity and Survival

description: Samples used to determine the effects of Spiroplasma on the fecundity and egg to adult survival of Anopheles mosquitoes.
DOI: 10.6084/m9.figshare.5384089.v1
title: Dataset1Prevalence.xlsx

description: The prevalence of Spiroplasma insolitum in wild caught Anopheles gambiae sl mosquitos from several sites in Kenya.
DOI: 10.6084/m9.figshare.5384101.v3
title: Dataset 2: Spiroplasma transmission and effects on survival and fecundity

description: Samples used to determine the effects of Spiroplasma on the fecundity and egg to adult survival of Anopheles mosquitoes.
DOI: 10.6084/m9.figshare.5384101.v2
title: Dataset2 Fecundity and Survival

description: Samples used to determine the effects of Spiroplasma on the fecundity and egg to adult survival of Anopheles mosquitoes.
DOI: 10.6084/m9.figshare.5383990
title: When and where do elections matter? A global test of the democratization by elections hypothesis, 1900–2010

description: Successive multiparty elections in sub-Saharan Africa are associated with incremental democratization. Yet tests in other regions are less than encouraging. Non-significant findings on Latin America and post-communist Eurasia, as well as conceptual criticism regarding the theory’s application in the contemporary Middle East, suggest that this may be a case of African exceptionalism. This article moves these debates forward by posing a comprehensive, global set of tests on the democratizing effect of elections. We seek to establish the scope conditions of the argument geographically, temporally, and substantively. Although we find a correlation between reiterated multiparty elections and improvements in the liberal-democratic components of electoral regimes globally since 1900, the relationship is only substantial in the period since the onset of the third wave of democracy. Experiences with iterated multiparty elections have substantive importance for democratization in sub-Saharan Africa, the post-communist region, Latin America and the Caribbean, and Asia. For the Middle East and North Africa, the relationship is weaker and less robust. Finally, the results suggest that reiterated sequences of multiparty elections are associated with improvements to liberal and deliberative components of democracy more so than egalitarian components.
DOI: 10.6084/m9.figshare.5383969
title: Dataset 1. Information on the 276 SNPs genotyped in 177 genes in P. falciparum parasite populations from The Gambia, Kilifi and Rachuonyo South

description: <b>Dataset 1:</b> <b>Information on the 276 SNPs genotyped in 177 genes in <i>P. falciparum </i>parasite populations from The Gambia, Kilifi and Rachuonyo South. </b>The columns contain the following information: study_location, site of sample collection; sample_id, unique sample identifier; gene_symbol, gene name (if available); chr_valid, chromosome; coord_valid= base position of SNP on chromosome; sequence_code, SNP name; assay_code, name of assay; rsnumber, unique SNP identifier in dbSNP; reference_allele, 3D7 reference allele, alternative_allele, alternative allele; single letter code, IUPAC code for SNPs; result, genotype call after processing; allele1, IUPAC code for allele 1; allele2, IUPAC code for allele 2; allele_ratio1, proportion of allele 1; allele_ratio2, proportion of allele 2; pass_fail, coding of SNP based on availability of valid genotype (pass) or lack of a valid genotype (fail). Geospatial data for homestead location is considered sensitive data and therefore cannot be made open access. However, it can be accessed through a request to our data governance committee, using the email address mmunene@uat/newsite.