cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6534416.v1
title: A Spatial Markov Model for Climate Extremes

description: Spatial climate data are often presented as summaries of areal regions such as grid cells, either because they are the output of numerical climate models or to facilitate comparison with numerical climate model output. Extreme value analysis can benefit greatly from spatial methods that borrow information across regions. For Gaussian outcomes, a host of methods that respect the areal nature of the data are available, including conditional and simultaneous autoregressive models. However, to our knowledge, there is no such method in the spatial extreme value analysis literature. In this article, we propose a new method for areal extremes that accounts for spatial dependence using latent clustering of neighboring regions. We show that the proposed model has desirable asymptotic dependence properties and leads to relatively simple computation. Applying the proposed method to North American climate data reveals several local and continental-scale changes in the distribution of precipitation and temperature extremes over time. Supplementary material for this article is available online.
DOI: 10.6084/m9.figshare.6534386
title: Arboles_grandes_y_viejos_EAFIT.xlsx

description: Esta base de datos corresponde a los árboles grandes y viejos que cuentan con cavidades arbóreas en la universidad EAFIT. Cada individuo fue identificado al nivel de especie junto con el reporte de cada tipo y cantidad de cavidades, se registra también su ubicación geográfica, tamaño de circunferencia (criterio básico para definir un árbol como grande y viejo), estado del individuo y observaciones adicionales.<br>This data corresponds to big old trees that have tree hollows from EAFIT University. Each individual was identified to the species level, type and quantity of hollows was recorded as well as location, circunference (basic criteria for defining a tree as big and old), status of the indiviual and aditional observations.
DOI: 10.6084/m9.figshare.6534386.v1
title: Arboles_grandes_y_viejos_EAFIT.xlsx

description: Esta base de datos corresponde a los árboles grandes y viejos que cuentan con cavidades arbóreas en la universidad EAFIT. Cada individuo fue identificado al nivel de especie junto con el reporte de cada tipo y cantidad de cavidades, se registra también su ubicación geográfica, tamaño de circunferencia (criterio básico para definir un árbol como grande y viejo), estado del individuo y observaciones adicionales.<br>This data corresponds to big old trees that have tree hollows from EAFIT University. Each individual was identified to the species level, type and quantity of hollows was recorded as well as location, circunference (basic criteria for defining a tree as big and old), status of the indiviual and aditional observations.
DOI: 10.6084/m9.figshare.6534323
title: Survey A and B Questions

description: All of the questions for the two-part survey that were answered by UCLA undergraduates via Google Forms.
DOI: 10.6084/m9.figshare.6534323.v1
title: Survey A and B Questions

description: All of the questions for the two-part survey that were answered by UCLA undergraduates via Google Forms.
DOI: 10.6084/m9.figshare.6534146
title: Data for pyjac-V2 paper

description: The data used in the creation of the the paper: "Using SIMD and SIMT vectorization to evaluate sparse chemical kinetic Jacobian matrices and thermochemical source terms" by Nicholas Curtis (UConn), Kyle Niemeyer (OSU) and Chih-Jen Sung (UConn).
DOI: 10.6084/m9.figshare.6534146.v2
title: Data for pyjac-V2 paper

description: The data used in the creation of the the paper: "Using SIMD and SIMT vectorization to evaluate sparse chemical kinetic Jacobian matrices and thermochemical source terms" by Nicholas Curtis (UConn), Kyle Niemeyer (OSU) and Chih-Jen Sung (UConn).
DOI: 10.6084/m9.figshare.6534146.v1
title: Data for pyjac-V2 paper

description: The data used in the creation of the the paper: "Using SIMD and SIMT vectorization to evaluate sparse chemical kinetic Jacobian matrices and thermochemical source terms" by Nicholas Curtis (UConn), Kyle Niemeyer (OSU) and Chih-Jen Sung (UConn).
DOI: 10.6084/m9.figshare.6534089
title: Efficient Sampling for Gaussian Linear Regression With Arbitrary Priors

description: This article develops a slice sampler for Bayesian linear regression models with arbitrary priors. The new sampler has two advantages over current approaches. One, it is faster than many custom implementations that rely on auxiliary latent variables, if the number of regressors is large. Two, it can be used with any prior with a density function that can be evaluated up to a normalizing constant, making it ideal for investigating the properties of new shrinkage priors without having to develop custom sampling algorithms. The new sampler takes advantage of the special structure of the linear regression likelihood, allowing it to produce better effective sample size per second than common alternative approaches.
DOI: 10.6084/m9.figshare.6534089.v1
title: Efficient sampling for Gaussian linear regression with arbitrary priors

description: This paper develops a slice sampler for Bayesian linear regression models with arbitrary priors. The new sampler has two advantages over current approaches. One, it is faster than many custom implementations that rely on auxiliary latent variables, if the number of regressors is large. Two, it can be used with any prior with a density function that can be evaluated up to a normalizing constant, making it ideal for investigating the properties of new shrinkage priors without having to develop custom sampling algorithms. The new sampler takes advantage of the special structure of the linear regression likelihood, allowing it to produce better effective sample size per second than common alternative approaches.
DOI: 10.6084/m9.figshare.6534089.v3
title: Efficient Sampling for Gaussian Linear Regression With Arbitrary Priors

description: This article develops a slice sampler for Bayesian linear regression models with arbitrary priors. The new sampler has two advantages over current approaches. One, it is faster than many custom implementations that rely on auxiliary latent variables, if the number of regressors is large. Two, it can be used with any prior with a density function that can be evaluated up to a normalizing constant, making it ideal for investigating the properties of new shrinkage priors without having to develop custom sampling algorithms. The new sampler takes advantage of the special structure of the linear regression likelihood, allowing it to produce better effective sample size per second than common alternative approaches.
DOI: 10.6084/m9.figshare.6531311
title: Appendix 4-figure 2: DNA and tRNA methyltransferase gene phylogeny

description: Levels and patterns of mCG in P. pyralis are corroborated by the presence of de novo and maintenance DNMTs (DNMT3 and DNMT1, respectively). Notably, P. pyralis possesses two copies of DNMT1, and 3 copies of DNMT3, in contrast to a single copy of DNMT1 and DNMT3 in the firefly Aquatica lateralis. The evolutionary history was inferred by using the Maximum Likelihood method with the LG (+G = 5)[187]. Evolutionary analyses were conducted in MEGA7 [188]. Size of circles at nodes corresponds to bootstrap support (100 bootstrap replicates). Branch lengths are in amino acid substitutions per site. T. castaneum= Tribolium castaneum, D. melanogaster= Drosophila melanogaster, N. vespilloides= Nicrophorus vespilloides.
DOI: 10.6084/m9.figshare.6531308
title: S1_Database

description: Despite the flourishing research on the relationships between affect and language, the characteristics of pain-related words, a specific type of negative words, have never been systematically investigated from a psycholinguistic and emotional perspective, despite their psychological relevance. This study offers psycholinguistic, affective, and pain-related norms for words expressing physical and social pain. This may provide a useful tool for the selection of stimulus materials in future studies on negative emotions and/or pain. We explored the relationships between psycholinguistic, affective, and pain-related properties of 512 Italian words (nouns, adjectives, and verbs) conveying physical and social pain by asking 1020 Italian participants to provide ratings of Familiarity, Age of Acquisition, Imageability, Concreteness, Context Availability, Valence, Arousal, Pain-Relatedness, Intensity, and Unpleasantness. We also collected data concerning Length, Written Frequency (Subtlex-IT), N-Size, Orthographic Levenshtein Distance 20, Neighbor Mean Frequency, and Neighbor Maximum Frequency of each word. Interestingly, the words expressing social pain were rated as more negative, arousing, pain-related, and conveying more intense and unpleasant experiences than the words conveying physical pain.
DOI: 10.6084/m9.figshare.6531293
title: Single-cell and neuronal networks alterations in an in vitro model of Fragile X syndrome

description: Preprocessed, multi-site extracellular electrical recordings from neuronal cell cultures developing <i>ex vivo</i> on substrate-integrated microelectrode arrays (MEAs).<br>Intracellular patch-clamp recordings from single cultured neurons.
DOI: 10.6084/m9.figshare.6531113
title: SIM-16-0472-Cure-Rate-Historical

description: All programming files associated with the paper titled "Bayesian Design of a Survival Trial with a Cured Fraction using Historical Data"
DOI: 10.6084/m9.figshare.6531113.v1
title: SIM-16-0472-Cure-Rate-Historical

description: All programming files associated with the paper titled "Bayesian Design of a Survival Trial with a Cured Fraction using Historical Data"
DOI: 10.6084/m9.figshare.6530951
title: Supplementary Material for: The University of California, San Francisco Documentation System for Retinoblastoma: Preparing to Improve Staging Methods for This Disease

description: <b><i>Background/Aims:</i></b> Current retinoblastoma staging systems do not adequately describe the disease, especially in eyes with multiple tumors. The aims of this study were to develop methods for documenting individual tumors and to score disease burden over time. <b><i>Methods:</i></b> A coding system was devised to describe each tumor according to affected eye, meridian, anteroposterior location, activity, growth pattern, type of seed, and treatment. A scoring system for quantifying disease burden was developed, taking account of tumor number, size, spread, and secondary effects on the eye. <b><i>Results:</i></b> Our coding system allowed contemporaneous tumor documentation, producing datasets that enabled generation of fundus diagrams, Kaplan-Meier curves, and tables summarizing disease progression in individual tumors and eyes. Our data showed disparities between ocular and tumor documentation, e.g., indicating earlier tumor development in the left eye but younger age at presentation if disease was worse in the right eye. Actuarial rates of local treatment failure were lower when individual tumors were analyzed than when data were reported in terms of whole eyes. <b><i>Conclusion:</i></b> Our methods for documenting individual retinoblastomas have facilitated the review of patients’ progress in our routine practice and may provide data that could be used to refine retinoblastoma classifications in the future.
DOI: 10.6084/m9.figshare.6530948
title: Supplementary Material for: Genetic Diversity of <b><i>Mycobacterium tuberculosis</i></b> Isolates in the Metropolitan Area of Rome

description: <b><i>Background:</i></b> The presence in a geographic area of <i>Mycobacterium tuberculosis</i> <i>(Mtb)</i> strains belonging to different phylogeographic lineages and showing different drug susceptibility patterns may suggest recent transmission, with implications in terms of patient clinical management and disease control. The aim of this study was to carry out a preliminary epidemiological investigation of tuberculosis (TB) cases in Rome. <b><i>Methods:</i></b> A total of 232 <i>Mtb</i> isolates, collected from new or previously treated patients, admitted between 2008 and 2014 at 2 hospital settings in Rome with a diagnosis of TB, were analyzed by spoligotyping and analyzing 24 variable-number tandem repeats (VNTR) mycobacterial interspersed repetitive-unit (MIRU) loci. The SITVIT2 database and the MIRU-VNTRplus web applications were used to identify the strain genotypes and to generate phylogenetic trees. <b><i>Results:</i></b> Based on the position on the phylogenetic tree, 97.4% of the strains were associated with 1 of the 7 main lineages. The Euro-American lineage was the most commonly represented (81.9%) within both Italian and foreign-born populations, although all main lineages were present. The highest frequency of drug-resistant strains was found among the East-Asian lineage (Beijing genotype) isolated from foreign-born patients. <b><i>Conclusions:</i></b> Dynamics of TB transmission in Rome indicate recent spread of <i>Mtb</i> strains belonging to phylogeographic lineages and clades usually found in countries and geographic areas with a high incidence of TB, similarly to what is observed in most metropolitan areas in Western Europe. Knowledge from molecular and classical epidemiology provides an important tool for disease control.
DOI: 10.6084/m9.figshare.6530861
title: Supplementary Material for: Surrogacy of Time to Progression for Overall Survival in Advanced Hepatocellular Carcinoma Treated with Systemic Therapy: A Systematic Review and Meta-Analysis of Randomized Controlled Trials

description: Time to progression (TTP) is widely used as the endpoint in early-phase trials of advanced hepatocellular carcinoma (HCC). However, the relevance of using TTP as a surrogate marker for overall survival (OS) in pivotal trials remains uncertain. The PubMed database and ASCO Meeting Library were searched for reports of randomized controlled trials that investigated patients with advanced HCC, included data for both OS and TTP, and were launched between 2009 and 2016. The correlation between hazard ratios (HRs) for TTP and OS was determined using weighted linear regression. Correlations between median OS and TTP, and between median OS and postprogression survival (PPS), defined as the period obtained by subtracting the median TTP from the median OS, were also evaluated. The database search yielded 24 trials with 50 arms. Overall, TTP HR correlated with OS HR (<i>R</i> = 0.73); however, the coefficient in the regression equation was 0.48. The correlation between median OS and median TTP was not so strong (<i>R</i> = 0.50), whereas the correlation between median OS and median PPS was strong (<i>R</i> = 0.78). In advanced HCC, the OS HR can be predicted from the TTP HR, which is useful when considering whether to proceed to a pivotal trial based on the results of early-phase trials. TTP may be a better endpoint than OS for evaluating a novel agent in a pivotal trial, because an improvement in antitumor effect cannot fully reflect an improvement in OS due to the strong impact of PPS on OS.
DOI: 10.6084/m9.figshare.6530861.v1
title: Supplementary Material for: Surrogacy of Time to Progression for Overall Survival in Advanced Hepatocellular Carcinoma Treated with Systemic Therapy: A Systematic Review and Meta-Analysis of Randomized Controlled Trials

description: Time to progression (TTP) is widely used as the endpoint in early-phase trials of advanced hepatocellular carcinoma (HCC). However, the relevance of using TTP as a surrogate marker for overall survival (OS) in pivotal trials remains uncertain. The PubMed database and ASCO Meeting Library were searched for reports of randomized controlled trials that investigated patients with advanced HCC, included data for both OS and TTP, and were launched between 2009 and 2016. The correlation between hazard ratios (HRs) for TTP and OS was determined using weighted linear regression. Correlations between median OS and TTP, and between median OS and postprogression survival (PPS), defined as the period obtained by subtracting the median TTP from the median OS, were also evaluated. The database search yielded 24 trials with 50 arms. Overall, TTP HR correlated with OS HR (<i>R</i> = 0.73); however, the coefficient in the regression equation was 0.48. The correlation between median OS and median TTP was not so strong (<i>R</i> = 0.50), whereas the correlation between median OS and median PPS was strong (<i>R</i> = 0.78). In advanced HCC, the OS HR can be predicted from the TTP HR, which is useful when considering whether to proceed to a pivotal trial based on the results of early-phase trials. TTP may be a better endpoint than OS for evaluating a novel agent in a pivotal trial, because an improvement in antitumor effect cannot fully reflect an improvement in OS due to the strong impact of PPS on OS.
DOI: 10.6084/m9.figshare.6530825
title: Hierarchical Representations of Freebase Topics

description: The dataset contains more than 21M hierarchical relationships about ≈10M topics extracted from Freebase knowledgebase. The topics span the various categories of Freebase including Science & Technology, Arts & Entertainment, Sports, Society, Products & Services, Transportation, Time & Space, Special Interests, and Commons. The relationships describe the hierarchies of topics in terms of Types, Domains, and Categories. For example, ‘Albert Einstein’ can be found as a topic that is a sub-class of ‘Person’, belonging to the ‘People’ domain and ‘Society’ category. While another entity named as ‘Albert Einstein’ can also be found as a sub-class of ‘Book’, belonging to the ‘Books’ domain and ‘Arts & Entertainment’ category. The dataset is published in JSON and CSV formats, sample files are provided to help explore how the dataset is structured.<br> The dataset is believed to be useful for studying the inter-related connections among topics in different domains of knowledge. The first author may be contacted at (mahmoud.elbattah@nuigalway.ie) for more information. The following paper may kindly be cited in case of using the dataset. Mahmoud Elbattah, Mohamed Roushdy, Mostafa Aref, Abdel-Badeeh M. Salem. “Large-Scale Entity Clustering Using Graph-Based Structural Similarity within Knowledge Graphs”, Big Data Analytics: Tools, Technology for Effective Planning, CRC Press. https://www.researchgate.net/publication/321716589_Large-Scale_Entity_Clustering_Based_on_Structural_Similarity_within_Knowledge_Graphs
DOI: 10.6084/m9.figshare.6530825.v1
title: Hierarchical Representations of Freebase Topics

description: The dataset contains more than 21M hierarchical relationships about ≈10M topics extracted from Freebase knowledgebase. The topics span the various categories of Freebase including Science & Technology, Arts & Entertainment, Sports, Society, Products & Services, Transportation, Time & Space, Special Interests, and Commons. The relationships describe the hierarchies of topics in terms of Types, Domains, and Categories. For example, ‘Albert Einstein’ can be found as a topic that is a sub-class of ‘Person’, belonging to the ‘People’ domain and ‘Society’ category. While another entity named as ‘Albert Einstein’ can also be found as a sub-class of ‘Book’, belonging to the ‘Books’ domain and ‘Arts & Entertainment’ category. The dataset is published in JSON and CSV formats, sample files are provided to help explore how the dataset is structured.<br> The dataset is believed to be useful for studying the inter-related connections among topics in different domains of knowledge. The first author may be contacted at (mahmoud.elbattah@nuigalway.ie) for more information. The following paper may kindly be cited in case of using the dataset. Mahmoud Elbattah, Mohamed Roushdy, Mostafa Aref, Abdel-Badeeh M. Salem. “Large-Scale Entity Clustering Using Graph-Based Structural Similarity within Knowledge Graphs”, Big Data Analytics: Tools, Technology for Effective Planning, CRC Press. https://www.researchgate.net/publication/321716589_Large-Scale_Entity_Clustering_Based_on_Structural_Similarity_within_Knowledge_Graphs
DOI: 10.6084/m9.figshare.6530825.v3
title: Hierarchical Representations of Freebase Topics

description: The dataset contains more than 21M hierarchical relationships about ≈10M topics extracted from Freebase knowledgebase. The topics span the various categories of Freebase including Science & Technology, Arts & Entertainment, Sports, Society, Products & Services, Transportation, Time & Space, Special Interests, and Commons. The relationships describe the hierarchies of topics in terms of Types, Domains, and Categories. For example, ‘Albert Einstein’ can be found as a topic that is a sub-class of ‘Person’, belonging to the ‘People’ domain and ‘Society’ category. While another entity named as ‘Albert Einstein’ can also be found as a sub-class of ‘Book’, belonging to the ‘Books’ domain and ‘Arts & Entertainment’ category. The dataset is published in JSON and CSV formats, sample files are provided to help explore how the dataset is structured.<br> The dataset is believed to be useful for studying the inter-related connections among topics in different domains of knowledge. The first author may be contacted at (mahmoud.elbattah@nuigalway.ie) for more information. The following paper may kindly be cited in case of using the dataset. Mahmoud Elbattah, Mohamed Roushdy, Mostafa Aref, Abdel-Badeeh M. Salem. “Large-Scale Entity Clustering Using Graph-Based Structural Similarity within Knowledge Graphs”, Big Data Analytics: Tools, Technology for Effective Planning, CRC Press. https://www.researchgate.net/publication/321716589_Large-Scale_Entity_Clustering_Based_on_Structural_Similarity_within_Knowledge_Graphs
DOI: 10.6084/m9.figshare.6530825.v2
title: Hierarchical Representations of Freebase Topics

description: The dataset contains more than 21M hierarchical relationships about ≈10M topics extracted from Freebase knowledgebase. The topics span the various categories of Freebase including Science & Technology, Arts & Entertainment, Sports, Society, Products & Services, Transportation, Time & Space, Special Interests, and Commons. The relationships describe the hierarchies of topics in terms of Types, Domains, and Categories. For example, ‘Albert Einstein’ can be found as a topic that is a sub-class of ‘Person’, belonging to the ‘People’ domain and ‘Society’ category. While another entity named as ‘Albert Einstein’ can also be found as a sub-class of ‘Book’, belonging to the ‘Books’ domain and ‘Arts & Entertainment’ category. The dataset is published in JSON and CSV formats, sample files are provided to help explore how the dataset is structured.<br> The dataset is believed to be useful for studying the inter-related connections among topics in different domains of knowledge. The first author may be contacted at (mahmoud.elbattah@nuigalway.ie) for more information. The following paper may kindly be cited in case of using the dataset. Mahmoud Elbattah, Mohamed Roushdy, Mostafa Aref, Abdel-Badeeh M. Salem. “Large-Scale Entity Clustering Using Graph-Based Structural Similarity within Knowledge Graphs”, Big Data Analytics: Tools, Technology for Effective Planning, CRC Press. https://www.researchgate.net/publication/321716589_Large-Scale_Entity_Clustering_Based_on_Structural_Similarity_within_Knowledge_Graphs