cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5813787
title: Parameter Estimation and Variable Selection for Big Systems of Linear Ordinary Differential Equations: A Matrix-Based Approach

description: Ordinary differential equations (ODEs) are widely used to model the dynamic behavior of a complex system. Parameter estimation and variable selection for a “Big System” with linear ODEs are very challenging due to the need of nonlinear optimization in an ultra-high dimensional parameter space. In this article, we develop a parameter estimation and variable selection method based on the ideas of similarity transformation and separable least squares (SLS). Simulation studies demonstrate that the proposed matrix-based SLS method could be used to estimate the coefficient matrix more accurately and perform variable selection for a linear ODE system with thousands of dimensions and millions of parameters much better than the direct least squares method and the vector-based two-stage method that are currently available. We applied this new method to two real datasets—a yeast cell cycle gene expression dataset with 30 dimensions and 930 unknown parameters and the Standard & Poor 1500 index stock price data with 1250 dimensions and 1,563,750 unknown parameters—to illustrate the utility and numerical performance of the proposed parameter estimation and variable selection method for big systems in practice. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.6534170
title: Priors for the Long Run

description: We propose a class of prior distributions that discipline the long-run behavior of vector autoregressions (VARs). These priors can be naturally elicited using economic theory, which provides guidance on the joint dynamics of macroeconomic time series in the long run. Our priors for the long run are conjugate, and can thus be easily implemented using dummy observations and combined with other popular priors. In VARs with standard macroeconomic variables, a prior based on the long-run predictions of a wide class of theoretical models yields substantial improvements in the forecasting performance. 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.6534170.v1
title: Priors for the Long Run

description: We propose a class of prior distributions that discipline the long-run behavior of Vector Autoregressions (VARs). These priors can be naturally elicited using economic theory, which provides guidance on the joint dynamics of macroeconomic time series in the long run. Our priors for the long run are conjugate, and can thus be easily implemented using dummy observations and combined with other popular priors. In VARs with standard macroeconomic variables, a prior based on the long-run predictions of a wide class of theoretical models yields substantial improvements in the forecasting performance.
DOI: 10.6084/m9.figshare.6534170.v2
title: Priors for the Long Run

description: We propose a class of prior distributions that discipline the long-run behavior of vector autoregressions (VARs). These priors can be naturally elicited using economic theory, which provides guidance on the joint dynamics of macroeconomic time series in the long run. Our priors for the long run are conjugate, and can thus be easily implemented using dummy observations and combined with other popular priors. In VARs with standard macroeconomic variables, a prior based on the long-run predictions of a wide class of theoretical models yields substantial improvements in the forecasting performance. 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.6949499.v3
title: Fully Bayesian Analysis of RNA-seq Counts for the Detection of Gene Expression Heterosis

description: Heterosis, or hybrid vigor, is the enhancement of the phenotype of hybrid progeny relative to their inbred parents. Heterosis is extensively used in agriculture, and the underlying mechanisms are unclear. To investigate the molecular basis of phenotypic heterosis, researchers search tens of thousands of genes for heterosis with respect to expression in the transcriptome. Difficulty arises in the assessment of heterosis due to composite null hypotheses and nonuniform distributions for <i>p</i>-values under these null hypotheses. Thus, we develop a general hierarchical model for count data and a fully Bayesian analysis in which an efficient parallelized Markov chain Monte Carlo algorithm ameliorates the computational burden. We use our method to detect gene expression heterosis in a two-hybrid plant-breeding scenario, both in a real RNA-seq maize dataset and in simulation studies. In the simulation studies, we show our method has well-calibrated posterior probabilities and credible intervals when the model assumed in analysis matches the model used to simulate the data. Although model misspecification can adversely affect calibration, the methodology is still able to accurately rank genes. Finally, we show that hyperparameter posteriors are extremely narrow and an empirical Bayes (eBayes) approach based on posterior means from the fully Bayesian analysis provides virtually equivalent posterior probabilities, credible intervals, and gene rankings relative to the fully Bayesian solution. This evidence of equivalence provides support for the use of eBayes procedures in RNA-seq data analysis if accurate hyperparameter estimates can be obtained. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.6949499.v2
title: Fully Bayesian Analysis of RNA-seq Counts for the Detection of Gene Expression Heterosis

description: Heterosis, or hybrid vigor, is the enhancement of the phenotype of hybrid progeny relative to their inbred parents. Heterosis is extensively used in agriculture, and the underlying mechanisms are unclear. To investigate the molecular basis of phenotypic heterosis, researchers search tens of thousands of genes for heterosis with respect to expression in the transcriptome. Difficulty arises in the assessment of heterosis due to composite null hypotheses and nonuniform distributions for <i>p</i>-values under these null hypotheses. Thus, we develop a general hierarchical model for count data and a fully Bayesian analysis in which an efficient parallelized Markov chain Monte Carlo algorithm ameliorates the computational burden. We use our method to detect gene expression heterosis in a two-hybrid plant-breeding scenario, both in a real RNA-seq maize dataset and in simulation studies. In the simulation studies, we show our method has well-calibrated posterior probabilities and credible intervals when the model assumed in analysis matches the model used to simulate the data. Although model misspecification can adversely affect calibration, the methodology is still able to accurately rank genes. Finally, we show that hyperparameter posteriors are extremely narrow and an empirical Bayes (eBayes) approach based on posterior means from the fully Bayesian analysis provides virtually equivalent posterior probabilities, credible intervals, and gene rankings relative to the fully Bayesian solution. This evidence of equivalence provides support for the use of eBayes procedures in RNA-seq data analysis if accurate hyperparameter estimates can be obtained. Supplementary materials for this article are available online.
DOI: 10.15468/dl.pvsmz4
title: Occurrence Download

description: A dataset containing 148 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "MULTIPOLYGON (((146.22701 -36.472308, 146.229255 -36.472308, 146.229255 -36.467816, 146.22701 -36.467816, 146.22701 -36.472308)), ((146.22701 -36.472308, 146.222518 -36.472308, 146.222518 -36.483537, 146.22701 -36.483537, 146.22701 -36.472308)))"
 ]
}

 The dataset includes 148 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0054714-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bxbtxz
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((148.818662 -36.472308, 148.818662 -36.476799, 148.820907 -36.476799, 148.820907 -36.472308, 148.818662 -36.472308))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0054716-240626123714530/datasets/export for details.
DOI: 10.6084/m9.figshare.25763916
title: metabolome_C-SCOPE.xlsx

description: Capillary electrophoresis combined with time-of-flight mass spectrometry (CE-TOFMS) and capillary electrophoresis combined with triple quadrupole mass spectrometry (QqQMS) measurements in cation and anion mode were used to generate metabolomics data, which were analyzed using MetaboAnalyst. Of the 116 metabolites identified.
DOI: 10.3886/e208373
title: Yemeni Synthetic Society

description: A synthetic society that replicates the characteristics of the local society can provide a valuable testing ground for the purpose of building an agent-based simulation model aimed at assessing and extrapolating the impact of Qat consumption of Yemeni society regarding to health, economy, and social aspects, as well as predicting the effects of local public policies on Qat consumption in Yemen. While synthetic society datasets are available for several countries, there is currently no synthetic society data for Yemen. This study proposes the creation of a synthetic society dataset for individuals at a detailed level in Yemen. This synthetic society was generated using a genetic algorithm based on multiple census data, several general statistical studies, and surveys on households and Qat consumption in Yemen, which include detailed or aggregated socio-demographic attributes such as age, sex, income, education level, employment status, stage of consumption, etc. We designed an efficient fitness function computation based on a hybrid distance, enabling us to incorporate over one hundred statistics and generate an artificial society comprising more than one hundred thousand artificial agents with an SRMSE of 0.231 compared to the statistics of the real society.<br><br><br>
description: People of yemen<br><br>.
description: other;
DOI: 10.3886/e208373v1
title: Yemeni Synthetic Society

description: A synthetic society that replicates the characteristics of the local society can provide a valuable testing ground for the purpose of building an agent-based simulation model aimed at assessing and extrapolating the impact of Qat consumption of Yemeni society regarding to health, economy, and social aspects, as well as predicting the effects of local public policies on Qat consumption in Yemen. While synthetic society datasets are available for several countries, there is currently no synthetic society data for Yemen. This study proposes the creation of a synthetic society dataset for individuals at a detailed level in Yemen. This synthetic society was generated using a genetic algorithm based on multiple census data, several general statistical studies, and surveys on households and Qat consumption in Yemen, which include detailed or aggregated socio-demographic attributes such as age, sex, income, education level, employment status, stage of consumption, etc. We designed an efficient fitness function computation based on a hybrid distance, enabling us to incorporate over one hundred statistics and generate an artificial society comprising more than one hundred thousand artificial agents with an SRMSE of 0.231 compared to the statistics of the real society.<br><br><br>
description: People of yemen<br><br>.
description: other;
DOI: 10.15468/dl.szm48x
title: Occurrence Download

description: A dataset containing 2430786 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Machine Observation, Human Observation, Material sample, Material citation, Specimen, Fossil, Living Specimen, Occurrence evidence, Observation)",
 "Country is India",
 "Geometry POLYGON((78.40607 36.22586,73.1769 35.28624,73.50372 30.87413,77.01707 30.22048,80.2853 27.85101,81.63345 29.40342,81.22492 30.62901,79.38654 31.97716,79.71336 33.16189,78.40607 36.22586))",
 "HasCoordinate is true",
 "Issue is one of (Coordinate rounded, Geodetic datum assumed WGS84, Coordinate uncertainty meters invalid, Country coordinate mismatch, Continent derived from coordinates, Country derived from coordinates, Recorded date mismatch, Recorded date invalid, The taxon concept ID was not used in backbone matching, The taxon ID was not used in backbone matching, Taxon match fuzzy, Taxon match higher rank, Institution match none, Institution collection mismatch, Collection match fuzzy, Institution match fuzzy, Collection match none, Occurrence status inferred from individual count, Multimedia URI invalid, Type status invalid, Identified date invalid, Modified date invalid)",
 "OccurrenceStatus is Present",
 "TaxonKey is Passeriformes"
 ]
}

 The dataset includes 2430786 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0054657-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.25763283
title: metabolome_LC-BasicScan.xlsx

description: Liquid chromatography combined with combined with time-of-flight mass spectrometry (LC-TOFMS) measurements were used to generate metabolomics data, which were analyzed using MetaboAnalyst. Of the 115 metabolites identified.
DOI: 10.15468/dl.e487c4
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((148.722092 -36.476799, 148.722092 -36.483537, 148.726584 -36.483537, 148.726584 -36.476799, 148.722092 -36.476799))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0054718-240626123714530/datasets/export for details.
DOI: 10.15468/dl.kymtha
title: Occurrence Download

description: A dataset containing 1134 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Micrurus mipartitus (Duméril, Bibron & Duméril, 1854)"
 ]
}

 The dataset includes 1134 records from 94 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0054717-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/nyr6j9p7mv.1
title: Compositional Data Analysis: A Guide to Geochemistry and Geology

description: The world of geochemistry and geology is complex, particularly for analyzing compositional data. In this blog, we explore the use of CodaPack, a powerful tool for compositional data analysis (CoDa). This guide will cover everything from data preparation to principal component analysis, providing you with a comprehensive understanding of how to utilize CodaPack effectively. With a focus on specifications, comparisons, pros, cons, and overall recommendations, this blog aims to enhance your analytical skills in geochemistry and geology.
DOI: 10.15468/dl.vfxyv4
title: Occurrence Download

description: A dataset containing 18 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "MULTIPOLYGON (((148.737813 -36.472308, 148.749042 -36.472308, 148.749042 -36.476799, 148.74455 -36.476799, 148.74455 -36.479045, 148.751288 -36.479045, 148.751288 -36.476799, 148.753533 -36.476799, 148.753533 -36.479045, 148.758025 -36.479045, 148.758025 -36.483537, 148.760271 -36.483537, 148.760271 -36.485782, 148.764762 -36.485782, 148.764762 -36.49252, 148.767008 -36.49252, 148.767008 -36.490274, 148.7715 -36.490274, 148.7715 -36.485782, 148.767008 -36.485782, 148.767008 -36.483537, 148.773746 -36.483537, 148.773746 -36.476799, 148.764762 -36.476799, 148.764762 -36.470062, 148.753533 -36.470062, 148.753533 -36.463324, 148.751288 -36.463324, 148.751288 -36.467816, 148.749042 -36.467816, 148.749042 -36.470062, 148.742304 -36.470062, 148.742304 -36.467816, 148.737813 -36.467816, 148.737813 -36.472308)), ((148.737813 -36.472308, 148.735567 -36.472308, 148.735567 -36.476799, 148.737813 -36.476799, 148.737813 -36.472308)))"
 ]
}

 The dataset includes 18 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0054720-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c7tag6
title: Occurrence Download

description: A dataset containing 3614 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Continent is one of (South America, North America)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Theobroma L.",
 "Year 1990-2024"
 ]
}

 The dataset includes 3614 records from 143 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0054721-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qus8s7
title: Occurrence Download

description: A dataset containing 1206087 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Machine Observation, Human Observation, Material sample, Material citation, Specimen, Fossil, Living Specimen, Occurrence evidence, Observation)",
 "Country is India",
 "Geometry POLYGON((97.58987 27.49757,97.36213 30.19794,95.34498 30.47448,91.42456 27.92052,91.52217 26.96075,89.61889 26.22872,90.13945 24.92733,92.14032 25.30148,92.51447 24.87853,93.71825 25.7895,95.50766 27.12342,97.58987 27.49757))",
 "HasCoordinate is true",
 "Issue is one of (Coordinate rounded, Geodetic datum assumed WGS84, Coordinate uncertainty meters invalid, Country coordinate mismatch, Continent derived from coordinates, Country derived from coordinates, Recorded date mismatch, Recorded date invalid, The taxon concept ID was not used in backbone matching, The taxon ID was not used in backbone matching, Taxon match fuzzy, Taxon match higher rank, Institution match none, Institution collection mismatch, Collection match fuzzy, Institution match fuzzy, Collection match none, Occurrence status inferred from individual count, Multimedia URI invalid, Type status invalid, Identified date invalid, Modified date invalid)",
 "OccurrenceStatus is Present",
 "TaxonKey is Passeriformes"
 ]
}

 The dataset includes 1206087 records from 35 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0054653-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yqyzev
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((148.944426 -36.476799, 148.944426 -36.479045, 148.948918 -36.479045, 148.948918 -36.476799, 148.944426 -36.476799))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0054722-240626123714530/datasets/export for details.
DOI: 10.5281/zenodo.13221418
title: Understanding Disorder in Monolayer Graphene Devices with Gate-Defined Superlattices
DOI: 10.5281/zenodo.13221419
title: Understanding Disorder in Monolayer Graphene Devices with Gate-Defined Superlattices
DOI: 10.15468/dl.b7a4rx
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((149.040996 -36.479045, 149.040996 -36.483537, 149.043241 -36.483537, 149.043241 -36.479045, 149.040996 -36.479045))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0054723-240626123714530/datasets/export for details.
DOI: 10.15468/dl.55pyyw
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((148.906248 -36.481291, 148.906248 -36.485782, 148.908494 -36.485782, 148.908494 -36.481291, 148.906248 -36.481291))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0054724-240626123714530/datasets/export for details.
DOI: 10.15468/dl.ft9krh
title: Occurrence Download

description: A dataset containing 142 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is South Africa",
 "TaxonKey is Compsomelissa Alfken, 1924"
 ]
}

 The dataset includes 142 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0054725-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5517/ccdc.csd.cc2jgf4l
title: CCDC 2337559: Experimental Crystal Structure Determination

description: Related Article: Polina E. Savinykh, Yuliya A. Golubeva, Ksenia S. Smirnova, Lyubov’ S. Klyushova, Alexey S. Berezin, Elizaveta V. Lider|2024|Polyhedron|261|117141|doi:10.1016/j.poly.2024.117141
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2jgf5m
title: CCDC 2337560: Experimental Crystal Structure Determination

description: Related Article: Polina E. Savinykh, Yuliya A. Golubeva, Ksenia S. Smirnova, Lyubov’ S. Klyushova, Alexey S. Berezin, Elizaveta V. Lider|2024|Polyhedron|261|117141|doi:10.1016/j.poly.2024.117141
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2jgf6n
title: CCDC 2337561: Experimental Crystal Structure Determination

description: Related Article: Polina E. Savinykh, Yuliya A. Golubeva, Ksenia S. Smirnova, Lyubov’ S. Klyushova, Alexey S. Berezin, Elizaveta V. Lider|2024|Polyhedron|261|117141|doi:10.1016/j.poly.2024.117141
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2jgf7p
title: CCDC 2337562: Experimental Crystal Structure Determination

description: Related Article: Polina E. Savinykh, Yuliya A. Golubeva, Ksenia S. Smirnova, Lyubov’ S. Klyushova, Alexey S. Berezin, Elizaveta V. Lider|2024|Polyhedron|261|117141|doi:10.1016/j.poly.2024.117141
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.