cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/2nhhdjx225
title: Data and scripts for longitudinal structural variant phylogenies in metastatic prostate cancer

description: This study evaluates whether structural variants (SVs) capture key evolutionary and resistance signals in mCRPC. We analyzed paired longitudinal tumor WGS (pre-BAT and on-BAT) with matched normals from COMBAT subjects treated with bipolar androgen therapy (BAT). SVs were called and genotyped, and SVCFit estimated structural-variant cellular fraction (SVCF), clustered SVs by prevalence, and inferred clonal phylogenies and clone proportions over time. Data show branched evolution and therapy-associated clonal shifts. In representative subjects, highly rearranged lineages contracted on BAT, while SV-defined clones expanded. Outputs include SV callsets, per-SV SVCF/CCF, cluster labels, trees, and figures for reuse.

This repository comprises the source data and computational workflows supporting "Longitudinal structural variant phylogenies define tumor evolution under therapeutic selection pressure in metastatic prostate cancer" by Liu et. al. (2026). 

1. Clinical Cohort Data (COMBAT). 
-- annotsv: Functional SV annotations generated via AnnotSV (Geoffroy et. al. 2018).
-- SVCFit_output: SV annotated with inferred SVCF, phasing, zygosity and overlapping CNVs (BED format).
-- cluster_result.csv: clusters of deduplicated SVs based on inferred SVCF.
-- sv2cluster.csv: clusters of all SVs based on inferred SVCF.
-- samp_pur.csv: Purity of all processed tumor samples estimated by FACETS (Shen et. al. 2016).
-- pair.bed: Matched pre- and on-BAT biopsy samples. 
* The raw sequencing data and germline variant calls used in the current study are available from the corresponding author upon reasonable request. These are not publicly available due to informed consent restrictions.

2. Synthetic Benchmarking Data (VISOR_benchmark) 
-- truth: Ground truth BED files defining spiked-in SVs: exact breakpoints , SV types (deletions, duplications, homozygosity).
-- depth: Test of the impact of variable breakpoint depth for SVCF estimation.
-- facet: CNV profiles generated via FACETS across five distinct experimental conditions to model heterogeneous tumor mixtures.
-- svclone_rdata: Serialized R objects containing subclonal deconvolution results (SVClone/ccube).
-- SV_vcfs: SV calls from Manta (Chen et. al. 2016). 
-- SNP: SNP calls from GATK4 (McKenna et. al. 2010). 

3. In Silico Validation (Prostate_mixture) Controlled admixtures of prostate cancer reads designed to evaluate sensitivity in polyclonal environments
-- prostate_vcfs: SV call sets for 3-, 4-, and 5-clone mixtures (3m, 4m, 5m) by Manta.
-- facet: CNV profiles generated via FACETS across all clone mixtures.
-- SNP: SNP calls from GATK4 across all clone mixtures.

4. Scripts
-- COMBAT: Clinical pipelines for alignment, consensus SV calling (integrating Manta, Delly, GRIDSS, and SURVIVOR), and functional annotation.
-- VISOR: Scripts for synthetic genome generation, read simulation, and benchmarking execution.
-- Prostate_mixture: Utilities for BAM mixing, interval splitting, and downstream processing.
DOI: 10.15468/cr5qrr
title: Overview of Campopleginae (Hymenoptera: Ichneumonidae) species described from 2016 to 2025 with revised taxon metrics

description: This dataset contains the digitized treatments in Plazi based on the original journal article Santos, Alvaro Doria Dos (2025): Overview of Campopleginae (Hymenoptera: Ichneumonidae) species described from 2016 to 2025 with revised taxon metrics. Zootaxa 5722 (2): 199-228, DOI: 10.11646/zootaxa.5722.2.3, URL: https://doi.org/10.11646/zootaxa.5722.2.3AbstractThe subfamily Campopleginae, one of the largest groups within the family Ichneumonidae, faces persistent challenges in maintaining updated taxonomic records due to the rapid pace of new species descriptions. This study compiles and consolidates recent taxonomic information, presenting a comprehensive list of species described between 2016 and 2025, along with a dataset documenting nomenclatural changes. In total, two new genera and 242 new species of Darwin wasps were identified from 67 articles published during this period. By unifying scattered data, this work addresses a critical gap in the literature and provides a reference tool that reflects the dynamic growth of Campopleginae taxonomy.
DOI: 10.17632/2nhhdjx225.2
title: Data and scripts for longitudinal structural variant phylogenies in metastatic prostate cancer

description: This study evaluates whether structural variants (SVs) capture key evolutionary and resistance signals in mCRPC. We analyzed paired longitudinal tumor WGS (pre-BAT and on-BAT) with matched normals from COMBAT subjects treated with bipolar androgen therapy (BAT). SVs were called and genotyped, and SVCFit estimated structural-variant cellular fraction (SVCF), clustered SVs by prevalence, and inferred clonal phylogenies and clone proportions over time. Data show branched evolution and therapy-associated clonal shifts. In representative subjects, highly rearranged lineages contracted on BAT, while SV-defined clones expanded. Outputs include SV callsets, per-SV SVCF/CCF, cluster labels, trees, and figures for reuse.

This repository comprises the source data and computational workflows supporting "Longitudinal structural variant phylogenies define tumor evolution under therapeutic selection pressure in metastatic prostate cancer" by Liu et. al. (2026). 

1. Clinical Cohort Data (COMBAT). 
-- annotsv: Functional SV annotations generated via AnnotSV (Geoffroy et. al. 2018).
-- SVCFit_output: SV annotated with inferred SVCF, phasing, zygosity and overlapping CNVs (BED format).
-- cluster_result.csv: clusters of deduplicated SVs based on inferred SVCF.
-- sv2cluster.csv: clusters of all SVs based on inferred SVCF.
-- samp_pur.csv: Purity of all processed tumor samples estimated by FACETS (Shen et. al. 2016).
-- pair.bed: Matched pre- and on-BAT biopsy samples. 
* The raw sequencing data and germline variant calls used in the current study are available from the corresponding author upon reasonable request. These are not publicly available due to informed consent restrictions.

2. Synthetic Benchmarking Data (VISOR_benchmark) 
-- truth: Ground truth BED files defining spiked-in SVs: exact breakpoints , SV types (deletions, duplications, homozygosity).
-- depth: Test of the impact of variable breakpoint depth for SVCF estimation.
-- facet: CNV profiles generated via FACETS across five distinct experimental conditions to model heterogeneous tumor mixtures.
-- svclone_rdata: Serialized R objects containing subclonal deconvolution results (SVClone/ccube).
-- SV_vcfs: SV calls from Manta (Chen et. al. 2016). 
-- SNP: SNP calls from GATK4 (McKenna et. al. 2010). 

3. In Silico Validation (Prostate_mixture) Controlled admixtures of prostate cancer reads designed to evaluate sensitivity in polyclonal environments
-- prostate_vcfs: SV call sets for 3-, 4-, and 5-clone mixtures (3m, 4m, 5m) by Manta.
-- facet: CNV profiles generated via FACETS across all clone mixtures.
-- SNP: SNP calls from GATK4 across all clone mixtures.

4. Scripts
-- COMBAT: Clinical pipelines for alignment, consensus SV calling (integrating Manta, Delly, GRIDSS, and SURVIVOR), and functional annotation.
-- VISOR: Scripts for synthetic genome generation, read simulation, and benchmarking execution.
-- Prostate_mixture: Utilities for BAM mixing, interval splitting, and downstream processing.
DOI: 10.17632/k923k4rhgx.2
title: Replication files for water resource tax and corporate bank debt

description: This folder contains Stata code and associated data files for conducting regression analysis in the paper, "Water Resource Tax and Corporate Bank Debt: Evidence from China." The data used in this paper are publicly available, and the code is compatible with Stata version MP17.
DOI: 10.15468/dl.phz2xu
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Diplaspis hydrocotylea",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008023-260120142942310/datasets/export for details.
DOI: 10.17632/4dx4dr4t3c
title: Seminario de investigación#2

description: Data para Seminario de Investigación 2
DOI: 10.17632/4dx4dr4t3c.2
title: Seminario de investigación#2

description: Data para Seminario de Investigación 2
DOI: 10.17632/7f3ym373j4
title: Harnessing digital with design-based learning experience

description: Dataset for an experiment following robotics competition on an university
DOI: 10.17632/7f3ym373j4.2
title: Harnessing digital with design-based learning experience

description: Dataset for an experiment following robotics competition on an university
DOI: 10.17632/f439kp2r2v
title: Seminario doctoral

description: Data para la creacion del poster del seminario Doctoral 1
DOI: 10.17632/f439kp2r2v.2
title: Seminario doctoral

description: Data para la creacion del poster del seminario Doctoral 1
DOI: 10.17632/txpznrgm3b
title: Modelling electricity markets when renewable power increases

description: This data set contains files to allow the replication of results found in the article "Modelling electricity markets when renewable power increases" by Clas Eriksson, Johan Lindén and Christos Papahristodoulou. The abstract below describes the article, its research question and its findings. 

The files in the data set are the following. 
 readme.txt - containing an overview of the material and instructions for replication
 elsim16.r - a program in the R programming language, used for simulating the theoretical model in the article
 plots16.zip - a compressed directory containing all graphs generated by the simulation model in the eps and png formats

Abstract of the article
We analyze theoretically a simple model of the electricity market where the supply of Variable Renewable Electricity (VRE) and demand are both shifting stochastically over time. The correlation between these shifts is crucial for the equilibrium price of electricity. Based on hourly equilibria we compute yearly producer surpluses, consumer utility and the value factor of VRE, under different conditions. While an increasing correlation between VRE and demand causes a decline in average price and total producer surplus, the VRE producer surplus increases, because these producers sell much when price is high. Higher VRE and peak capacities reduce the average price and the total producer surplus, but a negative correlation can counteract this, by causing high prices more frequently. In addition, the value factor of VRE does not decline monotonously, contrary to findings in previous studies.
DOI: 10.17632/txpznrgm3b.1
title: Modelling electricity markets when renewable power increases

description: This data set contains files to allow the replication of results found in the article "Modelling electricity markets when renewable power increases" by Clas Eriksson, Johan Lindén and Christos Papahristodoulou. The abstract below describes the article, its research question and its findings. 

The files in the data set are the following. 
 readme.txt - containing an overview of the material and instructions for replication
 elsim16.r - a program in the R programming language, used for simulating the theoretical model in the article
 plots16.zip - a compressed directory containing all graphs generated by the simulation model in the eps and png formats

Abstract of the article
We analyze theoretically a simple model of the electricity market where the supply of Variable Renewable Electricity (VRE) and demand are both shifting stochastically over time. The correlation between these shifts is crucial for the equilibrium price of electricity. Based on hourly equilibria we compute yearly producer surpluses, consumer utility and the value factor of VRE, under different conditions. While an increasing correlation between VRE and demand causes a decline in average price and total producer surplus, the VRE producer surplus increases, because these producers sell much when price is high. Higher VRE and peak capacities reduce the average price and the total producer surplus, but a negative correlation can counteract this, by causing high prices more frequently. In addition, the value factor of VRE does not decline monotonously, contrary to findings in previous studies.
DOI: 10.17632/2dm24z6yrr.1
title: Replication Package for "Cultural Industry Meets Tourism: Productive Intersectoral Spillovers and Cluster Synergies" (C. Bernini, S. Emili, F. Galli)

description: The files contained in this folder allow replication of the analysis presented in “Cultural Industry Meets Tourism: Productive Intersectoral Spillovers and Cluster Synergies” (C. Bernini, S. Emili, F. Galli).

Although the original data are confidential, following the procedures described in the README and the accompanying scripts allows reconstruction of the final dataset used for model estimation. For transparency and replication purposes, the folder also includes an example dataset with randomly generated (perturbed) data.
DOI: 10.15468/jsidn7
title: University of Vermont Zadock Thompson Zoological Collection-Invertebrates

description: The Zadock Thompson entomological collection is the oldest and most complete collection of its kind in the state of Vermont. It is also the largest insect collection in the state, with approximately 280,000 pinned specimens, and 20,000 DNA-grade specimens preserved in ethanol. The species represented in the collection represent the diversity of insect&rsquo;s populations in Vermont, though the range of the specimens is worldwide. The collection consists of approximately 40% Coleoptera, 10% Hemiptera, 10% Diptera, 10% Lepidoptera, 5% Hymenoptera and 5% Odonata, and a selection of various other orders of insects; as well as 60,000 Arachnids. The collection is now the only large arthropod collection in the state, since the ruin of the State Invertebrate Collection by flooding from Tropical Storm Irene. The Thompson collection has repeatedly and regularly been accessed by scientists studying taxonomy, nomenclature, phylogenetics, population ecology, and biodiversity of species living in Vermont, as well as being regularly used for biological class instruction, and by non-biologists, including artists and photographers. Understanding the consequences of climate change on biodiversity and distribution of animals is becoming increasingly important, and thus the scientific value of historical collections such as the Zadock Thompson Zoological Collection increases.
DOI: 10.17632/pvfwf6xmc5
title: The OEGMA-based hydrogel is active against all species of the ESKAPE pathogens, Streptococcus mutans and the pathogenic yeast Candida albicans

description: Wound dressings serve as a crucial first barrier against microbial contamination, particularly in severe wounds requiring rapid antimicrobial protection. Building on our previously established hydrogel system based on copolymers of oligo(ethylene glycol) methyl ether methacrylate (OEGMA) and 2-(dimethylamino)ethyl methacrylate (DMAEMA) crosslinked during quaternization with 1,6-dibromohexane, we extend the biological evaluation of this contact-active material to a broader spectrum of clinically relevant pathogens. The hydrogel was assessed against the complete multidrug resistant ESKAPE group, the Gram-positive bacterium Staphylococcus mutans, and the opportunistic yeast Candida albicans. Pronounced contact-mediated antimicrobial activity was observed against all tested organisms, resulting in a significant reduction of microbial viability. Importantly, the material retained excellent biocompatibility, showing no adverse effects on mammalian skin fibroblasts or human blood cells. The combination of broad-spectrum antimicrobial efficacy, biological compatibility, and a robust yet simple fabrication approach highlights the potential of this hydrogel as a next-generation wound dressing and a promising first-line option for emergency wound care of critical injuries.
DOI: 10.17632/pvfwf6xmc5.1
title: The OEGMA-based hydrogel is active against all species of the ESKAPE pathogens, Streptococcus mutans and the pathogenic yeast Candida albicans

description: Wound dressings serve as a crucial first barrier against microbial contamination, particularly in severe wounds requiring rapid antimicrobial protection. Building on our previously established hydrogel system based on copolymers of oligo(ethylene glycol) methyl ether methacrylate (OEGMA) and 2-(dimethylamino)ethyl methacrylate (DMAEMA) crosslinked during quaternization with 1,6-dibromohexane, we extend the biological evaluation of this contact-active material to a broader spectrum of clinically relevant pathogens. The hydrogel was assessed against the complete multidrug resistant ESKAPE group, the Gram-positive bacterium Staphylococcus mutans, and the opportunistic yeast Candida albicans. Pronounced contact-mediated antimicrobial activity was observed against all tested organisms, resulting in a significant reduction of microbial viability. Importantly, the material retained excellent biocompatibility, showing no adverse effects on mammalian skin fibroblasts or human blood cells. The combination of broad-spectrum antimicrobial efficacy, biological compatibility, and a robust yet simple fabrication approach highlights the potential of this hydrogel as a next-generation wound dressing and a promising first-line option for emergency wound care of critical injuries.
DOI: 10.17632/9kvv7bv25m.6
title: Food Restriction Patterns and Their Impact on Growth and Nutrition in Chinese Pediatric Atopic Dermatitis

description: Supplemental material for "Food Restriction Patterns and Their Impact on Growth and Nutrition in Chinese
Pediatric Atopic Dermatitis: A Cross-Sectional Study"
DOI: 10.17632/cmhv4zf887
title: Supplementary data

description: The results of the tests conducted on the 30 different rock samples.
DOI: 10.17632/cmhv4zf887.1
title: Supplementary data

description: The results of the tests conducted on the 30 different rock samples.
DOI: 10.17632/8z9x65555z
title: Cause-of-death mortality burdens incorporating lifespan inequality contributions for the United States

description: Do file and dataset for dominance analysis on US cause-deleted age-at-death distributions.

Abstract: Comparisons of cause-of-death mortality burdens ignore contributions to lifespan inequality or assess them separately from life expectancy impacts. We compare cause-of-death mortality burdens that take account of contributions to both life expectancy and lifespan inequality. Using 2021 U.S. National Center for Health Statistics mortality data stratified by sex and race/ethnic group, we distinguish eight causes of death (deaths of despair, homicides, accidents, CVD, cancer, COVID-19, infectious diseases, and respiratory diseases), construct a cause-deleted life table for each and use it to simulate an age-at-death distribution if that cause were eliminated. We rank these distributions and the respective causes using (higher-order) stochastic dominance analysis founded on value judgments concerning the distribution of lifespan. If longer and more equal lifespans are considered better, then we find that among non-Hispanic (NH) Whites, deaths of despair impose a larger mortality burden than those generated by homicides, COVID-19 (males), cancers (males), infectious diseases and respiratory diseases. If concern about lifespan inequality is stronger around younger ages at death, then the mortality burden of deaths of despair is even larger than that of CVD for NH White males. For NH Black males, the mortality burden of homicides is larger than that of respiratory diseases if there is concern about lifespan inequality and it is larger than the burdens of COVID-19 and cancers if there is greater concern about inequality between younger ages of death. These and other results can inform inequality-sensitive decision-makers looking to prioritize interventions that target causes of death that contribute most to the mortality burden through both reduced life expectancy and increased lifespan dispersion.
DOI: 10.17632/8z9x65555z.1
title: Cause-of-death mortality burdens incorporating lifespan inequality contributions for the United States

description: Do file and dataset for dominance analysis on US cause-deleted age-at-death distributions.

Abstract: Comparisons of cause-of-death mortality burdens ignore contributions to lifespan inequality or assess them separately from life expectancy impacts. We compare cause-of-death mortality burdens that take account of contributions to both life expectancy and lifespan inequality. Using 2021 U.S. National Center for Health Statistics mortality data stratified by sex and race/ethnic group, we distinguish eight causes of death (deaths of despair, homicides, accidents, CVD, cancer, COVID-19, infectious diseases, and respiratory diseases), construct a cause-deleted life table for each and use it to simulate an age-at-death distribution if that cause were eliminated. We rank these distributions and the respective causes using (higher-order) stochastic dominance analysis founded on value judgments concerning the distribution of lifespan. If longer and more equal lifespans are considered better, then we find that among non-Hispanic (NH) Whites, deaths of despair impose a larger mortality burden than those generated by homicides, COVID-19 (males), cancers (males), infectious diseases and respiratory diseases. If concern about lifespan inequality is stronger around younger ages at death, then the mortality burden of deaths of despair is even larger than that of CVD for NH White males. For NH Black males, the mortality burden of homicides is larger than that of respiratory diseases if there is concern about lifespan inequality and it is larger than the burdens of COVID-19 and cancers if there is greater concern about inequality between younger ages of death. These and other results can inform inequality-sensitive decision-makers looking to prioritize interventions that target causes of death that contribute most to the mortality burden through both reduced life expectancy and increased lifespan dispersion.
DOI: 10.15468/dl.6799jf
title: Occurrence Download

description: A dataset containing 96 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Diplolophium africanum",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 96 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008025-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gxvqcc
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Parachondria basicarinata"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008026-260120142942310/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.27238629
title: code for paper "Temperature thresholds of extreme heat-induced yield loss in maize and soybean reveal geographic heterogeneity across the Northern Hemisphere"

description: code for paper "Temperature thresholds of extreme heat-induced yield loss in maize and soybean reveal geographic heterogeneity across the Northern Hemisphere" by Zhao Q. et al. DOI: 10.1038/s43016-026-01298-0
DOI: 10.6084/m9.figshare.27238629.v3
title: code for paper "Temperature thresholds of extreme heat-induced yield loss in maize and soybean reveal geographic heterogeneity across the Northern Hemisphere"

description: code for paper "Temperature thresholds of extreme heat-induced yield loss in maize and soybean reveal geographic heterogeneity across the Northern Hemisphere" by Zhao Q. et al. DOI: 10.1038/s43016-026-01298-0