cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.16431687
title: The data and code for: "Snow avalanches and the impact of climate-linked extreme events on mountain wildlife  population dynamics and resilience"

description: Climate is changing rapidly in mountain environments, giving rise to increasing variability in weather, incidence of extreme events and alteration of the cryosphere. Natural hazards, such as snow avalanches, and the ecological communities they impact may be particularly sensitive to such change. While avalanches may impose both ‘good’ and ‘bad’ effects on mountain ecosystems, the direct impacts that lead to mortality have particularly important implications for future viability and resilience of slow-growing alpine wildlife populations. Here, we studied a sentinel species of coastal Alaskan mountain environments – the mountain goat (Oreamnos americanus) – using long-term field data from individually marked animals (600 individuals over 44 years) in a quantitative modeling framework to understand how avalanches influence demographic processes. Specifically, we developed and parameterized a sex- and age-specific population modeling approach to simulate the effects of avalanche-caused mortality on population growth rate (λ). We examined a range of ecologically relevant scenarios based on empirically-observed states of avalanche-caused mortality. During years when avalanche impacts are severe, populations can experience significant additive mortality and population declines (up to 15%). Due to low reproductive rates, such impacts can lead to long demographic recovery times (up to 11 years, or ~1.5 mountain goat generations). Thus, during the course of a typical mountain goat lifetime, significant avalanche-linked perturbations can be expected to occur, suggesting that meaningful demographic signatures of avalanche impacts are generationally recurrent and routinely imbedded in population histories. From a conservation perspective, such impacts are striking, and highlight the utility of employing a quantitative modeling approach to predict possible effects of avalanches, and extreme events more broadly, on mountain ungulate population dynamics and viability. Our work explicitly builds upon recent findings about the importance of avalanches on mountain-adapted animal populations and has implications for the cultural and ecological communities that depend on them.
DOI: 10.5281/zenodo.16431688
title: The data and code for: "Snow avalanches and the impact of climate-linked extreme events on mountain wildlife  population dynamics and resilience"

description: Climate is changing rapidly in mountain environments, giving rise to increasing variability in weather, incidence of extreme events and alteration of the cryosphere. Natural hazards, such as snow avalanches, and the ecological communities they impact may be particularly sensitive to such change. While avalanches may impose both ‘good’ and ‘bad’ effects on mountain ecosystems, the direct impacts that lead to mortality have particularly important implications for future viability and resilience of slow-growing alpine wildlife populations. Here, we studied a sentinel species of coastal Alaskan mountain environments – the mountain goat (Oreamnos americanus) – using long-term field data from individually marked animals (600 individuals over 44 years) in a quantitative modeling framework to understand how avalanches influence demographic processes. Specifically, we developed and parameterized a sex- and age-specific population modeling approach to simulate the effects of avalanche-caused mortality on population growth rate (λ). We examined a range of ecologically relevant scenarios based on empirically-observed states of avalanche-caused mortality. During years when avalanche impacts are severe, populations can experience significant additive mortality and population declines (up to 15%). Due to low reproductive rates, such impacts can lead to long demographic recovery times (up to 11 years, or ~1.5 mountain goat generations). Thus, during the course of a typical mountain goat lifetime, significant avalanche-linked perturbations can be expected to occur, suggesting that meaningful demographic signatures of avalanche impacts are generationally recurrent and routinely imbedded in population histories. From a conservation perspective, such impacts are striking, and highlight the utility of employing a quantitative modeling approach to predict possible effects of avalanches, and extreme events more broadly, on mountain ungulate population dynamics and viability. Our work explicitly builds upon recent findings about the importance of avalanches on mountain-adapted animal populations and has implications for the cultural and ecological communities that depend on them.
DOI: 10.15468/dl.um8eme
title: Occurrence Download

description: A dataset containing 1271270 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence, Observation)",
 "TaxonKey is one of (Cettia cetti)",
 "Country is one of (Åland Islands, Albania, Andorra, Austria, Belarus, Belgium, Bosnia and Herzegovina, Bulgaria, Croatia, Czechia, Denmark, Estonia, Faroe Islands, Finland, France, Germany, Gibraltar, Greece, Guernsey, Holy See, Hungary, Iceland, Ireland, Isle of Man, Italy, Jersey, Latvia, Liechtenstein, Lithuania, Luxembourg, Malta, Moldova, Republic of, Monaco, Montenegro, Netherlands, North Macedonia, Norway, Poland, Portugal, Romania, Russian Federation, San Marino, Serbia, Slovakia, Slovenia, Spain, Svalbard and Jan Mayen, Sweden, Switzerland, Ukraine, United Kingdom of Great Britain and Northern Ireland)"
 ]
}

 The dataset includes 1271270 records from 1671 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0048719-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14740207
title: Discovering the Complete Enhancer Map of Human Herpesviruses Using a Natural Language Processing Model: supplemental files

description: Abstract

Enhancers are distal cis-regulatory elements that dictate complex transcriptional repertoire. Herpes viruses show programmed latent and lytic gene expression based on the infected tissue and physiological cell state. Kaposi sarcoma-associated herpes virus (KSHV), an oncogenic dsDNA virus, possesses several enhancers that regulate latency and lytic gene expression. Here, we present a natural language processing model (NLP)-based tool, ENHAvir, that was trained with only six KSHV viral enhancer sequences and successfully predicted enhancer elements in other viruses and the human genome. ENHAvir identified known enhancers and predicted novel enhancer elements in the human herpes viruses; HSV-1, HSV-2, VZV, HCMV, HHV-6, HHV-7, and EBV. In the case of EBV, the activity of all predicted enhancers, BamHI-W repeats/BWRF1, BPLF-1, BALF-3, BKRF1, and terminal repeat (TR), was confirmed in enhancer reporter assay. The EBV TR presents features of a “viral super-enhancer” that is responsive to the viral activator ZTA and lytic inducers, suggesting a role in the latency to lytic transition. Interestingly, ENHAvir also precisely identified enhancers in the human genome. Once we obtained the enhancer sequences of all herpes viruses, we were able to compare them with human enhancers. This analysis revealed conserved enhancer signatures and the involvement of Alu elements.

 

Zenodo contents

This repository contains supplemental files of ENHAvir 2.0 training data, MEME analyses, and the phylogenetic tree raw file.
DOI: 10.5281/zenodo.17500116
title: Discovering the Complete Enhancer Map of Human Herpesviruses Using a Natural Language Processing Model: supplemental files

description: Abstract

Enhancers are distal cis-regulatory elements that dictate complex transcriptional repertoire. Herpes viruses show programmed latent and lytic gene expression based on the infected tissue and physiological cell state. Kaposi sarcoma-associated herpes virus (KSHV), an oncogenic dsDNA virus, possesses several enhancers that regulate latency and lytic gene expression. Here, we present a natural language processing model (NLP)-based tool, ENHAvir, that was trained with only six KSHV viral enhancer sequences and successfully predicted enhancer elements in other viruses and the human genome. ENHAvir identified known enhancers and predicted novel enhancer elements in the human herpes viruses; HSV-1, HSV-2, VZV, HCMV, HHV-6, HHV-7, and EBV. In the case of EBV, the activity of all predicted enhancers, BamHI-W repeats/BWRF1, BPLF-1, BALF-3, BKRF1, and terminal repeat (TR), was confirmed in enhancer reporter assay. The EBV TR presents features of a “viral super-enhancer” that is responsive to the viral activator ZTA and lytic inducers, suggesting a role in the latency to lytic transition. Interestingly, ENHAvir also precisely identified enhancers in the human genome. Once we obtained the enhancer sequences of all herpes viruses, we were able to compare them with human enhancers. This analysis revealed conserved enhancer signatures and the involvement of Alu elements.

 

Zenodo contents

This repository contains supplemental files of ENHAvir 2.0 training data, MEME analyses, and the phylogenetic tree raw file.
DOI: 10.15468/dl.ecbt8c
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((6.257206552842356 43.01743564239936,7.236247352996281 43.01743564239936,7.236247352996281 43.99647644255329,6.257206552842356 43.99647644255329,6.257206552842356 43.01743564239936))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Pantala flavescens"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010629-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f92d2j
title: Occurrence Download

description: A dataset containing 25076 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Catopsilia pomona"
 ]
}

 The dataset includes 25076 records from 137 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010631-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17500136
title: Davini Zero-Contradiction Law — Adaptive Pause Validation
title: Oscillator Resilience under Environmental Noise

description: This record is part of the Davini Zero-Contradiction Law™ Validation Archive, documenting the first full real-time validation phase of the Zero-Contradiction Law (ZC*).

Series I: Adaptive Pause Validation — Oscillator Resilience under Environmental Noise demonstrates how coupled systems preserve coherence and recover stability after perturbation, validating the ZC* constant as a universal equilibrium indicator.

 

Six interconnected real-time experiments (T₁–T₆) simulate environmental stress, delay, and cross-domain coupling across physical and informational oscillators.

Results confirm the predicted adaptive pause behavior: under incoherent environmental input, systems temporarily suspend interaction (pause) rather than collapse, resuming stable synchronization near ZC ≈ 0.64* once coherence returns.

 

Contents include:

 



ZC* functional definition and parameters

Dual-oscillator, delay, and cross-scale models

Python scripts and CSV datasets (5 000 samples per test)

Reproducible figures and mean-variance reports for each T₁–T₆ run


 

 

All code and data reflect live computational validation of the Davini Zero-Contradiction Law across physical–informational coupling layers.

 

Access: Restricted — full datasets and scripts available for peer or institutional review upon request.
DOI: 10.5281/zenodo.17498028
title: Paleo-Saltwater Dominates Coastal Aquifer Salinization: A Continental-Scale Study in China
DOI: 10.5281/zenodo.17498027
title: Paleo-Saltwater Dominates Coastal Aquifer Salinization: A Continental-Scale Study in China
DOI: 10.6084/m9.figshare.19406792
title: Data from: Fire and summer temperatures interact to shape seed dormancy thresholds

description: Data for the following paper: Zomer M, Moreira B, Pausas JG. Fire and summer temperatures interact to shape seed dormancy thresholds. Annals of Botany <br><br>It includes 3 files in ASCII format: readme file, and two data files.<br>Abstract<br>In Mediterranean ecosystems, the heat shock of wildfire disrupts physical seed dormancy in many plant species. This triggers germination in the post-fire environment where seedling establishment is optimal due to decreased competition and increased resource availability. However, to maintain the soil seedbank until a fire occurs, the minimum heat capable of breaking seed dormancy (i.e., the lower heat threshold) must be above the maximum temperatures typically observed in the soil during the summer. We therefore hypothesized that summer temperatures have shaped heat requirements for physical dormancy release. Specifically, we predicted that seeds from populations growing under warmer summers will have higher values of the lower heat threshold.To evaluate this prediction, we collected seeds from two Cistus species in 31 populations (20 Cistus albidus; 11 Cistus salviifolius) along a climate gradient of summer temperatures on the eastern coast of Spain. For each population, seeds were treated to 10-minute heat shocks, from 30°C to 120°C in 5-degree increments (19 treatments), to simulate increasing heat doses from summer to fire-related temperatures. Seeds were then germinated in the lab. For all populations, maximum germination was observed when applying temperatures associated with fire. Lower heat thresholds varied among-populations, with a positive relation between summer temperatures at seed population origin and the heat dose required to break dormancy. Our results suggest that fire drives maximum dormancy release for successful post-fire germination, while summer temperatures determine lower heat thresholds for ensuring inter-fire seed bank persistence. Significant among-population variation of thresholds also suggests that post-fire seeder species have some potential to modify their dormancy-breaking requirements in response to changing climate.<br>
DOI: 10.6084/m9.figshare.19406792.v1
title: Data from: Fire and summer temperatures interact to shape seed dormancy thresholds

description: Data for the following paper: Zomer M, Moreira B, Pausas JG. Fire and summer temperatures interact to shape seed dormancy thresholds. Annals of Botany <br><br>It includes 3 files in ASCII format: readme file, and two data files.<br>Abstract<br>In Mediterranean ecosystems, the heat shock of wildfire disrupts physical seed dormancy in many plant species. This triggers germination in the post-fire environment where seedling establishment is optimal due to decreased competition and increased resource availability. However, to maintain the soil seedbank until a fire occurs, the minimum heat capable of breaking seed dormancy (i.e., the lower heat threshold) must be above the maximum temperatures typically observed in the soil during the summer. We therefore hypothesized that summer temperatures have shaped heat requirements for physical dormancy release. Specifically, we predicted that seeds from populations growing under warmer summers will have higher values of the lower heat threshold.To evaluate this prediction, we collected seeds from two Cistus species in 31 populations (20 Cistus albidus; 11 Cistus salviifolius) along a climate gradient of summer temperatures on the eastern coast of Spain. For each population, seeds were treated to 10-minute heat shocks, from 30°C to 120°C in 5-degree increments (19 treatments), to simulate increasing heat doses from summer to fire-related temperatures. Seeds were then germinated in the lab. For all populations, maximum germination was observed when applying temperatures associated with fire. Lower heat thresholds varied among-populations, with a positive relation between summer temperatures at seed population origin and the heat dose required to break dormancy. Our results suggest that fire drives maximum dormancy release for successful post-fire germination, while summer temperatures determine lower heat thresholds for ensuring inter-fire seed bank persistence. Significant among-population variation of thresholds also suggests that post-fire seeder species have some potential to modify their dormancy-breaking requirements in response to changing climate.<br>
DOI: 10.15468/dl.v4s24p
title: Occurrence Download

description: A dataset containing 11766966 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 11766966 records from 3287 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010628-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sktfkc
title: Occurrence Download

description: A dataset containing 2746 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Marsypianthes chamaedrys",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 2746 records from 172 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018409-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j2rh49
title: Occurrence Download

description: A dataset containing 62 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Anopheles pursati"
 ]
}

 The dataset includes 62 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018410-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ggywpt
title: Occurrence Download

description: A dataset containing 95 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is TRUE",
 "HasGeospatialIssue is FALSE",
 "TaxonKey is Caperea marginata",
 "Year is greater than or equal to 2010",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 95 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018411-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mwpyat
title: Occurrence Download

description: A dataset containing 26189 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is TRUE",
 "HasGeospatialIssue is FALSE",
 "TaxonKey is Eschrichtius robustus",
 "Year is greater than or equal to 2010",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 26189 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018412-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mhzxwm
title: Occurrence Download

description: A dataset containing 177 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Martianthus leucocephalus",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 177 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018414-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.v83m9n
title: Occurrence Download

description: A dataset listing the 6343 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-180 0,180 0,180 10,-180 10,-180 0))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Mammalia"
 ]
}

 The dataset's 6343 records were derived from 1134 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018387-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ap6kzv
title: Occurrence Download

description: A dataset containing 2210 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Combretum micranthum",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is Fossil"
 ]
 }
 }
 ]
}

 The dataset includes 2210 records from 78 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018413-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qyzum5
title: Occurrence Download

description: A dataset containing 7190 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is TRUE",
 "HasGeospatialIssue is FALSE",
 "TaxonKey is Balaenoptera borealis",
 "Year is greater than or equal to 2010",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 7190 records from 78 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018417-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uftc5h
title: Occurrence Download

description: A dataset containing 393 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Medusantha crinita",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 393 records from 56 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018419-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q5vjfu
title: Occurrence Download

description: A dataset containing 8741 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Detarium microcarpum",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is Fossil"
 ]
 }
 }
 ]
}

 The dataset includes 8741 records from 98 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018420-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/3kj-qzm-e2w
title: Helix pomatia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/404-zaj-l7h
title: Atlanta californiensis Seapy & Richter, 1993

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/reh-zv7-hrx
title: Pachysphaera sphaerica (G. B. Sowerby I, 1841)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ddp-cgq-g9x
title: Swiftopecten swiftii (Bernardi, 1858)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/rpt-nre-r2f
title: Macularia sylvatica (Draparnaud, 1801)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/p0y-sex-l2t
title: Tylotoechus degneri (Laidlaw, 1957)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.