cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.17704455
title: mixtree-analysis-data

description: This is the data folder for the mixtree-analysis (https://doi.org/10.5281/zenodo.17704759). It is uploaded as a separate files as these are too heavy for GitHub. 

## Dataframe Documentation

### `param_grid.rds`- **Description:** Contains all combinations of simulation (`sim_config`) and test (`test_config`) parameters.  - **Columns:**    - `param_id`: unique identifier for each parameter combination    - `params`: list of parameters used for tree and forest generation  

### `tree_grid.rds`- **Description:** Reference transmission trees generated for each `param_id` in `param_grid`.  - **Columns:**    - `tree_id`: `<param_id>_<replicate_id>` identifier    - `tree`: transmission tree object  

### `forest_grid.rds`- **Description:** Forests generated from each reference tree in `tree_grid` using parameter sets from `param_grid` with matching epidemic size.  - **Columns:**    - `forest_id`: `<tree_id>_<param_id>` identifier    - `forest`: list of transmission trees forming the forest  

### `test_grid.rds`- **Description:** Unique pairs of forests derived from the same reference tree for statistical testing.  - **Columns:**    - `forest_id_A`: identifier of the first forest    - `forest_id_B`: identifier of the second forest  

### `results.rds`- **Description:** Statistical test results applied to each forest pair in `test_grid`.  - **Columns:**    - `forest_id_A`, `forest_id_B`: identifiers of compared forests    - `method`: test applied (`permanova` or `chisq`)    - `forest_size`: number of trees per forest    - `p_value`: resulting p-value  

### `results_grid.rds`- **Description:** Combines `results` with simulation parameters from `param_grid` for each forest pair.  - **Columns:**    - `tree_id`: reference tree identifier    - `forest_id_*`: identifiers of compared forests    - `param_id_*`: parameter set identifiers used to generate forests    - `off_R_*`: basic reproduction number (R0) of offspring distribution    - `off_k_*`: dispersion parameter (k) of offspring distribution    - `forest_size`: number of trees per forest    - `epidemic_size`: number of vertices per tree    - `method`: statistical test applied    - `p_value`: resulting p-value
DOI: 10.5281/zenodo.17704456
title: mixtree-analysis-data

description: This is the data folder for the mixtree-analysis (https://doi.org/10.5281/zenodo.17704759). It is uploaded as a separate files as these are too heavy for GitHub. 

## Dataframe Documentation

### `param_grid.rds`- **Description:** Contains all combinations of simulation (`sim_config`) and test (`test_config`) parameters.  - **Columns:**    - `param_id`: unique identifier for each parameter combination    - `params`: list of parameters used for tree and forest generation  

### `tree_grid.rds`- **Description:** Reference transmission trees generated for each `param_id` in `param_grid`.  - **Columns:**    - `tree_id`: `<param_id>_<replicate_id>` identifier    - `tree`: transmission tree object  

### `forest_grid.rds`- **Description:** Forests generated from each reference tree in `tree_grid` using parameter sets from `param_grid` with matching epidemic size.  - **Columns:**    - `forest_id`: `<tree_id>_<param_id>` identifier    - `forest`: list of transmission trees forming the forest  

### `test_grid.rds`- **Description:** Unique pairs of forests derived from the same reference tree for statistical testing.  - **Columns:**    - `forest_id_A`: identifier of the first forest    - `forest_id_B`: identifier of the second forest  

### `results.rds`- **Description:** Statistical test results applied to each forest pair in `test_grid`.  - **Columns:**    - `forest_id_A`, `forest_id_B`: identifiers of compared forests    - `method`: test applied (`permanova` or `chisq`)    - `forest_size`: number of trees per forest    - `p_value`: resulting p-value  

### `results_grid.rds`- **Description:** Combines `results` with simulation parameters from `param_grid` for each forest pair.  - **Columns:**    - `tree_id`: reference tree identifier    - `forest_id_*`: identifiers of compared forests    - `param_id_*`: parameter set identifiers used to generate forests    - `off_R_*`: basic reproduction number (R0) of offspring distribution    - `off_k_*`: dispersion parameter (k) of offspring distribution    - `forest_size`: number of trees per forest    - `epidemic_size`: number of vertices per tree    - `method`: statistical test applied    - `p_value`: resulting p-value
DOI: 10.15468/dl.pvgwbh
title: Occurrence Download

description: A dataset containing 10927 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "PublishingCountry is Colombia",
 {
 "and" : [
 "Country is Colombia",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 }
 ]
 },
 {
 "and" : [
 "GadmGid is one of (COL.19_2)",
 "StateProvince is one of (La Guajira)",
 "TaxonKey is one of (Mammalia [GBIF Backbone Taxonomy])"
 ]
 }
 ]
}

 The dataset includes 10927 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006582-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17617389
title: UTR Research Archive v3.1 — Supporting Documents

description: This dataset contains the complete supplementary and developmental materials associated with the UTR Trilogy v3.1, including earlier monographs, extracted chapters, mathematical foundations, resonance and consciousness modules, nervous system mapping, cosmic intelligence notes, integration documents, and multiple working drafts.

It provides full transparency into the evolution of the Universal Theory of Resilience (UTR) and accompanies the primary publication: UTR Trilogy v3.1 — Illustrated Special Edition
DOI: 10.5281/zenodo.17611094
title: Universal Theory of Resilience (UTR) v2.0: A Unified Framework for Adaptive Intelligence in Antagonistic Environments

description: Zenodo Description (Final Version)

Universal Theory of Resilience (UTR) v2.0 presents a unified, cross-domain framework explaining how stability, awareness, and intelligence emerge in systems exposed to persistent antagonism. Building on first-principles axioms, UTR v2.0 refines the theory into a fully operational, testable model applicable to physical, biological, cognitive, artificial, and social systems.

The framework introduces six core axioms—Distinction, Antagonism, Local Oscillation, Meta-Resonance, Stabilizing Structures, and Predictive Memory—each defined with operational clarity and domain examples. These axioms together form the UTR Cycle, a recursive computational process through which systems detect disruption, integrate information, deploy adaptive countermeasures, and build predictive memory. This cycle gives rise to Adaptive Stability, the functional equivalent of resilience and intelligence.

UTR v2.0 includes a formalized “Corrupted Reality” ontology, cross-domain application matrices (immune systems, cognition, AI, and organizations), a full implementation framework for engineering resilient systems, and a research agenda outlining pathways for mathematical formalization, empirical validation, and long-term theoretical development.

This version represents the first complete, integrated formulation of UTR, suitable for scientific reference, interdisciplinary research, and practical system design.
DOI: 10.5281/zenodo.17604848
title: Axiom of Antagonistic Physics: How Physical Law Disrupts the Binary Mechanics of Existence

description: The Axiom of Antagonistic Physics proposes that the fundamental forces of the universe—gravity, light, time, and entropy—act as antagonistic influences on the binary mechanics that structure existence. Instead of supporting equilibrium, these forces continually disrupt the natural balance between change and stability, producing corrupted binary states. From these distortions arise duality, contradiction, cognitive turbulence, and social instability.

This axiom builds on the Universal Theory of Resilience, which describes reality as governed by a primordial binary distinction engine (e.g., Change ⇌ Stability, Order ⇌ Chaos, Life ⇌ Mind). In an untouched state, these binaries operate in harmony. However, the unrelenting pressures of physical law—curvature, entropy, temporal drift, and energetic stress—push the system out of phase, creating tension at every level of existence.

As a result, biological systems experience stress, consciousness becomes conflicted, and societies fall into fragmentation and contradiction. Duality is therefore not fundamental but emergent: a symptom of the antagonistic interference of physical law upon the binary foundations of reality.
DOI: 10.5281/zenodo.17604246
title: Kappa Framework (v3) — Distinction, Efficiency, and Resonance

description: The Kappa Framework (v3) defines κ_quantum and κ_res as fundamental measures linking distinction efficiency, coherence ratios, and resonant integration. This module forms one of the three mathematical pillars of the Universal Theory of Resilience. Included are the combined explanatory PDF and the soft-blue A3 conceptual plate.
DOI: 10.15468/dl.6xxnjv
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "Geometry POLYGON((-106.16212 25.47784,-93.50723 25.47784,-93.50723 36.21837,-106.16212 36.21837,-106.16212 25.47784))",
 "HasGeospatialIssue is false",
 "License is one of (CC0 1.0, CC-BY 4.0)",
 "TaxonKey is Sus scrofa",
 "Year 2015-2015"
 ]
}

 The dataset includes 16 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006583-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17599319
title: Universal Theory of Resilience – Research Continuum (Version 1.5)

description: Universal Theory of Resilience – Research Continuum (Version 1.5)Author: Jamie Morris

This deposit contains the complete Version 1.5 research continuum for the Universal Theory of Resilience (UTR). The Continuum unifies quantum physics, geometry, thermodynamics, biology, cognition, collective behaviour, and cosmology using a single invariant: κ (kappa) — the measure of distinction, coherence, and multiscale resilience.

Version 1.5 includes all seven phases of the theory:

Phase I — Distinction

Phase II — Experimental Framework

Phase III — Gravitational κ

Phase IV — Biological κ

Phase V — Cognitive κ

Phase VI — Collective κ

Phase VII — Universal κ

This release introduces two major additions:

Master Equation Sheet (A3) — a unified view of all κ equations

All-Phases Map (A3) — a complete conceptual map of the seven-phase progression

The dataset contains:

The full Continuum archive (v1.5 ZIP)

A complete Book PDF (v1.5)

High-resolution A3 diagrams and plates

Metadata, README files, and documentation

The Universal Theory of Resilience provides a cross-domain framework describing how systems maintain structure across scales — from quantum particles to living organisms, minds, civilizations, and cosmological structures. κ offers a unified mathematical and conceptual language for understanding coherence, persistence, and emergent intelligence.
DOI: 10.5281/zenodo.17594121
title: Universal Theory of Resilience — Official Titles

description: This foundational study introduces the Distinction Parameter (κ), a proposed universal measure of informational efficiency in quantum systems.It outlines three precision experiments designed to test whether physical reality arises from discrete informational boundaries rather than continuous fields.The framework links quantum action, entropy, and geometry within a single measurable invariant, establishing the empirical base for the Universal Theory of Resilience continuum.
description: Resonant Consciousness extends the Distinction Model into the domain of awareness, proposing that consciousness is a resonant state of informational coherence between energy and time.The work formalizes the Energy–Awareness link, expressed through κ₍res₎ = (E₍coh₎/E₍total₎) × (τ₍aware₎/τ₍decoh₎).This phase unifies physical, informational, and experiential domains, showing that recognition and measurement are two expressions of the same universal resonance.
description: Jamie’s Lens explores perception as the mechanism through which the universe organizes and recognizes itself.Building on the Distinction and Resonant Consciousness models, it interprets observation not as passive reception but as active creation—the continual formation of pattern and meaning.This revised edition integrates the κ-framework to present perception and physics as complementary aspects of a single informational geometry.
description: This record consolidates all works within the Universal Theory of Resilience continuum—spanning quantum, informational, and cosmological scales.It includes metadata, cross-references, and contextual notes linking Phases I–III and Jamie’s Lens (Revised Edition) into a unified research lineage.The continuum describes how reality sustains and recognizes itself through the dynamic balance of distinction and resonance.
DOI: 10.5281/zenodo.17590196
title: Experimental Framework for Testing the Distinction Model (Module of the Universal Theory of Resilience Continuum)

description: A theoretical and experimental framework exploring how light–time symmetry and binary distinction may underpin consciousness, structure, and resilience within the Universal Theory of Resilience continuum.
DOI: 10.15468/dl.ehc28f
title: Occurrence Download

description: A dataset containing 71 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "Geometry POLYGON((-106.16212 25.47784,-93.50723 25.47784,-93.50723 36.21837,-106.16212 36.21837,-106.16212 25.47784))",
 "HasGeospatialIssue is false",
 "License is one of (CC0 1.0, CC-BY 4.0)",
 "TaxonKey is Sus scrofa",
 "Year 2025-2025"
 ]
}

 The dataset includes 71 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006584-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57892/100-251
title: E3C Hyper-reduction for hyperelasticity - Simulation Results

description: Results related to paper 2025 S. Wulfinghoff Homogenization in Hyperelasticity using Empirically Corrected Cluster Cubature (E3C) Hyper-Reduction
DOI: 10.15468/dl.sxm3xe
title: Occurrence Download

description: A dataset containing 327689 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Echinochloa P.Beauv."
 ]
}

 The dataset includes 327689 records from 2441 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001162-250424135625364/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fzzh86
title: Occurrence Download

description: A dataset containing 22971 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Calopteryx xanthostoma",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 22971 records from 518 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024652-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q34x3f
title: Occurrence Download

description: A dataset containing 999 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Acmella oleracea (L.) R.K.Jansen"
 ]
}

 The dataset includes 999 records from 184 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009836-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cja47q
title: Occurrence Download

description: A dataset containing 1195 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Specimen, Material sample, Human Observation, Occurrence evidence)",
 "Country is China",
 "TaxonKey is Eucommia ulmoides Oliv."
 ]
}

 The dataset includes 1195 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013717-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15487048
title: Avian promiscuity in the last European primeval forest

description: Primeval forests provide a reference point to understand the origins and evolution of mating systems because they offer a unique, undisturbed environment where natural selection and ecological interactions play out in their original context. We established rates of extra-pair paternity (EPP) for two bird species referential to evolutionary ecology: blue tit and great tit, breeding in natural cavities of the sole remnant of European lowland primeval forests preserved in Białowieża National Park. Genotype-by-sequencing of 889 blue tits and 1,256 great tits revealed that 48% of blue tit broods and 39% great tit broods were of mixed paternity, with 15% blue tit and 14% great tit nestlings not sired by their social father. These referential levels align with median values of EPP reported in nestbox studies in secondary and managed forests, suggesting that certain reproductive strategies are advantageous across diverse environments. Observed promiscuity levels did not affect reproductive success or parental investment, indicating no or limited adaptive value for promiscuity in the context of a primeval forest ecosystem. Our study underscores how primeval habitats provide unparalleled insights into natural selection and mating strategies in wild populations, highlighting the stability and resilience of these strategies across different environmental contexts.
DOI: 10.5281/zenodo.15487049
title: Avian promiscuity in the last European primeval forest

description: Primeval forests provide a reference point to understand the origins and evolution of mating systems because they offer a unique, undisturbed environment where natural selection and ecological interactions play out in their original context. We established rates of extra-pair paternity (EPP) for two bird species referential to evolutionary ecology: blue tit and great tit, breeding in natural cavities of the sole remnant of European lowland primeval forests preserved in Białowieża National Park. Genotype-by-sequencing of 889 blue tits and 1,256 great tits revealed that 48% of blue tit broods and 39% great tit broods were of mixed paternity, with 15% blue tit and 14% great tit nestlings not sired by their social father. These referential levels align with median values of EPP reported in nestbox studies in secondary and managed forests, suggesting that certain reproductive strategies are advantageous across diverse environments. Observed promiscuity levels did not affect reproductive success or parental investment, indicating no or limited adaptive value for promiscuity in the context of a primeval forest ecosystem. Our study underscores how primeval habitats provide unparalleled insights into natural selection and mating strategies in wild populations, highlighting the stability and resilience of these strategies across different environmental contexts.
DOI: 10.15468/dl.d939zt
title: Occurrence Download

description: A dataset containing 602181 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Observation",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year 2010-2025"
 ]
}

 The dataset includes 602181 records from 54 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004064-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5066/p14wpcuq
title: Yucaipa Integrated Hydrologic Model: simulating future climate scenarios in the Yucaipa Valley Watershed, San Bernardino and Riverside Counties, California

description: Managing water resources in semiarid watersheds is challenging because of limited water supply and uncertain impacts of future climate conditions on groundwater resources. This paper examines the impact of future climate changes on the urban Yucaipa Valley watershed in southern California using an integrated hydrological model referred to herein as the Yucaipa model. Coupled Groundwater and Surface-water FLOW (GSFLOW) modeling software was used to simulate the nonlinear relationships between climate trends and precipitation partitioning into evapotranspiration (ET), runoff, and subsurface storage. Four global climate models (also known as general circulation models or GCMs), each with two greenhouse-gas (GHG) scenarios: Representative Concentration Pathway 4.5 (RCP45) (low emissions) and RCP85 (high emissions) are used to project varying future climate conditions. GCMs include the Canadian Earth System Model (CanESM2), Centre National de Recherches Météorologiques Climate Model version 5 (CNRM-CM5), Hadley Centre Global Environment Model version 2 – Earth System (HadGEM2-ES), and Model for Interdisciplinary Research on Climate version 5 (MIROC5) models. RCP85 scenarios tend to be wetter and warmer than RCP45, and in some cases the increased precipitation offsets increased loss to ET. The Yucaipa model's simulated hydrological conditions using climate projections predict decreased groundwater in storage in most scenarios due to increased natural ET, vegetation consumptive use, and streamflow out of the watershed. Only scenarios with substantial increases in annual precipitation were able to maintain groundwater in storage approximately the same as at the end of the historical period. The study also highlights increased future aridity despite increased precipitation, and larger precipitation events, which increase the risk of urban floods and decrease stream leakage.
DOI: 10.6084/m9.figshare.29109137
title: SA1_prol_1

description: NU1 cells Chipseq data
DOI: 10.15468/dl.tgc7vs
title: Occurrence Download

description: A dataset listing the 2 species recorded in GBIF matching the query:
{
 "and" : [
 "Continent is Europe",
 "Country is Portugal",
 "TaxonKey is Lycaena bleusei Oberthür, 1884"
 ]
}

 The dataset's 2 records were derived from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009688-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yvxypv
title: Occurrence Download

description: A dataset containing 500 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Specimen, Occurrence evidence)",
 "Depth 500.0-9999.0m",
 "Geometry POLYGON((90 0,180 0,180 70,90 70,90 0))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Synaphobranchidae"
 ]
}

 The dataset includes 500 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009535-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jn248x
title: Occurrence Download

description: A dataset containing 2979 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-28.30049 38.79841,-28.37024 38.74897,-28.30683 38.65495,-28.05954 38.56081,-27.7742 38.45164,-27.70445 38.57072,-28.30049 38.79841))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Araneae"
 ]
}

 The dataset includes 2979 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009536-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.