cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.18166549
title: Rapid Personalized Computational Modeling of the Wrist - Data

description: Project Description

This work was performed at Mayo Clinic in Rochester, MN, USA.

It is part of a bigger project to use four-dimensional computed tomography data to develop and calibrate computational models of the human hand and wrist for recreating joint dynamics, with the ultimate goal being to improve the diagnosis and treatment of soft-tissue injuries of the hand and wrist. The work is funded by several NIH grants, as well as internal funding from Mayo Clinic. The project includes a data collected from a previous study on in vivo healthy controls collected with previous IRB approval (NCT03193996) using a combination of static computed tomography (3DCT) and dynamic computed tomography (4DCT = 3DCT + time). In this case, a subset of three asymptomatic individuals from that dataset were used. A novel computational workflow was used that combined non-linear morphing algorithms based on generalized regression neural networks (GRNNs) with algorithmic techniques to automatically create computational finite element models of each individuals native geometries. This workflow was applied to the three asymptomatic participants to develop models with personalized wrist bone geometries and material properties. Each model was then used with an optimization routine as well as a Monte Carlo (MC) analysis to demonstrate the utility of these models towards developing Digital Twins and for in silico clinical trials.

In total the work has provided the raw geometries and kinematics for the three participants, the calibrated computational model for Participant 2, and the working MATLAB code to develop new personalized models from the original bony geometries. This work is shared with IRB approval (25-012254).

This repository contains all of the raw data including the geometries and the kinematics for the three participants. The full set of deliverables are including in the following links:

Data: www.doi.org/10.5281/zenodo.18166549

Model: www.doi.org/10.5281/zenodo.18166611

Software/Code: www.doi.org/10.5281/zenodo.18166629






Licensing

This work is provided under a Creative Commons Attribution 4.0 International. You are free to use the work for your own purposes; however, we ask that you cite the work that made it possible:

Thor E. Andreassen, Taylor P. Trentadue, Andrew R. Thoreson, Kai-Nan An, Sanjeev Kakar, Kristin D. Zhao, "Rapid Development of Efficient Participant-Specific Computational Models of the Wrist", arXiv, 25 May 2025, DOI: 10.48550/arXiv.2505.19282

and

Thor E. Andreassen, Taylor P. Trentadue, Andrew R. Thoreson, Kai-Nan An, Sanjeev Kakar, Kristin D. Zhao, "Rapid Personalized Computational Modeling of the Wrist - Data", Zenodo, 14 January 2026, DOI: 10.5281/zenodo.18166549

File Structure

All files are organized within folders and name accordingly. For descriptions of the files and folder, please download the README.txt file to see the details.
DOI: 10.15468/dl.m22c98
title: Occurrence Download

description: A dataset containing 258 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Glicophyllum selerianum"
 ]
}

 The dataset includes 258 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003445-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8zx4rm
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{"type":"and","predicates":[{"type":"within","geometry":"POLYGON ((100.1 2.784176, 100.029655 2.778607, 99.961044 2.762037, 99.89585700000001 2.734876, 99.835703 2.697792, 99.782061 2.651699, 99.736254 2.597734, 99.69940800000001 2.537225, 99.672431 2.471664, 99.655985 2.402665, 99.65047300000001 2.331928, 99.656029 2.261194, 99.672515 2.192205, 99.699524 2.12666, 99.73639 2.066171, 99.782205 2.012227, 99.83583900000001 1.966156, 99.895974 1.929092, 99.961128 1.901946, 100.029699 1.885387, 100.1 1.879821, 100.170301 1.885387, 100.238872 1.901946, 100.304026 1.929092, 100.364161 1.966156, 100.417795 2.012227, 100.46361 2.066171, 100.500476 2.12666, 100.527485 2.192205, 100.543971 2.261194, 100.549527 2.331928, 100.544015 2.402665, 100.527569 2.471664, 100.500592 2.537225, 100.463746 2.597734, 100.417939 2.651699, 100.364297 2.697792, 100.304143 2.734876, 100.238956 2.762037, 100.170345 2.778607, 100.1 2.784176))"},{"type":"equals","key":"CLASS_KEY","value":"212","matchCase":false},{"type":"greaterThanOrEquals","key":"YEAR","value":"2015","matchCase":false},{"type":"not","predicate":{"type":"in","key":"BASIS_OF_RECORD","values":["MATERIAL_CITATION","MATERIAL_SAMPLE","PRESERVED_SPECIMEN"],"matchCase":false}},{"type":"lessThanOrEquals","key":"COORDINATE_UNCERTAINTY_IN_METERS","value":"10000","matchCase":false},{"type":"equals","key":"LICENSE","value":"CC BY 4.0","matchCase":false}]}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003444-260120142942310/datasets/export for details.
DOI: 10.5281/zenodo.14590345
title: Supplementary data for "Comprehensive aerial surveys find a reduction in Permian Basin methane intensity from 2020-2023"

description: Supplementary data, mostly detailed numerical results, from Sherwin et al. 2025, "Comprehensive aerial surveys find a reduction in Permian Basin methane intensity from 2020-2023".
DOI: 10.5281/zenodo.18331639
title: Supplementary data for "Comprehensive aerial surveys find a reduction in Permian Basin methane intensity from 2020-2023"

description: Supplementary data, mostly detailed numerical results, from Sherwin et al. 2025, "Comprehensive aerial surveys find a reduction in Permian Basin methane intensity from 2020-2023".
DOI: 10.5281/zenodo.18331653
title: County Health Rankings & Roadmaps relational data annual release
DOI: 10.7266/09mdfxq0
title: CTD data salinity, temperature, depth collected aboard the R/V Point Sur cruise PS25_17 (DP10, in-situ deep seawater and associated fauna) in the Gulf of Mexico from 2025-04-22 to 2025-05-02
DOI: 10.7910/dvn/uqyn1d
title: Replication Data for EJPR Publication: Women Talking: Bringing the Environment into UK Parliamentary Speeches

description: Replication data for Women Talking:
Bringing the Environment into UK Parliamentary Speeches published in the European Journal of Political Research
DOI: 10.15468/dl.pwz83a
title: Occurrence Download

description: A dataset containing 77208 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Salvelinus fontinalis"
 ]
}

 The dataset includes 77208 records from 207 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003402-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18331544
title: Technical Validation of the Q-Strings Framework: Scalability and Ground State Convergence in TFIM (6-20 Qubits)

description: We present Q-Strings, a computational framework for the simulation of string-inspired dynamics using variational quantum algorithms. We implement a mapping of vibrational degrees of freedom onto a quantum register, achieving ground state convergence through the Variational Quantum Eigensolver (VQE).

This technical dataset provides validation metrics and scalability results for the Transverse Field Ising Model (TFIM) across 6, 10, 15, and 20 qubits. The results highlight a specific configuration where optimal θ parameters show symmetric convergence to π values (14-decimal precision) and Von Neumann entropy profiles consistent with the system's topology (S_{VN}  ≈ 1.144 for N=20).

Data Availability: The technical checkpoint files (JSON format) containing the specific θ parameters and Hamiltonian mappings are strictly proprietary to protect the framework's architectural novelty. These records are maintained for institutional audit or peer-review purposes and are available only upon formal, reasonable request to the author.
DOI: 10.5281/zenodo.18331543
title: Technical Validation of the Q-Strings Framework: Scalability and Ground State Convergence in TFIM (6-20 Qubits)

description: We present Q-Strings, a computational framework for the simulation of string-inspired dynamics using variational quantum algorithms. We implement a mapping of vibrational degrees of freedom onto a quantum register, achieving ground state convergence through the Variational Quantum Eigensolver (VQE).

This technical dataset provides validation metrics and scalability results for the Transverse Field Ising Model (TFIM) across 6, 10, 15, and 20 qubits. The results highlight a specific configuration where optimal θ parameters show symmetric convergence to π values (14-decimal precision) and Von Neumann entropy profiles consistent with the system's topology (S_{VN}  ≈ 1.144 for N=20).

Data Availability: The technical checkpoint files (JSON format) containing the specific θ parameters and Hamiltonian mappings are strictly proprietary to protect the framework's architectural novelty. These records are maintained for institutional audit or peer-review purposes and are available only upon formal, reasonable request to the author.
DOI: 10.7910/dvn/lfwzmc
title: Village Common Forest management Dataset

description: From May 2021 to October 2022, this study assessed the livelihood status in the CHTs' VCFs and compared the impact of NGO-led restoration efforts with non-intervention regions. A total of 30 VCFs were sampled out of 314, including 15 with NGO intervention and 15 without.
DOI: 10.5281/zenodo.14974979
title: Climate Time Series: precipitation, SST, ONI and random time series

description: Dataset composed of climate monthly time series ranging from 1950 to 2016.

Variables:



Norheastern Brazil precipitation



NEB_highest: region with the highest Pearson correlation with ONI and TNAtl

NEB_mean: average precipitation of the whole region of interest

NEB_lowest: region with the lowest Pearson correlation with ONI and TNAtl



Southern Ural Mountains region precipitation (SRUNK)

Oceanic Niño Index (ONI)

Tropical North Atlantic SST (TNAtl)

Gaussian Random Time Series (random_ts)

Prior time series processed by a Wavelet filter (except for the the random_ts)



wavelet_NEB_highest

wavelet_NEB_mean

wavelet_NEB_lowest

wavelet_SRUNK

wavelet_AtlN

wavelet_ONI




======================================================================

The dataset was created and used in the following paper:

Evaluation of Time Series Causal Detection Methods on the Influence of Pacific and Atlantic Ocean over Northeastern Brazil Precipitation (pdf)(pdf)

JEC Cruz, MT Kayano, AJP Calheiros, SR Garcia, MG QuilesInternational Conference on Computational Science and Its Applications (ICCSA), 2023

 

more information can be found in https://jkreuz.github.io/publications/
DOI: 10.5281/zenodo.14974978
title: Climate Time Series: precipitation, SST, ONI and random time series

description: Dataset composed of climate monthly time series ranging from 1950 to 2016.

Variables:



Norheastern Brazil precipitation



NEB_highest: region with the highest Pearson correlation with ONI and TNAtl

NEB_mean: average precipitation of the whole region of interest

NEB_lowest: region with the lowest Pearson correlation with ONI and TNAtl



Southern Ural Mountains region precipitation (SRUNK)

Oceanic Niño Index (ONI)

Tropical North Atlantic SST (TNAtl)

Gaussian Random Time Series (random_ts)

Prior time series processed by a Wavelet filter (except for the the random_ts)



wavelet_NEB_highest

wavelet_NEB_mean

wavelet_NEB_lowest

wavelet_SRUNK

wavelet_AtlN

wavelet_ONI




======================================================================

The dataset was created and used in the following paper:

Evaluation of Time Series Causal Detection Methods on the Influence of Pacific and Atlantic Ocean over Northeastern Brazil Precipitation (pdf)(pdf)

JEC Cruz, MT Kayano, AJP Calheiros, SR Garcia, MG QuilesInternational Conference on Computational Science and Its Applications (ICCSA), 2023

 

more information can be found in https://jkreuz.github.io/publications/
DOI: 10.15468/dl.mnwhpd
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cleyera serrulata"
 ]
}

 The dataset includes 12 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003450-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gsa8pp
title: Occurrence Download

description: A dataset containing 573 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Megalonyx jeffersoni"
 ]
}

 The dataset includes 573 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003448-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.neczzj
title: Occurrence Download

description: A dataset containing 135 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "NetworkKey is 99d66b6c-9087-452f-a9d4-f15f2c2d0e7e",
 "TaxonKey is Chordata"
 ]
 },
 {
 "and" : [
 "TaxonKey is one of (Junco hyemalis [GBIF Backbone Taxonomy])",
 "InstitutionCode is one of (SBMNH)"
 ]
 }
 ]
}

 The dataset includes 135 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003449-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17909/kzyx-pn27
title: MIRI imaging of gam Oph

description: MIRI imaging of gam Oph, a reference star (zet Ser) and the sky background with the F1500W and F2550W filters.
DOI: 10.7910/dvn/qaelw6
title: Replication Data for: Network Pharmacology and Molecular Simulations Reveal Amentoflavone and Myo-Inositol as Potential Multi-Target Antivirals from Selaginella bryopteris

description: File associated a Molecular Simulation
DOI: 10.7910/dvn/5vurms
title: Supplementary Figures and Tables for "Quantifying the causal impact of diseases on lactation features in Holstein cattle based on causal inference approaches"

description: Supplementary Figures and Tables for "Quantifying the causal impact of diseases on lactation features in Holstein cattle based on causal inference approaches"

Supplementary Tables S1-S26
Supplementary Figures S1-S3
DOI: 10.5281/zenodo.17968258
title: Experimental Validation of ϕ-Geometry and Hermetic Equilibrium in Self-Organizing Particle Systems

description: Following the theoretical discovery that coupled chaotic oscillators spontaneously converge toGolden Ratio (ϕ ≈ 1.61803) coupling for optimal information flow, we investigate whether thisgeometric optimum manifests in physical particle systems. We construct a spatial extension whereparticle positions represent physical coordinates and internal states represent information carriers.The system implements inverse ϕ-control: spatial arrangement self-adjusts to maintain HermeticEquilibrium (control ratio R = σ2m/σ2s ≈ 1.096). Remarkably, the system simultaneously maintainsperfect ϕ-attraction (α/β = 1.6180339836±5.1×10−9) while achieving Hermetic Equilibrium (R =1.096028 ± 2.8 × 10−5). This represents the first experimental demonstration that ϕ-geometry andbalanced information flow are fundamental, co-emergent properties of optimally coupled complexsystems.
DOI: 10.5281/zenodo.17968259
title: Experimental Validation of ϕ-Geometry and Hermetic Equilibrium in Self-Organizing Particle Systems

description: Following the theoretical discovery that coupled chaotic oscillators spontaneously converge toGolden Ratio (ϕ ≈ 1.61803) coupling for optimal information flow, we investigate whether thisgeometric optimum manifests in physical particle systems. We construct a spatial extension whereparticle positions represent physical coordinates and internal states represent information carriers.The system implements inverse ϕ-control: spatial arrangement self-adjusts to maintain HermeticEquilibrium (control ratio R = σ2m/σ2s ≈ 1.096). Remarkably, the system simultaneously maintainsperfect ϕ-attraction (α/β = 1.6180339836±5.1×10−9) while achieving Hermetic Equilibrium (R =1.096028 ± 2.8 × 10−5). This represents the first experimental demonstration that ϕ-geometry andbalanced information flow are fundamental, co-emergent properties of optimally coupled complexsystems.
DOI: 10.15468/dl.hcppr5
title: Occurrence Download

description: A dataset containing 68633 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is European Green Crab surveys - DFO Pacific",
 {
 "or" : [
 "Geometry POLYGON((-139.71179 55.46799,-132.32165 55.46799,-132.32165 58.22322,-139.71179 58.22322,-139.71179 55.46799))",
 "Geometry POLYGON((-151.3172 44.47561,-119.53379 44.47561,-119.53379 61.48784,-151.3172 61.48784,-151.3172 44.47561))"
 ]
 },
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Carcinus maenas"
 ]
}

 The dataset includes 68633 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003442-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7910/dvn/wtmgty
title: Replication Data for: Re-Imagining the Epistemic Possibilities of GPT for Public Administration Research in Competitive Settings

description: The replication package contains the code and data to produce the main tables and figures of the paper.
DOI: 10.5683/sp3/gy5k1c
title: United States historical business data
title: US business database

description: Product contains one data file (.txt format) for each year from 1997-2023 containing 11-15 million records per year. Records provide information about business location (including address, census block, census tract & lat/long coordinates), number of employees, sales volume, NAICS & SIC codes, unique identifier across time for businesses and parent entities.
description: These files are too large to open in Excel; you will need to work with them programmatically or using statistical analysis software. Contact the Map & Data Library if you require assistance working with these files.
description: Added 2023 and 2024 Business Full Files
DOI: 10.6084/m9.figshare.25905279
title: TMX2 potentiates cell viability of hepatocellular carcinoma by promoting autophagy and mitophagy

description: The dysregulation of membrane protein expression has been implicated in tumorigenesis and progression, including hepatocellular carcinoma (HCC). In this study, we aimed to identify membrane proteins that modulate HCC viability. To achieve this, we performed a CRISPR activation screen targeting human genes encoding membrane-associated proteins, revealing TMX2 as a potential driver of HCC cell viability. Gain- and loss-of-function experiments demonstrated that TMX2 promoted growth and tumorigenesis of HCC. Clinically, TMX2 was an independent prognostic factor for HCC patients. It was significantly upregulated in HCC tissues and associated with poor prognosis of HCC patients. Mechanistically, TMX2 was demonstrated to promote macroautophagy/autophagy by facilitating KPNB1 nuclear export and TFEB nuclear import. In addition, TMX2 interacted with VDAC2 and VADC3, assisting in the recruitment of PRKN to defective mitochondria to promote cytoprotective mitophagy during oxidative stress. Most interestingly, HCC cells responded to oxidative stress by upregulating TMX2 expression and cell autophagy. Knockdown of <i>TMX2</i> enhanced the anti-tumor effect of lenvatinib. In conclusion, our findings emphasize the pivotal role of TMX2 in driving the HCC cell viability by promoting both autophagy and mitophagy. These results suggest that TMX2 May serve as a prognostic marker and promising therapeutic target for HCC treatment. <b>Abbreviation</b>: CCCP: Carbonyl cyanide 3-chlorophenylhydrazone; Co-IP: co-immunoprecipitation; CRISPR: clustered regularly interspaced short palindromic repeat; ER: endoplasmic reticulum; HCC: hepatocellular carcinoma; KPNB1: karyopherin subunit beta 1; PRKN: parkin RBR E3 ubiquitin protein ligase; ROS: reactive oxygen species; TFEB: transcription factor EB; TMX2: thioredoxin related transmembrane protein 2; VDAC2: voltage dependent anion channel 2; VDAC3: voltage dependent anion channel 3; WB: western blot.
DOI: 10.6084/m9.figshare.25905279.v1
title: TMX2 potentiates cell viability of hepatocellular carcinoma by promoting autophagy and mitophagy

description: The dysregulation of membrane protein expression has been implicated in tumorigenesis and progression, including hepatocellular carcinoma (HCC). In this study, we aimed to identify membrane proteins that modulate HCC viability. To achieve this, we performed a CRISPR activation screen targeting human genes encoding membrane-associated proteins, revealing TMX2 as a potential driver of HCC cell viability. Gain- and loss-of-function experiments demonstrated that TMX2 promoted growth and tumorigenesis of HCC. Clinically, TMX2 was an independent prognostic factor for HCC patients. It was significantly upregulated in HCC tissues and associated with poor prognosis of HCC patients. Mechanistically, TMX2 was demonstrated to promote macroautophagy/autophagy by facilitating KPNB1 nuclear export and TFEB nuclear import. In addition, TMX2 interacted with VDAC2 and VADC3, assisting in the recruitment of PRKN to defective mitochondria to promote cytoprotective mitophagy during oxidative stress. Most interestingly, HCC cells responded to oxidative stress by upregulating TMX2 expression and cell autophagy. Knockdown of <i>TMX2</i> enhanced the anti-tumor effect of lenvatinib. In conclusion, our findings emphasize the pivotal role of TMX2 in driving the HCC cell viability by promoting both autophagy and mitophagy. These results suggest that TMX2 May serve as a prognostic marker and promising therapeutic target for HCC treatment. <b>Abbreviation</b>: CCCP: Carbonyl cyanide 3-chlorophenylhydrazone; Co-IP: co-immunoprecipitation; CRISPR: clustered regularly interspaced short palindromic repeat; ER: endoplasmic reticulum; HCC: hepatocellular carcinoma; KPNB1: karyopherin subunit beta 1; PRKN: parkin RBR E3 ubiquitin protein ligase; ROS: reactive oxygen species; TFEB: transcription factor EB; TMX2: thioredoxin related transmembrane protein 2; VDAC2: voltage dependent anion channel 2; VDAC3: voltage dependent anion channel 3; WB: western blot.