cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.15171312
title: HybridCT Dataset -- ground truth, training, predicted data, and model parameters

description: This dataset consists of three parts:





Ground truth data: Microphysical cloud properties from Large Eddy Simulation for LWC (liquid water content) and reff (effective droplet radius) in 80x80x4 km domain with 40 m resolution.

Training data: collection of input data and labels for training the HybridCT `emulator`



Input: Synthetic multi-angle radiance fields which are generated from the ground truth cloud fields via radiative transfer simulations. The synthetic multi-angle images represent the viewing angle geometry of the Multi-angle Imaging Spectroradiometer (MISR) onboard the Terra spacecraft at its red channel (670 nm).

Labels: Multi-angle optical thickness fields directly computed from the ground truth cloud fields.



Predicted data: Multi-angle optical thickness fields predicted by the HybridCT `emulator` which serve as input for the `reconstruction`.

Model artifacts: parameters for the trained U-Net machine learning model to predict optical thickness maps from multi-angle radiance input.
DOI: 10.5281/zenodo.15171311
title: HybridCT Dataset -- ground truth, training, predicted data, and model parameters

description: This dataset consists of three parts:





Ground truth data: Microphysical cloud properties from Large Eddy Simulation for LWC (liquid water content) and reff (effective droplet radius) in 80x80x4 km domain with 40 m resolution.

Training data: collection of input data and labels for training the HybridCT `emulator`



Input: Synthetic multi-angle radiance fields which are generated from the ground truth cloud fields via radiative transfer simulations. The synthetic multi-angle images represent the viewing angle geometry of the Multi-angle Imaging Spectroradiometer (MISR) onboard the Terra spacecraft at its red channel (670 nm).

Labels: Multi-angle optical thickness fields directly computed from the ground truth cloud fields.



Predicted data: Multi-angle optical thickness fields predicted by the HybridCT `emulator` which serve as input for the `reconstruction`.

Model artifacts: parameters for the trained U-Net machine learning model to predict optical thickness maps from multi-angle radiance input.
DOI: 10.5281/zenodo.17786045
title: Downstream datasets of mRNABERT
DOI: 10.5281/zenodo.17786044
title: Downstream datasets of mRNABERT
DOI: 10.7914/sc77-gs90
title: Fagnano fault Unveiled: Earthquake and Geodetic Observations, Tierra de Fuego, Chilean Patagonia

description: The network focuses on the Fagnano Fault, aiming to detect background level seismicity in the area delimited by the Azopardo Bay to the West and the Fagnano Lake to the East. The study was supported by the Chilean Research and Development National Agency (ANID), initiation FONDECYT project 11220513 (PI: Francisco Delgado). This network consists of 10 Digos Datacube3 datalogger equipped with 3 component geophones, for a duration of 3 months.
DOI: 10.15468/dl.mapa56
title: Occurrence Download

description: A dataset containing 80 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Türkiye",
 "TaxonKey is Halcyon smyrnensis",
 "Year 2025-2025"
 ]
}

 The dataset includes 80 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021709-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17786387
title: Raw Values of Metabolite Abundance Profiles (CSV Dataset)
DOI: 10.5281/zenodo.17786388
title: Raw Values of Metabolite Abundance Profiles (CSV Dataset)
DOI: 10.15468/dl.m24wg6
title: Occurrence Download

description: A dataset containing 4346 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Türkiye",
 "OccurrenceStatus is Present",
 "TaxonKey is Cettia cetti",
 "Year 2024-2025"
 ]
}

 The dataset includes 4346 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021710-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/dsv/13954802
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.5281/zenodo.17786261
title: lncAPNet enables the deciphering of lncRNA–mRNA connections in patient transcriptomic data

description: Motivation

Long non-coding RNAs (lncRNAs) regulate gene expression through chromatin remodeling, transcriptional control, and post-transcriptional modulation, influencing physiological cell homeostasis but also disease onset. Yet most transcriptomic and network-based studies rely on descriptive linear co-expression analyses, missing nonlinear and mechanistic insights. Emerging ML/DL methods offer promise but remain limited by data sparsity, noise, insufficient biological priors, and poor interpretability, constraining systems-level lncRNA-mRNA motif discovery.

Results

In this manuscript, we introduce lncAPNet, an extended version of APNet workflow, which integrates graph-based nonlinear inference of lncRNA–mRNA interactions using NetBID2’s activity logic within an lncRNA-focused SJARACNe co-expression network, coupled with PASNet, a biologically informed sparse deep learning model. This framework enables explainable identification of lncRNA drivers in two different cancer type case studies, Chronic Lymphocytic Leukemia (CLL) and Prostate Adenocarcinoma (PRAD), uncovering lncRNA drivers that illuminate lncRNA-mediated programs in cancer progression.

Availability and implementation

lncAPNet’s R scripts, Python scripts, and methodologies are available at github repository:

https://github.com/BiodataAnalysisGroup/lncAPNet
DOI: 10.5281/zenodo.17786260
title: lncAPNet enables the deciphering of lncRNA–mRNA connections in patient transcriptomic data

description: Motivation

Long non-coding RNAs (lncRNAs) regulate gene expression through chromatin remodeling, transcriptional control, and post-transcriptional modulation, influencing physiological cell homeostasis but also disease onset. Yet most transcriptomic and network-based studies rely on descriptive linear co-expression analyses, missing nonlinear and mechanistic insights. Emerging ML/DL methods offer promise but remain limited by data sparsity, noise, insufficient biological priors, and poor interpretability, constraining systems-level lncRNA-mRNA motif discovery.

Results

In this manuscript, we introduce lncAPNet, an extended version of APNet workflow, which integrates graph-based nonlinear inference of lncRNA–mRNA interactions using NetBID2’s activity logic within an lncRNA-focused SJARACNe co-expression network, coupled with PASNet, a biologically informed sparse deep learning model. This framework enables explainable identification of lncRNA drivers in two different cancer type case studies, Chronic Lymphocytic Leukemia (CLL) and Prostate Adenocarcinoma (PRAD), uncovering lncRNA drivers that illuminate lncRNA-mediated programs in cancer progression.

Availability and implementation

lncAPNet’s R scripts, Python scripts, and methodologies are available at github repository:

https://github.com/BiodataAnalysisGroup/lncAPNet
DOI: 10.6084/m9.figshare.30760784
title: Supplementary Material for: Long-term Control After Intermittent Reintroduction of Enfortumab Vedotin in Metastatic Urothelial Carcinoma: A Case Report

description: Introduction
Enfortumab vedotin (EV), an antibody–drug conjugate targeting Nectin-4, has become a standard treatment option for metastatic urothelial carcinoma (mUC) following failure of platinum-based chemotherapy and immune checkpoint inhibitors. However, adverse events such as skin toxicity often necessitate dose modification or temporary discontinuation.

Case Presentation
We report the case of a 72-year-old woman with mUC who achieved a long-team partial response to EV despite experiencing grade 2 skin toxicity that required temporary treatment interruption. After symptom resolution, EV was successfully reintroduced at a reduced dose, and clinical response was maintained.

Conclusion
Temporary discontinuation of EV due to adverse events (AEs) followed by intermittent reintroduction resulted in long-term disease control in this patient with mUC. This case suggests that rechallenging EV after treatment interruption may be a feasible approach in selected patients, underscoring the importance of careful AE management in real-world practice.
DOI: 10.6084/m9.figshare.30760784.v1
title: Supplementary Material for: Long-term Control After Intermittent Reintroduction of Enfortumab Vedotin in Metastatic Urothelial Carcinoma: A Case Report

description: Introduction
Enfortumab vedotin (EV), an antibody–drug conjugate targeting Nectin-4, has become a standard treatment option for metastatic urothelial carcinoma (mUC) following failure of platinum-based chemotherapy and immune checkpoint inhibitors. However, adverse events such as skin toxicity often necessitate dose modification or temporary discontinuation.

Case Presentation
We report the case of a 72-year-old woman with mUC who achieved a long-team partial response to EV despite experiencing grade 2 skin toxicity that required temporary treatment interruption. After symptom resolution, EV was successfully reintroduced at a reduced dose, and clinical response was maintained.

Conclusion
Temporary discontinuation of EV due to adverse events (AEs) followed by intermittent reintroduction resulted in long-term disease control in this patient with mUC. This case suggests that rechallenging EV after treatment interruption may be a feasible approach in selected patients, underscoring the importance of careful AE management in real-world practice.
DOI: 10.6084/m9.figshare.30760787
title: Supplementary Material for: Predictors of Delayed Graft Function in Living and Deceased Donor Kidney transplantation: A Single-Centre Retrospective Cohort Study from India

description: Introduction: Delayed graft function (DGF) remains a common early complication, particularly after deceased donor kidney transplantation (DDKT). We sought to identify predictors in an Indian centre.
Methods: We retrospectively analysed 324 consecutive transplants (living donor 174; deceased donor 150) performed between 2021 and 2023. The primary endpoint was DGF, defined as dialysis within seven postoperative days. Patient characteristics were compared using appropriate parametric or non-parametric tests after normality assessment. Multivariable logistic regression identified independent predictors.
Results: Early graft function categories were: living donor kidney transplantation (LDKT)— Immediate graft function (IGF) 159/174 (91.4%), DGF 15/174 (8.6%); DDKT—IGF 81/150 (54.0%), DGF 69/150 (46.0%). Independent predictors of early dysfunction included higher donor terminal creatinine, extended-criteria donor status, recipient diabetes, higher HLA mismatch, perioperative hypotension, and longer cold ischaemia time.
Conclusion: Among largely non-modifiable donor factors, cold ischaemia time and perioperative haemodynamics emerged as actionable risk factors for early graft dysfunction, especially in deceased donor recipients. Targeted intraoperative monitoring and streamlined organ allocation pathways may mitigate these risks.
DOI: 10.6084/m9.figshare.30760787.v1
title: Supplementary Material for: Predictors of Delayed Graft Function in Living and Deceased Donor Kidney transplantation: A Single-Centre Retrospective Cohort Study from India

description: Introduction: Delayed graft function (DGF) remains a common early complication, particularly after deceased donor kidney transplantation (DDKT). We sought to identify predictors in an Indian centre.
Methods: We retrospectively analysed 324 consecutive transplants (living donor 174; deceased donor 150) performed between 2021 and 2023. The primary endpoint was DGF, defined as dialysis within seven postoperative days. Patient characteristics were compared using appropriate parametric or non-parametric tests after normality assessment. Multivariable logistic regression identified independent predictors.
Results: Early graft function categories were: living donor kidney transplantation (LDKT)— Immediate graft function (IGF) 159/174 (91.4%), DGF 15/174 (8.6%); DDKT—IGF 81/150 (54.0%), DGF 69/150 (46.0%). Independent predictors of early dysfunction included higher donor terminal creatinine, extended-criteria donor status, recipient diabetes, higher HLA mismatch, perioperative hypotension, and longer cold ischaemia time.
Conclusion: Among largely non-modifiable donor factors, cold ischaemia time and perioperative haemodynamics emerged as actionable risk factors for early graft dysfunction, especially in deceased donor recipients. Targeted intraoperative monitoring and streamlined organ allocation pathways may mitigate these risks.
DOI: 10.6084/m9.figshare.30760790
title: Supplementary Material for: Characteristics and long-term prognosis of celiac disease: comparisons between patients diagnosed either in childhood or adulthood

description: Introduction: It is plausible but not yet proven that early celiac disease diagnosis prevents long-term complications of untreated disease. Our aim was to compare phenotype and health outcomes in currently adult celiac disease patients diagnosed either in childhood (&lt;18 years) or adulthood.

Methods: Data on 1059 patients were collected from medical records at diagnosis and with questionnaires and structured interviews after long-term follow-up. Associations between timing of diagnosis and long-term health were studied with regression models. 

Results: Patients diagnosed in childhood (n=239) were more often males (32% vs. 23%, p=0.004), currently younger (27 vs. 54 years, p&lt;0.001), more often screen-detected (20% vs. 14%, p&lt;0.001), and reported lower adherence to gluten-free diet in adulthood (92% vs. 97%, p&lt;0.001) than those diagnosed in adulthood (n=820). After adjusting for clinico-demographic variables and dietary adherence, patients diagnosed in childhood had fewer miscarriages (OR 0.41 [95% CI 0.21-0.80]) but more allergies (1.75 [1.11-2.76]), dermatological diseases excluding dermatitis herpetiformis (1.99 [1.11-3.58]), asthma (2.28 [1.16-4.48]), and depression (2.84 [1.24-6.50]) in adulthood. The groups were comparable in other comorbidities including type 1 diabetes and autoimmune thyroidal diseases, persistent symptoms, and quality of life.

Conclusion: Diagnosis in childhood compared to adulthood was associated with disease phenotype and its effects on long-term comorbidities are complex.
DOI: 10.6084/m9.figshare.30760790.v1
title: Supplementary Material for: Characteristics and long-term prognosis of celiac disease: comparisons between patients diagnosed either in childhood or adulthood

description: Introduction: It is plausible but not yet proven that early celiac disease diagnosis prevents long-term complications of untreated disease. Our aim was to compare phenotype and health outcomes in currently adult celiac disease patients diagnosed either in childhood (&lt;18 years) or adulthood.

Methods: Data on 1059 patients were collected from medical records at diagnosis and with questionnaires and structured interviews after long-term follow-up. Associations between timing of diagnosis and long-term health were studied with regression models. 

Results: Patients diagnosed in childhood (n=239) were more often males (32% vs. 23%, p=0.004), currently younger (27 vs. 54 years, p&lt;0.001), more often screen-detected (20% vs. 14%, p&lt;0.001), and reported lower adherence to gluten-free diet in adulthood (92% vs. 97%, p&lt;0.001) than those diagnosed in adulthood (n=820). After adjusting for clinico-demographic variables and dietary adherence, patients diagnosed in childhood had fewer miscarriages (OR 0.41 [95% CI 0.21-0.80]) but more allergies (1.75 [1.11-2.76]), dermatological diseases excluding dermatitis herpetiformis (1.99 [1.11-3.58]), asthma (2.28 [1.16-4.48]), and depression (2.84 [1.24-6.50]) in adulthood. The groups were comparable in other comorbidities including type 1 diabetes and autoimmune thyroidal diseases, persistent symptoms, and quality of life.

Conclusion: Diagnosis in childhood compared to adulthood was associated with disease phenotype and its effects on long-term comorbidities are complex.
DOI: 10.6084/m9.figshare.30760793
title: Supplementary Material for: Lymphatic Metastasis Predicts Better Response to Nivolumab in Recurrent or Metastatic Gastric Cancer: Insights from Tumor-Draining Lymph Node Immunity and Long-Term Outcomes

description: Background: Nivolumab has become an essential therapeutic agent for patients with advanced or recurrent gastric cancer. However, the impact of metastatic patterns on its clinical efficacy has not been fully elucidated. This study aimed to clarify the association between distinct metastatic patterns and outcomes of nivolumab monotherapy.
Methods: Ninety-two patients with advanced or recurrent gastric cancer who received nivolumab were retrospectively analyzed. Clinicopathological variables, including performance status, HER2 expression, and predominant metastatic pattern, were correlated with survival outcomes and response rates.
Results: The median observation period was 48.3 months. The median overall and progression-free survival for the entire cohort were 5.80 and 2.43 months, respectively. Patients with ECOG performance status 2–3 had significantly shorter survival than those with PS 0–1. HER2-positive status was associated with longer PFS. When stratified by metastatic pattern, the lymph node metastasis group showed markedly longer survival (median OS 35.1 months, PFS 11.9 months) than the peritoneal (OS 4.66, PFS 2.36 months) and hematogenous/other groups (OS 5.80, PFS 2.10 months). The objective response and disease control rates were also significantly higher in the lymph node group.
Conclusion: The pattern of metastatic spread, particularly lymphatic involvement, appears to influence the efficacy of nivolumab in advanced or recurrent gastric cancer. Recognizing metastatic patterns may assist in optimizing patient selection and therapeutic strategies for immune checkpoint blockade.
DOI: 10.6084/m9.figshare.30760793.v1
title: Supplementary Material for: Lymphatic Metastasis Predicts Better Response to Nivolumab in Recurrent or Metastatic Gastric Cancer: Insights from Tumor-Draining Lymph Node Immunity and Long-Term Outcomes

description: Background: Nivolumab has become an essential therapeutic agent for patients with advanced or recurrent gastric cancer. However, the impact of metastatic patterns on its clinical efficacy has not been fully elucidated. This study aimed to clarify the association between distinct metastatic patterns and outcomes of nivolumab monotherapy.
Methods: Ninety-two patients with advanced or recurrent gastric cancer who received nivolumab were retrospectively analyzed. Clinicopathological variables, including performance status, HER2 expression, and predominant metastatic pattern, were correlated with survival outcomes and response rates.
Results: The median observation period was 48.3 months. The median overall and progression-free survival for the entire cohort were 5.80 and 2.43 months, respectively. Patients with ECOG performance status 2–3 had significantly shorter survival than those with PS 0–1. HER2-positive status was associated with longer PFS. When stratified by metastatic pattern, the lymph node metastasis group showed markedly longer survival (median OS 35.1 months, PFS 11.9 months) than the peritoneal (OS 4.66, PFS 2.36 months) and hematogenous/other groups (OS 5.80, PFS 2.10 months). The objective response and disease control rates were also significantly higher in the lymph node group.
Conclusion: The pattern of metastatic spread, particularly lymphatic involvement, appears to influence the efficacy of nivolumab in advanced or recurrent gastric cancer. Recognizing metastatic patterns may assist in optimizing patient selection and therapeutic strategies for immune checkpoint blockade.
DOI: 10.6084/m9.figshare.30760796
title: Supplementary Material for: Abscopal Effect Induced by LAG-3/PD-1 Inhibition and Radiation Therapy in Metastatic Acral Melanoma: A Case Report

description: Introduction: Acral melanoma (AM) is a rare and biologically distinct subtype of melanoma that exhibits poor responsiveness to immune checkpoint inhibitors (ICIs) and limited treatment options. Relatlimab, a LAG-3 inhibitor, in combination with nivolumab, a PD-1 inhibitor, has recently emerged as a dual ICI strategy targeting T-cell exhaustion.
Case Presentation: We report the first documented case of an abscopal effect induced by LAG-3 inhibition and radiation therapy in a man in his 40’s with metastatic amelanotic AM of the right foot. The patient progressed after four cycles of relatlimab plus nivolumab, prompting palliative radiation therapy to a bulky, bleeding foot lesion. Remarkably, the tumor began to regress within one week of initiating radiation. Two months later, the lesion had nearly resolved, and follow-up imaging demonstrated complete disappearance of pulmonary metastases, consistent with a systemic abscopal response.
Conclusion: This case illustrates the potential synergistic effect of sequential LAG-3/PD-1 inhibition followed by radiation therapy in eliciting systemic immune activation in AM. It represents the first reported instance of an abscopal effect associated with relatlimab-based immunotherapy, suggesting that strategic sequencing of immunotherapy and radiation may be critical in overcoming immune resistance in this challenging melanoma subtype.
DOI: 10.6084/m9.figshare.30760796.v1
title: Supplementary Material for: Abscopal Effect Induced by LAG-3/PD-1 Inhibition and Radiation Therapy in Metastatic Acral Melanoma: A Case Report

description: Introduction: Acral melanoma (AM) is a rare and biologically distinct subtype of melanoma that exhibits poor responsiveness to immune checkpoint inhibitors (ICIs) and limited treatment options. Relatlimab, a LAG-3 inhibitor, in combination with nivolumab, a PD-1 inhibitor, has recently emerged as a dual ICI strategy targeting T-cell exhaustion.
Case Presentation: We report the first documented case of an abscopal effect induced by LAG-3 inhibition and radiation therapy in a man in his 40’s with metastatic amelanotic AM of the right foot. The patient progressed after four cycles of relatlimab plus nivolumab, prompting palliative radiation therapy to a bulky, bleeding foot lesion. Remarkably, the tumor began to regress within one week of initiating radiation. Two months later, the lesion had nearly resolved, and follow-up imaging demonstrated complete disappearance of pulmonary metastases, consistent with a systemic abscopal response.
Conclusion: This case illustrates the potential synergistic effect of sequential LAG-3/PD-1 inhibition followed by radiation therapy in eliciting systemic immune activation in AM. It represents the first reported instance of an abscopal effect associated with relatlimab-based immunotherapy, suggesting that strategic sequencing of immunotherapy and radiation may be critical in overcoming immune resistance in this challenging melanoma subtype.