cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.25295959.v1
title: A multi-faceted approach to unravel coding and non-coding gene fusions and target chimeric proteins in ataxia

description: Ataxia represents a heterogeneous group of neurodegenerative disorders characterized by a loss of balance and coordination, often resulting from mutations in genes vital for cerebellar function and maintenance. Recent advances in genomics have identified gene fusion events as critical contributors to various cancers and neurodegenerative diseases. However, their role in ataxia pathogenesis remains largely unexplored. Our study Hdelved into this possibility by analyzing RNA sequencing data from 1443 diverse samples, including cell and mouse models, patient samples, and healthy controls. We identified 7067 novel gene fusions, potentially pivotal in disease onset. These fusions, notably in-frame, could produce chimeric proteins, disrupt gene regulation, or introduce new functions. We observed conservation of specific amino acids at fusion breakpoints and identified potential aggregate formations in fusion proteins, known to contribute to ataxia. Through AI-based protein structure prediction, we identified topological changes in three high-confidence fusion proteins—TEN1-ACOX1, PEX14-NMNAT1, and ITPR1-GRID2—which could potentially alter their functions. Subsequent virtual drug screening identified several molecules and peptides with high-affinity binding to fusion sites. Molecular dynamics simulations confirmed the stability of these protein-ligand complexes at fusion breakpoints. Additionally, we explored the role of non-coding RNA fusions as miRNA sponges. One such fusion, <i>RP11-547P4-FLJ33910</i>, showed strong interaction with hsa-miR-504-5p, potentially acting as its sponge. This interaction correlated with the upregulation of hsa-miR-504-5p target genes, some previously linked to ataxia. In conclusion, our study unveils new aspects of gene fusions in ataxia, suggesting their significant role in pathogenesis and opening avenues for targeted therapeutic interventions. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.25245702
title: CDH1 gene as biomarker towards breast cancer prediction*

description: Breast cancer is considered to be happened due to genetic aberration. Out of several genes expressed, it is found that cadherin 1, type 1 (CDH1) is responsible in several ways to control the metabolic order in human. Deregulation of the function of protein E-cadherin, expressed from CDH1 plays an important role in lobular breast cancer. In order to understand the root cause of this recent claim, we focus on CDH1 gene: whether the genetic information translated due to any deviation/alteration/modification in its sequence is related to the occurrence of the different types breast cancer. Towards this end, quantitative analysis of different biophysical and bio-chemical properties of CDH1 gene in genomic and proteomic levels from the available genomic (cDNA) sequences of CDH1 gene (obtained from the COSMIC Database for 78 patients, suffering from various types of breast cancer) clearly emphasizes that alternation/modification in the sequence of the CDH1 gene can be detrimental. Furthermore, Random forest, K-nearest neighbour and stochastic gradient descent (SGD) algorithms are applied on the derived dataset to classify the types of breast cancer, and to validate our hypothesis regarding the acute role of CDH1 as potential bio marker for breast cancer. Analysis of the mutated CDH1 gene sequences, and their related parameters using aforesaid machine learning techniques clearly establish that CDH1 gene can take the deterministic role in predicting the chances of occurrences of different types of breast cancer with an accuracy of &gt;90%. Such an observation opens a new paradigm in diagnostic approach of breast cancer.
DOI: 10.6084/m9.figshare.25245702.v1
title: CDH1 gene as biomarker towards breast cancer prediction*

description: Breast cancer is considered to be happened due to genetic aberration. Out of several genes expressed, it is found that cadherin 1, type 1 (CDH1) is responsible in several ways to control the metabolic order in human. Deregulation of the function of protein E-cadherin, expressed from CDH1 plays an important role in lobular breast cancer. In order to understand the root cause of this recent claim, we focus on CDH1 gene: whether the genetic information translated due to any deviation/alteration/modification in its sequence is related to the occurrence of the different types breast cancer. Towards this end, quantitative analysis of different biophysical and bio-chemical properties of CDH1 gene in genomic and proteomic levels from the available genomic (cDNA) sequences of CDH1 gene (obtained from the COSMIC Database for 78 patients, suffering from various types of breast cancer) clearly emphasizes that alternation/modification in the sequence of the CDH1 gene can be detrimental. Furthermore, Random forest, K-nearest neighbour and stochastic gradient descent (SGD) algorithms are applied on the derived dataset to classify the types of breast cancer, and to validate our hypothesis regarding the acute role of CDH1 as potential bio marker for breast cancer. Analysis of the mutated CDH1 gene sequences, and their related parameters using aforesaid machine learning techniques clearly establish that CDH1 gene can take the deterministic role in predicting the chances of occurrences of different types of breast cancer with an accuracy of &gt;90%. Such an observation opens a new paradigm in diagnostic approach of breast cancer.
DOI: 10.6084/m9.figshare.25514846
title: MOCS, a novel classifier system integrated multimoics analysis refining molecular subtypes and prognosis for skin melanoma

description: Purpose: The present investigation focuses on Skin Cutaneous Melanoma (SKCM), a melanocytic carcinoma characterized by marked aggression, significant heterogeneity, and a complex etiological background, factors which collectively contribute to the challenge in prognostic determinations. We defined a novel classifier system specifically tailored for SKCM based on multiomics. Methods: We collected 423 SKCM samples with multi omics datasets to perform a consensus cluster analysis using 10 machine learning algorithms and verified in 2 independent cohorts. Clinical features, biological characteristics, immune infiltration pattern, therapeutic response and mutation landscape were compared between subtypes. Results: Based on consensus clustering algorithms, we identified two Multi-Omics-Based-Cancer-Subtypes (MOCS) in SKCM in TCGA project and validated in GSE19234 and GSE65904 cohorts. MOCS2 emerged as a subtype with poor prognosis, characterized by a complex immune microenvironment, dysfunctional anti-tumor immune state, high cancer stemness index, and genomic instability. MOCS2 exhibited resistance to chemotherapy agents like erlotinib and sunitinib while sensitive to rapamycin, NSC87877, MG132, and FH355. Additionally, ELSPBP1 was identified as the target involving in glycolysis and M2 macrophage infiltration in SKCM. Conclusions: MOCS classification could stably predict prognosis of SKCM; patients with a high cancer stemness index combined with genomic instability may be predisposed to an immune exhaustion state.
DOI: 10.6084/m9.figshare.25514846.v1
title: MOCS, a novel classifier system integrated multimoics analysis refining molecular subtypes and prognosis for skin melanoma

description: Purpose: The present investigation focuses on Skin Cutaneous Melanoma (SKCM), a melanocytic carcinoma characterized by marked aggression, significant heterogeneity, and a complex etiological background, factors which collectively contribute to the challenge in prognostic determinations. We defined a novel classifier system specifically tailored for SKCM based on multiomics. Methods: We collected 423 SKCM samples with multi omics datasets to perform a consensus cluster analysis using 10 machine learning algorithms and verified in 2 independent cohorts. Clinical features, biological characteristics, immune infiltration pattern, therapeutic response and mutation landscape were compared between subtypes. Results: Based on consensus clustering algorithms, we identified two Multi-Omics-Based-Cancer-Subtypes (MOCS) in SKCM in TCGA project and validated in GSE19234 and GSE65904 cohorts. MOCS2 emerged as a subtype with poor prognosis, characterized by a complex immune microenvironment, dysfunctional anti-tumor immune state, high cancer stemness index, and genomic instability. MOCS2 exhibited resistance to chemotherapy agents like erlotinib and sunitinib while sensitive to rapamycin, NSC87877, MG132, and FH355. Additionally, ELSPBP1 was identified as the target involving in glycolysis and M2 macrophage infiltration in SKCM. Conclusions: MOCS classification could stably predict prognosis of SKCM; patients with a high cancer stemness index combined with genomic instability may be predisposed to an immune exhaustion state.
DOI: 10.6084/m9.figshare.28869584.v1
title: Matlab codes of "Numerically efficient model for the nucleation, growth, and coalescence of bubbles in magma".

description: This item is provided as part of the submission of the manuscript entitled "Numerically efficient model for the nucleation, growth, and coalescence of bubbles in magma".
DOI: 10.6084/m9.figshare.25256516
title: Identification of phytocompounds as potent inhibitors of sodium/glucose cotransporter-2 leading to diabetes treatment

description: Type-II diabetes, a major metabolic disorder has threatened the very existence of a healthy life since long ago. Commercially available antidiabetic drugs are known for several adverse effects. The present study attempted to identify potential phytocompounds as inhibitors of sodium/glucose cotransporter-2 (SGLT2), a major protein that helps in glucose re-absorption from renal tubules. A total of 28 phytocompounds were collected based on the literature survey. 3D co-ordinates of phytocompounds were collected from PubChem database. Molecular docking was carried out with SGLT2 protein and the best 3 docking complexes were subjected to molecular dynamics simulation for 100 ns. Free energy changes were also analyzed using MM/PBSA analysis. Phytocompounds were also analyzed for their drug-likeness and ADMET properties. Docking study observed a strong binding affinity of phytocompounds (&gt; −7.0 kcal/mol). More than 10 phytocompounds showed better binding affinity compared to reference drugs. Further analysis of three best docking complexes when analyzed by MD simulation showed better stability and compactness of the complexes compared to reference drug, empagliflozin. MM/PBSA analysis also revealed that van der Waals force and electrostatic energy are the major binding energy involved in the complex formation. Like docking energy, free energy analysis also observed stronger binding energies (ΔGGAS) in SGLT2-phytocompound complexes compared to empagliflozin complex. All the phytocompounds showed drug-likeness and considerable ADMET properties. The study, therefore, suggests that Trifolirhizin-6′-monoacetate, Aspalathin, and Quercetin-3-glucoside could be a possible inhibitor of SGLT2 protein. However, further studies need to be carried out to reveal the exact mode of activity.
DOI: 10.6084/m9.figshare.25256516.v1
title: Identification of phytocompounds as potent inhibitors of sodium/glucose cotransporter-2 leading to diabetes treatment

description: Type-II diabetes, a major metabolic disorder has threatened the very existence of a healthy life since long ago. Commercially available antidiabetic drugs are known for several adverse effects. The present study attempted to identify potential phytocompounds as inhibitors of sodium/glucose cotransporter-2 (SGLT2), a major protein that helps in glucose re-absorption from renal tubules. A total of 28 phytocompounds were collected based on the literature survey. 3D co-ordinates of phytocompounds were collected from PubChem database. Molecular docking was carried out with SGLT2 protein and the best 3 docking complexes were subjected to molecular dynamics simulation for 100 ns. Free energy changes were also analyzed using MM/PBSA analysis. Phytocompounds were also analyzed for their drug-likeness and ADMET properties. Docking study observed a strong binding affinity of phytocompounds (&gt; −7.0 kcal/mol). More than 10 phytocompounds showed better binding affinity compared to reference drugs. Further analysis of three best docking complexes when analyzed by MD simulation showed better stability and compactness of the complexes compared to reference drug, empagliflozin. MM/PBSA analysis also revealed that van der Waals force and electrostatic energy are the major binding energy involved in the complex formation. Like docking energy, free energy analysis also observed stronger binding energies (ΔGGAS) in SGLT2-phytocompound complexes compared to empagliflozin complex. All the phytocompounds showed drug-likeness and considerable ADMET properties. The study, therefore, suggests that Trifolirhizin-6′-monoacetate, Aspalathin, and Quercetin-3-glucoside could be a possible inhibitor of SGLT2 protein. However, further studies need to be carried out to reveal the exact mode of activity.
DOI: 10.6084/m9.figshare.25359360
title: Cytotoxic monastrol derivatives as adjective inhibitors of drug-resistant Eg5: a molecular dynamics perspective

description: The mitotic kinesin Eg5 is a motor protein involved in the formation of bipolar spindle and cell division. Eg5 is overexpressed in various cancer cells and Eg5 targeting agents are promising candidates for cancer therapy. Subsequent to the discovery of monastrol as a small-molecule Eg5 modulator, numerous inhibitors/modulators have been reported from which a few entered clinical trials. Mutagenic investigations specified declined sensitivity of Eg5 allosteric site to monastrol due to the occurrence of drug-resistant mutations in some cell cultures. Accordingly, identification of tight binders to the mutant Eg5 allosteric site is an invaluable strategy to devise more efficient Eg5 modulators. We have previously synthesized a few dihydropyrimidinethione (DHPMT)-based 5-carboxamide monastrol derivatives (<b>1</b>-<b>5</b>) with higher cytotoxicities against AGS (IC<sub>50</sub> 9.90-98.48 µM) and MCF-7 (IC<sub>50</sub> 15.20-149.13 µM) cancer cell lines than monastrol. Within a current study, a structural insight was offered into the binding mechanism of intended derivatives inside the mutant Eg5 loop5/α2/α3 allosteric pocket. Molecular docking of the DHPMT <i>R</i> and <i>S</i>-enantiomers unraveled top-scored Eg5 complexes. Molecular dynamics (MD) simulations were carried out on 5 superior complexes as (<i>R)</i>-<b>2</b>/D130V-Eg5, (<i>R)</i>-<b>4</b>/D130V-Eg5, (<i>R)</i>-<b>5</b>/D130V-Eg5, (<i>R)</i>-<b>5</b>/L214I-Eg5, (<i>R)</i>-<b>5</b>/R119L-Eg5, and the control groups monastrol/D130V-Eg5, monastrol/L214I-Eg5, monastrol/R119L-Eg5. Free energy calculations were conducted through conformational sampling of MD-driven binding trajectories. Our results provided structural details on probable interaction mechanism of the cytotoxic DHPMTs that are difficult to address experimentally. The outputs of the current study propose new monastrol derivatives as probable resistance-overwhelming Eg5 modulators. MD simulations revealed that <i>R</i>-enantiomer of <b>5</b> overwhelmed drug-resistant D130V-Eg5. Induced fit L5 loop conformation led to the accommodation of <b>5</b> inside Eg5 allosteric site. Cooperative lipophilic contacts accommodated DHPMTs inside D130V-Eg5 allosteric site. Ser120 pointed toward <b>5</b> and made a stable H-bond particularly within the 60-100 ns. Major fluctuations of D130V-Eg5 allosteric pocket occurred at L5 loop upon binding to <b>5</b>.
DOI: 10.6084/m9.figshare.25359360.v1
title: Cytotoxic monastrol derivatives as adjective inhibitors of drug-resistant Eg5: a molecular dynamics perspective

description: The mitotic kinesin Eg5 is a motor protein involved in the formation of bipolar spindle and cell division. Eg5 is overexpressed in various cancer cells and Eg5 targeting agents are promising candidates for cancer therapy. Subsequent to the discovery of monastrol as a small-molecule Eg5 modulator, numerous inhibitors/modulators have been reported from which a few entered clinical trials. Mutagenic investigations specified declined sensitivity of Eg5 allosteric site to monastrol due to the occurrence of drug-resistant mutations in some cell cultures. Accordingly, identification of tight binders to the mutant Eg5 allosteric site is an invaluable strategy to devise more efficient Eg5 modulators. We have previously synthesized a few dihydropyrimidinethione (DHPMT)-based 5-carboxamide monastrol derivatives (<b>1</b>-<b>5</b>) with higher cytotoxicities against AGS (IC<sub>50</sub> 9.90-98.48 µM) and MCF-7 (IC<sub>50</sub> 15.20-149.13 µM) cancer cell lines than monastrol. Within a current study, a structural insight was offered into the binding mechanism of intended derivatives inside the mutant Eg5 loop5/α2/α3 allosteric pocket. Molecular docking of the DHPMT <i>R</i> and <i>S</i>-enantiomers unraveled top-scored Eg5 complexes. Molecular dynamics (MD) simulations were carried out on 5 superior complexes as (<i>R)</i>-<b>2</b>/D130V-Eg5, (<i>R)</i>-<b>4</b>/D130V-Eg5, (<i>R)</i>-<b>5</b>/D130V-Eg5, (<i>R)</i>-<b>5</b>/L214I-Eg5, (<i>R)</i>-<b>5</b>/R119L-Eg5, and the control groups monastrol/D130V-Eg5, monastrol/L214I-Eg5, monastrol/R119L-Eg5. Free energy calculations were conducted through conformational sampling of MD-driven binding trajectories. Our results provided structural details on probable interaction mechanism of the cytotoxic DHPMTs that are difficult to address experimentally. The outputs of the current study propose new monastrol derivatives as probable resistance-overwhelming Eg5 modulators. MD simulations revealed that <i>R</i>-enantiomer of <b>5</b> overwhelmed drug-resistant D130V-Eg5. Induced fit L5 loop conformation led to the accommodation of <b>5</b> inside Eg5 allosteric site. Cooperative lipophilic contacts accommodated DHPMTs inside D130V-Eg5 allosteric site. Ser120 pointed toward <b>5</b> and made a stable H-bond particularly within the 60-100 ns. Major fluctuations of D130V-Eg5 allosteric pocket occurred at L5 loop upon binding to <b>5</b>.
DOI: 10.15468/dl.vckdm5
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GbifId is 5003971302",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029710-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/d84snc5fbz
title: research data of 《Research on the optimization of ecological security pattern of the Yellow River driven by strategy gradient and Harris Hawk algorithm》

description: 此数据是论文《Research on the optimization of ecological security pattern of the Yellow River driven by strategy gradient and Harris Hawk algorithm》中的研究数据
DOI: 10.17632/d84snc5fbz.1
title: research data of 《Research on the optimization of ecological security pattern of the Yellow River driven by strategy gradient and Harris Hawk algorithm》

description: 此数据是论文《Research on the optimization of ecological security pattern of the Yellow River driven by strategy gradient and Harris Hawk algorithm》中的研究数据
DOI: 10.15468/dl.79j37j
title: Occurrence Download

description: A dataset containing 482 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Corydalis solida",
 "Country is United States of America",
 "HasCoordinate is true"
 ]
}

 The dataset includes 482 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029711-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/zkhb2fwsrp
title: Mitochondrial glutamine import sustains mitochondrial translation independent of glutaminolysis in cancer

description: Mol Cell WB,IF,HE raw data 20250929
DOI: 10.17632/zkhb2fwsrp.1
title: Mitochondrial glutamine import sustains mitochondrial translation independent of glutaminolysis in cancer

description: Mol Cell WB,IF,HE raw data 20250929
DOI: 10.5281/zenodo.5794495
title: Executive compensation and corporate governance UK-Spain

description: Panel data containing a set of year-variables regarding executive compensation and corporate governance characteristics of a sample UK and Spanish listed firms.
description: Funder Ministerio de Ciencia e Innovación - Funding ECO2017-84209-P
DOI: 10.5281/zenodo.5794494
title: Executive compensation and corporate governance UK-Spain

description: Panel data containing a set of year-variables regarding executive compensation and corporate governance characteristics of a sample UK and Spanish listed firms.
description: Funder Ministerio de Ciencia e Innovación - Funding ECO2017-84209-P
DOI: 10.17617/3.uth7rg
title: Data for the manuscript entitled "Uniaxial stress tuning of the anomalous Hall effect in Mn3Ge"

description: This dataset contains the experimental data used in the manuscript entitled "Uniaxial stress tuning of the anomalous Hall effect in Mn3Ge". It is composed by Hall resistivity curves as a function of temperature, magnetic field and uniaxial stress and X-ray diffraction data as function of uniaxial stress.
DOI: 10.17632/6wr22w78c3
title: Innovations in Contemporary Opera

description: The presented materials visualize the findings of a research study focusing on innovations in contemporary opera, based on data regarding the winners of MT NOW.
DOI: 10.17632/6wr22w78c3.1
title: Innovations in Contemporary Opera

description: The presented materials visualize the findings of a research study focusing on innovations in contemporary opera, based on data regarding the winners of MT NOW.
DOI: 10.17632/yc5hx88kg2
title: Volumetric Behaviour Analysis (VBA) of Hong Kong Public Housing Flats - 2D Annotated Floor Plans - Case 1PHTR1
DOI: 10.17632/yc5hx88kg2.1
title: Volumetric Behaviour Analysis (VBA) of Hong Kong Public Housing Flats - 2D Annotated Floor Plans - Case 1PHTR1
DOI: 10.17632/ndphwwjmgv
title: GBV WORDS

description: Words related to gender-based online violence based on suervey to 511 Gen Z respondent in Indonesia.
DOI: 10.17632/ndphwwjmgv.1
title: GBV WORDS

description: Words related to gender-based online violence based on suervey to 511 Gen Z respondent in Indonesia.
DOI: 10.17632/5mbybym79v
title: Olfactory epithelia of juvenile southern bluefin tuna, Thunnus maccoyii

description: This dataset includes raw data from the study "Novel sensory epithelial topography of the olfactory lamellae in southern bluefin tuna, Thunnus maccoyii (Scombridae)". Total number, total area, and average size of sensory islets covering the surface of the olfactory lamellae (n=12), which are divided into distinct zones, of juvenile T. maccoyii (n=4) are provided.
DOI: 10.17632/5mbybym79v.1
title: Olfactory epithelia of juvenile southern bluefin tuna, Thunnus maccoyii

description: This dataset includes raw data from the study "Novel sensory epithelial topography of the olfactory lamellae in southern bluefin tuna, Thunnus maccoyii (Scombridae)". Total number, total area, and average size of sensory islets covering the surface of the olfactory lamellae (n=12), which are divided into distinct zones, of juvenile T. maccoyii (n=4) are provided.
DOI: 10.17632/xtynymtmgk
title: Data for: Monsoonally hydrological control on seasonally riverine magnesium isotopes in the tectonically-active Tibetan Plateau

description: Raw data for all figures in the manuscript by Yang Xu et al. to be published by Geochimica et Cosmochimica Acta as "Monsoonally hydrological control on seasonally riverine magnesium isotopes in the tectonically-active Tibetan Plateau".