cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5517/ccdc.csd.cc2gfs3t
title: CCDC 2277356: Experimental Crystal Structure Determination

description: Related Article: Mikayla L. Horvath, Caylee E. Jumbelic, Rosemarie A. Burynski, M. Brody Mistrot, Robert D. Pike, Brian J. Smith, Hasan Arslan|2023|Chem.Commun.|59|11799|doi:10.1039/D3CC03406B
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2gg4cg
title: CCDC 2277705: Experimental Crystal Structure Determination

description: Related Article: Chao Zhang, Ting-Wei Wang, Zu-Jia Lu, Zhen-Xin Yi, Bao-Long Kuang, Shu Bu, Zhi-Ming Xie, Yan Li, Kun Wang, Jian-Guo Zhang|2023|Dalton Trans.|52|13716|doi:10.1039/D3DT02429F
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2gg4gk
title: CCDC 2277708: Experimental Crystal Structure Determination

description: Related Article: Chao Zhang, Ting-Wei Wang, Zu-Jia Lu, Zhen-Xin Yi, Bao-Long Kuang, Shu Bu, Zhi-Ming Xie, Yan Li, Kun Wang, Jian-Guo Zhang|2023|Dalton Trans.|52|13716|doi:10.1039/D3DT02429F
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2gkztv
title: CCDC 2281408: Experimental Crystal Structure Determination

description: Related Article: F. Meurer, T. Dimova, M. Bodensteiner, I. Kolev|2023|Acta Crystallogr.,Sect.E:Cryst.Commun.|79|916|doi:10.1107/S2056989023007831
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6073/pasta/ba324950e5f6a1bcde24ce36fbe25218
title: DEPRECATED: Hubbard Brook Experimental Forest: Snow Water Measurements, 1955 - present

description: DEPRECATED: This data package continues in knb-lter-hbr.27, which integrates snow water and snow depth (https://portal.edirepository.org/nis/mapbrowse?scope=knb-lter-hbr&identifier=27). Snow measurements have been collected approximately weekly during the winter season using transects adjacent to the established network of standard rain gages from 1956 to the present. Maximum snow depth, water content and snow cover duration data are recorded at points along a transect known as a “snow course”, which includes 10 points spaced at 2-m intervals within a designated 0.25 ha area. Data from one course are averaged for each collection date and snow water content is scaled up to a whole watershed value. These data were gathered as part of the Hubbard Brook Ecosystem Study (HBES). The HBES is a collaborative effort at the Hubbard Brook Experimental Forest, which is operated and maintained by the USDA Forest Service, Northern Research Station.
DOI: 10.7270/q26h4kf1
title: BindingDB Entry 547: Histone demethylase inhibitors

description: Small molecule binding data for protein Lysine-specific demethylase 4C, Lysine-specific demethylase 5A, and Lysine-specific demethylase 5B, Uniprot P29375, Q9H3R0, and Q9UGL1
DOI: 10.34740/kaggle/dsv/6669668
title: Balochi Language to English Translation Dataset
DOI: 10.5281/zenodo.8185915
title: Simulations for SA and SC of SWAT+ model

description: This repository contains the simulations run with SWATPlusR to perform the Sensitivity analysis and the Soft calibration for a SWAT+ model constructed for the Upper Tagus River basin. In this repository you will find: The raw simulations for the Sensitivity analysis --&gt; SA_runs.rar The files created when extracting the data from the simulations for the Sensitivity analysis --&gt; var_extract.zip The raw simulations for the Soft calibration: For each iteration, the file that contains the entire output from the 1000 simulations is the ronda_X_lsu.rds The file channels_ordered_all.rds contains the streamflow simulated for the evaluated subbasins for the three soft calibration iterations. More info and the code used to analyse this data can be found in the GitHub repository (https://github.com/alejandrosgz/https://github.com/alejandrosgz/HSJ_SA_SC_SWATPlus)
DOI: 10.5281/zenodo.8185916
title: Simulations for SA and SC of SWAT+ model

description: This repository contains the simulations run with SWATPlusR to perform the Sensitivity analysis and the Soft calibration for a SWAT+ model constructed for the Upper Tagus River basin. More info and the code used to analyse this data can be found in the GitHub repository (https://github.com/alejandrosgz/WRR_SA_SC_hydrological_modelling) or Zenodo repository (https://zenodo.org/record/8221458).
DOI: 10.5281/zenodo.8432546
title: Simulations for SA and SC of SWAT+ model

description: This repository contains the simulations run with SWATPlusR to perform the Sensitivity analysis and the Soft calibration for a SWAT+ model constructed for the Upper Tagus River basin. In this repository you will find: The raw simulations for the Sensitivity analysis --&gt; SA_runs.rar The files created when extracting the data from the simulations for the Sensitivity analysis --&gt; var_extract.zip The raw simulations for the Soft calibration: For each iteration, the file that contains the entire output from the 1000 simulations is the ronda_X_lsu.rds The file channels_ordered_all.rds contains the streamflow simulated for the evaluated subbasins for the three soft calibration iterations. More info and the code used to analyse this data can be found in the GitHub repository (https://github.com/alejandrosgz/https://github.com/alejandrosgz/HSJ_SA_SC_SWATPlus)
DOI: 10.5281/zenodo.8432715
title: Dependency Practices for Vulnerability Mitigation

description: This is the replication package for our paper on dependency practices for mitigating vulnerabilities. Here is a short description of what is contained in this package: <strong>Vul. Extraction</strong> The code to extract vulnerability info from the npm advisories in json format. <strong>Data</strong> The preliminary datasets curated for the project. The raw data can be extracted from libraries.io and the npm advisories on github.com. <strong>Model Code</strong> The code for feature extraction, feature preprocessing and model training. <strong>Visualization Scripts</strong> The visualizer.py file includes the visualization scripts used for the paper. <strong>Analysis Code</strong> The analysis code used for findings of RQ1. <strong>Survey Responses</strong> The raw anonymized survey responses for RQ3.
DOI: 10.5281/zenodo.8432714
title: Dependency Practices for Vulnerability Mitigation

description: This is the replication package for our paper on dependency practices for mitigating vulnerabilities. Here is a short description of what is contained in this package: <strong>Vul. Extraction</strong> The code to extract vulnerability info from the npm advisories in json format. <strong>Data</strong> The preliminary datasets curated for the project. The raw data can be extracted from libraries.io and the npm advisories on github.com. <strong>Model Code</strong> The code for feature extraction, feature preprocessing and model training. <strong>Visualization Scripts</strong> The visualizer.py file includes the visualization scripts used for the paper. <strong>Analysis Code</strong> The analysis code used for findings of RQ1. <strong>Survey Responses</strong> The raw anonymized survey responses for RQ3.
DOI: 10.6084/m9.figshare.22274658
title: Transcription factors TP63 facilitates malignant progression of thyroid cancer by upregulating KRT17 expression and inducing epithelial-mesenchymal transition

description: Thyroid cancer (TC) is a relatively prevalent endocrine tumor among women, the incidence of which is rapidly rising. In this present study, we aimed to provide new therapeutic targets from the aspect of transcription factor-target gene interaction. TP63 and KRT17 were both highly expressed in TC tissues and cells. The results of ChIP and dual-luciferase assays confirmed TP63 to bind the KRT17 promoter. Cell function assays revealed that knockdown of TP63 could repress TC cell progression. Furthermore, the rescue assay verified that TP63 could facilitate KRT17 expression to activate the AKT signaling pathway, which in turn stimulated TC cell invasion and migration, and induced EMT. All these results verified that TP63 facilitates TC malignant progression by promoting KRT17 expression and inducing EMT.
DOI: 10.6084/m9.figshare.22274658.v1
title: Transcription factors TP63 facilitates malignant progression of thyroid cancer by upregulating KRT17 expression and inducing epithelial-mesenchymal transition

description: Thyroid cancer (TC) is a relatively prevalent endocrine tumor among women, the incidence of which is rapidly rising. In this present study, we aimed to provide new therapeutic targets from the aspect of transcription factor-target gene interaction. TP63 and KRT17 were both highly expressed in TC tissues and cells. The results of ChIP and dual-luciferase assays confirmed TP63 to bind the KRT17 promoter. Cell function assays revealed that knockdown of TP63 could repress TC cell progression. Furthermore, the rescue assay verified that TP63 could facilitate KRT17 expression to activate the AKT signaling pathway, which in turn stimulated TC cell invasion and migration, and induced EMT. All these results verified that TP63 facilitates TC malignant progression by promoting KRT17 expression and inducing EMT.
DOI: 10.6084/m9.figshare.21867750
title: Insights into H<sub>2</sub>O<sub>2</sub>-induced signaling in Jurkat cells from analysis of gene expression

description: Hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>) is a ubiquitous oxidant produced in a regulated manner by various enzymes in mammalian cells. H<sub>2</sub>O<sub>2</sub> reversibly oxidizes thiol groups of cysteine residues to mediate intracellular signaling. While examples of H<sub>2</sub>O<sub>2-</sub>dependent signaling have been reported, the exact molecular mechanism(s) of signaling and the pathways affected are not well understood. Here, the transcriptomic response of Jurkat T cells to H<sub>2</sub>O<sub>2</sub> was investigated to determine global effects on gene expression. With a low H<sub>2</sub>O<sub>2</sub> concentration (10 µM) that did not induce an oxidative stress response or cell death, extensive changes in gene expression occurred after 4 h (6803 differentially expressed genes). Of the genes with a greater then 2-fold change in expression, 85% were upregulated suggesting that in a physiological setting H<sub>2</sub>O<sub>2</sub> predominantly activates gene expression. Pathway analysis identified gene expression signatures associated with FOXO and NTRK signaling. These signatures were associated with an overlapping set of transcriptional regulators. Overall, our results provide a snapshot of gene expression changes in response to H<sub>2</sub>O<sub>2,</sub> which, along with further studies, will lead to new insights into the specific pathways that are activated in response to endogenous production of H<sub>2</sub>O<sub>2</sub>, and the molecular mechanisms of H<sub>2</sub>O<sub>2</sub> signaling.
DOI: 10.6084/m9.figshare.21867750.v1
title: Insights into H<sub>2</sub>O<sub>2</sub>-induced signaling in Jurkat cells from analysis of gene expression

description: Hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>) is a ubiquitous oxidant produced in a regulated manner by various enzymes in mammalian cells. H<sub>2</sub>O<sub>2</sub> reversibly oxidizes thiol groups of cysteine residues to mediate intracellular signaling. While examples of H<sub>2</sub>O<sub>2-</sub>dependent signaling have been reported, the exact molecular mechanism(s) of signaling and the pathways affected are not well understood. Here, the transcriptomic response of Jurkat T cells to H<sub>2</sub>O<sub>2</sub> was investigated to determine global effects on gene expression. With a low H<sub>2</sub>O<sub>2</sub> concentration (10 µM) that did not induce an oxidative stress response or cell death, extensive changes in gene expression occurred after 4 h (6803 differentially expressed genes). Of the genes with a greater then 2-fold change in expression, 85% were upregulated suggesting that in a physiological setting H<sub>2</sub>O<sub>2</sub> predominantly activates gene expression. Pathway analysis identified gene expression signatures associated with FOXO and NTRK signaling. These signatures were associated with an overlapping set of transcriptional regulators. Overall, our results provide a snapshot of gene expression changes in response to H<sub>2</sub>O<sub>2,</sub> which, along with further studies, will lead to new insights into the specific pathways that are activated in response to endogenous production of H<sub>2</sub>O<sub>2</sub>, and the molecular mechanisms of H<sub>2</sub>O<sub>2</sub> signaling.
DOI: 10.6084/m9.figshare.21901701
title: Relationship between toxicity and oxidative stress of the nanoencapsulated colchicine in a model of <i>Drosophila melanogaster</i>

description: Drug repurposing allows searching for new biological targets, especially against emerging diseases such as Covid-19. Drug colchicine (COL) presents recognized anti-inflammatory action, while the nanotechnology purpose therapies with low doses, efficacy, and decrease the drug’s side-effects. This study aims to evaluate the effects of COL and colchicine nanocapsules (NCCOL) on survival, LC50, activity locomotor, and oxidative stress parameters, elucidating the toxicity profile in acute and chronic exposure in <i>Drosophila melanogaster</i>. Three-day-old flies were investigated into groups: Control, 0.001, 0.0025, 0.005, and 0.010 mg/mL of COL or NCCOL. The survival rate, open field test, LC50, oxidative stress markers (reactive species (RS) production, thiobarbituric acid reactive substances), antioxidant enzyme activity (catalase (CAT), superoxide dismutase (SOD), glutathione S-transferase), protein thiols, nonprotein thiols, acetylcholinesterase activity, and cell viability were measured. As a result, acute exposure to the COL decreases the number of crosses in the open field and increases CAT activity. NCCOL reduced RS levels, increased lipoperoxidation and SOD activity. Chronic exposure to the COL and NCCOL in high concentrations implied high mortality and enzymatic inhibition of the CAT and AChE, and only the COL caused locomotor damage in the open field test. Thus, NCCOL again reduced the formation of RS while COL increased. In this comparative study, NCCOL was less toxic to the antioxidant system than COL and showed notable involvement of oxidative stress as one of their toxicity mechanisms. Future studies are needed to elucidate all aspects of nanosafety related to the NCCOL. HighlightsDrug repositioning contributes to research involving emerging diseases.Nanoencapsulation of drugs aims to increase bioavailability.Certain concentrations of nanocolchicine affect <i>Drosophila</i> antioxidant enzymes.Oxidative stress pathways are involved in colchicine drug toxicity.The nanosafety of nanomaterials is essential for further research on a larger scale. Drug repositioning contributes to research involving emerging diseases. Nanoencapsulation of drugs aims to increase bioavailability. Certain concentrations of nanocolchicine affect <i>Drosophila</i> antioxidant enzymes. Oxidative stress pathways are involved in colchicine drug toxicity. The nanosafety of nanomaterials is essential for further research on a larger scale.
DOI: 10.6084/m9.figshare.21731228
title: Non-thermal plasma elicits ferrous chloride-catalyzed DMPO-OH

description: Non-thermal plasma (NTP) induces the generation of reactive oxygen species (ROS) and reactive nitrogen species, such as hydroxyl radicals (<sup>•</sup>OH), hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>), singlet oxygen, superoxide, ozone, and nitric oxide, at near-physiological temperatures. These molecules promote blood coagulation, wound healing, disinfection, and selective cancer cell death. Based on these evidences, clinical trials of NTP have been conducted for treating chronic wounds and head and neck cancers. Although clinical applications have progressed, the stoichiometric quantification of NTP-induced ROS remains unclear in the liquid phase in the presence of FeCl<sub>2</sub> or FeCl<sub>3</sub> in combination with biocompatible reducing agents, which may modulate the final biological effects of NTP. In this study, we employed electron paramagnetic resonance spectroscopy to quantify ROS using spin-trapping probe, 5,5-dimethyl-1-pyrroline-<i>N</i>-oxide (DMPO) and H<sub>2</sub>O<sub>2</sub>, using luminescent probe in the presence of FeCl<sub>2</sub> or FeCl<sub>3</sub>. NTP-induced DMPO-OH levels were elevated 10–100 µM FeCl<sub>2</sub> or 500 and 1000 µM FeCl<sub>3</sub>. NTP-induced DMPO-OH with 10 µM FeCl<sub>2</sub> or FeCl<sub>3</sub> was significantly scavenged by ascorbate, α-tocopherol, dithiothreitol, reduced glutathione, or oxidized glutathione, whereas dehydroascorbate was ineffective in 2 mM DMPO. NTP-induced H<sub>2</sub>O<sub>2</sub> was significantly degraded by 100 µM FeCl<sub>2</sub> and FeCl<sub>3</sub> in an iron-dependent manner. Meanwhile, decomposition of H<sub>2</sub>O<sub>2</sub> by catalase decayed DMPO-OH efficiently in the presence of iron, indicating iron causes DMPO-OH production and degradation simultaneously. These results suggest that NTP-induced DMPO-OH is generated by the H<sub>2</sub>O<sub>2</sub>-consuming, iron-dependent Fenton reaction and ferryl intermediates. The potential iron-mediated ROS production by NTP is also discussed to clarify the interaction between NTP-induced ROS and biomolecules.
DOI: 10.6084/m9.figshare.21901701.v1
title: Relationship between toxicity and oxidative stress of the nanoencapsulated colchicine in a model of <i>Drosophila melanogaster</i>

description: Drug repurposing allows searching for new biological targets, especially against emerging diseases such as Covid-19. Drug colchicine (COL) presents recognized anti-inflammatory action, while the nanotechnology purpose therapies with low doses, efficacy, and decrease the drug’s side-effects. This study aims to evaluate the effects of COL and colchicine nanocapsules (NCCOL) on survival, LC50, activity locomotor, and oxidative stress parameters, elucidating the toxicity profile in acute and chronic exposure in <i>Drosophila melanogaster</i>. Three-day-old flies were investigated into groups: Control, 0.001, 0.0025, 0.005, and 0.010 mg/mL of COL or NCCOL. The survival rate, open field test, LC50, oxidative stress markers (reactive species (RS) production, thiobarbituric acid reactive substances), antioxidant enzyme activity (catalase (CAT), superoxide dismutase (SOD), glutathione S-transferase), protein thiols, nonprotein thiols, acetylcholinesterase activity, and cell viability were measured. As a result, acute exposure to the COL decreases the number of crosses in the open field and increases CAT activity. NCCOL reduced RS levels, increased lipoperoxidation and SOD activity. Chronic exposure to the COL and NCCOL in high concentrations implied high mortality and enzymatic inhibition of the CAT and AChE, and only the COL caused locomotor damage in the open field test. Thus, NCCOL again reduced the formation of RS while COL increased. In this comparative study, NCCOL was less toxic to the antioxidant system than COL and showed notable involvement of oxidative stress as one of their toxicity mechanisms. Future studies are needed to elucidate all aspects of nanosafety related to the NCCOL. HighlightsDrug repositioning contributes to research involving emerging diseases.Nanoencapsulation of drugs aims to increase bioavailability.Certain concentrations of nanocolchicine affect <i>Drosophila</i> antioxidant enzymes.Oxidative stress pathways are involved in colchicine drug toxicity.The nanosafety of nanomaterials is essential for further research on a larger scale. Drug repositioning contributes to research involving emerging diseases. Nanoencapsulation of drugs aims to increase bioavailability. Certain concentrations of nanocolchicine affect <i>Drosophila</i> antioxidant enzymes. Oxidative stress pathways are involved in colchicine drug toxicity. The nanosafety of nanomaterials is essential for further research on a larger scale.
DOI: 10.6084/m9.figshare.21731228.v1
title: Non-thermal plasma elicits ferrous chloride-catalyzed DMPO-OH

description: Non-thermal plasma (NTP) induces the generation of reactive oxygen species (ROS) and reactive nitrogen species, such as hydroxyl radicals (<sup>•</sup>OH), hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>), singlet oxygen, superoxide, ozone, and nitric oxide, at near-physiological temperatures. These molecules promote blood coagulation, wound healing, disinfection, and selective cancer cell death. Based on these evidences, clinical trials of NTP have been conducted for treating chronic wounds and head and neck cancers. Although clinical applications have progressed, the stoichiometric quantification of NTP-induced ROS remains unclear in the liquid phase in the presence of FeCl<sub>2</sub> or FeCl<sub>3</sub> in combination with biocompatible reducing agents, which may modulate the final biological effects of NTP. In this study, we employed electron paramagnetic resonance spectroscopy to quantify ROS using spin-trapping probe, 5,5-dimethyl-1-pyrroline-<i>N</i>-oxide (DMPO) and H<sub>2</sub>O<sub>2</sub>, using luminescent probe in the presence of FeCl<sub>2</sub> or FeCl<sub>3</sub>. NTP-induced DMPO-OH levels were elevated 10–100 µM FeCl<sub>2</sub> or 500 and 1000 µM FeCl<sub>3</sub>. NTP-induced DMPO-OH with 10 µM FeCl<sub>2</sub> or FeCl<sub>3</sub> was significantly scavenged by ascorbate, α-tocopherol, dithiothreitol, reduced glutathione, or oxidized glutathione, whereas dehydroascorbate was ineffective in 2 mM DMPO. NTP-induced H<sub>2</sub>O<sub>2</sub> was significantly degraded by 100 µM FeCl<sub>2</sub> and FeCl<sub>3</sub> in an iron-dependent manner. Meanwhile, decomposition of H<sub>2</sub>O<sub>2</sub> by catalase decayed DMPO-OH efficiently in the presence of iron, indicating iron causes DMPO-OH production and degradation simultaneously. These results suggest that NTP-induced DMPO-OH is generated by the H<sub>2</sub>O<sub>2</sub>-consuming, iron-dependent Fenton reaction and ferryl intermediates. The potential iron-mediated ROS production by NTP is also discussed to clarify the interaction between NTP-induced ROS and biomolecules.
DOI: 10.7270/q2cj8gk0
title: BindingDB Entry 1379: Histone demethylase inhibitors

description: Small molecule binding data for protein Homo sapiens lysine demethylase 2B (KDM2B), Lysine-specific demethylase 4A, Lysine-specific demethylase 4C, Lysine-specific demethylase 5A, and Lysine-specific demethylase 5B, Uniprot O75164, P29375, Q8NHM5, Q9H3R0, and Q9UGL1