cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9894419.v1
title: Trimetazidine ameliorates sunitinib-induced cardiotoxicity in mice via the AMPK/mTOR/autophagy pathway

description: <b>Context:</b> Sunitinib (SU) is a multi-targeted tyrosine kinase inhibitor anticancer agent whose clinical use is often limited by cardiovascular complications. Trimetazidine (TMZ) is an anti-angina agent that has been demonstrated cardioprotective effects in numerous cardiovascular conditions, but its potential effects in SU-induced cardiotoxicity have not been investigated. <b>Objective:</b> This study investigates the effect of TMZ in sunitinib-induced cardiotoxicity <i>in vivo</i> and <i>in vitro</i> and molecular mechanisms. <b>Materials and methods:</b> Male 129S1/SvImJ mice were treated with vehicle, SU (40 mg/kg/d) or SU and TMZ (20 mg/kg/d) via oral gavage for 28 days, and cardiovascular functions and cardiac protein expressions were examined. H9c2 cardiomyocytes were treated with vehicle, SU (2–10 μM) or SU and TMZ (40–120 μM) for 48 h, and cell viability, apoptosis, autophagy, and protein expression was tested. <b>Results:</b> SU induces hypertension (systolic blood pressure [SBP] + 28.33 ± 5.00 mmHg) and left ventricular dysfunction (left ventricular ejection fraction [LVEF] − 11.16 ± 2.53%) in mice. In H9c2 cardiomyocytes, SU reduces cell viability (IC<sub>50</sub> 4.07 μM) and inhibits the AMPK/mTOR/autophagy pathway (<i>p</i> &lt; 0.05). TMZ co-administration with SU reverses SU-induced cardiotoxicity in mice (SBP − 23.75 ± 4.69 mmHg, LVEF + 10.95 ± 3.317%), alleviates cell viability loss in H9c2 cardiomyocytes (<i>p</i> &lt; 0.01) and activates the AMPK/mTOR/autophagy pathway <i>in vivo</i> (<i>p</i> &lt; 0.001) and <i>in vitro</i> (<i>p</i> &lt; 0.05). <b>Discussion and conclusions:</b> Our results suggest TMZ as a potential cardioprotective approach for cardiovascular complications during SU regimen, and potentially for cardiotoxicity of other anticancer chemotherapies associated with cardiomyocyte autophagic pathways.
DOI: 10.6084/m9.figshare.11467302
title: The protease activity of human ATG4B is regulated by reversible oxidative modification

description: Macroautophagy/autophagy plays a pivotal role in cytoplasmic material recycling and metabolic turnover, in which ATG4B functions as a “scissor” for processing pro-LC3 and lipidated LC3 to drive the autophagy progress. Mounting evidence has demonstrated the tight connection between ROS and autophagy during various pathological situations. Coincidentally, several studies have shown that ATG4B is potentially regulated by redox modification, but the underlying molecular mechanism and its relationship with autophagy is ambiguous. In this study, we verified that ATG4B activity was definitely regulated in a reversible redox manner. We also determined that Cys292 and Cys361 are essential sites of ATG4B to form reversible intramolecular disulfide bonds that respond to oxidative stress. Interestingly, we unraveled a new phenomenon that ATG4B concurrently formed disulfide-linked oligomers at Cys292 and Cys361, and that both sites underwent redox modifications thereby modulating ATG4B activity. Finally, increased autophagic flux and decreased oxidation sensitivity were observed in Cys292 and Cys361 double site-mutated cells under normal growth conditions. In conclusion, our research reveals a novel molecular mechanism that oxidative modification at Cys292 and Cys361 sites regulates ATG4B function, which modulates autophagy.<b>Abbreviations</b>: Air-ox: air-oxidation; ATG4B: autophagy related 4B cysteine peptidase; BCNU: 1,3-bis(2-chloroethyl)-1-nitrosourea; CBB: Coomassie Brilliant Blue; CM: complete medium; CQ: chloroquine; DTT: dithiothreitol; GSH: reduced glutathione; GSNO: S-nitrosoglutathione; GSSG: oxidized glutathione; HMW: high molecular weight; H<sub>2</sub>O<sub>2</sub>: hydrogen peroxide; NAC: N-acetyl-L-cysteine; NEM: N-ethylmaleimide; PE: phosphatidylethanolamine; PTM: post-translational modification; ROS, reactive oxygen species; WT: wild type
DOI: 10.6084/m9.figshare.11467302.v1
title: The protease activity of human ATG4B is regulated by reversible oxidative modification

description: Macroautophagy/autophagy plays a pivotal role in cytoplasmic material recycling and metabolic turnover, in which ATG4B functions as a “scissor” for processing pro-LC3 and lipidated LC3 to drive the autophagy progress. Mounting evidence has demonstrated the tight connection between ROS and autophagy during various pathological situations. Coincidentally, several studies have shown that ATG4B is potentially regulated by redox modification, but the underlying molecular mechanism and its relationship with autophagy is ambiguous. In this study, we verified that ATG4B activity was definitely regulated in a reversible redox manner. We also determined that Cys292 and Cys361 are essential sites of ATG4B to form reversible intramolecular disulfide bonds that respond to oxidative stress. Interestingly, we unraveled a new phenomenon that ATG4B concurrently formed disulfide-linked oligomers at Cys292 and Cys361, and that both sites underwent redox modifications thereby modulating ATG4B activity. Finally, increased autophagic flux and decreased oxidation sensitivity were observed in Cys292 and Cys361 double site-mutated cells under normal growth conditions. In conclusion, our research reveals a novel molecular mechanism that oxidative modification at Cys292 and Cys361 sites regulates ATG4B function, which modulates autophagy.<b>Abbreviations</b>: Air-ox: air-oxidation; ATG4B: autophagy related 4B cysteine peptidase; BCNU: 1,3-bis(2-chloroethyl)-1-nitrosourea; CBB: Coomassie Brilliant Blue; CM: complete medium; CQ: chloroquine; DTT: dithiothreitol; GSH: reduced glutathione; GSNO: S-nitrosoglutathione; GSSG: oxidized glutathione; HMW: high molecular weight; H<sub>2</sub>O<sub>2</sub>: hydrogen peroxide; NAC: N-acetyl-L-cysteine; NEM: N-ethylmaleimide; PE: phosphatidylethanolamine; PTM: post-translational modification; ROS, reactive oxygen species; WT: wild type
DOI: 10.6084/m9.figshare.21428803
title: Semaphorin 3A Inhibits Endoplasmic Reticulum Stress Induced by High Glucose in Müller Cells

description: This study aimed to explore the effect of the Semaphorin3A (Sema3A)/Neuropilin-1 (Nrp-1) pathway on Müller cell activities and endoplasmic reticulum (ER) stress induced by high glucose (HG) in vitro. The primary Müller cells of C57BL/6J mice were isolated and cultured in normal or high glucose medium. The expression of endogenous Sema3A and its coreceptor Nrp-1 was measured by Western blot. Müller cells were incubated with exogenous recombinant Sema3A protein or transfected with lentiviral vectors expressing small hairpin RNA (shRNA) to knock down the expression of endogenous Sema3A. The proliferation of Müller cells was detected by CCK-8 assay and EdU staining. The migratory ability was detected by the Transwell migration assay. The level of endoplasmic reticulum (ER) stress was analyzed through the detection of GRP78/BiP, IRE1α, phosphorylated IRE1αS724 (p-IRE1αS724), and the splicing rate of XBP1 (XBP1s/XBP1) by using immunofluorescence, Western blot or quantitative polymerase chain reaction (qPCR). HG induced the upregulation of endogenous Sema3A and Nrp-1 receptors in Müller cells. The expression of GRP78/BiP and IRE1α was upregulated by HG, with an increased splicing rate of XBP1. Exogenous Sema3A inhibited HG-induced Müller cell proliferation, migration, and GRP78/BiP-IRE1α-XBP1 axis activation. Knockdown of Sema3A promoted proliferation, migration, and ER stress induced by high glucose in Müller cells. Sema3A inhibited the increased proliferative and migratory activities induced by high glucose by attenuating ER stress in Müller cells.
DOI: 10.6084/m9.figshare.21428803.v2
title: Semaphorin 3A Inhibits Endoplasmic Reticulum Stress Induced by High Glucose in Müller Cells

description: This study aimed to explore the effect of the Semaphorin3A (Sema3A)/Neuropilin-1 (Nrp-1) pathway on Müller cell activities and endoplasmic reticulum (ER) stress induced by high glucose (HG) in vitro. The primary Müller cells of C57BL/6J mice were isolated and cultured in normal or high glucose medium. The expression of endogenous Sema3A and its coreceptor Nrp-1 was measured by Western blot. Müller cells were incubated with exogenous recombinant Sema3A protein or transfected with lentiviral vectors expressing small hairpin RNA (shRNA) to knock down the expression of endogenous Sema3A. The proliferation of Müller cells was detected by CCK-8 assay and EdU staining. The migratory ability was detected by the Transwell migration assay. The level of endoplasmic reticulum (ER) stress was analyzed through the detection of GRP78/BiP, IRE1α, phosphorylated IRE1αS724 (p-IRE1αS724), and the splicing rate of XBP1 (XBP1s/XBP1) by using immunofluorescence, Western blot or quantitative polymerase chain reaction (qPCR). HG induced the upregulation of endogenous Sema3A and Nrp-1 receptors in Müller cells. The expression of GRP78/BiP and IRE1α was upregulated by HG, with an increased splicing rate of XBP1. Exogenous Sema3A inhibited HG-induced Müller cell proliferation, migration, and GRP78/BiP-IRE1α-XBP1 axis activation. Knockdown of Sema3A promoted proliferation, migration, and ER stress induced by high glucose in Müller cells. Sema3A inhibited the increased proliferative and migratory activities induced by high glucose by attenuating ER stress in Müller cells.
DOI: 10.6084/m9.figshare.21953195
title: Use of Capillary Electrophoresis Migration Position for the Presumptive Identification of Hemoglobin Variants Prevalent in China

description: Capillary electrophoresis (CE) is increasingly being used to screen for hemoglobinopathies. We here report the migration position of hemoglobin (Hb) variants prevalent in China determined by CE. The CE migration position showed excellent precision and minor inter-individual variation. We conclude that the CE migration position can be used as a reliable indicator for identifying Hb variants and can also help to establish a well-characterized library of Hb variants for their refined presumptive identification.
DOI: 10.6084/m9.figshare.21953195.v1
title: Use of Capillary Electrophoresis Migration Position for the Presumptive Identification of Hemoglobin Variants Prevalent in China

description: Capillary electrophoresis (CE) is increasingly being used to screen for hemoglobinopathies. We here report the migration position of hemoglobin (Hb) variants prevalent in China determined by CE. The CE migration position showed excellent precision and minor inter-individual variation. We conclude that the CE migration position can be used as a reliable indicator for identifying Hb variants and can also help to establish a well-characterized library of Hb variants for their refined presumptive identification.
DOI: 10.6084/m9.figshare.20382161
title: Additional file 2 of DNA methylation-mediated differential expression of DLX4 isoforms has opposing roles in leukemogenesis

description: Additional file 2: Table S2. mRNA expression analyzed by RNA-seq in K562 cell after BP1 overexpression (original data).
DOI: 10.6084/m9.figshare.20382161.v1
title: Additional file 2 of DNA methylation-mediated differential expression of DLX4 isoforms has opposing roles in leukemogenesis

description: Additional file 2: Table S2. mRNA expression analyzed by RNA-seq in K562 cell after BP1 overexpression (original data).
DOI: 10.6084/m9.figshare.21430828
title: Additional file 5 of scTAM-seq enables targeted high-confidence analysis of DNA methylation in single cells

description: Additional file 5: Table S4. Non-HhaI amplicons used for cell selection.
DOI: 10.6084/m9.figshare.21430828.v1
title: Additional file 5 of scTAM-seq enables targeted high-confidence analysis of DNA methylation in single cells

description: Additional file 5: Table S4. Non-HhaI amplicons used for cell selection.
DOI: 10.6084/m9.figshare.14615218
title: Additional file 2 of KDM6A-ARHGDIB axis blocks metastasis of bladder cancer by inhibiting Rac1

description: Additional file 2.
DOI: 10.6084/m9.figshare.20382397
title: Calibration of simulation parameters for wind erosion gas-solid two-phase flow in arid and semiarid soils

description: ABSTRACT To construct a coupled simulation model of soil wind erosion and two-phase flow in arid and semiarid regions, the proper contact parameters of the soil discrete element simulation model are obtained based on the angle of repose (AoR) calibration test. The coupled simulation model is established by combining computational fluid dynamics. The response value of the wind speed of sand initiation is used to verify the model’s accuracy. Due to the characteristics of arid and semiarid soils, this paper uses the Hertz-Mindlin with JKR contact model in EDEM software to calibrate the soil parameters based on soil physical tests and designs the Plackett-Burman, steepest climb, and Box-Behnken tests according to Design-Expert software to obtain the soil AoR second-order regression. With the AoR of 33.52° as the target, the best combination of parameters is obtained: soil-soil collision recovery of 0.64, soil-steel static friction coefficient of 0.31, JKR surface energy of 3.302 J m-2. Finally, by using calibrated parameters and the threshold wind velocity as the response value, the wind-sand air-solid two-phase flow test is conducted in ANSYS Fluent and EDEM, with the relative error between the starting wind speed recorded by the high-speed camera in the wind tunnel test and the threshold wind velocity shown in the simulation model calculated to be 8.7%, and the calibrated soil parameters met the requirements of the coupled simulation.
DOI: 10.6084/m9.figshare.20382397.v1
title: Calibration of simulation parameters for wind erosion gas-solid two-phase flow in arid and semiarid soils

description: ABSTRACT To construct a coupled simulation model of soil wind erosion and two-phase flow in arid and semiarid regions, the proper contact parameters of the soil discrete element simulation model are obtained based on the angle of repose (AoR) calibration test. The coupled simulation model is established by combining computational fluid dynamics. The response value of the wind speed of sand initiation is used to verify the model’s accuracy. Due to the characteristics of arid and semiarid soils, this paper uses the Hertz-Mindlin with JKR contact model in EDEM software to calibrate the soil parameters based on soil physical tests and designs the Plackett-Burman, steepest climb, and Box-Behnken tests according to Design-Expert software to obtain the soil AoR second-order regression. With the AoR of 33.52° as the target, the best combination of parameters is obtained: soil-soil collision recovery of 0.64, soil-steel static friction coefficient of 0.31, JKR surface energy of 3.302 J m-2. Finally, by using calibrated parameters and the threshold wind velocity as the response value, the wind-sand air-solid two-phase flow test is conducted in ANSYS Fluent and EDEM, with the relative error between the starting wind speed recorded by the high-speed camera in the wind tunnel test and the threshold wind velocity shown in the simulation model calculated to be 8.7%, and the calibrated soil parameters met the requirements of the coupled simulation.
DOI: 10.6084/m9.figshare.14615218.v1
title: Additional file 2 of KDM6A-ARHGDIB axis blocks metastasis of bladder cancer by inhibiting Rac1

description: Additional file 2.
DOI: 10.6084/m9.figshare.14615374
title: Additional file 2 of SCUBE3 serves as an independent poor prognostic factor in breast cancer

description: Additional file 2. The original data.
DOI: 10.6084/m9.figshare.14615374.v1
title: Additional file 2 of SCUBE3 serves as an independent poor prognostic factor in breast cancer

description: Additional file 2. The original data.
DOI: 10.6084/m9.figshare.8848208
title: Determination of Plant Growth Regulators in Chinese Herbal Medicine: A Comparison of Liquid (QuEChERS) and Solid (MSPD) Extraction Methods

description: This work aimed to compare the methods for the determination of twenty plant growth regulators (PGRs) from Chinese herbal medicines by applying liquid and solid extraction methods simultaneously. Quick, easy, cheap, effective, rugged and safe (QuEChERS) and matrix solid-phase dispersion (MSPD) were chosen as the liquid and solid extraction methods, respectively. Due to the complex matrix of herbal medicine, carbon nanotubes were selected as the solutions/sorbents for the extraction and purification. The extracts were analyzed by ultra-performance liquid chromatography-triple quadrupole-mass spectrometry (UPLC-MS/MS). Both methods resulted in good efficiency for the extraction and purification. The recoveries fell in the range of 71-117% with relative standard deviations (RSDs) less than 19%. The limits of detection were in the range of 0.01 to 3 μg kg-1 with the two methods. The standards were prepared using the matrix matched standards due to the considerable matrix effects of the herbal medicines. Compared to the liquid method, the solid method required a smaller amount of sample, which is critical for PGR analysis of rare valuable herbal medicines. The two methods were applied for the determination of the twenty PGRs in different Chinese herbal medicine successfully.
DOI: 10.6084/m9.figshare.8848208.v1
title: Determination of Plant Growth Regulators in Chinese Herbal Medicine: A Comparison of Liquid (QuEChERS) and Solid (MSPD) Extraction Methods

description: This work aimed to compare the methods for the determination of twenty plant growth regulators (PGRs) from Chinese herbal medicines by applying liquid and solid extraction methods simultaneously. Quick, easy, cheap, effective, rugged and safe (QuEChERS) and matrix solid-phase dispersion (MSPD) were chosen as the liquid and solid extraction methods, respectively. Due to the complex matrix of herbal medicine, carbon nanotubes were selected as the solutions/sorbents for the extraction and purification. The extracts were analyzed by ultra-performance liquid chromatography-triple quadrupole-mass spectrometry (UPLC-MS/MS). Both methods resulted in good efficiency for the extraction and purification. The recoveries fell in the range of 71-117% with relative standard deviations (RSDs) less than 19%. The limits of detection were in the range of 0.01 to 3 μg kg-1 with the two methods. The standards were prepared using the matrix matched standards due to the considerable matrix effects of the herbal medicines. Compared to the liquid method, the solid method required a smaller amount of sample, which is critical for PGR analysis of rare valuable herbal medicines. The two methods were applied for the determination of the twenty PGRs in different Chinese herbal medicine successfully.
DOI: 10.15468/z7zg34
title: Mollusca Collections from the South China Sea Repository and Reference Centre (RRC), Institute of Oceanography and Environment (INOS), Universiti Malaysia Terengganu (UMT)

description: This dataset is a partial compilation of mollusca collections in the South China Sea Repository and Reference Centre, Institute of Oceanography and Environment, Universiti Malaysia Terengganu.
DOI: 10.15468/u6kj6b
title: Pierid butterfly specimens (Part 3: Appias, Elodina, Leuciacria, Udaiana) at Museum Zoologi Bogor, Indonesia

description: Dataset of pierid butterfly specimens (Part 1: Aoa, Belenois, Cepora, Prioneris, Saletara) deposited at Museum Zoologi Bogor, Indonesia
DOI: 10.15468/47wve9
title: Eurema butterfly specimens at Museum Zoologi Bogor, Indonesia

description: Dataset of Eurema butterfly specimens deposited at Museum Zoologi Bogor, Indonesia
DOI: 10.15468/isqrqq
title: Troides butterfly specimens at Museum Zoologi Bogor, Indonesia

description: Dataset of Troides butterfly specimens deposited at Museum Zoologi Bogor, Indonesia
DOI: 10.15468/aj9bp7
title: Idea butterfly specimens at Museum Zoologi Bogor, Indonesia

description: Dataset of Idea butterfly specimens deposited at Museum Zoologi Bogor, Indonesia
DOI: 10.15468/7vtqff
title: Microlepidoptera database in some regions of the Lower Volga of the European part of Russia

description: The aim of the research is to describe the taxonomic composition and species diversity of the moth fauna of the Lower Volga region within the boundaries of Saratov and Volgograd Provinces (the south-eastern part of European Russia). The research was carried out in April-Novermber 1979-2023. Collections were made using a variety of methods (light trapping, Malaise traps, window traps, etc. For each observation the coordinates of the place of finding, abundance, dates were recorded. The dataset contains data on 983 species of microlepidoptera from 59 families. In total, 3471 specimens of moths have been studied.
DOI: 10.15468/dcczuv
title: Spiders of the Kreidova Flora Nature Reserve (Eastern Ukraine)

description: The database includes records of 157 spider species in 27 families collected in the Kreidova Flora Department of the Ukrainian Steppe Nature Reserve and its vicinity. The Department territory covers chalk hills on the right high bank of the Siverskyi Donets River.
DOI: 10.5281/zenodo.10725528
title: Dataset for Provenance of Tibetan Geoid Ridge and its Implication to the Collision Evolution between India and Tibet

description: Original Data for the Article "Provenance of Tibetan Geoid Ridge and its Implication to the Collision Evolution between India and Tibet" by Peilong Yan, Nan Zhang, Xi Liu and Bo Wan

PEILONG YAN, PEKING UNIVERSITY, FEB. 2024

All files presented here are the seismic tomography data interpolated to the CitcomS 65*65*65 mesh.

GYPSUM-S and SEMUCB-WM1 are the global whole mantle data of these two seismic tomography models.

GYPSUM-S_TibetanTZ is the global whole mantle data without seismic low-velocity anomalies in the Tibetan region (Red rectagle in Figure 3a in the main text).

GYPSUM-S+EARA2014, GYPSUM-S+SEMUCBWM1 and GYPSUM-S+SL2013sv are the global whole mantle data of GYPSUM-S with the Tibetan region replaced by EARA2014, SEMUCB-WM1 and SL2013sv models.

GYPSUM-S+EARA2014_cold, GYPSUM-S+SEMUCBWM1_cold and GYPSUM-S+SL2013sv_cold are the global whole mantle data of GYPSUM-S with the Tibetan region replaced by EARA2014, SEMUCB-WM1 and SL2013sv high-velocity anomalies.

Seismic velocity anomalies are transferred to thermal anomalies, please check the article's main text for more details.
DOI: 10.5281/zenodo.10725529
title: Dataset for Provenance of Tibetan Geoid Ridge and its Implication to the Collision Evolution between India and Tibet

description: Original Data for the Article "Provenance of Tibetan Geoid Ridge and its Implication to the Collision Evolution between India and Tibet" by Peilong Yan, Nan Zhang, Xi Liu and Bo Wan

PEILONG YAN, PEKING UNIVERSITY, FEB. 2024

All files presented here are the seismic tomography data interpolated to the CitcomS 65*65*65 mesh.

GYPSUM-S and SEMUCB-WM1 are the global whole mantle data of these two seismic tomography models.

GYPSUM-S_TibetanTZ is the global whole mantle data without seismic low-velocity anomalies in the Tibetan region (Red rectagle in Figure 3a in the main text).

GYPSUM-S+EARA2014, GYPSUM-S+SEMUCBWM1 and GYPSUM-S+SL2013sv are the global whole mantle data of GYPSUM-S with the Tibetan region replaced by EARA2014, SEMUCB-WM1 and SL2013sv models.

GYPSUM-S+EARA2014_cold, GYPSUM-S+SEMUCBWM1_cold and GYPSUM-S+SL2013sv_cold are the global whole mantle data of GYPSUM-S with the Tibetan region replaced by EARA2014, SEMUCB-WM1 and SL2013sv high-velocity anomalies.

Seismic velocity anomalies are transferred to thermal anomalies, please check the article's main text for more details.
DOI: 10.15468/gajarm
title: Campagnes en mer d'observations de cétacés (Abyss) - Synthèse des données d''observation issues des campagnes en mer d''Abyss sur la période 2008-2012

description: Synthèse des données d'observation issues des campagnes en mer d'Abyss sur la période 2008-2012. Les observations sont fortuites et les transects ne sont pas prédéterminés. Utilisation d'un epad (précision métrique, environ 15m). Données exportées depuis Google fusion.