cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/gcn4p9hbpm.1
title: Integrated proteomics and metabolomics reveal phytosesquiterpene lactones DET and DETD-35 inhibit triple-negative breast cancer cell activity by depleting ATP synthesis and reprogramming primary metabolism

description: Phytosesquiterpene lactones DET and DETD-35 are reported to induce oxidative stress towards inhibiting the activities of triple-negative breast cancer (TNBC) cells. However, how DET and DETD-35 affect mitochondrial proteome and associated oxidative phosphorylation in TNBC cells is unclear. In this study, the mechanisms through which DET and DETD-35 inhibit MDA-MB-231 TNBC cells were dissected. DET and DETD-35 promoted mitochondrial superoxide production by upregulating expression of SOD1 and SOD2, and induced permeability transition pore opening, and attenuated intracellular ATP levels. Neither compound interfered with mitochondrial respiration/bioenergetics in normal mammary MCF-10A cells. Comparative mitochondria proteome and bioinformatic analyses showed significant deregulation of proteins related to the oxidative phosphorylation, depolarization of mitochondria, and apoptosis signaling in DET- or DETD-35-treated TNBC cells, and primary metabolomics revealed that both compounds deregulated metabolites dynamics and the corresponding metabolic pathways in TNBC cells. Knockdown of the PRKCA gene/protein involved in inducing mitochondrial toxicity in TNBC cells reversed cytotoxicity and apoptosis and decreased the levels of several metabolites induced by DET or DETD-35 in the cancer cells. Integrated Pearson’s correlation and IPA network analyses of differentially expressed proteins and metabolites revealed the networks of ATP synthesis, energy homeostasis, and mitochondrial activities (respiration, depolarization, and transmembrane potential) highly correlated to the compound effects. Notable, DET/DETD-35 inhibited mitochondrial ATPase activity, and molecular modeling further predicted the binding sites of either compound with ATP synthase at the subunits α/βand c/a interfaces. In summary, the mechanisms through which these phytosesquiterpene lactones disrupt mitochondrial biogenetics to inhibit TNBC cell activities were delineated.
DOI: 10.17632/gcn4p9hbpm.2
title: Integrated proteomics and metabolomics reveal phytosesquiterpene lactones DET and DETD-35 inhibit triple-negative breast cancer cell activity by depleting ATP synthesis and reprogramming primary metabolism

description: Phytosesquiterpene lactones DET and DETD-35 are reported to induce oxidative stress towards inhibiting the activities of triple-negative breast cancer (TNBC) cells. However, how DET and DETD-35 affect mitochondrial proteome and associated oxidative phosphorylation in TNBC cells is unclear. In this study, the mechanisms through which DET and DETD-35 inhibit MDA-MB-231 TNBC cells were dissected. DET and DETD-35 promoted mitochondrial superoxide production by upregulating expression of SOD1 and SOD2, and induced permeability transition pore opening, and attenuated intracellular ATP levels. Neither compound interfered with mitochondrial respiration/bioenergetics in normal mammary MCF-10A cells. Comparative mitochondria proteome and bioinformatic analyses showed significant deregulation of proteins related to the oxidative phosphorylation, depolarization of mitochondria, and apoptosis signaling in DET- or DETD-35-treated TNBC cells, and primary metabolomics revealed that both compounds deregulated metabolites dynamics and the corresponding metabolic pathways in TNBC cells. Knockdown of the PRKCA gene/protein involved in inducing mitochondrial toxicity in TNBC cells reversed cytotoxicity and apoptosis and decreased the levels of several metabolites induced by DET or DETD-35 in the cancer cells. Integrated Pearson’s correlation and IPA network analyses of differentially expressed proteins and metabolites revealed the networks of ATP synthesis, energy homeostasis, and mitochondrial activities (respiration, depolarization, and transmembrane potential) highly correlated to the compound effects. Notable, DET/DETD-35 inhibited mitochondrial ATPase activity, and molecular modeling further predicted the binding sites of either compound with ATP synthase at the subunits α/βand c/a interfaces. In summary, the mechanisms through which these phytosesquiterpene lactones disrupt mitochondrial biogenetics to inhibit TNBC cell activities were delineated.
DOI: 10.17632/gcn4p9hbpm.3
title: Integrated proteomics and metabolomics reveal phytosesquiterpene lactones DET and DETD-35 inhibit triple-negative breast cancer cell activity by depleting ATP synthesis and reprogramming primary metabolism

description: Phytosesquiterpene lactones DET and DETD-35 are reported to induce oxidative stress towards inhibiting the activities of triple-negative breast cancer (TNBC) cells. However, how DET and DETD-35 affect mitochondrial proteome and associated oxidative phosphorylation in TNBC cells is unclear. In this study, the mechanisms through which DET and DETD-35 inhibit MDA-MB-231 TNBC cells were dissected. DET and DETD-35 promoted mitochondrial superoxide production by upregulating expression of SOD1 and SOD2, and induced permeability transition pore opening, and attenuated intracellular ATP levels. Neither compound interfered with mitochondrial respiration/bioenergetics in normal mammary MCF-10A cells. Comparative mitochondria proteome and bioinformatic analyses showed significant deregulation of proteins related to the oxidative phosphorylation, depolarization of mitochondria, and apoptosis signaling in DET- or DETD-35-treated TNBC cells, and primary metabolomics revealed that both compounds deregulated metabolites dynamics and the corresponding metabolic pathways in TNBC cells. Knockdown of the PRKCA gene/protein involved in inducing mitochondrial toxicity in TNBC cells reversed cytotoxicity and apoptosis and decreased the levels of several metabolites induced by DET or DETD-35 in the cancer cells. Integrated Pearson’s correlation and IPA network analyses of differentially expressed proteins and metabolites revealed the networks of ATP synthesis, energy homeostasis, and mitochondrial activities (respiration, depolarization, and transmembrane potential) highly correlated to the compound effects. Notable, DET/DETD-35 inhibited mitochondrial ATPase activity, and molecular modeling further predicted the binding sites of either compound with ATP synthase at the subunits α/βand c/a interfaces. In summary, the mechanisms through which these phytosesquiterpene lactones disrupt mitochondrial biogenetics to inhibit TNBC cell activities were delineated.
DOI: 10.17632/gcn4p9hbpm.4
title: Integrated proteomics and metabolomics reveal phytosesquiterpene lactones DET and DETD-35 inhibit triple-negative breast cancer cell activity by depleting ATP synthesis and reprogramming primary metabolism

description: Phytosesquiterpene lactones DET and DETD-35 are reported to induce oxidative stress towards inhibiting the activities of triple-negative breast cancer (TNBC) cells. However, how DET and DETD-35 affect mitochondrial proteome and associated oxidative phosphorylation in TNBC cells is unclear. In this study, the mechanisms through which DET and DETD-35 inhibit MDA-MB-231 TNBC cells were dissected. DET and DETD-35 promoted mitochondrial superoxide production by upregulating expression of SOD1 and SOD2, and induced permeability transition pore opening, and attenuated intracellular ATP levels. Neither compound interfered with mitochondrial respiration/bioenergetics in normal mammary MCF-10A cells. Comparative mitochondria proteome and bioinformatic analyses showed significant deregulation of proteins related to the oxidative phosphorylation, depolarization of mitochondria, and apoptosis signaling in DET- or DETD-35-treated TNBC cells, and primary metabolomics revealed that both compounds deregulated metabolites dynamics and the corresponding metabolic pathways in TNBC cells. Knockdown of the PRKCA gene/protein involved in inducing mitochondrial toxicity in TNBC cells reversed cytotoxicity and apoptosis and decreased the levels of several metabolites induced by DET or DETD-35 in the cancer cells. Integrated Pearson’s correlation and IPA network analyses of differentially expressed proteins and metabolites revealed the networks of ATP synthesis, energy homeostasis, and mitochondrial activities (respiration, depolarization, and transmembrane potential) highly correlated to the compound effects. Notable, DET/DETD-35 inhibited mitochondrial ATPase activity, and molecular modeling further predicted the binding sites of either compound with ATP synthase at the subunits α/βand c/a interfaces. In summary, the mechanisms through which these phytosesquiterpene lactones disrupt mitochondrial biogenetics to inhibit TNBC cell activities were delineated.
DOI: 10.17632/jxg6gf87fy.1
title: A Large-scale High-resolution velocity and strain rate field in the Northeastern Tibetan Plateau

description: (1) velocity-*-eu-90m.grd: the InSAR LOS velocity field in the ascending and descending tracks with respect to Eurasian plate in a resolution of ~90 m.
(2) Ve-90m.grd Vn-90m.grd Vu-90m.grd: the 3D velocities with a resolution of ~90m derived from InSAR LOS ascending, descending velocities and GNSS north-east velocities.
(3) *-rate-1km.grd: the horizontal strain rate fields with a resolution of ~1km calculated from the method of Ou et al. (2022).
DOI: 10.15468/dl.cgfehm
title: Occurrence Download

description: A dataset containing 12083292 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "Country is Ecuador"
 ]
}

 The dataset includes 12083292 records from 2213 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011022-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5518/471
title: Magnetic properties and field-driven dynamics of chiral domain walls in epitaxial Pt/Co/AuxPt1-x trilayers - dataset

description: Chiral domain walls in ultrathin perpendicularly magnetised layers have a N\'{e}el structure stabilised by a Dzyaloshinskii-Moriya interaction (DMI) that is generated at the interface between the ferromagnet and a heavy metal. Different interface materials or properties are required above and below a ferromagnetic film in order to generate the structural inversion asymmetry needed to ensure that the DMI arising at the two interfaces does not cancel. Here we report on the magnetic properties of epitaxial Pt/Co/Au$_x$Pt$_{1-x}$ trilayers grown by sputtering onto sapphire substrates with 0.6~nm thick Co. As $x$ rises from 0 to 1 a structural inversion asymmetry is progressively generated. We characterise the epilayer structure with x-ray diffraction and cross-sectional transmission electron microscopy, revealing (111) stacking. The saturation magnetization falls as the proximity magnetisation in Pt is reduced, whilst the perpendicular magnetic anisotropy $K_\mathrm{u}$ rises. The micromagnetic DMI strength $D$ was determined using the bubble expansion technique and also rises from a negligible value when $x=0$ to $\sim 1$~mJ/m$^2$ for $x = 1$. The depinning field at which field-driven domain wall motion crosses from the creep to the depinning regime rises from $\sim 40$ to $\sim 70$~mT, attributed to greater spatial fluctuations of the domain wall energy with increasing Au concentration. Meanwhile, the increase in DMI causes the Walker field to rise from $\sim 10$ to $\sim 280$~mT, meaning that only in the $x = 1$ sample is the steady flow regime accessible. The full dependence of domain wall velocity on driving field bears little resemblance to the prediction of a simple one-dimensional model, but can be described very well using micromagnetic simulations with a realistic model of disorder. These reveal a rise in Gilbert damping as $x$ increases.
DOI: 10.15468/dl.w4ek4h
title: Occurrence Download

description: A dataset containing 3769 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen, Living Specimen)",
 "OccurrenceStatus is Present",
 "TaxonKey is Chamaecyparis pisifera (Siebold & Zucc.) Endl."
 ]
}

 The dataset includes 3769 records from 245 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041306-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8bc8t5
title: Occurrence Download

description: A dataset containing 6419 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Noccaea brachypetala (Jord.) F.K.Mey.)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "HasGeospatialIssue is false",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Specimen)"
 ]
 }
 }
 ]
}

 The dataset includes 6419 records from 110 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041305-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13121699
title: SOSE output analyzed in "Evaluation of MITgcm-based ocean reanalysis for the Southern Ocean" (Part 2-8)

description: SOSE output analyzed in "Evaluation of MITgcm-based ocean reanalysis for the Southern Ocean" submitted to GMD. Complete theta data is 174GB. Thus, this dataset is separated into smaller files. These data can be accessed by accessing Zenode links (see below) or downloading from  http://sose.ucsd.edu/ (recommended).
DOI: 10.5281/zenodo.13121700
title: SOSE output analyzed in "Evaluation of MITgcm-based ocean reanalysis for the Southern Ocean" (Part 2-8)

description: SOSE output analyzed in "Evaluation of MITgcm-based ocean reanalysis for the Southern Ocean" submitted to GMD. Complete theta data is 174GB. Thus, this dataset is separated into smaller files. These data can be accessed by accessing Zenode links (see below) or downloading from  http://sose.ucsd.edu/ (recommended).
DOI: 10.6084/m9.figshare.25826126.v1
title: HO-1-induced autophagy establishes a HO-1-p62-Nrf2 positive feedback loop to reduce gut permeability in cholestatic liver disease

description: The gut-liver axis disruption is a unified pathogenetic principle of cholestatic liver disease (CSLD). Increased gut permeability is the leading cause of gut-liver axis disruption. HO-1 is capable of protecting against gut-liver axis injury. However, it has rarely been reported whether autophagy is involved in HO-1 protecting gut-liver barrier integrity and the underlying mechanism. Mice underwent bile duct ligation (BDL) was established as CSLD model in vivo. Caco-2 cells with LPS treatment was established as in vitro cell model. Immunofluorescence, western blot and transepithelial electrical resistance (TER) assay were used to observe epithelial tight junction (TJ) and autophagy. Liver injury and fibrosis were evaluated as well through H&E staining, masson staining, sirius red staining and ELISA. Our study demonstrated that the epithelial TJ and TER were notably reduced both in BDL mice and in LPS treated intestinal epithelial cells. Increased HO-1 expression could significantly induce intestinal epithelial cell autophagy. Additionally, this increased autophagy level reversed the reduction effects of BDL or LPS on epithelial TJ and TER <i>in vivo</i> and <i>in vitro</i>, therefore decreased transaminase level in serum and relieved liver fibrosis in BDL mice. Besides, increased autophagy level in turn upregulated the expression of HO-1 by p62 degradation of Keap1 and subsequent activation of Nrf2 pathway. Collectively, these results indicate that HO-1 reduces gut permeability by enhancing autophagy level in CSLD, the increased autophagy establishes a HO-1-p62-Nrf2 positive feedback loop to further improve gut-liver axis disruption. Therefore, our study confirms the critical role of autophagy in HO-1 ameliorating gut-liver axis injury during CSLD, highlighting HO-1 as a promising therapeutic target.
DOI: 10.6084/m9.figshare.25826126
title: HO-1-induced autophagy establishes a HO-1-p62-Nrf2 positive feedback loop to reduce gut permeability in cholestatic liver disease

description: The gut-liver axis disruption is a unified pathogenetic principle of cholestatic liver disease (CSLD). Increased gut permeability is the leading cause of gut-liver axis disruption. HO-1 is capable of protecting against gut-liver axis injury. However, it has rarely been reported whether autophagy is involved in HO-1 protecting gut-liver barrier integrity and the underlying mechanism. Mice underwent bile duct ligation (BDL) was established as CSLD model in vivo. Caco-2 cells with LPS treatment was established as in vitro cell model. Immunofluorescence, western blot and transepithelial electrical resistance (TER) assay were used to observe epithelial tight junction (TJ) and autophagy. Liver injury and fibrosis were evaluated as well through H&E staining, masson staining, sirius red staining and ELISA. Our study demonstrated that the epithelial TJ and TER were notably reduced both in BDL mice and in LPS treated intestinal epithelial cells. Increased HO-1 expression could significantly induce intestinal epithelial cell autophagy. Additionally, this increased autophagy level reversed the reduction effects of BDL or LPS on epithelial TJ and TER <i>in vivo</i> and <i>in vitro</i>, therefore decreased transaminase level in serum and relieved liver fibrosis in BDL mice. Besides, increased autophagy level in turn upregulated the expression of HO-1 by p62 degradation of Keap1 and subsequent activation of Nrf2 pathway. Collectively, these results indicate that HO-1 reduces gut permeability by enhancing autophagy level in CSLD, the increased autophagy establishes a HO-1-p62-Nrf2 positive feedback loop to further improve gut-liver axis disruption. Therefore, our study confirms the critical role of autophagy in HO-1 ameliorating gut-liver axis injury during CSLD, highlighting HO-1 as a promising therapeutic target.
DOI: 10.15468/dl.gczh5t
title: Occurrence Download

description: A dataset containing 282 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Neltuma alba (Griseb.) C.E.Hughes & G.P.Lewis"
 ]
}

 The dataset includes 282 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041307-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dsu4nd
title: Occurrence Download

description: A dataset containing 163 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aethomys ineptus (Thomas & Wroughton, 1908)"
 ]
}

 The dataset includes 163 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041308-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25592/uhhfdm.14743
title: CT of Maranta leuconeura branch

description: CT dataset (.nii) and metadata sheet of the branching of an aerial shoot of Maranta leuconeura.
description: Linnea Hesse was supported by the European Social Fund and the Ministry of Science, Research and the Arts Baden-Württemberg within the framework of the 'Margarete von Wrangell Habilitation Programme'. Linnea Hesse and Sébastien Bär received additional support by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation; HE 9048/1-1).
DOI: 10.15468/dl.hhatxb
title: Occurrence Download

description: A dataset containing 1673 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen, Living Specimen)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Chamaecyparis pisifera (Siebold & Zucc.) Endl."
 ]
}

 The dataset includes 1673 records from 145 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041309-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.aaf2c2
title: Occurrence Download

description: A dataset containing 33406 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Noccaea caerulescens (J.Presl & C.Presl) F.K.Mey.)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "HasGeospatialIssue is false",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Specimen)"
 ]
 }
 }
 ]
}

 The dataset includes 33406 records from 252 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041310-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fzv8u6
title: Occurrence Download

description: A dataset containing 3135 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen, Living Specimen)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Chamaecyparis obtusa (Siebold & Zucc.) Endl."
 ]
}

 The dataset includes 3135 records from 145 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041311-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.12820740
title: Computational Artifacts for the Paper "Are Noise-resilient Logical Timers useful for Performance Analysis?"

description: This repository contains computational artifacts for the paper "Are Noise-resilient Logical Timers useful for Performance Analysis?" to be submitted to ProTools@SC24.

See also the SC24 reproducibility initiative.

 

Contains



Source code of Score-P , including implementation of the logical clock algorithm from the paper

Software to post-process the Cube files generated by measurements

Benchmarks



Source code

Configuration skripts

Measurement results, including output logs, Cube files

Post-processing skripts and results




 
description: In modern HPC systems, performance measurements are often disturbed by noise.Because repeating measurements to increase confidence in their results is costly, alternative noise-resilient techniques are desirable. Therefore, we implement a logical clock, which does not rely on real-time measurements, in Score-P. We explore several methods to model computational work with the clock increment, counting OpenMP loop iterations, LLVM basic blocks/statements, or hardware counters.We demonstrate the strengths and weaknesses of using logical time stamps in a trace analysis workflow with Score-P and Scalasca, by evaluating the performance problems we can find in three MPI+OpenMP mini-apps.By design, logical measurements reliably show algorithmic issues, such as load imbalance, but cannot capture external aspects of program execution, for example memory contention.In summary, logical-time based measurements are a specialized but valuable addition to the performance analyst's toolbox.