cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.14272/cgjmihzefdrigg-uhfffaoysa-n.1
title: 4-methyl-N-morpholin-4-ylbenzenesulfonamide
title: InChI=1S/C11H16N2O3S/c1-10-2-4-11(5-3-10)17(14,15)12-13-6-8-16-9-7-13/h2-5,12H,6-9H2,1H3

description: This is a physical chemical entity[CHEBI_24431] associated with a molecule[CHEBI_25367]. The molecule[CHEBI_25367] can be described by the following structural desciptors[cheminf_000085]: InChI descriptor[cheminf_000113]: InChI=1S/C11H16N2O3S/c1-10-2-4-11(5-3-10)17(14,15)12-13-6-8-16-9-7-13/h2-5,12H,6-9H2,1H3, and canonical SMILES descriptor[cheminf_000007]: Cc1ccc(cc1)S(=O)(=O)NN1CCOCC1, and by the IUPAC name[cheminf_000107]: 4-methyl-N-morpholin-4-ylbenzenesulfonamide. The physical chemical entity[CHEBI_24431] has a component solvent[CHEBI_46787] which is described by the canonical SMILES descriptor[cheminf_000007]: [2H]C(Cl)(Cl)Cl The physical chemical entity[CHEBI_24431] has the following Sample ID as registered in the research data repository chemotion (www.chemotion-repository.net, https://doi.org/10.25504/FAIRsharing.iagXcR): CRS-28312 The physical chemical entity[CHEBI_24431] can be described by the physical descriptors [CHEMINF_000025]: Melting point descriptor[CHEMINF_000256]: Boiling point descriptor[CHEMINF_000257]: Refractive index descriptor[CHEMINF_000253]: The physical chemical entity[CHEBI_24431] can be further described by the following assays[OBI:0000070][CHMO:0001133]: CHMO:0000593 | 1H nuclear magnetic resonance spectroscopy (1H NMR) CHMO:0000595 | 13C nuclear magnetic resonance spectroscopy (13C NMR) The physical chemical entity[CHEBI_24431] was deposited to the Molecule Archive of the Karlsruhe Insitute of Technology (KIT) with the following Sample ID: ComP-18269 Used ontologies: CHEBI - Chemical Entities of Biological Interest CHEMINF - chemical information ontology (information entities about chemical entities) CHMO - Chemical Methods Ontology OBI - Ontology for Biomedical Investigations
DOI: 10.6084/m9.figshare.15090525
title: Exendin-4 stimulates autophagy in pancreatic β-cells via the RAPGEF/EPAC-Ca<sup>2+</sup>-PPP3/calcineurin-TFEB axis

description: Macroautophagy/autophagy is critical for the regulation of pancreatic β-cell mass and its deregulation has been implicated in the pathogenesis of type 2 diabetes (T2D). We have previously shown that treatment of pancreatic β-cells with the GLP1R (glucagon like peptide 1 receptor) agonist exendin-4 stimulates autophagic flux in a setting of chronic nutrient excess. The aim of this study was to identify the underlying pathways contributing to enhanced autophagic flux. Pancreatic β-cells (INS-1E),mouse and human islets were treated with glucolipotoxic stress (0.5 mM palmitate and 25 mM glucose) in the presence of exendin-4. Consistent with our previous work, exendin-4 stimulated autophagic flux. Using chemical inhibitors and siRNA knockdown, we identified RAPGEF4/EPAC2 (Rap guanine nucleotide exchange factor 4) and downstream calcium signaling to be essential for regulation of autophagic flux by exendin-4. This pathway was independent of AMPK and MTOR signaling. Further analysis identified PPP3/calcineurin and its downstream regulator TFEB (transcription factor EB) as key proteins mediating exendin-4 induced autophagy. Importantly, inhibition of this pathway prevented exendin-4-mediated cell survival and overexpression of TFEB mimicked the cell protective effects of exendin-4 in INS-1E and human islets. Moreover, treatment of <i>db/db</i> mice with exendin-4 for 21 days increased the expression of lysosomal markers within the pancreatic islets. Collectively our data identify the RAPGEF4/EPAC2-calcium-PPP3/calcineurin-TFEB axis as a key mediator of autophagic flux, lysosomal function and cell survival in pancreatic β-cells. Pharmacological modulation of this axis may offer a novel therapeutic target for the treatment of T2D. <b>Abbreviations</b>: AKT1/protein kinase B: AKT serine/threonine kinase 1; AMPK: 5’ AMP-activated protein kinase; CAMKK: calcium/calmodulin-dependent protein kinase kinase; cAMP: cyclic adenosine monophosphate; CASP3: caspase 3; CREB: cAMP response element-binding protein; CTSD: cathepsin D; Ex4: exendin-4(1-39); GLP-1: glucagon like peptide 1; GLP1R: glucagon like peptide 1 receptor; GLT: glucolipotoxicity; INS: insulin; MTOR: mechanistic target of rapamycin kinase; NFAT: nuclear factor of activated T-cells; PPP3/calcineurin: protein phosphatase 3; PRKA/PKA: protein kinase cAMP activated; RAPGEF3/EPAC1: Rap guanine nucleotide exchange factor 3; RAPGEF4/EPAC2: Rap guanine nucleotide exchange factor 4; SQSTM1/p62: sequestosome 1; T2D: type 2 diabetes; TFEB: transcription factor EB
DOI: 10.6084/m9.figshare.15090525.v1
title: Exendin-4 stimulates autophagy in pancreatic β-cells via the RAPGEF/EPAC-Ca<sup>2+</sup>-PPP3/calcineurin-TFEB axis

description: Macroautophagy/autophagy is critical for the regulation of pancreatic β-cell mass and its deregulation has been implicated in the pathogenesis of type 2 diabetes (T2D). We have previously shown that treatment of pancreatic β-cells with the GLP1R (glucagon like peptide 1 receptor) agonist exendin-4 stimulates autophagic flux in a setting of chronic nutrient excess. The aim of this study was to identify the underlying pathways contributing to enhanced autophagic flux. Pancreatic β-cells (INS-1E),mouse and human islets were treated with glucolipotoxic stress (0.5 mM palmitate and 25 mM glucose) in the presence of exendin-4. Consistent with our previous work, exendin-4 stimulated autophagic flux. Using chemical inhibitors and siRNA knockdown, we identified RAPGEF4/EPAC2 (Rap guanine nucleotide exchange factor 4) and downstream calcium signaling to be essential for regulation of autophagic flux by exendin-4. This pathway was independent of AMPK and MTOR signaling. Further analysis identified PPP3/calcineurin and its downstream regulator TFEB (transcription factor EB) as key proteins mediating exendin-4 induced autophagy. Importantly, inhibition of this pathway prevented exendin-4-mediated cell survival and overexpression of TFEB mimicked the cell protective effects of exendin-4 in INS-1E and human islets. Moreover, treatment of <i>db/db</i> mice with exendin-4 for 21 days increased the expression of lysosomal markers within the pancreatic islets. Collectively our data identify the RAPGEF4/EPAC2-calcium-PPP3/calcineurin-TFEB axis as a key mediator of autophagic flux, lysosomal function and cell survival in pancreatic β-cells. Pharmacological modulation of this axis may offer a novel therapeutic target for the treatment of T2D. <b>Abbreviations</b>: AKT1/protein kinase B: AKT serine/threonine kinase 1; AMPK: 5’ AMP-activated protein kinase; CAMKK: calcium/calmodulin-dependent protein kinase kinase; cAMP: cyclic adenosine monophosphate; CASP3: caspase 3; CREB: cAMP response element-binding protein; CTSD: cathepsin D; Ex4: exendin-4(1-39); GLP-1: glucagon like peptide 1; GLP1R: glucagon like peptide 1 receptor; GLT: glucolipotoxicity; INS: insulin; MTOR: mechanistic target of rapamycin kinase; NFAT: nuclear factor of activated T-cells; PPP3/calcineurin: protein phosphatase 3; PRKA/PKA: protein kinase cAMP activated; RAPGEF3/EPAC1: Rap guanine nucleotide exchange factor 3; RAPGEF4/EPAC2: Rap guanine nucleotide exchange factor 4; SQSTM1/p62: sequestosome 1; T2D: type 2 diabetes; TFEB: transcription factor EB
DOI: 10.6084/m9.figshare.16441371
title: C5orf51 is a component of the MON1-CCZ1 complex and controls RAB7A localization and stability during mitophagy

description: Depolarized mitochondria can be degraded via mitophagy, a selective form of autophagy. The RAB GTPase RAB7A was recently shown to play a key role in this process. RAB7A regulates late endocytic trafficking under normal growth conditions but is translocated to the mitochondrial surface following depolarization. However, how RAB7A activity is regulated during mitophagy is not understood. Here, using a proximity-dependent biotinylation approach (miniTurbo), we identified C5orf51 as a specific interactor of GDP-locked RAB7A. C5orf51 also interacts with the RAB7A guanine nucleotide exchange factor (GEF) complex members MON1 and CCZ1. In the absence of C5orf51, localization of RAB7A on depolarized mitochondria is compromised and the protein is degraded by the proteasome. Furthermore, depletion of C5orf51 also inhibited ATG9A recruitment to depolarized mitochondria. Together, these results indicate that C5orf51 is a positive regulator of RAB7A in its shuttling between late endosomes and mitochondria to enable mitophagy. <b>Abbreviations</b>: ATG9A: autophagy related 9A; Baf A<sub>1</sub>: bafilomycin A<sub>1</sub>; BioID: proximity-dependent biotin identification; CCCP: carbonyl cyanide m-chlorophenylhydrazone; CCZ1: CCZ1 homolog, vacuolar protein trafficking and biogenesis associated; DQ-BSA: dye quenched-bovine serum albumin; FYCO1: FYVE and coiled-coil domain autophagy adaptor 1; GAP: GTPase activating protein; GEF: guanine nucleotide exchange factor; KO: knockout; LRPPRC: leucine rich pentatricopeptide repeat containing; MG132: carbobenzoxy-Leu-Leu-leucinal; MON1: MON1 homolog, secretory trafficking associated; mtDNA: mitochondrial DNA; PINK1: PTEN induced kinase 1; PRKN/PARKIN: parkin RBR E3 ubiquitin protein ligase; RMC1: regulator of MON1-CCZ1; TBC1D15: TBC1 domain family member 15; TBC1D17: TBC1 domain family member 17; TOMM20: translocase of outer mitochondrial membrane 20; WDR91: WD repeat domain 91; WT: wild type.
DOI: 10.6084/m9.figshare.16441371.v1
title: C5orf51 is a component of the MON1-CCZ1 complex and controls RAB7A localization and stability during mitophagy

description: Depolarized mitochondria can be degraded via mitophagy, a selective form of autophagy. The RAB GTPase RAB7A was recently shown to play a key role in this process. RAB7A regulates late endocytic trafficking under normal growth conditions but is translocated to the mitochondrial surface following depolarization. However, how RAB7A activity is regulated during mitophagy is not understood. Here, using a proximity-dependent biotinylation approach (miniTurbo), we identified C5orf51 as a specific interactor of GDP-locked RAB7A. C5orf51 also interacts with the RAB7A guanine nucleotide exchange factor (GEF) complex members MON1 and CCZ1. In the absence of C5orf51, localization of RAB7A on depolarized mitochondria is compromised and the protein is degraded by the proteasome. Furthermore, depletion of C5orf51 also inhibited ATG9A recruitment to depolarized mitochondria. Together, these results indicate that C5orf51 is a positive regulator of RAB7A in its shuttling between late endosomes and mitochondria to enable mitophagy. <b>Abbreviations</b>: ATG9A: autophagy related 9A; Baf A<sub>1</sub>: bafilomycin A<sub>1</sub>; BioID: proximity-dependent biotin identification; CCCP: carbonyl cyanide m-chlorophenylhydrazone; CCZ1: CCZ1 homolog, vacuolar protein trafficking and biogenesis associated; DQ-BSA: dye quenched-bovine serum albumin; FYCO1: FYVE and coiled-coil domain autophagy adaptor 1; GAP: GTPase activating protein; GEF: guanine nucleotide exchange factor; KO: knockout; LRPPRC: leucine rich pentatricopeptide repeat containing; MG132: carbobenzoxy-Leu-Leu-leucinal; MON1: MON1 homolog, secretory trafficking associated; mtDNA: mitochondrial DNA; PINK1: PTEN induced kinase 1; PRKN/PARKIN: parkin RBR E3 ubiquitin protein ligase; RMC1: regulator of MON1-CCZ1; TBC1D15: TBC1 domain family member 15; TBC1D17: TBC1 domain family member 17; TOMM20: translocase of outer mitochondrial membrane 20; WDR91: WD repeat domain 91; WT: wild type.
DOI: 10.14272/rjlccsuqzuoztj-uhfffaoysa-m.1
title: berberine-tetraethylene glycol-azide
title: InChI=1S/C27H31N4O7.BrH/c1-32-24-3-2-19-14-23-21-16-26-25(37-18-38-26)15-20(21)4-6-31(23)17-22(19)27(24)36-13-12-35-11-10-34-9-8-33-7-5-29-30-28;/h2-3,14-17H,4-13,18H2,1H3;1H/q+1;/p-1

description: This is a physical chemical entity[CHEBI_24431] associated with a molecule[CHEBI_25367]. The molecule[CHEBI_25367] can be described by the following structural desciptors[cheminf_000085]: InChI descriptor[cheminf_000113]: InChI=1S/C27H31N4O7.BrH/c1-32-24-3-2-19-14-23-21-16-26-25(37-18-38-26)15-20(21)4-6-31(23)17-22(19)27(24)36-13-12-35-11-10-34-9-8-33-7-5-29-30-28;/h2-3,14-17H,4-13,18H2,1H3;1H/q+1;/p-1, and canonical SMILES descriptor[cheminf_000007]: [N-]=[N+]=NCCOCCOCCOCCOc1c(OC)ccc2c1c[n+]1CCc3c(-c1c2)cc1c(c3)OCO1.[Br-], and by the IUPAC name[cheminf_000107]: 16-[2-[2-[2-(2-azidoethoxy)ethoxy]ethoxy]ethoxy]-17-methoxy-5,7-dioxa-13-azoniapentacyclo[11.8.0.02,10.04,8.015,20]henicosa-1(13),2,4(8),9,14,16,18,20-octaene;bromide. The physical chemical entity[CHEBI_24431] has a component solvent[CHEBI_46787] which is described by the canonical SMILES descriptor[cheminf_000007]: The physical chemical entity[CHEBI_24431] has the following Sample ID as registered in the research data repository chemotion (www.chemotion-repository.net, https://doi.org/10.25504/FAIRsharing.iagXcR): CRS-14899 The physical chemical entity[CHEBI_24431] can be described by the physical descriptors [CHEMINF_000025]: Melting point descriptor[CHEMINF_000256]: Boiling point descriptor[CHEMINF_000257]: Refractive index descriptor[CHEMINF_000253]: The physical chemical entity[CHEBI_24431] can be further described by the following assays[OBI:0000070][CHMO:0001133]: CHMO:0000593 | 1H nuclear magnetic resonance spectroscopy (1H NMR) CHMO:0000595 | 13C nuclear magnetic resonance spectroscopy (13C NMR) The physical chemical entity[CHEBI_24431] was deposited to the Molecule Archive of the Karlsruhe Insitute of Technology (KIT) with the following Sample ID: ComP-15748 Used ontologies: CHEBI - Chemical Entities of Biological Interest CHEMINF - chemical information ontology (information entities about chemical entities) CHMO - Chemical Methods Ontology OBI - Ontology for Biomedical Investigations
DOI: 10.5255/ukda-sn-856507
title: Code to Create a Combined British Household Panel Survey and Understanding Society Data File, 1991-2020

description: The Modelling Housing Career Trajectories in Great Britain project used a range of datasets to examine how people’s pathways through the British housing system have changed since the 1990s. The project made extensive use of secondary household panel survey data from the British Household Panel Survey (BHPS, 1991-2008) and its successor, Understanding Society (UKHLS, 2009-present). This collection consists of project R code written to (1) extract and then (2) combine data from across the various files of BHPS and UKHLS into one ‘master’ longitudinal dataset containing annual records for all observed individuals from 1991 to 2020. A number of key individual and household-level variables (including age, sex, country of birth, partnership status, highest educational qualification, employment status, incomes and region) are then (3) cleaned and harmonised. Users can download and adapt the deposited code as needed for their own social science applications.
DOI: 10.6084/m9.figshare.23151547
title: Plot File from Cycle index polynomials and generalized quantum separability tests

description: Mathematica File Containing Plots
DOI: 10.6084/m9.figshare.23151547.v1
title: Plot File from Cycle index polynomials and generalized quantum separability tests

description: Mathematica File Containing Plots
DOI: 10.48331/scielo.ecqnf8/mvp7eb
title: ApresentacaoSciELO_CSP_LucianaDiasdeLima_PDF.pptx.pdf

description: :unav
DOI: 10.48331/scielo.ecqnf8
title: Modelos de sucessão de editores. Parte 2 – Experiência de periódicos da Rede SciELO

description: Apresentação da Profa Luciana Dias de Lima no Seminário ABEC Brasil – SciELO 25 Anos: Modelos de sucessão de editores. Parte 2 – Experiência de periódicos da Rede SciELO. Página do evento: https://25.scielo.org/seminarios/abec-editores-pt2/
DOI: 10.6084/m9.figshare.23151811
title: Sequence data for barcoding.zip from Recent origin and diversification accompanied by repeated host shifts of thallus-mining flies (Diptera: Agromyzidae) on liverworts and hornworts

description: Despite the vast diversity of phytophagous insects that feed on vascular plants (tracheophytes), insects that feed on bryophytes remain understudied. Agromyzidae, one of the most species-rich phytophagous clades in Diptera, consists mainly of leaf-mining species that feed on tracheophytes. However, a recent discovery of thallus-mining species on liverworts and hornworts within the <i>Liriomyza</i> group of Phytomyzinae provides an opportunity to study host shifts between tracheophytes and bryophytes. This study aimed to explore the origin and diversification of thallus-miners and estimate the pattern and timing of host shifts. Phylogenetic analysis of Phytomyzinae has revealed that the thallus-mining agromyzids formed a separate clade, which was sister to a fern pinnule-miner. The diversification of bryophyte-associated agromyzids since the Oligocene involved multiple host shifts across various bryophyte taxa. The diversification of the thallus-mining <i>Phytoliriomyza</i> may have occurred at the same time as the leaf-mining agromyzid flies on herbaceous plants, indicating a dynamic history of interactions between bryophytes and herbivores in angiosperms-dominated ecosystems.
DOI: 10.6084/m9.figshare.23151811.v1
title: Sequence data for barcoding.zip from Recent origin and diversification accompanied by repeated host shifts of thallus-mining flies (Diptera: Agromyzidae) on liverworts and hornworts

description: Despite the vast diversity of phytophagous insects that feed on vascular plants (tracheophytes), insects that feed on bryophytes remain understudied. Agromyzidae, one of the most species-rich phytophagous clades in Diptera, consists mainly of leaf-mining species that feed on tracheophytes. However, a recent discovery of thallus-mining species on liverworts and hornworts within the <i>Liriomyza</i> group of Phytomyzinae provides an opportunity to study host shifts between tracheophytes and bryophytes. This study aimed to explore the origin and diversification of thallus-miners and estimate the pattern and timing of host shifts. Phylogenetic analysis of Phytomyzinae has revealed that the thallus-mining agromyzids formed a separate clade, which was sister to a fern pinnule-miner. The diversification of bryophyte-associated agromyzids since the Oligocene involved multiple host shifts across various bryophyte taxa. The diversification of the thallus-mining <i>Phytoliriomyza</i> may have occurred at the same time as the leaf-mining agromyzid flies on herbaceous plants, indicating a dynamic history of interactions between bryophytes and herbivores in angiosperms-dominated ecosystems.
DOI: 10.6084/m9.figshare.23151814
title: Table S2. from Recent origin and diversification accompanied by repeated host shifts of thallus-mining flies (Diptera: Agromyzidae) on liverworts and hornworts

description: List of studied fly species with their host plants and GenBank/DDBJ accession numbers for five genes.
DOI: 10.6084/m9.figshare.23151814.v1
title: Table S2. from Recent origin and diversification accompanied by repeated host shifts of thallus-mining flies (Diptera: Agromyzidae) on liverworts and hornworts

description: List of studied fly species with their host plants and GenBank/DDBJ accession numbers for five genes.
DOI: 10.6084/m9.figshare.23151817
title: Table S1. from Recent origin and diversification accompanied by repeated host shifts of thallus-mining flies (Diptera: Agromyzidae) on liverworts and hornworts

description: Primers used for PCR amplification and DNA sequencing (*: sequencing only)
DOI: 10.6084/m9.figshare.23151817.v1
title: Table S1. from Recent origin and diversification accompanied by repeated host shifts of thallus-mining flies (Diptera: Agromyzidae) on liverworts and hornworts

description: Primers used for PCR amplification and DNA sequencing (*: sequencing only)
DOI: 10.6084/m9.figshare.23151820
title: Data of phylogenetic divergence time analysis.zip from Recent origin and diversification accompanied by repeated host shifts of thallus-mining flies (Diptera: Agromyzidae) on liverworts and hornworts

description: Despite the vast diversity of phytophagous insects that feed on vascular plants (tracheophytes), insects that feed on bryophytes remain understudied. Agromyzidae, one of the most species-rich phytophagous clades in Diptera, consists mainly of leaf-mining species that feed on tracheophytes. However, a recent discovery of thallus-mining species on liverworts and hornworts within the <i>Liriomyza</i> group of Phytomyzinae provides an opportunity to study host shifts between tracheophytes and bryophytes. This study aimed to explore the origin and diversification of thallus-miners and estimate the pattern and timing of host shifts. Phylogenetic analysis of Phytomyzinae has revealed that the thallus-mining agromyzids formed a separate clade, which was sister to a fern pinnule-miner. The diversification of bryophyte-associated agromyzids since the Oligocene involved multiple host shifts across various bryophyte taxa. The diversification of the thallus-mining <i>Phytoliriomyza</i> may have occurred at the same time as the leaf-mining agromyzid flies on herbaceous plants, indicating a dynamic history of interactions between bryophytes and herbivores in angiosperms-dominated ecosystems.
DOI: 10.6084/m9.figshare.23151820.v1
title: Data of phylogenetic divergence time analysis.zip from Recent origin and diversification accompanied by repeated host shifts of thallus-mining flies (Diptera: Agromyzidae) on liverworts and hornworts

description: Despite the vast diversity of phytophagous insects that feed on vascular plants (tracheophytes), insects that feed on bryophytes remain understudied. Agromyzidae, one of the most species-rich phytophagous clades in Diptera, consists mainly of leaf-mining species that feed on tracheophytes. However, a recent discovery of thallus-mining species on liverworts and hornworts within the <i>Liriomyza</i> group of Phytomyzinae provides an opportunity to study host shifts between tracheophytes and bryophytes. This study aimed to explore the origin and diversification of thallus-miners and estimate the pattern and timing of host shifts. Phylogenetic analysis of Phytomyzinae has revealed that the thallus-mining agromyzids formed a separate clade, which was sister to a fern pinnule-miner. The diversification of bryophyte-associated agromyzids since the Oligocene involved multiple host shifts across various bryophyte taxa. The diversification of the thallus-mining <i>Phytoliriomyza</i> may have occurred at the same time as the leaf-mining agromyzid flies on herbaceous plants, indicating a dynamic history of interactions between bryophytes and herbivores in angiosperms-dominated ecosystems.
DOI: 10.3886/e191724v1
title: A modified Maritime Human Factors Analysis and Classification System for towing vessel accident analysis

description: Human error and underlying factors play a crucial role in maritime accident analysis. This paper compares three versions of the Maritime Human Factors Analysis and Classification System model (HFACS-MA) and benchmarks them to a US Department of Defense (US-DoD) version. The first HFACS-MA version was chosen; further modified by adding one extra code, code (i.9), to account for “Equipment design and specification”; and applied to analyze (21) accidents, involving towing vessels on the US Gulf Coast between Jan. 1, 2019, and Dec. 31, 2020. The results show that the dominant latent failure factors include strong current; an estimate of the situation's inability; erroneous assumption, prediction, prejudice, inappropriate procedure, regulations, instructions; and maintenance check-ups, among others, whereas the dominant active failure factor was routine violations, in good agreement with previous investigations. <br>
description: Response Rates: The Maritime Human Factors Analysis and Classification System model (HFACS-MA).<br>