cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19248198.v1
title: Chloroquine treatment induces secretion of autophagy-related proteins and inclusion of Atg8-family proteins in distinct extracellular vesicle populations

description: Chloroquine (CQ), a lysosomotropic agent, is commonly used to inhibit lysosomal degradation and macroautophagy/autophagy. Here we investigated the cell-extrinsic effects of CQ on secretion. We showed that lysosomal and autophagy inhibition by CQ altered the secretome, and induced the release of Atg8 orthologs and autophagy receptors. Atg8-family proteins, in particular, were secreted inside small extracellular vesicles (sEVs) in a lipidation-dependent manner. CQ treatment enhanced the release of Atg8-family proteins inside sEVs. Using full-length ATG16L1 and an ATG16L1 mutant that enables Atg8-family protein lipidation on double but not on single membranes, we demonstrated that LC3B is released in two distinct sEV populations: one enriched with SDCBP/Syntenin-1, CD63, and endosomal lipidated LC3B, and another that contains LC3B but is not enriched with SDCBP/Syntenin-1 or CD63, and which our data supports as originating from a double-membrane source. Our findings underscore the context-dependency of sEV heterogeneity and composition, and illustrate the integration of autophagy and sEV composition in response to lysosomal inhibition. <b>Abbreviations:</b> ACTB: actin beta; ANOVA: analysis of variance; ATG4B: autophagy related 4B cysteine peptidase; Atg8: autophagy related 8; ATG16L1: autophagy related 16 like 1; ATP5F1A/ATP5a: ATP synthase F1 subunit alpha; CALCOCO2: calcium binding and coiled-coil domain 2; CASP3: caspase 3; CASP7: caspase 7; CQ: chloroquine; CD9: CD9 molecule; CD63: CD63 molecule; DAPI: 4’,6-diamidino-2-phenylindole; DQ-BSA: dye quenched-bovine serum albumin; ER: endoplasmic reticulum; ERN1/IRE1a: endoplasmic reticulum to nucleus signaling 1; EV: extracellular vesicles; FBS: fetal bovine serum; FDR: false discovery rate; GABARAP: GABA type A receptor-associated protein; GABARAPL2: GABA type A receptor associated protein like 2; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GFP: green fluorescent protein; GO: gene ontology; HCQ: hydroxychloroquine; HSP90AA1: heat shock protein 90 alpha family class A member 1; IP: immunoprecipitation; KO: knockout; LAMP2: lysosomal associated membrane protein 2; LIR: LC3-interacting region; LMNA: lamin A/C; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; MS: mass spectrometry; NBR1: NBR1 autophagy cargo receptor; NCOA4: nuclear receptor coactivator 4; NTA: nanoparticle tracking analysis; PE: phosphatidylethanolamine; PECA: probe-level expression change averaging; SDCBP/syntenin-1: syndecan binding protein; SD: standard deviation; SE: secreted; sEV: small extracellular vesicles; SQSTM1/p62: sequestosome 1; TAX1BP1: Tax1 binding protein 1; TEM: transmission electron microscopy; TMT: tandem-mass tag; TSG101: tumor susceptibility 101; ULK1: unc-51 like autophagy activating kinase 1; WC: whole cell
DOI: 10.6084/m9.figshare.7713770.v2
title: De-escalation versus standard dual antiplatelet therapy in patients undergoing percutaneous coronary intervention: a systematic review and meta-analysis

description: Switching from a potent P2Y<sub>12</sub> blocker to clopidogrel is not uncommon for antiplatelet therapy in patients undergoing percutaneous coronary intervention. This meta-analysis aimed to investigate the efficacy and safety of this de-escalation strategy. Medical literature databases were searched for analysis comparing continued potent antiplatelet therapy and switching to clopidogrel with no language restrictions from inception to 07/May/2018. The primary endpoints of major adverse cardiovascular events (MACE) and major bleeding together with additional efficacy outcomes were assessed by random-effects and fixed-effects meta-analysis. A total of 17 896 patients in 13 studies were eligible for analysis, while 17 579 (98.2%) patients presented as acute coronary syndrome and 4105 (23%) patients received the de-escalation therapy. Incidence of MACE was virtually identical in both de-escalation and standard potent antiplatelet therapy groups (odds ratio 0.91, 95% CI 0.73–1.14; <i>P</i> = 0.43). Insignificant difference was also observed in major bleeding (0.99, 0.62–1.60; <i>P</i> = 0.97), all-cause death (0.95, 0.61–1.46; <i>P</i> = 0.81), cardiovascular death (0.66, 0.31–1.42; <i>P</i> = 0.29), myocardial infarction (1.12, 0.80–1.58; <i>P</i> = 0.51), stent thrombosis (1.09, 0.50–2.36; <i>P</i> = 0.83), unplanned revascularization (1.09, 0.83–1.41; <i>P</i> = 0.54), and stroke (1.16, 0.62–2.19; <i>P</i> = 0.64). In conclusion, de-escalation of antiplatelet therapy is associated with nonsignificant differences in both ischemic events and major bleeding compared with standard potent antiplatelet therapy in patients undergoing percutaneous coronary intervention. The feasibility and even superiority of this strategy need to be elucidated by further randomized trials.
DOI: 10.6084/m9.figshare.19767869
title: Additional file 1 of 2D-DIGE based proteome analysis of wheat-Thinopyrum intermedium 7XL/7DS translocation line under drought stress

description: Additional file 1.
DOI: 10.6084/m9.figshare.19768000.v1
title: Additional file 1 of Optimized sample preparation and data analysis for TMT proteomic analysis of cerebrospinal fluid applied to the identification of Alzheimer’s disease biomarkers

description: Additional file 1. List of complete GO-terms relating to both significantly increased and decreased proteins (clinical AD vs. control) in EMIF-AD. Description of data: GO biological process terms were generated with the PANTHER statistical overrepresentation test. For significantly increased proteins, an FDR-correction was performed.
DOI: 10.17028/rd.lboro.19248365
title: Supplementary information files for Synergistic induced charge transfer switch by oxygen vacancy and pyrrolic nitrogen in MnFe<sub>2</sub>O<sub>4</sub>/g-C<sub>3</sub>N<sub>4</sub> heterojunctions for efficient transformation of bicarbonate to acetate in photo-assisted MES

description: Supplementary files for article Synergistic induced charge transfer switch by oxygen vacancy and pyrrolic nitrogen in MnFe<sub>2</sub>O<sub>4</sub>/g-C<sub>3</sub>N<sub>4</sub> heterojunctions for efficient transformation of bicarbonate to acetate in photo-assisted MES.<br>Inorganic carbon (HCO<sub>3</sub><sup>-</sup>) was efficiently converted into acetate (204.4 ± 0.5 mM with a coulombic efficiency of 96 ± 3% over 24 days operation) in a photo-assisted microbial electrosynthesis system (MES) using a urea-treated MnFe<sub>2</sub>O<sub>4</sub>/g-C<sub>3</sub>N<sub>4</sub> cathode and the nonphotosynthetic bacteria Serratia marcescens Q1. The remarkable photocatalytic performance of MnFe<sub>2</sub>O<sub>4</sub>/g-C<sub>3</sub>N<sub>4</sub> heterojunction was resulted from the charge transfer mechanism switch (from type II to Z-scheme) induced by the synergistic effect of oxygen vacancies and pyrrolic N after urea treatment. The increased pyrrolic N was conductive to photoinduced electron transfer while the oxygen vacancies provided a higher fraction of surface-active sites for H<sub>2</sub> evolution, which was metabolized in-situ with bicarbonate by S. marcescens Q1 to yield acetate via the Wood–Ljungdahl pathway. This study provides a simple and feasible strategy for switching the photocatalytic charge transfer in a spinel-based heterojunction and offers new insights for ingeniously synthesizing photocatalysts with high CO<sub>2</sub> conversion in MES.<br>
DOI: 10.6084/m9.figshare.19248385.v1
title: Hcp2b of T6SS affects colonization of avian pathogenic <i>Escherichia coli</i> and host keratin filament expression

description: T6SS (type VI secretion system) is a type of nano-syringe that exists in APEC (avian pathogenic <i>Escherichia coli</i>). Hcp (haemolysin-coregulated protein) of T6SS participates in the regulation of virulence during APEC infection. However, whether <i>hcp</i> plays a role in bacterial colonization by expression in host cells remains unclear. In this study, we analysed the biological characteristics of the mutant <i>hcp2b</i> strain. Our results showed that the <i>hcp2b</i> gene was involved in the regulation of bacterial motility, biofilm formation, anti-serum and anti-oxidative stress. Moreover, our data indicate that the colonization of the <i>hcp2b</i> mutation strain (Δ<i>hcp2b</i>) in the lung, liver and kidney of chickens decreased significantly. Hence, overexpression of Hcp2b protein in DF-1 cells was used to analyse the effect of Hcp2b on colonization of APEC. Proteomics analysis showed that overexpression of Hcp2b induced differentially expressed proteins in DF-1 cells (230 were significantly upregulated and 96 were significantly downregulated) and differentially expressed proteins were enriched in keratin filament. In conclusion, our data indicated that <i>hcp2b</i> promoted the colonization of APEC by affecting the expression of keratin filament.
DOI: 10.6084/m9.figshare.19248385
title: Hcp2b of T6SS affects colonization of avian pathogenic <i>Escherichia coli</i> and host keratin filament expression

description: T6SS (type VI secretion system) is a type of nano-syringe that exists in APEC (avian pathogenic <i>Escherichia coli</i>). Hcp (haemolysin-coregulated protein) of T6SS participates in the regulation of virulence during APEC infection. However, whether <i>hcp</i> plays a role in bacterial colonization by expression in host cells remains unclear. In this study, we analysed the biological characteristics of the mutant <i>hcp2b</i> strain. Our results showed that the <i>hcp2b</i> gene was involved in the regulation of bacterial motility, biofilm formation, anti-serum and anti-oxidative stress. Moreover, our data indicate that the colonization of the <i>hcp2b</i> mutation strain (Δ<i>hcp2b</i>) in the lung, liver and kidney of chickens decreased significantly. Hence, overexpression of Hcp2b protein in DF-1 cells was used to analyse the effect of Hcp2b on colonization of APEC. Proteomics analysis showed that overexpression of Hcp2b induced differentially expressed proteins in DF-1 cells (230 were significantly upregulated and 96 were significantly downregulated) and differentially expressed proteins were enriched in keratin filament. In conclusion, our data indicated that <i>hcp2b</i> promoted the colonization of APEC by affecting the expression of keratin filament.
DOI: 10.6084/m9.figshare.6141413
title: Characterisation of superalkaline-earth-metal halides, hydroxide and chalcogenides

description: A new series of superalkaline-earth-metal compounds Al<sub>14</sub>X (X = F<sub>2</sub>, Cl<sub>2</sub>, Br<sub>2</sub>, I<sub>2</sub>, (OH)<sub>2</sub>, O, S) has been investigated at the TPSS/Def2-TZVPP level. It is found that both interaction position and mode between Al<sub>14</sub> and X ligands influence isomer stability of the resulting superatom compounds. On the one hand, the top and bottom sites of Al<sub>14</sub> have higher reactivity relative to middle ones. On the other hand, different ligands favour different binding patterns when combining with Al<sub>14</sub>. For example, the halogen ligands prefer to occupy on-top sites of Al<sub>14</sub>. In contrast, the end-on bound configurations are the least favourable ones for Al<sub>14</sub> oxide. Natural population analysis indicates that the Al<sub>14</sub> cluster donates electrons to X ligands. Atoms in molecules analysis also suggests ionic bond character of the connection(s) between Al<sub>14</sub> and X moieties. Thus, the Al<sub>14</sub>X compounds are much like divalent salts where superatom Al<sub>14</sub> behaves just like an alkaline-earth-metal atom. Furthermore, considerable dissociation energies and large highest occupied molecular orbital and lowest unoccupied molecular orbital gaps confirm stability of these superatom compounds.
DOI: 10.6084/m9.figshare.16635064
title: Model data for article " Zonal structure of tropical Pacific surface salinity anomalies affects ENSO intensity and asymmetry"

description: This is model data submitted to AGU Journal, entitled by “Impacts of salinity on ENSO intensity and asymmetry”.
DOI: 10.6084/m9.figshare.16635070
title: Three mitochondrial genomes of early-winged insects (Ephemeroptera: Baetidae and Leptophlebiidae)

description: Mayflies (Ephemeroptera) are a semi-aquatic insect order with comparatively few genomic data available despite their phylogenetic position at the root of the winged-insects and possession of ancestral traits. Here, we provide three mitochondrial genomes (mtgenomes) from representatives of the two most species-rich families, <i>Baetis rutilocylindratus</i> and <i>Cloeon dipterum</i> (Baetidae), and <i>Habrophlebiodes zijinensis</i> (Leptophlebiidae). All mtgenomes had a complete set of 13 protein-coding genes and a conserved orientation except for two inverted tRNAs in <i>H. zijinensis.</i> Phylogenetic reconstructions using 21 mayfly mtgenomes and representatives of seven additional orders recovered both Baetidae and Leptophlebiidae as well supported monophyletic clades, with Ephemeroptera as the sister-taxon to all other winged insects (i.e. Odonata and Neoptera).
DOI: 10.6084/m9.figshare.17151241.v1
title: Changes in cortisol and dehydroepiandrosterone levels immediately after urban park visits

description: The purpose of this study is to explore physiological and psychological changes immediately after a short-term visit to urban parks in an uncontrolled condition. Sixty park visitors completed a short questionnaire evaluating their subjective well-being (SWB) and donated a saliva sample immediately before and after their park visit. In addition, participants wore a pedometer to track their physical activity level during the park visit. Results indicated the levels of all biomarkers (cortisol, dehydroepiandrosterone [DHEA], and cortisol/DHEA ratio) decreased while SWB scores increased after the park visit. The duration of park visit was identified as a key variable significantly associated with cortisol reduction, and changes in SWB scores after the park visit were significantly associated with changes in cortisol level. A park visit duration of 21.8 min has the predictive ability to discriminate park visitors who exhibit reductions in cortisol levels after the park visit from those who do not.
DOI: 10.6084/m9.figshare.4052178
title: Analysis of Gap Times Based on Panel Count Data With Informative Observation Times and Unknown Start Time

description: In biomedical studies, one is often interested in repeat events with longitudinal observations occurring only intermittently, resulting in panel count data. The first stage of labor, measured through unit-increments of cervical dilation in pregnant women, provides such an example. Obstetricians are interested in assessing the gap time distribution of per-unit increments of cervical dilation for better management of labor process. Typically, only intermittent medical examinations for cervical dilation occur after (already dilated) women get admitted to hospital. The observation frequency is very likely correlated to how fast/slow she dilates. Thus, one could view such data as panel count data with informative observation times and unknown start time. Here, we propose semiparametric proportional rate models for the event process and the observation process, with a multiplicative subject-specific frailty variable capturing the correlation between the two processes. Inference procedures for the gap times between consecutive events are proposed when the start times are known as well when unknown, using likelihood-based approach and estimating equations. The methodology is assessed through simulation study and through large sample property. A detailed analysis using the proposed methods is applied to data from two studies: the Collaborative Perinatal Project and the Consortium on Safe Labor. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.8246567.v1
title: MOESM1 of Metabolic engineering to enhance biosynthesis of both docosahexaenoic acid and odd-chain fatty acids in Schizochytrium sp. S31

description: Additional file 1: Fig. S1. Comparison of acetyl-CoA carboxylase activity after adding C16-CoA into cell-free extract of Schizochytrium sp. S31. 0 represents adding 0 μM of C16-CoA; 50 represents adding 50 μM of C16-CoA; 100 represents adding 100 μM of C16-CoA. * indicated p &lt; 0.05. ** indicated p &lt; 0.01. Fig. S2. Expression of a codon-optimized ELO3 gene from Mortierella alpina in Schizochytrium. A) Schematic map of the ELO3 gene expression cassette, with the indicated primers. 1: 18s upstream; 2: CaMV 35s promoter; 3: ELO3 gene; 4: Nos terminator; 5: α tubulin promoter from Schizochytrium; 6: bleomycin resistance gene; 7: CYC1 terminator; 8: 18s downstream; B) Genomic PCR detection with primer 1 and primer 2. M: 1 kb marker from Vazyme company; 1: S-E strain; 2: wild type. C) RT-PCR detection with primer 3 and primer 4. M: 1 kb marker from Thermo Scientific company; 1: S-E strain; 2: wild type. Fig. S3. Expression of a malic enzyme gene from C. cohnii in Schizochytrium. A) Schematic map of the malic enzyme expression cassette, with the indicated primers. 1: 18s upstream; 2: CaMV 35s promoter; 3: neomycin resistance gene; 4: CaMV poly(A) terminator; 5: malic enzyme gene; 6: 18s downstream; B) Genomic PCR detection with primer 5 and primer 6. M: 1kb marker; 1: water; 2: wild type; 3: S-M strain; C) RT-PCR detection with primer 7 and primer 8. 1: water; 2: wild type; 3 S-M strain. Fig. S4. Malic enzyme activity and NADPH content in the wild type and S-M strains. A) The malic enzyme activity. Blue: wild type; Purple: S-M strain. * indicated p &lt; 0.05; B) NADPH content. Blue: wild type; Purple: S-M strain. * indicated p &lt; 0.05, **indicated p &lt; 0.01. Fig. S5. Expression of a codon-optimized ELO3 gene from M. alpina in S-M strain. A) Schematic map of the ELO3 gene expression cassette, with the indicated primers. 1: CaMV 35s promoter; 2: ELO3 gene; 3: Nos terminator; 4: α tubulin promoter from Schizochytrium; 5: bleomycin resistance gene 6: CYC1 terminator; B) Genomic PCR detection with primer 1 and primer 2. M: 1 kb marker; 1: S-M-E strain; 2: S-M strain; C) RT-PCR detection with primer 3 and primer 4. M: 1 kb marker; 1: S-M strain; 2: S-M-E strain. Fig. S6. MS spectrums of methyl fatty acids detected among strains. Fig. S7. Principal component analysis of LC–MS targeted metabolomics of S-M and S-M-E strains. A) 48 h; B) 72 h. Purple: S-M strain; Green: S-M-E strain.
DOI: 10.6084/m9.figshare.19248198
title: Chloroquine treatment induces secretion of autophagy-related proteins and inclusion of Atg8-family proteins in distinct extracellular vesicle populations

description: Chloroquine (CQ), a lysosomotropic agent, is commonly used to inhibit lysosomal degradation and macroautophagy/autophagy. Here we investigated the cell-extrinsic effects of CQ on secretion. We showed that lysosomal and autophagy inhibition by CQ altered the secretome, and induced the release of Atg8 orthologs and autophagy receptors. Atg8-family proteins, in particular, were secreted inside small extracellular vesicles (sEVs) in a lipidation-dependent manner. CQ treatment enhanced the release of Atg8-family proteins inside sEVs. Using full-length ATG16L1 and an ATG16L1 mutant that enables Atg8-family protein lipidation on double but not on single membranes, we demonstrated that LC3B is released in two distinct sEV populations: one enriched with SDCBP/Syntenin-1, CD63, and endosomal lipidated LC3B, and another that contains LC3B but is not enriched with SDCBP/Syntenin-1 or CD63, and which our data supports as originating from a double-membrane source. Our findings underscore the context-dependency of sEV heterogeneity and composition, and illustrate the integration of autophagy and sEV composition in response to lysosomal inhibition. <b>Abbreviations:</b> ACTB: actin beta; ANOVA: analysis of variance; ATG4B: autophagy related 4B cysteine peptidase; Atg8: autophagy related 8; ATG16L1: autophagy related 16 like 1; ATP5F1A/ATP5a: ATP synthase F1 subunit alpha; CALCOCO2: calcium binding and coiled-coil domain 2; CASP3: caspase 3; CASP7: caspase 7; CQ: chloroquine; CD9: CD9 molecule; CD63: CD63 molecule; DAPI: 4’,6-diamidino-2-phenylindole; DQ-BSA: dye quenched-bovine serum albumin; ER: endoplasmic reticulum; ERN1/IRE1a: endoplasmic reticulum to nucleus signaling 1; EV: extracellular vesicles; FBS: fetal bovine serum; FDR: false discovery rate; GABARAP: GABA type A receptor-associated protein; GABARAPL2: GABA type A receptor associated protein like 2; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GFP: green fluorescent protein; GO: gene ontology; HCQ: hydroxychloroquine; HSP90AA1: heat shock protein 90 alpha family class A member 1; IP: immunoprecipitation; KO: knockout; LAMP2: lysosomal associated membrane protein 2; LIR: LC3-interacting region; LMNA: lamin A/C; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; MS: mass spectrometry; NBR1: NBR1 autophagy cargo receptor; NCOA4: nuclear receptor coactivator 4; NTA: nanoparticle tracking analysis; PE: phosphatidylethanolamine; PECA: probe-level expression change averaging; SDCBP/syntenin-1: syndecan binding protein; SD: standard deviation; SE: secreted; sEV: small extracellular vesicles; SQSTM1/p62: sequestosome 1; TAX1BP1: Tax1 binding protein 1; TEM: transmission electron microscopy; TMT: tandem-mass tag; TSG101: tumor susceptibility 101; ULK1: unc-51 like autophagy activating kinase 1; WC: whole cell
DOI: 10.17028/rd.lboro.19248365.v1
title: Supplementary information files for Synergistic induced charge transfer switch by oxygen vacancy and pyrrolic nitrogen in MnFe<sub>2</sub>O<sub>4</sub>/g-C<sub>3</sub>N<sub>4</sub> heterojunctions for efficient transformation of bicarbonate to acetate in photo-assisted MES

description: Supplementary files for article Synergistic induced charge transfer switch by oxygen vacancy and pyrrolic nitrogen in MnFe<sub>2</sub>O<sub>4</sub>/g-C<sub>3</sub>N<sub>4</sub> heterojunctions for efficient transformation of bicarbonate to acetate in photo-assisted MES.<br>Inorganic carbon (HCO<sub>3</sub><sup>-</sup>) was efficiently converted into acetate (204.4 ± 0.5 mM with a coulombic efficiency of 96 ± 3% over 24 days operation) in a photo-assisted microbial electrosynthesis system (MES) using a urea-treated MnFe<sub>2</sub>O<sub>4</sub>/g-C<sub>3</sub>N<sub>4</sub> cathode and the nonphotosynthetic bacteria Serratia marcescens Q1. The remarkable photocatalytic performance of MnFe<sub>2</sub>O<sub>4</sub>/g-C<sub>3</sub>N<sub>4</sub> heterojunction was resulted from the charge transfer mechanism switch (from type II to Z-scheme) induced by the synergistic effect of oxygen vacancies and pyrrolic N after urea treatment. The increased pyrrolic N was conductive to photoinduced electron transfer while the oxygen vacancies provided a higher fraction of surface-active sites for H<sub>2</sub> evolution, which was metabolized in-situ with bicarbonate by S. marcescens Q1 to yield acetate via the Wood–Ljungdahl pathway. This study provides a simple and feasible strategy for switching the photocatalytic charge transfer in a spinel-based heterojunction and offers new insights for ingeniously synthesizing photocatalysts with high CO<sub>2</sub> conversion in MES.<br>
DOI: 10.6084/m9.figshare.21345753
title: R code of RSPB-2022-1850 from Tree-ring evidence of ecological stress memory

description: R code used to do linear mixed model and plot Figure 2 in our parper
DOI: 10.6084/m9.figshare.21345753.v1
title: R code of RSPB-2022-1850 from Tree-ring evidence of ecological stress memory

description: R code used to do linear mixed model and plot Figure 2 in our parper