cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13220224.v1
title: Equine lentivirus counteracts SAMHD1 restriction by Rev-mediated degradation of SAMHD1 via the BECN1-dependent lysosomal pathway

description: The innate immune restriction factor SAMHD1 can inhibit diverse viruses in myeloid cells. Mechanistically, SAMHD1 inhibits lentiviral replication including HIV-1 by depleting the nucleotide pool to interfere with their reverse transcription. Equine infectious anemia virus (EIAV) is an ancient lentivirus that preferentially attacks macrophages. However, the mechanism by which EIAV successfully establishes infection in macrophages with functional SAMHD1 remains unclear. Here, we demonstrate that while equine SAMDH1 can limit EIAV replication in equine macrophages at the reverse transcription stage, the antiviral effect is counteracted by the well-known transcriptional regulator Rev, which downregulates equine SAMHD1 through the lysosomal pathway. Remarkably, Rev hijacks BECN1 (beclin 1) and PIK3C3 to mediate SAMHD1 degradation in a canonical macroautophagy/autophagy-independent pathway. Our study illustrates that equine lentiviral Rev possesses important functions in evading cellular innate immunity in addition to its RNA regulatory function, and may provide new insights into the co-evolutionary arms race between SAMHD1 and lentiviruses. <b>Abbreviations</b>:3-MA: 3-methyladenine; AA: amino acid; ACTB: actin beta; AD: activation domain; ATG: autophagy related; Baf A1: bafilomycin A<sub>1</sub>; BD: binding domain; BECN1: beclin 1; BH3: BCL2-homology-3 domain; BiFC: bimolecular fluorescence complementation; CCD: coiled-coil domain; class III PtdIns3K: class III phosphatidylinositol 3-kinase; CQ: chloroquine; Co-IP: co-immunoprecipitation; dNTPase: dGTP-stimulated deoxynucleoside triphosphate triphosphohydrolase; ECD: evolutionarily conserved domain; EIAV: equine infectious anemia virus; eMDMs: equine monocyte-derived macrophages; GFP: green fluorescent protein; HD: histidine-aspartic; HIV-1: human immunodeficiency virus-1; hpi: hours post infection; hpt: hours post transfection; KO: knockout; LAMP2: lysosomal associated membrane protein 2; LMB: leptomycin B; PMA: phorbol 12-myristate 13-acetate; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; ND: unknown non-essential domain; NES: nuclear export signal; NLS: localization signal; NS: statistically non-significant; PIK3C3: phosphatidylinositol 3-kinase catalytic subunit type 3; RBD: RNA binding domain; RT: reverse transcriptase; siRNAs: small interfering RNAs; SAMHD1: SAM and HD domain containing deoxynucleoside triphosphate triphosphohydrolase 1; SIV: simian immunodeficiency virus; VN: C-terminal residues of Venus 174 to 238; VC: N-terminal residues 2 to 173 of Venus
DOI: 10.6084/m9.figshare.12695910
title: Additional file 8 of Comparative transcriptome analyses reveal two distinct transcriptional modules associated with pollen shedding time in pine

description: Additional file 8: Data Set 1. Expression levels of 640 genes in all analysed samples.
DOI: 10.6084/m9.figshare.12695913
title: Additional file 9 of Comparative transcriptome analyses reveal two distinct transcriptional modules associated with pollen shedding time in pine

description: Additional file 9: Data Set 2. Normalised Z-scores of 640 genes in male cones of EPs and LPs.
DOI: 10.6084/m9.figshare.13220221.v1
title: ESRRA (estrogen related receptor alpha) is a critical regulator of intestinal homeostasis through activation of autophagic flux via gut microbiota

description: The orphan nuclear receptor ESRRA (estrogen related receptor alpha) is critical in mitochondrial biogenesis and macroautophagy/autophagy function; however, the roles of ESRRA in intestinal function remain uncharacterized. Herein we identified that ESRRA acts as a key regulator of intestinal homeostasis by amelioration of colonic inflammation through activation of autophagic flux and control of host gut microbiota. <i>Esrra</i>-deficient mice presented with increased susceptibility to dextran sodium sulfate (DSS)-induced colitis with upregulation of intestinal inflammation. In addition, <i>esrra</i>-null mice had depressed AMP-activated protein kinase phosphorylation (AMPK), lower levels of TFEB (transcription factor EB), and accumulation of SQSTM1/p62 (sequestosome 1) with defective mitochondria in intestinal tissues. <i>Esrra</i>-deficient mice showed distinct gut microbiota composition and significantly higher microbial diversity than wild-type (WT) mice. Cohousing or fecal microbiota transplantation from WT mice to <i>Esrra</i>-deficient mice ameliorated DSS-induced colitis severity. Importantly, patients with ulcerative colitis (UC) had significantly decreased <i>ESRRA</i> expression in intestinal mucosal tissues that correlated with disease activity, suggesting clinical relevance of ESRRA in UC. Taken together, our results show that ESRRA contributes to intestinal homeostasis through autophagy activation and gut microbiota control to protect the host from detrimental inflammation and dysfunctional mitochondria.
DOI: 10.6084/m9.figshare.13220224.v2
title: Equine lentivirus counteracts SAMHD1 restriction by Rev-mediated degradation of SAMHD1 via the BECN1-dependent lysosomal pathway

description: The innate immune restriction factor SAMHD1 can inhibit diverse viruses in myeloid cells. Mechanistically, SAMHD1 inhibits lentiviral replication including HIV-1 by depleting the nucleotide pool to interfere with their reverse transcription. Equine infectious anemia virus (EIAV) is an ancient lentivirus that preferentially attacks macrophages. However, the mechanism by which EIAV successfully establishes infection in macrophages with functional SAMHD1 remains unclear. Here, we demonstrate that while equine SAMDH1 can limit EIAV replication in equine macrophages at the reverse transcription stage, the antiviral effect is counteracted by the well-known transcriptional regulator Rev, which downregulates equine SAMHD1 through the lysosomal pathway. Remarkably, Rev hijacks BECN1 (beclin 1) and PIK3C3 to mediate SAMHD1 degradation in a canonical macroautophagy/autophagy-independent pathway. Our study illustrates that equine lentiviral Rev possesses important functions in evading cellular innate immunity in addition to its RNA regulatory function, and may provide new insights into the co-evolutionary arms race between SAMHD1 and lentiviruses. <b>Abbreviations</b>:3-MA: 3-methyladenine; AA: amino acid; ACTB: actin beta; AD: activation domain; ATG: autophagy related; Baf A1: bafilomycin A<sub>1</sub>; BD: binding domain; BECN1: beclin 1; BH3: BCL2-homology-3 domain; BiFC: bimolecular fluorescence complementation; CCD: coiled-coil domain; class III PtdIns3K: class III phosphatidylinositol 3-kinase; CQ: chloroquine; Co-IP: co-immunoprecipitation; dNTPase: dGTP-stimulated deoxynucleoside triphosphate triphosphohydrolase; ECD: evolutionarily conserved domain; EIAV: equine infectious anemia virus; eMDMs: equine monocyte-derived macrophages; GFP: green fluorescent protein; HD: histidine-aspartic; HIV-1: human immunodeficiency virus-1; hpi: hours post infection; hpt: hours post transfection; KO: knockout; LAMP2: lysosomal associated membrane protein 2; LMB: leptomycin B; PMA: phorbol 12-myristate 13-acetate; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; ND: unknown non-essential domain; NES: nuclear export signal; NLS: localization signal; NS: statistically non-significant; PIK3C3: phosphatidylinositol 3-kinase catalytic subunit type 3; RBD: RNA binding domain; RT: reverse transcriptase; siRNAs: small interfering RNAs; SAMHD1: SAM and HD domain containing deoxynucleoside triphosphate triphosphohydrolase 1; SIV: simian immunodeficiency virus; VN: C-terminal residues of Venus 174 to 238; VC: N-terminal residues 2 to 173 of Venus
DOI: 10.6084/m9.figshare.21080605
title: Additional file 4 of Dynamic regulation of HIF-1 signaling in the rhesus monkey heart after ischemic injury

description: Additional file 4: Table S2. The list of the top 25 DEGs enriched in inflammatory response, cell proliferation, cardiac fibrosis, and mitochondrial metabolism after MI
DOI: 10.6084/m9.figshare.21080611.v1
title: Additional file 6 of Dynamic regulation of HIF-1 signaling in the rhesus monkey heart after ischemic injury

description: Additional file 6: Table S4. The list of 89 significantly changed HIF-1 target genes in the ischemic monkey heart
DOI: 10.6084/m9.figshare.21080614
title: Additional file 7 of Dynamic regulation of HIF-1 signaling in the rhesus monkey heart after ischemic injury

description: Additional file 7: Table S5. The list of HIF-1 target genes positively or negatively correlated with myocardial copper status
DOI: 10.6084/m9.figshare.7453112
title: Monitoring of drug treatment and psychosocial intervention with SPECT in Alzheimer patients Implications for neurologically appropriate psychosocial interventions. An observational study. The Osaki-Tajiri Project

description: ABSTRACT We previously examined cerebral blood flow (CBF) with single-photon emission computed tomography (SPECT) in Alzheimer’s disease (AD) with reference to drug treatment (donepezil) and psychosocial intervention. Objective: The aim is to provide “brain-based” evidence for psychosocial interventions using SPECT. Methods: The participants were 27 consecutive outpatients with AD who received the drug and psychosocial intervention, and SPECT three times (baseline, pre-/post-intervention) at 6 month-intervals. The significance level of changes in CBF (Z score) and the extent of significantly changed areas, calculated with the eZIS system, were used as monitoring parameters. The participants were classified into three groups: improve (post-intervention CBF increased), worsening (progressive decline), and no change. Results: Six, 8, and 13 patients were classified as improve, worsening, and no change, respectively. All subjects in the improve group showed improvement in cognitive test scores for the MMSE and/or the CGI scores associated with the brain area with a CBF increase (right parietal lobe), suggesting appropriate psychosocial intervention (visuospatial intervention). Conclusion: These results suggest that monitoring of CBF with the eZIS system may be clinically applicable for monitoring of drug treatment and psychosocial intervention in AD patients.
DOI: 10.6084/m9.figshare.12695750.v1
title: Additional file 5 of Single-cell RNA-seq analysis reveals ploidy-dependent and cell-specific transcriptome changes in Arabidopsis female gametophytes

description: Additional file 5:Table S4. Primer pairs used for qRT-PCR and GFP validation.
DOI: 10.6084/m9.figshare.13220224
title: Equine lentivirus counteracts SAMHD1 restriction by Rev-mediated degradation of SAMHD1 via the BECN1-dependent lysosomal pathway

description: The innate immune restriction factor SAMHD1 can inhibit diverse viruses in myeloid cells. Mechanistically, SAMHD1 inhibits lentiviral replication including HIV-1 by depleting the nucleotide pool to interfere with their reverse transcription. Equine infectious anemia virus (EIAV) is an ancient lentivirus that preferentially attacks macrophages. However, the mechanism by which EIAV successfully establishes infection in macrophages with functional SAMHD1 remains unclear. Here, we demonstrate that while equine SAMDH1 can limit EIAV replication in equine macrophages at the reverse transcription stage, the antiviral effect is counteracted by the well-known transcriptional regulator Rev, which downregulates equine SAMHD1 through the lysosomal pathway. Remarkably, Rev hijacks BECN1 (beclin 1) and PIK3C3 to mediate SAMHD1 degradation in a canonical macroautophagy/autophagy-independent pathway. Our study illustrates that equine lentiviral Rev possesses important functions in evading cellular innate immunity in addition to its RNA regulatory function, and may provide new insights into the co-evolutionary arms race between SAMHD1 and lentiviruses. <b>Abbreviations</b>:3-MA: 3-methyladenine; AA: amino acid; ACTB: actin beta; AD: activation domain; ATG: autophagy related; Baf A1: bafilomycin A<sub>1</sub>; BD: binding domain; BECN1: beclin 1; BH3: BCL2-homology-3 domain; BiFC: bimolecular fluorescence complementation; CCD: coiled-coil domain; class III PtdIns3K: class III phosphatidylinositol 3-kinase; CQ: chloroquine; Co-IP: co-immunoprecipitation; dNTPase: dGTP-stimulated deoxynucleoside triphosphate triphosphohydrolase; ECD: evolutionarily conserved domain; EIAV: equine infectious anemia virus; eMDMs: equine monocyte-derived macrophages; GFP: green fluorescent protein; HD: histidine-aspartic; HIV-1: human immunodeficiency virus-1; hpi: hours post infection; hpt: hours post transfection; KO: knockout; LAMP2: lysosomal associated membrane protein 2; LMB: leptomycin B; PMA: phorbol 12-myristate 13-acetate; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; ND: unknown non-essential domain; NES: nuclear export signal; NLS: localization signal; NS: statistically non-significant; PIK3C3: phosphatidylinositol 3-kinase catalytic subunit type 3; RBD: RNA binding domain; RT: reverse transcriptase; siRNAs: small interfering RNAs; SAMHD1: SAM and HD domain containing deoxynucleoside triphosphate triphosphohydrolase 1; SIV: simian immunodeficiency virus; VN: C-terminal residues of Venus 174 to 238; VC: N-terminal residues 2 to 173 of Venus
DOI: 10.6084/m9.figshare.12695796
title: Additional file 20 of Multi-omics sequencing provides insight into floral transition in Catalpa bungei. C.A. Mey

description: Additional file 20: Table S11. Summary of AS events from DEGs in NF.
DOI: 10.6084/m9.figshare.21084727
title: Measuring Housing Vitality from Multi-Source Big Data and Machine Learning

description: Measuring timely high-resolution socioeconomic outcomes is critical for policymaking and evaluation, but hard to reliably obtain. With the help of machine learning and cheaply available data such as social media and nightlight, it is now possible to predict such indices in fine granularity. This article demonstrates an adaptive way to measure the time trend and spatial distribution of housing vitality (number of occupied houses) with the help of multiple easily accessible datasets: energy, nightlight, and land-use data. We first identified the high-frequency housing occupancy status from energy consumption data and then matched it with the monthly nightlight data. We then introduced the Factor-Augmented Regularized Model for prediction (FarmPredict) to deal with the dependence and collinearity issue among predictors by effectively lifting the prediction space, which is suitable to most machine learning algorithms. The heterogeneity issue in big data analysis is mitigated through the land-use data. FarmPredict allows us to extend the regional results to the city level, with a 76% out-of-sample explanation of the spatial and timeliness variation in the house usage. Since energy is indispensable for life, our method is highly transferable with the only requirement of publicly accessible data. Our article provides an alternative approach with statistical machine learning to predict socioeconomic outcomes without the reliance on existing census and survey data. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.7453112.v1
title: Monitoring of drug treatment and psychosocial intervention with SPECT in Alzheimer patients Implications for neurologically appropriate psychosocial interventions. An observational study. The Osaki-Tajiri Project

description: ABSTRACT We previously examined cerebral blood flow (CBF) with single-photon emission computed tomography (SPECT) in Alzheimer’s disease (AD) with reference to drug treatment (donepezil) and psychosocial intervention. Objective: The aim is to provide “brain-based” evidence for psychosocial interventions using SPECT. Methods: The participants were 27 consecutive outpatients with AD who received the drug and psychosocial intervention, and SPECT three times (baseline, pre-/post-intervention) at 6 month-intervals. The significance level of changes in CBF (Z score) and the extent of significantly changed areas, calculated with the eZIS system, were used as monitoring parameters. The participants were classified into three groups: improve (post-intervention CBF increased), worsening (progressive decline), and no change. Results: Six, 8, and 13 patients were classified as improve, worsening, and no change, respectively. All subjects in the improve group showed improvement in cognitive test scores for the MMSE and/or the CGI scores associated with the brain area with a CBF increase (right parietal lobe), suggesting appropriate psychosocial intervention (visuospatial intervention). Conclusion: These results suggest that monitoring of CBF with the eZIS system may be clinically applicable for monitoring of drug treatment and psychosocial intervention in AD patients.
DOI: 10.6084/m9.figshare.12695772
title: Additional file 13 of Multi-omics sequencing provides insight into floral transition in Catalpa bungei. C.A. Mey

description: Additional file 13: Table S4. All predicted transcription factors in EF during floral transition.
DOI: 10.6084/m9.figshare.12838964.v1
title: Additional file 1 of A ten-gene signature-based risk assessment model predicts the prognosis of lung adenocarcinoma

description: Additional file 1.
DOI: 10.6084/m9.figshare.12695778
title: Additional file 15 of Multi-omics sequencing provides insight into floral transition in Catalpa bungei. C.A. Mey

description: Additional file 15: Table S6. Summary of all genes from the MEdarkturquoise module.
DOI: 10.6084/m9.figshare.14269219
title: Syntheses and structural characterization of eight inorganic-organic hybrid solids based on N-Brønsted bases and halometallates of Zn, Cu, Sb and Bi

description: Eight organic-inorganic hybrid salts [(HL1)(SbCl<sub>4</sub>)] <b>(1)</b> (L1 = N,N-dimethylbenzylamine), [(HL2)<sub>2</sub>(ZnCl<sub>4</sub>)] <b>(2)</b> (L2 = 4-chlorobenzylamine), [(HL2)(L2)(CuCl<sub>3</sub>)(H<sub>2</sub>O)<sub>2</sub>] (<b>3)</b>, [(HL3)<sub>2</sub>(Sb<sub>2</sub>OCl<sub>6</sub>)] (<b>4)</b> (L3 = quinoline), [(HL4)<sub>4</sub>(Bi<sub>2</sub>Cl<sub>10</sub>)] (<b>5)</b> (L4 = 2-methylquinoline), [(HL5)(SbCl<sub>4</sub>)] (<b>6)</b> (L5 = 5,7-dimethyl-1,8-naphthyridine-2-amine), [(H<sub>2</sub>L6)(SbCl<sub>5</sub>)] (<b>7)</b> (L6 = 3,6-bis(imidazol-1-yl)pyridazine) and [(H<sub>2</sub>L7)<sub>2</sub>(CuBr<sub>4</sub>)<sub>2</sub>] · 7H<sub>2</sub>O (<b>8)</b> (L7 = di(2-benzimidazol-1-ylethyl)ether) were prepared and characterized by IR, XRD, EA and TG analysis. XRD analysis told that all of the complexes were 3 D net built from non-covalent bonds from the cations and the halometallates. The aryl rings of the cations in all of the compounds are essentially planar. The H<sub>2</sub>O also had crucial role in structure extension in <b>3</b> and <b>8</b>. Extensive intermolecular interactions have been used in the self-assembly of diverse motifs, ranging from strong N-H···X (X = Br, Cl), N-H···O, N-H···N, O-H···O, O-H···Br H-bonds to weak CH<sub>2</sub>···O, CH<sub>3</sub>-Cl/CH<sub>2</sub>-Cl/CH-Cl, Cl-Cl, O-Br, CH<sub>3</sub>-π, CH<sub>2</sub>-π, Cl-π and π-π associations. The arrangements of the anions and cations in the solid are ruled not only by the size and symmetry of the cations, but also by the non-covalent bonds in the crystal structures.
DOI: 10.6084/m9.figshare.12695790
title: Additional file 19 of Multi-omics sequencing provides insight into floral transition in Catalpa bungei. C.A. Mey

description: Additional file 19: Table S10. Summary of AS events from DEGs in EF.
DOI: 10.6084/m9.figshare.14269219.v1
title: Syntheses and structural characterization of eight inorganic-organic hybrid solids based on N-Brønsted bases and halometallates of Zn, Cu, Sb and Bi

description: Eight organic-inorganic hybrid salts [(HL1)(SbCl<sub>4</sub>)] <b>(1)</b> (L1 = N,N-dimethylbenzylamine), [(HL2)<sub>2</sub>(ZnCl<sub>4</sub>)] <b>(2)</b> (L2 = 4-chlorobenzylamine), [(HL2)(L2)(CuCl<sub>3</sub>)(H<sub>2</sub>O)<sub>2</sub>] (<b>3)</b>, [(HL3)<sub>2</sub>(Sb<sub>2</sub>OCl<sub>6</sub>)] (<b>4)</b> (L3 = quinoline), [(HL4)<sub>4</sub>(Bi<sub>2</sub>Cl<sub>10</sub>)] (<b>5)</b> (L4 = 2-methylquinoline), [(HL5)(SbCl<sub>4</sub>)] (<b>6)</b> (L5 = 5,7-dimethyl-1,8-naphthyridine-2-amine), [(H<sub>2</sub>L6)(SbCl<sub>5</sub>)] (<b>7)</b> (L6 = 3,6-bis(imidazol-1-yl)pyridazine) and [(H<sub>2</sub>L7)<sub>2</sub>(CuBr<sub>4</sub>)<sub>2</sub>] · 7H<sub>2</sub>O (<b>8)</b> (L7 = di(2-benzimidazol-1-ylethyl)ether) were prepared and characterized by IR, XRD, EA and TG analysis. XRD analysis told that all of the complexes were 3 D net built from non-covalent bonds from the cations and the halometallates. The aryl rings of the cations in all of the compounds are essentially planar. The H<sub>2</sub>O also had crucial role in structure extension in <b>3</b> and <b>8</b>. Extensive intermolecular interactions have been used in the self-assembly of diverse motifs, ranging from strong N-H···X (X = Br, Cl), N-H···O, N-H···N, O-H···O, O-H···Br H-bonds to weak CH<sub>2</sub>···O, CH<sub>3</sub>-Cl/CH<sub>2</sub>-Cl/CH-Cl, Cl-Cl, O-Br, CH<sub>3</sub>-π, CH<sub>2</sub>-π, Cl-π and π-π associations. The arrangements of the anions and cations in the solid are ruled not only by the size and symmetry of the cations, but also by the non-covalent bonds in the crystal structures.
DOI: 10.6084/m9.figshare.12695787.v1
title: Additional file 18 of Multi-omics sequencing provides insight into floral transition in Catalpa bungei. C.A. Mey

description: Additional file 18: Table S9. Summary of identification of splicing junctions using NGS and SMRT data.
DOI: 10.6084/m9.figshare.12695796.v1
title: Additional file 20 of Multi-omics sequencing provides insight into floral transition in Catalpa bungei. C.A. Mey

description: Additional file 20: Table S11. Summary of AS events from DEGs in NF.
DOI: 10.6084/m9.figshare.21084727.v1
title: Measuring Housing Vitality from Multi-Source Big Data and Machine Learning

description: Measuring timely high-resolution socioeconomic outcomes is critical for policymaking and evaluation, but hard to reliably obtain. With the help of machine learning and cheaply available data such as social media and nightlight, it is now possible to predict such indices in fine granularity. This article demonstrates an adaptive way to measure the time trend and spatial distribution of housing vitality (number of occupied houses) with the help of multiple easily accessible datasets: energy, nightlight, and land-use data. We first identified the high-frequency housing occupancy status from energy consumption data and then matched it with the monthly nightlight data. We then introduced the Factor-Augmented Regularized Model for prediction (FarmPredict) to deal with the dependence and collinearity issue among predictors by effectively lifting the prediction space, which is suitable to most machine learning algorithms. The heterogeneity issue in big data analysis is mitigated through the land-use data. FarmPredict allows us to extend the regional results to the city level, with a 76% out-of-sample explanation of the spatial and timeliness variation in the house usage. Since energy is indispensable for life, our method is highly transferable with the only requirement of publicly accessible data. Our article provides an alternative approach with statistical machine learning to predict socioeconomic outcomes without the reliance on existing census and survey data. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.25195733
title: Tables 2 to 11

description: The appendix includes tables summarizing the validity dimensions of a research questionnaire on motivation, determinant factors, and barriers to Foreign Direct Investment (FDI), as well as the sectoral distribution of Portuguese outward investment, features of outward investment in Central and Eastern European countries, and determinants of FDI for six specific firms.