cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7937864
title: Changes in intestinal microbiota in HIV-1-infected subjects following cART initiation: influence of CD4+ T cell count

description: The roles of immunodeficiency and combined antiretroviral therapy (cART) in shaping the gut microbiota in HIV-1-infected subjects (HISs) have not been described thoroughly by time-series investigations. In this study, 36 antiretroviral-naïve HISs were enrolled to prospectively assess alterations in the fecal microbiota and plasma markers of microbial translocation and inflammation with cART. At baseline, the species α-diversity of the fecal microbiota was significantly lower in HISs with a CD4<sup>+</sup> T cell count &lt;300/mm<sup>3</sup> than in HISs with a CD4<sup>+</sup> T cell count &gt;300/mm<sup>3</sup> (Shannon index: Median 2.557 vs. 2.981, <i>P</i> = 0.006; Simpson index: Median 0.168 vs. 0.096, <i>P</i> = 0.004). Additionally, the baseline α-diversity indices correlated with CD4<sup>+</sup> T cell counts (Shannon index: <i>r</i> = 0.474, <i>P</i> = 0.004; Simpson index: <i>r</i> = −0.467, <i>P</i> = 0.004) and the specific plasma biomarkers for microbial translocation and inflammation. After cART introduction, the species α-diversity of fecal microbiota in HISs with CD4<sup>+</sup> T cell counts &lt;300/mm<sup>3</sup> was significantly restored (Shannon index: Median 2.557 vs. 2.791, <i>P</i> = 0.007; Simpson index: Median 0.168 vs. 0.112, <i>P</i> = 0.004), while the variances were insignificant among HISs with CD4+ T cell counts &gt;300/mm<sup>3</sup> (Shannon index: Median 2.981 vs. 2.934, <i>P</i> = 0.179; Simpson index: Median 0.096 vs. 0.119, <i>P</i> = 0.082). Meanwhile, with cART introduction, alterations in the gut microbial composition were more significant in the subgroup with CD4<sup>+</sup> T cell counts &gt;300/mm<sup>3</sup>, corresponding to increases in the specific plasma inflammatory markers. These findings implicated the interactive roles of immunodeficiency and cART for affecting gut microbiota in HIV-1-infected individuals, providing new insights into intestinal microbiome dysbiosis related to HIV-1 infection.
DOI: 10.15468/dl.zta63p
title: Occurrence Download

description: A dataset containing 1393 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 {
 "or" : [
 "TaxonKey is Gleditsia sinensis Lam.",
 "TaxonKey is Kochia scoparia (L.) Schrad.",
 "TaxonKey is Portulaca oleracea L."
 ]
 }
 ]
}

 The dataset includes 1393 records from 39 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003175-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.7937066
title: Novel bovine hepacivirus in dairy cattle, China

description: Novel bovine hepacivirus in dairy cattle, China
DOI: 10.6084/m9.figshare.7937066.v1
title: Novel bovine hepacivirus in dairy cattle, China

description: Novel bovine hepacivirus in dairy cattle, China
DOI: 10.6084/m9.figshare.7937864.v1
title: Changes in intestinal microbiota in HIV-1-infected subjects following cART initiation: influence of CD4+ T cell count

description: The roles of immunodeficiency and combined antiretroviral therapy (cART) in shaping the gut microbiota in HIV-1-infected subjects (HISs) have not been described thoroughly by time-series investigations. In this study, 36 antiretroviral-naïve HISs were enrolled to prospectively assess alterations in the fecal microbiota and plasma markers of microbial translocation and inflammation with cART. At baseline, the species α-diversity of the fecal microbiota was significantly lower in HISs with a CD4<sup>+</sup> T cell count &lt;300/mm<sup>3</sup> than in HISs with a CD4<sup>+</sup> T cell count &gt;300/mm<sup>3</sup> (Shannon index: Median 2.557 vs. 2.981, <i>P</i> = 0.006; Simpson index: Median 0.168 vs. 0.096, <i>P</i> = 0.004). Additionally, the baseline α-diversity indices correlated with CD4<sup>+</sup> T cell counts (Shannon index: <i>r</i> = 0.474, <i>P</i> = 0.004; Simpson index: <i>r</i> = −0.467, <i>P</i> = 0.004) and the specific plasma biomarkers for microbial translocation and inflammation. After cART introduction, the species α-diversity of fecal microbiota in HISs with CD4<sup>+</sup> T cell counts &lt;300/mm<sup>3</sup> was significantly restored (Shannon index: Median 2.557 vs. 2.791, <i>P</i> = 0.007; Simpson index: Median 0.168 vs. 0.112, <i>P</i> = 0.004), while the variances were insignificant among HISs with CD4+ T cell counts &gt;300/mm<sup>3</sup> (Shannon index: Median 2.981 vs. 2.934, <i>P</i> = 0.179; Simpson index: Median 0.096 vs. 0.119, <i>P</i> = 0.082). Meanwhile, with cART introduction, alterations in the gut microbial composition were more significant in the subgroup with CD4<sup>+</sup> T cell counts &gt;300/mm<sup>3</sup>, corresponding to increases in the specific plasma inflammatory markers. These findings implicated the interactive roles of immunodeficiency and cART for affecting gut microbiota in HIV-1-infected individuals, providing new insights into intestinal microbiome dysbiosis related to HIV-1 infection.
DOI: 10.6084/m9.figshare.7936793
title: An epizootic of <i>Chlamydia psittaci</i> equine reproductive loss associated with suspected spillover from native Australian parrots

description: <i>Chlamydia psittaci</i> is an avian pathogen capable of spill-over infections to humans. A parrot <i>C. psittaci</i> strain was recently detected in an equine reproductive loss case associated with a subsequent cluster of human <i>C. psittaci</i> infections. In this study, we screened for <i>C. psittaci</i> in cases of equine reproductive loss reported in regional New South Wales, Australia during the 2016 foaling season. <i>C. psittaci</i> specific-PCR screening of foetal and placental tissue samples from cases of equine abortion (<i>n</i> = 161) and foals with compromised health status (<i>n</i> = 38) revealed <i>C. psittaci</i> positivity of 21.1% and 23.7%, respectively. There was a statistically significant geographical clustering of cases ~170 km inland from the mid-coast of NSW (<i>P</i> &lt; 0.001). Genomic analysis and molecular typing of <i>C. psittaci</i> positive samples from this study and the previous Australian equine index case revealed that the equine strains from different studs in regional NSW were clonal, while the phylogenetic analysis revealed that the <i>C. psittaci</i> strains from both Australian equine disease clusters belong to the parrot-associated 6BC clade, again indicative of spill-over of <i>C. psittaci</i> infections from native Australian parrots. The results of this work suggest that <i>C. psittaci</i> may be a more significant agent of equine reproductive loss than thought. A range of studies are now required to evaluate (a) the exact role that <i>C. psittaci</i> plays in equine reproductive loss; (b) the range of potential avian reservoirs and factors influencing infection spill-over; and (c) the risk that these equine infections pose to human health.
DOI: 10.6084/m9.figshare.7936793.v1
title: An epizootic of <i>Chlamydia psittaci</i> equine reproductive loss associated with suspected spillover from native Australian parrots

description: <i>Chlamydia psittaci</i> is an avian pathogen capable of spill-over infections to humans. A parrot <i>C. psittaci</i> strain was recently detected in an equine reproductive loss case associated with a subsequent cluster of human <i>C. psittaci</i> infections. In this study, we screened for <i>C. psittaci</i> in cases of equine reproductive loss reported in regional New South Wales, Australia during the 2016 foaling season. <i>C. psittaci</i> specific-PCR screening of foetal and placental tissue samples from cases of equine abortion (<i>n</i> = 161) and foals with compromised health status (<i>n</i> = 38) revealed <i>C. psittaci</i> positivity of 21.1% and 23.7%, respectively. There was a statistically significant geographical clustering of cases ~170 km inland from the mid-coast of NSW (<i>P</i> &lt; 0.001). Genomic analysis and molecular typing of <i>C. psittaci</i> positive samples from this study and the previous Australian equine index case revealed that the equine strains from different studs in regional NSW were clonal, while the phylogenetic analysis revealed that the <i>C. psittaci</i> strains from both Australian equine disease clusters belong to the parrot-associated 6BC clade, again indicative of spill-over of <i>C. psittaci</i> infections from native Australian parrots. The results of this work suggest that <i>C. psittaci</i> may be a more significant agent of equine reproductive loss than thought. A range of studies are now required to evaluate (a) the exact role that <i>C. psittaci</i> plays in equine reproductive loss; (b) the range of potential avian reservoirs and factors influencing infection spill-over; and (c) the risk that these equine infections pose to human health.
DOI: 10.6084/m9.figshare.7936943
title: Upregulation of HBV transcription by sodium taurocholate cotransporting polypeptide at the postentry step is inhibited by the entry inhibitor Myrcludex B

description: Sodium taurocholate cotransporting polypeptide (NTCP) is a functional receptor for hepatitis B virus (HBV) entry. However, little is known regarding whether NTCP is involved in regulating the postentry steps of the HBV life cycle. Here, we found that NTCP expression upregulated HBV transcription at the postentry step and that the NTCP-targeting entry inhibitor Myrcludex B (MyrB) effectively suppressed HBV transcription both in an HBV in vitro infection system and in mice hydrodynamically injected with an HBV expression plasmid. Mechanistically, NTCP upregulated HBV transcription via farnesoid X receptor α (FxRα)-mediated activation of the HBV EN2/core promoter at the postentry step in a manner that was dependent on the bile acid (BA)-transport function of NTCP, which was blocked by MyrB. Our findings uncover a novel role for NTCP in the HBV life cycle and provide a reference for the use of novel NTCP-targeting entry inhibitors to suppress HBV infection and replication.
DOI: 10.6084/m9.figshare.7936943.v1
title: Upregulation of HBV transcription by sodium taurocholate cotransporting polypeptide at the postentry step is inhibited by the entry inhibitor Myrcludex B

description: Sodium taurocholate cotransporting polypeptide (NTCP) is a functional receptor for hepatitis B virus (HBV) entry. However, little is known regarding whether NTCP is involved in regulating the postentry steps of the HBV life cycle. Here, we found that NTCP expression upregulated HBV transcription at the postentry step and that the NTCP-targeting entry inhibitor Myrcludex B (MyrB) effectively suppressed HBV transcription both in an HBV in vitro infection system and in mice hydrodynamically injected with an HBV expression plasmid. Mechanistically, NTCP upregulated HBV transcription via farnesoid X receptor α (FxRα)-mediated activation of the HBV EN2/core promoter at the postentry step in a manner that was dependent on the bile acid (BA)-transport function of NTCP, which was blocked by MyrB. Our findings uncover a novel role for NTCP in the HBV life cycle and provide a reference for the use of novel NTCP-targeting entry inhibitors to suppress HBV infection and replication.
DOI: 10.15468/dl.9qt6fn
title: Occurrence Download

description: A dataset containing 187 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Darina solenoides (P.P.King, 1832)"
 ]
}

 The dataset includes 187 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0106006-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-66200
title: Redemption tidings, vol. 46, nos. 1-53, 1 Jan. - 31 Dec. 1970

description: [description english/roman)] Issued weekly.
DOI: 10.6084/m9.figshare.7936964
title: <i>Candida blankii</i>: an emergent opportunistic yeast with reduced susceptibility to antifungals

description: <i>Candida blankii</i>: an emergent opportunistic yeast with reduced susceptibility to antifungals
DOI: 10.15468/dl.5crjdx
title: Occurrence Download

description: A dataset containing 436 species occurrences available in GBIF matching the query:
{
 "and" : [
 "VerbatimScientificName is Anodorhynchus leari",
 "BasisOfRecord is one of (Machine Observation, Human Observation)",
 "Year 2011-2021",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen, Specimen, Material citation, Material sample)"
 ]
 }
 }
 ]
}

 The dataset includes 436 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0090000-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.7936847
title: A multi-omic analysis reveals the regulatory role of CD180 during the response of macrophages to <i>Borrelia burgdorferi</i>

description: Macrophages are cells of the innate immune system with the ability to phagocytose and induce a global pattern of responses that depend on several signaling pathways. We have determined the biosignature of murine bone marrow-derived macrophages and human blood monocytes using transcriptomic and proteomic approaches. We identified a common pattern of genes that are transcriptionally regulated and overall indicate that the response to <i>B. burgdorferi</i> involves the interaction of spirochetal antigens with several inflammatory pathways corresponding to primary (triggered by pattern-recognition receptors) and secondary (induced by proinflammatory cytokines) responses. We also show that the Toll-like receptor family member CD180 is downregulated by the stimulation of macrophages, but not monocytes, with the spirochete. Silencing <i>Cd180</i> results in increased phagocytosis while tempering the production of the proinflammatory cytokine TNF. <i>Cd180</i>-silenced cells produce increased levels of <i>Itgam</i> and surface CD11b, suggesting that the regulation of CD180 by the spirochete initiates a cascade that increases CR3-mediated phagocytosis of the bacterium while repressing the consequent inflammatory response.
DOI: 10.6084/m9.figshare.7936847.v2
title: A multi-omic analysis reveals the regulatory role of CD180 during the response of macrophages to <i>Borrelia burgdorferi</i>

description: Macrophages are cells of the innate immune system with the ability to phagocytose and induce a global pattern of responses that depend on several signaling pathways. We have determined the biosignature of murine bone marrow-derived macrophages and human blood monocytes using transcriptomic and proteomic approaches. We identified a common pattern of genes that are transcriptionally regulated and overall indicate that the response to <i>B. burgdorferi</i> involves the interaction of spirochetal antigens with several inflammatory pathways corresponding to primary (triggered by pattern-recognition receptors) and secondary (induced by proinflammatory cytokines) responses. We also show that the Toll-like receptor family member CD180 is downregulated by the stimulation of macrophages, but not monocytes, with the spirochete. Silencing <i>Cd180</i> results in increased phagocytosis while tempering the production of the proinflammatory cytokine TNF. <i>Cd180</i>-silenced cells produce increased levels of <i>Itgam</i> and surface CD11b, suggesting that the regulation of CD180 by the spirochete initiates a cascade that increases CR3-mediated phagocytosis of the bacterium while repressing the consequent inflammatory response.
DOI: 10.6084/m9.figshare.7936964.v1
title: <i>Candida blankii</i>: an emergent opportunistic yeast with reduced susceptibility to antifungals

description: <i>Candida blankii</i>: an emergent opportunistic yeast with reduced susceptibility to antifungals
DOI: 10.15468/dl.ahxhfg
title: Occurrence Download

description: A dataset containing 61 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lyncodon patagonicus (de Blainville, 1842)"
 ]
}

 The dataset includes 61 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0076121-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.7936847.v1
title: A multi-omic analysis reveals the regulatory role of CD180 during the response of macrophages to <i>Borrelia burgdorferi</i>

description: Macrophages are cells of the innate immune system with the ability to phagocytose and induce a global pattern of responses that depend on several signaling pathways. We have determined the biosignature of murine bone marrow-derived macrophages and human blood monocytes using transcriptomic and proteomic approaches. We identified a common pattern of genes that are transcriptionally regulated and overall indicate that the response to <i>B. burgdorferi</i> involves the interaction of spirochetal antigens with several inflammatory pathways corresponding to primary (triggered by pattern-recognition receptors) and secondary (induced by proinflammatory cytokines) responses. We also show that the Toll-like receptor family member CD180 is downregulated by the stimulation of macrophages, but not monocytes, with the spirochete. Silencing <i>Cd180</i> results in increased phagocytosis while tempering the production of the proinflammatory cytokine TNF. <i>Cd180</i>-silenced cells produce increased levels of <i>Itgam</i> and surface CD11b, suggesting that the regulation of CD180 by the spirochete initiates a cascade that increases CR3-mediated phagocytosis of the bacterium while repressing the consequent inflammatory response.
DOI: 10.6084/m9.figshare.7936946
title: Large-scale sequence analysis reveals novel human-adaptive markers in PB2 segment of seasonal influenza A viruses

description: To elucidate the adaptive strategies of influenza A viruses (IAVs) to human, we proposed a computational approach to identify human-adaptive mutations in seasonal IAVs, which have not been analyzed comprehensively. We compared representative PB2 sequences of 1425 avian IAVs and 2176 human IAVs and identified a total of 42 human-adaptive markers, including 28 and 31 markers in PB2 proteins of seasonal viruses H1N1 and H3N2, respectively. Notably, this comprehensive list encompasses almost all the markers identified in prior computational studies and 21 novel markers including an experimentally verified mutation K526R, suggesting the predictive power of our method. The strength of our analysis derives from the enormous amount of recently available sequences as well as the recognition that human-adaptive mutations are not necessarily conserved across subtypes. We also utilized mutual information to profile the inter-residue coevolution in PB2 protein. A total of 35 and 46 coevolving site pairs are identified in H1N1 and H3N2, respectively. Interestingly, 13 out of the 28 (46.4%) identified markers in H1N1 and 16 out of the 31 (51.6%) in H3N2 are embraced in the coevolving pairs. Many of them are paired with well-characterized human-adaptive mutations, indicating potential epistatic effect of these coevolving residues in human adaptation. Additionally, we reconstructed the PB2 evolutionary history of seasonal IAVs and demonstrated the distinct adaptive pathway of PB2 segment after reassortment from H1 to H3 lineage. Our study may provide clues for further experimental validation of human-adaptive mutations and shed light on the human adaptation process of seasonal IAVs.
DOI: 10.6084/m9.figshare.7936946.v1
title: Large-scale sequence analysis reveals novel human-adaptive markers in PB2 segment of seasonal influenza A viruses

description: To elucidate the adaptive strategies of influenza A viruses (IAVs) to human, we proposed a computational approach to identify human-adaptive mutations in seasonal IAVs, which have not been analyzed comprehensively. We compared representative PB2 sequences of 1425 avian IAVs and 2176 human IAVs and identified a total of 42 human-adaptive markers, including 28 and 31 markers in PB2 proteins of seasonal viruses H1N1 and H3N2, respectively. Notably, this comprehensive list encompasses almost all the markers identified in prior computational studies and 21 novel markers including an experimentally verified mutation K526R, suggesting the predictive power of our method. The strength of our analysis derives from the enormous amount of recently available sequences as well as the recognition that human-adaptive mutations are not necessarily conserved across subtypes. We also utilized mutual information to profile the inter-residue coevolution in PB2 protein. A total of 35 and 46 coevolving site pairs are identified in H1N1 and H3N2, respectively. Interestingly, 13 out of the 28 (46.4%) identified markers in H1N1 and 16 out of the 31 (51.6%) in H3N2 are embraced in the coevolving pairs. Many of them are paired with well-characterized human-adaptive mutations, indicating potential epistatic effect of these coevolving residues in human adaptation. Additionally, we reconstructed the PB2 evolutionary history of seasonal IAVs and demonstrated the distinct adaptive pathway of PB2 segment after reassortment from H1 to H3 lineage. Our study may provide clues for further experimental validation of human-adaptive mutations and shed light on the human adaptation process of seasonal IAVs.
DOI: 10.6084/m9.figshare.7937006
title: Associating H<sub>2</sub>O<sub>2-</sub>and NO-related changes in the proteome of <i>Mycobacterium smegmatis</i> with enhanced survival in macrophage

description: <i>Mycobacterium</i> manages to evade the host cell immune system, partially owing to its ability to survive redox stress after macrophage engulfment. Exposure to redox stress has been linked to later replication, persistence, and latent infection. In this work, mass spectrometry was used to elucidate the cell-wide changes that occur in response to sublethal doses of hydrogen peroxide and nitric oxide over time, with <i>Mycobacterium smegmatis</i> being used as a model organism. A total of 3135 proteins were confidently assigned, of which 1713, 1674, and 1713 were identified under NO, H<sub>2</sub>O<sub>2</sub>, and control conditions, respectively. Both treatment conditions resulted in changes of protein expression from the DosR regulon as well as those related to lipid metabolism. Complementary to the changes in the proteome, sublethal exposure to NO and H<sub>2</sub>O<sub>2</sub> improved the survival of the bacteria after macrophage infection. Our data indicate that pre-exposure to sublethal doses of these redox stressors causes an alteration in the expression of proteins related to lipid metabolism, suggesting a link between altered lipid metabolism and enhanced survival in macrophages.