cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7937006.v1
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.
DOI: 10.25549/pcra-c14-66124
title: Redemption tidings, vol. 46, nos. 1-53, 1 Jan. - 31 Dec. 1970

description: [description english/roman)] Issued weekly.
DOI: 10.6084/m9.figshare.7937822
title: A novel genotype of “<i>Anaplasma capra</i>” in wildlife and its phylogenetic relationship with the human genotypes

description: A novel genotype of “<i>Anaplasma capra</i>” in wildlife and its phylogenetic relationship with the human genotypes
DOI: 10.6084/m9.figshare.7937822.v1
title: A novel genotype of “<i>Anaplasma capra</i>” in wildlife and its phylogenetic relationship with the human genotypes

description: A novel genotype of “<i>Anaplasma capra</i>” in wildlife and its phylogenetic relationship with the human genotypes
DOI: 10.5281/zenodo.11005401
title: heliconius_elevatus_decontaminated_FSCR.fasta.gz

description: .
DOI: 10.5281/zenodo.11005402
title: heliconius_elevatus_decontaminated_FSCR.fasta.gz

description: .
DOI: 10.6084/m9.figshare.7936937
title: Sequence analysis of integrated hepatitis B virus DNA during HBeAg-seroconversion

description: Hepatitis B virus (HBV) integration into the host cell genome occurs early on in infection and reportedly induces pro-oncogenic changes in hepatocytes that drive HCC initiation. However, it remains unclear when these changes occur during hepatocarcinogenesis. Extensive expansion of hepatocyte clones with a selective advantage was shown to occur prior to cancer formation during the HBeAg-seroconversion phase of chronic HBV infection. We hypothesized that since integrations occur during the early stages of infection, cell phenotype could be altered and induce a selection advantage (e.g., through insertional mutagenesis or <i>cis</i>-mediated activation of downstream genes). Here, we analyzed the enrichment of genomic and functional patterns in the cellular host sequence adjacent to HBV DNA integration events. We examined 717 unique integration events detected in patients who have and have not undergone HBeAg-seroconversion (<i>n</i> = 41) or in an in vitro model system. We also used an in silico model to control for detection biases. We showed that the sites of HBV DNA integration were distributed throughout the entire host genome without obvious enrichment of specific structural or functional genomic features in the adjacent cellular genome during HBeAg-seroconversion. Currently, this is the most comprehensive characterization of HBV DNA integration events prior to hepatocarcinogenesis. Our results suggest no significant selection for (or against) specific cellular sites of HBV DNA integration occur during the clonal expansion phase of chronic HBV infection. Thus, HBV DNA integration events likely represent passenger events rather than active drivers of liver cancer, which was previously suggested.
DOI: 10.6084/m9.figshare.7936937.v1
title: Sequence analysis of integrated hepatitis B virus DNA during HBeAg-seroconversion

description: Hepatitis B virus (HBV) integration into the host cell genome occurs early on in infection and reportedly induces pro-oncogenic changes in hepatocytes that drive HCC initiation. However, it remains unclear when these changes occur during hepatocarcinogenesis. Extensive expansion of hepatocyte clones with a selective advantage was shown to occur prior to cancer formation during the HBeAg-seroconversion phase of chronic HBV infection. We hypothesized that since integrations occur during the early stages of infection, cell phenotype could be altered and induce a selection advantage (e.g., through insertional mutagenesis or <i>cis</i>-mediated activation of downstream genes). Here, we analyzed the enrichment of genomic and functional patterns in the cellular host sequence adjacent to HBV DNA integration events. We examined 717 unique integration events detected in patients who have and have not undergone HBeAg-seroconversion (<i>n</i> = 41) or in an in vitro model system. We also used an in silico model to control for detection biases. We showed that the sites of HBV DNA integration were distributed throughout the entire host genome without obvious enrichment of specific structural or functional genomic features in the adjacent cellular genome during HBeAg-seroconversion. Currently, this is the most comprehensive characterization of HBV DNA integration events prior to hepatocarcinogenesis. Our results suggest no significant selection for (or against) specific cellular sites of HBV DNA integration occur during the clonal expansion phase of chronic HBV infection. Thus, HBV DNA integration events likely represent passenger events rather than active drivers of liver cancer, which was previously suggested.
DOI: 10.6084/m9.figshare.7937060.v1
title: Evolutionary evidence for multi-host transmission of cetacean morbillivirus

description: Cetacean morbillivirus (CeMV) has emerged as the pathogen that poses the greatest risk of triggering epizootics in cetacean populations worldwide, and has a high propensity for interspecies transmission, including sporadic infection of seals. In this study, we investigated the evolutionary history of CeMV by deep sequencing wild-type viruses from tissue samples representing cetacean species with different spatiotemporal origins. Bayesian phylogeographic analysis generated an estimated evolutionary rate of 2.34 × 10<sup>−4</sup> nucleotide substitutions/site/year and showed that CeMV evolutionary dynamics are neither host-restricted nor location-restricted. Moreover, the dolphin morbillivirus strain of CeMV has undergone purifying selection without evidence of species-specific mutations. Cell-to-cell fusion and growth kinetics assays demonstrated that CeMV can use both dolphin and seal CD150 as a cellular receptor. Thus, it appears that CeMV can readily spread among multiple cetacean populations and may pose an additional spillover risk to seals.
DOI: 10.15468/dl.bwkjcw
title: Occurrence Download

description: A dataset containing 814 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "Geometry POLYGON((-139.12517 -8.14496,-33.10661 -8.14496,-33.10661 34.28145,-139.12517 34.28145,-139.12517 -8.14496))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Trachemys venusta (Gray, 1855)"
 ]
}

 The dataset includes 814 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0106005-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fgekry
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Primulina lungzhouensis (W.T.Wang) Mich.Möller & A.Weber"
 ]
}

 The dataset includes 12 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0095444-230530130749713/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.7936820
title: Two genetically diverse H7N7 avian influenza viruses isolated from migratory birds in central China

description: After the emergence of H7N9 avian influenza viruses (AIV) in early 2013 in China, active surveillance of AIVs in migratory birds was undertaken, and two H7N7 strains were subsequently recovered from the fresh droppings of migratory birds; the strains were from different hosts and sampling sites. Phylogenetic and sequence similarity network analyses indicated that several genes of the two H7N7 viruses were closely related to those in AIVs circulating in domestic poultry, although different gene segments were implicated in the two isolates. This strongly suggested that genes from viruses infecting migratory birds have been introduced into poultry-infecting strains. A Bayesian phylogenetic reconstruction of all eight segments implied that multiple reassortments have occurred in the evolution of these viruses, particularly during late 2011 and early 2014. Antigenic analysis using a hemagglutination inhibition test showed that the two H7N7 viruses were moderately cross-reactive with H7N9-specific anti-serum. The ability of the two H7N7 viruses to remain infectious under various pH and temperature conditions was evaluated, and the viruses persisted the longest at near-neutral pH and in cold temperatures. Animal infection experiments showed that the viruses were avirulent to mice and could not be recovered from any organs. Our results indicate that low pathogenic, divergent H7N7 viruses circulate within the East Asian-Australasian flyway. Virus dispersal between migratory birds and domestic poultry may increase the risk of the emergence of novel unprecedented strains.
DOI: 10.6084/m9.figshare.7936820.v1
title: Two genetically diverse H7N7 avian influenza viruses isolated from migratory birds in central China

description: After the emergence of H7N9 avian influenza viruses (AIV) in early 2013 in China, active surveillance of AIVs in migratory birds was undertaken, and two H7N7 strains were subsequently recovered from the fresh droppings of migratory birds; the strains were from different hosts and sampling sites. Phylogenetic and sequence similarity network analyses indicated that several genes of the two H7N7 viruses were closely related to those in AIVs circulating in domestic poultry, although different gene segments were implicated in the two isolates. This strongly suggested that genes from viruses infecting migratory birds have been introduced into poultry-infecting strains. A Bayesian phylogenetic reconstruction of all eight segments implied that multiple reassortments have occurred in the evolution of these viruses, particularly during late 2011 and early 2014. Antigenic analysis using a hemagglutination inhibition test showed that the two H7N7 viruses were moderately cross-reactive with H7N9-specific anti-serum. The ability of the two H7N7 viruses to remain infectious under various pH and temperature conditions was evaluated, and the viruses persisted the longest at near-neutral pH and in cold temperatures. Animal infection experiments showed that the viruses were avirulent to mice and could not be recovered from any organs. Our results indicate that low pathogenic, divergent H7N7 viruses circulate within the East Asian-Australasian flyway. Virus dispersal between migratory birds and domestic poultry may increase the risk of the emergence of novel unprecedented strains.
DOI: 10.6084/m9.figshare.7937060
title: Evolutionary evidence for multi-host transmission of cetacean morbillivirus

description: Cetacean morbillivirus (CeMV) has emerged as the pathogen that poses the greatest risk of triggering epizootics in cetacean populations worldwide, and has a high propensity for interspecies transmission, including sporadic infection of seals. In this study, we investigated the evolutionary history of CeMV by deep sequencing wild-type viruses from tissue samples representing cetacean species with different spatiotemporal origins. Bayesian phylogeographic analysis generated an estimated evolutionary rate of 2.34 × 10<sup>−4</sup> nucleotide substitutions/site/year and showed that CeMV evolutionary dynamics are neither host-restricted nor location-restricted. Moreover, the dolphin morbillivirus strain of CeMV has undergone purifying selection without evidence of species-specific mutations. Cell-to-cell fusion and growth kinetics assays demonstrated that CeMV can use both dolphin and seal CD150 as a cellular receptor. Thus, it appears that CeMV can readily spread among multiple cetacean populations and may pose an additional spillover risk to seals.
DOI: 10.6084/m9.figshare.7936823
title: Capsular serovars of virulent <i>Capnocytophaga canimorsus</i> are shared by the closely related species <i>C. canis</i> and <i>C. cynodegmi</i>

description: <i>Capnocytophaga canimorsus</i> is a dog oral commensal bacterium that causes rare but life-threatening generalized infections in humans who have been in contact with its animal hosts. Two other dog commensals, <i>Capnocytophaga canis</i> and <i>Capnocytophaga cynodegmi</i>, cause rare, mild local infections. To date, nine capsular serovars have been described in <i>C. canimorsus</i>. Here, we serotyped 112 strains of <i>Capnocytophaga</i> spp. isolated from human infections. The <i>C. canimorsus</i> strains (86 of 96, 89.6%) belonged to serovars A, B, or C with relative frequencies of approximately 30% for each serovar. The high prevalence of the A, B, and C serovars in strains isolated from humans, compared to the previously described low prevalence of these serovars among dog isolates (7.6%), confirms that these three serovars are more virulent to humans than other serovars and suggests that the low incidence of disease may be linked to the low prevalence of the A, B, and C serovars in dogs. We serotyped six strains of <i>C. canis</i> and ten strains of <i>C. cynodegmi</i> and, surprisingly, found one <i>C. canis</i> and three <i>C. cynodegmi</i> strains to be of capsular serovar B. This observation prompted us to test 34 dog-isolated <i>C. canis</i> and 16 dog-isolated <i>C. cynodegmi</i> strains. We found four <i>C. canis</i> strains belonging to serovar A and one belonging to serovar F. In contrast, no dog-isolated <i>C. cynodegmi</i> strain could be typed with the available antisera. This work demonstrates that virulence-associated capsular polysaccharides (A, B, and C) are not specific to the <i>C. canimorsus</i> species.
DOI: 10.6084/m9.figshare.7936823.v1
title: Capsular serovars of virulent <i>Capnocytophaga canimorsus</i> are shared by the closely related species <i>C. canis</i> and <i>C. cynodegmi</i>

description: <i>Capnocytophaga canimorsus</i> is a dog oral commensal bacterium that causes rare but life-threatening generalized infections in humans who have been in contact with its animal hosts. Two other dog commensals, <i>Capnocytophaga canis</i> and <i>Capnocytophaga cynodegmi</i>, cause rare, mild local infections. To date, nine capsular serovars have been described in <i>C. canimorsus</i>. Here, we serotyped 112 strains of <i>Capnocytophaga</i> spp. isolated from human infections. The <i>C. canimorsus</i> strains (86 of 96, 89.6%) belonged to serovars A, B, or C with relative frequencies of approximately 30% for each serovar. The high prevalence of the A, B, and C serovars in strains isolated from humans, compared to the previously described low prevalence of these serovars among dog isolates (7.6%), confirms that these three serovars are more virulent to humans than other serovars and suggests that the low incidence of disease may be linked to the low prevalence of the A, B, and C serovars in dogs. We serotyped six strains of <i>C. canis</i> and ten strains of <i>C. cynodegmi</i> and, surprisingly, found one <i>C. canis</i> and three <i>C. cynodegmi</i> strains to be of capsular serovar B. This observation prompted us to test 34 dog-isolated <i>C. canis</i> and 16 dog-isolated <i>C. cynodegmi</i> strains. We found four <i>C. canis</i> strains belonging to serovar A and one belonging to serovar F. In contrast, no dog-isolated <i>C. cynodegmi</i> strain could be typed with the available antisera. This work demonstrates that virulence-associated capsular polysaccharides (A, B, and C) are not specific to the <i>C. canimorsus</i> species.
DOI: 10.6084/m9.figshare.7936982
title: Genetics, pathogenicity and transmissibility of novel reassortant H5N6 highly pathogenic avian influenza viruses first isolated from migratory birds in western China

description: Genetics, pathogenicity and transmissibility of novel reassortant H5N6 highly pathogenic avian influenza viruses first isolated from migratory birds in western China
DOI: 10.6084/m9.figshare.7936982.v1
title: Genetics, pathogenicity and transmissibility of novel reassortant H5N6 highly pathogenic avian influenza viruses first isolated from migratory birds in western China

description: Genetics, pathogenicity and transmissibility of novel reassortant H5N6 highly pathogenic avian influenza viruses first isolated from migratory birds in western China
DOI: 10.15468/dl.bh9n7c
title: Occurrence Download

description: A dataset containing 47 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Xenoglossa gabbii (Cresson, 1879)"
 ]
}

 The dataset includes 47 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004245-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-66274
title: Redemption tidings, vol. 46, nos. 1-53, 1 Jan. - 31 Dec. 1970

description: [description english/roman)] Issued weekly.
DOI: 10.6084/m9.figshare.7937120
title: Optimized HepaRG is a suitable cell source to generate the human liver chimeric mouse model for the chronic hepatitis B virus infection

description: The human liver chimeric mouse with primary human hepatocytes (PHHs) engraftment has been demonstrated to be a useful animal model to study hepatitis B virus (HBV) pathogenesis and evaluate anti-HBV drugs. However, the disadvantages of using PHHs include the inability for cellular expansion in vitro, limited donor availability, individual differences, and ethical issues, necessitating the development of alternatives. To obtain in vitro expandable hepatocytes, we optimized the hepatic differentiation procedure of the human liver progenitor cell line, HepaRG, using four functional small molecules (4SM) and enriched the precursor hepatocyte-like cells (HLCs). HepaRG cells of different hepatic differentiation states were engrafted to immunodeficient mice (FRGS) with weekly 4SM treatment. The HepaRG-engrafted mice were challenged with HBV and/or treated with several antivirals to evaluate their effects. We demonstrated that the 4SM treatment enhanced hepatic differentiation and promoted cell proliferation capacity both in vitro and in vivo. Mice engrafted with enriched HepaRG of prehepatic differentiation and treated with 4SM displayed approximately 10% liver chimerism at week 8 after engraftment and were maintained at this level for another 16 weeks. Therefore, we developed a HepaRG-based human liver chimeric mouse model: HepaRG-FRGS. Our experimental results showed that the liver chimerism of the mice was adequate to support chronic HBV infection for 24 weeks and to evaluate antivirals. We also demonstrated that HBV infection in HepaRG cells was dependent on their hepatic differentiation state and liver chimerism in vivo. Overall, HepaRG-FRGS mice provide a novel human liver chimeric mouse model to study chronic HBV infection and evaluate anti-HBV drugs.
DOI: 10.6084/m9.figshare.7937120.v1
title: Optimized HepaRG is a suitable cell source to generate the human liver chimeric mouse model for the chronic hepatitis B virus infection

description: The human liver chimeric mouse with primary human hepatocytes (PHHs) engraftment has been demonstrated to be a useful animal model to study hepatitis B virus (HBV) pathogenesis and evaluate anti-HBV drugs. However, the disadvantages of using PHHs include the inability for cellular expansion in vitro, limited donor availability, individual differences, and ethical issues, necessitating the development of alternatives. To obtain in vitro expandable hepatocytes, we optimized the hepatic differentiation procedure of the human liver progenitor cell line, HepaRG, using four functional small molecules (4SM) and enriched the precursor hepatocyte-like cells (HLCs). HepaRG cells of different hepatic differentiation states were engrafted to immunodeficient mice (FRGS) with weekly 4SM treatment. The HepaRG-engrafted mice were challenged with HBV and/or treated with several antivirals to evaluate their effects. We demonstrated that the 4SM treatment enhanced hepatic differentiation and promoted cell proliferation capacity both in vitro and in vivo. Mice engrafted with enriched HepaRG of prehepatic differentiation and treated with 4SM displayed approximately 10% liver chimerism at week 8 after engraftment and were maintained at this level for another 16 weeks. Therefore, we developed a HepaRG-based human liver chimeric mouse model: HepaRG-FRGS. Our experimental results showed that the liver chimerism of the mice was adequate to support chronic HBV infection for 24 weeks and to evaluate antivirals. We also demonstrated that HBV infection in HepaRG cells was dependent on their hepatic differentiation state and liver chimerism in vivo. Overall, HepaRG-FRGS mice provide a novel human liver chimeric mouse model to study chronic HBV infection and evaluate anti-HBV drugs.
DOI: 10.15468/dl.6zx7b3
title: Occurrence Download

description: A dataset containing 34415 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Centropomus undecimalis (Bloch, 1792)"
 ]
}

 The dataset includes 34415 records from 146 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0127142-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.