cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7936841.v1
title: Serological survey of neutralizing antibodies to eight major enteroviruses among healthy population

description: Human enteroviruses (EVs) are the most common causative agents infecting human, causing many harmful diseases, such as hand, foot, and mouth disease (HFMD), herpangina (HA), myocarditis, encephalitis, and aseptic meningitis. EV-related diseases pose a serious worldwide threat to public health. To gain comprehensive insight into the seroepidemiology of major prevalent EVs in humans, we firstly performed a serological survey for neutralizing antibodies (nAbs) against Enterovirus A71 (EV-A71), Coxsackie virus A16 (CV-A16), Coxsackie virus A6 (CV-A6), Coxsackie virus A10 (CV-A10), Coxsackie virus B3 (CV-B3), Coxsackie virus B5 (CV-B5), Echovirus 25 (ECHO25), and Echovirus 30 (ECHO30) among the healthy population in Xiamen City in 2016, using micro-neutralization assay. A total of 515 subjects aged 5 months to 83 years were recruited by stratified random sampling. Most major human EVs are widely circulated in Xiamen City and usually infect infants and children. The overall seroprevalence of these eight EVs were ranged from 14.4% to 42.7%, and most of them increased with age and subsequently reached a plateau. The co-existence of nAbs against various EVs are common among people ≥ 7 years of age, due to the alternate infections or co-infections with different serotypes of EVs, while most children were negative for nAb against EVs, especially those &lt; 1 year of age. This is the first report detailing the seroepidemiology of eight prevalent EVs in the same population, which provides scientific data supporting further studies on the improvement of EV-related disease prevention and control.
DOI: 10.15468/dl.ivp6kc
title: Occurrence Download

description: A dataset containing 292 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Selaginella leptophylla Baker"
 ]
}

 The dataset includes 292 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002821-170714134226665/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.7936991
title: Evidence of a fixed internal gene constellation in influenza A viruses isolated from wild birds in Argentina (2006–2016)

description: Wild aquatic birds are the major reservoir of influenza A virus. Cloacal swabs and feces samples (<i>n</i> = 6595) were collected from 62 bird species in Argentina from 2006 to 2016 and screened for influenza A virus. Full genome sequencing of 15 influenza isolates from 6 waterfowl species revealed subtypes combinations that were previously described in South America (H1N1, H4N2, H4N6 (<i>n</i> = 3), H5N3, H6N2 (<i>n</i> = 4), and H10N7 (<i>n</i> = 2)), and new ones not previously identified in the region (H4N8, H7N7 and H7N9). Notably, the internal gene segments of all 15 Argentine isolates belonged to the South American lineage, showing a divergent evolution of these viruses in the Southern Hemisphere. Time-scaled phylogenies indicated that South American gene segments diverged between ~ 30 and ~ 140 years ago from the most closely related influenza lineages, which include the avian North American (PB1, HA, NA, MP, and NS-B) and Eurasian lineage (PB2), and the equine H3N8 lineage (PA, NP, and NS-A). Phylogenetic analyses of the hemagglutinin and neuraminidase gene segments of the H4, H6, and N8 subtypes revealed recent introductions and reassortment between viruses from the Northern and Southern Hemispheres in the Americas. Remarkably and despite evidence of recent hemagglutinin and neuraminidase subtype introductions, the phylogenetic composition of internal gene constellation of these influenza A viruses has remained unchanged. Considering the extended time and the number of sampled species of the current study, and the paucity of previously available data, our results contribute to a better understanding of the ecology and evolution of influenza virus in South America.
DOI: 10.6084/m9.figshare.7936991.v2
title: Evidence of a fixed internal gene constellation in influenza A viruses isolated from wild birds in Argentina (2006–2016)

description: Wild aquatic birds are the major reservoir of influenza A virus. Cloacal swabs and feces samples (<i>n</i> = 6595) were collected from 62 bird species in Argentina from 2006 to 2016 and screened for influenza A virus. Full genome sequencing of 15 influenza isolates from 6 waterfowl species revealed subtypes combinations that were previously described in South America (H1N1, H4N2, H4N6 (<i>n</i> = 3), H5N3, H6N2 (<i>n</i> = 4), and H10N7 (<i>n</i> = 2)), and new ones not previously identified in the region (H4N8, H7N7 and H7N9). Notably, the internal gene segments of all 15 Argentine isolates belonged to the South American lineage, showing a divergent evolution of these viruses in the Southern Hemisphere. Time-scaled phylogenies indicated that South American gene segments diverged between ~ 30 and ~ 140 years ago from the most closely related influenza lineages, which include the avian North American (PB1, HA, NA, MP, and NS-B) and Eurasian lineage (PB2), and the equine H3N8 lineage (PA, NP, and NS-A). Phylogenetic analyses of the hemagglutinin and neuraminidase gene segments of the H4, H6, and N8 subtypes revealed recent introductions and reassortment between viruses from the Northern and Southern Hemispheres in the Americas. Remarkably and despite evidence of recent hemagglutinin and neuraminidase subtype introductions, the phylogenetic composition of internal gene constellation of these influenza A viruses has remained unchanged. Considering the extended time and the number of sampled species of the current study, and the paucity of previously available data, our results contribute to a better understanding of the ecology and evolution of influenza virus in South America.
DOI: 10.15468/dl.g7jvjs
title: Occurrence Download

description: A dataset containing 135 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Polydora angustifolia (Steetz) H.Rob."
 ]
}

 The dataset includes 135 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0090008-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-64168
title: Redemption tidings, vol. 44, nos. 1-52, 4 Jan. - 26 Dec. 1968

description: [description english/roman)] Issued weekly.
DOI: 10.6084/m9.figshare.7936811
title: <i>Bordetella pertussis</i> pertactin knock-out strains reveal immunomodulatory properties of this virulence factor

description: Whooping cough, caused by <i>Bordetella pertussis</i>, has resurged and presents a global health burden worldwide. <i>B. pertussis</i> strains unable to produce the acellular pertussis vaccine component pertactin (Prn), have been emerging and in some countries represent up to 95% of recent clinical isolates. Knowledge on the effect that Prn deficiency has on infection and immunity to <i>B. pertussis</i> is crucial for the development of new strategies to control this disease. Here, we characterized the effect of Prn production by <i>B. pertussis</i> on human and murine dendritic cell (DC) maturation as well as in a murine model for pertussis infection. We incubated human monocyte-derived DCs (moDCs) with multiple isogenic Prn knockout (Prn-KO) and corresponding parental <i>B. pertussis</i> strains constructed either in laboratory reference strains with a Tohama I background or in a recently circulating clinical isolate. Results indicate that, compared to the parental strains, Prn-KO strains induced an increased production of pro-inflammatory cytokines by moDCs. This pro-inflammatory phenotype was also observed upon stimulation of murine bone marrow-derived DCs. Moreover, RNA sequencing analysis of lungs from mice infected with <i>B. pertussis</i> Prn-KO revealed increased expression of genes involved in cell death. These in vitro and in vivo findings indicate that <i>B. pertussis</i> strains which do not produce Prn induce a stronger pro-inflammatory response and increased cell death upon infection, suggesting immunomodulatory properties for Prn.
DOI: 10.6084/m9.figshare.7936811.v1
title: <i>Bordetella pertussis</i> pertactin knock-out strains reveal immunomodulatory properties of this virulence factor

description: Whooping cough, caused by <i>Bordetella pertussis</i>, has resurged and presents a global health burden worldwide. <i>B. pertussis</i> strains unable to produce the acellular pertussis vaccine component pertactin (Prn), have been emerging and in some countries represent up to 95% of recent clinical isolates. Knowledge on the effect that Prn deficiency has on infection and immunity to <i>B. pertussis</i> is crucial for the development of new strategies to control this disease. Here, we characterized the effect of Prn production by <i>B. pertussis</i> on human and murine dendritic cell (DC) maturation as well as in a murine model for pertussis infection. We incubated human monocyte-derived DCs (moDCs) with multiple isogenic Prn knockout (Prn-KO) and corresponding parental <i>B. pertussis</i> strains constructed either in laboratory reference strains with a Tohama I background or in a recently circulating clinical isolate. Results indicate that, compared to the parental strains, Prn-KO strains induced an increased production of pro-inflammatory cytokines by moDCs. This pro-inflammatory phenotype was also observed upon stimulation of murine bone marrow-derived DCs. Moreover, RNA sequencing analysis of lungs from mice infected with <i>B. pertussis</i> Prn-KO revealed increased expression of genes involved in cell death. These in vitro and in vivo findings indicate that <i>B. pertussis</i> strains which do not produce Prn induce a stronger pro-inflammatory response and increased cell death upon infection, suggesting immunomodulatory properties for Prn.
DOI: 10.6084/m9.figshare.7936991.v1
title: Evidence of a fixed internal gene constellation in influenza A viruses isolated from wild birds in Argentina (2006–2016)

description: Wild aquatic birds are the major reservoir of influenza A virus. Cloacal swabs and feces samples (<i>n</i> = 6595) were collected from 62 bird species in Argentina from 2006 to 2016 and screened for influenza A virus. Full genome sequencing of 15 influenza isolates from 6 waterfowl species revealed subtypes combinations that were previously described in South America (H1N1, H4N2, H4N6 (<i>n</i> = 3), H5N3, H6N2 (<i>n</i> = 4), and H10N7 (<i>n</i> = 2)), and new ones not previously identified in the region (H4N8, H7N7 and H7N9). Notably, the internal gene segments of all 15 Argentine isolates belonged to the South American lineage, showing a divergent evolution of these viruses in the Southern Hemisphere. Time-scaled phylogenies indicated that South American gene segments diverged between ~ 30 and ~ 140 years ago from the most closely related influenza lineages, which include the avian North American (PB1, HA, NA, MP, and NS-B) and Eurasian lineage (PB2), and the equine H3N8 lineage (PA, NP, and NS-A). Phylogenetic analyses of the hemagglutinin and neuraminidase gene segments of the H4, H6, and N8 subtypes revealed recent introductions and reassortment between viruses from the Northern and Southern Hemispheres in the Americas. Remarkably and despite evidence of recent hemagglutinin and neuraminidase subtype introductions, the phylogenetic composition of internal gene constellation of these influenza A viruses has remained unchanged. Considering the extended time and the number of sampled species of the current study, and the paucity of previously available data, our results contribute to a better understanding of the ecology and evolution of influenza virus in South America.
DOI: 10.6084/m9.figshare.7937111
title: Novel AR-12 derivatives, P12-23 and P12-34, inhibit flavivirus replication by blocking host de novo pyrimidine biosynthesis

description: The genus <i>Flavivirus</i> contains many important pathogens, including dengue virus (DENV), Zika virus (ZIKV), and Japanese encephalitis virus (JEV). AR-12 is a celecoxib-derived anticancer agent that possesses antiviral activity against a broad range of viruses. We pharmacologically exploited this unique activity to develop additional antiviral agents, resulting in the production of the AR-12 derivatives P12-23 and P12-34. At nanomolar concentrations, these compounds were effective in suppressing DENV, ZIKV and JEV replication, exhibiting 10-fold improvements in the efficacy and selectivity indices as compared to AR-12. Regarding the mode of antiviral action, P12-23 and P12-34 inhibited viral RNA replication but had no effect on viral binding, entry or translation. Moreover, these AR-12 derivatives co-localized with mitochondrial markers, and their antiviral activity was lost in mitochondria-depleted cells. Interestingly, exogenous uridine or orotate, the latter being a metabolite of the mitochondrial enzyme dihydroorotate dehydrogenase (DHODH), abolished the antiviral activity of AR-12 and its derivatives. As DHODH is a key enzyme in the de novo pyrimidine biosynthesis pathway, these AR-12 derivatives may act by targeting pyrimidine biosynthesis in host cells to inhibit viral replication. Importantly, treatment with P12-34 significantly improved the survival of mice that were subcutaneously challenged with DENV. Thus, P12-34 may warrant further evaluation as a therapeutic to control flaviviral outbreaks.
DOI: 10.6084/m9.figshare.7937111.v1
title: Novel AR-12 derivatives, P12-23 and P12-34, inhibit flavivirus replication by blocking host de novo pyrimidine biosynthesis

description: The genus <i>Flavivirus</i> contains many important pathogens, including dengue virus (DENV), Zika virus (ZIKV), and Japanese encephalitis virus (JEV). AR-12 is a celecoxib-derived anticancer agent that possesses antiviral activity against a broad range of viruses. We pharmacologically exploited this unique activity to develop additional antiviral agents, resulting in the production of the AR-12 derivatives P12-23 and P12-34. At nanomolar concentrations, these compounds were effective in suppressing DENV, ZIKV and JEV replication, exhibiting 10-fold improvements in the efficacy and selectivity indices as compared to AR-12. Regarding the mode of antiviral action, P12-23 and P12-34 inhibited viral RNA replication but had no effect on viral binding, entry or translation. Moreover, these AR-12 derivatives co-localized with mitochondrial markers, and their antiviral activity was lost in mitochondria-depleted cells. Interestingly, exogenous uridine or orotate, the latter being a metabolite of the mitochondrial enzyme dihydroorotate dehydrogenase (DHODH), abolished the antiviral activity of AR-12 and its derivatives. As DHODH is a key enzyme in the de novo pyrimidine biosynthesis pathway, these AR-12 derivatives may act by targeting pyrimidine biosynthesis in host cells to inhibit viral replication. Importantly, treatment with P12-34 significantly improved the survival of mice that were subcutaneously challenged with DENV. Thus, P12-34 may warrant further evaluation as a therapeutic to control flaviviral outbreaks.
DOI: 10.15468/dl.d547em
title: Occurrence Download

description: A dataset containing 36267 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-74.88587 40.78387,-74.72118 40.49499,-74.42149 40.1575,-74.01651 40.1629,-73.94091 40.1872,-73.90312 40.45179,-74.01381 40.54628,-73.88692 40.51119,-73.75732 40.55708,-73.54133 40.54088,-73.08506 40.62728,-72.30749 40.85677,-71.81072 41.05656,-71.86471 41.11596,-72.02401 41.07546,-72.078 41.14296,-72.1752 41.11866,-72.2319 41.18615,-72.35879 41.17535,-72.63148 41.00796,-73.14985 41.00256,-73.23895 40.95936,-73.39554 41.03226,-73.61963 41.39404,-74.11641 41.41834,-74.80757 41.11596,-74.88587 40.78387))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "PublishingOrg is ccd1ddc0-6c21-11de-8224-b8a03c50a862"
 ]
}

 The dataset includes 36267 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0073435-220831081235567/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.7936985
title: Broad and long-lasting immune protection against various Chikungunya genotypes demonstrated by participants in a cross-sectional study in a Cambodian rural community

description: Chikungunya virus (CHIKV) is an alphavirus circulating worldwide. Its presence in Asia has been reported since the 1950s, constituting the Asian genotype. Since 2005, strains from the Eastern, Central, and Southern African (ECSA) genotype have caused several outbreaks across Asia. Viruses from the ECSA genotype were also detected in Cambodia in late 2011 and led to an outbreak in a rural community in 2012. A former investigation from 2012 found a higher risk of infection in people younger than 40 years, suggesting a pre-existing herd immunity in the older Cambodian population due to infection with an Asian genotype. In 2016, we collected serum from equivalent numbers of individuals born before 1975 and born after 1980 that were also part of the 2012 study. We analyzed the 154 serum samples from 2016 for neutralization against the Cambodian ECSA isolate and three strains belonging to the Asian genotype. This experiment revealed that 22.5% (18/80) of the younger study participants had no CHIKV antibodies, whereas 5.4% (4/74) of the older population remained naive. Study participants infected during the ECSA outbreak had twofold neutralizing titers against the ECSA and the most ancient Asian genotype virus (Thailand 1958) compared to the other two Asian genotype viruses. The neutralization data also support the older population’s exposure to an Asian genotype virus during the 1960s. The observed cross-reactivity confirms that the investigated CHIKV strains belong to a single serotype despite the emergence of novel ECSA genotype viruses and supports the importance of the development of a Chikungunya vaccine.
DOI: 10.6084/m9.figshare.7936985.v1
title: Broad and long-lasting immune protection against various Chikungunya genotypes demonstrated by participants in a cross-sectional study in a Cambodian rural community

description: Chikungunya virus (CHIKV) is an alphavirus circulating worldwide. Its presence in Asia has been reported since the 1950s, constituting the Asian genotype. Since 2005, strains from the Eastern, Central, and Southern African (ECSA) genotype have caused several outbreaks across Asia. Viruses from the ECSA genotype were also detected in Cambodia in late 2011 and led to an outbreak in a rural community in 2012. A former investigation from 2012 found a higher risk of infection in people younger than 40 years, suggesting a pre-existing herd immunity in the older Cambodian population due to infection with an Asian genotype. In 2016, we collected serum from equivalent numbers of individuals born before 1975 and born after 1980 that were also part of the 2012 study. We analyzed the 154 serum samples from 2016 for neutralization against the Cambodian ECSA isolate and three strains belonging to the Asian genotype. This experiment revealed that 22.5% (18/80) of the younger study participants had no CHIKV antibodies, whereas 5.4% (4/74) of the older population remained naive. Study participants infected during the ECSA outbreak had twofold neutralizing titers against the ECSA and the most ancient Asian genotype virus (Thailand 1958) compared to the other two Asian genotype viruses. The neutralization data also support the older population’s exposure to an Asian genotype virus during the 1960s. The observed cross-reactivity confirms that the investigated CHIKV strains belong to a single serotype despite the emergence of novel ECSA genotype viruses and supports the importance of the development of a Chikungunya vaccine.
DOI: 10.15468/dl.7tmh9e
title: Occurrence Download

description: A dataset containing 18089 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Morpho Fabricius, 1807"
 ]
}

 The dataset includes 18089 records from 110 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041109-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-64252
title: Redemption tidings, vol. 44, nos. 1-52, 4 Jan. - 26 Dec. 1968

description: [description english/roman)] Issued weekly.
DOI: 10.6084/m9.figshare.7936895
title: Identification and characterization of a novel rodent bocavirus from different rodent species in China

description: Members in the genus <i>Bocaparvovirus</i> are closely related to human health and have a wide host range. The diverse hosts raise the possibility of crossing species barrier, which is a feature of emerging viruses. Among the mammalian hosts, rodents are generally acknowledged to be important reservoirs of emerging viruses. Here, rodent samples collected from six provinces and autonomous regions of China (Liaoning, Inner Mongolia, Tibet, Xinjiang, Guangxi and Yunnan) were used to investigate the prevalence and distribution of bocaparvoviruses. By using next-generation sequencing first, a partial non-structural protein 1 (NS1) gene belonging to a possible novel bocaparvovirus was discovered. Following this, PCR-based screening of NS1 gene was conducted in 485 rodent samples, with 106 positive results found in seven rodent species (<i>Rattus norvegicus</i>, <i>Mus musculus</i>, <i>Apodemus agrarius</i>, <i>Cricetulus barabensis</i>, <i>Rattus flavipectus</i>, <i>Rattus rattus</i> and <i>Rhombomys opimus</i>). Finally, six nearly full-length genomes and three complete CDS were obtained and the newly identified bocaparvovirus was tentatively named rodent bocavirus (RoBoV). RoBoV has three ORFs: NS1, NP1, and VP, which are characteristics of bocaparvoviruses. Phylogenetic analyses revealed that porcine bocavirus isolate PBoV-KU14, a member of <i>Ungulate bocaparvovirus 4</i>, was the most related virus to RoBoV, with 92.1–92.9% amino acid identities in NS1 protein. Alignments of RoBoV-related sequences showed RoBoV isolates could be classified into two clades, demonstrating an inter-host genetic diversity. The results indicate a potential interspecies transmission of RoBoV between rodents and swine and expand our knowledge on bocaparvoviruses in rodent populations.