cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20522232.v2
title: An outbreak of a novel recombinant Coxsackievirus A4 in a kindergarten, Shandong province, China, 2021

description: In 2021, twenty children exhibiting influenza-like illnesses were reported from a kindergarten in Shandong Province, China. Eleven genomes of Coxsackievirus A4 (CV-A4) were obtained from the pediatric cases, sharing &lt;93% genome sequence identities with known CV-A4 strains. Further analyses suggested potential genetic recombination in the P3 region of the novel strains.
DOI: 10.15468/dl.h66r77
title: Occurrence Download

description: A dataset containing 1096 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eucalyptus flocktoniae",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1096 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0040895-251025141854904/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.17081967
title: Cell membrane-anchored anti-HIV single-chain antibodies and bifunctional inhibitors targeting the gp41 fusion protein: new strategies for HIV gene therapy

description: Emerging studies indicate that infusion of HIV-resistant cells could be an effective strategy to achieve a sterilizing or functional cure. We recently reported that glycosylphosphatidylinositol (GPI)-anchored nanobody or a fusion inhibitory peptide can render modified cells resistant to HIV-1 infection. In this study, we comprehensively characterized a panel of newly isolated HIV-1-neutralizing antibodies as GPI-anchored inhibitors. Fusion genes encoding the single-chain variable fragment (scFv) of 3BNC117, N6, PGT126, PGT128, 10E8, or 35O22 were constructed with a self-inactivating lentiviral vector, and they were efficiently expressed in the lipid raft sites of target cell membrane without affecting the expression of HIV-1 receptors (CD4, CCR5 and CXCR4). Significantly, transduced cells exhibited various degrees of resistance to cell-free HIV-1 infection and cell-associated HIV-1 transmission, as well as viral Env-mediated cell–cell fusion, with the cells modified by GPI-10E8 showing the most potent and broad anti-HIV activity. In mechanism, GPI-10E8 also interfered with the processing of viral Env in transduced cells and attenuated the infectivity of progeny viruses. By genetically linking 10E8 with a fusion inhibitor peptide, we subsequently designed a group of eight bifunctional constructs as cell membrane-based inhibitors, designated CMI01∼CMI08, which rendered cells completely resistant to HIV-1, HIV-2, and simian immunodeficiency virus (SIV). In human CD4<sup>+</sup> T cells, GPI-10E8 and its bifunctional derivatives blocked both CCR5- and CXCR4-tropic HIV-1 isolates efficiently, and the modified cells displayed robust survival selection under HIV-1 infection. Therefore, our studies provide new strategies for generating HIV-resistant cells, which can be used alone or with other gene therapy approaches.
DOI: 10.6084/m9.figshare.17081967.v2
title: Cell membrane-anchored anti-HIV single-chain antibodies and bifunctional inhibitors targeting the gp41 fusion protein: new strategies for HIV gene therapy

description: Emerging studies indicate that infusion of HIV-resistant cells could be an effective strategy to achieve a sterilizing or functional cure. We recently reported that glycosylphosphatidylinositol (GPI)-anchored nanobody or a fusion inhibitory peptide can render modified cells resistant to HIV-1 infection. In this study, we comprehensively characterized a panel of newly isolated HIV-1-neutralizing antibodies as GPI-anchored inhibitors. Fusion genes encoding the single-chain variable fragment (scFv) of 3BNC117, N6, PGT126, PGT128, 10E8, or 35O22 were constructed with a self-inactivating lentiviral vector, and they were efficiently expressed in the lipid raft sites of target cell membrane without affecting the expression of HIV-1 receptors (CD4, CCR5 and CXCR4). Significantly, transduced cells exhibited various degrees of resistance to cell-free HIV-1 infection and cell-associated HIV-1 transmission, as well as viral Env-mediated cell–cell fusion, with the cells modified by GPI-10E8 showing the most potent and broad anti-HIV activity. In mechanism, GPI-10E8 also interfered with the processing of viral Env in transduced cells and attenuated the infectivity of progeny viruses. By genetically linking 10E8 with a fusion inhibitor peptide, we subsequently designed a group of eight bifunctional constructs as cell membrane-based inhibitors, designated CMI01∼CMI08, which rendered cells completely resistant to HIV-1, HIV-2, and simian immunodeficiency virus (SIV). In human CD4<sup>+</sup> T cells, GPI-10E8 and its bifunctional derivatives blocked both CCR5- and CXCR4-tropic HIV-1 isolates efficiently, and the modified cells displayed robust survival selection under HIV-1 infection. Therefore, our studies provide new strategies for generating HIV-resistant cells, which can be used alone or with other gene therapy approaches.
DOI: 10.6084/m9.figshare.19207551
title: The SARS-CoV-2 inactivated vaccine enhances the broad neutralization against variants in individuals recovered from COVID-19 up to one year

description: The SARS-CoV-2 inactivated vaccine enhances the broad neutralization against variants in individuals recovered from COVID-19 up to one year
DOI: 10.6084/m9.figshare.19207551.v3
title: The SARS-CoV-2 inactivated vaccine enhances the broad neutralization against variants in individuals recovered from COVID-19 up to one year

description: The SARS-CoV-2 inactivated vaccine enhances the broad neutralization against variants in individuals recovered from COVID-19 up to one year
DOI: 10.6084/m9.figshare.18743676
title: Changing epidemiology of shigellosis in Taiwan, 2010-2019: an emerging threat to HIV-infected patients and men who have sex with men

description: Shigellosis appears to increase in certain at-risk populations in developed countries. Based on the nationwide surveillance, the annual incidence of shigellosis in Taiwan (1999-2019) was 0.38-5.77 cases per 100,000 people. Indigenous shigellosis has mostly affected men who have sex with men (MSM) and people living with HIV (PLWH) since 2015. In this retrospective study, compared with those diagnosed before 2015, indigenous cases diagnosed during 2015–2019 mostly occurred in male adults (96.0% vs 47.1%, <i>P </i>&lt; 0.001), with a longer hospital stay (median 5.0 vs 3.5 days, <i>P </i>= 0.029) and different coinfections. The predominant strains in 2015 and 2016 were ciprofloxacin-resistant <i>Shigella sonnei</i> and azithromycin non-susceptible <i>Shigella flexneri</i> (<i>S. flexneri</i>) 3a, which had been replaced by ciprofloxacin-resistant <i>S. flexneri</i> 2a since 2018. Notably, six indigenous cases were caused by cefotaxime-resistant <i>S. flexneri</i>. Inappropriate use of empiric antibiotic treatment was common. In conclusion, there is an ongoing spread of ciprofloxacin-resistant shigellosis among PLWH and MSM and cefotaxime-resistant <i>S. flexneri</i> is an emerging threat in Taiwan.
DOI: 10.6084/m9.figshare.18743676.v3
title: Changing epidemiology of shigellosis in Taiwan, 2010-2019: an emerging threat to HIV-infected patients and men who have sex with men

description: Shigellosis appears to increase in certain at-risk populations in developed countries. Based on the nationwide surveillance, the annual incidence of shigellosis in Taiwan (1999-2019) was 0.38-5.77 cases per 100,000 people. Indigenous shigellosis has mostly affected men who have sex with men (MSM) and people living with HIV (PLWH) since 2015. In this retrospective study, compared with those diagnosed before 2015, indigenous cases diagnosed during 2015–2019 mostly occurred in male adults (96.0% vs 47.1%, <i>P </i>&lt; 0.001), with a longer hospital stay (median 5.0 vs 3.5 days, <i>P </i>= 0.029) and different coinfections. The predominant strains in 2015 and 2016 were ciprofloxacin-resistant <i>Shigella sonnei</i> and azithromycin non-susceptible <i>Shigella flexneri</i> (<i>S. flexneri</i>) 3a, which had been replaced by ciprofloxacin-resistant <i>S. flexneri</i> 2a since 2018. Notably, six indigenous cases were caused by cefotaxime-resistant <i>S. flexneri</i>. Inappropriate use of empiric antibiotic treatment was common. In conclusion, there is an ongoing spread of ciprofloxacin-resistant shigellosis among PLWH and MSM and cefotaxime-resistant <i>S. flexneri</i> is an emerging threat in Taiwan.
DOI: 10.6084/m9.figshare.19207551.v2
title: The SARS-CoV-2 inactivated vaccine enhances the broad neutralization against variants in individuals recovered from COVID-19 up to one year

description: The SARS-CoV-2 inactivated vaccine enhances the broad neutralization against variants in individuals recovered from COVID-19 up to one year
DOI: 10.6084/m9.figshare.19746822
title: Genomic dissection of the microevolution of Australian epidemic <i>Bordetella pertussis</i>

description: Whooping cough (pertussis) is a highly contagious respiratory disease caused by the bacterium <i>Bordetella pertussis.</i> Despite high vaccine coverage, pertussis has re-emerged in many countries including Australia and caused two large epidemics in Australia since 2007. Here, we undertook a genomic and phylogeographic study of 385 Australian <i>B. pertussis</i> isolates collected from 2008 to 2017. The Australian <i>B. pertussis</i> population was found to be composed of mostly <i>ptxP3</i> strains carrying different <i>fim3</i> alleles, with <i>ptxP3-fim3A</i> genotype expanding far more than <i>ptxP3-fim3B.</i> Within the former, there were six co-circulating epidemic lineages (EL1 to EL6). The multiple ELs emerged, expanded, and then declined at different time points over the two epidemics. In population genetics terms, both hard and soft selective sweeps through vaccine selection pressures have determined the population dynamics of Australian <i>B. pertussis.</i> Relative risk estimation suggests that once a new <i>B. pertussis</i> lineage emerged, it was more likely to spread locally within the first 1.5 years. However, after 1.5 years, any new lineage was likely to expand to a wider region. Phylogenetic analysis revealed the expansion of <i>ptxP3</i> strains was also associated with replacement of the type III secretion system allele <i>bscI1</i> with <i>bscI3</i>. <i>bscI3</i> is associated with decreased T3SS secretion and may allow <i>B. pertussis</i> to reduce immune recognition. This study advanced our understanding of the epidemic population structure and spatial and temporal dynamics of <i>B. pertussis</i> in a highly immunized population.
DOI: 10.6084/m9.figshare.19746822.v2
title: Genomic dissection of the microevolution of Australian epidemic <i>Bordetella pertussis</i>

description: Whooping cough (pertussis) is a highly contagious respiratory disease caused by the bacterium <i>Bordetella pertussis.</i> Despite high vaccine coverage, pertussis has re-emerged in many countries including Australia and caused two large epidemics in Australia since 2007. Here, we undertook a genomic and phylogeographic study of 385 Australian <i>B. pertussis</i> isolates collected from 2008 to 2017. The Australian <i>B. pertussis</i> population was found to be composed of mostly <i>ptxP3</i> strains carrying different <i>fim3</i> alleles, with <i>ptxP3-fim3A</i> genotype expanding far more than <i>ptxP3-fim3B.</i> Within the former, there were six co-circulating epidemic lineages (EL1 to EL6). The multiple ELs emerged, expanded, and then declined at different time points over the two epidemics. In population genetics terms, both hard and soft selective sweeps through vaccine selection pressures have determined the population dynamics of Australian <i>B. pertussis.</i> Relative risk estimation suggests that once a new <i>B. pertussis</i> lineage emerged, it was more likely to spread locally within the first 1.5 years. However, after 1.5 years, any new lineage was likely to expand to a wider region. Phylogenetic analysis revealed the expansion of <i>ptxP3</i> strains was also associated with replacement of the type III secretion system allele <i>bscI1</i> with <i>bscI3</i>. <i>bscI3</i> is associated with decreased T3SS secretion and may allow <i>B. pertussis</i> to reduce immune recognition. This study advanced our understanding of the epidemic population structure and spatial and temporal dynamics of <i>B. pertussis</i> in a highly immunized population.
DOI: 10.6084/m9.figshare.18743676.v2
title: Changing epidemiology of shigellosis in Taiwan, 2010-2019: an emerging threat to HIV-infected patients and men who have sex with men

description: Shigellosis appears to increase in certain at-risk populations in developed countries. Based on the nationwide surveillance, the annual incidence of shigellosis in Taiwan (1999-2019) was 0.38-5.77 cases per 100,000 people. Indigenous shigellosis has mostly affected men who have sex with men (MSM) and people living with HIV (PLWH) since 2015. In this retrospective study, compared with those diagnosed before 2015, indigenous cases diagnosed during 2015–2019 mostly occurred in male adults (96.0% vs 47.1%, <i>P </i>&lt; 0.001), with a longer hospital stay (median 5.0 vs 3.5 days, <i>P </i>= 0.029) and different coinfections. The predominant strains in 2015 and 2016 were ciprofloxacin-resistant <i>Shigella sonnei</i> and azithromycin non-susceptible <i>Shigella flexneri</i> (<i>S. flexneri</i>) 3a, which had been replaced by ciprofloxacin-resistant <i>S. flexneri</i> 2a since 2018. Notably, six indigenous cases were caused by cefotaxime-resistant <i>S. flexneri</i>. Inappropriate use of empiric antibiotic treatment was common. In conclusion, there is an ongoing spread of ciprofloxacin-resistant shigellosis among PLWH and MSM and cefotaxime-resistant <i>S. flexneri</i> is an emerging threat in Taiwan.
DOI: 10.6084/m9.figshare.20424267
title: Effect of pneumococcal conjugate vaccine availability on <i>Streptococcus pneumoniae</i> infections and genetic recombination in Zhejiang, China from 2009 to 2019

description: Pneumococcal pneumonia is one of the main reasons for child death worldwide. Pneumococcal conjugate vaccines (PCVs) are considered the most effective strategy for pneumococcal disease (PD) prevention, but how a pause in PCV vaccination affects the prevalence of PD or the genetic evolution of <i>Streptococcus pneumoniae</i> genetic evolution is unknown. Based on the unique PCV introduction timeline (vaccine unavailable during April 2015-April 2017) in China, we aimed to evaluate the effect of interrupted PCV availability on PD and pneumococcal genome variation. Pneumococcal isolates (n = 386) were collected retrospectively from eight sites in Zhejiang, China from 2009 to 2019 in which 184 pathogenic (isolates from sterile and infection sites) strains were identified. An interrupted time series analysis was conducted to estimate changes in PD and the recombination frequency of whole genome-sequenced strains was estimated via SNP calling. We found that both PD and pneumococcal genome variation were affected by interrupted PCV availability. The proportion (∼70%) of vaccine-type pneumococcal LRTI (VT-LRTI) in all LRTI cases decreased to ∼30% in the later PCV7 period and rebounded to ∼70% in children once PCV7 became unavailable in April 2015 (<i>p </i>= 0.0007). The major clone CC271 strains showed slowed (<i>p </i>= 0.0293) recombination frequency (decreased from 2.82 ± 1.16–0.72 ± 0.21) upon PCV removal. Our study illustrated for the first time that VT-LRTI fluctuated upon interrupted vaccine availability in China and causing a decreased of recombination frequency of vaccine types. Promoting a nationwide continuous vaccination programme and strengthening <i>S. pneumoniae</i> molecular epidemiology surveillance are essential for PD prevention.
DOI: 10.6084/m9.figshare.20424267.v1
title: Effect of pneumococcal conjugate vaccine availability on <i>Streptococcus pneumoniae</i> infections and genetic recombination in Zhejiang, China from 2009 to 2019

description: Pneumococcal pneumonia is one of the main reasons for child death worldwide. Pneumococcal conjugate vaccines (PCVs) are considered the most effective strategy for pneumococcal disease (PD) prevention, but how a pause in PCV vaccination affects the prevalence of PD or the genetic evolution of <i>Streptococcus pneumoniae</i> genetic evolution is unknown. Based on the unique PCV introduction timeline (vaccine unavailable during April 2015-April 2017) in China, we aimed to evaluate the effect of interrupted PCV availability on PD and pneumococcal genome variation. Pneumococcal isolates (n = 386) were collected retrospectively from eight sites in Zhejiang, China from 2009 to 2019 in which 184 pathogenic (isolates from sterile and infection sites) strains were identified. An interrupted time series analysis was conducted to estimate changes in PD and the recombination frequency of whole genome-sequenced strains was estimated via SNP calling. We found that both PD and pneumococcal genome variation were affected by interrupted PCV availability. The proportion (∼70%) of vaccine-type pneumococcal LRTI (VT-LRTI) in all LRTI cases decreased to ∼30% in the later PCV7 period and rebounded to ∼70% in children once PCV7 became unavailable in April 2015 (<i>p </i>= 0.0007). The major clone CC271 strains showed slowed (<i>p </i>= 0.0293) recombination frequency (decreased from 2.82 ± 1.16–0.72 ± 0.21) upon PCV removal. Our study illustrated for the first time that VT-LRTI fluctuated upon interrupted vaccine availability in China and causing a decreased of recombination frequency of vaccine types. Promoting a nationwide continuous vaccination programme and strengthening <i>S. pneumoniae</i> molecular epidemiology surveillance are essential for PD prevention.
DOI: 10.6084/m9.figshare.20224186
title: Combining intramuscular and intranasal homologous prime-boost with a chimpanzee adenovirus-based COVID-19 vaccine elicits potent humoral and cellular immune responses in mice

description: The efficacy of many coronavirus disease 2019 (COVID-19) vaccines has been shown to decrease to varying extents against new severe acute respiratory syndrome coronavirus 2 variants, which are responsible for the continuing COVID-19 pandemic. Combining intramuscular and intranasal vaccination routes is a promising approach for achieving more potent immune responses. We evaluated the immunogenicity of prime-boost protocols with a chimpanzee adenovirus serotype 68 vector-based vaccine, ChAdTS-S, administered via both intranasal and intramuscular routes in BALB/c mice. Intramuscular priming followed by an intranasal booster elicited the highest levels of IgG, IgA, and pseudovirus neutralizing antibody titres among all the protocols tested at day 42 after prime immunization compared with the intranasal priming/intramuscular booster and prime-boost protocols using only one route. In addition, intramuscular priming followed by an intranasal booster induced high T-cell responses, measured using the IFN-γ ELISpot assay, that were similar to those observed upon intramuscular vaccination. All ChAdTS-S vaccination groups induced Th1-skewing of the T-cell response according to intracellular cytokine staining and Meso Scale Discovery cytokine profiling assays on day 56 after priming. This study provides reference data for assessing vaccination schemes of adenovirus-based COVID-19 vaccines with high immune efficacy.
DOI: 10.6084/m9.figshare.20224186.v2
title: Combining intramuscular and intranasal homologous prime-boost with a chimpanzee adenovirus-based COVID-19 vaccine elicits potent humoral and cellular immune responses in mice

description: The efficacy of many coronavirus disease 2019 (COVID-19) vaccines has been shown to decrease to varying extents against new severe acute respiratory syndrome coronavirus 2 variants, which are responsible for the continuing COVID-19 pandemic. Combining intramuscular and intranasal vaccination routes is a promising approach for achieving more potent immune responses. We evaluated the immunogenicity of prime-boost protocols with a chimpanzee adenovirus serotype 68 vector-based vaccine, ChAdTS-S, administered via both intranasal and intramuscular routes in BALB/c mice. Intramuscular priming followed by an intranasal booster elicited the highest levels of IgG, IgA, and pseudovirus neutralizing antibody titres among all the protocols tested at day 42 after prime immunization compared with the intranasal priming/intramuscular booster and prime-boost protocols using only one route. In addition, intramuscular priming followed by an intranasal booster induced high T-cell responses, measured using the IFN-γ ELISpot assay, that were similar to those observed upon intramuscular vaccination. All ChAdTS-S vaccination groups induced Th1-skewing of the T-cell response according to intracellular cytokine staining and Meso Scale Discovery cytokine profiling assays on day 56 after priming. This study provides reference data for assessing vaccination schemes of adenovirus-based COVID-19 vaccines with high immune efficacy.
DOI: 10.6084/m9.figshare.19829478
title: Gene essentiality profiling reveals a novel determinant of stresses preventing protein aggregation in <i>Salmonella</i>

description: Adaptation to various stresses during infection is important for <i>Salmonella</i> Typhimurium virulence, while the fitness determinants under infection-relevant stress conditions remain unknown. Here, we simulated conditions <i>Salmonella</i> encountered within the host or in the environment by 15 individual stresses as well as two model cell lines (epithelium and macrophage) to decipher the genes and pathways required for fitness. By high-resolution Tn-seq analysis, a total of 1242 genes were identified as essential for fitness under at least one stress condition. The comparative analysis of fitness determinants in 17 stress conditions indicated the essentiality of genes varied in different mimicking host niches. A total of 12 genes were identified as fitness determinants in all stress conditions, including <i>recB</i>, <i>recC</i>, and <i>xseA</i> (encode three exonuclease subunits necessary for DNA recombination repair) and a novel essential fitness gene <i>yheM</i>. YheM is a putative sulfurtransferase subunit that is responsible for tRNA modification, and our results showed that <i>Salmonella</i> lacking <i>yheM</i> accumulated more aggregates of endogenous protein than wild-type. Moreover, we established a scoring scheme for sRNA essentiality analysis and found STnc2080 of unknown function was essential for resistance to LL-37. In summary, we systematically dissected <i>Salmonella</i> gene essentiality profiling and demonstrated the general and specific adaptive requirements in infection-relevant niches. Our data not only provide valuable insights on how <i>Salmonella</i> responds to environmental stresses during infections but also highlight the potential clinical application of fitness determinants in vaccine development.