cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8320715
title: Immunization with a recombinant antigen composed of conserved blocks from TSA56 provides broad genotype protection against scrub typhus

description: Scrub typhus is an acute febrile disease caused by <i>Orientia tsutsugamushi</i> infection. Despite the wide range of approaches explored during the last seventy years, an effective prophylactic vaccine is not yet available. Here, we developed a novel recombinant antigen derived from conserved regions of 56 kDa type-specific antigen (TSA56), a major outer membrane protein responsible for genetic heterogeneity and antigenicity, and evaluated it as a protective vaccine antigen. Our findings demonstrate that immunization with conserved blocks of TSA56 (cTSA56) not only provides protective immunity against lethal challenges with the homologous genotype, but also confers significantly better protection against heterologous genotypes than TSA56. Adoptive transfer of CD4<sup>+</sup> or CD8<sup>+</sup> T cells from immunized mice provided significantly enhanced protection against lethal challenge, whereas immune B cells failed to do so, indicating that cellular immunity against the conserved epitopes plays a protective role. Moreover, immunization with a 10-mer peptide mixture, screened from CD8<sup>+</sup> T cell epitopes within the conserved region of TSA56, provided enhanced protection against lethal challenge with <i>O. tsutsugamushi</i>. Therefore, this novel recombinant antigen is a promising candidate for scrub typhus vaccine against a wide range of <i>O. tsutsugamushi</i> genotypes.
DOI: 10.6084/m9.figshare.8320715.v1
title: Immunization with a recombinant antigen composed of conserved blocks from TSA56 provides broad genotype protection against scrub typhus

description: Scrub typhus is an acute febrile disease caused by <i>Orientia tsutsugamushi</i> infection. Despite the wide range of approaches explored during the last seventy years, an effective prophylactic vaccine is not yet available. Here, we developed a novel recombinant antigen derived from conserved regions of 56 kDa type-specific antigen (TSA56), a major outer membrane protein responsible for genetic heterogeneity and antigenicity, and evaluated it as a protective vaccine antigen. Our findings demonstrate that immunization with conserved blocks of TSA56 (cTSA56) not only provides protective immunity against lethal challenges with the homologous genotype, but also confers significantly better protection against heterologous genotypes than TSA56. Adoptive transfer of CD4<sup>+</sup> or CD8<sup>+</sup> T cells from immunized mice provided significantly enhanced protection against lethal challenge, whereas immune B cells failed to do so, indicating that cellular immunity against the conserved epitopes plays a protective role. Moreover, immunization with a 10-mer peptide mixture, screened from CD8<sup>+</sup> T cell epitopes within the conserved region of TSA56, provided enhanced protection against lethal challenge with <i>O. tsutsugamushi</i>. Therefore, this novel recombinant antigen is a promising candidate for scrub typhus vaccine against a wide range of <i>O. tsutsugamushi</i> genotypes.
DOI: 10.6084/m9.figshare.8847446
title: Characterization of swine-origin H1N1 canine influenza viruses

description: Host switch events of influenza A viruses (IAVs) continuously pose a zoonotic threat to humans. In 2013, swine-origin H1N1 IAVs emerged in dogs soon after they were detected in swine in the Guangxi province of China. This host switch was followed by multiple reassortment events between these H1N1 and previously circulating H3N2 canine IAVs (IAVs-C) in dogs. To evaluate the phenotype of these newly identified viruses, we characterized three swine-origin H1N1 IAVs-C and one reassortant H1N1 IAV-C. We found that H1N1 IAVs-C predominantly bound to human-type receptors, efficiently transmitted via direct contact in guinea pigs and replicated in human lung cells. Moreover, the swine-origin H1N1 IAVs-C were lethal in mice and were transmissible by respiratory droplets in guinea pigs. Importantly, sporadic human infections with these viruses have been detected, and preexisting immunity in humans might not be sufficient to prevent infections with these new viruses. Our results show the potential of H1N1 IAVs-C to infect and transmit in humans, suggesting that these viruses should be closely monitored in the future.
DOI: 10.6084/m9.figshare.8847446.v3
title: Characterization of swine-origin H1N1 canine influenza viruses

description: Host switch events of influenza A viruses (IAVs) continuously pose a zoonotic threat to humans. In 2013, swine-origin H1N1 IAVs emerged in dogs soon after they were detected in swine in the Guangxi province of China. This host switch was followed by multiple reassortment events between these H1N1 and previously circulating H3N2 canine IAVs (IAVs-C) in dogs. To evaluate the phenotype of these newly identified viruses, we characterized three swine-origin H1N1 IAVs-C and one reassortant H1N1 IAV-C. We found that H1N1 IAVs-C predominantly bound to human-type receptors, efficiently transmitted via direct contact in guinea pigs and replicated in human lung cells. Moreover, the swine-origin H1N1 IAVs-C were lethal in mice and were transmissible by respiratory droplets in guinea pigs. Importantly, sporadic human infections with these viruses have been detected, and preexisting immunity in humans might not be sufficient to prevent infections with these new viruses. Our results show the potential of H1N1 IAVs-C to infect and transmit in humans, suggesting that these viruses should be closely monitored in the future.
DOI: 10.6084/m9.figshare.10289369
title: Mechanisms underlying the virulence regulation of new <i>Vibrio alginolyticus</i> ncRNA Vvrr1 with a comparative proteomic analysis

description: The incidence of <i>Vibrio alginolyticus</i> infections has increased in recent years due to the influence of climate change and rising sea temperature. Vibrio virulence regulatory RNA 1 (Vvrr1) is a newly found noncoding RNA (ncRNA) predicted to be closely related to the adhesion ability of <i>V. alginolyticus</i> based on the previous RNA-seq. In this study, the target genes of Vvrr1 were fully screened and verified by constructing Vvrr1-overexpressing strains and using the proteome sequencing technology. Pyruvate kinase I (<i>pykF</i>) gene was predicted to be a chief target gene of Vvrr1 involved in virulence regulation. The adhesion ability, biofilm formation and virulence were significantly reduced in the Vvrr1-overexpressing and the <i>pykF</i>-silenced strain compared with the wild strains. Similar to the overexpression of Vvrr1, the silencing of pykF also reduced the expression level of virulence genes, such as <i>ndk</i>, <i>eno</i>, <i>sdhB</i>, <i>glpF</i>, and <i>cysH</i>. Meanwhile, by constructing the “<i>pykF-GFP</i>” fusion expression plasmid and using the GFP reporter gene analysis in <i>Escherichia coli</i>, the fluorescence intensity of the strain containing Vvrr1 whole ncRNA sequence vector was found to be significantly weakened. These indicated that Vvrr1 participated in the virulence regulation mechanism of <i>V. alginolyticus</i> by interacting with the virulence gene <i>pykF</i>.
DOI: 10.6084/m9.figshare.10289369.v1
title: Mechanisms underlying the virulence regulation of new <i>Vibrio alginolyticus</i> ncRNA Vvrr1 with a comparative proteomic analysis

description: The incidence of <i>Vibrio alginolyticus</i> infections has increased in recent years due to the influence of climate change and rising sea temperature. Vibrio virulence regulatory RNA 1 (Vvrr1) is a newly found noncoding RNA (ncRNA) predicted to be closely related to the adhesion ability of <i>V. alginolyticus</i> based on the previous RNA-seq. In this study, the target genes of Vvrr1 were fully screened and verified by constructing Vvrr1-overexpressing strains and using the proteome sequencing technology. Pyruvate kinase I (<i>pykF</i>) gene was predicted to be a chief target gene of Vvrr1 involved in virulence regulation. The adhesion ability, biofilm formation and virulence were significantly reduced in the Vvrr1-overexpressing and the <i>pykF</i>-silenced strain compared with the wild strains. Similar to the overexpression of Vvrr1, the silencing of pykF also reduced the expression level of virulence genes, such as <i>ndk</i>, <i>eno</i>, <i>sdhB</i>, <i>glpF</i>, and <i>cysH</i>. Meanwhile, by constructing the “<i>pykF-GFP</i>” fusion expression plasmid and using the GFP reporter gene analysis in <i>Escherichia coli</i>, the fluorescence intensity of the strain containing Vvrr1 whole ncRNA sequence vector was found to be significantly weakened. These indicated that Vvrr1 participated in the virulence regulation mechanism of <i>V. alginolyticus</i> by interacting with the virulence gene <i>pykF</i>.
DOI: 10.6084/m9.figshare.10318703
title: Zika virus threshold determines transmission by European <i>Aedes albopictus</i> mosquitoes

description: Since its emergence in Yap Island in 2007, Zika virus (ZIKV) has affected all continents except Europe. Despite the hundreds of cases imported to European countries from ZIKV-infested regions, no local cases have been reported in localities where the ZIKV-competent mosquito <i>Aedes albopictus</i> is well established. Here we analysed the vector competence of European <i>Aedes</i> (<i>aegypti</i> and <i>albopictus</i>) mosquitoes to different genotypes of ZIKV. We demonstrate that <i>Ae. albopictus</i> from France was less susceptible to the Asian ZIKV than to the African ZIKV. Critically we show that effective crossing of anatomical barriers (midgut and salivary glands) after an infectious blood meal depends on a viral load threshold to trigger: (i) viral dissemination from the midgut to infect mosquito internal organs and (ii) viral transmission from the saliva to infect a vertebrate host. A viral load in body ≥4800 viral copies triggered dissemination and ≥12,000 viral copies set out transmission. Only 27.3% and 18.2% of <i>Ae. albopictus</i> Montpellier mosquitoes meet respectively these two criteria. Collectively, these compelling results stress the poor ability of <i>Ae. albopictus</i> to sustain a local transmission of ZIKV in Europe and provide a promising tool to evaluate the risk of ZIKV transmission in future outbreaks.
DOI: 10.6084/m9.figshare.10318703.v1
title: Zika virus threshold determines transmission by European <i>Aedes albopictus</i> mosquitoes

description: Since its emergence in Yap Island in 2007, Zika virus (ZIKV) has affected all continents except Europe. Despite the hundreds of cases imported to European countries from ZIKV-infested regions, no local cases have been reported in localities where the ZIKV-competent mosquito <i>Aedes albopictus</i> is well established. Here we analysed the vector competence of European <i>Aedes</i> (<i>aegypti</i> and <i>albopictus</i>) mosquitoes to different genotypes of ZIKV. We demonstrate that <i>Ae. albopictus</i> from France was less susceptible to the Asian ZIKV than to the African ZIKV. Critically we show that effective crossing of anatomical barriers (midgut and salivary glands) after an infectious blood meal depends on a viral load threshold to trigger: (i) viral dissemination from the midgut to infect mosquito internal organs and (ii) viral transmission from the saliva to infect a vertebrate host. A viral load in body ≥4800 viral copies triggered dissemination and ≥12,000 viral copies set out transmission. Only 27.3% and 18.2% of <i>Ae. albopictus</i> Montpellier mosquitoes meet respectively these two criteria. Collectively, these compelling results stress the poor ability of <i>Ae. albopictus</i> to sustain a local transmission of ZIKV in Europe and provide a promising tool to evaluate the risk of ZIKV transmission in future outbreaks.
DOI: 10.6084/m9.figshare.8847446.v2
title: Characterization of swine-origin H1N1 canine influenza viruses

description: Host switch events of influenza A viruses (IAVs) continuously pose a zoonotic threat to humans. In 2013, swine-origin H1N1 IAVs emerged in dogs soon after they were detected in swine in the Guangxi province of China. This host switch was followed by multiple reassortment events between these H1N1 and previously circulating H3N2 canine IAVs (IAVs-C) in dogs. To evaluate the phenotype of these newly identified viruses, we characterized three swine-origin H1N1 IAVs-C and one reassortant H1N1 IAV-C. We found that H1N1 IAVs-C predominantly bound to human-type receptors, efficiently transmitted via direct contact in guinea pigs and replicated in human lung cells. Moreover, the swine-origin H1N1 IAVs-C were lethal in mice and were transmissible by respiratory droplets in guinea pigs. Importantly, sporadic human infections with these viruses have been detected, and preexisting immunity in humans might not be sufficient to prevent infections with these new viruses. Our results show the potential of H1N1 IAVs-C to infect and transmit in humans, suggesting that these viruses should be closely monitored in the future.
DOI: 10.6084/m9.figshare.9822845
title: Host factor SMYD3 is recruited by Ebola virus nucleoprotein to facilitate viral mRNA transcription

description: The polymerase complex of Ebola virus (EBOV) is the functional unit for transcription and replication of viral genome. Nucleoprotein (NP) is a multifunctional protein with high RNA binding affinity and recruits other viral proteins to form functional polymerase complex. In our study, we investigated host proteins associated with EBOV polymerase complex using NP as bait in a transcription and replication competent minigenome system by mass spectrometry analysis and identified SET and MYND domain-containing protein 3 (SMYD3) as a novel host protein which was required for the replication of EBOV. SMYD3 specifically interacted with NP and was recruited to EBOV inclusion bodies through NP. The depletion of SMYD3 dramatically suppressed EBOV mRNA production. A mimic of non-phosphorylated VP30, which is a transcription activator, could partially rescue the viral mRNA production downregulated by the depletion of SMYD3. In addition, SMYD3 promoted NP-VP30 interaction in a dose-dependent manner. These results revealed that SMYD3 was a novel host factor recruited by NP to supporting EBOV mRNA transcription through increasing the binding of VP30 to NP. Thus, our study provided a new understanding of mechanism underlying the transcription of EBOV genome, and a novel anti-EBOV drug design strategy by targeting SMYD3.
DOI: 10.6084/m9.figshare.9822845.v1
title: Host factor SMYD3 is recruited by Ebola virus nucleoprotein to facilitate viral mRNA transcription

description: The polymerase complex of Ebola virus (EBOV) is the functional unit for transcription and replication of viral genome. Nucleoprotein (NP) is a multifunctional protein with high RNA binding affinity and recruits other viral proteins to form functional polymerase complex. In our study, we investigated host proteins associated with EBOV polymerase complex using NP as bait in a transcription and replication competent minigenome system by mass spectrometry analysis and identified SET and MYND domain-containing protein 3 (SMYD3) as a novel host protein which was required for the replication of EBOV. SMYD3 specifically interacted with NP and was recruited to EBOV inclusion bodies through NP. The depletion of SMYD3 dramatically suppressed EBOV mRNA production. A mimic of non-phosphorylated VP30, which is a transcription activator, could partially rescue the viral mRNA production downregulated by the depletion of SMYD3. In addition, SMYD3 promoted NP-VP30 interaction in a dose-dependent manner. These results revealed that SMYD3 was a novel host factor recruited by NP to supporting EBOV mRNA transcription through increasing the binding of VP30 to NP. Thus, our study provided a new understanding of mechanism underlying the transcription of EBOV genome, and a novel anti-EBOV drug design strategy by targeting SMYD3.
DOI: 10.6084/m9.figshare.8247533
title: Down-regulation of cell membrane localized NTCP expression in proliferating hepatocytes prevents hepatitis B virus infection

description: Hepatocyte proliferation could result in the loss of covalently closed circular DNA (cccDNA) and the emergence of cccDNA-cleared nascent hepatocytes, which appear refractory to hepatitis B virus (HBV) reinfection with unknown mechanism(s). Sodium taurocholate cotransporting polypeptide (NTCP) is the functional receptor for HBV entry. In this study, down-regulation of cell membrane localized NTCP expression in proliferating hepatocytes was found to prevent HBV infection in HepG2-NTCP-tet cells and in liver-humanized mice. In patients, lower NTCP protein expression was correlated well with higher levels of hepatocyte proliferation and less HBsAg expression in HBV-related focal nodular hyperplasia (FNH) tissues. Clinically, significantly lower NTCP protein expression was correlated with more active hepatocyte proliferation in CHB patients with severe active necroinflammation and better antiviral treatment outcome. Mechanistically, the activation of cell cycle regulatory genes p53, S-phase kinase-associated protein 2 (SKP2) and cyclin D1 during cell proliferation, as well as proliferative and inflammatory cytokine Interleukin-6 (IL-6) could transcriptionally down-regulate NTCP expression. From these aspects, we conclude that within the milieu of hepatocyte proliferation, down-regulation of cell membrane localized NTCP expression level renders nascent hepatocytes resistant to HBV reinfection. This may accelerate virus clearance during immune-mediated cell death and compensatory proliferation of survival hepatocytes.
DOI: 10.6084/m9.figshare.8247533.v1
title: Down-regulation of cell membrane localized NTCP expression in proliferating hepatocytes prevents hepatitis B virus infection

description: Hepatocyte proliferation could result in the loss of covalently closed circular DNA (cccDNA) and the emergence of cccDNA-cleared nascent hepatocytes, which appear refractory to hepatitis B virus (HBV) reinfection with unknown mechanism(s). Sodium taurocholate cotransporting polypeptide (NTCP) is the functional receptor for HBV entry. In this study, down-regulation of cell membrane localized NTCP expression in proliferating hepatocytes was found to prevent HBV infection in HepG2-NTCP-tet cells and in liver-humanized mice. In patients, lower NTCP protein expression was correlated well with higher levels of hepatocyte proliferation and less HBsAg expression in HBV-related focal nodular hyperplasia (FNH) tissues. Clinically, significantly lower NTCP protein expression was correlated with more active hepatocyte proliferation in CHB patients with severe active necroinflammation and better antiviral treatment outcome. Mechanistically, the activation of cell cycle regulatory genes p53, S-phase kinase-associated protein 2 (SKP2) and cyclin D1 during cell proliferation, as well as proliferative and inflammatory cytokine Interleukin-6 (IL-6) could transcriptionally down-regulate NTCP expression. From these aspects, we conclude that within the milieu of hepatocyte proliferation, down-regulation of cell membrane localized NTCP expression level renders nascent hepatocytes resistant to HBV reinfection. This may accelerate virus clearance during immune-mediated cell death and compensatory proliferation of survival hepatocytes.
DOI: 10.5281/zenodo.18080730
title: Dataset for "Determination of 2-MCPD, 3-MCPD and GE in Edible Oils by the One-Tube Alkaline Transesterification Coupled with Gas Chromatography-Mass Spectrometry"

description: This dataset provides the foundational data for the findings presented in the JAOCS manuscript titled “Determination of 2‑MCPD, 3‑MCPD and GE in Edible Oils by One‑Tube Alkaline Transesterification Coupled with Gas Chromatography–Mass Spectrometry.” The study introduces an efficient, rapid, cost‑effective, and low‑interference analytical method for the determination of these contaminants in edible oils. This dataset includes all primary analytical measurements used to produce the figures and support the conclusions of the paper.

Data Contents



Experimental Design: Optimization of mass spectrometry parameters and quantification of glycidyl esters (GE).

Spectrometry Data: Spectral data with m/z 245 and 245 selected as quantification ions.

Calibration Data: Calculation of GE mass derived from 3‑MCPDE conversion.


Relationship to the ManuscriptThis dataset serves as the direct source for Figures 1–3 and Tables 1–3 in the manuscript. It enables independent verification of the proposed method and facilitates performance comparison between the “two‑tube” approach and conventional GC‑MS/MS methodology.

The complete dataset is available under the permanent identifier:DOI: 10.5281/zenodo.18080731
DOI: 10.5281/zenodo.18080731
title: Dataset for "Determination of 2-MCPD, 3-MCPD and GE in Edible Oils by the One-Tube Alkaline Transesterification Coupled with Gas Chromatography-Mass Spectrometry"

description: This dataset provides the foundational data for the findings presented in the JAOCS manuscript titled “Determination of 2‑MCPD, 3‑MCPD and GE in Edible Oils by One‑Tube Alkaline Transesterification Coupled with Gas Chromatography–Mass Spectrometry.” The study introduces an efficient, rapid, cost‑effective, and low‑interference analytical method for the determination of these contaminants in edible oils. This dataset includes all primary analytical measurements used to produce the figures and support the conclusions of the paper.

Data Contents



Experimental Design: Optimization of mass spectrometry parameters and quantification of glycidyl esters (GE).

Spectrometry Data: Spectral data with m/z 245 and 245 selected as quantification ions.

Calibration Data: Calculation of GE mass derived from 3‑MCPDE conversion.


Relationship to the ManuscriptThis dataset serves as the direct source for Figures 1–3 and Tables 1–3 in the manuscript. It enables independent verification of the proposed method and facilitates performance comparison between the “two‑tube” approach and conventional GC‑MS/MS methodology.

The complete dataset is available under the permanent identifier:DOI: 10.5281/zenodo.18080731
DOI: 10.6084/m9.figshare.8984156.v2
title: Target-independent high-throughput sequencing methods provide evidence that already known human viral pathogens play a main role in respiratory infections with unexplained etiology

description: Despite the advanced PCR-based assays available, a fraction of the pediatric respiratory infections remain unexplained every epidemic season, and there is a perception that novel viruses might be present in these specimens. We systematically collected samples from a prospective cohort of pediatric patients with respiratory infections, that returned negative results by validated molecular RT–PCR assays, and studied them with a target-independent, high-throughput sequencing-based approach. We also included a matched cohort of children with no symptoms of respiratory infection, as a contrast study population. More than fifty percent of the specimens from the group of patients with unexplained respiratory infections were resolved. However, the higher rate of detection was not due to the presence of novel viruses, but to the identification of well-known viral respiratory pathogens. Our results show that already known viral pathogens are responsible for the majority of cases that remain unexplained after the epidemic season. High-throughput sequencing approaches that use pathogen-specific probes are easier to standardize because they ensure reproducible library enrichment and sequencing. In consequence, these techniques might be desirable from a regulatory standpoint for diagnostic laboratories seeking to benefit from the many advantages of these sequencing technologies.