cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.16699075
title: Comparison of three <i>Coxiella burnetii</i> infectious routes in mice

description: Evidence suggests that <i>Coxiella burnetii</i>, which is shed in the milk, urine, feces, and birth products of infected domestic ruminants, can lead to Q fever disease following consumption of unpasteurized dairy products; however, <i>C. burnetii</i> is not believed to be a major gastrointestinal pathogen. Most infections are associated with inhalation of aerosols generated from the excreta of domestic ruminants. We recently demonstrated that <i>C. burnetii</i> delivered by oral gavage (OG) resulted in dissemination and an immune response; however, it is unclear how infection via the oral route compares to other well-established routes. Therefore, we delivered three strains of <i>C. burnetii</i> (representing three pertinent sequence types in the United States, such as ST16, ST20, and ST8) to immunocompetent mice in four doses via aerosol challenge (AC), intraperitoneal injection (IP), or OG. Low dose (10^5) of ST16 by OG was insufficient to cause infection, yet doses 1,000- or 100-fold lower by IP or AC, respectively, induced a robust immune response and dissemination. Despite being able to induce an immune response in a dose-dependent manner, administration of <i>C. burnetii</i> via OG is the least efficient route tested. Not only were the immune responses and bacterial loads diminished in mice exposed by OG relative to AC or IP, the efficiency of transmission was also inferior. High doses (10^8) were not sufficient to ensure transmission to 100% of the ST20 or ST8 cohorts. These results may provide some basis for why ingestion of <i>C. burnetii</i> as a mode of Q fever transmission is not often reported.
DOI: 10.6084/m9.figshare.14494907.v1
title: Genomic population structure of <i>Helicobacter pylori</i> Shanghai isolates and identification of genomic features uniquely linked with pathogenicity

description: Severe <i>Helicobacter pylori</i>-linked gastric disorders are especially prevalent in the East Asia region. The ability of <i>H. pylori</i> to cause different clinical outcomes is thought to be associated with unique sets of its genetic features. However, only few genetic features have been definitively linked to specific gastrointestinal pathologies. Genome heterogeneity of clinical <i>H. pylori</i> strains from patients with four different gastric disorders was studied to explore the population structure and molecular genomic features and their association with pathogenicity. Population analysis showed that 92.9% of the Shanghai <i>H. pylori</i> isolates were clustered in the East Asia group. Among 2,866 genes detected in all genomes, 1,146 genes formed the core genome, whereas 209 unique genes were detected in individual disease groups. The unique genes of peptic ulcer and gastric cancer groups represented the inorganic ion transport and metabolism function gene clusters. Sixteen virulence genes were detected with statistically different detection rates among the four disease groups. Furthermore, 127 clustered regularly interspaced short palindromic repeats were found with significantly different rates in the four disease groups. A total of 337 putative genomic islands were identified, and three genomic islands were individually found in more than 10% of strains. The genomic islands included several metabolism-associated genes and many genes with unknown function. In total, 88 sequence types were detected among the 112 Shanghai <i>H. pylori</i> isolates. Our study provides an essential milestone in the mapping of specific genomic features and their functions to identify factors needed to induce specific gastric disorders in <i>H. pylori.</i>
DOI: 10.6084/m9.figshare.17041679.v1
title: Emergent SARS-CoV-2 variants: comparative replication dynamics and high sensitivity to thapsigargin

description: The struggle to control the COVID-19 pandemic is made challenging by the emergence of virulent SARS-CoV-2 variants. To gain insight into their replication dynamics, emergent Alpha (A), Beta (B) and Delta (D) SARS-CoV-2 variants were assessed for their infection performance in single variant- and co-infections. The effectiveness of thapsigargin (TG), a recently discovered broad-spectrum antiviral, against these variants was also examined. Of the 3 viruses, the D variant exhibited the highest replication rate and was most able to spread to in-contact cells; its replication rate at 24 h post-infection (hpi) based on progeny viral RNA production was over 4 times that of variant A and 9 times more than the B variant. In co-infections, the D variant boosted the replication of its co-infected partners at the expense of its own initial performance. Furthermore, co-infection with AD or AB combination conferred replication synergy where total progeny (RNA) output was greater than the sum of corresponding single-variant infections. All variants were highly sensitive to TG inhibition. A single pre-infection priming dose of TG effectively blocked all single-variant infections and every combination (AB, AD, BD variants) of co-infection at greater than 95% (relative to controls) at 72 hpi. Likewise, TG was effective in inhibiting each variant in active preexisting infection. In conclusion, against the current backdrop of the dominant D variant that could be further complicated by co-infection synergy with new variants, the growing list of viruses susceptible to TG, a promising host-centric antiviral, now includes a spectrum of contemporary SARS-CoV-2 viruses.
DOI: 10.6084/m9.figshare.17288352
title: Functionality of the human antibody response to <i>Candida albicans</i>

description: <i>Candida albicans</i> is a common commensal on human mucosal surfaces, but can become pathogenic, e.g. if the host is immunocompromised. While neutrophils, macrophages and T cells are regarded as major players in the defense against pathogenic <i>C. albicans</i>, the role of B cells and the protective function of their antibodies are less well characterized. In this study, we show that human serum antibodies are able to enhance the association of human THP-1 monocyte-like cells with <i>C. albicans</i> cells. Human serum antibodies are also capable of inhibiting the adherence and damage dealt to epithelial cells. Furthermore, human serum antibodies impair <i>C. albicans</i> invasion of human oral epithelial cells by blocking induced endocytosis and consequently host cell damage. While aspartic proteases secreted by <i>C. albicans</i> are able to cleave human IgG, this process does not appear to affect the protective function of human antibodies. Thus, humans are equipped with a robust antibody response to <i>C. albicans</i>, which can enhance antifungal activities and prevent fungal-mediated epithelial damage.
DOI: 10.6084/m9.figshare.17288352.v1
title: Functionality of the human antibody response to <i>Candida albicans</i>

description: <i>Candida albicans</i> is a common commensal on human mucosal surfaces, but can become pathogenic, e.g. if the host is immunocompromised. While neutrophils, macrophages and T cells are regarded as major players in the defense against pathogenic <i>C. albicans</i>, the role of B cells and the protective function of their antibodies are less well characterized. In this study, we show that human serum antibodies are able to enhance the association of human THP-1 monocyte-like cells with <i>C. albicans</i> cells. Human serum antibodies are also capable of inhibiting the adherence and damage dealt to epithelial cells. Furthermore, human serum antibodies impair <i>C. albicans</i> invasion of human oral epithelial cells by blocking induced endocytosis and consequently host cell damage. While aspartic proteases secreted by <i>C. albicans</i> are able to cleave human IgG, this process does not appear to affect the protective function of human antibodies. Thus, humans are equipped with a robust antibody response to <i>C. albicans</i>, which can enhance antifungal activities and prevent fungal-mediated epithelial damage.
DOI: 10.6084/m9.figshare.15050601
title: Establishing an invertebrate <i>Galleria mellonella</i> greater wax moth larval model of <i>Neisseria gonorrhoeae</i> infection

description: <i>Neisseria gonorrhoeae</i> (gonococcus) causes the human sexually transmitted disease gonorrhea. Studying gonococcal pathogenesis and developing new vaccines and therapies to combat the increasing prevalence of multi-antibiotic resistant bacteria has made use of many <i>ex vivo</i> models based on human cells and tissues, and <i>in vivo</i> vertebrate models, for example, rodent, pig and human. The focus of the current study was to examine the utility of the invertebrate greater wax moth <i>Galleria mellonella</i> as an <i>in vivo</i> model of gonococcal infection. We observed that a threshold of ~10<sup>6</sup> – 10<sup>7</sup> gonococci/larva was required to kill &gt;50% of larvae (P &lt; 0.05), and increased toxicity correlated with reduced health index scores and pronounced histopathological changes such as increases in the total lesion grade, melanized nodules, hemocyte reaction, and multifocal adipose body degeneration. Larval death was independent of the expression of pilus or Opa protein or LOS sialylation within a single gonococcal species studied, but the model could demonstrate relative toxicity of different isolates. <i>N. meningitidis, N. lacatamica</i> and gonococci all killed larvae equally, but were significantly less toxic (P &gt; 0.05) than <i>Pseudomonas aeruginosa</i>. Larvae primed with nontoxic doses of gonococci were more susceptible to subsequent challenge with homologous and heterologous bacteria, and larval survival was significantly reduced (P &lt; 0.05) in infected larvae after depletion of their hemocytes with clodronate-liposomes. The model was used to test the anti-gonococcal properties of antibiotics and novel antimicrobials. Ceftriaxone (P &lt; 0.05) protected larvae from infection with different gonococcal isolates, but not azithromycin or monocaprin or ligand-coated silver nanoclusters (P &gt; 0.05).
DOI: 10.6084/m9.figshare.17153057
title: The induced knockdown of GmCAD receptor protein encoding gene in <i>Galleria mellonella</i> decreased the insect susceptibility to a <i>Photorhabdus akhurstii</i> oral toxin

description: <i>Photorhabdus</i> bacteria secrete a repertoire of protein toxins that can kill the host insect. Among them, toxin complex (Tc) proteins have gained significant attention due to their wider conservation across the different bacterial genera. In our laboratory, a C-terminal domain of TcaB protein was characterized from <i>P. akhurstii</i> bacterium that conferred the potent oral insecticidal effect on <i>Galleria mellonella</i>. However, the role of insect gut receptors in the TcaB intoxication process was yet to be investigated. In the current study, we examined the transcription of candidate midgut receptors in TcaB-infected larvae and subsequently cloned a cadherin-like gene, <i>GmCAD</i>, from <i>G. mellonella. GmCAD</i> was highly transcribed in the fourth-instar larval stage and specifically in the midgut tissues. Our ligand blot and binding ELISA assays indicated that TcaB binds to the truncated peptides from the GmCAD transmembrane-proximal region with greater affinity than that from the transmembrane-distal region. Oral administration of bacterially expressed <i>GmCAD</i> dsRNA in <i>G. mellonella</i> severely attenuated the expression of target mRNA, which in turn alleviated the negative effect of TcaB on insect survival (TcaB-induced mortality in CAD dsRNA pretreated larvae reduced by 72–83% compared to control), implying the association of GmCAD in the TcaB intoxication process. Present findings form a basis of future research related to the insect gut receptor interactions with <i>Photorhabdus</i> toxins.
DOI: 10.6084/m9.figshare.17153057.v2
title: The induced knockdown of GmCAD receptor protein encoding gene in <i>Galleria mellonella</i> decreased the insect susceptibility to a <i>Photorhabdus akhurstii</i> oral toxin

description: <i>Photorhabdus</i> bacteria secrete a repertoire of protein toxins that can kill the host insect. Among them, toxin complex (Tc) proteins have gained significant attention due to their wider conservation across the different bacterial genera. In our laboratory, a C-terminal domain of TcaB protein was characterized from <i>P. akhurstii</i> bacterium that conferred the potent oral insecticidal effect on <i>Galleria mellonella</i>. However, the role of insect gut receptors in the TcaB intoxication process was yet to be investigated. In the current study, we examined the transcription of candidate midgut receptors in TcaB-infected larvae and subsequently cloned a cadherin-like gene, <i>GmCAD</i>, from <i>G. mellonella. GmCAD</i> was highly transcribed in the fourth-instar larval stage and specifically in the midgut tissues. Our ligand blot and binding ELISA assays indicated that TcaB binds to the truncated peptides from the GmCAD transmembrane-proximal region with greater affinity than that from the transmembrane-distal region. Oral administration of bacterially expressed <i>GmCAD</i> dsRNA in <i>G. mellonella</i> severely attenuated the expression of target mRNA, which in turn alleviated the negative effect of TcaB on insect survival (TcaB-induced mortality in CAD dsRNA pretreated larvae reduced by 72–83% compared to control), implying the association of GmCAD in the TcaB intoxication process. Present findings form a basis of future research related to the insect gut receptor interactions with <i>Photorhabdus</i> toxins.
DOI: 10.6084/m9.figshare.13377014.v1
title: A novel phosphoinositide kinase Fab1 regulates biosynthesis of pathogenic aflatoxin in <i>Aspergillus flavus</i>

description: <i>Aspergillus flavus</i> (<i>A. flavus</i>) is one of the most important model environmental fungi which can produce a potent toxin and carcinogen known as aflatoxin. Aflatoxin contamination causes massive agricultural economic loss and a critical human health issue each year. Although a functional vacuole has been highlighted for its fundamental importance in fungal virulence, the molecular mechanisms of the vacuole in regulating the virulence of <i>A. flavus</i> remain largely unknown. Here, we identified a novel vacuole-related protein in <i>A. flavus</i>, the ortholog of phosphatidylinositol-3-phosphate-5-kinase (Fab1) in <i>Saccharomyces cerevisiae</i>. This kinase was located at the vacuolar membrane, and loss of <i>fab1</i> function was found to affect the growth, conidia and sclerotial development, cellular acidification and metal ion homeostasis, aflatoxin production and pathogenicity of <i>A. flavus</i>. Further functional analysis revealed that Fab1 was required to maintain the vacuole size and cell morphology. Additional quantitative proteomic analysis suggested that Fab1 was likely to play an important role in maintaining vacuolar/cellular homeostasis, with vacuolar dysregulation upon <i>fab1</i> deletion leading to impaired aflatoxin synthesis in this fungus. Together, these results provide insight into the molecular mechanisms by which this pathogen produces aflatoxin and mediates its pathogenicity, and may facilitate dissection of the vacuole-mediated regulatory network in <i>A. flavus</i>.
DOI: 10.5281/zenodo.10822732
title: NoVAGraphS FSA User-Agent Corpus

description: Paper:  Di Nuovo E., Sanguinetti M., Balestrucci P.F,Anselma L., Bernareggi C., Mazzei A. (2024),Educational Dialogue Systems for Visually Impaired Students: Introducing a Task-Oriented User-Agent Corpus. Accepted paper at the 2024 Joint International Conference on Computational Linguistics, Language Resources and Evaluation (LREC-COLING 2024)

Contact person: Elisa Di Nuovo, elisa.dinuovo@gmail.com


Dataset Summary

Collection of user-agent interactions revolving around the description of Finite State Automata.

Daset Description

The corpus consists of a CSV file encoded in UTF-8 comprising the following columns:



CODE_ID: the id of the interaction

Turn: the turn number within the interaction

Participant: it identifies the sender (U for the user, S for the agent)

Text: the utterance content

VIP: it determines whether the user is a Visually-Impaired Person

Token count: the number of tokens in the utterance (counted using Spacy tokenizer)

DAs_GOLD and Errors_GOLD: the columns including the assigned labels for Dialog Acts and Errors, respectively

FSA_ID: the id of the Finite State Automaton that is being referred to within the conversation (it corresponds to the PNG and HTML file names containing the relevant information on the FSA)


Additional Data



Two PNG files with the graphical representation of the automata

Two HTML files containing the state tables of the automata

RASA configuration files used to train the DIET classifier on the DAs


Access Request

To access the data users need to fill out the following Google form
DOI: 10.6084/m9.figshare.17162491
title: UvKmt6-mediated H3K27 trimethylation is required for development, pathogenicity, and stress response in <i>Ustilaginoidea virens</i>

description: Polycomb repressive complex 2 (PRC2) is responsible for the trimethylation of lysine 27 of histone H3 (H3K27me3)-mediated transcriptional silencing. At present, its biological roles in the devastating rice pathogenic fungus <i>Ustilaginoidea virens</i> remain unclear. In this study, we analyzed the function of a putative PRC2 catalytic subunit UvKmt6. The results showed that disruption of <i>UvKMT6</i> resulted in reduced growth, conidiation and pathogenicity in <i>U. virens</i>. Furthermore, UvKmt6 is essential for establishment of H3K27me3 modification, which covers 321 genes in the genome. Deletion of <i>UvKMT6</i> led to transcriptional derepression of 629 genes, 140 of which were occupied with H3K27me3 modification. Consistent with RNA-seq and ChIP-seq analysis, UvKmt6 was further confirmed to participate in the transcriptional repression of genes encoding effectors and genes associated with secondary metabolites production, such as <i>PKS</i>s, <i>NRPS</i>s and <i>Cytochrome P450s</i>. Notably, we found that UvKmt6 is involved in transcriptional repression of oxidative, osmotic, cell wall and nutrient starvation stresses response-related genes. From the perspective of gene expression and phenotype, in addition to the relatively conservative role in fungal development, virulence and production of secondary metabolites, we further reported that UvKmt6-mdediated H3K27me3 plays a critical role in the response to various stresses in <i>U. virens</i>.
DOI: 10.6084/m9.figshare.17162491.v1
title: UvKmt6-mediated H3K27 trimethylation is required for development, pathogenicity, and stress response in <i>Ustilaginoidea virens</i>

description: Polycomb repressive complex 2 (PRC2) is responsible for the trimethylation of lysine 27 of histone H3 (H3K27me3)-mediated transcriptional silencing. At present, its biological roles in the devastating rice pathogenic fungus <i>Ustilaginoidea virens</i> remain unclear. In this study, we analyzed the function of a putative PRC2 catalytic subunit UvKmt6. The results showed that disruption of <i>UvKMT6</i> resulted in reduced growth, conidiation and pathogenicity in <i>U. virens</i>. Furthermore, UvKmt6 is essential for establishment of H3K27me3 modification, which covers 321 genes in the genome. Deletion of <i>UvKMT6</i> led to transcriptional derepression of 629 genes, 140 of which were occupied with H3K27me3 modification. Consistent with RNA-seq and ChIP-seq analysis, UvKmt6 was further confirmed to participate in the transcriptional repression of genes encoding effectors and genes associated with secondary metabolites production, such as <i>PKS</i>s, <i>NRPS</i>s and <i>Cytochrome P450s</i>. Notably, we found that UvKmt6 is involved in transcriptional repression of oxidative, osmotic, cell wall and nutrient starvation stresses response-related genes. From the perspective of gene expression and phenotype, in addition to the relatively conservative role in fungal development, virulence and production of secondary metabolites, we further reported that UvKmt6-mdediated H3K27me3 plays a critical role in the response to various stresses in <i>U. virens</i>.
DOI: 10.5281/zenodo.10822733
title: NoVAGraphS FSA User-Agent Corpus

description: Paper:  Di Nuovo E., Sanguinetti M., Balestrucci P.F,Anselma L., Bernareggi C., Mazzei A. (2024),Educational Dialogue Systems for Visually Impaired Students: Introducing a Task-Oriented User-Agent Corpus. Accepted paper at the 2024 Joint International Conference on Computational Linguistics, Language Resources and Evaluation (LREC-COLING 2024)

Contact person: Elisa Di Nuovo, elisa.dinuovo@gmail.com


Dataset Summary

Collection of user-agent interactions revolving around the description of Finite State Automata.

Daset Description

The corpus consists of a CSV file encoded in UTF-8 comprising the following columns:



CODE_ID: the id of the interaction

Turn: the turn number within the interaction

Participant: it identifies the sender (U for the user, S for the agent)

Text: the utterance content

VIP: it determines whether the user is a Visually-Impaired Person

Token count: the number of tokens in the utterance (counted using Spacy tokenizer)

DAs_GOLD and Errors_GOLD: the columns including the assigned labels for Dialog Acts and Errors, respectively

FSA_ID: the id of the Finite State Automaton that is being referred to within the conversation (it corresponds to the PNG and HTML file names containing the relevant information on the FSA)


Additional Data



Two PNG files with the graphical representation of the automata

Two HTML files containing the state tables of the automata

RASA configuration files used to train the DIET classifier on the DAs


Access Request

To access the data users need to fill out the following Google form
DOI: 10.6084/m9.figshare.16415536.v1
title: S-adenosyl-L-homocysteine hydrolase FgSah1 is required for fungal development and virulence in <i>Fusarium graminearum</i>

description: The S-adenosyl-L-homocysteine hydrolase (Sah1) plays a crucial role in methylation and lipid metabolism in yeast and mammals, yet its function remains elusive in filamentous fungi. In this study, we characterized Sah1 in the phytopathogenic fungus <i>F. graminearum</i> by generating knockout and knockout-complemented strains of <i>FgSAH1</i>. We found that the FgSah1-GFP fusion protein was localized to the cytoplasm, and that deletion of <i>FgSAH1</i> resulted in defects in vegetative growth, asexual and sexual reproduction, stress responses, virulence, lipid metabolism, and tolerance against fungicides. Moreover, the accumulations of S-adenosyl-L-homocysteine (AdoHcy) and S-adenosyl-L-methionine (AdoMet) (the methyl group donor in most methyl transfer reactions) in Δ<i>FgSah1</i> were seven- and ninefold higher than those in the wild-type strain, respectively. All of these defective phenotypes in Δ<i>FgSah1</i> mutants were rescued by target gene complementation. Taken together, these results demonstrate that <i>FgSah1</i> plays essential roles in methylation metabolism, fungal development, full virulence, multiple stress responses, lipid metabolism, and fungicide sensitivity in <i>F. graminearum</i>. To our knowledge, this is the first report on the systematic functional characterization of Sah1 in <i>F. graminearum</i>.