cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.16563397.v2
title: Viral intra-host evolution in immunocompetent children contributes to human norovirus diversification at the global scale

description: Norovirus is a major cause of acute gastroenteritis. Human noroviruses present &gt;30 different genotypes, with a single genotype (GII.4) predominating worldwide. Concurrent outbreaks of norovirus are often associated with the emergence of new viruses. While different hypotheses have been presented, the source of new mutations in noroviruses is still unknown. In this study, we applied high-resolution sequencing to determine the intra-host viral diversity presented by noroviruses during the acute and shedding phase of infection in children. Profiling viral intra-host diversification at nearly full genome level indicated that GII.4 viruses presented dynamic intra-host variation, while non-GII.4 viruses presented minimal variation throughout the infection. Notably, the intra-host genetic variation during the shedding phase recapitulates the genetic diversity observed at the global level, particularly those mapping at the VP1 antigenic sites. Thus the intra-host evolution in healthy children explains the source of norovirus mutations that results in diversification at the global scale.
DOI: 10.6084/m9.figshare.14806340
title: Experimental infections with Zika virus strains reveal high vector competence of <i>Aedes albopictus</i> and <i>Aedes aegypti</i> populations from Gabon (Central Africa) for the African virus lineage

description: The two main Zika virus (ZIKV) vectors, <i>Aedes albopictus</i> and <i>Aedes aegypti</i> (invasive and native species, respectively), are present in Gabon (Central Africa). The aim of this study was to determine the entomological ZIKV risk associated with these mosquito species in Gabon by evaluating their vector competence for an African (i.e. representative of the endemic strains circulating in sub-Saharan Africa) and two Asian (i.e. representatives of exogenous epidemic strains that could be introduced) ZIKV strains. The transmission efficiency of one <i>Ae. aegypti</i> and two <i>Ae. albopictus</i> field-collected populations from Libreville and Franceville was assayed at day 7, 14 and 21 after experimental oral infection. The two mosquito species could transmit all three ZIKV strains already at day 7 post-infection, but transmission efficiency was higher for the African strain than the non-African strains (&gt;60% versus &lt;14%; incubation period of 14–21 days). The two mosquito species exhibited comparable vector competence for ZIKV, although the amount of viral particles (African strain) in saliva was significantly higher in <i>Ae. albopictus</i> than <i>Ae. aegypti</i> at day 14 post-infection. These findings suggest that overall, ZIKV risk in Gabon is mainly related to virus strains that circulate endemically across sub-Saharan Africa, although the transmission of non-African strains remain possible in case of introduction. Due to its high infestation indexes and ecological/geographical ranges, this risk appears mainly associated with <i>Ae. albopictus</i>. Vector surveillance and control methods against this invasive mosquito must be strengthened in the region to limit the risk of future outbreaks.
DOI: 10.6084/m9.figshare.14806340.v1
title: Experimental infections with Zika virus strains reveal high vector competence of <i>Aedes albopictus</i> and <i>Aedes aegypti</i> populations from Gabon (Central Africa) for the African virus lineage

description: The two main Zika virus (ZIKV) vectors, <i>Aedes albopictus</i> and <i>Aedes aegypti</i> (invasive and native species, respectively), are present in Gabon (Central Africa). The aim of this study was to determine the entomological ZIKV risk associated with these mosquito species in Gabon by evaluating their vector competence for an African (i.e. representative of the endemic strains circulating in sub-Saharan Africa) and two Asian (i.e. representatives of exogenous epidemic strains that could be introduced) ZIKV strains. The transmission efficiency of one <i>Ae. aegypti</i> and two <i>Ae. albopictus</i> field-collected populations from Libreville and Franceville was assayed at day 7, 14 and 21 after experimental oral infection. The two mosquito species could transmit all three ZIKV strains already at day 7 post-infection, but transmission efficiency was higher for the African strain than the non-African strains (&gt;60% versus &lt;14%; incubation period of 14–21 days). The two mosquito species exhibited comparable vector competence for ZIKV, although the amount of viral particles (African strain) in saliva was significantly higher in <i>Ae. albopictus</i> than <i>Ae. aegypti</i> at day 14 post-infection. These findings suggest that overall, ZIKV risk in Gabon is mainly related to virus strains that circulate endemically across sub-Saharan Africa, although the transmission of non-African strains remain possible in case of introduction. Due to its high infestation indexes and ecological/geographical ranges, this risk appears mainly associated with <i>Ae. albopictus</i>. Vector surveillance and control methods against this invasive mosquito must be strengthened in the region to limit the risk of future outbreaks.
DOI: 10.6084/m9.figshare.16551592.v1
title: Genomic characterization of carbapenem-non-susceptible <i>Pseudomonas aeruginosa</i> in Singapore

description: <i>Pseudomonas aeruginosa</i> is a clinically important pathogen implicated in many hospital-acquired infections. Its propensity to acquire broad-spectrum resistance has earned the organism its status as a severe public health threat requiring urgent control measures. While whole-genome sequencing-based genomic surveillance provides a means to track antimicrobial resistance, its use in molecular epidemiological surveys of <i>P. aeruginosa</i> remains limited, especially in the Southeast Asian region. We sequenced the whole genomes of 222 carbapenem-non-susceptible <i>P. aeruginosa</i> (CNPA) isolates collected in 2006–2020 at the largest public acute care hospital in Singapore. Antimicrobial susceptibilities were determined using broth microdilution. Clonal relatedness, multi-locus sequence types, and antimicrobial resistance determinants (acquired and chromosomal) were determined. In this study, CNPA exhibited broad-spectrum resistance (87.8% multi-drug resistance), retaining susceptibility only to polymyxin B (95.0%) and amikacin (55.0%). Carbapenemases were detected in 51.4% of the isolates, where IMP and NDM metallo-<i>β</i>-lactamases were the most frequent. Carbapenem resistance was also likely associated with OprD alterations or efflux mechanisms (ArmZ/NalD mutations), which occurred in strains with or without carbapenemases. The population of CNPA in the hospital was diverse; the 222 isolates grouped into 68 sequence types (ST), which included various high-risk clones. We detected an emerging clone, the NDM-1-producing ST308, in addition to the global high-risk ST235 clone which was the predominant clone in our population. Our results thus provide a “snapshot” of the circulating lineages of CNPA locally and the prevailing genetic mechanisms contributing to carbapenem resistance. This database also serves as the baseline for future prospective surveillance studies.
DOI: 10.6084/m9.figshare.16563397.v1
title: Viral intra-host evolution in immunocompetent children contributes to human norovirus diversification at the global scale

description: Norovirus is a major cause of acute gastroenteritis. Human noroviruses present &gt;30 different genotypes, with a single genotype (GII.4) predominating worldwide. Concurrent outbreaks of norovirus are often associated with the emergence of new viruses. While different hypotheses have been presented, the source of new mutations in noroviruses is still unknown. In this study, we applied high-resolution sequencing to determine the intra-host viral diversity presented by noroviruses during the acute and shedding phase of infection in children. Profiling viral intra-host diversification at nearly full genome level indicated that GII.4 viruses presented dynamic intra-host variation, while non-GII.4 viruses presented minimal variation throughout the infection. Notably, the intra-host genetic variation during the shedding phase recapitulates the genetic diversity observed at the global level, particularly those mapping at the VP1 antigenic sites. Thus the intra-host evolution in healthy children explains the source of norovirus mutations that results in diversification at the global scale.
DOI: 10.6084/m9.figshare.16617055
title: High estradiol and low testosterone levels are associated with critical illness in male but not in female COVID-19 patients: a retrospective cohort study

description: Male sex was repeatedly identified as a risk factor for death and intensive care admission. However, it is yet unclear whether sex hormones are associated with disease severity in COVID-19 patients. In this study, we analysed sex hormone levels (estradiol and testosterone) of male and female COVID-19 patients (<i>n</i> = 50) admitted to an intensive care unit (ICU) in comparison to control non-COVID-19 patients at the ICU (<i>n</i> = 42), non-COVID-19 patients with the most prevalent comorbidity (coronary heart diseases) present within the COVID-19 cohort (<i>n</i> = 39) and healthy individuals (<i>n</i> = 50). We detected significantly elevated estradiol levels in critically ill male COVID-19 patients compared to all control cohorts. Testosterone levels were significantly reduced in critically ill male COVID-19 patients compared to control cohorts. No statistically significant differences in sex hormone levels were detected in critically ill female COVID-19 patients, albeit similar trends towards elevated estradiol levels were observed. Linear regression analysis revealed that among a broad range of cytokines and chemokines analysed, IFN-γ levels are positively associated with estradiol levels in male and female COVID-19 patients. Furthermore, male COVID-19 patients with elevated estradiol levels were more likely to receive ECMO treatment. Thus, we herein identified that disturbance of sex hormone metabolism might present a hallmark in critically ill male COVID-19 patients.
DOI: 10.6084/m9.figshare.16617055.v1
title: High estradiol and low testosterone levels are associated with critical illness in male but not in female COVID-19 patients: a retrospective cohort study

description: Male sex was repeatedly identified as a risk factor for death and intensive care admission. However, it is yet unclear whether sex hormones are associated with disease severity in COVID-19 patients. In this study, we analysed sex hormone levels (estradiol and testosterone) of male and female COVID-19 patients (<i>n</i> = 50) admitted to an intensive care unit (ICU) in comparison to control non-COVID-19 patients at the ICU (<i>n</i> = 42), non-COVID-19 patients with the most prevalent comorbidity (coronary heart diseases) present within the COVID-19 cohort (<i>n</i> = 39) and healthy individuals (<i>n</i> = 50). We detected significantly elevated estradiol levels in critically ill male COVID-19 patients compared to all control cohorts. Testosterone levels were significantly reduced in critically ill male COVID-19 patients compared to control cohorts. No statistically significant differences in sex hormone levels were detected in critically ill female COVID-19 patients, albeit similar trends towards elevated estradiol levels were observed. Linear regression analysis revealed that among a broad range of cytokines and chemokines analysed, IFN-γ levels are positively associated with estradiol levels in male and female COVID-19 patients. Furthermore, male COVID-19 patients with elevated estradiol levels were more likely to receive ECMO treatment. Thus, we herein identified that disturbance of sex hormone metabolism might present a hallmark in critically ill male COVID-19 patients.
DOI: 10.6084/m9.figshare.13686149
title: Isolation of SARS-CoV-2 strains carrying a nucleotide mutation, leading to a stop codon in the ORF 6 protein

description: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was isolated from the oro/pharyngeal swabs of two Italian COVID-19 patients, physicians in a COVID-19 division hospital, with different courses of the disease. The complete genome sequences show that the two isolates belong to the B1.1 lineage, but contain a nucleotide mutation in the ORF6, leading to a stop codon and to the deletion of 6 amino acids in the C terminus. This deletion was unique, compared to the currently available sequences deposited in the GISAID and GenBank database. It did not affect the in vitro viral replication, neither the neutralizing activities of the patients' antibodies. Based on homology analysis with other Coronaviruses, the two isolated lacked the ORF6 aminoacidic portion responsible for the inhibition of the antiviral Interferon (IFN)-based host response. IFN seems to have a dual role of in SARS-CoV-2 infected patients: not only antiviral activity, but also a detrimental role in case of excessive production. A deletion in the SARS-CoV-2 ORF6 protein might have a specific, still unknown role in the viral pathogenesis.
DOI: 10.6084/m9.figshare.13686149.v2
title: Isolation of SARS-CoV-2 strains carrying a nucleotide mutation, leading to a stop codon in the ORF 6 protein

description: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was isolated from the oro/pharyngeal swabs of two Italian COVID-19 patients, physicians in a COVID-19 division hospital, with different courses of the disease. The complete genome sequences show that the two isolates belong to the B1.1 lineage, but contain a nucleotide mutation in the ORF6, leading to a stop codon and to the deletion of 6 amino acids in the C terminus. This deletion was unique, compared to the currently available sequences deposited in the GISAID and GenBank database. It did not affect the in vitro viral replication, neither the neutralizing activities of the patients' antibodies. Based on homology analysis with other Coronaviruses, the two isolated lacked the ORF6 aminoacidic portion responsible for the inhibition of the antiviral Interferon (IFN)-based host response. IFN seems to have a dual role of in SARS-CoV-2 infected patients: not only antiviral activity, but also a detrimental role in case of excessive production. A deletion in the SARS-CoV-2 ORF6 protein might have a specific, still unknown role in the viral pathogenesis.
DOI: 10.5519/qd.scu9wa5g
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1 records)
DOI: 10.6084/m9.figshare.15043244
title: The synergistic effect of prebiotics, probiotics and antioxidants on dogs with chronic kidney disease

description: The use of probiotics, prebiotics and antioxidants could be found beneficial for dogs with chronic kidney disease (CKD). The aim of our case-control study is to evaluate the synergistic effect of a diet integrated with a supplement containing probiotics (<i>Lactobacillus acidophilus</i>), prebiotics (fructoligosaccharides) and antioxidants (<i>Olea Europaea</i> extract) on the nutritional status and on serum and urinary parameters of dogs with CKD. A total of 30 dogs classified with IRIS CKD stage 3 were enrolled and randomly assigned to a control (CG, <i>n</i> = 15) and a treated (TG <i>n</i> = 15) group. The trial consisted in a 7-days adaptation period, followed by 90 days where animals in the TR group received the supplement, while in the CG group the placebo. No significant changes in body weight and body condition score were recorded. We recorded a significant improvement of the protein plasmatic level and a decrease in blood phosphorus, systolic pressure, BUN, proteinuria and urine protein-to-creatinine ratio throughout the trial in the TG compared to the CG group. Furthermore, the parameters related to inflammation and oxidative stress (C-reactive protein and Reactive Oxygen Metabolite- derived compound, respectively) were lower in the TG than in the CG group throughout the study. Our results showed that the supplement allows to maintain the correct nutritional status and to improve blood and kidney parameters in dogs with advance stage of CKD. This supplement could be considered as a new nutritional approach for treating this condition.HIGHLIGHTSDiet supplemented with prebiotics, probiotics and antioxidants is safe for dogs with CKD.The synergic effect of prebiotics, probiotics and antioxidants included in the supplement under study shows the maintenance of a good nutritional status and the improvement of blood and urinary parameters in dogs with CKD. Diet supplemented with prebiotics, probiotics and antioxidants is safe for dogs with CKD. The synergic effect of prebiotics, probiotics and antioxidants included in the supplement under study shows the maintenance of a good nutritional status and the improvement of blood and urinary parameters in dogs with CKD.
DOI: 10.6084/m9.figshare.14686077
title: Characterisation of biological growth curves of different varieties of an endangered native hen breed kept under free range conditions

description: The aim of this study is to model the growth samples of four varieties (White, Black, Partridge, Franciscan) of Spanish Utrerana hen breed, which is endangered, by using Brody, Von Bertalanffy, Verhulst, Logistic and Gompertz models. For this purpose, a total of 16,235 weight data observations from 2004 animals reared in free range system were collected. Logistic was the best suited model for predicting the biological growth curve of White variety in both sexes, while Von Bertalanffy was the best fitting model for the rest of individuals of the breed, based on the 5 goodness-of-fit and flexibility criteria: Pseudo-<i>R</i><sup>2</sup>, mean squared error, Akaike information criterion, Bayesian information criterion and the biological coherence of the estimated parameters. Black variety was the heaviest, with values of 2605.96 and 2032.61 g (for males and females, respectively) for <i>a</i> parameter, while White variety presented the lowest maturity weight (<i>a</i> = 2442.99 and 1874.24 g, for males and females, respectively). Conclusively, this growth characterisation is essential for the conservation of the Utrerana hen, to search for new market niches and a greater profitability to this differentiated product.HighlightsNon-linear models can explain the Utrerana hen growth.Females reach maturity earlier than males.Utrerana hen shows a strong sexual dimorphism. Non-linear models can explain the Utrerana hen growth. Females reach maturity earlier than males. Utrerana hen shows a strong sexual dimorphism.
DOI: 10.6084/m9.figshare.14686077.v1
title: Characterisation of biological growth curves of different varieties of an endangered native hen breed kept under free range conditions

description: The aim of this study is to model the growth samples of four varieties (White, Black, Partridge, Franciscan) of Spanish Utrerana hen breed, which is endangered, by using Brody, Von Bertalanffy, Verhulst, Logistic and Gompertz models. For this purpose, a total of 16,235 weight data observations from 2004 animals reared in free range system were collected. Logistic was the best suited model for predicting the biological growth curve of White variety in both sexes, while Von Bertalanffy was the best fitting model for the rest of individuals of the breed, based on the 5 goodness-of-fit and flexibility criteria: Pseudo-<i>R</i><sup>2</sup>, mean squared error, Akaike information criterion, Bayesian information criterion and the biological coherence of the estimated parameters. Black variety was the heaviest, with values of 2605.96 and 2032.61 g (for males and females, respectively) for <i>a</i> parameter, while White variety presented the lowest maturity weight (<i>a</i> = 2442.99 and 1874.24 g, for males and females, respectively). Conclusively, this growth characterisation is essential for the conservation of the Utrerana hen, to search for new market niches and a greater profitability to this differentiated product.HighlightsNon-linear models can explain the Utrerana hen growth.Females reach maturity earlier than males.Utrerana hen shows a strong sexual dimorphism. Non-linear models can explain the Utrerana hen growth. Females reach maturity earlier than males. Utrerana hen shows a strong sexual dimorphism.
DOI: 10.6084/m9.figshare.15043244.v1
title: The synergistic effect of prebiotics, probiotics and antioxidants on dogs with chronic kidney disease

description: The use of probiotics, prebiotics and antioxidants could be found beneficial for dogs with chronic kidney disease (CKD). The aim of our case-control study is to evaluate the synergistic effect of a diet integrated with a supplement containing probiotics (<i>Lactobacillus acidophilus</i>), prebiotics (fructoligosaccharides) and antioxidants (<i>Olea Europaea</i> extract) on the nutritional status and on serum and urinary parameters of dogs with CKD. A total of 30 dogs classified with IRIS CKD stage 3 were enrolled and randomly assigned to a control (CG, <i>n</i> = 15) and a treated (TG <i>n</i> = 15) group. The trial consisted in a 7-days adaptation period, followed by 90 days where animals in the TR group received the supplement, while in the CG group the placebo. No significant changes in body weight and body condition score were recorded. We recorded a significant improvement of the protein plasmatic level and a decrease in blood phosphorus, systolic pressure, BUN, proteinuria and urine protein-to-creatinine ratio throughout the trial in the TG compared to the CG group. Furthermore, the parameters related to inflammation and oxidative stress (C-reactive protein and Reactive Oxygen Metabolite- derived compound, respectively) were lower in the TG than in the CG group throughout the study. Our results showed that the supplement allows to maintain the correct nutritional status and to improve blood and kidney parameters in dogs with advance stage of CKD. This supplement could be considered as a new nutritional approach for treating this condition.HIGHLIGHTSDiet supplemented with prebiotics, probiotics and antioxidants is safe for dogs with CKD.The synergic effect of prebiotics, probiotics and antioxidants included in the supplement under study shows the maintenance of a good nutritional status and the improvement of blood and urinary parameters in dogs with CKD. Diet supplemented with prebiotics, probiotics and antioxidants is safe for dogs with CKD. The synergic effect of prebiotics, probiotics and antioxidants included in the supplement under study shows the maintenance of a good nutritional status and the improvement of blood and urinary parameters in dogs with CKD.