cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.29499282.v2
title: Impact of virus-mediated bacterial interactions on acute gastroenteritis symptoms: A new scoring system for clinical assessment

description: Acute gastroenteritis (AGE) exerts a substantial healthcare burden and economic loss annually, mainly due to viral infections. The objective of the study was to elucidate the impact of the interactions between the AGE virus and gut microbiota on patient clinical symptoms, thereby facilitating the early diagnosis and treatment of AGE. Clinical information and fecal samples were collected from 289 AGE patients (exclude fungal, parasitic, and bacterial infections), of whom 23.5% were infected with AGE viruses. A scoring method was developed to assess the severity of virus-induced AGE in patients. The results indicate significant differences (<i>p</i> &lt; 0.05 indicates a significant difference, as determined by Kruskal–Wallis test, <i>p</i> = 0.03) in clinical symptom scores among the None-virus, Single-virus, and Dual-virus group. The Single-virus (14.82) and Dual-virus (15.33) groups exhibited more severe clinical symptom, with scoring values higher than None-virus group (12.40). Although significant differences in microbial community composition were observed between the Single-virus and Dual-virus groups (as determined by Adonis analysis, Variation = 0.11, <i>p</i> = 0.034), the diversity index (e.g. Chao1) did not significantly differ among the None-virus (288.14), Single-virus (345.74), and Dual-virus (282.70) groups. Notably, the patients with a higher <i>Prevotella</i>/<i>Bacteroide</i>s index displayed more severe clinical symptom, as the index in the Single-virus and Dual-virus groups was over 10-times greater than in the None-virus group. In summary, this study shows that clinical symptoms of patients with viral AGE could be exacerbated through promoting bacterial competitions, and this understanding would facilitate the early diagnosis and treatment of viral AGE.
DOI: 10.6084/m9.figshare.27610104
title: <b>Cuttlefish camouflage under extreme flooding events</b>

description: Extreme events are becoming increasingly frequent and intense, leading to cascading negative effects on marine ecosystems. Here, we aimed to investigate the impact of ecologically relevant extreme flooding conditions (exposure to acute salinity values of 17 and 7) and non-extreme conditions (salinity values of 35, 28, and 24), during 4 days at late embryogenesis, on the survival and camouflage abilities of the European cuttlefish (<i>Sepia officinalis</i>) hatchlings.
DOI: 10.6084/m9.figshare.28142540
title: The highly pathogenic strain of porcine deltacoronavirus disrupts the intestinal barrier and causes diarrhea in newborn piglets

description: Porcine deltacoronavirus (PDCoV) is increasingly prevalent in newborn piglets with diarrhea. With the development of research on the virus and the feasibility of PDCoV cross-species transmission, the biosafety and the development of pig industry have been greatly affected. In this study, a PDCoV strain CH/LNFX/2022 was isolated from diarrheal newborn piglets at a farm in China. A genome-wide based phylogenetic analysis suggests that 97.5% to 99.2% homology existed in the whole genomes of other strains. Five amino acid mutations are seen for the first time in the S protein. By constructing 3D models, it was found that the S1-NTD/CTD and S2-HR-C regions produced structural alterations. Protein functional analysis showed that the structural changes of the three regions changed the epitope of S protein, the O-GalNAc glycosylation site and the 3C-like protease cleavage site. In addition, oral administration of 10<sup>7</sup> TCID<sub>50</sub> CH/LNFX/2022 to newborn piglets successfully reproduced obvious clinical signs of piglets, such as diarrhea and dehydration. Meanwhile, PDCoV antigen was detected by immunofluorescence in the small intestine, and microscopic lesions and intestinal mucosal barrier destruction were detected by histological observation and scanning electron microscopy. Our study confirmed that porcine coronavirus strains increased pathogenicity through evolution, damaged the intestinal barrier of newborn piglets, and caused diarrhea in pigs. This study provided the candidate strains and theoretical basis for establishing the prevention and control system of vaccine and diagnostic methods for piglet diarrhea.
DOI: 10.6084/m9.figshare.28142540.v1
title: The highly pathogenic strain of porcine deltacoronavirus disrupts the intestinal barrier and causes diarrhea in newborn piglets

description: Porcine deltacoronavirus (PDCoV) is increasingly prevalent in newborn piglets with diarrhea. With the development of research on the virus and the feasibility of PDCoV cross-species transmission, the biosafety and the development of pig industry have been greatly affected. In this study, a PDCoV strain CH/LNFX/2022 was isolated from diarrheal newborn piglets at a farm in China. A genome-wide based phylogenetic analysis suggests that 97.5% to 99.2% homology existed in the whole genomes of other strains. Five amino acid mutations are seen for the first time in the S protein. By constructing 3D models, it was found that the S1-NTD/CTD and S2-HR-C regions produced structural alterations. Protein functional analysis showed that the structural changes of the three regions changed the epitope of S protein, the O-GalNAc glycosylation site and the 3C-like protease cleavage site. In addition, oral administration of 10<sup>7</sup> TCID<sub>50</sub> CH/LNFX/2022 to newborn piglets successfully reproduced obvious clinical signs of piglets, such as diarrhea and dehydration. Meanwhile, PDCoV antigen was detected by immunofluorescence in the small intestine, and microscopic lesions and intestinal mucosal barrier destruction were detected by histological observation and scanning electron microscopy. Our study confirmed that porcine coronavirus strains increased pathogenicity through evolution, damaged the intestinal barrier of newborn piglets, and caused diarrhea in pigs. This study provided the candidate strains and theoretical basis for establishing the prevention and control system of vaccine and diagnostic methods for piglet diarrhea.
DOI: 10.6084/m9.figshare.28955586
title: Circulation characteristics of bat coronaviruses linked to bat ecological factors in Korea, 2021–2022

description: Considering that bat ecology alterations may be linked with pathogen spillover, research on bat coronaviruses, particularly on the infection and transmission pattern among bats in relation with their ecology, is essential. We captured bats distributed in Korea from 2021 to 2022, examined coronaviruses in oral swabs, feces, urine, and ectoparasites, and were able to detect alphacoronavirus. We investigated coronaviruses, but noted no substantial differences in the body condition index in the coronavirus-positive bats. Binary logistic regression analysis revealed that bat ecological factors that were significantly associated with coronavirus-positive were roost type, sample type, and bat species. Coronavirus-positive ectoparasite cases suggested additional study on the potential role of them as the viral transmission vectors or fomites. Reinfection of a different coronavirus in recaptured bats was evident, suggesting the possibility that coronavirus circulation can evade the potential protective immunity acquired from previous coronavirus infections. The present findings provide comprehensive information on the coronaviruses transmission dynamics within bat populations linked with bat ecology.
DOI: 10.6084/m9.figshare.28955586.v2
title: Circulation characteristics of bat coronaviruses linked to bat ecological factors in Korea, 2021–2022

description: Considering that bat ecology alterations may be linked with pathogen spillover, research on bat coronaviruses, particularly on the infection and transmission pattern among bats in relation with their ecology, is essential. We captured bats distributed in Korea from 2021 to 2022, examined coronaviruses in oral swabs, feces, urine, and ectoparasites, and were able to detect alphacoronavirus. We investigated coronaviruses, but noted no substantial differences in the body condition index in the coronavirus-positive bats. Binary logistic regression analysis revealed that bat ecological factors that were significantly associated with coronavirus-positive were roost type, sample type, and bat species. Coronavirus-positive ectoparasite cases suggested additional study on the potential role of them as the viral transmission vectors or fomites. Reinfection of a different coronavirus in recaptured bats was evident, suggesting the possibility that coronavirus circulation can evade the potential protective immunity acquired from previous coronavirus infections. The present findings provide comprehensive information on the coronaviruses transmission dynamics within bat populations linked with bat ecology.
DOI: 10.6084/m9.figshare.29499282.v1
title: Impact of virus-mediated bacterial interactions on acute gastroenteritis symptoms: A New scoring system for clinical assessment

description: Acute gastroenteritis (AGE) exerts a substantial healthcare burden and economic loss annually, mainly due to viral infections. The objective of the study was to elucidate the impact of the interactions between the AGE virus and gut microbiota on patient clinical symptoms, thereby facilitating the early diagnosis and treatment of AGE. Clinical information and faecal samples were collected from 289 AGE patients (exclude fungal, parasitic and bacterial infections), of whom 23.5% were infected with AGE viruses. A scoring method was developed to assess the severity of virus-induced AGE in patients. The results indicate significant differences (<i>p</i> &lt; 0.05indicates a significant difference, as determined by Kruskal-Wallis test, <i>p</i> = 0.03) in clinical symptom scores among the None-virus, Single-virus and Dual-virus group. The Single-virus (14.82) and Dual-virus (15.33) groups exhibited more severe clinical symptom, with scoring values higher than None-virus group (12.40). Although significant differences in microbial community composition were observed between the Single-virus and Dual-virus groups (as determined by Adonis analysis, Variation = 0.11, <i>p</i> = 0.034), the diversity index (e.g. Chao1) did not significantly differ among the None-virus (288.14), Single-virus (345.74), and Dual-virus (282.70) groups. Notably, the patients with a higher <i>Prevotella</i>/<i>Bacteroide</i>s index displayed more severe clinical symptom, as the index in the Single-virus and Dual-virus groups were over 10-times greater than in the None-virus group. In summary, this study shows that clinical symptoms of patients with viral AGE could be exacerbated through promoting bacterial competitions, and this understanding would facilitate the early diagnosis and treatment of viral AGE.
DOI: 10.6084/m9.figshare.27610104.v10
title: <b>Cuttlefish camouflage under extreme flooding events</b>

description: Extreme events are becoming increasingly frequent and intense, leading to cascading negative effects on marine ecosystems. Here, we aimed to investigate the impact of ecologically relevant extreme flooding conditions (exposure to acute salinity values of 17 and 7) and non-extreme conditions (salinity values of 35, 28, and 24), during 4 days at late embryogenesis, on the survival and camouflage abilities of the European cuttlefish (<i>Sepia officinalis</i>) hatchlings.
DOI: 10.6084/m9.figshare.27610104.v11
title: <b>Cuttlefish camouflage under extreme flooding events</b>

description: Extreme events are becoming increasingly frequent and intense, leading to cascading negative effects on marine ecosystems. Here, we aimed to investigate the impact of ecologically relevant extreme flooding conditions (exposure to acute salinity values of 17 and 7) and non-extreme conditions (salinity values of 35, 28, and 24), during 4 days at late embryogenesis, on the survival and camouflage abilities of the European cuttlefish (<i>Sepia officinalis</i>) hatchlings.
DOI: 10.6084/m9.figshare.28955586.v1
title: Circulation characteristics of bat coronaviruses linked to bat ecological factors in Korea, 2021-2022.

description: Considering that bat ecology alterations may be linked with pathogen spillover, research on bat coronaviruses, particularly on the infection and transmission pattern among bats in relation with their ecology, is essential. We captured bats distributed in Korea from 2021 to 2022, examined coronaviruses in oral swabs, faeces, urine, and ectoparasites, and were able to detect alphacoronavirus. We investigated coronaviruses, but noted no substantial differences in the body condition index in the coronavirus-positive bats. Binary logistic regression analysis revealed that bat ecological factors that were significantly associated with coronavirus-positive were roost type, sample type, and bat species. Coronavirus-positive ectoparasite cases suggested additional study on the potential role of them as the viral transmission vectors or fomites. Reinfection of a different coronavirus in recaptured bats was evident, suggesting the possibility that coronavirus circulation can evade the potential protective immunity acquired from previous coronavirus infections. The present findings provide comprehensive information on the coronaviruses transmission dynamics within bat populations linked with bat ecology.
DOI: 10.6084/m9.figshare.29086186
title: Novel prognostic scoring models for hepatitis B virus-related acute-on-chronic liver failure: A comparison with classical models

description: Early diagnosis and accurate prognostic evaluation are important for guiding clinical treatment and reducing mortality in patients with hepatitis B virus (HBV)-related acute-on-chronic liver failure (ACLF). The present study established novel prognostic scoring models to guide the clinical treatment of patients with HBV-ACLF. We performed a retrospective analysis of clinical data from two cohorts of patients diagnosed with HBV-ACLF. By comparing differences in baseline characteristics and clinical indicators between the survival (<i>n</i> = 102) and dead (<i>n</i> = 64) groups in the derivation cohort(<i>n</i> = 166), four laboratory indicators (age, INR, TBIL, and HBeAg status) and three clinical signs (extrahepatic infection, ascites, and hepatic encephalopathy) were identified as independent risk factors. Logistic regression and nomogram models were used to construct three novel predictive models. By comparing the death and survival groups, we found that the three new models had higher predictions for AUROC (average of 0.856) than the three old models (average of 0.773). Model 1 had the strongest predictive power for the short-term survival rate of HBV-ACLF patients. Finally, we verified the predictive value of the new models for HBV-ACLF in a validation cohort (<i>n</i> = 42), and the Model 2 demonstrated good predictive accuracy for the 30-day survival rate of patients. The novel model based on seven predictors could accurately predict short-term mortality in patients with HBV-ACLF, which is promising for guiding clinical management and addressing the aetiological differences in Asian populations.
DOI: 10.6084/m9.figshare.29086186.v1
title: Novel prognostic scoring models for hepatitis B virus-related acute-on-chronic liver failure: A comparison with classical models

description: Early diagnosis and accurate prognostic evaluation are important for guiding clinical treatment and reducing mortality in patients with hepatitis B virus (HBV)-related acute-on-chronic liver failure (ACLF). The present study established novel prognostic scoring models to guide the clinical treatment of patients with HBV-ACLF. We performed a retrospective analysis of clinical data from two cohorts of patients diagnosed with HBV-ACLF. By comparing differences in baseline characteristics and clinical indicators between the survival (<i>n</i> = 102) and dead (<i>n</i> = 64) groups in the derivation cohort(<i>n</i> = 166), four laboratory indicators (age, INR, TBIL, and HBeAg status) and three clinical signs (extrahepatic infection, ascites, and hepatic encephalopathy) were identified as independent risk factors. Logistic regression and nomogram models were used to construct three novel predictive models. By comparing the death and survival groups, we found that the three new models had higher predictions for AUROC (average of 0.856) than the three old models (average of 0.773). Model 1 had the strongest predictive power for the short-term survival rate of HBV-ACLF patients. Finally, we verified the predictive value of the new models for HBV-ACLF in a validation cohort (<i>n</i> = 42), and the Model 2 demonstrated good predictive accuracy for the 30-day survival rate of patients. The novel model based on seven predictors could accurately predict short-term mortality in patients with HBV-ACLF, which is promising for guiding clinical management and addressing the aetiological differences in Asian populations.
DOI: 10.6084/m9.figshare.29826307
title: The stress of carrying CRISPR-Cas

description: <i>Streptococcus anginosus</i> (<i>S. anginosus</i>) is a commensal that can cause severe invasive bacterial infections. A considerable percentage of <i>S. anginosus</i> strains harbour CRISPR-Cas systems, which apart from being a bacterial immunity system, can play an important role in adaptation to environmental stress. The functionality of <i>S. anginosus</i> CRISPR-Cas systems has not been investigated previously. To address this, we created a set of deletion mutants in the CRISPR-Cas type II-A system of the <i>S. anginosus</i> SK52 type strain, targeting the nuclease Cas9 and CRISPR array. We were able to confirm CRISPR-Cas activity by testing these strains in a plasmid clearance assay. Furthermore, the impact of the CRISPR-Cas system on the viability of <i>S. anginosus</i> was investigated under various stress conditions, such as UV light, hydrogen peroxide exposure, and high temperatures in wild-type <i>S. anginosus</i> and CRISPR-Cas mutant strains. Under these conditions, survival was significantly lower in the strains carrying <i>cas9</i>. Bacterial growth and metabolic activity in Alamar Blue assays were also negatively affected by the presence of <i>cas9</i> in <i>S. anginosus</i>. In summary, we found that the presence of a functional CRISPR-Cas system in <i>S. anginosus</i> leads to measurable metabolic and fitness costs in the wild-type strain. Carrying <i>cas9</i> was associated with an impaired stress response in our experiments and may explain why many strains of this species lack CRISPR-Cas.
DOI: 10.6084/m9.figshare.29826307.v1
title: The stress of carrying CRISPR-Cas

description: <i>Streptococcus anginosus</i> (<i>S. anginosus</i>) is a commensal that can cause severe invasive bacterial infections. A considerable percentage of <i>S. anginosus</i> strains harbour CRISPR-Cas systems, which apart from being a bacterial immunity system, can play an important role in adaptation to environmental stress. The functionality of <i>S. anginosus</i> CRISPR-Cas systems has not been investigated previously. To address this, we created a set of deletion mutants in the CRISPR-Cas type II-A system of the <i>S. anginosus</i> SK52 type strain, targeting the nuclease Cas9 and CRISPR array. We were able to confirm CRISPR-Cas activity by testing these strains in a plasmid clearance assay. Furthermore, the impact of the CRISPR-Cas system on the viability of <i>S. anginosus</i> was investigated under various stress conditions, such as UV light, hydrogen peroxide exposure, and high temperatures in wild-type <i>S. anginosus</i> and CRISPR-Cas mutant strains. Under these conditions, survival was significantly lower in the strains carrying <i>cas9</i>. Bacterial growth and metabolic activity in Alamar Blue assays were also negatively affected by the presence of <i>cas9</i> in <i>S. anginosus</i>. In summary, we found that the presence of a functional CRISPR-Cas system in <i>S. anginosus</i> leads to measurable metabolic and fitness costs in the wild-type strain. Carrying <i>cas9</i> was associated with an impaired stress response in our experiments and may explain why many strains of this species lack CRISPR-Cas.
DOI: 10.6084/m9.figshare.29327547
title: Predicting the evolutionary and epidemiological dynamics of SARS-CoV-2 in South Africa

description: Since the outbreak of coronavirus disease 2019 (COVID-19), the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continuously mutated and evolved, causing several waves of infection. Predicting the evolutionary and epidemiological dynamics of SARS-CoV-2 remains a challenge. This study combines the epidemic data of different variants of SARS-CoV-2 in South Africa to predict their evolutionary and epidemiological dynamics. Based on the susceptible-infectious-recovered-susceptible (SIRS) transmission dynamics, we consider the transmission rate as an evolutionary trait and the disease-deduced mortality and recovery rates as trade-off functions of the trait. Using the adaptive dynamics method, combined with the epidemic data of the five most recent variants in South Africa, we find that South Africa will be continuously invaded and infected by the new mutant strain with a higher transmission rate. In addition, we find that changing the recovery rate by enhancing treatment, for example, will alter the trade-off function and thereby affect the evolutionary dynamics of SARS-CoV-2, which may evolve into a continuously stable strategy. This study is the first to use evolutionary dynamics theory to predict the future evolutionary and epidemiological dynamics of SARS-CoV-2, which is helpful for the government to predict the epidemic dynamics of COVID-19 and to take effective measures in advance, and it is proposed that advancing treatment time and improving treatment efficiency will contribute to disease control.
DOI: 10.6084/m9.figshare.29327547.v1
title: Predicting the evolutionary and epidemiological dynamics of SARS-CoV-2 in South Africa

description: Since the outbreak of coronavirus disease 2019 (COVID-19), the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continuously mutated and evolved, causing several waves of infection. Predicting the evolutionary and epidemiological dynamics of SARS-CoV-2 remains a challenge. This study combines the epidemic data of different variants of SARS-CoV-2 in South Africa to predict their evolutionary and epidemiological dynamics. Based on the susceptible-infectious-recovered-susceptible (SIRS) transmission dynamics, we consider the transmission rate as an evolutionary trait and the disease-deduced mortality and recovery rates as trade-off functions of the trait. Using the adaptive dynamics method, combined with the epidemic data of the five most recent variants in South Africa, we find that South Africa will be continuously invaded and infected by the new mutant strain with a higher transmission rate. In addition, we find that changing the recovery rate by enhancing treatment, for example, will alter the trade-off function and thereby affect the evolutionary dynamics of SARS-CoV-2, which may evolve into a continuously stable strategy. This study is the first to use evolutionary dynamics theory to predict the future evolutionary and epidemiological dynamics of SARS-CoV-2, which is helpful for the government to predict the epidemic dynamics of COVID-19 and to take effective measures in advance, and it is proposed that advancing treatment time and improving treatment efficiency will contribute to disease control.