cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5517/ccdc.csd.cc27lm5n
title: CCDC 2073471: Experimental Crystal Structure Determination

description: Related Article: Kai Yang, Shi-He Luo, Si-Hong Chen, Xi-Ying Cao, Yong-Jun Zhou, Yan-Lan Lin, Yan-Ping Huo, Zhao-Yang Wang|2021|Org.Biomol.Chem.|19|8133|doi:10.1039/D1OB01424B
DOI: 10.5517/ccdc.csd.cc27lm7q
title: CCDC 2073473: Experimental Crystal Structure Determination

description: Related Article: Kai Yang, Shi-He Luo, Si-Hong Chen, Xi-Ying Cao, Yong-Jun Zhou, Yan-Lan Lin, Yan-Ping Huo, Zhao-Yang Wang|2021|Org.Biomol.Chem.|19|8133|doi:10.1039/D1OB01424B
DOI: 10.5517/ccdc.csd.cc27lz1w
title: CCDC 2073808: Experimental Crystal Structure Determination

description: Related Article: Kai Yang, Shi-He Luo, Si-Hong Chen, Xi-Ying Cao, Yong-Jun Zhou, Yan-Lan Lin, Yan-Ping Huo, Zhao-Yang Wang|2021|Org.Biomol.Chem.|19|8133|doi:10.1039/D1OB01424B
DOI: 10.5517/ccdc.csd.cc27mx60
title: CCDC 2074712: Experimental Crystal Structure Determination

description: Related Article: Juzhang Yan, Xiurong Zheng, Yangqing Zheng, Ruoting Zhan, Huicai Huang|2021|Org.Biomol.Chem.|19|8102|doi:10.1039/D1OB01200B
DOI: 10.5517/ccdc.csd.cc27tg7s
title: CCDC 2080045: Experimental Crystal Structure Determination

description: Related Article: Biligma D. Tsyrenova, Victor N. Khrustalev, Valentine G. Nenajdenko|2021|Org.Biomol.Chem.|19|8140|doi:10.1039/D1OB01084K
DOI: 10.5517/ccdc.csd.cc27tg8t
title: CCDC 2080046: Experimental Crystal Structure Determination

description: Related Article: Biligma D. Tsyrenova, Victor N. Khrustalev, Valentine G. Nenajdenko|2021|Org.Biomol.Chem.|19|8140|doi:10.1039/D1OB01084K
DOI: 10.5517/ccdc.csd.cc27tg9v
title: CCDC 2080047: Experimental Crystal Structure Determination

description: Related Article: Biligma D. Tsyrenova, Victor N. Khrustalev, Valentine G. Nenajdenko|2021|Org.Biomol.Chem.|19|8140|doi:10.1039/D1OB01084K
DOI: 10.5517/ccdc.csd.cc2890m7
title: CCDC 2094038: Experimental Crystal Structure Determination

description: Related Article: Ling-Hui Lu, Guangchuan Ou, Xiongjie Zhao, Yufei Wang, Xuelian Chen, Wenjun Liao, Shundan Li, Chao Wu|2021|Org.Biomol.Chem.|19|8128|doi:10.1039/D1OB01287H
DOI: 10.6084/m9.figshare.13029039.v15
title: Genomic epidemiology of emerging ESBL-producing <i>Salmonella</i> Kentucky <i>bla</i> <sub>CTX-M-14b</sub> in Europe

description: Global dissemination of ciprofloxacin-resistant <i>Salmonella</i> Kentucky has been observed over the past decades. In recent years, there have been reports of extended-spectrum β-lactamase (ESBL) producing <i>S</i>. Kentucky. Routine surveillance at the European Centre for Disease Prevention and Control (ECDC) detected cases with a ciprofloxacin-resistant <i>S</i>. Kentucky with the ESBL-gene <i>bla</i> <sub>CTX-M-14b</sub>. Ensuing research identified 78 cases in 2013–2018 in eight European countries. Compared to other <i>S</i>. Kentucky and non-typhoidal <i>Salmonella</i> infections, reported to the European Surveillance System, these cases were more likely to be elderly and to present urinary-tract infections. Bayesian time-scaled phylogeny on whole genome sequences of isolates from these cases and supplementary isolates from public sequence databases was used to infer the origin and spread of this clone. We dated the origin of the <i>bla</i> <sub>CTX-M-14b</sub> clone to approximately 2005 in Northern Africa, most likely in Egypt. The geographic origin predicted by the phylogenetic analysis is consistent with the patients’ travel history. Next to multiple introductions of the clone to Europe from Egypt, our analysis suggests that in some parts of Europe the clone might have formed a stable population, from which further spread has occurred. Comparative genomics indicated that the <i>bla</i> <sub>CTX-M-14b</sub> gene is present on the bacterial chromosome, within the type VI secretion system region. The <i>bla</i> <sub>CTX-M-14b</sub> gene is integrated downstream of the <i>hcp1</i> gene, on a 2854 bp plasmid fragment containing also IS<i>Ecp1</i>. This is the first report of a chromosomally integrated CTX-M gene in <i>Salmonella</i> spp. in Europe, previous studies having identified similar genes only on plasmids.
DOI: 10.6084/m9.figshare.12853655.v1
title: The burden, admission, and outcome of COVID-19 in Africa: protocol for a systematic review and meta-analysis

description: <i>Background</i>: According to the World Health Organization (WHO), the outbreak of coronavirus disease in 2019 (COVID-19) has been declared as pandemic and public health emergency that infected more than 5 million people worldwide at the time of writing this protocol. Strong evidence for the burden, admission, and outcome of COVID-19 has not been published in Africa. Therefore, this protocol will be served as a guideline to conduct a systematic review and meta-analysis of the burden, admission, and outcome of COVID-19 in Africa. <i>Methods</i>: Published and unpublished studies on the burden, admission, and outcome of COVID-19 in Africa and written in any language will be included. Databases (PubMed / MEDLINE, Google Scholar, Google, EMBASE, Web of Science, Microsoft Academic, WHO COVID-19 database, Cochran Library, Africa Wide Knowledge, and Africa Index Medicus) from December 2019 to May 2020 will be searched. Two independent reviewers will select, screen, extract data, and assess the risk of bias. The proportion will be measured using a random-effects model. Subgroup analysis will be conducted to manage hetrogeinity. The presence of publication bias will be assessed using Egger's test and visual inspection of the funnel plots. This systematic and meta-analysis review protocol will be reported per the PRISMA-P guidelines. <i>Conclusion</i>: This systematic review and meta-analysis protocol will be expected to quantify the burden, admission, and outcome of COVID-19 in Africa. <i>Systematic review registration</i>: This protocol was submitted for registration with the International Prospective Register of Systematic Reviews (PROSPERO) in March 2020 and accepted with the registration number: CRD42020179321(https://www.crd.york.ac.uk/PROSPERO).
DOI: 10.6084/m9.figshare.11889867.v1
title: Trypsin promotes porcine deltacoronavirus mediating cell-to-cell fusion in a cell type-dependent manner

description: Porcine deltacoronavirus (PDCoV) is a newly emerging threat to the global porcine industry. PDCoV has been successfully isolated using various medium additives including trypsin, and although we know it is important for viral replication, the mechanism has not been fully elucidated. Here, we systematically investigated the role of trypsin in PDCoV replication including cell entry, cell-to-cell membrane fusion and virus release. Using pseudovirus entry assays, we demonstrated that PDCoV entry is not trypsin dependent. Furthermore, unlike porcine epidemic diarrhea virus (PEDV), in which trypsin is important for the release of virus from infected cells, PDCoV release was not affected by trypsin. We also demonstrated that trypsin promotes PDCoV replication by enhancing cell-to-cell membrane fusion. Most importantly, our study illustrates two distinct spreading patterns from infected cells to uninfected cells during PDCoV transmission, and the role of trypsin in PDCoV replication in cells with different virus spreading types. Overall, these results clarify that trypsin promotes PDCoV replication by mediating cell-to-cell fusion transmission but is not crucial for viral entry. This knowledge can potentially contribute to improvement of virus production efficiency in culture, not only for vaccine preparation but also to develop antiviral treatments.
DOI: 10.6084/m9.figshare.11993181.v2
title: Emerging COVID-19 coronavirus: glycan shield and structure prediction of spike glycoprotein and its interaction with human CD26

description: The recent outbreak of pneumonia-causing COVID-19 in China is an urgent global public health issue with an increase in mortality and morbidity. Here we report our modelled homo-trimer structure of COVID-19 spike glycoprotein in both closed (ligand-free) and open (ligand-bound) conformation, which is involved in host cell adhesion. We also predict the unique N- and O-linked glycosylation sites of spike glycoprotein that distinguish it from the SARS and underlines shielding and camouflage of COVID-19 from the host the defence system. Furthermore, our study also highlights the key finding that the S1 domain of COVID-19 spike glycoprotein potentially interacts with the human CD26, a key immunoregulatory factor for hijacking and virulence. These findings accentuate the unique features of COVID-19 and assist in the development of new therapeutics.
DOI: 10.6084/m9.figshare.13140206.v1
title: SARS-CoV-2 infection, disease and transmission in domestic cats

description: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is the cause of Coronavirus Disease 2019 (COVID-19) and responsible for the current pandemic. Recent SARS-CoV-2 susceptibility studies in cats show that the virus can replicate in these companion animals and transmit to other cats. Here, we present an in-depth study of SARS-CoV-2 infection, disease and transmission in domestic cats. Cats were challenged with SARS-CoV-2 via intranasal and oral routes. One day post challenge (DPC), two sentinel cats were introduced. Animals were monitored for clinical signs, clinicopathological abnormalities and viral shedding. <i>Postmortem</i> examinations were performed at 4, 7 and 21 DPC. Viral RNA was not detected in blood but transiently in nasal, oropharyngeal and rectal swabs and bronchoalveolar lavage fluid as well as various tissues. Tracheobronchoadenitis of submucosal glands with the presence of viral RNA and antigen was observed in airways of the infected cats. Serology showed that both, principals and sentinels, developed antibodies to SARS-CoV-2. All animals were clinically asymptomatic during the course of the study and capable of transmitting SARS-CoV-2 to sentinels. The results of this study are critical for understanding the clinical course of SARS-CoV-2 in a naturally susceptible host species, and for risk assessment.
DOI: 10.6084/m9.figshare.11835717.v1
title: What happens when we modify mosquitoes for disease prevention? A systematic review

description: The release of modified mosquitoes to suppress/replace vectors constitutes a promising tool for vector control and disease prevention. Evidence regarding these innovative modification techniques is scarce and disperse. This work conducted a systematic review, gathering and analysing research articles from PubMed and Biblioteca Virtual em Saúde databases whose results report efficacy and non-target effects of using modified insects for disease prevention, until 2016. More than 1500 publications were screened and 349 were analysed. Only 12/3.4% articles reported field-based evidence and 41/11.7% covered modification strategies’ post-release efficacy. Variability in the effective results (90/25.7%) questioned its reproducibility in different settings. We also found publications reporting reversal outcomes 38/10.9%, (e.g. post-release increase of vector population). Ecological effects were also reported, such as horizontal transfer events (54/15.5%), and worsening pathogenesis induced by natural <i>wolbachia</i> (10/2.9%). Present work revealed promising outcomes of modifying strategies. However, it also revealed a need for field-based evidence mainly regarding epidemiologic and long-term impact. It pointed out some eventual irreversible and important effects that must not be ignored when considering open-field releases, and that may constitute constraints to generate the missing field evidence. Present work constitutes a baseline of knowledge, offering also a methodological approach that may facilitate future updates.
DOI: 10.6084/m9.figshare.11533008.v2
title: Contribution of Fc-dependent cell-mediated activity of a vestigial esterase-targeting antibody against H5N6 virus infection

description: The highly pathogenic avian influenza A (H5N6) virus has caused sporadic human infections with a high case fatality rate. Due to the continuous evolution of this virus subtype and its ability to transmit to humans, there is an urgent need to develop effective antiviral therapeutics. In this study, a murine monoclonal antibody 9F4 was shown to display broad binding affinity against H5Nx viruses. Furthermore, 9F4 can neutralize H5N6 pseudotyped particles and prevent entry into host cells. Additionally, ADCC/ADCP deficient L234A, L235A (LALA) and CDC deficient K322A mutants were generated and displayed comparable binding affinity and neutralizing activity as wild type 9F4 (9F4-WT). Notably, 9F4-WT, 9F4-LALA and 9F4-K322A exhibit <i>in vivo</i> protective efficacies against H5N6 infections in that they were able to reduce viral loads in mice. However, only 9F4-WT and 9F4-K322A but not 9F4-LALA were able to reduce viral pathogenesis in H5N6 challenged mice. Furthermore, depletion of phagocytic cells in mice lungs nullifies 9F4-WT's protection against H5N6 infections, suggesting a crucial role of the host's immune cells in 9F4 antiviral activity. Collectively, these findings reveal the importance of ADCC/ADCP function for 9F4-WT protection against HPAIV H5N6 and demonstrate the potential of 9F4 to confer protection against the reassortant H5-subtype HPAIVs.
DOI: 10.6084/m9.figshare.11799054.v1
title: Identification of pyrvinium pamoate as an anti-tuberculosis agent <i>in vitro</i> and <i>in vivo</i> by SOSA approach amongst known drugs

description: Tuberculosis (TB), caused by <i>Mycobacterium tuberculosis</i> (<i>M.tb</i>) bacteria, is a leading infectious cause of mortality worldwide. The emergence of drug-resistant <i>M. tb</i> has made control of TB more difficult. The selective optimization of side activities (SOSA) approach uses old drugs for new pharmacological targets. In the present study by using SOSA approach, we have successfully identified pyrvinium pamoate (PP) which is capable of inhibiting the growth of mycobacteria, including <i>M. tb</i> H37Rv, <i>Mycobacterium smegmatis</i>, Bacille Calmette-Guérin (BCG), <i>M. tb</i> H37Ra, and drug-resistant <i>M. tb</i> clinical isolates <i>in vitro</i> from 1280 known drugs library. The MIC<sub>99</sub> of PP, the minimum inhibitory concentration that inhibits more than 99% of <i>M. tb</i> H37Rv and the drug-resistant <i>M. tb</i> clinical isolates, ranges from 1.55 to 4.8 µg/mL. Importantly, PP could reduce the bacterial colony-forming units (CFUs) in lung, spleen and liver tissues, and effectively inhibit inflammatory response in <i>M. tb</i> H37Rv, multidrug-resistant (MDR) <i>M. tb</i> and extensively drug-resistant (XDR) <i>M.tb</i>-infected mice. Our results clearly show that the PP has the potential application for treatment of TB.
DOI: 10.6084/m9.figshare.12853658.v1
title: Households as hotspots of Lassa fever? Assessing the spatial distribution of Lassa virus-infected rodents in rural villages of Guinea

description: The Natal multimammate mouse (<i>Mastomys natalensis</i>) is the reservoir host of Lassa virus (LASV), an arenavirus that causes Lassa haemorrhagic fever in humans in West Africa. While previous studies suggest that spillover risk is focal within rural villages due to the spatial behaviour of the rodents, the level of clustering was never specifically assessed. Nevertheless, detailed information on the spatial distribution of infected rodents would be highly valuable to optimize LASV-control campaigns, which are limited to rodent control or interrupting human–rodent contact considering that a human vaccine is not available. Here, we analysed data from a four-year field experiment to investigate whether LASV-infected rodents cluster in households in six rural villages in Guinea. Our analyses were based on the infection status (antibody or PCR) and geolocation of rodents (<i>n </i>=<i> </i>864), and complemented with a phylogenetic analysis of LASV sequences (<i>n </i>=<i> </i>119). We observed that the majority of infected rodents were trapped in a few houses (20%) and most houses were rodent-free at a specific point in time (60%). We also found that LASV strains circulating in a specific village were polyphyletic with respect to neighbouring villages, although most strains grouped together at the sub-village level and persisted over time. In conclusion, our results suggest that: (i) LASV spillover risk is heterogeneously distributed within villages in Guinea; (ii) viral elimination in one particular village is unlikely if rodents are not controlled in neighbouring villages. Such spatial information should be incorporated into eco-epidemiological models that assess the cost-efficiency of LASV control strategies.
DOI: 10.6084/m9.figshare.11902212.v1
title: Evidence that the second human pegivirus (HPgV-2) is primarily a lymphotropic virus and can replicate independent of HCV replication

description: The second human pegivirus HPgV-2 is a novel blood-borne virus that is strongly associated with the hepatitis C virus (HCV) infection. However, the molecular evidence for their association as well as the natural history and tissue tropism of HPgV-2 remain to be elucidated. In this longitudinal study, a total of 753 patients including 512 HIV-1 and HCV co-infected patients were enrolled to characterize the natural history of HPgV-2 infection. Peripheral blood mononuclear cells (PBMCs) and liver biopsies were collected to determine the tissue tropism of HPgV-2 using immunohistochemical staining of the HPgV-2 antigen and in situ hybridization of HPgV-2 RNA. We documented both persistent HPgV-2 infection with the presence of HPgV-2 viral RNA and antibodies up to 4.6 years and resolved HPgV-2 infection, accompanied by a simultaneous decline of anti-HPgV-2 antibodies and clearance of HPgV-2 viremia. Furthermore, we observed the clearance of HCV, but not HPgV-2, by treatment with direct-acting antivirals (DAAs). Biochemical tests and pathological analyses did not reveal any indication of hepatic impairment caused by HPgV-2. HPgV-2 RNA and nonstructural antigen were detected in the lymphocytes, but not in the hepatocytes present in the liver biopsy samples. In addition, both positive- and negative-strand HPgV-2 RNAs were detected in PBMCs, especially in B cells. The present study is the first to provide evidence that HPgV-2 is a lymphotropic, but not a hepatotropic virus and that HPgV-2 replication is independent of HCV viremia. These new findings let us gain insights into the evolution and persistent infection of RNA viruses in humans.
DOI: 10.6084/m9.figshare.12011181.v1
title: Tropism, pathology, and transmission of equine parvovirus-hepatitis

description: Equine parvovirus-hepatitis (EqPV-H) has recently been associated with cases of Theiler's disease, a form of fulminant hepatic necrosis in horses. To assess whether EqPV-H is the cause of Theiler's disease, we first demonstrated hepatotropism by PCR on tissues from acutely infected horses. We then experimentally inoculated horses with EqPV-H and 8 of 10 horses developed hepatitis. One horse showed clinical signs of liver failure. The onset of hepatitis was temporally associated with seroconversion and a decline in viremia. Liver histology and <i>in situ</i> hybridization showed lymphocytic infiltrates and necrotic EqPV-H-infected hepatocytes. We next investigated potential modes of transmission. Iatrogenic transmission via allogeneic stem cell therapy for orthopedic injuries was previously suggested in a case series of Theiler's disease, and was demonstrated here for the first time. Vertical transmission and mechanical vectoring by horse fly bites could not be demonstrated in this study, potentially due to limited sample size. We found EqPV-H shedding in oral and nasal secretions, and in feces. Importantly, we could demonstrate EqPV-H transmission via oral inoculation with viremic serum. Together, our findings provide additional information that EqPV-H is the likely cause of Theiler's disease and that transmission of EqPV-H occurs via both iatrogenic and natural routes.
DOI: 10.6084/m9.figshare.12601348.v3
title: Biologically-based modeling of radiation risk and biomarker prevalence for papillary thyroid cancer in Japanese a-bomb survivors 1958–2005

description: Thyroid cancer of papillary histology (PTC) is the dominant type in radio-epidemiological cohorts established after nuclear accidents or warfare. Studies on post-Chernobyl PTC and on thyroid cancer in the life span study (LSS) of Japanese a-bomb survivors consistently revealed high radiation risk after exposure during childhood and adolescence. For post-Chernobyl risk assessment overexpression of the CLIP2 gene was proposed as molecular biomarker to separate radiogenic from sporadic PTC. Based on such binary marker a biologically-based risk model of PTC carcinogenesis has been developed for observational Chernobyl data. The model featured two independent molecular pathways of disease development, of which one was associated with radiation exposure. To gain credibility the concept for a mechanistic risk model must be based on general biological features which transcend findings in a single cohort. The purpose of the present study is therefore to demonstrate portability of the model concept by application to PTC incidence data in the LSS. By exploiting the molecular two-path concept we improve the determination of the probability of radiation causing cancer (POC). The current analysis uses thyroid cancer incidence data of the LSS with thyroid cancer diagnoses and papillary histology (<i>n</i> = 292) from the follow-up period between 1958 and 2005. Risk analysis was performed with both descriptive and biologically-based models. Judged by goodness-of-fit all applied models described the data almost equally well. They yielded similar risk estimates in cohorts post-Chernobyl and LSS. The preferred mechanistic model was selected by biological plausibility. It reflected important features of an imperfect radiation marker which are not easily addressed by descriptive models. Precise model predictions of marker prevalence in strata of epidemiological covariables can be tested by molecular measurements. Application of the radiation-related molecular pathway from our preferred model in retrospective risk assessment decreases the threshold dose for 50% POC from 0.33 (95% confidence interval (CI) 0.18; 0.64) Gy to 0.04 (95% CI 0.01; 0.19) Gy for females and from 0.43 (95% CI 0.17; 1.84) Gy to 0.19 (95% CI 0.05; 1.00) Gy for males. These improvements are still not sufficient to separate radiation-induced from sporadic PTC cases at very low doses &lt;0.015 Gy typical for the Fukushima accident. Successful application of our preferred mechanistic model to LSS incidence data confirms and improves the biological two-path concept of radiation-induced PTC. Model predictions suggest further molecular validation studies to consolidate the basis of biologically-based risk estimation.