Puumala Hantavirus Excretion Kinetics in Bank Voles (Myodes glareolus)

One-sentence summary for table of contents: Virus may be transmitted by saliva, urine, and feces, and saliva may play a role in transmission to humans

Mortality Rate Patterns for Hemorrhagic Fever with Renal Syndrome Caused by Puumala Virus

To investigate nephropathia epidemica in Sweden during 1997–2007, we determined case-fatality rates for 5,282 patients with this disease. Overall, 0.4% died of acute nephropathia epidemica <3 months after diagnosis. Case-fatality rates increased with age. Only women showed an increased case-fatality rate during the first year after diagnosis

Data integration and handling

Modern technology allows researchers to generate data at an ever increasing rate, outpacing the capacity of researchers to analyse it. Developing automated support systems for the collection, management and distribution of information is therefore an important step to reduce error rates and accelerate progress to enable high-quality research based on big data volumes. This thesis encompasses five articles, describing strategies for the creation of technical research platforms, as well as descriptions of the technical platforms themselves. The key conclusion of the thesis is that technical solutions for many issues have been available for a long time. These technical solutions are however overlooked, or simply ignored, if they fail to recognise the social dimensions of the issues they try to solve. The Molecular Methods database is an example of a technically sound but only partially successful solution in regards to social viability. Thousands of researchers have used the website to access protocols, but only a handful have shared their own work on MolMeth. Experiences from the Molecular Methods database and other projects have provided a foundation for studies supporting the development of the eB3Kit The eB3Kit is a portable, robust and scalable informatics platform for structured data management. Deploying the platform enables research groups to carry out advanced research projects with very limited means. With the eB3Kit researchers can integrate data from a wide variety of sources, including the local laboratory information management system and analyse it using the Galaksio interface. Galaksio provides user friendly access to the Galaxy workflow management system and provides eB3Kit users with access to tools developed by a far larger user community than the one actively developing the eB3Kit. Using a workflow management system improves reproducibility and enables bioinformaticians to prepare workflows without directly accessing ethically or commercially sensitive data. Therefore, it is especially well- suited for applications where researchers are worried about privacy and during disease outbreaks where persistent storage and analysis capacity must be established quickly

A Model System for In Vitro Studies of Bank Vole Borne Viruses

The bank vole (Myodes glareolus) is a common small mammal in Europe and a natural host for several important emerging zoonotic viruses, e.g. Puumala hantavirus (PUUV) that causes hemorrhagic fever with renal syndrome (HFRS). Hantaviruses are known to interfere with several signaling pathways in infected human cells, and HFRS is considered an immune-mediated disease. There is no in vitro-model available for infectious experiments in bank vole cells, nor tools for analyses of bank vole immune activation and responses. Consequently, it is not known if there are any differences in the regulation of virus induced responses in humans compared to natural hosts during infection. We here present an in vitro-model for studies of bank vole borne viruses and their interactions with natural host cell innate immune responses. Bank vole embryonic fibroblasts (VEFs) were isolated and shown to be susceptible for PUUV-infection, including a wild-type PUUV strain (only passaged in bank voles). The significance of VEFs as a model system for bank vole associated viruses was further established by infection studies showing that these cells are also susceptible to tick borne encephalitis, cowpox and Ljungan virus. The genes encoding bank vole IFN-β and Mx2 were partially sequenced and protocols for semi-quantitative RT-PCR were developed. Interestingly, PUUV did not induce an increased IFN-β or Mx2 mRNA expression. Corresponding infections with CPXV and LV induced IFN-β but not Mx2, while TBEV induced both IFN-β and Mx2

EXACT2: the semantics of biomedical protocols

© 2014 Soldatova et al.; licensee BioMed Central. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.This article has been made available through the Brunel Open Access Publishing Fund.Background: The reliability and reproducibility of experimental procedures is a cornerstone of scientific practice. There is a pressing technological need for the better representation of biomedical protocols to enable other agents (human or machine) to better reproduce results. A framework that ensures that all information required for the replication of experimental protocols is essential to achieve reproducibility. Methods: We have developed the ontology EXACT2 (EXperimental ACTions) that is designed to capture the full semantics of biomedical protocols required for their reproducibility. To construct EXACT2 we manually inspected hundreds of published and commercial biomedical protocols from several areas of biomedicine. After establishing a clear pattern for extracting the required information we utilized text-mining tools to translate the protocols into a machine amenable format. We have verified the utility of EXACT2 through the successful processing of previously ‘unseen’ (not used for the construction of EXACT2) protocols. Results: The paper reports on a fundamentally new version EXACT2 that supports the semantically-defined representation of biomedical protocols. The ability of EXACT2 to capture the semantics of biomedical procedures was verified through a text mining use case. In this EXACT2 is used as a reference model for text mining tools to identify terms pertinent to experimental actions, and their properties, in biomedical protocols expressed in natural language. An EXACT2-based framework for the translation of biomedical protocols to a machine amenable format is proposed. Conclusions: The EXACT2 ontology is sufficient to record, in a machine processable form, the essential information about biomedical protocols. EXACT2 defines explicit semantics of experimental actions, and can be used by various computer applications. It can serve as a reference model for for the translation of biomedical protocols in natural language into a semantically-defined format.This work has been partially funded by the Brunel University BRIEF award and a grant from Occams Resources

Strengthening the interaction of the virology community with the International Committee on Taxonomy of Viruses (ICTV) by linking virus names and their abbreviations to virus species

The International Committee on Taxonomy of Viruses (ICTV) is tasked with classifying viruses into taxa (phyla to species) and devising taxon names. Virus names and virus name abbreviations are currently not within the ICTV’s official remit and are not regulated by an official entity. Many scientists, medical/veterinary professionals, and regulatory agencies do not address evolutionary questions nor are they concerned with the hierarchical organization of the viral world, and therefore, have limited use for ICTV-devised taxa. Instead, these professionals look to the ICTV as an expert point source that provides the most current taxonomic affiliations of viruses of interests to facilitate document writing. These needs are currently unmet as an ICTV-supported, easily searchable database that includes all published virus names and abbreviations linked to their taxa is not available. In addition, in stark contrast to other biological taxonomic frameworks, virus taxonomy currently permits individual species to have several members. Consequently, confusion emerges among those who are not aware of the difference between taxa and viruses, and because certain well-known viruses cannot be located in ICTV publications or be linked to their species. In addition, the number of duplicate names and abbreviations has increased dramatically in the literature. To solve this conundrum, the ICTV could mandate listing all viruses of established species and all reported unclassified viruses in forthcoming online ICTV Reports and create a searchable webpage using this information. The International Union of Microbiology Societies could also consider changing the mandate of the ICTV to include the nomenclature of all viruses in addition to taxon considerations. With such a mandate expansion, official virus names and virus name abbreviations could be catalogued and virus nomenclature could be standardized. As a result, the ICTV would become an even more useful resource for all stakeholders in virology

Pathology of Puumala hantavirus infection in macaques

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