A review of The Publishing Trap as a training tool for researchers, doctoral students and academics

This article explores the potential of using an educational board game as a fun and stimulating learning resource to support researchers and academics in Higher Education. The Publishing Trap was developed by Chris Morrison and Jane Secker (@UKCopyrightLit) to highlight the impact of publishing and scholarly communication choices that researchers make throughout their career. After trialling the game with Library staff at Leeds Beckett University, Rachel Thornton summarises the experience and participants’ feedback, and considers the game’s usefulness as a training tool

Running a successful network to support methodologists and guideline developers: sharing experiences from UK evidence synthesis networks

Running a successful network to support methodologists and guideline developers: sharing experiences from UK evidence synthesis networks Facilitators: Judith Thornton (NICE); Ruaraidh Hill (University of Liverpool), Emma McFarlane (NICE), Li Chia Chen (University of Manchester) BACKGROUND AND INTRODUCTION We established the ‘North West Evidence Synthesis Network’ (NWESN) to bring together guideline developers, health researchers and policy makers from across our region in order to share knowledge and expertise and raise awareness of methodological developments. Several other UK networks have been initiated including the ‘Liverpool Evidence Synthesis Network’ (LivEN). Feedback from members has been positive with both personal and institutional benefits. Other networks include: • Health Research Methodology and Implementation (HeRMI) • Bangor Evidence Synthesis Hub (BESH) • Peninsula Systematic Review discussion group (PenSR) OBJECTIVES • To advocate the role of networks • To discuss the practicalities to establishing/running networks • To explore what guideline developers needs from networks DESCRIPTION OF THE WORKSHOP Short presentations to compare and contrast the remit, structure and function of different networks. Group discussions to explore: • What guideline developers want from networks • Challenges to establishing/running networks and strategies to overcome these. • Future directions for networking • How networks can be better connected Group feedback and conclusions TARGET GROUPS All staff involved in evidence synthesis and guideline development. IMPLICATIONS FOR GUIDELINE DEVELOPERS Our presentation at the Global Evidence Summit 2017 demonstrated the benefits of membership of the NWESN. Implications for guideline developers included general education and updating on new methods; a key benefit is the opportunity to share skills, information and support across researchers and institutions. CONCLUSIONS The workshop intends to raise awareness of the benefits of networks and what they can offer methodologists and guideline developers. We hope to encourage more people to connect with and establish methodological networks

VarSite: disease variants and protein structure

VarSite is a web server mapping known disease-associated variants from UniProt and ClinVar, together with natural variants from gnomAD, onto protein 3D structures in the Protein Data Bank (PDB). The analyses are primarily image-based and provide both an overview for each human protein, as well as a report for any specific variant of interest. The information can be useful in assessing whether a given variant might be pathogenic or benign. The structural annotations for each position in the protein include protein secondary structure, interactions with ligand, metal, DNA/RNA, or other protein, and various measures of a given variant's possible impact on the protein's function. The 3D locations of the disease-associated variants can be viewed interactively via the 3dmol.js JavaScript viewer, as well as in RasMol and PyMOL. Users can search for specific variants, or sets of variants, by providing the DNA coordinates of the base change(s) of interest. Additionally, various agglomerative analyses are given, such as the mapping of disease and natural variants onto specific Pfam or CATH domains. The server is freely accessible to all at: https://www.ebi.ac.uk/thornton-srv/databases/VarSite. This article is protected by copyright. All rights reserved

The Divisive Power of Humour: Comedy, Taste and Symbolic Boundaries

Using British and Dutch interview data, this article demonstrates how people from different social classes draw strong symbolic boundaries on the basis of comedy taste. Eschewing the omnivorousness described in recent studies of cultural consumption, comedy audiences make negative aesthetic and moral judgements on the basis of comedy taste, and often make harsh judgements without the disclaimers, apologies and ambivalence so typical of ‘taste talk’ in contemporary culture. The article demonstrates how, in particular, Dutch and British middle class audiences use their comedy taste to communicate distinction and cultural superiority. We discuss several reasons why such processes of social distancing exist in comedy taste and not other cultural areas: the traditionally low status of comedy; the strong relation between humour and personhood; the continuity between comedy tastes and humour styles in everyday life; as well as the specific position of comedy in the British and Dutch cultural fields

Identifying risk factors for exposure to culturable allergenic moulds in energy efficient homes by using highly specific monoclonal antibodies.

PublishedThis is the author accepted manuscript. The final version is available from Elsevier via the DOI in this record.The aim of this study was to determine the accuracy of monoclonal antibodies (mAbs) in identifying culturable allergenic fungi present in visible mould growth in energy efficient homes, and to identify risk factors for exposure to these known allergenic fungi. Swabs were taken from fungal contaminated surfaces and culturable yeasts and moulds isolated by using mycological culture. Soluble antigens from cultures were tested by ELISA using mAbs specific to the culturable allergenic fungi Aspergillus and Penicillium spp., Ulocladium, Alternaria, and Epicoccum spp., Cladosporium spp., Fusarium spp., and Trichoderma spp. Diagnostic accuracies of the ELISA tests were determined by sequencing of the internally transcribed spacer 1 (ITS1)-5.8S-ITS2-encoding regions of recovered fungi following ELISA. There was 100% concordance between the two methods, with ELISAs providing genus-level identity and ITS sequencing providing species-level identities (210 out of 210 tested). Species of Aspergillus/Penicillium, Cladosporium, Ulocladium/Alternaria/Epicoccum, Fusarium and Trichoderma were detected in 82% of the samples. The presence of condensation was associated with an increased risk of surfaces being contaminated by Aspergillus/Penicillium spp. and Cladosporium spp., whereas moisture within the building fabric (water ingress/rising damp) was only associated with increased risk of Aspergillus/Penicillium spp. Property type and energy efficiency levels were found to moderate the risk of indoor surfaces becoming contaminated with Aspergillus/Penicillium and Cladosporium which in turn was modified by the presence of condensation, water ingress and rising damp, consistent with previous literature.Richard Sharpe's PhD scholarship was funded by the European Social Fund Convergence Program for Cornwall and the Isles of Scilly, and was undertaken in collaboration with Coastline Housing. The European Centre for Environment and Human Health (part of the University of Exeter Medical School) is part financed by the European Regional Development Fund Program 2007–2013 and European Social Fund Convergence Program for Cornwall and the Isles of Scill

1,000 structures and more from the MCSG

Background: The Midwest Center for Structural Genomics (MCSG) is one of the large-scale centres of the Protein Structure Initiative (PSI). During the first two phases of the PSI the MCSG has solved over a thousand protein structures. A criticism of structural genomics is that target selection strategies mean that some structures are solved without having a known function and thus are of little biomedical significance. Structures of unknown function have stimulated the development of methods for function prediction from structure.Results: We show that the MCSG has met the stated goals of the PSI and use online resources and readily available function prediction methods to provide functional annotations for more than 90% of the MCSG structures. The structure-to-function prediction method ProFunc provides likely functions for many of the MCSG structures that cannot be annotated by sequence-based methods.Conclusions: Although the focus of the PSI was structural coverage, many of the structures solved by the MCSG can also be associated with functional classes and biological roles of possible biomedical value

Differential Subcellular Localization of the Splice Variants of the Zinc Transporter ZnT5 Is Dictated by the Different C-Terminal Regions

Zinc is emerging as an important intracellular signaling molecule, as well as fulfilling essential structural and catalytic functions through incorporation in a myriad of zinc metalloproteins so it is important to elucidate the molecular mechanisms of zinc homeostasis, including the subcellular localizations of zinc transporters.Two splice variants of the human SLC30A5 Zn transporter gene (ZnT5) have been reported in the literature. These variants differ at their N- and C-terminal regions, corresponding with the use of different 5' and 3' exons. We demonstrate that full length human ZnT5 variant B is a genuine transcript in human intestinal cells and confirm expression of both variant A and variant B in a range of untreated human tissues by splice variant-specific RT-PCR. Using N- or C-terminal GFP or FLAG fusions of both isoforms of ZnT5 we identify that the differential subcellular localization to the Golgi apparatus and ER respectively is a function of their alternative C-terminal sequences. These different C-terminal regions result from the incorporation into the mature transcript of either the whole of exon 14 (variant B) or only the 5' region of exon 14 plus exons 15-17 (variant A).We thus propose that exons 15 to 17 include a signal that results in trafficking of ZnT5 to the Golgi apparatus and that the 3' end of exon 14 includes a signal that leads to retention in the ER

Cholestatic hepatitis as a possible new side-effect of oxycodone: a case report

<p>Abstract</p> <p>Introduction</p> <p>Oxycodone is a widely-used semisynthetic opioid analgesic that has been used for over eighty years. Oxycodone is known to cause side effects such as nausea, pruritus, dizziness, constipation and somnolence. As far as we are aware cholestatic hepatitis as a result of oxycodone use has not been reported so far in the world literature.</p> <p>Case presentation</p> <p>A 34-year-old male presented with cholestatic jaundice and severe pruritus after receiving oxycodone for analgesia post-T11 vertebrectomy. Extensive laboratory investigations and imaging studies did not reveal any other obvious cause for his jaundice and a liver biopsy confirmed canalicular cholestatis suggestive of drug-induced hepatotoxicity. The patient's symptoms and transaminases normalised on withdrawal of oxycodone confirming that oxycodone was the probable cause of the patient's hepatotoxicity.</p> <p>Conclusion</p> <p>We conclude that cholestatic hepatitis is possibly a rare side effect of oxycodone use. Physicians should be aware of the possibility of this potentially serious picture of drug-induced hepatotoxicity.</p

Dioxin-Induced Changes in Epididymal Sperm Count and Spermatogenesis

A single in utero exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) on gestation day 15 decreased epididymal sperm count in adult rats and thus was used to establish a tolerable daily intake for TCDD. However, several laboratories have been unable to replicate these findings. Moreover, conflicting reports of TCDD effects on daily sperm production suggest that spermatogenesis may not be as sensitive to the adverse effects of TCDD as previously thought. We performed a PubMed search using relevant search terms linking dioxin exposure with adverse effects on reproduction and spermatogenesis. Developmental exposure to TCDD is consistently linked with decreased cauda epididymal sperm counts in animal studies, although at higher dose levels than those used in some earlier studies. However, the evidence linking in utero TCDD exposure and spermatogenesis is not convincing. Animal studies provide clear evidence of an adverse effect of in utero TCDD exposure on epididymal sperm count but do not support the conclusion that spermatogenesis is adversely affected. The mechanisms underlying decreased epididymal sperm count are unknown; however, we postulate that epididymal function is the key target for the adverse effects of TCDD.Uma única exposição in utero a 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) no 15º dia de gestação diminuiu a contagem de esperma epididimal em ratos adultos e por isso foi utilizada para estabelecer uma dosagem diária tolerável para TCDD. No entanto, diversos laboratórios não conseguiram reproduzir esses resultados. Além disso, relatórios conflitantes dos efeitos de TCDD na produção diária de esperma sugere que espermatogênese pode não ser tão sensível aos efeitos adversos do TCDD como antes se pensava. Foi feita uma pesquisa no PubMed usando termos de pesquisa relevantes, relacionados à exposição à dioxina com efeitos adversos na reprodução e na espermatogênese. Exposição em desenvolvimento ao TCDD é consistentemente relacionada à diminuição da contagem da cauda epididimal de esperma, mas não apoia a conclusão de que a espermatogênese é afetada. Os mecanismos por trás da diminuição da contagem de esperma epididimal são desconhecidos; no entanto, contestamos que a função epididimal é a chave para efeitos adversos do TCDD