Redefining the Institutional Repository

Institutional Repositories have grown in importance over the last 10 years to offer a core University and Library service, however, their role is developing faster now than it has ever done. Funder Open Access requirements, internal reporting, research data. Ref2020 and more are increasing the demands on the traditional repository, putting pressure on staff resources and challenging the underlying software. This webinar will outline these issues as well as look at how the needs and use of repositories may change in the future

Discovery services: next generation of searching scholarly information

The new breed of resource discovery services is an evolutionary step forward in providing library users with a ‘one-stop shop’ where they can find information sources for their research. They provide a single search box that can search a library’s online and physical content including articles, books, journals, newspaper articles, e-books, specialist collections and more. These discovery services have built on the concepts of both federated searching and next-generation catalogues

Changing Publishing Ecologies: A Landscape Study of New University Presses and Academic-Led Publishing: A Report to JISC

Introduction A new wave of university presses is emerging. Common characteristics are that they are open access (OA), digital first, library-based, and they often offer a smaller set of services than a traditional publisher, blurring the line between publisher and platform. In tandem, a small but notable number of academics and researchers have set up their own publishing initiatives, often demonstrating an innovative or unique approach either in workflow, peer review, technology or business model. These new publishing initiatives have a potentially disruptive effect on the scholarly communication environment, providing new avenues for the dissemination of research outputs and acting as pathfinders for the evolution of academic publishing and the scholarly record. In this report, we have captured the current landscape of new university presses (NUPs) and academic-led presses (ALPs) emerging within the UK. Taking different approaches for these two types of press we have captured the take-up, reasoning and characteristics of these initiatives, as well as future plans. The report concludes with a series of recommendations to help support and foster new developments in this space, to share best practice and collaboration and to identify the tools and services that will facilitate further innovation. Jisc supports universities and researchers in the provision of new digital services and innovation. We will work with the community and stakeholders to decide how we can take forward some of the recommendations listed in this report for the benefit of our members and the research community

Climate Change in a Differential Equations Course: Using Bifurcation Diagrams to Explore Small Changes with Big Effects

The environmental phenomenon of climate change is of critical importance to today\u27s science and global communities. Differential equations give a powerful lens onto this phenomenon, and so we should commit to discussing the mathematics of this environmental issue in differential equations courses. Doing so highlights the power of linking differential equations to environmental and social justice causes, and also brings important science to the forefront in the mathematics classroom. In this paper, we provide an extended problem, appropriate for a first course in differential equations, that uses bifurcation analysis to study climate change. Specifically, through studying hysteresis, this problem highlights how it may be the case that damage done to the environment by a small change cannot be reversed merely by undoing that small change. In addition to the problem itself, we elaborate on the mathematics, discuss implementation strategies, and provide examples of student work. Students in a mathematics classroom do not necessarily expect to confront such issues of social justice or environmental concerns, but we see it as our moral obligation as educators to include such lessons in our classes so that our students can become well-informed global citizens

Development and implementation of the physiotherapy-led exercise interventions for the treatment of rotator cuff disorders for the ‘Getting it Right:Addressing Shoulder Pain’ (GRASP) trial

The Getting it Right: Addressing Shoulder Pain (GRASP) trial is a large-scale, multicentre, randomised controlled trial investigating the clinical and cost-effectiveness of a progressive exercise intervention versus a best-practice advice intervention, with or without corticosteroid injection, for treating people with a rotator cuff disorder. Interventions were developed using the Medical Research Council guidance on complex interventions, and included a stakeholder meeting of 26 clinicians, researchers, and patient representatives. The best-practice advice (1 session) and progressive exercise (≤6 sessions over 16 weeks) interventions both involve face-to-face, one-to-one physiotherapist appointments and include self-management advice, home-exercise instruction, and behaviour-change strategies to target exercise adherence. The results of the GRASP trial are anticipated in 2020. This large scale evaluation on 704 participants will provide high quality evidence to best inform clinical practice for the management of people with shoulder pain due to a rotator cuff disorder. A critical stage of evaluating the complex interventions in the GRASP trial is ensuring details of the development and content of the interventions are available to clinicians and researchers to facilitate their implementation

Global impact of nitrate photolysis in sea-salt aerosol on NOx, OH, and O3 in the marine boundary layer

Recent field studies have suggested that sea-salt particulate nitrate (NITs) photolysis may act as a significant local source of nitrogen oxides (NOx) over oceans. We present a study of the global impact of this process on oxidant concentrations in the marine boundary layer (MBL) using the GEOS-Chem model, after first updating the model to better simulate observed gas-particle phase partitioning of nitrate in the marine boundary layer. Model comparisons with long-term measurements of NOx from the Cape Verde Atmospheric Observatory (CVAO) in the eastern tropical North Atlantic provide support for an in situ source of NOx from NITs photolysis, with NITs photolysis coefficients about 25-50 times larger than corresponding HNO3 photolysis coefficients. Short-term measurements of nitrous acid (HONO) at this location show a clear daytime peak, with average peak mixing ratios ranging from 3 to 6 pptv. The model reproduces the general shape of the diurnal HONO profile only when NITs photolysis is included, but the magnitude of the daytime peak mixing ratio is under-predicted. This under-prediction is somewhat reduced if HONO yields from NITs photolysis are assumed to be close to unity. The combined NOx and HONO analysis suggests that the upper limit of the ratio of NITs : HNO3 photolysis coefficients is about 100. The largest simulated relative impact of NITs photolysis is in the tropical and subtropical marine boundary layer, with peak local enhancements ranging from factors of 5 to 20 for NOx, 1.2 to 1.6 for OH, and 1.1 to 1.3 for ozone. Since the spatial extent of the sea-salt aerosol (SSA) impact is limited, global impacts on NOx, ozone, and OH mass burdens are small ( ∼ 1-3 %). We also present preliminary analysis showing that particulate nitrate photolysis in accumulation-mode aerosols (predominantly over continental regions) could lead to ppbv-level increases in ozone in the continental boundary layer. Our results highlight the need for more comprehensive long-term measurements of NOx, and related species like HONO and sea-salt particulate nitrate, to better constrain the impact of particulate nitrate photolysis on marine boundary layer oxidant chemistry. Further field and laboratory studies on particulate nitrate photolysis in other aerosol types are also needed to better understand the impact of this process on continental boundary layer oxidant chemistry

Assessing agreement between malaria slide density readings

BACKGROUND: Several criteria have been used to assess agreement between replicate slide readings of malaria parasite density. Such criteria may be based on percent difference, or absolute difference, or a combination. Neither the rationale for choosing between these types of criteria, nor that for choosing the magnitude of difference which defines acceptable agreement, are clear. The current paper seeks a procedure which avoids the disadvantages of these current options and whose parameter values are more clearly justified. METHODS AND RESULTS: Variation of parasite density within a slide is expected, even when it has been prepared from a homogeneous sample. This places lower limits on sensitivity and observer agreement, quantified by the Poisson distribution. This means that, if a criterion of fixed percent difference criterion is used for satisfactory agreement, the number of discrepant readings is over-estimated at low parasite densities. With a criterion of fixed absolute difference, the same happens at high parasite densities. For an ideal slide, following the Poisson distribution, a criterion based on a constant difference in square root counts would apply for all densities. This can be back-transformed to a difference in absolute counts, which, as expected, gives a wider range of acceptable agreement at higher average densities. In an example dataset from Tanzania, observed differences in square root counts correspond to a 95% limits of agreement of -2,800 and +2,500 parasites/microl at average density of 2,000 parasites/microl, and -6,200 and +5,700 parasites/microl at 10,000 parasites/microl. However, there were more outliers beyond those ranges at higher densities, meaning that actual coverage of these ranges was not a constant 95%, but decreased with density. In a second study, a trial of microscopist training, the corresponding ranges of agreement are wider and asymmetrical: -8,600 to +5,200/microl, and -19,200 to +11,700/microl, respectively. By comparison, the optimal limits of agreement, corresponding to Poisson variation, are +/- 780 and +/- 1,800 parasites/microl, respectively. The focus of this approach on the volume of blood read leads to other conclusions. For example, no matter how large a volume of blood is read, some densities are too low to be reliably detected, which in turn means that disagreements on slide positivity may simply result from within-slide variation, rather than reading errors. CONCLUSIONS: The proposed method defines limits of acceptable agreement in a way which allows for the natural increase in variability with parasite density. This includes defining the levels of between-reader variability, which are consistent with random variation: disagreements within these limits should not trigger additional readings. This approach merits investigation in other settings, in order to determine both the extent of its applicability, and appropriate numerical values for limits of agreement

The Yeast La Related Protein Slf1p Is a Key Activator of Translation during the Oxidative Stress Response

The mechanisms by which RNA-binding proteins control the translation of subsets of mRNAs are not yet clear. Slf1p and Sro9p are atypical-La motif containing proteins which are members of a superfamily of RNA-binding proteins conserved in eukaryotes. RIP-Seq analysis of these two yeast proteins identified overlapping and distinct sets of mRNA targets, including highly translated mRNAs such as those encoding ribosomal proteins. In paralell, transcriptome analysis of slf1Δ and sro9Δ mutant strains indicated altered gene expression in similar functional classes of mRNAs following loss of each factor. The loss of SLF1 had a greater impact on the transcriptome, and in particular, revealed changes in genes involved in the oxidative stress response. slf1Δ cells are more sensitive to oxidants and RIP-Seq analysis of oxidatively stressed cells enriched Slf1p targets encoding antioxidants and other proteins required for oxidant tolerance. To quantify these effects at the protein level, we used label-free mass spectrometry to compare the proteomes of wild-type and slf1Δ strains following oxidative stress. This analysis identified several proteins which are normally induced in response to hydrogen peroxide, but where this increase is attenuated in the slf1Δ mutant. Importantly, a significant number of the mRNAs encoding these targets were also identified as Slf1p-mRNA targets. We show that Slf1p remains associated with the few translating ribosomes following hydrogen peroxide stress and that Slf1p co-immunoprecipitates ribosomes and members of the eIF4E/eIF4G/Pab1p ‘closed loop’ complex suggesting that Slf1p interacts with actively translated mRNAs following stress. Finally, mutational analysis of SLF1 revealed a novel ribosome interacting domain in Slf1p, independent of its RNA binding La-motif. Together, our results indicate that Slf1p mediates a translational response to oxidative stress via mRNA-specific translational control