Applying quantitative bias analysis to estimate the plausible effects of selection bias in a cluster randomised controlled trial: secondary analysis of the Primary care Osteoarthritis Screening Trial (POST).

BACKGROUND: Selection bias is a concern when designing cluster randomised controlled trials (c-RCT). Despite addressing potential issues at the design stage, bias cannot always be eradicated from a trial design. The application of bias analysis presents an important step forward in evaluating whether trial findings are credible. The aim of this paper is to give an example of the technique to quantify potential selection bias in c-RCTs. METHODS: This analysis uses data from the Primary care Osteoarthritis Screening Trial (POST). The primary aim of this trial was to test whether screening for anxiety and depression, and providing appropriate care for patients consulting their GP with osteoarthritis would improve clinical outcomes. Quantitative bias analysis is a seldom-used technique that can quantify types of bias present in studies. Due to lack of information on the selection probability, probabilistic bias analysis with a range of triangular distributions was also used, applied at all three follow-up time points; 3, 6, and 12 months post consultation. A simple bias analysis was also applied to the study. RESULTS: Worse pain outcomes were observed among intervention participants than control participants (crude odds ratio at 3, 6, and 12 months: 1.30 (95% CI 1.01, 1.67), 1.39 (1.07, 1.80), and 1.17 (95% CI 0.90, 1.53), respectively). Probabilistic bias analysis suggested that the observed effect became statistically non-significant if the selection probability ratio was between 1.2 and 1.4. Selection probability ratios of > 1.8 were needed to mask a statistically significant benefit of the intervention. CONCLUSIONS: The use of probabilistic bias analysis in this c-RCT suggested that worse outcomes observed in the intervention arm could plausibly be attributed to selection bias. A very large degree of selection of bias was needed to mask a beneficial effect of intervention making this interpretation less plausible

Hierarchical Re-estimation of Topic Models for Measuring Topical Diversity

A high degree of topical diversity is often considered to be an important characteristic of interesting text documents. A recent proposal for measuring topical diversity identifies three elements for assessing diversity: words, topics, and documents as collections of words. Topic models play a central role in this approach. Using standard topic models for measuring diversity of documents is suboptimal due to generality and impurity. General topics only include common information from a background corpus and are assigned to most of the documents in the collection. Impure topics contain words that are not related to the topic; impurity lowers the interpretability of topic models and impure topics are likely to get assigned to documents erroneously. We propose a hierarchical re-estimation approach for topic models to combat generality and impurity; the proposed approach operates at three levels: words, topics, and documents. Our re-estimation approach for measuring documents' topical diversity outperforms the state of the art on PubMed dataset which is commonly used for diversity experiments.Comment: Proceedings of the 39th European Conference on Information Retrieval (ECIR2017

Reimagining laboratory‐based immunology education in the time of COVID‐19

The pandemic has brought challenges to teaching lab and research skills. Here Nigel Francis and colleagues explore the diverse approaches taken to replace lab-based immunology teaching, explain how networks of educators have driven this innovation and discuss the importance of retaining best practice into the future

Impaired hypertrophy in myoblasts is improved with testosterone administration

We investigated the ability of testosterone (T) to restore differentiation in multiple population doubled (PD) murine myoblasts, previously shown to have reduced differentiation in monolayer and bioengineered skeletal muscle cultures vs. their parental controls (CON) (Sharples et al., 2011, 2012 [7] and [26]). Cells were exposed to low serum conditions in the presence or absence of T (100 nM) ± PI3K inhibitor (LY294002) for 72 h and 7 days (early and late muscle differentiation respectively). Morphological analyses were performed to determine myotube number, diameter (μm) and myonuclear accretion as indices of differentiation and myotube hypertrophy. Changes in gene expression for myogenin, mTOR and myostatin were also performed. Myotube diameter in CON and PD cells increased from 17.32 ± 2.56 μm to 21.02 ± 1.89 μm and 14.58 ± 2.66 μm to 18.29 ± 3.08 μm (P ≤ 0.05) respectively after 72 h of T exposure. The increase was comparable in both PD (+25%) and CON cells (+21%) suggesting a similar intrinsic ability to respond to exogenous T administration. T treatment also significantly increased myonuclear accretion (% of myotubes expressing 5+ nuclei) in both cell types after 7 days exposure (P ≤ 0.05). Addition of PI3K inhibitor (LY294002) in the presence of T attenuated these effects in myotube morphology (in both cell types) suggesting a role for the PI3K pathway in T stimulated hypertrophy. Finally, PD myoblasts showed reduced responsiveness to T stimulated mRNA expression of mTOR vs. CON cells and T also reduced myostatin expression in PD myoblasts only. The present study demonstrates testosterone administration improves hypertrophy in myoblasts that basally display impaired differentiation and hypertrophic capacity vs. their parental controls, the action of testosterone in this model was mediated by PI3K/Akt pathway

T2{}^2K2{}^2: The Twitter Top-K Keywords Benchmark

Information retrieval from textual data focuses on the construction of vocabularies that contain weighted term tuples. Such vocabularies can then be exploited by various text analysis algorithms to extract new knowledge, e.g., top-k keywords, top-k documents, etc. Top-k keywords are casually used for various purposes, are often computed on-the-fly, and thus must be efficiently computed. To compare competing weighting schemes and database implementations, benchmarking is customary. To the best of our knowledge, no benchmark currently addresses these problems. Hence, in this paper, we present a top-k keywords benchmark, T${}^2$K${}^2$, which features a real tweet dataset and queries with various complexities and selectivities. T${}^2$K${}^2$ helps evaluate weighting schemes and database implementations in terms of computing performance. To illustrate T${}^2$K${}^2$'s relevance and genericity, we successfully performed tests on the TF-IDF and Okapi BM25 weighting schemes, on one hand, and on different relational (Oracle, PostgreSQL) and document-oriented (MongoDB) database implementations, on the other hand

The design-by-adaptation approach to universal access: learning from videogame technology

This paper proposes an alternative approach to the design of universally accessible interfaces to that provided by formal design frameworks applied ab initio to the development of new software. This approach, design-byadaptation, involves the transfer of interface technology and/or design principles from one application domain to another, in situations where the recipient domain is similar to the host domain in terms of modelled systems, tasks and users. Using the example of interaction in 3D virtual environments, the paper explores how principles underlying the design of videogame interfaces may be applied to a broad family of visualization and analysis software which handles geographical data (virtual geographic environments, or VGEs). One of the motivations behind the current study is that VGE technology lags some way behind videogame technology in the modelling of 3D environments, and has a less-developed track record in providing the variety of interaction methods needed to undertake varied tasks in 3D virtual worlds by users with varied levels of experience. The current analysis extracted a set of interaction principles from videogames which were used to devise a set of 3D task interfaces that have been implemented in a prototype VGE for formal evaluation

Keele Aches and Pains Study Protocol: validity, acceptability and feasibility of the Keele STarT MSK Tool for subgrouping musculoskeletal patients in primary care

Musculoskeletal conditions represent a considerable burden worldwide, and are predominantly managed in primary care. Evidence suggests that many musculoskeletal conditions share similar prognostic factors. Systematically assessing patient’s prognosis, and matching treatments based on prognostic subgroups (stratified care), has been shown to be clinically and cost effective. This study (Keele Aches and Pains Study: KAPS) aims to refine and examine the validity of a brief questionnaire (Keele STarT MSK Tool), designed to enable risk-stratification of primary care patients with the five most common musculoskeletal pain presentations. We will also describe the subgroups of patients, and explore the acceptability and feasibility of using the tool, and how the tool is best implemented in clinical practice. The study design is mixed methods: a prospective, quantitative observational cohort study with a linked qualitative focus group and interview study. Patients who have consulted their General Practitioner or Healthcare Practitioner (GP/HCP) about a relevant musculoskeletal condition will be recruited from General practice. Participating patients will complete a baseline questionnaire (shortly after consultation), plus questionnaires 2 and 6 months later. A sub-sample of patients, along with participating GPs and HCPs, will be invited to take part in qualitative focus groups and interviews. The Keele STarT MSK Tool will be refined based on face, discriminant, construct and predictive validity at baseline and 2 months, and validated using data from 6 month follow-up. Patient and clinician perspectives about using the tool will be explored. This study will provide a validated prognostic tool (the Keele STarT MSK Tool) with established cut-points to stratify patients with the five most common musculoskeletal presentations into low, medium and high risk subgroups. The qualitative analysis of patient and healthcare perspectives will inform how to embed the tool into clinical practice using established general practice IT systems and clinician support packages

Pond management enhances the local abundance and species richness of farmland bird communities

Agricultural intensification and the associated loss of non-cropped habitats have caused a major decline in UK farmland bird populations since the 1970s. As a consequence, there is an urgent need to implement effective conservation and habitat restoration measures in agricultural landscapes. Over the last 40–50 years, due to the cessation of traditional management practices, the majority of UK farmland ponds have become highly terrestrialised, resulting in major reductions in the diversity and abundance of aquatic plant and invertebrate assemblages. Recent research undertaken at farmland ponds in early summer, has shown restored open-canopy, macrophyte-dominated ponds support an increased abundance and diversity of farmland birds, compared to non-managed, overgrown ponds. Here, we expand on this previous research with a year-long field study to assess the implications of pond management for farmland birds by comparing bird diversity, abundance and activity at managed open-canopy ponds with those at unmanaged overgrown ponds. Driven strongly by pond management and connectivity to semi-natural landscape features such as hedgerows and woodland patches, bird abundance and species richness, as well as foraging and parental behaviour, were all significantly higher at managed open-canopy ponds. Further, a wider landscape analysis found that terrestrial land-use patterns in the vicinity of the ponds were not significant predictors of bird communities at the pond sites. In light of the numerous potential benefits to conservation-listed birds and other wildlife, we conclude that farmland pond management has been undervalued as a conservation measure to assist farmland birds. Consequently, we conclude that future agri-environment schemes, should more fully embrace farmland ponds

LiQD Cornea: Pro-regeneration collagen mimetics as patches and alternatives to corneal transplantation

Transplantation with donor corneas is the mainstay for treating corneal blindness, but a severe worldwide shortage necessitates the development of other treatment options. Corneal perforation from infection or inflammation is sealed with cyanoacrylate glue. However, the resulting cytotoxicity requires transplantation. LiQD Cornea is an alternative to conventional corneal transplantation and sealants. It is a cell-free, liquid hydrogel matrix for corneal regeneration, comprising short collagen-like peptides conjugated with polyethylene glycol and mixed with fibrinogen to promote adhesion within tissue defects. Gelation occurs spontaneously at body temperature within 5 min. Light exposure is not required-particularly advantageous because patients with corneal inflammation are typically photophobic. The self-assembling, fully defined, synthetic collagen analog is much less costly than human recombinant collagen and reduces the risk of immune rejection associated with xenogeneic materials. In situ gelation potentially allows for clinical application in outpatient clinics instead of operating theaters, maximizing practicality, and minimizing health care costs