Learning Temporal Transformations From Time-Lapse Videos

Based on life-long observations of physical, chemical, and biologic phenomena in the natural world, humans can often easily picture in their minds what an object will look like in the future. But, what about computers? In this paper, we learn computational models of object transformations from time-lapse videos. In particular, we explore the use of generative models to create depictions of objects at future times. These models explore several different prediction tasks: generating a future state given a single depiction of an object, generating a future state given two depictions of an object at different times, and generating future states recursively in a recurrent framework. We provide both qualitative and quantitative evaluations of the generated results, and also conduct a human evaluation to compare variations of our models.Comment: ECCV201

Bringing genetics into primary care: findings from a national evaluation of pilots in England

Objectives: Developments in genetic knowledge and clinical applications are seen as rendering traditional modes of organizing genetics provision increasingly inappropriate. In common with a number of developed world countries the UK has sought to increase the role of primary care in delivering such services. However, efforts to reconfigure service delivery face multiple challenges associated with divergent policy objectives, organizational boundaries and professional cultures. This paper presents findings from an evaluation of an English initiative to integrate genetics into 'mainstream' clinical provision in the National Health Service. Methods: Qualitative research in 11 case-study sites focusing on attempts by pilots funded by the initiative to embed knowledge and provision within primary care illustrating barriers faced and the ways in which these were surmounted. Results: Lack of intrinsic interest in clinical genetics among primary care staff was compounded by national targets that focused their attention elsewhere and by service structures that rendered genetics a peripheral concern demanding minimal engagement. Established divisions between the commissioning of mainstream and specialist services, along with the pressures of shorter-term targets, impeded ongoing funding. Conclusions: More wide-ranging policy and organizational support is required if the aim of entrenching genetics knowledge and practice across the Health Service is to be realized

The Forcing Strong Metric Dimension of a Graph

For any two vertices u, v in a connected graph G, the interval I(u, v) consists of all vertices which are lying in some u − v shortest path in G. A vertex x in a graph G strongly resolves a pair of vertices u, v if either u ∈ I(x, v) or v ∈ I(x, u). A set of vertices W of V (G) is called a strong resolving set if every pair of vertices of G is strongly resolved by some vertex of W. The minimum cardinality of a strong resolving set in G is called the strong metric dimension number of G and it is denoted by sdim(G). For a strong resolving set W of G, a subset S ofW is called the forcing subset of W if W is the unique strong resolving set containing S. The forcing number f(W, sdim(G)) of W in G is the minimum cardinality of a forcing subset for W, while the forcing strong metric dimension, fsdim(G), of G is the smallest forcing number among all strong resolving sets of G. The forcing strong metric dimensions of some well-known graphs are determined. It is shown that for any positiveintegers a and b, with 0 ≤ a ≤ b, there is nontrivial connected graph G with sdim(G) = b and fsdim(G) = a if and only if {a, b} not equal to {0, 1}

A structural perspective of the role of IP6 in immature and mature retroviral assembly

The small cellular molecule inositol hexakisphosphate (IP6) has been known for ~20 years to promote the in vitro assembly of HIV-1 into immature virus-like particles. However, the molecular details underlying this effect have been determined only recently, with the identification of the IP6 binding site in the immature Gag lattice. IP6 also promotes formation of the mature capsid protein (CA) lattice via a second IP6 binding site, and enhances core stability, creating a favorable environment for reverse transcription. IP6 also enhances assembly of other retroviruses, from both the Lentivirus and the Alpharetrovirus genera. These findings suggest that IP6 may have a conserved function throughout the family Retroviridae. Here, we discuss the different steps in the viral life cycle that are influenced by IP6, and describe in detail how IP6 interacts with the immature and mature lattices of different retroviruses

The medium-term sustainability of organisational innovations in the national health service

Background: There is a growing recognition of the importance of introducing new ways of working into the UK's National Health Service (NHS) and other health systems, in order to ensure that patient care is provided as effectively and efficiently as possible. Researchers have examined the challenges of introducing new ways of working-'organisational innovations'-into complex organisations such as the NHS, and this has given rise to a much better understanding of how this takes place-and why seemingly good ideas do not always result in changes in practice. However, there has been less research on the medium-and longer-term outcomes for organisational innovations and on the question of how new ways of working, introduced by frontline clinicians and managers, are sustained and become established in day-to-day practice. Clearly, this question of sustainability is crucial if the gains in patient care that derive from organisational innovations are to be maintained, rather than lost to what the NHS Institute has called the 'improvement-evaporation effect'. Methods: The study will involve research in four case-study sites around England, each of which was successful in sustaining its new model of service provision beyond an initial period of pilot funding for new genetics services provided by the Department of Health. Building on findings relating to the introduction and sustainability of these services already gained from an earlier study, the research will use qualitative methods-in-depth interviews, observation of key meetings, and analysis of relevant documents-to understand the longer-term challenges involved in each case and how these were surmounted. The research will provide lessons for those seeking to sustain their own organisational innovations in wide-ranging clinical areas and for those designing the systems and organisations that make up the NHS, to make them more receptive contexts for the sustainment of innovation. Discussion: Through comparison and contrast across four sites, each involving different organisational innovations, different forms of leadership, and different organisational contexts to contend with, the findings of the study will have wide relevance. The research will produce outputs that are useful for managers and clinicians responsible for organisational innovation, policy makers and senior managers, and academics

Evaluating Maintainability Prejudices with a Large-Scale Study of Open-Source Projects

Exaggeration or context changes can render maintainability experience into prejudice. For example, JavaScript is often seen as least elegant language and hence of lowest maintainability. Such prejudice should not guide decisions without prior empirical validation. We formulated 10 hypotheses about maintainability based on prejudices and test them in a large set of open-source projects (6,897 GitHub repositories, 402 million lines, 5 programming languages). We operationalize maintainability with five static analysis metrics. We found that JavaScript code is not worse than other code, Java code shows higher maintainability than C# code and C code has longer methods than other code. The quality of interface documentation is better in Java code than in other code. Code developed by teams is not of higher and large code bases not of lower maintainability. Projects with high maintainability are not more popular or more often forked. Overall, most hypotheses are not supported by open-source data.Comment: 20 page

Cross-sectional evaluation of a longitudinal consultation skills course at a new UK medical school

Background: Good communication is a crucial element of good clinical care, and it is important to provide appropriate consultation skills teaching in undergraduate medical training to ensure that doctors have the necessary skills to communicate effectively with patients and other key stakeholders. This article aims to provide research evidence of the acceptability of a longitudinal consultation skills strand in an undergraduate medical course, as assessed by a cross-sectional evaluation of students' perceptions of their teaching and learning experiences. Methods: A structured questionnaire was used to collect student views. The questionnaire comprised two parts: 16 closed questions to evaluate content and process of teaching and 5 open-ended questions. Questionnaires were completed at the end of each consultation skills session across all year groups during the 2006-7 academic year (5 sessions in Year 1, 3 in Year 2, 3 in Year 3, 10 in Year 4 and 10 in Year 5). 2519 questionnaires were returned in total. Results: Students rated Tutor Facilitation most favourably, followed by Teaching, then Practice & Feedback, with suitability of the Rooms being most poorly rated. All years listed the following as important aspects they had learnt during the session: • how to structure the consultation • importance of patient-centredness • aspects of professionalism (including recognising own limits, being prepared, generally acting professionally). All years also noted that the sessions had increased their confidence, particularly through practice. Conclusions: Our results suggest that a longitudinal and integrated approach to teaching consultation skills using a well structured model such as Calgary-Cambridge, facilitates and consolidates learning of desired process skills, increases student confidence, encourages integration of process and content, and reinforces appreciation of patient-centredness and professionalism

The fate of steroid estrogens: Partitioning during wastewater treatment and onto river sediments

This is the author's accepted manuscript. The final published article is available from the link below. Copyright @ 2010 Springer Science+Business Media B.V.The partitioning of steroid estrogens in wastewater treatment and receiving waters is likely to influence their discharge to, and persistence in, the environment. This study investigated the partitioning behaviour of steroid estrogens in both laboratory and field studies. Partitioning onto activated sludge from laboratory-scale Husmann units was rapid with equilibrium achieved after 1 h. Sorption isotherms and Kd values decreased in the order 17α-ethinyl estradiol > 17α-estradiol > estrone > estriol without a sorption limit being achieved (1/n >1). Samples from a wastewater treatment works indicated no accumulation of steroid estrogens in solids from primary or secondary biological treatment, however, a range of steroid estrogens were identified in sediment samples from the River Thames. This would indicate that partitioning in the environment may play a role in the long-term fate of estrogens, with an indication that they will be recalcitrant in anaerobic conditions.EPSR

Performance of regression models as a function of experiment noise

A challenge in developing machine learning regression models is that it is difficult to know whether maximal performance has been reached on a particular dataset, or whether further model improvement is possible. In biology this problem is particularly pronounced as sample labels (response variables) are typically obtained through experiments and therefore have experiment noise associated with them. Such label noise puts a fundamental limit to the performance attainable by regression models. We address this challenge by deriving a theoretical upper bound for the coefficient of determination (R2) for regression models. This theoretical upper bound depends only on the noise associated with the response variable in a dataset as well as its variance. The upper bound estimate was validated via Monte Carlo simulations and then used as a tool to bootstrap performance of regression models trained on biological datasets, including protein sequence data, transcriptomic data, and genomic data. Although we study biological datasets in this work, the new upper bound estimates will hold true for regression models from any research field or application area where response variables have associated noise