A stitch in time: Efficient computation of genomic DNA melting bubbles

Background: It is of biological interest to make genome-wide predictions of the locations of DNA melting bubbles using statistical mechanics models. Computationally, this poses the challenge that a generic search through all combinations of bubble starts and ends is quadratic. Results: An efficient algorithm is described, which shows that the time complexity of the task is O(NlogN) rather than quadratic. The algorithm exploits that bubble lengths may be limited, but without a prior assumption of a maximal bubble length. No approximations, such as windowing, have been introduced to reduce the time complexity. More than just finding the bubbles, the algorithm produces a stitch profile, which is a probabilistic graphical model of bubbles and helical regions. The algorithm applies a probability peak finding method based on a hierarchical analysis of the energy barriers in the Poland-Scheraga model. Conclusions: Exact and fast computation of genomic stitch profiles is thus feasible. Sequences of several megabases have been computed, only limited by computer memory. Possible applications are the genome-wide comparisons of bubbles with promotors, TSS, viral integration sites, and other melting-related regions.Comment: 16 pages, 10 figure

Gangs and guilt: Towards a new theory of horror film

The most basic and unanimous statement made in scholarship on horror films is that horror films are ‘about’ fear: the primary purpose of horror films is to scare viewers. Based on horror films from the 1970s until the present in which child gangs play a significant part, this essay advances a new theory of horror film, namely that horror films primarily seek to elicit not fear but guilt. The analysis focuses on four topics: themes, camera angles, horror’s cinematic casting of ‘abnormality,’ and the rift, unique to the horror genre, between audience ‘alignment’ and ‘allegiance.

Reflective Journaling: A Theoretical Model and Digital Prototype for Developing Resilience and Creativity

Reflection is commonly discussed as a tool for personal and professional development that is becoming increasingly important in today’s global and digital world. In this paper, we propose a model that suggests ways in which reflection, in the form of Reflective Journaling, can support the development of creativity and resilience, which are needed to enable individuals to function effectively in a fast-changing environment. In addition, the model proposes ways in which external support and progress monitoring can be used in conjunction with skills in adaptive resilience and structured creativity, to support the maintenance of reflective journaling as a habit, in the longer term, thus creating virtuous cycles of skills and behaviours that can reinforce each other. Based on our model, and additional user research, we describe the design of a first digital prototype that aims to support the use of Reflective Journaling and to develop creativity and resilience through suggested mechanisms. Initial evaluations of our prototype are positive. It has been well-received by early test users, and has the potential to address all the connections defined. We therefore suggest that the theoretical model can be used to develop digital tools, such as the one included, to help those who wish to develop the habit of reflective journaling, and through that a range of other skills associated with resilience and creative thinking. We see this as a starting point for investigating this potential in more depth

Using Latent Class Analyses to Examine Health Disparities among Young Children in Socially Disadvantaged Families during the COVID-19 Pandemic

Rising income inequality is strongly linked to health disparities, particularly in regions where uneven distribution of wealth and income has long been a concern. Despite emerging evidence of COVID-19-related health inequalities for adults, limited evidence is available for children and their parents. This study aimed to explore subtypes of families of preschoolers living in the disadvantaged neighborhoods of Hong Kong based on patterns of family hardship and to compare their patterns of parenting behavior, lifestyle practices, and wellbeing during the COVID-19 pandemic. Data were collected from 1338 preschoolers and their parents during March to June 2020. Latent class analysis was performed based on 11 socioeconomic and disease indicators. Multivariate logistic regressions were used to examine associations between identified classes and variables of interest during the COVID-19 pandemic. Four classes of family hardship were identified. Class 1 (45.7%) had the lowest disease and financial burden. Class 2 (14.0%) had the highest financial burden. Class 3 (5.9%) had the highest disease burden. Class 4 (34.5%) had low family income but did not receive government welfare assistance. Class 1 (low hardship) had lower risks of child maltreatment and adjustment problems than Class 2 (poverty) and Class 3 (poor health). However, children in Class 1 (low hardship) had higher odds of suffering psychological aggression and poorer physical wellbeing than those in Class 4 (low income), even after adjusting for child age and gender. The findings emphasize the need to adopt flexible intervention strategies in the time of large disease outbreak to address diverse problems and concerns among socially disadvantaged families

The Effect of Transposable Element Insertions on Gene Expression Evolution in Rodents

Background:Many genomes contain a substantial number of transposable elements (TEs), a few of which are known to be involved in regulating gene expression. However, recent observations suggest that TEs may have played a very important role in the evolution of gene expression because many conserved non-genic sequences, some of which are know to be involved in gene regulation, resemble TEs. Results:Here we investigate whether new TE insertions affect gene expression profiles by testing whether gene expression divergence between mouse and rat is correlated to the numbers of new transposable elements inserted near genes. We show that expression divergence is significantly correlated to the number of new LTR and SINE elements, but not to the numbers of LINEs. We also show that expression divergence is not significantly correlated to the numbers of ancestral TEs in most cases, which suggests that the correlations between expression divergence and the numbers of new TEs are causal in nature. We quantify the effect and estimate that TE insertion has accounted for ~20% (95% confidence interval: 12% to 26%) of all expression profile divergence in rodents. Conclusions:We conclude that TE insertions may have had a major impact on the evolution of gene expression levels in rodents

The Minimal Solution to the mu/B_mu Problem in Gauge Mediation

We provide a minimal solution to the mu/B_mu problem in the gauge mediated supersymmetry breaking by introducing a Standard Model singlet filed S with a mass around the messenger scale which couples to the Higgs and messenger fields. This singlet is nearly supersymmetric and acquires a relatively small Vacuum Expectation Value (VEV) from its radiatively generated tadpole term. Consequently, both mu and B_mu parameters receive the tree-level and one-loop contributions, which are comparable due to the small S VEV. Because there exists a proper cancellation in such two kinds of contributions to B_mu, we can have a viable Higgs sector for electroweak symmetry breaking.Comment: 15 pages, 2 figures, version published on JHE

Extreme behavioural shifts by baboons exploiting risky, resource-rich, human-modified environments

Abstract A range of species exploit anthropogenic food resources in behaviour known as ‘raiding’. Such behavioural flexibility is considered a central component of a species’ ability to cope with human-induced environmental changes. Here, we study the behavioural processes by which raiding male chacma baboons (Papio ursinus) exploit the opportunities and mitigate the risks presented by raiding in the suburbs of Cape Town, South Africa. Ecological sampling and interviews conducted with ‘rangers’ (employed to manage the baboons’ space use) revealed that baboons are at risk of being herded out of urban spaces that contain high-energy anthropogenic food sources. Baboon-attached motion/GPS tracking collars showed that raiding male baboons spent almost all of their time at the urban edge, engaging in short, high-activity forays into the urban space. Moreover, activity levels were increased where the likelihood of deterrence by rangers was greater. Overall, these raiding baboons display a time-activity balance that is drastically altered in comparison to individuals living in more remote regions. We suggest our methods can be used to obtain precise estimates of management impact for this and other species in conflict with people

IMPLEmenting a clinical practice guideline for acute low back pain evidence-based manageMENT in general practice (IMPLEMENT) : cluster randomised controlled trial study protocol

Background: Evidence generated from reliable research is not frequently implemented into clinical practice. Evidence-based clinical practice guidelines are a potential vehicle to achieve this. A recent systematic review of implementation strategies of guideline dissemination concluded that there was a lack of evidence regarding effective strategies to promote the uptake of guidelines. Recommendations from this review, and other studies, have suggested the use of interventions that are theoretically based because these may be more effective than those that are not. An evidencebased clinical practice guideline for the management of acute low back pain was recently developed in Australia. This provides an opportunity to develop and test a theory-based implementation intervention for a condition which is common, has a high burden, and for which there is an evidence-practice gap in the primary care setting. Aim: This study aims to test the effectiveness of a theory-based intervention for implementing a clinical practice guideline for acute low back pain in general practice in Victoria, Australia. Specifically, our primary objectives are to establish if the intervention is effective in reducing the percentage of patients who are referred for a plain x-ray, and improving mean level of disability for patients three months post-consultation. Methods/Design: This study protocol describes the details of a cluster randomised controlled trial. Ninety-two general practices (clusters), which include at least one consenting general practitioner, will be randomised to an intervention or control arm using restricted randomisation. Patients aged 18 years or older who visit a participating practitioner for acute non-specific low back pain of less than three months duration will be eligible for inclusion. An average of twenty-five patients per general practice will be recruited, providing a total of 2,300 patient participants. General practitioners in the control arm will receive access to the guideline using the existing dissemination strategy. Practitioners in the intervention arm will be invited to participate in facilitated face-to-face workshops that have been underpinned by behavioural theory. Investigators (not involved in the delivery of the intervention), patients, outcome assessors and the study statistician will be blinded to group allocation. Trial registration: Australian New Zealand Clinical Trials Registry ACTRN012606000098538 (date registered 14/03/2006).The trial is funded by the NHMRC by way of a Primary Health Care Project Grant (334060). JF has 50% of her time funded by the Chief Scientist Office3/2006). of the Scottish Government Health Directorate and 50% by the University of Aberdeen. PK is supported by a NHMRC Health Professional Fellowship (384366) and RB by a NHMRC Practitioner Fellowship (334010). JG holds a Canada Research Chair in Health Knowledge Transfer and Uptake. All other authors are funded by their own institutions

Anomalous U(1) symmetry and lepton flavor violation

We show that in a large class of models based on anomalous U(1) symmetry which addresses the fermion mass hierarchy problem, leptonic flavor changing processes are induced that are in the experimentally interesting range. The flavor violation occurs through the renormalization group evolution of the soft SUSY breaking parameters between the string scale and the U(1)_A breaking scale. We derive general expressions for the evolution of these parameters in the presence of higher dimensional operators. Several sources for the flavor violation are identified: flavor-dependent contributions to the soft masses from the U(1)_A gaugino, scalar mass corrections proportional to the trace of U(1)_A charge, non-proportional A-terms from vertex corrections, and the U(1)_A D-term. Quantitative estimates for the decays \mu -> e \gamma and \tau -> \mu \gamma are presented in supergravity models which accommodate the relic abundance of neutralino dark matter.Comment: References added, typos corrected, 28 pages LaTeX, includes 14 eps figure

Star Clusters

This review concentrates almost entirely on globular star clusters. It emphasises the increasing realisation that few of the traditional problems of star cluster astronomy can be studied in isolation: the influence of the Galaxy affects dynamical evolution deep in the core, and the spectrum of stellar masses; in turn the evolution of the core determines the highest stellar densities, and the rate of encounters. In this way external tidal effects indirectly influence the formation and evolution of blue stragglers, binary pulsars, X-ray sources, etc. More controversially, the stellar density appears to influence the relative distribution of normal stars. In the opposite sense, the evolution of individual stars governs much of the early dynamics of a globular cluster, and the existence of large numbers of primordial binary stars has changed important details of our picture of the dynamical evolution. New computational tools which will become available in the next few years will help dynamical theorists to address these questions.Comment: 10 pages, 3 figures, Te