A transient assay for recombination demonstrates that Arabidopsis SNM1 and XRCC3 enhance non-homologous recombination

Replacement of endogenous genes by homologous recombination is rare in plants; the majority of genetic modifications are the result of transforming DNA molecules undergoing random genomic insertion by way of non-homologous recombination. Factors that affect chromatin remodeling and DNA repair are thought to have the potential to enhance the frequency of homologous recombination in plants. Conventional tools to study the frequencies of genetic recombination often rely on stable transformation-based approaches, with these systems being rarely capable of high-throughput or combinatorial analysis. We developed a series of vectors that use chemiluminescent (LUC and REN) reporter genes to assay the relative frequency of homologous and non-homologous recombination in plants. These transient assay vectors were used to screen 14 candidategenes for their effects on recombination frequencies in Nicotiana benthamiana plants. Over-expression of Arabidopsis genes with sequence similarity to SNM1 from yeast and XRCC3 from humans enhanced the frequency of non-homologous recombination when assayed using two different donor vectors. Transient N. benthamiana leaf systems were also used in an alternative assay for preliminary measurements of homologous recombination frequencies, which were found to be enhanced by over-expression of RAD52, MIM and RAD51 from yeast, as well as CHR24 from Arabidopsis. The findings for the assays described here are in line with previous studies that analyzed recombination frequencies using stable transformation. The assays we report have revealed functions in non-homologous recombination for the Arabidopsis SNM1 and XRCC3 genes, so the suppression of these genes' expression offers a potential means to enhance the gene targeting frequency in plants. Furthermore, our findings also indicate that plant gene targeting frequencies could be enhanced by over-expression of RAD52, MIM, CHR24, and RAD51 genes.

Measuring and influencing physical activity with Smartphone technology : a systematic review

Background Rapid developments in technology have encouraged the use of smartphones in physical activity research, although little is known regarding their effectiveness as measurement and intervention tools. Objective This study systematically reviewed evidence on smartphones and their viability for measuring and influencing physical activity. Data Sources Research articles were identified in September 2013 by literature searches in Web of Knowledge, PubMed, PsycINFO, EBSCO, and ScienceDirect. Study Selection The search was restricted using the terms (physical activity OR exercise OR fitness) AND (smartphone* OR mobile phone* OR cell phone*) AND (measurement OR intervention). Reviewed articles were required to be published in international academic peer-reviewed journals, or in full text from international scientific conferences, and focused on measuring physical activity through smartphone processing data and influencing people to be more active through smartphone applications. Study Appraisal and Synthesis Methods Two reviewers independently performed the selection of articles and examined titles and abstracts to exclude those out of scope. Data on study characteristics, technologies used to objectively measure physical activity, strategies applied to influence activity; and the main study findings were extracted and reported. Results A total of 26 articles (with the first published in 2007) met inclusion criteria. All studies were conducted in highly economically advantaged countries; 12 articles focused on special populations (e.g. obese patients). Studies measured physical activity using native mobile features, and/or an external device linked to an application. Measurement accuracy ranged from 52 to 100 % (n = 10 studies). A total of 17 articles implemented and evaluated an intervention. Smartphone strategies to influence physical activity tended to be ad hoc, rather than theory-based approaches; physical activity profiles, goal setting, real-time feedback, social support networking, and online expert consultation were identified as the most useful strategies to encourage physical activity change. Only five studies assessed physical activity intervention effects; all used step counts as the outcome measure. Four studies (three pre–post and one comparative) reported physical activity increases (12–42 participants, 800–1,104 steps/day, 2 weeks–6 months), and one case-control study reported physical activity maintenance (n = 200 participants; >10,000 steps/day) over 3 months. Limitations Smartphone use is a relatively new field of study in physical activity research, and consequently the evidence base is emerging. Conclusions Few studies identified in this review considered the validity of phone-based assessment of physical activity. Those that did report on measurement properties found average-to-excellent levels of accuracy for different behaviors. The range of novel and engaging intervention strategies used by smartphones, and user perceptions on their usefulness and viability, highlights the potential such technology has for physical activity promotion. However, intervention effects reported in the extant literature are modest at best, and future studies need to utilize randomized controlled trial research designs, larger sample sizes, and longer study periods to better explore the physical activity measurement and intervention capabilities of smartphones.

An approach for extending Building Information Models (BIM) to specifications

The Construction industry accounts for a tenth of global GDP. Still, challenges such as slow adoption of new work processes, islands of information, and legal disputes, remain frequent, industry-wide occurrences despite various attempts to address them. In response, IT-based approaches have been adopted to explore collaborative ways of executing construction projects. Building Information Modelling (BIM) is an exemplar of integrative technologies whose 3D-visualisation capabilities have fostered collaboration especially between clients and design teams. Yet, the ways in which specification documents are created and used in capturing clients' expectations based on industry standards have remained largely unchanged since the 18th century. As a result, specification-related errors are still common place in an industry where vast amounts of information are consumed as well as produced in the course project implementation in the built environment. By implication, processes such as cost planning which depend on specification-related information remain largely inaccurate even with the use of BIM-based technologies. This paper briefly distinguishes between non-BIM-based and BIM-based specifications and reports on-going efforts geared towards the latter. We review exemplars aimed at extending Building Information Models to specification information embedded within the objects in a product library and explore a viable way of reasoning about a semi-automated process of specification using our product library.

Artificial neural networks to predict activity type and energy expenditure in youth

Previous studies have demonstrated that pattern recognition approaches to accelerometer data reduction are feasible and moderately accurate in classifying activity type in children. Whether pattern recognition techniques can be used to provide valid estimates of physical activity (PA) energy expenditure in youth remains unexplored in the research literature. Purpose: The objective of this study is to develop and test artificial neural networks (ANNs) to predict PA type and energy expenditure (PAEE) from processed accelerometer data collected in children and adolescents. Methods: One hundred participants between the ages of 5 and 15 yr completed 12 activity trials that were categorized into five PA types: sedentary, walking, running, light-intensity household activities or games, and moderate-to-vigorous intensity games or sports. During each trial, participants wore an ActiGraph GTIM on the right hip, and (V) Over dotO(2) was measured using the Oxycon Mobile (Viasys Healthcare, Yorba Linda, CA) portable metabolic system. ANNs to predict PA type and PAEE (METs) were developed using the following features: 10th, 25th, 50th, 75th, and 90th percentiles and the lag one autocorrelation. To determine the highest time resolution achievable, we extracted features from 10-, 15-, 20-, 30-, and 60-s windows. Accuracy was assessed by calculating the percentage of windows correctly classified and root mean square en-or (RMSE). Results: As window size increased from 10 to 60 s, accuracy for the PA-type ANN increased from 81.3% to 88.4%. RMSE for the MET prediction ANN decreased from 1.1 METs to 0.9 METs. At any given window size, RMSE values for the MET prediction ANN were 30-40% lower than the conventional regression-based approaches. Conclusions: ANNs can be used to predict both PA type and PAEE in children and adolescents using count data from a single waist mounted accelerometer.

Contemporary cultures of service delivery to families : implications for music therapy

Family-centred and early intervention and prevention programs are a strong focus of current policy objectives within Australia, and a significant area of practice within the music therapy community. Recent shifts in the culture of policy and practice increasingly reflect ecological understandings by focussing on integrated and place-based approaches to service delivery. Further, current funding opportunities are strongly concerned with the extent to which interventions are able to reach out to highly vulnerable families that typically do not engage with services easily. Music therapy holds unique promise within these cultural shifts and thus advocates must develop a solid understanding of the concepts and related language in order to confidently engage with both funding and service systems. This paper uses an integrative review to first define and summarise current knowledge in three key areas relevant to contemporary Australian policy and practice: hard-to-reach families, home visiting as assertive outreach, and integrated or place-based service delivery. Evidence for the effectiveness of music therapy in relation to these key themes is then presented. Finally, the paper discusses the implications for the future of music therapy within the current Australian early intervention and prevention policy context and makes recommendations for moving forward on both practice and research fronts. While there is growing evidence and theory to suggest that music therapy may be uniquely efficacious in this area, greater Australian Journal of Music Therapy Vol 25, 2014 149 advocacy, documentation, research and adjustment of practices and language will further cement the position of the industry.

Effects of physical activity intervention in youth : a review

Effects of physical activity interventions in youth: A review. International SportMed Journal. Vol.2 No.5 2001. The purpose of this paper is to review the peer-reviewed literature pertinent to physical activity interventions for children and adolescents. In order to provide a more quantitative conclusion regarding the effectiveness of these interventions, a meta-analytic approach was utilized in which effect sizes (the efficacy of each intervention or magnitude of the intervention effect was expressed as a standardized effect size, which represents the influence of the treatment or intervention on the dependent variable) from each study are pooled to provide a global estimate of effectiveness. A search of the relevant peer-reviewed literature was conducted using several computer-based databases, including MEDLINE, PYSCHLIT, SOCIAL SCIENCE INDEX, and SPORTS DISCUS. Manual searches were also made using the reference lists from recovered articles. Applying strict criteria for quality of design and assessment of physical activity, 10 studies were located, yielding a total of 44 effect sizes. The mean effect size was 0.47 (95% C.I. 0.28 – 0.66) suggesting that interventions have produced moderate increases in physical activity behavior. Effect sizes ranged from –0.61 to 2.5. Interventions focusing on increasing the amount of physical activity performed during regular physical education were more effective than those targeting overall levels of physical activity. Interventions were almost entirely school-based. Accordingly, the development and evaluation of community-based approaches for promoting physical activity among young people, especially older adolescents, remains an urgent priority for future research.

University of Glasgow at ImageCLEFPhoto 2009 : optimising similarity and diversity in image retrieval

In this paper we describe the approaches adopted to generate the runs submitted to ImageCLEFPhoto 2009 with an aim to promote document diversity in the rankings. Four of our runs are text based approaches that employ textual statistics extracted from the captions of images, i.e. MMR [1] as a state of the art method for result diversification, two approaches that combine relevance information and clustering techniques, and an instantiation of Quantum Probability Ranking Principle. The fifth run exploits visual features of the provided images to re-rank the initial results by means of Factor Analysis. The results reveal that our methods based on only text captions consistently improve the performance of the respective baselines, while the approach that combines visual features with textual statistics shows lower levels of improvements.

The 3rd Knowledge Cities World Summit Proceedings

FROM KCWS 2010 Ch airs and Summit Proceeding Ed ito rs ‘Knowledge’ is a resource, which relies on the past for a better future. In the 21st century, more than ever before, cities around the world depend on the knowledge of their citizens, their institutions and their firms and enterprises. The knowledge image, the human competence and the reputation of their public and private institutions and corporations profiles a city. It attracts investment, qualified labour and professionals, as well as students and researchers. And it creates local life spaces and professional milieus, which offer the quality of life to the citizens that are seeking to cope with the challenges of modern life in a competitive world. Integrating knowledge-based development in urban strategies and policies, beyond the provision of schools and locations for higher education, has become a new ambitious arena of city politics. Coming from theory to practice, and bringing together the manifold knowledge stakeholders in a city and preparing joint visions for the knowledge city is a new challenge for city managers, urban planners and leaders of the civic society . It requires visionary power, creativity, holistic thinking, the willingness to cooperate with all groups of the local civil society, and the capability to moderate communication processes to overcome conflicts and to develop joint action for a sustainable future. This timely Melbourne 2010 – The Third Knowledge City World Summit makes an important reminder that ‘knowledge’ is the key notion in the 21st Century development. Considering this notion, the summit aims to shed light on the multi-faceted dimensions and various scales of building the ‘knowledge city’ and on ‘knowledge-based development’ paradigms. At this summit, the theoretical and practical maturing of knowledge-based development paradigms will be advanced through the interplay between the world’s leading academic’s theories and the practical models and strategies of practitioners’ and policy makers’ drawn from around the world. As chairs of The Melbourne 2010 Summit, we have compiled this summit proceeding in order to disseminate the knowledge generated and shared in Melbourne with the wider research, governance, and practice communities. The papers in the proceedings reflect the broad range of contributions to the summit. They report on recent developments in planning and managing knowledge cities and ICT infrastructure, they assess the role of knowledge institutions in regional innovation systems and of the intellectual capital of cities and regions; they describe the evolution of knowledge-based approaches to urban development in differing cultural environments; they finally bridge the discourse on the knowledge city to other urban development paradigms such as the creative city, the ubiquitous city or the compact city. The diversity of papers presented shows how different scholars from planning cultures around the world interpret the knowledge dimension in urban and regional development. All papers of this proceeding have gone through a double-blind peer review process and been reviewed by our summit editorial review and advisory board members. We cordially thank the members of the Summit Proceeding Editorial Review and Advisory Board for their diligent work in the review of the papers. We hope the papers in this proceeding will inspire and make a significant contribution to the research, governance, and practice circles.

Mid-Aged Adults' Sitting Time in Three Contexts

BACKGROUND: To develop evidence-based approaches for reducing sedentary behavior, there is a need to identify the specific settings where prolonged sitting occurs, associated factors, and variations. PURPOSE: To examine the sociodemographic and health factors associated with mid-aged adults' sitting time in three contexts and variations between weekdays and weekend days. METHODS: A mail survey was sent to 17,000 adults (aged 40-65 years) in 2007; 11,037 responses were received (68.5%); and 7719 were analyzed in 2010. Respondents indicated time spent sitting on a usual weekday and weekend day for watching TV, general leisure, and home computer use. Multivariate linear mixed models with area-level random intercepts were used to examine (1) associations between sociodemographic and health variables and sitting time, and (2) interaction effects of weekday/weekend day with each of gender, age, education, and employment status, on sitting time. RESULTS: For each context, longer sitting times were reported by those single and living alone, and those whose health restricted activity. For watching TV, longer sitting times were reported by men; smokers; and those with high school or lower education, not in paid employment, in poor health, and with BMI ≥25. For general leisure, longer sitting times were reported by women, smokers, and those not employed full-time. For home computer use, longer sitting times were reported by men; and those aged 40-44 years, with university qualifications; in the mid-income range; and with BMI ≥30. Sitting times tended to be longer on weekend days than weekdays, although the extent of this differed among sociodemographic groups. CONCLUSIONS: Sociodemographic and health factors associated with sitting time differ by context and between weekdays and weekend days.

Pituitary tumours : all silent on the epigenetics front

Investigation of the epigenome of sporadic pituitary tumours is providing a more detailed understanding of aberrations that characterise this tumour type. Early studies, in this and other tumour types adopted candidate-gene approaches to characterise CpG island methylation as a mechanism responsible for or associated with gene silencing. However, more recently, investigators have adopted approaches that do not require a priori knowledge of the gene and transcript, as example differential display techniques, and also genome-wide, array-based approaches, to 'uncover' or 'unmask' silenced genes. Furthermore, through use of chromatin immunoprecipitation as a selective enrichment technique; we are now beginning to identify modifications that target the underlying histones themselves and that have roles in gene-silencing events. Collectively, these studies provided convincing evidence that change to the tumour epigenome are not simply epiphenomena but have functional consequences in the context of pituitary tumour evolution. Our ability to perform these types of studies has been and is increasingly reliant upon technological advances in the genomics and epigenomics arena. In this context, other more recent advances and developing technologies, and, in particular, next generation or flow cell re-sequencing techniques offer exciting opportunities for our future studies of this tumour type.

An investigation of the impact of various geographical scales for the specification of spatial dependence

Ecological studies are based on characteristics of groups of individuals, which are common in various disciplines including epidemiology. It is of great interest for epidemiologists to study the geographical variation of a disease by accounting for the positive spatial dependence between neighbouring areas. However, the choice of scale of the spatial correlation requires much attention. In view of a lack of studies in this area, this study aims to investigate the impact of differing definitions of geographical scales using a multilevel model. We propose a new approach -- the grid-based partitions and compare it with the popular census region approach. Unexplained geographical variation is accounted for via area-specific unstructured random effects and spatially structured random effects specified as an intrinsic conditional autoregressive process. Using grid-based modelling of random effects in contrast to the census region approach, we illustrate conditions where improvements are observed in the estimation of the linear predictor, random effects, parameters, and the identification of the distribution of residual risk and the aggregate risk in a study region. The study has found that grid-based modelling is a valuable approach for spatially sparse data while the SLA-based and grid-based approaches perform equally well for spatially dense data.

Application of meshfree methods to numerically simulate microscale deformations of different plant food materials during drying

Plant food materials have a very high demand in the consumer market and therefore, improved food products and efficient processing techniques are concurrently being researched in food engineering. In this context, numerical modelling and simulation techniques have a very high potential to reveal fundamentals of the underlying mechanisms involved. However, numerical modelling of plant food materials during drying becomes quite challenging, mainly due to the complexity of the multiphase microstructure of the material, which undergoes excessive deformations during drying. In this regard, conventional grid-based modelling techniques have limited applicability due to their inflexible grid-based fundamental limitations. As a result, meshfree methods have recently been developed which offer a more adaptable approach to problem domains of this nature, due to their fundamental grid-free advantages. In this work, a recently developed meshfree based two-dimensional plant tissue model is used for a comparative study of microscale morphological changes of several food materials during drying. The model involves Smoothed Particle Hydrodynamics (SPH) and Discrete Element Method (DEM) to represent fluid and solid phases of the cellular structure. Simulation are conducted on apple, potato, carrot and grape tissues and the results are qualitatively and quantitatively compared and related with experimental findings obtained from the literature. The study revealed that cellular deformations are highly sensitive to cell dimensions, cell wall physical and mechanical properties, middle lamella properties and turgor pressure. In particular, the meshfree model is well capable of simulating critically dried tissues at lower moisture content and turgor pressure, which lead to cell wall wrinkling. The findings further highlighted the potential applicability of the meshfree approach to model large deformations of the plant tissue microstructure during drying, providing a distinct advantage over the state of the art grid-based approaches.

Making smart decisions : key steps towards a typology for emergency communication during natural hazards

Governments, authorities, and organisations dedicate significant resources to encourage communities to prepare for and respond to natural hazards such as cyclones, earthquakes, floods, and bushfires. However, recent events, media attention, and ongoing academic research continue to highlight cases of non-compliance including swift water rescues. Individuals who fail to comply with instructions issued during natural hazards significantly impede the emergency response because they divert resources to compliance-enforcement and risk the lives of emergency service workers who may be required to assist them. An initial investigation of the field suggests several assumptions or practices that influence emergency management policy, communication strategy, and community behaviours during natural hazards: 1) that community members will comply with instructions issued by governments and agencies that represent the most authoritative voice, 2) that communication campaigns are shaped by intuition rather than evidence-based approaches (Wood et al., 2012), and 3) that emergency communication is linear and directional. This extended abstract represents the first stage of a collaborative research project that integrates industry and cross-disciplinary perspectives to provide evidence-based approaches for emergency and risk communication during the response and recovery phases of a natural hazard. Specifically, this abstract focuses on the approach taken and key elements that will form the development of a typology of compliance-gaining messages during the response phase of natural hazards, which will be the focus of the conference presentation.

Locality-sensitive hashing for protein classification

Determination of sequence similarity is a central issue in computational biology, a problem addressed primarily through BLAST, an alignment based heuristic which has underpinned much of the analysis and annotation of the genomic era. Despite their success, alignment-based approaches scale poorly with increasing data set size, and are not robust under structural sequence rearrangements. Successive waves of innovation in sequencing technologies – so-called Next Generation Sequencing (NGS) approaches – have led to an explosion in data availability, challenging existing methods and motivating novel approaches to sequence representation and similarity scoring, including adaptation of existing methods from other domains such as information retrieval. In this work, we investigate locality-sensitive hashing of sequences through binary document signatures, applying the method to a bacterial protein classification task. Here, the goal is to predict the gene family to which a given query protein belongs. Experiments carried out on a pair of small but biologically realistic datasets (the full protein repertoires of families of Chlamydia and Staphylococcus aureus genomes respectively) show that a measure of similarity obtained by locality sensitive hashing gives highly accurate results while offering a number of avenues which will lead to substantial performance improvements over BLAST..

Workplace physical activity interventions : a systematic review

Objective. To assess the effectiveness of workplace interventions in improving physical activity. Data Source. EBSCO research database (and all subdatabases). Study Inclusion and Exclusion Criteria. Articles were published from 2000 to 2010 in English, had appropriate designs, and measured employees' physical activity, energy consumption, and/or body mass index (BMI) as primary outcomes. Articles that did not meet the inclusion criteria were excluded. Data Extraction. Data extracted included study design, study population, duration, intervention activities, outcomes, and results. Data Synthesis. Data were synthesized into one table. Results of each relevant outcome including p values were combined. Results. Twelve (60%) of 20 selected interventions reported an improvement in physical activity level, steps, or BMI, and there was one slowed step reduction in the intervention group. Among these, 10 were less than 6 months in duration; 9 used pedometers; 6 applied Internet-based approaches; and 5 included activities targeting social and environmental levels. Seven of 8 interventions with pre-posttest and quasi-experimental controlled design showed improvement on at least one outcome. However, 7 of 12 randomized controlled trials (RCTs) did not prove effective in any outcome. Conclusion. Interventions that had less rigorous research designs, used pedometers, applied Internet-based approaches, and included activities at social and environmental levels were more likely to report being effective than those without these characteristics.