Characterizing Scales of Genetic Recombination and Antibiotic Resistance in Pathogenic Bacteria Using Topological Data Analysis

Pathogenic bacteria present a large disease burden on human health. Control of these pathogens is hampered by rampant lateral gene transfer, whereby pathogenic strains may acquire genes conferring resistance to common antibiotics. Here we introduce tools from topological data analysis to characterize the frequency and scale of lateral gene transfer in bacteria, focusing on a set of pathogens of significant public health relevance. As a case study, we examine the spread of antibiotic resistance in Staphylococcus aureus. Finally, we consider the possible role of the human microbiome as a reservoir for antibiotic resistance genes.Comment: 12 pages, 6 figures. To appear in AMT 2014 Special Session on Advanced Methods of Interactive Data Mining for Personalized Medicin

What do young athletes implicitly understand about psychological skills?

One reason sport psychologists teach psychological skills is to enhance performance in sport; but the value of psychological skills for young athletes is questionable because of the qualitative and quantitative differences between children and adults in their understanding of abstract concepts such as mental skills. To teach these skills effectively to young athletes, sport psychologists need to appreciate what young athletes implicitly understand about such skills because maturational (e.g., cognitive, social) and environmental (e.g., coaches) factors can influence the progressive development of children and youth. In the present qualitative study, we explored young athletes’ (aged 10–15 years) understanding of four basic psychological skills: goal setting, mental imagery, self-talk, and relaxation. Young athletes (n = 118: 75 males and 43 females) completed an open-ended questionnaire to report their understanding of these four basic psychological skills. Compared with the older youth athletes, the younger youth athletes were less able to explain the meaning of each psychological skill. Goal setting and mental imagery were better understood than self-talk and relaxation. Based on these findings, sport psychologists should consider adapting interventions and psychoeducational programs to match young athletes’ age and developmental level

Only two out of five articles by New Zealand researchers are free-to-access: a multiple API study of access, citations, cost of Article Processing Charges (APC), and the potential to increase the proportion of open access

We studied journal articles published by researchers at all eight New Zealand universities in 2017 to determine how many were freely accessible on the web. We wrote software code to harvest data from multiple sources, code that we now share to enable others to reproduce our work on their own sample set. In May 2019, we ran our code to determine which of the 2017 articles were open at that time and by what method; where those articles would have incurred an Article Processing Charge (APC) we calculated the cost if those charges had been paid. Where articles were not freely available we determined whether the policies of publishers in each case would have allowed deposit in a non-commercial repository (Green open access). We also examined citation rates for different types of access. We found that, of our 2017 sample set, about two out of every five articles were freely accessible without payment or subscription (41%). Where research was explicitly said to be funded by New Zealand’s major research funding agencies, the proportion was slightly higher at 45%. Where open articles would have incurred an APC we estimated an average cost per article of USD1,682 (for publications where all articles require an APC, that is, Gold open access) and USD2,558 (where APC payment is optional, Hybrid open access) at a total estimated cost of USD1.45m. Of the paid options, Gold is by far more common for New Zealand researchers (82% Gold, 18% Hybrid). In terms of citations, our analysis aligned with previous studies that suggest a correlation between publications being freely accessible and, on balance, slightly higher rates of citation. This is not seen across all types of open access, however, with Diamond OA achieving the lowest rates. Where articles were not freely accessible we found that a very large majority of them (88% or 3089 publications) could have been legally deposited in an institutional repository. Similarly, only in a very small number of cases had a version deposited in the repository of a New Zealand university made the difference between the publication being freely accessible or not (125 publications). Given that most New Zealand researchers support research being open, there is clearly a large gap between belief and practice in New Zealand’s research ecosystem

The research journey: Travels across the idiomatic and axiomatic toward a better understanding of complexity

In this paper, seven researchers reflect on the journeys their research projects have taken when they engage with and synthesize complex problems. These journeys embody an adaptive approach to tackling problems characterized by their interconnectedness and emergence, and that transcend traditional units of analysis such as ecosystems. In this paper we argue that making such a process deliberate and explicit will help researchers better combine different research paradigms such as expert-driven and participant-directed work, thus resulting in both broad explanations and specific phenomenon; research tensions traditionally defined as oppositional must be approached as complimentary. This paper includes researchers. personal journeys as they dealt with the emergent properties of complex problems and participant involvement. This paper argues that that research journey should be more than accidental but is a methodological necessity and should guide the theoretical and practical approaches to complex problems

Impacts of local human activities on the Antarctic environment

We review the scientific literature, especially from the past decade, on the impacts of human activities on the Antarctic environment. A range of impacts has been identified at a variety of spatial and temporal scales. Chemical contamination and sewage disposal on the continent have been found to be long-lived. Contemporary sewage management practices at many coastal stations are insufficient to prevent local contamination but no introduction of non-indigenous organisms through this route has yet been demonstrated. Human activities, particularly construction and transport, have led to disturbances of flora and fauna. A small number of non-indigenous plant and animal species has become established, mostly on the northern Antarctic Peninsula and southern archipelagos of the Scotia Arc. There is little indication of recovery of overexploited fish stocks, and ramifications of fishing activity oil bycatch species and the ecosystem could also be far-reaching. The Antarctic Treaty System and its instruments, in particular the Convention for the Conservation of Antarctic Marine Living Resources and the Environmental Protocol, provide a framework within which management of human activities take place. In the face of the continuing expansion of human activities in Antarctica, a more effective implementation of a wide range of measures is essential, in order to ensure comprehensive protection of the Antarctic environment, including its intrinsic, wilderness and scientific values which remains a fundamental principle of the Antarctic Treaty System. These measures include effective environmental impact assessments, long-term monitoring, mitigation measures for non-indigenous species, ecosystem-based management of living resources, and increased regulation of National Antarctic Programmes and tourism activities

Examining the validity of the Athlete Engagement Questionnaire (AEQ) within a Portuguese sport setting

Sport psychology literature suggests that understanding engagement levels is pivotal to promote positive sporting experiences among athletes. The purpose of this study was to examine the psychometric properties of the Athlete Engagement Questionnaire among Portuguese sport athletes. Two distinct samples of Portuguese athletes from different competitive levels were collected, and the results of a confirmatory factor analysis demonstrated a good fit of the model to the data. A review of the psychometric properties indicated that all factors showed good composite reliability, convergent validity, and discriminant validity. In addition, a multi-groups analysis showed the invariance of the model in two independent samples providing evidence of cross validity. Implications of these results for scholars and coaches are discussed and guidelines for future studies are suggested

Birthing practices of traditional birth attendants in South Asia in the context of training programmes

Traditional Birth Attendants (TBA) training has been an important component of public health policy interventions to improve maternal and child health in developing countries since the 1970s. More recently, since the 1990s, the TBA training strategy has been increasingly seen as irrelevant, ineffective or, on the whole, a failure due to evidence that the maternal mortality rate (MMR) in developing countries had not reduced. Although, worldwide data show that, by choice or out of necessity, 47 percent of births in the developing world are assisted by TBAs and/or family members, funding for TBA training has been reduced and moved to providing skilled birth attendants for all births. Any shift in policy needs to be supported by appropriate evidence on TBA roles in providing maternal and infant health care service and effectiveness of the training programmes. This article reviews literature on the characteristics and role of TBAs in South Asia with an emphasis on India. The aim was to assess the contribution of TBAs in providing maternal and infant health care service at different stages of pregnancy and after-delivery and birthing practices adopted in home births. The review of role revealed that apart from TBAs, there are various other people in the community also involved in making decisions about the welfare and health of the birthing mother and new born baby. However, TBAs have changing, localised but nonetheless significant roles in delivery, postnatal and infant care in India. Certain traditional birthing practices such as bathing babies immediately after birth, not weighing babies after birth and not feeding with colostrum are adopted in home births as well as health institutions in India. There is therefore a thin precarious balance between the application of biomedical and traditional knowledge. Customary rituals and perceptions essentially affect practices in home and institutional births and hence training of TBAs need to be implemented in conjunction with community awareness programmes

Anthropogenic Space Weather

Anthropogenic effects on the space environment started in the late 19th century and reached their peak in the 1960s when high-altitude nuclear explosions were carried out by the USA and the Soviet Union. These explosions created artificial radiation belts near Earth that resulted in major damages to several satellites. Another, unexpected impact of the high-altitude nuclear tests was the electromagnetic pulse (EMP) that can have devastating effects over a large geographic area (as large as the continental United States). Other anthropogenic impacts on the space environment include chemical release ex- periments, high-frequency wave heating of the ionosphere and the interaction of VLF waves with the radiation belts. This paper reviews the fundamental physical process behind these phenomena and discusses the observations of their impacts.Comment: 71 pages, 35 figure

Data visualization in yield component analysis: an expert study

Even though data visualization is a common analytical tool in numerous disciplines, it has rarely been used in agricultural sciences, particularly in agronomy. In this paper, we discuss a study on employing data visualization to analyze a multiplicative model. This model is often used by agronomists, for example in the so-called yield component analysis. The multiplicative model in agronomy is normally analyzed by statistical or related methods. In practice, unfortunately, usefulness of these methods is limited since they help to answer only a few questions, not allowing for a complex view of the phenomena studied. We believe that data visualization could be used for such complex analysis and presentation of the multiplicative model. To that end, we conducted an expert survey. It showed that visualization methods could indeed be useful for analysis and presentation of the multiplicative model

Social learning in LEADER: Exogenous, endogenous and hybrid evaluation in rural development

This paper considers the relationship between the centralised exogenous, institutions and the embedded, endogenous institutions of rural governance in Europe through an examination the evaluation procedures of the European LEADER programme. LEADER is presented in the literature as progressive in terms of innovation and stakeholder engagement. Yet while the planning and management of LEADER embraces heterogeneity and participation, programmatic evaluation is centralised and held at arms length from delivery organisations. The paper reviews previous efforts to improve evaluation in LEADER and considers alternative strategies for evaluation, contrasting LEADER practice with participatory evaluation methodologies in the wider international context. Can evaluation in itself be valuable as a mode of social learning and hence a driver for endogenous development in rural communities in Europe? The paper concludes by examining the challenges in producing a hybrid form of evaluation which accommodates endogenous and exogenous values