Annotation of two large contiguous regions from the Haemonchus contortus genome using RNA-seq and comparative analysis with Caenorhabditis elegans

The genomes of numerous parasitic nematodes are currently being sequenced, but their complexity and size, together with high levels of intra-specific sequence variation and a lack of reference genomes, makes their assembly and annotation a challenging task. Haemonchus contortus is an economically significant parasite of livestock that is widely used for basic research as well as for vaccine development and drug discovery. It is one of many medically and economically important parasites within the strongylid nematode group. This group of parasites has the closest phylogenetic relationship with the model organism Caenorhabditis elegans, making comparative analysis a potentially powerful tool for genome annotation and functional studies. To investigate this hypothesis, we sequenced two contiguous fragments from the H. contortus genome and undertook detailed annotation and comparative analysis with C. elegans. The adult H. contortus transcriptome was sequenced using an Illumina platform and RNA-seq was used to annotate a 409 kb overlapping BAC tiling path relating to the X chromosome and a 181 kb BAC insert relating to chromosome I. In total, 40 genes and 12 putative transposable elements were identified. 97.5% of the annotated genes had detectable homologues in C. elegans of which 60% had putative orthologues, significantly higher than previous analyses based on EST analysis. Gene density appears to be less in H. contortus than in C. elegans, with annotated H. contortus genes being an average of two-to-three times larger than their putative C. elegans orthologues due to a greater intron number and size. Synteny appears high but gene order is generally poorly conserved, although areas of conserved microsynteny are apparent. C. elegans operons appear to be partially conserved in H. contortus. Our findings suggest that a combination of RNA-seq and comparative analysis with C. elegans is a powerful approach for the annotation and analysis of strongylid nematode genomes

Northern Eurasia Future Initiative (NEFI): facing the challenges and pathways of global change in the 21st century

During the past several decades, the Earth system has changed significantly, especially across Northern Eurasia. Changes in the socio-economic conditions of the larger countries in the region have also resulted in a variety of regional environmental changes that can have global consequences. The Northern Eurasia Future Initiative (NEFI) has been designed as an essential continuation of the Northern Eurasia Earth Science Partnership Initiative (NEESPI), which was launched in 2004. NEESPI sought to elucidate all aspects of ongoing environmental change, to inform societies and, thus, to better prepare societies for future developments. A key principle of NEFI is that these developments must now be secured through science-based strategies co-designed with regional decision makers to lead their societies to prosperity in the face of environmental and institutional challenges. NEESPI scientific research, data, and models have created a solid knowledge base to support the NEFI program. This paper presents the NEFI research vision consensus based on that knowledge. It provides the reader with samples of recent accomplishments in regional studies and formulates new NEFI science questions. To address these questions, nine research foci are identified and their selections are briefly justified. These foci include: warming of the Arctic; changing frequency, pattern, and intensity of extreme and inclement environmental conditions; retreat of the cryosphere; changes in terrestrial water cycles; changes in the biosphere; pressures on land-use; changes in infrastructure; societal actions in response to environmental change; and quantification of Northern Eurasia's role in the global Earth system. Powerful feedbacks between the Earth and human systems in Northern Eurasia (e.g., mega-fires, droughts, depletion of the cryosphere essential for water supply, retreat of sea ice) result from past and current human activities (e.g., large scale water withdrawals, land use and governance change) and potentially restrict or provide new opportunities for future human activities. Therefore, we propose that Integrated Assessment Models are needed as the final stage of global change assessment. The overarching goal of this NEFI modeling effort will enable evaluation of economic decisions in response to changing environmental conditions and justification of mitigation and adaptation efforts

Mid-term results of previously cemented hip arthroplasties revised with uncemented modular femoral components: a retrospective study

BACKGROUND: We evaluated the mid-term results of previously cemented hip arthroplasties revised with uncemented modular femoral components. METHODS: The study included 40 patients (36 females (90 %) and 4 males (10 %), mean age 67.6 years, range 39–87 years) who underwent revision of a previously cemented hip prosthesis with an uncemented modular femoral stem between 2005 and 2009. The indications for revision were femoral aseptic loosening in 38 (95 %) cases and acetabular protrusion in 2 (5 %). According to the Paprosky classification, the femoral defect was type 1 in 10 (25 %) patients, type 2 in 16 (40 %), type 3a in 11 (27.5 %), type 3b in 2 (5 %) and type 4 in 1 (2.5 %). The Harris hip score was used for the clinical evaluation. Femoral vertical subsidence, the cortical index and femoral stem stability were assessed radiologically. The mean follow-up period was 84 months (range 61–95 months). RESULTS: The mean Harris hip score was 41.4 (range 35.4–44.4) preoperatively and 80.9 (range 65.6–98.3) at the final follow-up examination (p < 0.05). Mean vertical subsidence was 5.7 mm (range 2.5–10.5 mm) in seven (17.5 %) patients. Stable bone fixation was observed in 38 (95 %) patients, fibrous stable fixation in 2 (5 %) and no instability in any patient. Radiographs taken during the early postoperative period revealed that the cortical index was a mean of 1.34 (range 1.11–1.73) and a mean of 1.55 on the final follow-up radiographic examinations (range 1.16–1.91) (p < 0.01). CONCLUSIONS: Satisfactory results were achieved using uncemented modular femoral components during revision of previously cemented femoral components. Many modular femoral stems provide primary stability by filling femoral bone losses and help determine stem length, offset and anteversion

Adaptation of a Mindfulness-Based Intervention for Incarcerated Young Men: a Feasibility Study

Objectives: Incarcerated young men commonly experience problems with impulsivity and emotional dysregulation. Mindfulness training could help but the evidence is limited. This study developed and piloted an adapted mindfulness-based intervention for this group (n = 48). Methods: Feasibility of recruitment, retention, and data collection were assessed, and the effectiveness of mindfulness training measured using validated questionnaires. Twenty-five qualitative interviews were conducted to explore experiences of the course, and barriers and facilitators to taking part. Results: The findings indicated that recruitment and retention to mindfulness training groups was a challenge despite trying various adaptive strategies to improve interest, relevance, and acceptability. Quantitative data collection was feasible at baseline and post-course. There were significant improvements following training in impulsivity (effect size [ES] 0.72, 95% CI 0.32–1.11, p = 0.001), mental wellbeing (ES 0.50; 95% CI 0.18–0.80; p = 0.003), inner resilience (comprehensibility ES 0.35; 95% CI − 0.02–0.68; p = 0.03), and mindfulness (ES 0.32; 95% CI 0.03–0.60; p = 0.03). The majority (70%) of participants reported finding the course uncomfortable or disconcerting at first but if they chose to remain, this changed as they began to experience benefit. The body scan and breathing techniques were reported as being most helpful. Positive experiences included better sleep, less stress, feeling more in control, and improved relationships. Conclusions: Developing and delivering mindfulness training for incarcerated young men is feasible and may be beneficial, but recruitment and retention may limit reach. Further studies are required that include a control group

Reproductive health and access to healthcare facilities: risk factors for depression and anxiety in women with an earthquake experience

<p>Abstract</p> <p>Background</p> <p>The reproductive and mental health of women contributes significantly to their overall well-being. Three of the eight Millennium Development Goals are directly related to reproductive and sexual health while mental disorders make up three of the ten leading causes of disease burden in low and middle-income countries. Among mental disorders, depression and anxiety are two of the most prevalent. In the context of slower progress in achieving Millennium Development Goals in developing countries and the ever-increasing man-made and natural disasters in these areas, it is important to understand the association between reproductive health and mental health among women with post-disaster experiences.</p> <p>Methods</p> <p>This was a cross-sectional study with a sample of 387 women of reproductive age (15-49 years) randomly selected from the October 2005 earthquake affected areas of Pakistan. Data on reproductive health was collected using the Centers for Disease Control reproductive health assessment toolkit. Depression and anxiety were measured using the Hopkins Symptom Checklist-25, while earthquake experiences were captured using the Harvard Trauma Questionnaire. The association of either depression or anxiety with socio-demographic variables, earthquake experiences, reproductive health and access to health facilities was estimated using multivariate logistic regression.</p> <p>Results</p> <p>Post-earthquake reproductive health events together with economic deprivation, lower family support and poorer access to health care facilities explained a significant proportion of differences in the experiencing of clinical levels of depression and anxiety. For instance, women losing resources for subsistence, separation from family and experiencing reproductive health events such as having a stillbirth, having had an abortion, having had abnormal vaginal discharge or having had genital ulcers, were at significant risk of depression and anxiety.</p> <p>Conclusion</p> <p>The relationship between women's post-earthquake mental health and reproductive health, socio-economic status, and health care access is complex and explained largely by the socio-cultural role of women. It is suggested that interventions that consider gender differences and that are culturally appropriate are likely to reduce the incidence.</p

Smoking cessation opportunities in severe mental illness (tobacco intensive motivational and estimate risk — TIMER—): study protocol for a randomized controlled trial

There is an increased risk of premature death in people with severe mental illness (SMI). Respiratory disorders and cardiovascular disease are leading causes of increased mortality rates in these patients, and tobacco consumption remains the most preventable risk factor involved. Developing new tools to motivate patients towards cessation of smoking is a high priority. Information on the motivational value of giving the lung age and prevention opportunities is unknown in this high-risk population. In the context of community care, screening and early detection of lung damage could potentially be used, together with mobile technology, in order to produce a prevention message, which may provide patients with SMI with a better chance of quitting smoking.This study receives funding by the Spanish Ministry of Economy, Industry and Competitiveness, Instituto Carlos III (FIS PI16/00802)

Sandy coastlines under threat of erosion

Sandy beaches occupy more than one-third of the global coastline(1) and have high socioeconomic value related to recreation, tourism and ecosystem services(2). Beaches are the interface between land and ocean, providing coastal protection from marine storms and cyclones(3). However the presence of sandy beaches cannot be taken for granted, as they are under constant change, driven by meteorological(4,5), geological(6) and anthropogenic factors(1,7). A substantial proportion of the world's sandy coastline is already eroding(1,7), a situation that could be exacerbated by climate change(8,9). Here, we show that ambient trends in shoreline dynamics, combined with coastal recession driven by sea level rise, could result in the near extinction of almost half of the world's sandy beaches by the end of the century. Moderate GHG emission mitigation could prevent 40% of shoreline retreat. Projected shoreline dynamics are dominated by sea level rise for the majority of sandy beaches, but in certain regions the erosive trend is counteracted by accretive ambient shoreline changes; for example, in the Amazon, East and Southeast Asia and the north tropical Pacific. A substantial proportion of the threatened sandy shorelines are in densely populated areas, underlining the need for the design and implementation of effective adaptive measures. Erosion is a major problem facing sandy beaches that will probably worsen with climate change and sea-level rise. Half the world's beaches, many of which are in densely populated areas, could disappear by the end of the century under current trends; mitigation could lessen retreat by 40%.info:eu-repo/semantics/publishedVersio

Seasonality in Human Zoonotic Enteric Diseases: A Systematic Review

BACKGROUND: Although seasonality is a defining characteristic of many infectious diseases, few studies have described and compared seasonal patterns across diseases globally, impeding our understanding of putative mechanisms. Here, we review seasonal patterns across five enteric zoonotic diseases: campylobacteriosis, salmonellosis, vero-cytotoxigenic Escherichia coli (VTEC), cryptosporidiosis and giardiasis in the context of two primary drivers of seasonality: (i) environmental effects on pathogen occurrence and pathogen-host associations and (ii) population characteristics/behaviour. METHODOLOGY/PRINCIPAL FINDINGS: We systematically reviewed published literature from 1960-2010, resulting in the review of 86 studies across the five diseases. The Gini coefficient compared temporal variations in incidence across diseases and the monthly seasonality index characterised timing of seasonal peaks. Consistent seasonal patterns across transnational boundaries, albeit with regional variations was observed. The bacterial diseases all had a distinct summer peak, with identical Gini values for campylobacteriosis and salmonellosis (0.22) and a higher index for VTEC (Gini  0.36). Cryptosporidiosis displayed a bi-modal peak with spring and summer highs and the most marked temporal variation (Gini = 0.39). Giardiasis showed a relatively small summer increase and was the least variable (Gini = 0.18). CONCLUSIONS/SIGNIFICANCE: Seasonal variation in enteric zoonotic diseases is ubiquitous, with regional variations highlighting complex environment-pathogen-host interactions. Results suggest that proximal environmental influences and host population dynamics, together with distal, longer-term climatic variability could have important direct and indirect consequences for future enteric disease risk. Additional understanding of the concerted influence of these factors on disease patterns may improve assessment and prediction of enteric disease burden in temperate, developed countries