TreeToReads - a pipeline for simulating raw reads from phylogenies.

BackgroundUsing phylogenomic analysis tools for tracking pathogens has become standard practice in academia, public health agencies, and large industries. Using the same raw read genomic data as input, there are several different approaches being used to infer phylogenetic tree. These include many different SNP pipelines, wgMLST approaches, k-mer algorithms, whole genome alignment and others; each of these has advantages and disadvantages, some have been extensively validated, some are faster, some have higher resolution. A few of these analysis approaches are well-integrated into the regulatory process of US Federal agencies (e.g. the FDA's SNP pipeline for tracking foodborne pathogens). However, despite extensive validation on benchmark datasets and comparison with other pipelines, we lack methods for fully exploring the effects of multiple parameter values in each pipeline that can potentially have an effect on whether the correct phylogenetic tree is recovered.ResultsTo resolve this problem, we offer a program, TreeToReads, which can generate raw read data from mutated genomes simulated under a known phylogeny. This simulation pipeline allows direct comparisons of simulated and observed data in a controlled environment. At each step of these simulations, researchers can vary parameters of interest (e.g., input tree topology, amount of sequence divergence, rate of indels, read coverage, distance of reference genome, etc) to assess the effects of various parameter values on correctly calling SNPs and reconstructing an accurate tree.ConclusionsSuch critical assessments of the accuracy and robustness of analytical pipelines are essential to progress in both research and applied settings

Dyadic influence of hope and optimism on patient marital satisfaction among couples with advanced breast cancer

PURPOSE: An estimated 10-40 % of breast cancer (BC) patients report negative changes to their partnered relationships. Literature suggests that for these patients, marital satisfaction is related to depression and other quality of life factors which are associated with survivorship and treatment response. However, existing literature does not provide a clear explanation of the factors that strengthen vs. create strain in couples facing cancer. Given the benefits of a satisfying relationship to patient quality of life, it is important to better understand factors that put patients at greater risk for marital difficulties. This study examined the differential and combined roles of hope and optimism among BC patients and their partners on patient marital satisfaction. METHOD: Fifty-six breast cancer patient-partner dyads completed study questionnaires as part of a larger study. Regression analyses were used to examine the main and interaction effects of patient and partner hope and optimism on patient marital satisfaction. RESULTS AND CONCLUSION: Higher patient and partner hope predicted greater patient marital satisfaction, whereas optimism did not. These results are divergent from the literature on optimism and well-being, which shows the importance of studying these two traits concurrently. Interaction effects suggest certain combinations of patient and partner hope and optimism are more beneficial than others for patient marital satisfaction and suggest a dyadic approach is important for investigation of well-being in breast cancer

Children: a vital component for achieving total sanitation and associated benefits (Bangladesh case study)

While the impact of poor sanitation is often measured by the effects on children, most sanitation interventions target adults. Global monitoring of sanitation coverage against the Millennium Development Goals (MDGs) generally also overlooks sanitation among young children. In Bangladesh, the faeces of only 22% of children under age three were disposed of safely in 2006, and children in more marginalized households were least likely to have their faeces safely disposed of. Even in households with improved sanitation, 22% of children’s faeces were reported to be left in the open. These inequities are emblematic of trends seen in developing countries worldwide. This paper provides a policy and programming-relevant overview of child sanitation in Bangladesh, a country with relatively more interventions focused on increasing demand, improving supply, and creating an enabling environment for the safe disposal of child faeces

Integrating environmental sustainability into the water and sanitation sector: lessons from tsunami disaster response

During the recovery phase following a disaster, humanitarian aid organizations are uniquely positioned to implement water and sanitation activities that go beyond disaster recovery to provide beneficiaries with systems that are more environmentally sustainable than pre-disaster conditions. Oftentimes, however, the pressure to rapidly restore post-disaster water and sanitation systems leads to a lack of coordinated planning and missed opportunities to implement innovative technologies that can make communities more resilient to future disasters and reduce long-term ecosystem impacts. Following the 2004 Indian Ocean tsunami, several humanitarian aid agencies recognized the importance of integrating environmental sustainability concepts into their water and sanitation relief operations. This paper examines methods and strategies for addressing environmental stewardship within the humanitarian aid water and sanitation sector through global partnerships with environmental organizations, with case studies from Indonesia, Sri Lanka, and Maldives. Lessons learned from application of environmental stewardship approaches in this disaster response can be used to remodel and improve future humanitarian aid relief operations

Water circulation and impact on water quality in the southwest of Efate Island, Vanuatu

In Small Island Developing States (SIDS), water pollution is not monitored or assessed frequently enough to fully understand the processes, impacts of water quality issues and what solutions are available This study investigated flushing time in Erakor lagoon and Port Vila Bay, Vanuatu using a numerical model developed in Delft3D. Microbial contamination by Escherichia coli was detected in multiple locations in the lagoon system with counts exceeding thresholds related to human health concerns. Modelling demonstrated a poor flushing time overall with a further decrease as the influence of waves and wind increased, especially in Vila Bay. Sea level rise resulted in an increase in flushing time downstream of the lagoon near the open sea, while with a decrease upstream and in Vila Bay. Based on these results, we recommend long-term continuous monitoring and identification of higher risks areas to prioritise decisions around wastewater management

High-resolution temporal profiling of transcripts during Arabidopsis leaf senescence reveals a distinct chronology of processes and regulation

Leaf senescence is an essential developmental process that impacts dramatically on crop yields and involves altered regulation of thousands of genes and many metabolic and signaling pathways, resulting in major changes in the leaf. The regulation of senescence is complex, and although senescence regulatory genes have been characterized, there is little information on how these function in the global control of the process. We used microarray analysis to obtain a highresolution time-course profile of gene expression during development of a single leaf over a 3-week period to senescence. A complex experimental design approach and a combination of methods were used to extract high-quality replicated data and to identify differentially expressed genes. The multiple time points enable the use of highly informative clustering to reveal distinct time points at which signaling and metabolic pathways change. Analysis of motif enrichment, as well as comparison of transcription factor (TF) families showing altered expression over the time course, identify clear groups of TFs active at different stages of leaf development and senescence. These data enable connection of metabolic processes, signaling pathways, and specific TF activity, which will underpin the development of network models to elucidate the process of senescence

Ultrasonographic Visualization of the Ovaries to Detect Ovarian Cancer According to Age, Menopausal Status and Body Type

Because the effects of age, menopausal status, weight and body mass index (BMI) on ovarian detectability by transvaginal ultrasound (TVS) have not been established, we determined their contributions to TVS visualization of the ovaries. A total of 29,877 women that had both ovaries visualized on their first exam were followed over 202,639 prospective TVS exams. All images were reviewed by a physician. While visualization of both ovaries decreased with age, one or both ovaries could be visualized in two of every three women over 80 years of age. Around 93% of pre-menopausal women and ~69% of post-menopausal women had both ovaries visualized. Both ovaries were visualized in ~72% of women weighing over 300 lbs. and in ~70% of women with a BMI over 40. Conclusions: Age had the greatest influence on the visualization of the ovaries. The ovaries can be visualized well past the menopause. Body habitus was not limiting to TVS ovarian imaging, and TVS should be considered capable of imaging one or both ovaries in two of every three women over 80 years of age. Thus, older and obese patients remain good candidates for TVS exams

Ecological genetics in the North Atlantic: environmental gradients and adaptation at specific loci

The North Atlantic intertidal community provides a rich set of organismal and environmental material for the study of ecological genetics. Clearly defined environmental gradients exist at multiple spatial scales: there are broad latitudinal trends in temperature, meso-scale changes in salinity along estuaries, and smaller scale gradients in desiccation and temperature spanning the intertidal range. The geology and geography of the American and European coasts provide natural replication of these gradients, allowing for population genetic analyses of parallel adaptation to environmental stress and heterogeneity. Statistical methods have been developed that provide genomic neutrality tests of population differentiation and aid in the process of candidate gene identification. In this paper, we review studies of marine organisms that illustrate associations between an environmental gradient and specific genetic markers. Such highly differentiated markers become candidate genes for adaptation to the environmental factors in question, but the functional significance of genetic variants must be comprehensively evaluated. We present a set of predictions about locus-specific selection across latitudinal, estuarine, and intertidal gradients that are likely to exist in the North Atlantic. We further present new data and analyses that support and contradict these simple selection models. Some taxa show pronounced clinal variation at certain loci against a background of mild clinal variation at many loci. These cases illustrate the procedures necessary for distinguishing selection driven by internal genomic vs. external environmental factors. We suggest that the North Atlantic intertidal community provides a model system for identifying genes that matter in ecology due to the clarity of the environmental stresses and an extensive experimental literature on ecological function. While these organisms are typically poor genetic and genomic models, advances in comparative genomics have provided access to molecular tools that can now be applied to taxa with well-defined ecologies. As many of the organisms we discuss have tight physiological limits driven by climatic factors, this synthesis of molecular population genetics with marine ecology could provide a sensitive means of assessing evolutionary responses to climate change

Climate change impacts on the coral reefs of the UK Overseas Territory of the Pitcairn Islands: Resilience and adaptation considerations

The coral reefs of the Pitcairn Islands are in one of the most remote areas of the Pacific Ocean, and yet they are exposed to the impacts of anthropogenic climate change. The Pitcairn Islands Marine Protected Area was designated in 2016 and is one of the largest in the world, but the marine environment around these highly isolated islands remains poorly documented. Evidence collated here indicates that while the Pitcairn Islands' reefs have thus far been relatively sheltered from the effect of warming sea temperatures, there is substantial risk of future coral decalcification due to ocean acidification. The projected acceleration in the rate of sea level rise, and the reefs' exposure to risks from distant ocean swells and cold-water intrusions, add further uncertainty as to whether these islands and their reefs will continue to adapt and persist into the future. Coordinated action within the context of the Pitcairn Islands Marine Protected Area can help enhance the resilience of the reefs in the Pitcairn Islands. Options include management of other human pressures, control of invasive species and active reef interventions. More research, however, is needed in order to better assess what are the most appropriate and feasible options to protect these reefs