Genome-wide SNP identification by high-throughput sequencing and selective mapping allows sequence assembly positioning using a framework genetic linkage map

Determining the position and order of contigs and scaffolds from a genome assembly within an organism’s genome remains a technical challenge in a majority of sequencing projects. In order to exploit contemporary technologies for DNA sequencing. We developed a strategy for whole genome single nucleotide polymorphism sequencing allowing the positioning of sequence contigs onto a linkage map using the bin mapping method. The strategy was tested on a draft genome of the fungal pathogen Venturia inaequalis, the causal agent of apple scab, and further validated using sequence contigs derived from the diploid plant genome Fragaria vesca. Using our novel method we were able to anchor 70% and 92% of sequences assemblies for V. inaequalis and F. vesca, respectively, to genetic linkage maps. We demonstrated the utility of this approach by accurately determining the bin map positions of the majority of the large sequence contigs from each genome sequence and validated our method by mapping single sequence repeat markers derived from sequence contigs on a full mapping population.Deciduous Fruit Producers Trust THRIP Program National Research Foundation Claude Harris Leon FoundationWeb of Scienc

Boltzmann brains and the scale-factor cutoff measure of the multiverse

To make predictions for an eternally inflating "multiverse", one must adopt a procedure for regulating its divergent spacetime volume. Recently, a new test of such spacetime measures has emerged: normal observers - who evolve in pocket universes cooling from hot big bang conditions - must not be vastly outnumbered by "Boltzmann brains" - freak observers that pop in and out of existence as a result of rare quantum fluctuations. If the Boltzmann brains prevail, then a randomly chosen observer would be overwhelmingly likely to be surrounded by an empty world, where all but vacuum energy has redshifted away, rather than the rich structure that we observe. Using the scale-factor cutoff measure, we calculate the ratio of Boltzmann brains to normal observers. We find the ratio to be finite, and give an expression for it in terms of Boltzmann brain nucleation rates and vacuum decay rates. We discuss the conditions that these rates must obey for the ratio to be acceptable, and we discuss estimates of the rates under a variety of assumptions.Comment: 32 pp, 2 figs. Modified to conform to the version accepted by Phys. Rev. D. The last paragraph of Sec. V-A, about Boltzmann brains in Minkowski space, has been significantly enlarged. Two sentences were added to the introduction concerning the classical approximation and the hope of finding a motivating principle for the measure. Several references were adde

Evaluation of gellan gum fluid gels as modified release oral liquids

Oral liquids are often preferred for drug administration to patients for whom swallowing is difficult, however formulating modified release versions can be challenging. A potential route to achieve modified release in oral liquids is by using fluid (sheared) gels formed by introducing a shear field during gelation in gel-forming biopolymers. These fluid gels can act as pourable viscoelastic fluids but retain true gel micro/nano structure. Here, we have demonstrated that fluid gels have potential as paediatric oral liquids preventing release of ibuprofen in simulated gastric fluid. Subsequent release at pH 7.4 was affected by the duration of exposure and magnitude of acid pH with a linear relationship between onset of release and the preceding acidic exposure duration. Delayed release was a result of increasing gel stiffness, a consequence of the acidity of the initial release media and exposure time. A much faster release rate was measured when exposure time in acid was 10 min compared with 60 min. This study highlights the potential to design fluid gels that are tuned to have a specified stiffness at a particular pH and exposure time. This could enable the preparation oral liquids with modified release behaviour

Understanding future water challenges in a highly regulated Indian river basin — modelling the impact of climate change on the hydrology of the upper Narmada

The Narmada river basin is a highly regulated catchment in central India, supporting a population of over 16 million people. In such extensively modified hydrological systems, the influence of anthropogenic alterations is often underrepresented or excluded entirely by large-scale hydrological models. The Global Water Availability Assessment (GWAVA) model is applied to the Upper Narmada, with all major dams, water abstractions and irrigation command areas included, which allows for the development of a holistic methodology for the assessment of water resources in the basin. The model is driven with 17 Global Circulation Models (GCMs) from the Coupled Model Intercomparison Project Phase 5 (CMIP5) ensemble to assess the impact of climate change on water resources in the basin for the period 2031–2060. The study finds that the hydrological regime within the basin is likely to intensify over the next half-century as a result of future climate change, causing long-term increases in monsoon season flow across the Upper Narmada. Climate is expected to have little impact on dry season flows, in comparison to water demand intensification over the same period, which may lead to increased water stress in parts of the basin

Feasibility study to assess the delivery of a novel isometric exercise intervention for people with stage 1 hypertension in the NHS: protocol for the IsoFIT-BP study including amendments to mitigate the risk of COVID-19.

BackgroundHypertension  (HTN) affects approximately 25% of the UK population and is a leading cause of mortality. Associated annual health care costs run into billions. National treatment guidance includes initial lifestyle advice, followed by anti-hypertensive medication if blood pressure (BP) remains high. However, adoption and adherence to recommended exercise guidelines, dietary advice and anti-hypertensive medication is poor. Four short bouts of isometric exercise (IE) performed 3 days per week (d/wk) at home elicits clinically significant reductions in BP in those with normal to high-normal BP. This study will determine the feasibility of delivering personalised IE to patients with stage 1 hypertension for whom lifestyle changes would be recommended before medication within NHS primary care.MethodsThis is a randomised controlled feasibility study. Participants were 18+ years, with stage 1 hypertension, not on anti-hypertensive medication and without significant medical contraindications. Trial arms will be standard lifestyle advice (control) or isometric wall squat exercise and standard lifestyle advice. Primary outcomes include the feasibility of healthcare professionals to deliver isometric exercise prescriptions in a primary care NHS setting and estimation of the variance of change in systolic BP. Secondary outcomes include accuracy of protocol delivery, execution of and adherence to protocol, recruitment rate, attrition, perception of intervention viability, cost, participant experience and accuracy of home BP. The study will last 18 months. Sample size of 100 participants (50 per arm) allows for 20% attrition and 6.5% incomplete data, based upon 74 (37 each arm) participants (two-sided 95% confidence interval, width of 1.33 and standard deviation of 4) completing 4 weeks. Ethical approval IRAS ID is 274676.DiscussionBefore the efficacy of this novel intervention to treat stage 1 hypertension can be investigated in any large randomised controlled trial, it is necessary to ascertain if it can be delivered and carried out in a NHS primary care setting. Findings could support IE viability as a prophylactic/alternative treatment option.Trial registrationISRCTN13472393 , registered 18 August 2020

The Aligned z ~ 1 Radio Galaxy 3C 280

The z~1 radio galaxy 3C280 has a striking rest-frame UV morphology, with multiple line and continuum components precisely aligned with the radio structure, including an obvious semi-circular arc. We explore the nature of these various components by bringing together HST and ground-based imaging, ground-based spectroscopy, and radio mapping. From plausible decompositions of the spectra, we show that the continuum of the nuclear component is likely dominated by a combination of nebular thermal continuum, quasar light, and light from old stars. A component that falls directly on the probable path of the radio jet shows mostly nebular thermal continuum and includes contributions from a relatively young stellar population with an age around 100 Myr. The arc appears to be completely dominated by line emission and nebular thermal continuum, with no evidence for a significant stellar contribution. Though much of the aligned light is in UV components, the underlying old elliptical is also well-aligned with the radio axis. The elliptical is well-fit by a de Vaucouleurs profile, probably has a moderately old stellar population (~3 Gyr), and is a massive system with a velocity dispersion of sigma ~ 270 km/s that implies it contains a supermassive black hole. Although the arc and the extended emission surrounding the eastern lobe suggest that interactions between the radio lobe and jet must have been important in creating the UV morphology, the ionization and kinematic properties in these componentsare more consistent with photoionization than shock excitation. 3C280 may be a transition object between the compact steep-spectrum radio galaxies which seem to be shock-dominated, and the extended radio sources which may have evolved past this phase and rarely show shock signatures.Comment: 43 pages, including 14 figures; to appear in ApJ, vol 60

Quality of medication use in primary care - mapping the problem, working to a solution: a systematic review of the literature

Background: The UK, USA and the World Health Organization have identified improved patient safety in healthcare as a priority. Medication error has been identified as one of the most frequent forms of medical error and is associated with significant medical harm. Errors are the result of the systems that produce them. In industrial settings, a range of systematic techniques have been designed to reduce error and waste. The first stage of these processes is to map out the whole system and its reliability at each stage. However, to date, studies of medication error and solutions have concentrated on individual parts of the whole system. In this paper we wished to conduct a systematic review of the literature, in order to map out the medication system with its associated errors and failures in quality, to assess the strength of the evidence and to use approaches from quality management to identify ways in which the system could be made safer. Methods: We mapped out the medicines management system in primary care in the UK. We conducted a systematic literature review in order to refine our map of the system and to establish the quality of the research and reliability of the system. Results: The map demonstrated that the proportion of errors in the management system for medicines in primary care is very high. Several stages of the process had error rates of 50% or more: repeat prescribing reviews, interface prescribing and communication and patient adherence. When including the efficacy of the medicine in the system, the available evidence suggested that only between 4% and 21% of patients achieved the optimum benefit from their medication. Whilst there were some limitations in the evidence base, including the error rate measurement and the sampling strategies employed, there was sufficient information to indicate the ways in which the system could be improved, using management approaches. The first step to improving the overall quality would be routine monitoring of adherence, clinical effectiveness and hospital admissions. Conclusion: By adopting the whole system approach from a management perspective we have found where failures in quality occur in medication use in primary care in the UK, and where weaknesses occur in the associated evidence base. Quality management approaches have allowed us to develop a coherent change and research agenda in order to tackle these, so far, fairly intractable problems

The selection of search sources influences the findings of a systematic review of people’s views: a case study in public health

Background For systematic reviews providing evidence for policy decisions in specific geographical regions, there is a need to minimise regional bias when seeking out relevant research studies. Studies on people’s views tend to be dispersed across a range of bibliographic databases and other search sources. It is recognised that a comprehensive literature search can provide unique evidence not found from a focused search; however, the geographical focus of databases as a potential source of bias on the findings of a research review is less clear. This case study describes search source selection for research about people’s views and how supplementary searches designed to redress geographical bias influenced the findings of a systematic review. Our research questions are: a) what was the impact of search methods employed to redress potential database selection bias on the overall findings of the review? and b) how did each search source contribute to the identification of all the research studies included in the review? Methods The contribution of 25 search sources in locating 28 studies included within a systematic review on UK children’s views of body size, shape and weight was analysed retrospectively. The impact of utilising seven search sources chosen to identify UK-based literature on the review’s findings was assessed. Results Over a sixth (5 out of 28) of the studies were located only through supplementary searches of three sources. These five studies were of a disproportionally high quality compared with the other studies in the review. The retrieval of these studies added direction, detail and strength to the overall findings of the review. All studies in the review were located within 21 search sources. Precision for 21 sources ranged from 0.21% to 1.64%. Conclusions For reducing geographical bias and increasing the coverage and context-specificity of systematic reviews of people’s perspectives and experiences, searching that is sensitive and aimed at reducing geographical bias in database sources is recommended

Single cell analysis reveals satellite cell heterogeneity for proinflammatory chemokine expression

Background: The expression of proinflammatory signals at the site of muscle injury are essential for efficient tissue repair and their dysregulation can lead to inflammatory myopathies. Macrophages, neutrophils, and fibroadipogenic progenitor cells residing in the muscle are significant sources of proinflammatory cytokines and chemokines. However, the inducibility of the myogenic satellite cell population and their contribution to proinflammatory signaling is less understood.Methods: Mouse satellite cells were isolated and exposed to lipopolysaccharide (LPS) to mimic sterile skeletal muscle injury and changes in the expression of proinflammatory genes was examined by RT-qPCR and single cell RNA sequencing. Expression patterns were validated in skeletal muscle injured with cardiotoxin by RT-qPCR and immunofluorescence.Results: Satellite cells in culture were able to express Tnfa, Ccl2, and Il6, within 2 h of treatment with LPS. Single cell RNA-Seq revealed seven cell clusters representing the continuum from activation to differentiation. LPS treatment led to a heterogeneous pattern of induction of C-C and C-X-C chemokines (e.g., Ccl2, Ccl5, and Cxcl0) and cytokines (e.g., Tgfb1, Bmp2, Il18, and Il33) associated with innate immune cell recruitment and satellite cell proliferation. One cell cluster was enriched for expression of the antiviral interferon pathway genes under control conditions and LPS treatment. Activation of this pathway in satellite cells was also detectable at the site of cardiotoxin induced muscle injury.Conclusion: These data demonstrate that satellite cells respond to inflammatory signals and secrete chemokines and cytokines. Further, we identified a previously unrecognized subset of satellite cells that may act as sensors for muscle infection or injury using the antiviral interferon pathway

Advancing translational research with the Semantic Web

<p>Abstract</p> <p>Background</p> <p>A fundamental goal of the U.S. National Institute of Health (NIH) "Roadmap" is to strengthen <it>Translational Research</it>, defined as the movement of discoveries in basic research to application at the clinical level. A significant barrier to translational research is the lack of uniformly structured data across related biomedical domains. The Semantic Web is an extension of the current Web that enables navigation and meaningful use of digital resources by automatic processes. It is based on common formats that support aggregation and integration of data drawn from diverse sources. A variety of technologies have been built on this foundation that, together, support identifying, representing, and reasoning across a wide range of biomedical data. The Semantic Web Health Care and Life Sciences Interest Group (HCLSIG), set up within the framework of the World Wide Web Consortium, was launched to explore the application of these technologies in a variety of areas. Subgroups focus on making biomedical data available in RDF, working with biomedical ontologies, prototyping clinical decision support systems, working on drug safety and efficacy communication, and supporting disease researchers navigating and annotating the large amount of potentially relevant literature.</p> <p>Results</p> <p>We present a scenario that shows the value of the information environment the Semantic Web can support for aiding neuroscience researchers. We then report on several projects by members of the HCLSIG, in the process illustrating the range of Semantic Web technologies that have applications in areas of biomedicine.</p> <p>Conclusion</p> <p>Semantic Web technologies present both promise and challenges. Current tools and standards are already adequate to implement components of the bench-to-bedside vision. On the other hand, these technologies are young. Gaps in standards and implementations still exist and adoption is limited by typical problems with early technology, such as the need for a critical mass of practitioners and installed base, and growing pains as the technology is scaled up. Still, the potential of interoperable knowledge sources for biomedicine, at the scale of the World Wide Web, merits continued work.</p