Transcriptome sequencing, annotation and polymorphism detection in the hop bush, Dodonaea viscosa

The hop bush, Dodonaea viscosa, is a trans-oceanic species distributed oversix continents. It evolved in Australia where it is found over a wide range of habitat types and is an ecologically important species. Limited genomic resources are currently available for this species, thus our understanding of its evolutionary history and ecological adaptation is restricted. Here, we present a comprehensive transcriptome dataset for future genomic studies into this species.We performed Illumina sequencing of cDNA prepared from leaf tissue collected from seven populations of D. viscosa ssp. angustissima and spatulata distributed along an environmental gradient in South Australia. Sequenced reads were assembled to provide a transcriptome resource. Contiguous sequences (contigs) were annotated using BLAST searches against the NCBI non-redundant database and gene ontology definitions were assigned. Single nucleotide polymorphisms were detected for the establishment of a genetic marker set. A comparison between the two subspecies was also carried out.Illumina sequencing returned 268,672,818 sequence reads, which were de novoassembled into 105,125 contigs. Contigs with significant BLAST alignments (E value < 1e(-5))numbered at 44,191, with 38,311 of these having their most significant hits to sequences from land plant species. Gene Ontology terms were assigned to 28,440 contigs and KEGG analysis identified 146 pathways that the gene products from 5,070 contigs are potentially involved in. The subspecies comparison identified 8,494 fixed SNP differences across 3,979 contiguous sequences, indicating a level of genetic differentiation between them. Across all samples, 248,235 SNPs were detected.We have established a significant genomic data resource for D. viscosa,providing a comprehensive transcriptomic reference. Genetic differences among morphologically distinct subspecies were found. A wide range of putative gene regions were identified along with a large set of variable SNP markers, providing a basis for studies into the evolution and ecological adaptation of D. viscosa.Matthew J. Christmas, Ed Biffin and Andrew J. Low

Designing an intervention for improving primary care management of sleep problems (REST: Resources for Effective Sleep Treatment)

Brief outline of context An improvement project was begun in a Primary Care Trust in Lincolnshire a large rural county in the East Midlands of the United Kingdom comprising almost 700,000 patients. The projects included patients, general practitioners and their primary care teams, pharmacists and research and audit teams. Brief outline of problem Hypnotic prescribing rates from general practice Prescribing Analysis and Cost Data was identified by the executive as high in Lincolnshire compared to the rest of the East Midlands and the United Kingdom. Published research has shown that the clinical benefits of hypnotic drugs are small with significant risks of complications from adverse cognitive, psychiatric or psychomotor effects which may persist for several months after stopping the drug. The extent of the problem, its nature and the barriers to improvement were not well understood given that previous attempts to improve prescribing rates in this area of practice had failed. Assessment of problem and analysis of its causes Previous efforts to improve this aspect of quality and safety in healthcare in Lincolnshire and nationally have been hampered because of practitioner and patient attitudes, lack of organisational support or systems for change and an emphasis on other areas of healthcare. To understand the barriers to improving prescribing more fully we used questionnaires to general practitioners and patients and measured variation in prescribing rates across practices. Unforeseen and hitherto invisible problems were revealed by the responses. In addition, the views of patients prescribed hypnotics in the previous six months exposed high rates of inappropriate long term prescribing (94.9%had taken benzodiazepine or Z drug hypnotics for four weeks or more), side effects (41.8%reported at least one side effect), a wish to stop taking drugs (Z-drugs vs. benzodiazepines: 22.7 vs. 12.3%; p=0.001) and previous attempts by patients to come off medication (Z-drugs vs. benzodiazepines: 52.4% vs. 41.0%; p=0.001). Potential barriers to improvement included attitudes of general practitioners which supported prescribing of newer (Z drug) hypnotics for the majority of indications. More positively, practitioners were aware of their practice prescribing rates to the extent that they were able to identify whether they were in a high, intermediate or low prescribing practice. Most doctors held a negative perception of hypnotics and were positive to the idea of reducing prescribing in this area. Practitioners’ favoured methods for reducing prescribing helped inform potential strategies for change and will be presented. On the basis of these results it was felt that systematic efforts at implementation and improvement were likely to be successful given appropriate organisational support from the Primary Care Trust. Strategy for change: How did you implement the proposed change? What staff or other groups were involved? How did you disseminate the results of your analysis and your plans for change to the groups involved with/affected by the planned change? What was the timetable for change? A change project was developed, Resources for Effective Sleep Treatment (REST), with a number of stakeholders including partner organisation and patients. The aims of this project are to produce measurable improvements in the management of insomnia, specifically to: a. Reduce rate and (costs) of z-drug prescribing by 50% in 3 years b. Reduce the rate (costs) of benzodiazepine hypnotic prescribing by 25% in 3 years c. Increase use of recorded non-pharmacological measures in insomnia by at least 100% in 3 years. d. Improve the user experience of management of insomnia. We will use evidence based methods to develop an effective spread and adoption strategy to effect a sustained and sustainable change in practice in relation to management of insomnia. We will initially work with 10 pilot practices (10% of the total) using rapid experimentation (plan, do, study, act) cycles. We plan to work with these willing adopter practices and practitioners to develop a network of good practice, measurement and improvement tools, opinion leaders and champions for good practice using rapid cycle of change. We will also undertake focus groups with prescribing practitioners and patients to help understand more fully the barriers and facilitators, to identify good practice and to design appropriate improvement methods and interventions in this area of practice. Tailored interventions for practices involving clinician, pharmacy, secondary care and administrative support could help bring about change in clinical management. Measurement of improvement We will gather and analyse prescribing and improvement data from all practices in the county to enable systematic spread and adoption of improvements in prescribing and improvement methods more generally in the county. Lessons learned This project has emphasised the importance of gathering data at the onset of quality improvement initiatives to understand invisible barriers or facilitators for change and of involvement of patients and practitioners in their initial and ongoing development. Message for others Quality improvement projects benefit from research as well as quality improvement expertise in order to analyse, present and utilise information for their appropriate design

Targeted capture to assess neutral genomic variation in the narrow-leaf hopbush across a continental biodiversity refugium

The Adelaide geosyncline, a mountainous region in central southern Australia, is purported to be an important continental refugium for Mediterranean and semi-arid Australian biota, yet few population genetic studies have been conducted to test this theory. Here, we focus on a plant species distributed widely throughout the region, the narrow-leaf hopbush, Dodonaea viscosa ssp. angustissima, and examine its genetic diversity and population structure. We used a hybrid-capture target enrichment technique to selectively sequence over 700 genes from 89 individuals across 17 sampling locations. We compared 815 single nucleotide polymorphisms among individuals and populations to investigate population genetic structure. Three distinct genetic clusters were identified; a Flinders/Gammon ranges cluster, an Eastern cluster, and a Kangaroo Island cluster. Higher genetic diversity was identified in the Flinders/Gammon Ranges cluster, indicating that this area is likely to have acted as a refugium during past climate oscillations. We discuss these findings and consider the historical range dynamics of these populations. We also provide methodological considerations for population genomics studies that aim to use novel genomic approaches (such as target capture methods) on non-model systems. The application of our findings to restoration of this species across the region are also considered.Matthew J. Christmas, Ed Biffin, Martin F. Breed & Andrew J. Low

UK Defence Research Agency the Two UK \u27Space Technology Research Vehicles\u27: First In-Orbit Results

The UK Defence Research Agency is about to launch two 50kg \u27Space Technology Research Vehicles\u27 which have as their major objective the demonstration and in-orbit evaluation of new technologies which have application to future space missions, both large and small. The STRVs are due for launch together on an Ariane 4 in June 1994 and will go into a geostationary transfer orbit which provides a very harsh (and therefore good) environment for the evaluation of the new technology. Areas of research for the mission include the use of advanced structural materials, use of new radiation hardened computers, sensors, solar cells and microelectronics, use of ADA software in a restricted memory space, demonstration of cryocoolers, measurement of electrostatic charge, elimination of electrostatic charge, measurement of atomic oxygen erosion, measurement of the incidence of cosmic rays and total dose radiation, improved battery charging techniques, and also the demonstration of key components from the UK ion thruster system. The two satellites not only carry a suite of 14 experiments between them, including experiments from BMDO, ESA and various universities but they also incorporate new technologies into the bus itself. This paper will give a full overview of the mission including a description of the in-orbit performance of the two spacecraft. Some of the main results from the early part of the mission with respect to spacecraft, subsystem and experiment performance will be presented together with a preview of the mission plan to follow during the remainder of the one year mission

On Random Sampling and Fourier Transform Estimation in Sea Waves Prediction

Improving the safety of a wide range of launch and recovery operations is of great international maritime interest. Deterministic sea wave prediction (DSWP) is a relatively new branch of science that can offer such opportunities by predicting the actual shape of the sea surface and its evolution for short time in the future. Fourier transform technique is the main building block in DSWP, which requires measurements of the sea surface. Nonetheless, uniformly sampled measurements of the sea surface cannot be practically achieved for various reasons. Conventional X-band radars are the most realistic candidate to provide a low-cost convenient source of two-dimensional wave profile information for DSWP purposes. Ship movement and mechanically rotating scanning antennas are among sources of irregularity in sea surface sampling. This in turn introduces errors when traditional Fourier transform based wave prediction methods are used. In this paper we show that by modelling the radar sampling instants as random variables and using the estimator of Tarczynski and Allay to process the samples, a reliable solution for DSWP can be constituted

A novel Markov logic rule induction strategy for characterizing sports video footage

The grounding of high-level semantic concepts is a key requirement of video annotation systems. Rule induction can thus constitute an invaluable intermediate step in characterizing protocol-governed domains, such as broadcast sports footage. We here set out a novel “clause grammar template” approach to the problem of rule-induction in video footage of court games that employs a second-order meta grammar for Markov Logic Network construction. The aim is to build an adaptive system for sports video annotation capable, in principle, both of learning ab initio and also adaptively transferring learning between distinct rule domains. The method is tested with respect to both a simulated game predicate generator and also real data derived from tennis footage via computer-vision based approaches including HOG3D based player-action classification, Hough-transform based court detection, and graph-theoretic ball-tracking. Experiments demonstrate that the method exhibits both error resilience and learning transfer in the court domain context. Moreover the clause template approach naturally generalizes to any suitably-constrained, protocol-governed video domain characterized by feature noise or detector error

Sea State Estimation from Uncalibrated, Monoscopic Video

This is the final version. Available on open access from Springer via the DOI in this recordVideo of the ocean surface is used as a means for estimating the sea state. Time series of pixel intensity values are given as input to a method that uses the Kalman filter and the least squares approximate solution for estimating the uncalibrated video amplitude spectrum. A method is proposed for scaling this spectrum to metres with the use of an empirical model of the ocean. The significant wave height is estimated from the calibrated video amplitude spectrum. The results are tested against two sets of video data, and buoy measurements in both cases are solely used for indicating the true state. For significant wave height values between 0.5 and 3.6 m, the maximum observed value of root mean square error is 0.37 m and of mean absolute percentage error 16%

Sea state from ocean video with singular spectrum analysis and extended Kalman filter

This is the final version. Available on open access from Springer via the DOI in this recordA method for estimating key parameters of ocean waves (the dominant frequency and the significant wave height) from uncalibrated monoscopic video is proposed, based on temporal variation of the wave field, specifically time series of pixel intensities. The methodology tracks the principal component of the movement of water in the video, which we propose is associated with the dominant frequency of the ocean. To accomplish this, the singular spectrum analysis algorithm and the extended Kalman filter are used. Then, the shape of an empirical spectrum is used in order to translate the dominant frequency output into a significant wave height estimation

Cytomegalovirus drives Vδ2neg γδ T cell inflation in many healthy virus carriers with increasing age

Cytomegalovirus (CMV) usually causes lifelong asymptomatic infection, but over time can distort immune profiles. Recent reports describe selective expansion of Vδ2(neg) γδ T cells in healthy and immunocompromised CMV carriers. Having shown previously that virus-specific CD8(+) and CD4(+) T cell responses are increased significantly in elderly CMV carriers, probably driven by chronic stimulation, we hypothesized that Vδ2(neg) γδ T cells may also be expanded with age. Our results show that Vδ2(neg) γδ T cells are increased significantly in CMV-seropositive healthy individuals compared to CMV-seronegative controls in all age groups. The differences were most significant in older age groups (P < 0·0001). Furthermore, while Vδ2(neg) γδ T- cells comprise both naive and memory cells in CMV-seronegative donors, highly differentiated effector memory cells are the dominant phenotype in CMV carriers, with naive cells reduced significantly in numbers in CMV-seropositive elderly. Although phenotypically resembling conventional CMV-specific T cells, Vδ2(neg) γδ T cells do not correlate with changes in magnitude of CMV-specific CD4(+) or CD8(+) T cell frequencies within those individuals, and do not possess ex-vivo immediate effector function as shown by CMV-specific CD4(+) and CD8(+) T cells. However, after short-term culture, Vδ2(neg) γδ T cells demonstrate effector T cell functions, suggesting additional requirements for activation. In summary, Vδ2(neg) γδ T cells are expanded in many older CMV carriers, demonstrating a further level of lymphocyte subset skewing by CMV in healthy individuals. As others have reported shared reactivity of Vδ2(neg) γδ T cells towards tumour cells, the composition of γδ T cell subsets may also have implications for risk of developing cancer in elderly people