Performance analysis of a parallel, multi-node pipeline for DNA sequencing

Post-sequencing DNA analysis typically consists of read mapping followed by variant calling and is very time-consuming, even on a multi-core machine. Recently, we proposed Halvade, a parallel, multi-node implementation of a DNA sequencing pipeline according to the GATK Best Practices recommendations. The MapReduce programming model is used to distribute the workload among different workers. In this paper, we study the impact of different hardware configurations on the performance of Halvade. Benchmarks indicate that especially the lack of good multithreading capabilities in the existing tools (BWA, SAMtools, Picard, GATK) cause suboptimal scaling behavior. We demonstrate that it is possible to circumvent this bottleneck by using multiprocessing on high-memory machines rather than using multithreading. Using a 15-node cluster with 360 CPU cores in total, this results in a runtime of 1 h 31 min. Compared to a single-threaded runtime of similar to 12 days, this corresponds to an overall parallel efficiency of 53%

USING LINEAR MATRIX INEQUALITY METHOD TO DESIGN MINIMUM-LENGHT FINITE IMPULSE RESPONSE LOOP FILTERS IN FIXED WiMAX PLL

We designed Finite Impulse Response (FIR), digital filters by Semi-Definite Programming (SDP) using SeDuMi (self-dual minimization) toolbox software. The stability is assured using Linear Matrix Inequality (LMI) constraints. The minimum length FIR filter algorithm was used to proof that the order of the FIR filter, which was designed, is optimal for our design specifications. The proposed method gave better result with regard to all specifications of control signal, where we had the faster system and more stable than the other systems

Satellite Images Unsupervised Classification Using Two Methods Fast Otsu and K-means

Two unsupervised classifiers for optimum multithreshold are presented; fast Otsu and k-means. The unparametric methods produce an efficient procedure to separate the regions (classes) by select optimum levels, either on the gray levels of image histogram (as Otsu classifier), or on the gray levels of image intensities(as k-mean classifier), which are represent threshold values of the classes. In order to compare between the experimental results of these classifiers, the computation time is recorded and the needed iterations for k-means classifier to converge with optimum classes centers. The variation in the recorded computation time for k-means classifier is discussed

Exploring health professionals’ and women's awareness of models of maternity care evidence

A Cochrane systematic review has shown midwife-led continuity models of care provide explicit benefits for mothers and babies compared with other models of maternity care, with a comparable level of safety. The Cochrane review has had much international impact. This study explored the local impact of the review, alongside other midwife-led care evidence and guidelines. Electronic surveys were undertaken exploring women's and health professionals' awareness of models of maternity care evidence, including midwife-led care and homebirth, and how they utilise evidence to guide their choices and practice. A low awareness of much of the available evidence was shown among the women and the professionals. There is a need for better dissemination of information to professionals as they are women's preferred source of information about the options available for place of birth and midwife-led care

XPS and STM studies of the oxidation of hydrogen chloride at Cu(100) surfaces

The dissociative chemisorption of HCl on clean and oxidized Cu(100) surfaces has been investigated using x-ray photoelectron spectroscopy (XPS) and scanning tunneling microscopy (STM). Whereas the dissociation of HCl at the clean surface is limited to the formation of a (√ 2 × √ 2)-R45° Cl(a) monolayer, the presence of surface oxygen removes this barrier, leading to chlorine coverages up to twice that obtained at the clean surface. Additional features in the STM images that appear at these coverages are tentatively assigned to the nucleation of CuCl islands. The rate of reaction of the HCl was slightly higher on the oxidized surface but unaffected by the initial oxygen concentration or the availability of clean copper sites. Of the two distinct domains of adsorbed oxygen identified at room temperature on the Cu(100) surfaces, the (√ 2 × √ 2)-R45° structure reacts slightly faster with HCl than the missing row (√ 2 × 2 √ 2)-R45° O(a) structure. The results address the first stages in the formation of a copper chloride and present an interesting comparison with the HCl/O(a) reaction at Cu(110) surfaces, where oxygen also increased the extent of HCl reactions. The results emphasize the importance of the exothermic reaction to form water in the HCl/O(a) reaction on copper

The Role of Systematic Covariance and Coskewness in the Pricing of Real Estate: Evidence from Equity REITs

This study explores the impact of systematic risk (beta) and systematic coskewness on EREIT returns. The test uses the Skewness Preference CAPM, which includes the impact of the third moment on returns. The findings are that systematic risk impacts return in the predicted manner. However, there is no evidence that systematic coskewness is a determinant of EREIT return, which is contrary to prior findings using other financial instruments. Also, the problem of multicollinearity noted in earlier tests of the model does not occur herein.

Assessing the validity of decision support systems : a case study from the sustainable management of the West Bank Aquifer

Decision support systems (DSS) have been widely advocated as key tools for the integrated management of water resources, which emerged as a critical need for addressing the various technical, economic, social, environmental and politicoinstitutional challenges facing the management of water resources. This thesis aims at developing a framework for assessing the validity of DSS in application to water resources management, more particularly reviewing Multi-Criteria Analysis (MCA) and Cost-Benefit Analysis (CBA) as a basis for decision-making. This is critical at times of increasing demand for tools such as DSS, and therefore the increasing importance of overcoming a major DSS limitation, which is validity. The proposed framework consists of two complementary approaches: (1) assessing intra-model validity (MCA), an approach which consists of studying the level of confidence in the comprehensiveness of management options (MO) and basic indicators (BI), analysing uncertainty in the performance values and weights assigned to BI, undertaking a sensitivity analysis of MO ranking to BI performance values and weights, and, based on results, generating as well as evaluating strategy alternatives; (2) assessing DSS inter-model validity, an approach which consists of comparing models (MCA and CBA). The application of the framework to the Sustainable Management of the West Bank Aquifer (SUSMAQ) generates results very much consistent with literature findings: importance of sensitivity analysis as a practical alternative to uncertainty analysis, sensitivity of MO ranking to BI performance values more than to BI weights, importance of accounting for indirect benefits and for the choice of discount rate in CBA, complementarity if not equivalence of MCA and CBA, etc. Although the aim of the thesis is methodological, the application uses validity assessment results to test various strategies for the management of water resources in the West Bank, as an illustrative example only.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Impact of frailty on outcomes after percutaneous coronary intervention: a prospective cohort study.

Background: Average life expectancy is rising, resulting in increasing numbers of elderly, frail individuals presenting with coronary artery disease and requiring percutaneous coronary intervention (PCI). PCI can be of value for this population, but little is known about the balance of benefit versus risk, particularly in the frail. Objective: To determine the relationship between frailty and clinical outcomes in patients undergoing PCI. Methods: Patients undergoing PCI, for either stable angina or acute coronary syndrome, were prospectively assessed for frailty using the Canadian Study of Health and Ageing Clinical Frailty Scale. Demographics, clinical and angiographic data were extracted from the hospital database. Mortality was obtained from the Office of National Statistics. Results: Frailty was assessed in 745 patients undergoing PCI. The mean age of patients was 62±12 years and 70% were males. The median frailty score was 3 (IQR 2–4). A frailty score ≥5, indicating significant frailty, was present in 81 (11%) patients. Frail patients required longer hospitalisation after PCI. Frailty was also associated with increased 30-day (HR 4.8, 95% CI 1.4 to 16.3, p=0.013) and 1 year mortality (HR 5.9, 95% CI 2.5 to 13.8, p<0.001). Frailty was a predictor of length of hospital stay and mortality, independent of age, gender and comorbidities. Conclusions: A simple assessment of frailty can help predict mortality and the length of hospital stay, and may therefore guide healthcare providers to plan PCI and appropriate resources for frail patients

Health practitioners' perceptions of the barriers and enablers to the implementation of reproductive genetic carrier screening: A systematic review.

BACKGROUND: As interest in reproductive genetic carrier screening rises, with increased availability, the role of healthcare practitioners is central in guiding uptake aligned with a couples' values and beliefs. Therefore, practitioners' views on implementation are critical to the success of any reproductive genetic carrier screening programme. AIM: To explore healthcare practitioners' perceptions of the barriers and enablers to implementation. MATERIALS & METHODS: We undertook a systematic review of the literature searching seven databases using health practitioner, screening and implementation terms returning 490 articles. RESULTS: Screening led to the inclusion of 26 articles for full-text review. We found three interconnected themes relating to reproductive genetic carrier screening: (i) use and impact, (ii) practitioners' beliefs and expectations and (iii) resources. DISCUSSION: Barriers and enablers to implementation were present within each theme and grouping these determinants by (a) community for example lack of public interest, (b) practitioner for example lack of practitioner time and (c) organisation for example lack of effective metrics, reveals a preponderance of practitioner barriers and organisational enablers. Linking barriers with potential enablers leaves several barriers unresolved (e.g., costs for couples) implying additional interventions may be required. CONCLUSION: Future research should draw on the findings from this study to develop and test strategies to facilitate appropriate offering of reproductive genetic carrier screening by healthcare practitioners