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%

The European Network for Translational Research in Atrial Fibrillation (EUTRAF): objectives and initial results.

Atrial fibrillation (AF) is the most common sustained arrhythmia in the general population. As an age-related arrhythmia AF is becoming a huge socio-economic burden for European healthcare systems. Despite significant progress in our understanding of the pathophysiology of AF, therapeutic strategies for AF have not changed substantially and the major challenges in the management of AF are still unmet. This lack of progress may be related to the multifactorial pathogenesis of atrial remodelling and AF that hampers the identification of causative pathophysiological alterations in individual patients. Also, again new mechanisms have been identified and the relative contribution of these mechanisms still has to be established. In November 2010, the European Union launched the large collaborative project EUTRAF (European Network of Translational Research in Atrial Fibrillation) to address these challenges. The main aims of EUTRAF are to study the main mechanisms of initiation and perpetuation of AF, to identify the molecular alterations underlying atrial remodelling, to develop markers allowing to monitor this processes, and suggest strategies to treat AF based on insights in newly defined disease mechanisms. This article reports on the objectives, the structure, and initial results of this network

A national survey of medical education fellowships

Purpose: The purpose of our study was to determine the prevalence, focus, time commitment, graduation requirements and programme evaluation methods of medical education fellowships throughout the United States. Medical education fellowships are defined as a single cohort of medical teaching faculty who participate in an extended faculty development programme. Methods: A 26-item online questionnaire was distributed to all US medical schools (n=127) in 2005 and 2006. The questionnaire asked each school if it had a medical education fellowship and the characteristics of the fellowship programme. Results: Almost half (n=55) of the participating schools (n=120, response rate 94.5 %) reported having fellowships. Duration (10–584 hours) and length (<1 month–48 months) varied; most focused on teaching skills, scholarly dissemination and curriculum design, and required the completion of a scholarly project. A majority collected participant satisfaction; few used other programme evaluation strategies. Conclusions: The number of medical education fellowships increased rapidly during the 1990s and 2000s. Across the US, programmes are similar in participant characteristics and curricular focus but unique in completion requirements. Fellowships collect limited programme evaluation data, indicating a need for better outcome data. These results provide benchmark data for those implementing or revising existing medical education fellowships

Welding of dissimilar alloys for high temperature heat exchangers for SOFC

Reduction in the cost of balance of plant applications is one of the top priority focus areas for the successful implementation of solid oxide fuel cell technology. High temperature heat exchangers are employed to heat cathode air utilizing either hot gases coming from the anode side of the stack or other hot gases generated by external processes. In order to reduce the cost of heat exchangers, it may be necessary to apply several different materials, each in a different temperature zone, for the construction of the heat exchanger. This technique would require the joining of dissimilar materials in the construction. In this work, welding of commercial candidate dissimilar materials is explored. Filler materials were identified using equilibrium phase diagrams and thermodynamic simulation software. Autogenous welding was performed and the welding defects were characterized. Finally, experimental weld microstructures were compared to phases predicted by the simulations

A Light Sterile Neutrino in the TopFlavor Model

A scenario based on the TopFlavor model is presented to explain the origin of a light sterile neutrino as indicated by all combined neutrino oscillation experiments. The model is phenomenologically well motivated and compatible with all available low-energy data. The derived nuetrino mass matrix can qualitatively explain the observed hierarchy in the neutrino mass splittings as indicated by the neutrino oscillation data. Numerical results are obtained for special cases.Comment: Plain Latex file, 12 page

Mechanical and surgical interventions for treating primary postpartum haemorrhage.

BACKGROUND:Primary postpartum haemorrhage (PPH) is commonly defined as bleeding from the genital tract of 500 mL or more within 24 hours of birth. It is one of the most common causes of maternal mortality worldwide and causes significant physical and psychological morbidity. An earlier Cochrane Review considering any treatments for the management of primary PPH, has been split into separate reviews. This review considers treatment with mechanical and surgical interventions. OBJECTIVES:To determine the effectiveness and safety of mechanical and surgical interventions used for the treatment of primary PPH. SEARCH METHODS:We searched Cochrane Pregnancy and Childbirth's Trials Register, ClinicalTrials.gov, the WHO International Clinical Trials Registry Platform (ICTRP) (26 July 2019) and reference lists of retrieved studies. SELECTION CRITERIA:Randomised controlled trials (RCTs) of mechanical/surgical methods for the treatment of primary PPH compared with standard care or another mechanical/surgical method. Interventions could include uterine packing, intrauterine balloon insertion, artery ligation/embolism, or uterine compression (either with sutures or manually). We included studies reported in abstract form if there was sufficient information to permit risk of bias assessment. Trials using a cluster-RCT design were eligible for inclusion, but quasi-RCTs or cross-over studies were not. DATA COLLECTION AND ANALYSIS:Two review authors independently assessed studies for inclusion and risk of bias, independently extracted data and checked data for accuracy. We used GRADE to assess the certainty of the evidence. MAIN RESULTS:We included nine small trials (944 women) conducted in Pakistan, Turkey, Thailand, Egypt (four trials), Saudi Arabia, Benin and Mali. Overall, included trials were at an unclear risk of bias. Due to substantial differences between the studies, it was not possible to combine any trials in meta-analysis. Many of this review's important outcomes were not reported. GRADE assessments ranged from very low to low, with the majority of outcome results rated as very low certainty. Downgrading decisions were mainly based on study design limitations and imprecision; one study was also downgraded for indirectness. External uterine compression versus normal care (1 trial, 64 women) Very low-certainty evidence means that we are unclear about the effect on blood transfusion (risk ratio (RR) 2.33, 95% confidence interval (CI) 0.66 to 8.23). Uterine arterial embolisation versus surgical devascularisation plus B-Lynch (1 trial, 23 women) The available evidence for hysterectomy to control bleeding (RR 0.73, 95% CI 0.15 to 3.57) is unclear due to very low-certainty evidence. The available evidence for intervention side effects is also unclear because the evidence was very low certainty (RR 1.09; 95% CI 0.08 to 15.41). Intrauterine Tamponade Studies included various methods of intrauterine tamponade: the commercial Bakri balloon, a fluid-filled condom-loaded latex catheter ('condom catheter'), an air-filled latex balloon-loaded catheter ('latex balloon catheter'), or traditional packing with gauze. Balloon tamponade versus normal care (2 trials, 356 women) One study(116 women) used the condom catheter. This study found that it may increase blood loss of 1000 mL or more (RR 1.52, 95% CI 1.15 to 2.00; 113 women), very low-certainty evidence. For other outcomes the results are unclear and graded as very low-certainty evidence: mortality due to bleeding (RR 6.21, 95% CI 0.77 to 49.98); hysterectomy to control bleeding (RR 4.14, 95% CI 0.48 to 35.93); total blood transfusion (RR 1.49, 95% CI 0.88 to 2.51); and side effects. A second study of 240 women used the latex balloon catheter together with cervical cerclage. Very low-certainty evidence means we are unclear about the effect on hysterectomy (RR 0.14, 95% CI 0.01 to 2.74) and additional surgical interventions to control bleeding (RR 0.20, 95% CI 0.01 to 4.12). Bakri balloon tamponade versus haemostatic square suturing of the uterus (1 trial, 13 women) In this small trial there was no mortality due to bleeding, serious maternal morbidity or side effects of the intervention, and the results are unclear for blood transfusion (RR 0.57, 95% CI 0.14 to 2.36; very low certainty). Bakri balloon tamponade may reduce mean 'intraoperative' blood loss (mean difference (MD) -426 mL, 95% CI -631.28 to -220.72), very low-certainty evidence. Comparison of intrauterine tamponade methods (3 trials, 328 women) One study (66 women) compared the Bakri balloon and the condom catheter, but it was uncertain whether the Bakri balloon reduces the risk of hysterectomy to control bleeding due to very low-certainty evidence (RR 0.50, 95% CI 0.05 to 5.25). Very low-certainty evidence also means we are unclear about the results for the risk of blood transfusion (RR 0.97, 95% CI 0.88 to 1.06). A second study (50 women) compared Bakri balloon, with and without a traction stitch. Very low-certainty evidence means we are unclear about the results for hysterectomy to control bleeding (RR 0.20, 95% CI 0.01 to 3.97). A third study (212 women) compared the condom catheter to gauze packing and found that it may reduce fever (RR 0.47, 95% CI 0.38 to 0.59), but again the evidence was very low certainty. Modified B-Lynch compression suture versus standard B-Lynch compression suture (1 trial, 160 women) Low-certainty evidence suggests that a modified B-Lynch compression suture may reduce the risk of hysterectomy to control bleeding (RR 0.33, 95% CI 0.11 to 0.99) and postoperative blood loss (MD -244.00 mL, 95% CI -295.25 to -192.75). AUTHORS' CONCLUSIONS:There is currently insufficient evidence from RCTs to determine the relative effectiveness and safety of mechanical and surgical interventions for treating primary PPH. High-quality randomised trials are urgently needed, and new emergency consent pathways should facilitate recruitment. The finding that intrauterine tamponade may increase total blood loss > 1000 mL suggests that introducing condom-balloon tamponade into low-resource settings on its own without multi-system quality improvement does not reduce PPH deaths or morbidity. The suggestion that modified B-Lynch suture may be superior to the original requires further research before the revised technique is adopted. In high-resource settings, uterine artery embolisation has become popular as the equipment and skills become more widely available. However, there is little randomised trial evidence regarding efficacy and this requires further research. We urge new trial authors to adopt PPH core outcomes to facilitate consistency between primary studies and subsequent meta-analysis

Stochastic computing based on volatile GeSe ovonic threshold switching selectors

Stochastic computing (SC) is a special type of digital compute strategy where values are represented by the probability of 1 and 0 in stochastic bit streams, which leads to superior hardware simplicity and error-tolerance. In this paper, we propose and demonstrate SC with GeSe based Ovonic Threshold Switching (OTS) selector devices by exploiting their probabilistic switching behavior. The stochastic bit streams generated by OTS are demonstrated with good computation accuracy in both multiplication operation and image processing circuit. Moreover, the bit distribution has been statistically studied and linked to the collective defect de/localization behavior in the chalcogenide material. Weibull distribution of the delay time supports the origin of such probabilistic switching, facilitates further optimization of the operation condition, and lays the foundation for device modelling and circuit design. Considering its other advantages such as simple structure, fast speed, and volatile nature, OTS is a promising material for implementing SC in a wide range of novel applications, such as image processors, neural networks, control systems and reliability analysis

GeSe-based Ovonic Threshold Switching Volatile True Random Number Generator

In this paper, we propose and demonstrate a novel technique for true random number generator (TRNG) application using GeSe-based Ovonic threshold switching (OTS) selector devices. The inherent variability in OTS threshold voltage results in a bimodal distribution of on/off states which can be easily converted into digital bits. The experimental evaluation shows that the proposed TRNG enables the generation of high-quality random bits that passed 12 tests in the National Institute of Standards and Technology statistical test suite without complex external circuits for post-processing. The randomness is further evidenced by the prediction rate of ∼50% using machine learning algorithm. Compared with the TRNGs based on non-volatile memories, the volatile nature of OTS avoids the reset operation, thus further simplifying the operation and improving the generation frequency

Experimental investigation of pressure-drop characteristics across multi-layer porous metal structures

This study investigates the effect of airflow (in the range of 0–70 m s-1) on the pressure-drop characteristics for a novel multi-layered, nickel-based porous metal, as a function of thickness (affected by sectioning) and density (affected by compression). In addition to generating unique data for these materials, the study highlights the need for precise pinpointing of the different flow regimes (Darcy, Forchheimer and Turbulent) in order to enable accurate determination of the permeability (K) and form drag coefficient (C) defined by the Forchheimer equation and to understand the complex dependence of length-normalised pressure drop on sample thickness

Circulating CD34+ Progenitor Cells and Risk of Mortality in a Population with Coronary Artery Disease

RATIONALE: Low circulating progenitor cell (PC) numbers and activity may reflect impaired intrinsic regenerative/reparative potential, but it remains uncertain whether this translates into a worse prognosis. OBJECTIVES: To investigate whether low numbers of PCs associate with a greater risk of mortality in a population at high cardiovascular risk. METHODS & RESULTS: Patients undergoing coronary angiography were recruited into two cohorts (1, n=502 and 2, n=403) over separate time periods. PCs were enumerated by flow cytometry as CD45(med+) blood mononuclear cells expressing CD34, with additional quantification of subsets co-expressing CD133, VEGFR2 and CXCR4. Coefficient of variation for CD34 cells was 2.9% and 4.8%, 21.6% and 6.5% for the respective subsets. Each cohort was followed for a mean of 2.7 and 1.2 years, respectively, for the primary endpoint of all-cause death. There was an inverse association between CD34+ and CD34+/CD133+ cell counts and risk of death in Cohort 1 (β=−0.92, p=0.043 and β=−1.64, p=0.019, respectively) that was confirmed in Cohort 2 (β=−1.25, p=0.020 and β=−1.81, p=0.015, respectively). Covariate adjusted HRs in the pooled cohort (n=905) were 3.54 (1.67-7.50) and 2.46 (1.18-5.13), respectively. CD34+/CD133+ cell counts improved risk prediction metrics beyond standard risk factors. CONCLUSION: Reduced circulating PC counts, identified primarily as CD34+ mononuclear cells or its subset expressing CD133 are associated with risk of death in individuals with coronary artery disease, suggesting that impaired endogenous regenerative capacity is associated with increased mortality. These findings have implications for biological understanding, risk prediction and cell selection for cell based therapies