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%

Overview on Hepatitis B vaccination

Background: Hepatitis B virus (HBV) infection is increasing globally, posing a serious public health problem. Hepatitis B virus (HBV) infection and mortality are among the leading causes of death worldwide. Concerns for public health are amplified by the fact that about a third of the world's population is afflicted with HBV. HBV infection may result in cirrhosis, hepatocellular cancer, or both (HCC).Immunization is the most cost-effective strategy available worldwide for controlling and preventing hepatitis B in terms of benefit-cost ratio. Objective: This review article discusses the most critical components of the HBV vaccine and the most efficient strategies for increasing HBV vaccinatio

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

Aberrant crossed corticospinal facilitation in muscles distant from a spinal cord injury.

Crossed facilitatory interactions in the corticospinal pathway are impaired in humans with chronic incomplete spinal cord injury (SCI). The extent to which crossed facilitation is affected in muscles above and below the injury remains unknown. To address this question we tested 51 patients with neurological injuries between C2-T12 and 17 age-matched healthy controls. Using transcranial magnetic stimulation we elicited motor evoked potentials (MEPs) in the resting first dorsal interosseous, biceps brachii, and tibialis anterior muscles when the contralateral side remained at rest or performed 70% of maximal voluntary contraction (MVC) into index finger abduction, elbow flexion, and ankle dorsiflexion, respectively. By testing MEPs in muscles with motoneurons located at different spinal cord segments we were able to relate the neurological level of injury to be above, at, or below the location of the motoneurons of the muscle tested. We demonstrate that in patients the size of MEPs was increased to a similar extent as in controls in muscles above the injury during 70% of MVC compared to rest. MEPs remained unchanged in muscles at and within 5 segments below the injury during 70% of MVC compared to rest. However, in muscles beyond 5 segments below the injury the size of MEPs increased similar to controls and was aberrantly high, 2-fold above controls, in muscles distant (>15 segments) from the injury. These aberrantly large MEPs were accompanied by larger F-wave amplitudes compared to controls. Thus, our findings support the view that corticospinal degeneration does not spread rostral to the lesion, and highlights the potential of caudal regions distant from an injury to facilitate residual corticospinal output after SCI

Characterizing chronic pain phenotypes in multiple sclerosis : a nationwide survey study

Acknowledgements The National Multiple Sclerosis Society (NMSS) provided participant recruitment support by distributing study advertisements via their email listserv. The Michigan Institute for Clinical & Health Research (MICHR: NIH award number UL1TR002240) provided participant recruitment support through the UMHealthResearch.org website. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. The authors thank Shubhangi Kulkarni, MS, for her contribution in coordinating this study and collecting these data. The authors have no conflicts of interest to report.Peer reviewedPostprin

Coexistence of HBsAg/Anti-HBs and HBeAg/Anti-HBe in Sudanese Patients with Chronic Hepatitis B Virus Infection: A Cross-Sectional Study

Background: Seroconversion of hepatitis B surface antigen (HBsAg) to hepatitis B surface antibody (anti-HBs) is a recognized goal of HBV therapy. This dynamic transition responsible for the coexistence of HBsAg and anti-HBs is rarely detected in clinical cases. However, with vaccination and the use of various antiviral drugs, as well as the development of new medical technologies, recognizing the coexistence of HBsAg and anti-HBs has become more common. In addition, mutations in viral genomes, immune status, and human genetic factors may also contribute to such coexistence. The current study was designed to determine the prevalence of the coexistence of HBsAg and anti-HBs and HBeAg and anti-HBe in CHB patients in Sudan. Methods and Results: This was a descriptive cross-sectional study conducted in Khartoum state from November 2018 to January 2019. The study included 70 HBV-infected patients who were positive for HBsAg for more than six months. Blood samples were tested for HBsAg/Anti-HBs and HBeAg/Anti-HBe using Commercial ELISA Kits (Foresight, United Kingdom) and (PRECHEK, USA). Demographic data were collected using a structured questionnaire, and any antiviral agent and laboratory results were also recorded for each participant. The current study showed that one case (1.4%) was reactive for the coexistence of HBsAg/HBsAb and two cases (2.8%) for the coexistence of HBeAg/HBeAb. There was no statistical difference between the coexistence of HBsAg/HBsAb and HBeAg/HBeAb with age, gender, residence, and treatment status. Conclusion: Our study indicates that the frequencies of the coexistence of HBsAg/HBsAb and HBeAg/HBeAb among Sudanese patients with chronic HBV infection were low compared to previous studies in a different population

Continuity of midwifery care and gestational weight gain in obese women: a randomised controlled trial

Background: The increased prevalence of obesity in pregnant women in Australia and other developed countries is a significant public health concern. Obese women are at increased risk of serious perinatal complications and guidelines recommend weight gain restriction and additional care. There is limited evidence to support the effectiveness of dietary and physical activity lifestyle interventions in preventing adverse perinatal outcomes and new strategies need to be evaluated. The primary aim of this project is to evaluate the effect of continuity of midwifery care on restricting gestational weight gain in obese women to the recommended range. The secondary aims of the study are to assess the impact of continuity of midwifery care on: women&rsquo;s experience of pregnancy care; women&rsquo;s satisfaction with care and a range of psychological factors.Methods/Design: A two arm randomised controlled trial (RCT) will be conducted with primigravid women recruited from maternity services in Victoria, Australia. Participants will be primigravid women, with a BMI&ge;30 who are less than 17 weeks gestation. Women allocated to the intervention arm will be cared for in a midwifery continuity of care model and receive an informational leaflet on managing weight gain in pregnancy. Women allocated to the control group will receive routine care in addition to the same informational leaflet. Weight gain during pregnancy, standards of care, medical and obstetric information will be extracted from medical records. Data collected at recruitment (self administered survey) and at 36 weeks by postal survey will include sociodemographic information and the use of validated scales to measure secondary outcomes.Discussion: Continuity of midwifery care models are well aligned with current Victorian, Australian and many international government policies on maternity care. Increasingly, midwifery continuity models of care are being introduced in low risk maternity care, and information on their application in high risk populations is required. There is an identified need to trial alternative antenatal interventions to reduce perinatal risk factors for women who are obese and the findings from this project may have application in other maternity services. In addition this study will inform a larger trial that will focus on birth and postnatal outcomes.<br /

Fog computing security: a review of current applications and security solutions

Fog computing is a new paradigm that extends the Cloud platform model by providing computing resources on the edges of a network. It can be described as a cloud-like platform having similar data, computation, storage and application services, but is fundamentally different in that it is decentralized. In addition, Fog systems are capable of processing large amounts of data locally, operate on-premise, are fully portable, and can be installed on heterogeneous hardware. These features make the Fog platform highly suitable for time and location-sensitive applications. For example, Internet of Things (IoT) devices are required to quickly process a large amount of data. This wide range of functionality driven applications intensifies many security issues regarding data, virtualization, segregation, network, malware and monitoring. This paper surveys existing literature on Fog computing applications to identify common security gaps. Similar technologies like Edge computing, Cloudlets and Micro-data centres have also been included to provide a holistic review process. The majority of Fog applications are motivated by the desire for functionality and end-user requirements, while the security aspects are often ignored or considered as an afterthought. This paper also determines the impact of those security issues and possible solutions, providing future security-relevant directions to those responsible for designing, developing, and maintaining Fog systems