Accelerating cardiac bidomain simulations using graphics processing units

Anatomically realistic and biophysically detailed multiscale computer models of the heart are playing an increasingly important role in advancing our understanding of integrated cardiac function in health and disease. Such detailed simulations, however, are computationally vastly demanding, which is a limiting factor for a wider adoption of in-silico modeling. While current trends in high-performance computing (HPC) hardware promise to alleviate this problem, exploiting the potential of such architectures remains challenging since strongly scalable algorithms are necessitated to reduce execution times. Alternatively, acceleration technologies such as graphics processing units (GPUs) are being considered. While the potential of GPUs has been demonstrated in various applications, benefits in the context of bidomain simulations where large sparse linear systems have to be solved in parallel with advanced numerical techniques are less clear. In this study, the feasibility of multi-GPU bidomain simulations is demonstrated by running strong scalability benchmarks using a state-of-the-art model of rabbit ventricles. The model is spatially discretized using the finite element methods (FEM) on fully unstructured grids. The GPU code is directly derived from a large pre-existing code, the Cardiac Arrhythmia Research Package (CARP), with very minor perturbation of the code base. Overall, bidomain simulations were sped up by a factor of 11.8 to 16.3 in benchmarks running on 6-20 GPUs compared to the same number of CPU cores. To match the fastest GPU simulation which engaged 20 GPUs, 476 CPU cores were required on a national supercomputing facility.

Dynamic respiratory endoscopy of Standardbred racehorses during qualifying races

REASON FOR PERFORMING STUDY

Examination of the equine upper airway during racing has not previously been documented.

OBJECTIVE

To describe the feasibility and appearance of the upper airways by overground respiratory endoscopic examination during racing conditions.

METHODS

Overground videoendoscopic examinations were performed on 46 Standardbred racehorses during qualifying races. Examined horses' speeds were recorded throughout the race with a portable GPS device.

RESULTS

The procedure did not interfere with performance as there were no significant differences in race times between races in which horses were examined with the endoscope in place and prior unexamined races. Airway obstructions during or after the race were documented in 21 horses. Most previously reported causes of upper airway obstruction were observed; surprisingly bilateral ventro-medial arytenoid displacement (VMAD; n = 5) was seen during exercise as frequently as dorsal displacement of the soft palate (DDSP). Although DDSP (n = 10) was the most common diagnosis made, many displacements (n = 5) occurred after the race. Horses that demonstrated DDSP after the race had slower speeds than unaffected horses during the race.

CONCLUSIONS

Racing endoscopy permits the diagnosis of upper airway obstructions without affecting performance. The occurrence of DDSP immediately after exercise may be clinically relevant. During racing VMAD may be an important anomaly.

POTENTIAL RELEVANCE

Racing endoscopy could be used to correlate the sensitivity of diagnostic endoscopy during race-training or treadmill examination. The pathogenesis and significance of VMAD deserves further investigation.

An audit highlighting a lack of awareness of the UK national guidelines for HIV testing, 2008

Following the publication of the UK national guidelines for HIV testing 2008, we carried out a local audit to determine the level of awareness of these guidelines among doctors working in Sunderland Royal Hospital, Sunderland, UK. An email questionnaire was distributed. Over two-thirds of respondents were unaware of the publication of the guidelines. Only 36% of respondents felt comfortable in offering a patient testing for HIV. The majority of doctors who responded lacked knowledge and confidence in issues surrounding HIV management and diagnosis, suggesting that better dissemination of information and training is still needed.

Effects of nanomaterials on luciferase with significant protection and increased enzyme activity observed for zinc oxide nanomaterials

This principle goal of this research was to examine the effects of various nanomaterials on the activity and behavior of the firefly enzyme luciferase. Nanomaterials have been found to stabilize, and in some instances, shown to increase the activity of enzymes. In this study gold, manganese oxide (MnO), and zinc oxide (ZnO) nanomaterials were utilized in order to test their effects on enzyme activity. Luciferase was used because its activity is easy to analyze, as it typically produces a large amount of bioluminescence easily detected by a Microtiter plate reader. Following incubation with the various nanomaterials, luciferase was subjected to degradation by several protein denaturing agents, such as heat, SDS, urea, ethanol, protease, hydrogen peroxide, and pH changes. Results indicated that luciferase activity is indeed affected when combined with nanomaterials, accompanied by both increases and decreases in enzyme activity depending on the type of nanomaterial and denaturing agent used. In most of the experiments, when incubated with ZnO nanomaterials, luciferase depicted significant increases in activity and bioluminescence. Additional experiments, in which human A375 cells were treated with luciferase-nanomaterial mixtures, also depicted increased enzyme activity and bioluminescence for luciferase incubated with ZnO nanomaterials. Ultimately, our findings indicated that when luciferase was subjected to multiple types of denaturation, zinc oxide nanomaterials dramatically preserved and increased enzyme activity and bioluminescence.

Screening for alcohol use disorders in a genitourinary medicine setting

The new National Institute for Health and Clinical Excellence (NICE) guidance cites genitourinary (GU) medicine clinics as one setting where screening for alcohol-use disorders should be part of routine clinical practice. Northumberland GU medicine service has routinely used the Fast Alcohol Screening Tool (FAST) since June 2009. An audit of all first attendees to the service in April 2010 (n = 256) was carried out. This audit found that the FAST questionnaire was acceptable to both patients and staff (uptake of 95.7%). Statistically significant associations between excessive alcohol and higher rates of unprotected sex (P < 0.01), an increased number of sexual partners (P < 0.01) and higher rates of sexually transmitted infection (STI) diagnosis (P < 0.05) were also demonstrated.

Trichomonas vaginalis: an unusual presentation

We report a case of Trichomonas vaginalis (TV) presenting as vulval ulceration in a 41-year-old woman. There was complete resolution of her symptoms only after oral tinidazole. The delayed diagnosis and importance of using the correct tests for the diagnosis of TV are discussed.