Efficiency analysis methodology of FPGAs based on lost frequencies, area and cycles

We propose a methodology to study and to quantify efficiency and the impact of overheads on runtime performance. Most work on High-Performance Computing (HPC) for FPGAs only studies runtime performance or cost, while we are interested in how far we are from peak performance and, more importantly, why. The efficiency of runtime performance is defined with respect to the ideal computational runtime in absence of inefficiencies. The analysis of the difference between actual and ideal runtime reveals the overheads and bottlenecks. A formal approach is proposed to decompose the efficiency into three components: frequency, area and cycles. After quantification of the efficiencies, a detailed analysis has to reveal the reasons for the lost frequencies, lost area and lost cycles. We propose a taxonomy of possible causes and practical methods to identify and quantify the overheads. The proposed methodology is applied on a number of use cases to illustrate the methodology. We show the interaction between the three components of efficiency and show how bottlenecks are revealed

Performance and toolchain of a combined GPU/FPGA desktop

Low-power, high-performance computing nowadays relies on accelerator cards to speed up the calculations. Combining the power of GPUs with the flexibility of FPGAs enlarges the scope of problems that can be accelerated. We describe the performance analysis of a desktop equipped with a GPU Tesla 2050 and an FPGA Virtex- 6 LX 240T. The balance between the I/O and the raw peak performance is analyzed using the roofline model. A well-tuned accelerator- based codesign, identifying the parallelism, the computation and data patterns of different classes of algorithms, will enable to maximize the performance of the combined GPU/FPGA system

Study of combining GPU/FPGA accelerators for high-performance computing

This contribution presents the performance modeling of a super desktop with GPU and FPGA accelerators, using OpenCL for the GPU and a high-level synthesis compiler for the FPGAs. The performance model is used to evaluate the different high-level synthesis optimizations, taking into account the resource usage, and to compare the compute power of the FPGA with the GP

Genomic characterization and detection of potential therapeutic targets for peritoneal mesothelioma in current practice

Peritoneal mesothelioma (PeM) is an aggressive tumor with limited treatment options. The current study aimed to evaluate the value of next generation sequencing (NGS) of PeM samples in current practice. Foundation Medicine F1CDx NGS was performed on 20 tumor samples. This platform assesses 360 commonly somatically mutated genes in solid tumors and provides a genomic signature. Based on the detected mutations, potentially effective targeted therapies were identified. NGS was successful in 19 cases. Tumor mutational burden (TMB) was low in 10 cases, and 11 cases were microsatellite stable. In the other cases, TMB and microsatellite status could not be determined. BRCA1 associated protein 1 (BAP1) mutations were found in 32% of cases, cyclin dependent kinase inhibitor 2A/B (CDKN2A/B) and neurofibromin 2 (NF2) mutations in 16%, and ataxia-telangiectasia mutated serine/threonine kinase (ATM) in 11%. Based on mutations in the latter two genes, potential targeted therapies are available for approximately a quarter of cases (i.e., protein kinase inhibitors for three NF2 mutated tumors, and polyADP-ribose polymerase inhibitors for two ATM mutated tumors). Extensive NGS analysis of PeM samples resulted in the identification of potentially effective targeted therapies for about one in four patients. Although these therapies are currently not available for patients with PeM, ongoing developments might result in new treatment options in the future.</p

Genomic characterization and detection of potential therapeutic targets for peritoneal mesothelioma in current practice

Peritoneal mesothelioma (PeM) is an aggressive tumor with limited treatment options. The current study aimed to evaluate the value of next generation sequencing (NGS) of PeM samples in current practice. Foundation Medicine F1CDx NGS was performed on 20 tumor samples. This platform assesses 360 commonly somatically mutated genes in solid tumors and provides a genomic signature. Based on the detected mutations, potentially effective targeted therapies were identified. NGS was successful in 19 cases. Tumor mutational burden (TMB) was low in 10 cases, and 11 cases were microsatellite stable. In the other cases, TMB and microsatellite status could not be determined. BRCA1 associated protein 1 (BAP1) mutations were found in 32% of cases, cyclin dependent kinase inhibitor 2A/B (CDKN2A/B) and neurofibromin 2 (NF2) mutations in 16%, and ataxia-telangiectasia mutated serine/threonine kinase (ATM) in 11%. Based on mutations in the latter two genes, potential targeted therapies are available for approximately a quarter of cases (i.e., protein kinase inhibitors for three NF2 mutated tumors, and polyADP-ribose polymerase inhibitors for two ATM mutated tumors). Extensive NGS analysis of PeM samples resulted in the identification of potentially effective targeted therapies for about one in four patients. Although these therapies are currently not available for patients with PeM, ongoing developments might result in new treatment options in the future.</p

Cost-effectiveness of hepatitis C virus screening, and subsequent monitoring or treatment among pregnant women in the Netherlands

Background The prevalence of diagnosed chronic hepatitis C virus (HCV) infection among pregnant women in the Netherlands is 0.26%, yet many cases remain undiagnosed. HCV screening and treatment of pregnant HCV carriers could reduce the burden of disease and limit vertical transmission from mother to child. We assessed the impact of HCV screening and subsequent treatment with new direct-acting antivirals (DAAs) among pregnant women in the Netherlands. Methods An HCV natural history Markov transition state model was developed, to evaluate the public-health and economic impact of HCV screening and treatment. Besides all 179,000 pregnant women in the Netherlands (cohort 1), we modelled 3 further cohorts: all 79,000 first-time pregnant women (cohort 2), 33,000 pregnant migrant women (cohort 3) and 16,000 first-time pregnant migrant women (cohort 4). Each cohort was analyzed in various scenarios:i no intervention, i.e., the current practice,ii screen-and-treat, i.e., the most extensive approach involving treatment of all individuals found HCV-positive, andiii screen-and-treat/monitor, i.e., a strategy involving treatment of symptomatic (F1-F4) patients and follow-up of asymptomatic (F0) HCV carriers with subsequent treatment only at progression. Results For all cohorts, comparison betweenscenarios(ii) and (i) resulted in ICERs between euro9,306 and euro10,173 per QALY gained and 5 year budget impacts varying between euro6,283,830 and euro19,220,405. For all cohorts, comparison betweenscenarios(iii) and (i) resulted in ICERs between euro1,739 and euro2,749 per QALY gained and budget impacts varying between euro1,468,670 and euro5,607,556. For all cohorts, the ICERs (scenario iiiversusii) involved in delayed treatment of asymptomatic (F0) HCV carriers varied between euro56,607 and euro56,892, well above the willingness-to-pay (WTP) threshold of euro20,000 per QALY gained and even above a threshold of euro50,000 per QALY gained. Conclusion Universal screening for HCV among all pregnant women in the Netherlands is cost-effective. However, it would be reasonable to consider smaller risk groups in view of the budget impact of the intervention

Prevalence and Risk Factors for Delirium in Elderly Patients With Severe Burns: A Retrospective Cohort Study

Little is known about delirium in elderly burn center patients. The aim of this study is to provide information on the prevalence of delirium and risk factors contributing to the onset of delirium. All patients aged 70 years or older admitted with burn injuries to the Burn Center, Maasstad Hospital, in 2011 to 2017 were eligible for inclusion. We retrospectively collected data regarding the presence of delirium, potential risk factors contributing to the onset of delirium and outcome after delirium. We included elderly 90 patients in this study. The prevalence of delirium in our population was 13% (N = 12). Risk factors for delirium were advanced age, increased American Society for Anesthesiologists score, physical impairment and the use of anticholinergic drugs during admission. Patients with delirium had a poorer outcome, with prolonged hospital stay and increased mortality 6 and 12 months after discharge. Delirium is diagnosed in 13% of the elderly patients admitted to our burn center. Risk factors for delirium found in this study are advanced age, poor physical health status, physical impairment, and the use of anticholinergic drugs. Delirium is related to poor outcomes, including prolonged hospital stay and mortality after discharge