COMET: Communication-optimised multi-threaded error-detection technique

© 2016 ACM. Relentless technology scaling has made transistors more vulnerable to soft, or transient, errors. To keep systems robust against these, current error detection techniques use different types of redundancy at the hardware or the software level. A consequence of these additional protection mechanisms is that these systems tend to become slower. In particular, software error-detection techniques degrade performance considerably, limiting their uptake. This paper focuses on software redundant multi-threading error detection, a compiler-based technique that makes use of redundant cores within a multi-core system to perform error checking. Implementations of this scheme feature two threads that execute almost the same code: the main thread runs the original code and the checker thread executes code to verify the correctness of the original. The main thread communicates the values that require checking to the checker thread to use in its comparisons. We identify a major performance bottleneck in existing schemes: poorly performing inter-core communication and the generated code associated with it. Our study shows this is a major performance impediment within existing techniques since the two threads require extremely fine-grained communication, on the order of every few instructions. We alleviate this bottleneck with a series of code generation optimisations at the compiler level. We propose COMET (Communication-Optimised Multi-threaded Error-detection Technique), which improves performance across the NAS parallel benchmarks by 31.4% (on average) compared to the state-of-the-art, without affecting fault-coverage

Lynx: Using OS and hardware support for fast fine-grained inter-core communication

Designing high-performance software queues for fast intercore communication is challenging, but critical for maximising software parallelism. State-of-the-art single-producer / single-consumer queues for streaming applications contain multiple sections, requiring the producer and consumer to operate independently on different sections from each other. While these queues perform well for coarse-grained data transfers, they perform poorly in the fine-grained case. This paper proposes Lynx, a novel SP/SC queue, specifically tuned for fine-grained communication. Lynx is built from the ground up, reducing the generated code on the critical-path to just two operations per enqueue and dequeue. To achieve this it relies on existing commodity processor hardware and operating system exception handling support to deal with infrequent queue maintenance operations. Lynx outperforms the state-of-the art by up to 1.57× in total 64-bit throughput reaching a peak throughput of 15.7GB/s on a common desktop system. Real applications using Lynx get a performance improvement of up to 1.4×.This work was supported by the Engineering and Physical Sciences Research Council (EPSRC), through grant reference EP/K026399/1.This is the author accepted manuscript. The final version is available from Association for Computing Machinery via http://dx.doi.org/10.1145/2925426.2926274

Maintaining Digestive Health in Diabetes: The Role of the Gut Microbiome and the Challenge of Functional Foods.

Over the last decades, the incidence of diabetes has increased in developed countries and beyond the genetic impact, environmental factors, which can trigger the activation of the gut immune system, seem to affect the induction of the disease process. Since the composition of the gut microbiome might disturb the normal interaction with the immune system and contribute to altered immune responses, the restoration of normal microbiota composition constitutes a new target for the prevention and treatment of diabetes. Thus, the interaction of gut microbiome and diabetes, focusing on mechanisms connecting gut microbiota with the occurrence of the disorder, is discussed in the present review. Finally, the challenge of functional food diet on maintaining intestinal health and microbial flora diversity and functionality, as a potential tool for the onset inhibition and management of the disease, is highlighted by reporting key animal studies and clinical trials. Early onset of the disease in the oral cavity is an important factor for the incorporation of a functional food diet in daily routine

Exercise tolerance and quality of life in patients with known or suspected coronary artery disease

Background: Coronary artery disease (CAD) is known to impact on patients’ physical and mental health. The relationship between performance on treadmill exercise tolerance test (ETT) and health-related quality of life (HRQL)has never been specifically investigated in the setting of CAD. Methods: Consecutive patients undergoing an ETT with the Bruce protocol during a diagnostic workup for CAD (n = 1,631, age 55 ± 12 years) were evaluated. Exercise-related indices were recorded. Detailed information on cardiovascular risk factors and past medical history were obtained. HRQLwas assessed with the use of the validated 36-Item Short Form Survey (SF-36) questionnaire. Results: Increasing age and the presence of cardiovascular risk factors and comorbidities correlated with lower scores on the physical and mental health component of SF-36(all P < 0.05). Subjects with arrhythmias during exercise and slow recovery of systolic blood pressure had lower scores on the physical health indices or the Social Role Functioning component (P < 0.05). Achieved target heart rate and good exercise tolerance were independently associated with better scores of the physical and mental health domains of SF-36 and overall HRQLscores (β = 0.05 for target HR and PCS-36, β = 1.86 and β = 1.66 per increasing stage of exercise tolerance and PCS-36 and MCS-36, respectively, P < 0.001 for all associations). Ischemic ECG changes were associated with worse scores on Physical Functioning (β = − 3.2, P = 0.02) and Bodily Pain (β = − 4.55, P = 0.026). Conclusion: ETT parameters are associated with HRQL indices in patients evaluated for possible CAD. Physical conditioning may increase patient well-being and could serve as a complementary target in conjunction with cardiovascular drug therapy

Economic evaluation of pharmacogenomic-guided antiplatelet treatment in Spanish patients suffering from acute coronary syndrome participating in the U-PGx PREPARE study

BackgroundCardiovascular diseases and especially Acute Coronary Syndrome (ACS) constitute a major health issue impacting millions of patients worldwide. Being a leading cause of death and hospital admissions in many European countries including Spain, it accounts for enormous amounts of healthcare expenditures for its management. Clopidogrel is one of the oldest antiplatelet medications used as standard of care in ACS.MethodsIn this study, we performed an economic evaluation study to estimate whether a genome-guided clopidogrel treatment is cost-effective compared to conventional one in a large cohort of 243 individuals of Spanish origin suffering from ACS and treated with clopidogrel. Data were derived from the U-PGx PREPARE clinical trial. Effectiveness was measured as survival of individuals while study data on safety and efficacy, as well as on resource utilization associated with each adverse drug reaction were used to measure costs to treat these adverse drug reactions. A generalized linear regression model was used to estimate cost differences for both study groups.ResultsBased on our findings, PGx-guided treatment group is cost-effective. PGx-guided treatment demonstrated to have 50% less hospital admissions, reduced emergency visits and almost 13% less ADRs compared to the non-PGx approach with mean QALY 1.07 (95% CI, 1.04-1.10) versus 1.06 (95% CI, 1.03-1.09) for the control group, while life years for both groups were 1.24 (95% CI, 1.20-1.26) and 1.23 (95% CI, 1.19-1.26), respectively. The mean total cost of PGx-guided treatment was 50% less expensive than conventional therapy with clopidogrel [euro883 (95% UI, euro316-euro1582), compared to euro1,755 (95% UI, euro765-euro2949)].ConclusionThese findings suggest that PGx-guided clopidogrel treatment represents a cost-effective option for patients suffering from ACS in the Spanish healthcare setting.Personalised Therapeutic

Correction: A european spectrum of pharmacogenomic biomarkers: Implications for clinical pharmacogenomics (PLoS ONE (2016) 11:9 (e0162866) DOI: 10.1371/journal.pone.0162866)

The thirty-Third author's name is spelled incorrectly. The correct name is: Jadranka Sertić

Androgen receptor expresion in breast cancer: Relationship with clinicopathological characteristics of the tumors, prognosis, and expression of metalloproteases and their inhibitors

<p>Abstract</p> <p>Background</p> <p>In the present study we analyze, in patients with breast cancer, the tumor expression of androgen receptors (AR), its relationship with clinicopathological characteristics and with the expression of several matrix metalloproteases (MMPs) and their inhibitors (TIMPs), as well as with prognosis.</p> <p>Methods</p> <p>An immunohistochemical study was performed using tissue microarrays and specific antibodies against AR, MMPs -1, -2, -7, -9, -11, -13, -14, and TIMPs -1, -2 and -3. More than 2,800 determinations on tumor specimens from 111 patients with primary invasive ductal carcinoma of the breast (52 with axillary lymph node metastases and 59 without them) and controls were performed. Staining results were categorized using a score based on the intensity of the staining and a specific software program calculated the percentage of immunostained cells automatically.</p> <p>Results</p> <p>A total of 83 cases (74.8%) showed a positive immunostaining for AR, but with a wide variation in the staining score values. There were no significant associations between the total immunostaining scores for AR and any clinicopathological parameters. However, score values for MMP-1, -7 and -13, were significantly higher in AR-positive tumors than in AR-negative tumors. Likewise, when we considered the cellular type expressing each factor, we found that AR-positive tumors had a higher percentage of cases positive for MMP-1, -7, -11, and TIMP-2 in their malignant cells, as well as for MMP-1 in intratumoral fibroblasts. On the other hand, multivariate analysis demonstrated that patients with AR-positive tumors have a significant longer overall survival than those with AR-negative breast carcinomas (<it>p </it>= 0.03).</p> <p>Conclusion</p> <p>Our results confirm that AR are commonly expressed in breast cancer, and are correlated with the expression of some MMPs and TIMP-2. Although we found a specific value of AR expression to be a prognostic indicator in breast cancer, the functional role of AR in these neoplasms is still unclear and further data are needed in order to clarify their biological signification in breast cancer.</p

A European spectrum of pharmacogenomic biomarkers: Implications for clinical pharmacogenomics

Pharmacogenomics aims to correlate inter-individual differences of drug efficacy and/or toxicity with the underlying genetic composition, particularly in genes encoding for protein factors and enzymes involved in drug metabolism and transport. In several European populations, particularly in countries with lower income, information related to the prevalence of pharmacogenomic biomarkers is incomplete or lacking. Here, we have implemented the microattribution approach to assess the pharmacogenomic biomarkers allelic spectrum in 18 European populations, mostly from developing European countries, by analyzing 1,931 pharmacogenomics biomarkers in 231 genes. Our data show significant interpopulation pharmacogenomic biomarker allele frequency differences, particularly in 7 clinically actionable pharmacogenomic biomarkers in 7 European populations, affecting drug efficacy and/or toxicity of 51 medication treatment modalities. These data also reflect on the differences observed in the prevalence of high-risk genotypes in these populations, as far as common markers in the CYP2C9, CYP2C19, CYP3A5, VKORC1, SLCO1B1 and TPMT pharmacogenes are concerned. Also, our data demonstrate notable differences in predicted genotype-based warfarin dosing among these populations. Our findings can be exploited not only to develop guidelines for medical prioritization, but most importantly to facilitate integration of pharmacogenomics and to support pre-emptive pharmacogenomic testing. This may subsequently contribute towards significant cost-savings in the overall healthcare expenditure in the participating countries, where pharmacogenomics implementation proves to be cost-effective

Character pathology and neuropsychological test performance in remitted opiate dependence

<p>Abstract</p> <p>Background</p> <p>Cognitive deficits and personality pathology are prevalent in opiate dependence, even during periods of remission, and likely contribute to relapse. Understanding the relationship between the two in vulnerable, opiate-addicted patients may contribute to the design of better treatment and relapse prevention strategies.</p> <p>Methods</p> <p>The Millon Multiaxial Clinical Inventory (MCMI) and a series of neuropsychological tests were administered to three subject groups: 29 subjects receiving methadone maintenance treatment (MM), 27 subjects in protracted abstinence from methadone maintenance treatment (PA), and 29 healthy non-dependent comparison subjects. Relationships between MCMI scores, neuropsychological test results, and measures of substance use and treatment were examined using bivariate correlation and regression analysis.</p> <p>Results</p> <p>MCMI scores were greater in subjects with a history of opiate dependence than in comparison subjects. A significant negative correlation between MCMI scores and neuropsychological test performance was identified in all subjects. MCMI scores were stronger predictors of neuropsychological test performance than measures of drug use.</p> <p>Conclusion</p> <p>Formerly methadone-treated opiate dependent individuals in protracted opiate abstinence demonstrate a strong relationship between personality pathology and cognitive deficits. The cause of these deficits is unclear and most likely multi-factorial. This finding may be important in understanding and interpreting neuropsychological testing deficiencies in opiate-dependent subjects.</p