Fast and Robust Vectorized In-Place Sorting of Primitive Types

Modern CPUs provide single instruction-multiple data (SIMD) instructions. SIMD instructions process several elements of a primitive data type simultaneously in fixed-size vectors. Classical sorting algorithms are not directly expressible in SIMD instructions. Accelerating sorting algorithms with SIMD instruction is therefore a creative endeavor. A promising approach for sorting with SIMD instructions is to use sorting networks for small arrays and Quicksort for large arrays. In this paper we improve vectorization techniques for sorting networks and Quicksort. In particular, we show how to use the full capacity of vector registers in sorting networks and how to make vectorized Quicksort robust with respect to different key distributions. To demonstrate the performance of our techniques we implement an in-place hybrid sorting algorithm for the data type int with AVX2 intrinsics. Our implementation is at least 30% faster than state-of-the-art high-performance sorting alternatives

Fast and Robust Vectorized In-Place Sorting of Primitive Types

Modern CPUs provide single instruction-multiple data (SIMD) instructions. SIMD instructions process several elements of a primitive data type simultaneously in fixed-size vectors. Classical sorting algorithms are not directly expressible in SIMD instructions. Accelerating sorting algorithms with SIMD instruction is therefore a creative endeavor. A promising approach for sorting with SIMD instructions is to use sorting networks for small arrays and Quicksort for large arrays. In this paper we improve vectorization techniques for sorting networks and Quicksort. In particular, we show how to use the full capacity of vector registers in sorting networks and how to make vectorized Quicksort robust with respect to different key distributions. To demonstrate the performance of our techniques we implement an in-place hybrid sorting algorithm for the data type int with AVX2 intrinsics. Our implementation is at least 30% faster than state-of-the-art high-performance sorting alternatives

Implementation of a vectorized Quicksort using AVX-512 intrinsics

Jahrzehntelang wurden Verbesserungen der Rechengeschwindigkeit erreicht, indem die Taktfrequenz der CPU erhöht wurde. Im Laufe der letzten Jahre wurde dieser Mechanismus durch physikalische Einflüsse gebremst. Daher müssen moderne Single-Thread-Anwendungen stärker CPU-Funktionen ausnutzen, um von den Fortschritten neuer Prozessorgenerationen zu profitieren. Eine dieser Funktionen ist die Vektorverarbeitung, um mehrere Datenelemente gleichzeitig zu verarbeiten. Diese Arbeit untersucht die Verwendung von AVX-512-Befehlen zur Sortierung von primitiven Typen der Länge 32 bit. Die Nutzung von Vektorinstruktionen für die Sortierung ist eine Herausforderung, da Sortieralgorithmen erst vektorisierungsfreundlich umgestaltet werden müssen. Glücklicherweise hat Mark Blacher einen effizienten vektorisierten Sortieralgorithmus auf Basis von Sortiernetzwerken und einem nichtquadratischen Quicksort entwickelt. In dieser Arbeit wird Blachers AVX2-basierte vektorisierte Implementierung auf den moderneren AVX-512-Befehlssatz portiert. Im Geschwindigkeitsvergleich schlägt Blachers AVX2-Version die in dieser Arbeit entwickelte AVX-512-Implementierung. Diese ist jedoch in der Lage, den bisherigen AVX-512-Sortieralgorithmus von Bramas zu übertreffen

Effect of a reduction in glomerular filtration rate after nephrectomy on arterial stiffness and central hemodynamics: rationale and design of the EARNEST study

Background: There is strong evidence of an association between chronic kidney disease (CKD) and cardiovascular disease. To date, however, proof that a reduction in glomerular filtration rate (GFR) is a causative factor in cardiovascular disease is lacking. Kidney donors comprise a highly screened population without risk factors such as diabetes and inflammation, which invariably confound the association between CKD and cardiovascular disease. There is strong evidence that increased arterial stiffness and left ventricular hypertrophy and fibrosis, rather than atherosclerotic disease, mediate the adverse cardiovascular effects of CKD. The expanding practice of live kidney donation provides a unique opportunity to study the cardiovascular effects of an isolated reduction in GFR in a prospective fashion. At the same time, the proposed study will address ongoing safety concerns that persist because most longitudinal outcome studies have been undertaken at single centers and compared donor cohorts with an inappropriately selected control group.<p></p> Hypotheses: The reduction in GFR accompanying uninephrectomy causes (1) a pressure-independent increase in aortic stiffness (aortic pulse wave velocity) and (2) an increase in peripheral and central blood pressure.<p></p> Methods: This is a prospective, multicenter, longitudinal, parallel group study of 440 living kidney donors and 440 healthy controls. All controls will be eligible for living kidney donation using current UK transplant criteria. Investigations will be performed at baseline and repeated at 12 months in the first instance. These include measurement of arterial stiffness using applanation tonometry to determine pulse wave velocity and pulse wave analysis, office blood pressure, 24-hour ambulatory blood pressure monitoring, and a series of biomarkers for cardiovascular and bone mineral disease.<p></p> Conclusions: These data will prove valuable by characterizing the direction of causality between cardiovascular and renal disease. This should help inform whether targeting reduced GFR alongside more traditional cardiovascular risk factors is warranted. In addition, this study will contribute important safety data on living kidney donors by providing a longitudinal assessment of well-validated surrogate markers of cardiovascular disease, namely, blood pressure and arterial stiffness. If any adverse effects are detected, these may be potentially reversed with the early introduction of targeted therapy. This should ensure that kidney donors do not come to long-term harm and thereby preserve the ongoing expansion of the living donor transplant program.<p></p&gt

Vascular function assessed with cardiovascular magnetic resonance predicts survival in patients with advanced chronic kidney disease

<p>Abstract</p> <p>Background</p> <p>Increased arterial stiffness is associated with mortality in patients with chronic kidney disease. Cardiovascular magnetic resonance (CMR) permits assessment of the central arteries to measure aortic function.</p> <p>Methods</p> <p>We studied the relationship between central haemodynamics and outcome using CMR in 144 chronic kidney disease patients with estimated glomerular filtration rate <15 ml/min (110 on dialysis). Aortic distensibilty and volumetric arterial strain were calculated from cross sectional aortic volume and pulse pressure measured during the scan.</p> <p>Results</p> <p>Median follow up after the scan was 24 months. There were no significant differences in aortic distensibilty or aortic volumetric arterial strain between pre-dialysis and dialysis patients. Aortic distensibilty and volumetric arterial strain negatively correlated with age. Aortic distensibilty and volumetric arterial strain were lower in diabetics, patients with ischaemic heart disease and peripheral vascular disease. During follow up there were 20 deaths. Patients who died had lower aortic distensibilty than survivors. In a survival analysis, diabetes, systolic blood pressure and aortic distensibilty were independent predictors of mortality. There were 12 non-fatal cardiovascular events during follow up. Analysing the combined end point of death or a vascular event, diabetes, aortic distensibilty and volumetric arterial strain were predictors of events.</p> <p>Conclusion</p> <p>Deranged vascular function measured with CMR correlates with cardiovascular risk factors and predicts outcome. CMR measures of vascular function are potential targets for interventions to reduce cardiovascular risk.</p

Impact of COVID-19 on cardiovascular testing in the United States versus the rest of the world

Objectives: This study sought to quantify and compare the decline in volumes of cardiovascular procedures between the United States and non-US institutions during the early phase of the coronavirus disease-2019 (COVID-19) pandemic. Background: The COVID-19 pandemic has disrupted the care of many non-COVID-19 illnesses. Reductions in diagnostic cardiovascular testing around the world have led to concerns over the implications of reduced testing for cardiovascular disease (CVD) morbidity and mortality. Methods: Data were submitted to the INCAPS-COVID (International Atomic Energy Agency Non-Invasive Cardiology Protocols Study of COVID-19), a multinational registry comprising 909 institutions in 108 countries (including 155 facilities in 40 U.S. states), assessing the impact of the COVID-19 pandemic on volumes of diagnostic cardiovascular procedures. Data were obtained for April 2020 and compared with volumes of baseline procedures from March 2019. We compared laboratory characteristics, practices, and procedure volumes between U.S. and non-U.S. facilities and between U.S. geographic regions and identified factors associated with volume reduction in the United States. Results: Reductions in the volumes of procedures in the United States were similar to those in non-U.S. facilities (68% vs. 63%, respectively; p = 0.237), although U.S. facilities reported greater reductions in invasive coronary angiography (69% vs. 53%, respectively; p < 0.001). Significantly more U.S. facilities reported increased use of telehealth and patient screening measures than non-U.S. facilities, such as temperature checks, symptom screenings, and COVID-19 testing. Reductions in volumes of procedures differed between U.S. regions, with larger declines observed in the Northeast (76%) and Midwest (74%) than in the South (62%) and West (44%). Prevalence of COVID-19, staff redeployments, outpatient centers, and urban centers were associated with greater reductions in volume in U.S. facilities in a multivariable analysis. Conclusions: We observed marked reductions in U.S. cardiovascular testing in the early phase of the pandemic and significant variability between U.S. regions. The association between reductions of volumes and COVID-19 prevalence in the United States highlighted the need for proactive efforts to maintain access to cardiovascular testing in areas most affected by outbreaks of COVID-19 infection

Consensus guidelines for the use and interpretation of angiogenesis assays

The formation of new blood vessels, or angiogenesis, is a complex process that plays important roles in growth and development, tissue and organ regeneration, as well as numerous pathological conditions. Angiogenesis undergoes multiple discrete steps that can be individually evaluated and quantified by a large number of bioassays. These independent assessments hold advantages but also have limitations. This article describes in vivo, ex vivo, and in vitro bioassays that are available for the evaluation of angiogenesis and highlights critical aspects that are relevant for their execution and proper interpretation. As such, this collaborative work is the first edition of consensus guidelines on angiogenesis bioassays to serve for current and future reference

Optimization for Classical Machine Learning Problems on the GPU

Constrained optimization problems arise frequently in classical machine learning. There exist frameworks addressing constrained optimization, for instance, CVXPY and GENO. However, in contrast to deep learning frameworks, GPU support is limited. Here, we extend the GENO framework to also solve constrained optimization problems on the GPU. The framework allows the user to specify constrained optimization problems in an easy-to-read modeling language. A solver is then automatically generated from this specification. When run on the GPU, the solver outperforms state-of-the-art approaches like CVXPY combined with a GPU-accelerated solver such as cuOSQP or SCS by a few orders of magnitude

Vascular function in patients with end-stage renal disease and/or coronary artery disease: A cardiac magnetic resonance imaging study

Decreased arterial compliance in end-stage renal disease (ESRD) is associated with increased cardiovascular risk. Our aim was to examine aortic compliance in patients with ESRD using cardiac magnetic resonance imaging (MRI) and to compare these with patients with advanced atherosclerotic disease who are known to be at high cardiovascular risk. We examined a total of 83 subjects matched for age: 24 had ESRD and were on dialysis therapy for 3plusminus6 years, 24 had severe coronary artery disease (CAD), 11 had both ESRD and CAD (4plusminus5 years on dialysis therapy), and 24 healthy subjects with no evidence of CAD. Vascular and cardiac function was assessed using cardiac MRI. Aortic compliance was significantly reduced in patients with CAD compared to control subjects (11.3plusminus6.3 mldot10-3/mm Hg vs 15.6plusminus6.0 mldot10-3/mm Hg, P=0.009). Patients with ESRD also exhibited significantly reduced aortic compliance compared to healthy controls (12.4plusminus5.8 mldot10-3/mm Hg vs 15.6plusminus6.0 ml 10-3/mm Hg, P=0.012), whereas there was no significant difference in aortic compliance between patients with CAD and ESRD. Even in the absence of symptomatic CAD, patients with ESRD have significantly reduced aortic compliance compared to normal subjects. Patients with ESRD have equivalent aortic compliance to patients with advanced CAD. These findings suggest that a significantly reduced aortic compliance is one of many mechanisms promoting premature cardiovascular events in patients with ESRD compared to age-matched controls from the general population