Strategies for Optimize Off-Lattice Aggregate Simulations

We review some computer algorithms for the simulation of off-lattice clusters grown from a seed, with emphasis on the diffusion-limited aggregation, ballistic aggregation and Eden models. Only those methods which can be immediately extended to distinct off-lattice aggregation processes are discussed. The computer efficiencies of the distinct algorithms are compared.Comment: 6 pages, 7 figures and 3 tables; published at Brazilian Journal of Physics 38, march, 2008 (http://www.sbfisica.org.br/bjp/files/v38_81.pdf

Amplitude analysis of four-body decays using a massively-parallel fitting framework

The GooFit Framework is designed to perform maximum-likelihood fits for arbitrary functions on various parallel back ends, for example a GPU. We present an extension to GooFit which adds the functionality to perform time-dependent amplitude analyses of pseudoscalar mesons decaying into four pseudoscalar final states. Benchmarks of this functionality show a significant performance increase when utilizing a GPU compared to a CPU. Furthermore, this extension is employed to study the sensitivity on the $D^0 - \bar{D}^0$ mixing parameters $x$ and $y$ in a time-dependent amplitude analysis of the decay $D^0 \rightarrow K^+\pi^-\pi^+\pi^-$. Studying a sample of 50 000 events and setting the central values to the world average of $x = (0.49 \pm0.15) \%$ and $y = (0.61 \pm0.08) \%$, the statistical sensitivities of $x$ and $y$ are determined to be $\sigma(x) = 0.019 \%$ and $\sigma(y) = 0.019 \%$.Comment: Proceedings of the 22nd International Conference on Computing in High Energy and Nuclear Physics, CHEP 201

Benchmarking the Security Protocol and Data Model (SPDM) for component authentication

Efforts to secure computing systems via software traditionally focus on the operating system and application levels. In contrast, the Security Protocol and Data Model (SPDM) tackles firmware level security challenges, which are much harder (if at all possible) to detect with regular protection software. SPDM includes key features like enabling peripheral authentication, authenticated hardware measurements retrieval, and secure session establishment. Since SPDM is a relatively recent proposal, there is a lack of studies evaluating its performance impact on real-world applications. In this article, we address this gap by: (1) implementing the protocol on a simple virtual device, and then investigating the overhead introduced by each SDPM message; and (2) creating an SPDM-capable virtual hard drive based on VirtIO, and comparing the resulting read/write performance with a regular, unsecured implementation. Our results suggest that SPDM bootstrap time takes the order of tens of milliseconds, while the toll of introducing SPDM on hard drive communication highly depends on specific workload patterns. For example, for mixed random read/write operations, the slowdown is negligible in comparison to the baseline unsecured setup. Conversely, for sequential read or write operations, the data encryption process becomes the bottleneck, reducing the performance indicators by several orders of magnitude.Comment: 10 pages, 8 figure

The familial hypercholesterolaemia phenotype: Monogenic familial hypercholesterolaemia, polygenic hypercholesterolaemia and other causes

Familial Hypercholesterolaemia (FH) is a monogenic disorder characterised by high LDL-C concentrations and increased cardiovascular risk. However, in clinically defined FH cohorts worldwide, an FH-causing variant is only found in 40-50% of the cases. The aim of this work was to characterise the genetic cause of the FH phenotype in Portuguese clinical FH patients. Methods and Results Between 1999 and 2017, 731 index patients (311 children and 420 adults) who met the Simon Broome diagnostic criteria had been referred to our laboratory. LDLR, APOB, PCSK9, APOE, LIPA, LDLRAP1, ABCG5/8 genes were analysed by PCR amplification and Sanger sequencing. The 6-SNP LDL-C genetic risk score (GRS) for polygenic hypercholesterolaemia was validated in the Portuguese population and cases with a GRS over the 25th percentile were considered to have a high likelihood of polygenic hypercholesterolaemia. An FH-causing mutation was found in 39% of patients (94% in LDLR, 5% APOB and 1% PCSK9), while at least 29% have polygenic hypercholesterolaemia and 1% have other lipid disorders. A genetic cause for the FH phenotype was found in 503 patients (69%). All known causes of the FH phenotype should be investigated in FH cohorts to ensure accurate diagnosis and appropriate management. This article is protected by copyright. All rights reserved

Five-Year Outcome in Stroke Patients Submitted to Thrombolysis

BACKGROUND AND PURPOSE: Little is known on long-term follow-up after thrombolysis in ischemic stroke patients because the majority of studies evaluated outcome at 3 to 12 months. We aimed to assess 5-year outcome after intravenous thrombolysis (IVT). METHODS: Cohort study based on the prospective registry of all consecutive ischemic stroke patients submitted to IVT in our Stroke Unit. Five-year outcome, including living settings, functional outcome, stroke recurrence, and mortality, was ascertained by telephonic interviews and additional review of clinical records. Multivariate analyses were performed to identify predictors of outcome and mortality. Excellent outcome was defined as modified Rankin scale 0 to 1. RESULTS: Five-year outcome was available for 155/164 patients submitted to IVT. At 5 years, 32.9% of patients had an excellent outcome (95% confidence interval (CI) =25.5-43.3) and mortality was 43.9% (95%CI=36.1-51.7). Increasing age (odds ratio =0.93, 95% CI =0.90-0.97) and increasing National Institute of Health Stroke Scale (NIHSS) 24 h after thrombolysis (odds ratio =0.81, 95% CI =0.74-0.90) were independently associated with a lower likelihood of an excellent 5-year outcome. Age (hazards ratio =1.07, 95% CI =1.03-1.11) and excellent functional outcome 3 months after thrombolysis (hazards ratio =0.28, 95%CI=0.12-0.66) were independently associated with mortality during follow-up. CONCLUSIONS: One third of ischemic stroke patients have excellent 5-year outcome after IVT. Younger age, lower NIHSS 24 h after IVT, and excellent 3-month functional outcome are independent predictors of excellent 5-year outcome

A framework for database optimization and workload control

Nowadays, database optimizers take advantage of indexes and materialized views (MVs) to produce query execution plans. While indexes and MVs can speed up the execution of queries, there are costs to store and manage them. This paper presents a mathematical model and a greedy implementation to recommend a set of indexes and MVs in order to optimize the database, given a database workload and a disk space constraint. Our approach is generic, so it can be used to any relational database system that takes advantage of MVs in plan selection. While it was developed for frequently updated databases, it also produced interesting results in read only databases and to estimate the behavior of new databases (with predefined workloads)