High Performance Algorithms for Counting Collisions and Pairwise Interactions

The problem of counting collisions or interactions is common in areas as computer graphics and scientific simulations. Since it is a major bottleneck in applications of these areas, a lot of research has been carried out on such subject, mainly focused on techniques that allow calculations to be performed within pruned sets of objects. This paper focuses on how interaction calculation (such as collisions) within these sets can be done more efficiently than existing approaches. Two algorithms are proposed: a sequential algorithm that has linear complexity at the cost of high memory usage; and a parallel algorithm, mathematically proved to be correct, that manages to use GPU resources more efficiently than existing approaches. The proposed and existing algorithms were implemented, and experiments show a speedup of 21.7 for the sequential algorithm (on small problem size), and 1.12 for the parallel proposal (large problem size). By improving interaction calculation, this work contributes to research areas that promote interconnection in the modern world, such as computer graphics and robotics.Comment: Accepted in ICCS 2019 and published in Springer's LNCS series. Supplementary content at https://mjsaldanha.com/articles/1-hpc-ssp

Different Impacts of Cardiovascular Risk Factors on Oxidative Stress

The objective of the study was to evaluate oxidative stress (OS) status in subjects with different cardiovascular risk factors. With this in mind, we have studied three models of high cardiovascular risk: hypertension (HT) with and without metabolic syndrome, familial hypercholesterolemia (FH) and familial combined hyperlipidemia (FCH) with and without insulin resistance. Oxidative stress markers (oxidized/reduced glutathione ratio, 8-oxo-deoxyguanosine and malondialdehide) together with the activity of antioxidant enzyme triad (superoxide dismutase, catalase, glutathione peroxidase) and activation of both pro-oxidant enzyme (NAPDH oxidase components) and AGTR1 genes, as well as antioxidant enzyme genes (CuZn-SOD, CAT, GPX1, GSR, GSS and TXN) were measured in mononuclear cells of controls (n = 20) and patients (n = 90) by assessing mRNA levels. Activity of some of these antioxidant enzymes was also tested. An increase in OS and pro-oxidant gene mRNA values was observed in patients compared to controls. The hypertensive group showed not only the highest OS values, but also the highest pro-oxidant activation compared to those observed in the other groups. In addition, in HT a significantly reduced antioxidant activity and mRNA induction of antioxidant genes were found when compared to controls and the other groups. In FH and FCH, the activation of pro-oxidant enzymes was also higher and antioxidant ones lower than in the control group, although it did not reach the values obtained in hypertensives. The thioredoxin system was more activated in patients as compared to controls, and the highest levels were in hypertensives. The increased oxidative status in the presence of cardiovascular risk factors is a consequence of both the activation of pro-oxidant mechanisms and the reduction of the antioxidant ones. The altered response of the main cytoplasmic antioxidant systems largely contributes to OS despite the apparent attempt of the thioredoxin system to control it

Observation of the lowest energy gamma-ray in any superdeformed nucleus : 196Bi

New results on the superdeformed $^{196}$Bi nucleus a re reported. We have observed with the EUROBALL IV $\gamma$-ray spectrometer array a superdeformed trans ition of 124 keV which is the lowest observed energy $\gamma$-ray in any superdeformed nucleus. We have de velopped microscopic cranked Hartree-Fock-Bogoliubov calculations using the SLy4 effective force and a realistic surface p airing which strongly support the $K^\pi=2^-$($\pi$[651]1/2$\otimes \nu$[752]5/2) assignment of this su perdeformed band

A single-sample method for normalizing and combining full-resolution copy numbers from multiple platforms, labs and analysis methods

Motivation: The rapid expansion of whole-genome copy number (CN) studies brings a demand for increased precision and resolution of CN estimates. Recent studies have obtained CN estimates from more than one platform for the same set of samples, and it is natural to want to combine the different estimates in order to meet this demand. Estimates from different platforms show different degrees of attenuation of the true CN changes. Similar differences can be observed in CNs from the same platform run in different labs, or in the same lab, with different analytical methods. This is the reason why it is not straightforward to combine CN estimates from different sources (platforms, labs and analysis methods)

Copy number variant detection in inbred strains from short read sequence data

Summary: We have developed an algorithm to detect copy number variants (CNVs) in homozygous organisms, such as inbred laboratory strains of mice, from short read sequence data. Our novel approach exploits the fact that inbred mice are homozygous at virtually every position in the genome to detect CNVs using a hidden Markov model (HMM). This HMM uses both the density of sequence reads mapped to the genome, and the rate of apparent heterozygous single nucleotide polymorphisms, to determine genomic copy number. We tested our algorithm on short read sequence data generated from re-sequencing chromosome 17 of the mouse strains A/J and CAST/EiJ with the Illumina platform. In total, we identified 118 copy number variants (43 for A/J and 75 for CAST/EiJ). We investigated the performance of our algorithm through comparison to CNVs previously identified by array-comparative genomic hybridization (array CGH). We performed quantitative-PCR validation on a subset of the calls that differed from the array CGH data sets

Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridization.

BACKGROUND: Large-scale high throughput studies using microarray technology have established that copy number variation (CNV) throughout the genome is more frequent than previously thought. Such variation is known to play an important role in the presence and development of phenotypes such as HIV-1 infection and Alzheimer's disease. However, methods for analyzing the complex data produced and identifying regions of CNV are still being refined. RESULTS: We describe the presence of a genome-wide technical artifact, spatial autocorrelation or 'wave', which occurs in a large dataset used to determine the location of CNV across the genome. By removing this artifact we are able to obtain both a more biologically meaningful clustering of the data and an increase in the number of CNVs identified by current calling methods without a major increase in the number of false positives detected. Moreover, removing this artifact is critical for the development of a novel model-based CNV calling algorithm - CNVmix - that uses cross-sample information to identify regions of the genome where CNVs occur. For regions of CNV that are identified by both CNVmix and current methods, we demonstrate that CNVmix is better able to categorize samples into groups that represent copy number gains or losses. CONCLUSION: Removing artifactual 'waves' (which appear to be a general feature of array comparative genomic hybridization (aCGH) datasets) and using cross-sample information when identifying CNVs enables more biological information to be extracted from aCGH experiments designed to investigate copy number variation in normal individuals.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Neutron Spectrometry with Scintillating Bolometers of LiF and Sapphire

Two scintillating bolometers of LiF (33 g) and Al2O3 (50 g) at 20 mK, inside a lead shielding at the Canfranc Underground Laboratory, were irradiated with neutrons from a source of 252Cf. The analysis of nuclear recoils registered by sapphire and (n, a) captures by 6Li shows the feasibility of these cryogenic devices to measure the spectral flux of a neutron field. Data unfolding was done assuming that the spectral flux is a piecewise constant function defined on six energy groups. It can be solved by using non-negative least squares without additional assumptions on the neutron flux. The model provides consistent results with the spectra of the observed events in bolometers, giving a fast neutron flux of F(E > 0.1 MeV) = 0.20 n s-1cm-2 with a 15% uncertainty after 3 hours of live time. After our analysis, it can be concluded that nuclear recoils in sapphire are more useful than (n, a) captures in LiF for spectrometry of fast neutrons

Relative spins and excitation energies of superdeformed bands in 190Hg: Further evidence for octupole vibration

An experiment using the Eurogam Phase II gamma-ray spectrometer confirms the existence of an excited superdeformed (SD) band in 190Hg and its very unusual decay into the lowest SD band over 3-4 transitions. The energies and dipole character of the transitions linking the two SD bands have been firmly established. Comparisons with RPA calculations indicate that the excited SD band can be interpreted as an octupole-vibrational structure.Comment: 12 pages, latex, 4 figures available via WWW at http://www.phy.anl.gov/bgo/bc/hg190_nucl_ex.htm

Search for Fingerprints of Tetrahedral Symmetry in 156Gd^{156}Gd

Theoretical predictions suggest the presence of tetrahedral symmetry as an explanation for the vanishing intra-band E2-transitions at the bottom of the odd-spin negative parity band in $^{156}Gd$. The present study reports on experiment performed to address this phenomenon. It allowed to determine the intra-band E2 transitions and branching ratios B(E2)/B(E1) of two of the negative-parity bands in $^{156}Gd$.Comment: presented by Q.T. Doan at XLII Zakopane School of Physics: Breaking Frontiers: Submicron Structures in Physics and Biology, May 2008. 5 pages, minor corrections. To be published in the proceeding

Cyclin L1 (CCNL1) gene alterations in human head and neck squamous cell carcinoma

We evaluated the expression and amplification of cyclin L1 (CCNL1) gene, a potential oncogene localised in the commonly amplified 3q25–28 region, in human head and neck squamous cell carcinomas (HNSCCs). Overexpression was observed in 55 out of 96 cases (57%) and amplification in nine out of 35 tumours (26%) with no relationships to the clinico-pathological parameters. The Cyclin L1 antibody we developed labels nuclear speckles in tumour cells compatible with a role for CCNL1 in RNA splicing