Investigation of tetrahedron elements using automatic meshing in finite element analysis

This investigation examines the quality of finite element analysis (FEA) results based on the use of tetrahedron elements. For some classes of problems analyzed by the finite element method (FEM), the use of various polynomial order tetrahedra is considered quite acceptable. However, in other classes of problems, particularly stress analysis, users have a strong bias against these types of elements. Various case studies are performed, comparing results based on several types of three-dimensional elements

On Steering Swarms

The main contribution of this paper is a novel method allowing an external observer/controller to steer and guide swarms of identical and indistinguishable agents, in spite of the agents' lack of information on absolute location and orientation. Importantly, this is done via simple global broadcast signals, based on the observed average swarm location, with no need to send control signals to any specific agent in the swarm

αCP binding to a cytosine-rich subset of polypyrimidine tracts drives a novel pathway of cassette exon splicing in the mammalian transcriptome.

Alternative splicing (AS) is a robust generator of mammalian transcriptome complexity. Splice site specification is controlled by interactions of cis-acting determinants on a transcript with specific RNA binding proteins. These interactions are frequently localized to the intronic U-rich polypyrimidine tracts (PPT) located 5' to the majority of splice acceptor junctions. αCPs (also referred to as polyC-binding proteins (PCBPs) and hnRNPEs) comprise a subset of KH-domain proteins with high affinity and specificity for C-rich polypyrimidine motifs. Here, we demonstrate that αCPs promote the splicing of a defined subset of cassette exons via binding to a C-rich subset of polypyrimidine tracts located 5' to the αCP-enhanced exonic segments. This enhancement of splice acceptor activity is linked to interactions of αCPs with the U2 snRNP complex and may be mediated by cooperative interactions with the canonical polypyrimidine tract binding protein, U2AF65. Analysis of αCP-targeted exons predicts a substantial impact on fundamental cell functions. These findings lead us to conclude that the αCPs play a direct and global role in modulating the splicing activity and inclusion of an array of cassette exons, thus driving a novel pathway of splice site regulation within the mammalian transcriptome

Boosted Decision Trees as an Alternative to Artificial Neural Networks for Particle Identification

The efficacy of particle identification is compared using artificial neutral networks and boosted decision trees. The comparison is performed in the context of the MiniBooNE, an experiment at Fermilab searching for neutrino oscillations. Based on studies of Monte Carlo samples of simulated data, particle identification with boosting algorithms has better performance than that with artificial neural networks for the MiniBooNE experiment. Although the tests in this paper were for one experiment, it is expected that boosting algorithms will find wide application in physics.Comment: 6 pages, 5 figures; Accepted for publication in Nucl. Inst. & Meth.

Transmission Phase of a Quantum Dot with Kondo Correlation Near the Unitary Limit

The complex transmission amplitude -- both magnitude and phase -- of a quantum dot (QD) with Kondo correlation was measured near the unitary limit. Contrary to previous phase measurements, performed far from this limit [Ji et al., Science 290, 779 (2000)], the transmission phase was observed to evolve linearly over a range of about 1.5 pi when the Fermi energy was scanned through a Kondo pair -- a pair of spin degenerate energy levels. Moreover, the phase in Coulomb blockade (CB) peak, adjancent to the Kondo pair, retained a memory of the Kondo correlation and did not exhibit the familiar behavior in the CB regime. These results do not agree with theoretical predictions, suggesting that a full explanation may go beyond the framework of the Anderson model.Comment: 4 pages, 4 figure

Incorporation of genetic model parameters for cost-effective designs of genetic association studies using DNA pooling

<p>Abstract</p> <p>Background</p> <p>Studies of association methods using DNA pooling of single nucleotide polymorphisms (SNPs) have focused primarily on the effects of "machine-error", number of replicates, and the size of the pool. We use the non-centrality parameter (NCP) for the analysis of variance test to compute the approximate power for genetic association tests with DNA pooling data on cases and controls. We incorporate genetic model parameters into the computation of the NCP. Parameters involved in the power calculation are disease allele frequency, frequency of the marker SNP allele in coupling with the disease locus, disease prevalence, genotype relative risk, sample size, genetic model, number of pools, number of replicates of each pool, and the proportion of variance of the pooled frequency estimate due to machine variability. We compute power for different settings of number of replicates and total number of genotypings when the genetic model parameters are fixed. Several significance levels are considered, including stringent significance levels (due to the increasing popularity of 100 K and 500 K SNP "chip" data). We use a factorial design with two to four settings of each parameter and multiple regression analysis to assess which parameters most significantly affect power.</p> <p>Results</p> <p>The power can increase substantially as the genotyping number increases. For a fixed number of genotypings, the power is a function of the number of replicates of each pool such that there is a setting with maximum power. The four most significant parameters affecting power for association are: (1) genotype relative risk, (2) genetic model, (3) sample size, and (4) the interaction term between disease and SNP marker allele probabilities.</p> <p>Conclusion</p> <p>For a fixed number of genotypings, there is an optimal number of replicates of each pool that increases as the number of genotypings increases. Power is not substantially reduced when the number of replicates is close to but not equal to the optimal setting.</p

Conjugate Hard X-ray Footpoints in the 2003 October 29 X10 Flare: Unshearing Motions, Correlations, and Asymmetries

We present a detailed imaging and spectroscopic study of the conjugate hard X-ray (HXR) footpoints (FPs) observed with RHESSI in the 2003 October 29 X10 flare. The double FPs first move toward and then away from each other, mainly parallel and perpendicular to the magnetic neutral line, respectively. The transition of these two phases of FP unshearing motions coincides with the direction reversal of the motion of the loop-top (LT) source, and with the minima of the estimated loop length and LT height. The FPs show temporal correlations between HXR flux, spectral index, and magnetic field strength. The HXR flux exponentially correlates with the magnetic field strength, which also anti-correlates with the spectral index before the second HXR peak's maximum, suggesting that particle acceleration sensitively depends on the magnetic field strength and/or reconnection rate. Asymmetries are observed between the FPs: on average, the eastern FP is 2.2 times brighter in HXR flux and 1.8 times weaker in magnetic field strength, and moves 2.8 times faster away from the neutral line than the western FP; the estimated coronal column density to the eastern FP from the LT source is 1.7 times smaller. The two FPs have marginally different spectral indexes. The eastern-to-western FP HXR flux ratio and magnetic field strength ratio are anti-correlated only before the second HXR peak's maximum. Neither magnetic mirroring nor column density alone can explain the totality of these observations, but their combination, together with other transport effects, might provide a full explanation. We have also developed novel techniques to remove particle contamination from HXR counts and to estimate effects of pulse pileup in imaging spectroscopy, which can be applied to other RHESSI flares in similar circumstances.Comment: 22 pages, 14 figures, 4 tables; ApJ 2009, in pres

Systems Biology Approaches to Decoding the Genome of Liver Cancer

Molecular classification of cancers has been significantly improved patient outcomes through the implementation of treatment protocols tailored to the abnormalities present in each patient's cancer cells. Breast cancer represents the poster child with marked improvements in outcome occurring due to the implementation of targeted therapies for estrogen receptor or human epidermal growth factor receptor-2 positive breast cancers. Important subtypes with characteristic molecular features as potential therapeutic targets are likely to exist for all tumor lineages including hepatocellular carcinoma (HCC) but have yet to be discovered and validated as targets. Because each tumor accumulates hundreds or thousands of genomic and epigenetic alterations of critical genes, it is challenging to identify and validate candidate tumor aberrations as therapeutic targets or biomarkers that predict prognosis or response to therapy. Therefore, there is an urgent need to devise new experimental and analytical strategies to overcome this problem. Systems biology approaches integrating multiple data sets and technologies analyzing patient tissues holds great promise for the identification of novel therapeutic targets and linked predictive biomarkers allowing implementation of personalized medicine for HCC patients

Episodic X-ray Emission Accompanying the Activation of an Eruptive Prominence: Evidence of Episodic Magnetic Reconnection

We present an X-ray imaging and spectroscopic study of a partially occulted C7.7 flare on 2003 April 24 observed by RHESSI that accompanied a prominence eruption observed by TRACE. (1) The activation and rise of the prominence occurs during the preheating phase of the flare. The initial X-ray emission appears as a single coronal source at one leg of the prominence and it then splits into a double source. Such a source splitting happens three times, each coinciding with an increased X-ray flux and plasma temperature, suggestive of fast reconnection in a localized current sheet and an enhanced energy release rate. In the late stage of this phase, the prominence displays a helical structure. These observations are consistent with the tether-cutting and/or kink instability model for triggering solar eruptions. (2) The eruption of the prominence takes place during the flare impulsive phase. Since then, there appear signatures predicted by the classical CSHKP model of two-ribbon flares occurring in a vertical current sheet trailing an eruption. These signatures include an EUV cusp and current-sheet-like feature (or ridge) above it. There is also X-ray emission along the EUV ridge both below and above the cusp, which in both regions appears closer to the cusp at higher energies in the thermal regime. This trend is reversed in the nonthermal regime. (3) Spectral analysis indicates thermal X-rays from all sources throughout the flare, while during the impulsive phase there is additional nonthermal emission which primarily comes from the coronal source below the cusp. This source also has a lower temperature, a higher emission measure, and a much harder nonthermal spectrum than the upper sources.Comment: 8 pages, 5 figures, submitted to Ap