Exact subgrid interface correction schemes for elliptic interface problems

Abstract We introduce a non-conforming finite element method for second order elliptic interface problems. Our approach applies to problems in which discontinuous coefficients and singular sources on the interface may give rise to jump discontinuities in either the solution or its normal derivative. Given a standard background mesh and an interface that passes between elements, the key idea is to construct a singular correction function which satisfies the prescribed jump conditions, providing accurate sub-grid resolution of the discontinuities. Utilizing the closest point extension and an implicit interface representation by the signed distance function, an algorithm is established to construct the correction function. The result is a function which is supported only on the interface elements, represented by the regular basis functions, and bounded independently of the interface location with respect to the background mesh. In the particular case of a constant second order coefficient, our regularization by singular function is straightforward, and the resulting left-hand-side is identical to that of a regular problem without introducing any instability. The influence of the regularization appears solely on the right-hand-side, which simplifies the implementation. In the more general case of discontinuous second order coefficients, a normalization is invoked which introduces a constraint equation on the interface. This results in a problem statement similar to that of a saddle-point problem. We employ two-level-iteration as the solution strategy, which exhibits aspects similar to those of iterative preconditioning strategies. Elliptic interface problems appear in many physical applications, including Stefan problems, fluids problems, materials issues, free boundary problems, and shape optimization In the above, as a model problem, we can take a Poisson equation with piecewise constant coefficient, a i > 0 on each Ω i ; −∇·(a i ∇u) = f on Ω i for i = 1, 2 with the boundary data given on ∂Ω. For well-posedness, we need additional information on the behavior of the solution on the interface. Let g and h be

Migration, assignment, and scheduling of jobs in virtualized environment

Abstract Migration is an interesting issue for managing resource utilization and performance in clusters. Recent advances in server virtualization have made migration a practical method to achieve these goals. Especially, the live migration of virtualized servers made their pausing times negligible. However, migration of a virtual machine (VM) can slow down other collocated VMs in multiresource shared systems, where all the system resources are shared among collocated VMs. In parallel execution environment, such sudden slow-down phase of systems is called system noise; it may slow down overall systems while increasing the variability of system performance. When we consider the virtual machine assignment problem as resource allocation, those performance issues are hard to be properly treated. In this work, we address how to consider performance in assigning VMs. To achieve this goal, we model a migration process of a VM instance as a pair of jobs that run at the hosts of sender and receiver. We propose a method to analyze the migration time and the performance impact on multiresource shared systems for completing given VM assignment plan. This study may contribute to create more robust performance in virtualized environment

LINE FUSION GENES: a database of LINE expression in human genes

BACKGROUND: Long Interspersed Nuclear Elements (LINEs) are the most abundant retrotransposons in humans. About 79% of human genes are estimated to contain at least one segment of LINE per transcription unit. Recent studies have shown that LINE elements can affect protein sequences, splicing patterns and expression of human genes. DESCRIPTION: We have developed a database, LINE FUSION GENES, for elucidating LINE expression throughout the human gene database. We searched the 28,171 genes listed in the NCBI database for LINE elements and analyzed their structures and expression patterns. The results show that the mRNA sequences of 1,329 genes were affected by LINE expression. The LINE expression types were classified on the basis of LINEs in the 5' UTR, exon or 3' UTR sequences of the mRNAs. Our database provides further information, such as the tissue distribution and chromosomal location of the genes, and the domain structure that is changed by LINE integration. We have linked all the accession numbers to the NCBI data bank to provide mRNA sequences for subsequent users. CONCLUSION: We believe that our work will interest genome scientists and might help them to gain insight into the implications of LINE expression for human evolution and disease. AVAILABILITY

Selection of internal reference genes for SYBR green qRT-PCR studies of rhesus monkey (Macaca mulatta) tissues

<p>Abstract</p> <p>Background</p> <p>The rhesus monkey (<it>Macaca mulatta</it>) is a valuable and widely used model animal for biomedical research. However, quantitative analyses of rhesus gene expression profiles under diverse experimental conditions are limited by a shortage of suitable internal controls for the normalization of mRNA levels. In this study, we used a systematic approach for the selection of potential reference genes in the rhesus monkey and compared their suitability to that of the corresponding genes in humans.</p> <p>Results</p> <p>Eight housekeeping genes (HKGs) (<it>GAPDH, SDHA, ACTB, RPL13A, RPL32, UBA52, PGK1Y</it>, and <it>YWHAZ</it>) from rhesus monkeys and humans were selected to test for normalization of expression levels in six different tissue types (brain, colon, kidney, liver, lung, and stomach). Their stability and suitability as reference genes were validated by <it>geNorm</it>, <it>NormFinder </it>and <it>BestKeeper </it>programs. Intriguingly, <it>RPL13A </it>and <it>RPL32 </it>were selected as ideal reference genes only in rhesus monkeys.</p> <p>Conclusion</p> <p>The results clearly indicated the necessity of using different reference genes for normalization of expression levels between rhesus monkeys and humans in various tissues.</p

Patterns of Recurrence after Breast-Conserving Treatment for Early Stage Breast Cancer by Molecular Subtype

Purpose: To study clinical features and patterns of recurrence after breast-conserving treatment (BCT) for three molecular subtypes of early stage breast cancer. Methods: The sample studied included 596 patients with T1-2N0-1 breast cancer who received BCT. Three groups were defined by receptor status. Luminal: estrogen receptor (ER) or progesterone receptor (PR) positive; triple negative (TN): ER, PR, and epidermal growth factor receptor-2 (HER2) receptor negative; and HER2 overexpressing: ER and PR negative but HER2 receptor positive. Results: The number of patients in each group was 408 (68.5%), 105 (17.6%), and 83 (13.9%), respectively. The median follow-up period was 79 months. The TN and HER2 subtypes occurred in younger patients (p=0.0007) and had higher nuclear grade and poorer histologic grade (p&lt;0.0001 and 0.0071, respectively). During the follow-up period, locoregional recurrence was detected as th

Protective and therapeutic effects of an extract mixture of alder tree, labiate herb, milk thistle green bean-rice bran fermentation, and turnip against ethanol-induced toxicity in the rat

An herbal extract mixture and yogurt added to the herbal extract mixture were tested for their protective and therapeutic effects on ethanol-induced liver injury. The herbal extract mixture, yogurt and commercial drugs were used for treatment for two weeks prior to administering a single oral dose of ethanol (3 g/kg body weight). The herbal extract mixture and yogurt added to the herbal extract mixture were found to provide protection against ethanol-induced toxicity comparable to the commercial drug treatment, according to the serum and histopathological analysis. It was also shown that co-treatment with herbal extract mixture and yogurt against a triple oral dose of ethanol (2 g/kg body weight, over one week) provided protection against ethanol toxicity. After the initial set of experiments, the herbal extract mixture and yogurt treatments were extended for three more weeks. When compared to the positive control, further treatment with both the herbal extract and yogurt significantly reduced liver injury and resulted in a lower grade of lipid deposition

Normal Ambulatory 24-Hour Esophageal pH Values in Koreans -A Multicenter Study-

Ambulatory 24-hr esophageal pH monitoring is considered the gold standard for diagnosing gastroesophageal reflux disease. The aim of this study was to establish normal values for gastroesophageal acid exposure in healthy Koreans. Fifty healthy volunteers (24 males and 26 females; mean age, 45 yr) without reflux symptoms and without reflux esophagitis or hiatal hernia on upper endoscopy underwent ambulatory 24-hr esophageal pH monitoring after esophageal manometry. The 95th percentiles for the reflux parameters were: the percent total time pH <4, 3.7%; the percent upright time pH <4, 5.7%; the percent supine time pH <4, 1.0%; the number of reflux episodes with pH <4, 76.5; the number of reflux episodes with pH <4 for >5 min, 1.5; the duration of the longest episode, 12.5 min; and the composite score, 14.2. Age and gender were not associated with any of the pH parameters. In conclusion, physiological gastroesophageal reflux occurs in healthy Koreans. These normal esophageal pH values will provide reference data for clinical and research studies in Korea