Performance enhancement of an immersed boundary method based FSI solver using OpenMP

This work presents a high-fidelity in-house Fluid Structure Interaction (FSI) solver devel- oped by combining discrete forcing Immersed Boundary Method (IBM) with a RK-4 based structural solver. Classification of the grid points as fluid, solid and IB points in the IBM framework and the solution of the pressure correction equations are the two most computationally expensive section in the numerical solver. These computational efforts can be significantly reduced by implementing OpenMP techniques. However, the successive over-relaxation (SOR) iterative method used in the serial code is not suitable for OpenMP parallelization as it shows data dependencies from previous iterations. Therefore, the Red-Black (RB) SOR is implemented to avoid the data dependencies

Spherical averages in the space of marked lattices

A marked lattice is a $d$-dimensional Euclidean lattice, where each lattice point is assigned a mark via a given random field on ${\mathbb Z}^d$. We prove that, if the field is strongly mixing with a faster-than-logarithmic rate, then for every given lattice and almost every marking, large spheres become equidistributed in the space of marked lattices. A key aspect of our study is that the space of marked lattices is not a homogeneous space, but rather a non-trivial fiber bundle over such a space. As an application, we prove that the free path length in a crystal with random defects has a limiting distribution in the Boltzmann-Grad limit

Combinatorial Roles of Heparan Sulfate Proteoglycans and Heparan Sulfates in Caenorhabditis elegans Neural Development

Heparan sulfate proteoglycans (HSPGs) play critical roles in the development and adult physiology of all metazoan organisms. Most of the known molecular interactions of HSPGs are attributed to the structurally highly complex heparan sulfate (HS) glycans. However, whether a specific HSPG (such as syndecan) contains HS modifications that differ from another HSPG (such as glypican) has remained largely unresolved. Here, a neural model in C. elegans is used to demonstrate for the first time the relationship between specific HSPGs and HS modifications in a defined biological process in vivo. HSPGs are critical for the migration of hermaphrodite specific neurons (HSNs) as genetic elimination of multiple HSPGs leads to 80% defect of HSN migration. The effects of genetic elimination of HSPGs are additive, suggesting that multiple HSPGs, present in the migrating neuron and in the matrix, act in parallel to support neuron migration. Genetic analyses suggest that syndecan/sdn-1 and HS 6-O-sulfotransferase, hst-6, function in a linear signaling pathway and glypican/lon-2 and HS 2-O-sulfotransferase, hst-2, function together in a pathway that is parallel to sdn-1 and hst-6. These results suggest core protein specific HS modifications that are critical for HSN migration. In C. elegans, the core protein specificity of distinct HS modifications may be in part regulated at the level of tissue specific expression of genes encoding for HSPGs and HS modifying enzymes. Genetic analysis reveals that there is a delicate balance of HS modifications and eliminating one HS modifying enzyme in a compromised genetic background leads to significant changes in the overall phenotype. These findings are of importance with the view of HS as a critical regulator of cell signaling in normal development and disease

Sinter formation during directed energy deposition of titanium alloy powders

During directed energy deposition (DED) additive manufacturing, powder agglomeration and sintering can occur outside of the melt pool when using titanium alloy powders. Using in situ synchrotron radiography we investigate the mechanisms by which sintering of Ti6242 powder occurs around the pool, performing a parametric study to determine the influence of laser power and stage traverse speed on sinter build-up. The results reveal that detrimental sinter can be reduced using a high laser power or increased stage traverse speed, although the latter also reduces deposition layer thickness. The mechanism of sinter formation during DED was determined to be in-flight heating of the powder particles in the laser beam. Calculations of particle heating under the processing conditions explored in this study confirm that powder particles can reasonably exceed 700 °C, the threshold for Ti surface oxide dissolution, and thus the powder is prone to sintering if not incorporated into the melt pool. The build-up of sinter powder layer on deposit surfaces led to lack of fusion pores. To mitigate sinter formation and its detrimental effects on DED component quality, it is essential that the powder delivery spot area is smaller than the melt pool, ensuring most powder lands in the melt pool

Annotation and query of tissue microarray data using the NCI Thesaurus

<p>Abstract</p> <p>Background</p> <p>The Stanford Tissue Microarray Database (TMAD) is a repository of data serving a consortium of pathologists and biomedical researchers. The tissue samples in TMAD are annotated with multiple free-text fields, specifying the pathological diagnoses for each sample. These text annotations are not structured according to any ontology, making future integration of this resource with other biological and clinical data difficult.</p> <p>Results</p> <p>We developed methods to map these annotations to the NCI thesaurus. Using the NCI-T we can effectively represent annotations for about 86% of the samples. We demonstrate how this mapping enables ontology driven integration and querying of tissue microarray data. We have deployed the mapping and ontology driven querying tools at the TMAD site for general use.</p> <p>Conclusion</p> <p>We have demonstrated that we can effectively map the diagnosis-related terms describing a sample in TMAD to the NCI-T. The NCI thesaurus terms have a wide coverage and provide terms for about 86% of the samples. In our opinion the NCI thesaurus can facilitate integration of this resource with other biological data.</p

The novel mTOR inhibitor RAD001 (Everolimus) induces antiproliferative effects in human pancreatic neuroendocrine tumor cells

Background/Aim: Tumors exhibiting constitutively activated PI(3) K/Akt/mTOR signaling are hypersensitive to mTOR inhibitors such as RAD001 (everolimus) which is presently being investigated in clinical phase II trials in various tumor entities, including neuroendocrine tumors (NETs). However, no preclinical data about the effects of RAD001 on NET cells have been published. In this study, we aimed to evaluate the effects of RAD001 on BON cells, a human pancreatic NET cell line that exhibits constitutively activated PI(3) K/Akt/mTOR signaling. Methods: BON cells were treated with different concentrations of RAD001 to analyze its effect on cell growth using proliferation assays. Apoptosis was examined by Western blot analysis of caspase-3/PARP cleavage and by FACS analysis of DNA fragmentation. Results: RAD001 potently inhibited BON cell growth in a dose-dependent manner which was dependent on the serum concentration in the medium. RAD001-induced growth inhibition involved G0/G1-phase arrest as well as induction of apoptosis. Conclusion: In summary, our data demonstrate antiproliferative and apoptotic effects of RAD001 in NET cells in vitro supporting its clinical use in current phase II trials in NET patients. Copyright (c) 2007 S. Karger AG, Basel

The Seroepidemiology of Haemophilus influenzae Type B Prior to Introduction of an Immunization Programme in Kathmandu, Nepal.

Haemophilus influenzae type b (Hib) is now recognized as an important pathogen in Asia. To evaluate disease susceptibility, and as a marker of Hib transmission before routine immunization was introduced in Kathmandu, 71 participants aged 7 months-77 years were recruited and 15 cord blood samples were collected for analysis of anti-polyribosylribitol phosphate antibody levels by enzyme-linked immunosorbent assay. Only 20% of children under 5 years old had levels considered protective (>0.15 µg/ml), rising to 83% of 15-54 year-olds. Prior to introduction of Hib vaccine in Kathmandu, the majority of young children were susceptible to disease