Convergence acceleration of implicit schemes in the presence of high aspect ratio grid cells

The performance of Navier-Stokes codes are influenced by several phenomena. For example, the robustness of the code may be compromised by the lack of grid resolution, by a need for more precise initial conditions or because all or part of the flowfield lies outside the flow regime in which the algorithm converges efficiently. A primary example of the latter effect is the presence of extended low Mach number and/or low Reynolds number regions which cause convergence deterioration of time marching algorithms. Recent research into this problem by several workers including the present authors has largely negated this difficulty through the introduction of time-derivative preconditioning. In the present paper, we employ the preconditioned algorithm to address convergence difficulties arising from sensitivity to grid stretching and high aspect ratio grid cells. Strong grid stretching is particularly characteristic of turbulent flow calculations where the grid must be refined very tightly in the dimension normal to the wall, without a similar refinement in the tangential direction. High aspect ratio grid cells also arise in problems that involve high aspect ratio domains such as combustor coolant channels. In both situations, the high aspect ratio cells can lead to extreme deterioration in convergence. It is the purpose of the present paper to address the reasons for this adverse response to grid stretching and to suggest methods for enhancing convergence under such circumstances. Numerical algorithms typically possess a maximum allowable or optimum value for the time step size, expressed in non-dimensional terms as a CFL number or vonNeumann number (VNN). In the presence of high aspect ratio cells, the smallest dimension of the grid cell controls the time step size causing it to be extremely small, which in turn results in the deterioration of convergence behavior. For explicit schemes, this time step limitation cannot be exceeded without violating stability restrictions of the scheme. On the other hand, for implicit schemes, which are typically unconditionally stable, there appears to be room for improvement through careful tailoring of the time step definition based on results of linear stability analyses. In the present paper, we focus on the central-differenced alternating direction implicit (ADI) scheme. The understanding garnered from this analyses can then be applied to other implicit schemes. In order to systematically study the effects of aspect ratio and the methods of mitigating the associated problems, we use a two pronged approach. We use stability analyses as a tool for predicting numerical convergence behavior and numerical experiments on simple model problems to verify predicted trends. Based on these analyses, we determine that efficient convergence may be obtained at all aspect ratios by getting a combination of things right. Primary among these are the proper definition of the time step size, proper selection of viscous preconditioner and the precise treatment of boundary conditions. These algorithmic improvements are then applied to a variety of test cases to demonstrate uniform convergence at all aspect ratios

Poly(ADP-ribose)glycohydrolase is an upstream regulator of Ca2+ fluxes in oxidative cell death

Oxidative DNA damage to cells activates poly(ADP-ribose)polymerase-1 (PARP-1) and the poly(ADP-ribose) formed is rapidly degraded to ADP-ribose by poly(ADP-ribose)glycohydrolase (PARG). Here we show that PARP-1 and PARG control extracellular Ca2+ fluxes through melastatin-like transient receptor potential 2 channels (TRPM2) in a cell death signaling pathway. TRPM2 activation accounts for essentially the entire Ca2+ influx into the cytosol, activating caspases and causing the translocation of apoptosis inducing factor (AIF) from the inner mitochondrial membrane to the nucleus followed by cell death. Abrogation of PARP-1 or PARG function disrupts these signals and reduces cell death. ADP-ribose-loading of cells induces Ca2+ fluxes in the absence of oxidative damage, suggesting that ADP-ribose is the key metabolite of the PARP-1/PARG system regulating TRPM2. We conclude that PARP-1/PARG control a cell death signal pathway that operates between five different cell compartments and communicates via three types of chemical messengers: a nucleotide, a cation, and proteins

The BRCT Domain of PARP-1 Is Required for Immunoglobulin Gene Conversion

During affinity maturation, genomic integrity is maintained through specific targeting of DNA mutations. The DNA damage sensor PARP-1 helps determine whether a DNA lesion results in faithful or mutagenic repair

Body Shaping and Volume Restoration: The Role of Hyaluronic Acid

Driven by the rising popularity of minimally invasive techniques, the demand for cosmetic procedures is increasing. Cosmetic body-shaping procedures can be categorized into those that remove tissue and those that add volume. This review focuses on the latter of these categories, particularly on the use of resorbable hyaluronic acid gels specifically developed for minimally invasive volume enhancement. Pilot studies of hyaluronic acid involving its injection to contour various body deformities and its recent use in female breast augmentation are discussed. Injectable hyaluronic acid is effective and well tolerated. It represents an attractive treatment option for volume restoration or augmentation by providing predictable long-lasting results after minimally invasive administration. Alternative treatment options for volume enhancement also are summarized including fat transfer, silicone implants, and the use of injectable nonresorbable products such as silicone, polyalkylimide, and polyacrylamide gels. As patients continue to opt for nonsurgical procedures that offer predictable results, the development of minimally invasive products such as hyaluronic acid is increasingly important

Tamoxifen-Induced Cre-loxP Recombination Is Prolonged in Pancreatic Islets of Adult Mice

Tamoxifen (Tm)-inducible Cre recombinases are widely used to perform gene inactivation and lineage tracing studies in mice. Although the efficiency of inducible Cre-loxP recombination can be easily evaluated with reporter strains, the precise length of time that Tm induces nuclear translocation of CreERTm and subsequent recombination of a target allele is not well defined, and difficult to assess. To better understand the timeline of Tm activity in vivo, we developed a bioassay in which pancreatic islets with a Tm-inducible reporter (from Pdx1PB-CreERTm;R26RlacZ mice) were transplanted beneath the renal capsule of adult mice previously treated with three doses of 1 mg Tm, 8 mg Tm, or corn oil vehicle. Surprisingly, recombination in islet grafts, as assessed by expression of the β-galactosidase (β-gal) reporter, was observed days or weeks after Tm treatment, in a dose-dependent manner. Substantial recombination occurred in islet grafts long after administration of 3×8 mg Tm: in grafts transplanted 48 hours after the last Tm injection, 77.9±0.4% of β-cells were β-gal+; in β-cells placed after 1 week, 46.2±5.0% were β-gal+; after 2 weeks, 26.3±7.0% were β-gal+; and after 4 weeks, 1.9±0.9% were β-gal+. Islet grafts from mice given 3×1 mg Tm showed lower, but notable, recombination 48 hours (4.9±1.7%) and 1 week (4.5±1.9%) after Tm administration. These results show that Tm doses commonly used to induce Cre-loxP recombination may continue to label significant numbers of cells for weeks after Tm treatment, possibly confounding the interpretation of time-sensitive studies using Tm-dependent models. Therefore, investigators developing experimental approaches using Tm-inducible systems should consider both maximal recombination efficiency and the length of time that Tm-induced Cre-loxP recombination occurs

Potential biological role of poly (ADP-ribose) polymerase (PARP) in male gametes

Maintaining the integrity of sperm DNA is vital to reproduction and male fertility. Sperm contain a number of molecules and pathways for the repair of base excision, base mismatches and DNA strand breaks. The presence of Poly (ADP-ribose) polymerase (PARP), a DNA repair enzyme, and its homologues has recently been shown in male germ cells, specifically during stage VII of spermatogenesis. High PARP expression has been reported in mature spermatozoa and in proven fertile men. Whenever there are strand breaks in sperm DNA due to oxidative stress, chromatin remodeling or cell death, PARP is activated. However, the cleavage of PARP by caspase-3 inactivates it and inhibits PARP's DNA-repairing abilities. Therefore, cleaved PARP (cPARP) may be considered a marker of apoptosis. The presence of higher levels of cPARP in sperm of infertile men adds a new proof for the correlation between apoptosis and male infertility. This review describes the possible biological significance of PARP in mammalian cells with the focus on male reproduction. The review elaborates on the role played by PARP during spermatogenesis, sperm maturation in ejaculated spermatozoa and the potential role of PARP as new marker of sperm damage. PARP could provide new strategies to preserve fertility in cancer patients subjected to genotoxic stresses and may be a key to better male reproductive health

2ʹ-Deoxyadenosine 5ʹ-diphosphoribose is an endogenous TRPM2 superagonist

Transient receptor potential melastatin 2 (TRPM2) is a ligand-gated Ca2+-permeable nonselective cation channel. Whereas physiological stimuli, such as chemotactic agents, evoke controlled Ca2+ signals via TRPM2, pathophysiological stimuli such as reactive oxygen species and genotoxic stress result in prolonged TRPM2-mediated Ca2+ entry and, consequently, apoptosis. To date, adenosine 5'-diphosphoribose (ADPR) has been assumed to be the main agonist for TRPM2. Here we show that 2'-deoxy-ADPR was a significantly better TRPM2 agonist, inducing 10.4-fold higher whole-cell currents at saturation. Mechanistically, this increased activity was caused by a decreased rate of inactivation and higher average open probability. Using high-performance liquid chromatography (HPLC) and mass spectrometry, we detected endogenous 2'-deoxy-ADPR in Jurkat T lymphocytes. Consistently, cytosolic nicotinamide mononucleotide adenylyltransferase 2 (NMNAT-2) and nicotinamide adenine dinucleotide (NAD)-glycohydrolase CD38 sequentially catalyzed the synthesis of 2'-deoxy-ADPR from nicotinamide mononucleotide (NMN) and 2'-deoxy-ATP in vitro. Thus, 2'-deoxy-ADPR is an endogenous TRPM2 superagonist that may act as a cell signaling molecule