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Khan, Sabbir

Publications and source records attributed to Khan, Sabbir.

CD36 mediates lipid accumulation in pancreatic beta cells under the duress of glucolipotoxic conditions: Novel roles of lysine deacetylases

The cluster of differentiation 36 (CD36) is implicated in the intake of long-chain fatty acids and fat storage in various cell types including the pancreatic beta cell, thus contributing to the pathogenesis of metabolic stress and diabetes. Recent evidence indicates that CD36 undergoes post-translational modifications such as acetylation-deacetylation. However, putative roles of such modifications in its functional activation and onset of beta cell dysregulation under the duress of glucolipotoxicity (GLT) remain largely unknown. Using pharmacological approaches, we validated, herein, the hypothesis that acetylation-deacetylation signaling steps are involved in CD36-mediated lipid accumulation and downstream apoptotic signaling in pancreatic beta (INS-1832/13) cells under GLT. Exposure of these cells to GLT resulted in significant lipid accumulation without affecting the CD36 expression. Sulfo-n-succinimidyl oleate (SSO), an irreversible inhibitor of CD36, significantly attenuated lipid accumulation under GLT conditions, thus implicating CD36 in this metabolic step. Furthermore, trichostatin A (TSA) or valproic acid (VPA), known inhibitors of lysine deacetylases, markedly suppressed GLT-associated lipid accumulation with no discernible effects on CD36 expression. Lastly, SSO or TSA prevented caspase 3 activation in INS-1832/13 cells exposed to GLT conditions. Based on these findings, we conclude that an acetylation-deacetylation signaling step might regulate CD36 functional activity and subsequent lipid accumulation and caspase 3 activation in pancreatic beta cells exposed to GLT conditions. Identification of specific lysine deacetylases that control CD36 function should provide novel clues for the prevention of beta-cell dysfunction under GLT.

60 APPLIED LIFE SCIENCES↗

Optimizing a Multiple Right-Hand Side Dslash Kernel for Intel Knights Corner

Lattice Quantum Chromo-dynamics (LQCD) stands unique as the only computationally tractable, non-perturbative, and model-independent quantum field theory of the strong nuclear force. LQCD achieves tractability by discretizing our familiar 4-dimensional space-time onto a hypercubic lattice. The core component of the linear solver used in LQCD is the Wilson-Dirac operator whose finite difference component is called the Dslash operator. Dslash is a nearest neighbor stencil operator summing matrix-vector multiplications over lattice points. The arithmetic intensity of a regular Dslash operator acting on a single vector in single precision is between 0.88-2.29 (depending on the tricks employed) making it memory bandwidth bound on most current architectures, including Xeon Phi. Maximizing the performance of Dslash on Xeon Phi requires deliberate exploitation of its architectural features. One key feature of Xeon Phi is its powerful vector processing unit with lengthy vector registers. There is a class of LQCD computations which aims to solve the Dirac equation for the same lattice gauge fields multiple times. In this case one can gain additional reuse of the gauge field, and potentially simplified vectorization, through applying Dslash to several vectors at the same time; often referred to as Multiple Right Hand Side (MRHS) Dslash. Previous work in this area focused on applying this approach to the Highly Improved Staggered operator, and in cases to the multi-Grid algorithm for Wilson clover fermions. Here, we present two approaches to MRHS Dslash: a vector register blocking approach and one using the software package QPhiX with a custom Code Generator for low-level intrinsics. We explore the Knights Corner instruction set, memory hierarchy, and threading capabilities. For standard lattice sizes used in testing, we observed significant speedups, with sustained performance of over 700 GFLOPS (single precision) in one instance. We achieved up to 27% of theoretical peak performance compared to a maximum of 12% obtained by the previous single RHS method in QPhiX.

Joó, Bálint↗