A framework for post-silicon realization of arbitrary instruction extensions on reconfigurable data-paths

In this paper we present a framework for realizing arbitrary instruction set extensions (IE) that are identified post-silicon. The proposed framework has two components viz., an IE synthesis methodology and the architecture of a reconfigurable data-path for realization of the such IEs. The IE synthesis methodology ensures maximal utilization of resources on the reconfigurable data-path. In this context we present the techniques used to realize IEs for applications that demand high throughput or those that must process data streams. The reconfigurable hardware called HyperCell comprises a reconfigurable execution fabric. The fabric is a collection of interconnected compute units. A typical use case of HyperCell is where it acts as a co-processor with a host and accelerates execution of IEs that are defined post-silicon. We demonstrate the effectiveness of our approach by evaluating the performance of some well-known integer kernels that are realized as IEs on HyperCell. Our methodology for realizing IEs through HyperCells permits overlapping of potentially all memory transactions with computations. We show significant improvement in performance for streaming applications over general purpose processor based solutions, by fully pipelining the data-path. (C) 2014 Elsevier B.V. All rights reserved.

Local Structural and Environmental Factors Define the Efficiency of an RNA Pseudoknot Involved in Programmed Ribosomal Frameshift Process

In programmed -1 ribosomal frameshift, an RNA pseudoknot stalls the ribosome at specific sequence and restarts translation in a new reading frame. A precise understanding of structural characteristics of these pseudoknots and their PRF inducing ability has not been clear to date. To investigate this phenomenon, we have studied various structural aspects of a -1 PRF inducing RNA pseudoknot from BWYV using extensive molecular dynamics simulations. A set of functional and poorly functional forms, for which previous mutational data were available, were chosen for analysis. These structures differ from each other by either single base substitutions or base-pair replacements from the native structure. We have rationalized how certain mutations in RNA pseudoknot affect its function; e.g., a specific base substitution in loop 2 stabilizes the junction geometry by forming multiple noncanonical hydrogen bonds, leading to a highly rigid structure that could effectively resist ribosome-induced unfolding, thereby increasing efficiency. While, a CG to AU pair substitution in stem 1 leads to loss of noncanonical hydrogen bonds between stems and loop, resulting in a less stable structure and reduced PRF inducing ability, inversion of a pair in stem 2 alters specific base-pair geometry that might be required in ribosomal recognition of nucleobase groups, negatively affecting pseudoknot functioning. These observations illustrate that the ability of an RNA pseudoknot to induce -1 PRF with an optimal rate depends on several independent factors that contribute to either the local conformational variability or geometry

Synthesis of Instruction Extensions on HyperCell, a Reconfigurable Datapath

In this paper we present HyperCell as a reconfigurable datapath for Instruction Extensions (IEs). HyperCell comprises an array of compute units laid over a switch network. We present an IE synthesis methodology that enables post-silicon realization of IE datapaths on HyperCell. The synthesis methodology optimally exploits hardware resources in HyperCell to enable software pipelined execution of IEs. Exploitation of temporal reuse of data in HyperCell results in significant reduction of input/output bandwidth requirements of HyperCell.

Mycobacteria-responsive sonic hedgehog signaling mediates programmed death-ligand 1-and prostaglandin E-2-induced regulatory T cell expansion

CD4(+)CD25(+)FoxP3(+) regulatory T cells (Tregs) are exploited by mycobacteria to subvert the protective host immune responses. The Treg expansion in the periphery requires signaling by professional antigen presenting cells and in particularly dendritic cells (DC). However, precise molecular mechanisms by which mycobacteria instruct Treg expansion via DCs are not established. Here we demonstrate that mycobacteria-responsive sonic hedgehog (SHH) signaling in human DCs leads to programmed death ligand-1 (PD-L1) expression and cyclooxygenase (COX)-2-catalyzed prostaglandin E-2 (PGE(2)) that orchestrate mycobacterial infection-induced expansion of Tregs. While SHH-responsive transcription factor GLI1 directly arbitrated COX-2 transcription, specific microRNAs, miR-324-5p and miR-338-5p, which target PD-L1 were downregulated by SHH signaling. Further, counter-regulatory roles of SHH and NOTCH1 signaling during mycobacterial-infection of human DCs was also evident. Together, our results establish that Mycobacterium directs a fine-balance of host signaling pathways and molecular regulators in human DCs to expand Tregs that favour immune evasion of the pathogen.