Advances in parallel programming for electronic design automation

The continued miniaturization of the technology node increases not only the chip capacity but also the circuit design complexity. How does one efficiently design a chip with millions or billions transistors? This has become a challenging problem in the integrated circuit (IC) design industry, especially for the developers of electronic design automation (EDA) tools. To boost the performance of EDA tools, one promising direction is via parallel computing. In this dissertation, we explore different parallel computing approaches, from CPU to GPU to distributed computing, for EDA applications. Nowadays multi-core processors are prevalent from mobile devices to laptops to desktop, and it is natural for software developers to utilize the available cores to maximize the performance of their applications. Therefore, in this dissertation we first focus on multi-threaded programming. We begin by reviewing a C++ parallel programming library called Cpp-Taskflow. Cpp-Taskflow is designed to facilitate programming parallel applications, and has been successfully applied to an EDA timing analysis tool. We will demonstrate Cpp-Taskflow’s programming model and interface, software architecture and execution flow. Then, we improve Cpp-Taskflow in several aspects. First, we enhance Cpp-Taskflow’s usability through restructuring the software architecture. Second, we introduce task graph composition to support composability and modularity, which makes it easier for users to construct large and complex parallel patterns. Third, we add a new task type in Cpp-Taskflow to let users control the graph execution flow. This feature empowers the graph model with the ability to describe complex control flow. Aside from the above enhancements, we have designed a new scheduler to adaptively manage the threads based on available parallelism. The new scheduler uses a simple and effective strategy which can not only prevent resource from being underutilized, but also mitigate resource over-subscription. We have evaluated the new scheduler on both micro-benchmarks and a very-large-scale integration (VLSI) application, and the results show that the new scheduler can achieve good performance and is very energy-efficient. Next we study the applicability of heterogeneous computing, specifically the graphics processing unit (GPU), to EDA. We demonstrate how to use GPU to accelerate VLSI placement, and we show that GPU can bring substantial performance gain to VLSI placement. Finally, as the design size keeps increasing, a more scalable solution will be distributed computing. We introduce a distributed power grid analysis framework built on top of DtCraft. This framework allows users to flexibly partition the design and automatically deploy the computations across several machines. In addition, we propose a job scheduler that can efficiently utilize cluster resource to improve the framework’s performance

Novel loci and pathways significantly associated with longevity

Only two genome-wide significant loci associated with longevity have been identified so far, probably because of insufficient sample sizes of centenarians, whose genomes may harbor genetic variants associated with health and longevity. Here we report a genome-wide association study (GWAS) of Han Chinese with a sample size 2.7 times the largest previously published GWAS on centenarians. We identified 11 independent loci associated with longevity replicated in Southern-Northern regions of China, including two novel loci (rs2069837-IL6; rs2440012-ANKRD20A9P) with genome-wide significance and the rest with suggestive significance (P < 3.65 × 10(−5)). Eight independent SNPs overlapped across Han Chinese, European and U.S. populations, and APOE and 5q33.3 were replicated as longevity loci. Integrated analysis indicates four pathways (starch, sucrose and xenobiotic metabolism; immune response and inflammation; MAPK; calcium signaling) highly associated with longevity (P ≤ 0.006) in Han Chinese. The association with longevity of three of these four pathways (MAPK; immunity; calcium signaling) is supported by findings in other human cohorts. Our novel finding on the association of starch, sucrose and xenobiotic metabolism pathway with longevity is consistent with the previous results from Drosophilia. This study suggests protective mechanisms including immunity and nutrient metabolism and their interactions with environmental stress play key roles in human longevity

An Antimicrobial Peptide Regulates Tumor-Associated Macrophage Trafficking via the Chemokine Receptor CCR2, a Model for Tumorigenesis

Tumor-associated macrophages (TAMs) constitute a significant part of infiltrating inflammatory cells that are frequently correlated with progression and poor prognosis of a variety of cancers. Tumor cell-produced human β-defensin-3 (hBD-3) has been associated with TAM trafficking in oral cancer; however, its involvement in tumor-related inflammatory processes remains largely unknown., applying a cross-desensitization strategy of CCR2 and its pharmacological inhibitor (RS102895), respectively, was also carried out. outcome and demonstrates the importance of the innate immune system in the development of tumors

好アルカリ性Bacillus A-007株のK^+ : 促進ATPaseについて

1.好アルカリ性Bacillus A-007株の生育にとってK^+は必須であった.2.K^+-濃度を制限した培地(1.5mMK^+)で生育させた細胞の膜画分に, K^+により促進されるATPase活性が認められた.3.K^+促進ATPaseは, 動力学的特性及びウワバイン, NaN_3, PCMBに対する感受件において, 同菌株のH^+-ATPaseと明らかに異なっていた.1. K^+ was essential for the growth of an alkalophilic Bacillus A-007. 2. Membrane fraction, which was prepared from the cells grown in K^+ -limited medium (1.5mM K^+), showed K^+ -stimulated ATPase activity. 3. The K^+ -stimulated ATPase was clearly different from H^+ -ATPase on kinetical profile and ouabain-, NaN_3- and PCMB-sensvtivity

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals &lt;1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data