Combined hardware–software multi-parallel prefiltering on the Convey HC-1 for fast homology detection

Protein databases used in research are huge and still grow at a fast pace. Many comparisons need to be done when searching similar (homologous) sequences for a given query sequence in these databases. Comparing a query sequence against all sequences of a huge database using the well-known Smith–Waterman algorithm is very time-consuming. Hidden Markov Models pose an opportunity for reducing the number of entries of a database and also enable to find distantly homologous sequences. Fewer entries are achieved by clustering similar sequences in a Hidden Markov Model. Such an approach is used by the bioinformatics tool HHblits. To further reduce the runtime, HHblits uses two-level prefiltering to reduce the number of time-consuming Viterbi comparisons. Still, prefiltering is very time-consuming. Highly parallel architectures and huge bandwidth are required for processing and transferring the massive amounts of data. In this article, we present an approach exploiting the reconfigurable, hybrid computer architecture Convey HC-1 for migrating the most time-consuming part. The Convey HC-1 with four FPGAs and high memory bandwidth of up to 76.8 GB/s serves as the platform of choice. Other bioinformatics applications have already been successfully supported by the HC-1. Limited by FPGA size only, we present a design that calculates four first-level prefiltering scores per FPGA concurrently, i.e. 16 calculations in total. This score calculation for the query profile against database sequences is done by a modified Smith–Waterman scheme that is internally parallelized 128 times in contrast to the original Streaming ‘Single Instruction Multiple Data (SIMD)’ Extensions (SSE)-supported implementation where only 16-fold parallelism can be exploited and where memory bandwidth poses the limiting factor. Preloading the query profile, we are able to transform the memory-bound implementation to a compute- and resource-bound FPGA design. We tightly integrated the FPGA-based coprocessor into the hybrid computing system by employing task-parallelism for the two-level prefiltering. Despite much lower clock rates, the FPGAs outperform SSE-based execution for the calculation of the prefiltering scores by a factor of 7.9.     

管道清管器运行速度控制技术研究进展

随着对管道安全问题和降本增效理念的逐步重视，管道清管操作已成为全世界油气管道运行中必不可少的作业规程，清管器的运行速度是需要重点控制的参数之一，当其处于合理区间内时（原油管道1~5m/s，天然气管道2~7m/s），清管效果最佳。本文基于对管道清管数学模型的研究，首先论述了不同的被动控制方法，认为该方法较为灵活，应用广泛，对不同入口条件下清管器速度的准确计算是能否控制清管器速度处于合理区间的关键；然后对不同的主动控制方法进行了研究，研究表明：射流清管器速度控制的核心是旁通率的优选，其依赖于压降系数、皮碗与管壁间摩擦力的准确计算，建立简便可靠的摩擦力工程计算模型将有助于射流清管技术应用的进一步推广；最终本文对清管器智能调速技术进行综述和展望，指出发展稳定可靠的国产智能调速技术是未来重点研究方向。     

浅析混凝土搅拌站的防雷

近年来,我市因雷击而导致搅拌站系统瘫痪停产、影响工程进度的事件时有发生,在针对混凝土搅拌站配料秤的实际检定工作中,也常发现配料秤的称重传感器因雷击损坏而影响计量准确性。因此,对混凝土搅拌站防雷的研究具有重要意义。本文阐述了雷电对混凝土搅拌站的主要危害,分析了混凝土搅拌站常见的雷击原因及其防护措施,旨在引起生产方、安装方以及使用方对混凝土搅拌站防雷的共同重视。     

某两自由度弹药提升装置的建模、实验及仿真研究

弹药自动装填系统的研究已经成为火炮武器平台中机械系统设计的关键和难点,基于一种两自由度弹药提升装置,并根据该装置的工作原理构造数学模型,搭建实验平台,建立PID控制回路,同时创建该模型的虚拟样机模型,使用动力学仿真软件Recurdyn和Matlab/Simulink进行联合仿真,并通过实验与仿真的数据进行对比,验证该装置的可行性和所采用控制的有效性。     

Friction compensation controller for load varying machine tool feed drive

The load applied to a machine tool feed drive changes during the machining process as material is removed. This load change alters the Coulomb friction of the feed drive. Because Coulomb friction accounts for a large part of the total friction the friction compensation control accuracy of the feed drives is limited if this nonlinear change in the applied load is not considered. This paper presents a new friction compensation method that estimates the machine tool load in real time and considers its effect on friction characteristics. A friction observer based on a Kalman filter with load estimation is proposed for friction compensation control considering the applied load change. A specially designed feed drive testbed that enables the applied load to be modified easily was constructed for experimental verification. Control performance and friction estimation accuracy are demonstrated experimentally using the testbed.     

Current Status on Stem Cells and Cancers of the Gastric Epithelium

Gastric cancer is still a leading cause of cancer-related mortality worldwide in spite of declining incidence. Gastric cancers are, essentially, adenocarcinomas and one of the strongest risk factors is still infection with Helicobacter pylori. Within the last years, it became clear that gastric self-renewal and carcinogenesis are intimately linked, particularly during chronic inflammatory conditions. Generally, gastric cancer is now regarded as a disease resulting from dysregulated differentiation of stem and progenitor cells, mainly due to an inflammatory environment. However, the situation in the stomach is rather complex, consisting of two types of gastric units which show bidirectional self-renewal from an unexpectedly large variety of progenitor/stem cell populations. As in many other tumors, cancer stem cells have also been characterized for gastric cancer. This review focuses on the various gastric epithelial stem cells, how they contribute to self-renewal and which routes are known to gastric adenocarcinomas, including their stem cells.     

Direct Injection of CRISPR/Cas9-Related mRNA into Cytoplasm of Parthenogenetically Activated Porcine Oocytes Causes Frequent Mosaicism for Indel Mutations

Some reports demonstrated successful genome editing in pigs by one-step zygote microinjection of mRNA of CRISPR/Cas9-related components. Given the relatively long gestation periods and the high cost of housing, the establishment of a single blastocyst-based assay for rapid optimization of the above system is required. As a proof-of-concept, we attempted to disrupt a gene (GGTA1) encoding the α-1,3-galactosyltransferase that synthesizes the α-Gal epitope using parthenogenetically activated porcine oocytes. The lack of α-Gal epitope expression can be monitored by staining with fluorescently labeled isolectin BS-I-B₄ (IB4), which binds specifically to the α-Gal epitope. When oocytes were injected with guide RNA specific to GGTA1 together with enhanced green fluorescent protein (EGFP) and human Cas9 mRNAs, 65% (24/37) of the developing blastocysts exhibited green fluorescence, although almost all (96%, 23/24) showed a mosaic fluorescent pattern. Staining with IB4 revealed that the green fluorescent area often had a reduced binding activity to IB4. Of the 16 samples tested, six (five fluorescent and one non-fluorescent blastocysts) had indel mutations, suggesting a correlation between EGFP expression and mutation induction. Furthermore, it is suggested that zygote microinjection of mRNAs might lead to the production of piglets with cells harboring various mutation types.     

Glibenclamide for the Treatment of Ischemic and Hemorrhagic Stroke

Ischemic and hemorrhagic strokes are associated with severe functional disability and high mortality. Except for recombinant tissue plasminogen activator, therapies targeting the underlying pathophysiology of central nervous system (CNS) ischemia and hemorrhage are strikingly lacking. Sur1-regulated channels play essential roles in necrotic cell death and cerebral edema following ischemic insults, and in neuroinflammation after hemorrhagic injuries. Inhibiting endothelial, neuronal, astrocytic and oligodendroglial sulfonylurea receptor 1–transient receptor potential melastatin 4 (Sur1–Trpm4) channels and, in some cases, microglial K_ATP (Sur1–Kir6.2) channels, with glibenclamide is protective in a variety of contexts. Robust preclinical studies have shown that glibenclamide and other sulfonylurea agents reduce infarct volumes, edema and hemorrhagic conversion, and improve outcomes in rodent models of ischemic stroke. Retrospective studies suggest that diabetic patients on sulfonylurea drugs at stroke presentation fare better if they continue on drug. Additional laboratory investigations have implicated Sur1 in the pathophysiology of hemorrhagic CNS insults. In clinically relevant models of subarachnoid hemorrhage, glibenclamide reduces adverse neuroinflammatory and behavioral outcomes. Here, we provide an overview of the preclinical studies of glibenclamide therapy for CNS ischemia and hemorrhage, discuss the available data from clinical investigations, and conclude with promising preclinical results that suggest glibenclamide may be an effective therapeutic option for ischemic and hemorrhagic stroke.     

Control theory for stochastic distributed parameter systems,an engineering perspective

The main purpose of this paper is to survey some recent progresses on control theory for stochastic distributed parameter systems, i.e., systems governed by stochastic differential equations in infinite dimensions, typically by stochastic partial differential equations. We will explain the new phenomenon and difficulties in the study of controllability and optimal control problems for one dimensional stochastic parabolic equations and stochastic hyperbolic equations. In particular, we shall see that both the formulation of corresponding stochastic control problems and the tools to solve them may differ considerably from their deterministic/finite-dimensional counterparts. More importantly, one has to develop new tools, say, the stochastic transposition method introduced in our previous works, to solve some problems in this field.     

Adaptive actuator failure compensation design for unknown chaotic multi‐input systems

In this paper, an adaptive control approach is designed for compensating the faults in the actuators of chaotic systems and maintaining the acceptable system stability. We propose a state‐feedback model reference adaptive control scheme for unknown chaotic multi‐input systems. Only the dimensions of the chaotic systems are required to be known. Based on Lyapunov stability theory, new adaptive control laws are synthesized to accommodate actuator failures and system nonlinearities. An illustrative example is studied. The simulation results show the effectiveness of the design method. Copyright © 2014 John Wiley & Sons, Ltd.