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.     

不同晶相结构ZrO2负载铜基催化剂用于二乙醇胺脱氢反应

通过制备不同晶相结构〔单斜相(m-ZrO_2)、四方相(t-ZrO_2)和无定型(a-ZrO_2)〕ZrO_2载体,再通过沉积沉淀法制得Cu/m-ZrO_2、Cu/t-ZrO_2和Cu/a-ZrO_2催化剂,分别用于催化二乙醇胺脱氢合成亚氨基二乙酸反应。采用XRD、氮气物理吸附脱附、XPS、H_2-TPR、CO_2-TPD对催化剂的结构进行了表征。结果表明,Cu/m-ZrO_2催化剂界面更加有利于Cu~+/Cu~0稳定存在,具有更多的碱性位点,且抗氧化性较好。在二乙醇胺脱氢反应中,Cu/m-ZrO_2催化剂性能最好,反应时间为2.5 h,亚氨基二乙酸收率为97.64%。     

CAN-BUS系统应用一例

CAN-BUS系统自问世以来,已将近30年,当代各品牌车辆纷纷采用,但大部分技术人员对CAN总线系统既熟悉又陌生。经常能听到,但具体操作又显得有些力不从心。本文通过对奇瑞A3品牌轿车CAN总线的巧妙应用,引导大家进一步理解和应用CAN总线。     

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.     

共享交通的时空轨迹检索与群体发现

为解决共享交通下的共乘用户群体发现效率低、准确率不高问题，依据R-树原理建立GeoOD-Tree索引，并在此基础上提出以最大化共乘率为目标的群体发现策略。首先，对原始时空轨迹数据进行特征提取与标定处理，挖掘有效出行起讫点（OD）轨迹；其次，针对用户起讫点轨迹的特征，建立GeoOD-Tree索引进行有效的存储管理；最后，给出以最大化共乘行程为目标的群体发现模型，并运用K最近邻（KNN）查询对搜索空间剪枝压缩，提高群体发现效率。采用西安市近12000辆出租车营运轨迹数据，选取动态时间规整（DTW）等典型算法与所提算法在查询效率与准确率上进行性能对比分析。与DTW算法相比，所提算法的准确率提高了10.12%，查询效率提高了约15倍。实验结果表明提出的群体发现策略能有效提高共乘用户群体发现的准确率和效率，可有效提升共乘出行方式的出行率。     

Investigation on phase shifting for a 4 K Stirling pulse tube cryocooler with He-3 as working fluid

He-3 is generally recognized for its ability to provide more excellent thermophysical performance than He-4, especially in the 4 K temperature range. However, this was not always the case in our preliminary experiments on a three-stage Stirling-type pulse tube cryocooler (SPTC). Our ongoing studies, as reported in this paper, demonstrate that the different working fluids also affect the performance through their phase shifting capability. This feature has been passed over in large part by researchers considering refrigerant substitution. Unlike previous theoretical analyses that focus primarily on regenerator losses, this report investigates the effects of the working fluid on the phase angle at the cold end in order to quantitatively reveal the relationship between the lowest attainable temperature and the cooling capacity. The analysis agrees well with our experimental results on a three-stage SPTC. While running with the operating parameters optimized for He-3, the lowest temperature of the SPTC decreased from 5.4 K down to 4.03 K. This is the lowest refrigeration temperature ever achieved with a three-stage SPTC.     

Barium titanate‐based nanodielectrics of two chemically recyclable thermosets

In this work was investigated the effect of the addition of barium titanate (BaTiO₃) on electrical properties of two chemically recyclable thermosets, polyhemiaminal (PHA) and polyhexahydro‐s‐triazine (PHT), both fabricated from 4,4′‐oxydianiline (ODA), an ether derivative of aniline and paraformaldehyde. Thermal and mechanical properties as well as chemical recyclability of the two polymers and their nanocomposites/nanodielectrics were also investigated. In addition, a quantitative analysis was conducted of the nanoparticle dispersion in the PHA‐/PHT‐based BaTiO₃‐containing nanocomposites using transmission electron microscopy imaging and the nearest‐neighbor distance index and this index was used to analyze the investigated properties in connection with the proper mechanisms. Regarding the electrical properties for both neat polymers, conductivity values of the order of 10^?8 S m^?1 at 100 Hz were observed and dielectric constant values close to 2.80 for both polymers at 1 kHz. The addition of 0.5 wt% of BaTiO₃ ferroelectric nanoparticles increased by about 44% the dielectric constant (1 kHz) and conductivity (10² Hz) of the PHA‐based nanocomposite. PHA and PHT exhibited glass transition temperature (T_g) values in the range 125–180 °C. An increase of 7 °C in T_g was observed after the incorporation of 0.5 wt% of BaTiO₃ into PHA. Concerning the mechanical properties, values in the range 4.00–4.45 GPa for reduced modulus and 0.30–0.43 GPa for nanohardness for PHA and PHT polymers were observed. Independently of filler content or polymer matrix, both mechanical properties were enhanced after the addition of BaTiO₃. The chemical recycling of PHA/PHT and all nanocomposites in the initial ODA reagent after sulfuric acid treatment was successfully characterized using the NMR and Fourier transform infrared spectroscopic techniques. © 2018 Society of Chemical Industry     

Dielectric,ferroelectric, and piezoelectric properties of lead-free Ba0.95Ca0.05Ti1-xZrxO3 ceramics

Abstract

Ba_0.95Ca_0.05Ti_1-xZr_xO₃ (BCTZO) ceramics were prepared by a solid state reaction method. The samples were characterized by X-ray diffraction (XRD), Scanning electron microscopy (SEM) and X-ray absorption near edge structure (XANES). The ceramics exhibit a pure perovskite structure. The average grain size gradually decreases with increasing Zr concentration. XANES results indicate that the intensities of pre-edge peaks dropped with increasing Zr concentration. The BCTZO ceramic of x?=?0.05 has the optimum electrical properties with the maximum dielectric constant (ε'_m), remanent polarization (2P_r), coercive electric field (2E_c) and piezoelectric charge constant (d₃₃) of 7,244, 12.54 (μC/cm²), 5.29 (kV/cm) and 288 (pC/N), respectively.