Batch RNAi selector: a standalone program to predict specific siRNA candidates in batches with enhanced sensitivity

RNA interference (RNAi) is a popular and effective method for silencing gene expression. siRNAs should be gene-specific and effective to achieve specific and potent gene silencing. However, most currently available siRNA design programs are web-based programs that either require each sequence be submitted individually, making large-batch analyses difficult to conduct, or only provide limited options for searching off-target candidates (e.g. NCBI-BLAST). We have developed a stand-alone, enhanced RNAi design program that overcomes these shortcomings. We have implemented WU-BLAST, FASTA and SSEARCH homology searches for siRNA candidates to improve gene specific siRNA selection and to identity siRNA candidates that could lead to off-target gene silencing. We also included many new features such as siRNA score calculation and calculation of siRNA internal stability to help select highly potent siRNAs. This program is freely available for academic and commercial use (), and can be installed and run on any Linux machine. Our program automates the search for siRNAs and the resulting data files including a list of siRNA primers with scores and database search results for each siRNA candidate are stored locally for easy retrieval and inspection when needed.     

Apportioning: a technique for efficient reachability analysis ofconcurrent object-oriented programs

The object-oriented paradigm in software engineering provides support for the construction of modular and reusable program components and is attractive for the design of large and complex distributed systems. Reachability analysis is an important and well-known tool for static analysis of critical properties in concurrent programs, such as deadlock freedom. It involves the systematic enumeration of all possible global states of program execution and provides the same level of assurance for properties of the synchronization structure in concurrent programs, such as formal verification. However, direct application of traditional reachability analysis to concurrent object-oriented programs has many problems, such as incomplete analysis for reusable classes (not safe) and increased computational complexity (not efficient). We propose a novel technique called apportioning, for safe and efficient reachability analysis of concurrent object-oriented programs, that is based upon a simple but powerful idea of classification of program analysis points as local (having influence within a class) and global (having possible influence outside a class). We have developed a number of apportioning-based algorithms, having different degrees of safety and efficiency. We present the details of one of these algorithms, formally show its safety for an appropriate class of programs, and present experimental results to demonstrate its efficiency for various examples     

Development of environmentally responsive hydrogels with metal affinity behavior

This work describes initial efforts to incorporate affinity ligands within an environmentally responsive hydrogel. Metal affinity ligands were chosen as model affinity groups and thermally responsive N‐isopropyl acrylamide/acrylamide copolymers were used as the base hydrogels. The ? NH₂ group of the acrylamide serves as a reactive group for functionalization with metal affinity ligands. The gels were synthesized by free radical polymerization and Cu²⁺ was bound to the gel via 1,4‐butanediol diglycidyl ether (BDE) as a linker and iminodiacetic acid (IDA) as a chelating ligand. The base acrylamide gels were also functionalized with metal affinity ligands to allow for comparison with thermally responsive affinity gels. The results show the effectiveness of this technique for both these types of gels, and an improved method to immobilize metal affinity groups on to thermally sensitive N‐isopropyl acrylamide gels was also developed. It was seen that the yields for the reaction with BDE decreased with increased reaction time in both kinds of gels, whereas reaction with IDA showed a decrease in yields with increase in temperature for N‐isoporpyl acrylamide gels and increase in yields for acrylamide gels. Further techniques were developed to overcome diffusional resistances and stresses in the thermally responsive N‐isopropyl acrylamide gels so as to improve the distribution of Cu²⁺ ions. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci, 2007     

Two-Color Capillary Electrophoresis with On-Column Excitation and Wave-Guide Based Fluorescent Detection

An optical wave-guide based two-color capillary electrophoresis laser induced fluorescence (CE-LIF) instrument is described. The wave-guide based approach allows for on column excitation and detection with two-color discrimination. The instrument is designed to allow either electrokinetic or hydrodynamic injections. In its present configuration, the attainable limit of detection (LOD, S/N = 3) was 50 X 10⁻²¹ moles of fluorescein with a 488-nm excitation source. This study was designed to test the instrument design for applications in protein analyses. Fluorescent dyes with two different wavelengths were simultaneously separated and detected as were complexes formed by labeled antibodies to NFκB p65 and cdc2p34. Quantification of both proteins in THP-1 cell lysates performed using this approach illustrates a rapid screening application of this instrument.     

SAT-Solving the Coverability Problem for Petri Nets

Net unfoldings have attracted great attention as a powerful technique for combating state space explosion in model checking, and have been applied to verification of finite state systems including 1-safe (finite) Petri nets and synchronous products of finite transition systems. Given that net unfoldings represent the state space in a distributed, implicit manner the verification algorithm is necessarily a two step process: generation of the unfolding and reasoning about it. In his seminal work McMillan (K.L. McMillan, Symbolic Model Checking. Kluwer Academic Publishers, 1993) showed that deadlock detection on unfoldings of 1-safe Petri nets is NP-complete. Since the deadlock problem on Petri nets is PSPACE-hard it is generally accepted that the two step process will yield savings (in time and space) provided the unfoldings are small.In this paper we show how unfoldings can be extended to the context of infinite-state systems. More precisely, we show how unfoldings can be constructed to represent sets of backward reachable states of unbounded Petri nets in a symbolic fashion. Furthermore, based on unfoldings, we show how to solve the coverability problem for unbounded Petri nets using a SAT-solver. Our experiments show that the use of unfoldings, in spite of the two-step process for solving coverability, has better time and space characteristics compared to a traditional reachability based implementation that considers all interleavings for solving the coverability problem.     

TCP onloading for data center servers

To meet the increasing networking needs of server workloads, servers are starting to offload packet processing to peripheral devices to achieve TCP/IP acceleration. Researchers at Intel Labs have experimented with alternative solutions that improve the server's ability to process TCP/IP packets efficiently and at very high rates.     

Essential oil nanoemulsions: antibacterial activity in contaminated fruit juices

Many human acid tolerant bacterial and fungal pathogens can be transmitted through the consumption of the contaminated fruit juices. We aim to formulate essential oil nanoemulsions (basil, black seed, turmeric, clove & cinnamon), determine their ability to clear contamination by food borne bacterial pathogens from fruit juices. The antibacterial activity of the optimised formulations was tested in the fruit juices against bacterial pathogens causing gastrointestinal tract infections. The minimum bactericidal concentration (MBC) of clove emulsions ranged from 15.6 to 25 μL mL⁻¹. Cinnamon oil emulsion had an MBC ranging between 15 and 31 μL mL⁻¹. At MBC, cinnamon oil emulsions caused a 6log₁₀ decrease in viable counts by 8 h and maintained the sterility of fruit juices for 7 days at ambient temperature. Thus, clove and cinnamon microemulsions can be used as juice additives to control food borne bacterial pathogens and maintain the bacterial sterility of fruit juices.     

便携式应用的半导体产品封装发展回顾

半导体封装主要是提供一个媒介,把精细的硅芯片连接到较粗糙间距的印制电路板上,并保护器件免于受潮。这些年间,虽然这个功能并未改变,但封装技术已远较从前复杂。由于芯片的性能逐步复杂封装已肩负着全部散热的责任,这些热量不能成为限制部件电子性能的因素。而且对便携式应用而言,由于空间越来越宝贵,也需要更小和更薄的封装。随着硅片工作频率的提高,走线电感需要减小。与此同时,封装方案必须具备成本效益以满足当前消费电子应用的价格目标。鉴于硅技术不断发展,封装不得不变得更轻薄、散热性能更佳、速度更快及成本更低!1引线封装市场上…