In vitro selection of non-crosshybridizing oligonucleotides for computation

Since they minimize errors from cross-hybridizations, DNA oligonucleotides that annealas designed are beneficial to DNA computing. By in vitro selection, huge libraries of non-crosshybridizing oligonucleotides might be evolved in the test tube. As a first step, a fitness function corresponding to non-crosshybridization was based upon the duplex stability of randomly matched oligonucleotides. By melting pairs that have a low thermal stability, a protocol based on DNA polymerization selectively amplifies maximally mismatched oligonucleotides over those that were more closely matched. Experiments confirmed this property of the protocol, and in addition, a reaction temperature window was identified in which discrimination between matched and mismatched might be obtained. The protocol was iterated on a set of random starting material, and there was evidence that non-crosshybridizing libraries were in fact being created. These results are a step toward practical manufacture of very large libraries of non-crosshybridizing oligonucleotides in the test tube. This revised version was published online in June 2006 with corrections to the Cover Date.     

Simulations of DNA Computing with In Vitro Selection

An attractive feature of DNA-based computers is the large number of possible sequences (4 ⁿ ) of a given length n with which to represent information. The problem, however, is that any given sequence is not necessarily independent of the other sequences, and thus, reactions among them can interfere with the reliability and efficiency of the computation. Independent sequences might be manufactured in the test tube using evolutionary methods. To this end, an in vitro selection has been developed that selects maximally mismatched DNA sequences. In order to understand the behavior of the protocol, a computer simulation of the protocol was done, results of which showed that Watson-Crick pairs of independent oligonucleotides were preferentially selected. In addition, to explore the computational capability of the selection protocol, a design is presented that generates the Fibonacci sequence of numbers.     

A study of control skills in an industrial task,and in a simulation,using the verbal protocol technique

The control skills of gas grid control engineers were studied in a real and simulated version of the same task. Verbal protocol data were used in both tasks as the main source of evidence of the controllers' behaviour. The protocol data were analysed by frequency counting methods, and by identifying recurring sequences of control behaviour. The results indicated that the controllers' behaviour was not unnaturally distorted by the use of a simulator. Possible biases inherent in the controllers' behaviour were also discussed. Analysis of the prediction, decision and action selection routines employed by the controllers indicated that in certain circum stances control performance could be sub-optimal. Some of the organizing principles underlying the controllers' behaviour were considered.     

一种基于形式化描述的测试序列生成改进方法

动生成测试序列始终是软件工程中一项极为困难的工作．国际标准化组织（ＩＳＯ）一直致力于协议一致性测试方法与形式化描述技术的研究．本文讨论了基于形式化描述的协议测试序列生成方法中的问题,特别是提出了“部分Ｔ序列叠加算法”对使用ＵＩＯ序列生成测试序列的方法做了进一步改进,大大减少了测试开销．     

Kolmogorov-Loveland Stochasticity and Kolmogorov Complexity

Merkle et al. (Ann. Pure Appl. Logic 138(1–3):183–210, 2006) showed that all Kolmogorov-Loveland stochastic infinite binary sequences have constructive Hausdorff dimension 1. In this paper, we go even further, showing that from an infinite sequence of dimension less than H(\frac 12+d)\mathcal {H}(\frac {1}{2}+\delta) (ℋ being the Shannon entropy function) one can extract by an effective selection rule a biased subsequence with bias at least δ. We also prove an analogous result for finite strings.     

异地协同产品开发系统中资源选择策略研究

全球经济一体化使得企业之间必须建立动态联盟，实现异地协同产品开发．才能抓住快速多变的市场机遇。本文论述了异地协同产品开发的协议过程，并针对签约结点的选择提出了综合能力分析方法模型。这种综合能力评比的方法．为资源的合理选择提供了有效的策略。     

A DNA-based memory with <Emphasis Type="Italic">in vitro</Emphasis> learning and associative recall

A DNA-based memory was implemented with in vitro learning and associative recall.The learning protocol stored the sequences to which it was exposed, and memories were recalled by sequence content through DNA-to-DNA template annealing reactions. Experiments demonstrated that biological DNA could be learned, that sequences similar to the training DNA were recalled correctly, and that unlike sequences were differentiated. Theoretically, the memory has a pattern separation capability that is very large, and can learn long DNA sequences. The learning and recall protocols are massively parallel, as well as simple, inexpensive, and quick. The memory has several potential applications in detection and classification of biological sequences, as well as a massive storage capacity for non-biological data.     

k-Top Scoring Pair Algorithm for feature selection in SVM with applications to microarray data classification

Top Scoring Pair (TSP) and its ensemble counterpart, k-Top Scoring Pair (k-TSP), were recently introduced as competitive options for solving classification problems of microarray data. However, support vector machine (SVM) which was compared with these approaches is not equipped with feature or variable selection mechanism while TSP itself is a kind of variable selection algorithm. Moreover, an ensemble of SVMs should also be considered as a possible competitor to k-TSP. In this work, we conducted a fair comparison between TSP and SVM-recursive feature elimination (SVM-RFE) as the feature selection method for SVM. We also compared k-TSP with two ensemble methods using SVM as their base classifier. Results on ten public domain microarray data indicated that TSP family classifiers serve as good feature selection schemes which may be combined effectively with other classification methods.     

Local model checking and protocol analysis

This paper describes a local model-checking algorithm for the alternation-free fragment of the modal mu-calculus that has been implemented in the Concurrency Factory and discusses its application to the analysis of a real-time communications protocol. The protocol considered is RETHER, a software-based, real-time Ethernet protocol developed at SUNY at Stony Brook. Its purpose is to provide guaranteed bandwidth and deterministic, periodic network access to multimedia applications over commodity Ethernet hardware. Our model-checking results show that (for a particular network configuration) RETHER makes good on its bandwidth guarantees to real-time nodes without exposing non-real-time nodes to the possibility of starvation. Our data also indicate that, in many cases, the state-exploration overhead of the local model checker is significantly smaller than the total amount that would result from a global analysis of the protocol. In the course of specifying and verifying RETHER, we also identified an alternative design of the protocol that warranted further study due to its potentially smaller run-time overhead in servicing requests for data transmission. Again, using local model checking, we showed that this alternative design also possesses the properties of interest. This observation points out one of the often-overlooked benefits of formal verification: by forcing designers to understand their designs rigorously and abstractly, these techniques often enable the designers to uncover interesting design alternatives.     

A combinatorial testing strategy for concurrent programs

One approach to testing concurrent programs is called reachability testing, which derives test sequences automatically and on‐the‐fly, without constructing a static model. Existing reachability testing algorithms are exhaustive in that they are intended to exercise all possible synchronization sequences of a concurrent program with a given input. In this paper, we present a new testing strategy, called t‐way reachability testing, that adopts the dynamic framework of reachability testing but selectively exercises a subset of synchronization sequences. The selection of the synchronization sequences is based on a combinatorial testing strategy called t‐way testing. We present an algorithm that implements t‐way reachability testing, and report the results of several case studies that were conducted to evaluate its effectiveness. The results indicate that t‐way reachability testing can substantially reduce the number of synchronization sequences exercised during reachability testing while still effectively detecting faults. Copyright © 2007 John Wiley & Sons, Ltd.