'98 Escherichia coli SWISS-2DPAGE database update

The combination of two-dimensional polyacrylamide gel electrophoresis (2-D PAGE), computer image analysis and several protein identification techniques allowed the Escherichia coli SWISS-2DPAGE database to be established. This is part of the ExPASy molecular biology server accessible through the WWW at the URL address http://www.expasy.ch/ch2d/ch2d-top.html . Here we report recent progress in the development of the E. coli SWISS-2DPAGE database. Proteins were separated with immobilized pH gradients in the first dimension and sodium dodecyl sulfate-polyacrylamide gel electrophoresis in the second dimension. To increase the resolution of the separation and thus the number of identified proteins, a variety of wide and narrow range immobilized pH gradients were used in the first dimension. Micropreparative gels were electroblotted onto polyvinylidene difluoride membranes and spots were visualized by amido black staining. Protein identification techniques such as amino acid composition analysis, gel comparison and microsequencing were used, as well as a recently described Edman "sequence tag" approach. Some of the above identification techniques were coupled with database searching tools. Currently 231 polypeptides are identified on the E. coli SWISS-2DPAGE map: 64 have been identified by N-terminal microsequencing, 39 by amino acid composition, and 82 by sequence tag. Of 153 proteins putatively identified by gel comparison, 65 have been confirmed. Many proteins have been identified using more than one technique. Faster progress in the E. coli proteome project will now be possible with advances in biochemical methodology and with the completion of the entire E. coli genome.     

Solution structure of glutathione bound to human glutathione transferase P1-1: comparison of NMR measurements with the crystal structure

The conformation of the bound glutathione (GSH) in the active site of the human glutathione transferase P1-1 (EC 2.5.1.18) has been studied by transferred NOE measurements and compared with those obtained by X-ray diffraction data. Two-dimensional TRNOESY and TRROESY experiments have been performed under fast-exchange conditions. The family of GSH conformers, compatible with TRNOE distance constraints, shows a backbone structure very similar to the crystal model. Interesting differences have been found in the side chain regions. After restrained energy minimization of a representative NMR conformer in the active site, the sulfur atom is not found in hydrogen-bonding distance of the hydroxyl group of Tyr 7. This situation is similar to the one observed in an "atypical" crystal complex grown at low pH and low temperature. The NMR conformers display also a poorly defined structure of the glutamyl moiety, and the presence of an unexpected intermolecular NOE could indicate a different interaction of this substrate portion with the G-site. The NMR data seem to provide a snapshot of GSH in a precomplex where the GSH glutamyl end is bound in a different fashion. The existence of this precomplex is supported by pre-steady-state kinetic experiments [Caccuri, A. M., Lo Bello, M., Nuccetelli, M., Nicotra, M., Rossi, P., Antonini, G., Federici, G., and Ricci, G. (1998) Biochemistry 37, 3028-3034] and preliminary time-resolved fluorescence data.     

Chemiotropic behavior of female olive fly (Bactrocera oleae GMEL.) onOlea europaea L

An interpretation is given of a number of observations on the chemiotropic behavior ofBactrocera oleae in connection with olive maceration water and the fly's return to the olive groves after the first summer rains. To this end, the headspace of both maceration water and leaf leaching water, simulating rainfall, were examined. In both cases, the presence of ammonia, which is generally known to attract fruit flies (Diptera, Tephritidae), was detected and, for the first time, in addition to other compounds that are inert for the fly, the presence of styrene was also detected. This aromatic hydrocarbon was found to be a strong attractant. It is shown that both ammonia and styrene are products of the metabolism of microbial flora present on the olive and leaf surface.     

Reduction of false positives in lung nodule detection using a two-level neural classification

The authors have developed a neural-digital computer-aided diagnosis system, based on a parameterized two-level convolution neural network (CNN) architecture and on a special multilabel output encoding procedure. The developed architecture was trained, tested, and evaluated specifically on the problem of diagnosis of lung cancer nodules found on digitized chest radiographs. The system performs automatic "suspect" localization, feature extraction, and diagnosis of a particular pattern-class aimed at a high degree of "true-positive fraction" detection and low "false-positive fraction" detection. In this paper, the authors aim at the presentation of the two-level neural classification method in reducing false-positives in their system. They employed receiver operating characteristics (ROC) method with the area under the ROC curve (A(z)) as the performance index to evaluate all the simulation results. The two-level CNN showed superior performance (A(z)=0.93) to the single-level CNN (A(z)=0.85). The proposed two-level CNN architecture is proven to be promising and to be extensible, problem-independent, and therefore, applicable to other medical or difficult diagnostic tasks in two-dimensional (2-D) image environments.     

A study of maintenance policies for second-hand products

This paper proposes two maintenance schemes for reused products. In order to reduce the purchasing cost or conform to the concept of environmental protection, reuse is considered as one of the most efficient strategies. However, the initial quality of reused product is often inferior to the new one and then product failures will occur frequently during usage period. Therefore, two periodical preventive maintenance (PM) policies in this paper are developed to decrease the high failure rate of the second-hand products. When a second-hand product with Weibull life time distribution of known age is intended to be used for a pre-specified period of time, the optimal number of PM actions and the corresponding maintenance degree are derived such that the expected total maintenance cost is minimized. The impact of providing preventive maintenance is illustrated through numerical examples.     

A low-order model of biological neural networks

A biologically plausible low-order model (LOM) of biological neural networks is proposed. LOM is a recurrent hierarchical network of models of dendritic nodes and trees; spiking and nonspiking neurons; unsupervised, supervised covariance and accumulative learning mechanisms; feedback connections; and a scheme for maximal generalization. These component models are motivated and necessitated by making LOM learn and retrieve easily without differentiation, optimization, or iteration, and cluster, detect, and recognize multiple and hierarchical corrupted, distorted, and occluded temporal and spatial patterns. Four models of dendritic nodes are given that are all described as a hyperbolic polynomial that acts like an exclusive-OR logic gate when the model dendritic nodes input two binary digits. A model dendritic encoder that is a network of model dendritic nodes encodes its inputs such that the resultant codes have an orthogonality property. Such codes are stored in synapses by unsupervised covariance learning, supervised covariance learning, or unsupervised accumulative learning, depending on the type of postsynaptic neuron. A masking matrix for a dendritic tree, whose upper part comprises model dendritic encoders, enables maximal generalization on corrupted, distorted, and occluded data. It is a mathematical organization and idealization of dendritic trees with overlapped and nested input vectors. A model nonspiking neuron transmits inhibitory graded signals to modulate its neighboring model spiking neurons. Model spiking neurons evaluate the subjective probability distribution (SPD) of the labels of the inputs to model dendritic encoders and generate spike trains with such SPDs as firing rates. Feedback connections from the same or higher layers with different numbers of unit-delay devices reflect different signal traveling times, enabling LOM to fully utilize temporally and spatially associated information. Biological plausibility of the component models is discussed. Numerical examples are given to demonstrate how LOM operates in retrieving, generalizing, and unsupervised and supervised learning.     

What Security Questions Do Developers Ask? A Large-Scale Study of Stack Overflow Posts

Security has always been a popular and critical topic. With the rapid development of information technology, it is always attracting people’s attention. However, since security has a long history, it covers a wide range of topics which change a lot, from classic cryptography to recently popular mobile security. There is a need to investigate security-related topics and trends, which can be a guide for security researchers, security educators and security practitioners. To address the above-mentioned need, in this paper, we conduct a large-scale study on security-related questions on Stack Overflow. Stack Overflow is a popular on-line question and answer site for software developers to communicate, collaborate, and share information with one another. There are many different topics among the numerous questions posted on Stack Overflow and security-related questions occupy a large proportion and have an important and significant position. We first use two heuristics to extract from the dataset the questions that are related to security based on the tags of the posts. And then we use an advanced topic model, Latent Dirichlet Allocation (LDA) tuned using Genetic Algorithm (GA), to cluster different security-related questions based on their texts. After obtaining the different topics of security-related questions, we use their metadata to make various analyses. We summarize all the topics into five main categories, and investigate the popularity and difficulty of different topics as well. Based on the results of our study, we conclude several implications for researchers, educators and practitioners.     

The relationship between online game playing motivation and selection of online game characters – the case of Taiwan

The alarming growth rate in the online game industry calls for a need of understanding the determinants of online gamers’ behaviour. Investigating how online gamers choose different online characters assists online game vendors to design characters that match the needs of different online gamers. Recently, numerous online game designers have introduced celebrity figures as characters for certain online games. The popularity of those celebrities has resulted in greater awareness of these games, and hopefully further increases the playability of online games. While different online gamers are motivated by different desires for playing, it is insufficiently researched whether these online celebrity characters have actually altered players’ choice in giving preference to these games. Thus, this study conducts an experimental design to study the reasons behind players’ choice of characters by studying how online games perceive the interpersonal attractiveness of celebrity online characters, and how online gamers with different playing motivations display different behaviours in their choice of online game characters. Results from the survey filled out by participants after the experiments show that the attractiveness of celebrity online characters is significantly higher than that of non-celebrity characters. Further, online game players with a social playing motivation tend to choose celebrities as their online game characters.     

Why and how developers fork what from whom in GitHub

Forking is the creation of a new software repository by copying another repository. Though forking is controversial in traditional open source software (OSS) community, it is encouraged and is a built-in feature in GitHub. Developers freely fork repositories, use codes as their own and make changes. A deep understanding of repository forking can provide important insights for OSS community and GitHub. In this paper, we explore why and how developers fork what from whom in GitHub. We collect a dataset containing 236,344 developers and 1,841,324 forks. We make surveys, and analyze programming languages and owners of forked repositories. Our main observations are: (1) Developers fork repositories to submit pull requests, fix bugs, add new features and keep copies etc. Developers find repositories to fork from various sources: search engines, external sites (e.g., Twitter, Reddit), social relationships, etc. More than 42 % of developers that we have surveyed agree that an automated recommendation tool is useful to help them pick repositories to fork, while more than 44.4 % of developers do not value a recommendation tool. Developers care about repository owners when they fork repositories. (2) A repository written in a developer’s preferred programming language is more likely to be forked. (3) Developers mostly fork repositories from creators. In comparison with unattractive repository owners, attractive repository owners have higher percentage of organizations, more followers and earlier registration in GitHub. Our results show that forking is mainly used for making contributions of original repositories, and it is beneficial for OSS community. Moreover, our results show the value of recommendation and provide important insights for GitHub to recommend repositories.     

Using ontologies to perform threat analysis and develop defensive strategies for mobile security

Existing studies on the detection of mobile malware have focused mainly on static analyses performed to examine the code-structure signature of viruses, rather than the dynamic behavioral aspects. By contrast, the unidentified behavior of new mobile viruses using the self-modification, polymorphic, and mutation techniques for variants have largely been ignored. The problem of precision regarding malware variant detection has become one of the key concerns in mobile security. Accordingly, the present study proposed a threat risk analysis model for mobile viruses, using a heuristic approach incorporating both malware behavior analysis and code analysis to generate a virus behavior ontology associated with the Protégé platform. The proposed model can not only explicitly identify an attack profile in accordance with structural signature of mobile viruses, but also overcome the uncertainty regarding the probability of an attack being successful. This model is able to achieve this by extending frequent episode rules to investigate the attack profile of a given malware, using specific event sequences associated with the sandbox technique for mobile applications (apps) and hosts. For probabilistic analysis, defense evaluation metrics for each node were used to simulate the results of an attack. The simulations focused specifically on the attack profile of a botnet to assess the threat risk. The validity of the proposed approach was demonstrated numerically by using two malware cyber-attack examples. Overall, the results presented in this paper prove that the proposed scheme offers an effective countermeasure, evaluated using a set of security metrics, for mitigating network threats by considering the interaction between the attack profiles and defense needs.