Gas-phase compaction and unfolding of protein structures

Ion-mobility mass spectrometry is emerging as a powerful tool for studying the structures of less established protein assemblies. The method provides simultaneous measurement of the mass and size of intact protein assemblies, providing information not only on the subunit composition and network of interactions but also on the overall topology and shape of protein complexes. However, how the experimental parameters affect the measured collision cross-sections remains elusive. Here, we present an extensive systematic study on a range of proteins and protein complexes with differing sizes, structures, and oligomerization states. Our results indicate that the experimental parameters, T-wave height and velocity, influence the determined collision cross-section independently and in opposite directions. Increasing the T-wave height leads to compaction of the protein structures, while higher T-wave velocities lead to their expansion. These different effects are attributed to differences in energy transmission and dissipation rates. Moreover, by analyzing proteins in their native and denatured states, we could identify the lower and upper boundaries of the collision cross-section, which reflect the "maximally packed" and "ultimately unfolded" states. Together, our results provide grounds for selecting optimal experimental parameters that will enable preservation of the nativelike conformation, providing structural information on uncharacterized protein assemblies.     

Diffusion-related implications for langasite resonator operation

Oxygen and gallium diffusivities in langasite were experimentally determined by analysis of diffusion profiles of 18O and 71Ga tracers by SIMS analysis as functions of temperature and doping. Strontium-enhanced diffusivities and activation energies of approximately 1.2+/-0.2 eV confirm the predominant role of oxygen vacancies in controlling the electrical conductivity of langasite at elevated temperature and oxygen partial pressure. The potential impact of high levels of porosity and the use of an oxygen primary ion beam on the accuracy of some of the data is discussed. The gallium diffusivity, with activation energy of 3.13 eV, was found to be more than two orders of magnitude lower than that of oxygen. Surface exchange measurements enabled estimation of gallium loss at elevated temperatures and oxygen partial pressure; the level is not believed to be of major concern for resonator performance.     

Evolution of efficient real-time non-linear image filters for FPGAs

Image processing represents a research field in which high-quality solutions have been obtained using various soft computing techniques. Evolutionary algorithms constitute a class of stochastic search methods that are applicable in both optimization and design tasks. In the area of circuit design Cartesian Genetic Programming has often been utilized in combination with an algorithm of Evolutionary Strategy. Digital image filters represent a specific class of circuits whose design can be performed by means of this approach. Switching filters are advanced non-linear filtering techniques in which the main idea is to detect and filter the noise pixels while keeping the uncorrupted pixels unchanged in order to increase the quality of the resulting image. The aim of this article is to present a robust design technique based on Cartesian Genetic Programming for the automatic synthesis of switching image filters intended for real-time processing applications. The robustness of the proposed evolutionary approach is evaluated using four design problems including the removal of salt and pepper noise, random shot noise, impulse burst noise and impulse burst noise combined with random shot noise. An extensive evaluation is performed in order to compare the properties of the evolved switching filters with the best conventional solutions. The evaluation has shown that the evolved switching filters exhibit a very good trade off between the quality of filtering and the implementation cost in field programmable gate arrays.     

Experiments with routing on printed circuit boards

Several ways of utilizing Lee's wave algorithm for routing on printed circuit boards were compared. It was proved that the order of net processing influenced the quality of the solution of a given interconnection problem. Moreover, it was found that the choice of ‘source’ and ‘target’ formations influenced both the computational time and the quality of the solution. The results obtained allowed the performance of the SYSDEB77 system for routing on two-layer boards to be improved.     

Generating heavy particles with energy and momentum conservation

We propose a novel algorithm, called REGGAE, for the generation of momenta of a given sample of particle masses, evenly distributed in Lorentz-invariant phase space and obeying energy and momentum conservation. In comparison to other existing algorithms, REGGAE is designed for the use in multiparticle production in hadronic and nuclear collisions where many hadrons are produced and a large part of the available energy is stored in the form of their masses. The algorithm uses a loop simulating multiple collisions which lead to production of configurations with reasonably large weights.

Program summary

Program title: REGGAE (REscattering-after-Genbod GenerAtor of Events)Catalogue identifier: AEJR_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJR_v1_0.htmlProgram obtainable from: CPC Program Library, Queen?s University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 1523No. of bytes in distributed program, including test data, etc.: 9608Distribution format: tar.gzProgramming language: C++Computer: PC Pentium 4, though no particular tuning for this machine was performed.Operating system: Originally designed on Linux PC with g++, but it has been compiled and ran successfully on OS X with g++ and MS Windows with Microsoft Visual C++ 2008 Express Edition, as well.RAM: This depends on the number of particles which are generated. For 10 particles like in the attached example it requires about 120 kB.Classification: 11.2Nature of problem: The task is to generate momenta of a sample of particles with given masses which obey energy and momentum conservation. Generated samples should be evenly distributed in the available Lorentz-invariant phase space.Solution method: In general, the algorithm works in two steps. First, all momenta are generated with the GENBOD algorithm. There, particle production is modeled as a sequence of two-body decays of heavy resonances. After all momenta are generated this way, they are reshuffled. Each particle undergoes a collision with some other partner such that in the pair center of mass system the new directions of momenta are distributed isotropically. After each particle collides only a few times, the momenta are distributed evenly across the whole available phase space. Starting with GENBOD is not essential for the procedure but it improves the performance.Running time: This depends on the number of particles and number of events one wants to generate. On a LINUX PC with 2 GHz processor, generation of 1000 events with 10 particles each takes about 3 s.     

Developing and evaluating language courseware

The paper sets out twenty proposals for the development and evaluation of Computer Assisted Language Learning (CALL) programs. These proposals emerge from special characteristics of language instruction and of the use of computers to assist in language instruction. We combine theoretically-based assumptions with empirical findings drawn from investigation of language courseware for Hebrew speakers in Israel. We first list four unique features of language instruction: (1) the object-language-meta-language distinction; (2) computer as written medium vs. language as primary spoken medium; (3) teaching of second language skills vs. linguistics; (4) the computer as an electronic tool vs. the computer as a cognitive entity simulating the speaker. We then show how these unique characteristics of language instruction (mother-tongue and foreign language) impose special proposals on language courseware. These proposals should be observed in the development of language courseware and in the evaluation of such programs. Clearly, these proposals integrate with general courseware proposals. Michal Ephratt (Ph.D., computational linguistics) completed post-doctoral studies at the University of Rochester. She has been on the staff of the Dept. of Hebrew Linguistics, University of Haifa, since 1988. Some of her publications include Root-Pattern Array: The Main Tool of Hebrew Word Formation (Hebrew University, 1985); and What's in a Joke? in Advances in Artificial Intelligence, Natural Language and Knowledge-based Systems (Springer-Verlag, 1990).This paper is based on work the author did as a consultant in the National Courseware Evaluation Department of the Ministry of Education. I wish to thank Esther Diamant, head of the department, for making the study possible.     

Proplant: Multiagent system for production planning

The so-called ''tribase'' acquaintance model of the agent's behavior is presented in this paper. This represents an extension of the twin-base model (Cao et al., 1997). Based on practical experience, the new model tries to cope with parallel processing, precedence constraints, and sparse resources. The idea of substituting the interagent negotiation processes by the periodical internal planning activity of the agents is stressed. A multiagent system, ProPlanT, as an application of the tribase model for the project-oriented production planning developed for TESLA TV company is described in detail. Three types of agents production planning agent (PPA), production management agent (PMA), and production agent (PA) are distinguished. The corresponding tribase models and potential role of metaagents are discussed.     

AutoMed: an automated mediator for multi-issue bilateral negotiations

In this paper, we present AutoMed, an automated mediator for multi-issue bilateral negotiation under time constraints. AutoMed elicits the negotiators preferences and analyzes them. It monitors the negotiations and proposes possible solutions for resolving the conflict. We conducted experiments in a simulated environment. The results show that negotiations mediated by AutoMed are concluded significantly faster than non-mediated ones and without any of the negotiators opting out. Furthermore, the subjects in the mediated negotiations are more satisfied with the resolutions than the subjects in the non-mediated negotiations.     

Image auto-annotation with automatic selection of the annotation length

Developing a satisfactory and effective method for auto-annotating images that works under general conditions is a challenging task. The advantages of such a system would be manifold: it can be used to annotate existing, large databases of images, rendering them accessible to text search engines; or it can be used as core for image retrieval based on a query image’s visual content. Manual annotation of images is a difficult, tedious and time consuming task. Furthermore, manual annotations tend to show great inter-person variance: considering an image, the opinions about what elements are significant and deserve an annotation vary strongly. The latter poses a problem for the evaluation of an automatic method, as an annotation’s correctness is greatly subjective. In this paper we present an automatic method for annotating images, which addresses one of the existing methods’ major limitation, namely a fixed annotation length. The proposed method, PATSI, automatically chooses the resulting annotation’s length for each query image. It is held as simple as possible and a build-in parameter optimization procedure renders PATSI de-facto parameter free. Finally, PATSI is evaluated on standard datasets, outperforming various state-of-the-art methods.