Quantitative online prediction of peptide binding to the major histocompatibility complex

With its implications for vaccine discovery, the accurate prediction of T cell epitopes is one of the key aspirations of computational vaccinology. We have developed a robust multivariate statistical method, based on partial least squares, for the quantitative prediction of peptide binding to major histocompatibility complexes (MHC), the principal checkpoint on the antigen presentation pathway. As a service to the immunobiology community, we have made a Perl implementation of the method available via a World Wide Web server. We call this server MHCPred. Access to the server is freely available from the URL: http://www.jenner.ac.uk/MHCPred. We have exemplified our method with a model for peptides binding to the common human MHC molecule HLA-B*3501.

Representational difference analysis:Critical appraisal and method development for the identification of unique DNA sequences from prokaryotes

Representational difference analysis (RDA) has great potential for preferential amplification of unique but uncharacterised DNA sequences present in one source such as a whole genome, but absent from a related genome or other complex population of sequences. While a few examples of its successful exploitation have been published, the method has not been well dissected and robust, detailed published protocols are lacking. Here we examine the method in detail, suggest improvements and provide a protocol that has yielded key unique sequences from a pathogenic bacterial genome. © 2003 Elsevier Science B.V. All rights reserved.

Hierarchical Logical Description and Neural Recognition of Complex Patterns

Authors suggested earlier hierarchical method for definition of class description at pattern recognition problems solution. In this paper development and use of such hierarchical descriptions for parallel representation of complex patterns on the base of multi-core computers or neural networks is proposed.

Evolutionary Clustering of Complex Systems and Processes

In a paper the method of complex systems and processes clustering based use of genetic algorithm is offered. The aspects of its realization and shaping of fitness-function are considered. The solution of clustering task of Ukraine areas on socio-economic indexes is represented and comparative analysis with outcomes of classical methods is realized.

Intellect Sensing of Neural Network that Trained to Classify Complex Signals

An experimental comparison of information features used by neural network is performed. The sensing method was used. Suboptimal classifier agreeable to the gaussian model of the training data was used as a probe. Neural nets with architectures of perceptron and feedforward net with one hidden layer were used. The experiments were carried out with spatial ultrasonic data, which are used for car’s passenger safety system neural controller learning. In this paper we show that a neural network doesn’t fully make use of gaussian components, which are first two moment coefficients of probability distribution. On the contrary, the network can find more complicated regularities inside data vectors and thus shows better results than suboptimal classifier. The parallel connection of suboptimal classifier improves work of modular neural network whereas its connection to the network input improves the specialization effect during training.

Numerical modelling of complex femtosecond laser inscribed fiber gratings - comparison wih experiment

We present experimental studies and numerical modeling based on a combination of the Bidirectional Beam Propagation Method and Finite Element Modeling that completely describes the wavelength spectra of point by point femtosecond laser inscribed fiber Bragg gratings, showing excellent agreement with experiment. We have investigated the dependence of different spectral parameters such as insertion loss, all dominant cladding and ghost modes and their shape relative to the position of the fiber Bragg grating in the core of the fiber. Our model is validated by comparing model predictions with experimental data and allows for predictive modeling of the gratings. We expand our analysis to more complicated structures, where we introduce symmetry breaking; this highlights the importance of centered gratings and how maintaining symmetry contributes to the overall spectral quality of the inscribed Bragg gratings. Finally, the numerical modeling is applied to superstructure gratings and a comparison with experimental results reveals a capability for dealing with complex grating structures that can be designed with particular wavelength characteristics.

Entropy Based Approach to Finding Interacting Genes Responsible for Complex Human Disease

2000 Mathematics Subject Classification: 62P10, 92D10, 92D30, 94A17, 62L10.

A knowledge based system of principled negotiation for complex business contract

Automated negotiation systems can do better than human being in many aspects, and thus are applied into many domains ranging from business to computer science. However, little work about automating negotiation of complex business contract has been done so far although it is a kind of the most important negotiation in business. In order to address this issue, in this paper we developed an automated system for this kind of negotiation. This system is based on the principled negotiation theory, which is the most effective method of negotiation in the domain of business. The system is developed as a knowledge-based one because a negotiating agent in business has to be economically intelligent and capable of making effective decisions based on business experiences and knowledge. Finally, the validity of the developed system is shown in a real negotiation scenario where on behalf of human users, the system successfully performed a negotiation of a complex business contract between a wholesaler and a retailer. © 2013 Springer-Verlag Berlin Heidelberg.

Complex Oscillations and Limit Cycles in Autonomous Two-Component Incommensurate Fractional Dynamical Systems

MSC 2010: 26A33, 34D05, 37C25

Simple room temperature method for polymer optical fibre cleaving

In this paper, we report on a new method to cleave polymer optical fibre. The most common way to cut a polymer optical fibre is chopping it with a razor blade; however, in this approach both the fibre and the blade must be preheated in order to turn the material ductile, and thus, prevent crazing. In this paper, we make use of the temperature-time equivalence in polymers to replace the use of heating by an increase of the cleaving time and use a sawing motion to reduce fibre end face damage. In this way, the polymer fibre can be cleaved at room temperature in seconds with the resulting end face being of similar quality to those produced by more complex and expensive heated systems.

Determining the change of Brillouin frequency shift by using the similarity matching method

We have proposed a similarity matching method (SMM) to obtain the change of Brillouin frequency shift (BFS), in which the change of BFS can be determined from the frequency difference between detecting spectrum and selected reference spectrum by comparing their similarity. We have also compared three similarity measures in the simulation, which has shown that the correlation coefficient is more accurate to determine the change of BFS. Compared with the other methods of determining the change of BFS, the SMM is more suitable for complex Brillouin spectrum profiles. More precise result and much faster processing speed have been verified in our simulation and experiments. The experimental results have shown that the measurement uncertainty of the BFS has been improved to 0.72 MHz by using the SMM, which is almost one-third of that by using the curve fitting method, and the speed of deriving the BFS change by the SMM is 120 times faster than that by the curve fitting method.

What counts versus what can be counted:the complex interplay of market orientation and marketing performance measurement

Market orientation (MO) and marketing performance measurement (MPM) are two of the most widespread strategic marketing concepts among practitioners. However, some have questioned the benefits of extensive investments in MO and MPM. More importantly, little is known about which combinations of MO and MPM are optimal in ensuring high business performance. To address this research gap, the authors analyze a unique data set of 628 firms with a novel method of configurational analysis: fuzzy-set qualitative comparative analysis. In line with prior research, the authors find that MO is an important determinant of business performance. However, to reap its benefits, managers need to complement it with appropriate MPM, the level and focus of which vary across firms. For example, whereas large firms and market leaders generally benefit from comprehensive MPM, small firms may benefit from measuring marketing performance only selectively or by focusing on particular dimensions of marketing performance. The study also finds that many of the highest-performing firms do not follow any of the particular best practices identified.

Lattice Boltzmann method for flow and heat transfer in microgeometries

Recent technological developments have made it possible to design various microdevices where fluid flow and heat transfer are involved. For the proper design of such systems, the governing physics needs to be investigated. Due to the difficulty to study complex geometries in micro scales using experimental techniques, computational tools are developed to analyze and simulate flow and heat transfer in microgeometries. However, conventional numerical methods using the Navier-Stokes equations fail to predict some aspects of microflows such as nonlinear pressure distribution, increase mass flow rate, slip flow and temperature jump at the solid boundaries. This necessitates the development of new computational methods which depend on the kinetic theory that are both accurate and computationally efficient. In this study, lattice Boltzmann method (LBM) was used to investigate the flow and heat transfer in micro sized geometries. The LBM depends on the Boltzmann equation which is valid in the whole rarefaction regime that can be observed in micro flows. Results were obtained for isothermal channel flows at Knudsen numbers higher than 0.01 at different pressure ratios. LBM solutions for micro-Couette and micro-Poiseuille flow were found to be in good agreement with the analytical solutions valid in the slip flow regime (0.01 < Kn < 0.1) and direct simulation Monte Carlo solutions that are valid in the transition regime (0.1 < Kn < 10) for pressure distribution and velocity field. The isothermal LBM was further extended to simulate flows including heat transfer. The method was first validated for continuum channel flows with and without constrictions by comparing the thermal LBM results against accurate solutions obtained from analytical equations and finite element method. Finally, the capability of thermal LBM was improved by adding the effect of rarefaction and the method was used to analyze the behavior of gas flow in microchannels. The major finding of this research is that, the newly developed particle-based method described here can be used as an alternative numerical tool in order to study non-continuum effects observed in micro-electro-mechanical-systems (MEMS).

Inspection of parts with complex geometry and welds with structural health monitoring techniques

Structural Health Monitoring (SHM) systems were developed to evaluate the integrity of a system during operation, and to quickly identify the maintenance problems. They will be used in future aerospace vehicles to improve safety, reduce cost and minimize the maintenance time of a system. Many SHM systems were already developed to evaluate the integrity of plates and used in marine structures. Their implementation in manufacturing processes is still expected. The application of SHM methods for complex geometries and welds are two important challenges in this area of research. This research work started by studying the characteristics of piezoelectric actuators, and a small energy harvester was designed. The output voltages at different frequencies of vibration were acquired to determine the nonlinear characteristics of the piezoelectric stripe actuators. The frequency response was evaluated experimentally. AA battery size energy harvesting devices were developed by using these actuators. When the round and square cross section devices were excited at 50 Hz frequency, they generated 16 V and 25 V respectively. The Surface Response to Excitation (SuRE) and Lamb wave methods were used to estimate the condition of parts with complex geometries. Cutting tools and welded plates were considered. Both approaches used piezoelectric elements that were attached to the surfaces of considered parts. The variation of the magnitude of the frequency response was evaluated when the SuRE method was used. The sum of the square of the differences was calculated. The envelope of the received signal was used for the analysis of wave propagation. Bi-orthogonal wavelet (Binlet) analysis was also used for the evaluation of the data obtained during Lamb wave technique. Both the Lamb wave and SuRE approaches along with the three methods for data analysis worked effectively to detect increasing tool wear. Similarly, they detected defects on the plate, on the weld, and on a separate plate without any sensor as long as it was welded to the test plate.

Lattice Boltzmann Method for Flow and Heat Transfer in Microgeometries

Recent technological developments have made it possible to design various microdevices where fluid flow and heat transfer are involved. For the proper design of such systems, the governing physics needs to be investigated. Due to the difficulty to study complex geometries in micro scales using experimental techniques, computational tools are developed to analyze and simulate flow and heat transfer in microgeometries. However, conventional numerical methods using the Navier-Stokes equations fail to predict some aspects of microflows such as nonlinear pressure distribution, increase mass flow rate, slip flow and temperature jump at the solid boundaries. This necessitates the development of new computational methods which depend on the kinetic theory that are both accurate and computationally efficient. In this study, lattice Boltzmann method (LBM) was used to investigate the flow and heat transfer in micro sized geometries. The LBM depends on the Boltzmann equation which is valid in the whole rarefaction regime that can be observed in micro flows. Results were obtained for isothermal channel flows at Knudsen numbers higher than 0.01 at different pressure ratios. LBM solutions for micro-Couette and micro-Poiseuille flow were found to be in good agreement with the analytical solutions valid in the slip flow regime (0.01 < Kn < 0.1) and direct simulation Monte Carlo solutions that are valid in the transition regime (0.1 < Kn < 10) for pressure distribution and velocity field. The isothermal LBM was further extended to simulate flows including heat transfer. The method was first validated for continuum channel flows with and without constrictions by comparing the thermal LBM results against accurate solutions obtained from analytical equations and finite element method. Finally, the capability of thermal LBM was improved by adding the effect of rarefaction and the method was used to analyze the behavior of gas flow in microchannels. The major finding of this research is that, the newly developed particle-based method described here can be used as an alternative numerical tool in order to study non-continuum effects observed in micro-electro-mechanical-systems (MEMS).