Identifying candidate subunit vaccines using an alignment-independent method based on principal amino acid properties

Subunit vaccine discovery is an accepted clinical priority. The empirical approach is time- and labor-consuming and can often end in failure. Rational information-driven approaches can overcome these limitations in a fast and efficient manner. However, informatics solutions require reliable algorithms for antigen identification. All known algorithms use sequence similarity to identify antigens. However, antigenicity may be encoded subtly in a sequence and may not be directly identifiable by sequence alignment. We propose a new alignment-independent method for antigen recognition based on the principal chemical properties of protein amino acid sequences. The method is tested by cross-validation on a training set of bacterial antigens and external validation on a test set of known antigens. The prediction accuracy is 83% for the cross-validation and 80% for the external test set. Our approach is accurate and robust, and provides a potent tool for the in silico discovery of medically relevant subunit vaccines.

Incremental tensor biased discriminant analysis:a new color-based visual tracking method

Most existing color-based tracking algorithms utilize the statistical color information of the object as the tracking clues, without maintaining the spatial structure within a single chromatic image. Recently, the researches on the multilinear algebra provide the possibility to hold the spatial structural relationship in a representation of the image ensembles. In this paper, a third-order color tensor is constructed to represent the object to be tracked. Considering the influence of the environment changing on the tracking, the biased discriminant analysis (BDA) is extended to the tensor biased discriminant analysis (TBDA) for distinguishing the object from the background. At the same time, an incremental scheme for the TBDA is developed for the tensor biased discriminant subspace online learning, which can be used to adapt to the appearance variant of both the object and background. The experimental results show that the proposed method can track objects precisely undergoing large pose, scale and lighting changes, as well as partial occlusion. © 2009 Elsevier B.V.

Case-based Reasoning Method for Real-time Expert Diagnostics Systems

The method of case-based reasoning for a solution of problems of real-time diagnostics and forecasting in intelligent decision support systems (IDSS) is considered. Special attention is drawn to case library structure for real-time IDSS (RT IDSS) and algorithm of k-nearest neighbors type. This work was supported by RFBR.

Power conversion and signal transmission integration method based on dual modulation of DC-DC converters

For the development of communication systems such as Internet of Things, integrating communication with power supplies is an attractive solution to reduce supply cost. This paper presents a novel method of power/signal dual modulation (PSDM), by which signal transmission is integrated with power conversion. This method takes advantage of the intrinsic ripple initiated in switch mode power supplies as signal carriers, by which cost-effective communications can be realized. The principles of PSDM are discussed, and two basic dual modulation methods (specifically PWM/FSK and PWM/PSK) are concluded. The key points of designing a PWM/FSK system, including topology selection, carrier shape, and carrier frequency, are discussed to provide theoretical guidelines. A practical signal modulation-demodulation method is given, and a prototype system provides experimental results to verify the effectiveness of the proposed solution.

A Method of Estimating Usability of a User Interface Based on its Model

The article presents a new method to estimating usability of a user interface based on its model. The principal features of the method are: creation of an expandable knowledge base of usability defects, detection defects based on the interface model, within the design phase, and information to the developer not only about existence of defects but also advice on their elimination.

The Inflation Index Prognosis Based on the Method of Decision-Marking “Tree”

The description of the support system for marking decision in terms of prognosing the inflation level based on the multifactor dependence represented by the decision – marking “tree” is given in the paper. The interrelation of factors affecting the inflation level – economic, financial, political, socio-demographic ones, is considered. The perspectives for developing the method of decision – marking “tree”, and pointing out the so- called “narrow” spaces and further analysis of possible scenarios for inflation level prognosing in particular, are defined.

Developing of Distributed Virtual Laboratories for Smart Sensor System Design Based on Multi-Dimensional Access Method

In the article it is considered preconditions and main principles of creation of virtual laboratories for computer-aided design, as tools for interdisciplinary researches. Virtual laboratory, what are offered, is worth to be used on the stage of the requirements specification or EFT-stage, because it gives the possibility of fast estimating of the project realization, certain characteristics and, as a result, expected benefit of its applications. Using of these technologies already increase automation level of design stages of new devices for different purposes. Proposed computer technology gives possibility to specialists from such scientific fields, as chemistry, biology, biochemistry, physics etc, to check possibility of device creating on the basis of developed sensors. It lets to reduce terms and costs of designing of computer devices and systems on the early stages of designing, for example on the stage of requirements specification or EFT-stage. An important feature of this project is using the advanced multi-dimensional access method for organizing the information base of the Virtual laboratory.

A laser induced breakdown spectroscopy quantitative analysis method based on the robust least squares support vector machine regression model

Data fluctuation in multiple measurements of Laser Induced Breakdown Spectroscopy (LIBS) greatly affects the accuracy of quantitative analysis. A new LIBS quantitative analysis method based on the Robust Least Squares Support Vector Machine (RLS-SVM) regression model is proposed. The usual way to enhance the analysis accuracy is to improve the quality and consistency of the emission signal, such as by averaging the spectral signals or spectrum standardization over a number of laser shots. The proposed method focuses more on how to enhance the robustness of the quantitative analysis regression model. The proposed RLS-SVM regression model originates from the Weighted Least Squares Support Vector Machine (WLS-SVM) but has an improved segmented weighting function and residual error calculation according to the statistical distribution of measured spectral data. Through the improved segmented weighting function, the information on the spectral data in the normal distribution will be retained in the regression model while the information on the outliers will be restrained or removed. Copper elemental concentration analysis experiments of 16 certified standard brass samples were carried out. The average value of relative standard deviation obtained from the RLS-SVM model was 3.06% and the root mean square error was 1.537%. The experimental results showed that the proposed method achieved better prediction accuracy and better modeling robustness compared with the quantitative analysis methods based on Partial Least Squares (PLS) regression, standard Support Vector Machine (SVM) and WLS-SVM. It was also demonstrated that the improved weighting function had better comprehensive performance in model robustness and convergence speed, compared with the four known weighting functions.

An edge-based matching kernel through discrete-time quantum walks

In this paper, we propose a new edge-based matching kernel for graphs by using discrete-time quantum walks. To this end, we commence by transforming a graph into a directed line graph. The reasons of using the line graph structure are twofold. First, for a graph, its directed line graph is a dual representation and each vertex of the line graph represents a corresponding edge in the original graph. Second, we show that the discrete-time quantum walk can be seen as a walk on the line graph and the state space of the walk is the vertex set of the line graph, i.e., the state space of the walk is the edges of the original graph. As a result, the directed line graph provides an elegant way of developing new edge-based matching kernel based on discrete-time quantum walks. For a pair of graphs, we compute the h-layer depth-based representation for each vertex of their directed line graphs by computing entropic signatures (computed from discrete-time quantum walks on the line graphs) on the family of K-layer expansion subgraphs rooted at the vertex, i.e., we compute the depth-based representations for edges of the original graphs through their directed line graphs. Based on the new representations, we define an edge-based matching method for the pair of graphs by aligning the h-layer depth-based representations computed through the directed line graphs. The new edge-based matching kernel is thus computed by counting the number of matched vertices identified by the matching method on the directed line graphs. Experiments on standard graph datasets demonstrate the effectiveness of our new kernel.

Fogalmak, módszerek. Páros összehasonlításokon alapuló rangsorolási módszerek (Ranking methods based on paired comparisons)

A páronként összehasonlított alternatívák rangsorolásának problémája egyaránt felmerül a szavazáselmélet, a statisztika, a tudománymetria, a pszichológia és a sport területén. A nemzetközi szakirodalom alapján részletesen áttekintjük a megoldási lehetőségeket, bemutatjuk a gyakorlati alkalmazások során fellépő kérdések kezelésének, a valós adatoknak megfelelő matematikai környezet felépítésének módjait. Kiemelten tárgyaljuk a páros összehasonlítási mátrix megadását, az egyes pontozási eljárásokat és azok kapcsolatát. A tanulmány elméleti szempontból vizsgálja a Perron-Frobenius tételen alapuló invariáns, fair bets, PageRank, valamint az irányított gráfok csúcsainak rangsorolásra javasolt internal slackening és pozíciós erő módszereket. A közülük történő választáshoz az axiomatikus megközelítést ajánljuk, ennek keretében bemutatjuk az invariáns és a fair bets eljárások karakterizációját, és kitérünk a módszerek vitatható tulajdonságaira. _____ The ranking of the alternatives or selecting the best one are fundamental issues of social choice theory, statistics, psychology and sport. Different solution concepts, and various mathematical models of applications are reviewed based on the international literature. We are focusing on the de¯nition of paired comparison matrix, on main scoring procedures and their relation. The paper gives a theoretical analysis of the invariant, fair bets and PageRank methods, which are founded on Perron-Frobenius theorem, as well as the internal slackening and positional power procedures used for ranking the nodes of a directed graph. An axiomatic approach is proposed for the choice of an appropriate method. Besides some known characterizations for the invariant and fair bets methods, we also discuss the violation of some properties, meaning their main weakness.

An energy based nanomechnical properties evaluation method for cementitious materials

Advances in multiscale material modeling of structural concrete have created an upsurge of interest in the accurate evaluation of mechanical properties and volume fractions of its nano constituents. The task is accomplished by analyzing the response of a material to indentation, obtained as an outcome of a nanoindentation experiment, using a procedure called the Oliver and Pharr (OP) method. Despite its widespread use, the accuracy of this method is often questioned when it is applied to the data from heterogeneous materials or from the materials that show pile-up and sink-in during indentation, which necessitates the development of an alternative method. ^ In this study, a model is developed within the framework defined by contact mechanics to compute the nanomechanical properties of a material from its indentation response. Unlike the OP method, indentation energies are employed in the form of dimensionless constants to evaluate model parameters. Analysis of the load-displacement data pertaining to a wide range of materials revealed that the energy constants may be used to determine the indenter tip bluntness, hardness and initial unloading stiffness of the material. The proposed model has two main advantages: (1) it does not require the computation of the contact area, a source of error in the existing method; and (2) it incorporates the effect of peak indentation load, dwelling period and indenter tip bluntness on the measured mechanical properties explicitly. ^ Indentation tests are also carried out on samples from cement paste to validate the energy based model developed herein by determining the elastic modulus and hardness of different phases of the paste. As a consequence, it has been found that the model computes the mechanical properties in close agreement with that obtained by the OP method; a discrepancy, though insignificant, is observed more in the case of C-S-H than in the anhydrous phase. Nevertheless, the proposed method is computationally efficient, and thus it is highly suitable when the grid indentation technique is required to be performed. In addition, several empirical relations are developed that are found to be crucial in understanding the nanomechanical behavior of cementitious materials.^

An automatic method of above-water iceberg 3-D profiling based on autonomous surface craft (ASC) using surface images and LIDAR

This thesis reports on a novel method to build a 3-D model of the above-water portion of icebergs using surface imaging. The goal is to work towards the automation of iceberg surveys, allowing an Autonomous Surface Craft (ASC) to acquire shape and size information. After collecting data and images, the core software algorithm is made up of three parts: occluding contour finding, volume intersection, and parameter estimation. A software module is designed that could be used on the ASC to perform automatic and fast processing of above-water surface image data to determine iceberg shape and size measurement and determination. The resolution of the method is calculated using data from the iceberg database of the Program of Energy Research and Development (PERD). The method was investigated using data from field trials conducted through the summer of 2014 by surveying 8 icebergs during 3 expeditions. The results were analyzed to determine iceberg characteristics. Limitations of this method are addressed including its accuracy. Surface imaging system and LIDAR system are developed to profile the above-water iceberg in 2015.

Habitat map of Danajon Bank, Philippines, derived from a high-spatial-resolution multi-spectral satellite image and georeferenced point intercept transect and spot-check survey field data, using an object-based image classification method

A mosaic of two WorldView-2 high resolution multispectral images (Acquisition dates: October 2010 and April 2012), in conjunction with field survey data, was used to create a habitat map of the Danajon Bank, Philippines (10°15'0'' N, 124°08'0'' E) using an object-based approach. To create the habitat map, we conducted benthic cover (seafloor) field surveys using two methods. Firstly, we undertook georeferenced point intercept transects (English et al., 1997). For ten sites we recorded habitat cover types at 1 m intervals on 10 m long transects (n= 2,070 points). Second, we conducted geo-referenced spot check surveys, by placing a viewing bucket in the water to estimate the percent cover benthic cover types (n = 2,357 points). Survey locations were chosen to cover a diverse and representative subset of habitats found in the Danajon Bank. The combination of methods was a compromise between the higher accuracy of point intercept transects and the larger sample area achievable through spot check surveys (Roelfsema and Phinn, 2008, doi:10.1117/12.804806). Object-based image analysis, using the field data as calibration data, was used to classify the image mosaic at each of the reef, geomorphic and benthic community levels. The benthic community level segregated the image into a total of 17 pure and mixed benthic classes.

Accuracy of a method based on atomic absorption spectrometry to determine inorganic arsenic in food : Outcome of the collaborative trial IMEP-41

Peer reviewed

A cardiovascular occlusion method based on the use of a smart hydrogel

Smart hydrogels for biomedical applications are highly researched materials. However, integrating them into a device for implantation is difficult. This paper investigates an integrated delivery device designed to deliver an electro-responsive hydrogel to a target location inside a blood vessel with the purpose of creating an occlusion. The paper describes the synthesis and characterization of a Pluronic/methacrylic acid sodium salt electro-responsive hydrogel. Application of an electrical bias decelerates the expansion of the hydrogel. An integrated delivery system was manufactured to deliver the hydrogel to the target location in the body. Ex vivo and in vivo experiments in the carotid artery of sheep were used to validate the concept. The hydrogel was able to completely occlude the blood vessel reducing the blood flow from 245 to 0 ml/min after implantation. Ex vivo experiments showed that the hydrogel was able to withstand physiological blood pressures of > 270 mm·Hg without dislodgement. The results showed that the electro-responsive hydrogel used in this paper can be used to create a long-term occlusion in a blood vessel without any apparent side effects. The delivery system developed is a promising device for the delivery of electro-responsive hydrogels.