A new feature encoding scheme for HIV-1 protease cleavage site prediction

HIV-1 protease has been the subject of intense research for deciphering HIV-1 virus replication process for decades. Knowledge of the substrate specificity of HIV-1 protease will enlighten the way of development of HIV-1 protease inhibitors. In the prediction of HIV-1 protease cleavage site techniques, various feature encoding techniques and machine learning algorithms have been used frequently. In this paper, a new feature amino acid encoding scheme is proposed to predict HIV-1 protease cleavage sites. In the proposed method, we combined orthonormal encoding and Taylor’s venn-diagram. We used linear support vector machines as the classifier in the tests. We also analyzed our technique by comparing some feature encoding techniques. The tests are carried out on PR-1625 and PR-3261 datasets. Experimental results show that our amino acid encoding technique leads to better classification performance than other encoding techniques on a standalone classifier.     

Dynamic modeling and fuzzy logic control of vibrations of a railway vehicle for different track irregularities

Safe and comfortable transportation of passengers and goods on railways can be achieved by solving the vibration problem. In this study, the dynamic modeling of the full railway vehicle is used to perform vibration analysis in order to observe displacements and accelerations. The full railway vehicle model consists of 54 degrees of freedom which are defined by differential equations. Additionally, wheel–rail contact problem (i.e. creepage factors and hertzian spring stiffness of rails) is analyzed by finite element method. Dynamic modeling and vibration analysis are carried out using Matlab–Simulink software. Using the developed model, the car body vibrations, caused by a lateral and two vertical sinusoidal track irregularities, are controlled by fuzzy logic controllers placed between the car body and bogies. The fuzzy logic algorithm herein is used for realizing the active control of car body vibrations. The simulations of vibration analysis are obtained in time and frequency domains and compared with passive controlled status. The robustness of the designed controller is verified by simulations, carried out for the cases of car body mass variations. The results show the effectiveness of the proposed algorithm.     

Effect of cathodic arc plasma treatment on the properties of WC–Co based hard metals

In this study, ion bombardment in a cathodic arc physical vapor deposition system was applied on WC–Co hard metal surfaces aiming to benefit from the diffusion acceleration effect, and to investigate the role of this effect on the surface composition, morphology and corrosion resistance of the materials. Chromium ions obtained via cathodic arc evaporation were accelerated under low (− 150 V) and high (− 1000 V) bias voltages in order to apply coating–bombardment cycles to sample surfaces. Substrate temperatures were measured by an optical pyrometer during the processes. The treated samples were characterized by scanning electron microscopy (SEM) and X-ray diffractometry (XRD). Temperature measurements showed that the sample temperature could be controlled precisely by adjusting the bias voltage. Temperatures in the range of 750–1200 °C were measured during the treatment depending on the duration of the high bias voltage cycles. XRD analysis showed η phase formation in the near surface regions of all treated samples. The amount of the formed η phase was shown to be dependent on the heating–cooling regime that varied with the applied mode of bias. The corrosion behavior of the samples was investigated by immersing treated and untreated samples in a solution of 5% H₃PO₄ containing 1 g/l Zn^{+ 2} for 24 h at 50 °C. The samples were investigated via SEM observations after immersion. Cathodic arc plasma treated samples showed a better resistance to corrosion in this environment.     

Various approaches for constructing an ensemble of metamodels using local measures

Metamodels are approximate mathematical models used as surrogates for computationally expensive simulations. Since metamodels are widely used in design space exploration and optimization, there is growing interest in developing techniques to enhance their accuracy. It has been shown that the accuracy of metamodel predictions can be increased by combining individual metamodels in the form of an ensemble. Several efforts were focused on determining the contribution (or weight factor) of a metamodel in the ensemble using global error measures. In addition, prediction variance is also used as a local error measure to determine the weight factors. This paper investigates the efficiency of using local error measures, and also presents the use of the pointwise cross validation error as a local error measure as an alternative to using prediction variance. The effectiveness of ensemble models are tested on several problems with varying dimensionality: five mathematical benchmark problems, two structural mechanics problems and an automobile crash problem. It is found that the spatial ensemble models show better performances than the global ensemble for the low-dimensional problems, while the global ensemble is a more accurate model than the spatial ensembles for the high-dimensional problems. Ensembles based on pointwise cross validation error and prediction variance provide similar accuracy. The ensemble models based on local measures reduce cross validation errors drastically, but their performances are not that impressive in reducing the error evaluated at random test points, because the pointwise cross validation error is not a good surrogate for the error at a point.     

Stills,not full motion,for interactive spatial training: American,Turkish and Taiwanese female pre-service teachers learn spatial visualization

This study investigated how female elementary education pre-service teachers in the United States, Turkey and Taiwan learned spatial skills from structured activities involving discrete, as opposed to continuous, transformations in interactive computer programs, and how these activities transferred to non-related standardized tests of spatial visualization and mental rotation. The study used a pretest, intervention, posttest research design with experimental and comparison groups. The experimental group participated in transformational geometry visualization exercises, once a week for six weeks, for approximately 20 minutes each session. Instruments were standardized measures of spatial visualization and mental rotation; intervention activity worksheets directed the participants through 2D and 3D transformational geometry tasks in computer environments. For Turkish and Taiwanese participants, the experimental group improved significantly more than the control group in spatial visualization, while the American participants showed no such significant improvement.     

Preparation of nano-size ZrB2 powder by self-propagating high-temperature synthesis

Preparation of nano-size ZrB₂ powder by SHS has been investigated. Zr and B elemental powders were mixed with 10–50 wt.% NaCl, and prepared pellets were reacted under argon. Adiabatic temperatures were calculated by HSC software. Increasing NaCl content led to a continuous decrease in adiabatic temperatures and reaction wave velocity. Products were subjected to XRD, SEM and FESEM analyses. Average crystallite size of ZrB₂, which was 303 nm without NaCl, decreased to 32 nm with 40% NaCl addition. Distinct decrease in ZrB₂ particle size was also observed from SEM analyses. 30% NaCl addition was found to be optimum for ensuring a stable SHS reaction and providing the formation of nano-size ZrB₂ particles. It was revealed from particle size distribution measurements that ZrB₂ powder obtained by 30 wt.% NaCl addition contained particles mostly finer than 200 nm. A mechanism, similar to solution-precipitation was proposed for the particle size refining effect of NaCl.     

Resonant frequency of an air gap tuned circular disc microstrip antenna

In this study, the formulation and the computation of the resonant frequency of an air gap tuned circular disc microstrip antenna are simplified, with improved accuracy, by using a new and very simple effective permittivity expression which is valid for thin and thick gaps. Very good agreement between the theoretical and the experimental resonant frequency values is obtained for the various structural parameters and operational modes.     

The effects of alternating current electrocoagulation on dye removal from aqueous solutions

The main goal of this study is to investigate the effects of alternating current (AC) on dye removal from aqueous solutions by electrocoagulation (EC). An EC system with parallel-connected aluminium electrodes was operated in batch mode. Two different aqueous dye solutions were used: one was obtained from Dianix Yellow CC (DY) and the other was obtained using Procion Yellow (PY). The experiments employing direct current (DC) were carried out using a DC power supply. The AC experiments were conducted using rectangular wave, which is produced with an adjustable time relay connected to the output of DC power supply. This current is called alternating pulse current (APC) in order to refer AC system in this study. Total organic carbon (TOC) and dye removal efficiencies were measured to assess treatment efficiency. Operating cost was calculated for both power supply systems and alternating pulse current was found superior to direct current for the treatment of reactive and disperse dyes used in this study.