Volume 23, Issue 2
Generalized Net Model of Cluster Analysis Using CLIQUE: Clustering in Quest131-138
Veselina Bureva, Stanislav Popov, Velichka Traneva, Stoyan Tranev
doi: 10.7546/ijba.2019.23.2.000506
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Veselina Bureva, Stanislav Popov, Velichka Traneva, Stoyan Tranev (2019) Generalized Net Model of Cluster Analysis Using CLIQUE: Clustering in Quest, Int J Bioautomation, 23 (2), 131-138, doi: 10.7546/ijba.2019.23.2.000506
Abstract: The purpose of the cluster analysis is to find groups of objects with similar characteristics. Different methods are already developed. In the current research work a CLIQUE: Clustering in quest algorithm is investigated. The presented method combines subspace grid-based and density-based techniques to determine clusters of objects. Generalized net of cluster analysis using CLIQUE: Clustering in quest algorithm is constructed. The presented Generalized net can be used for description and monitoring the parallel processes in the cluster analysis.

Keywords: Cluster, Cluster analysis, Clique, Generalized nets
Dynamics of Changes in Visual Evoked Potentials Values with the Advance of Retinal Changes in Patients with Diabetes Mellitus139-152
Elena Mermeklieva
doi: 10.7546/ijba.2019.23.2.000639
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Elena Mermeklieva (2019) Dynamics of Changes in Visual Evoked Potentials Values with the Advance of Retinal Changes in Patients with Diabetes Mellitus, Int J Bioautomation, 23 (2), 139-152, doi: 10.7546/ijba.2019.23.2.000639
Abstract: Abstract: Aim: The aim of the study was to explore objectively the visual analyzer (VA) function by pattern visual evoked potentials (PVEPs) in patients with diabetes mellitus (DM) in different stages of diabetic retinopathy (DR) and to compare the results with controls and between the different groups. Material and methods: This is a prospective observation study with 3-year duration (2014-2017). A group of 185 people was studied. Patients with DM were 138. They were divided into two main groups - patients without DR and patients with DR. The first group consisted of two subgroups – patients with newly-diagnosed DM (33 people) and patients with DM duration longer than 1 year (mean DM duration 6.8 ± 4.2 years) (36 people). The second main group consists of patients with DR, divided into two subgroups – patients with initial DR (34 people) and patients with advanced DR (35 people). Controls for the EF studies were 47 healthy individuals. PVEPs were performed. The main variables that were considered in the results analysis were the latency and amplitude, reflecting the configuration of the wave forms. Results: PVEPs results were affected even in patients without DR. The changes in PVEPs values became more distinct in patients with initial DR group as а number of components with significant difference as well as a degree of significant difference, to reach their maximum number and significance manifestation peak in patients with advanced DR, the most affected by DM group. Conclusion: PVEPs studies could be used as an objective methods for registration of early changes in the VA function as a DM complication. Also, to monitor the changes in dynamics as they are non-invasive, harmless, fast, inexpensive and repeatable.

Keywords: Visual evoked potentials, Diabetes mellitus, Diabetic retinopathy
A Microorganism Transcriptional Regulation Algorithm Based on Generalized Regression Neural Network153-162
Hui Li
doi: 10.7546/ijba.2019.23.2.000676
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Hui Li (2019) A Microorganism Transcriptional Regulation Algorithm Based on Generalized Regression Neural Network, Int J Bioautomation, 23 (2), 153-162, doi: 10.7546/ijba.2019.23.2.000676
Abstract: Considering the importance of operon in microorganism transcriptional regulation, this paper sets up a new operon prediction model based on artificial neural network (ANN). Specifically, multiple genome information, ranging from intergenic distance (IGD), orthologous protein cluster (OPC), conserved gene pair (CGP) to system evolution spectrum (SES), were preprocessed by log-likelihood fraction and wavelet transform, and then inputted to the GRNN for operon prediction. The experimental results in E. coli K-12 and B. subtilis 168 show that our model is a valid and feasible way to predict operon. The research findings shed new light on the prediction of operon information of new species.

Keywords: Microorganism transcriptional regulation, Operon prediction, Generalized regression neural network
A Numerical Study on a Model for HIV Infection of CD4+T-cells by Shifted Chebyshev Polynomials163-174
Kourosh Parand, Mohammad Mahdi Moayeri, Sobhan Latifi
doi: 10.7546/ijba.2019.23.2.000498
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Kourosh Parand, Mohammad Mahdi Moayeri, Sobhan Latifi (2019) A Numerical Study on a Model for HIV Infection of CD4+T-cells by Shifted Chebyshev Polynomials, Int J Bioautomation, 23 (2), 163-174, doi: 10.7546/ijba.2019.23.2.000498
Abstract: In this paper, we propose a new method to approximate the solution of a model for Human immunodeficiency virus (HIV) infection of CD4+T-cells. A collocation method based on shifted Chebyshev orthogonal polynomials is implemented for solving the model. Using the proposed method, the model is converted to a system of nonlinear algebraic equations. In addition, the accuracy of our method are investigated by comparing our results with the state-of-the-art methods, and the results indicate that our method improves the precision of the solution and has a uniform accuracy in comparison with previous methods in the same interval.

Keywords: Shifted-Chebyshev polynomials, HIV infection, CD4+T-cells, Collocation methods, Nonlinear differential equations
Application of Intuitionistic Fuzzy Sets for Conflict Resolution Modeling and Agent Based Simulation175-184
Shpend Ismaili, Stefka Fidanova
doi: 10.7546/ijba.2019.23.2.000544
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Shpend Ismaili, Stefka Fidanova (2019) Application of Intuitionistic Fuzzy Sets for Conflict Resolution Modeling and Agent Based Simulation, Int J Bioautomation, 23 (2), 175-184, doi: 10.7546/ijba.2019.23.2.000544
Abstract: Very topical nowadays is the modeling and simulation of conflict situations. The aim is their peaceful prevention and conflict resolution. Different mathematical approaches are used. One of them is the application of multi-agent systems. The multiagent system consists of software agents, which are autonomous subjects working together. In our application the agents represents police officers and civilians in case of protest. In this work we propose application of intuitionistic fuzzy sets for representation of the movement and interaction of the agents. The intuitionistic fuzzy sets are extension of the fuzzy sets including level of uncertainty. Thus the model becomes more realistic. The conflict situation can cause disturbances and casualties. Crowd simulation is very difficult and important research topic.

Keywords: Multiagent system, Conflict resolution, Intuitionistic fuzzy set
Manually Defined Continuous Positive Airway Pressure versus Mathematically Calculated for Obstructive Sleep Apnea185-192
Krassimir Rankov, Nikolay Zaekov, Milena Nikolova
doi: 10.7546/ijba.2019.23.2.000523
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Krassimir Rankov, Nikolay Zaekov, Milena Nikolova (2019) Manually Defined Continuous Positive Airway Pressure versus Mathematically Calculated for Obstructive Sleep Apnea, Int J Bioautomation, 23 (2), 185-192, doi: 10.7546/ijba.2019.23.2.000523
Abstract: The determination of therapeutic pressure in patients with Obstructive sleep apnea (OSA) is crucial. Manual adjustment of Continuous positive airway pressure (CPAP) under polysomnography (PSG) is considered the better practice. Recently, different formulas were presented for predicting CPAP using body mass index (BMI), neck circumference (NC) and apnea/hypopnea index (AHI). The aim of the study was to assess the correlation between the values of pressure calculated by two formulas as well as manual obtained pressure values. Forty patients (33 male, 7 female) with suspected OSA were examined by PSG. Manual titration was applied using standard protocol. For predicting CPAP were used two equations hereinafter referred to as Eq. (1) and Eq. (2). For men the determined pressure was higher when using the Eq. (1) whereas with the Eq. (2) the pressure was lower than predicted. For women the differences were larger. The pressures calculated with the Eq. (1) and the Eq. (2) for both genders were lower and higher, respectively, than those experimentally obtained. From a practical point of view, when it is not possible to determine pressure experimentally, the Eq. (2) should be preferred because higher pressure prescription is better for OSA therapy.

Keywords: Obstructive sleep apnea, Continuous positive airway pressure, Titration, Prediction
Extraction, Separation and Purification of Acidic Polysaccharide from Morchella esculenta by High Voltage Pulsed Electric Field193-202
Chao Liu
doi: 10.7546/ijba.2019.23.2.000678
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Chao Liu (2019) Extraction, Separation and Purification of Acidic Polysaccharide from Morchella esculenta by High Voltage Pulsed Electric Field, Int J Bioautomation, 23 (2), 193-202, doi: 10.7546/ijba.2019.23.2.000678
Abstract: The intracellular acidic polysaccharide from Morchella esculenta mycelium produced by submerged fermentation is extracted and separated. In the process of extracting the polysaccharide by the high voltage pulsed electric field (HVPEF), heat is not generated and the structure of the polysaccharide is not destroyed. The response surface method is used to investigate the electric field intensity, the pulse number and the liquid-to-material ratio. The optimum extraction process of the acidic polysaccharide is obtained as follows: the electric field intensity is 18 kV/cm, the pulse number is 7 and the liquid-to-material ratio is 27 mL/g. At this time, the polysaccharide yield reaches a maximum value of 56.03 µg/mL. The crude polysaccharide is separated and purified by using DEAE-52 cellulose ion exchange column and Sephadex G-100 to obtain an acidic polysaccharide F1 with high purity. The molecular weight is 1.9895x105 Da. Its functional and structural characteristics need to be further studied.

Keywords: Morchella esculenta, Intracellular polysaccharide, High voltage pulsed electric field, Extraction, Separation and purification
Lysing Agents for Characteristic Polluting Microorganisms in Jet Fuels203-214
Yun Xiong, Xinfeng Sun, Peng Zhu, Mingming Niu, Peng Su
doi: 10.7546/ijba.2019.23.2.000679
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Yun Xiong, Xinfeng Sun, Peng Zhu, Mingming Niu, Peng Su (2019) Lysing Agents for Characteristic Polluting Microorganisms in Jet Fuels, Int J Bioautomation, 23 (2), 203-214, doi: 10.7546/ijba.2019.23.2.000679
Abstract: The adenosine triphosphate (ATP) bioluminescence assay is a feasible way to quantify the characteristic polluting microorganisms of the jet fuels. The effect of this method hinges on the release of ATP through the effective lysis of microorganisms. To achieve a good microbial lysis effect, this paper explores the fungi lysis effects of two quaternary ammonium salts, benzyldodecyldimethylammonium bromide (BAB) and benzalkonium chloride (BAC), and discusses the impacts of the two cationic surfactants on luciferase activity. The results show that BAB was more effective than BAC in the lysis of the characteristic polluting fungi, putting the optimal BAB concentration at 0.05%; traditional lysing agents like cetyl trimethyl ammonium bromide (CTAB) and trichloroacetic acid (TCA) had poor effects on fungi lysis; 0.025% Hibitine and 0.05% BAB exerted a synergistic effect on the lysis of characteristic polluting fungi, and were identified as the preliminary components of the lysing agent for the characteristic polluting microorganisms of jet fuels; the optimized luciferase-luciferin reaction system effectively mitigated the suppression effect of the lysis agent on enzymatic activity, and the ATP standard curves with or without lysing agent had no significant difference (p = 0.9768 > 0.05). The optimized luciferase-luciferin reaction system, coupled with the mixture of BAB and Hibitine, outshines the traditional plate culture method and HY-LiTE JET A1 Fuel Test in detection efficiency and cost.

Keywords: Jet fuels, Microbial contamination, Adenosine triphosphate, Adenosine triphosphate bioluminescence assay, Luciferase
Estimation of Substrate and Biomass Concentrations in a Chemostat using an Extended Kalman Filter215-232
Oussama Hadj-Abdelkader, Amine Hadj-Abdelkader
doi: 10.7546/ijba.2019.23.2.000551
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Oussama Hadj-Abdelkader, Amine Hadj-Abdelkader (2019) Estimation of Substrate and Biomass Concentrations in a Chemostat using an Extended Kalman Filter, Int J Bioautomation, 23 (2), 215-232, doi: 10.7546/ijba.2019.23.2.000551
Abstract: This paper presents the estimation of substrate and biomass concentrations inside a Chemostat used for waste-water treatment. These concentrations represent the state variables of the process model. Most research in this field used only deterministic models, not accounting for uncertainties and noises on the states and on the output. Hence, the estimation of these concentrations may not be sufficiently accurate. For a more realistic description, we used here a stochastic formulation. Unlike the other research works, we used a stochastic differential equations (SDE) model which provides a better representation of the system in his natural processing scale. This model also includes the aleatory effects in the process which had been discarded in the other works. We then deal with the state estimation problem using an Extended Kalman filter, which proceeds with a linearization of the model around a deterministic trajectory. The classical prediction and update steps of the filter are then carried-out and led to good results. Notice that the system in study has some interesting properties such as discrete-time observations, high noise intensities and slow-time evolution. Results are presented, discussed and compared with the related state-of-the-art researches.

Keywords: Extended Kalman filter, State estimation, Chemostat, Waste-water treatment, Stochastic differential equations
Gene Sequence Input Formatting and MapReduce Computing233-246
Xiaolong Feng, Jing Gao
doi: 10.7546/ijba.2019.23.2.000675
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Xiaolong Feng, Jing Gao (2019) Gene Sequence Input Formatting and MapReduce Computing, Int J Bioautomation, 23 (2), 233-246, doi: 10.7546/ijba.2019.23.2.000675
Abstract: Considering the limitations of the application programming interface (API) of Hadoop in gene sequence computing, this paper puts forward an input formatting method that reads the format of gene sequence as key-value pairs in the form of records. This method relies on the rewriting of Hadoop source code, which is an extension of platform function, and eliminates the need to preprocess data with other tools. On this basis, a MapReduce computing model was designed for distributed parallel computing of gene sequence alignment tasks. Experimental verification shows that the proposed method can read many kinds of gene sequence files effectively on Hadoop, and the proposed model can realize distributed parallel computing of gene sequence alignment. The research findings provide a valuable reference for bioinformatics computing tasks on Hadoop platform.

Keywords: Input formatting, MapReduce, Gene sequence, Sequence alignment, Short reads mapping

Sponsored by National Science Fund of Bulgaria, Grant No KP-06-NP/9/2018

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