Bioautomation

Volume 20, Issue 3
Bioinformatics
In silico Repositioning of Alendronate and Cytarabine Drugs to Cure Mutations of FPPS, HAP, PTPRS, PTPRE, PTN4, GGPPS Gene and Mutant DNA, DPOLB, TOP2a, DPOLA, DNMT, RNA, TYSY, RIR Genes	317-328
Anum Munir, Shumaila Azam, Sahar Fazal, Zanib Khan, Azhar Mehmood [ +/- abstract ][ full text ]
Osteoporosis occurs because of the Calcitonin-Related Polypeptide Alpha (CALCA) gene. At present, Caltrate600, Boniva and Alendronate are viewed as dynamic drugs to cure osteoporosis. Chronic lymphocytic leukemia occurs because of the ABL1 proto oncogene. Currently, Rituximab, Fludarabine and Cytarabine are utilized as monoclonal antibodies against this ailment. Drug repositioning is a new rising field of reusing previous drugs, safeguarding retired drugs and developing licenses to make lives easy. The main objective of this research was repositioning of Alendronate and Cytarabine in order to use them in other diseases, too. Interactions of each of these drugs with many off-target proteins were identified. Alendronate presented strong interactions with FPPS, Hydroxylapatite, PTPRS, PTPRE, PTN4 and GGPPS. Cytarabine demonstrated strong interactions with DNA and DPOLB. After screening a great number of drugs which are accustomed to cure mutations of those off-target genes and proteins, their ill effects were compared, and it is suggested that Alendronate and Cytarabine have less side effects than different other drugs utilized for the same interacting targets. Both Alendronate and Cytarabine can be repositioned to cure well known carcinomas and different diseases.
Secondary Structural Models (16S rRNA) of Polyhydroxyalkanoates Producing Bacillus Species Isolated from Different Rhizospheric Soil: Phylogenetics and Chemical Analysis	329-338
Swati Mohapatra, Surya Narayan Rath, Sukanta Kumar Pradhan, Devi Prasad Samantaray, Chandi Charan Rath [ +/- abstract ][ full text ]
Polyhydroxyalkanoates (PHAs) producing bacterial isolates are gaining more importance over the world due to the synthesis of a biodegradable polymer which is extremely desirable to substitute synthetic plastics. PHAs are produced by various microorganisms under certain stress conditions. In this study, sixteen bacterial isolates characterized previously by partial 16S rRNA gene sequencing (NCBI Accession No. KF626466 to KF626481) were again stained by Nile red after three years of preservation in order to confirm their ability to accumulate PHAs. Also, phylogenetic analysis carried out in the present investigation evidenced that the bacterial species belonging to genus Bacillus are the dominant flora of the rhizospheric region, with a potentiality of biodegradable polymer (PHAs) production. Again, RNA secondary structure prediction hypothesized that there is no direct correlation between RNA folding pattern stability with a rate of PHAs production among the selected isolates of genus Bacillus.
Fingerprint Image Segmentation Algorithm Based on Contourlet Transform Technology	339-350
Guanghua Zhang, Zhongyang Xiong, Shuyin Xia, Yueguo Luo, Changyuan Xing [ +/- abstract ][ full text ]
This paper briefly introduces two classic algorithms for fingerprint image processing, which include the soft threshold denoise algorithm of wavelet domain based on wavelet domain and the fingerprint image enhancement algorithm based on Gabor function. Contourlet transform has good texture sensitivity and can be used for the segmentation enforcement of the fingerprint image. The method proposed in this paper has attained the final fingerprint segmentation image through utilizing a modified denoising for a high-frequency coefficient after Contourlet decomposition, highlighting the fingerprint ridge line through modulus maxima detection and finally connecting the broken fingerprint line using a value filter in direction. It can attain richer direction information than the method based on wavelet transform and Gabor function and can make the positioning of detailed features more accurate. However, its ridge should be more coherent. Experiments have shown that this algorithm is obviously superior in fingerprint features detection.
Cloning and Sequence Analysis of Gene Encoding psbZ from Silybum marianum (L.) Gaertn	351-358
Yousef Mohammadi, Ahmad Razban Haghighi, Shiva Gheytaranpour Sehrigh [ +/- abstract ][ full text ]
Photosystem II is known as the core of photosynthesis and among of the photosystem II protein complex, PsbZ protein is very important because of its role in connection PSII and LHCII. For identifying and sequencing of the psbZ gene in Silybum marianum plant, seeds were prepared from botanical garden in Tabriz, Iran. DNA was extracted by CTAB method and by using the PCR amplification the fragment length was estimated to be 705 bp. The amplified fragment was cloned in pGEM-T vector and E. coli transformation was carried out. The plasmid was extracted and the sequence was recorded at NCBI with accession number of GQ225868. BLAST of psbZ, glycine tRNA and psbZ-tRNA GLY intergenic spacer showed that each region is highly conserved among species. BLAST of predicted PsbZ protein also represents a severe conservation among species. Because of the importance of PsbZ protein in photosynthesis, it is necessary to create targeted mutations to determine the active sites of proteins.
Biomedical systems
Research on the Application of GSR and ECG in the Usability Testing of an Aggregation Reading App	359-372
Sha Liu, Bao-Yue Zhang, Cong Liu [ +/- abstract ][ full text ]
Usability testing is a very important step in improving App design and development. The traditional usability testing methods are based on users'expressions and behaviors, which hardly show users' emotional experience and cognitive load in real time. The introduction of an electrophysiological technique can make up for the deficiency of the traditional usability testing methods. In this study, a usability testing was carried out with the old and the new version of an App software. The behavior and the subjective evaluation of the participants were recorded, and their GSR and ECG signals were collected. Then, 14 physiological characteristics, such as GSR-Mean, LF, HF, LF/HF, etc., were extracted from the GSR and ECG signals. These characteristics were analyzed, and a significance test of difference of the two versions was made. This research indicated that there is a certain application value of GSR and HRV in usability testing and evaluation of an App product. But the meanings of the physiological characteristics must be explained in combination with the behavior and subjective evaluation of users. The result can prove that physiological characteristics have obvious advantages in real-time monitoring users' emotional changes, which can be helpful to find the usability problems of the product.
Design and Evaluation of Swing Phase Controllers for Single-axis Knee	373-388
Solomon Seid, S. Sujatha, Sujatha Chandramohan [ +/- abstract ][ full text ]
A prosthetic swing-phase control mechanism simulates the action of thigh musculature to aid in increased gait function. In this work, a hydraulic damper and a magnetorheological (MR) damper are designed as controllers with an objective of evaluating their performance in controlling swing-phase damping in an above-knee prosthesis. Parametric models are utilized to represent dynamic properties of the dampers. Based on the models, control parameters that govern damping force and displacement of the dampers are identified. Parameters of the dampers are determined through optimization that minimizes the error between the prosthesis knee angle trajectories and a desired knee angle trajectory for normal level ground walking from experimental data. Experimental data of thigh and hip motions are introduced as inputs into a dynamic system to determine sets of control parameters. Furthermore, input thigh motion is also deviated to evaluate robustness of the controllers in real application. Comparison of the desired knee angle trajectory with those of the knee angle trajectories obtained from control parameters is done with respect to maximum achievable knee flexion angle, duration of swing phase, shank velocity at the end of swing phase and mean angle difference. Evaluation results of the dampers show a better competence of MR damper over hydraulic damper.
Changes in EMG Activities of Upper Arm Muscles and in Shoulder Joint Angles in Post-stroke Patients	389-408
Rositsa Raikova, Silvija Angelova, Simeon Ribagin [ +/- abstract ][ full text ]
The aim of the paper is to compare the electromyographic signals (EMGs) and the joint angles of the affected upper limb muscles of stroke survivors to those of their non-affected limb as well as to those of the dominant and the non-dominant limbs of healthy volunteers. Twenty five volunteers, ten post-stroke survivors and fifteen healthy subjects as control group, participated in the experiments. EMGs of muscles of the upper limbs and two angles in the shoulder joint were registered and processed during three static and two dynamic tasks. The results showed a big variability of all investigated parameters (mean and median frequencies, ranges of motions, maximal normalized EMGs) both for the patients and for the healthy subjects, for right and for left hand. This makes difficult a deduction of definitive conclusions about the changes in motor control of the upper limbs due to stroke. Moreover, natural differences in motor control exist for dominant and non-dominant limb. On the whole, the power-frequency analysis and the relevant statistical analysis indicated that the muscles of the affected limb had lower median frequencies than those of the healthy limb. Examination of full elbow flexions in the sagittal plane showed that the range of the motion in the shoulder joint of both limbs of the patients increased when compared to the healthy subjects and that this increase was larger for the affected limb. The post-stroke survivors used more of their muscle power although no increased co-contraction was observed.
Specific Antitumor Effect of the Combined Action of Algal Heteropolysaccharide and Electroporation	407-416
Lyudmila Kabaivanova, Juliana Ivanova, Viktoria Pehlivanova, Biliana Nikolova [ +/- abstract ][ full text ]
Marine organisms are potentially prolific sources of highly bioactive secondary metabolites that might represent useful leads in the development of new pharmaceutical agents. In this study the biological effect of the freeze-dried heteropolysaccharide, isolated and purified from the red microalga Rhodella reticulata strain using electroporation was evaluated. Two different types of cells - tumor and non-tumor were treated with the heteropolysaccharide alone or together with the application of electroporation. The effect of the treatment was evaluated in parallel: with proliferation test for estimating cell viability and with immunofluorescent cytoskeleton staining to establish changes in morphology. Evidence for cell line specific viability reduction (70% from the control in case of cancer cell line treatment and only 30% in non-tumor cells) in a dose dependent manner was presented. These findings will arouse further interest in heteropolysaccharide as a new anticancer drug suitable for clinical trials.
Application of BP Neural Network Algorithm in Biomedical Diagnostic Analysis	417-426
Junbing Li [ +/- abstract ][ full text ]
The research on the application of a neural network in medical diagnosis includes two aspects: theoretical research on a neural network algorithm and research on its application in medical diagnosis. These two closely related research contents are complementary to each other, the former provides the theoretical basis for the latter and the latter takes the former as the basis and provides practical guidance to the former at the same time. The Back Propagation (BP) has the most extensive application in medical diagnosis, but the BP neural network learning algorithm has the shortcomings of slow convergence and the unit quantity being difficult to determine at the hidden layer in the application of medical diagnosis. This paper has made a detailed analysis of and exploration into these problems and proposed targeted solutions and applied them to specific medical diagnosis cases.