Volume 16, number 1
Editorial
Editorial Board News
Soft Matter Physics and the Physics of Living Matter
Highlights of Medical Physics in Bulgaria
New books
Forthcoming Events
Еuropean Medical Physics and Engineering Conference 2012
Bioinformatics
A Computational Approach to Identifying miRNAs Implicated in Drosophila Neurodevelopment1-12
Momchil Nenov, Svetoslav Nikolov, Ginka Genova
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miRNAs are known to regulate many aspects of neurodevelopment. They participate at different stages of this process from early embryogenesis to adult stage. Their various and specific functions begin to be unraveled in many model systems. Important part of neurogenesis, which generates mature neurons from progenitor cells, is the nerve growth and the formation of synapses. As they underlie the neuronal network formation, perturbation of their proper regulation causes different neuro-developmental diseases in human. In our study we used the model organism Drosophila to identify by a computational approach miRNAs, targeting genes, which control axonal growth and synaptogenesis. We screened preselected groups of genes, known to regulate these processes and identified several micro-RNAs as likely candidates for their expression control. We found five miRNAs, which have been reported earlier to associate with dFMRP (Drosophila Fragile X mental Retardation Protein 1) and which target only a small number of specific genes. We also identified several new miRNA candidates likely implicated in synaptogenesis.
Integrated Features by Administering the Support Vector Machine (SVM) of Translational Initiations Sites in Alternative Polymorphic Contex13-22
Nurul Arneida Husin, Nanna Suryana Herman, Burairah Hussin
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Many algorithms and methods have been proposed for classification problems in bioinformatics. In this study, the discriminative approach in particular support vector machines (SVM) is employed to recognize the studied TIS patterns. The applied discriminative approach is used to learn about some discriminant functions of samples that have been labelled as positive or negative. After learning, the discriminant functions are employed to decide whether a new sample is true or false. In this study, support vector machines (SVM) is employed to recognize the patterns for studied translational initiation sites in alternative weak context. The method has been optimized with the best parameters selected; c=100, E=10-6 and ex=2 for non linear kernel function. Results show that with top 5 features and non linear kernel, the best prediction accuracy achieved is 95.8%. J48 algorithm is applied to compare with SVM with top 15 features and the results show a good prediction accuracy of 95.8%. This indicates that the top 5 features selected by the IGR method and that are performed by SVM are sufficient to use in the prediction of TIS in weak contexts.
Bioprocess systems
Optimization of E. coli Cultivation Model Parameters Using Firefly Algorithm23-32
Olympia Roeva
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In this paper, a novel meta-heuristics algorithm, namely the Firefly Algorithm (FA), is adapted and applied for a model parameter identification of an E. coli fed-batch cultivation process. A system of ordinary nonlinear differential equations is used to model the biomass growth and substrate utilization. Parameter optimization is performed using real experimental data set from an E. coli MC4110 fed-batch cultivation process. The FA adjustments are done based on several pre-tests according to the optimization problem considered here. The simulation results indicate that the applied algorithm is effective and efficient. As a result, a model with high degree of accuracy is obtained applying the FA.
Biomedical systems
Study of Biochemical Changes and Elevated Levels of Enzymes in Salmonella typhi Infected Patients in Pakistani Population33-42
Amen Shamim, Ayesha Shamim, Bilal Hussain
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Typhoid fever causes significant biochemical changes and hepatic complications. As many studies have indicated several biochemical parameters that are involved in developing the risk of typhoid fever. The current study was designed to evaluate these risk factors in general Pakistani population. Serum biochemistry and liver enzymes were studied to investigate the relationship of these risk factors to Typhoid fever. Total 100 subjects were studied, 50 healthy individuals and 50 typhoid patients. Blood samples were collected from Allied and National Hospital, Faisalabad, Pakistan. In this study, Nested PCR was used to test the samples. Elevated level of ALT (P<0.0001) and AST (P<0.0001) were observed in typhoid patients. Typhoid patients had significantly higher concentrations of Triglyceride (P=0.0044), Globulin (P=0.0004) and Total protein (P=0.0978) while LDL (P=0.0197), Albumin (P<0.0001), Glucose (P=0.0006), HDL-cholesterol (P<0.0001) and Cholesterol (P=0.04) were significantly lower than those of healthy individuals. This study appears to be ample evidence based on the physiological and biochemical parameters in typhoid patients to explain influence of typhoid morbidity. Extensive research in this field would enable us to make modern drugs to treat typhoid fever patients.
Recent Australian Advances in the Radiotherapy of Skin Cancer43-52
Gerald B. Fogarty
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This paper is an expository report on some recent and current research on clinical problems in the control of skin cancer in Australia, which has a high prevalence and an increasing incidence of this disease.
Biomedical Physics
Optical Biopsy of Human Skin - A Tool for Cutaneous Tumours' Diagnosis53-72
Ekaterina Borisova, Petya Pavlova, Elmira Pavlova, Petranka Troyanova, Latchezar Avramov
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A short review of the recent status of optical biopsy of human skin as a tool for cutaneous tumour detection will be presented. Basically laser- and light- induced fluorescence and diffuse reflectance techniques incorporated in so called "optical biopsy" technique used for skin tissue analysis will be described and some original results and findings from our own investigations will be commented as well. Fluorescence spectroscopy gives information mainly about changes in the biochemical content, and diffuse reflectance about morphological changes and pigments' concentrations in the human skin. Both techniques are applied separately and as a common tool for early skin cancer diagnosis, give high accuracy and objective diagnosis, applicable into the clinical practice. Skin optical biopsy diagnostic clinical trial is currently under implementation in the frames of University Hospital "Tsaritsa Yoanna - ISUL" and with broadening of the database with fluorescence and reflectance spectra of major skin benign and malignant pathologies we expect to receive objective tool for detection and evaluation of skin lesion type, which could become a basis for reliable system for skin cancer detection. Optical biopsy system is developed in the frames of Institute of Electronics, Bulgarian Academy of Sciences, and consists of autofluorescence and diffuse reflectance channels for early skin tumour detection. Fibro-optical probe allows receiving of noninvasive spectral information for the tissues' condition, which allows making highly-sensitive diagnosis of tissues in real time.

Sponsored by National Science Fund of Bulgaria, Grant No DNP 03/32

© 2012, BAS, Institute of Biophysics and Biomedical Engineering