World Academy of Science, Engineering and Technology

Authors: R. Haddad, K. Morris, V. Buchanan-Wollaston

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Biochemical and molecular analysis of some antioxidant enzyme genes revealed different level of gene expression on oilseed (Brassica napus). For molecular and biochemical analysis, leaf tissues were harvested from plants at eight different developmental stages, from young to senescence. The levels of total protein and chlorophyll were increased during maturity stages of plant, while these were decreased during the last stages of plant growth. Structural analysis (nucleotide and deduced amino acid sequence, and phylogenic tree) of a complementary DNA revealed a high level of similarity for a family of Catalase genes. The expression of the gene encoded by different Catalase isoforms was assessed during different plant growth phase. No significant difference between samples was observed, when Catalase activity was statistically analyzed at different developmental stages. EST analysis exhibited different transcripts levels for a number of other relevant antioxidant genes (different isoforms of SOD and glutathione). The high level of transcription of these genes at senescence stages was indicated that these genes are senescenceinduced genes.

Keywords: Biochemical analysis, Oilseed, Expression pattern, Growth phases

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Authors: Duane Barker, John Holliday

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In a 10-week (May – August, 2008) Phase I trial, 840, 1+ rainbow trout, Oncorhynchus mykiss, received a commercial oral immunomodulator, Fin Immune™, at four different dosages (0, 10, 20 and 30 mg g-1) to evaluate immune response and growth. The overall objective of was to determine an optimal dosage of this product for rainbow trout that provides enhanced immunity with maximal growth and health. Biweekly blood samples were taken from 10 randomly selected fish in each tank (30 samples per treatment) to evaluate the duration of enhanced immunity conferred by Fin-Immune™. The immunological assessment included serum white blood cell (lymphocyte, neutrophil) densities and blood hematocrit (packed cell volume %). Of these three variables, only lymphocyte density increased significantly among trout fed Fin- Immune™ at 20 and 30 mg g-1 which peaked at week 6. At week 7, all trout were switched to regular feed (lacking Fin-Immune™) and by week 10, lymphocyte levels decreased among all levels but were still greater than at week 0. There was growth impairment at the highest dose of Fin-Immune™ tested (30 mg g-1) which can be associated with a physiological compensatory mechanism due to a dose-specific threshold level. Thus, our main objective of this Phase I study was achieved, the 20 mg g-1 dose of Fin-Immune™ should be the most efficacious (of those we tested) to use for a Phase II disease challenge trial.

Keywords: Blood Lymphocyte, Neutrophil Response of Cultured Rainbow Trout, Oncorhynchus mykiss, Oral Immunomodulator – 'Fin-ImmuneTM'.

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Authors: Choeng-Ryul Choi, Chang-Nyung Kim, Tae-Hyub Hong

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A numerical method is developed for simulating the motion of particles with arbitrary shapes in an effectively infinite or bounded viscous flow. The particle translational and angular motions are numerically investigated using a fluid-structure interaction (FSI) method based on the Arbitrary-Lagrangian-Eulerian (ALE) approach and the dynamic mesh method (smoothing and remeshing) in FLUENT ( ANSYS Inc., USA). Also, the effects of arbitrary shapes on the dynamics are studied using the FSI method which could be applied to the motions and deformations of a single blood cell and multiple blood cells, and the primary thrombogenesis caused by platelet aggregation. It is expected that, combined with a sophisticated large-scale computational technique, the simulation method will be useful for understanding the overall properties of blood flow from blood cellular level (microscopic) to the resulting rheological properties of blood as a mass (macroscopic).

Keywords: Blood Flow, Fluid-Structure Interaction (FSI), Micro-Channels, Arbitrary Shapes, Red Blood Cells (RBCs)

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Authors: Morteza Moazami-Goudarzi, Ali Taheri, Mohammad Pooyan, Reza Mahboobi

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In this paper we are to find the optimum multiwavelet for compression of electrocardiogram (ECG) signals and then, selecting it for using with SPIHT codec. At present, it is not well known which multiwavelet is the best choice for optimum compression of ECG. In this work, we examine different multiwavelets on 24 sets of ECG data with entirely different characteristics, selected from MIT-BIH database. For assessing the functionality of the different multiwavelets in compressing ECG signals, in addition to known factors such as Compression Ratio (CR), Percent Root Difference (PRD), Distortion (D), Root Mean Square Error (RMSE) in compression literature, we also employed the Cross Correlation (CC) criterion for studying the morphological relations between the reconstructed and the original ECG signal and Signal to reconstruction Noise Ratio (SNR). The simulation results show that the Cardinal Balanced Multiwavelet (cardbal2) by the means of identity (Id) prefiltering method to be the best effective transformation. After finding the most efficient multiwavelet, we apply SPIHT coding algorithm on the transformed signal by this multiwavelet.

Keywords: ECG compression, Prefiltering, Cardinal Balanced Multiwavelet.

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Authors: Parvinder S. Sandhu, Porush Bassi, Amanpreet Singh Brar

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Various models have been derived by studying large number of completed software projects from various organizations and applications to explore how project sizes mapped into project effort. But, still there is a need to prediction accuracy of the models. As Neuro-fuzzy based system is able to approximate the non-linear function with more precision. So, Neuro-Fuzzy system is used as a soft computing approach to generate model by formulating the relationship based on its training. In this paper, Neuro-Fuzzy technique is used for software estimation modeling of on NASA software project data and performance of the developed models are compared with the Halstead, Walston-Felix, Bailey-Basili and Doty Models mentioned in the literature.

Keywords: Effort Estimation, Neural-Fuzzy Model, Halstead Model, Walston-Felix Model, Bailey-Basili Model, Doty Model.

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Authors: Desmond B. Keenan

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The clinical usefulness of heart rate variability is limited to the range of Holter monitoring software available. These software algorithms require a normal sinus rhythm to accurately acquire heart rate variability (HRV) measures in the frequency domain. Premature ventricular contractions (PVC) or more commonly referred to as ectopic beats, frequent in heart failure, hinder this analysis and introduce ambiguity. This investigation demonstrates an algorithm to automatically detect ectopic beats by analyzing discrete wavelet transform coefficients. Two techniques for filtering and replacing the ectopic beats from the RR signal are compared. One technique applies wavelet hard thresholding techniques and another applies linear interpolation to replace ectopic cycles. The results demonstrate through simulation, and signals acquired from a 24hr ambulatory recorder, that these techniques can accurately detect PVC-s and remove the noise and leakage effects produced by ectopic cycles retaining smooth spectra with the minimum of error.

Keywords: Heart rate variability, vagal tone, sympathetic, parasympathetic, wavelets, ectopic beats, spectral analysis.

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Authors: Alpha Agape Gopalai, Darwin Gouwanda, S.M.N. Arosha Senanayake

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This paper explores the opportunity of using tri-axial wireless accelerometers for supervised monitoring of sports movements. A motion analysis system for the upper extremities of lawn bowlers in particular is developed. Accelerometers are placed on parts of human body such as the chest to represent the shoulder movements, the back to capture the trunk motion, back of the hand, the wrist and one above the elbow, to capture arm movements. These sensors placement are carefully designed in order to avoid restricting bowler-s movements. Data is acquired from these sensors in soft-real time using virtual instrumentation; the acquired data is then conditioned and converted into required parameters for motion regeneration. A user interface was also created to facilitate in the acquisition of data, and broadcasting of commands to the wireless accelerometers. All motion regeneration in this paper deals with the motion of the human body segment in the X and Y direction, looking into the motion of the anterior/ posterior and lateral directions respectively.

Keywords: Motion Regeneration, Virtual Instrumentation, Wireless Accelerometers

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Authors: D. Gouwanda, S. M. N. A. Senanayake

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This paper presents a real time force sensing instrument that is designed for human gait analysis purposes. It is capable of recording and monitoring ground reaction forces exerted by human foot during various activities such as walking, running and jumping in real time. In overall, force sensing mat mainly consists of three elements: the force sensing mat, signal conditioning circuit and data acquisition device. Force sensing mat is the mat that contains an array of force sensing elements. To control and process the incoming signal from the force sensing mat, Force-Logger and Force-Reloader are developed using National Instrument Labview. This paper describes the architecture of the force sensing mat, signal conditioning circuit and the real time streaming of the incoming data from the force sensing mat. Additionally, a preliminary experiment dataset is presented in this paper.

Keywords: Force platform, force sensing resistor, human gait analysis.

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Authors: Antonino Greco, Nadia Mammone, Francesco Carlo Morabito, Mario Versaci

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The goal of this work is to improve the efficiency and the reliability of the automatic artifact rejection, in particular from the Electroencephalographic (EEG) recordings. Artifact rejection is a key topic in signal processing. The artifacts are unwelcome signals that may occur during the signal acquisition and that may alter the analysis of the signals themselves. A technique for the automatic artifact rejection, based on the Independent Component Analysis (ICA) for the artifact extraction and on some high order statistics such as kurtosis and Shannon-s entropy, was proposed some years ago in literature. In this paper we enhance this technique introducing the Renyi-s entropy. The performance of our method was tested exploiting the Independent Component scalp maps and it was compared to the performance of the method in literature and it showed to outperform it.

Keywords: Artifact, EEG, Renyi's entropy, independent component analysis, kurtosis.

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Authors: Ime R. Udotong, Ofonime U. M. John, Justina I. R. Udotong

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The microbiological and physicochemical characteristics of wetland soils in Eket Local Government Area were studied between May 2001 and June 2003. Total heterotrophic bacterial counts (THBC), total fungal counts (TFC), and total actinomycetes counts (TAC) were determined from soil samples taken from four locations at two depths in the wet and dry seasons. Microbial isolates were characterized and identified. Particle size and chemical parameters were also determined using standard methods. THBC ranged from 5.2 (+0.17) x106 to 1.7 (+0.18) x107 cfu/g and from 2.4 (+0.02) x106 to 1.4 (+0.04) x107cfu/g in the wet and dry seasons, respectively. TFC ranged from 1.8 (+0.03) x106 to 6.6 (+ 0.18) x106 cfu/g and from 1.0 (+0.04) x106 to 4.2 (+ 0.01) x106 cfu/g in the wet and dry seasons, respectively .TAC ranged from 1.2 (+0.53) x106 to 6.0 (+0.05) x106 cfu/g and from 0.6 (+0.01) x106 to 3.2 (+ 0.12) x106 cfu/g in the wet and dry season, respectively. Acinetobacter, Alcaligenes, Arthrobacter, Bacillus, Beijerinckja, Enterobacter, Micrococcus, Flavobacterium, Serratia, Enterococcus, and Pseudomonas species were predominant bacteria while Aspergillus, Fusarium, Mucor, Penicillium, and Rhizopus were the dominant fungal genera isolated. Streptomyces and Norcadia were the actinomycetes genera isolated. The particle size analysis showed high sand fraction but low silt and clay. The pH and % organic matter were generally acidic and low, respectively at all locations. Calcium dominated the exchangeable bases with low electrical conductivity and micronutrients. These results provide the baseline data of Eket wetland soils for its management for sustainable agriculture.

Keywords: Wetland soils, Microbial counts, physicochemicalcharacteristics, Sustainable agriculture.

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Authors: Lukas Horny, Rudolf Zitny, Hynek Chlup, Tomas Adamek, Michal Sara

Abstract:

An inflation–extension test with human vena cava inferior was performed with the aim to fit a material model. The vein was modeled as a thick–walled tube loaded by internal pressure and axial force. The material was assumed to be an incompressible hyperelastic fiber reinforced continuum. Fibers are supposed to be arranged in two families of anti–symmetric helices. Considered anisotropy corresponds to local orthotropy. Used strain energy density function was based on a concept of limiting strain extensibility. The pressurization was comprised by four pre–cycles under physiological venous loading (0 – 4kPa) and four cycles under nonphysiological loading (0 – 21kPa). Each overloading cycle was performed with different value of axial weight. Overloading data were used in regression analysis to fit material model. Considered model did not fit experimental data so good. Especially predictions of axial force failed. It was hypothesized that due to nonphysiological values of loading pressure and different values of axial weight the material was not preconditioned enough and some damage occurred inside the wall. A limiting fiber extensibility parameter Jm was assumed to be in relation to supposed damage. Each of overloading cycles was fitted separately with different values of Jm. Other parameters were held the same. This approach turned out to be successful. Variable value of Jm can describe changes in the axial force – axial stretch response and satisfy pressure – radius dependence simultaneously.

Keywords: Constitutive model, damage, fiber reinforcedcomposite, limiting fiber extensibility, preconditioning, vena cavainferior.

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Authors: Abdellali Kelil, Shengrui Wang, Ryszard Brzezinski

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The literature reports a large number of approaches for measuring the similarity between protein sequences. Most of these approaches estimate this similarity using alignment-based techniques that do not necessarily yield biologically plausible results, for two reasons. First, for the case of non-alignable (i.e., not yet definitively aligned and biologically approved) sequences such as multi-domain, circular permutation and tandem repeat protein sequences, alignment-based approaches do not succeed in producing biologically plausible results. This is due to the nature of the alignment, which is based on the matching of subsequences in equivalent positions, while non-alignable proteins often have similar and conserved domains in non-equivalent positions. Second, the alignment-based approaches lead to similarity measures that depend heavily on the parameters set by the user for the alignment (e.g., gap penalties and substitution matrices). For easily alignable protein sequences, it's possible to supply a suitable combination of input parameters that allows such an approach to yield biologically plausible results. However, for difficult-to-align protein sequences, supplying different combinations of input parameters yields different results. Such variable results create ambiguities and complicate the similarity measurement task. To overcome these drawbacks, this paper describes a novel and effective approach for measuring the similarity between protein sequences, called SAF for Substitution and Alignment Free. Without resorting either to the alignment of protein sequences or to substitution relations between amino acids, SAF is able to efficiently detect the significant subsequences that best represent the intrinsic properties of protein sequences, those underlying the chronological dependencies of structural features and biochemical activities of protein sequences. Moreover, by using a new efficient subsequence matching scheme, SAF more efficiently handles protein sequences that contain similar structural features with significant meaning in chronologically non-equivalent positions. To show the effectiveness of SAF, extensive experiments were performed on protein datasets from different databases, and the results were compared with those obtained by several mainstream algorithms.

Keywords: Protein, Similarity, Substitution, Alignment.

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Authors: Carmen Grigoraş, Victor Grigoraş, Daniela Boişteanu

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The standard investigational method for obstructive sleep apnea syndrome (OSAS) diagnosis is polysomnography (PSG), which consists of a simultaneous, usually overnight recording of multiple electro-physiological signals related to sleep and wakefulness. This is an expensive, encumbering and not a readily repeated protocol, and therefore there is need for simpler and easily implemented screening and detection techniques. Identification of apnea/hypopnea events in the screening recordings is the key factor for the diagnosis of OSAS. The analysis of a solely single-lead electrocardiographic (ECG) signal for OSAS diagnosis, which may be done with portable devices, at patient-s home, is the challenge of the last years. A novel artificial neural network (ANN) based approach for feature extraction and automatic identification of respiratory events in ECG signals is presented in this paper. A nonlinear principal component analysis (NLPCA) method was considered for feature extraction and support vector machine for classification/recognition. An alternative representation of the respiratory events by means of Kohonen type neural network is discussed. Our prospective study was based on OSAS patients of the Clinical Hospital of Pneumology from Iaşi, Romania, males and females, as well as on non-OSAS investigated human subjects. Our computed analysis includes a learning phase based on cross signal PSG annotation.

Keywords: Artificial neural networks, feature extraction, obstructive sleep apnea syndrome, pattern recognition, signalprocessing.

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Authors: Jingming Wu, Junqi Yue, Ruikang Hu, Zhaoguang Yang, Lifeng Zhang

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Fecal coliform bacteria are widely used as indicators of sewage contamination in surface water. However, there are some disadvantages in these microbial techniques including time consuming (18-48h) and inability in discriminating between human and animal fecal material sources. Therefore, it is necessary to seek a more specific indicator of human sanitary waste. In this study, the feasibility was investigated to apply caffeine and human pharmaceutical compounds to identify the human-source contamination. The correlation between caffeine and fecal coliform was also explored. Surface water samples were collected from upstream, middle-stream and downstream points respectively, along Rochor Canal, as well as 8 locations of Marina Bay. Results indicate that caffeine is a suitable chemical tracer in Singapore because of its easy detection (in the range of 0.30-2.0 ng/mL), compared with other chemicals monitored. Relative low concentrations of human pharmaceutical compounds (< 0.07 ng/mL) in Rochor Canal and Marina Bay water samples make them hard to be detected and difficult to be chemical tracer. However, their existence can help to validate sewage contamination. In addition, it was discovered the high correlation exists between caffeine concentration and fecal coliform density in the Rochor Canal water samples, demonstrating that caffeine is highly related to the human-source contamination.

Keywords: Caffeine, Human Pharmaceutical Compounds, Chemical Tracer, Sewage Contamination.

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Authors: Hynek Chlup, Lukas Horny, Rudolf Zitny, Svatava Konvickova, Tomas Adamek

Abstract:

Coronary artery bypass grafts (CABG) are widely studied with respect to hemodynamic conditions which play important role in presence of a restenosis. However, papers which concern with constitutive modeling of CABG are lacking in the literature. The purpose of this study is to find a constitutive model for CABG tissue. A sample of the CABG obtained within an autopsy underwent an inflation–extension test. Displacements were recoredered by CCD cameras and subsequently evaluated by digital image correlation. Pressure – radius and axial force – elongation data were used to fit material model. The tissue was modeled as onelayered composite reinforced by two families of helical fibers. The material is assumed to be locally orthotropic, nonlinear, incompressible and hyperelastic. Material parameters are estimated for two strain energy functions (SEF). The first is classical exponential. The second SEF is logarithmic which allows interpretation by means of limiting (finite) strain extensibility. Presented material parameters are estimated by optimization based on radial and axial equilibrium equation in a thick-walled tube. Both material models fit experimental data successfully. The exponential model fits significantly better relationship between axial force and axial strain than logarithmic one.

Keywords: Constitutive model, coronary artery bypass graft, digital image correlation, fiber reinforced composite, inflation test, saphenous vein.

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Authors: Manfred Hartmann, Andreas Graef, Hannes Perko, Christoph Baumgartner, Tilmann Kluge

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In this paper we introduce a novel method for the characterization of synchronziation and coupling effects in multivariate time series that can be used for the analysis of EEG or ECoG signals recorded during epileptic seizures. The method allows to visualize the spatio-temporal evolution of synchronization and coupling effects that are characteristic for epileptic seizures. Similar to other methods proposed for this purpose our method is based on a regression analysis. However, a more general definition of the regression together with an effective channel selection procedure allows to use the method even for time series that are highly correlated, which is commonly the case in EEG/ECoG recordings with large numbers of electrodes. The method was experimentally tested on ECoG recordings of epileptic seizures from patients with temporal lobe epilepsies. A comparision with the results from a independent visual inspection by clinical experts showed an excellent agreement with the patterns obtained with the proposed method.

Keywords: EEG, epilepsy, regression analysis, seizurepropagation.

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Authors: Ali Zifan, Mohammad Hassan Moradi, Sohrab Saberi, Farzad Towhidkhah

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Electrocardiogram (ECG) segmentation is necessary to help reduce the time consuming task of manually annotating ECG-s. Several algorithms have been developed to segment the ECG automatically. We first review several of such methods, and then present a new single lead segmentation method based on Adaptive piecewise constant approximation (APCA) and Piecewise derivative dynamic time warping (PDDTW). The results are tested on the QT database. We compared our results to Laguna-s two lead method. Our proposed approach has a comparable mean error, but yields a slightly higher standard deviation than Laguna-s method.

Keywords: Adaptive Piecewise Constant Approximation, Dynamic programming, ECG segmentation, Piecewise DerivativeDynamic Time Warping.

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Authors: Ramaswamy Palaniappan

Abstract:

This paper reports a new approach on identifying the individuality of persons by using parametric classification of multiple mental thoughts. In the approach, electroencephalogram (EEG) signals were recorded when the subjects were thinking of one or more (up to five) mental thoughts. Autoregressive features were computed from these EEG signals and classified by Linear Discriminant classifier. The results here indicate that near perfect identification of 400 test EEG patterns from four subjects was possible, thereby opening up a new avenue in biometrics.

Keywords: Autoregressive, Biometrics, Electroencephalogram, Linear discrimination, Mental thoughts.

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Authors: H. B. Nguendo Yongsi, Thora M. Herrmann, A. Lutumba Ntetu, Rémy Sietchiping, Christopher Bryant

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Health problems linked to urban growth are current major concerns of developing countries. In 2002 and 2005, an interdisciplinary program “Populations et Espaces ├á Risques SANitaires" (PERSAN) was set up under the patronage of the Development and Research Institute. Centered on health in Cameroon-s urban environment, the program mainly sought to (i) identify diarrhoea risk factors in Yaoundé, (ii) to measure their prevalence and apprehend their spatial distribution. The crosssectional epidemiological study that was carried out revealed a diarrheic prevalence of 14.4% (437 cases of diarrhoea on the 3,034 children examined). Also, among risk factors studied, household refuse management methods used by city dwellers were statistically associated to these diarrhoeas. Moreover, it happened that levels of diarrhoeal attacks varied consistently from one neighbourhood to another because of the discrepancy urbanization process of the Yaoundé metropolis.

Keywords: Diarrhea, health risk, household refuses handling, sanitation, Yaoundé.

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Authors: R. Sullivan, T. Holden, G. Tremberger, Jr, E. Cheung, C. Branch, J. Burrero, G. Surpris, S. Quintana, A. Rameau, N. Gadura, H. Yao, R. Subramaniam, P. Schneider, S. A. Rotenberg, P. Marchese, A. Flamhlolz, D. Lieberman, T. Cheung

Abstract:

Migration in breast cancer cell wound healing assay had been studied using image fractal dimension analysis. The migration of MDA-MB-231 cells (highly motile) in a wound healing assay was captured using time-lapse phase contrast video microscopy and compared to MDA-MB-468 cell migration (moderately motile). The Higuchi fractal method was used to compute the fractal dimension of the image intensity fluctuation along a single pixel width region parallel to the wound. The near-wound region fractal dimension was found to decrease three times faster in the MDA-MB- 231 cells initially as compared to the less cancerous MDA-MB-468 cells. The inner region fractal dimension was found to be fairly constant for both cell types in time and suggests a wound influence range of about 15 cell layer. The box-counting fractal dimension method was also used to study region of interest (ROI). The MDAMB- 468 ROI area fractal dimension was found to decrease continuously up to 7 hours. The MDA-MB-231 ROI area fractal dimension was found to increase and is consistent with the behavior of a HGF-treated MDA-MB-231 wound healing assay posted in the public domain. A fractal dimension based capacity index has been formulated to quantify the invasiveness of the MDA-MB-231 cells in the perpendicular-to-wound direction. Our results suggest that image intensity fluctuation fractal dimension analysis can be used as a tool to quantify cell migration in terms of cancer severity and treatment responses.

Keywords: Higuchi fractal dimension, box-counting fractal dimension, cancer cell migration, wound healing.

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Authors: Martin Rozanek, Karel Roubik

Abstract:

The study deals with the modelling of the gas flow during heliox therapy. A special model has been developed to study the effect of the helium upon the gas flow in the airways during the spontaneous breathing. Lower density of helium compared with air decreases the Reynolds number and it allows improving the flow during the spontaneous breathing. In the cases, where the flow becomes turbulent while the patient inspires air the flow is still laminar when the patient inspires heliox. The use of heliox decreases the work of breathing and improves ventilation. It allows in some cases to prevent the intubation of the patients.

Keywords: Gas flow, heliox, Reynolds number, turbulent flow.

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Authors: Christopher Paterson, Richard Curry, Alan Purvis, Simon Johnson

Abstract:

Emerging Bio-engineering fields such as Brain Computer Interfaces, neuroprothesis devices and modeling and simulation of neural networks have led to increased research activity in algorithms for the detection, isolation and classification of Action Potentials (AP) from noisy data trains. Current techniques in the field of 'unsupervised no-prior knowledge' biosignal processing include energy operators, wavelet detection and adaptive thresholding. These tend to bias towards larger AP waveforms, AP may be missed due to deviations in spike shape and frequency and correlated noise spectrums can cause false detection. Also, such algorithms tend to suffer from large computational expense. A new signal detection technique based upon the ideas of phasespace diagrams and trajectories is proposed based upon the use of a delayed copy of the AP to highlight discontinuities relative to background noise. This idea has been used to create algorithms that are computationally inexpensive and address the above problems. Distinct AP have been picked out and manually classified from real physiological data recorded from a cockroach. To facilitate testing of the new technique, an Auto Regressive Moving Average (ARMA) noise model has been constructed bases upon background noise of the recordings. Along with the AP classification means this model enables generation of realistic neuronal data sets at arbitrary signal to noise ratio (SNR).

Keywords: Action potential detection, Low SNR, Phase spacediagrams/trajectories, Unsupervised/no-prior knowledge.

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Authors: Nadezhda M. Usmanova, Nikolai V. Tomilin

Abstract:

Mammalian genomes contain large number of retroelements (SINEs, LINEs and LTRs) which could affect expression of protein coding genes through associated transcription factor binding sites (TFBS). Activity of the retroelement-associated TFBS in many genes is confirmed experimentally but their global functional impact remains unclear. Human SINEs (Alu repeats) and mouse SINEs (B1 and B2 repeats) are known to be clustered in GCrich gene rich genome segments consistent with the view that they can contribute to regulation of gene expression. We have shown earlier that Alu are involved in formation of cis-regulatory modules (clusters of TFBS) in human promoters, and other authors reported that Alu located near promoter CpG islands have an increased frequency of CpG dinucleotides suggesting that these Alu are undermethylated. Human Alu and mouse B1/B2 elements have an internal bipartite promoter for RNA polymerase III containing conserved sequence motif called B-box which can bind basal transcription complex TFIIIC. It has been recently shown that TFIIIC binding to B-box leads to formation of a boundary which limits spread of repressive chromatin modifications in S. pombe. SINEassociated B-boxes may have similar function but conservation of TFIIIC binding sites in SINEs located near mammalian promoters has not been studied earlier. Here we analysed abundance and distribution of retroelements (SINEs, LINEs and LTRs) in annotated sequences of the Database of mammalian transcription start sites (DBTSS). Fractions of SINEs in human and mouse promoters are slightly lower than in all genome but >40% of human and mouse promoters contain Alu or B1/B2 elements within -1000 to +200 bp interval relative to transcription start site (TSS). Most of these SINEs is associated with distal segments of promoters (-1000 to -200 bp relative to TSS) indicating that their insertion at distances >200 bp upstream of TSS is tolerated during evolution. Distribution of SINEs in promoters correlates negatively with the distribution of CpG sequences. Using analysis of abundance of 12-mer motifs from the B1 and Alu consensus sequences in genome and DBTSS it has been confirmed that some subsegments of Alu and B1 elements are poorly conserved which depends in part on the presence of CpG dinucleotides. One of these CpG-containing subsegments in B1 elements overlaps with SINE-associated B-box and it shows better conservation in DBTSS compared to genomic sequences. It has been also studied conservation in DBTSS and genome of the B-box containing segments of old (AluJ, AluS) and young (AluY) Alu repeats and found that CpG sequence of the B-box of old Alu is better conserved in DBTSS than in genome. This indicates that Bbox- associated CpGs in promoters are better protected from methylation and mutation than B-box-associated CpGs in genomic SINEs. These results are consistent with the view that potential TFIIIC binding motifs in SINEs associated with human and mouse promoters may be functionally important. These motifs may protect promoters from repressive histone modifications which spread from adjacent sequences. This can potentially explain well known clustering of SINEs in GC-rich gene rich genome compartments and existence of unmethylated CpG islands.

Keywords: Retroelement, promoter, CpG island, DNAmethylation.

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Authors: M. Mottaghi, F. Ghalichi, H. Badri Ghavifekr, H. Niroomand Oskui

Abstract:

This paper presents design and characterization of a microaccelerometer designated for integration into cataract surgical probe to detect hardness of different eye tissues during cataract surgery. Soft posterior lens capsule of eye can be easily damaged in comparison with hard opaque lens since the surgeon can not see directly behind cutting needle during the surgery. Presence of microsensor helps the surgeon to avoid rupturing posterior lens capsule which if occurs leads to severe complications such as glaucoma, infection, or even blindness. The microsensor having overall dimensions of 480 μm x 395 μm is able to deliver significant capacitance variations during encountered vibration situations which makes it capable to distinguish between different types of tissue. Integration of electronic components on chip ensures high level of reliability and noise immunity while minimizes space and power requirements. Physical characteristics and results on performance testing, proves integration of microsensor as an effective tool to aid the surgeon during this procedure.

Keywords: Cataract surgery, MEMS, Microsensor, Phacoemulsification.

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Authors: Richard Grünes, Karel Roubik

Abstract:

The article deals with technical support of intracranial single unit activity measurement. The parameters of the whole measuring set were tested in order to assure the optimal conditions of extracellular single-unit recording. Metal microelectrodes for measuring the single-unit were tested during animal experiments. From signals recorded during these experiments, requirements for the measuring set parameters were defined. The impedance parameters of the metal microelectrodes were measured. The frequency-gain and autonomous noise properties of preamplifier and amplifier were verified. The measurement and the description of the extracellular single unit activity could help in prognoses of brain tissue damage recovery.

Keywords: Measuring set, metal microelectrodes, single-unit, noise, impedance parameters, gain characteristics.

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Authors: Abdulsalam I. Rafida

Abstract:

The main objective of this research was to investigate the biosorption capacity for biofilms of sulphate reducing bacteria (SRB) to remove heavy metals, such as Zn, Pb and Cd from rainwater using laboratory-scale reactors containing mixed support media. Evidence showed that biosorption had contributed to removal of heavy metals including Zn, Pb and Cd in presence of SRB and SRB were also found in the aqueous samples from reactors. However, the SRB and specific families (Desulfobacteriaceae and Desulfovibrionaceae) were found mainly in the biomass samples taken from all reactors at the end of the experiment. EDX-analysis of reactor solids at end of experiment showed that heavy metals Zn, Pb and Cd had also accumulated in these precipitates.

Keywords: Sulphate reducing bacteria (SRB), biosorption capacity.

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Authors: S. Amirhassan Monadjemi, Narges Zarrabi, Naser Neamatbakhsh

Abstract:

As days go by, we hear more and more about HIV, Ebola, Bird Flu and other dreadful viruses which were unknown a few decades ago. In both detecting and fighting viral diseases ordinary methods have come across some basic and important difficulties. Vaccination is by a sense introduction of the virus to the immune system before the occurrence of the real case infection. It is very successful against some viruses (e.g. Poliomyelitis), while totally ineffective against some others (e.g. HIV or Hepatitis-C). On the other hand, Anti-virus drugs are mostly some tools to control and not to cure a viral disease. This could be a good motivation to try alternative treatments. In this study, some key features of possible physical-based alternative treatments for viral diseases are presented. Electrification of body parts or fluids (especially blood) with micro electric signals with adjusted current or frequency is also studied. The main approach of this study is to find a suitable energy field, with appropriate parameters that are able to kill or deactivate viruses. This would be a lengthy, multi-disciplinary research which needs the contribution of virology, physics, and signal processing experts. It should be mentioned that all the claims made by alternative cures researchers must be tested carefully and are not advisable at the time being.

Keywords: Alternative Cure, Viral disease, HIV, signals, energy filed.

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Authors: Desmond B. Keenan, Paul Grossman

Abstract:

In order to provide accurate heart rate variability indices of sympathetic and parasympathetic activity, the low frequency and high frequency components of an RR heart rate signal must be adequately separated. This is not always possible by just applying spectral analysis, as power from the high and low frequency components often leak into their adjacent bands. Furthermore, without the respiratory spectra it is not obvious that the low frequency component is not another respiratory component, which can appear in the lower band. This paper describes an adaptive filter, which aids the separation of the low frequency sympathetic and high frequency parasympathetic components from an ECG R-R interval signal, enabling the attainment of more accurate heart rate variability measures. The algorithm is applied to simulated signals and heart rate and respiratory signals acquired from an ambulatory monitor incorporating single lead ECG and inductive plethysmography sensors embedded in a garment. The results show an improvement over standard heart rate variability spectral measurements.

Keywords: Heart rate variability, vagal tone, sympathetic, parasympathetic, spectral analysis, adaptive filter.

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Authors: K. Gauthaman, T.S. Mohamed Saleem, V. Ravi, Sita Sharan Patel, S. Niranjali Devaraj

Abstract:

The present study was designed to investigate the cardio protective role of chronic oral administration of alcoholic extract of Terminalia arjuna in in-vivo ischemic reperfusion injury and the induction of HSP72. Rabbits, divided into three groups, and were administered with the alcoholic extract of the bark powder of Terminalia arjuna (TAAE) by oral gavage [6.75mg/kg: (T1) and 9.75mg/kg: (T2), 6 days /week for 12 weeks]. In open-chest Ketamine pentobarbitone anaesthetized rabbits, the left anterior descending coronary artery was occluded for 15 min of ischemia followed by 60 min of reperfusion. In the vehicle-treated group, ischemic-reperfusion injury (IRI) was evidenced by depression of global hemodynamic function (MAP, HR, LVEDP, peak LV (+) & (- ) (dP/dt) along with depletion of HEP compounds. Oxidative stress in IRI was evidenced by, raised levels of myocardial TBARS and depletion of endogenous myocardial antioxidants GSH, SOD and catalase. Western blot analysis showed a single band corresponding to 72 kDa in homogenates of hearts from rabbits treated with both the doses. In the alcoholic extract of the bark powder of Terminalia arjuna treatment groups, both the doses had better recovery of myocardial hemodynamic function, with significant reduction in TBARS, and rise in SOD, GSH, catalase were observed. The results of the present study suggest that the alcoholic extract of the bark powder of Terminalia arjuna in rabbit induces myocardial HSP 72 and augments myocardial endogenous antioxidants, without causing any cellular injury and offered better cardioprotection against oxidative stress associated with myocardial IR injury.

Keywords: Antioxidants, HSP72, Ischemic reperfusion injury, Terminalia arjuna.

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Authors: Christer Ahlstrom, Katja Höglund, Peter Hult, Jens Häggström, Clarence Kvart, Per Ask

Abstract:

It is sometimes difficult to differentiate between innocent murmurs and pathological murmurs during auscultation. In these difficult cases, an intelligent stethoscope with decision support abilities would be of great value. In this study, using a dog model, phonocardiographic recordings were obtained from 27 boxer dogs with various degrees of aortic stenosis (AS) severity. As a reference for severity assessment, continuous wave Doppler was used. The data were analyzed with recurrence quantification analysis (RQA) with the aim to find features able to distinguish innocent murmurs from murmurs caused by AS. Four out of eight investigated RQA features showed significant differences between innocent murmurs and pathological murmurs. Using a plain linear discriminant analysis classifier, the best pair of features (recurrence rate and entropy) resulted in a sensitivity of 90% and a specificity of 88%. In conclusion, RQA provide valid features which can be used for differentiation between innocent murmurs and murmurs caused by AS.

Keywords: Bioacoustics, murmur, phonocardiographic signal, recurrence quantification analysis.

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