Journal of
Systemics, Cybernetics and Informatics
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 ISSN: 1690-4524 (Online)




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TABLE OF CONTENTS





Low-energy Scheduling Algorithms for Wearable Fall Pre-impact Detection System
M.N. Nyan, Francis E.H. Tay, D Guo, L Xu, K.L. Yap, L.K. Goh, B. Veeravalli
Pages: 1-7
Abstract | Full Text
ABSTRACT:
In this paper, novel low-energy static and dynamic scheduling algorithms with low computational complexities for heterogeneous multiprocessor systems are proposed. Since battery life of the system plays a critical role in wearable embedded systems, the algorithms are useful for energy consumption reduction in Body Area Network (BAN)-based wearable multiprocessor systems in healthcare applications. Our developed BAN-based fall pre-impact detection system is used in this investigation. Based on simulation results using the algorithms, it is found that the battery life can be extended up to 41.6 percent more of its normal life without the algorithms.


A Project-Centric Course on Cyberinfrastructure to Support High School STEM Education
Daphne Rainey, Lisa Coyne, Jason Gibson, Stephen Cammer, Julie Schulman, Betsy Tretola, Oswald Crasta
Pages: 8-13
Abstract | Full Text
ABSTRACT:
Recent rapid advances in information technology pose new challenges for teachers in the Science, Technology, Engineering, and Mathematics (STEM) fields to incorporate the latest knowledge and technical expertise into courses in a way that will be applicable to students as future scientists. A demonstration project was designed, developed, and deployed by university faculty and high school teachers for their students to explore the use of the components of cyberinfrastructure. The project explored the introduction of cyberinfrastructure through the use of bioinformatics and the use of team science. This paper describes the high school course that was deployed at Galileo Magnet High School (GMHS) in collaboration with the scientists at Virginia Tech University, and details its overall assessment. Implementation of a project-centric teaching paradigm to engage students in applying the concepts of cyberinfrastructure by integrating the disciplines of biology, computer science, mathematics, and statistics through bioinformatics was an integral part of this study.


A Biomedical Computation Revealed that an Extra-Systolic Heartbeat Exhibits a Lower Scaling Exponent: DFA as a Beneficial Biomedical Tool
Toru Yazawa, Tomoo Katsuyama
Pages: 14-18
Abstract | Full Text
ABSTRACT:
We made our own DFA (detrended fluctuation analysis) program. We applied it for checking characteristics for the heartbeat of various individuals. Healthy subjects showed a normal scaling exponent, which is near 1.0 (ranging 0.9 to 1.19 in our own temporary guideline). This is in agreement with the original report by Peng et al. long time ago. In the present study, we investigated the person who has an extra-systole heartbeat, and revealed that their arrhythmic heartbeat exhibited a low scaling exponent (around 0.7). Alternans, which is the heart beating in period-2 rhythms, exhibited a much low scaling exponent (around 0.6). We may conclude that if it would be possible to make a device that equips a DFA program, it might be useful to check the heart condition, and contribute not only in nonlinear physics but also in biomedical fields; especially as a device for health check, which is applicable for people who are spending an ordinary life, before they get seriously heart sick.


Complete Platform for Remote Health Management
Bozena Kaminska, Yindar Chuo, Marcin Marzencki, Benny Hung, Camille Jaggernauth, Kouhyar Tavakolian, Philip Lin
Pages: 19-24
Abstract | Full Text
ABSTRACT:
Practical usability of the majority of the current wearable body sensor systems for multiple parameter physiological signal acquisition is limited by the multiple physical connections between the sensors and the data acquisition modules. In order to improve the user comfort and enable the use of this type of systems on active mobile subjects, we propose a wireless body sensor system that incorporates multiple sensors on a single node. This multi-sensor node includes signal acquisition, processing, and wireless data transmission fitted on multiple layers of a thin flexible substrate with very small footprint. Considerations for design include size, form factor, reliable body attachment, good signal coupling, and user convenience. The prototype device measures 55mm by 15mm and is 3mm thick. The unit is attached to the patient’s chest, and is capable of performing simultaneous measurements of parameters such as body motion, activityintensity, tilt, respiration, cardiac vibration, cardiac potential (ECG), heart-rate, body surface temperature. In this paper, we discuss the architecture of this system, including the multisensor hardware, the firmware, a mobile phone receiver unit, and assembly of the first prototype.


The Prediction of Tertiary Structure of RNA Based upon Secondary Structure by Using the Relaxation Method and Texture Mapping Method
C.C. Lin, R.C.T. Lee
Pages: 25-33
Abstract | Full Text
ABSTRACT:
In this paper, we propose a method to predict tertiary structure of an RNA sequence. Our prediction method would first find the secondary structure of the given RNA sequence. We then use the relaxation method to predict the 3-space structure of it. Experimental results show that our method is quite feasible. We tested our approach on 731 RNA’s. 179 of them got a complete match, 391 of them got 90% match and 161 of them got 80% match.


Delivering Chronic Heart Failure Telemanagement via Multiple Interactive Platforms
Joseph Finkelstein, Jeffrey Wood
Pages: 34-39
Abstract | Full Text
ABSTRACT:
Existing telemonitoring systems provide limited support in implementing personalized treatment plans. We developed a Home Automated Telemanagement (HAT) system for patients with congestive heart failure (CHF) to provide support in following individualized treatment plans as well as to monitor symptoms, weight changes, and quality of life, while educating the patient on their disease. The system was developed for both a laptop computer and a Nintendo Wii. The system is designed to be placed in the patient’s home and to communicate all patient data to a central server implementing real-time clinical decision support. The system questions the patient daily on their condition, monitors their weight, and provides the patient with instant feedback on their condition in the form of a 3-zone CHF action plan. Their medication regimen and suggested actions are determined by their care management team and integrated into the system, keeping a personalized approach to disease management while taking advantage of the technology available. The systems are designed to be as simple as possible, making it usable by patients with no prior computer or videogame experience. A feasibility assessment in African American patients with CHF and without prior computer or videogame experience demonstrated high level of acceptance of the CHF HAT laptop and Wii systems. Keywords: telem


Quantifying Stability Using Frequency Domain Data from Wireless Inertial Measurement Units
Stephen Slaughter, Rachel Hales, Cheryl Hinze, Catherine Pfeiffer
Pages: 40-43
Abstract | Full Text
ABSTRACT:
The quantification of gait stability can provide valuable information when evaluating subjects for age related and neuromuscular disease changes. Using tri-axial inertial measurement units (IMU) for acceleration and rotational data provide a non-linear profile for this type of movement. As subjects traverse various surfaces representing decreasing stability, the different phasing of gait data make comparisons difficult. By converting from time to frequency domain data, the phase effects can be ignored, allowing for significant correlations. In this study, 12 subjects provided gait information over various surfaces while wearing an IMU. Instabilities were determined by comparing frequency domain data over less stable surfaces to frequency domain data of neural network (NN) models representing the normal gait for any given participant. Time dependent data from 2 axes of acceleration and 2 axes of rotation were converted using a discrete Fourier transform (FFT) algorithm. The data over less stable surfaces were compared to the normal gait NN model by averaging the Pearson product moment correlation (r) values. This provided a method to quantify the decreased stability. Data showed progressively decreasing correlation coefficient values as subjects encountered progressively less stable surface environments. This methodology has allowed for the quantification of instability in gait situations for application in real-time fall prevention situations.



Chaotic Inertia Weight Particle Swarm Optimization for PCR Primer Design
Cheng-Huei Yang, Yu-Huei Cheng, Li-Yeh Chuang, Cheng-Hong Yang
Pages: 44-49
Abstract | Full Text
ABSTRACT:
In order to provide feasible primer sets for performing a polymerase chain reaction (PCR) experiment, many primer design methods have been proposed. However, the majority of these methods require a long time to obtain an optimal solution since large quantities of template DNA need to be analyzed, and the designed primer sets usually do not provide a specific PCR product size. In recent years, particle swarm optimization (PSO) has been applied to solve many problems and yielded good results. In this paper, a logistic map is proposed to determine the value of inertia weight of PSO (CIWPSO) to design feasible primers. Accuracies for the primer design of the Homo sapiens RNA binding motif protein 11 (RBM11), mRNA (NM_144770), and the Homo sapiens G protein-coupled receptor 78 (GPR78), mRNA (NM_080819) were calculated. Five hundred runs of PSO and the CIWPSO primer design method were performed on different PCR product lengths and the different methods of calculating the melting temperature. A comparison of the accuracy results for PSO and CIWPSO primer design showed that CIWPSO is superior to the PSO for primer design. The proposed method could effectively find optimal or near-optimal primer sets.


Effect of Excess Gravitational Force on Cultured Myotubes in Vitro
Shigehiro Hashimoto, Haruka Hino, Takeshi Iwagawa
Pages: 50-57
Abstract | Full Text
ABSTRACT:
An effect of an excess gravitational force on cultured myoblasts has been studied in an experimental system with centrifugal force in vitro. Mouse myoblasts (C2C12) were seeded on a culture dish of 35 mm diameter, and cultured in the Dulbecco’s Modified Eagle’s Medium until the sub-confluent condition. To apply the excess gravitational force on the cultured cells, the dish was set in a conventional centrifugal machine. Constant gravitational force was applied to the cultured cells for three hours. Variations were made on the gravitational force (6 G, 10 G, 100 G, 500 G, and 800 G) with control of the rotational speed of the rotator in the centrifugal machine. Morphology of the cells was observed with a phasecontrast microscope for eight days. The experimental results show that the myotube thickens day by day after the exposure to the excess gravitational force field. The results also show that the higher excess gravitational force thickens myotubes. The microscopic study shows that myotubes thicken with fusion each other.


GEGEINTOOL: A Computer-Based Tool for Automated Analysis of Gene-Gene Interactions in Large Epidemiological Studies in Cardiovascular Genomics
Oscar Coltell, José M. Ordovás, Carmen Saiz, Manuel Forner, Francisco Gabriel, Dolores Corella
Pages: 58-61
Abstract | Full Text
ABSTRACT:
Current methods of data analysis of gene-gene interactions in complex diseases, after taking into account environmental factors using traditional approaches, are inefficient. High-throughput methods of analysis in large scale studies including thousands of subjects and hundreds of SNPs should be implemented. We developed an integrative computer tool, GEGEINTOOL (GEne- GEne INTeraction tOOL), for large-scale analysis of gene-gene interactions, in human studies of complex diseases including a large number of subjects, SNPs, as well as environmental factors. That resource uses standard statistical packages (SPSS, etc.) to build and fit the gene-gene interaction models by means of syntax scripts in predicting one or more continuous or dichotomic phenotypes. Codominant, dominant and recessive genetic interaction models including control for covariates are automatically created for each SNP in order to test the best model. From the standard outputs, GEGEINTOOL extracts a selected set of parameters (regression coefficients, p-values, adjusted means, etc.), and groups them in a single MS Excel Spreadsheet. The tool allows editing the set of filter parameters, filtering the selected results depending on p-values, as well as plotting the selected gene-gene interactions to check consistency. In conclusion, GEGEINTOOL is a useful and friendly tool for exploring and identifying gene-gene interactions in complex diseases.


In vitro and in silico Approaches to the Identification of New Compounds with Antibacterial Profile
Carlos R. Rodrigues, Bruno Leal, Kely N. De Oliveira, Ariane S. S. R. Ferreira, Alice Bernardino, Ricardo J. Nunes, Vitor Ferreira, Maria C. De Souza, Anna C. Cunha, Helena C. Castro
Pages: 62-65
Abstract | Full Text
ABSTRACT:
The emergence of multidrug-resistant bacterial strains is a world problem that increases the need for new and more effective antimicrobials. On that purpose, derivatives of cyclic systems may serve as new leads for discovering new active molecules. In this work we evaluated the antibacterial profile of 243 molecules derived from the systems thienopyridine, pyrazolopiridine, quinolone, chalcone, hydrazone and lapachone against Gram-positive and Gram-negative susceptible and multiresistant strains also comparing them with antibiotics of clinical use. Our results showed that among the 243 molecules tested, only eight derivatives were active with promissing MIC values (2-64mg/mL). Our theoretical in silico analysis showed that all active compounds fulfilled Lipinski rule of five (molecular weight = 344.37–409.24, clogP = 3.15–4.11, nHBA = 6–7, and nHBD = 2), similarly to commercial drugs as well as presented better druglikeness values (from -3.68 to 0.12) than chloramphenicol (-4.61) and linezolid (-4.08). Most of the active derivatives presented a low in silico toxicity risk profile, similar to oxacillin, ampicillin, and penicillin G, and even lower than that observed for chloramphenicol and linezolid. Theoretically HOMO and the electrostatic protential distribution may be contributing for this safer profile. This study used computacional tools and may help to deal with an important world health problem.


Analysis of CR1 Repeats in the Zebra Finch Genome
George E. Liu, Yali Hou, Twain Brown
Pages: 66-71
Abstract | Full Text
ABSTRACT:
Most bird species have smaller genomes and fewer repeats than mammals. Chicken Repeat 1 (CR1) repeat is one of the most abundant families of repeats, ranging from ~133,000 to ~187,000 copies accounting for ~50 to ~80% of the interspersed repeats in the zebra finch and chicken genomes, respectively. CR1 repeats are believed to have arisen from the retrotransposition of a small number of master elements, which gave rise to multiple CR1 subfamilies in the chicken. In this study, we performed a global assessment of the divergence distributions, phylogenies, and consensus sequences of CR1 repeats in the zebra finch genome. We identified and validated 34 CR1 subfamilies and further analyzed the correlation between these subfamilies. We also discovered 4 novel lineage-specific CR1 subfamilies in the zebra finch when compared to the chicken genome. We built various evolutionary trees of these subfamilies and concluded that CR1 repeats may play an important role in reshaping the structure of bird genomes.


Meta-Classification of Multi-Gene Data with Alternative Feature Mapping
Victor C. Liang, Vincent T. Y. Ng
Pages: 72-77
Abstract | Full Text
ABSTRACT:
In order to overcome the limitation on small size of gene datasets, many meta-classification methods which ensemble classifiers from different datasets have been developed. However, due to discrepancies of the characteristics among multiple heterogeneous datasets, the number of common and significant genes is usually small. Instead of matching common genes between heterogeneous datasets, we propose a novel solution, alternative feature mapping approach (AFM), to utilize related and discriminative gene expressions while not necessarily having exact matches. Genes in the training dataset are clustered and mapped to the test dataset as gene groups. Through analyzing the correlation within gene groups, significant genes can be matched and dataset dissimilarity factors can be used as weights for meta-classification. We conducted experiments consisting of 10 heterogeneous datasets with different cancer types and platforms. Our experiments show that classification performance is greatly improved using suitable significant genes selected by AFM, and weight voting method based on AFM provides more reliability for meta-classification.


Serious Gaming to Improve the Safety of Central Venous Catheter Placement
Daniel Katz, Samuel Demaria
Pages: 78-81
Abstract | Full Text
ABSTRACT:
Approximately 5 million central venous catheters (CVCs) are placed by physicians annually in the United States, with a complication rate of 15%.1 Guidelines and recommendations are continually being established and updated regarding CVC placement.2 While much has been done regarding training the technical skills of CVC placement using part-task trainers (i.e., mannequins), successfully finding and cannulating a central vein is but one part of the process. In fact, many steps designed to prevent untoward complications involve non-technical skills which are perhaps more important in training practitioners to safely place CVCs. First in aviation and now in healthcare, practitioners are being trained in realistic and highly interactive simulated environments so they can learn not just technical skills , but the key management and non-technical steps which make their task safer.3 One modality being used to improve performance is video gaming simulation, or “serious gaming.” Gaming as a learning tool is being increasingly utilized in health care fields and can lead to better skill-based outcomes.4 As such, we have developed a game based around the placement of CVCs that will be used as a new teaching modality in a pilot program for instructing residents in safe CVC placement.