Search results for: adaptive genetic regions

Authors: Janice Haworth, Karamoko Camara, Marie-Therèse Dramou, Kokoly Haba, Daniel Léno, Augustin Mara, Adama Noël Oulari, Silafa Tolno, Noël Zoumanigui

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The traditional rhythms of the West African country of Guinea have played a centuries-long role in defining the different people groups that make up the country. Throughout their history, before and since colonization by the French, the different ethnicities have used their traditional music as a distinct part of their historical identities. That is starting to change. Guinea is an impoverished nation created in the early twentieth-century with little regard for the history and cultures of the people who were included. The traditional rhythms of the different people groups and their heritages have remained. Fifteen individual traditional Guinean rhythms were chosen to represent popular rhythms from the four geographical regions of Guinea. Each rhythm was traced back to its native village and video recorded on-site by as many different local performing groups as could be located. The cyclical patterns rhythms were transcribed via a circular, spatial design and then copied into a box notation system where sounds happening at the same time could be studied. These rhythms were analyzed for their consistency-over-performance in a Fundamental Rhythm Pattern analysis so rhythms could be compared for how they are changing through different performances. The analysis showed that the traditional rhythm performances of the Middle and Forest Guinea regions were the most cohesive and showed the least evidence of change between performances. The role of music in each of these regions is both limited and focused. The Coastal and High Guinea regions have much in common historically through their ethnic history and modern-day trade connections, but the rhythm performances seem to be less consistent and demonstrate more changes in how they are performed today. In each of these regions the role and usage of music is much freer and wide-spread. In spite of advances being made as a country, different ethnic groups still frequently only respond and participate (dance and sing) to the music of their native ethnicity. There is some evidence that this self-imposed musical barrier is beginning to change and evolve, partially through the development of better roads, more access to electricity and technology, the nation-wide Ebola health crisis, and a growing self-identification as a unified nation.

Keywords: cultural identity, Guinea, traditional rhythms, west Africa

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Authors: N. R. Badurally Adam, S. R. Monebhurrun, M. Z. Dauhoo, A. Khoodaruth

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Transport energy demand is vital for the economic growth of any country. Globalisation and better standard of living plays an important role in transport energy demand. Recently, transport energy demand in Mauritius has increased significantly, thus leading to an abuse of natural resources and thereby contributing to global warming. Forecasting the transport energy demand is therefore important for controlling and managing the demand. In this paper, we develop a model to predict the transport energy demand. The model developed is based on a system of five stochastic differential equations (SDEs) consisting of five endogenous variables: fuel price, population, gross domestic product (GDP), number of vehicles and transport energy demand and three exogenous parameters: crude birth rate, crude death rate and labour force. An interval of seven years is used to avoid any falsification of result since Mauritius is a developing country. Data available for Mauritius from year 2003 up to 2009 are used to obtain the values of design variables by applying genetic algorithm. The model is verified and validated for 2010 to 2012 by substituting the values of coefficients obtained by GA in the model and using particle swarm optimisation (PSO) to predict the values of the exogenous parameters. This model will help to control the transport energy demand in Mauritius which will in turn foster Mauritius towards a pollution-free country and decrease our dependence on fossil fuels.

Keywords: genetic algorithm, modeling, particle swarm optimization, stochastic differential equations, transport energy demand

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Authors: Kausik Halder, Nabendu Chaki, Ranjan Dasgupta

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We present a modelling framework that supports the engineering of early requirements specifications for design of learner centric dynamic Learning Management System. The framework is based on i* modelling tool and Means End Analysis, that adopts primitive concepts for modelling early requirements (such as actor, goal, and strategic dependency). We show how pedagogical and computational requirements for designing a learner centric Learning Management system can be adapted for the automatic early requirement engineering specifications. Finally, we presented a model on a Learner Quanta based adaptive Courseware. Our early requirement analysis shows that how means end analysis reveals gaps and inconsistencies in early requirements specifications that are by no means trivial to discover without the help of formal analysis tool.

Keywords: adaptive courseware, early requirement engineering, means end analysis, organizational modelling, requirement modelling

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Authors: Fakhrosadat Sajjadian

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In the USA, about 5% of women diagnosed with breast cancer annually are affected by Inflammatory Breast Cancer (IBC), which is a highly aggressive type of Locally Advanced Breast Cancer (LABC). It is a type of LABC that is clinically and pathologically different, known for its rapid growth, invasiveness, and ability to promote the growth of blood vessels. Almost all women are found to have lymph nodes affected upon diagnosis, while around 36% show obvious distant metastases. Even with the latest improvements in multimodality therapies, the outlook for patients with IBC remains bleak, as the average disease-free survival time is less than 2.5 years. Recent research on the genetic factors responsible for the IBC phenotype has resulted in the discovery of genes that play a role in the advancement of this illness. The development of primary human cell lines and animal models has assisted in this research. These advancements offer new possibilities for future actions in identifying and treating IBC.

Keywords: breast cancer, inflammation, diagnosis, IBC, LABC

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Authors: R. Nagarani

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An intrinsic property of software in a real-world environment is its need to evolve, which is usually accompanied by the increase of software complexity and deterioration of software quality, making software maintenance a tough problem. Refactoring is regarded as an effective way to address this problem. Many refactoring approaches at the method and class level have been proposed. But the extent of research on software refactoring at the package level is less. This work presents a novel approach to refactor the package structures of object oriented software using genetic algorithm based community detection. It uses software networks to represent classes and their dependencies. It uses a constrained community detection algorithm to obtain the optimized community structures in software networks, which also correspond to the optimized package structures. It finally provides a list of classes as refactoring candidates by comparing the optimized package structures with the real package structures.

Keywords: community detection, complex network, genetic algorithm, package, refactoring

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Authors: Hanaa A. S. Oraby, Amal A. M. Hassan, Mahmoud M. Sakr, Atef A. A. Haiba

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Applying the profiling approach for the assessment of proteomic variations due to genetic modification of the Egyptian tomato cultivar "Edkawy", three complementary approaches were used. These methods are amino acids analysis, gel electrophoresis, and Gas chromatography coupled with mass spectrometry (GC/MS). The results of the present study Show evidence of proteomic variations between both modified tomato and its non-modified counterpart. Amino acids concentrations, and the protein patterns separation on the 1D SDS-PAGE were not similar in the case of transformed tomato compared to that of the non-transformed counterpart. These detected differences are most likely derived from the process of transformation. Results also revealed that the efficiency of GC/MS approach to identify a mixture of unknown proteins is limited. GC/MS analysis was only able to identify few number of protein molecules. Therefore, more advanced and specific technologies like MALDI-TOF-MS are recommended to be employed.

Keywords: GMOs, unintended effects, proteomic variations, 1D SDS-PAGE, GC/MS

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Authors: Serkan Tezgel

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Effectively managing threats and power that transcend national boundaries requires a reformulation from the traditional post-modern navy to an adaptive and institutional transnational navy. By analyzing existing soft power concept, post-modern navy, and sea power, this study proposes the transnational navy, founded on the triangle of main attributes of transnational companies, 'Global Competitiveness, Local Responsiveness, Worldwide Learning and Innovation Sharing', a new model which will lead to a positive peace with an institutional network. This transnational model necessitates 'Transnational Navies' to help establish peace with collective and transnational understanding during a transition period 'Reactive Postmodern Navy' has been experiencing. In this regard, it is fairly claimed that a new paradigm shift will revolve around sea power to establish good order at sea with collective and collaborative initiatives and bound to breed new theories and ideas in the forthcoming years. However, there are obstacles to overcome. Postmodern navies, currently shaped by 'Collective Maritime Security' and 'Collective Defense' concepts, can not abandon reactive applications and acts. States deploying postmodern navies to realize their policies on international platforms and seapower structures shaped by the axis of countries’ absolute interests resulted in multipolar alliances and coalitions, but the establishment of the peace. These obstacles can be categorized into three tiers in establishing a unique transnational model navy: Strategic, Organizational and Management challenges. To overcome these obstacles and challenges, postmodern navies should transform into cooperative, collective and independent soft transnational navies with the transnational mentality, global commons, and institutional network. Such an adaptive institution can help the world navigate to a positive peace.

Keywords: postmodern navy, transnational navy, transnational mentality, institutional network

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Authors: S. Khan, A. Khan, Abdul R. Soomrani, Raja F. Zafar, A. Waqas, G. Akbar

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This paper proposes a low-complexity image interpolation method. Image interpolation is used to convert a low dimension video/image to high dimension video/image. The objective of a good interpolation method is to upscale an image in such a way that it provides better edge preservation at the cost of very low complexity so that real-time processing of video frames can be made possible. However, low complexity methods tend to provide real-time interpolation at the cost of blurring, jagging and other artifacts due to errors in slope calculation. Non-linear methods, on the other hand, provide better edge preservation, but at the cost of high complexity and hence they can be considered very far from having real-time interpolation. The proposed method is a linear method that uses gradient orientation for slope calculation, unlike conventional linear methods that uses the contrast of nearby pixels. Prewitt edge detection is applied to separate uniform regions and edges. Simple line averaging is applied to unknown uniform regions, whereas unknown edge pixels are interpolated after calculation of slopes using gradient orientations of neighboring known edge pixels. As a post-processing step, bilateral filter is applied to interpolated edge regions in order to enhance the interpolated edges.

Keywords: edge detection, gradient orientation, image upscaling, linear interpolation, slope tracing

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Authors: Piotr Kacejko, Mariusz Duk, Miroslaw Wendeker

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This paper presents an adaptive controller to track the maximum power point of a photovoltaic modules (PV) under fast irradiation change on the city-bus roof. Photovoltaic systems have been a prominent option as an additional energy source for vehicles. The Municipal Transport Company (MPK) in Lublin has installed photovoltaic panels on its buses roofs. The solar panels turn solar energy into electric energy and are used to load the buses electric equipment. This decreases the buses alternators load, leading to lower fuel consumption and bringing both economic and ecological profits. A DC–DC boost converter is selected as the power conditioning unit to coordinate the operating point of the system. In addition to the conversion efficiency of a photovoltaic panel, the maximum power point tracking (MPPT) method also plays a main role to harvest most energy out of the sun. The MPPT unit on a moving vehicle must keep tracking accuracy high in order to compensate rapid change of irradiation change due to dynamic motion of the vehicle. Maximum power point track controllers should be used to increase efficiency and power output of solar panels under changing environmental factors. There are several different control algorithms in the literature developed for maximum power point tracking. However, energy performances of MPPT algorithms are not clarified for vehicle applications that cause rapid changes of environmental factors. In this study, an adaptive MPPT algorithm is examined at real ambient conditions. PV modules are mounted on a moving city bus designed to test the solar systems on a moving vehicle. Some problems of a PV system associated with a moving vehicle are addressed. The proposed algorithm uses a scanning technique to determine the maximum power delivering capacity of the panel at a given operating condition and controls the PV panel. The aim of control algorithm was matching the impedance of the PV modules by controlling the duty cycle of the internal switch, regardless of changes of the parameters of the object of control and its outer environment. Presented algorithm was capable of reaching the aim of control. The structure of an adaptive controller was simplified on purpose. Since such a simple controller, armed only with an ability to learn, a more complex structure of an algorithm can only improve the result. The presented adaptive control system of the PV system is a general solution and can be used for other types of PV systems of both high and low power. Experimental results obtained from comparison of algorithms by a motion loop are presented and discussed. Experimental results are presented for fast change in irradiation and partial shading conditions. The results obtained clearly show that the proposed method is simple to implement with minimum tracking time and high tracking efficiency proving superior to the proposed method. This work has been financed by the Polish National Centre for Research and Development, PBS, under Grant Agreement No. PBS 2/A6/16/2013.

Keywords: adaptive control, photovoltaic energy, city bus electric load, DC-DC converter

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Authors: Maamar Ali Saud Al Tobi, Geraint Bevan, K. P. Ramachandran, Peter Wallace, David Harrison

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Centrifugal pumps are complex machines which can experience different types of fault. Condition monitoring can be used in centrifugal pump fault detection through vibration analysis for mechanical and hydraulic forces. Vibration analysis methods have the potential to be combined with artificial intelligence systems where an automatic diagnostic method can be approached. An automatic fault diagnosis approach could be a good option to minimize human error and to provide a precise machine fault classification. This work aims to introduce an approach to centrifugal pump fault diagnosis based on artificial intelligence and genetic algorithm systems. An overview of the future works, research methodology and proposed experimental setup is presented and discussed. The expected results and outcomes based on the experimental work are illustrated.

Keywords: centrifugal pump setup, vibration analysis, artificial intelligence, genetic algorithm

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Authors: Alireza Pouladkhan, Mohammad Yavari Foroushani, Ali Mortazavi

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This paper presents a finite element model for a sandwich plate containing a piezoelectric core. A sandwich plate with a piezoelectric core is constructed using the shear mode of piezoelectric materials. The orientation of poling vector has a significant effect on deflection and stress induced in the piezo-actuated adaptive sandwich plate. In the present study, the influence of this factor for a clamped-clamped-free-free and simple-simple-free-free square sandwich plate is investigated using Finite Element Method. The study uses ABAQUS (v.6.7) software to derive the finite element model of the sandwich plate. By using this model, the study gives the influences of the poling vector angle on the response of the smart structure and determines the maximum transverse displacement and maximum stress induced.

Keywords: finite element method, sandwich plate, poling vector, piezoelectric materials, smart structure, electric enthalpy

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Authors: Mandeep Kaur, Fatehgarh Sahib

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The purpose of economic load dispatch is to allocate the required load demand between the available generation units such that the cost of operation is minimized. It is an optimization problem to find the most economical schedule of the generating units while satisfying load demand and operational constraints. The multiobjective optimization problem in which the engineer’s goal is to maximize or minimize not a single objective function but several objective functions simultaneously. The purpose of multiobjective problems in the mathematical programming framework is to optimize the different objective functions. Many approaches and methods have been proposed in recent years to solve multiobjective optimization problems. Weighting method has been applied to convert multiobjective optimization problems into scalar optimization. MATLAB 7.10 has been used to write the code for the complete algorithm with the help of genetic algorithm (GA). The validity of the proposed method has been demonstrated on a three-unit power system.

Keywords: economic load dispatch, genetic algorithm, generating units, multiobjective optimization, weighting method

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Authors: Sanjeev Kumar Shukla, Govind Singh, Prabhat Pant Shahzad Ahmad

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Background: Graves’ disease is an autoimmune disorder with a genetic predisposition, and CD40 plays a pathogenic role in various autoimmune diseases. A single nucleotide polymorphism at position –1 of the Kozak sequence of the 5 untranslated regions of the CD40 gene of exon 1 has been reported to be associated with the development of Graves’ Disease. Objective: The aim of the present study was to investigate whether CD40 gene polymorphism confers susceptibility to Graves’ disease in the Kumaon region. CD40 gene polymorphisms were studied in Graves’ Disease patients (n=50) and healthy control subjects without anti-thyroid autoantibodies or a family history of autoimmune disorders (n=50). Material and Method: CD40 gene polymorphisms were studied in fifty Graves’ Disease patients and fifty healthy control subjects. All samples were collected from STG Hospital, Haldwani, Nainital. A C/T polymorphism at position –1 of the CD40 gene was measured using the polymerase chain reaction-restriction fragment length polymorphism. Results: There was no significant difference in allele or genotype frequency of the CD40 SNP between Graves’ Disease and control subjects. There was a significant decrease in the TT genotype frequency in the Graves’ Disease patients who developed Graves’ Disease after 40 years old than those under 40 years of age. These data suggest that the SNP of the CD40 gene is associated with susceptibility to the later onset of Graves’ Disease. Conclusion: The CD40 gene was a different susceptibility gene for Graves’ Disease within certain families because it was both linked and associated with Graves’ Disease.

Keywords: autoimmune diseases, pathogenesis, diagnosis, therapy

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Authors: Andreina Giustiniani, Massimiliano Oliveri

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Rhythmic activity in different frequencies could subserve distinct functional roles during visual perception and visual mental imagery. In particular, alpha band activity is thought to play a role in active inhibition of both task-irrelevant regions and processing of non-relevant information. In the present blind placebo-controlled study we applied alpha transcranial alternating current stimulation (tACS) in the occipital cortex both during a basic visual perception and a visual working memory task. To understand if the role of alpha is more related to a general inhibition of distractors or to an inhibition of task-irrelevant regions, we added a non visual distraction to both the tasks.Sixteen adult volunteers performed both a simple perception and a working memory task during 10 Hz tACS. The electrodes were placed over the left and right occipital cortex, the current intensity was 1 mA peak-to-baseline. Sham stimulation was chosen as control condition and in order to elicit the skin sensation similar to the real stimulation, electrical stimulation was applied for short periods (30 s) at the beginning of the session and then turned off. The tasks were split in two sets, in one set distracters were included and in the other set, there were no distracters. Motor interference was added by changing the answer key after subjects completed the first set of trials.The results show that alpha tACS improves working memory only when no motor distracters are added, suggesting a role of alpha tACS in inhibiting non-relevant regions rather than in a general inhibition of distractors. Additionally, we found that alpha tACS does not affect accuracy and hit rates during the visual perception task. These results suggest that alpha activity in the occipital cortex plays a different role in perception and working memory and it could optimize performance in tasks in which attention is internally directed, as in this working memory paradigm, but only when there is not motor distraction. Moreover, alpha tACS improves working memory performance by means of inhibition of task-irrelevant regions while it does not affect perception.

Keywords: alpha activity, interference, perception, working memory

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Authors: Rajamani Doraiswami, Lahouari Cheded

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Fault diagnosis of Linear Parameter-Varying (LPV) system using an adaptive Kalman filter is proposed. The LPV model is comprised of scheduling parameters, and the emulator parameters. The scheduling parameters are chosen such that they are capable of tracking variations in the system model as a result of changes in the operating regimes. The emulator parameters, on the other hand, simulate variations in the subsystems during the identification phase and have negligible effect during the operational phase. The nominal model and the influence vectors, which are the gradient of the feature vector respect to the emulator parameters, are identified off-line from a number of emulator parameter perturbed experiments. A Kalman filter is designed using the identified nominal model. As the system varies, the Kalman filter model is adapted using the scheduling variables. The residual is employed for fault diagnosis. The proposed scheme is successfully evaluated on simulated system as well as on a physical process control system.

Keywords: identification, linear parameter-varying systems, least-squares estimation, fault diagnosis, Kalman filter, emulators

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Authors: Atitallah Sofien, Bouyahia Olfa, Attar Souleima, Missaoui Nada, Ben Rabeh Rania, Yahyaoui Salem, Mazigh Sonia, Boukthir Samir

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Introduction: Ciliopathies are a spectrum of diseases that have in common a defect in the synthesis of ciliary proteins. It is a rare cause of neonatal cholestasis. Clinical presentation varies extremely, and the main affected organs are the kidneys, liver, and pancreas. Methodology: This is a descriptive case report of a newborn who was admitted for exploration of neonatal cholestasis in the Paediatric Department C at the Children’s Hospital of Tunis, where the investigations concluded with a rare genetic mutation. Results: This is the case of a newborn male with no family history of hepatic and renal diseases, born to consanguineous parents, and from a well-monitored uneventful pregnancy. He developed jaundice on the second day of life, for which he received conventional phototherapy in the neonatal intensive care unit. He was admitted at 15 days for mild bronchiolitis. On clinical examination, intense jaundice was noted with normal stool and urine colour. Initial blood work showed an elevation in conjugated bilirubin and a high gamma-glutamyl transferase level. Transaminases and prothrombin time were normal. Abdominal sonography revealed hepatomegaly, splenomegaly, and undifferentiated renal cortex with bilateral medullar micro-cysts. Kidney function tests were normal. The infant received ursodeoxycholic acid and vitamin therapy. Genetic testing showed a homozygous mutation in the DCDC2 gene that hadn’t been documented before confirming the diagnosis of renal-hepatic ciliopathy. The patient has regular follow-ups, and his conjugated bilirubin and gamma-glutamyl transferase levels have been decreasing. Conclusion: Genetic testing has revolutionized the approach to etiological diagnosis in pediatric cholestasis. It enables personalised treatment strategies to better enhance the quality of life of patients and prevent potential complications following adequate long-term monitoring.

Keywords: cholestasis, newborn, ciliopathy, DCDC2, genetic

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Authors: Ibrahim Ilker Ozyigit, Fatih Tabanli, Sezin Adinir

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In this study, Ascochyta blight resistance was investigated in 34 registered chickpea varieties, which are widely planting in different regions of Turkey. For this aim, molecular marker techniques, such as STMS, RAPD and ISSR were used. Ta2, Ta146 and Ts54 primers were used for STMS, while UBC733 and UBC681 primers for RAPD, and UBC836 and UBC858 primers for ISSR. Ta2, Ts54 and Ta146 (STMS), and UBC733 (RAPD) primers demonstrated the distinctive feature for Ascochyta blight resistance. Ta2, Ts54 and Ta146 primers yielded the quite effective results in detection of resistant and sensitive varieties. Besides, UBC 733 primer distinguished all kinds of standard did not give any reliable results for other varieties since it demonstrated all as resistant. In addition, monomorphic bands were obtained from UBC681 (RAPD), and UBC836 and UBC858 (ISSR) primers, not demonstrating reliable results in detection of resistance against Ascochyta blight disease. Obtained results informed us about both disease resistance and genetic diversity in registered Turkish chickpea varieties. This project was funded through the Scientific Research Projects of Marmara University under Grant Number FEN-C-YLP-070617-0365 and The Scientific and Technological Research Council of Turkey (TUBITAK) under Grant Number 113O070.

Keywords: plant genetics, ISSR, RAPD, STMS

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Authors: Biswabandhu Bankura, Srikanta Guria, Madhusudan Das

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Purpose: Thyroid peroxidase (TPO) is the key enzyme in the biosynthesis of thyroid hormones. We aimed to identify the spectrum of mutations in the TPO gene leading to hypothyroidism in the population of West Bengal to establish the genetic etiology of the disease. Methods: 200 hypothyroid patients (case) and their corresponding sex and age matched 200 normal individuals (control) were screened depending on their clinical manifestations. Genomic DNA was isolated from peripheral blood samples and TPO gene (Exon 7 to Exon 14) was amplified by PCR. The PCR products were subjected to sequencing to identify mutations. Results: Single nucleotide changes such as Glu 641 Lys, Asp 668 Asn, Thr 725 Pro, Asp 620 Asn, Ser 398 Thr, and Ala 373 Ser were found. Changes in the TPO were assayed in vitro to compare mutant and wild-type activities. Five mutants were enzymatically inactive in the guaiacol and iodide assays. This is a strong indication that the mutations are present at crucial positions of the TPO gene, resulting in inactivated TPO. Key Findings: The results of this study may help to develop a genetic screening protocol for goiter and hypothyroidism in the population of West Bengal.

Keywords: thyroid peroxidase, hypothyroidism, mutation, in vitro assay, transfection

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Authors: Misty Attwood, Helgi Schioth

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Transmembrane proteins are important components in many essential cell processes such as signal transduction, cell-cell signalling, transport of solutes, structural adhesion activities, and protein trafficking. Due to their involvement in diverse critical activities, transmembrane proteins are implicated in different disease pathways and hence are the focus of intense interest in understanding functional activities, their pathogenesis in disease, and their potential as pharmaceutical targets. Further, as the structure and function of proteins are correlated, investigating a group of proteins with the same tertiary structure, i.e., the same number of transmembrane regions, may give understanding about their functional roles and potential as therapeutic targets. In this in silico bioinformatics analysis, we identify and comprehensively characterize the previously unstudied group of proteins with five transmembrane-spanning regions (5TM). We classify nearly 60 5TM proteins in which 31 are members of ten families that contain two or more family members and all members are predicted to contain the 5TM architecture. Furthermore, nine singlet proteins that contain the 5TM architecture without paralogues detected in humans were also identifying, indicating the evolution of single unique proteins with the 5TM structure. Interestingly, more than half of these proteins function in localization activities through movement or tethering of cell components and more than one-third are involved in transport activities, particularly in the mitochondria. Surprisingly, no receptor activity was identified within this family in sharp contrast with other TM families. Three major 5TM families were identified and include the Tweety family, which are pore-forming subunits of the swelling-dependent volume regulated anion channel in astrocytes; the sidoreflexin family that acts as mitochondrial amino acid transporters; and the Yip1 domain family engaged in vesicle budding and intra-Golgi transport. About 30% of the proteins have enhanced expression in the brain, liver, or testis. Importantly, 60% of these proteins are identified as cancer prognostic markers, where they are associated with clinical outcomes of various tumour types, indicating further investigation into the function and expression of these proteins is important. This study provides the first comprehensive analysis of proteins with 5TM regions and provides details of the unique characteristics and application in pharmaceutical development.

Keywords: 5TM, cancer prognostic marker, drug targets, transmembrane protein

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Authors: Safa A. Mohammed Ali, Ammar S. Ahamed, Mohammed Khair Abdalla

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The objectives of this study were to estimate the means and genetic parameters of birth and weaning weight of calves of pure Holstein-Friesian cows raised in Sudan. The traits studied were:*Weight at birth *Weight at weaning. The study also included some of the important factors that affected these traits. The data were analyzed using Harvey’s Least Squares and Maximum Likelihood programme. The results obtained showed that the overall mean weight at birth of the calves under study was 34.36±0.94kg. Male calves were found to be heavier than females; the difference between the sexes was highly significant (P<0.001). The mean weight at birth of male calves was 34.27±1.17 kg while that of females was 32.51±1.14kg. The effect of sex of calves, sire and parity of dam were highly significant (P<0.001). The overall mean of weight at weaning was 67.10 ± 5.05 kg, weight at weaning was significantly (p<0.001) effected by sex of calves, sire, year and season of birth have highly significant (P<0.001) effect on either trait. Also estimates heritabilities of birth weight was (0.033±0.015) lower than heritabilities of weaning weight (0.224±0.039), and genetic correlation was 0.563, the phenotypic correlation 0.281, and the environmental correlation 0.268.

Keywords: birth, weaning, weight, friesian

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Authors: M. Kouyate, M. Sangare, S. Samake, S. Keita, H. G. Kim, D. H. Geschwind

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Background & Objectives: Human genetic studies can be expensive, even unaffordable, in developing countries, partly due to the sequencing costs. Our aim is to pilot the use of bioinformatics tools to guide scientifically valid, locally relevant, and economically sound autism genetic research in Mali. Methods: The following databases, NCBI, HGMD, and LSDB, were used to identify hot point mutations. Phenotype, transmission pattern, theoretical protein expression in the brain, the impact of the mutation on the 3D structure of the protein) were used to prioritize selected autism genes. We used the protein database, Modeller, and clustal W. Results: We found Mef2c (Gly27Ala/Leu38Gln), Pten (Thr131IIle), Prodh (Leu289Met), Nme1 (Ser120Gly), and Dhcr7 (Pro227Thr/Glu224Lys). These mutations were associated with endonucleases BseRI, NspI, PfrJS2IV, BspGI, BsaBI, and SpoDI, respectively. Gly27Ala/Leu38Gln mutations impacted the 3D structure of the Mef2c protein. Mef2c protein sequences across species showed a high percentage of similarity with a highly conserved MADS domain. Discussion: Mef2c, Pten, Prodh, Nme1, and Dhcr 7 gene mutation frequencies in the Malian population will be very informative. PCR coupled with restriction enzyme digestion can be used to screen the targeted gene mutations. Sanger sequencing will be used for confirmation only. This will cut down considerably the sequencing cost for gene-to-gene mutation screening. The knowledge of the 3D structure and potential impact of the mutations on Mef2c protein informed the protein family and altered function (ex. Leu38Gln). Conclusion & Future Work: Bio-informatics will positively impact autism research in Mali. Our approach can be applied to another neuropsychiatric disorder.

Keywords: bioinformatics, endonucleases, autism, Sanger sequencing, point mutations

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Authors: Alireza Nikbakht Shahbazi, Emadeddin Shirali

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Since optimization issues of water resources are complicated due to the variety of decision making criteria and objective functions, it is sometimes impossible to resolve them through regular optimization methods or, it is time or money consuming. Therefore, the use of modern tools and methods is inevitable in resolving such problems. An accurate and essential utilization policy has to be determined in order to use natural resources such as water reservoirs optimally. Water reservoir programming studies aim to determine the final cultivated land area based on predefined agricultural models and water requirements. Dam utilization rule curve is also provided in such studies. The basic information applied in water reservoir programming studies generally include meteorological, hydrological, agricultural and water reservoir related data, and the geometric characteristics of the reservoir. The system of Dez dam water resources was simulated applying the basic information in order to determine the capability of its reservoir to provide the objectives of the performed plan. As a meta-exploratory method, genetic algorithm was applied in order to provide utilization rule curves (intersecting the reservoir volume). MATLAB software was used in order to resolve the foresaid model. Rule curves were firstly obtained through genetic algorithm. Then the significance of using rule curves and the decrease in decision making variables in the system was determined through system simulation and comparing the results with optimization results (Standard Operating Procedure). One of the most essential issues in optimization of a complicated water resource system is the increasing number of variables. Therefore a lot of time is required to find an optimum answer and in some cases, no desirable result is obtained. In this research, intersecting the reservoir volume has been applied as a modern model in order to reduce the number of variables. Water reservoir programming studies has been performed based on basic information, general hypotheses and standards and applying monthly simulation technique for a statistical period of 30 years. Results indicated that application of rule curve prevents the extreme shortages and decrease the monthly shortages.

Keywords: optimization, rule curve, genetic algorithm method, Dez dam reservoir

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Authors: Hyunchul Ahn, William X. S. Wong

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Corporate credit rating prediction is one of the most important topics, which has been studied by researchers in the last decade. Over the last decade, researchers are pushing the limit to enhance the exactness of the corporate credit rating prediction model by applying several data-driven tools including statistical and artificial intelligence methods. Among them, multiclass support vector machine (MSVM) has been widely applied due to its good predictability. However, heuristics, for example, parameters of a kernel function, appropriate feature and instance subset, has become the main reason for the critics on MSVM, as they have dictate the MSVM architectural variables. This study presents a hybrid MSVM model that is intended to optimize all the parameter such as feature selection, instance selection, and kernel parameter. Our model adopts genetic algorithm (GA) to simultaneously optimize multiple heterogeneous design factors of MSVM.

Keywords: corporate credit rating prediction, Feature selection, genetic algorithms, instance selection, multiclass support vector machines

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Authors: Biji Jacob

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Vector quantization algorithm which uses minimum distance calculation for codebook generation, a time consuming calculation performed on each pixel values leads to computation complexity. The codebook is updated by comparing the distance of each vector to their centroid vector and measure for their closeness. In this paper vector quantization is modified based on vector difference algorithm for image enhancement purpose. In the proposed scheme, vector differences between the vectors are considered as the new generation vectors or new codebook vectors. The codebook is updated by comparing the new generation vector with a threshold value having minimum error with the parent vector. The minimum error decides the fitness of each newly generated vector. Thus the codebook is generated in an adaptive manner and the fitness value is determined for the suppression of the degraded portion of the image and thereby leads to the enhancement of the image through the adaptive searching capability of the vector quantization through vector difference algorithm. Experimental results shows that the vector difference scheme efficiently modifies the vector quantization algorithm for enhancing the image with peak signal to noise ratio (PSNR), mean square error (MSE), Euclidean distance (E_dist) as the performance parameters.

Keywords: codebook, image enhancement, vector difference, vector quantization

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Authors: Yushinta Fujaya, Andi Ivo Asphama, Andi Parenrengi, Andi Tenriulo

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Blue Swimming crab (Portunus pelagicus) is an important commercial species throughout the subtropical waters and as such constitutes part of the fisheries resources. Data are lacking on the morphological variations of selected fast-growing crabs reared in a pond. This study aimed to analyze the morphological and molecular character of a selected fast-growing crab reared in ponds in South of Sulawesi. The crab seeds were obtained from local fish-trap and hatchery. A study on the growth was carried out in the population of crabs. The dimensions analyzed were carapace width (CW) measured after 3 months of grow out. Morphological character states were examined based on the pattern of spots on the carapace. Molecular analysis was performed using RAPD (Random Amplified Polymorphic DNA). Genetic distance was analysed using TFPGA (Tools for Population Genetic Analyses) version 1.3. The results showed that there were variations in the growth of crabs. These crabs clustered morphologically into three quite distinct groups. The crab with white spots irregularly spread over its carapace was the largest size while the crab with large white spots scattered over the carapace was the smaller size (3%). The crab with small white spots scattered over the carapace was the smallest size found in this study. Molecular analysis showed that there are morphologically and genetically different between groups of crabs. Genetic distances among crabs ranged from 0.1527 to 0.5856. Thus, this study provides information the use of white spots pattern over carapace as indicators to identify the type of blue swimming crabs.

Keywords: crab, portunus pelagicus, morphology, RAPD, Carapace

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Authors: Lydia Tan, Philippe Lemey, Lieselot Houspie, Marco Viveen, Darren Martin, Frank Coenjaerts

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Introduction: Human respiratory syncytial virus (hRSV) is the leading cause of severe respiratory tract infections in infants under the age of two. Genomic substitutions and related evolutionary dynamics of hRSV are of great influence on virus transmission behavior. The evolutionary patterns formed are due to a precarious interplay between the host immune response and RSV, thereby selecting the most viable and less immunogenic strains. Studying genomic profiles can teach us which genes and consequent proteins play an important role in RSV survival and transmission dynamics. Study design: In this study, genetic diversity and evolutionary rate analysis were conducted on 36 RSV subgroup B whole genome sequences and 37 subgroup A genome sequences. Clinical RSV isolates were obtained from nasopharyngeal aspirates and swabs of children between 2 weeks and 5 years old of age. These strains, collected during epidemic seasons from 2001 to 2011 in the Netherlands and Belgium by either conventional or 454-sequencing. Sequences were analyzed for genetic diversity, recombination events, synonymous/non-synonymous substitution ratios, epistasis, and translational consequences of mutations were mapped to known 3D protein structures. We used Bayesian statistical inference to estimate the rate of RSV genome evolution and the rate of variability across the genome. Results: The A and B profiles were described in detail and compared to each other. Overall, the majority of the whole RSV genome is highly conserved among all strains. The attachment protein G was the most variable protein and its gene had, similar to the non-coding regions in RSV, more elevated (two-fold) substitution rates than other genes. In addition, the G gene has been identified as the major target for diversifying selection. Overall, less gene and protein variability was found within RSV-B compared to RSV-A and most protein variation between the subgroups was found in the F, G, SH and M2-2 proteins. For the F protein mutations and correlated amino acid changes are largely located in the F2 ligand-binding domain. The small hydrophobic phosphoprotein and nucleoprotein are the most conserved proteins. The evolutionary rates were similar in both subgroups (A: 6.47E-04, B: 7.76E-04 substitution/site/yr), but estimates of the time to the most recent common ancestor were much lower for RSV-B (B: 19, A: 46.8 yrs), indicating that there is more turnover in this subgroup. Conclusion: This study provides a detailed description of whole RSV genome mutations, the effect on translation products and the first estimate of the RSV genome evolution tempo. The immunogenic G protein seems to require high substitution rates in order to select less immunogenic strains and other conserved proteins are most likely essential to preserve RSV viability. The resulting G gene variability makes its protein a less interesting target for RSV intervention methods. The more conserved RSV F protein with less antigenic epitope shedding is, therefore, more suitable for developing therapeutic strategies or vaccines.

Keywords: drug target selection, epidemiology, respiratory syncytial virus, RSV

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Authors: Eriko Ochiai, Fumiko Satoh, Keiko Miyashita, Yu Kakimoto, Motoki Osawa

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Sudden and unexpected deaths from unknown causes occur in infants and youths. Recently, molecular links between a part of these deaths and several genetic diseases are examined in the postmortem. For instance, hereditary long QT syndrome and Burgada syndrome are occasionally fatal through critical ventricular tachyarrhythmia. There are a large number of target genes responsible for such diseases, the conventional analysis using the Sanger’s method has been laborious. In this report, we attempted to analyze sudden deaths comprehensively using the next generation sequencing (NGS) technique. Multiplex PCR to subject’s DNA was performed using Ion AmpliSeq Library Kits 2.0 and Ion AmpliSeq Inherited Disease Panel (Life Technologies). After the library was constructed by emulsion PCR, the amplicons were sequenced 500 flows on Ion Personal Genome Machine System (Life Technologies) according to the manufacture instruction. SNPs and indels were analyzed to the sequence reads that were mapped on hg19 of reference sequences. This project has been approved by the ethical committee of Tokai University School of Medicine. As a representative case, the molecular analysis to a 40 years old male who received a diagnosis of Brugada syndrome demonstrated a total of 584 SNPs or indels. Non-synonymous and frameshift nucleotide substitutions were selected in the coding region of heart disease related genes of ANK2, AKAP9, CACNA1C, DSC2, KCNQ1, MYLK, SCN1B, and STARD3. In particular, c.629T-C transition in exon 3 of the SCN1B gene, resulting in a leu210-to-pro (L210P) substitution is predicted “damaging” by the SIFT program. Because the mutation has not been reported, it was unclear if the substitution was pathogenic. Sudden death that failed in determining the cause of death constitutes one of the most important unsolved subjects in forensic pathology. The Ion AmpliSeq Inherited Disease Panel can amplify the exons of 328 genes at one time. We realized the difficulty in selection of the true source from a number of candidates, but postmortem genetic testing using NGS analysis deserves of a diagnostic to date. We now extend this analysis to SIDS suspected subjects and young sudden death victims.

Keywords: postmortem genetic testing, sudden death, SIDS, next generation sequencing

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Authors: Thomas Bryan, Veton Kepuska, Ivica Kostanic

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A simple adaptive voice activity detector (VAD) is implemented using Gabor and gammatone atomic decomposition of speech for high Gaussian noise environments. Matching pursuit is used for atomic decomposition, and is shown to achieve optimal speech detection capability at high data compression rates for low signal to noise ratios. The most active dictionary elements found by matching pursuit are used for the signal reconstruction so that the algorithm adapts to the individual speakers dominant time-frequency characteristics. Speech has a high peak to average ratio enabling matching pursuit greedy heuristic of highest inner products to isolate high energy speech components in high noise environments. Gabor and gammatone atoms are both investigated with identical logarithmically spaced center frequencies, and similar bandwidths. The algorithm performs equally well for both Gabor and gammatone atoms with no significant statistical differences. The algorithm achieves 70% accuracy at a 0 dB SNR, 90% accuracy at a 5 dB SNR and 98% accuracy at a 20dB SNR using 30dB SNR as a reference for voice activity.

Keywords: atomic decomposition, gabor, gammatone, matching pursuit, voice activity detection

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Authors: Sadaf Ilyas

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Recombinant cytokines have been employed successfully as potential therapeutic agent. Some cytokine therapies are already used as a part of clinical practice, ranging from early exploratory trials to well established therapies that have already received approval. Interleukin 15 is a pleiotropic cytokine having multiple roles in peripheral innate and adaptive immune cell function. It regulates the activation, proliferation and maturation of NK cells, T-cells, monocytes/macrophages and granulocytes, and the interactions between them thus acting as a bridge between innate and adaptive immune responses. Unraveling the biology of IL-15 has revealed some interesting surprises that may point toward some of the first therapeutic applications for this cytokine. In this study, the human interleukin 15 gene was isolated, amplified and ligated to a TA vector which was then transfected to a bacterial host, E. coli Top10F’. The sequence of cloned gene was confirmed and it showed 100% homology with the reported sequence. The confirmed gene was then subcloned in pET Expression system to study the IPTG induced expression of IL-15 gene. Positive expression was obtained for number of clones that showed 15 kd band of IL-15 in SDS-PAGE analysis, indicating the successful strain development that can be studied further to assess the potential therapeutic intervention of this cytokine in relevance to human diseases.

Keywords: Interleukin 15, pET expression system, immune therapy, protein purification

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Authors: Kuo-Cheng Liu

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In the perceptual image coding, the objective is to shape the coding distortion such that the amplitude of distortion does not exceed the error visibility threshold, or to remove perceptually redundant signals from the image. While most researches focus on color image coding, the perceptual-based quantizer developed for luminance signals are always directly applied to chrominance signals such that the color image compression methods are inefficient. In this paper, the internal generative mechanism is integrated into the design of a color image compression method. The internal generative mechanism working model based on the structure-based spatial masking is used to assess the subjective distortion visibility thresholds that are visually consistent to human eyes better. The estimation method of structure-based distortion visibility thresholds for color components is further presented in a locally adaptive way to design quantization process in the wavelet color image compression scheme. Since the lowest subband coefficient matrix of images in the wavelet domain preserves the local property of images in the spatial domain, the error visibility threshold inherent in each coefficient of the lowest subband for each color component is estimated by using the proposed spatial error visibility threshold assessment. The threshold inherent in each coefficient of other subbands for each color component is then estimated in a local adaptive fashion based on the distortion energy allocation. By considering that the error visibility thresholds are estimated using predicting and reconstructed signals of the color image, the coding scheme incorporated with locally adaptive perceptual color quantizer does not require side information. Experimental results show that the entropies of three color components obtained by using proposed IGM-based color image compression scheme are lower than that obtained by using the existing color image compression method at perceptually lossless visual quality.

Keywords: internal generative mechanism, structure-based spatial masking, visibility threshold, wavelet domain

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