Search results for: genetic markers

Authors: Seyed Reza Aghili, Tahereh Shokohi, Shirin Sadat Hashemi Fesharaki, Mohammad Ali Boroumand, Bahar Salmanian

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Introduction: Intravenous catheter-associated fungal infection as nosocomial infection continue to be a deep problem among hospitalized patients, decreasing quality of life and adding healthcare costs. The capacity of catheters in the spread of candidemia in heart failure patients is obvious. The aim of this study was to evaluate the prevalence and genetic identification of Candida species in heart disorder patients. Material and Methods: This study was conducted in Tehran Hospital of Cardiology Center (Tehran, Iran, 2014) during 1.5 years on the patients hospitalized for at least 7 days and who had central or peripheral vein catheter. Culture of catheters, blood and skin of the location of catheter insertion were applied for detecting Candida colonies in 223 patients. Identification of Candida species was made on the basis of a combination of various phenotypic methods and confirmed by sequencing the ITS1-5.8S-ITS2 region amplified from the genomic DNA using PCR and the NCBI BLAST. Results: Of the 223 patients samples tested, we identified totally 15 Candida isolates obtained from 9 (4.04%) catheter cultures, 3 (1.35%) blood cultures and 2 (0.90%) skin cultures of the catheter insertion areas. On the base of ITS region sequencing, out of nine Candida isolates from catheter, 5(55.6%) C. albicans, 2(22.2%) C. glabrata, 1(11.1%) C. membranifiaciens and 1 (11.1%) C. tropicalis were identified. Among three Candida isolates from blood culture, C. tropicalis, C. carpophila and C. membranifiaciens were identified. Non-candida yeast isolated from one blood culture was Cryptococcus albidus. One case of C. glabrata and one case of Candida albicans were isolated from skin culture of the catheter insertion areas in patients with positive catheter culture. In these patients, ITS region of rDNA sequence showed a similarity between Candida isolated from the skin and catheter. However, the blood samples of these patients were negative for fungal growth. We report two cases of catheter-related candidemia caused by C. membranifiaciens and C. tropicalis on the base of genetic similarity of species isolated from blood and catheter which were treated successfully with intravenous fluconazole and catheter removal. In phenotypic identification methods, we could only identify C. albicans and C. tropicalis and other yeast isolates were diagnosed as Candida sp. Discussion: Although more than 200 species of Candida have been identified, only a few cause diseases in humans. There is some evidence that non-albicans infections are increasing. Many risk factors, including prior antibiotic therapy, use of a central venous catheter, surgery, and parenteral nutrition are considered to be associated with candidemia in hospitalized heart failure patients. Identifying the route of infection in candidemia is difficult. Non-albicans candida as the cause of candidemia is increasing dramatically. By using conventional method, many non-albicans isolates remain unidentified. So, using more sensitive and specific molecular genetic sequencing to clarify the aspects of epidemiology of the unknown candida species infections is essential. The positive blood and catheter cultures for candida isolates and high percentage of similarity of their ITS region of rDNA sequence in these two patients confirmed the diagnosis of intravenous catheter-associated candidemia.

Keywords: catheter-associated infections, heart failure patient, molecular genetic sequencing, ITS region of rDNA, Candidemia

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Authors: Niousha Bagheri Khulenjani, Mohammad Saniee Abadeh

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Learning from very big datasets is a significant problem for most present data mining and machine learning algorithms. MicroRNA (miRNA) is one of the important big genomic and non-coding datasets presenting the genome sequences. In this paper, a hybrid method for the classification of the miRNA data is proposed. Due to the variety of cancers and high number of genes, analyzing the miRNA dataset has been a challenging problem for researchers. The number of features corresponding to the number of samples is high and the data suffer from being imbalanced. The feature selection method has been used to select features having more ability to distinguish classes and eliminating obscures features. Afterward, a Convolutional Neural Network (CNN) classifier for classification of cancer types is utilized, which employs a Genetic Algorithm to highlight optimized hyper-parameters of CNN. In order to make the process of classification by CNN faster, Graphics Processing Unit (GPU) is recommended for calculating the mathematic equation in a parallel way. The proposed method is tested on a real-world dataset with 8,129 patients, 29 different types of tumors, and 1,046 miRNA biomarkers, taken from The Cancer Genome Atlas (TCGA) database.

Keywords: cancer classification, feature selection, deep learning, genetic algorithm

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Authors: Eldho Paul, Brijesh Paul

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This work proposes an auction mechanism based solution methodology for the optimum scheduling of trucks in a cross-docking centre. The cross-docking centre is an important element of lean supply chain. It reduces the amount of storage and transportation costs in the distribution system compared to an ordinary warehouse. Better scheduling of trucks in a cross-docking center is the best way to reduce storage and transportation costs. Auction mechanism is commonly used for allocation of limited resources in different real-life applications. Here, we try to schedule inbound trucks by integrating auction mechanism with the functioning of a cross-docking centre. A mathematical model is developed for the optimal scheduling of inbound trucks based on the auction methodology. The determination of exact solution for problems involving large number of trucks was found to be computationally difficult, and hence a genetic algorithm based heuristic methodology is proposed in this work. A comparative study of exact and heuristic solutions is done using five classes of data sets. It is observed from the study that the auction-based mechanism is capable of providing good solutions to scheduling problem in cross-docking centres.

Keywords: auction mechanism, cross-docking centre, genetic algorithm, scheduling of trucks

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Authors: Aktar-Uz-Zaman, M. Tuhina-Khatun, Mohamed Hanafi Musa

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Three rust diseases: leaf (brown) rust caused by Puccinia triticina Eriks, stripe (yellow) rust caused by Puccinia striiformis West, and stem (black) rust caused by Puccinia graminis f. sp. tritici are economically important diseases of wheat in world wide. Yield loss due to leaf rust is 40% in susceptible cultivars. Yield losses caused by the stem rust pathogens in the mid of 20 century reached 20-30% in Eastern and Central Europe and the most virulent stem rust race Ug99 emerged first in Uganda and after that in Kenya, Ethiopia, Yemen, in the Middle East and South Asia. Yield losses were estimated up to 100%, whereas, up to 80% have been reported in Kenya during 1999. In case of stripe rust, severity level has been recorded 60% - 70% as compared to 100% severity of susceptible check in disease screening nurseries in Kenya. Improvement of resistant varieties or cultivars is the sustainable, economical and environmentally friendly approaches for increasing the global wheat production to suppress the rust diseases. More than 68 leaf rust, 49 stripe rust and 53 stem rust resistance genes have been identified in the global wheat cultivars or varieties using different molecular breeding approaches. Among these, Lr1, Lr9, Lr10, Lr19, Lr21, Lr24, Lr25, Lr28, Lr29, Lr34, Lr35, Lr37, Lr39, Lr47, Lr51, Lr3bg, Lr18, Lr40, Lr46, and Lr50 leaf rust resistance genes have been identified by using molecular, enzymatic and microsatellite markers from African, Asian, European cultivars of hexaploid wheat (Triticum aestivum), durum wheat and diploid wheat species. These genes are located on 20, of the 21 chromosomes of hexaploid wheat. Similarly, Sr1, Sr2, Sr24, and Sr3, Sr31 stem rust resistance genes have been recognized from wheat cultivars of Pakistan, India, Kenya, and Uganda etc. A race of P. striiformis (stripe rust) Yr9, Yr18, and Yr29 was first observed in East Africa, Italy, Pakistan and India wheat cultivars. These stripe rust resistance genes are located on chromosomes 1BL, 4BL, 6AL, 3BS and 6BL in bread wheat cultivars. All these identified resistant genes could be used for notable improvement of susceptible wheat cultivars in the future.

Keywords: hexaploid wheat, resistance genes, rust disease, triticum aestivum

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Authors: Elisaveta Kirilova, Wilfried Becker, Jordanka Ivanova, Tatyana Petrova

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The study is a continuation of the research on the hygrothermal piezoelectric response of a smart patch/layer joint with undesirable interface defect (gap) at dynamic time harmonic mechanical and electrical load and environmental conditions. In order to find the axial displacements, shear stress and interface debond length in a closed analytical form for different positions of the interface gap, the 1D modified shear lag analysis is used. The debond length is represented as a function of many parameters (frequency, magnitude, electric displacement, moisture and temperature, joint geometry, position of the gap along the interface, etc.). Then the Genetic algorithm (GA) is implemented to find this position of the gap along the interface at which a vanishing/minimal debond length is ensured, e.g to find the most harmless position for the safe work of the structure. The illustrative example clearly shows that analytical shear-lag solutions and GA method can be combined successfully to give an effective prognosis of interface shear stress and interface delamination in patch/layer structure at combined loading with existing defects. To show the effect of the position of the interface gap, all obtained results are given in figures and discussed.

Keywords: genetic algorithm, minimal delamination, optimal gap position, shear lag solution

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Authors: Abdu Qayyum, Hafiz Muhammad Saeed, Mamoona Hanif, Etrat Noor, Waqas Malik, Shoaib Liaqat

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Salinity is extremely serious problem that has a drastic effect on maize crop, environment and causes economic losses of country. An advance technique to overcome salinity is to develop salt tolerant geno types which require screening of huge germ plasm to start a breeding program. Therefore, present study was undertaken to screen out 25 maize hybrids of different origin for salinity tolerance at seedling stage under three levels of salt stress 250 and 300 mM NaCl including one control. The existence of variation for tolerance to enhanced NaCl salinity levels at seedling stage in maize proved that hybrids had differing ability to grow under saline environment and potential variability within specie. Almost all the twenty five maize hybrids behaved varyingly in response to different salinity levels. However, the maize hybrids H6, H13, H21, H23 and H24 expressed better performance under salt stress in terms of all six characters and proved to be as highly tolerant while H22, H17 H20, H18, H4, H9, and H8 were identified as moderately tolerant. Hybrids H14, H5, H11 and H3 H12, H2, were expressed as most sensitive to salinity suggesting that screening is an effective tool to exploit genetic variation among maize hybrids and salt tolerance in maize can be enhanced through selection and breeding procedure.

Keywords: salinity, hybrids, maize, variation

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Authors: Hosein Hamisheh Bahar, Mohammad Hossein Fazel Zarandi, Akbar Esfahanipour

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In this paper, a hybrid expert system is developed by using fuzzy genetic network programming with reinforcement learning (GNP-RL). In this system, the frame-based structure of the system uses the trading rules extracted by GNP. These rules are extracted by using technical indices of the stock prices in the training time period. For developing this system, we applied fuzzy node transition and decision making in both processing and judgment nodes of GNP-RL. Consequently, using these method not only did increase the accuracy of node transition and decision making in GNP's nodes, but also extended the GNP's binary signals to ternary trading signals. In the other words, in our proposed Fuzzy GNP-RL model, a No Trade signal is added to conventional Buy or Sell signals. Finally, the obtained rules are used in a frame-based system implemented in Kappa-PC software. This developed trading system has been used to generate trading signals for ten companies listed in Tehran Stock Exchange (TSE). The simulation results in the testing time period shows that the developed system has more favorable performance in comparison with the Buy and Hold strategy.

Keywords: fuzzy genetic network programming, hybrid expert system, technical trading signal, Tehran stock exchange

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Authors: Galal H. Senussi, Muamar Benisa, Sanja Vasin

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In our business field today, one of the most important issues for any enterprises is cost minimization and profit maximization. Second issue is how to develop a strong and capable model that is able to give us desired forecasting of these two issues. Many researches deal with these issues using different methods. In this study, we developed a model for multi-criteria production program optimization, integrated with Artificial Neural Network. The prediction of the production cost and profit per unit of a product, dealing with two obverse functions at same time can be extremely difficult, especially if there is a great amount of conflict information about production parameters. Feed-Forward Neural Networks are suitable for generalization, which means that the network will generate a proper output as a result to input it has never seen. Therefore, with small set of examples the network will adjust its weight coefficients so the input will generate a proper output. This essential characteristic is of the most important abilities enabling this network to be used in variety of problems spreading from engineering to finance etc. From our results as we will see later, Feed-Forward Neural Networks has a strong ability and capability to map inputs into desired outputs.

Keywords: project profitability, multi-objective optimization, genetic algorithm, Pareto set, neural networks

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Authors: Mohsen Rezaei Aghdam

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Recombinant DNA technology has meaningfully augmented the conventional crop improvement and has a great possibility to contribution plant breeders to encounter the augmented food request foretold for the 21st century. Predictable changes in weather and its erraticism, chiefly extreme fevers and vicissitudes in rainfall are expected to brand crop upgrading even more vital for food manufacture. Tissue attitude has been downtrodden to create genetic erraticism from which harvest plants can be better, to improve the state of health of the recognized physical and to upsurge the number of wanted germplasms obtainable to the plant breeder. This appraisal delivers an impression of the chances obtainable by the integration of vegetable biotechnology into plant development efforts and increases some of the social subjects that need to be considered in their application. Public-private companies offer chances to catalyze new approaches and investment while accelerating integrated research and development and commercial supply chain-based solutions. Novel varieties derivative by encouraged mutatgenesis are used commonly: rice in Thailand. These paper combinations obtainable data about the influence of change breeding-derived crop changes around the world, traveler magnetism the possibility of mutation upbringing as a flexible and feasible approach appropriate to any crop if that suitable objectives and selection approaches are used.

Keywords: crop, improve, genetic, agricultural

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Authors: M. Kislu Noman, Syed Mohammed Shamsul Islam, Shahriar Hassan, Raihana Pervin

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With the increasing rate of wireless devices and high bandwidth operations, wireless networking and communications are becoming over crowded. To cope with such crowdy and messy situation, massive MIMO is designed to work with hundreds of low costs serving antennas at a time as well as improve the spectral efficiency at the same time. TDD has been used for gaining beamforming which is a major part of massive MIMO, to gain its best improvement to transmit and receive pilot sequences. All the benefits are only possible if the channel state information or channel estimation is gained properly. The common methods to estimate channel matrix used so far is LS, MMSE and a linear version of MMSE also proposed in many research works. We have optimized these methods using genetic algorithm to minimize the mean squared error and finding the best channel matrix from existing algorithms with less computational complexity. Our simulation result has shown that the use of GA worked beautifully on existing algorithms in a Rayleigh slow fading channel and existence of Additive White Gaussian Noise. We found that the GA optimized LS is better than existing algorithms as GA provides optimal result in some few iterations in terms of MSE with respect to SNR and computational complexity.

Keywords: channel estimation, LMMSE, LS, MIMO, MMSE

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Authors: Okan Cakir, Okan Tatli

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Acute motor and sensory axonal neuropathy (AMSAN) syndrome usually occurs following a postviral infection in two to four weeks and is a polyneuropathy characterized by axonal and sensorial degeneration as a rare variant of Gullian-Barre syndrome. In our case, we wanted to mention that a rare case of AMSAN Syndrome due to prior surgery. A 61-year-old male case admitted to emergency department with complaints of weakness in feet, numbness and incapability to walk. In his history, it was learned that endovascular aneurysm repair (EVAR) had applied for abdominal aort aneurysm two weeks ago before admission, his complaints had been for a couple of days increasingly and bilaterally, and there had been no infection disease history for four weeks. In physical examination, general status was good, vital signs were stable, and there was a mild paresis in dorsal flexion of feet in bilaterally lower extremities. No nuchal rigidity was determined. Other system examinations were normal. Urea:52 mg/dL (normal range: 15-44 mg/dL), creatinine: 1,05 mg/dL (normal range: 0,81-1,4 mg/dL), potassium: 3,68 mmol/L (normal range: 3,5-5,5 mmol/L), glycaemia: 142 mg/dL, calcium: 9,71 mg/dL (normal range: 8,5-10,5 mg/dL), erythrocyte sedimentation rate (ESR): 74 mm/h (normal range: 0-15 mm/h) were determined in biochemical tests. The case was consulted to neurology department and hospitalized. In performing electromyography, it was reported as a bilateral significant axonal degeneration with sensory-motor polyneuropathy. Normal ranges of glycaemia and protein levels were detected in lumbal punction. Viral markers and bucella, toxoplasma, and rubella markers were in normal range. Intravenous immunoglobulin (IVIG) was applied as a treatment, physical treatment programme was planned and the case discharged from neurology department. In our case, we mentioned that it should be considered polyneuropathy as an alternative diagnosis in cases admitting symptoms like weakness and numbness had a history of prior surgery.

Keywords: AMSAN Syndrome, emergency department, prior surgery, weakness

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Authors: Davood Rajabi, Mojgan Yazdani

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Non-linear Muskingum model is an efficient method for flood routing, however, the efficiency of this method is influenced by three applied parameters. Therefore, efficiency assessment of Imperialist Competition Algorithm (ICA) to evaluate optimum parameters of non-linear Muskingum model was addressed through this study. In addition to ICA, Genetic Algorithm (GA) and Particle Swarm Optimization (PSO) were also used aiming at an available criterion to verdict ICA. In this regard, ICA was applied for Wilson flood routing; then, routing of two flood events of DoAab Samsami River was investigated. In case of Wilson flood that the target function was considered as the sum of squared deviation (SSQ) of observed and calculated discharges. Routing two other floods, in addition to SSQ, another target function was also considered as the sum of absolute deviations of observed and calculated discharge. For the first floodwater based on SSQ, GA indicated the best performance, however, ICA was on first place, based on SAD. For the second floodwater, based on both target functions, ICA indicated a better operation. According to the obtained results, it can be said that ICA could be used as an appropriate method to evaluate the parameters of Muskingum non-linear model.

Keywords: Doab Samsami river, genetic algorithm, imperialist competition algorithm, meta-exploratory algorithms, particle swarm optimization, Wilson flood

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Authors: Swarkar Sharma, Ekta Rai, Ankit Mahajan, Parvinder Kumar, Manoj K Dhar, Sushil Razdan, Kumarasamy Thangaraj, Carol Wise, Shiro Ikegawa M.D., K.K. Pandita M.D.

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Rare disorders are poorly understood hence, remain uncharacterized or patients are misdiagnosed and get poor medical attention. A rare mysterious skeletal disorder that remained unidentified for decades and rendered many people physically challenged and disabled for life has been reported in an isolated remote village ‘Arai’ of Poonch district of Jammu and Kashmir. This village is located deep in mountains and the population residing in the region is highly consanguineous. In our survey of the region, 70 affected people were reported, showing similar phenotype, in the village with a population of approximately 5000 individuals. We were able to collect samples from two multi generational extended families from the village. Through Whole Exome sequencing (WES), we identified a rare variation NM_003880.3:c.156C>A NP_003871.1:p.Cys52Ter, which results in introduction of premature stop codon in WISP3 gene. We found this variation perfectly segregating with the disease in one of the family. However, this variation was absent in other family. Interestingly, a novel splice site mutation at position c.643+1G>A of WISP3 gene, perfectly segregating with the disease was observed in the second family. Thus, exploiting WES and putting different evidences together (familial histories and genetic data, clinical features, radiological and biochemical tests and findings), the disease has finally been diagnosed as a very rare recessive hereditary skeletal disease “Progressive Pseudorheumatoid Arthropathy of Childhood” (PPAC) also known as “Spondyloepiphyseal Dysplasia Tarda with Progressive Arthropathy” (SEDT-PA). This genetic characterization and identification of the disease causing mutations will aid in genetic counseling, critically required to curb this rare disorder and to prevent its appearance in future generations in the population. Further, understanding of the role of WISP3 gene the biological pathways should help in developing treatment for the disorder.

Keywords: whole exome sequencing, Next Generation Sequencing, rare disorders

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Authors: M. Karthigayan, M. Rizon, Sazali Yaacob, R. Nagarajan, M. Muthukumaran, Thinaharan Ramachandran, Sargunam Thirugnanam

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In this paper, using a set of irregular and regular ellipse fitting equations using Genetic algorithm (GA) are applied to the lip and eye features to classify the human emotions. Two South East Asian (SEA) faces are considered in this work for the emotion classification. There are six emotions and one neutral are considered as the output. Each subject shows unique characteristic of the lip and eye features for various emotions. GA is adopted to optimize irregular ellipse characteristics of the lip and eye features in each emotion. That is, the top portion of lip configuration is a part of one ellipse and the bottom of different ellipse. Two ellipse based fitness equations are proposed for the lip configuration and relevant parameters that define the emotions are listed. The GA method has achieved reasonably successful classification of emotion. In some emotions classification, optimized data values of one emotion are messed or overlapped to other emotion ranges. In order to overcome the overlapping problem between the emotion optimized values and at the same time to improve the classification, a fuzzy clustering method (FCM) of approach has been implemented to offer better classification. The GA-FCM approach offers a reasonably good classification within the ranges of clusters and it had been proven by applying to two SEA subjects and have improved the classification rate.

Keywords: ellipse fitness function, genetic algorithm, emotion recognition, fuzzy clustering

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Authors: Lamis Naddaf, Yuval Tabach

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In this research, we identified the missense genetic variants that have the potential to enhance resistance against cancer. Such field has not been widely explored, as researchers tend to investigate mutations that cause diseases, in response to the suffering of patients, rather than those mutations that protect from them. In conjunction with the genomic revolution, and the advances in genetic engineering and synthetic biology, identifying the protective variants will increase the power of genotype-phenotype predictions and can have significant implications on improved risk estimation, diagnostics, prognosis and even for personalized therapy and drug discovery. To approach our goal, we systematically investigated the sites of the coding genomes and picked up the alleles that showed a correlation with the species’ cancer resistance. We predicted 250 protecting variants (PVs) with a 0.01 false discovery rate and more than 20 thousand PVs with a 0.25 false discovery rate. Cancer resistance in Mammals and reptiles was significantly predicted by the number of PVs a species has. Moreover, Genes enriched with the protecting variants are enriched in pathways relevant to tumor suppression like pathways of Hedgehog signaling and silencing, which its improper activation is associated with the most common form of cancer malignancy. We also showed that the PVs are more abundant in healthy people compared to cancer patients within different human races.

Keywords: comparative genomics, machine learning, cancer resistance, cancer-protecting alleles

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Authors: Yaxuan Wang

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It has long been a mystery that why the Mongolian possessive suffix, which is constrained by Condition A of binding theory, has the ability to probe a potential antecedent outside of its binding domain. This squib argues that binding theory alone is not sufficient to explain the linguistic facts and proposes an analysis adopting the Agree operation. The current analysis correctly predicts all the possible and impossible structures, with an additional hypothesis that Mongolian possessive suffixes serve as an antecedent for PROs in adjunct. The findings thus provide insights into how Agree operates in Mongolian language.

Keywords: syntax, Mongolian, agreement, possessive particles

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Authors: Rozeena Baig, R. Rehana Rehman, Rifat Ahmed

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Background: Osteoporosis, characterized by low bone mineral density, poses a global health concern. Diagnosis increases the likelihood of developing osteoporosis, a multifactorial disorder marked by low bone mass, elevating the risk of fractures in the lumbar spine, femoral neck, hip, vertebras, and distal forearm, particularly in postmenopausal women due to bone loss influenced by various pathophysiological factors. Objectives: The aim is to investigate the association of serum cytokine, bone turnover marker, bone mineral density and TLR4 gene polymorphism in pre and post-menopausal women and to find if any of these can be the potential predictor of osteoporosis in postmenopausal women. Material and methods: The study participants consisted of Group A (n=91) healthy pre-menopausal women and Group B (n=102) healthy postmenopausal women having ≥ 5 years’ history of menopause. ELISA was performed for cytokine (TNFα) and bone turnover markers (carboxytelopeptides), respectively. Bone Mineral Density (BMD)was measured through a dual X-ray absorptiometry (DEXA) scan. Toll-like Receptors 4 (TLR4) gene polymorphisms (A896G; Asp299Gly) and (C1196T; Thr399Ile) were investigated by PCR and Sanger sequencing. Results: Statistical analysis reveals a positive correlation of age and BMI with T scores in the premenopausal group, whereas in post-menopausal group found a significant negative correlation between age and T-score at hip (r = - 0.352**), spine (r = - .306**), and femoral neck (r = - 0.344**) and a significant negative correlation of BMI with TNF-α (- 0.316**). No association and significant differences were observed for TLR4 genotype and allele frequencies among studied groups However, both SNPs exhibited significant association with each other. Conclusions: This study concludes that BMI, BMD and TNF-α are the potential predictors of osteoporosis in post-menopausal women. However, CTX and TLR4 gene polymorphism did not appear as potential predictors of bone loss in this study and apparently cannot help in predicting bone loss in post-menopausal women.

Keywords: osteoporosis, post-menopausal, pre-menopausal woemn, genetics mutaiont, TLR4 genepolymorphsum

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Authors: Yuechao Lei, Lei Zhang

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The interface shear between asphalt overlay and existing rigid airport pavements occurs due to differences in the mechanical properties of materials subjected to aircraft loading. Interlayer contact influences the mechanical characteristics of the asphalt overlay directly. However, the effective interlayer relative displacement obtained accurately using existing displacement sensors of the loading apparatus remains challenging. This study aims to utilize digital image correlation technology to enhance the accuracy of interfacial contact parameters by obtaining effective interlayer relative displacements. Composite structure specimens were prepared, and fixtures for interlayer shear tests were designed and fabricated. Subsequently, a digital image recognition scheme for required markers was designed and optimized. Effective interlayer relative displacement values were obtained through image recognition and calculation of surface markers on specimens. Finite element simulations validated the mechanical response of composite specimens with interlayer shearing. Results indicated that an optimized marking approach using the wall mending agent for surface application and color coding enhanced the image recognition quality of marking points on the specimen surface. Further image extraction provided effective interlayer relative displacement values during interlayer shear, thereby improving the accuracy of interface contact parameters. For composite structure specimens utilizing Styrene-Butadiene-Styrene (SBS) modified asphalt as the tack coat, the corresponding maximum interlayer shear stress strength was 0.6 MPa, and fracture energy was 2917 J/m2. This research provides valuable insights for investigating the impact of interlayer contact in composite pavement structures on the mechanical characteristics of asphalt overlay.

Keywords: interlayer contact, effective relative displacement, digital image correlation technology, composite pavement structure, asphalt overlay

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Authors: Christian Angerer, Markus Lienkamp

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Electric vehicles offer a high variety of possible drivetrain topologies with up to 4 motors. Multi-motor-designs can have several advantages regarding traction, vehicle dynamics, safety and even efficiency. With a rising number of motors, the whole drivetrain becomes more complex. All permutations of gearings, drivetrain-layouts, motor-types and –sizes lead up in a very large solution space. Single elements of this solution space can be analyzed by simulation methods. In addition to longitudinal vehicle behavior, which most optimization-approaches are restricted to, also lateral dynamics are important for vehicle dynamics, stability and efficiency. In order to compete large solution spaces and to find an optimal result, genetic algorithm based optimization is state-of-the-art. As lateral dynamics simulation is way more CPU-intensive, optimization takes much more time than in case of longitudinal-only simulation. Therefore, this paper shows an approach how to create meta-models from a 14-degree of freedom vehicle model in order to enable a numerically efficient drivetrain-layout optimization process under consideration of lateral dynamics. Different meta-modelling approaches such as neural networks or DoE are implemented and comparatively discussed.

Keywords: driving dynamics, drivetrain layout, genetic optimization, meta-modeling, lateral dynamicx

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Authors: Anil Kumar, Diwakar Aggarwal, M. Sudhakara Reddy

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The wood of Eucalyptus, Populus and bamboos are some important species used as raw material for the manufacture of pulp. However, higher levels of lignin pose a problem during Kraft pulping and yield of pulp is also lower. In order to increase the yield of pulp per unit wood and reduce the use of chemicals during kraft pulping it is important to reduce the lignin content and/or increase cellulose content in wood. Cellulose biosynthesis in wood takes place by the coordinated action of many enzymes. The two important enzymes are KORRIGAN and SUCROSE SYNTHASE. KORRIGAN (Endo-1,4--glucanase) is implicated in the process of editing growing cellulose chains and improvement of the crystallinity of produced cellulose, whereas SUCROSE SYNTHASE is involved in providing substrate (UDP-glucose) for growing cellulose chains. The present study was aimed at the cloning, characterization and overexpression of these genes in Eucalyptus and Populus. An efficient shoot organogenesis protocol from leaf explants taken from micro shoots of the species has been developed. Agrobacterium mediated genetic transformation using Agrobacterium tumefaciens strain EHA105 and LBA4404 harboring binary vector pBI121 was achieved. Both the genes were cloned from cDNA library of Populus deltoides. These were subsequently characterized using various bioinformatics tools. The cloned genes were then inserted into pBI121 under the CaMV35S promotors replacing GUS gene. The constructs were then mobilized into above strains of Agrobacterium and used for the transformation work. Subsequently, genetic transformation of these clones with target genes following already developed protocol is in progress. Four transgenic lines of Eucalyptus tereticornis overexpressing Korrigan gene under the strong constitutive promoters CaMV35S have been developed, which are being further evaluated. Work on development of more transgenic lines overexpressing these genes in Populus and Eucalyptus is also in progress. This presentation will focus on important developments in this direction.

Keywords: Eucalyptus tereticornis, genetic transformation, Kraft pulping Populus deltoides

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Authors: Basheer Idrees Balarabe, Aminu Hamisu Kura, Nabila Shehu

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As the power demand rapidly increases, the generation and transmission systems are affected because of inadequate resources, environmental restrictions and other losses. The role of transient stability control in maintaining the steady-state operation in the occurrence of large disturbance and fault is to describe the ability of the power system to survive serious contingency in time. The application of a Unified power flow controller (UPFC) plays a vital role in controlling the active and reactive power flows in a transmission line. In this research, a genetic algorithm (GA) method is applied to determine the optimal location of the UPFC device in a power system network for the enhancement of the power-system Transient Stability. Optimal location of UPFC has Significantly Improved the transient stability, the damping oscillation and reduced the peak over shoot. The GA optimization Technique proposed was iteratively searches the optimal location of UPFC and maintains the unusual bus voltages within the satisfy limits. The result indicated that transient stability is improved and achieved the faster steady state. Simulations were performed on the IEEE 14 Bus test systems using the MATLAB/Simulink platform.

Keywords: UPFC, transient stability, GA, IEEE, MATLAB and SIMULINK

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Authors: Aftab Khan, Ashfaq Khan

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The research paper focuses on an interesting challenge faced in Blind Image Deblurring (BID). It relates to the estimation of arbitrarily shaped or non-parametric Point Spread Functions (PSFs) of motion blur caused by camera handshake. These PSFs exhibit much more complex shapes than their parametric counterparts and deblurring in this case requires intricate ways to estimate the blur and effectively remove it. This research work introduces a novel blind deblurring scheme visualized for deblurring images corrupted by arbitrarily shaped PSFs. It is based on Genetic Algorithm (GA) and utilises the Blind/Reference-less Image Spatial QUality Evaluator (BRISQUE) measure as the fitness function for arbitrarily shaped PSF estimation. The proposed BID scheme has been compared with other single image motion deblurring schemes as benchmark. Validation has been carried out on various blurred images. Results of both benchmark and real images are presented. Non-reference image quality measures were used to quantify the deblurring results. For benchmark images, the proposed BID scheme using BRISQUE converges in close vicinity of the original blurring functions.

Keywords: blind deconvolution, blind image deblurring, genetic algorithm, image restoration, image quality measures

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Authors: Lamis Naddaf, Yuval Tabach

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We identified missense genetic variants with the potential to enhance resistance against cancer. Such a field has not been widely explored as researchers tend to investigate the mutations that cause diseases, in response to the suffering of patients, rather than those mutations that protect from them. In conjunction with the genomic revolution and the advances in genetic engineering and synthetic biology, identifying the protective variants will increase the power of genotype-phenotype predictions and have significant implications for improved risk estimation, diagnostics, prognosis, and even personalized therapy and drug discovery. To approach our goal, we systematically investigated the sites of the coding genomes and selected the alleles that showed a correlation with the species’ cancer resistance. Interestingly, we found several amino acids that are more generally preferred (like the Proline) or avoided (like the Cysteine) by the resistant species. Furthermore, Cancer resistance in mammals and reptiles is significantly predicted by the number of the predicted protecting variants (PVs) a species has. Moreover, PVs-enriched-genes are enriched in pathways relevant to tumor suppression. For example, they are enriched in the Hedgehog signaling and silencing pathways, which its improper activation is associated with the most common form of cancer malignancy. We also showed that the PVs are mostly more abundant in healthy people compared to cancer patients within different human races.

Keywords: cancer resistance, protecting variant, naked mole rat, comparative genomics

Procedia PDF Downloads 112

Authors: Ankush Kalra, Mirza Masroor, Usha Manaktala, B. C. Koner, T. K. Mishra

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Introduction: Pre-eclampsia affects 3-5% of pregnancies worldwide and increases maternal-fetal morbidity and mortality. Reduced placental perfusion induces the release of biomolecules by the placenta into maternal circulation causing endothelial dysfunction. Zinc dependent matrix metalloproteinase-2 (MMP-2) may be up-regulated and interact with circulating factors of oxidative stress and inflammation to produce endothelial dysfunction in pre-eclampsia. Aim: To study the functional genetic polymorphism of MMP-2 gene (g-1306 C>T) in pre-eclampsia and its effect on serum MMP-2 levels in these patients. Method: Hundred pre-eclampsia patients and hundred age and gestation period matched healthy pregnant women with their consent were recruited in the study. Serum MMP-2 levels in all subjects were estimated using standard ELISA kits. MMP-2 gene (g.- 1306 C>T) SNPs were genotyped using whole blood by ASO-PCR. Result: The pre-eclampsia patients had higher serum levels of MMP-2 compared to the healthy pregnant (p < 0.05). Also the MMP-2 genotype was associated with significant alteration in the serum MMP-2 concentration in these patients (p < 0.05). Conclusion: This study results suggest an association of MMP-2 genetic polymorphism and serum levels of MMP-2 to the path physiology of hypertensive disorder of pregnancy.

Keywords: allele specific oligonucleotide polymerase chain reaction (ASO-PCR), enzyme linked immunosorbent assay (ELISA), matrix metalloproteinase-2 (MMP-2), pre-eclampsia

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Authors: Haile Berihulay, Chenglong Luo

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Avian influenza, commonly known as bird flu, is a highly contagious viral disease primarily affecting poultry and wild birds, with significant implications for both animal health and public safety. The influenza virus (IV) is notorious for its ability to mutate and infect multiple species, including humans, leading to severe consequences. Avian influenza poses considerable pandemic risks due to the potential evolution of low pathogenic avian influenza (LPAI) into highly pathogenic avian influenza (HPAI), which can cause rapid outbreaks in domestic flocks. While AVI viruses typically do not replicate well in humans, strains such as H5N1 and H7N9 have crossed the species barrier, raising alarm over human infections. The recent documentation of human transmission of the H5N8 strain from birds underscores the ongoing threat posed by avian influenza. This review necessitates a thorough discussion about the genetic foundation of viral pathogens, identifying key candidate genes linked to disease resilience, and discussing powerful tools. This review can help researchers to comprehensively overview the disease severity and combat related to AIV, which causes significant economic impact and set effective control strategies to mitigate the risks associated with avian influenza outbreaks.

Keywords: Avian, candidate genes, chicken, molecular, pathogen, virus

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Authors: Barbara Farinon, Maurizio E. Picarella, Lorenzo Mancini, Andrea Mazzucato

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Italy is notoriously a secondary center of diversification for cultivated tomatoes (Solanum lycopersicum L.). The study of phenotypic and genetic diversity in landrace collections is important for germplasm conservation and biodiversity protection. Here, we set up to study the germplasm collected in the region of Lazio in Central Italy with a focus on the distinctiveness among landraces and the attribution of membership to unnamed accessions. Our regional collection included 30 accessions belonging to six different locally recognized landraces and 21 unnamed accessions. All accessions were gathered in Lazio and belonged to the collection held at the Regional Agency for the Development and Innovation of Agriculture in Lazio (ARSIAL, in the application of the Regional Act n. 15/2000, funded by Lazio Rural Development Plan 2014 – 2020 Agro-environmental Measure, Action 10.2.1) and at the University of Tuscia. We included 13 control genotypes as references. The collection showed wide phenotypic variability for several traits, such as fruit weight (range 14-277 g), locule number (2-12), shape index (0.54-2.65), yield (0.24-3.08 kg/plant), and soluble solids (3.4-7.5 °B). A few landraces showed uncommon phenotypes, such as potato leaf, colorless fruit epidermis, or delayed ripening. Multivariate analysis of 25 cardinal phenotypic variables grouped the named varieties and allowed to assign of some of the unnamed to recognized groups. A case study for distinctiveness is presented for the flattened-ribbed types that presented overlapping distribution according to the phenotypic data. Molecular markers retrieved by previous studies revealed differences compared to the phenotyping clustering, indicating that the named varieties “Scatolone di Bolsena” and “Pantano Romanesco” belong to the Marmande group, together with the reference landrace from Tuscany “Costoluto Fiorentino”. Differently, the landrace “Spagnoletta di Formia e Gaeta” was clearly distinct from the former at the molecular level. Therefore, a genotypic analysis of the analyzed collection appears needed to better define the molecular distinctiveness among the flattened-ribbed accessions, as well as to properly attribute the membership group of the unnamed accessions.

Keywords: distinctiveness, flattened-ribbed fruits, regional landraces, tomato

Procedia PDF Downloads 139

Authors: Chih-Hsin Lin, Shyh-Yuan Lee, Yuan-Min Lin

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For many tissue engineering applications, an important goal is to create functional tissues in-vitro, and such tissues to be viable, they have to be vascularized. Endothelial cells (EC) and endothelial progenitor cells (EPC) are promising candidates for vascularization. However, both of them have limited expansion capacity and autologous cells currently do not exist for either ECs or EPCs. Therefore, we use bone marrow mesenchymal stem cells (MSC) as a source material for ECs. Growth supplements are commonly used to induce MSC differentiation, and further improvements in differentiation conditions can be made by modifying the cell's growth environment. An example is pre-treatment of the growth dish with gas plasma, in order to modify the surface functional groups of the material that the cells are seeded on. In this work, we compare the effects of different gas plasmas on the growth and differentiation of MSCs. We treat the dish with different plasmas (CO2, N2, and O2) and then induce MSC differentiation with endothelial growth medium-2 (EGM-2). We find that EGM-2 by itself upregulates EC marker CD31 mRNA expression, but not VEGFR2, CD34, or vWF. However, these additional EC marker expressions were increased for cells seeded on plasma treated substrates. Specifically, for EC markers, we found that N2 plasma treatment upregulated CD31 and VEGFR-2 mRNA expressions; CO2 plasma treatment upregulated CD34 and vWF mRNA expressions. The osteogenic markers ALP and osteopontin mRNA expressions were markedly enhanced on all plasma-treated dishes. We also found that plasma treatment in conjunction with EGM-2 growth medium can enhance MSCs differentiation into endothelial-like cells and osteogenic-like cells. Our work shows that the effect of the growth medium (EGM-2) on MSCs differentiation is influenced by the plasma modified surface chemistry of the substrate. In conclusion, plasma surface modification can enhance EGM-2 effectiveness and induced both endothelial and osteogenic differentiation. Our findings provide a method to enhance EGM-2 based cell differentiation, with consequences for tissue engineering and stem cell biology applications.

Keywords: endothelial differentiation, EGM-2, osteogenesis, plasma treatment, surface modification

Procedia PDF Downloads 333

Authors: Anchal Rana

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Indian Himalayas with their diverse climatic conditions are home to many rare and endangered medicinal flora. One such species is Polygonatum verticillatum Linn., popularly known as King Solomon’s Seal or Solomon’s Seal. Its mention as an incredible medicinal herb comes from 5000 years ago in Indian Materia Medica as a component of Ashtavarga, a poly-herbal formulation comprising of eight herbs illustrated as world’s first ever revitalizing and rejuvenating nutraceutical food, which is now commercialised in the name ‘Chaywanprash’. It is an erect tall (60 to 120 cm) perennial herb with sessile, linear leaves and white pendulous flowers. The species grows well in an altitude range of 1600 to 3600 m amsl, and propagates mostly through rhizomes. The rhizomes are potential source for significant phytochemicals like flavonoids, phenolics, lectins, terpenoids, allantoin, diosgenin, β-Sitosterol and quinine. The presence of such phytochemicals makes the species an asset for antioxidant, cardiotonic, demulcent, diuretic, energizer, emollient, aphrodisiac, appetizer, glactagogue, etc. properties. Having profound concentrations of macro and micronutrients, species has fine prospects of being used as a diet supplement. However, due to unscientific and gregarious uprooting, it has been assigned a status of ‘vulnerable’ and ‘endangered’ in the Conservation Assessment and Management Plan (CAMP) process conducted by Foundation for Revitalisation of Local Health Traditions (FRLHT) during 2010, according to IUCN Red-List Criteria. Further, destructive harvesting, land use disturbances, heavy livestock grazing, climatic changes and habitat fragmentation have substantially contributed towards anomaly of the species. It, therefore, became imperative to conserve the diversity of the species and make judicious use in future research and commercial programme and schemes. A Gene Bank was therefore established at High Altitude Herbal Garden of the Forest Research Institute, Dehradun, India situated at Chakarata (30042’52.99’’N, 77051’36.77’’E, 2205 m amsl) consisting 149 accessions collected from thirty-one geographical locations spread over three Himalayan States of Jammu and Kashmir, Himachal Pradesh, and Uttarakhand. The present investigations purport towards sampling and collection of divergent germplasm followed by planting and cultivation techniques. The ultimate aim is thereby focussed on analysing genetic diversity of the species and capturing promising genotypes for carrying out further genetic improvement programme so to contribute towards sustainable development and healthcare.

Keywords: Polygonatum verticillatum Linn., phytochemicals, genetic diversity, conservation, gene bank

Procedia PDF Downloads 173

Authors: Jean Pierre Kabue, Emma Meader, Afsatou Ndama Traore, Paul R. Hunter, Natasha Potgieter

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Norovirus is now considered the most common cause of outbreaks of nonbacterial gastroenteritis. Limited data are available for Norovirus strains in Africa, especially in rural and peri-urban areas. Despite the excessive burden of diarrhea disease in developing countries, Norovirus infections have been to date mostly reported in developed countries. There is a need to investigate intensively the role of viral agents associated with diarrhea in different settings in Africa continent. To determine the prevalence and genetic diversity of Norovirus strains circulating in the rural communities in the Limpopo Province, South Africa and investigate the genetic relationship between Norovirus strains, a cross-sectional study was performed on human stools collected from rural communities. Between July 2014 and April 2015, outpatient children under 5 years of age from rural communities of Vhembe District, South Africa, were recorded for the study. A total of 303 stool specimens were collected from those with diarrhea (n=253) and without (n=50) diarrhea. NoVs were identified using real-time one-step RT-PCR. Partial Sequence analyses were performed to genotype the strains. Phylogenetic analyses were performed to compare identified NoVs genotypes to the worldwide circulating strains. Norovirus detection rate was 41.1% (104/253) in children with diarrhea. There was no significant difference (OR=1.24; 95% CI 0.66-2.33) in Norovirus detection between symptomatic and asymptomatic children. Comparison of the median CT values for NoV in children with diarrhea and without diarrhea revealed significant statistical difference of estimated GII viral load from both groups, with a much higher viral burden in children with diarrhea. To our knowledge, this is the first study reporting on the differences in estimated viral load of GII and GI NoV positive cases and controls. GII.Pe (n=9) were the predominant genotypes followed by GII.Pe/GII.4 Sydney 2012 (n=8) suspected recombinant and GII.4 Sydney 2012 variants(n=7). Two unassigned GII.4 variants and an unusual RdRp genotype GII.P15 were found. With note, the rare GIIP15 identified in this study has a common ancestor with GIIP15 strain from Japan previously reported as GII/untypeable recombinant strain implicated in a gastroenteritis outbreak. To our knowledge, this is the first report of this unusual genotype in the African continent. Though not confirmed predictive of diarrhea disease in this study, the high detection rate of NoV is an indication of subsequent exposure of children from rural communities to enteric pathogens due to poor sanitation and hygiene practices. The results reveal that the difference between asymptomatic and symptomatic children with NoV may possibly be related to the NoV genogroups involved. The findings emphasize NoV genetic diversity and predominance of GII.Pe/GII.4 Sydney 2012, indicative of increased NoV activity. An uncommon GII.P15 and two unassigned GII.4 variants were also identified from rural settings of the Vhembe District/South Africa. NoV surveillance is required to help to inform investigations into NoV evolution, and to support vaccine development programmes in Africa.

Keywords: asymptomatic, common, outpatients, norovirus genetic diversity, sporadic gastroenteritis, South African rural communities, symptomatic

Procedia PDF Downloads 196

Authors: Hieu Van Dong, Giang Thi Huong Tran, Giap Van Nguyen, Tung Duy Dao, Vuong Nghia Bui, Le Thi My Huynh, Yohei Takeda, Haruko Ogawa, Kunitoshi Imai

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Chicken anemia virus (CAV) has a ubiquitous and worldwide distribution in chicken production. Our group previously reported high seroprevalence of CAV in chickens in northern Vietnam. In the present study, 330 tissue samples collected from commercial and breeder chicken farms in eleven provinces in northern Vietnam were tested for the CAV infection. We found that 157 out of 330 (47.58%) chickens were positive with CAV genes by real-time PCR method. Nine CAV strains obtained from the different location and time were forwarded to the full-length sequence of CAV VP1 gene. Phylogenetic analysis of the Vietnamese CAV vp1 gene indicated that the CAVs circulating in northern Vietnam were divided into three distinct genotypes, II, III, and V, but not clustered with the vaccine strains. Among the three genotypes, genotype III was the major one widely spread in Vietnam, and that included three sub-genotypes, IIIa, IIIb, and IIIc. The Vietnamese CAV strains were closely related to the Chinese, Taiwanese, and USA strains. All the CAV isolates had glutamine at amino acid position 394 in the VP1 gene, suggesting that they might be highly pathogenic strains. One strain was defined to be genotype V, which had not been reported for Vietnamese CAVs. Additional studies are required to further evaluate the pathogenicity of CAV strains circulating in Vietnam.

Keywords: chicken anemia virus, genotype, genetic characteristics, Vietnam

Procedia PDF Downloads 167