Search results for: genetic testing

Authors: Assiya Madenovna Borsynbayeva, Kairat Altynbekovich Turgenbayev, Nikolay Petrovich Ivanov

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In this article presents the results of rapid diagnostics of tuberculosis in comparison with classical bacteriological method. The proposed method of rapid diagnosis of tuberculosis than bacteriological method allows shortening the time of diagnosis to 7 days, to visualize the growth of mycobacteria in the semi-liquid medium and differentiate the type of mycobacterium. Fast definition of Mycobacterium tuberculosis and its derivatives in the culture medium is a new and promising direction in the diagnosis of tuberculosis.

Keywords: animal diagnosis of tuberculosis, bacteriological diagnostics, antigen, specific antibodies, immunological reaction

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Authors: A. Y. Purnama, N. Yasufuku

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The bridge structure is a building that has to be maintained, especially for the elastomeric bearing. The girder of the bridge needs to be lifted upward to maintain this elastomeric bearing, that needs high cost. Nowadays, integral abutment bridges are becoming popular. The integral abutment bridge is less costly because the elastomeric bearings are eliminated, which reduces the construction cost and maintenance costs. However, when this elastomeric bearing removed, the girder movement due to environmental thermal forces directly support by pile foundation, and it needs to be considered in the design. In case of pile foundation in a stiff soil, in the top area of the pile cannot move freely due to the fixed condition by soil stiffness. Pre-bored pile system can be used to increase the flexibility of pile foundation using a pre-bored hole that filled with elastic materials, but the behavior of soil-pile interaction and soil response due to this system is still rarely explained. In this paper, an experimental study using small-scale laboratory model test conducted in a half size model. Single flexible pile model embedded in sandy soil with the pre-bored ring, which filled with the filler material. The testing box made from an acrylic glass panel as observation area of the pile shaft to monitor the displacement of the pile during the lateral loading. The failure behavior of the soil inside the pre-bored ring and around the pile shaft was investigated to determine the point of pile rotation and the movement of this point due to the pre-bored ring system along the pile shaft. Digital images were used to capture the deformations of the soil and pile foundation during the loading from the acrylic glass on the side of the testing box. The results were presented in the form of lateral load resistance charts against the pile shaft displacement. The failure pattern result also established due to the cyclic lateral loading. The movement of the rotational point was measured due to the pre-bored system filled with appropriate filler material. Based on the findings, design considerations for pre-bored pile system due to cyclic lateral loading can be introduced.

Keywords: failure behavior, pre-bored pile system, cyclic lateral loading, sandy soil

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Authors: Meng-Fei Cheng, Wei Fneg

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New Taiwan high school standards emphasize employing scientific models and modeling practices in physics learning. However, to our knowledge. Few studies address how scientific models and modeling are approached in current science teaching, and they do not examine the views of scientific models portrayed in the textbooks. To explore the views of scientific models and modeling in textbooks, this study investigated the atomic unit in different textbook versions as an example and provided suggestions for modeling curriculum. This study adopted a quantitative analysis of qualitative data in the atomic units of four mainstream version of Taiwan high school physics textbooks. The models were further analyzed using five dimensions of the views of scientific models (nature of models, multiple models, purpose of the models, testing models, and changing models); each dimension had three levels (low, medium, high). Descriptive statistics were employed to compare the frequency of describing the five dimensions of the views of scientific models in the atomic unit to understand the emphasis of the views and to compare the frequency of the eight scientific models’ use to investigate the atomic model that was used most often in the textbooks. Descriptive statistics were further utilized to investigate the average levels of the five dimensions of the views of scientific models to examine whether the textbooks views were close to the scientific view. The average level of the five dimensions of the eight atomic models were also compared to examine whether the views of the eight atomic models were close to the scientific views. The results revealed the following three major findings from the atomic unit. (1) Among the five dimensions of the views of scientific models, the most portrayed dimension was the 'purpose of models,' and the least portrayed dimension was 'multiple models.' The most diverse view was the 'purpose of models,' and the most sophisticated scientific view was the 'nature of models.' The least sophisticated scientific view was 'multiple models.' (2) Among the eight atomic models, the most mentioned model was the atomic nucleus model, and the least mentioned model was the three states of matter. (3) Among the correlations between the five dimensions, the dimension of 'testing models' was highly related to the dimension of 'changing models.' In short, this study examined the views of scientific models based on the atomic units of physics textbooks to identify the emphasized and disregarded views in the textbooks. The findings suggest how future textbooks and curriculum can provide a thorough view of scientific models to enhance students' model-based learning.

Keywords: atomic models, textbooks, science education, scientific model

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Authors: Filip Rusak, Yulia Arzhaeva, Dadong Wang

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Machine learning based Computer-Aided Diagnosis (CAD) is gaining much popularity in medical imaging and diagnostic radiology. However, it requires a large amount of high quality and labeled training image datasets. The training images may come from different sources and be acquired from different radiography machines produced by different manufacturers, digital or digitized copies of film radiographs, with various sizes as well as different pixel intensity distributions. In this paper, a content-aware image augmentation method is presented to deal with these variations. The results of the proposed method have been validated graphically by plotting the removed and added seams of pixels on original images. Two different chest X-ray (CXR) datasets are used in the experiments. The CXRs in the datasets defer in size, some are digital CXRs while the others are digitized from analog CXR films. With the proposed content-aware augmentation method, the Seam Carving algorithm is employed to resize CXRs and the corresponding labels in the form of image masks, followed by histogram matching used to normalize the pixel intensities of digital radiography, based on the pixel intensity values of digitized radiographs. We implemented the algorithms, resized the well-known Montgomery dataset, to the size of the most frequently used Japanese Society of Radiological Technology (JSRT) dataset and normalized our digital CXRs for testing. This work resulted in the unified off-the-shelf CXR dataset composed of radiographs included in both, Montgomery and JSRT datasets. The experimental results show that even though the amount of augmentation is large, our algorithm can preserve the important information in lung fields, local structures, and global visual effect adequately. The proposed method can be used to augment training and testing image data sets so that the trained machine learning model can be used to process CXRs from various sources, and it can be potentially used broadly in any medical imaging applications.

Keywords: computer-aided diagnosis, image augmentation, lung segmentation, medical imaging, seam carving

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Authors: Amna Abdalla Mohammed Khalid, Pietro Parisse, Silvia Onesti, Loredana Casalis

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Basic cellular processes as DNA replication are crucial to cell life. Understanding at the molecular level the mechanisms that govern DNA replication in proliferating cells is fundamental to understand disease connected to genomic instabilities, as a genetic disease and cancer. A key step for DNA replication to take place, is unwinding the DNA double helix and this carried out by proteins called helicases. The archaeal MCM (minichromosome maintenance) complex from Methanothermobacter thermautotrophicus have being studied using Atomic Force Microscopy (AFM), imaging in air and liquid (Physiological environment). The accurate analysis of AFM topographic images allowed to understand the static conformations as well the interaction dynamic of MCM and DNA double helix in the present of ATP.

Keywords: DNA, protein-DNA interaction, MCM (mini chromosome manteinance) complex, atomic force microscopy (AFM)

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Authors: Polina Prokopovich

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Despite the well-established dependence of cartilage mechanical properties on the frequency of the applied load, most research in the field is carried out in either load-free or constant load conditions because of the complexity of the equipment required for the determination of time-dependent properties. These simpler analyses provide a limited representation of cartilage properties thus greatly reducing the impact of the information gathered hindering the understanding of the mechanisms involved in this tissue replacement, development and pathology. More complex techniques could represent better investigative methods, but their uptake in cartilage research is limited by the highly specialised training required and cost of the equipment. There is, therefore, a clear need for alternative experimental approaches to cartilage testing to be deployed in research and clinical settings using more user-friendly and financial accessible devices. Frequency dependent material properties can be determined through rheometry that is an easy to use requiring a relatively inexpensive device; we present how a commercial rheometer can be adapted to determine the viscoelastic properties of articular cartilage. Frequency-sweep tests were run at various applied normal loads on immature, mature and trypsinased (as model of osteoarthritis) cartilage samples to determine the dynamic shear moduli (G*, G′ G″) of the tissues. Moduli increased with increasing frequency and applied load; mature cartilage had generally the highest moduli and GAG depleted samples the lowest. Hydraulic permeability (KH) was estimated from the rheological data and decreased with applied load; GAG depleted cartilage exhibited higher hydraulic permeability than either immature or mature tissues. The rheometer-based methodology developed was validated by the close comparison of the rheometer-obtained cartilage characteristics (G*, G′, G″, KH) with results obtained with more complex testing techniques available in literature. Rheometry is relatively simpler and does not require highly capital intensive machinery and staff training is more accessible; thus the use of a rheometer would represent a cost-effective approach for the determination of frequency-dependent properties of cartilage for more comprehensive and impactful results for both healthcare professional and R&D.

Keywords: tissue, rheometer, biomaterial, cartilage

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Authors: Deniz Dincel, Sena Ardicli, Hale Samli, Mustafa Ogan, Faruk Balci

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The aim of the study was to determine the effects of some environmental and genetic factors on growth, fertility traits, milk yield and composition in Saanen goats. For this purpose, the total of 173 Saanen goats and kids were investigated for growth, fertility and milk traits in Marmara Region of Turkey. Fertility parameters (n=70) were evaluated during two years. Milk samples were collected during the lactation and the milk yield/components (n=59) of each goat were calculated. In terms of CSN3 and AGPAT6 gene; the genotypes were defined by PCR-RFLP. Saanen kids (n=86-112) were measured from birth to 6 months of life. The birth, weaning, 60ᵗʰ, 90ᵗʰ, 120ᵗʰ and 180tᵗʰ days of average live weights were calculated. The effects of maternal age on pregnancy rate (p < 0.05), birth rate (p < 0.05), infertility rate (p < 0.05), single born kidding (p < 0.001), twinning rate (p < 0.05), triplet rate (p < 0.05), survival rate of kids until weaning (p < 0.05), number of kids per parturition (p < 0.01) and number of kids per mating (p < 0.01) were found significant. The impacts of year on birth rate (p < 0.05), abortion rate (p < 0.001), single born kidding (p < 0.01), survival rate of kids until weaning (p < 0.01), number of kids per mating (p < 0.01) were found significant for fertility traits. The impacts of lactation length on all milk yield parameters (lactation milk, protein, fat, totally solid, solid not fat, casein and lactose yield) (p < 0.001) were found significant. The effects of age on all milk yield parameters (lactation milk, protein, fat, total solid, solid not fat, casein and lactose yield) (p < 0.001), protein rate (p < 0.05), fat rate (p < 0.05), total solid rate (p < 0.01), solid not fat rate (p < 0.05), casein rate (p < 0.05) and lactation length (p < 0.01), were found significant too. However, the effect of AGPAT6 gene on milk yield and composition was not found significant in Saanen goats. The herd was found monomorphic (FF) for CSN3 gene. The effects of sex on live weights until 90ᵗʰ days of life (birth, weaning and 60ᵗʰ day of average weight) were found significant statistically (p < 0.001). The maternal age affected only birth weight (p < 0,001). The effects month at birth on all of the investigated day [the birth, 120ᵗʰ, 180ᵗʰ days (p < 0.05); the weaning, 60ᵗʰ, 90ᵗʰ days (p < 0,001)] were found significant. The birth type was found significant on the birth (p < 0,001), weaning (p < 0,01), 60ᵗʰ (p < 0,01) and 90ᵗʰ (p < 0,01) days of average live weights. As a result, screening the other regions of CSN3, AGPAT6 gene and also investigation the phenotypic association of them should be useful to clarify the efficiency of target genes. Environmental factors such as maternal age, year, sex and birth type were found significant on some growth, fertility and milk traits in Saanen goats. So consideration of these factors could be used as selection criteria in dairy goat breeding.

Keywords: fertility, growth, milk yield, Saanen goats

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Authors: Yan Torres, Fernanda Simoes, Francisco Petrucci-Fonseca, Freddie-Jeanne Richard

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The non-invasive samples are an alternative of collecting genetic samples directly. Non-invasive samples are collected without the manipulation of the animal (e.g., scats, feathers and hairs). Nevertheless, the use of non-invasive samples has some limitations. The main issue is degraded DNA, leading to poorer extraction efficiency and genotyping. Those errors delayed for some years a widespread use of non-invasive genetic information. Possibilities to limit genotyping errors can be done using analysis methods that can assimilate the errors and singularities of non-invasive samples. Genotype matching and population estimation algorithms can be highlighted as important analysis tools that have been adapted to deal with those errors. Although, this recent development of analysis methods there is still a lack of empirical performance comparison of them. A comparison of methods with dataset different in size and structure can be useful for future studies since non-invasive samples are a powerful tool for getting information specially for endangered and rare populations. To compare the analysis methods, four different datasets used were obtained from the Dryad digital repository were used. Three different matching algorithms (Cervus, Colony and Error Tolerant Likelihood Matching - ETLM) are used for matching genotypes and two different ones for population estimation (Capwire and BayesN). The three matching algorithms showed different patterns of results. The ETLM produced less number of unique individuals and recaptures. A similarity in the matched genotypes between Colony and Cervus was observed. That is not a surprise since the similarity between those methods on the likelihood pairwise and clustering algorithms. The matching of ETLM showed almost no similarity with the genotypes that were matched with the other methods. The different cluster algorithm system and error model of ETLM seems to lead to a more criterious selection, although the processing time and interface friendly of ETLM were the worst between the compared methods. The population estimators performed differently regarding the datasets. There was a consensus between the different estimators only for the one dataset. The BayesN showed higher and lower estimations when compared with Capwire. The BayesN does not consider the total number of recaptures like Capwire only the recapture events. So, this makes the estimator sensitive to data heterogeneity. Heterogeneity in the sense means different capture rates between individuals. In those examples, the tolerance for homogeneity seems to be crucial for BayesN work properly. Both methods are user-friendly and have reasonable processing time. An amplified analysis with simulated genotype data can clarify the sensibility of the algorithms. The present comparison of the matching methods indicates that Colony seems to be more appropriated for general use considering a time/interface/robustness balance. The heterogeneity of the recaptures affected strongly the BayesN estimations, leading to over and underestimations population numbers. Capwire is then advisable to general use since it performs better in a wide range of situations.

Keywords: algorithms, genetics, matching, population

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Authors: Catherine K. Derow

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Possibly a slime mold somehow mutated or already was mutated at progeniture and so stayed as a metazoan when it developed into the fruiting stage and so the slime mold(s) we are evolved and similar to are genetically differ from the slime molds in existence now. This may be why there are genetic links between humans and other metazoa now alive and slime molds now alive but we are now divergent branches of the evolutionary tree compared to the original slime mold, or perhaps slime mold-like organisms, that gave rise to metazoan animalia and perhaps algae and plantae as slime molds were undifferentiated enough in many ways that could allow their descendants to evolve into these three separate phylogenetic categories. Or it may be a slime mold was born or somehow progenated as multicellular, as the particular organism was mutated enough to have say divided in a a 'pseudo-embryonic' stage, and this could have happened for algae, plantae as well as animalia or all the branches may be from the same line but the missing link might be covered in 'phylogenetic sequence comparison noise'.

Keywords: metazoan evolution, unicellular bridge to metazoans, evolution, slime mold

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Authors: M. Derraz, M.Farhaoui

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In the water treatment processes, the determination of the optimal dose of the coagulant is an issue of particular concern. Coagulant dosing is correlated to raw water quality which depends on some parameters (turbidity, ph, temperature, conductivity…). The objective of this study is to provide water treatment operators with a tool that enables to predict and replace, sometimes, the manual method (jar testing) used in this plant to predict the optimum coagulant dose. The model is constructed using actual process data for a water treatment plant located in the middle of Morocco (Meknes).

Keywords: coagulation process, aluminum sulfate, model, coagulant dose

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Authors: Wenli Tsou, Jessica Wu

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Courses of English for specific academic purposes (ESAP) have become popular for higher education in Taiwan; however, no standardized tests have been developed for evaluating learners’ English proficiency in individual designated fields. Assuming a learner’s proficiency in a specific academic area is built up with one’s general proficiency in English with specific knowledge and vocabulary in the content areas, an adequate ESAP proficiency test may be constructed by some selected test items related to the designated academic areas. In this study, through collaboration between a language testing institution and a university in Taiwan, three sets of ESAP tests, covering three disciplinary areas of business and the workplace, science and engineering, and health and medicine majors, were developed and administered to sophomore students (N=1704) who were enrolled in ESAP courses at a university in southern Taiwan. For this study, the courses were grouped into the above-mentioned three disciplines, and students took the specialized proficiency test based on the ESAP course they were taking. Because students were free to select which ESAP course to take, each course had both major and non-major students. Toward the end of the one-semester course, ending in January, 2015, each student took two tests, one of general English (General English Proficiency Test, or GEPT) and the other ESAP. Following each test, students filled out a survey, reporting their test taking experiences. After comparing students’ two test scores, it was found that business majors and health and medical students performed better in ESAP than the non-majors in the class, whereas science and engineering majors did about the same as their non-major counterparts. In addition, test takers with CERF B2 (upper intermediate) level or above performed well in both tests, while students who are below B2 did slightly better in ESAP. The findings suggest that students’ test performance have been enhanced by their specialist content and vocabulary knowledge. Furthermore, results of the survey show that the difficulty levels reported by students are consistent with their test performances. Based on the item analysis, the findings can be used to develop proficiency tests for specific disciplines and to identify ability indicators for college students in their designated fields.

Keywords: english for specific academic purposes (ESAP), general english proficiency test (GEPT), higher education, proficiency test

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Authors: Paula I. Buonfiglio, Carlos David Bruque, Lucia Salatino, Vanesa Lotersztein, Sebastián Menazzi, Paola Plazas, Ana Belén Elgoyhen, Viviana Dalamón

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Hearing loss (HL) is the most prevalent sensorineural disorder affecting about 10% of the global population, with more than half due to genetic causes. About 1 in 500-1000 newborns present congenital HL. Most of the patients are non-syndromic with an autosomal recessive mode of inheritance. To date, more than 100 genes are related to HL. Therefore, the Whole-exome sequencing (WES) technique has become a cost-effective alternative approach for molecular diagnosis. Nevertheless, new challenges arise from the detection of novel variants, in particular missense changes, which can lead to a spectrum of genotype-to-phenotype correlations, which is not always straightforward. In this work, we aimed to identify the genetic causes of HL in isolated and familial cases by designing a multistep approach to analyze target genes related to hearing impairment. Moreover, we performed in silico and in vivo analyses in order to further study the effect of some of the novel variants identified in the hair cell function using the zebrafish model. A total of 650 patients were studied by Sanger Sequencing and Gap-PCR in GJB2 and GJB6 genes, respectively, diagnosing 15.5% of sporadic cases and 36% of familial ones. Overall, 50 different sequence variants were detected. Fifty of the undiagnosed patients with moderate HL were tested for deletions in STRC gene by Multiplex ligation-dependent probe amplification technique (MLPA), leading to 6% of diagnosis. After this initial screening, 50 families were selected to be analyzed by WES, achieving diagnosis in 44% of them. Half of the identified variants were novel. A missense variant in MYO6 gene detected in a family with postlingual HL was selected to be further analyzed. A protein modeling with AlphaFold2 software was performed, proving its pathogenic effect. In order to functionally validate this novel variant, a knockdown phenotype rescue assay in zebrafish was carried out. Injection of wild-type MYO6 mRNA in embryos rescued the phenotype, whereas using the mutant MYO6 mRNA (carrying c.2782C>A variant) had no effect. These results strongly suggest the deleterious effect of this variant on the mobility of stereocilia in zebrafish neuromasts, and hence on the auditory system. In the present work, we demonstrated that our algorithm is suitable for the sequential multigenic approach to HL in our cohort. These results highlight the importance of a combined strategy in order to identify candidate variants as well as the in silico and in vivo studies to analyze and prove their pathogenicity and accomplish a better understanding of the mechanisms underlying the physiopathology of the hearing impairment.

Keywords: diagnosis, genetics, hearing loss, in silico analysis, in vivo analysis, WES, zebrafish

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Authors: Bahar Ayberk

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The study was conducted to determine the relationship between physical fitness and academic performance among university students. A far-famed saying ‘Sound mind in a sound body’ referring to the potential quality of increased physical fitness in the intellectual development of individuals seems to be endorsed. There is a growing body of literature the impact of physical fitness on academic achievement, especially in elementary and middle-school aged children. Even though there are numerous positive effects related to being physically active and physical fitness, their effect on academic achievement is not very much clear for university students. The subjects for this study included 25 students (20 female and 5 male) enrolled in Yeditepe University, Physiotherapy and Rehabilitation Department of Health Science Faculty. All participants filled in a questionnaire about their socio-demographic status, general health status, and physical activity status. Health-related physical fitness testing, included several core components: 1) body composition evaluation (body mass index, waist-to-hip ratio), 2) cardiovascular endurance evaluation (queen’s college step test), 3) muscle strength and endurance evaluation (sit-up test, push-up test), 4) flexibility evaluation (sit and reach test). Academic performance evaluation was based on student’s Cumulative Grade Point Average (CGPA). The prevalence of the subjects participating physical activity was found to be 40% (n = 10). CGPA scores were significantly higher among students having regular physical activity when we compared the students having regular physical activities or not (respectively 2,71 ± 0.46, 3.02 ± 0.28 scores, p = 0.076). The result of the study also revealed that there is positive correlation relationship between sit-up, push up and academic performance points (CGPA) (r = 0.43, p ≤ 0.05 ) and negative correlation relationship between cardiovascular endurance parameter (Queen's College Step Test) and academic performance points (CGPA) (r = -0.47, p ≤ 0.05). In conclusion, the findings confirmed that physical fitness level was generally associated with academic performance in the study group. Cardiovascular endurance and muscle strength and endurance were associated with student’s CGPA, whereas body composition and flexibility were unrelated to CGPA.

Keywords: academic performance, health-related physical fitness, physical activity, physical fitness testing

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Authors: Thibaud Berthomier, Ali Mansour, Luc Bressollette, Frédéric Le Roy, Dominique Mottier, Léo Fréchier, Barthélémy Hermenault

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Deep Venous Thrombosis (DVT) occurs when a thrombus is formed within a deep vein (most often in the legs). This disease can be deadly if a part or the whole thrombus reaches the lung and causes a Pulmonary Embolism (PE). This disorder, often asymptomatic, has multifactorial causes: immobilization, surgery, pregnancy, age, cancers, and genetic variations. Our project aims to relate the thrombus epidemiology (origins, patient predispositions, PE) to its structure using ultrasound images. Ultrasonography and elastography were collected using Toshiba Aplio 500 at Brest Hospital. This manuscript compares two classification approaches: spectral clustering and scattering operator. The former is based on the graph and matrix theories while the latter cascades wavelet convolutions with nonlinear modulus and averaging operators.

Keywords: deep venous thrombosis, ultrasonography, elastography, scattering operator, wavelet, spectral clustering

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Authors: Svetlana Zhikrivetskaya, Nataliya Shirokova, Roman Bikanov, Elizaveta Musatova, Yana Kovaleva, Nataliya Vetrova, Ekaterina Pomerantseva

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Nowadays there is a growing number of couples with conceiving problems due to male or female infertility. Genetic abnormalities are responsible for about 31% of all cases of male infertility. These abnormalities include both chromosomal aberrations or aneuploidies and mutations in certain genes. Chromosomal abnormalities can be easily identified, thus the development of screening panels able to reveal genetic reasons of male infertility on gene level is of current interest. There are approximately 2,000 genes involved in male fertility that is the reason why it is very important to determine the most clinically relevant in certain population and ethnic conditions. An infertility screening panel containing 48 mutations in genes AMHR2, CFTR, DNAI1, HFE, KAL1, TSSK2 and AZF locus which are the most clinically relevant for the European population according to databases NCBI and ClinVar was designed. The aim of this research was to confirm clinic relevance of these mutations in the Russian population. Genotyping was performed in 220 patients with different types of male infertility and in 57 healthy males with normozoospermia. Mutations were identified by end-point PCR with TaqMan probes in microfluidic plates. The frequency of 5 mutations in healthy males and 13 mutations in patients with infertility was revealed and estimated. The frequency of mutation c.187C>G in HFE gene was significantly lower for healthy males (8.8%) compared with patients (17.7%) and the values for the European population according to ExAc database (13.7%) and dbSNP (17.2%). Analysis of c.3454G>C, and c.1545_1546delTA mutations in the CFTR gene revealed increased frequency (0.9 and 0.2%, respectively) in patients with infertility compared with data for the European population (0.04%, respectively (ExAc, European (Non-Finnish) and for the Aggregated Populations (0.002% (ExAc), because there is no data for European population for c.1545_1546delTA mutation. The frequency of del508 mutation (CFTR) in patients (1.59%) were lower comparing with male infertility Europeans (3.34-6.25% depending on nationality) and at the same level with healthy Europeans (1.06%, ExAc, European (Non-Finnish). Analysis of c.845G>A (HFE) mutation resulted in decreased frequency in patients (1.8%) in contrast with the European population data (5.1%, respectively, ExAc, European (Non-Finnish). Moreover, obtained data revealed no statistically significant frequency difference for c.845G>A mutation (HFE) between healthy males in the Russian and the European populations. Allele frequencies of mutations c.350G>A (CFTR), c.193A>T (HFE), c.774C>T, and c.80A>G (gene TSSK2) showed no significantly difference among patients with infertility, healthy males and Europeans. Analysis of AZF locus revealed increased frequency for AZFc microdeletion in patients with male infertility. Thereby, the new data of the allele frequencies in infertility patients in the Russian population was obtained. As well as the frequency differences of mutations associated with male infertility among patients, healthy males in the Russian population and the European one were estimated. The revealed differences showed that for high effectiveness of screening panel detecting genetically caused male infertility it is very important to consider ethnic and population characteristics of patients which will be screened.

Keywords: allele frequency, azoospermia, male infertility, mutation, population

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Authors: C. W. Kan

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Fabrics can be treated to equip them with certain functional properties in which water repellency is one of the important functional effects. In this study, commercial water repellent agent was used under different application conditions to cotton fabric. Finally, the water repellent effect was evaluated by standard testing method. Thus, the aim of this study is to illustrate the proper application of water repellent finishing to cotton fabric and the results could provide guidance note to the students in learning this topic. Acknowledgment: Authors would like to thank the financial support from the Hong Kong Polytechnic University for this work.

Keywords: learning materials, water repellent, textiles, cotton

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Authors: Chi-Wai Kan, Kam-Hong Chau, Ho-Shing Law

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Wicking property is important for textile finishing and wears comfort. Good wicking properties can ensure uniformity and efficiency of the textiles treatment. In view of wear comfort, quick wicking fabrics facilitate the evaporation of sweat. Therefore, the wetness sensation of the skin is minimised to prevent discomfort. The testing method for vertical wicking was standardised by the American Association of Textile Chemists and Colorists (AATCC) in 2011. The traditional vertical wicking test involves human error to observe fast changing and/or unclear wicking height. This study introduces optoelectronic devices to achieve an automatic Vertical Wicking Tester (VWT) and reduce human error. The VWT can record the wicking time and wicking height of samples. By reducing the difficulties of manual judgment, the reliability of the vertical wicking experiment is highly increased. Furthermore, labour is greatly decreased by using the VWT. The automatic measurement of the VWT has optoelectronic devices to trace the liquid wicking with a simple operation procedure. The optoelectronic devices detect the colour difference between dry and wet samples. This allows high sensitivity to a difference in irradiance down to 10 μW/cm². Therefore, the VWT is capable of testing dark fabric. The VWT gives a wicking distance (wicking height) of 1 mm resolution and a wicking time of one-second resolution. Acknowledgment: This is a research project of HKRITA funded by Innovation and Technology Fund (ITF) with title “Development of an Automatic Measuring System for Vertical Wicking” (ITP/055/20TP). Author would like to thank the financial support by ITF. Any opinions, findings, conclusions or recommendations expressed in this material/event (or by members of the project team) do not reflect the views of the Government of the Hong Kong Special Administrative Region, the Innovation and Technology Commission or the Panel of Assessors for the Innovation and Technology Support Programme of the Innovation and Technology Fund and the Hong Kong Research Institute of Textiles and Apparel. Also, we would like to thank the support and sponsorship from Lai Tak Enterprises Limited, Kingis Development Limited and Wing Yue Textile Company Limited.

Keywords: AATCC method, comfort, textile measurement, wetness sensation

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Authors: Yu-Ju Hsieh, Lin-Hung Lin, Wen-Hui Chang

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This study was designed as an interventional research and intended to validate whether the introduction of drinking vinegar every day can reduce and even prevent urinary tract infection in Taiwan home stayed disabilities who using indwelling catheter. The data was collected from the subjects who have received home care case at northern Taiwan, according to the questionnaire and a medical records retroactive methodology, the subjects were informed and consent to drink 15ml of table vinegar in a daily diet, and through routine urine testing and culture study. Home care nurses would assist collecting urine at the point of before and after a meal from total 35 studied subjects per month, and total collected 4 times for testing. The results showed that when the average age of study subjects was 65.46 years and catheter indwelling time was 15 years, drinking table vinegar could inhibit the activity of E. coli O157: H7 and reduce its breeding. Before drinking table vinegar daily, the subjects’ urine pH value was 7.0-8.0, and the average was 7.5, and the urine PH value dropped to 6.5 after drinking table vinegar for a month. There were two purple urine cases whose urine were changed from purple to normal color after two weeks of drinking, and the protein and bacteria values of urine gradually improved. Urine smell unpleasant before attending to this study, and the symptom improved significantly only after 1 week, and the urine smell returned to normal ammonia and became clean after 1 month later. None of these subjects received treatment in a hospital due to urinary tract infection, and there were no signs of bleeding in all cases during this study. The subjects of this study are chronic patients with a long-term bedridden catheterization; drinking cranberry juice is an economic burden for them, and also highly prohibited for diabetes patients. By adapting to use cheaper table vinegar to acidified urine and improve its smell and ease Purple Urine Syndrome, to furthermore, proven urinary tract infection, it can also to reduce the financial burden on families, the cost of social resources and the rate of re-admission.

Keywords: table vinegar, urinary tract infection, disability patients, long-term indwelling catheter

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Authors: Himanshu Sharma, Karthik Kumar, Harish Kumar

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The major problem in crop cultivation is the occurrence of multiple crop diseases. During the growth stage, timely identification of crop diseases is paramount to ensure the high yield of crops, lower production costs, and minimize pesticide usage. In most cases, crop diseases produce observable characteristics and symptoms. The Surveyors usually diagnose crop diseases when they walk through the fields. However, surveyor inspections tend to be biased and error-prone due to the nature of the monotonous task and the subjectivity of individuals. In addition, visual inspection of each leaf or plant is costly, time-consuming, and labour-intensive. Furthermore, the plant pathologists and experts who can often identify the disease within the plant according to their symptoms in early stages are not readily available in remote regions. Therefore, this study specifically addressed early detection of leaf scald, red rot, and eyespot types of diseases within sugarcane plants. The study proposes a computer vision-based approach using a convolutional neural network (CNN) for automatic identification of crop diseases. To facilitate this, firstly, images of sugarcane diseases were taken from google without modifying the scene, background, or controlling the illumination to build the training dataset. Then, the testing dataset was developed based on the real-time collected images from the sugarcane field from India. Then, the image dataset is pre-processed for feature extraction and selection. Finally, the CNN-based Visual Geometry Group (VGG) model was deployed on the training and testing dataset to classify the images into diseased and healthy sugarcane plants and measure the model's performance using various parameters, i.e., accuracy, sensitivity, specificity, and F1-score. The promising result of the proposed model lays the groundwork for the automatic early detection of sugarcane disease. The proposed research directly sustains an increase in crop yield.

Keywords: automatic classification, computer vision, convolutional neural network, image processing, sugarcane disease, visual geometry group

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Authors: Wuthichai Wongthatsanekorn, Nuntana Matheekrieangkrai

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This research proposes Bee Algorithm (BA) to optimize Ready Mixed Concrete (RMC) truck scheduling problem from single batch plant to multiple construction sites. This problem is considered as an NP-hard constrained combinatorial optimization problem. This paper provides the details of the RMC dispatching process and its related constraints. BA was then developed to minimize total waiting time of RMC trucks while satisfying all constraints. The performance of BA is then evaluated on two benchmark problems (3 and 5construction sites) according to previous researchers. The simulation results of BA are compared in term of efficiency and accuracy with Genetic Algorithm (GA) and all problems show that BA approach outperforms GA in term of efficiency and accuracy to obtain optimal solution. Hence, BA approach could be practically implemented to obtain the best schedule.

Keywords: bee colony optimization, ready mixed concrete problem, ruck scheduling, multiple construction sites

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Authors: Jiraporn Weenuttranon

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The objectives of the consumer behavior of bakery products in Bangkok are to study consumer behavior of the bakery product, to study the essential factors that could possibly affect the consumer behavior and to study recommendations for the development of the bakery products. This research is a survey research. Populations are buyer’s bakery products in Bangkok. The probability sample size is 400. The research uses a questionnaire for self-learning by using information technology. The researcher created a reliability value at 0.71 levels of significance. The data analysis will be done by using the percentage, mean, and standard deviation and testing the hypotheses by using chi-square.

Keywords: consumer, behavior, bakery, standard deviation

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Authors: Ben Soltane Cheima, Ittansa Yonas Kelbesa

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Speaker Identification (SI) is the task of establishing identity of an individual based on his/her voice characteristics. The SI task is typically achieved by two-stage signal processing: training and testing. The training process calculates speaker specific feature parameters from the speech and generates speaker models accordingly. In the testing phase, speech samples from unknown speakers are compared with the models and classified. Even though performance of speaker identification systems has improved due to recent advances in speech processing techniques, there is still need of improvement. In this paper, a Closed-Set Tex-Independent Speaker Identification System (CISI) based on a Multiple Classifier System (MCS) is proposed, using Mel Frequency Cepstrum Coefficient (MFCC) as feature extraction and suitable combination of vector quantization (VQ) and Gaussian Mixture Model (GMM) together with Expectation Maximization algorithm (EM) for speaker modeling. The use of Voice Activity Detector (VAD) with a hybrid approach based on Short Time Energy (STE) and Statistical Modeling of Background Noise in the pre-processing step of the feature extraction yields a better and more robust automatic speaker identification system. Also investigation of Linde-Buzo-Gray (LBG) clustering algorithm for initialization of GMM, for estimating the underlying parameters, in the EM step improved the convergence rate and systems performance. It also uses relative index as confidence measures in case of contradiction in identification process by GMM and VQ as well. Simulation results carried out on voxforge.org speech database using MATLAB highlight the efficacy of the proposed method compared to earlier work.

Keywords: feature extraction, speaker modeling, feature matching, Mel frequency cepstrum coefficient (MFCC), Gaussian mixture model (GMM), vector quantization (VQ), Linde-Buzo-Gray (LBG), expectation maximization (EM), pre-processing, voice activity detection (VAD), short time energy (STE), background noise statistical modeling, closed-set tex-independent speaker identification system (CISI)

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Authors: Y. Mohammed, A. I. Kabuga

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Sexually transmitted infections (STIs) have continued to be a major public health problem in sub-Saharan Africa especially with the recent resurgence of syphilis. Syphilis is a systemic disease caused by the bacterium, spirochete Treponema pallidum and has been reported as one of the common sexually transmitted infections (STIs) in Nigeria. Presence of genital ulcer disease from syphilis facilitates human immunodeficiency virus (HIV) transmission and their ¬diagnosis is essential for the proper management. Venereal Disease Research Laboratory (VDRL) test is used as a screening test for the diagnosis of syphilis. However, unusual VDRL test results have been reported in HIV-infected persons with syphilis. There are reports showing higher than expected VDRL titers as well as biological false positive in most of the studies. A negative Rapid Plasma Reagin (RPR) test or VDRL test result may not rule out syphilis in patients with HIV infection. For laboratory confirmation of syphilis, one specific Treponemal test, namely, Fluroscent Treponemal Antibody Absorption (FTA-ABS) test or Treponema Pallidum Haemagglutination Assay (TPHA) should be done along with VDRL. A prospective cross sectional study was conducted for 2 years from Jun, 2012 to Jun 2014 to determine the prevalence of syphilis in HIV-seroreactive patients at 5 selected HIV/AIDS treatment and counseling centers in Kano State, North Western, Nigeria. New HIV-Seroreactive patients who gave informed consent to participate in the study were recruited. Venereal Diseases Research Laboratory (VDRL) test for Syphilis screening was performed on the same sera samples which were collected for HIV testing. A total of 238 patients, 113 (47%) males and 125 (53%) females, were enrolled. In the present study, 238 HIV-seropositive patients were screened for syphilis by VDRL test. Out of these 238 cases, 72 (32%) patients were positive for TPHA and 8 (3.4%) patients were reactive for VDRL in various titers with an overall prevalence of 3.4%. All the eight patients who were reactive for VDRL test were also positive for TPHA test. In Conclusions, with high prevalence of syphilis among HIV-infected people from this study, it is recommended that serological testing for syphilis should be carried out in all patients with newly diagnosed HIV infection. Detection and treatment of STI should have a central role in HIV prevention and control. This will help in proper management of patients having STIs and HIV co infection.

Keywords: HIV, infections, STIs, syphilis

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Authors: Nasreen Abdulmannan

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Fetal abnormalities are categorized as a structural abnormality, non-structural abnormality, or a combination of both. Fetal structural abnormalities (FSA) include, but are not limited, to Down syndrome, congenital diaphragmatic hernia, and cleft lip and palate. These abnormalities can be detected in the first weeks of pregnancy, which is almost around 9 - 20 weeks gestational. Etiological factors for FSA are unknown; however, transmitted genetic risk can be one of these factors. Consanguineous marriage often referred to as inbreeding, represents a significant risk factor for FSA due to the increased likelihood of deleterious genetic traits shared by both biological parents. In a country such as the Kingdom of Saudi Arabia (KSA), consanguineous marriage is high, which creates a significant risk of children being born with congenital abnormalities. Historically, the practice of consanguinity occurred commonly among European royalty. For example, Great Britain’s Queen Victoria married her German first cousin, Prince Albert of Coburg. Although a distant blood relationship, the United Kingdom’s Queen Elizabeth II married her cousin, Prince Philip of Greece and Denmark—both of them direct descendants of Queen Victoria. In Middle Eastern countries, a high incidence of consanguineous unions still exists, including in the KSA. Previous studies indicated that a significant gap exists in understanding the lived experiences of Saudi women dealing with an FSA-complicated pregnancy. Eleven participants were interviewed using a semi-structured interview format for this qualitative phenomenological study investigating the lived experiences of pregnant Saudi women carrying a child with FSA. This study explored the gaps in current literature regarding the lived experiences of pregnant Saudi women whose pregnancies were complicated by FSA. In addition, the researcher acquired knowledge about the available support and resources as well as the Saudi cultural perspective on FSA. This research explored the lived experiences of pregnant Saudi women utilizing Giorgi’s (2009) approach to data collection and data management. Findings for this study cover five major themes: (1) initial maternal reaction to the FSA diagnosis per ultrasound screening; (2) strengthening of the maternal relationship with God; (3) maternal concern for their child’s future; (4) feeling supported by their loved ones; and (5) lack of healthcare provider support and guidance. Future research in the KSA is needed to explore the network support for these mothers. This study recommended further clinical nursing research, nursing education, clinical practice, and healthcare policy/procedures to provide opportunities for improvement in nursing care and increase awareness in KSA society.

Keywords: fetal structural abnormalities, psychological distress, health provider, health care

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Authors: Mariam Bibi, Rubab Mehboob, Mehreen Sirshar

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Satisfying the customer requirements is the ultimate goal of producing or developing any product. The quality of the product is decided on the bases of the level of customer satisfaction. There are different techniques which have been reported during the survey which enhance the quality of the product through software defect prediction and by locating the missing software requirements. Some mining techniques were proposed to assess the individual performance indicators in collaborative environment to reduce errors at individual level. The basic intention is to produce a product with zero or few defects thereby producing a best product quality wise. In the analysis of survey the techniques like Genetic algorithm, artificial neural network, classification and clustering techniques and decision tree are studied. After analysis it has been discovered that these techniques contributed much to the improvement and enhancement of the quality of the product.

Keywords: data mining, defect prediction, missing requirements, software quality

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Authors: Mikhail S. Zastrozhin, Valery V. Smirnov, Dmitry A. Sychev, Ludmila M. Savchenko, Evgeny A. Bryun, Mark O. Nechaev

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Cytochrome P-450 isoenzyme 3A4 takes part in the biotransformation of medical drugs. The activity of CYP isoenzymes depends on genetic (polymorphisms of genes which encoded it) and phenotypic factors (a kind of food, a concomitant drug therapy). The aim of the study was to evaluate a carbamazepine effect on the CYP3A4 activity in patients with alcohol addiction. The study included 25 men with alcohol dependence, who received haloperidol during the exacerbation of the addiction. CYP3A4 activity was assessed by urinary 6-beta-hydroxycortisol/cortisol ratios measured by high performance liquid chromatography with mass spectrometry. The study modeled a graph and an equation of the logarithmic regression, that reflects the dependence of CYP3A4 activity on a dose of carbamazepine: y = 5,5 * 9,1 * 10-5 * x2. The study statistically significant demonstrates the effect of carbamazepine on CYP2D6 isozyme activity in patients with alcohol addiction.

Keywords: CYP3A4, biotransformation, carbamazepine, alcohol abuse

Procedia PDF Downloads 269

Authors: Thomas Bryan, Veton Kepuska, Ivica Kostanic

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Speaker recognition is performed in high Additive White Gaussian Noise (AWGN) environments using principals of Computational Auditory Scene Analysis (CASA). CASA methods often classify sounds from images in the time-frequency (T-F) plane using spectrograms or cochleargrams as the image. In this paper atomic decomposition implemented by matching pursuit performs a transform from time series speech signals to the T-F plane. The atomic decomposition creates a sparsely populated T-F vector in “weight space” where each populated T-F position contains an amplitude weight. The weight space vector along with the atomic dictionary represents a denoised, compressed version of the original signal. The arraignment or of the atomic indices in the T-F vector are used for classification. Unsupervised feature learning implemented by a sparse autoencoder learns a single dictionary of basis features from a collection of envelope samples from all speakers. The approach is demonstrated using pairs of speakers from the TIMIT data set. Pairs of speakers are selected randomly from a single district. Each speak has 10 sentences. Two are used for training and 8 for testing. Atomic index probabilities are created for each training sentence and also for each test sentence. Classification is performed by finding the lowest Euclidean distance between then probabilities from the training sentences and the test sentences. Training is done at a 30dB Signal-to-Noise Ratio (SNR). Testing is performed at SNR’s of 0 dB, 5 dB, 10 dB and 30dB. The algorithm has a baseline classification accuracy of ~93% averaged over 10 pairs of speakers from the TIMIT data set. The baseline accuracy is attributable to short sequences of training and test data as well as the overall simplicity of the classification algorithm. The accuracy is not affected by AWGN and produces ~93% accuracy at 0dB SNR.

Keywords: time-frequency plane, atomic decomposition, envelope sampling, Gabor atoms, matching pursuit, sparse dictionary learning, sparse autoencoder

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Authors: Mohamed Chabi

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The purpose of this study is to determine Whether paper assessment especially in the subject mathematics will ever be completely replaced by online assessment using Learning Management System and Content Management System such as blackboard. In the subject mathematics, the assessment is the exercise of judgment on the quality of students’ work, as a way of supporting student learning and appraising its outcomes. Testing students has moved from the traditional scribbling and sketching on paper towards working online on a screen and keyboard.

Keywords: paper assessment, online assessment, learning management system, content management system, mathematics

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Authors: Santhosh Srinivasan, Vipul Garhiya, Shahul Hamid Khan

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Environmental performance along with social performance is becoming vital factors for industries to achieve global standards. With a good environmental policy global industries are differentiating them from their competitors. This paper concentrates on multi stage, multi product and multi period manufacturing network. Single objective mathematical models for a total cost for the entire forward supply chain and reverse chain are considered. Here five different problems are considered by varying the number of facilities for illustration. M-MOGA, Shuffle Frog Leaping algorithm (SFLA) and CPLEX are used for finding the optimal solution for the mathematical model.

Keywords: closed loop supply chain, genetic algorithm, random search, multi period, green supply chain

Procedia PDF Downloads 387

Authors: Oya Bulut, Oguzhan Avci, Zafer Bulut, Atilla Simsek

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Livestock breeders have focused on the improvement of production traits with little or no attention for improvement of disease resistance traits. In order to determine the association between the genetic structure of the individual gene loci with possibility of the occurrence and the development of diseases, MHC (major histocompatibility complex) are frequently used. Because of their importance in the immune system, MHC locus is considered as candidate genes for resistance/susceptibility against to different diseases. Major histocompatibility complex (MHC) molecules play a critical role in both innate and adaptive immunity and have been considered candidate molecular markers of an association between polymorphisms and resistance/susceptibility to diseases. The purpose of this study is to give some information about MHC genes become an important area of study in recent years in terms of animal husbandry and determine the relation between MHC genes and resistance/susceptibility to disease.

Keywords: MHC, polymorphism, disease, resistance

Procedia PDF Downloads 626