Search results for: allele specific PCR

Authors: Atsuko Okazaki, Jurg Ott

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Some genetic diseases (‘digenic traits’) are due to the interaction between two DNA variants. For example, certain forms of Retinitis Pigmentosa (a genetic form of blindness) occur in the presence of two mutant variants, one in the ROM1 gene and one in the RDS gene, while the occurrence of only one of these mutant variants leads to a completely normal phenotype. Detecting such digenic traits by genetic methods is difficult. A common approach to finding disease-causing variants is to compare 100,000s of variants between individuals with a trait (cases) and those without the trait (controls). Such genome-wide association studies (GWASs) have been very successful but hinge on genetic effects of single variants, that is, there should be a difference in allele or genotype frequencies between cases and controls at a disease-causing variant. Frequent pattern mining (FPM) methods offer an avenue at detecting digenic traits even in the absence of single-variant effects. The idea is to enumerate pairs of genotypes (genotype patterns) with each of the two genotypes originating from different variants that may be located at very different genomic positions. What is needed is for genotype patterns to be significantly more common in cases than in controls. Let Y = 2 refer to cases and Y = 1 to controls, with X denoting a specific genotype pattern. We are seeking association rules, ‘X → Y’, with high confidence, P(Y = 2|X), significantly higher than the proportion of cases, P(Y = 2) in the study. Clearly, generally available FPM methods are very suitable for detecting disease-associated genotype patterns. We use fpgrowth as the basic FPM algorithm and built a framework around it to enumerate high-frequency digenic genotype patterns and to evaluate their statistical significance by permutation analysis. Application to a published dataset on opioid dependence furnished results that could not be found with classical GWAS methodology. There were 143 cases and 153 healthy controls, each genotyped for 82 variants in eight genes of the opioid system. The aim was to find out whether any of these variants were disease-associated. The single-variant analysis did not lead to significant results. Application of our FPM implementation resulted in one significant (p < 0.01) genotype pattern with both genotypes in the pattern being heterozygous and originating from two variants on different chromosomes. This pattern occurred in 14 cases and none of the controls. Thus, the pattern seems quite specific to this form of substance abuse and is also rather predictive of disease. An algorithm called Multifactor Dimension Reduction (MDR) was developed some 20 years ago and has been in use in human genetics ever since. This and our algorithms share some similar properties, but they are also very different in other respects. The main difference seems to be that our algorithm focuses on patterns of genotypes while the main object of inference in MDR is the 3 × 3 table of genotypes at two variants.

Keywords: digenic traits, DNA variants, epistasis, statistical genetics

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Authors: M. A. C. S. Sampath Fernando, James M. Curran, Renate Meyer

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Forensic DNA analysis has received much attention over the last three decades, due to its incredible usefulness in human identification. The statistical interpretation of DNA evidence is recognised as one of the most mature fields in forensic science. Peak heights in an Electropherogram (EPG) are approximately proportional to the amount of template DNA in the original sample being tested. A stutter is a minor peak in an EPG, which is not masking as an allele of a potential contributor, and considered as an artefact that is presumed to be arisen due to miscopying or slippage during the PCR. Stutter peaks are mostly analysed in terms of stutter ratio that is calculated relative to the corresponding parent allele height. Analysis of mixture profiles has always been problematic in evidence interpretation, especially with the presence of PCR artefacts like stutters. Unlike binary and semi-continuous models; continuous models assign a probability (as a continuous weight) for each possible genotype combination, and significantly enhances the use of continuous peak height information resulting in more efficient reliable interpretations. Therefore, the presence of a sound methodology to distinguish between stutters and real alleles is essential for the accuracy of the interpretation. Sensibly, any such method has to be able to focus on modelling stutter peaks. Bayesian nonparametric methods provide increased flexibility in applied statistical modelling. Mixture models are frequently employed as fundamental data analysis tools in clustering and classification of data and assume unidentified heterogeneous sources for data. In model-based clustering, each unknown source is reflected by a cluster, and the clusters are modelled using parametric models. Specifying the number of components in finite mixture models, however, is practically difficult even though the calculations are relatively simple. Infinite mixture models, in contrast, do not require the user to specify the number of components. Instead, a Dirichlet process, which is an infinite-dimensional generalization of the Dirichlet distribution, is used to deal with the problem of a number of components. Chinese restaurant process (CRP), Stick-breaking process and Pólya urn scheme are frequently used as Dirichlet priors in Bayesian mixture models. In this study, we illustrate an infinite mixture of simple linear regression models for modelling stutter ratio and introduce some modifications to overcome weaknesses associated with CRP.

Keywords: Chinese restaurant process, Dirichlet prior, infinite mixture model, PCR stutter

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Authors: Özlem Ateş Sönmezoğlu, Begüm Terzi, Ahmet Yıldırım, Leyla Gündüz

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Durum wheat quality is defined as its suitability for pasta processing, that is pasta making quality. Another factor that determines the quality of durum wheat is the nutritional value of wheat or its final products. Wheat is a basic source of calories, proteins and minerals for humans in many countries of the world. For this reason, improvement of wheat nutritional value is of great importance. In recent years, deficiencies in protein and micronutrients, particularly in iron and zinc, have seriously increased. Therefore, basic foods such as wheat must be improved for micronutrient content. The effects of some major genes for grain quality established. Gpc-B1 locus is one of the genes increased protein and micronutrients content, and used in improvement studies of durum wheat nutritional value. The aim of this study was to increase the protein content and the micronutrient (Fe, Zn ve Mn) contents of an advanced durum wheat line (TMB 1) that was previously improved for its protein quality. For this purpose, TMB1 advanced durum wheat line were used as the recurrent parent and also, UC1113-Gpc-B1 line containing the Gpc-B1 gene was used as the gene source. In all of the generations, backcrossed plants carrying the targeted gene region were selected by marker assisted selection (MAS). BC4F1 plants MAS method was employed in combination with embryo culture and rapid plant growth in a controlled greenhouse conditions in order to shorten the duration of the transition between generations in backcross breeding. The Gpc-B1 gene was selected specific molecular markers. Since Yr-36 gene associated with Gpc-B1 allele, it was also transferred to the Gpc-B1 transferred lines. Thus, the backcrossed plants selected by MAS are resistance to yellow rust disease. This research has been financially supported by TÜBİTAK (112T910).

Keywords: Durum wheat, Gpc-B1, MAS, Triticum durum, Yr-36

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Authors: Techale B., Hongxu Dong, Mihrete Getinet, Aregash Gabizew, Andrew H. Paterson, Kassahun Bantte

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The genetic architecture of drought tolerance is expected to involve multiple loci that are unlikely to all segregate for alternative alleles in a single bi-parental population. Therefore, the identification of quantitative trait loci (QTL) that are expressed in diverse genetic backgrounds of multiple bi-parental populations provides evidence about both background-specific and common genetic variants. The purpose of this study was to map QTL related to drought tolerance using three connected mapping populations of different genetic backgrounds to gain insight into the genomic landscape of this important trait in elite Ethiopian germplasm. The three bi-parental populations, each with 207 F₂:₃ lines, were evaluated using an alpha lattice design with two replications under two moisture stress environments. Drought tolerance related traits were analyzed separately for each population using composite interval mapping, finding a total of 105 QTLs. All the QTLs identified from individual populations were projected on a combined consensus map, comprising a total of 25 meta QTLs for seven traits. The consensus map allowed us to deduce locations of a larger number of markers than possible in any individual map, providing a reference for genetic studies in different genetic backgrounds. The mQTL identified in this study could be used for marker-assisted breeding programs in sorghum after validation. Only one trait, reduced leaf senescence, showed a striking bias of allele distribution, indicating substantial standing variation among present varieties that might be employed in improving drought tolerance of Ethiopian and other sorghums.

Keywords: Drought tolerance , Mapping populations, Meta QTL, QTL mapping, Sorghum

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Authors: Sofia Meacham

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In this abstract paper, the Domain-Specific Languages (DSL) evaluation will be presented based on existing literature and years of experience developing DSLs for several domains. The domains we worked on ranged from AI, business applications, and finances/accounting to health. In general, DSLs have been utilised in many domains to provide tailored and efficient solutions to address specific problems. Although they are a reputable method among highly technical circles and have also been used by non-technical experts with success, according to our knowledge, there isn’t a commonly accepted method for evaluating them. There are some methods that define criteria that are adaptations from the general software engineering quality criteria. Other literature focuses on the DSL usability aspect of evaluation and applies methods such as Human-Computer Interaction (HCI) and goal modeling. All these approaches are either hard to introduce, such as the goal modeling, or seem to ignore the domain-specific focus of the DSLs. From our experience, the DSLs have domain-specificity in their core, and consequently, the methods to evaluate them should also include domain-specific criteria in their core. The domain-specific criteria would require synergy between the domain experts and the DSL developers in the same way that DSLs cannot be developed without domain-experts involvement. Methods from agile and other software engineering practices, such as co-creation workshops, should be further emphasised and explored to facilitate this direction. Concluding, our latest experience and plans for DSLs evaluation will be presented and open for discussion.

Keywords: domain-specific languages, DSL evaluation, DSL usability, DSL quality metrics

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Authors: Jae Hyun Lee

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Manufacturing companies use life-cycle inventory databases to analyze sustainability of their manufacturing processes. Life cycle inventory data provides reference data which may not be accurate for a specific company. Collecting accurate data of manufacturing processes for a specific company requires enormous time and efforts. An information model of typical manufacturing processes can reduce time and efforts to get appropriate reference data for a specific company. This paper shows an attempt to build an abstract information model which can be used to develop information models for specific manufacturing processes.

Keywords: process information model, sustainability, OWL, manufacturing

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Authors: Ramune Kasperaviciene, Jurgita Motiejuniene, Dalia Venckiene

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Familiarising students with strategies for transferring cultural meanings (intertextual units, culture-specific idioms, culture-specific items, etc.) should be part of a comprehensive translator training programme. The present paper focuses on strategies for transferring such meanings into other languages and explores possibilities for introducing these methods and practice to translation students. The authors (university translation teachers) analyse the means of transferring cultural meanings from English into Lithuanian in a specific travel book, attribute these means to theoretically grounded strategies, and make calculations related to the frequency of adoption of specific strategies; translation students are familiarised with concepts and methods related to transferring cultural meanings and asked to put their theoretical knowledge into practice, i.e. interpret and translate certain culture-specific items from the same source text, and ground their decisions on theory; the comparison of the strategies employed by the professional translator of the source text (as identified by the authors of this study) and by the students is made. As a result, both students and teachers gain valuable experience, and new practices of conducting translation classes for a specific purpose evolve. Conclusions highlight the differences and similarities of non-professional and professional choices, summarise the possibilities for introducing methods of transferring cultural meanings to students, and round up with specific considerations of the impact of theoretical knowledge and the degree of experience on decisions made in the translation process.

Keywords: cultural meanings, culture-specific items, strategies for transferring cultural meanings, translator training

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Authors: Bela Siska Afrida, Wisnu Barlianto, Desy Wulandari, Ery Olivianto

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Background: Allergic asthma, caused by IgE-mediated allergic reactions, remains a global health issue with high morbidity and mortality rates. Immunotherapy is the only etiology-based approach to treating asthma, but no standard biomarkers have been established to evaluate the therapy’s effectiveness. This study aims to determine the correlation between the ratios of serum levels of HDM-specific IgE/total IgE and Asthma Control Test (ACT) score as a biomarker of the response to immunotherapy in pediatric allergic asthma patients. Patient and Methods: This retrospective cohort study involved 26 pediatric allergic asthma patients who underwent HDM-specific subcutaneous immunotherapy for 14 weeks at the Pediatric Allergy Immunology Outpatient Clinic at Saiful Anwar General Hospital, Malang. Serum levels of HDM-Specific IgE and Total IgE were measured before and after immunotherapy using Chemiluminescence Immunoassay and Enzyme-linked Immunosorbent Assay (ELISA) method. Changes in asthma control were assessed using the ACT score. The Wilcoxon Signed Ranked Test and Spearman correlation test were used for data analysis. Results: There were 14 boys and 12 girls with a mean age of 6.48 ± 2.54 years. The study showed a significant decrease in serum HMD-specific levels before immunotherapy [9.88 ± 5.74 kuA/L] compared to those of 14 weeks after immunotherapy [4.51 ± 3.98 kuA/L], p = 0.000. Serum Total IgE levels significant decrease before immunotherapy [207.6 ± 120.8IU/ml] compared to those of 14 weeks after immunotherapy [109.83 ± 189.39 IU/mL], p = 0.000. The ratios of serum HDM-specific IgE/total IgE levels significant decrease before immunotherapy [0.063 ± 0.05] compared to those of 14 weeks after immunotherapy [0.041 ± 0.039], p = 0.012. There was also a significant increase in ACT scores before and after immunotherapy (each 15.5 ± 1.79 and 20.96 ± 2.049, p = 0.000). The correlation test showed a weak negative correlation between the ratios of HDM-specific IgE/total IgE levels and ACT score (p = 0.034 and r = -0.29). Conclusion: In conclusion, this study showed that a decrease in HDM-specific IgE levels, total IgE levels, and HDM-specific IgE/total IgE ratios, and an increase in ACT score, was observed after 14 weeks of HDM-specific subcutaneous immunotherapy. The weak negative correlation between the HDM-specific IgE/total IgE ratio and the ACT score suggests that this ratio can serve as a potential biomarker of the effectiveness of immunotherapy in treating pediatric allergic asthma patients.

Keywords: HDM-specific IgE/total IgE ratio, ACT score, immunotherapy, allergic asthma

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Authors: Ahlam Inayatullah Badrul Munir, M. Husaini A. Rahman, Mohd Sukri Hassan

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Real-time PCR is a molecular biology technique that is currently being widely used for halal services to differentiating between porcine and bovine DNA. The useful of technique become very important for student or workers (who works in the laboratory) to learn how the technique could be run smoothly without fail. Same concept with conventional PCR, real-time PCR also needed DNA template, primer, enzyme polymerase, dNTP, and buffer. The difference is in real-time PCR, have additional component namely fluorescent dye. The most common use of fluorescent dye in real-time PCR is SYBR green. The purpose of this study was to find out how sensitive, specific and efficient real-time PCR technique was combined with SYBR green method and specific primers of CYT b. The results showed that real-time PCR technique using SYBR Green, capable of detecting porcine and bovine DNA concentrations up to 0.0001 µl/ng. The level of efficiency for both types of DNA was 91% (90-110). Not only that in specific primer CYT b bovine primer could detect only bovine DNA, and porcine primer could detect only porcine primer. So, from the study could be concluded that real-time PCR technique that was combined with specific primer CYT b and SYBR green method, was sensitive, specific and efficient to detect porcine and bovine DNA.

Keywords: sensitivity, specificity, efficiency, real-time PCR, SYBR green, Cytochrome b, porcine DNA, bovine DNA

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Authors: Ji Sun Kim, Jae Ho Baek, Kyeong Ho Kim, Ji Hae Ha, Seong Soo Hong, Jung-Wook Park, Man Sig Lee

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Carbon supported palladium catalysts have been used in many industrial reactions, especially for hydrogenation in the fine chemical industry. Porous carbons had been widely used as catalyst supports due to its higher surface area and larger pore volume. The specific surface area, pore structure and surface chemical functional groups of porous carbon affects metal dispersion and particle size. In this paper, we confirm the effect of support texture on the dispersion of Pd. Pd catalyst supported on activated carbon having various specific surface area were characterized by BET, XRD and FE-TEM. Catalyst activity and dispersion of prepared catalyst were evaluated on the basis of the CO adsorption capacity by CO-chemisorption. As concluding remark to this part of our study, let us note that specific area of carbon play important role on the synthesis of Pd/C catalyst/.

Keywords: carbon, dispersion, Pd/C, specific are, support

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Authors: Karima Tayaa, Amina Bouaziz

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The rapid expansion in the scientific fields and the growth of communication technology increased the use of English as international language in the world. Hence, over the past few decades, many researchers have been emphasizing on how the teaching and learning of English as a foreign or as an additional language can best help students to perform successfully. English for specific purpose is today quite literally regarded as the most global language discipline which existed practically in every country in the world. ESP (English for Specific Purposes) involves teaching and learning the specific skills and language needed by particular learners for a particular purpose. The P in ESP is always a professional purpose which is a set of skills that learners currently need in their work or will need in their professional careers. It has had an early origin since 1960’s and has grown to become one of the most prominent of English language teaching today. Moreover, ESP learners are usually adults who have some quittances with English and learn the language so as to communicate and perform particular profession. Related activities are based on specific purposes and needs. They are integrated into subject matter area important to the learners. Unlike general English which focuses on teaching general language courses and all four language skills are equally stressed, ESP and practically needs analysis determine which language skills are the most needed by the learners and syllabus designed accordingly. This paper looked into the origin, characteristics, development of ESP, the difference between ESP and general English. Finally, the paper critically reviews the role of needs analysis in the ESP.

Keywords: English language teaching, English for general purposes, English for specific purposes, needs analysis

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Authors: Arianna Sacerdoti

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There is a rich and frequent representation of uniqueness in Statius’ poem called Thebaid. This topos interweave with a psychoanalytical study about groups and individual but is also a literary device. This paper will analyze all the passages in the 'Thebaid' referred to uniqueness and exceptionality. Antigone, Adrastus and other characters are, in fact, often characterized as the only ones to behave in a specific way or to do something. Also, the insomniac characters are often the only ones who do not sleep. The material of such a tòpos is very rich throughout the 'Thebaid'. The methodology will be text-oriented. Conclusions will enlighten Statius’ specific use of this tòpos, as related to his models, and will be interdisciplinary. In concluding, this is a study linking philology and psychoanalysis and focused on a topic which deserves a specific analysis.

Keywords: statius, Silius Italicus, uniqueness, epic

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Authors: Ajay B. C., Meena H. N., Dagla M. C., Narendra Kumar, Makwana A. D., Bera S. K., Kalariya K. A., Singh A. L.

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The high-energy value, protein content and minerals makes peanut a rich source of nutrition at comparatively low cost. Basic information on genetics and inheritance of these mineral elements is very scarce. Hence, in the present study inheritance (using additive-dominance model) and association of mineral elements was studied in two peanut crosses. Dominance variance (H) played an important role in the inheritance of P, K, Fe and Zn in peanut pods. Average degree of dominance for most of the traits was greater than unity indicating over dominance for these traits. Significant associations were also observed among mineral elements both in F2 and F3 generations but pod yield had no associations with mineral elements (with few exceptions). Di-allele/bi-parental mating could be followed to identify high yielding and mineral dense segregates.

Keywords: correlation, dominance variance, mineral elements, peanut

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Authors: A. Hol

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Nowadays, within quickly changing business environments, companies are often faced with specific problems where knowledge required to make timely decisions is often available however is not always readily accessible by the decision makers, in a required form. To identify if in any way via innovative system development companies could be assisted so that they can make quicker industry specific decisions in a given time and space, researchers conducted in depth case study investigation during which they studied company’s e-transformation recommendations, company’s current issues and problems as well as the nature of company’s pressing decisions. This study utilizes Scenario Based Analysis with the aim to help identify parameters crucial for the development of the system that could support decision making in a given time and space. Based on the findings, Context Specific e-transformation decision making framework is proposed.

Keywords: e-transformation, business context, decision making, e-T Guide, ICT

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Authors: Bunakiye R. Japheth, Ogude U. Cyril

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Since the process of transforming user requirements to modeling constructs are not very well supported by domain-specific frameworks, it became necessary to integrate domain requirements with the specific architectures to achieve an integrated customizable solutions space via artifact orientation. Domain-specific modeling language specifications of model-driven engineering technologies focus more on requirements within a particular domain, which can be tailored to aid the domain expert in expressing domain concepts effectively. Modeling processes through domain-specific language formalisms are highly volatile due to dependencies on domain concepts or used process models. A capable solution is given by artifact orientation that stresses on the results rather than expressing a strict dependence on complicated platforms for model creation and development. Based on this premise, domain-specific methods for producing artifacts without having to take into account the complexity and variability of platforms for model definitions can be integrated to support customizable development. In this paper, we discuss methods for the integration capabilities and necessities within a common structure and semantics that contribute a metamodel for artifact-orientation, which leads to a reusable software layer with concrete syntax capable of determining design intents from domain expert. These concepts forming the language formalism are established from models explained within the oil and gas pipelines industry.

Keywords: control process, metrics of engineering, structured abstraction, semantic model

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Authors: John Hawkins, Graham Burton

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Contextual targeting is a common strategy for advertising that places marketing messages in media locations that are expected to be aligned with the target audience. There are multiple major challenges to contextual targeting: the ideal categorisation scheme needs to be known, as well as the most appropriate subsections of that scheme for a given campaign or creative. In addition, the campaign reach is typically limited when targeting becomes narrow, so a balance must be struck between requirements. Finally, refinement of the process is limited by the use of evaluation methods that are either rapid but non-specific (click through rates), or reliable but slow and costly (conversions or brand recall studies). In this study we evaluate the use of attention measurement as a technique for understanding the performance of targeting on the basis of specific contextual topics. We perform the analysis using a large scale dataset of impressions categorised using the iAB V2.0 taxonomy. We evaluate multiple levels of the categorisation hierarchy, using categories at different positions within an initial creative specific ranking. The results illustrate that measuring attention time is an affective signal for the performance of a specific creative within a specific context. Performance is sustained across a ranking of categories from one period to another.

Keywords: contextual targeting, digital advertising, attention measurement, marketing performance

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Authors: C. Andreu Sabater, D. Drago, C. Key-aberg, W. Moukrim, B. Naccache

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Present study concerns the optimization of a new vertical axis wind turbine system associated to a dynamoelectric motor. The system is composed by three Savonius wind turbines, arranged in an equilateral triangle. The idea is to propose a new concept of wind turbines through a technical approach allowing find a specific power never obtained before and therefore, a significant reduction of installation costs. In this work different wind flows across the system have been simulated, as well as precise definition of parameters and relations established between them. It will allow define the optimal rotor specific power for a given volume. Calculations have been developed with classical Savonius dimensions.

Keywords: VAWT, savonius, specific power, optimization, weibull

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Authors: Peter Burggräf, Moritz Krunke, Hanno Voet

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Due to shortening product and technology lifecycles, many companies use standardization approaches in product development and factory planning to reduce costs and time to market. Unlike large companies, where modular systems are already widely used, small and medium-sized companies often show a much lower degree of standardization due to lower scale effects and missing capacities for the development of these standards. To overcome these challenges, the development of industry sector specific standards in cooperations or by third parties is an interesting approach. This paper analyzes which branches that are mainly dominated by small or medium-sized companies might be especially interesting for the development of factory standards using the example of the German industry. For this, a key performance indicator based approach was developed that will be presented in detail with its specific results for the German industry structure.

Keywords: factory planning, factory standards, industry sector specific standardization, production planning

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Authors: Rudolf Hela, Lenka Bodnarova

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Paper focuses on experimental testing of possibilities of mechanical activation of fly ash and observation of influence of specific surface and granulometry on final properties of fresh and hardened concrete. Mechanical grinding prepared various fineness of fly ash, which was classed by specific surface in accordance with Blain and their granulometry was determined by means of laser granulometer. Then, sets of testing specimens were made from mix designs of identical composition with 25% or Portland cement CEM I 42.5 R replaced with fly ash with various specific surface and granulometry. Mix design with only Portland cement was used as reference. Mix designs were tested on consistency of fresh concrete and compressive strength after 7, 28, 60, and 90 days.

Keywords: concrete, fly ash, latent hydraulicity, mechanically activated fly ash

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Authors: Mustafa Malki, Ewan R. Pearson

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Tools utilized by health care practitioners to flag potential adverse drug reactions secondary to drug-drug interactions ignore individual genetic variation, which has the potential to markedly alter the severity of these interactions. To our best knowledge, there have been limited published studies on the impact of genetic variation on drug-drug interactions. Therefore, our aim in this project is the discovery of previously unrecognized, clinically important drug-drug-gene interactions (DDGIs) within the list of most commonly used drug combinations in the UK. The UKBB database was utilized to identify the top most frequently prescribed drug combinations in the UK with at least one route of interaction (over than 200 combinations were identified). We have recognised 37 common and unique interacting genes considering all of our drug combinations. Out of around 600 potential genetic variants found in these 37 genes, 100 variants have met the selection criteria (common variant with minor allele frequency ≥ 5%, independence, and has passed HWE test). The association between these variants and the use of each of our top drug combinations has been tested with a case-control analysis under the log-additive model. As the data is cross-sectional, drug intolerance has been identified from the genotype distribution as presented by the lower percentage of patients carrying the risky allele and on the drug combination compared to those free of these risk factors and vice versa with drug tolerance. In GoDARTs database, the same list of common drug combinations identified by the UKBB was utilized here with the same list of candidate genetic variants but with the addition of 14 new SNPs so that we have a total of 114 variants which have met the selection criteria in GoDARTs. From the list of the top 200 drug combinations, we have selected 28 combinations where the two drugs in each combination are known to be used chronically. For each of our 28 combinations, three drug response phenotypes have been identified (drug stop/switch, dose decrease, or dose increase of any of the two drugs during their interaction). The association between each of the three phenotypes belonging to each of our 28 drug combinations has been tested against our 114 candidate genetic variants. The results show replication of four findings between both databases : (1) Omeprazole +Amitriptyline +rs2246709 (A > G) variant in CYP3A4 gene (p-values and ORs with the UKBB and GoDARTs respectively = 0.048,0.037,0.92,and 0.52 (dose increase phenotype)) (2) Simvastatin + Ranitidine + rs9332197 (T > C) variant in CYP2C9 gene (0.024,0.032,0.81, and 5.75 (drug stop/switch phenotype)) (3) Atorvastatin + Doxazosin + rs9282564 (T > C) variant in ABCB1 gene (0.0015,0.0095,1.58,and 3.14 (drug stop/switch phenotype)) (4) Simvastatin + Nifedipine + rs2257401 (C > G) variant in CYP3A7 gene (0.025,0.019,0.77,and 0.30 (drug stop/switch phenotype)). In addition, some other non-replicated, but interesting, significant findings were detected. Our work also provides a great source of information for researchers interested in DD, DG, or DDG interactions studies as it has highlighted the top common drug combinations in the UK with recognizing 114 significant genetic variants related to drugs' pharmacokinetic.

Keywords: adverse drug reactions, common drug combinations, drug-drug-gene interactions, pharmacogenomics

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Authors: Thusitha Mabotuwana, Christopher S. Hall

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Radiologists routinely make follow-up imaging recommendations, usually based on established clinical practice guidelines, such as the Fleischner Society guidelines for managing lung nodules. In order to ensure optimal care, it is important to make guideline-compliant recommendations, and also for patients to follow-up on these imaging recommendations in a timely manner. However, determining such compliance rates after a specific finding has been observed usually requires many time-consuming manual steps. To address some of these limitations with current approaches, in this paper we discuss a methodology to automatically detect finding-specific follow-up recommendations from radiology reports and create a visualization for relevant subsequent exams showing the modality transitions. Nearly 5% of patients who had a lung related follow-up recommendation continued to have at least eight subsequent outpatient CT exams during a seven year period following the recommendation. Radiologist and section chiefs can use the proposed tool to better understand how a specific patient population is being managed, identify possible deviations from established guideline recommendations and have a patient-specific graphical representation of the imaging pathways for an abstract view of the overall treatment path thus far.

Keywords: follow-up recommendations, follow-up tracking, care pathways, imaging pathway visualization

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Authors: Yozna Gurung

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This paper presents preliminary findings from an on-going study on the use of Internal State Terms (IST) in the production of narratives of Hindi-English bilinguals in an attempt to identify children at risk for Specific Language Impairment. Narratives were examined for macrostructure (story structure and story complexity) and internal state terms or mental state terms (IST/MST). 31 students generated stories based on six pictures that were matched for content and story structure in L1 (Hindi) and L2 (English) using a wordless picture narrative. From 30 sample population, 2 students are at risk of Specific Language Impairment, according to this study i.e 6.45%. They showed least development in story grammar as well as IST in both their languages.

Keywords: internal state terms, macrostructure, specific language impairment, wordless picture narrative

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Authors: Chandra Gupt Porwal

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Excessive vibration means increased wear, increased repair efforts, bad product selection & quality and high energy consumption. This may be sometimes experienced by cavitation or suction/discharge re-circulation which could occur only when net positive suction head available NPSHA drops below the net positive suction head required NPSHR. Cavitation can cause axial surging if it is excessive, will damage mechanical seals, bearings, possibly other pump components frequently and shorten the life of the impeller. Efforts have been made to explain Suction Energy (SE), Specific Speed (Ns), Suction Specific Speed (Nss), NPSHA, NPSHR & their significance, possible reasons of cavitation /internal re-circulation, its diagnostics and remedial measures to arrest and prevent cavitation in this paper. A case study is presented by the author highlighting that the root cause of unwanted noise and vibration is due to cavitation, caused by high specific speeds or inadequate net- positive suction head available which results in damages to material surfaces of impeller & suction bells and degradation of machine performance, its capacity and efficiency too. The author strongly recommends revisiting the technical specifications of CW pumps to provide sufficient NPSH margin ratios > 1.5, for future projects and Nss be limited to 8500 -9000 for cavitation free operation.

Keywords: best efficiency point (BEP), net positive suction head NPSHA, NPSHR, specific speed NS, suction specific speed NSS

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Authors: I. Boroňová, J. Bernasovská, J. Kľoc, Z. Tomková, E. Petrejčíková, S. Mačeková, J. Poráčová, M. M. Blaščáková

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Osteoporosis is a common multifactorial disease with a strong genetic component characterized by reduced bone mass and increased risk of fractures. Genetic factors play an important role in the pathogenesis of osteoporosis. The aim of our study was to identify the genotype and allele distribution of T245G polymorphism in OPG gene in Slovak postmenopausal women. A total of 200 unrelated Slovak postmenopausal women with diagnosed osteoporosis and 200 normal controls were genotyped for T245G (rs3134069) polymorphism of OPG gene. Genotyping was performed using the Custom Taqman®SNP Genotyping assays. Genotypes and alleles frequencies showed no significant differences (p=0.5551; p=0.6022). The results of the present study confirm the importance of T245G polymorphism in OPG gene in the pathogenesis of osteoporosis.

Keywords: OPG gene, T245G polymorphism, osteoporosis, T245G polymorphism, real-time PCR

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Authors: Wilhelm Hoeflinger, Thomas Laminger, Johannes Wolfslehner

Abstract:

For vacuum cleaned dust filters, used e. g. in textile industry, there exist no calculation methods to determine design parameters (e. g. traverse speed of the nozzle, filter area...). In this work a method to calculate the optimum traverse speed of the nozzle of an industrial-size flat dust filter at a given mean pressure drop and filter face velocity was elaborated. Well-known equations for the design of a cleanable multi-chamber bag-house-filter were modified in order to take into account a continuously regeneration of a dust filter by a nozzle. Thereby, the specific filter medium resistance and the specific cake resistance values are needed which can be derived from filter tests under constant operation conditions. A lab-scale filter test rig was used to derive the specific filter media resistance value and the specific cake resistance value for vacuum cleaned filter operation. Three different filter media were tested and the determined parameters were compared to each other.

Keywords: design of dust filter, dust removing, filter regeneration, operation parameters

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Authors: Mahdy Elhusseiny, Richard Gearhart, Mariam Alyammahi

Abstract:

In this study we analyse the impact of a number of major macroeconomic variables on industry-specific excess rates of return. In later specifications, we include time and recession fixed effects, to potentially capture time-specific trends that may have been changing over our panel. We have a number of results that bear mentioning. Seasonal and temporal factors found to have very large role in sector-specific excess returns. Increases in M1(money supply) decreases bank, insurance, real estate, and telecommunications, while increases industrial and transportation excess returns. The results indicate that the market return increases every sector-specific rate of return. The 2007 to 2009 recession significantly reduced excess returns in the bank, real estate, and transportation sectors.

Keywords: macroeconomic factors, industry returns, fixed effects, temporal factors

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Authors: Thanyaporn Senarai, Rapeepun Vanichviriyakit, Shinji Miyata, Chihiro Sato, Prapee Sretarugsa, Wattana Weerachatyanukul, Ken Kitajima

Abstract:

In this study, we characterized a region-specific 250 kDa protein that was secreted of MSD fluid, which is believed to play dual functions in forming a spermatophoric wall for sperm physical protection, and in sperm membrane modification as part of sperm maturation process. The partial amino acid sequence and N-terminal sequencing revealed that the MSD-specific 250 kDa protein showed a high similarity with a plasma-rich protein, α-2 macroglobulin (α2M), so termed pp-α2M. This protein was a large glycoprotein contained predominantly mannose and GlcNAc. The expression of pp-α2M mRNA was detected in spermatic duct (SD), androgenic gland (AG) and hematopoietic tissue, while the protein expression was rather specific to the apical cytoplasm of MSD epithelium. The secretory pp-α2M in MSD fluid was acquired onto the MSD sperm membrane and was also found within the matrix of the acrosome. Distally, pp-α2M was removed from spermathecal sperm membrane, while its level kept constant in the sperm AC. Together the results indicate that pp-α2M is a 250 kDa region-specific secretory protein which plays roles in sperm physical protection and also acts as maturation factor in the P. pelagicus sperm.

Keywords: alpha-2 macroglobulin, blue swimming crab, sperm maturation, spermatic duct

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Authors: Tuhina-khatun, Mohamed Hanafi Musa, Mohd Rafii Yosup, Wong Mui Yun, Aktar-uz-Zaman, Mahbod Sahebi

Abstract:

Suppression subtractive hybridization (SSH) method is valuable tool for identifying differentially regulated genes in disease specific or tissue specific genes important for cellular growth and differentiation. It is a widely used method for separating DNA molecules that distinguish two closely related DNA samples. SSH is one of the most powerful and popular methods for generating subtracted cDNA or genomic DNA libraries. It is based primarily on a suppression polymerase chain reaction (PCR) technique and combines normalization and subtraction in a solitary procedure. The normalization step equalizes the abundance of DNA fragments within the target population, and the subtraction step excludes sequences that are common to the populations being compared. This dramatically increases the probability of obtaining low-abundance differentially expressed cDNAs or genomic DNA fragments and simplifies analysis of the subtracted library. SSH technique is applicable to many comparative and functional genetic studies for the identification of disease, developmental, tissue specific, or other differentially expressed genes, as well as for the recovery of genomic DNA fragments distinguishing the samples under comparison.

Keywords: suppression subtractive hybridization, differentially expressed genes, disease specific genes, tissue specific genes

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Authors: Sunil Kumar, Uday C. Ghoshal

Abstract:

Background and aims: Serotonin (5-hydroxtryptamine, 5-HT) is an important factor in gut function, playing key roles in intestinal peristalsis and secretion, and in sensory signaling in the brain-gut axis. Removal from its sites of action is mediated by a specific protein called the serotonin reuptake transporter (SERT). Polymorphisms in the promoter region of the SERT gene have effects on transcriptional activity, resulting in altered 5-HT reuptake efficiency. Functional polymorphisms may underlie disturbance in gut function in individuals suffering with disorders such as irritable bowel syndrome (IBS). The aim of this study was to assess the potential association between SERT polymorphisms and the diarrhea predominant IBS (D-IBS) phenotype Subjects: A total of 36 northern Indian female patients and 55 female northern Indian healthy controls (HC) were subjected to genotyping. Methods: Leucocyte DNA of all subjects was analyzed by polymerase chain reaction based technologies for SERT polymorphisms, specifically the insertion/deletion polymorphism in the promoter (SERT-P). Statistical analysis was performed to assess association of SERT polymorphism allele with the D-IBS phenotype. Results: The frequency of distribution of SERT-P gene was comparable between female patients with IBS and HC (p = 0.086). However, frequency of SERT-P deletion/deletion genotype was significantly higher in female patients with D-IBS compared to C-IBS and A-IBS [17/19 (89.5%) vs. 4/12 (33.3%) vs. 1/5 (20%), p=0.001, respectively]. The mucosal level of serotonin was higher in D-IBS compared to C-IBS and A-IBS [Median, range (159.26, 98.78–212.1) vs. 110.4, 67.87–143.53 vs. 92.34, 78.8–166.3 pmol/mL, p=0.001, respectively]. The mucosal level of serotonin was higher in female patients with IBS with SERT-P deletion/deletion genotype compared deletion/insertion and insertion/insertion [157.65, 67.87–212.1 vs. 110.4, 78.1–143.32 vs. 100.5, 69.1–132.03 pmol/mL, p=0.001, respectively]. Patients with D-IBS with deletion/deletion genotype more often reported symptoms of abdominal pain, discomfort (p=0.025) and bloating (p=0.039). Symptoms development following lactose ingestion was strongly associated with D-IBS and SERT-P deletion/deletion genotype (p=0.004). Conclusions: Significant association was observed between D-IBS and the SERT-P deletion/deletion genotype, suggesting that the serotonin transporter is a potential candidate gene for D-IBS in women.

Keywords: serotonin, SERT, inflammatory bowel disease, genetic polymorphism

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Authors: Shahram Nanekarania, Majid Goodarzia

Abstract:

Calpastatin and callipyge have been known as one of the candidate genes in meat quality and quantity. Calpastatin gene has been located to chromosome 5 of sheep and callipyge gene has been localized in the telomeric region on ovine chromosome 18. The objective of this study was identification of calpastatin and callipyge genes polymorphism and analysis of genotype structure in population of Lori sheep kept in Iran. Blood samples were taken from 120 Lori sheep breed and genomic DNA was extracted by salting out method. Polymorphism was identified using the PCR-RFLP technique. The PCR products were digested with MspI and FaqI restriction enzymes for calpastatin gene and callipyge gene, respectively. In this population, three patterns were observed and AA, AB, BB genotype have been identified with the 0.32, 0.63, 0.05 frequencies for calpastatin gene. The results obtained for the callipyge gene revealed that only the wild-type allele A was observed, indicating that only genotype AA was present in the population under consideration.

Keywords: polymorphism, calpastatin, callipyge, PCR-RFLP, Lori sheep

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