Search results for: variant calling

Authors: Rofida Gamal, Mostafa Mohammed, Mariam Adel, Marwa Gamal, Marwa kamal, Ayat Saber, Maha Mamdouh, Amira Emad, Mai Ramadan

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Lynch Syndrome is an inherited genetic condition associated with an increased risk of colorectal and other cancers. Detecting Lynch Syndrome in individuals is crucial for early intervention and preventive measures. This study proposes a computational pipeline for Lynch Syndrome detection by integrating alignment, variant calling, and annotation. The pipeline leverages popular tools such as FastQC, Trimmomatic, BWA, bcftools, and ANNOVAR to process the input FASTQ file, perform quality trimming, align reads to the reference genome, call variants, and annotate them. It is believed that the computational pipeline was applied to a dataset of Lynch Syndrome cases, and its performance was evaluated. It is believed that the quality check step ensured the integrity of the sequencing data, while the trimming process is thought to have removed low-quality bases and adaptors. In the alignment step, it is believed that the reads were accurately mapped to the reference genome, and the subsequent variant calling step is believed to have identified potential genetic variants. The annotation step is believed to have provided functional insights into the detected variants, including their effects on known Lynch Syndrome-associated genes. The results obtained from the pipeline revealed Lynch Syndrome-related positions in the genome, providing valuable information for further investigation and clinical decision-making. The pipeline's effectiveness was demonstrated through its ability to streamline the analysis workflow and identify potential genetic markers associated with Lynch Syndrome. It is believed that the computational pipeline presents a comprehensive and efficient approach to Lynch Syndrome detection, contributing to early diagnosis and intervention. The modularity and flexibility of the pipeline are believed to enable customization and adaptation to various datasets and research settings. Further optimization and validation are believed to be necessary to enhance performance and applicability across diverse populations.

Keywords: Lynch Syndrome, computational pipeline, alignment, variant calling, annotation, genetic markers

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Authors: Malul Miki, Rafi Bar-El, Eithan Hourie

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In this article, we test the influence of an occupation as a calling on the value of job security and its connection with wage levels. Our sample consists of 495 workers in Israel from 10 occupations in the public sector, who are assumed to have a relatively high level of job security, and the private sector, who are assumed to have less job security or none at all. These 10 occupations are social workers, lecturers, lawyers, administration workers, accountants, high school teachers, bank workers, high-tech worker, nurses and psychologists. Using regression analysis, we find that those who have occupations that the literature has defined as a calling value job security less than those in ordinary employment. In addition, salary level has no effect on this relationship. Finally, those who work in occupations that are regarded as a calling have less status quo bias than those in ordinary employment.

Keywords: calling, loss aversion, job security, status quo bias

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Authors: Yonguk L. Park, Jeonghoon Seol

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The Republic of Korea is facing a special situation as it is the only divided country in the world. Even though Korea is facing such unstable circumstances in terms of a foreign diplomacy situation, Korea is one of the countries who, in concern for world peace, have been sending troops overseas. The troops spend more than a year at sea and may suffer from different types of psychological disorders. The purpose of this study is to try to find factors that promote psychological well-being of troops and improve their psychological health. We investigated the effect of dispatch sailors’ occupational calling and social support on anxiety before they are sent overseas and also examined the interaction between occupational calling and social support on anxiety. One hundred thirty-eight dispatched sailors participated in this study, wherein they completed the Korean calling scale, multifaceted social support scale, and anxiety scale –Y form. We analyzed the data using hierarchical regression. The results showed that after controlling gender, marital status, and the previous experiences of dispatch, those who have a higher level of occupational calling and perceived social support experienced a low level of anxiety before they are sent (β = -.276, β = -.395). Furthermore, we examined the interaction effect. If the troops’ perceived social support is high, they experience a low level of anxiety—even if they have a low level of occupational calling. This study confirms that both occupational calling and social support reduce the level of anxiety of the troops. The research provides meaningful information in understanding those who serve in the Navy’s distinctive situations and contributes to improving their psychological well-being. We suggest that sailors undergo training to have a higher occupational calling and healthy relationships with friends, families, and co-workers who provide emotional and social support.

Keywords: navy, occupational calling, social support, anxiety

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Authors: Yuan-Lin Liu, Ye Li, Tian Xia

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Taxi-calling APPs have been used widely, while brought both benefits and a variety of issues for the taxi market. Many countries do not know whether the benefits are remarkable than the issues or not. This paper established a comparison between the basic scenario (2009-2012) and a taxi-calling software usage scenario (2012-2015) to explain the impact of taxi-calling APPs. The impacts of taxi-calling APPs illustrated by the comparison results are: 1) The supply and demand distribution is more balanced, extending from the city center to the suburb. The availability of taxi service has been improved in low density areas, thin market attribute has also been improved; 2)The ratio of short distance taxi trip decreased, long distance service increased, the utilization of mileage increased, and the rate of empty decreased; 3) The popularity of taxi-calling APPs was able to reduce the average empty distance, cruise time, empty mileage rate and average times of loading passengers, can also enhance the average operating speed, improve the taxi operating level, and reduce social cost although there are some disadvantages. This paper argues that the taxi industry and government can establish an integrated third-party credit information platform based on credit evaluated by the data of the drivers’ driving behaviors to supervise the drivers. Taxi-calling APPs under fully covered supervision in the mobile Internet environment will become a new trend.

Keywords: taxi, taxi-calling APPs, credit, scenario comparison

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Authors: Chen Wang, Jared Evans, Yan Asmann

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With the quick evolvement of next-generation sequencing techniques, whole-exome or exome-panel data have become a cost-effective way for detection of small exonic mutations, but there has been a growing desire to accurately detect copy number variations (CNVs) as well. In order to address this research and clinical needs, we developed a sequencing coverage pattern-based method not only for copy number detections, data integrity checks, CNV calling, and visualization reports. The developed methodologies include complete automation to increase usability, genome content-coverage bias correction, CNV segmentation, data quality reports, and publication quality images. Automatic identification and removal of poor quality outlier samples were made automatically. Multiple experimental batches were routinely detected and further reduced for a clean subset of samples before analysis. Algorithm improvements were also made to improve somatic CNV detection as well as germline CNV detection in trio family. Additionally, a set of utilities was included to facilitate users for producing CNV plots in focused genes of interest. We demonstrate the somatic CNV enhancements by accurately detecting CNVs in whole exome-wide data from the cancer genome atlas cancer samples and a lymphoma case study with paired tumor and normal samples. We also showed our efficient reuses of existing exome sequencing data, for improved germline CNV calling in a family of the trio from the phase-III study of 1000 Genome to detect CNVs with various modes of inheritance. The performance of the developed method is evaluated by comparing CNV calling results with results from other orthogonal copy number platforms. Through our case studies, reuses of exome sequencing data for calling CNVs have several noticeable functionalities, including a better quality control for exome sequencing data, improved joint analysis with single nucleotide variant calls, and novel genomic discovery of under-utilized existing whole exome and custom exome panel data.

Keywords: bioinformatics, computational genetics, copy number variations, data reuse, exome sequencing, next generation sequencing

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Authors: Yohannes Bisa Biramo

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This study examined the meditational role of surface acting and deep acting on the relationship between calling orientation and work engagement of teachers in secondary schools of Wolaita Zone, Wolaita, Ethiopia. A predictive non-experimental correlational design was performed among 300 secondary school teachers. Stratified random sampling followed by a systematic random sampling technique was used as the basis for selecting samples from the target population. To analyze the data, Structural Equation Modeling (SEM) was used to test the association between the independent variables and the dependent variables. Furthermore, the goodness of fit of the study variables was tested using SEM to see and explain the path influence of the independent variable on the dependent variable. Confirmatory factor analysis (CFA) was conducted to test the validity of the scales in the study and to assess the measurement model fit indices. The analysis result revealed that calling was significantly and positively correlated with surface acting, deep acting and work engagement. Similarly, surface acting was significantly and positively correlated with deep acting and work engagement. And also, deep acting was significantly and positively correlated with work engagement. With respect to mediation analysis, the result revealed that surface acting mediated the relationship between calling and work engagement and also deep acting mediated the relationship between calling and work engagement. Besides, by using the model of the present study, the school leaders and practitioners can identify a core area to be considered in recruiting and letting teachers teach, in giving induction training for newly employed teachers and in performance appraisal.

Keywords: calling, surface acting, deep acting, work engagement, mediation, teachers

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Authors: Mohammed Althobiti, Patrick Booms, Dorota Fiszer, Philip Hopkins

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Malignant hyperthermia (MH) is a pharmacogenetic disorder of skeletal muscle. MH results from anaesthetics induced breakdown of calcium homeostasis. RYR1 and CACN1AS mutations represent the aetiology in ~70% of the MH population. Previous studies indicate that up to 25% of MH patients carry no variants in these genes. Therefore, the aim of this study is to investigate the relationships between MH susceptibility and genes encoding skeletal muscle Ca2+ channels as well as accessory proteins. The JSRP, encoding JP-45, was previously sequenced and novel genetic variants were identified. The variant p.P108L (c.323C > T) was identified in exon 4 and encodes a change from a proline at amino acid 108 to leucine residue. The variant P108L was detected in two patients out of 50 with 4% frequency in the sample population. The alignment of DNA sequences in different species indicates highly conserved proline sequences involved in the substitution of the P108L variant. In this study, the variant P108L co-segregates with the SNP p.V92A (c.275T > C) at the same exon, both variants being inherited in the same two patients only. This indicates that the two variants may represent a haplotype. Therefore, a set of single nucleotide polymorphisms and statistical analysis will be used to investigate the effects of haplotypes on MH susceptibility. Furthermore, investigating the effect of the P108L variant in combination with RYR1 mutations or other genetic variants in other genes as a combination of two or more genetic variants, haplotypes may then provide stronger genetic evidence indicating that JSRP1 is associated with MH susceptibility. In conclusion, these preliminary results lend a potential modifier role of the variant P108L in JSRP1 in MH susceptibility and further investigations are suggested to confirm these results.

Keywords: JSRP1, malignant hyperthermia, RyR1, skeletal muscle

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Authors: Zi-Han Li, Zi-Jun Sun, Dong-Yuan Chang, Li Zhu, Min Chen, Ming-Hui Zhao

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Aims: A genome-wide association study (GWAS) reported that patients with the rs55703767 minor allele in collagen type IV α3 chain encoding gene COL4A3 showed protection against diabetic kidney disease (DKD) in type 1 diabetes mellitus (T1DM). However, the role of rs55703767 in type 2 DKD has not been elucidated. The aim of the current study was to investigate the association between COL4A3 variant rs55703767 and DKD risk in Chinese patients with type 2 diabetes mellitus (T2DM). Methods: This nested case-control study was performed on 1311 patients who had T2DM for at least 10 years, including 580 with DKD and 731 without DKD. We detected the genotypes of all patients by TaqMan SNP Genotyping Assay and analyzed the association between COL4A3 variant rs55703767 and DKD risk. Results: Genetic analysis revealed that there was no significant difference between T2DM patients with DKD and those without DKD regarding allele or genotype frequencies of rs55703767, and the effect of this variant was not hyperglycemia specific. Conclusion: Our findings suggested that there was no detectable association between the COL4A3 variant rs55703767 and the susceptibility to DKD in the Chinese T2DM population.

Keywords: collagen type IV α3 chain, gene polymorphism, type 2 diabetes, diabetic kidney disease

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Authors: Fern Baedyananda, Arkom Chaiwongkot, Somchai Niruthisard, Nakarin Kitkumthorn, Parvapan Bhattarakosol

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High-risk human papillomavirus (HPV) infections cause transformation of the host cells by down-regulating and inhibiting host regulatory proteins such as p53 and pRb by overexpressing the viral oncoproteins E6 and E7. However, the E1 protein which is the only enzyme encoded by HPV has also been shown to cause DNA instability leading to the integration of the virus into the host genome and triggering carcinogenic events. A 63bp duplication in the E1 helicase region has been detected in European patients. However, the clinical prognosis of these patients is still controversial. This study was performed to determine the presence of the HPV-16 E1 63bp duplication in patient cervical samples in Thai women and determine the sequence of the variant in the Thai population. Detection of the HPV-16 E1 duplication in the helicase region was performed in 90 patient cell samples across normal, cervical intraepithelial neoplasia I-III, and squamous cervical carcinoma stages by PCR. The PCR products were purified and sequenced to determine the presence of duplication variants.The variant form was found in 10% of all CIN 1 patients. In this study, the presence of the 63 bp duplication variant in the Thai population was found to be present and was further characterized. Interestingly, all samples that exhibited the variant form of HPV-16 E1 were classified as CIN I. Presence of the variant, constricted to mild dysplasia signifies the importance of HPV-16 E1 in carcinogenesis.

Keywords: carcinogenesis, cervical cancer, human papillomavirus, HPV-16 E1

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Authors: Rim Frikha, Maha Ben Jema, Moez Elloumi, Tarek Rebai

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Background: Acute lymphoblastic leukemia (ALL); a common blood cancer characterized by the interaction between genetic and environmental factors. Methylenetetrahydrofolate reductase (MTHFR) is an essential folate metabolic enzyme in the processes of DNA synthesis and methylation. A common functional variant of the MTHFR gene, the A1298C, which induces disturbances in folate metabolism, may affect susceptibility to ALL. Objective: The present study aimed to assess the prevalence of MTHFR polymorphism A1298 > C in Tunisian children with ALL. Materials and Methods: A total of 28 Tunisian ALL children were enrolled in this study. Genomic DNA was extracted from whole venous blood collected in ethylenediaminetetraacetic acid (EDTA). Genotyping was carried out with restriction fragment length polymorphism (RFLP) using MboII restriction enzyme. Genotype distribution and allele frequency of MTHFR A1298C was calculated in ALL patients. Results: The A1298C variant of MTHFR was found in 11(19.6%) heterozygous and one homozygous patient (3.5%). Conclusions: This result highlights that A1298C polymorphism of MTHFR is common in Tunisian childhood ALL and suggests that this variant may have a potential role in leukemogenesis. Genotyping of large samples and different ethnicities are required to validate these findings.

Keywords: methylenetetrahydrofolate reductase, acute lymphoblastic leukemia, A1298C variant, prevalence

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Authors: Isobel Hambleton, Mark Carrington

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Trypanosoma brucei, the causal agent of a range of diseases in humans and livestock, evades the mammalian immune system through a population survival strategy based on the expression of a series of antigenically distinct variant surface glycoproteins (VSGs). RNAi mediated knockdown of the active VSG gene triggers a precytokinesis cell cycle arrest. To determine whether this phenotype is the result of reduced VSG transcript or depleted VSG protein, we used morpholino antisense oligonucleotides to block translation of VSG mRNA. The same precytokinesis cell cycle arrest was observed, suggesting that VSG protein abundance is monitored closely throughout the cell cycle. An inducible expression system has been developed to test various GPI-anchored proteins for their ability to rescue this cell cycle arrest. This system has been used to demonstrate that wild-type VSG expressed from a T7 promoter rescues this phenotype. This indicates that VSG expression from one of the specialised bloodstream expression sites (BES) is not essential for cell division. The same approach has been used to define the minimum essential features of a VSG necessary for function.

Keywords: bloodstream expression site, morpholino, precytokinesis cell cycle arrest, variant surface glycoprotein

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Authors: Fatimazahrae Elbakri, Azeddine Ibrahimi, Meryem Lemrani, Dris Belghyti

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Leishmaniasis represents a major public health problem because of the number of cases recorded each year and the wide distribution of the disease. It is a parasitic disease of flagellated protozoa transmitted by the bite of certain species of sandfly, causing a spectrum of clinical pathology in humans ranging from disfiguring skin lesions to fatal visceral leishmaniasis. Cutaneous leishmaniasis due to Leishmania major is a polymorphic disease; in fact, the infection can be asymptomatic, localized, or disseminated. The objective of this work is to determine the genomic diversity that contributes to clinical variability by trying to identify the variation in chromosome number and to extract SNPs and SNPs and InDels; it is based on four sequences (WGS) of Leishmania major available on NCBI in Fastq form, from three countries: Tunisia, Algeria, and Israel, the analysis is set up from a pipeline to facilitate the discovery of genetic diversity, in particular SNP and chromosomal somy.

Keywords: Leshmania major, cutaneous Leishmania, NGS, genomic, somy, variant calling

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Authors: Hamza Iftikhar

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The research study focuses on the transgender community's gender recognition challenges. It is one of the issues for the transgender community, interacting directly with the difficulties of gender identity and the lives of these people who are facing gender disapproval from society. This study investigates the major flaws of the transgender act. The study's goal is to look into the strange implications of self-perceived identity as a policy tool for transgender recognition. This policy tool jeopardises the rights of Pakistan's indigenous gender-variant people as well as the country's legal and social framework. Qualitative research using semi structured interviews will be carried out. This study proposes developing a scheme for mainstreaming gender-variant people on the basis of the Pakistani Constitution, Supreme Court guidelines, and internationally recognised principles of law. This would necessitate a thorough review of current law using a new approach and reference point.

Keywords: transgender act, self perceived identity, gender variant, policy tool

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Authors: P. Jayashree, S. Rajkumar

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With the trend of virtual and augmented reality environments booming to provide a life like experience, gaming is a major tool in supporting such learning environments. In this work, a variant of Voronoi heuristics, employing supervised learning for the TRON game is proposed. The paper discusses the features that would be really useful when a machine learning bot is to be used as an opponent against a human player. Various game scenarios, nature of the bot and the experimental results are provided for the proposed variant to prove that the approach is better than those that are currently followed.

Keywords: artificial Intelligence, automation, machine learning, TRON game, Voronoi heuristics

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Authors: Robert van Ling, Alexander Schwahn, Shanhua Lin, Ken Cook, Frank Steiner, Rowan Moore, Mauro de Pra

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Purpose: Demonstration of fast high resolution charge variant analysis for monoclonal antibody (mAb) therapeutics within 5 minutes. Methods: Three commercially available mAbs were used for all experiments. The charge variants of therapeutic mAbs (Bevacizumab, Cetuximab, Infliximab, and Trastuzumab) are analyzed on a strong cation exchange column with a linear pH gradient separation method. The linear gradient from pH 5.6 to pH 10.2 is generated over time by running a linear pump gradient from 100% Thermo Scientific™ CX-1 pH Gradient Buffer A (pH 5.6) to 100% CX-1 pH Gradient Buffer B (pH 10.2), using the Thermo Scientific™ Vanquish™ UHPLC system. Results: The pH gradient method is generally applicable to monoclonal antibody charge variant analysis. In conjunction with state-of-the-art column and UHPLC technology, ultra fast high-resolution separations are consistently achieved in under 5 minutes for all mAbs analyzed. Conclusion: The linear pH gradient method is a platform method for mAb charge variant analysis. The linear pH gradient method can be easily optimized to improve separations and shorten cycle times. Ultra-fast charge variant separation is facilitated with UHPLC that complements, and in some instances outperforms CE approaches in terms of both resolution and throughput.

Keywords: charge variants, ion exchange chromatography, monoclonal antibody, UHPLC

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Authors: Vaclav Novak, Katerina Krizova, Petr Sarec

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Modern agriculture has to face many issues from which soil degradation and lack of organic matter in the soil are only a few of them. Apart from Climate Change, human utilization of landscape is the cause of a majority part of these problems. Cattle production in Czechia has been reduced by more than half in recent 30 years. However, cattle manure is considered as staple organic fertilizer, and its role in attempts for sustainable agriculture is irreplaceable. This study aims to describe the impact of so-called activators of biological manure transformation (Z´fix, Olmix Group) mainly on physical soil properties but also on crop status. The experiment has been established in 2017; nevertheless, initial measurements of implement draft have been performed before the treated manure application. In 2018, the physical soil properties and crop status (sugar beet) has been determined and compared with the untreated manure and control variant. Significant results have been observed already in the first year, where the implement draft decreased by 9.2 % within the treated manure variant in comparison with the control variant.

Keywords: field experiment, implement draft, vegetation index, sugar beet

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Authors: Mohammed N. Al Kindi, Mazin Al Khabouri, Khalsa Al Lamki, Tommasso Pappuci, Giovani Romeo, Nadia Al Wardy

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Hereditary hearing loss is a heterogeneous group of complex disorders with an overall incidence of one in every five hundred newborns presented as syndromic and non-syndromic forms. Cadherin-related 23 (CDH23) is one of the listed deafness causative genes. CDH23 is found to be expressed in the stereocilia of hair cells and the retina photoreceptor cells. Defective CDH23 has been associated mostly with prelingual severe-to-profound sensorineural hearing loss (SNHL) in either syndromic (USH1D) or non-syndromic SNHL (DFNB12). An Omani family diagnosed clinically with severe-profound sensorineural hearing loss was genetically analysed by whole exome sequencing technique. A novel homozygous missense variant, c.A7451C (p.D2484A), in exon 53 of CDH23 was detected. One hundred and thirty control samples were analysed where all were negative for the detected variant. The variant was analysed in silico for pathogenicity verification using several mutation prediction software. The variant proved to be a pathogenic mutation and is reported for the first time in Oman and worldwide. It is concluded that in silico mutation prediction analysis might be used as a useful molecular diagnostics tool benefiting both genetic counseling and mutation verification. The aspartic acid 2484 alanine missense substitution might be the main disease-causing mutation that damages CDH23 function and could be used as a genetic hearing loss marker for this particular Omani family.

Keywords: Cdh23, d2484a, in silico, Oman

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Authors: Rim Sghiri, Samia Al Shouli, Hana Benhassine, Nejla Elamri, Zahid Shakoor, Foued Slama, Adel Almogren, Hala Zeglaoui, Elyes Bouajina, Ramzi Zemni

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Objectives: Little is known about genes predisposing to systemic bone loss (SBL) in rheumatoid arthritis (RA). Therefore, we examined the association between SBL and a variant of CD40 gene, which is known to play a critical role in both immune response and bone homeostasis among patients with RA. Methods: CD40 rs48104850 was genotyped in 176 adult RA patients. Bone mineral density (BMD) was measured using dual-energy X-ray absorptiometry (DXA). Results: Low BMD was observed in 116 (65.9%) patients. Among them, 60 (34.1%) had low femoral neck (FN) Z score, 72 (40.9%) had low total femur (TF) Z score, and 105 (59.6%) had low lumbar spine (LS) Z score. CD40 rs4810485 was found to be associated with reduced TF Z score with the CD40 rs4810485 T allele protecting against reduced TF Z score (OR = 0.40, 95% CI = 0.23-0.68, p = 0.0005). This association was confirmed in the multivariate logistic regression analysis (OR=0.31, 95% CI= 0.16-0.59, p=3.84 x 10₋₄). Moreover, median FN BMD was reduced among RA patients with CD40 rs4810485 GG genotype compared to RA patients harbouring CD40 rs4810485 TT and GT genotypes (0.788± 0.136 versus 0.826± 0.146g/cm², p=0.001). Conclusion: This study, for the first time ever, demonstrated an association between a CD40 genetic variant and SBL among patients with RA.

Keywords: rheumatoid arthritis, CD40 gene, bone mineral density, systemic bone loss, rs48104850

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Authors: Manendra Singh Parihar, Sandip Ghosh Chowdhury

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Austenitic stainless steels are widely used and give a good combination of properties. When this steel is plastically deformed, a phase transformation of the metastable Face Centred Cubic Austenite to the stable Body Centred Cubic (α’) or to the Hexagonal close packed (ԑ) martensite may occur, leading to the enhancement in the mechanical properties like strength. The work was based on variant selection and corresponding texture analysis for the strain induced martensitic transformation during deformation of the parent austenite FCC phase to form the product HCP and the BCC martensite phases separately, obeying their respective orientation relationships. The automated method for reconstruction of the parent phase orientation using the EBSD data of the product phase orientation is done using the MATLAB and TSL-OIM software. The method of triplets was used which involves the formation of a triplet of neighboring product grains having a common variant and linking them using a misorientation-based criterion. This led to the proper reconstruction of the pre-transformation phase orientation data and thus to its micro structure and texture. The computational speed of current method is better compared to the previously used methods of reconstruction. The reconstruction of austenite from ԑ and α’ martensite was carried out for multiple samples and their IPF images, pole figures, inverse pole figures and ODFs were compared. Similar type of results was observed for all samples. The comparison gives the idea for estimating the correct sequence of the transformation i.e. γ → ε → α’ or γ → α’, during deformation of AISI 304 austenitic stainless steel.

Keywords: variant selection, reconstruction, EBSD, austenitic stainless steel, martensitic transformation

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Authors: Sara A. Al-Jaberi, Salma Ben-Salem, Meriam Messedi, Fatma Ayadi, Lihadh Al-Gazali, Bassam R. Ali

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Background: The chemokine receptor components play crucial roles in the immune system and some of them serve as co-receptors for the HIV virus. Several studies have documented those variants in chemokine receptors are correlated with susceptibility and resistance to infection with HIV virus. For example, mutations in the chemokine receptor 5 gene (CCR5) resulting in loss-of-function (such as the homozygous CCR5Δ32) confer high degree of resistance to HIV infection. Heterozygotes for these variants exhibit slow progression to AIDS. The prevalence of CCR5 polymorphisms varies among ethnic and geographical groups. For example, the CCR5 Δ32 variant is present in 10–15% of north Europeans but is rarely encountered among Africans. This study aims to identify the prevalence of some CCR5 variants in two geographically distant Arab populations (namely Emiratis and Tunisians). Methodology: The prevalence of CCR5 gene variants including CCR5Δ32, FS299, C101X, A29S and C178R has been determined using PCR and direct DNA sequencing. A total of 403 unrelated healthy individuals (253 Emiratis and 150 Tunisians) were genotyped for the CCR5Δ32 variant using PCR amplification and gel electrophoresis. In addition, 200 Emiratis have been screened for other SNPs using Sanger DNA sequencing. Results: Among Emiratis, the allele frequency of the CCR5Δ32 variant has been found to be 0.002. In addition, two variants L55Q and A159 were found at a frequency of 0.002.Moreover, the prevalence of the CCR5Δ32 variant in Tunisians was estimated to be 0.013 which is relatively higher than its frequency in Emiratis but lower than Europeans. Conclusion: We conclude that the allele frequency of the most critical CCR5 polymorphism (Δ32) is extremely low among Emiratis compared to other Arabs and North Europeans. In addition, very low allele frequencies of other CCR5 polymorphisms have been detected among Emiratis.

Keywords: chemokine receptors, CCR5Δ32, CCR5 polymorphisms, Emiratis, Arab populations

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Authors: Lukáš Plošek, Jaroslav Hynšt, Jaroslav Záhora, Jakub Elbl, Antonín Kintl, Ivana Charousová, Silvia Kovácsová

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Compost can influence soil fertility and plant health. At the same time compost can play an important role in the nitrogen cycle and it can influence leaching of mineral nitrogen from soil to underground water. This paper deals with the influence of compost addition and mineral nitrogen fertilizer on leaching of mineral nitrogen, nitrogen availability in microbial biomass and plant biomass production in the lysimetric experiment. Twenty-one lysimeters were filed with topsoil and subsoil collected in the area of protection zone of underground source of drinking water - Březová nad Svitavou. The highest leaching of mineral nitrogen was detected in the variant fertilized only mineral nitrogen fertilizer (624.58 mg m-2), the lowest leaching was recorded in the variant with high addition of compost (315.51 mg m-2). On the other hand, losses of mineral nitrogen are not in connection with the losses of available form of nitrogen in microbial biomass. Because loss of mineral nitrogen was detected in variant with the least change in the availability of N in microbial biomass. The leaching of mineral nitrogen, yields as well as the results concerning nitrogen availability from the first year of long term experiment suggest that compost can positive influence the leaching of nitrogen into underground water.

Keywords: nitrogen, compost, biomass production, lysimeter

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Authors: Elizabeth Godwin Mahenge

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This study seeks to investigate the portrayal of albinism in Swahili literature. People with albinism have faced many life-threatening challenges, from being hunted for their body parts of being assigned derogatory names that depict them as ghosts as or less than humans. Many studies have been conducted on the perception of people towards Persons with Albinism [PWA] worldwide. Findings showed there is negative perception or negative portrayal of PWA in different societies worldwide. These negative connotations raised hot debates around the world among different societies and associations of/for PWA. People with disability in different parts of the world started arguing the labeling and name calling same applied to persons with disability in Tanzania (albinism included). They went the same debate about name calling hence in 2010, the Tanzanian Parliament passed the bill on Persons with Disability Act which banned derogative names attached to disability in general and to albinism in particular. In Tanzanian societies, there have been a mixed feelings with regards to albinism. Some do have negative perceptions because of the killings with connection to superstitious believes, while in other societies are perceived positively as blessed children a family. From these two contradictory perceptions that exist in this society, the study seeks to find out how Swahili literature portrays albinism.

Keywords: albinism, portrayal, disability, Kiswahili literature

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Authors: Elena V. Lysenko

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Motivating as the leading function of a modern Human Resources Management involves issues of increasing the effectiveness of the organization in a broader context. During the formation of motivational systems, the top-management of organization should pay equal attention to both external motivation (incentive system) and internal (self-motivation). The balance of internal and external motivation harmonizes the relations between employers and employees, increases the level of job satisfaction by the organization staff, which in turn leads the organization to success and ensures the organization`s profitability and competitiveness in the market environment. The article is devoted to the study of personnel motivation system in the small metal trade company, which is located in Yekaterinburg, Russian Federation. The study took place during November-December, 2016 ordered by the Company Director to analyze the motivational potential of work (managerial aspect of motivation) and motivation of personnel (personnel aspect of motivation) with the purpose to construct a system of employees’ motivation. The research tools included 6 specially selected tests of motivation, which are: “Motivation profile of your job”, “Constructive motivational attitudes”, Tests about Motivation of achievements (1st variant: Test by А.Mehrabian by the theory of D.С.McClelland and 2nd variant: Test about leading needs according with the theory of D.С.MacClelland), Tests by T.Elers (1st variant: “Determination of the motivation towards success or to avoid failure” and 2nd variant: “Trends to achieve results or to avoid failure”). The results of the study showed only one, but fundamental problem of the whole organization: high level of both motivational potential in work and self-motivation, especially in terms of achievement motivation, but serious lack of productivity. According the results which study showed this problem is derived from insufficient staff competence. The research suggests basic guidelines in order to build the new personnel motivation system for this Company, which is planned to be developed in the nearest future.

Keywords: incentive system, motivation of achievements, motivation system, self-motivation

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Authors: Hsiao-Yung Wang

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This essay aims to examine how the transgender imagery has been constructed in the Taiwanese news media and its evolution from 1953 to 2016. It also explores the discourse patterns and rhetorical strategies in the transgender-related issues which contributed to levels of evaluation in forming ‘social deviance.’ Samples for analysis were selected from mainstream newspapers, including China Times, United Daily and Apple Daily. The time frame for sample selection is from August 1953 (when the first transgender case was reported in Taiwan) to June 2016. To enhance understanding of media representation as nominalistic-based, the author refers to the representative of critical rhetoric Raymie McKerrow for his study on remembrance and forgetfulness in public discourse (especially in his model of ‘critique of domination’); thereby categorizing the 64 years of transgender discourse into five periods: (1) transgender as ‘intersex’ of surgical-reparative medical treatment; (2) transgender as ‘freak gender-bender’ with criminal behaviors; (3) transgender as ‘ladyboy’ (‘katoey in a Thai term) of bar girls or sex workers; (4) transgender as ‘cross dresser’ of transvestite performance; and (5) transgender as ‘life-style or human right’ of spontaneous gender identification. Based on the research findings, this essay argues that the characterization of transgender reporting as a site for the production of compulsory sexism and gender stereotype by the specific forms of name-calling. Besides, the evolution of word-image addressing to transgender issues also pinpoints media as a reflection of fashion of the day. While the transgender imagery might be crystallized as ‘still social problems’ or ‘gender transgression’ in insidious rhetoric; and while the so-called ‘phobia’ persistently embodies in media discourse to exercise name-calling in an ambiguous (rather than in a bullying) way or under the cover of humanist-liberalist rationales, these emergent rhetorical dilemma should be resolved without any delay.

Keywords: critical rhetoric, media representation, McKerrow, nominalistic, social deviance, transgender

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Authors: Vijay Kumar Kutala, Addepalli Pavani, M. Amresh Rao, Naushad Sm

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In this study, we evaluated the impact of CYP2C9*2 and CYP2C9*3 variants on binding and hydroxylation of warfarin. In silico data revealed that warfarin forms two hydrogen bonds with protein backbone i.e. I205 and S209, one hydrogen bond with protein side chain i.e. T301 and stacking interaction with F100 in CYP2C9*1. In CYP2C9*2 and CYP2C9*3 variants, two hydrogen bonds with protein backbone are disrupted. In double variant, all the hydrogen bonds are disrupted. The distances between C7 of S-warfarin and Fe-O in CYP2C9*1, CYP2C9*2, CYP2C9*3 and CYP2C9*2/*3 were 5.81A°, 7.02A°, 7.43° and 10.07°, respectively. The glide scores (Kcal/mol) were -7.698, -7.380, -6.821 and -6.986, respectively. Increase in warfarin/7-hydroxy warfarin ratio was observed with increase in variant alleles. To conclude, CYP2C9*2 and CYP2C9*3 variants result in disruption of hydrogen bonding interactions with warfarin and longer distance between C7 and Fe-O thus impairing warfarin 7-hydroxylation due to lower binding affinity of warfarin.

Keywords: warfarin, CYP2C9 polymorphism, personalized medicine, in Silico

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Authors: Gareth Baxter

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We use a mathematical model of language change to examine two recently observed patterns of language change: one in which most speakers change gradually, following the mean of the community change, and one in which most individuals use predominantly one variant or another, and change rapidly if they change at all. The model is based on Croft’s Utterance Selection account of language change, which views language change as an evolutionary process, in which different variants (different ‘ways of saying the same thing’) compete for usage in a population of speakers. Language change occurs when a new variant replaces an older one as the convention within a given population. The present model extends a previous simpler model to include effects related to speaker aging and interspeaker variation in behaviour. The two patterns of individual change (one more centralized and the other more polarized) were recently observed in historical language changes, and it was further observed that slower changes were more associated with the centralized pattern, while quicker changes were more polarized. Our model suggests that the two patterns of change can be explained by different balances between the preference of speakers to use one variant over another and the degree of accommodation to (propensity to adapt towards) other speakers. The correlation with the rate of change appears naturally in our model, and results from the fact that both differential weighting of variants and the degree of accommodation affect the time for change to occur, while also determining the patterns of change. This work represents part of an ongoing effort to examine phenomena in language change through the use of mathematical models. This offers another way to evaluate qualitative explanations that cannot be practically tested (or cannot be tested at all) in a real-world, large-scale speech community.

Keywords: agent based modeling, cultural evolution, language change, social behavior modeling, social influence

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Authors: Manik Sharma

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Understanding the anatomy and normal anatomical variations of the lower limb arterial system is undeniably important not only to understand the pathology involving the vessels of the lower limb but also as a part of endovascular intervention and surgical planning in cases that demand them as a part of treatment. There have been very few cases of duplication of SFA cited in the literature, close to six worldwide and this being the seventh case in the world and first to be reported in the Indian population. We incidentally came across this normal variant during US lower limb (US-LL) duplex scan in a patient with claudicating pain in bilateral lower limbs hence suspected of having peripheral vascular disease. It was confirmed on CT-Peripheral Angiography (CT-PA), which was done successively.

Keywords: peripheral vascular disease, claudicating pain, normal anatomical variants, endovascular intervention, duplication, CT-peripheral angiography, duplex scan, Iohexol

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Authors: Alena Semeradtova, Marcel Stofik, Lucie Mareckova, Petr Maly, Ondrej Stanek, Jan Maly

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Recently, novel strategies based on so-called molecular evolution were shown to be effective for the production of various peptide ligand libraries with high affinities to molecular targets of interest comparable or even better than monoclonal antibodies. The major advantage of these peptide scaffolds is mainly their prevailing low molecular weight and simple structure. This study describes a new high-affinity binding molecules based immunesensor using a simple optical system for human serum albumin (HSA) detection as a model molecule. We present a comparison of two variants of recombinant binders based on albumin binding domain of the protein G (ABD) performed on micropatterned glass chip. Binding domains may be tailored to any specific target of interest by molecular evolution. Micropatterened glass chips were prepared using UV-photolithography on chromium sputtered glasses. Glass surface was modified by (3-aminopropyl)trietoxysilane and biotin-PEG-acid using EDC/NHS chemistry. Two variants of high-affinity binding molecules were used to detect target molecule. Firstly, a variant is based on ABD domain fused with TolA chain. This molecule is in vivo biotinylated and each molecule contains one molecule of biotin and one ABD domain. Secondly, the variant is ABD domain based on streptavidin molecule and contains four gaps for biotin and four ABD domains. These high-affinity molecules were immobilized to the chip surface via biotin-streptavidin chemistry. To eliminate nonspecific binding 1% bovine serum albumin (BSA) or 6% fetal bovine serum (FBS) were used in every step. For both variants range of measured concentrations of fluorescently labelled HSA was 0 – 30 µg/ml. As a control, we performed a simultaneous assay without high-affinity binding molecules. Fluorescent signal was measured using inverse fluorescent microscope Olympus IX 70 with COOL LED pE 4000 as a light source, related filters, and camera Retiga 2000R as a detector. The fluorescent signal from non-modified areas was substracted from the signal of the fluorescent areas. Results were presented in graphs showing the dependence of measured grayscale value on the log-scale of HSA concentration. For the TolA variant the limit of detection (LOD) of the optical immunosensor proposed in this study is calculated to be 0,20 µg/ml for HSA detection in 1% BSA and 0,24 µg/ml in 6% FBS. In the case of streptavidin-based molecule, it was 0,04 µg/ml and 0,07 µg/ml respectively. The dynamical range of the immunosensor was possible to estimate just in the case of TolA variant and it was calculated to be 0,49 – 3,75 µg/ml and 0,73-1,88 µg/ml respectively. In the case of the streptavidin-based the variant we didn´t reach the surface saturation even with the 480 ug/ml concentration and the upper value of dynamical range was not estimated. Lower value was calculated to be 0,14 µg/ml and 0,17 µg/ml respectively. Based on the obtained results, it´s clear that both variants are useful for creating the bio-recognizing layer on immunosensors. For this particular system, it is obvious that the variant based on streptavidin molecule is more useful for biosensing on glass planar surfaces. Immunosensors based on this variant would exhibit better limit of detection and wide dynamical range.

Keywords: high affinity binding molecules, human serum albumin, optical immunosensor, protein G, UV-photolitography

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Authors: Manendra Singh Parihar, Sandip Ghosh Chowdhury

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Austenitic stainless steels are widely used and give a good combination of properties. When this steel is plastically deformed, a phase transformation of the metastable Face Centred Cubic Austenite to the stable Body Centred Cubic (α’) or to the Hexagonal close packed (ԑ) martensite may occur, leading to the enhancement in the mechanical properties like strength. The work was based on variant selection and corresponding texture analysis for the strain induced martensitic transformation during deformation of the parent austenite FCC phase to form the product HCP and the BCC martensite phases separately, obeying their respective orientation relationships. The automated method for reconstruction of the parent phase orientation using the EBSD data of the product phase orientation is done using the MATLAB and TSL-OIM software. The method of triplets was used which involves the formation of a triplet of neighboring product grains having a common variant and linking them using a misorientation-based criterion. This led to the proper reconstruction of the pre-transformation phase orientation data and thus to its microstructure and texture. The computational speed of current method is better compared to the previously used methods of reconstruction. The reconstruction of austenite from ԑ and α’ martensite was carried out for multiple samples and their IPF images, pole figures, inverse pole figures and ODFs were compared. Similar type of results was observed for all samples. The comparison gives the idea for estimating the correct sequence of the transformation i.e. γ → ε → α’ or γ → α’, during deformation of AISI 304 austenitic stainless steel.

Keywords: variant selection, reconstruction, EBSD, austenitic stainless steel, martensitic transformation

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Authors: Naoki Yamamoto, Hidenobu Ozaki, Taiichiro Ookawa, Youming Liu, Kazunori Okada, Aiping Zheng

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Rice sheath blight is one of the destructive fungal diseases in rice. We have thought that rice sheath blight resistance is a polygenic trait. Host-pathogen interactions and secondary metabolites such as lignin and phytoalexins are likely to be involved in defense against R. solani. However, to our knowledge, it is still unknown how sheath blight resistance can be enhanced in rice breeding. To seek for an alternative genetic factor that contribute to sheath blight resistance, we mined relevant allelic variations from rice core collections created in Japan. Based on disease lesion length on detached leaf sheath, we selected 30 varieties of the top tail-end and the bottom tail-end, respectively, from the core collections to perform genome-wide association mapping. Re-sequencing reads for these varieties were used for calling single nucleotide polymorphisms among the 60 varieties to create a SNP panel, which contained 1,137,131 homozygous variant sites after filitering. Association mapping highlighted a locus on the long arm of chromosome 11, which is co-localized with three sheath blight QTLs, qShB11-2-TX, qShB11, and qSBR-11-2. Based on the localization of the trait-associated alleles, we identified an ankyryn repeat-containing protein gene (ANK-M) as an uncharacterized candidate factor for rice sheath blight resistance. Allelic distributions for ANK-M in the whole rice population supported the reliability of trait-allele associations. Gene expression characteristics were checked to evaluiate the functionality of ANK-M. Since an ANK-M homolog (OsPIANK1) in rice seems a basal defense regulator against rice blast and bacterial leaf blight, ANK-M may also play a role in the rice immune system.

Keywords: allele mining, GWAS, QTL, rice sheath blight

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