Search results for: gene selection

Authors: Cheng-Cao Sun, Shu-Jun Li, Cuili Yang, Yongyong Xi, Liang Wang, Feng Zhang, De-Jia Li

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MicroRNAs (miRNAs) act as key regulators of multiple cancers. Hsa-miR-329 (miR-329) functions as a tumor suppressor in some malignancies. However, its role on lung cancer remains poorly understood. In this study, we investigated the role of miR-329 on the development of lung cancer. The results indicated that miR-329 was decreased in primary lung cancer tissues compared with matched adjacent normal lung tissues and very low levels were found in a non-small cell lung cancer (NSCLC) cell lines. Ectopic expression of miR-329 in lung cancer cell lines substantially repressed cell growth as evidenced by cell viability assay, colony formation assay and BrdU staining, through inhibiting cyclin D1, cyclin D2, and up-regulatiing p57(Kip2) and p21(WAF1/CIP1). In addition, miR-329 promoted NSCLC cell apoptosis, as indicated by up-regulation of key apoptosis gene cleaved caspase-3, and down-regulation of anti-apoptosis gene Bcl2. Moreover, miR-329 inhibited cellular migration and invasiveness through inhibiting matrix metalloproteinases (MMP)-7 and MMP-9. Further, oncogene MET was revealed to be a putative target of miR-329, which was inversely correlated with miR-329 expression. Furthermore, down-regulation of MET by siRNA performed similar effects to over-expression of miR-329. Collectively, our results demonstrated that miR-329 played a pivotal role in lung cancer through inhibiting cell proliferation, migration, invasion, and promoting apoptosis by targeting oncogenic MET.

Keywords: hsa-miRNA-329(miR-329), MET, non-small cell lung cancer (NSCLC), proliferation, apoptosis

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Authors: Yoftahe Nigussie Worku

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This research focuses on advancing fire tube boiler technology by systematically optimizing design parameters to achieve efficient saturated steam production. The main objective is to design a high-performance boiler with a production capacity of 2000kg/h at a 12-bar design pressure while minimizing costs. The methodology employs iterative analysis, utilizing relevant formulas, and considers material selection and production methods. The study successfully results in a boiler operating at 85.25% efficiency, with a fuel consumption rate of 140.37kg/hr and a heat output of 1610kW. Theoretical importance lies in balancing efficiency, safety considerations, and cost minimization. The research addresses key questions on parameter optimization, material choices, and safety-efficiency balance, contributing valuable insights to fire tube boiler design.

Keywords: safety consideration, efficiency, production methods, material selection

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Authors: Vandana Deopanée Tomar, Gurpreet Kaur Sidhu, Panchsheela Nogia, Rajesh Mehrotra, Sandhya Mehrotra

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The cyanobacterial CO₂ concentrating mechanism (CCM) operates to raise the levels of CO₂ in the vicinity of the main carboxylation enzyme Rubisco which is encapsulated in protein micro compartments called carboxysomes. Thus, due to the presence of CCM, cyanobacterial cells are able to work with high photosynthetic efficiency even at low Ci conditions and can accumulate 1000 folds high internal concentrations of Ci than external environment. Engineering of some useful CCM components into higher plants is one of the plausible approaches to improve their photosynthetic performance. The first step and the simplest approach for attaining this objective would be the transfer of cyanobacterial bicarbonate transporter such as SbtA to inner chloroplast envelope of C₃ plants. For this, SbtA transporter gene from Synechococcus elongatus PCC 7942 was fused to a transit peptide element to generate chimeric constructs in order to direct it to chloroplast inner envelope. Two transit peptides namely, TnaXTP (transit peptide from AT3G56160) and TMDTP (transit peptide from AT2G02590) were shortlisted from Arabidopsis thaliana genome and cloned in plant expression vector pCAMBIA1302 having mgfp5 as a reporter gene. Plant transformation was done by agro infiltration and Agrobacterium mediated co-culture. DNA, RNA, and protein were isolated from the leaves four days post infiltration, and the presence of transgene was confirmed by gene specific PCR (Polymerase Chain Reaction) analysis and by RT-PCR (Reverse Transcription Polymerase Chain Reaction). The expression was confirmed at the protein level by western blotting using anti-GFP primary antibody and horseradish peroxidase (HRP) conjugated secondary antibody. The localization of the protein was detected by confocal microscopy of isolated protoplasts. We observed chloroplastic expression for both the fusion constructs which suggest that the transit peptide sequences are capable of taking the cargo protein to the chloroplasts. These constructs are now being used to generate stable transgenic plants by Agrobacterium mediated transformation. The stability of transgene expression will be analyzed from T₀ to T₂ generation.

Keywords: agro infiltration, bicarbonate transporter, carbon concentrating mechanisms, cyanobacteria, SbtA

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Authors: M. Suwaibah, S. W. Tan, I. Aiini, K. Yusoff, A. R. Omar

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Respiratory diseases are the most important infectious diseases affecting poultry worldwide. One of the avian respiratory virus of global importance causing significant economic losses is Infectious Bronchitis Virus (IBV). The virus causes a wide spectrum disease known as Infectious Bronchitis (IB), affecting not only the respiratory system but also the kidney and the reproductive system, depending on its strain. IB and Newcastle disease are two of the most prevalent diseases affecting poultry in Malaysia. However, a study on the molecular characterization of Malaysian IBV is lacking. In this study, an IBV strain IBS130 which was isolated in 2015 was fully sequenced using next-gene sequencing approach. Sequence analysis of IBS130 based on the complete genome, polyprotein 1ab and S1 genes were compared with other IBV sequences available in Genbank, National Center for Biotechnology Information (NCBI). IBV strain IBS130 is characterised as QX-like strain based on whole genome and S1 gene sequence analysis. Comparisons of the virus with other IBV strains showed that the nucleotide identity ranged from 67% to 99.2%, depending on the region analysed. The similarity in whole genome nucleotide ranging from 84.9% to 90.7% with the least similar was from Singapore strains (84.9%) and highly similar with China QX-like strains. Meanwhile, the similarity in polyprotein 1ab ranging from 85.3% to 89.9% with the least similar to Singapore strains (85.3%) and highly similar with Mass strains from USA.

Keywords: infectious bronchitis virus, phylogenetic analysis, chicken, Malaysia

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Authors: J. E. O. Hernandez

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In the next 20 years, energy production by burning fuels will increase and so will the atmospheric concentration of CO2 and its well-known threats to life on Earth. The technologies available for capturing CO2 are still dubious and this keeps fostering an interest in bio-inspired approaches. The leading one is the application of carbonic anhydrase (CA) –a superfast biocatalyst able to convert up to one million molecules of CO2 into carbonates in water. However, natural CA underperforms when applied to real smoky CO2 in chimneys and, so far, the efforts to create superior CAs in the lab rely on screening methods running under pristine conditions at the micro level, which are far from resembling those in chimneys. For the evolution of man-made enzymes, selection rather than screening would be ideal but this is challenging because of the need for a suitable artificial environment that is also sustainable for our society. Herein we present the stepwise design and construction of a bioprocess (from bench-scale to semi-pilot) for evolutionary selection experiments. In this bioprocess, reaction and adsorption took place simultaneously at atmospheric pressure in a spray tower. The scrubbing solution was fed countercurrently by reusing municipal pressure and it was mainly prepared with water, carbonic anhydrase and calcium chloride. This bioprocess allowed for the enzymatic carbonation of smoky CO2; the reuse of process water and the recovery of solid carbonates without cooling of smoke, pretreatments, solvent amines and compression of CO2. The average yield of solid carbonates was 0.54 g min-1 or 12-fold the amount produced in serum bottles at lab bench scale. This bioprocess could be used as a tailor-made environment for driving the selection of superior CAs. The bioprocess and its match CA could be sustainably used to reduce global warming by CO2 emissions from exhausts.

Keywords: biological carbon capture and sequestration, carbonic anhydrase, directed evolution, global warming

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Authors: Belinda Brunner

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Objectives: Communicate common test constructs of well-known higher education admissions tests. Discuss influences on admissions test construct definition and design and discuss research on related to factors influencing success in academic study. Discuss how admissions tests can be used to identify relevant talent. Examine how admissions test can be used to facilitate educational mobility and inform selection decisions when the prerequisite curricula is not standardized Observations: Generally speaking, constructs of admissions tests can be placed along a continuum from curriculum-related knowledge to more general reasoning abilities. For example, subject-specific achievement tests are more closely aligned to a prescribed curriculum, while reasoning tests are typically not associated with a specific curriculum. This session will draw reference from the test-constructs of well-known international higher education admissions tests, such as the UK clinical aptitude test (UKCAT) which is used for medicine and dentistry admissions. Conclusions: The purpose of academic admissions testing is to identify potential students with the prerequisite skills set needed to succeed in the academic environment, but how can the test construct help achieve this goal? Determination of the appropriate test construct for tests used in the admissions selection decisions should be influenced by a number of factors, including the preceding academic curricula, other criteria influencing the admissions decision, and the principal purpose for testing. Attendees of this session will learn the types of aptitudes and knowledge that are assessed higher education admissions tests and will have the opportunity to gain insight into how careful and deliberate consideration of the desired test constructs can aid in identifying potential students with the greatest likelihood of success in medical school.

Keywords: admissions, measuring success, selection, identify skills

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Authors: Iman Kamranfar, Gang-Ping Xue, Salma Balazadeh, Bernd Mueller-Roeber

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Adverse environmental conditions such as salinity stress, high temperature and drought limit plant growth and typically lead to precocious tissue degeneration and leaf senescence, a process by which nutrients from photosynthetic organs are recycled for the formation of flowers and seeds to secure reaching the next generation under such harmful conditions. In addition, abiotic stress affects developmental patterns that help the plant to withstand unfavourable environmental conditions. We discovered an NAC (for NAM, ATAF1, 2, and CUC2) transcription factor (TF), called RAF in the following, which plays a central role in abiotic drought stress-triggered senescence and the control of developmental adaptations to stressful environments. RAF is an ABA-responsive TF; RAF overexpressors are hypersensitive to abscisic acid (ABA) and exhibit precocious senescence while knock-out mutants show delayed senescence. To explore the RAF gene regulatory network (GRN), we determined its preferred DNA binding sites by binding site selection assay (BSSA) and performed microarray-based expression profiling using inducible RAF overexpression lines and chromatin immunoprecipitation (ChIP)-PCR. Our studies identified several direct target genes, including those encoding for catabolic enzymes acting during stress-induced senescence. Furthermore, we identified various genes controlling drought stress-related developmental changes. Based on our results, we conclude that RAF functions as a central transcriptional regulator that coordinates developmental programs with stress-related inputs from the environment. To explore the potential agricultural applications of our findings, we are currently extending our studies towards crop species.

Keywords: abiotic stress, Arabidopsis, development, transcription factor

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Authors: Waranya Imprasittichai, Patsarawadee Paojinda, Sudaratana R. Krungkrai, Nirianne Marie Q. Palacpac, Toshihiro Horii, Jerapan Krungkrai

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Fusion of the last two enzymes in the pyrimidine biosynthetic pathway in the inversed order by having COOH-terminal orotate phosphoribosyltransferase (OPRT) and NH2-terminal orotidine 5'-monophosphate decarboxylase (OMPDC), as OMPDC-OPRT, are described in many organisms. In this study, we constructed gene fusions of Plasmodium falciparum OMPDC-OPRT (1,836 bp) in pTrcHisA vector and expressed as an 6xHis-tag bifunctional protein in three Escherichia coli strains (BL21, Rosetta, TOP10) at 18 °C, 25 °C and 37 °C. The recombinant bifunctional protein was partially purified by Ni-Nitrilotriacetic acid-affinity chromatography. Specific activities of OPRT and OMPDC domains in the bifunctional enzyme expressed in E. coli TOP10 cells were approximately 3-4-fold higher than those in BL21 cells. There were no enzymatic activities when the construct vector expressed in Rosetta cells. Maximal expression of the fused gene was observed at 18 °C and the bifunctional enzyme had specific activities of OPRT and OMPDC domains in a ratio of 1:2. These results provide greater yields and better catalytic activities of the bifunctional OMPDC-OPRT enzyme for further purification and kinetic study.

Keywords: bifunctional enzyme, orotate phosphoribosyltransferase, orotidine 5'-monophosphate decarboxylase, plasmodium falciparum

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Authors: Mudasir Ahmad Syed, Raashid Ahmd Wani, Mashooq Ahmad Dar, Uneeb Urwat, Riaz Ahmad Shah, Nazir Ahmad Ganai

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Salmonella enterica serovar Typhimurium (Salmonella Typhimurium) is a primary avian pathogen responsible for severe intestinal pathology in younger chickens and economic losses. However, the Salmonella Typhimurium is also able to cause infection in humans, described by typhoid fever and acute gastro-intestinal disease. A study was conducted at days to investigate pathological, histopathological, haemato-biochemical, immunological and expression kinetics of NRAMP (natural resistance associated macrophage protein) gene family (NRAMP1 and NRAMP2) in broiler chickens following experimental infection of Salmonella Typhimurium at 0,1,3,5,7,9,11,13 and 15 days respectively. Infection was developed in birds through oral route at 2×108 CFU/ml. Clinical symptoms appeared 4 days post infection (dpi) and after one-week birds showed progressive weakness, anorexia, diarrhea and lowering of head. On postmortem examination, liver showed congestion, hemorrhage and necrotic foci on surface, while as spleen, lungs and intestines revealed congestion and hemorrhages. Histopathological alterations were principally observed in liver in second week post infection. Changes in liver comprised of congestion, areas of necrosis, reticular endothelial hyperplasia in association with mononuclear cell and heterophilic infiltration. Hematological studies confirm a significant decrease (P<0.05) in RBC count, Hb concentration and PCV. White blood cell count showed significant increase throughout the experimental study. An increase in heterophils was found up to 7dpi and a decreased pattern was observed afterwards. Initial lymphopenia followed by lymphocytosis was found in infected chicks. Biochemical studies showed a significant increase in glucose, AST and ALT concentration and a significant decrease (P<0.05) in total protein and albumin level in the infected group. Immunological studies showed higher titers of IgG in infected group as compared to control group. The real time gene expression of NRAMPI and NRAMP2 genes increased significantly (P<0.05) in infected group as compared to controls. The peak expression of NRAMP1 gene was seen in liver, spleen and caecum of infected birds at 3dpi, 5dpi and 7dpi respectively, while as peak expression of NRAMP2 gene in liver, spleen and caecum of infected chicken was seen at 9dpi, 5dpi and 9dpi respectively. This study has role in diagnostics and prognostics in the poultry industry for the detection of salmonella infections at early stages of poultry development.

Keywords: biochemistry, histopathology, NRAMP, poultry, real time expression, Salmonella Typhimurium

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Authors: Bo Wang

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The geometric processing of multi-source remote sensing data using control data of different scale and different accuracy is an important research direction of multi-platform system for earth observation. In the existing block bundle adjustment methods, as the controlling information in the adjustment system, the approach using single observation scale and precision is unable to screen out the control information and to give reasonable and effective corresponding weights, which reduces the convergence and adjustment reliability of the results. Referring to the relevant theory and technology of quotient space, in this project, several subjects are researched. Multi-layer quotient space of multi-geometric features is constructed to describe and filter control data. Normalized granularity merging mechanism of multi-layer control information is studied and based on the normalized scale factor, the strategy to optimize the weight selection of control data which is less relevant to the adjustment system can be realized. At the same time, geometric positioning experiment is conducted using multi-source remote sensing data, aerial images, and multiclass control data to verify the theoretical research results. This research is expected to break through the cliché of the single scale and single accuracy control data in the adjustment process and expand the theory and technology of photogrammetry. Thus the problem to process multi-source remote sensing data will be solved both theoretically and practically.

Keywords: multi-source image geometric process, high precision geometric positioning, quotient space of multi-geometric features, optimized weight selection

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Authors: Norah Mohammed Alshahrani, Abdulaziz Almaleh

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Autism Spectrum Disorder (ASD) is a condition related to issues with brain development that affects how a person recognises and communicates with others which results in difficulties with interaction and communication socially and it is constantly growing. Early recognition of ASD allows children to lead safe and healthy lives and helps doctors with accurate diagnoses and management of conditions. Therefore, it is crucial to develop a method that will achieve good results and with high accuracy for the measurement of ASD in children. In this paper, ASD datasets of toddlers and children have been analyzed. We employed the following machine learning techniques to attempt to explore ASD and they are Random Forest (RF), Decision Tree (DT), Na¨ıve Bayes (NB) and Support Vector Machine (SVM). Then Feature selection was used to provide fewer attributes from ASD datasets while preserving model performance. As a result, we found that the best result has been provided by the Support Vector Machine (SVM), achieving 0.98% in the toddler dataset and 0.99% in the children dataset.

Keywords: autism spectrum disorder, machine learning, feature selection, support vector machine

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Authors: Hecson Christian, Joel Macwan

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Landfill site selection in an urban area is a critical issue in the planning process. With the growth of the urbanization, it has a mammoth impact on the economy, ecology, and environmental health of the region. Outsized amount of wastes are produced and the problem gets soared every day. Hence, selection of ideal site for sanitary landfill is a challenge for urban planners and solid waste managers. Disposal site is a function of many parameters. Among all, Geotechnical parameters are very vital as the same is related to surrounding open land. Moreover, the accessible safe and acceptable land is also scarce. Therefore, in this paper geotechnical parameters are used to develop a GIS model to identify an ideal location for landfill purpose. Metropolitan city of Surat is highly populated and fastest growing urban area in India. The research objectives are to conduct field experiments to collect data and to transfer the facts in GIS platform to evolve a model, to find ideal location. Planners’ preferences were obtained to use analytical hierarchical process (AHP) to find weights of each parameter. Integration of GIS and Multi-Criteria Decision Analysis (MCDA) techniques are applied to improve decision-making. It augments an environment for transformation and combination of geographical data and planners’ preferences. GIS performs deterministic overlay and buffer operations. MCDA methods evaluate alternatives based on the decision makers’ subjective values and priorities. Research results have shown many alternative locations. Economic analysis of selected site from actual operations point of view is not included in this research.

Keywords: GIS, AHP, MCDA, Geo-technical

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Authors: Ronak Khosravi, Mahmood Abbasi Layegh, Siamak Haghipour, Avin Esmaili

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In this paper, a study on classification of musical woodwind instruments using a small set of features selected from a broad range of extracted ones by the sequential forward selection method was carried out. Firstly, we extract 42 features for each record in the music database of 402 sound files belonging to five different groups of Flutes (end blown and internal duct), Single –reed, Double –reed (exposed and capped), Triple reed and Quadruple reed. Then, the sequential forward selection method is adopted to choose the best feature set in order to achieve very high classification accuracy. Two different classification techniques of support vector machines and relevance vector machines have been tested out and an accuracy of up to 96% can be achieved by using 21 time, frequency and coefficient features and relevance vector machine with the Gaussian kernel function.

Keywords: coefficient features, relevance vector machines, spectral features, support vector machines, temporal features

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Authors: Noora Al Muftah, Reda Rawi, Richard Thompson, Halima Bensmail

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Clinical responses to anticancer therapies are often restricted to a subset of patients. In some cases, mutated cancer genes are potent biomarkers of response to targeted agents. There is an urgent need to identify biomarkers that predict which patients with are most likely to respond to treatment. Systematic efforts to correlate tumor mutational data with biologic dependencies may facilitate the translation of somatic mutation catalogs into meaningful biomarkers for patient stratification. To identify genomic features associated with drug sensitivity and uncover new biomarkers of sensitivity and resistance to cancer therapeutics, we have screened and integrated a panel of several hundred cancer cell lines from different databases, mutation, DNA copy number, and gene expression data for hundreds of cell lines with their responses to targeted and cytotoxic therapies with drugs under clinical and preclinical investigation. We found mutated cancer genes were associated with cellular response to most currently available Glioma cancer drugs and some frequently mutated genes were associated with sensitivity to a broad range of therapeutic agents. By linking drug activity to the functional complexity of cancer genomes, systematic pharmacogenomic profiling in cancer cell lines provides a powerful biomarker discovery platform to guide rational cancer therapeutic strategies.

Keywords: cancer, gene network, Lasso, penalized regression, P-values, unbiased estimator

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Authors: M. F. Yilmaz, B. Ö. Çağlayan

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Fragility curve is an effective common used tool to determine the earthquake performance of structural and nonstructural components. Also, it is used to determine the nonlinear behavior of bridges. There are many historical bridges in the Turkish railway network; the earthquake performances of these bridges are needed to be investigated. To derive fragility curve Intensity measures (IMs) and Engineering demand parameters (EDP) are needed to be determined. And the relation between IMs and EDP are needed to be derived. In this study, a typical simply supported steel girder riveted railway bridge is studied. Fragility curves of this bridge are derived by two parameters lognormal distribution. Time history analyses are done for selected 60 real earthquake data to determine the relation between IMs and EDP. Moreover, efficiency, practicality, and sufficiency of three different IMs are discussed. PGA, Sa(0.2s) and Sa(1s), the most common used IMs parameters for fragility curve in the literature, are taken into consideration in terms of efficiency, practicality and sufficiency.

Keywords: railway bridges, earthquake performance, fragility analyses, selection of intensity measures

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Authors: Amirreza Razzaghipour Sorkhab

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One of the most common disorders among humans is hearing impairment. This paper provides an evidence base that recovers understanding of Meniere’s disease and highlights the physical and mental health correlates of the disorder. Meniere's disease is more common in the elderly. The term idiopathic endolymphatic hydrops has been attributed to this disease by some in the previous. Meniere’s disease demonstrations a genetic tendency, and a family history is found in 10% of cases, with an autosomal dominant inheritance pattern. The COCH gene may be one of the hereditary factors contributing to Meniere’s disease, and the possibility of a COCH mutation should be considered in patients with Meniere’s disease symptoms. Should be considered Missense mutations in the COCH gene cause the autosomal dominant sensorineural hearing loss and vestibular disorder. Meniere’s disease is a complex, heterogeneous disorder of the inner ear and that is characterized by episodes of vertigo lasting from minutes to hours, fluctuating sensorineural hearing loss, tinnitus, and aural fullness. The existing evidence supports the suggestion that age and sleep disorder are risk factors for Meniere's disease. Many factors have been reported to precipitate the progress of Menier, including endolymphatic hydrops, immunology, viral infection, inheritance, vestibular migraine, and altered intra-labyrinthine fluid dynamics. Although there is currently no treatment that has a proven helpful effect on hearing levels or on the long-term evolution of the disease, however, in the primary stages, the hearing may improve among attacks, but a permanent hearing loss occurs in the majority of cases. Current publications have proposed a role for the intratympanic use of medicine, mostly aminoglycosides, for the control of vertigo. more than 85% of patients with Meniere's disease are helped by either changes in lifestyle and medical treatment or minimally aggressive surgical procedures such as intratympanic steroid therapy, intratympanic gentamicin therapy, and endolymphatic sac surgery. However, unilateral vestibular extirpation methods (intratympanic gentamicin, vestibular nerve section, or labyrinthectomy) are more predictable but invasive approaches to control the vertigo attacks. Medical therapy aimed at reducing endolymph volume, such as low-sodium diet, diuretic use, is the typical initial treatment.

Keywords: meniere's disease, endolymphatic hydrops, hearing loss, vertigo, tinnitus, COCH gene

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Authors: Rini Rahul, Manoj Kumar

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Cadmium (Cd) is a poisonous trace metal, which is responsible for excess reactive oxygen species generation (ROS) in plants, thereby adversely affecting their productivity and commercial potential. Ricinus communis (castor) is an industry-efficient non-edible bioenergy crop used for phytoremediation and re-vegetation. We have determined the total Cd content in castor genotypes and established a relationship between the Cd tolerance mechanism and physiological parameters like chlorophyll fluorescence, the total photosynthetic activity, chlorophyll and carotenoid content as well as ROS generation and malondialdehyde content. This study is an effort to comprehend the interrelation between Cd toxicity (control, 250 µM and 500 µM), proline, various ROS scavenging enzymes (anti-oxidative in nature), nicotianamine synthase (NAS) and Natural resistance-associated macrophage protein (NRAMP) gene. The antioxidant enzyme activity increased for WM hence conferring Cd toxicity in this genotype. RcNRAMP genes showed differential expression in GCH2 and WM genotypes; this can also be one of the reasons for Cd toxicity and sensitivity in WM and GCH2, respectively. The cause of pronounced Cd tolerance in WM leaves can be because of enhanced expression of RcNAS1, RcNAS2 and RcNAS3 genes. Our results demonstrate that there is an interrelation between Cd toxicity (control, 250 µM and 500 µM), proline, various ROS scavenging enzymes (anti-oxidative in nature), NAS and NRAMP gene.

Keywords: ricinus communis, cadmium, reactive oxygen species, nicotianamine synthase, NRAMP, malondialdehyde

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Authors: Kinnsley Travis, Camerron M. Crowder

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Mapk8ip3 (Mitogen-Activated Protein Kinase 8 Interacting Protein 3) is a gene that codes for the JIP3 protein, which is a part of the JIP scaffolding protein family. This protein is involved in axonal vesicle transport, elongation and regeneration. Variants in the Mapk8ip3 gene are associated with a rare-genetic condition that results in a neurodevelopmental disorder that can cause a range of phenotypes including global developmental delay and intellectual disability. Currently, there are 18 known individuals diagnosed to have sequenced confirmed Mapk8ip3 genetic disorders. This project focuses on examining the impact of a subset of missense patient variants on the Jip3 protein function by overexpressing the mRNA of these variants in a zebrafish knockout model for Jip3. Plasmids containing cDNA with individual missense variants were reverse transcribed, purified, and injected into single-cell zebrafish embryos (Wild Type, Jip3 -/+, and Jip3 -/-). At 6-days post mRNA microinjection, morphological, behavioral, and microscopic phenotypes were examined in zebrafish larvae. Morphologically, we compared the size and shape of the zebrafish during their development over a 5-day period. Total locomotive activity was assessed using the Microtracker assay and patterns of movement over time were examined using the DanioVision assay. Lastly, we used confocal microscopy to examine sensory axons for swelling and shortened length, which are phenotypes observed in the loss-of-function knockout Jip3 zebrafish model. Using these assays during embryonic development, we determined the impact of various missense variants on Jip3 protein function, compared to knockout and wild-type zebrafish embryo models. Variants in the gene Mapk8ip3 cause rare-neurodevelopmental disorders due to an essential role in axonal vesicle transport, elongation and regeneration. A subset of missense variants was examined by overexpressing the mRNA of these variants in a Jip3 knock-out zebrafish. Morphological, behavioral, and microscopic phenotypes were examined in zebrafish larvae. Using these assays, the spectrum of disorders can be phenotypically determined and the impact of variant location can be compared to knockout and wild-type zebrafish embryo models.

Keywords: rare disease, neurodevelopmental disorders, mrna overexpression, zebrafish research

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Authors: Reem Alajmi, Hind Al Harbi, Tahany Ayaad, Zainab Al Musawi

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Hard ticks Hyalomma spp. (family: Ixodidae) are obligate ectoparasite in their all life stages on some domestic animals mainly camels and cattle. Ticks may lead to many economic and public health problems because of their blood feeding behavior. Also, they act as vectors for many bacterial, viral and protozoan agents which may cause serious diseases such as tick-born encephalitis, Rocky-mountain spotted fever, Q-fever and Lyme disease which can affect human and/or animals. In the present study, molecular identification of ticks that attack camels in Riyadh region, Saudi Arabia based on the partial sequence of mitochondrial 16s rRNA gene was applied. Also, the present study aims to detect natural infections of collected camel ticks with Rickessia spp. and Borelia spp. using PCR/hybridization of Citrate synthase encoding gene present in bacterial cells. Hard ticks infesting camels were collected from different camels located in a farm in Riyadh region, Saudi Arabia. Results of the present study showed that the collected specimens belong to two species: Hyalomma dromedari represent 99% of the identified specimens and Hyalomma marginatum which account for 1 % of identified ticks. The molecular identification was made through blasting the obtained sequence of this study with sequences already present and identified in GeneBank. All obtained sequences of H. dromedarii specimens showed 97-100% identity with the same gene sequence of the same species (Accession # L34306.1) which was used as a reference. Meanwhile, no intraspecific variations of H. marginatum mesured because only one specimen was collected. Results also had shown that the intraspecific variability between individuals of H. dromedarii obtained in 92 % of samples ranging from 0.2- 6.6%, while the remaining 7 % of the total samples of H. dromedarii showed about 10.3 % individual differences. However, the interspecific variability between H. dromedarii and H. marginatum was approximately 18.3 %. On the other hand, by using the technique of PCR/hybridization, we could detect natural infection of camel ticks with Rickettsia spp. and Borrelia spp. Results revealed the natural presence of both bacteria in collected ticks. Rickettsial spp. infection present in 29% of collected ticks, while 35% of collected specimen were infected with Borrelia spp. The valuable results obtained from the present study are a new record for the molecular identification of camel ticks in Riyadh, Saudi Arabia and their natural infection with both Rickettsia spp. and Borrelia spp. These results may help scientists to provide a good and direct control strategy of ticks in order to protect one of the most important economic animals which are camels. Also results of this project spotlight on the disease that might be transmitted by ticks to put out a direct protective plan to prevent spreading of these dangerous agents. Further molecular studies are needed to confirm the results of the present study by using other mitochondrial and nuclear genes for tick identification.

Keywords: Camel ticks, Rickessia spp. , Borelia spp. , mitochondrial 16s rRNA gene

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Authors: Alina Beraudi, Simona Catalani, Dalila De Pasquale, Eva Bianconi, Umberto Santoro, Susanna Stea, Pietro Apostoli

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Recently the European Community, in line with the international scientific community such as with the Consensus Statement, has determined to stop the use of metal-on-metal big head stemmed hip prosthesis. Among the factors accounted as responsible for the high failure rates of these hip implants are the release and accumulation of metal ions. Many studies have correlated the presence of these ions, besides other factors, with the induction of oxidative stress response. In our study on 12 subjects, we observed the patient specific capability to eliminate metal ions after revision surgery. While for cobalt all the patients were able to completely excrete cobalt ions within 5-7 months after metal-on-metal bearing removal, for chromium ions it didn’t happen. If on the one hand the toxicokinetic differences between the two types of ions are confirmed by toxicological and occupational studies, on the other hand, this peculiar way of exposition represents a novel and important point of view. Thus, two different approaches were performed to better understand the subject specific capability to transport metal ions (albumin study) and to manage the response to them (heme-oxygenase-1 study): - a mutational screening of ALBUMIN gene was conducted in 30 MoM prosthetic patients resulting in the absence of nucleotidic changes compared with the ALB reference sequence. To this study was also added the analysis of expression of modified albumin protein; - a gene and protein expression study on 44 patients of heme-oxygenase-1, that is one of the most important antioxidant enzyme induced by metallic ions, was performed. This study resulted in no statistically significant differences in the expression of the gene and protein heme-oxygenase-1 between prosthetic and non-prosthetic patients, as well as between patients with high and low ions levels. Our results show that the protein studied (albumin and heme-oxygenase-1) seem to be not involved in determining chromium and cobalt ions level. On the other hand, achromium and cobalt elimination rates are different, but similar in all patients analyzed, suggesting that this process could be not patient-related. We support the importance of researching more about ions transport within the organism once released by hip prosthesis, about the chemical species involved, the districts where they are contained and the mechanisms of elimination, not excluding the existence of a subjective susceptibility to these metals ions.

Keywords: chromium, cobalt, hip prosthesis, individual susceptibility

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Authors: Ricardo Alberto Chiong Zevallos, Eduardo Moraes Rego Reis

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Pancreatic adenocarcinoma (PDAC) patients have a less than 10% 5-year survival rate. PDAC has no defined diagnostic and prognostic biomarkers. Gemcitabine is the first-line drug in PDAC and several other cancers. Long non-coding RNAs (lncRNAs) contribute to the tumorigenesis and are potential biomarkers for PDAC. Although lncRNAs aren’t translated into proteins, they have important functions. LncRNAs can decoy or recruit proteins from the epigenetic machinery, act as microRNA sponges, participate in protein translocation through different cellular compartments, and even promote chemoresistance. The chromatin remodeling enzyme EZH2 is a histone methyltransferase that catalyzes the methylation of histone 3 at lysine 27, silencing local expression. EZH2 is ambivalent, it can also activate gene expression independently of its histone methyltransferase activity. EZH2 is overexpressed in several cancers and interacts with lncRNAs, being recruited to a specific locus. EZH2 can be recruited to activate an oncogene or silence a tumor suppressor. The lncRNAs misregulation in cancer can result in the differential recruitment of EZH2 and in a distinct epigenetic landscape, promoting chemoresistance. The relevance of the EZH2-lncRNAs interaction to chemoresistant PDAC was assessed by Real Time quantitative PCR (RT-qPCR) and RNA Immunoprecipitation (RIP) experiments with naïve and gemcitabine-resistant PDAC cells. The expression of several lncRNAs and EZH2 gene targets was evaluated contrasting naïve and resistant cells. Selection of candidate genes was made by bioinformatic analysis and literature curation. Indeed, the resistant cell line showed higher expression of chemoresistant-associated lncRNAs and protein coding genes. RIP detected lncRNAs interacting with EZH2 with varying intensity levels in the cell lines. During RIP, the nuclear fraction of the cells was incubated with an antibody for EZH2 and with magnetic beads. The RNA precipitated with the beads-antibody-EZH2 complex was isolated and reverse transcribed. The presence of candidate lncRNAs was detected by RT-qPCR, and the enrichment was calculated relative to INPUT (total lysate control sample collected before RIP). The enrichment levels varied across the several lncRNAs and cell lines. The EZH2-lncRNA interaction might be responsible for the regulation of chemoresistance-associated genes in multiple cancers. The relevance of the lncRNA-EZH2 interaction to PDAC was assessed by siRNA knockdown of a lncRNA, followed by the analysis of the EZH2 target expression by RT-qPCR. The chromatin immunoprecipitation (ChIP) of EZH2 and H3K27me3 followed by RT-qPCR with primers for EZH2 targets also assess the specificity of the EZH2 recruitment by the lncRNA. This is the first report of the interaction of EZH2 and lncRNAs HOTTIP and PVT1 in chemoresistant PDAC. HOTTIP and PVT1 were described as promoting chemoresistance in several cancers, but the role of EZH2 is not clarified. For the first time, the lncRNA LINC01133 was detected in a chemoresistant cancer. The interaction of EZH2 with LINC02577, LINC00920, LINC00941, and LINC01559 have never been reported in any context. The novel lncRNAs-EZH2 interactions regulate chemoresistant-associated genes in PDAC and might be relevant to other cancers. Therapies targeting EZH2 alone weren’t successful, and a combinatorial approach also targeting the lncRNAs interacting with it might be key to overcome chemoresistance in several cancers.

Keywords: epigenetics, chemoresistance, long non-coding RNAs, pancreatic cancer, histone modification

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Authors: Charalabos Antonatos, Mariza Panoutsopoulou, Georgios K. Georgakilas, Evangelos Evangelou, Yiannis Vasilopoulos

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The extended tissue damage and severe clinical outcomes of autoimmune diseases, accompanied by the high annual costs to the overall health care system, highlight the need for an efficient therapy. Increasing knowledge over the pathophysiology of specific chronic inflammatory diseases, namely Psoriasis (PsO), Inflammatory Bowel Diseases (IBD) consisting of Crohn’s disease (CD) and Ulcerative colitis (UC), and Rheumatoid Arthritis (RA), has provided insights into the underlying mechanisms that lead to the maintenance of the inflammation, such as Tumor Necrosis Factor alpha (TNF-α). Hence, the anti-TNFα biological agents pose as an ideal therapeutic approach. Despite the efficacy of anti-TNFα agents, several clinical trials have shown that 20-40% of patients do not respond to treatment. Nowadays, high-throughput technologies have been recruited in order to elucidate the complex interactions in multifactorial phenotypes, with the most ubiquitous ones referring to transcriptome quantification analyses. In this context, a random effects meta-analysis of available gene expression cDNA microarray datasets was performed between responders and non-responders to anti-TNFα therapy in patients with IBD, PsO, and RA. Publicly available datasets were systematically searched from inception to 10th of November 2020 and selected for further analysis if they assessed the response to anti-TNFα therapy with clinical score indexes from inflamed biopsies. Specifically, 4 IBD (79 responders/72 non-responders), 3 PsO (40 responders/11 non-responders) and 2 RA (16 responders/6 non-responders) datasetswere selected. After the separate pre-processing of each dataset, 4 separate meta-analyses were conducted; three disease-specific and a single combined meta-analysis on the disease-specific results. The MetaVolcano R package (v.1.8.0) was utilized for a random-effects meta-analysis through theRestricted Maximum Likelihood (RELM) method. The top 1% of the most consistently perturbed genes in the included datasets was highlighted through the TopConfects approach while maintaining a 5% False Discovery Rate (FDR). Genes were considered as Differentialy Expressed (DEGs) as those with P ≤ 0.05, |log2(FC)| ≥ log2(1.25) and perturbed in at least 75% of the included datasets. Over-representation analysis was performed using Gene Ontology and Reactome Pathways for both up- and down-regulated genes in all 4 performed meta-analyses. Protein-Protein interaction networks were also incorporated in the subsequentanalyses with STRING v11.5 and Cytoscape v3.9. Disease-specific meta-analyses detected multiple distinct pro-inflammatory and immune-related down-regulated genes for each disease, such asNFKBIA, IL36, and IRAK1, respectively. Pathway analyses revealed unique and shared pathways between each disease, such as Neutrophil Degranulation and Signaling by Interleukins. The combined meta-analysis unveiled 436 DEGs, 86 out of which were up- and 350 down-regulated, confirming the aforementioned shared pathways and genes, as well as uncovering genes that participate in anti-inflammatory pathways, namely IL-10 signaling. The identification of key biological pathways and regulatory elements is imperative for the accurate prediction of the patient’s response to biological drugs. Meta-analysis of such gene expression data could aid the challenging approach to unravel the complex interactions implicated in the response to anti-TNFα therapy in patients with PsO, IBD, and RA, as well as distinguish gene clusters and pathways that are altered through this heterogeneous phenotype.

Keywords: anti-TNFα, autoimmune, meta-analysis, microarrays

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Authors: Chen Chih-Cheng, Chen I-Cheng, Lee Yung-Tan, Kuo Yen-Whea, Yu Chin-Hung

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The purpose of this study is to construct a model for best spike player selection in a top volleyball tournament of the world. Data consisted of the records of 2013 World Grand Prix declared by International Volleyball Federation (FIVB). Simple Multiple-Attribute Rating Technique (SMART) was used for optimal decision-making model on the best spike player selection. The research results showed that the best spike player ranking by SMART is different than the ranking by FIVB. The results demonstrated the effectiveness and feasibility of the proposed model.

Keywords: simple multiple-attribute rating technique, World Grand Prix, best spike player, International Volleyball Federation

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Authors: Abdullah Bilal Ozturk, Nil Acarali, Hediye Irem Ozgunduz, Hava Gizem Kandilci, Hanifi Sarac

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In this study, zeolite, shellac and different boron chemicals were used as additive to dye and effects were comprehensively investigated. Considering previous studies additive materials that had not used before were determined for produce dye with physical properties. Literature research about the materials provides determining easily sufficient amount of additive materials. Accessible of additives or yearly production amounts are become important issue at selection of materials. Zeolite and boron chemicals are suitable selection in that easy access and has large amount of production in our country. Previous research about boron chemicals shows they have flame retardant effect on textile materials besides numerous usage areas. Also, from previous research, shellac was used widely for protection and insulation of metallic materials. Zeolite added to dye to increase adhesive effect of dye. In this study, corrosion tests were applied to find out if there are positive effects of zeolite, shellac, and boron chemicals to dye’s physical properties.

Keywords: dye, corrosion, zeolite, shellac, boron

Procedia PDF Downloads 332

Authors: Chia-Jung Li, Li-Te Lin, Kuan-Hao Tsui

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The study identifies SPP1 as a potential gene associated with ovarian aging, revealing a significant decline in its expression in aged ovaries. SPP1, also known as osteopontin (OPN), is a multifunctional glycoprotein involved with regulatory proteins and pro-inflammatory immune chemokines. However, its genetic links to ovarian aging have not been extensively explored. Spatial transcriptomic analyses were conducted on ovaries from young and aged female mice, along with a sample from a 73-year-old individual. Additionally, single-cell RNA sequencing analysis was performed to identify associations between SPP1 and key genes. The study focused on crucial genes, including ITGAV, ITGB1, CD44, MMP3, and FN1, with a particular emphasis on the correlation between SPP1 and ITGB1. The findings indicate a significant decline in SPP1 expression in aged ovaries, which was consistent in the 73-year-old sample. Single-cell RNA sequencing unveiled associations between SPP1 and key genes, emphasizing a strong co-expression correlation between SPP1 and ITGB1. While the study provides valuable insights, further research is necessary to understand the broader implications and potential applications of SPP1 in ovarian aging. Translating these findings to clinical settings requires careful consideration. The identification of SPP1 as a gene implicated in ovarian aging opens new avenues for advancing precision medicine and refining treatment strategies for conditions related to ovarian aging.

Keywords: SPP1, ovarian aging, spatial transcriptomic, single-cell RNA sequencing

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Authors: Olanrewaju Kafayat, O., Salman Kabir, K.

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The role of organic agriculture in providing food and income is now gaining wider recognition (Van Elzakker et al 2007). The increasing public concerns about food safety issues on the use of fertilizers, pesticide residues, growth hormones, GM organisms, and increasing awareness of environmental quality issues have led to an expanding demand for environmentally friendly products (Thompson, 1998; Rimal et al., 2005). As a result national governments are concerned about diet and health, and there has been renewed recognition of the role of public policy in promoting healthy diets, thus to provide healthier, safer, more confident citizens (Poole et al., 2007), With these benefits, a study into organic vegetables is very vital to all the major stakeholders. This study analyzed the willingness of consumers to pay for organic vegetables in Oyo state, Nigeria. Primary data was collected with the aid of structured questionnaire administered to 168 respondents. These were selected using multistage random sampling. The first stage involved the selection two (2) ADP zones out of the three (3) ADP zones in Oyo state, The second stage involved the random selection of two (2) local government areas each out of the two (2) ADP zones which are; Ibadan South West and Ogbomoso North and random selection of 4 wards each from the local government areas. The third stage involved random selection of 42 household each from of the local government areas. Descriptive statistics, the principal component analysis, and the logistic regression were used to analyze the data. Results showed 55 percent of the respondents were female while 80 percent were  50 years. 74 percent of the respondents agreed that organic vegetables are of better quality. 31 percent of the respondents were aware of organic vegetables as against 69 percent who were not aware. From the logistic model, educational attainment, amount spent on organic vegetables monthly, better quality of organic vegetables and accessibility to organic vegetables were significant and had a positive relationship on willingness to pay for organic vegetable. The variables that were significant and had a negative relationship with WTP are less attractiveness of organic vegetables and household size of the respondents. This study concludes that consumers with higher level of education were more likely to be aware and willing to pay for organic vegetables than those with low levels of education, the study therefore recommends creation of awareness on the relevance of consuming organic vegetables through effective marketing and educational campaigns.

Keywords: consumers awareness, willingness to pay, organic vegetables, Oyo State

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Authors: Sadaf Ilyas, Saba Riaz

Abstract:

The extensive use of antibiotics has led to increases emergence of antibiotic-resistant organisms. Pseudomonas is a notorious opportunistic pathogen involoved in nosocomial infections and exhibit innate resistance to many antibiotics. The present study was conducted to assess the prevalence, levels of antimicrobial susceptibility and resistance mechanisms of Pseudomonas. A total of thirty clinical strains of Pseudomonas were isolated from different clinical sites of infection. All clinical specimens were collected from Chughtais Lahore Lab. Jail road, during 8-07-2010 to 11-01-2011. Biochemical characterization was done using routine biochemical tests. Antimicrobial susceptibility was determined by Kirby-Baeur method. The plasmids were isolated from all the strains and digested with restriction enzyme PstI and EcoRI. Transfer of Multi-resistance plasmid was checked via transformation and conjugation to confirm the plasmid mediated resistance to antibiotics. The prevalence of Pseudomonas in clinical specimens was found out to be 14% of all bacterial infections. IPM has shown to be the most effective drug against Pseudomonas followed by CES, PTB and meropenem, wheareas most of the Pseudomonas strains have developed significant resistance against Penicillins and some Cephalasporins. Antibiotic resistance determinants were carried by plasmids, as they conferred resistance to transformed K1 strains. The isolates readily undergo conjugation, transferring the resistant genes to other strains, illustrating the high rates of cross infection and nosocomial infection in the immunocompromised patients.

Keywords: pseudomonas, antibiotics, drug resistance, horizontal gene transfer

Procedia PDF Downloads 341

Authors: Laura Gantley, Vanessa M. Conn, Stuart Webb, Kirsty Kirk, Marta Gabryelska, Duncan Holds, Brett W. Stringer, Simon J. Conn

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Trinucleotide repeat disorders comprise ~20 severe, inherited human neuromuscular and neurodegenerative disorders, which are a result of an abnormal expansion of repetitive sequences in the DNA. The most common of these, Huntington’s disease, results from the expansion of the CAG repeat region in exon 1 of the HTT gene via an unknown mechanism. Non-coding RNAs have been implicated in the initiation and progression of many diseases; thus, we focus on one circular RNA (circRNA) molecule arising from non-canonical splicing (back splicing) of HTT pre-mRNA. This circRNA and its mouse orthologue were transgenically overexpressed in human cells (SHSY-5Y and HEK293T) and mouse cells (Mb1), respectively. High-content imaging and flow cytometry demonstrated the overexpression of this circRNA reduces cell proliferation, reduces nuclear size independent of cellular size, and alters cell cycle progression. Analysis of protein by western blot and immunofluorescence demonstrated no change to HTT protein levels but altered nuclear-cytoplasmic distribution without impacting the expansion of the HTT repeat region. As these phenotypic and genotypic changes are found in Huntington’s disease patients, these results may suggest that this circRNA may play a functional role in the progression of Huntington’s disease.

Keywords: cell biology, circular RNAs, Huntington’s disease, molecular biology, neurodegenerative disorders

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Authors: H. Zidoum, A. AlShareedah, S. Al Sawafi, A. Al-Ansari, B. Al Lawati

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Systemic lupus erythematosus (SLE) is an autoimmune disease with genetic and environmental components. SLE is characterized by a wide variability of clinical manifestations and a course frequently subject to unpredictable flares. Despite recent progress in classification tools, the early diagnosis of SLE is still an unmet need for many patients. This study proposes an interpretable disease classification model that combines the high and efficient predictive performance of CatBoost and the model-agnostic interpretation tools of Shapley Additive exPlanations (SHAP). The CatBoost model was trained on a local cohort of 219 Omani patients with SLE as well as other control diseases. Furthermore, the SHAP library was used to generate individual explanations of the model's decisions as well as rank clinical features by contribution. Overall, we achieved an AUC score of 0.945, F1-score of 0.92 and identified four clinical features (alopecia, renal disorders, cutaneous lupus, and hemolytic anemia) along with the patient's age that was shown to have the greatest contribution on the prediction.

Keywords: feature selection, classification, systemic lupus erythematosus, model interpretation, SHAP, Catboost

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Authors: A. Robbin

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Language selection can be an efficient negotiation strategy employed by both service or product providers and their customers to achieve transactional success. The transactional scenario in Gbagi Market, Ibadan, Nigeria provides an appropriate setting for the exploration of the Nigerian multilingual situation with its own interesting linguistic peculiarities which questions the functionality of the ‘Lingua Franca’ in trade situations. This study examined English Language proficiency among Yoruba Traders in Gbagi Market, Ibadan and its use as determinants of transactional success during service encounters. Randomly selected Yoruba-English bilingual traders and customers were administered questionnaires and the data subjected to statistical and descriptive analysis using Giles Communication Accommodation Theory. Findings reveal that only fifty percent of the traders used for the study were proficient in speaking English language. Traders with minimal proficiency in Standard English, however, resulted in the use of the Nigerian Pidgin English. Both traders and customers select the Mother Tongue, which is the Yoruba Language during service encounters but are quick to converge to the other’s preferred language as the transactional exchange demands. The English language selection is not so much for the prestige or lingua franca status of the language as it is for its functions, which include ease of communication, negotiation, and increased sales. The use of English during service encounters is mostly determined by customer’s linguistic preference which the trader accommodates to for better negotiation and never as a first choice. This convergence is found to be beneficial as it ensures sales and return patronage. Although the English language is not a preferred code choice in Gbagi Market, it serves a functional trade strategy for transactional success during service encounters in the market.

Keywords: communication accommodation theory, language selection, proficiency, service encounter, transaction

Procedia PDF Downloads 156