Search results for: complete genome sequencing

Authors: Xinxiu Li, Chuqian Zheng, Yanyan Qian, Hong Fan

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Objectives: In hepatocellular carcinoma (HCC), oncogenes are continuously and robustly transcribed due to aberrant expression of essential components of the trans-acting super-enhancers (SE) complex. Preclinical and clinical trials are now being conducted on small-molecule inhibitors that target core-transcriptional components, including as transcriptional bromodomain protein 4 (BRD4) and cyclin-dependent kinase 7 (CDK7), in a number of malignant tumors. This study aims to explore whether co-overexpression of BRD4 and CDK7 is a potential marker of worse prognosis and a combined therapeutic target in HCC. Methods: The expression pattern of BRD4 and CDK7 and their correlation with prognosis in HCC were analyzed by RNA sequencing data and survival data of HCC patients from TCGA and GEO datasets. The protein levels of BRD4 and CDK7 were determined by immunohistochemistry (IHC), and survival data of patients were analyzed using the Kaplan-Meier method. The mRNA expression levels of genes in HCC cell lines were evaluated by quantitative PCR (q-PCR). CCK-8 and colony formation assays were conducted to assess cell proliferation of HCC upon treatment with BRD4 inhibitor JQ1 or/and CDK7 inhibitor THZ1. Results: It was shown that BRD4 and CDK7 were often overexpressed in HCCs and were associated with poor prognosis of HCC by analyzing the TCGA and GEO datasets. BRD4 or CDK7 overexpression was related to a lower survival rate. It's interesting to note that co-overexpression of CDK7 and BRD4 was a worse prognostic factor in HCC. Treatment with JQ1 or THZ1 alone had an inhibitory effect on cell proliferation; however, when JQ1 and THZ1 were combined, there was a more notable suppression of cell growth. At the same time, the combined use of JQ1 and THZ1 synergistically suppresses the expression of HCC driver genes. Conclusion: Our research revealed that BRD4 and CDK7 coupled can be a useful biomarker in HCC prognosis and the combination of JQ1 and THZ1 can be a promising therapeutic therapy against HCC.

Keywords: BRD4, CDK7, cell proliferation, combined inhibition

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Authors: Jiri Palecek, Radmila Hajkova, Alena Oulehlova, Hana Malachova

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The increase of emergency incidents and crisis situations requires proactive crisis management of authorities and for its solution. Application business continuity management systems help the crisis management authorities quickly and responsibly react to events and to plan more effectively and efficiently powers and resources. The main goal of this article is describing Military Continuity Management System (MCMS) based on the principles of Business Continuity Management System (BCMS) for dealing with floods in the territory of the selected municipalities. There are explained steps of loading, running and evaluating activities in the software application MCMS. Software MCMS provides complete control over the tasks, contribute a comprehensive and responsible approach solutions to solution floods in the municipality.

Keywords: business continuity management, floods plan, flood activity, level of flood activity

Procedia PDF Downloads 270

Authors: C. von Essen

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This study outlines and evaluates a constructivist design approach to the creation of educational video on postgraduate business degree programmes. Many online courses are tapping into the educational affordances of video, as this form of online learning has the potential to create rich, multimodal experiences. And yet, in many learning contexts video is still being used to transmit instruction to passive learners, rather than promote learner engagement and knowledge creation. Constructivism posits the notion that learning is shaped as students make connections between their experiences and ideas. This paper pivots on the following research question: how can we design educational video in ways which promote constructivist learning and stimulate analytic viewing? By exploring and categorizing over two thousand educational videos created since 2014 for over thirty postgraduate courses in business, economics, mathematics and statistics, this paper presents and critically reflects on a taxonomy of video styles and features. It links the pedagogical intent of video – be it concept explanation, skill demonstration, feedback, real-world application of ideas, community creation, or the cultivation of course narrative – to specific presentational characteristics such as visual effects including diagrammatic and real-life graphics and aminations, commentary and sound options, chronological sequencing, interactive elements, and presenter set-up. The findings of this study inform a framework which captures the pedagogical, technological and production considerations instructional designers and educational media specialists should be conscious of when planning and preparing the video. More broadly, the paper demonstrates how learning theory and technology can coalesce to produce informed and pedagogical grounded instructional design choices. This paper reveals how crafting video in a more conscious and critical manner can produce powerful, new educational design.

Keywords: educational video, constructivism, instructional design, business education

Procedia PDF Downloads 229

Authors: N. Nagalakshmi, Indira Bairy, M. Atulya, Jesil Mathew

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S. aureus has the ability to colonize and form biofilms on implanted biomaterials, which is difficult to disrupt, and current antimicrobial therapies for biofilms have largely proven unsuccessful in complete eradication of biofilm. The present study is aimed to determine the lysostaphin activity against biofilm producing MRSA clinical strains. The minimum biofilm inhibition activity of lysostaphin was studied against twelve strong biofilm producing isolates. The biofilm was produced in 96-wells micro-titer plate and biofilm was treated with lysostaphin (0.5 to 16 µg/ml), vancomycin (0.5 to 64 µg/ml) and linezolid (0.5 to 64 µg/ml). The biofilm inhibitory concentration of lysostaphin was found between 4 to 8 µg/ml whereas vancomycin and linezolid inhibited at concentration between 32 to 64 µg/ml. Results indicate that lysostaphin as potential antimicrobial activity against biofilm at lower concentration is comparable with routine antibiotics like vancomycin and linezolid.

Keywords: biofilm, lysostaphin, MRSA, minimum biofilm inhibitory concentration

Procedia PDF Downloads 356

Authors: Kênio Angelo Dantas Freitas Estrela

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Traditionally meaning holism is a theory that is related to the meaning attributed to words and their relationships to other words in a language. This theory can be more specifically defined as a defense of the mutual interdependence of all items of linguistic knowledge, so that, for example, to understand the meaning of a given expression, it is necessary to understand a large sector of the language in question or, even the complete language. The aim of this paper is to present a moderate version of meaning holism, which argues that, among other things, meaning holism does not imply the thesis of instability - if there is the change of belief about an object, there is a change of meaning - and, in this way, it is possible to attribute meanings to objects admitting changes of opinions and then beliefs. It will be shown how this version of holism gives an account of the main criticisms made of meaning holism in the last decades and also show how this theory can justify linguistic phenomena (like vagueness and polysemy) that are often treated as problems of language. Finally, it will also be argued that these linguistic phenomena are intrinsic to languages and that the moderate version of meaning holism can justify the occurrence of these phenomena.

Keywords: linguistics, meaning holism, philosophy of language, semantics

Procedia PDF Downloads 245

Authors: Othman E. Othman, Hassan R. Darwish, Amira M. Nowier

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Lactoferrin (LF) is a multifunctional protein involved in economically production traits like milk protein composition and skeletal structure in small ruminants including sheep and goat. So, LF gene - with its genetic polymorphisms associated with production traits - is considered a candidate genetic marker used in marker-assisted selection in goats. This study aimed to identify the different alleles and genotypes of this gene in three Egyptian goat breeds using PCR-SSCP (polymerase chain reaction-single-strand conformation polymorphism) and DNA sequencing. Genomic DNA was extracted from 120 animals belonging to Barki, Zaraibi, and Damascus goat breeds. Using specific primers, PCR amplified 247-bp fragments from exon 2 of LF goat gene. The PCR products were subjected to Single-Strand Conformation Polymorphism (SSCP) technique. The results showed the presence of two genotypes GG and AG in the tested animals. The frequencies of both genotypes varied among the three tested breeds with the highest frequencies of GG genotype in all tested goat breeds. The sequence analysis of PCR products representing these two detected genotypes declared the presence of an SNP (single nucleotide polymorphisms) substitution (G/A) among G and A alleles of this gene. The association between different LF genotypes and milk composition as well as body measurement was estimated. The comparison showed that the animals possess AG genotypes are superior over those with GG genotypes for different parameters of milk protein compositions and skeletal structures. This finding declared that allele A of LF gene is considered the promising marker for the productive traits in goat. In conclusion, the Egyptian goat breeds will be needed to enhance their milk protein composition and growth trait parameters through the increasing of allele A frequency in their herds depending on the superior production traits of this allele in goats.

Keywords: lLactoferrin gene, PCR-SSCP, SNPs, Egyptian goat

Procedia PDF Downloads 144

Authors: Ridwaan N. Milase, Leonardo J. Van Zyl, Marla Trindade

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American foulbrood (AFB) is the world’s most devastating honeybee disease that has drastically reduced the population of Apis mellifera capensis since 2009. The outbreak has jeopardized the South African bee keeping industry as well as the agricultural sector dependent on honeybees for honey production and pollination, leading to significant economic losses. AFB is caused by Paenibacillus larvae, a spore-forming, Gram positive facultative anaerobic and flagellated bacterium. The use of antibiotics within beehives has selected for resistant strains of P. larvae, while the current practice of burning spore contaminated beehives and equipment contributes to the economic losses in the honeybee-keeping industry. Therefore, phage therapy is proposed as a promising alternative to combat P. larvae strains affecting A. mellifera capensis. The genomes of two P. larvae strains isolated from infected combs in the Western Cape have been sequenced and annotated using bioinformatics tools. Genome analyses has revealed that these P. larvae strains are lysogens to more than 6 different prophages and possess different type of clustered regularly interspaced short palindromic repeat (CRISPRs) regions per strain. Active prophages from one of the two P. larvae strains were detected and identified using PCR. Electron microscopy was used to determine the family of the identified active prophages. Lytic bacteriophages that specifically target the two P. larvae strains were purified from sewage wastewater, beehive materials, and soil samples to investigate their potential development as anti-P. larvae agents. Another alternative treatment being investigated is the development of a prophage endolysin cocktail. Endolysin genes of the prophages have been targeted, cloned and expressed in Escherichia coli. The heterologously expressed endolysins have been purified and are currently being assessed for their lytic activity against P. larvae strains and other commensal microorganisms that compose the honeybee larvae microbiota. The study has shown that phage therapy and endolysins have a great potential as alternative control methods for AFB disease affecting A. mellifera capensis.

Keywords: American foulbrood, bacteriophage, honeybee, Paenibacillus larvae

Procedia PDF Downloads 169

Authors: Rowland Brucken

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This paper argues that nation-building theories that prioritize democratic governance best explain the successful post-independence development of Botswana. Three main competing schools of thought exist regarding the sequencing of policies that should occur to re-build weakened or failed states. The first posits that economic development should receive foremost attention, while democratization and a binding sense of nationalism can wait. A second group of experts identified constructing a sense of nationalism among a populace is necessary first, so that the state receives popular legitimacy and obedience that are prerequisites for development. Botswana, though, transitioned into a multi-party democracy and prosperous open economy due to the utilization of traditional democratic structures, enlightened and accountable leadership, and an educated technocratic civil service. With these political foundations already in place when the discovery of diamonds occurred, the resulting revenues were spent wisely on projects that grew the economy, improved basic living standards, and attracted foreign investment. Thus democratization preceded, and therefore provided an accountable basis for, economic development that might otherwise have been squandered by greedy and isolated elites to the detriment of the greater population. Botswana was one of the poorest nations in the world at the time of its independence in 1966, with little infrastructure, a dependence on apartheid South Africa for trade, and a largely subsistence economy. Over the next thirty years, though, its economy grew the fastest of any nation in the world. The transparent and judicious use of diamond returns is only a partial explanation, as the government also pursued economic diversification, mass education, and rural development in response to public needs. As nation-building has become a project undertaken by nations and multilateral agencies such as the United Nations and the North Atlantic Treaty Organization, Botswana may provide best practices that others should follow in attempting to reconstruct economically and politically unstable states.

Keywords: Botswana, democratization, economic development, nation-building

Procedia PDF Downloads 499

Authors: Razzaghifard P., Arya F., Chen S. Chien-I, Abdi B., Razzaghifard V., Arya A. H., Nazary A., Hosseinpour H., Ghabelnezam K.

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E-learning, also known as online learning, has indicated increased growth in recent years. One of the critical factors in the successful application of e-learning in higher education is students’ perceptions towards it. The main purpose of this paper is to investigate the perceptions of engineering students about e-learning in the UK. For the purpose of the present study, 145 second-year engineering students were randomly selected from the total population of 1280 participants. The participants were asked to complete a questionnaire containing 16 items. The data collected from the questionnaire were analyzed through the Statistical Package for Social Science (SPSS) software. The findings of the study revealed that the majority of participants have negative perceptions of e-learning. Most of the students had trouble interacting effectively during online classes. Furthermore, the majority of participants had negative experiences with the learning platform they used during e-learning. Suggestions were made on what could be done to improve the students’ perceptions of e-learning.

Keywords: e-learning, higher, education, engineering education, online learning

Procedia PDF Downloads 113

Authors: Aleš Florian, Lenka Ševelová, Jaroslav Žák

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Formation of tensile cracks in concrete slabs of rigid pavement can be (among others) the initiation point of the other, more serious failures which can ultimately lead to complete degradation of the concrete slab and thus the whole pavement. Two measures can be used for reliability assessment of this phenomenon - the probability of failure and/or the reliability index. Different methods can be used for their calculation. The simple ones are called moment methods and simulation techniques. Two methods - FOSM Method and Simple Random Sampling Method - are verified and their comparison is performed. The influence of information about the probability distribution and the statistical parameters of input variables as well as of the limit state function on the calculated reliability index and failure probability are studied in three points on the lower surface of concrete slabs of the older type of rigid pavement formerly used in the Czech Republic.

Keywords: failure, pavement, probability, reliability index, simulation, tensile crack

Procedia PDF Downloads 539

Authors: Brando Vagenende, Marie-Anne Guerry

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For stochastic matrices of any order, the geometric description of the convex set of eigenvalues is completely known. The purpose of this study is to investigate the subset of the monotone matrices. This type of matrix appears in contexts such as intergenerational occupational mobility, equal-input modeling, and credit ratings-based systems. Monotone matrices are stochastic matrices in which each row stochastically dominates the previous row. The monotonicity property of a stochastic matrix can be expressed by a nonnegative lower-order matrix with the same eigenvalues as the original monotone matrix (except for the eigenvalue 1). Specifically, the aim of this research is to focus on the properties of eigenvalues of monotone matrices. For those matrices up to order 3, there already exists a complete description of the convex set of eigenvalues. For monotone matrices of order at least 4, this study gives, through simulations, more insight into the geometric description of their eigenvalues. Furthermore, this research treats in a geometric and algebraic way the properties of eigenvalues of monotone matrices of order at least 4.

Keywords: eigenvalues of matrices, finite Markov chains, monotone matrices, nonnegative matrices, stochastic matrices

Procedia PDF Downloads 67

Authors: Jagdeep Singh, Prem Singh

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Milk is considered as an essential and complete food. The present study was conducted at Milk Plant Mohali especially in reference to the procurement section where the cash inflow was maximum, with the objective to achieve higher productivity and reduce wastage of milk. In milk plant it was observed that during the month of Jan-2014 to March-2014 the average procurement of milk was Rs. 4, 19, 361 liter per month and cost of procurement of milk is Rs 35/- per liter. The total cost of procurement thereby equal to Rs. 1crore 46 lakh per month, but there was mismatch in procurement-production of milk, which leads to an average loss of Rs. 12, 94, 405 per month. To solve the procurement-production problem Quality Control Tools like brainstorming, Flow Chart, Cause effect diagram and Pareto analysis are applied wherever applicable. With the successful implementation of Quality Control tools an average saving of Rs. 4, 59, 445 per month is done.

Keywords: milk, procurement-demand, quality control tools,

Procedia PDF Downloads 516

Authors: Abdolamir Allameh, Seyyed Mortaza Haghgoo, Adnan Khosravi, Esmaeil Mortaz, Mihan Pourabdollah-Toutkaboni, Sharareh Seifi

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Non-Small Cell Lung Carcinoma (NSCLC) is associated with a number of gene mutations in epidermal growth factor receptor (EGFR). The prognostic significance of mutations in exons 19 and 21, together with serum levels of EGFR, amphiregulin (AR), and Transforming Growth Factor-alpha (TGF-α) are implicated in diagnosis and treatment. The aim of this study was to examine the relationship of EGFR mutations in selected exons with the expression of relevant ligands in sera samples of NSCLC patients. For this, a group of NSCLC patients (n=98) referred to the hospital for lung surgery with a mean age of 59±10.5 were enrolled (M/F: 75/23). Blood specimen was collected from each patient. Besides, formalin fixed paraffin embedded tissues were processed for DNA extraction. Gene mutations in exons 19 and 21 were detected by direct sequencing, following DNA amplification which was done by PCR (Polymerase Chain Reaction). Also, serum levels of EGFR, AR, and TGF-α were measured by ELISA. The results of our study show that EGFR mutations were present in 37% of Iranian NSCLC patients. The most frequently identified mutations were deletions in exon 19 (72.2%) and substitutions in exon 21 (27.8%). The most frequently identified alteration, which is considered as a rare mutation, was the E872K mutation in exon 21, which was found in 90% (9 out of 10) cases. EGFR mutation detected in exon 21 was significantly (P<0.05) correlated with the levels of its ligands, EGFR and TGF-α in serum samples. Furthermore, it was found that increased serum AR (>3pg/ml) and TGF-α (>10.5 pg/ml) were associated with shorter overall survival (P<0.05). The results clearly showed a close relationship between EGFR mutations and serum EGFR and serum TGF-α. Increased serum EGFR was associated with TGF-α and AR and linked to poor prognosis of NSCLC. These findings are implicated in clinical decision-making related to EGFR-Tyrosine kinase inhibitors (TKIs).

Keywords: lung cancer, Iranian patients, epidermal growth factor, mutation, prognosis

Procedia PDF Downloads 71

Authors: M. Zain, Thaung H. Aung, Naveed Anwar

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During the service life, a structure may experience extreme loading conditions. The current study proposes a new methodology that covers the effect of uncertainty involved in gravity loadings on key structural elements of new and complex structures by emphasizing on a very realistic assumption that allows the 'Performance-Based Assessment' to be executed on the structure against the gravity loadings. The methodology does not require the complete removal of an element, instead, it permits the incremental reduction in the capacity of key structural elements and preserves the same stiffness of the member in each case of capacity loss. To demonstrate the application of the proposed methodology, a 13 story complex structure is selected that comprises of a diverse structural configuration. The results ensure the structural integrity against the applied gravity loadings, as well as the effectiveness of the proposed methodology.

Keywords: force-deformation relationship, gravity loading, incremental capacity reduction, multi-linear plastic link element, SAP2000, stiffness

Procedia PDF Downloads 444

Authors: Shen Jian, Hu Jie, Qi Jin, Liu Wei Jie, Chen Ji Yi, Peng Ying Hong

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In order to settle the problem of acquiring case in biological related to design problems, a biometrics instance acquisition method based on text mining is presented. Through the construction of corpus text vector space and knowledge mining, the feature selection, similarity measure and case retrieval method of text in the field of biology are studied. First, we establish a vector space model of the corpus in the biological field and complete the preprocessing steps. Then, the corpus is retrieved by using the vector space model combined with the functional keywords to obtain the biological domain examples related to the design problems. Finally, we verify the validity of this method by taking the example of text.

Keywords: text mining, vector space model, feature selection, biologically inspired design

Procedia PDF Downloads 252

Authors: Mustafa Cam, Nedim Ongun, Ufuk Kutluana

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Introduction: Restless LegsSyndrome (RLS) is a common, under-recognized disorder disrupts sleep and diminishes quality of life (1). The most common conditions highly associated with RLS include renalfailure, iron and folic acid deficiency, peripheral neuropathy, pregnancy, celiacdisease, Crohn’sdiseaseandrarelymalignancy (2).Despite a clear relation between low peripheral iron and increased prevalence and severity of RLS, the prevalence and clinical significance of RLS in iron-deficientanemic populations is unknown (2). We report here a case of RLS due to iron deficiency in the setting of neuroendocrinetumor. Report of Case: A 35 year-old man was referred to our clinic with general weakness, weight loss (10 kg in 2 months)and 2-month history of uncomfortable sensations in his legs with urge to move, partially relieved by movement. The symptoms were presented very day, worsening in the evening; the discomfort forced the patient to getup and walk around at night. RLS was severe, with a score of 22 at the International RLS ratingscale. The patient had no past medical history. The patient underwent a complete set of blood analyses and the following ab normal values were found (normal limitswithinbrackets): hemoglobin 9.9 g/dl (14-18), MCV 70 fL (80-94), ferritin 3,5 ng/mL (13-150). Brain and spinemagnetic resonance imaging was normal. The patient consultated with gastroenterology clinic and gastointestinal systemendoscopy was performed for theetiology of the iron deficiency anemia. After the gastricbiopsy, results allowed us to reach the diagnosis of neuroen docrine tumor and the patient referred to oncology clinic. Discussion: The first important consideration from this case report is that the patient was referred to our clinic because of his severe RLS symptoms dramatically reducing his quality of life. However, our clinical study clearly demonstrated that RLS was not the primary disease. Considering the information available for this patient, we believe that the most likely possibility is that RLS was secondary to iron deficiency, a very well-known and established cause of RLS in theliterature (3,4). Neuroendocrine tumors (NETs) are rare epithelial neoplasms with neuroendocrine differentiation that most commonly originate in the lungs and gastrointestinal tract (5). NETs vary widely in their clinical presentation; symptoms are often nonspecific and can be mistaken for those of other more common conditions (6). 50% of patients with reported disease stage have either regional or distant metastases at diagnosis (7). Accurate and earlier NET diagnosis is the first step in shortening the time to optimal care and improved outcomes for patients (8). The most important message from this case report is that RLS symptoms can sometimes be thesign of a life-threatening condition. Conclusion: Careful and complete collection of clinical and laboratory data should be carried out in RLS patients. Inparticular, if RLS onset coincides with weight loss and iron deficieny anemia, gastricendos copy should be performed. It is known about that malignancy is a rare etiology in RLS patients and to our knowledge; it is the first case with neuro endocrine tumor presenting with RLS.

Keywords: neurology, neuroendocrine tumor, restless legs syndrome, sleep

Procedia PDF Downloads 276

Authors: Shringika Soni, Utkarsh Jain, Nidhi Chauhan

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Aptamers are recently discovered ~80-100 bp long artificial oligonucleotides that not only demonstrated their applications in therapeutics; it is tremendously used in diagnostic and sensing application to detect different biomarkers and drugs. Synthesizing aptamers for proteins or genomic template is comparatively feasible in laboratory, but drugs or other chemical target based aptamers require major specification and proper optimization and validation. One has to optimize all selection, amplification, and characterization steps of the end product, which is extremely time-consuming. Therefore, we performed asymmetric PCR (polymerase chain reaction) for random oligonucleotides pool synthesis, and further use them in Systematic evolution of ligands by exponential enrichment (SELEX) for anti-psychotic drugs based aptamers synthesis. Anti-psychotic drugs are major tranquilizers to control psychosis for proper cognitive functions. Though their low medical use, their misuse may lead to severe medical condition as addiction and can promote crime in social and economical impact. In this work, we have approached the in-vitro SELEX method for ssDNA synthesis for anti-psychotic drugs (in this case ‘target’) based aptamer synthesis. The study was performed in three stages, where first stage included synthesis of random oligonucleotides pool via asymmetric PCR where end product was analyzed with electrophoresis and purified for further stages. The purified oligonucleotide pool was incubated in SELEX buffer, and further partition was performed in the next stage to obtain target specific aptamers. The isolated oligonucleotides are characterized and quantified after each round of partition, and significant results were obtained. After the repetitive partition and amplification steps of target-specific oligonucleotides, final stage included sequencing of end product. We can confirm the specific sequence for anti-psychoactive drugs, which will be further used in diagnostic application in clinical and forensic set-up.

Keywords: anti-psychotic drugs, aptamer, biosensor, ssDNA, SELEX

Procedia PDF Downloads 127

Authors: Hediyeh Talebi, Shokoofeh Ghiam, Changiz Eslahchi

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Traditionally, Alzheimer’s disease research has focused on genes with significant fold changes, potentially neglecting subtle but biologically important alterations. Our study introduces an integrative approach that highlights genes crucial to underlying biological processes, regardless of their fold change magnitude. Alzheimer's Single-cell RNA-seq data related to the peripheral blood mononuclear cells (PBMC) was extracted from the Gene Expression Omnibus (GEO). After quality control, normalization, scaling, batch effect correction, and clustering, differentially expressed genes (DEGs) were identified with adjusted p-values less than 0.05. These DEGs were categorized based on cell-type, resulting in four datasets, each corresponding to a distinct cell type. To distinguish between cells from healthy individuals and those with Alzheimer's, an adversarial autoencoder with a classifier was employed. This allowed for the separation of healthy and diseased samples. To identify the most influential genes in this classification, the weight matrices in the network, which includes the encoder and classifier components, were multiplied, and focused on the top 20 genes. The analysis revealed that while some of these genes exhibit a high fold change, others do not. These genes, which may be overlooked by previous methods due to their low fold change, were shown to be significant in our study. The findings highlight the critical role of genes with subtle alterations in diagnosing Alzheimer's disease, a facet frequently overlooked by conventional methods. These genes demonstrate remarkable discriminatory power, underscoring the need to integrate biological relevance with statistical measures in gene prioritization. This integrative approach enhances our understanding of the molecular mechanisms in Alzheimer’s disease and provides a promising direction for identifying potential therapeutic targets.

Keywords: alzheimer's disease, single-cell RNA-seq, neural networks, blood biomarkers

Procedia PDF Downloads 55

Authors: Mahmoud Owais

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Public Transit (P.T) is very important means to reduce traffic congestion, to improve urban environmental conditions and consequently affects people social lives. Planning, designing and management of P.T are the key issues for offering a competitive mode that can compete with the private transportation. These transportation planning, designing and management issues are addressed in the Transit Network Design Problem (TNDP). It deals with a complete hierarchy of decision making process. It includes strategic, tactical and operational decisions. The main body of TNDP is two stages, namely; route design stage and frequency setting. The TNDP is extensively studied in the last five decades; however the research gate is still widely open due to its many practical and modeling challenges. In this paper, a comprehensive background is given to illustrate the issues and challenges related to the TNDP to help in directing the incoming researches towards the untouched areas of the problem.

Keywords: frequency setting, network design, transit planning, urban planning

Procedia PDF Downloads 370

Authors: R. Behrooz, D. Jahanfar, D. Reza

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Organic farming is a fundamental principle in sustainable agriculture. Preventing excessive contamination of water and soil with pesticides and chemical fertilizers is important in order to produce healthy food. For this purpose, two potato cultivars (Sante and Marfona) and seven levels of fertilizer (non-fertilizer, chemical fertilizer, granulated chicken manure, common manure, compost, vermicompost and tea compost) were evaluated by factorial experiment based on randomized complete block design (RCBD) with three replications. According to the results, the effect of different manure was significant on number of tubers per plant, tuber weight per plant and tuber yield. The highest value of these traits was obtained by using of chicken manure which was significantly superior to other treatments. However, there was no significant difference between the two varieties. According to the results, the use of chicken manure has produced the highest potato yield even in comparison with the use of chemical fertilizer.

Keywords: organic farming, organic manure, potato, tuber yield

Procedia PDF Downloads 143

Authors: Hazim Abdulsada

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The inspection of underneath vehicle system has been given significant attention by governments after the threat of terrorism become more prevalent. New technologies such as mobile robots and computer vision are led to have more secure environment. This paper proposed that a mobile robot like Aria robot can be used to search and inspect the bombs under parking a lot vehicle. This robot is using fuzzy logic and subsumption algorithms to control the robot that movies underneath the vehicle. An OpenCV library and laser Hokuyo are added to Aria robot to complete the experiment for under vehicle inspection. This experiment was conducted at the indoor environment to demonstrate the efficiency of our methods to search objects and control the robot movements under vehicle. We got excellent results not only by controlling the robot movement but also inspecting object by the robot camera at same time. This success allowed us to know the requirement to construct a new cost effective robot with more functionality.

Keywords: fuzzy logic, mobile robots, Opencv, subsumption, under vehicle inspection

Procedia PDF Downloads 465

Authors: Satyendra Pratap Singh, S. P. Singh

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This paper presents a methodology using Gravitational Search Algorithm for optimal placement of Phasor Measurement Units (PMUs) in order to achieve complete observability of the power system. The objective of proposed algorithm is to minimize the total number of PMUs at the power system buses, which in turn minimize installation cost of the PMUs. In this algorithm, the searcher agents are collection of masses which interact with each other using Newton’s laws of gravity and motion. This new Gravitational Search Algorithm based method has been applied to the IEEE 14-bus, IEEE 30-bus and IEEE 118-bus test systems. Case studies reveal optimal number of PMUs with better observability by proposed method.

Keywords: gravitational search algorithm (GSA), law of motion, law of gravity, observability, phasor measurement unit

Procedia PDF Downloads 494

Authors: Dina Athariah, Desriani Desriani, Bugi Ratno Budiarto, Abinawanto Abinawanto, Dwi Wulandari

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Breast cancer is a regulated by many genes. Defect in PIK3CA gene especially at position of exon 9 (E542K and E545K), called hot spot mutation induce early transformation of breast cells. The early detection of breast cancer based on mutation profile of this hot spot region would be hampered by the existence of pseudogene, marked by its substitution mutation at base 1658 (E545A) and deletion at 1659 that have been previously proven in several cancers. To the best of the authors’ knowledge, until recently no studies have been reported about pseudogene phenomenon in breast cancer. Here, we reported PCR optimization to to obtain true exon 9 of PIK3CA gene from its pseudogene hence increasing the validity of data. Material and methods: two genomic DNA with Dev and En code were used in this experiment. Two pairs of primer were design for Standard PCR method. The size of PCR products for each primer is 200bp and 400bp. While other primer was designed for Nested-PCR followed with DNA sequencing method. For Nested-PCR, we optimized the annealing temperature in first and second run of PCR, and the PCR cycle for first run PCR (15x versus 25x). Result: standard PCR using both primer pairs designed is failed to detect the true PIK3CA gene, appearing a substitution mutation at 1658 and deletion at 1659 of PCR product in sequence chromatogram indicated pseudogene. Meanwhile, Nested-PCR with optimum condition (annealing temperature for the first round at 55oC, annealing temperatung for the second round at 60,7oC with 15x PCR cycles) and could detect the true PIK3CA gene. Dev sample were identified as WT while En sample contain one substitution mutation at position 545 of exon 9, indicating amino acid changing from E to K. For the conclusion, pseudogene also exists in breast cancer and the apllication of optimazed Nested-PCR in this study could detect the true exon 9 of PIK3CA gene.

Keywords: breast cancer, exon 9, hotspot mutation, PIK3CA, pseudogene

Procedia PDF Downloads 235

Authors: Allan Kiptanui Kimisto, Geoffrey Odhiambo Ongondo, Anastasia Wairimu Muia, Cyrus Ndungu Kimani

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The major challenge to proper sewage sludge treatment processes is the poor understanding of sludge microbiome diversities. This study applied the whole-genome. shotgun metagenomics technique to profile the microbial composition of sewage sludge in two active digestion lagoons at the Nyeri-Kangemi Wastewater Treatment Plant in Nyeri County, Kenya. Total microbial community DNA was extracted from samples using the available ZymoBIOMICS™ DNA Miniprep Kit and sequenced using Shotgun metagenomics. Samples were analyzed using MG-RAST software (Project ID: mgp100988), which allowed for comparing taxonomic diversity before β-diversities studies for Bacteria, Archaea and Eukaryotes. The study identified 57 phyla, 145 classes, 301 orders, 506 families, 963 genera, and 1980 species. Bacteria dominated the microbes and comprised 28 species, 51 classes, 110 orders, 243 families, 597 genera, and 1518 species. The Bacteroides(6.77%) were dominant, followed by Acinetobacter(1.44%) belonging to the Gammaproteobacteria and Acidororax (1.36%), Bacillus (1.24%) and Clostridium (1.02%) belonging to Betaproteobacteria. Archaea recorded 5 phyla, 13 classes, 19 orders, 29 families, 60 genera,and87 species, with the dominant genera being Methanospirillum (16.01%), methanosarcina (15.70%), and Methanoregula(14.80%) and Methanosaeta (8.74%), Methanosphaerula(5.48%) and Methanobrevibacter(5.03%) being the subdominant group. The eukaryotes were the least in abundance and comprised 24 phyla, 81 classes, 301 orders, 506 families, 963 genera, and 980 species. Arabidopsis (4.91%) and Caenorhabditis (4.81%) dominated the eukaryotes, while Dityostelium (3.63%) and Drosophila(2.08%) were the subdominant genera. All these microbes play distinct roles in the anaerobic treatment process of sewage sludge. The local sludge microbial composition and abundance variations may be due to age difference differences between the two digestion lagoons in operation at the plant and the different degradation rales played by the taxa. The information presented in this study can help in the genetic manipulation or formulation of optimal microbial ratios to improve their effectiveness in sewage sludge treatment. This study recommends further research on how the different taxa respond to environmental changes over time and space.

Keywords: shotgun metagenomics, sludge, bacteria, archaea, eukaryotes

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Authors: Soulef Amamria, Mohamed Sadok Bensalem, Mohamed Ghanmi

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The structural and sedimentological study of fault-related- folds in the Southern Tunisian Atlas is distinguished by a special geometry of the gravitational structures. This distinct geometry is observable in the example of a flap structure in Jebel Ben Zannouch with the formation of a stuck syncline. This geometry can be explained by the mechanism of major thrusting in Orbata anticline in the occidental extremity of Gafsa chains, with asymmetrical flank dips and hinge migration kinematics. These kinematics was originally controlled by the Breakthrough structure; the study of this special geometry of gravity flap structure depends on the sedimentation domain, shortening ratios, and erosion speed. This study constitutes one of the complete examples of kinematic model validation on a field scale.

Keywords: fault-related-folds, southern Tunisian Atlas, flap structure, breakthrough

Procedia PDF Downloads 90

Authors: S. H. Arnaud Kanga, O. Hili, S. Dabo-Niang

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Spatial prediction is an issue appealing and attracting several fields such as agriculture, environmental sciences, ecology, econometrics, and many others. Although multiple non-parametric prediction methods exist for spatial data, those are based on the conditional expectation. This paper took a different approach by examining a non-parametric spatial predictor of the conditional quantile. The study especially observes the stationary multidimensional spatial process over a rectangular domain. Indeed, the proposed quantile is obtained by inverting the conditional distribution function. Furthermore, the proposed estimator of the conditional distribution function depends on three kernels, where one of them controls the distance between spatial locations, while the other two control the distance between observations. In addition, the almost complete convergence and the convergence in mean order q of the kernel predictor are obtained when the sample considered is alpha-mixing. Such approach of the prediction method gives the advantage of accuracy as it overcomes sensitivity to extreme and outliers values.

Keywords: conditional quantile, kernel, nonparametric, stationary

Procedia PDF Downloads 146

Authors: Nurulhikma Md Isa, Intan Elya Suka, Nur Farhana Roslan, Chew Bee Lynn

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The evolutionarily conserved N-end rule pathway marks proteins for degradation by the Ubiquitin Proteosome System (UPS) based on the nature of their N-terminal residue. Proteins with a destabilizing N-terminal residue undergo a series of condition-dependent N-terminal modifications, resulting in their ubiquitination and degradation. Intensive research has been carried out in Arabidopsis previously. The group VII Ethylene Response Factor (ERFs) transcription factors are the first N-end rule pathway substrates found in Arabidopsis and their role in regulating oxygen sensing. ERFs also function as central hubs for the perception of gaseous signals in plants and control different plant developmental including germination, stomatal aperture, hypocotyl elongation and stress responses. However, nothing is known about the role of this pathway during fruit development and ripening aspect. The plant model system Arabidopsis cannot represent fleshy fruit model system therefore tomato is the best model plant to study. PROTEOLYSIS6 (PRT6) is an E3 ubiquitin ligase of the N-end rule pathway. Two homologs of PRT6 sequences have been identified in tomato genome database using the PRT6 protein sequence from model plant Arabidopsis thaliana. Homology search against Ensemble Plant database (tomato) showed Solyc09g010830.2 is the best hit with highest score of 1143, e-value of 0.0 and 61.3% identity compare to the second hit Solyc10g084760.1. Further homology search was done using NCBI Blast database to validate the data. The result showed best gene hit was XP_010325853.1 of uncharacterized protein LOC101255129 (Solanum lycopersicum) with highest score of 1601, e-value 0.0 and 48% identity. Both Solyc09g010830.2 and uncharacterized protein LOC101255129 were genes located at chromosome 9. Further validation was carried out using BLASTP program between these two sequences (Solyc09g010830.2 and uncharacterized protein LOC101255129) to investigate whether they were the same proteins represent PRT6 in tomato. Results showed that both proteins have 100 % identity, indicates that they were the same gene represents PRT6 in tomato. In addition, we used two different RNAi constructs that were driven under 35S and Polygalacturonase (PG) promoters to study the function of PRT6 during tomato developmental stages and ripening processes.

Keywords: ERFs, PRT6, tomato, ubiquitin

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Authors: Soumaya Sallem, Marc Olivas

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This contribution presents a method for detecting, locating, and characterizing soft faults in a complex wired network. The proposed method is based on multi-carrier reflectometry MCTDR (Multi-Carrier Time Domain Reflectometry) combined with a multi-objective genetic algorithm. In order to ensure complete network coverage and eliminate diagnosis ambiguities, the MCTDR test signal is injected at several points on the network, and the data is merged between different reflectometers (sensors) distributed on the network. An adapted multi-objective genetic algorithm is used to merge data in order to obtain more accurate faults location and characterization. The proposed method performances are evaluated from numerical and experimental results.

Keywords: wired network, reflectometry, network distributed diagnosis, multi-objective genetic algorithm

Procedia PDF Downloads 184

Authors: Noor Azlina Mohamed Yunus, Noorlaila Yunus, Kadulliah Ghazali

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In this an era of intense competition, Malaysia aspires to be a fully developed country by 2020 and desires its citizens to perform and execute excellent work behaviors. For that reason, organizations are focusing on employees’ positive and constructive behaviors such as organizational citizenship behavior (OCB). They expect employees to not only complete their required duties by providing excellent performance but also keenly go beyond their roles that are not specifying in their formal job descriptions to ensure organizational success. The role and duty to acquire employees to engage and connect in OCB is the responsibility of a leader. Thus, leaders can utilize their sources of power to enable subordinates to accomplish organizational objective including OCB. Therefore, this paper formulates a framework postulating leader’s sources of power as an antecedent of organizational citizenship behavior (OCB). The discussion on implications for future theory development is discussed.

Keywords: organizational citizenship behaviour (OCB), leader’s sources of power, call centre industry, conceptual paper

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Authors: Mehmet Ali Topçu, Aydın Ruşen

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Çinkur is the only plant in Turkey that produces zinc from primary ore containing zinc carbonate from its establishment until 1997. After this year, zinc concentrate coming from Iran was used in this plant. Therefore, there are two different leach residues namely Turkish leach residue (TLR) and Iranian leach residue (ILR), in Çinkur stock piles. This paper describes zinc recovery by sulphuric acid (H2SO4) treatment for each leach residue and includes comparison of blended of TLR and ILR. Before leach experiments; chemical, mineralogical and thermal analysis of three different leach residues was carried out by using atomic absorption spectrometry (AAS), X-Ray diffraction (XRD) and differential thermal analysis (DTA), respectively. Leaching experiments were conducted at optimum conditions; 100 oC, 150 g/L H2SO4 and 2 hours. In the experiments, stirring rate was kept constant at 600 r/min which ensures complete mixing in leaching solution. Results show that zinc recovery for Iranian LR was higher than Turkish LR due to having different chemical composition from each other.

Keywords: hydrometallurgy, leaching, metal extraction, metal recovery

Procedia PDF Downloads 345