Search results for: sequence alignment problem

Authors: Wajahat Ali, Shakeel Javaid

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In this study, we have developed a mathematical programming model for a solid transportation problem with three objective functions arranged in hierarchical order. The mathematical programming models with more than one objective function to be solved in hierarchical order is termed as a multi-level programming model. Our study explores a Multi-Level Solid Transportation Problem with Uncertain Parameters (MLSTPWU). The proposed MLSTPWU model consists of three objective functions, viz. minimization of transportation cost, minimization of total transportation time, and minimization of deterioration during transportation. These three objective functions are supposed to be solved by decision-makers at three consecutive levels. Three constraint functions are added to the model, restricting the total availability, total demand, and capacity of modes of transportation. All the parameters involved in the model are assumed to be uncertain in nature. A solution method based on fuzzy logic is also discussed to obtain the compromise solution for the proposed model. Further, a simulated numerical example is discussed to establish the efficiency and applicability of the proposed model.

Keywords: solid transportation problem, multi-level programming, uncertain variable, uncertain environment

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Authors: Nahed Al-Hajeri

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Time and cost is an integral part of every construction plan and can affect each party’s contractual obligations. The performance of both time and cost are usually important to the client and contractor during the project. Almost all construction projects are experiencing time overrun. These time overruns always contributed as expensive to both client and contractor. Construction of any project inside the gathering centers involves complex management skills related to work force, materials, plant, machineries, new technologies etc. It also involves many agencies interdependent on each other like the vendors, structural and functional designers including various types of specialized engineers and it includes support of contractors and specialized contractors. This paper mainly highlights the types of construction delays due to which project suffer time and cost overrun. This paper also speaks about the delay causes and factors that contribute to the construction sequence delay for the oil and gas projects. Construction delay is supposed to be one of the repeated problems in the construction projects and it has an opposing effect on project success in terms of time, cost and quality. Some effective methods are identified to minimize delays in construction projects such as: 1. Site management and supervision, 2. Effective strategic planning, 3. Clear information and communication channel. Our research paper studies the types of delay with some real examples with statistic results and suggests solutions to overcome this problem.

Keywords: non-compensable delay, delays caused by force majeure, compensable delay, delays caused by the owner or the owner’s representative, non-excusable delay, delay caused by the contractor or the contractor’s representative, concurrent delay, delays resulting from two separate causes at the same time

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Authors: Leili Esmaeilani, Jafar Ghaisari, Mohsen Ahmadian

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Hammerstein–Wiener model is a block-oriented model where a linear dynamic system is surrounded by two static nonlinearities at its input and output and could be used to model various processes. This paper contains an optimization approach method for analysing the problem of Hammerstein–Wiener systems identification. The method relies on reformulate the identification problem; solve it as constraint quadratic problem and analysing its solutions. During the formulation of the problem, effects of adding noise to both input and output signals of nonlinear blocks and disturbance to linear block, in the emerged equations are discussed. Additionally, the possible parametric form of matrix operations to reduce the equation size is presented. To analyse the possible solutions to the mentioned system of equations, a method to reduce the difference between the number of equations and number of unknown variables by formulate and importing existing knowledge about nonlinear functions is presented. Obtained equations are applied to an instance H–W system to validate the results and illustrate the proposed method.

Keywords: identification, Hammerstein-Wiener, optimization, quantization

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Authors: Serhat Tüzün, Tufan Demirel

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The objective of the present study is to select the most suitable location for a wind power plant station through Choquet integral method. The problem of selecting the location for a wind power station was considered as a multi-criteria decision-making problem. The essential and sub-criteria were specified and location selection was expressed in a hierarchic structure. Among the main criteria taken into account in this paper are wind potential, technical factors, social factors, transportation, and costs. The problem was solved by using different approaches of Choquet integral and the best location for a wind power station was determined. Then, the priority weights obtained from different Choquet integral approaches are compared and commented on.

Keywords: multi-criteria decision making, choquet integral, fuzzy sets, location of a wind power plant

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Authors: Jannis Kountouras, Nikolaos Kapetanakis, Stergios A. Polyzos, Apostolis Papaeftymiou, Panagiotis Katsinelos, Ioannis Venizelos, Christina Nikolaidou, Christos Zavos, Iordanis Romiopoulos, Elena Tsiaousi, Evangelos Kazakos, Michael Doulberis

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Background & Aims: Helicobacter pylori infection (Hp-I) has been recognized as a substantial risk agent involved in gastrointestinal (GI) tract oncogenesis by stimulating cancer stem cells (CSCs), oncogenes, immune surveillance processes, and triggering GI microbiota dysbiosis. We aimed to investigate the possible involvement of active Hp-I in the sequence: chronic inflammation–adenoma–colorectal cancer (CRC) development. Methods: Four pillars were investigated: (i) endoscopic and conventional histological examinations of patients with CRC, colorectal adenomas (CRA) versus controls to detect the presence of active Hp-I; (ii) immunohistochemical determination of the presence of Hp; expression of CD44, an indicator of CSCs and/or bone marrow-derived stem cells (BMDSCs); expressions of oncogene Ki67 and anti-apoptotic Bcl-2 protein; (iii) expression of CD45, indicator of immune surveillance locally (assessing mainly T and B lymphocytes locally); and (iv) correlation of the studied parameters with the presence or absence of Hp-I. Results: Among 50 patients with CRC, 25 with CRA, and 10 controls, a significantly higher presence of Hp-I in the CRA (68%) and CRC group (84%) were found compared with controls (30%). The presence of Hp-I with accompanying immunohistochemical expression of CD44 in biopsy specimens was revealed in a high proportion of patients with CRA associated with moderate/severe dysplasia (88%) and CRC patients with moderate/severe degree of malignancy (91%). Comparable results were also obtained for Ki67, Bcl-2, and CD45 immunohistochemical expressions. Concluding Remarks: Hp-I seems to be involved in the sequence: CRA – dysplasia – CRC, similarly to the upper GI tract oncogenesis, by several pathways such as the following: Beyond Hp-I associated insulin resistance, the major underlying mechanism responsible for the metabolic syndrome (MetS) that increase the risk of colorectal neoplasms, as implied by other Hp-I related MetS pathologies, such as non-alcoholic fatty liver disease and upper GI cancer, the disturbance of the normal GI microbiota (i.e., dysbiosis) and the formation of an irritative biofilm could contribute to a perpetual inflammatory upper GIT and colon mucosal damage, stimulating CSCs or recruiting BMDSCs and affecting oncogenes and immune surveillance processes. Further large-scale relative studies with a pathophysiological perspective are necessary to demonstrate in-depth this relationship.

Keywords: Helicobacter pylori, colorectal cancer, colorectal adenomas, gastrointestinal oncogenesis

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Authors: Shazi Farooqui, Anupam Sharma

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The Mahi River (~600km long) is an important west flowing the river of Central India. It originates in Madhya Pradesh and starts flowing in NW direction and enters into the state of Rajasthan. It flows across southern Rajasthan and then enters into Gujarat and finally debouches in the Gulf of Cambay. In Gujarat state, it flows through all four geomorphic zones i.e. eastern upland zone, shallow buried piedmont zone, alluvial zone and coastal zone. In lower reaches and particularly when it is flowing under the coastal regime, it provides an opportunity to study – 1. Land–Sea interaction and role of relative sea level changes, 2. Coastal/estuarine geological process, 3. Landscape evolution in marginal areas and so on. The Late Quaternary deposits of Mainland Gujarat is appreciably studied by Chamyal and his group of MS University of Baroda, and they have established that the 30-35m thick sediment package of the Mainland Gujarat is comprised of marine, fluvial and aeolian sediments. It is also established that in the estuarine zone, the upper few meter thick sediments package is of marine nature. However, its thickness, characters and the depositional environment including the role of climate and tectonics is still not clearly defined. To understand few aspects of the above mentioned, in the present study, a 17m subsurface sediment core has been retrieved from the estuarine zone of Mahi river basin. The Multiproxy studies which include the textural analysis (grain size), Loss on ignition (LOI), Bulk and clay mineralogy and geochemical studies have been carried out. In the entire sedimentary sequence, the grain size largely varies from coarse sand to clay; however, a solitary gravel bed is also noticed. The lower part (depth 9-17m), is mainly comprised of sub equal proportion of sand and silt. The sediments mainly have bimodal and leptokurtic distribution and deposited in alternate sand-silt package, probably indicating flood deposits. Relatively low moisture (1.8%) and organic carbon (2.4%) with increased carbonate values (12%) indicate that conditions must have to remain oxidizing. The middle part (depth 9–6m) has a 1m thick gravel bed at the bottom and overlain by coarse sand to very fine sand showing fining upward sequence. The presence of gravel bed suggests some kind of tectonic activity resulting into change in base level or enhanced precipitation in the catchment region. The upper part (depth 6–0m; top part of sequence) mainly comprised of fine sand to silt size grains (with appreciable clay content). The sediment of this part is Unimodal and very leptokurtic in nature suggesting wave and winnowing process and deposited in low energy suspension environment. This part has relatively high moisture (2.1%) and organic carbon (2.7%) with decreased carbonate content (4.2%) indicating change in the depositional environment probably under estuarine conditions. The presence of chlorite along with smectite clay mineral further supports the significant marine contribution in the formation of upper part of the sequence.

Keywords: grain size, statistical analysis, clay minerals, late quaternary, LOI

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Authors: Blair D. Macdonald

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After nearly one hundred years of its origin, foundational quantum mechanics remains one of the greatest unexplained mysteries in physicists today. Within this time, chaos theory and its geometry, the fractal, has developed. In this paper, the propagation behaviour with an iteration of a simple fractal, the Koch Snowflake, was described and analysed. From an arbitrary observation point within the fractal set, the fractal propagates forward by oscillation—the focus of this study and retrospectively behind by exponential growth from a point beginning. It propagates a potentially infinite exponential oscillating sinusoidal wave of discrete triangle bits sharing many characteristics of light and quantum entities. The model's wave speed is potentially constant, offering insights into the perception and a direction of time where, to an observer, when travelling at the frontier of propagation, time may slow to a stop. In isolation, the fractal is a superposition of component bits where position and scale present a problem of location. In reality, this problem is experienced within fractal landscapes or fields where 'position' is only 'known' by the addition of information or markers. The quantum' measurement problem', 'uncertainty principle,' 'entanglement,' and the classical-quantum interface are addressed; these are a problem of scale invariance associated with isolated fractality. Dual forward and retrospective perspectives of the fractal model offer the opportunity for unification between quantum mechanics and cosmological mathematics, observations, and conjectures. Quantum and cosmological problems may be different aspects of the one fractal geometry.

Keywords: measurement problem, observer, entanglement, unification

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Authors: Vyacheslav Furtak, Merja Roivainen, Olga Mirochnichenko, Majid Laassri, Bella Bidzhieva, Tatiana Zagorodnyaya, Vladimir Chizhikov, Konstantin Chumakov

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Molecular epidemiology and environmental surveillance are parts of a rational strategy to control infectious diseases. They have been widely used in the worldwide campaign to eradicate poliomyelitis, which otherwise would be complicated by the inability to rapidly respond to outbreaks and determine sources of the infection. The conventional scheme involves isolation of viruses from patients and the environment, followed by their identification by nucleotide sequences analysis to determine phylogenetic relationships. This is a tedious and time-consuming process that yields definitive results when it may be too late to implement countermeasures. Because of the difficulty of high-throughput full-genome sequencing, most such studies are conducted by sequencing only capsid genes or their parts. Therefore the important information about the contribution of other parts of the genome and inter- and intra-species recombination to viral evolution is not captured. Here we propose a new approach based on the rapid concentration of sewage samples with tangential flow filtration followed by deep sequencing and reconstruction of nucleotide sequences of viruses present in the samples. The entire nucleic acids content of each sample is sequenced, thus preserving in digital format the complete spectrum of viruses. A set of rapid algorithms was developed to separate deep sequence reads into discrete populations corresponding to each virus and assemble them into full-length consensus contigs, as well as to generate a complete profile of sequence heterogeneities in each of them. This provides an effective approach to study molecular epidemiology and evolution of natural viral populations.

Keywords: poliovirus, eradication, environmental surveillance, laboratory diagnosis

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Authors: Paula Andrea Segura Delgado, Martha Helena Ramírez-Bahena

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Research on how the brain learns has a transcendental application in the educational context. It is crucial for teacher training to understand the nature of brain changes and their direct influence on learning processes. This communication is based on a literature review focused on neuroscience, neuroeducation, and the impact of digital technology on the human brain. Information was gathered from both English and Spanish language sources, using online journals, books and reports. The general objective was to analyze the role of neuroscience knowledge in enriching our understanding of the learning process. In fact, the authors have focused on the impact of digital technology on the human brain as well as its influence in the field of education..Neuroscience knowledge can contribute significantly to improving the training of educators and therefore educational practices. Education as an instrument of change and school as an agent of socialization, it is necessary to understand what it aims to transform: the human brain. Understanding the functioning of the human brain has important repercussions on education: this elucidates cognitive skills, psychological processes and elements that influence the learning process (memory, executive functions, emotions and the circadian cycle); helps identify psychological and neurological deficits that can impede learning processes (dyslexia, autism, hyperactivity); It allows creating environments that promote brain development and contribute to the advancement of brain capabilities in alignment with the stages of neurobiological development. The digital age presents diverse opportunities to every social environment. The frequent use of digital technology (DT) has had a significant and abrupt impact on both the cognitive abilities and physico-chemical properties of the brain, significantly influencing educational processes. Hence, educational community, with the insights from advances in neuroscience, aspire to identify the positive and negative effects of digital technology on the human brain. This knowledge helps ensure the alignment of teacher training and practices with these findings. The knowledge of neuroscience enables teachers to develop teaching methods that are aligned with the way the brain works. For example, neuroscience research has shown that digital technology is having a significant impact on the human brain (addition, anxiety, high levels of dopamine, circadian cycle disorder, decrease in attention, memory, concentration, problems with their social relationships). Therefore, it is important to understand the nature of these changes, their impact on the learning process, and how educators should effectively adapt their approaches based on these brain's changes.

Keywords: digital technology, learn process, neuroscience knowledge, neuroeducation, training proffesors

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Authors: O. I. H. Dimitry, N. A. Mansour, A. L. G. Saad

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Natural sodium montmorillonite (NaMMT), Cloisite Na⁺ and two organophilic montmorillonites (OMMTs), Cloisites 20A and 15A were used. Polycaprolactone (PCL)/MMT composites containing 1, 3, 5, and 10 wt% of Cloisite Na⁺ and PCL/OMMT nanocomposites containing 5 and 10 wt% of Cloisites 20A and 15A were prepared via solution intercalation technique to study the influence of organic modifier loading on particle dispersion of PCL/ NaMMT composites. Thermal stabilities of the obtained composites were characterized by thermal analysis using the thermogravimetric analyzer (TGA) which showed that in the presence of nitrogen flow the incorporation of 5 and 10 wt% of filler brings some decrease in PCL thermal stability in the sequence: Cloisite Na+>Cloisite 15A > Cloisite 20A, while in the presence of air flow these fillers scarcely influenced the thermoxidative stability of PCL by slightly accelerating the process. The interaction between PCL and silicate layers was studied by Fourier transform infrared (FTIR) spectroscopy which confirmed moderate interactions between nanometric silicate layers and PCL segments. The electrical conductivity (σ) which describes the ionic mobility of the systems was studied as a function of temperature and showed that σ of PCL was enhanced on increasing the modifier loading at filler content of 5 wt%, especially at higher temperatures in the sequence: Cloisite Na⁺<Cloisite 20A<Cloisite 15A, and was then decreased to some extent with a further increase to 10 wt%. The activation energy E_σ obtained from the dependency of σ on temperature using Arrhenius equation was found to be lowest for the nanocomposite containing 5 wt% of Cloisite 15A. The dispersed behavior of clay in PCL matrix was evaluated by X-ray diffraction (XRD) and scanning electron microscopy (SEM) analyses which revealed partial intercalated structures in PCL/NaMMT composites and semi-intercalated/semi-exfoliated structures in PCL/OMMT nanocomposites containing 5 wt% of Cloisite 20A or Cloisite 15A.

Keywords: electrical conductivity, montmorillonite, nanocomposite, organoclay, polycaprolactone

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Authors: Neringa Bagdonaite

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Study Aims: The current study aimed to systematically analyse various research done in the area of female post-traumatic stress disorder (PTSD) and alcohol abuse, and to critically review these results on the basis of theoretical models as well as answer following questions: (I) What is the reciprocal relationship between PTSD and problem alcohol use among females; (II) What are the moderating/mediating factors of this relationship? Methods: The computer bibliographic databases Ebsco, Scopus, Springer, Web of Science, Medline, Science Direct were used to search for scientific articles. Systematic analyses sample consisted of peer-reviewed, English written articles addressing mixed gender and female PTSD and alcohol abuse issues from Jan 2012 to May 2017. Results: Total of 1011 articles were found in scientific databases related to searched keywords of which 29 met the selection criteria and were analysed. The results of longitudinal studies indicate that (I) various trauma, especially interpersonal trauma exposure in childhood is linked with increased risk of revictimization in later life and problem alcohol use; (II) revictimization in adolescence or adulthood, rather than victimization in childhood has a greater impact on the onset and progression of problematic alcohol use in adulthood. Cross-sectional and epidemiological studies also support significant relationships between female PTSD and problem alcohol use. Regards to the negative impact of alcohol use on PTSD symptoms results are yet controversial; some evidence suggests that alcohol does not exacerbate symptoms of PTSD over time, while others argue that problem alcohol use worsens PTSD symptoms and is linked to chronicity of both disorders, especially among women with previous alcohol use problems. Analysis of moderating/mediating factors of PTSD and problem alcohol use revealed, that higher motives/expectancies, specifically distress coping motives for alcohol use significantly moderates the relationship between PTSD and problematic alcohol use. Whereas negative affective states mediate relationship between symptoms of PTSD and alcohol use, but only among woman with alcohol use problems already developed. Conclusions: Interpersonal trauma experience, especially in childhood and its reappearance in lifetime is linked with PTSD symptoms and problem drinking among women. Moreover, problem alcohol use can be both a cause and a consequence of trauma and PTSD, and if used for coping it, increases the likelihood of chronicity of both disorders. In order to effectively treat both disorders, it’s worthwhile taking into account this dynamic interplay of women's PTSD symptoms and problem drinking.

Keywords: female, trauma, post-traumatic stress disorder, problem alcohol use, systemic analysis

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Authors: Khan Shahid, Shahid Zakia

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This article explores the fields of Theology and Islamic Philosophy in alignment with the SOUL (Sincere act, Optimization efforts, Ultimate goal, Law compliance) framework. It examines their historical development and demonstrates how embracing sincerity, optimization, ultimate goals, and law compliance enhances these disciplines within the Islamic context. By emphasizing the importance of Sincere acts, Optimization efforts, Ultimate goal, and Law compliance, this article provides a framework for enriching Theology and Islamic Philosophy.

Keywords: SOUL framework, Theology, Islamic Philosophy, Sincerity act, Optimization effort, Ultimate goal, Law compliance

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Authors: Annet Namusoke, Annet Namayanja, Peter Wasswa, Shakirah Nampijja

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Common bean cultivar G2333 which offers broad resistance for anthracnose has been widely used as a source of resistance in breeding for anthracnose resistance. The cultivar is pyramided with three genes namely CO-4, CO-5 and CO-7 and of these three genes, the CO-4 gene has been found to offer the broadest resistance. The main aim of this work was to identify and validate easily assayable PCR based co-dominant molecular markers for selection of the CO-4 gene in segregating populations derived from crosses of G2333 with RWR 1946 and RWR 2075, two commercial Andean cultivars highly susceptible to anthracnose. Marker sequences for the study were obtained by blasting the sequence of the COK-4 gene in the Phaseolus gene database. Primer sequence pairs that were not provided from the Phaseolus gene database were designed by the use of Primer3 software. PCR conditions were optimized and the PCR products were run on 6% HPAGE gel. Results of the polymorphism test indicated that out of 18 identified markers, only two markers namely BM588 and BM211 behaved co-dominantly. Phenotypic evaluation for reaction to anthracnose disease was done by inoculating 21days old seedlings of three parents, F1 and F2 populations with race 7 of Colletotrichum lindemuthianum in the humid chamber. DNA testing of the BM588 marker onto the F2 segregating population of the crosses RWR 1946 x G 2333 and RWR 2075 x G2333 further revealed that the marker BM588 co-segregated with disease resistance with co-dominance of two alleles of 200bp and 400bp, fitting the expected segregation ratio of 1:2:1. The BM588 marker was significantly associated with disease resistance and gave promising results for marker assisted selection of the CO-4 gene in the breeding lines. Activities to validate the BM211 marker are also underway.

Keywords: codominant, Colletotrichum lindemuthianum, MAS, Phaseolus vulgaris

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Authors: Christine K. Fulmer

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Social work education is competency based in nature. There is an expectation that graduates of social work programs throughout the world are to be prepared to practice at a level of competence, which is beneficial to both the well-being of individuals and community. Experiential learning is one way to prepare students for competent practice. The use of Problem-Based Learning (PBL) is a form experiential education that has been successful in a number of disciplines to bridge the gap between the theoretical concepts in the classroom to the real world. PBL aligns with the constructivist theoretical approach to learning, which emphasizes the integration of new knowledge with the beliefs students already hold. In addition, the basic tenants of PBL correspond well with the practice behaviors associated with social work practice including multi-disciplinary collaboration and critical thinking. This paper makes an argument for utilizing PBL in social work education.

Keywords: social work education, problem-based learning, pedagogy, experiential learning, constructivist theoretical approach

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Authors: Dalvinder Kaur Mangal

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For the past decade, noise corrupted output measurements have been a fundamental research problem to be investigated. On the other hand, the estimation of the parameters for linear dynamic systems when also the input is affected by noise is recognized as more difficult problem which only recently has received increasing attention. Representations where errors or measurement noises/disturbances are present on both the inputs and outputs are usually called errors-in-variables (EIV) models. These disturbances may also have additive effects which are also considered in this paper. Parameter estimation of false EIV problem using equation error, output error and iterative prefiltering identification schemes with and without additive uncertainty, when only the output observation is corrupted by noise has been dealt in this paper. The comparative study of these three schemes has also been carried out.

Keywords: errors-in-variable (EIV), false EIV, equation error, output error, iterative prefiltering, Gaussian noise

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Authors: Homa Ghave, Parmis Shahmaleki

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This paper presents a new multi-criteria stochastic mathematical model for a single machine scheduling with outsourcing allowed. There are multiple jobs processing in batch. For each batch, all of job or a quantity of it can be outsourced. The jobs have stochastic processing time and lead time and deterministic due dates arrive randomly. Because of the stochastic inherent of processing time and lead time, we use the chance constrained programming for modeling the problem. First, the problem is formulated in form of stochastic programming and then prepared in a form of deterministic mixed integer linear programming. The objectives are considered in the model to minimize the maximum tardiness and outsourcing cost simultaneously. Several procedures have been developed to deal with the multi-criteria problem. In this paper, we utilize the concept of satisfaction functions to increases the manager’s preference. The proposed approach is tested on instances where the random variables are normally distributed.

Keywords: single machine scheduling, multi-criteria mathematical model, outsourcing strategy, uncertain lead times and processing times, chance constrained programming, satisfaction function

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Authors: Mohammad Pourmohammadi Fallah, Maziar Salahi

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In the literature, a mixed-integer linear programming model for the integrated production planning and warehouse layout problem is proposed. To solve the model, the authors proposed a Lagrangian relax-and-fix heuristic that takes a significant amount of time to stop with gaps above 5$\%$ for large-scale instances. Here, we present two heuristic algorithms to solve the problem. In the first one, we use a greedy approach by allocating warehouse locations with less reservation costs and also less transportation costs from the production area to locations and from locations to the output point to items with higher demands. Then a smaller model is solved. In the second heuristic, first, we sort items in descending order according to the fraction of the sum of the demands for that item in the time horizon plus the maximum demand for that item in the time horizon and the sum of all its demands in the time horizon. Then we categorize the sorted items into groups of 3, 4, or 5 and solve a small-scale optimization problem for each group, hoping to improve the solution of the first heuristic. Our preliminary numerical results show the effectiveness of the proposed heuristics.

Keywords: capacitated lot-sizing, warehouse layout, mixed-integer linear programming, heuristics algorithm

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Authors: Abdoulie K. Ceesay

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Within the sequence of the whole genome, it is known that 99.9% of the human genome is similar, whilst our difference lies in just 0.1%. Among these minor dissimilarities, the most common type of genetic variations that occurs in a population is SNP, which arises due to nucleotide substitution in a protein sequence that leads to protein destabilization, alteration in dynamics, and other physio-chemical properties’ distortions. While causing variations, they are equally responsible for our difference in the way we respond to a treatment or a disease, including various cancer types. There are two types of SNPs; synonymous single nucleotide polymorphism (sSNP) and non-synonymous single nucleotide polymorphism (nsSNP). sSNP occur in the gene coding region without causing a change in the encoded amino acid, while nsSNP is deleterious due to its replacement of a nucleotide residue in the gene sequence that results in a change in the encoded amino acid. Predicting the effects of cancer related nsSNPs on protein stability, function, and dynamics is important due to the significance of phenotype-genotype association of cancer. In this thesis, Data of 5 oncogenes (ONGs) (AKT1, ALK, ERBB2, KRAS, BRAF) and 5 tumor suppressor genes (TSGs) (ESR1, CASP8, TET2, PALB2, PTEN) were retrieved from ClinVar. Five common in silico tools; Polyphen, Provean, Mutation Assessor, Suspect, and FATHMM, were used to predict and categorize nsSNPs as deleterious, benign, or neutral. To understand the impact of each variation on the phenotype, Maestro, PremPS, Cupsat, and mCSM-NA in silico structural prediction tools were used. This study comprises of in-depth analysis of 10 cancer gene variants downloaded from Clinvar. Various analysis of the genes was conducted to derive a meaningful conclusion from the data. Research done indicated that pathogenic variants are more common among ONGs. Our research also shows that pathogenic and destabilizing variants are more common among ONGs than TSGs. Moreover, our data indicated that ALK(409) and BRAF(86) has higher benign count among ONGs; whilst among TSGs, PALB2(1308) and PTEN(318) genes have higher benign counts. Looking at the individual cancer genes predisposition or frequencies of causing cancer according to our research data, KRAS(76%), BRAF(55%), and ERBB2(36%) among ONGs; and PTEN(29%) and ESR1(17%) among TSGs have higher tendencies of causing cancer. Obtained results can shed light to the future research in order to pave new frontiers in cancer therapies.

Keywords: tumor suppressor genes (TSGs), oncogenes (ONGs), non synonymous single nucleotide polymorphism (nsSNP), single nucleotide polymorphism (SNP)

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Authors: Thepnarintra Praphanphat

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The purposes of this study were to: 1) investigate operation conditions of SME automotive part industry in Bangkok and vicinity and 2) to compare operation problem levels of SME automotive part industry in Bangkok and vicinity according to the sizes of the enterprises. Samples in this study included 196 entrepreneurs of SME automotive part industry in Bangkok and vicinity derived from simple random sampling and calculation from R. V. Krejcie and D. W. Morgan’s tables. Research statistics included frequency, percentage, mean, standard deviation, and T-test. The results revealed that in general the problem levels of SME automotive part industry in Bangkok and vicinity were high. When considering in details, it was found that the problem levels were high at every aspect, i.e. personal, production, export, finance, and marketing respectively. The comparison of the problem levels according to the sizes of the enterprises revealed statistically significant differences at .05. When considering on each aspect, it was found that the aspect with the statistical difference at .05 included 5 aspects, i.e. production, marketing, finance, personal, and export. The findings also showed that small enterprises faced more severe problems than those of medium enterprises.

Keywords: automotive part industry, operation problems, SME, Perimeter

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Authors: Rajkumar Ghosh

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The paper presents a comprehensive study of the structural analysis of the Chaura Thrust in Himachal Pradesh, India. The research focuses on several key aspects, including the activation timing of the Main Central Thrust (MCT) and the South Tibetan Detachment System (STDS), the identification and characterization of mylonitised zones through microscopic examination, and the understanding of box fold characteristics and their implications in the regional geology of the Himachal Himalaya. The primary objective of the study is to provide field documentation of the Chaura Thrust, which was previously considered a blind thrust with limited field evidence. Additionally, the research aims to characterize box folds and their signatures within the broader geological context of the Himachal Himalaya, document the temperature range associated with grain boundary migration (GBM), and explore the overprinting structures related to multiple sets of Higher Himalayan Out-of-Sequence Thrusts (OOSTs). The research methodology employed geological field observations and microscopic studies. Samples were collected along the Jhakri-Chaura transect at regular intervals of approximately 1 km to conduct strain analysis. Microstructural studies at the grain scale along the Jhakri-Wangtu transect were used to document the GBM-associated temperature range. The study reveals that the MCT activated in two parts, as did the STDS, and provides insights into the activation ages of the Main Boundary Thrust (MBT) and the Main Frontal Thrust (MFT). Under microscopic examination, the study identifies two mylonitised zones characterized by S-C fabric, and it documents dynamic and bulging recrystallization, as well as sub-grain formation. Various types of crenulated schistosity are observed in photomicrographs, including a rare occurrence where crenulation cleavage and sigmoid Muscovite are found juxtaposed. The study also notes the presence of S/SE-verging meso- and micro-scale box folds around Chaura, which may indicate structural upliftment. Kink folds near Chaura are visible, while asymmetric shear sense indicators in augen mylonite are predominantly observed under microscopic examination. Moreover, the research highlights the documentation of the Higher Himalayan Out-of-Sequence Thrust (OOST) in Himachal Pradesh, which activated the MCT and occurred within a zone south of the Main Central Thrust Upper (MCTU). The presence of multiple sets of OOSTs suggests a zigzag pattern of strain accumulation in the area. The study emphasizes the significance of understanding the overprinting structures associated with OOSTs. Overall, this study contributes to the understanding of the structural analysis of the Chaura Thrust and its implications in the regional geology of the Himachal Himalaya. The research underscores the importance of microscopic studies in identifying mylonitised zones and various types of crenulated schistosity. Additionally, the study documents the GBM-associated temperature range and provides insights into the activation of the Higher Himalayan Out-of-Sequence Thrust (OOST) in Himachal Pradesh. The findings of the study were obtained through geological field observations, microscopic studies, and strain analysis, offering valuable insights into the activation timing, mylonitization characteristics, and overprinting structures related to the Chaura Thrust and the broader tectonic framework of the region.

Keywords: Main Central Thrust, Jhakri Thrust, Chaura Thrust, Higher Himalaya, Out-of-Sequence Thrust, Sarahan Thrust

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Authors: Chen-Ya Juan

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In recent years, the increasing number of children with special needs has brought a lot of attention by many scholars and experts in education, which enforced the preschool teachers face the harsh challenge in the classroom. To protect the right of equal education for all children, enhance the quality of children learning, and take care of the needs of children with special needs, the special education paraprofessional becomes one of the future employment trends for students of the department of the early childhood care and education. Problem-based learning is a problem-oriented instruction, which is different from traditional instruction. The instructor first designed an ambiguous problem direction, following the basic knowledge of early intervention, students had to find clues to solve the problem defined by themselves. In the class, the total instruction included 20 hours, two hours per week. The primary purpose of this paper is to investigate the relationship of student academic scores, self-awareness, learning motivation, learning attitudes, and early intervention knowledge. A total of 105 college students participated in this study and 97 questionnaires were effective. The effective response rate was 90%. The student participants included 95 females and two males. The average age of the participants was 19 years old. The questionnaires included 125 questions divided into four major dimensions: (1) Self-awareness, (2) learning motivation, (3) learning attitudes, and (4) early intervention knowledge. The results indicated (1) the scores of self-awareness were 58%; the scores of the learning motivations was 64.9%; the scores of the learning attitudes was 55.3%. (2) After the instruction, the early intervention knowledge has been increased to 64.2% from 38.4%. (3) Student’s academic performance has positive relationship with self-awareness (p < 0.05; R = 0.506), learning motivation (p < 0.05; R = 0.487), learning attitudes (p < 0.05; R = 0.527). The results implied that although students had gained early intervention knowledge by using PBL instruction, students had medium scores on self-awareness and learning attitudes, medium high in learning motivations.

Keywords: college students, children with special needs, problem-based learning, learning motivation

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Authors: Abu Salim Mustafa

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Rv3873 is a relatively large size protein (371 amino acids in length) and its gene is located in the immunodominant genomic region of difference (RD)1 that is present in the genome of Mycobacterium tuberculosis but deleted from the genomes of all the vaccine strains of Bacillus Calmette Guerin (BCG) and most other mycobacteria. However, when tested for cellular immune responses using peripheral blood mononuclear cells from tuberculosis patients and BCG-vaccinated healthy subjects, this protein was found to be a major stimulator of cell mediated immune responses in both groups of subjects. In order to further identify the sequence of immunodominant epitopes and explore their Human Leukocyte Antigen (HLA)-restriction for epitope recognition, 24 peptides (25-mers overlapping with the neighboring peptides by 10 residues) covering the sequence of Rv3873 were synthesized chemically using fluorenylmethyloxycarbonyl chemistry and tested in cell mediated immune responses. The results of these experiments helped in the identification of an immunodominant peptide P9 that was recognized by people expressing varying HLA-DR types. Furthermore, it was also predicted to be a promiscuous binder with multiple epitopes for binding to HLA-DR, HLA-DP and HLA-DQ alleles of HLA-class II molecules that present antigens to T helper cells, and to HLA-class I molecules that present antigens to T cytotoxic cells. In addition, the evaluation of peptide P9 using an immunogenicity predictor server yielded a high score (0.94), which indicated a greater probability of this peptide to elicit a protective cellular immune response. In conclusion, P9, a peptide with multiple epitopes and ability to bind several HLA class I and class II molecules for presentation to cells of the cellular immune response, may be useful as a peptide-based vaccine against tuberculosis.

Keywords: mycobacterium tuberculosis, PPE68, peptides, vaccine

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Authors: Shantanu Prakash, Suruchi Shukla, Amita Jain

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Introduction: The hepatitis C virus (HCV) is a major public health problem and a leading cause of chronic liver disease. Injection drug use and individuals receiving blood and blood products are the primary modes of HCV transmission. Our study aims to establish the prevalent genotypes/ subtypes of HCV circulating in Uttar Pradesh, North India, as reported from a tertiary care hospital. Methods: It is a retrospective observational analysis of consecutive 404 HCV RNA positive cases referred to our hospital during September 2014 to April 2017. The study was approved by an institutional ethics committee. Written informed consent was taken from each participant. Clinical and demographic details of these patients were recorded using predesigned questionnaires. All the laboratory testing was carried on stored serum sample of enrolled cases. Genotyping of all 404 strains was done by Sanger’s sequencing of the core region. The phylogenetic analysis of 179 HCV strains with high -quality sequencing data was performed. Results: The distribution of prevalent genotypes/ subtypes as noted in the present study was; Genotype (GT)1a [n-101(25%)], GT1b [n-12(2.9%)], GT1c [1(0.25%)], GT3a [275(68.07%)], GT3b [9(2.2%)], GT3g [2(0.49%)], GT3i [3(0.74%)], and GT4a [1(0.24%)]. HCV genotypes GT2, GT5 and GT6 were not detected from our region. Sequence analysis showed high genotypic variability in HCV GT3. Phylogenetic analysis showed that HCV GT3 and GT1 circulating in our region were related to Indian strains reported earlier. Conclusions: HCV genotypes 3a and 1a are commonest circulating genotypes in Uttar Pradesh (UP), India.

Keywords: Hepatitis C virus, genetic variation, bioinformatics, genotype, HCV

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Authors: Abdon Choque-Rivero

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The Jacobi system with the Dirichlet boundary condition is considered on a half-line lattice when the coefficients are real valued. The inverse problem of recovery of the coefficients from various data sets containing the so-called transmission eigenvalues is analyzed. The Marchenko method is utilized to solve the corresponding inverse problem.

Keywords: inverse scattering, discrete system, transmission eigenvalues, Marchenko method

Procedia PDF Downloads 131

Authors: Elham Jelodari Mamaghani, Christian Prins, Haoxun Chen

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In this paper, there is concentration on collaborative transportation planning (CTP) among multiple carriers with pickup and delivery requests and time windows. This problem is a vehicle routing problem with constraints from standard vehicle routing problems and new constraints from a real-world application. In the problem, each carrier has a finite number of vehicles, and each request is a pickup and delivery request with time window. Moreover, each carrier has reserved requests, which must be served by itself, whereas its exchangeable requests can be outsourced to and served by other carriers. This collaboration among carriers can help them to reduce total transportation costs. A mixed integer programming model is proposed to the problem. To solve the model, a hybrid algorithm that combines Genetic Algorithm and Simulated Annealing (GASA) is proposed. This algorithm takes advantages of GASA at the same time. After tuning the parameters of the algorithm with the Taguchi method, the experiments are conducted and experimental results are provided for the hybrid algorithm. The results are compared with those obtained by a commercial solver. The comparison indicates that the GASA significantly outperforms the commercial solver.

Keywords: centralized collaborative transportation, collaborative transportation with pickup and delivery, collaborative transportation with time windows, hybrid algorithm of GA and SA

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Authors: Maryam Abata, Moulhime El Bekkali, Said Mazer, Catherine Algani, Mahmoud Mehdi

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One major problem of most electronic systems operating in the millimeter wave band is the signal generation with a high purity and a stable carrier frequency. This problem is overcome by using the combination of a signal with a low frequency local oscillator (LO) and several stages of frequency multipliers. The use of these frequency multipliers to create millimeter-wave signals is an attractive alternative to direct generation signal. Therefore, the isolation problem of the local oscillator from the other stages is always present, which leads to have various mechanisms that can disturb the oscillator performance, thus a buffer amplifier is often included in oscillator outputs. In this paper, we present the study and design of a buffer amplifier in the mm-wave band using a 0.15μm pHEMT from UMS foundry. This amplifier will be used as a part of a frequency quadrupler at 60 GHz.

Keywords: Mm-wave band, local oscillator, frequency quadrupler, buffer amplifier

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Authors: Purva Joshi, Rohit Thanki, Omar Hanif

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Unmanned aerial vehicles (UAVs) are becoming increasingly important in various industrial applications and sectors. Nowadays, a multi UAV network is used for specific types of communication (e.g., military) and monitoring purposes. Therefore, it is critical to reducing propagation delay during communication between UAVs, which is essential in a multi UAV network. This paper presents how the propagation delay between the base station (BS) and the UAVs is reduced using a searching algorithm. Furthermore, the iterative-based K-nearest neighbor (k-NN) algorithm and Travelling Salesmen Problem (TSP) algorthm were utilized to optimize the distance between BS and individual UAV to overcome the problem of propagation delay in multi UAV networks. The simulation results show that this proposed method reduced complexity, improved reliability, and reduced propagation delay in multi UAV networks.

Keywords: multi UAV network, optimal distance, propagation delay, K - nearest neighbor, traveling salesmen problem

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Authors: Salinee Thumronglaohapun

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The proper number and appropriate locations of service centers can save cost, raise revenue and gain more satisfaction from customers. Establishing service centers is high-cost and difficult to relocate. In long-term planning periods, several factors may affect the service. One of the most critical factors is uncertain demand of customers. The opened service centers need to be capable of serving customers and making a profit although the demand in each period is changed. In this work, the capacitated location-allocation problem with stochastic demand is considered. A mathematical model is formulated to determine suitable locations of service centers and their allocation to maximize total profit for multiple planning periods. Two heuristic methods, a local search and genetic algorithm, are used to solve this problem. For the local search, five different chances to choose each type of moves are applied. For the genetic algorithm, three different replacement strategies are considered. The results of applying each method to solve numerical examples are compared. Both methods reach to the same best found solution in most examples but the genetic algorithm provides better solutions in some cases.

Keywords: location-allocation problem, stochastic demand, local search, genetic algorithm

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Authors: Hesham Shaalan

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Senior design projects teach students many important skills. One of the major goals is to prepare students to apply effective problem-solving techniques to a problem that represents a real-world situation. This includes the ability to define the problem, compare alternative solutions, identify the best solution, and design the system. This paper describes the design of a shipboard power plant as a senior project in the Marine Engineering program at the U.S. Merchant Marine Academy. The design project was supervised by faculty members who guided a multidisciplinary group of seniors. The research project was sponsored by the Office of Naval Research. Each group of seniors focused on one of the main design aspects of the project, including the electric power system, nuclear power plant, ship hull design, and economics.

Keywords: senior design project, shipboard power system, engineering education, marine engineering

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Authors: Abdulkerim Ilgun, Ahmad Javid Zia

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In developing countries, the urban populations are increasing rapidly and with this increment the residential areas are experiencing major problems. Construction of high-rise buildings in confined spaces is one of the most practical solutions for this problem. However, by living in high-rise buildings and sharing common residential areas, residents will face many problems. Irritating sound problem which is known as noise is one of the major problems mentioned above. The second most important problem is the weight of the high-rise buildings which makes the structure more vulnerable to earthquakes. To decrease earthquake loads it’s very important to decrease the weight of the buildings. To solve the problem of noise and keep the building weight at minimum level, experimentally designed soundproof gypsum partition wall which has optimum thickness has been used in high-rise story building and the results have been compared with ordinary brick partition walls. In this compression the effect of weights of soundproof gypsum walls and ordinary brick walls in accordance to structural engineering have been investigated.

Keywords: cellubor, gypsum board, gypsum partition walls, light partition walls, noise, sound

Procedia PDF Downloads 296