Search results for: genomic analyses

Authors: Sara Muhammad Elqudah, Vigh László Gergely

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Catastrophic events, such as earthquakes, are sudden, short, and devastating, threatening lives, demolishing futures, and causing huge economic losses. Current seismic analyses and design standards are based on life safety levels where only some residual strength and stiffness are left in the structure leaving it beyond economical repair. Consequently, it has become necessary to introduce and implement the concept of resilient design. Resilient design is about designing for ductility over time by resisting, absorbing, and recovering from the effects of a hazard in an appropriate and efficient time manner while maintaining the functionality of the structure in the aftermath of the incident. Resilient analysis is mainly based on the fragility, vulnerability, and functionality curves where eventually a resilience index is generated from these curves, and the higher this index is, the better is the performance of the structure. In this paper, seismic performances of a simple two story reinforced concrete building, located in a moderate seismic region, has been evaluated using the conventional seismic analyses methods, which are the linear static analysis, the response spectrum analysis, and the pushover analysis, and the generated results of these analyses methods are compared to those of the resilient analysis. Results highlight that the resilience analysis was the most convenient method in generating a more ductile and functional structure from a socio-economic perspective, in comparison to the standard seismic analysis methods.

Keywords: conventional analysis methods, functionality, resilient analysis, seismic performance

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Authors: Isabela Moreira Queiroz

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Slope stability analyses are largely carried out by deterministic methods and evaluated through a single security factor. Although it is known that the geotechnical parameters can present great dispersal, such analyses are considered fixed and known. The probabilistic methods, in turn, incorporate the variability of input key parameters (random variables), resulting in a range of values of safety factors, thus enabling the determination of the probability of failure, which is an essential parameter in the calculation of the risk (probability multiplied by the consequence of the event). Among the probabilistic methods, there are three frequently used methods in geotechnical society: FOSM (First-Order, Second-Moment), Rosenblueth (Point Estimates) and Monte Carlo. This paper presents a comparison between the results from deterministic and probabilistic analyses (FOSM method, Monte Carlo and Rosenblueth) applied to a hypothetical slope. The end was held to evaluate the behavior of the slope and consequent risk analysis, which is used to calculate the risk and analyze their mitigation and control solutions. It can be observed that the results obtained by the three probabilistic methods were quite close. It should be noticed that the calculation of the risk makes it possible to list the priority to the implementation of mitigation measures. Therefore, it is recommended to do a good assessment of the geological-geotechnical model incorporating the uncertainty in viability, design, construction, operation and closure by means of risk management. 

Keywords: probabilistic methods, risk assessment, risk management, slope stability

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Authors: Alsu F. Saifitdinova, Alexey S. Komissarov, Svetlana A. Galkina, Elena I. Koshel, Maria M. Kulak, Stephen J. O'Brien, Elena R. Gaginskaya

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The mystery of sex determination is one of the most ancient and still not solved until the end so far. In many species, sex determination is genetic and often accompanied by the presence of dimorphic sex chromosomes in the karyotype. Genomic sequencing gave the information about the gene content of sex chromosomes which allowed to reveal their origin from ordinary autosomes and to trace their evolutionary history. Female-specific W chromosome in birds as well as mammalian male-specific Y chromosome is characterized by the degeneration of gene content and the accumulation of repetitive DNA. Tandem repeats complicate the analysis of genomic data. Despite the best efforts chicken W chromosome assembly includes only 1.2 Mb from expected 55 Mb. Supplementing the information on the sex chromosome composition not only helps to complete the assembly of genomes but also moves us in the direction of understanding of the sex-determination systems evolution. A whole-genome survey to the assembly Gallus_gallus WASHUC 2.60 was applied for repeats search in assembled genome and performed search and assembly of high copy number repeats in unassembled reads of SRR867748 short reads datasets. For cytogenetic analysis conventional methods of fluorescent in situ hybridization was used for previously cloned W specific satellites and specifically designed directly labeled synthetic oligonucleotide DNA probe was used for bioinformatically identified repetitive sequence. Hybridization was performed with mitotic chicken chromosomes and manually isolated giant meiotic lampbrush chromosomes from growing oocytes. A novel chicken W specific satellite (GGAAA)n which is not co-localizes with any previously described classes of W specific repeats was identified and mapped with high resolution. In the composition of autosomes this repeat units was found as a part of upstream regions of gonad specific protein coding sequences. These findings may contribute to the understanding of the role of tandem repeats in sex specific differentiation regulation in birds and sex chromosome evolution. This work was supported by the postdoctoral fellowships from St. Petersburg State University (#1.50.1623.2013 and #1.50.1043.2014), the grant for Leading Scientific Schools (#3553.2014.4) and the grant from Russian foundation for basic researches (#15-04-05684). The equipment and software of Research Resource Center “Chromas” and Theodosius Dobzhansky Center for Genome Bioinformatics of Saint Petersburg State University were used.

Keywords: birds, lampbrush chromosomes, sex chromosomes, tandem repeats

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Authors: Matthew Baucum

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With the increasing popularity of fMRI as an experimental method, psychology and neuroscience can greatly benefit from advanced techniques for summarizing and synthesizing large amounts of data from brain imaging studies. One promising avenue is automated meta-analyses, in which natural language processing methods are used to identify the brain regions consistently associated with certain semantic concepts (e.g. “social”, “reward’) across large corpora of studies. This study builds on this approach by demonstrating how, in fMRI meta-analyses, individual voxels can be treated as vectors in a semantic space and evaluated for their “proximity” to terms of interest. In this technique, a low-dimensional semantic space is built from brain imaging study texts, allowing words in each text to be represented as vectors (where words that frequently appear together are near each other in the semantic space). Consequently, each voxel in a brain mask can be represented as a normalized vector sum of all of the words in the studies that showed activation in that voxel. The entire brain mask can then be visualized in terms of each voxel’s proximity to a given term of interest (e.g., “vision”, “decision making”) or collection of terms (e.g., “theory of mind”, “social”, “agent”), as measured by the cosine similarity between the voxel’s vector and the term vector (or the average of multiple term vectors). Analysis can also proceed in the opposite direction, allowing word cloud visualizations of the nearest semantic neighbors for a given brain region. This approach allows for continuous, fine-grained metrics of voxel-term associations, and relies on state-of-the-art “open vocabulary” methods that go beyond mere word-counts. An analysis of over 11,000 neuroimaging studies from an existing meta-analytic fMRI database demonstrates that this technique can be used to recover known neural bases for multiple psychological functions, suggesting this method’s utility for efficient, high-level meta-analyses of localized brain function. While automated text analytic methods are no replacement for deliberate, manual meta-analyses, they seem to show promise for the efficient aggregation of large bodies of scientific knowledge, at least on a relatively general level.

Keywords: FMRI, machine learning, meta-analysis, text analysis

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Authors: Seyedeh Khadijeh Amirian, Seyed Mohammad Reza Amirian, Narges Hekmati

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The current study aims at examining the relationship between English as a foreign language (EFL) students' self-concept and their willingness to communicate (WTC) in EFL classes. To this effect, two questionnaires, namely 'Willingness to Communicate' (MacIntyre et al., 2001) and 'Self-Concept Scale' (Liu and Wang, 2005), were distributed among 174 (45 males and 129 females) Iranian EFL university students. Correlation and regression analyses were conducted to examine the relationship between the two variables. The results indicated that there was a significantly positive correlation between EFL students' self-concept and their WTC in EFL classes (p < .0.05). Moreover, regression analyses indicated that self-concept has a significantly positive influence on students’ WTC in language classes (B= .302, p < .0.05) and explains .302 percent of the variance in the dependent variable (WTC). The results are discussed with regards to the individual differences in educational contexts, and implications are offered.

Keywords: EFL students, language classes, willingness to communicate, self-concept

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Authors: Hadeel Abdulatif, Maha Alkhaffaf

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E-government is the use of Information and Communication Technology to enrich the access to and delivery of government services to citizens, business partners and employees, Policy makers and regulatory bodies have to be cognizant of the degree of readiness of a populace in order to design and implement efficient e-government programs. This paper aims to provide a transparent situation analyses for the case of e-government official website in Jordan, it focuses on assessing e-government in Jordan; web site assessment by using international criteria for assessing e-government websites, However, the study analyses the environmental factor consisting of cultural and business environment factors. By reviewing the literature the researchers found that government's efforts towards e-government may vary according to the country's readiness and other key implementation factors which will lead to diverse e-government experience; thus, there is a need to study the impact of key factors to implement e-government in Jordan.

Keywords: e-government, environmental factors, website assessment, readiness

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Authors: Philna Coetzee, Clara Msiza

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In modern society, audit committees are seen as the custodians of accountability and the conscience of management and the board. But who holds the audit committee accountable for their actions or non-actions and how do we know what they are supposed to be doing and what they are doing? The purpose of this article is to provide greater insight into the latter part of this problem, namely, determine what best practises for audit committees and the disclosure of what is the realities are. In countries where governance is well established, the roles and responsibilities of the audit committee are mostly clearly guided by legislation and/or guidance documents, with countries increasingly providing guidance on this topic. With high cost involved to adhere to governance guidelines, the public (for public organisations) and shareholders (for private organisations) expect to see the value of their ‘investment’. For audit committees, the dividends on the investment should reflect in less fraudulent activities, less corruption, higher efficiency and effectiveness, improved social and environmental impact, and increased profits, to name a few. If this is not the case (which is reflected in the number of fraudulent activities in both the private and the public sector), stakeholders have the right to ask: where was the audit committee? Therefore, the objective of this article is to contribute to the body of knowledge by comparing the adherence of audit committee to best practices guidelines as stipulated in the King Report across public listed companies, national and provincial government departments, state-owned enterprises and local municipalities. After constructs were formed, based on the literature, factor analyses were conducted to reduce the number of variables in each construct. Thereafter, cluster analyses, which is an explorative analysis technique that classifies a set of objects in such a way that objects that are more similar are grouped into the same group, were conducted. The SPSS TwoStep Clustering Component was used, being capable of handling both continuous and categorical variables. In the first step, a pre-clustering procedure clusters the objects into small sub-clusters, after which it clusters these sub-clusters into the desired number of clusters. The cluster analyses were conducted for each construct and the measure, namely the audit opinion as listed in the external audit report, were included. Analysing 228 organisations' information, the results indicate that there is a clear distinction between the four spheres of business that has been included in the analyses, indicating certain strengths and certain weaknesses within each sphere. The results may provide the overseers of audit committees’ insight into where a specific sector’s strengths and weaknesses lie. Audit committee chairs will be able to improve the areas where their audit committee is lacking behind. The strengthening of audit committees should result in an improvement of the accountability of boards, leading to less fraud and corruption.

Keywords: audit committee disclosure, cluster analyses, governance best practices, strengths and weaknesses

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Authors: Lokesh Harshe

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The building construction sector is using 36% of global energy consumption with 39% of CO₂ emission. Professionals in the Built Environment Sector have long been aware of the industry’s contribution towards CO₂ emissions and are now moving towards more sustainable practices. As a result of this, many organizations have introduced rating systems to address the issue of global warming in the construction sector by ranking construction projects based on sustainability parameters. The pre-construction phase of any building project is the most essential time to make decisions for addressing the sustainability aspects. Traditionally, it is very difficult to collect data from different stakeholders and bring it together to form a decision based on factual data to perform sustainability analyses in the pre-construction phase. Building Information Modelling (BIM) is the solution where one single model is the result of the collaborative approach of BIM processes where all the information is shared, extracted, communicated, and stored on a single platform that everyone can access and make decisions based on real-time data. The focus of this research is on the Indian Green Rating System IGBC® with the objective of understanding IGBC® requirements and developing a framework to create the relationship between the rating processes and BIM. A Hypothetical (Architectural) model of a hostel building is developed using AutoCAD 2019 & Revit Arch. 2019, where the framework is applied to generate results on sustainability analysis using Green Building Studio (GBS) and Revit Add-ins. The results of any sustainability analysis are generated within a fraction of a minute, which is very quick in comparison with traditional sustainability analysis. This may save a considerable amount of time as well as cost. The future scope is to integrate Architectural, Structural, and MEP Models to perform accurate sustainability analyses with inputs from industry professionals working on real-life Green BIM projects.

Keywords: sustainability analyses, BIM, green rating systems, IGBC®, LEED

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Authors: Yeo Kyeong Lee, Hae Won Min, Ji Yeon Kang, Hee Sun Kim, Yeong Soo Shin

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Fire incidents have been steadily increased over the last year according to national emergency management agency of South Korea. Even though most of the fire incidents with property damage have been occurred in building, rehabilitation has not been properly done with consideration of structure safety. Therefore, this study aims at evaluating rehabilitation effects on fire damaged normal strength concrete beams through experiments and finite element analyses. For the experiments, reinforced concrete beams were fabricated having designed concrete strength of 21 MPa. Two different cover thicknesses were used as 40 mm and 50 mm. After cured, the fabricated beams were heated for 1hour or 2hours according to ISO-834 standard time-temperature curve. Rehabilitation was done by removing the damaged part of cover thickness and filling polymeric mortar into the removed part. Both fire damaged beams and rehabilitated beams were tested with four point loading system to observe structural behaviors and the rehabilitation effect. To verify the experiment, finite element (FE) models for structural analysis were generated using commercial software ABAQUS 6.10-3. For the rehabilitated beam models, integrated temperature-structural analyses were performed in advance to obtain geometries of the fire damaged beams. In addition to the fire damaged beam models, rehabilitated part was added with material properties of polymeric mortar. Three dimensional continuum brick elements were used for both temperature and structural analyses. The same loading and boundary conditions as experiments were implemented to the rehabilitated beam models and non-linear geometrical analyses were performed. Test results showed that maximum loads of the rehabilitated beams were 8~10% higher than those of the non-rehabilitated beams and even 1~6 % higher than those of the non-fire damaged beam. Stiffness of the rehabilitated beams were also larger than that of non-rehabilitated beams but smaller than that of the non-fire damaged beams. In addition, predicted structural behaviors from the analyses also showed good rehabilitation effect and the predicted load-deflection curves were similar to the experimental results. From this study, both experiments and analytical results demonstrated good rehabilitation effect on the fire damaged normal strength concrete beams. For the further, the proposed analytical method can be used to predict structural behaviors of rehabilitated and fire damaged concrete beams accurately without suffering from time and cost consuming experimental process.

Keywords: fire, normal strength concrete, rehabilitation, reinforced concrete beam

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Authors: Ahmad Idi

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The biosynthesis and properties of polyhydroxyalkanoate (PHA) are determined by the bacterial strain and the culture condition. Hence this study elucidates the structure and properties of PHA produced by a newly isolated strain of photosynthetic bacterium, Rhodobacter sphaeroides ADZ101 grown under the optimized culture condition. The properties of the accumulated PHA were determined via FTIR, NMR, TGA, and GCMS analyses. The results showed that acetate and ammonia chloride had the highest PHA accumulation with a ratio of 32.5 mM at neutral pH. The structural analyses showed that the polymer comprises both short and medium-chain length monomers ranging from C5, C13, C14, and C18, as well as the presence of novel PHA monomers. The thermal analysis revealed that the maximum temperature of decomposition occurred at 395°C and 454°C, indicating two major decomposition reactions. Thus this bacterial strain, optimized culture condition, and the abundance of novel monomers enhanced the thermostability of the accumulated PHA.

Keywords: bioplastic polyhydroxyalkanoates Rhodobacter sphaeroides ADZ101 thermostable PHA

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Authors: Juha Kettunen

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This study analyzes the quality and the size of the strategic network of higher education institutions. The study analyses the concept of fitness for purpose in quality assurance. It also analyses the transaction costs of networking that have consequences on the number of members in the network. Empirical evidence is presented of the Consortium on Applied Research and Professional Education, which is a European strategic network of six higher education institutions. The results of the study support the argument that the number of members in the strategic network should be relatively small to provide high quality results. The practical importance is that networking has been able to promote international research and development projects. The results of this study are important for those who want to design and improve international networks in higher education.

Keywords: balanced scorecard, higher education, social networking, strategic planning

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Authors: Clara Tramuta, Floris Irene, Daniela Manila Bianchi, Monica Pitti, Giulia Federica Cazzaniga, Lucia Decastelli

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This work presents the results obtained by the Regional Reference Centre for Salmonella Typing (CeRTiS) in a retrospective study aimed to investigate, through Pulsed-field Gel Electrophoresis (PFGE) analysis, the genetic relatedness of emerging Salmonella serotypes of human origin circulating in North-West of Italy. Furthermore, the goal of this work was to create a Regional database to facilitate foodborne outbreak investigation and to monitor them at an earlier stage. A total of 112 strains, isolated from 2016 to 2018 in hospital laboratories, were included in this study. The isolates were previously identified as Salmonella according to standard microbiological techniques and serotyping was performed according to ISO 6579-3 and the Kaufmann-White scheme using O and H antisera (Statens Serum Institut®). All strains were characterized by PFGE: analysis was conducted according to a standardized PulseNet protocol. The restriction enzyme XbaI was used to generate several distinguishable genomic fragments on the agarose gel. PFGE was performed on a CHEF Mapper system, separating large fragments and generating comparable genetic patterns. The agarose gel was then stained with GelRed® and photographed under ultraviolet transillumination. The PFGE patterns obtained from the 112 strains were compared using Bionumerics version 7.6 software with the Dice coefficient with 2% band tolerance and 2% optimization. For each serotype, the data obtained with the PFGE were compared according to the geographical origin and the year in which they were isolated. Salmonella strains were identified as follow: S. Derby n. 34; S. Infantis n. 38; S. Napoli n. 40. All the isolates had appreciable restricted digestion patterns ranging from approximately 40 to 1100 kb. In general, a fairly heterogeneous distribution of pulsotypes has emerged in the different provinces. Cluster analysis indicated high genetic similarity (≥ 83%) among strains of S. Derby (n. 30; 88%), S. Infantis (n. 36; 95%) and S. Napoli (n. 38; 95%) circulating in north-western Italy. The study underlines the genomic similarities shared by the emerging Salmonella strains in Northwest Italy and allowed to create a database to detect outbreaks in an early stage. Therefore, the results confirmed that PFGE is a powerful and discriminatory tool to investigate the genetic relationships among strains in order to monitoring and control Salmonellosis outbreak spread. Pulsed-field gel electrophoresis (PFGE) still represents one of the most suitable approaches to characterize strains, in particular for the laboratories for which NGS techniques are not available.

Keywords: emerging Salmonella serotypes, genetic characterization, human strains, PFGE

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Authors: Priscila A. Bernardes, Marcos E. Buzanskas, Luciana C. A. Regitano, Ricardo V. Ventura, Danisio P. Munari

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Genotype imputation has been used to reduce genomic selections costs. In order to increase haplotype detection accuracy in methods that considers the linkage disequilibrium, another approach could be used, such as combined genotype data from different panels. Therefore, this study aimed to evaluate the linkage disequilibrium and haplotype blocks in two high-density panels before and after the imputation to a combined panel in Nelore beef cattle. A total of 814 animals were genotyped with the Illumina BovineHD BeadChip (IHD), wherein 93 animals (23 bulls and 70 progenies) were also genotyped with the Affymetrix Axion Genome-Wide BOS 1 Array Plate (AHD). After the quality control, 809 IHD animals (509,107 SNPs) and 93 AHD (427,875 SNPs) remained for analyses. The combined genotype panel (CP) was constructed by merging both panels after quality control, resulting in 880,336 SNPs. Imputation analysis was conducted using software FImpute v.2.2b. The reference (CP) and target (IHD) populations consisted of 23 bulls and 786 animals, respectively. The linkage disequilibrium and haplotype blocks studies were carried out for IHD, AHD, and imputed CP. Two linkage disequilibrium measures were considered; the correlation coefficient between alleles from two loci (r²) and the |D’|. Both measures were calculated using the software PLINK. The haplotypes' blocks were estimated using the software Haploview. The r² measurement presented different decay when compared to |D’|, wherein AHD and IHD had almost the same decay. For r², even with possible overestimation by the sample size for AHD (93 animals), the IHD presented higher values when compared to AHD for shorter distances, but with the increase of distance, both panels presented similar values. The r² measurement is influenced by the minor allele frequency of the pair of SNPs, which can cause the observed difference comparing the r² decay and |D’| decay. As a sum of the combinations between Illumina and Affymetrix panels, the CP presented a decay equivalent to a mean of these combinations. The estimated haplotype blocks detected for IHD, AHD, and CP were 84,529, 63,967, and 140,336, respectively. The IHD were composed by haplotype blocks with mean of 137.70 ± 219.05kb, the AHD with mean of 102.10kb ± 155.47, and the CP with mean of 107.10kb ± 169.14. The majority of the haplotype blocks of these three panels were composed by less than 10 SNPs, with only 3,882 (IHD), 193 (AHD) and 8,462 (CP) haplotype blocks composed by 10 SNPs or more. There was an increase in the number of chromosomes covered with long haplotypes when CP was used as well as an increase in haplotype coverage for short chromosomes (23-29), which can contribute for studies that explore haplotype blocks. In general, using CP could be an alternative to increase density and number of haplotype blocks, increasing the probability to obtain a marker close to a quantitative trait loci of interest.

Keywords: Bos taurus indicus, decay, genotype imputation, single nucleotide polymorphism

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Authors: Aleksandra Majchrzak, Katarzyna Baruch, Monika Sobolewska, Bartlomiej Chojnacki, Adam Pilch

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Scaled modeling is very common in the areas of science such as aerodynamics or fluid mechanics, since defining characteristic numbers enables to determine relations between objects under test and their models. In acoustics, scaled modeling is aimed mainly at investigation of room acoustics, sound insulation and sound absorption phenomena. Despite such a range of application, there is no method developed that would enable scaling acoustical perforated panels freely, maintaining their sound absorption coefficient in a desired frequency range. However, conducted theoretical and numerical analyses have proven that it is not physically possible to obtain given sound absorption coefficient in a desired frequency range by directly scaling only all of the physical dimensions of a perforated panel, according to a defined characteristic number. This paper is a continuation of the research mentioned above and presents practical evaluation of theoretical and numerical analyses. The measurements of sound absorption coefficient of perforated panels were performed in order to verify previous analyses and as a result find the relations between full-scale perforated panels and their models which will enable to scale them properly. The measurements were conducted in a one-to-eight model of a reverberation chamber of Technical Acoustics Laboratory, AGH. Obtained results verify theses proposed after theoretical and numerical analyses. Finding the relations between full-scale and modeled perforated panels will allow to produce measurement samples equivalent to the original ones. As a consequence, it will make the process of designing acoustical perforated panels easier and will also lower the costs of prototypes production. Having this knowledge, it will be possible to emulate in a constructed model panels used, or to be used, in a full-scale room more precisely and as a result imitate or predict the acoustics of a modeled space more accurately.

Keywords: characteristic numbers, dimensional analysis, model study, scaled modeling, sound absorption coefficient

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Authors: Gurpreet Singh, Hazoor Singh, Buta Singh Sidhu

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In the current investigation plasma spray technique was used for depositing hydroxyapatite (HA) and HA – silicon oxide (SiO2) coatings on 316L SS substrate. In HA-SiO2 coating, 20 wt% SiO2 was mixed with HA. The feedstock and coatings were characterized by X-ray diffraction (XRD) and scanning electron microscopy (SEM)/energy-dispersive X-ray spectroscopy (EDX) analyses. The corrosion resistance of the uncoated, HA coated and HA + 20 wt% SiO2 coated 316L SS was investigated by electrochemical corrosion testing in simulated human body fluid (Ringer’s solution). The influence of SiO2 (20 wt%) on corrosion resistance was determined. After the corrosion testing, the samples were analyzed by XRD and SEM/EDX analyses. The addition of SiO2 reduces the crystallinity of the coating. The corrosion resistance of the 316L SS was found to increase after the deposition of the HA + 20 wt% SiO2 and HA coatings.

Keywords: HA, SiO2, corrosion, Ringer’s solution, 316L SS

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Authors: Won Mog Choi, Seong Kyeong Hong, Seok Young Jeong

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The stress on the buried pipeline under pavement is significantly affected by vehicle loads and elastic modulus of the soil surrounding the pipeline. The correct elastic modulus of soil has to be applied to the finite element model to investigate the effect of the vehicle loads on the buried pipeline using finite element analysis. The purpose of this study is to establish the approach to calculating the correct elastic modulus of soil using the optimization process. The optimal elastic modulus of soil, which minimizes the difference between the strain measured from vehicle driving test at the velocity of 35km/h and the strain calculated from finite element analyses, was calculated through the optimization process using multi-response surface methodology. Three elastic moduli of soil (road layer, original soil, dense sand) surrounding the pipeline were defined as the variables for the optimization. Further analyses with the optimal elastic modulus at the velocities of 4.27km/h, 15.47km/h, 24.18km/h were performed and compared to the test results to verify the applicability of multi-response surface methodology. The results indicated that the strain of the buried pipeline was mostly affected by the elastic modulus of original soil, followed by the dense sand and the load layer, as well as the results of further analyses with optimal elastic modulus of soil show good agreement with the test.

Keywords: pipeline, optimization, elastic modulus of soil, response surface methodology

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Authors: Davod Ahmadi, Narges Ebadi, Ethan Wang, Hugo Melgar-Quiñonez

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Compared to the other Least Developed Countries (LDCs), major countries in sub-Saharan Africa (SSA) have limited access to the clean water. People in this region, and more specifically females, suffer from acute water scarcity problems. They are compelled to spend too much of their time bringing water for domestic use like drinking and washing. Apart from domestic use, water through affecting agriculture and livestock contributes to the food security status of people in vulnerable regions like SSA. Livestock needs water to grow, and agriculture requires enormous quantities of water for irrigation. The main objective of this study is to explore the association between access to water and individuals’ food security status. Data from 2017 Gallup World Poll (GWP) for SSA were analyzed (n=35,000). The target population in GWP is the entire civilian, non-institutionalized, aged 15 and older population. All samples selection is probability based and nationally representative. The Gallup surveys an average of 1,000 samples of individuals per country. Three questions related to water (i.e., water quality, availability of water for crops and availability of water for livestock) were used as the exposure variables. Food Insecurity Experience Scale (FIES) was used as the outcome variable. FIES measures individuals’ food security status, and it is composed of eight questions with simple dichotomous responses (1=Yes and 0=No). Different statistical analyses such as descriptive, crosstabs and binary logistic regression, form the basis of this study. Results from descriptive analyses showed that more than 50% of the respondents had no access to enough water for crops and livestock. More than 85% of respondents were categorized as “food insecure”. Findings from cross-tabulation analyses showed that food security status was significantly associated with water quality (0.135; P=0.000), water for crops (0.106; P=0.000) and water for livestock (0.112; P=0.000). In regression analyses, the probability of being food insecure increased among people who expressed no satisfaction with water quality (OR=1.884 (OR=1.768-2.008)), not enough water for crops (OR=1.721 (1.616-1.834)) and not enough water for livestock (OR=1.706 (1.819)). In conclusion, it should note that water access affects food security status in SSA.

Keywords: water access, agriculture, livestock, FIES

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Authors: Atif Zafar, Fan Haijun

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A sequence of different Reservoir Engineering methods and tools in reservoir characterization and field development are presented in this paper. The real data of Jin Gas Field of L-Basin of Pakistan is used. The basic concept behind this work is to enlighten the importance of well test analysis in a broader way (i.e. reservoir characterization and field development) unlike to just determine the permeability and skin parameters. Normally in the case of reservoir characterization we rely on well test analysis to some extent but for field development plan, the well test analysis has become a forgotten tool specifically for locations of new development wells. This paper describes the successful implementation of well test analysis in Jin Gas Field where the main uncertainties are identified during initial stage of field development when location of new development well was marked only on the basis of G&G (Geologic and Geophysical) data. The seismic interpretation could not encounter one of the boundary (fault, sub-seismic fault, heterogeneity) near the main and only producing well of Jin Gas Field whereas the results of the model from the well test analysis played a very crucial rule in order to propose the location of second well of the newly discovered field. The results from different methods of well test analysis of Jin Gas Field are also integrated with and supported by other tools of Reservoir Engineering i.e. Material Balance Method and Volumetric Method. In this way, a comprehensive way out and algorithm is obtained in order to integrate the well test analyses with Geological and Geophysical analyses for reservoir characterization and field development. On the strong basis of this working and algorithm, it was successfully evaluated that the proposed location of new development well was not justified and it must be somewhere else except South direction.

Keywords: field development plan, reservoir characterization, reservoir engineering, well test analysis

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Authors: Umut Yıldız, Berkin Kurtuluş, Yunus Emre Muslubaş

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Thrust vectoring, especially in military aviation, is a concept that sees much use to improve maneuverability in already agile aircraft. As this concept is fairly new and cost intensive to design and test, computational methods are useful in easing the preliminary design process. Computational Fluid Dynamics (CFD) can be utilized in many forms to simulate nozzle flow, and there exist various CFD studies in both 2D mechanical and 3D injection based thrust vectoring, and yet, 3D mechanical thrust vectoring analyses, at this point in time, are lacking variety. Additionally, the freely available test data is constrained to limited pitch angles and geometries. In this study, based on a test case provided by NASA, both steady and unsteady 3D CFD simulations are conducted to examine the aerodynamic performance of a mechanical thrust vectoring nozzle model and to validate the utilized numerical model. Steady analyses are performed to verify the flow characteristics of the nozzle at pitch angles of 0, 10 and 20 degrees, and the results are compared with experimental data. It is observed that the pressure data obtained on the inner surface of the nozzle at each specified pitch angle and under different flow conditions with pressure ratios of 1.5, 2 and 4, as well as at azimuthal angle of 0, 45, 90, 135, and 180 degrees exhibited a high level of agreement with the corresponding experimental results. To validate the CFD model, the insights from the steady analyses are utilized, followed by unsteady analyses covering a wide range of pitch angles from 0 to 20 degrees. Throughout the simulations, a mesh morphing method using a carefully calculated mathematical shape deformation model that simulates the vectored nozzle shape exactly at each point of its travel is employed to dynamically alter the divergent part of the nozzle over time within this pitch angle range. The mesh morphing based vectored nozzle shapes were compared with the drawings provided by NASA, ensuring a complete match was achieved. This computational approach allowed for the creation of a comprehensive database of results without the need to generate separate solution domains. The database contains results at every 0.01° increment of nozzle pitch angle. The unsteady analyses, generated using the morphing method, are found to be in excellent agreement with experimental data, further confirming the accuracy of the CFD model.

Keywords: thrust vectoring, computational fluid dynamics, 3d mesh morphing, mathematical shape deformation model

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Authors: Iman Atighi, Jalal Soleimannejad, Reza Pourjafarabadi, Saeid Moradpour

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In the past, we could increase profit by increasing product prices. But in the new decade, a competitive market does not let us to increase profit with increased prices. Therefore, the only way to increase profit will be to reduce costs. A significant percentage of production costs are the maintenance costs, and analysis of these costs could achieve more profit. Most maintenance strategies such as RCM (Reliability-Center-Maintenance), TPM (Total Productivity Maintenance), PM (Preventive Maintenance) and etc., are trying to reduce maintenance costs. In this paper, decreasing the maintenance costs of Concentration Plant of Golgohar Iron Ore Mining & Industrial Company (GeG) was examined by using of MTBF (Mean Time Between Failures) and MTTR (Mean Time To Repair) analyses. These analyses showed that instead of buying new machines and increasing costs in order to promote capacity, the improving of MTBF and MTTR indexes would solve capacity problems in the best way and decrease costs.

Keywords: GeG company, maintainability, maintenance costs, reliability-center-maintenance

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Authors: Mahya Naghipoor

Abstract:

Purpose: Non-small cell lung cancer (NSCLC) is the most common lung cancer type. Epidermal growth factor receptor (EGFR) mutation is the main reason which causes NSCLC. Computed tomography (CT) is used for diagnosis and prognosis of lung cancers because of low price and little invasion. Semantic analyses of qualitative CT features are based on visual evaluation by radiologist. However, the naked eye ability may not assess all image features. On the other hand, radiomics provides the opportunity of quantitative analyses for CT images features. The aim of this review study was comparing accuracy of semantic and radiomics features in prognosis of EGFR mutation in NSCLC. Methods: For this purpose, the keywords including: non-small cell lung cancer, epidermal growth factor receptor mutation, semantic, radiomics, feature, receiver operating characteristics curve (ROC) and area under curve (AUC) were searched in PubMed and Google Scholar. Totally 29 papers were reviewed and the AUC of ROC analyses for semantic and radiomics features were compared. Results: The results showed that the reported AUC amounts for semantic features (ground glass opacity, shape, margins, lesion density and presence or absence of air bronchogram, emphysema and pleural effusion) were %41-%79. For radiomics features (kurtosis, skewness, entropy, texture, standard deviation (SD) and wavelet) the AUC values were found %50-%86. Conclusions: In conclusion, the accuracy of radiomics analysis is a little higher than semantic in prognosis of EGFR mutation in NSCLC.

Keywords: lung cancer, radiomics, computer tomography, mutation

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Authors: W. S. Thulasitha, N. Umasuthan, G. I. Godahewa, Jehee Lee

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In fish, innate immune defense is the first immune response against microbial pathogens which consists of several antimicrobial components. Galectins are one of the carbohydrate binding lectins that have the ability to identify pathogen by recognition of pathogen associated molecular patterns. Galectins play a vital role in the regulation of innate and adaptive immune responses. Rock bream Oplegnathus fasciatus is one of the most important cultured species in Korea and Japan. Considering the losses due to microbial pathogens, present study was carried out to understand the molecular and functional characteristics of a galectin in normal and pathogenic conditions, which could help to establish an understanding about immunological components of rock bream. Complete cDNA of rock bream galectin like protein B (rbGal like B) was identified from the cDNA library, and the in silico analysis was carried out using bioinformatic tools. Genomic structure was derived from the BAC library by sequencing a specific clone and using Spidey. Full length of rbGal like B (contig14775) cDNA containing 517 nucleotides was identified from the cDNA library which comprised of 435 bp in the open reading frame encoding a deduced protein composed of 145 amino acids. The molecular mass of putative protein was predicted as 16.14 kDa with an isoelectric point of 8.55. A characteristic conserved galactose binding domain was located from 12 to 145 amino acids. Genomic structure of rbGal like B consisted of 4 exons and 3 introns. Moreover, pairwise alignment showed that rock bream rbGal like B shares highest similarity (95.9 %) and identity (91 %) with Takifugu rubripes galectin related protein B like and lowest similarity (55.5 %) and identity (32.4 %) with Homo sapiens. Multiple sequence alignment demonstrated that the galectin related protein B was conserved among vertebrates. A phylogenetic analysis revealed that rbGal like B protein clustered together with other fish homologs in fish clade. It showed closer evolutionary link with Takifugu rubripes. Tissue distribution and expression patterns of rbGal like B upon immune challenges were performed using qRT-PCR assays. Among all tested tissues, level of rbGal like B expression was significantly high in gill tissue followed by kidney, intestine, heart and spleen. Upon immune challenges, it showed an up-regulated pattern of expression with Edwardsiella tarda, rock bream irido virus and poly I:C up to 6 h post injection and up to 24 h with LPS. However, In the presence of Streptococcus iniae rbGal like B showed an up and down pattern of expression with the peak at 6 - 12 h. Results from the present study revealed the phylogenetic position and role of rbGal like B in response to microbial infection in rock bream.

Keywords: galectin like protein B, immune response, Oplegnathus fasciatus, molecular characterization

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Authors: Amna Abdalla Mohammed Khalid, Pietro Parisse, Silvia Onesti, Loredana Casalis

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Basic cellular processes as DNA replication are crucial to cell life. Understanding at the molecular level the mechanisms that govern DNA replication in proliferating cells is fundamental to understand disease connected to genomic instabilities, as a genetic disease and cancer. A key step for DNA replication to take place, is unwinding the DNA double helix and this carried out by proteins called helicases. The archaeal MCM (minichromosome maintenance) complex from Methanothermobacter thermautotrophicus have being studied using Atomic Force Microscopy (AFM), imaging in air and liquid (Physiological environment). The accurate analysis of AFM topographic images allowed to understand the static conformations as well the interaction dynamic of MCM and DNA double helix in the present of ATP.

Keywords: DNA, protein-DNA interaction, MCM (mini chromosome manteinance) complex, atomic force microscopy (AFM)

Procedia PDF Downloads 284

Authors: Johnson Okoduwa Imumbhon, Mohammad Didarul Alam, Yiding Cao

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Structural analyses are commonly employed to test the integrity of aircraft component systems in the design stage to demonstrate the capability of the structural components to withstand what it was designed for, as well as to predict potential failure of the components. The analyses are also essential for weight minimization and selecting the most resilient materials that will provide optimal outcomes. This research focuses on testing the structural nature of a high-lift low Reynolds number airfoil profile design, the Selig S1223, under certain loading conditions for a drone model application. The wing (ribs, spars, and skin) of the drone model was made of carbon fiber-reinforced polymer and designed in SolidWorks, while the finite element analysis was carried out in ANSYS mechanical in conjunction with the lift and drag forces that were derived from the aerodynamic airfoil analysis. Additionally, modal analysis was performed to calculate the natural frequencies and the mode shapes of the wing structure. The structural strain and stress determined the minimal deformations under the wing loading conditions, and the modal analysis showed the prominent modes that were excited by the given forces. The research findings from the structural analysis of the S1223 high-lift airfoil indicated that it is applicable for use in an unmanned aerial vehicle as well as a novel reciprocating-airfoil-driven vertical take-off and landing (VTOL) drone model.

Keywords: CFRP, finite element analysis, high-lift, S1223, strain, stress, VTOL

Procedia PDF Downloads 186

Authors: Soo Dong Cho, In-Ohk Ouh, Byeong Sul Kang, Seyeon Park, In-Soo Cho, Jae Young Song

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An VP2 gene from the current prevalent CPV (Canine Parvovirus) strain (new CPV-2a) in the Republic of Korea was expressed in a baculovirus expression system. Genomic DNA was extracted from the isolate strain CPV-2a. The recombinant baculovirus, containing the coding sequences of VP2 with the histidine tag at the N-terminus, were generated by using the Bac-to-Bac system. For production of the recombinant VP2 proteins, SF9 cells were transfection into 6 wells. Propagation of recombinant baculoviruses and expression of the VP2 protein were performed in the Sf9 cell line maintained. The proteins were detected to Western blot anlaysis. CPV-2a VP2 was detected by Western blotting the monoclonal antibodies recognized 6x His and the band had a molecular weight of 65 KDa. We demonstrated that recombinant CPV-2a VP2 expression in baculovirus. The recombinant CPV-2a VP2 may able to development of specific diagnostic test and vaccination of against CPV2. This study provides a foundation for application of CPV2 on the development of new CPV2 subunit vaccine.

Keywords: baculovirus, canine parvovirus 2a, Dog, Korea

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Authors: M. Amelsakhi, A. Sohrabi-Bidar, A. Shareghi

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One of the most important issues about the structural damages caused by earthquake is the evaluating of the spectral response of the site on which the construction is built. This fact has demonstrated during many earlier earthquakes and many researchers’ reports have concerned with it. According to these reports, features of the site materials and geometry of the ground surface are considered the main factors. This study concentrates on the specific form of topographies like hills. Assessing of spectral responses of different points on the hills and beside demonstrates considerable differences between 1D and 2D methods of geotechnical analyses. A general trend of amplifications on the top of the hills and de-amplifications near the toe of the hills has been appeared within the acceleration, velocity and displacement response spectrums of horizontal motion. Evaluating of spectral responses of different sizes of the hills revealed that as much as the hill-size enlarges differences between spectral responses of 1D and 2D analyses transfers to longer range of periods and becomes wider.

Keywords: topography effect, amplification ratio, response spectrum, earth resources engineering

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Authors: M. A. I Perera, C. R. Wijesinghe, A. R. Weerasinghe

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his study was conducted to review and identify the unsupervised techniques that can be employed to analyze gene expression data in order to identify better subtypes of tumors. Identifying subtypes of cancer help in improving the efficacy and reducing the toxicity of the treatments by identifying clues to find target therapeutics. Process of gene expression data analysis described under three steps as preprocessing, clustering, and cluster validation. Feature selection is important since the genomic data are high dimensional with a large number of features compared to samples. Hierarchical clustering and K Means are often used in the analysis of gene expression data. There are several cluster validation techniques used in validating the clusters. Heatmaps are an effective external validation method that allows comparing the identified classes with clinical variables and visual analysis of the classes.

Keywords: cancer subtypes, gene expression data analysis, clustering, cluster validation

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Authors: Pouya Kaafi, Gholamreza Ghodrati Amiri

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Abnormal loads due to natural events, implementation errors and some other issues can lead to occurrence of progressive collapse in structures. Most of the past researches consist of 2- Dimensional (2D) models of steel frames without consideration of the floor system effects, which reduces the accuracy of the modeling. While employing a 3-Dimensional (3D) model and modeling the concrete slab system for the floors have a crucial role in the progressive collapse evaluation. In this research, a 3D finite element model of a 5-story steel building is modeled by the ABAQUS software once with modeling the slabs, and the next time without considering them. Then, the progressive collapse potential is evaluated. The results of the analyses indicate that the lack of the consideration of the slabs during the analyses, can lead to inaccuracy in assessing the progressive failure potential of the structure.

Keywords: abnormal loads, composite floor system, intermediate steel moment resisting frame system, progressive collapse

Procedia PDF Downloads 435

Authors: Henrique C. C. Andrade, Ana Beatriz C. G. Silva, Fernando Luiz B. Ribeiro, Samir Maghous, Jose Claudio F. Telles, Eduardo M. R. Fairbairn

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The present paper aims at developing a parallel computational model for numerical simulation of poromechanics analyses of heterogeneous reservoirs. In the context of macroscopic poroelastoplasticity, the hydromechanical coupling between the skeleton deformation and the fluid pressure is addressed by means of two constitutive equations. The first state equation relates the stress to skeleton strain and pore pressure, while the second state equation relates the Lagrangian porosity change to skeleton volume strain and pore pressure. A specific algorithm for local plastic integration using a tangent operator is devised. A modified Cam-clay type yield surface with associated plastic flow rule is adopted to account for both contractive and dilative behavior.

Keywords: finite element method, poromechanics, poroplasticity, reservoir analysis

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Authors: Rahele Hasani, Iraj Mehregan, Kambiz Larijani, Taher Nejadsattari, Romain Scalone

Abstract:

Essential oils of Heracleum persicum (Apiaceae) have been widely used from many years ago, but the difference of its properties among different populations have not been identified up to now. Hydrodistilation Clevenger type was used to obtaining the fruit essential oils of four populations of H. persicum from different localities in Iran, then they were characterized by GC-FID and GC-MS analyses. Some ecological factors were also measured. The oils of four populations were compared to determine the similarities and differences and the relationships between these factors and ecological factors. Based on the result, 18-32 different components were identified in four populations, while the percentage of the main components was higher in population with lower number of components. According to the statistical analyses of chemical components and ecological factors, it can be concluded that some ecological factors such as altitude, less humidity, high difference between day and night temperature and salty soil would lead to lower number of components in essential oil, whereas they consist the higher percentage.

Keywords: Chemotaxonomy, Persian hogweed, Ecological factors, Apiaceae.

Procedia PDF Downloads 405