Search results for: genome rearrangement distance

Authors: Sulafah Basahel

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Nowadays, Higher Education Institutions (HEIs) around the world are attempting to utilize Information and Communication Technologies (ICTs) to enhance learning process and strategies of knowledge delivery for students through Distance Education (DE) system. Stakeholders in DE system face a complex situation of different ill-defined and related issues that influence decision making process. In this study system thinking as a body of knowledge is used to explore the emergent properties that produced from these connections between issues and could have either positive or negative outcomes for the DE development. Checkland Soft System Methodology (SSM) - Mode 2 is employed in a cultural context of Saudi Arabia for more knowledge acquisition purposes among multiple stakeholders in DE rather than solving problems to achieve an overall development of DE system. This paper will discuss some political, cultural issues and connections between them that impact on effectiveness of stakeholders’ activities and relations. This study will significantly contribute to both system thinking and education fields by leading decision makers in DE to reconsider future plans, strategies and right actions for more successful educational practices.

Keywords: distance education, higher education institutions, ill-defined issues, soft system methodology-Mode 2

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Authors: Salman Naveed, Nitant Gandhi, Grant Billings, Zachary Jones, B. Todd Campbell, Michael Jones, Sachin Rustgi

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Cotton (Gossypium spp.) is the primary source of natural fiber in the U.S. and a major crop in the Southeastern U.S. Despite constant efforts to increase the cotton fiber yield, the yield gain has stagnated. Therefore, we undertook a novel approach to improve the cotton fiber yield by altering its growth habit from perennial to annual. In this effort, we identified genotypes with high-expression alleles of five floral induction and meristem identity genes (FT, SOC1, FUL, LFY, and AP1) from an upland cotton mini-core collection and crossed them in various combinations to develop cotton lines with annual growth habit, optimal flowering time and enhanced productivity. To facilitate the characterization of genotypes with the desired combinations of stacked alleles, we identified markers associated with the gene expression traits via genome-wide association analysis using a 63K SNP Array (Hulse-Kemp et al. 2015 G3 5:1187). Over 14,500 SNPs showed polymorphism and were used for association analysis. A total of 396 markers showed association with expression traits. Out of these 396 markers, 159 mapped to genes, 50 to untranslated regions, and 187 to random genomic regions. Biased genomic distribution of associated markers was observed where more trait-associated markers mapped to the cotton D sub-genome. Many quantitative trait loci coincided at specific genomic regions. This observation has implications as these traits could be bred together. The analysis also allowed the identification of candidate regulators of the expression patterns of these floral induction and meristem identity genes whose functions will be validated via virus-induced gene silencing.

Keywords: cotton, GWAS, QTL, expression traits

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Authors: Rawinun Praserttaweelap, Somyot Kiatwanidvilai

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Obstacle avoidance is the one key for the robot system in unknown environment. The robots should be able to know their position and safety region. This research starts on the path planning which are SLAM and AMCL in ROS system. In addition, the best parameters of the obstacle avoidance function are required. In situation on Hard Disk Drive Manufacturing, the distance between robots and obstacles are very serious due to the manufacturing constraint. The simulations are accomplished by the SLAM and AMCL with adaptive velocity and safety region calculation.

Keywords: obstacle avoidance, OA, Simultaneous Localization and Mapping, SLAM, Adaptive Monte Carlo Localization, AMCL, KLD sampling, KLD

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Authors: Kgolagano Mpejane

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The study applies a New Institutional Economics (NIE) analytical framework to trade in developing economies by assessing the impacts of institutional quality and institutional quality distance on agricultural trade using a panel data of 15 Southern African Development Community (SADC) countries from the years 1991-2010. The issue of institutions on agricultural trade has not been accorded the necessary attention in the literature, particularly in developing economies. Therefore, the paper empirically tests the gravity model of international trade by measuring the impact of political, economic and legal institutions on intra SADC agricultural trade. The gravity model is noted for its exploratory power and strong theoretical foundation. However, the model has statistical shortcomings in dealing with zero trade values and heteroscedasticity residuals leading to biased results. Therefore, this study employs a two stage Heckman selection model with a Probit equation to estimate the influence of institutions on agricultural trade. The selection stages include the inverse Mills ratio to account for the variable bias of the gravity model. The Heckman model accounts for zero trade values and is robust in the presence of heteroscedasticity. The empirical results of the study support the NIE theory premise that institutions matter in trade. The results demonstrate that institutions determine bilateral agricultural trade on different margins with political institutions having positive and significant influence on bilateral agricultural trade flows within the SADC region. Legal and economic institutions have significant and negative effects on SADC trade. Furthermore, the results of this study confirm that institutional quality distance influences agricultural trade. Legal and political institutional distance have a positive and significant influence on bilateral agricultural trade while the influence of economic, institutional quality is negative and insignificant. The results imply that nontrade barriers, in the form of institutional quality and institutional quality distance, are significant factors limiting intra SADC agricultural trade. Therefore, gains from intra SADC agricultural trade can be attained through the improvement of institutions within the region.

Keywords: agricultural trade, institutions, gravity model, SADC

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Authors: Hatib Shabbir

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Student support services play an important role in providing technical and motivational support to distance learner. ICT based systems have improved the efficiency and effectiveness of support services. In distance education, students being at distant require quick responses from their institution. In the manual system, it is practically hard to give prompt response to each and every student, so as a result student has to suffer a lot. The best way to minimize inefficiencies is to use automated systems. This project involves the development of centralized automated software that would not only replace the manual degree issuance system of 1.3 million students studying at AIOU but also provide online tracking to all the students applying for Degrees. DTS is also the first step towards the paperless culture which is adopted by the major organizations of the world. DTS would not only save university cost but also save students cost and time too by conveying all the information/objection through email and SMS. Moreover, DTS also monitors the performance of each and every individual working in the exam department AIOU and generates daily, monthly and yearly reports of every individual which helps a lot in continuous performance monitoring of the employees.

Keywords: aiou dts, dts aiou, dts, degree tracking aiou

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Authors: Anne C. Okwedadi, Samson Ng’ambi, Ian Jefferson

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Collapsible soils go through radical rearrangement of their particles when triggered by water, stress or/and vibration, causing loss of volume. This loss of volume in soil as seen in foundation failures has caused millions of dollars’ worth of damages to public facilities and infrastructure and so has an adverse effect on the society and people. Despite these consequences and the several studies that are available, more research is still required in the study of soil collapsibility. Discerning the pedogenesis (formation) of soils and investigating the combined effects of the different geological soil properties is key to elucidating and quantifying soils collapsibility. This study presents a novel laboratory testing regime that would be undertaken on soil samples where the effects of soil type, compactive variables (moisture content, density, void ratio, degree of saturation) and loading are analyzed. It is anticipated that results obtained would be useful in mapping the trend of the combined effect thus the basis for evaluating soil collapsibility or collapse potentials encountered in construction with volume loss problems attributed to collapse.

Keywords: collapsible soil, geomorphological process, soil collapsibility properties, soil test

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Authors: Byeongcheol Kang, Junyi Kim, Hyungsik Jung, Hyungjun Yang, Jaewoo An, Jonggeun Choe

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It is important to figure out reservoir properties for better production management. Due to the limited information, there are geological uncertainties on very heterogeneous or channel reservoir. One of the solutions is to generate multiple equi-probable realizations using geostatistical methods. However, some models have wrong properties, which need to be excluded for simulation efficiency and reliability. We propose a novel method of model selection scheme, based on distance-based clustering for reliable application of production optimization algorithm. Distance is defined as a degree of dissimilarity between the data. We calculate Hausdorff distance to classify the models based on their similarity. Hausdorff distance is useful for shape matching of the reservoir models. We use multi-dimensional scaling (MDS) to describe the models on two dimensional space and group them by K-means clustering. Rather than simulating all models, we choose one representative model from each cluster and find out the best model, which has the similar production rates with the true values. From the process, we can select good reservoir models near the best model with high confidence. We make 100 channel reservoir models using single normal equation simulation (SNESIM). Since oil and gas prefer to flow through the sand facies, it is critical to characterize pattern and connectivity of the channels in the reservoir. After calculating Hausdorff distances and projecting the models by MDS, we can see that the models assemble depending on their channel patterns. These channel distributions affect operation controls of each production well so that the model selection scheme improves management optimization process. We use one of useful global search algorithms, particle swarm optimization (PSO), for our production optimization. PSO is good to find global optimum of objective function, but it takes too much time due to its usage of many particles and iterations. In addition, if we use multiple reservoir models, the simulation time for PSO will be soared. By using the proposed method, we can select good and reliable models that already matches production data. Considering geological uncertainty of the reservoir, we can get well-optimized production controls for maximum net present value. The proposed method shows one of novel solutions to select good cases among the various probabilities. The model selection schemes can be applied to not only production optimization but also history matching or other ensemble-based methods for efficient simulations.

Keywords: distance-based clustering, geological uncertainty, particle swarm optimization (PSO), production optimization

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Authors: S. Benchelha, H. C. Aoudjehane, M. Hakdaoui, R. El Hamdouni, H. Mansouri, T. Benchelha, M. Layelmam, M. Alaoui

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The logistic regression (LR) and multivariate adaptive regression spline (MarSpline) are applied and verified for analysis of landslide susceptibility map in Oudka, Morocco, using geographical information system. From spatial database containing data such as landslide mapping, topography, soil, hydrology and lithology, the eight factors related to landslides such as elevation, slope, aspect, distance to streams, distance to road, distance to faults, lithology map and Normalized Difference Vegetation Index (NDVI) were calculated or extracted. Using these factors, landslide susceptibility indexes were calculated by the two mentioned methods. Before the calculation, this database was divided into two parts, the first for the formation of the model and the second for the validation. The results of the landslide susceptibility analysis were verified using success and prediction rates to evaluate the quality of these probabilistic models. The result of this verification was that the MarSpline model is the best model with a success rate (AUC = 0.963) and a prediction rate (AUC = 0.951) higher than the LR model (success rate AUC = 0.918, rate prediction AUC = 0.901).

Keywords: landslide susceptibility mapping, regression logistic, multivariate adaptive regression spline, Oudka, Taounate

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Authors: Felix E. Gbenoba, Opeyemi Dahunsi

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Self-instructional materials are at the heart of instructional delivery in Open and Distance Learning (ODL). The success of any ODL institution depends on the availability of instructional materials in quality and quantity. An ODL study material is expected to fully play the teacher plays in the face-to-face learning environment. In Nigeria, efforts to deliver ODL learning materials have been peculiarly challenging. Although researchers are unrelenting in hewing out ways to make ODL delivery in Africa generally and Nigeria in particular, meet the learners’ needs and acceptable global practices, the prospects of integrating instructional media into distance learning courses are largely unexplored. In the present study, we critically examine the prospects of integration of instructional media into ODL courses for pedagogic and other benefits it portends for delivery via the distance learning mode. Although efforts to integrate media in ODL have been recorded before now, the reality has not matched the expectation so far in Nigeria. This does not mean that the existing instructional materials have not produced any significant positive results in improving the overall learning (and teaching) experience in its institutions; it implies that increased integration as suggested here will further improve the experience as well as bring up the new challenges. Obstacles and problems of instructional materials and media development that could have affected the open educational resource initiatives are well established. The first aspect of this paper recalls the revolutionary strides that ODL brought to delivery of education in Nigeria particularly. The other aspect is on what instructional media are, their role, prospects and challenges for ODL in Nigeria; these are examined vis a vis the challenges of development, production and distribution of print instructional materials as the major format of instructional delivery at Nigeria’s only single mode ODL institution, NOUN. In the third aspect, we justify the need and benefits of integrating instructional media into the courses and make recommendations.

Keywords: instructional delivery, instructional media, ODL, media integration, Nigeria, self-instructional materials

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Authors: Aidan N. Smallwood, Celestine R. Weegenaar, Jack N. Evans

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The intensive care unit (ICU) is a particularly resource heavy environment, in terms of staff, drugs and equipment required. Whilst many areas of the hospital are attempting to cut down on plastic use and minimise their impact on the environment, this has proven challenging within the confines of intensive care. Concurrently, as globalization has progressed over recent decades, there has been a tendency towards centralised manufacturing with international distribution networks for products, often covering large distances. In this study, we have modelled the standard consumption of plastic single-use items over the course of the first 24-hours of an average individual patient’s stay in a 12 bed ICU in the United Kingdom (UK). We have identified the country of manufacture and calculated the minimum possible distance travelled by each item from factory to patient. We have assumed direct transport via the shortest possible straight line from country of origin to the UK and have not accounted for transport within either country. Assuming an intubated patient with invasive haemodynamic monitoring and central venous access, there are a total of 52 distincts, largely plastic, disposable products which would reasonably be required in the first 24-hours after admission. Each product type has only been counted once to account for multiple items being shipped as one package. Travel distances from origin were summed to give the total distance combined for all 52 products. The minimum possible total distance travelled from country of origin to the UK for all types of product was 273,353 km, equivalent to 6.82 circumnavigations of the globe, or 71% of the way to the moon. The mean distance travelled was 5,256 km, approximately the distance from London to Mecca. With individual packaging for each item, the total weight of consumed products was 4.121 kg. The CO2 produced shipping these items by air freight would equate to 30.1 kg, however doing the same by sea would produce 0.2 kg CO2. Extrapolating these results to the 211,932 UK annual ICU admissions (2018-2019), even with the underestimates of distance and weight of our assumptions, air freight would account for 6586 tons CO2 emitted annually, approximately 130 times that of sea freight. Given the drive towards cost saving within the UK health service, and the decline of the local manufacturing industry, buying from intercontinental manufacturers is inevitable However, transporting all consumables by sea where feasible would be environmentally beneficial, as well as being less costly than air freight. At present, the NHS supply chain purchases from medical device companies, and there is no freely available information as to the transport mode used to deliver the product to the UK. This must be made available to purchasers in order to give a fuller picture of life cycle impact and allow for informed decision making in this regard.

Keywords: CO2, intensive care, plastic, transport

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Authors: Siamak Dawazdah Emami, Amin Khodaei, Harith Bin Ahmad, Hairul A. Adbul-Rashid

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The Fano resonance effect on plasmonic nanoparticle materials results in such materials possessing a number of unique optical properties, and the potential applicability for sensing, nonlinear devices and slow-light devices. A Fano resonance is a consequence of coherent interference between superradiant and subradiant hybridized plasmon modes. Incident light on subradiant modes will initiate excitation that results in superradiant modes, and these superradient modes possess zero or finite dipole moments alongside a comparable negligible coupling with light. This research work details the derivation of an electrodynamics coupling model for the interaction of dipolar transitions and radiation via plasmonic nanoclusters such as quadrimers, pentamers and heptamers. The directivity calculation is analyzed in order to qualify the redirection of emission. The geometry of a configured array of nanostructures strongly influenced the transmission and reflection properties, which subsequently resulted in the directivity of each antenna being related to the nanosphere size and gap distances between the nanospheres in each model’s structure. A well-separated configuration of nanospheres resulted in the structure behaving similarly to monomers, with spectra peaks of a broad superradiant mode being centered within the vicinity of 560 nm wavelength. Reducing the distance between ring nanospheres in pentamers and heptamers to 20~60 nm caused the coupling factor and charge distributions to increase and invoke a subradiant mode centered within the vicinity of 690 nm. Increasing the outside ring’s nanosphere distance from the centered nanospheres caused the coupling factor to decrease, with the coupling factor being inversely proportional to cubic of the distance between nanospheres. This phenomenon led to a dramatic decrease of the superradiant mode at a 200 nm distance between the central nanosphere and outer rings. Effects from a superradiant mode vanished beyond a 240 nm distance between central and outer ring nanospheres.

Keywords: fano resonance, optical antenna, plasmonic, nano-clusters

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Authors: Sandra Smieszek, Jonathan Haines

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Introduction: Numerous research efforts have focused on searching for ‘longevity genes’. However, attempting to decipher the genetic component of the longevous phenotype have resulted in limited success and the mechanisms governing longevity remain to be explained. We conducted a genome-wide homozygosity analysis (GWHA) of the founder population of the Amish community in central Ohio. While genome-wide association studies using unrelated individuals have revealed many interesting longevity associated variants, these variants are typically of small effect and cannot explain the observed patterns of heritability for this complex trait. The Amish provide a large cohort of extended kinships allowing for in depth analysis via family-based approach excellent population due to its. Heritability of longevity increases with age with significant genetic contribution being seen in individuals living beyond 60 years of age. In our present analysis we show that the heritability of longevity is estimated to be increasing with age particularly on the paternal side. Methods: The present analysis integrated both phenotypic and genotypic data and led to the discovery of a series of variants, distinct for stratified populations across ages and distinct for paternal and maternal cohorts. Specifically 5437 subjects were analyzed and a subset of 893 successfully genotyped individuals was used to assess CHIP heritability. We have conducted the homozygosity analysis to examine if homozygosity is associated with increased risk of living beyond 90. We analyzed AMISH cohort genotyped for 614,957 SNPs. Results: We delineated 10 significant regions of homozygosity (ROH) specific for the age group of interest (>90). Of particular interest was ROH on chromosome 13, P < 0.0001. The lead SNPs rs7318486 and rs9645914 point to COL4A2 and our lead SNP. COL25A1 encodes one of the six subunits of type IV collagen, the C-terminal portion of the protein, known as canstatin, is an inhibitor of angiogenesis and tumor growth. COL4A2 mutations have been reported with a broader spectrum of cerebrovascular, renal, ophthalmological, cardiac, and muscular abnormalities. The second region of interest points to IRS2. Furthermore we built a classifier using the obtained SNPs from the significant ROH region with 0.945 AUC giving ability to discriminate between those living beyond to 90 years of age and beyond. Conclusion: In conclusion our results suggest that a history of longevity does indeed contribute to increasing the odds of individual longevity. Preliminary results are consistent with conjecture that heritability of longevity is substantial when we start looking at oldest fifth and smaller percentiles of survival specifically in males. We will validate all the candidate variants in independent cohorts of centenarians, to test whether they are robustly associated with human longevity. The identified regions of interest via ROH analysis could be of profound importance for the understanding of genetic underpinnings of longevity.

Keywords: regions of homozygosity, longevity, SNP, Amish

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Authors: Igor V. Grigoriev

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Understanding of biological processes encoded in fungi is instrumental in addressing future food, feed, and energy demands of the growing human population. Genomics is a powerful and quickly evolving tool to understand these processes. The Fungal Genomics Program of the US Department of Energy Joint Genome Institute (JGI) partners with researchers around the world to explore fungi in several large scale genomics projects, changing the fungal genomics landscape. The key trends of these changes include: (i) rapidly increasing scale of sequencing and analysis, (ii) developing approaches to go beyond culturable fungi and explore fungal ‘dark matter,’ or unculturables, and (iii) functional genomics and multi-omics data integration. Power of comparative genomics has been recently demonstrated in several JGI projects targeting mycorrhizae, plant pathogens, wood decay fungi, and sugar fermenting yeasts. The largest JGI project ‘1000 Fungal Genomes’ aims at exploring the diversity across the Fungal Tree of Life in order to better understand fungal evolution and to build a catalogue of genes, enzymes, and pathways for biotechnological applications. At this point, at least 65% of over 700 known families have one or more reference genomes sequenced, enabling metagenomics studies of microbial communities and their interactions with plants. For many of the remaining families no representative species are available from culture collections. To sequence genomes of unculturable fungi two approaches have been developed: (a) sequencing DNA from fruiting bodies of ‘macro’ and (b) single cell genomics using fungal spores. The latter has been tested using zoospores from the early diverging fungi and resulted in several near-complete genomes from underexplored branches of the Fungal Tree, including the first genomes of Zoopagomycotina. Genome sequence serves as a reference for transcriptomics studies, the first step towards functional genomics. In the JGI fungal mini-ENCODE project transcriptomes of the model fungus Neurospora crassa grown on a spectrum of carbon sources have been collected to build regulatory gene networks. Epigenomics is another tool to understand gene regulation and recently introduced single molecule sequencing platforms not only provide better genome assemblies but can also detect DNA modifications. For example, 6mC methylome was surveyed across many diverse fungi and the highest among Eukaryota levels of 6mC methylation has been reported. Finally, data production at such scale requires data integration to enable efficient data analysis. Over 700 fungal genomes and other -omes have been integrated in JGI MycoCosm portal and equipped with comparative genomics tools to enable researchers addressing a broad spectrum of biological questions and applications for bioenergy and biotechnology.

Keywords: fungal genomics, single cell genomics, DNA methylation, comparative genomics

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Authors: Lukman Andi Priyatna, Vivi Fauzia, Ferry Anggoro Ardy Nugroho

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Zinc oxide (ZnO) based nanostructures are ubiquitous in applications due to their favourable physicochemical properties and ease of fabrication. One widely accessible route to synthesize ZnO nanorods, which show promising performance in e.g. photoelectrochemical water splitting, is hydrothermal growth of ZnO seeds, obtained via an atomic nebulizer. Despite its popularity, study on the impact of the synthesis parameters in atomic nebulizer on the performance of the synthesized ZnO nanostructures is lacking. This study presents an investigation on the impact of the distance between substrates and atomic nebulizer nozzle on the photoelectrochemical water splitting performance of ZnO nanorods. Adjusting such a distance reveals an optimum separation which results in nanostructures with highest absorbance. Such high absorbance translates into improved photoelectrochemistry, as evaluated by higher photocurrent density, from 0.11 mA/cm² to 0.14 mA/cm² and higher Applied Bias Photon-to-Current Efficiency (ABPE) from 0.12% to 0.14%. These results underscore the importance of understanding and optimizing the experimental parameters during ZnO nanostructure synthesis. In a broader context, it advertises the need to carefully assess the corresponding fabrication parameters to optimize the performance of the obtained nanostructures.

Keywords: atomic nebulizer, photocurrent density, photoelectrochemical water splitting, ZnO nanorods

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Authors: Anatoly D. Pluzhnikov, Elena N. Pribludova, Alexander G. Ryndyk

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In conjunction with the problem of the target selection on a clutter background, the analysis of the scanning rate influence on the spatial-temporal signal structure, the generalized multivariate correlation function and the quality of the resolution with the increase pulse repetition frequency is made. The possibility of the object space-distance resolution, which is conditioned by the range-to-angle conversion with an increased scanning rate, is substantiated. The calculations for the real cylindrical array at high scanning rate are presented. The high scanning rate let to get the signal to noise improvement of the order of 10 dB for the space-time signal processing.

Keywords: antenna pattern, array, signal processing, spatial resolution

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Authors: Mahsa Namvari, Kari Ullakko

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It is well-known that the Co-doping of ferromagnetic shape memory alloys (FSMAs) is a crucial tool to control their multifunctional properties. The present work investigates the use of small quantities of Co to fine-tune the transformation, structure, microstructure, mechanical and magnetic properties of the polycrystalline Ni₄₉.₈Mn₂₈.₅Ga₂₁.₇ (at.%) alloy, At Co concentrations of 1-1.5 at.%, a microstructure with an average grain size of about 2.00 mm was formed with a twin structure, enabling the experimental observation of magnetic-field-induced twin variant rearrangement. At higher levels of Co-doping, the grain size was essentially reduced, and the crystal structure of the martensitic phase became 2M martensite. The decreasing grain size and changing crystal structure are attributed to the progress of γ-phase precipitates. Alongside the academic aspect, the results of the present work point to the commercial advantage of fabricating 10M Co-doped Ni-Mn-Ga actuating elements made from large grains of polycrystalline ingots obtained by a standard melting facility instead of grown single crystals.

Keywords: Ni-Mn-Ga, ferromagnetic shape memory, martensitic phase transformation, grain growth

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Authors: Hung-Chieh Chen, Kuo-Hui Wang, Tsu-Lin Yeh

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Proteomics represent the performance of genomic complement proteins and the protein level on functional genomics. This study adopted proteomic strategies for comparing serum proteins among three groups: elite sprinter (sprint runner group, SR), long-distance runners (long-distance runner group, LDR), and the untrained control group (control group, CON). Purposes: This study aims to identify elite sprinters and long-distance runners’ serum protein and to provide a comparison of their serum proteome’ composition. Methods: Serum protein fractionations that separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and analyzed by a quantitative nano-LC-MS/MS-based proteomic profiling. The one-way analysis of variance (ANOVA) and Scheffe post hoc comparison (α= 0.05) was used to determine whether there is any significant difference in each protein level among the three groups. Results: (1) After analyzing the 307 identified proteins, there were 26 unique proteins in the SR group, and 18 unique proteins in the LDR group. (2) For the LDR group, 7 coagulation function-associated proteins’ expression levels were investigated: vitronectin, serum paraoxonase/arylesterase 1, fibulin-1, complement C3, vitamin K-dependent protein, inter-alpha-trypsin inhibitor heavy chain H3 and von Willebrand factor, and the findings show the seven coagulation function-associated proteins were significantly lower than the group of SR. (3) Comparing to the group of SR, this study found that the LDR group’s expression levels of the 2 antioxidant proteins (afamin and glutathione peroxidase 3) were also significantly lower. (4) The LDR group’s expression levels of seven immune function-related proteins (Ig gamma-3 chain C region, Ig lambda-like polypeptide 5, clusterin, complement C1s subcomponent, complement factor B, complement C4-A, complement C1q subcomponent subunit A) were also significantly lower than the group of SR. Conclusion: This study identified the potential serum protein markers for elite sprinters and long-distance runners. The changes in the regulation of coagulation, antioxidant, or immune function-specific proteins may also provide further clinical applications for these two different track athletes.

Keywords: biomarkers, coagulation, immune response, oxidative stress

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Authors: S. Fahiminiya, J. Nadaf, F. Rauch, L. Jerome-Majewska, J. Majewski

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Background: Sequencing of protein coding regions of human genome (Whole Exome Sequencing; WES), has demonstrated a great success in the identification of causal mutations for several rare genetic disorders in human. Generally, most of WES studies have focused on rare variants in coding exons and splicing-sites where missense substitutions lead to the alternation of protein product. Although focusing on this category of variants has revealed the mystery behind many inherited genetic diseases in recent years, a subset of them remained still inconclusive. Here, we present the result of our WES studies where analyzing only rare variants in coding regions was not conclusive but further investigation revealed the involvement of non-coding variants and copy number variations (CNV) in etiology of the diseases. Methods: Whole exome sequencing was performed using our standard protocols at Genome Quebec Innovation Center, Montreal, Canada. All bioinformatics analyses were done using in-house WES pipeline. Results: To date, we successfully identified several disease causing mutations within gene coding regions (e.g. SCARF2: Van den Ende-Gupta syndrome and SNAP29: 22q11.2 deletion syndrome) by using WES. In addition, we showed that variants in non-coding regions and CNV have also important value and should not be ignored and/or filtered out along the way of bioinformatics analysis on WES data. For instance, in patients with osteogenesis imperfecta type V and in patients with glucocorticoid deficiency, we identified variants in 5'UTR, resulting in the production of longer or truncating non-functional proteins. Furthermore, CNVs were identified as the main cause of the diseases in patients with metaphyseal dysplasia with maxillary hypoplasia and brachydactyly and in patients with osteogenesis imperfecta type VII. Conclusions: Our study highlights the importance of considering non-coding variants and CNVs during interpretation of WES data, as they can be the only cause of disease under investigation.

Keywords: whole exome sequencing data, non-coding variants, copy number variations, rare diseases

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Authors: Khadija Raissi, Bechir Ben Gouissem

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In this paper, we perform the investigation of some routing protocols in Vehicular Ad-Hoc Network (VANET) context. Indeed, we study the efficiency of protocols like Dynamic Source Routing (DSR), Ad hoc On-demand Distance Vector Routing (AODV), Destination Sequenced Distance Vector (DSDV), Optimized Link State Routing convention (OLSR) and Vehicular Multi-hop algorithm for Stable Clustering (VMASC) in terms of packet delivery ratio (PDR) and throughput. The performance evaluation and comparison between the studied protocols shows that the VMASC is the best protocols regarding fast data transmission and link stability in VANETs. The validation of all results is done by the NS3 simulator.

Keywords: VANET, smart city, AODV, OLSR, DSR, OLSR, VMASC, routing protocols, NS3

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Authors: Hyunseo Choi, Jaewan Hong, Seil Lee, Yang Mo Koo

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Non-oriented (NO) electrical steel is one of the most important soft magnetic materials for rotating machines. Si has usually been added to electrical steels to reduce eddy current loss by increasing the electrical resistivity. Si content more than 3.5 wt% causes cracks during cold rolling due to increase of brittleness. Al also increases the electrical resistivity of the materials as much as Si. In addition, cold workability of Fe-Al is better than Fe-Si, so that Al can be added up to 6.0 wt%. However, the effect of Al contents on magnetic properties of electrical steels has not been studied in detail. Magnetic domains of {100} grains in electrical steels, ranging from 1.85 to 6.54 wt% Al, were observed by magneto-optic Kerr microscopy. Furthermore, the correlation of magnetic domains with magnetic properties was investigated. As Al contents increased, the magnetic domain size of {100} grains decreased due to lowered domain wall energy. Reorganization of magnetic domain structure became more complex as domain size decreased. Therefore, the addition of Al to electrical steel caused hysteresis loss to increase. Anomalous loss decreased and saturated after 4.68% Al.

Keywords: electrical steel, magnetic domain structure, Al addition, core loss, rearrangement of domains

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Authors: Feyza Şahi̇n, Harun Deni̇zli̇, Mustafa Zabun, Hüseyi̇n OnbaşIoğli

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Heat exchangers are devices that are widely used to transfer heat between fluids due to their temperature differences. As a type of heat exchanger, air coolers are heat exchangers that cool the air as it passes through the fins of the heat exchanger by transferring heat to the refrigerant in the coil tubes of the heat exchanger. An assembled fin and tube heat exchanger consists of a coil block and a casing with a fan mounted on it. The term “Fan hood” is used to define the distance between the fan and the coil block. Air coolers play a crucial role in cooling systems, and their heat transfer performance can vary depending on design parameters. These parameters can be related to the air side or the internal fluid side. For airside efficiency, the distance between the fan and the coil block affects the performance by creating dead zones at the corners of the casing and maldistribution of airflow. Therefore, a detailed study of the effect of the fan hood on the evaporator and the optimum fan hood distance is necessary for an efficient air cooler design. This study aims to investigate the value of the fan hood in a fin and tube-type air cooler heat exchanger through computational fluid dynamics (CFD) simulations and experimental investigations. CFD simulations will be used to study the airflow within the fan hood. These simulations will provide valuable insights to optimize the design of the fan hood. In addition, experimental tests will be carried out to validate the CFD results and to measure the performance of the fan hood under real conditions. The results will help us to understand the effect of fan hood design on evaporator efficiency and contribute to the development of more efficient cooling systems. This study will provide essential information for evaporator design and improving the energy efficiency of cooling systems.

Keywords: heat exchanger, fan hood, heat exchanger performance, air flow performance

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Authors: Triloki Nath, R. K. Gupta, L. P. Singh

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The aim of this paper is to find the new exact solution of the blast wave problem in one-dimensional unsteady adiabatic flow for generalized geometry in a compressible, inviscid ideal gas with dust particles. The density of the undisturbed region is assumed to vary according to a power law of the distance from the point of explosion. The exact solution of the problem in form of a power in the distance and the time is obtained. Further, the behaviour of the total energy carried out by the blast wave for planar, cylindrically symmetric and spherically symmetric flow corresponding to different Mach number of the fluid flow in dusty gas is presented. It is observed that the presence of dust particles in the gas yields more complex expression as compared to the ordinary Gasdynamics.

Keywords: shock wave, blast wave, dusty gas, strong shock

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Authors: Moiz S. Vohra, Nagalingam Arun Prasanth, Wei L. Tan, S. H. Yeo

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The understanding of generation and collapse of acoustic cavitation bubbles are prerequisites for application of cavitation erosion. Microbubbles generated due to rapid fluctuation of pressure induced by propagation of ultrasonic wave lead to formation of high velocity microjets and or shock waves upon collapse. Due to vast application of ultrasonic, it is important to characterize and understand cavitation collapse pressure under the radiating surface at different conditions. A comparative investigation is carried out to determine impact load and dynamic pressure distribution exerted upon bubble collapse using thin film pressure sensors. Measurements were recorded at different input conditions such as amplitude, stand-off distance, insertion depth of the horn inside the liquid and pulse on-off time of acoustic vibrations. Impact force of 2.97 N is recorded at amplitude of 108 μm and stand-off distance of 1 mm from the sensor film, whereas impulsive force as low as 0.4 N is recorded at amplitude of 12 μm and stand-off distance of 5 mm from the sensor film. The results drawn from the investigation indicated that variety of impact loads can be achieved by controlling generation and collapse of bubbles, making it suitable to use for numerous application.

Keywords: ultrasonic cavitation, bubble collapse, pressure mapping sensor, impact load

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Authors: Cuneyt Yucelbas, Seral Ozsen, Sule Yucelbas, Gulay Tezel

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Due to the fact that there exist only a small number of complex systems in artificial immune system (AIS) that work out nonlinear problems, nonlinear AIS approaches, among the well-known solution techniques, need to be developed. Gaussian function is usually used as similarity estimation in classification problems and pattern recognition. In this study, diagnosis of breast cancer, the second type of the most widespread cancer in women, was performed with different distance calculation functions that euclidean, gaussian and gaussian-euclidean hybrid function in the clonal selection model of classical AIS on Wisconsin Breast Cancer Dataset (WBCD), which was taken from the University of California, Irvine Machine-Learning Repository. We used 3-fold cross validation method to train and test the dataset. According to the results, the maximum test classification accuracy was reported as 97.35% by using of gaussian-euclidean hybrid function for fold-3. Also, mean of test classification accuracies for all of functions were obtained as 94.78%, 94.45% and 95.31% with use of euclidean, gaussian and gaussian-euclidean, respectively. With these results, gaussian-euclidean hybrid function seems to be a potential distance calculation method, and it may be considered as an alternative distance calculation method for hard nonlinear classification problems.

Keywords: artificial immune system, breast cancer diagnosis, Euclidean function, Gaussian function

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Authors: Somojit Saha, Rohit K. Chatterjee, Sarit K. Das, Avijit Kar

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A new force field is designed for propagation of the parametric contour into deep narrow cortical fold in the application of knowledge based reconstruction of cerebral cortex from MR image of brain. Designing of this force field is highly inspired by the Generalized Gradient Vector Flow (GGVF) model and markedly differs in manipulation of image information in order to determine the direction of propagation of the contour. While GGVF uses edge map as its main driving force, the newly designed force field uses the map of distance between zero valued pixels and their nearest non-zero valued pixel as its main driving force. Hence, it is called Zero-Non-Zero Distance (ZNZD) force field. The objective of this force field is forceful propagation of the contour beyond spurious convergence due to partial volume effect (PVE) in to narrow sulcal fold. Being function of the corresponding non-zero pixel value, the force field has got an inherent property to determine spuriousness of the edge automatically. It is effectively applied along with some morphological processing in the application of cortical reconstruction to breach the hindrance of PVE in narrow sulci where conventional GGVF fails.

Keywords: deformable model, external force field, partial volume effect, cortical reconstruction, MR image of brain

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Authors: T. Nakkeran, C. Dhamodharan, Win Myint Soe , Ramasamy Deverajan, M. Ganesh Babu

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This manuscript presents the results of an experimental investigation performed to study the material and mechanical properties of two weld joints fabricated within close proximity. The experiment was designed using welded S355 D Z35 with distances between two parallel adjacent weld toes at 8 mm. These distances were less than the distance that has normally been recommended in standards, codes, and specifications. The main idea of the analysis is to determine any significant effects when welding the joints with the close proximity of 8mm using the SAW welding process of the one joint with high heat put and one joint welded with the FCAW welding process and evaluating the destructing and nondestructive testing between the welded joints. Further, we have evaluated the joints with Mechanical Testing for evaluating by performing Tensile test, bend testing, Macrostructure, Microstructure, Hardness test, and Impact testing. After evaluating the final outcome of the result, no significant changes were observed for welding the close proximity of weld of 8mm distance between the joints as compared to the specification minimum distance between the weldments of any design should be 50mm.

Keywords: S355 carbon steel, weld proximity, SAW process, FCAW process, heat input, bend test, tensile test, hardness test, impact test, macro and microscopic examinations

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Authors: Nipun Manirajan, Heeralal Gargama, Sushil Guhe, Manoj Prabhakaran

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In railway industry, train sets are designed based on contractual requirements (mission profile), where reliability targets are measured in terms of mean distance between failures (MDBF). However, during the beginning of revenue services, trains do not achieve the designed mission profile distance (mileage) within the timeframe due to infrastructure constraints, scarcity of commuters or other operational challenges thereby not respecting the original design inputs. Since trains do not run sufficiently and do not achieve the designed mileage within the specified time, car builder has a risk of not achieving the contractual MDBF target. This paper proposes a constant failure rate based model to deal with the situations where mileage accumulation is not a part of the design mission profile. The model provides appropriate MDBF target to be demonstrated based on actual accumulated mileage. A case study of rolling stock running in the field is undertaken to analyze the failure data and MDBF target demonstration during low mileage accumulation. The results of case study prove that with the proposed method, reliability targets are achieved under low mileage accumulation.

Keywords: mean distance between failures, mileage-based reliability, reliability target appropriations, rolling stock reliability

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Authors: Zewdneh Zana Zate

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The study focuses on the evolutionary and ecological genomics of both wild and cultivated Coffea arabica L. at its center of origin, Ethiopia, aiming to uncover how this vital species may withstand future climate changes. Utilizing bioclimatic models, we project the future distribution of Arabica under varied climate scenarios for 2050 and 2080, identifying potential conservation zones and immediate risk areas. Through whole-genome resequencing of accessions from Ethiopian gene banks, this research assesses genetic diversity and divergence between wild and cultivated populations. It explores relationships, demographic histories, and potential hybridization events among Coffea arabica accessions to better understand the species' origins and its connection to parental species. This genomic analysis also seeks to detect signs of natural or artificial selection across populations. Integrating these genomic discoveries with ecological data, the study evaluates the current and future ecological and genomic vulnerabilities of wild Coffea arabica, emphasizing necessary adaptations for survival. We have identified key genomic regions linked to environmental stress tolerance, which could be crucial for breeding more resilient Arabica varieties. Additionally, our ecological modeling predicted a contraction of suitable habitats, urging immediate conservation actions in identified key areas. This research not only elucidates the evolutionary history and adaptive strategies of Arabica but also informs conservation priorities and breeding strategies to enhance resilience to climate change. By synthesizing genomic and ecological insights, we provide a robust framework for developing effective management strategies aimed at sustaining Coffea arabica, a species of profound global importance, in its native habitat under evolving climatic conditions.

Keywords: coffea arabica, climate change adaptation, conservation strategies, genomic resilience

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Authors: Shinsuke Udagawa, Masato Yamagishi, Masanori Ota

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The Schlieren method, which has been conventionally used to visualize high-speed flows, has disadvantages such as the complexity of the experimental setup and the inability to quantitatively analyze the amount of refraction of light. The Background Oriented Schlieren (BOS) method proposed by Meier is one of the measurement methods that solves the problems, as mentioned above. The refraction of light is used for BOS method same as the Schlieren method. The BOS method is characterized using a digital camera to capture the images of the background behind the observation area. The images are later analyzed by a computer to quantitatively detect the amount of shift of the background image. The experimental setup for BOS does not require concave mirrors, pinholes, or color filters, which are necessary in the conventional Schlieren method, thus simplifying the experimental setup. However, the defocusing of the observation results is caused in case of using BOS method. Since the focus of camera on the background image leads to defocusing of the observed object. The defocusing of object becomes greater with increasing the distance between the background and the object. On the other hand, the higher sensitivity can be obtained. Therefore, it is necessary to adjust the distance between the background and the object to be appropriate for the experiment, considering the relation between the defocus and the sensitivity. The purpose of this study is to experimentally clarify the effect of defocus on density field reconstruction. In this study, the visualization experiment of underexpanded jet using BOS measurement system with ronchi ruling as the background that we constructed, have been performed. The reservoir pressure of the jet and the distance between camera and axis of jet is fixed, and the distance between background and axis of jet has been changed as the parameter. The images have been later analyzed by using personal computer to quantitatively detect the amount of shift of the background image from the comparison between the background pattern and the captured image of underexpanded jet. The quantitatively measured amount of shift have been reconstructed into a density flow field using the Abel transformation and the Gradstone-Dale equation. From the experimental results, it is found that the reconstructed density image becomes blurring, and noise becomes decreasing with increasing the distance between background and axis of underexpanded jet. Consequently, it is cralified that the sensitivity constant should be greater than 20, and the circle of confusion diameter should be less than 2.7mm at least in this experimental setup.

Keywords: BOS method, underexpanded jet, abel transformation, density field visualization

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Authors: Sindile Ngubane-Mokiwa

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This paper addresses two questions: (1) what barriers do the blind students face with assessment and feedback in open distance learning contexts? And (2) How can these barriers be removed? The paper focuses on the distance education through which most students with disabilities elevate their chances of accessing higher education. Lack of genuine inclusion is also evident in the challenges the blind students face during the assessment. These barriers are experienced at both formative and summative stages. The insights in this paper emanate from a case study that was carried out through qualitative approaches. The data was collected through in-depth interview, life stories, and telephonic interviews. The paper provides a review of local, continental and international views on how best assessment barriers can be removed. A group of five blind students, comprising of two honours students, two master's students and one doctoral student participated in this study. The data analysis was done through thematic analysis. The findings revealed that (a) feedback to the assignment is often inaccessible; (b) the software used is incompatible; (c) learning and assessment are designed in exclusionary approaches; (d) assessment facilities are not conducive; and (e) lack of proactive innovative assessment strategies. The article concludes by recommending ways in which barriers to assessment can be removed. These include addressing inclusive assessment and feedback strategies in professional development initiatives.

Keywords: assessment design, barriers, disabilities, blind students, feedback, universal design for learning

Procedia PDF Downloads 360