Search results for: multiple sequence alignment

Authors: Ng Liang Shen, Hau Yuan Wen

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Arrhythmia analysis of ECG signal plays a major role in diagnosing most of the cardiac diseases. Therefore, a single arrhythmia detection of an electrocardiographic (ECG) record can determine multiple pattern of various algorithms and match accordingly each ECG beats based on Machine Learning supervised learning. These researchers used different features and classification methods to classify different arrhythmia types. A major problem in these studies is the fact that the symptoms of the disease do not show all the time in the ECG record. Hence, a successful diagnosis might require the manual investigation of several hours of ECG records. The point of this paper presents investigations cardiovascular ailment in Electrocardiogram (ECG) Signals for Cardiac Arrhythmia utilizing examination of ECG irregular wave frames via heart beat as correspond arrhythmia which with Machine Learning Pattern Recognition.

Keywords: electrocardiogram, ECG, classification, machine learning, pattern recognition, detection, QRS

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Authors: Garadi Ahmed, Boubakar S. Bouazza

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The Zero Cross-Correlation (C, w) code is a family of binary sequences of length C and constant Hamming-weight, the cross correlation between any two sequences equal zero. In this paper, we evaluate the performance of ZCC code based on Balanced Incomplete Block Design (BIBD) for Spectral Amplitude Coding Optical Code Division Multiple Access (SAC-OCDMA) system using direct detection. The BER obtained is better than 10-9 for five simultaneous users.

Keywords: spectral amplitude coding-optical code-division-multiple-access (SAC-OCDMA), phase induced intensity noise (PIIN), balanced incomplete block design (BIBD), zero cross-correlation (ZCC)

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Authors: A. Asgharzadeh, M. Maroufi

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5G mobile communication system has drawn more and more attention. The 5G system needs to provide three different types of services, including enhanced Mobile BroadBand (eMBB), massive machine-type communication (mMTC), and ultra-reliable and low-latency communication (URLLC). Universal Filtered Multi-Carrier (UFMC), Filter Bank Multicarrier (FBMC), and Filtered Orthogonal Frequency Division Multiplexing (f-OFDM) are suggested as a well-known candidate waveform for the coming 5G system. Themachine-to-machine (M2M) communications are one of the essential applications in 5G, and it involves exchanging of concise messages with a very short latency. However, in UFMC systems, the subcarriers are grouped into subbands but f-OFDM only one subband covers the entire band. Furthermore, in FBMC, a subband includes only one subcarrier, and the number of subbands is the same as the number of subcarriers. This paper mainly discusses the performance of UFMC with different parameters for the UFMC system. Also, paper shows that UFMC is the best choice outperforming OFDM in any case and FBMC in case of very short packets while performing similarly for long sequences with channel estimation techniques for Interleave Division Multiple Access (IDMA) systems.

Keywords: universal filtered multi-carrier technique, UFMC, interleave division multiple access, IDMA, fifth-generation, subband

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Authors: Kai-Yao Huang, Tzong-Yi Lee, Pin-Hao Ho, Tzu-Hao Chang, Cheng-Wei Chang

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Background: Human cytomegalovirus (HCMV) infects much people around the world, and there were many researches mention that many diseases were caused by HCMV. To understand the mechanism of HCMV lead to diseases during infection. We observe a microRNA (miRNA) – miRNA interaction between HCMV and host during infection. We found HCMV miRNA sequence component complementary with host miRNA precursors, and we also found that the host miRNA abundances were decrease in HCMV infection. Hence, we focus on the host miRNA which may target by the other HCMV miRNA to find theirs target mRNAs expression and analysis these mRNAs affect what kind of signaling pathway. Interestingly, we found the affected mRNA play an important role in some diseases related pathways, and these diseases had been annotated by HCMV infection. Results: From our analysis procedure, we found 464 human miRNAs might be targeted by 26 HCMV miRNAs and there were 291 human miRNAs shows the concordant decrease trend during HCMV infection. For case study, we found hcmv-miR-US22-5p may regulate hsa-mir-877 and we analysis the KEGG pathway which built by hsa-mir-877 validate target mRNA. Additionally, through survey KEGG Disease database found that these mRNA co-regulate some disease related pathway for instance cancer, nerve disease. However, there were studies annotated that HCMV infection casuse cancer and Alzheimer. Conclusions: This work supply a different scenario of miRNA target interactions(MTIs). In previous study assume miRNA only target to other mRNA. Here we wonder there is possibility that miRNAs might regulate non-mRNA targets, like other miRNAs. In this study, we not only consider the sequence similarity with HCMV miRNAs and human miRNA precursors but also the expression trend of these miRNAs. Then we analysis the human miRNAs validate target mRNAs and its associated KEGG pathway. Finally, we survey related works to validate our investigation.

Keywords: human cytomegalovirus, HCMV, microRNA, miRNA

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Authors: Raziyeh Shamsi

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In this paper, we present a multiple objective linear programming (MOLP) problem in full fuzzy case and find Data Envelopment Analysis(DEA) targets. In the presented model, we are seeking the least inputs and the most outputs in the production possibility set (PPS) with the variable return to scale (VRS) assumption, so that the efficiency projection is obtained for all decision making units (DMUs). Then, we provide an algorithm for finding DEA targets interactively in the full fuzzy case, which solves the full fuzzy problem without defuzzification. Owing to the use of interactive methods, the targets obtained by our algorithm are more applicable, more realistic, and they are according to the wish of the decision maker. Finally, an application of the algorithm in 21 educational institutions is provided.

Keywords: DEA, MOLP, full fuzzy, target

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Authors: Cosmas Maphosa, Ndileleni P. Mudzielwana, Lufuno Netshifhefhe

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Core business in a university centers on a curriculum. Teaching, learning, assessment and university products all have a bearing on the curriculum. In this discussion paper, the researchers engage in theoretical underpinnings of curriculum development in universities in South Africa. The paper is hinged on the realization that meaningful curriculum development is only possible if academic staff member has a thorough understanding of curriculum, curriculum design principles, and processes. Such understanding should be informed by theory. In this paper, the researchers consider curriculum, curriculum orientations, and the role of learning outcomes in curriculum development. Important and key considerations in module/course design are discussed and relevant examples given. The issue of alignment, as an important aspect of module/course design, is also explained and exemplified. Conclusions and recommendations are made.

Keywords: curriculum, curriculum development, knowledge, graduate attributes, competencies, teaching and learning

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Authors: Asma Alzahrani, Elizabeth Stojanovski

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This study investigated factors that influence mathematics achievement based on a sample of ninth-grade students (N  =  21,444) from the High School Longitudinal Study of 2009 (HSLS09). Key aspects studied included efficacy in mathematics, interest and enjoyment of mathematics, identity with mathematics and future utility beliefs and how these influence mathematics achievement. The predictability of mathematics achievement based on these factors was assessed using correlation coefficients and multiple linear regression. Spearman rank correlations and multiple regression analyses indicated positive and statistically significant relationships between the explanatory variables: mathematics efficacy, identity with mathematics, interest in and future utility beliefs with the response variable, achievement in mathematics.

Keywords: Mathematics achievement, math efficacy, mathematics interest, factors influence

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Authors: Othmane Touri, Sanaa El Filali, El Habib Benlahmar

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Natural Language Processing (NLP) has gained significant attention lately. It has proved its ability to analyze and extract insights from unstructured text data in various languages. It is found that one of the most popular NLP applications is sentiment analysis which aims to identify the sentiment expressed in a piece of text, such as positive, negative, or neutral, in multiple languages. While there are several multilingual NLP models available for sentiment analysis, there is a need to investigate their effectiveness in different contexts and applications. In this study, we aim to investigate the effectiveness of different multilingual NLP models for sentiment analysis on a dataset of online product reviews in multiple languages. The performance of several NLP models, including Google Cloud Natural Language API, Microsoft Azure Cognitive Services, Amazon Comprehend, Stanford CoreNLP, spaCy, and Hugging Face Transformers are being compared. The models based on several metrics, including accuracy, precision, recall, and F1 score, are being evaluated and compared to their performance across different categories of product reviews. In order to run the study, preprocessing of the dataset has been performed by cleaning and tokenizing the text data in multiple languages. Then training and testing each model has been applied using a cross-validation approach where randomly dividing the dataset into training and testing sets and repeating the process multiple times has been used. A grid search approach to optimize the hyperparameters of each model and select the best-performing model for each category of product reviews and language has been applied. The findings of this study provide insights into the effectiveness of different multilingual NLP models for Multilingual Sentiment Analysis and their suitability for different languages and applications. The strengths and limitations of each model were identified, and recommendations for selecting the most performant model based on the specific requirements of a project were provided. This study contributes to the advancement of research methods in multilingual NLP and provides a practical guide for researchers and practitioners in the field.

Keywords: NLP, multilingual, sentiment analysis, texts

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Authors: András Farkas, István Molnár, Jan Vrána, Veronika Burešová, Petr Cápal, András Cseh, Márta Molnár-Láng, Jaroslav Doležel

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Species of Aegilops played a central role in the evolution of wheat and are sources of traits related to yield quality and tolerance against biotic and abiotic stresses. These wild genes and alleles are desirable to use in crop improvement programs via introgressive hybridization. However, the success of chromosome mediated gene transfer to wheat are hampered by the pour knowledge on the genome structure of Aegilops relative to wheat and by the low number of cost-effective molecular markers specific for Aegilops chromosomes. The COS markers specific for genes conserved throughout evolution in both sequence and copy number between Triticeae/Aegilops taxa and define orthologous regions, thus enabling the comparison of regions on the chromosomes of related species. The present study compared individual chromosomes of Aegilops umbellulata (UU), Ae. comosa (MM), Ae. speltoides (SS) and Ae. caudata (CC) purified by flourescent labelling with oligonucleotid SSR repeats and biparametric flow cytometry with wheat by identifying orthologous chromosomal regions by COS markers. The linear order of bin-mapped COS markers along the wheat D chromosomes was identified by the use of chromosome-specific sequence data and virtual gene order. Syntenic regions of wheat identifying genome rearrangements differentiating the U, M, S or C genomes from the D genome of wheat were detected. The conserved orthologous set markers assigned to Aegilops chromosomes promise to accelerate gene introgression by facilitating the identification of alien chromatin. The syntenic relationships between the Aegilops species and wheat will facilitate the targeted development of new markers specific for U, M, S and C genomic regions and will contribute to the understanding of molecular processes related to the evolution of Aegilops.

Keywords: Aegilops, cos-markers, flow-sorting, wheat

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Authors: Fiona Lord

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This paper presents research on strengthening urban governance and planning practices for sustainable and regenerative city transformations looking at urban governance in Cambodia as a case study. Transformations to urban sustainability and regeneration require systemic and long-term transformation processes, across multiple levels of society and inclusive of multiple urban actors. This paper presents the emerging findings of a qualitative case study comparing the urban governance and planning practices in two of Cambodia's secondary cities - Battambang and Sihanoukville. The lessons learned have broader implications for how governance and planning can be strengthened to initiate and sustain urban sustainability transformations in other developing country cities of Cambodia and the Southeast Asia region.

Keywords: Cambodia, planning practices, urban governance, urban sustainability transformations

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Authors: Lucille Alonso, Florent Renard

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The characterizations of urban heat island (UHI) and their interactions with climate change and urban climates are the main research and public health issue, due to the increasing urbanization of the population. These solutions require a better knowledge of the UHI and micro-climate in urban areas, by combining measurements and modelling. This study is part of this topic by evaluating microclimatic conditions in dense urban areas in the Lyon Metropolitan Area (France) using a combination of data traditionally used such as topography, but also from LiDAR (Light Detection And Ranging) data, Landsat 8 satellite observation and Sentinel and ground measurements by bike. These bicycle-dependent weather data collections are used to build the database of the variable to be modelled, the air temperature, over Lyon’s hyper-center. This study aims to model the air temperature, measured during 6 mobile campaigns in Lyon in clear weather, using multiple linear regressions based on 33 explanatory variables. They are of various categories such as meteorological parameters from remote sensing, topographic variables, vegetation indices, the presence of water, humidity, bare soil, buildings, radiation, urban morphology or proximity and density to various land uses (water surfaces, vegetation, bare soil, etc.). The acquisition sources are multiple and come from the Landsat 8 and Sentinel satellites, LiDAR points, and cartographic products downloaded from an open data platform in Greater Lyon. Regarding the presence of low, medium, and high vegetation, the presence of buildings and ground, several buffers close to these factors were tested (5, 10, 20, 25, 50, 100, 200 and 500m). The buffers with the best linear correlations with air temperature for ground are 5m around the measurement points, for low and medium vegetation, and for building 50m and for high vegetation is 100m. The explanatory model of the dependent variable is obtained by multiple linear regression of the remaining explanatory variables (Pearson correlation matrix with a |r| < 0.7 and VIF with < 5) by integrating a stepwise sorting algorithm. Moreover, holdout cross-validation is performed, due to its ability to detect over-fitting of multiple regression, although multiple regression provides internal validation and randomization (80% training, 20% testing). Multiple linear regression explained, on average, 72% of the variance for the study days, with an average RMSE of only 0.20°C. The impact on the model of surface temperature in the estimation of air temperature is the most important variable. Other variables are recurrent such as distance to subway stations, distance to water areas, NDVI, digital elevation model, sky view factor, average vegetation density, or building density. Changing urban morphology influences the city's thermal patterns. The thermal atmosphere in dense urban areas can only be analysed on a microscale to be able to consider the local impact of trees, streets, and buildings. There is currently no network of fixed weather stations sufficiently deployed in central Lyon and most major urban areas. Therefore, it is necessary to use mobile measurements, followed by modelling to characterize the city's multiple thermal environments.

Keywords: air temperature, LIDAR, multiple linear regression, surface temperature, urban heat island

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Authors: Yichen Lin, Hsiao-Han Chen, Chi-Chen Jan

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Since 1990, the research area of Integrated Marketing Communications (IMC) has been presented from a different perspective. With advances in information technology and the rise of consumer consciousness, businesses are in a competitive environment. There is an urgent need to adopt more profitable and effective integrated marketing strategies to increase core competitiveness. The goal of the company's sustainable management is to increase consumers' willingness to purchase and to maximize profits. This research uses six aspects of IMC, which includes awareness integration, unified image, database integration, customer-based integration, stakeholders-based integration, and evaluation integration to examine the role of marketing strategies in the strengths and weaknesses of the six components of integrated marketing communications, their effectiveness, the most important components and the most important components that need improvement. At the same time, social media such as FaceBook, Instagram, Youtube, Line, or even TikTok have become marketing tools which firms adopt them more and more frequently in the marketing strategy. In the end of 2019, the outbreak of COVID-19 did really affect the global industries. Lockdown policies also accelerated closure of brick-mentor stores worldwide. Online purchases rose dramatically. Hence, the effectiveness of online marketing will be essential to maintain the business. This study uses multiple-case studies to extend the effects of social media and IMC. Moreover, the study would also explore the differences of social media and IMC during COVID-19. Through literature review and multiple-case studies, it is found that using social media combined with IMC did really help companies expand their business and make good connections with stakeholders. One of previous studies also used system theory to explore the interrelationship among Integrated Marketing Communication, collaborative marketing, and global brand building. Even during pandemic, firms could still maintain the operation and connect with their customers more tightly.

Keywords: integration marketing communications, multiple-case studies, social media, system theory

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Authors: Adham M. Salah, Tariq A. Nagem, Raed A. Abd-Alhameed, James M. Noras

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Recently, the demand for wireless communications systems to cover more than one frequency band (multi-band) with high data rate has been increased for both fixed and mobile services. Multiple Input Multiple Output (MIMO) technology is one of the significant solutions for attaining these requirements and to achieve the maximum channel capacity of the wireless communications systems. The main issue associated with MIMO antennas especially in portable devices is the compact space between the radiating elements which leads to limit the physical separation between them. This issue exacerbates the performance of the MIMO antennas by increasing the mutual coupling between the radiating elements. In other words, the mutual coupling will be stronger if the radiating elements of the MIMO antenna are closer. This paper presents a low–profile dual-band (2×1) MIMO antenna that works at 2.4GHz, 5.3GHz and 5.8GHz for wireless local area networks (WLAN) applications. A neutralization line (NL) technique for enhancing the isolation has been used by introducing a strip line with a length of λg/4 at the isolation frequency (2.4GHz) between the radiating elements. The overall dimensions of the antenna are 33.5 x 36 x 1.6 mm³. The fabricated prototype shows a good agreement between the simulated and measured results. The antenna impedance bandwidths are 2.38–2.75 GHz and 4.4–6 GHz for the lower and upper band respectively; the reflection coefficient and mutual coupling are better than -25 dB in both lower and higher bands. The MIMO antenna performance characteristics are reported in terms of the scattering parameters, envelope correlation coefficient (ECC), total active reflection coefficient, capacity loss, antenna gain, and radiation patterns. Analysis of these characteristics indicates that the design is appropriate for the WLAN terminal applications.

Keywords: ECC, neutralization line, MIMO antenna, multi-band, mutual coupling, WLAN

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Authors: K. R. Sultana, K. Pope, Y. S. Muzychka

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In recent years, the research of heat transfer or phase change phenomena of liquid water droplets experiences a growing interest in aircraft icing, power transmission line icing, marine icing and wind turbine icing applications. This growing interest speeding up the research from single to multiple droplet phenomena. Impingements of multiple droplets and the resulting solidification phenomena after impact on a very cold surface is computationally studied in this paper. The model used in the current study solves the flow equation, composed of energy balance and the volume fraction equations. The main aim of the study is to investigate the effects of several thermo-physical properties (density, thermal conductivity and specific heat) on droplets freezing. The outcome is examined by various important factors, for instance, liquid fraction, total freezing time, droplet temperature and total heat transfer rate in the interface region. The liquid fraction helps to understand the complete phase change phenomena during solidification. Temperature distribution and heat transfer rate help to demonstrate the overall thermal exchange behaviors between the droplets and substrate surface. Findings of this research provide an important technical achievement for ice modeling and prediction studies.

Keywords: droplets, CFD, thermos-physical properties, solidification

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Authors: Mohamed Barbary, Mohamed H. Abd El-Azeem

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Maneuvering extended object tracking (M-EOT) using high-resolution inverse synthetic aperture radar (ISAR) observations has been gaining momentum recently. This work presents a new robust implementation of the multiple models (MM) multi-Bernoulli (MB) filter for M-EOT, where the M-EOT’s ISAR observations are characterized using a skewed (SK) non-symmetrically normal distribution. To cope with the possible abrupt change of kinematic state, extension, and observation distribution over an extended object when a target maneuvers, a multiple model technique is represented based on MB-track-before-detect (TBD) filter supported by SK-sub-random matrix model (RMM) or sub-ellipses framework. Simulation results demonstrate this remarkable impact.

Keywords: maneuvering extended objects, ISAR, skewed normal distribution, sub-RMM, MM-MB-TBD filter

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Authors: Daniel Hristov

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The paper describes the principle of operation, simulation and physical validation of method for simultaneous acquisition of gain and phase states of multiple antenna elements and the corresponding feed lines across a Phased Array Antenna (PAA). The derived values for gain and phase are used for PAA-calibration. The method utilizes the Rotating-Element Electric- Field Vector (REV) principle currently used for gain and phase state estimation of single antenna element across an active antenna aperture. A significant reduction of procedure execution time is achieved with simultaneous setting of different phase delays to multiple phase shifters, followed by a single power measurement. The initial gain and phase states are calculated using spectral and correlation analysis of the measured power series.

Keywords: antenna, antenna arrays, calibration, phase measurement, power measurement

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Authors: Shivam Yadav, Neelam Atri

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Cyanobacteria are photoautotrophic prokaryotes able to grow in diverse ecological habitats, originated 2.5 - 3.5 billion years ago and brought oxygenic photosynthesis. Since then superoxide dismutases (SODs) acquired great significance due to their ability to catalyze detoxification of byproducts of oxygenic photosynthesis, i.e. superoxide radicals. Sequence information from several cyanobacterial genomes offers a unique opportunity to conduct a comprehensive comparative analysis of the superoxide dismutases family. In the present study, we extracted information regarding SODs from species of sequenced cyanobacteria and investigated their diversity, conservation, domain structure, and evolution. 144 putative SOD homologues were identified. SODs are present in all cyanobacterial species reflecting their significant role in survival. However, their distribution varies, fewer in unicellular marine strains whereas abundant in filamentous nitrogen-fixing cyanobacteria. Motifs and invariant amino acids typical in eukaryotic SODs were conserved well in these proteins. These SODs were classified into three major families according to their domain structures. Interestingly, they lack additional domains as found in proteins of other family. Phylogenetic relationships correspond well with phylogenies based on 16S rRNA and clustering occurs on the basis of structural characteristics such as domain organization. Similar conserved motifs and amino acids indicate that cyanobacterial SODs make use of a similar catalytic mechanism as eukaryotic SODs. Gene gain-and-loss is insignificant during SOD evolution as evidenced by absence of additional domain. This study has not only examined an overall background of sequence-structure-function interactions for the SOD gene family but also revealed variation among SOD distribution based on ecophysiological and morphological characters.

Keywords: comparative genomics, cyanobacteria, phylogeny, superoxide dismutases

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Authors: J. U. Santhosh Kumar, V. Krishna, Sebin Sebastian, G. S. Seethapathy, G. Ravikanth, R. Uma Shaanker

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Food is one of the basic needs of human beings. It requires the normal function of the body part and a healthy growth. Recently, food adulteration increases day by day to increase the quantity and make more benefit. Animal source foods can provide a variety of micronutrients that are difficult to obtain in adequate quantities from plant source foods alone. Particularly in the meat industry, products from animals are susceptible targets for fraudulent labeling due to the economic profit that results from selling cheaper meat as meat from more profitable and desirable species. This work presents an overview of the main PCR-based techniques applied to date to verify the authenticity of beef meat and meat products from beef species. We were analyzed 25 market beef samples in South India. We examined PCR methods based on the sequence of the cytochrome b gene for source species identification. We found all sample were sold as beef meat as Bos Taurus. However, interestingly Male meats are more valuable high price compare to female meat, due to this reason most of the markets samples are susceptible. We were used sex determination gene of cattle like TSPY(Y-encoded, testis-specific protein TSPY is a Y-specific gene). TSPY homologs exist in several mammalian species, including humans, horses, and cattle. This gene is Y coded testis protein genes, which only amplify the male. We used multiple PCR products form species-specific “fingerprints” on gel electrophoresis, which may be useful for meat authentication. Amplicons were obtained only by the Cattle -specific PCR. We found 13 market meat samples sold as female beef samples. These results suggest that the species-specific PCR methods established in this study would be useful for simple and easy detection of adulteration of meat products.

Keywords: authentication, meat products, species-specific, TSPY

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Authors: Johannes T. Tsoku, Teboho J. Mosikari, Diteboho Xaba, Thatoyaone Modise

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This paper examines the relationship between manufacturing growth and economic growth in South Africa using quarterly data ranging from 2001 to 2014. The paper employed the Johansen cointegration to test the Kaldor’s hypothesis. The Johansen cointegration results revealed that there is a long run relationship between GDP, manufacturing, service and employment. The Granger causality results revealed that there is a unidirectional causality running from manufacturing growth to GDP growth. The overall findings of the study confirm that Kaldor’s first law of growth is applicable in South African economy. Therefore, investment strategies and policies should be alignment towards promoting growth in the manufacturing sector in order to boost the economic growth of South Africa.

Keywords: cointegration, economic growth, Kaldor’s law, manufacturing growth

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Authors: Jaswinder Singh

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In this paper, comparative analysis is carried out to study the performance of wavelength/time/space optical CDMA codes using two well-known formats; those are CSRZ and DPSK-RZ using RSoft’s OptSIM. The analysis is carried out under the real-like scenario considering the presence of various non-linear effects such as XPM, SPM, SRS, SBS and FWM. Fiber dispersion and the multiple access interference are also considered. The codes used in this analysis are 3-D wavelength/time/space codes. These are converted into 2-D wavelength-time codes so that their requirement of space couplers and fiber ribbons is eliminated. Under the conditions simulated, this is found that CSRZ performs better than DPSK-RZ for fiber-optic CDMA applications.

Keywords: Optical CDMA, Multiple access interference (MAI), CSRZ, DPSK-RZ

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Authors: Tunjo Perič, Marin Fatović

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In this paper a new methodology for vendor selection and supply quotas determination (VSSQD) is proposed. The problem of VSSQD is solved by the model that combines revised weighting method for determining the objective function coefficients, and a multiple objective linear programming (MOLP) method based on the cooperative game theory for VSSQD. The criteria used for VSSQD are: (1) purchase costs and (2) product quality supplied by individual vendors. The proposed methodology is tested on the example of flour purchase for a bakery with two decision makers.

Keywords: cooperative game theory, multiple objective linear programming, revised weighting method, vendor selection

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Authors: Alexander A. Tokmakov

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Cell-free protein synthesis is widely used to synthesize recombinant proteins. It allows genome-scale expression of various polypeptides under strictly controlled uniform conditions. However, only a minor fraction of all proteins can be successfully expressed in the systems of protein synthesis that are currently used. The factors determining expression success are poorly understood. At present, the vast volume of data is accumulated in cell-free expression databases. It makes possible comprehensive bioinformatics analysis and identification of multiple features associated with successful cell-free expression. Here, we describe an approach aimed at identification of multiple physicochemical and structural properties of amino acid sequences associated with protein solubility and aggregation and highlight major correlations obtained using this approach. The developed method includes: categorical assessment of the protein expression data, calculation and prediction of multiple properties of expressed amino acid sequences, correlation of the individual properties with the expression scores, and evaluation of statistical significance of the observed correlations. Using this approach, we revealed a number of statistically significant correlations between calculated and predicted features of protein sequences and their amenability to cell-free expression. It was found that some of the features, such as protein pI, hydrophobicity, presence of signal sequences, etc., are mostly related to protein solubility, whereas the others, such as protein length, number of disulfide bonds, content of secondary structure, etc., affect mainly the expression propensity. We also demonstrated that amenability of polypeptide sequences to cell-free expression correlates with the presence of multiple sites of post-translational modifications. The correlations revealed in this study provide a plethora of important insights into protein folding and rationalization of protein production. The developed bioinformatics approach can be of practical use for predicting expression success and optimizing cell-free protein synthesis.

Keywords: bioinformatics analysis, cell-free protein synthesis, expression success, optimization, recombinant proteins

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Authors: Leigh Ann Wilson, Melanie Borrego

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The purpose of institutional learning outcomes (ILOs) is to assess what students across the university know and what they do not. The issue is gathering this information in a systematic and usable way. This presentation will explain how one institution has engineered this process for both student success and maximum faculty curriculum and course design input. At Brandman University, there are three levels of learning outcomes: course, program, and institutional. Institutional Learning Outcomes (ILOs) are mapped to specific courses. Faculty course developers write the signature assignments (SAs) in alignment with the Institutional Learning Outcomes for each course. These SAs use a specific rubric that is applied consistently by every section and every instructor. Each year, the 12-member General Education Team (GET), as a part of their work, conducts the calibration and assessment of the university-wide SAs and the related rubrics for one or two of the five ILOs. GET members, who are senior faculty and administrators who represent each of the university's schools, lead the calibration meetings. Specifically, calibration is a process designed to ensure the accuracy and reliability of evaluating signature assignments by working with peer faculty to interpret rubrics and compare scoring. These calibration meetings include the full time and adjunct faculty members who teach the course to ensure consensus on the application of the rubric. Each calibration session is chaired by a GET representative as well as the course custodian/contact where the ILO signature assignment resides. The overall calibration process GET follows includes multiple steps, such as: contacting and inviting relevant faculty members to participate; organizing and hosting calibration sessions; and reviewing and discussing at least 10 samples of student work from class sections during the previous academic year, for each applicable signature assignment. Conversely, the commitment for calibration teams consist of attending two virtual meetings lasting up to three hours in duration. The first meeting focuses on interpreting the rubric, and the second meeting involves comparing scores for sample work and sharing feedback about the rubric and assignment. Next, participants are expected to follow all directions provided and participate actively, and respond to scheduling requests and other emails within 72 hours. The virtual meetings are recorded for future institutional use. Adjunct faculty are paid a small stipend after participating in both calibration meetings. Full time faculty can use this work on their annual faculty report for "internal service" credit.

Keywords: assessment, assurance of learning, course design, institutional learning outcomes, rubrics, signature assignments

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Authors: Bruna Luisa Ramos Prado Vasques, Mariane Rembold Petraglia, Antonio Petraglia

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This paper investigates MIMO (Multiple-Input Multiple-Output) adaptive filtering techniques for the application of supervised source separation in the context of convolutive mixtures. From the observation that there is correlation among the signals of the different mixtures, an improvement in the NSAF (Normalized Subband Adaptive Filter) algorithm is proposed in order to accelerate its convergence rate. Simulation results with mixtures of speech signals in reverberant environments show the superior performance of the proposed algorithm with respect to the performances of the NLMS (Normalized Least-Mean-Square) and conventional NSAF, considering both the convergence speed and SIR (Signal-to-Interference Ratio) after convergence.

Keywords: adaptive filtering, multi-rate processing, normalized subband adaptive filter, source separation

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Authors: Danny Barash

Abstract:

Riboswitches are RNA genetic control elements that were originally discovered in bacteria and provide a unique mechanism of gene regulation. They work without the participation of proteins and are believed to represent ancient regulatory systems in the evolutionary timescale. One of the biggest challenges in riboswitch research is that many are found in prokaryotes but only a small percentage of known riboswitches have been found in certain eukaryotic organisms. The few examples of eukaryotic riboswitches were identified using sequence-based bioinformatics search methods that include some slight structural considerations. These pattern-matching methods were the first ones to be applied for the purpose of riboswitch detection and they can also be programmed very efficiently using a data structure called affix arrays, making them suitable for genome-wide searches of riboswitch patterns. However, they are limited by their ability to detect harder to find riboswitches that deviate from the known patterns. Several methods have been developed since then to tackle this problem. The most commonly used by practitioners is Infernal that relies on Hidden Markov Models (HMMs) and Covariance Models (CMs). Profile Hidden Markov Models were also carried out in the pHMM Riboswitch Scanner web application, independently from Infernal. Other computational approaches that have been developed include RMDetect by the use of 3D structural modules and RNAbor that utilizes Boltzmann probability of structural neighbors. We have tried to incorporate more sophisticated secondary structure considerations based on RNA folding prediction using several strategies. The first idea was to utilize window-based methods in conjunction with folding predictions by energy minimization. The moving window approach is heavily geared towards secondary structure consideration relative to sequence that is treated as a constraint. However, the method cannot be used genome-wide due to its high cost because each folding prediction by energy minimization in the moving window is computationally expensive, enabling to scan only at the vicinity of genes of interest. The second idea was to remedy the inefficiency of the previous approach by constructing a pipeline that consists of inverse RNA folding considering RNA secondary structure, followed by a BLAST search that is sequence-based and highly efficient. This approach, which relies on inverse RNA folding in general and our own in-house fragment-based inverse RNA folding program called RNAfbinv in particular, shows capability to find attractive candidates that are missed by Infernal and other standard methods being used for riboswitch detection. We demonstrate attractive candidates found by both the moving-window approach and the inverse RNA folding approach performed together with BLAST. We conclude that structure-based methods like the two strategies outlined above hold considerable promise in detecting riboswitches and other conserved RNAs of functional importance in a variety of organisms.

Keywords: riboswitches, RNA folding prediction, RNA structure, structure-based methods

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Authors: Abderrahmane Diaf, Kamel Benabdellaziz

Abstract:

Remote arid areas of the vast expanses of the African deserts hold huge subterranean reserves of brackish water resources waiting for economic development. This work presents design guidelines as well as initial performance data of new autonomous solar desalination equipment which could help local communities produce their own fresh water using solar energy only and, why not, contribute to transforming desert lands into lush gardens. The output of solar distillation equipment is typically low and in the range of 3 l/m2/day on the average. This new design with an integrated, water-based, environmentally-friendly solar heat storage system produced 5 l/m2/day in early spring weather. Equipment output during summer exceeded 9 liters per m2 per day.

Keywords: multiple trough distillation, solar desalination, solar distillation with heat storage, water based heat storage system

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Authors: Çağrı Özgün Kibiroğlu, Zeynep Turgut

Abstract:

This paper considers a hub location problem where the network service area partitioned into predetermined zones (represented by node clusters is given) and potential hub nodes capacity levels are determined a priori as a selection criteria of hub to investigate congestion effect on network. The objective is to design hub network by determining all required hub locations in the node clusters and also allocate non-hub nodes to hubs such that the total cost including transportation cost, opening cost of hubs and penalty cost for exceed of capacity level at hubs is minimized. A mixed integer linear programming model is developed introducing additional constraints to the traditional model of capacitated multiple allocation hub location problem and empirically tested.

Keywords: hub location problem, p-hub median problem, clustering, congestion

Procedia PDF Downloads 482

Authors: Richard Colwell, Thomas Englert

Abstract:

In cryogenic liquefaction processes, brazed aluminum core heat exchangers are used to minimize surface area/volume of the exchanger. Aluminum alloy (5083-H321; UNS A95083) piping must transition to higher melting point 304L stainless steel piping outside of the heat exchanger kettle or cold box for safety reasons. Since aluminum alloys and austenitic stainless steel cannot be directly welded to together, a transition joint consisting of 5 layers of different metals explosively bonded are used. Failures of two of these joints resulted in process shut-down and loss of revenue. Failure analyses, FEA analysis, and mock-up testing were performed by multiple teams to gain a further understanding into the failure mechanisms involved.

Keywords: explosion bonding, intermetallic compound, thermal strain, titanium-nickel Interface

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Authors: Daniel Botero, Oscar Rubiano, Pedro P. Barragan, Jaime Baron, Leonardo Rodriguez Perdomo, Jaime Rodriguez

Abstract:

In the last decade interval training (IT) has gained importance when is compare with strength training (ST). However, there are few studies analyzing the impact of these training over the autonomic nervous system (ANS). This work has aimed to compare the activity of the autonomic nervous system, when is expose to an IT or ST indoor cycling mode. After approval by the ethics committee, a cross-over clinical trial with 22 healthy participants (age 21 ± 3 years) was implemented. The selection of participants for the groups with sequence force-interval (F-I) and interval-force (I-F) was made randomly with assignation of 11 participants for each group. The temporal series of heart rate was obtained before and after each training using the POLAR TEAM® heart monitor. The evaluation of the ANS was performed with spectral analysis of the heart rate variability (HRV) using the fast Fourier transform (Kubios software). A training of 8 weeks in each sequence (4 weeks with each training) with an intermediate period of two weeks of washout was implemented for each group. The power parameter of the HRV in the low frequency band (LF = 0.04-0.15Hz related to the sympathetic nervous system), high frequency (HF = 0.15-0.4Hz, related to the parasympathetic) and LF/HF (with reference to a modulation of parasympathetic over the sympathetic), were calculated. Afterward, the difference between the parameters before and after was realized. Then, to evaluate statistical differences between each training was implemented the method of Wellek (Wellek and Blettner, 2012, Medicine, 109 (15), 276-81). To determine the difference of effect over parasympathetic when FT and IT are used, the T test is implemented obtaining a T value of 0.73 with p-value ≤ 0.1. For the sympathetic was obtained a T of 0.33 with p ≤ 0.1 and for LF/HF the T was 1.44 with a p ≥ 0.1. Then, the carry over effect was evaluated and was not present. Significant changes over autonomic activity with strength or interval training were not observed. However, a modulation of the parasympathetic over the sympathetic can be observed. Probably, these findings should be explained because the sample is little and/or the time of training was insufficient to generate changes.

Keywords: autonomic nervous, force training, indoor cycling, interval training

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Authors: S. Shahzadi, J. Rizk

Abstract:

This paper describes the pulse width modulated control of a three phase, 4 polar DC brushless motor. To implement this practically the Atmel’s AVR ATmega 328 microcontroller embedded on an Arduino Eleven board is utilized. The microcontroller programming is done in an open source Arduino IDE development environment. The programming logic effectively manipulated a six MOSFET bridge which was used to energize the stator windings as per control requirements. The results obtained showed accurate, precise and efficient pulse width modulated operation. Another advantage offered by this pulse width modulated control was the efficient speed control of the motor. By varying the time intervals between successive commutations, faster energizing of the stator windings was possible thereby leading to quicker rotor alignment with these energized phases and faster revolutions.

Keywords: brushless DC motors, commutation, MOSFET, PWM

Procedia PDF Downloads 499