Search results for: gene co-expression network

Authors: John Gibbs, Benjamin Flanders, Dylan Pozorski, Weixuan Liu

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Weight Painting–adjusting the influence a skeletal joint has on a given vertex in a character mesh–is an arduous and time con- suming part of the 3D animation pipeline. This process generally requires a trained technical animator and many hours of work to complete. Our skiNNer plug-in, which works within Autodesk’s Maya 3D animation software, uses Machine Learning and data pro- cessing techniques to create a deep neural network model that can accomplish the weight painting task in seconds rather than hours for bipedal quasi-humanoid character meshes. In order to create a properly trained network, a number of challenges were overcome, including curating an appropriately large data library, managing an arbitrary 3D mesh size, handling arbitrary skeletal architectures, accounting for extreme numeric values (most data points are near 0 or 1 for weight maps), and constructing an appropriate neural network model that can properly capture the high frequency alter- ation between high weight values (near 1.0) and low weight values (near 0.0). The arrived at neural network model is a cross between a traditional CNN, deep residual network, and fully dense network. The resultant network captures the unusually hard-edged features of a weight map matrix, and produces excellent results on many bipedal models.

Keywords: 3d animation, animation, character, rigging, skinning, weight painting, machine learning, artificial intelligence, neural network, deep neural network

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Authors: K. R. Thabethe, G. A. Adefolaju, M. J. Hosie

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Cervical cancer is the third most commonly diagnosed cancer globally and it is one of three AIDS defining malignancies. Highly active antiretroviral therapy (HAART) is a combination of three or more antiretroviral drugs and has been shown to play a significant role in reducing the incidence of some AIDS defining malignancies, although its effect on cervical cancer is still unclear. The aim of this study was to investigate the relationship between cervical cancer and HAART. This was achieved by studying the expression of two signalling molecules expressed in cervical cancer; MUC1 and P65. Following the 24 hour treatment of a cervical cancer cell line, HCS-2, with drugs which are commonly used as part of HAART at their clinical plasma concentrations, real-time qPCR and immunofluorescence were used in order to study gene and protein expression. A one way ANOVA followed by a Tukey Kramer Post Hoc test was conducted using JMP 11 software on both sets of data. The drug classified as a protease inhibitor (PI) (i.e. LPV/r) reduced MUC1 and P65 gene and protein expression more than the other drug tested. PIs are known to play a significant role in cell death, therefore the cells were thought to be more susceptible to cell death following treatment with PIs. In conclusion, the drugs used, especially the PI showed some anticancer effects by facilitating cell death through decreased gene and protein expression of MUC1 and P65 and present promising agents for cancer treatment.

Keywords: cervical cancer, haart, MUC1, P65

Procedia PDF Downloads 317

Authors: Dalia. G. Aseel

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Begomoviruses are economically important plant viruses that infect dicotyledonous plants and exclusively transmitted by the whitefly Bemisia tabaci. Here, replicative form was isolated from Okra, Cotton, Tomato plants and whitefly infected with Begomoviruses. Using coat protein specific primers (AV1), the viral infection was verified with amplicon at 450 bp. The sequence of OLCuV-AV1 gene was recorded and received an accession number (FJ441605) from Genebank. The phylogenetic tree of OLCuV was closely related to Okra leaf curl virus previously isolated from Cameroon and USA with nucleotide sequence identity of 92%. The protein purification was carried out using His-Tag methodology by using Affinity Chromatography. The purified protein was separated on SDS-PAGE analysis and an enriched expected size of band at 30 kDa was observed. Furthermore, RAPD and SDS-PAGE were used to detect genetic variability between different hosts of okra leaf curl virus (OLCuV), cotton leaf curl virus (CLCuV), tomato yellow leaf curl virus (TYLCuV) and the whitefly vector. Finally, the present study would help to understand the relationship between the whitefly and different economical crops in Egypt.

Keywords: okra leaf curl virus, AV1 gene, sequencing, phylogenetic, cloning, purified protein, genetic diversity and viral proteins

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Authors: Henok Mezemr Besfat, Haftom Gebreslassie Gebregwergs

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wireless network is one of the most important mediums of transmission of information from one device to another devices. Wireless communication has a broad range of applications, including mobile communications through cell phones and satellites, Internet of Things (IoT) connecting several devices, wireless sensor networks for traffic management and environmental monitoring, satellite communication for weather forecasting and TV without requiring any cable or wire or other electronic conductors, by using electromagnetic waves like IR, RF, satellite, etc. This paper summarizes different wireless network technologies, applications of different wireless technologies and different types of wireless networks. Generally, wireless technology will further enhance operations and experiences across sectors with continued innovation. This paper suggests different strategies that can improve wireless networks and technologies.

Keywords: wireless senser, wireless technology, wireless network, internet of things

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Authors: Alina Smalinskiene Janina Petkeviciene, Jurate Klumbiene, Vilma Kriaucioniene, Vaiva Lesauskaite

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The worldwide prevalence of obesity has been increasing dramatically in the last few decades, and Lithuania is no exception. In 2012, every fifth adult (19% of men and 20.5 % of women) was obese and every third was overweight Association studies have highlighted the influence of SNPs in obesity, with particular focus on FTO rs9939609. Thus far, no data on the possible association of this SNP to obesity in the adult Lithuanian population has been reported. Here, for the first time, we demonstrate an association between the FTO rs9939609 homozygous AA genotype and increased BMI when compared to homozygous TT. Furthermore, a positive association was determined between the FTO rs9939609 variant and risk of metabolic syndrome. Background: This study aimed to examine the associations between the fat mass and obesity associated (FTO) gene rs9939609 variant with obesity and metabolic syndrome in Lithuanian adult population. Materials and Methods: A cross-sectional health survey was carried out in randomly selected municipalities of Lithuania. The random sample was obtained from lists of 25–64 year-old inhabitants. The data from 1020 subjects were analysed. The rs9939609 SNP of the FTO gene was assessed using TaqMan assays (Applied Biosystems, Foster City, CA, USA). The Applied Biosystems 7900HT Real-Time Polymerase Chain Reaction System was used for detecting the SNPs. Results: The carriers of the AA genotype had the highest mean values of BMI and waist circumference (WC) and the highest risk of obesity. Interactions ‘genotype x age’ and ‘genotype x physical activity’ in determining BMI and WC were shown. Neither lipid and glucose levels, nor blood pressure were associated with the rs9939609 independently of BMI. In the age group of 25-44 years, association between the FTO genotypes and metabolic syndrome was found. Conclusion: The FTO rs9939609 variant was significantly associated with BMI and WC, and with the risk of obesity in Lithuanian population. The FTO polymorphism might have a greater influence on weight status in younger individuals and in subjects with a low level of physical activity.

Keywords: obesity metabolic syndrome, FTO gene, polymorphism, Lithuania

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Authors: Oluwaponmile David Alao

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Misdiagnosis has been the major problem in health sector. Heart attack has been one of diseases that have high level of misdiagnosis recorded on the part of physicians. In this paper, an intelligent system has been developed for diagnosis of heart attack in the health sector. Dataset of heart attack obtained from UCI repository has been used. This dataset is made up of thirteen attributes which are very vital in diagnosis of heart disease. The system is developed on the multilayer perceptron trained with back propagation neural network then simulated with feed forward neural network and a recognition rate of 87% was obtained which is a good result for diagnosis of heart attack in medical field.

Keywords: heart attack, artificial neural network, diagnosis, intelligent system

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Authors: İkbal Eski

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This investigation is researched on design of robust neural network predictors for analyzing vibration effects on moving parts of a drilling machine. Moreover, the research is divided two parts; first part is experimental investigation, second part is simulation analysis with neural networks. Therefore, a real time the drilling machine is used to vibrations during working conditions. The measured real vibration parameters are analyzed with proposed neural network. As results: Simulation approaches show that Radial Basis Neural Network has good performance to adapt real time parameters of the drilling machine.

Keywords: artificial neural network, vibration analyses, drilling machine, robust

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Authors: T. C. C. Soo, S. Bhassu

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Unlike the common presence of both innate and adaptive immunity in vertebrates, crustaceans, in particular, shrimps, have been discovered to possess only innate immunity. This further emphasizes the importance of innate immunity within shrimps in pathogenic resistance. Under the study of pathogenic immune challenge, different shrimp species actually exhibit varying degrees of immune resistance towards the same pathogen. Furthermore, even within the same shrimp species, different batches of challenged shrimps can have different strengths of immune defence. Several important pathways are activated within shrimps during pathogenic infection. One of them is JAK-STAT pathway that is activated during bacterial, viral and fungal infections by which STAT(Signal Transducer and Activator of Transcription) gene is the core element of the pathway. Based on theory of Central Dogma, the genomic information is transmitted in the order of DNA, RNA and protein. This study is focused in uncovering the important evolutionary patterns present within the DNA (non-coding region) and RNA (coding region). The three shrimp species involved are Macrobrachium rosenbergii, Penaeus monodon and Litopenaeus vannamei which all possess commercial significance. The shrimp species were challenged with a famous penaeid shrimp virus called white spot syndrome virus (WSSV) which can cause serious lethality. Tissue samples were collected during time intervals of 0h, 3h, 6h, 12h, 24h, 36h and 48h. The DNA and RNA samples were then extracted using conventional kits from the hepatopancreas tissue samples. PCR technique together with designed STAT gene conserved primers were utilized for identification of the STAT coding sequences using RNA-converted cDNA samples and subsequent characterization using various bioinformatics approaches including Ramachandran plot, ProtParam and SWISS-MODEL. The varying levels of immune STAT gene activation for the three shrimp species during WSSV infection were confirmed using qRT-PCR technique. For one sample, three biological replicates with three technical replicates each were used for qRT-PCR. On the other hand, DNA samples were important for uncovering the structural variations within the genomic region of STAT gene which would greatly assist in understanding the STAT protein functional variations. The partially-overlapping primers technique was used for the genomic region sequencing. The evolutionary inferences and event predictions were then conducted through the Bayesian Inference method using all the acquired coding and non-coding sequences. This was supplemented by the construction of conventional phylogenetic trees using Maximum likelihood method. The results showed that adaptive evolution caused STAT gene sequence mutations between different shrimp species which led to evolutionary divergence event. Subsequently, the divergent sites were correlated to the differing expressions of STAT gene. Ultimately, this study assists in knowing the shrimp species innate immune variability and selection of disease resistant shrimps for breeding purpose. The deeper understanding of STAT gene evolution from the perspective of both purifying and adaptive approaches not only can provide better immunological insight among shrimp species, but also can be used as a good reference for immunological studies in humans or other model organisms.

Keywords: gene evolution, JAK-STAT pathway, immunology, STAT gene

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Authors: Safak Baykal

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The purpose of this study is analyzing the relationship between self leadership and social capital of people with using Social Network Analysis. In this study, two aspects of social capital will be focused: bonding, homophilous social capital (BoSC) which implies better, strong, dense or closed network ties, and bridging, heterophilous social capital (BrSC) which implies weak ties, bridging the structural holes. The other concept of the study is Trust (Tr), namely interpersonal trust, willingness to ascribe good intentions to and have confidence in the words and actions of other people. In this study, the sample group, 61 people, was selected from a private firm from the defense industry. The relation between BoSC/BrSC and Tr is shown by using Social Network Analysis (SNA) and statistical analysis with Likert type-questionnaire. The results of the analysis show the Cronbach’s alpha value is 0.73 and social capital values (BoSC/BrSC) is highly correlated with Tr values of the people.

Keywords: bonding social capital, bridging social capital, trust, social network analysis (SNA)

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Authors: Ghorab Sara, Meziani Lila, Rubin Harvey Stuart

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The rapid growth of deep learning has led to intricate and resource-intensive deep neural networks widely used in computer vision tasks. However, their complexity results in high computational demands and memory usage, hindering real-time application. To address this, research focuses on model compression techniques. The paper provides an overview of recent advancements in compressing neural networks and categorizes the various methods into four main approaches: network pruning, quantization, network decomposition, and knowledge distillation. This paper aims to provide a comprehensive outline of both the advantages and limitations of each method.

Keywords: model compression, deep neural network, pruning, knowledge distillation, quantization, low-rank decomposition

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Authors: Mary Anne Roa

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Congestion in network occurs due to exceed in aggregate demand as compared to the accessible capacity of the resources. Network congestion will increase as network speed increases and new effective congestion control methods are needed, especially for today’s very high speed networks. To address this undeniably global issue, the study focuses on the development of a fuzzy-based congestion control model concerned with allocating the resources of a computer network such that the system can operate at an adequate performance level when the demand exceeds or is near the capacity of the resources. Fuzzy logic based models have proven capable of accurately representing a wide variety of processes. The model built is based on bandwidth, the aggregate incoming traffic and the waiting time. The theoretical analysis and simulation results show that the proposed algorithm provides not only good utilization but also low packet loss.

Keywords: congestion control, queue management, computer networks, fuzzy logic

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Authors: Yinebeb Mezgebu Dagnachew, Hwee Ying Lim, Liao Wupeng, Sheau Yng Lim, Lim Sheng Jie Natalie, Veronique Angeli

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Collagen is essential for maintaining lung structure and function, and its remodeling has been associated with respiratory diseases, including chronic obstructive pulmonary disease (COPD). However, the cellular mechanisms driving collagen remodeling and the functional implications of this process in the pathophysiology of pulmonary diseases remain poorly understood. Using a mouse model of Lyve-1 expressing macrophage depletion, we found that the absence of this subpopulation of tissue-resident macrophage led to the preferential deposition of type I collagen fibers around the alveoli and bronchi in the steady state. Further analysis by polarized light microscopy revealed that the collagen fibers accumulating in the lungs depleted of Lyve-1+ macrophages were thicker and crosslinked. A decrease in MMP-9 gene expression and proteolytic activity, together with an increase in Col1a1, Timp-3 and Lox gene expression, accompanied the collagen alterations. Next, we investigated the effect of the collagen remodeling on the pathophysiology of COPD and airway function in mouse lacking Lyve-1+ macrophage exposed chronically to cigarette smoke (CS), a well-established animal model of COPD. We showed that the deposition of collagen protected mouse against the destruction of alveoli (emphysema) and bronchi thickening after CS exposure and prevented loss of airway function. Thus, we demonstrate that interstitial Lyve-1+ macrophages regulate the composition, amount, and architecture of the collagen network in the lungs and that such collagen remodeling functionally impacts the development of COPD. This study further supports the potential of targeting collagen as a promising approach to treating respiratory diseases.

Keywords: lung, extracellular matrix, chronic obstructive pulmonary disease, matrix metalloproteinases, collagen

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Authors: Alexander Hempfing

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The desire to understand business cycle fluctuations, trade interdependencies and co-movement has a long tradition in economic thinking. From input-output economics to business cycle theory, researchers aimed to find appropriate answers from an empirical as well as a theoretical perspective. This paper empirically analyses how the production structure of the global economy and several states developed over time, what their distributional properties are and if there are network specific metrics that allow identifying structurally important nodes, on a global, national and sectoral scale. For this, the World Input-Output Database was used, and different statistical methods were applied. Empirical evidence is provided that the importance of the Eastern hemisphere in the global production network has increased significantly between 2000 and 2014. Moreover, it was possible to show that the sectoral eigenvector centrality indices on a global level are power-law distributed, providing evidence that specific national sectors exist which are more critical to the world economy than others while serving as a hub within the global production network. However, further findings suggest, that global production cannot be characterized as a scale-free network.

Keywords: economic integration, industrial organization, input-output economics, network economics, production networks

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Authors: M. R. Martinez-Torres, S. L. Toral, M. Olmedilla

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Typically, virtual communities exhibit the well-known phenomenon of participation inequality, which means that only a small percentage of users is responsible of the majority of contributions. However, the sustainability of the community requires that the group of active users must be continuously nurtured with new users that gain expertise through a participation process. This paper analyzes the time evolution of Open Source Software (OSS) communities, considering users that join/abandon the community over time and several topological properties of the network when modeled as a social network. More specifically, the paper analyzes the role of those users rejoining the community and their influence in the global characteristics of the network.

Keywords: open source communities, social network Analysis, time series, virtual communities

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Authors: Ali̇ Bayram, Semih Dalkilic, Remzi Yigiter

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N-methyl-D-aspartate (NMDA) receptor is a subtype of glutamate receptor and plays a pivotal role in learning, memory, neuronal plasticity, neurotoxicity and synaptic mechanisms. Animal experiments were suggested that glutamate-induced excitotoxic injuriy and NMDA receptor blockage lead to amnesia and other neurodegenerative diseases including Alzheimer’s disease (AD), Huntington’s disease, amyotrophic lateral sclerosis. Aim of this study is to investigate association between NMDA receptor coding gene GRIN2B expression level and Alzheimer disease. The study was approved by the local ethics committees, and it was conducted according to the principles of the Declaration of Helsinki and guidelines for the Good Clinical Practice. Peripheral blood was collected 50 patients who diagnosed AD and 49 healthy control individuals. Total RNA was isolated with RNeasy midi kit (Qiagen) according to manufacturer’s instructions. After checked RNA quality and quantity with spectrophotometer, GRIN2B expression levels were detected by quantitative real time PCR (QRT-PCR). Statistical analyses were performed, variance between two groups were compared with Mann Whitney U test in GraphpadInstat algorithm with 95 % confidence interval and p < 0.05. After statistical analyses, we have determined that GRIN2B expression levels were down regulated in AD patients group with respect to control group. But expression level of this gene in each group was showed high variability. İn this study, we have determined that NMDA receptor coding gene GRIN2B expression level was down regulated in AD patients when compared with healthy control individuals. According to our results, we have speculated that GRIN2B expression level was associated with AD. But it is necessary to validate these results with bigger sample size.

Keywords: Alzheimer’s disease, N-methyl-d-aspartate receptor, NR2B, GRIN2B, mRNA expression, RT-PCR

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Authors: Younghyun Jeon, Seungjoo Maeng

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In the Ad-hoc network, the great interests regarding MIMO scheme leads to their combination, which is also utilized into its applicable network. We manage the field of the problem into Reverse-link MIMO Ad-hoc Network (RMAN) and propose the methodology to maximize the data rate with its power consumption using Node-Cooperative beamforming technique. Based on the result of mathematical optimization formulation, we design the algorithm to construct optimal orthogonal weight vector according to channel feedback and control its transmission power according to QoS-pricing value level. In simulation results, we show the validity of the proposed mathematical optimization result and algorithm which mean that the sum-rate of each link is converged into some point.

Keywords: ad-hoc network, MIMO, cooperative beamforming, transmit power

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Authors: Sultan Noman Qasem

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This paper presents an evolutionary algorithm for solving multi-objective optimization problems-based artificial neural network (ANN). The multi-objective evolutionary algorithm used in this study is genetic algorithm while ANN used is radial basis function network (RBFN). The proposed algorithm named memetic elitist Pareto non-dominated sorting genetic algorithm-based RBFNN (MEPGAN). The proposed algorithm is implemented on medical diseases problems. The experimental results indicate that the proposed algorithm is viable, and provides an effective means to design multi-objective RBFNs with good generalization capability and compact network structure. This study shows that MEPGAN generates RBFNs coming with an appropriate balance between accuracy and simplicity, comparing to the other algorithms found in literature.

Keywords: radial basis function network, hybrid learning, multi-objective optimization, genetic algorithm

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Authors: Widyani Fatwa Dewi, Subroto Athor

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In a telecommunication service provider, quantity and interval of customer demand often difficult to predict due to high dependency on customer expansion strategy and technological development. Demand arrives when a customer needs to add capacity to an existing site or build a network in a new site. Because demand is uncertain for each period, and sometimes there is a null demand for several equipments, it is categorized as intermittent. This research aims to improve demand forecast quality in Indonesia's telecommunication service providers by using Artificial Neural Network. In Artificial Neural Network, the pattern or relationship within data will be analyzed using the training process, followed by the learning process as validation stage. Historical demand data for 36 periods is used to support this research. It is found that demand forecast by using Artificial Neural Network outperforms the existing method if it is reviewed on two criteria: the forecast accuracy, using Mean Absolute Deviation (MAD), Mean of the sum of the Squares of the Forecasting Error (MSE), Mean Error (ME) and service level which is shown through inventory cost. This research is expected to increase the reference for a telecommunication demand forecast, which is currently still limited.

Keywords: artificial neural network, demand forecast, forecast accuracy, intermittent, service level, telecommunication

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Authors: Donya Ashtiani Haghighi, Amirali Baniasadi

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Coronavirus (COVID-19) disease has spread abruptly all over the world since the end of 2019. Computed tomography (CT) scans and X-ray images are used to detect this disease. Different Deep Neural Network (DNN)-based diagnosis solutions have been developed, mainly based on Convolutional Neural Networks (CNNs), to accelerate the identification of COVID-19 cases. However, CNNs lose important information in intermediate layers and require large datasets. In this paper, Capsule Network (CapsNet) is used. Capsule Network performs better than CNNs for small datasets. Accuracy of 0.9885, f1-score of 0.9883, precision of 0.9859, recall of 0.9908, and Area Under the Curve (AUC) of 0.9948 are achieved on the Capsule-based framework with hyperparameter tuning. Moreover, different dropout rates are investigated to decrease overfitting. Accordingly, a dropout rate of 0.1 shows the best results. Finally, we remove one convolution layer and decrease the number of trainable parameters to 146,752, which is a promising result.

Keywords: capsule network, dropout, hyperparameter tuning, classification

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Authors: Eu Tteum Ha, Seyoung Kim, Jeongmin Kim, Kwang Ryel Ryu

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The smart home environment backed up by IoT (internet of things) technologies enables intelligent services based on the awareness of the situation a user is currently in. One of the convenient sensors for recognizing the situations within a home is the smart meter that can monitor the status of each electrical appliance in real time. This paper aims at learning a Bayesian network that models the causal relationship between the user situations and the status of the electrical appliances. Using such a network, we can infer the current situation based on the observed status of the appliances. However, learning the conditional probability tables (CPTs) of the network requires many training examples that cannot be obtained unless the user situations are closely monitored by any means. This paper proposes a method for learning the CPT entries of the network relying only on the user feedbacks generated occasionally. In our case study with a robot vacuum cleaner, the feedback comes in whenever the user gives an order to the robot adversely from its preprogrammed setting. Given a network with randomly initialized CPT entries, our proposed method uses this feedback information to adjust relevant CPT entries in the direction of increasing the probability of recognizing the desired situations. Simulation experiments show that our method can rapidly improve the recognition performance of the Bayesian network using a relatively small number of feedbacks.

Keywords: Bayesian network, IoT, learning, situation -awareness, smart home

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Authors: Oleg Vlasovets, Fabian Schaipp, Christian L. Mueller

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we conduct a network analysis and predict the sex of 1000 participants based on ”connectome” - pairwise Pearson’s correlation across 436 brain parcels. We solve the non-smooth convex optimization problem, known under the name of Graphical Lasso, where the solution includes a low-rank component. With this solution and machine learning model for a sex prediction, we explain the brain parcels-sex connectivity patterns.

Keywords: network analysis, neuroscience, machine learning, optimization

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Authors: Sifat Rahman Ahona, Rifat Tasnim, Naima Hassan

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Data aggregation is a helpful technique for reducing the data communication overhead in wireless sensor network. One of the important tasks of data aggregation is positioning of the aggregator points. There are a lot of works done on data aggregation. But, efficient positioning of the aggregators points is not focused so much. In this paper, authors are focusing on the positioning or the placement of the aggregation points in wireless sensor network. Authors proposed an algorithm to select the aggregators positions for a scenario where aggregator nodes are more powerful than sensor nodes.

Keywords: aggregation point, data communication, data aggregation, wireless sensor network

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Authors: Seung-Hwa Baek, In-Jung Nam, Sang-Han Lee

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The development of anti-melanogenic agents is important for the prevention of serious esthetic problem like a melasma, freckle, age spots, and chloasma. The aim of this study was to investigate the anti-melanogenic effect of sesamol, an active lignan isolated from sesame seed, by mushroom and cellular tyrosinase assay, melanin content and the analysis of melanogensis-related mRNA expressions in melana cells. Sesamol showed strong inhibitory activity against the mushroom tyrosinase in a dose-dependent manner. Intracellular tyrosinase inhibition activity was also confirmed by zymography. At a concentration of 50 μM, sesamol inhibited melanin production in melan-a cells with no cytoxicity while those of phenylthiourea (PTU) as a positive control were the same condition. Sesamol significantly inhibited the expression of melanogensis-related genes, such as tyrosinase, tyrosinase-related protein-1 (TRP-1), dopachrome tautomerase (Dct), microphthalmia-associated transcription factor (MITF) and melanocortin 1 receptor (MC1R). These findings indicate that sesamol could reduce melanin biosynthesis via the downregulation of tyrosinase activity and melanin production via subsequent gene expression of melanogenesis-related proteins. Together, these results suggest that the sesamol have strong potential in inhibiting melanin biosynthesis, in that the substance may be used as a new skin-whitening agent of cosmetic materials.

Keywords: sesamol, sesame seed, melanin biosynthesis, melanogenesis-related gene, skin-whitening agent

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Authors: Özlem Ateş Sönmezoğlu, Begüm Terzi, Ahmet Yıldırım, Ramazan Özbey

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The basic criteria which determine durum wheat quality is its suitability for pasta processing that is pasta making quality. Bright yellow color is a desired property in pasta products. Durum wheat pasta making quality is affected by grain pigment content and oxidative enzymes which affect adversely bright yellow color. Of the oxidative enzymes, lipoxygenase LOX is the most effective one on oxidative bleaching of yellow pigments in durum wheat products. Thus, wheat cultivars that are high in yellow pigments but low in LOX enzyme activity should be preferred for the production of pasta with high color quality. The aim of this study was to reduce lipoxygenase activities of the backcross durum wheat lines that were previously improved for their protein quality. For this purpose, two advanced lines with different parents (TMB2 and TMB3) were used recurrent parents. Also, Gediz-75 wheat with low LOX enzyme activity was used as the gene source. In all of the generations, backcrossed plants carrying the targeted gene region (Lpx-B1.1) were selected using SSR markers by marker assisted selection method. As a result, the study will be completed in three years instead of six years required in a classical backcross breeding study, leading to the development of high-quality candidate varieties. This research has been financially supported by TÜBİTAK (Project No: 112T910).

Keywords: durum wheat, lipoxygenase, LOX, Lpx-B1.1, MAS, Triticum durum

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Authors: Richard Draper

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A supercomputer can be constructed from identical building blocks which are small parallel processors connected by a network referred to as the local network. The routers have unused ports which are used to interconnect the building blocks. These connections are referred to as the global network. The address space has a global and a local component (g, l). The conventional way to connect the building blocks is to connect (g, l) to (g’,l). If there are K blocks, this requires K global ports in each router. If a block is of size M, the result is a machine with KM routers having diameter two. To increase the size of the machine to 2K blocks, each router connects to only half of the other blocks. The result is a larger machine but also one with greater diameter. This is a crude description of how the network of the CRAY XC® is designed. In this paper, a family of interconnection networks using routers with K global and M local ports is defined. Coordinates are (c,d, p) and the global connections are (c,d,p)↔(c’,p,d) which swaps p and d. The network is denoted D3(K,M) and is called a Swapped Dragonfly. D3(K,M) has KM2 routers and has diameter three, regardless of the size of K. To produce a network of size KM2 conventionally, diameter would be an increasing function of K. The family of Swapped Dragonflies has other desirable properties: 1) D3(K,M) scales linearly in K and quadratically in M. 2) If L < K, D3(K,M) contains many copies of D3(L,M). 3) If L < M, D3(K,M) contains many copies of D3(K,L). 4) D3(K,M) can perform an all-to-all exchange in KM2+KM time which is only slightly more than the time to do a one-to-all. This paper makes several contributions. It is the first time that a swap has been used to define a linearly scalable family of networks. Structural properties of this new family of networks are thoroughly examined. A synchronizing packet header is introduced. It specifies the path to be followed and it makes it possible to define highly parallel communication algorithm on the network. Among these is an all-to-all exchange in time KM2+KM. To demonstrate the effectiveness of the swap properties of the network of the CRAY XC® and D3(K,16) are compared.

Keywords: all-to-all exchange, CRAY XC®, Dragonfly, interconnection network, packet switching, swapped network, topology

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Authors: Mansur Abdulrasheed, Hussein I. Ibrahim, Ahmed F. Umar

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Nitrification, the microbial oxidation of ammonia to nitrate (NO3-) via nitrite (NO2-) is a vital process in the biogeochemical nitrogen cycle and is performed by two distinct functional groups; ammonia oxidisers (comprised of ammonia oxidising bacteria (AOB) and ammonia oxidising archaea (AOA)) and nitrite oxidising bacteria. Autotrophic nitrification is said to occur in acidic soils, even though most laboratory cultures of isolated ammonia and nitrite oxidising bacteria fail to grow below neutral pH. Published studies revealed that soil pH is a major driver for determining the distribution and abundance of AOB and AOA. To determine whether distinct populations of nitrite oxidising bacteria within the lineages of Nitrospira and Nitrobacter are adapted to a particular range of pH as observed in ammonia oxidising organisms, the community structure of Nitrospira-like and Nitrobacter-like NOB were examined across a pH gradient (4.5–7.5) by amplifying nitrite oxido-reductase (nxrA) and 16S rRNA genes followed by denaturing gradient gel electrophoresis (DGGE). The community structure of both Nitrospira and Nitrobacter changed with soil pH, with distinct populations observed in acidic and neutral soils. The abundance of Nitrospira-like 16S rRNA and Nitrobacter-like nxrA gene copies contrasted across the pH gradient. Nitrobacter-like nxrA gene abundance decreased with increasing soil pH, whereas Nitrospira-like 16S rRNA gene abundance increased with increasing pH. Findings indicated that abundance and distributions of soil NOB is influence by soil pH.

Keywords: nitrospira, nitrobacter, nitrite-oxidizing bacteria, nitrification, pH, soil

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Authors: Abtehal Y. Anaas, Mohd. Nazmi Bin Abd. Manap

Abstract:

Meat Tenderness is one of the most important factors affecting consumers' assessment of meat quality. Variation in meat tenderness is genetically controlled and varies among breeds, and it is also influenced by environmental factors that can affect its creation during rigor mortis and postmortem. The final postmortem meat tenderization relies on the extent of proteolysis of myofibrillar proteins caused by the endogenous activity of the proteolytic calpain system. This calpain system includes different calcium-dependent cysteine proteases, and an inhibitor, calpastatin. It is widely accepted that in farm animals including chickens, the μ-calpain gene (CAPN1) is a physiological candidate gene for meat tenderness. This study aimed to identify the association of single nucleotide polymorphism (SNP) markers in the CAPN1 gene with the tenderness of chicken breast meat from two Malaysian native and commercial broiler breed crosses. Ten, five months old native chickens and ten, 42 days commercial broilers were collected from the local market and breast muscles were removed two hours after slaughter, packed separately in plastic bags and kept at -20ºC for 24 h. The tenderness phenotype for all chickens’ breast meats was determined by Warner-Bratzler Shear Force (WBSF). Thawing and cooking losses were also measured in the same breast samples before using in WBSF determination. Polymerase chain reaction (PCR) was used to identify the previously reported C7198A and G9950A SNPs in the CAPN1 gene and assess their associations with meat tenderness in the two breeds. The broiler breast meat showed lower shear force values and lower thawing loss rates than the native chickens (p<0.05), whereas there were similar in the rates of cooking loss. The study confirms some previous results that the markers CAPN1 C7198A and G9950A were not significantly associated with the variation in meat tenderness in chickens. Therefore, further study is needed to confirm the functional molecular mechanism of these SNPs and evaluate their associations in different chicken populations.

Keywords: CAPNl, chicken, meat tenderness, meat quality, SNPs

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Authors: Xiaohan Bookman, Xiaoyan Zhu

Abstract:

The outputs of non-linear feed-forward neural network are positive, which could be treated as probability when they are normalized to one. If we take Entropy-Based Principle into consideration, the outputs for each sample could be represented as the distribution of this sample for different clusters. Entropy-Based Principle is the principle with which we could estimate the unknown distribution under some limited conditions. As this paper defines two processes in Feed-Forward Neural Network, our limited condition is the abstracted features of samples which are worked out in the abstraction process. And the final outputs are the probability distribution for different clusters in the clustering process. As Entropy-Based Principle is considered into the feed-forward neural network, a clustering method is born. We have conducted some experiments on six open UCI data sets, comparing with a few baselines and applied purity as the measurement. The results illustrate that our method outperforms all the other baselines that are most popular clustering methods.

Keywords: feed-forward neural network, clustering, max-entropy principle, probabilistic models

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Authors: Mohamed Abdel-Hamid, Olfat Gamil Shaker, Doha El-Sayed Ellakwa, Eman Fathy Abdel-Maksoud

Abstract:

Introduction: Despite advances in the knowledge of the molecular virology of hepatitis C virus (HCV), the mechanisms of hepatocellular injury in HCV infection are not completely understood. Hepatitis C viral infection (HCV) influences the susceptibility to apoptosis. This could lead to insufficient antiviral immune response and persistent viral infection. Aim of this study: was to examine whether BCL-2 gene polymorphism at codon 43 (+127G/A or Ala43Thr) has an impact on development of hepatocellular carcinoma caused by chronic hepatitis C Egyptian patients. Subjects and Methods: The study included three groups; group 1: composing of 30 patients with hepatocellular carcinoma (HCC), group 2 composing of 30 patients with HCV, group 3 composing of 30 healthy subjects matching the same age and socioeconomic status were taken as a control group. Gene polymorphism of BCL2 (Ala43Thr) were evaluated by PCR-RFLP technique and measured for all patients and controls. Results: The summed 43Thr genotype was more frequent and statistically significant in HCC patients as compared to control group. This genotype of BCL2 gene may inhibit the programmed cell death which leads to disturbance in tissue and cells homeostasis and reduction in immune regulation. This result leads to viral replication and HCV persistence. Moreover, virus produces variety of mechanisms to block genes participated in apoptosis. This mechanism proves that HCV patients who have 43Thr genotype are more susceptible to HCC. Conclusion: The data suggest for the first time that the BCL2 polymorphism is associated with the susceptibility to HCC in Egyptian populations and might be used as molecular markers for evaluating HCC risk. This study clearly demonstrated that Chronic HCV exhibit a deregulation of apoptosis with the disease progression. This provides an insight into the pathogenesis of chronic HCV infection, and may contribute to the therapy.

Keywords: BCL2 gene, Hepatitis C Virus, Hepatocellular carcinoma, sensitivity, specificity, apoptosis

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Authors: Monica Sharma, Harjit Pal Singh, Jasbinder Singh, Manju Bala

Abstract:

In Voice over Internet Protocol (VoIP) system, the speech signal is degraded when passed through the network layers. The speech signal is processed through the best effort policy based IP network, which leads to the network degradations including delay, packet loss and jitter. The packet loss is the major issue of the degradation in the VoIP signal quality; even a single lost packet may generate audible distortion in the decoded speech signal. In addition to these network degradations, the quality of the speech signal is also affected by the environmental noises and coder distortions. The signal quality of the VoIP system is improved through the interleaving technique. The performance of the system is evaluated for various types of noises at different network conditions. The performance of the enhanced VoIP signal is evaluated using perceptual evaluation of speech quality (PESQ) measurement for narrow band signal.

Keywords: VoIP, interleaving, packet loss, packet size, background noise

Procedia PDF Downloads 460