Search results for: Gene prediction

Authors: M. Karimpour, L. Hitihamillage, N. Elkhoury, S. Moridpour, R. Hesami

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Rail transport authorities around the world have been facing a significant challenge when predicting rail infrastructure maintenance work for a long period of time. Generally, maintenance monitoring and prediction is conducted manually. With the restrictions in economy, the rail transport authorities are in pursuit of improved modern methods, which can provide precise prediction of rail maintenance time and location. The expectation from such a method is to develop models to minimize the human error that is strongly related to manual prediction. Such models will help them in understanding how the track degradation occurs overtime under the change in different conditions (e.g. rail load, rail type, rail profile). They need a well-structured technique to identify the precise time that rail tracks fail in order to minimize the maintenance cost/time and secure the vehicles. The rail track characteristics that have been collected over the years will be used in developing rail track degradation prediction models. Since these data have been collected in large volumes and the data collection is done both electronically and manually, it is possible to have some errors. Sometimes these errors make it impossible to use them in prediction model development. This is one of the major drawbacks in rail track degradation prediction. An accurate model can play a key role in the estimation of the long-term behavior of rail tracks. Accurate models increase the track safety and decrease the cost of maintenance in long term. In this research, a short review of rail track degradation prediction models has been discussed before estimating rail track degradation for the curve sections of Melbourne tram track system using Adaptive Network-based Fuzzy Inference System (ANFIS) model.

Keywords: ANFIS, MGT, Prediction modeling, rail track degradation.

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Authors: Mansour A. Mohamed, George G. Karady, Ali M. Yousef

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This paper proposes transient angle stability agents to enhance power system stability. The proposed transient angle stability agents divided into two strategy agents. The first strategy agent is a prediction agent that will predict power system instability. According to the prediction agent-s output, the second strategy agent, which is a control agent, is automatically calculating the amount of active power reduction that can stabilize the system and initiating a control action. The control action considered is turbine fast valving. The proposed strategies are applied to a realistic power system, the IEEE 50- generator system. Results show that the proposed technique can be used on-line for power system instability prediction and control.

Keywords: Multi-agents, Fast Valving, Power System Transient Stability, Prediction methods,

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Authors: Surender Kumar Soni, Dhirendra Pratap Singh

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Wireless Sensor Networks can be used to monitor the physical phenomenon in such areas where human approach is nearly impossible. Hence the limited power supply is the major constraint of the WSNs due to the use of non-rechargeable batteries in sensor nodes. A lot of researches are going on to reduce the energy consumption of sensor nodes. Energy map can be used with clustering, data dissemination and routing techniques to reduce the power consumption of WSNs. Energy map can also be used to know which part of the network is going to fail in near future. In this paper, Energy map is constructed using the prediction based approach. Adaptive alpha GM(1,1) model is used as the prediction model. GM(1,1) is being used worldwide in many applications for predicting future values of time series using some past values due to its high computational efficiency and accuracy.

Keywords: Adaptive Alpha GM(1, 1) Model, Energy Map, Prediction Based Data Reduction, Wireless Sensor Networks

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Authors: Nabilah Filzah Mohd Radzuan, Zalinda Othman, Azuraliza Abu Bakar, Abdul Razak Hamdan

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Uncertain data is believed to be an important issue in building up a prediction model. The main objective in the time series uncertainty analysis is to formulate uncertain data in order to gain knowledge and fit low dimensional model prior to a prediction task. This paper discusses the performance of a number of techniques in dealing with uncertain data specifically those which solve uncertain data condition by minimizing the loss of compression properties.

Keywords: Compression properties, uncertainty, uncertain time series, mining technique, weather prediction.

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Authors: S. Channgam, A. Sae-Tang, T. Termsaithong

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In this research, the occurrences of large size events in various system sizes of the Bak-Tang-Wiesenfeld sandpile model are considered. The system sizes (square lattice) of model considered here are 25×25, 50×50, 75×75 and 100×100. The cross-correlation between the ratio of sites containing 3 grain time series and the large size event time series for these 4 system sizes are also analyzed. Moreover, a prediction method of the large-size event for the 50×50 system size is also introduced. Lastly, it can be shown that this prediction method provides a slightly higher efficiency than random predictions.

Keywords: Bak-Tang-Wiesenfeld sandpile model, avalanches, cross-correlation, prediction method.

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Authors: Ulas Vural, M. Ergun Okay, E. Mesut Yildiz

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Telecommunication service providers demand accurate and precise prediction of customer churn probabilities to increase the effectiveness of their customer relation services. The large amount of customer data owned by the service providers is suitable for analysis by machine learning methods. In this study, expenditure data of customers are analyzed by using an artificial neural network (ANN). The ANN model is applied to the data of customers with different billing duration. The proposed model successfully predicts the churn probabilities at 83% accuracy for only three months expenditure data and the prediction accuracy increases up to 89% when the nine month data is used. The experiments also show that the accuracy of ANN model increases on an extended feature set with information of the changes on the bill amounts.

Keywords: Customer relationship management, churn prediction, telecom industry, deep learning, Artificial Neural Networks, ANN.

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Authors: Roya Bakhtiar, Alireza Abdolmohammadi, Hadi Hajarian, Zahra Nikousefat, Davood, Kalantar-Neyestanaki

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The objective of the present study was to determine the polymorphism in the leptin (332G>A) and its association with biometric traits in Sanjabi sheep. For this purpose, blood samples from 96 rams were taken, and tail length, width tail, circumference tail, body length, body width, and height were simultaneously recorded. PCR was performed using specific primer to amplify 463 bp fragment including exon 3 of leptin gene, and PCR products were digested by Cail restriction enzymes. The 332G>A (at 332th nucleotide of exon 3 leptin gene) that caused an amino acid change from Arg to Gln was detected by Cail (CAGNNNCTG) endonuclease, as the endonuclease cannot cut this region if G nucleotide is located in this position. Three genotypes including GG (463), GA (463, 360and 103 bp) and GG (360 bp and 103 bp) were identified after digestion by enzyme. The estimated frequencies of three genotypes including GG, GA, and AA for 332G>A locus were 0.68, 0.29 and 0.03 and those were 0.18 and 0.82 for A and G alleles, respectively. In the current study, chi-square test indicated that 332G>A positions did not deviate from the Hardy–Weinberg (HW) equilibrium. The most important reason to show HW equation was that samples used in this study belong to three large local herds with a traditional breeding system having random mating and without selection. Shannon index amount was calculated which represent an average genetic variation in Sanjabi rams. Also, heterozygosity estimated by Nei index indicated that genetic diversity of mutation in the leptin gene is moderate. Leptin gene polymorphism in the 332G>A had significant effect on body length (P<0.05) trait, and individuals with GA genotype had significantly the higher body length compared to other individuals. Although animals with GA genotype had higher body width, this difference was not statistically significant (P>0.05). This non-synonymous SNP resulted in different amino acid changes at codon positions111(R/Q). As leptin activity is localized, at least in part, in domains between amino acid residues 106-1406, it is speculated that the detected SNP at position 332 may affect the activity of leptin and may lead to different biological functions. Based to our results, due to significant effect of leptin gene polymorphism on body size traits, this gene may be used a candidate gene for improving these traits.

Keywords: Body size, Leptin gene, PCR-RFLP, Sanjabi sheep.

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Authors: Amer A. Hasan, Mehri Igci, Ersin Borazan, Rozhgar A. Khailany, Emine Bayraktar, Ahmet Arslan

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Gastric Cancer (GC) has high morbidity and fatality rate in various countries. It is still one of the most frequent and deadly diseases. Gastrokine1 (GKN1) and gastrokine2 (GKN2) genes are highly expressed in the normal stomach epithelium and play important roles in maintaining the integrity and homeostasis of stomach mucosal epithelial cells. In this study, 47 paired samples that were grouped according to the types of gastric cancer and the clinical characteristics of the patients, including gender and average of age. They were investigated with gene expression analysis and mutation screening by monitoring RT-PCR, SSCP and nucleotide sequencing techniques. Both GKN1 and GKN2 genes were observed significantly reduced found by (Wilcoxon signed rank test; p<0.05). As a result of gene screening, no mutation (no different genotype) was detected. It is considered that gene mutations are not the cause of gastrokines inactivation. In conclusion, the mRNA expression level of GKN1 and GKN2 genes statistically was decreased regardless the gender, age, or cancer type of patients. Reduced of gastrokine genes seem to occur at the initial steps of gastric cancer development.

Keywords: Diagnostic biomarker, gastric cancer, nucleotide sequencing, semi-quantitative RT-PCR.

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Authors: Grzegorz Ulacha, Ryszard Stasiński

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In the paper an effective context based lossless coding technique is presented. Three principal and few auxiliary contexts are defined. The predictor adaptation technique is an improved CoBALP algorithm, denoted CoBALP+. Cumulated predictor error combining 8 bias estimators is calculated. It is shown experimentally that indeed, the new technique is time-effective while it outperforms the well known methods having reasonable time complexity, and is inferior only to extremely computationally complex ones.

Keywords: Adaptive prediction, context coding, image losslesscoding, prediction error bias correction.

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Authors: Hyun-Woo Cho

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Detection of incipient abnormal events is important to improve safety and reliability of machine operations and reduce losses caused by failures. Improper set-ups or aligning of parts often leads to severe problems in many machines. The construction of prediction models for predicting faulty conditions is quite essential in making decisions on when to perform machine maintenance. This paper presents a multivariate calibration monitoring approach based on the statistical analysis of machine measurement data. The calibration model is used to predict two faulty conditions from historical reference data. This approach utilizes genetic algorithms (GA) based variable selection, and we evaluate the predictive performance of several prediction methods using real data. The results shows that the calibration model based on supervised probabilistic principal component analysis (SPPCA) yielded best performance in this work. By adopting a proper variable selection scheme in calibration models, the prediction performance can be improved by excluding non-informative variables from their model building steps.

Keywords: Prediction, operation monitoring, on-line data, nonlinear statistical methods, empirical model.

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Authors: Rohayu Izanwati M. R., Muhamad Ridhwan M. R., Abbe Maleyki M. J., Ahmad Zubaidi A. L., Zahri M. K.

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PPARs function as regulators of lipid and lipoprotein metabolism. The aim of the study was to compare the lipid profile between two phases of fasting and to examine the frequency and relationship of peroxisome proliferator-activated receptor, PPARα gene polymorphisms to lipid profile in fasting respondents. We conducted a case-control study protocol, which included 21 healthy volunteers without gender discrimination at the age of 18 years old. 3 ml of blood sample was drawn before the fasting phase and during the fasting phase (in Ramadhan month). 1ml of serum for the lipid profile was analyzed by using the automated chemistry analyser (Olympus, AU 400) and the data were analysed using the Paired T-Test (SPSS ver.20). DNA was extracted and PCR was conducted utilising 6 sets of primer. Primers were designed within 6 exons of interest in PPARα gene. Genetic and metabolic characteristics of fasting respondents and controls were estimated and compared. Fasting respondents were significantly have lowered the LDL levels (p=0.03). There were no polymorphisms detected except in exon 1 with 5% of this population study respectively. The polymorphisms in exon 1 of the PPARα gene were found in low frequency. Regarding the 1375G/T and 1386G/T polymorphisms in the exon 1 of the PPARα gene, the T-allele in fasting phase had no association with the decreased LDL levels (Fisher Exact Test). However this association is more promising when the sample size is larger in order to elucidate the precise impact of the polymorphisms on lipid profile in the population. In conclusion, the PPARα gene polymorphisms do not appear to affect the LDL of fasting respondents.

Keywords: Fasting, LDL, Peroxisome proliferator activated receptor alpha (PPAR-α), Polymorphisms.

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Authors: Farahnaz Amini, Woo Yun Kin, Lazwani Kolandaiveloo

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Availability of different genetic tests after completion of Human Genome Project increases the physicians’ responsibility to keep themselves update on the potential implementation of these genetic tests in their daily practice. However, due to numbers of barriers, still many of physicians are not either aware of these tests or are not willing to offer or refer their patients for genetic tests. This study was conducted an anonymous, cross-sectional, mailed-based survey to develop a primary data of Malaysian physicians’ level of knowledge and perception of gene profiling. Questionnaire had 29 questions. Total scores on selected questions were used to assess the level of knowledge. The highest possible score was 11. Descriptive statistics, one way ANOVA and chi-squared test was used for statistical analysis. Sixty three completed questionnaires were returned by 27 general practitioners (GPs) and 36 medical specialists. Responders’ age ranges from 24 to 55 years old (mean 30.2 ± 6.4). About 40% of the participants rated themselves as having poor level of knowledge in genetics in general whilst 60% believed that they have fair level of knowledge; however, almost half (46%) of the respondents felt that they were not knowledgeable about available genetic tests. A majority (94%) of the responders were not aware of any lab or company which is offering gene profiling services in Malaysia. Only 4% of participants were aware of using gene profiling for detection of dosage of some drugs. Respondents perceived greater utility of gene profiling for breast cancer (38%) compared to the colorectal familial cancer (3%). The score of knowledge ranged from 2 to 8 (mean 4.38 ± 1.67). Non- significant differences between score of knowledge of GPs and specialists were observed, with score of 4.19 and 4.58 respectively. There was no significant association between any demographic factors and level of knowledge. However, those who graduated between years 2001 to 2005 had higher level of knowledge. Overall, 83% of participants showed relatively high level of perception on value of gene profiling to detect patient’s risk of disease. However, low perception was observed for both statements of using gene profiling for general population in order to alter their lifestyle (25%) as well as having the full sequence of a patient genome for the purpose of determining a patient’s best match for treatment (18%). The lack of clinical guidelines, limited provider knowledge and awareness, lack of time and resources to educate patients, lack of evidence-based clinical information and cost of tests were the most barriers of ordering gene profiling mentioned by physicians. In conclusion Malaysian physicians who participate in this study had mediocre level of knowledge and awareness in gene profiling. The low exposure to the genetic questions and problems might be a key predictor of lack of awareness and knowledge on available genetic tests. Educational and training workshop might be useful in helping Malaysian physicians incorporate genetic profiling into practice for eligible patients.

Keywords: Gene Profiling, Knowledge, Malaysia, Physician.

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Authors: K. Sreelakshmi, P. Ramakanthkumar

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Predicting short term wind speed is essential in order to prevent systems in-action from the effects of strong winds. It also helps in using wind energy as an alternative source of energy, mainly for Electrical power generation. Wind speed prediction has applications in Military and civilian fields for air traffic control, rocket launch, ship navigation etc. The wind speed in near future depends on the values of other meteorological variables, such as atmospheric pressure, moisture content, humidity, rainfall etc. The values of these parameters are obtained from a nearest weather station and are used to train various forms of neural networks. The trained model of neural networks is validated using a similar set of data. The model is then used to predict the wind speed, using the same meteorological information. This paper reports an Artificial Neural Network model for short term wind speed prediction, which uses back propagation algorithm.

Keywords: Short term wind speed prediction, Neural networks, Back propagation.

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Authors: Mohamed A. Mahfouz, M. A. Ismail

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Biclustering is a very useful data mining technique for identifying patterns where different genes are co-related based on a subset of conditions in gene expression analysis. Association rules mining is an efficient approach to achieve biclustering as in BIMODULE algorithm but it is sensitive to the value given to its input parameters and the discretization procedure used in the preprocessing step, also when noise is present, classical association rules miners discover multiple small fragments of the true bicluster, but miss the true bicluster itself. This paper formally presents a generalized noise tolerant bicluster model, termed as μBicluster. An iterative algorithm termed as BIDENS based on the proposed model is introduced that can discover a set of k possibly overlapping biclusters simultaneously. Our model uses a more flexible method to partition the dimensions to preserve meaningful and significant biclusters. The proposed algorithm allows discovering biclusters that hard to be discovered by BIMODULE. Experimental study on yeast, human gene expression data and several artificial datasets shows that our algorithm offers substantial improvements over several previously proposed biclustering algorithms.

Keywords: Machine learning, biclustering, bi-dimensional clustering, gene expression analysis, data mining.

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Authors: H. Merhni, A. Sbiti, I. Ratbi, A. Sefiani

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The proximal spinal muscular atrophy (SMA) is a group of neuromuscular disorders characterized by progressive muscle weakness due to the degeneration and loss of anterior motor neurons of the spinal cord. Depending on the age of onset of symptoms and their evolution, four types of SMA, varying in severity, result in a mutations of the SMN gene (survival of Motor neuron). We have analyzed the DNA of 295 patients referred to our genetic counseling; since January 1996 until October 2014; for suspected SMA. The homozygous deletion of exon 7 of the SMN gene was found in 133 patients; of which, 40.6% were born to consanguineous parents. In countries like Morocco, where the frequency of heterozygotes for SMA is high, genetic testing should be offered as first-line and, after careful clinical assessment, especially in newborns and infants with congenital hypotonia unexplained and prognosis compromise. The molecular diagnosis of SMA allows a quick and certainly diagnosis, provide adequate genetic counseling for families at risk and suggest, for couples who want prenatal diagnosis. The analysis of the SMN gene is a perfect example of genetic testing with an excellent cost/benefit ratio that can be of great interest in public health, especially in low-income countries. We emphasize in this work for the benefit of the generalization of molecular diagnosis of SMA by the technique of PCR-enzymatic digestion in other centers in Morocco.

Keywords: Exon7, PCR-digestion, SMA, SMN gene.

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Authors: Fariba Esfandiary, Ghafoor Aghaie, Ali Dolati Mehr

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Wheat prediction was carried out using different meteorological variables together with agro meteorological indices in Ardebil district for the years 2004-2005 & 2005–2006. On the basis of correlation coefficients, standard error of estimate as well as relative deviation of predicted yield from actual yield using different statistical models, the best subset of agro meteorological indices were selected including daily minimum temperature (Tmin), accumulated difference of maximum & minimum temperatures (TD), growing degree days (GDD), accumulated water vapor pressure deficit (VPD), sunshine hours (SH) & potential evapotranspiration (PET). Yield prediction was done two months in advance before harvesting time which was coincide with commencement of reproductive stage of wheat (5th of June). It revealed that in the final statistical models, 83% of wheat yield variability was accounted for variation in above agro meteorological indices.

Keywords: Wheat yields prediction, agro meteorological indices, statistical models

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Authors: Shogo Kato, Daisuke Okamoto, Satoko Tsuru, Yoshinori Iizuka, Ryoko Shimono

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Healthcare safety has been perceived important. It is essential to prevent troubles in healthcare processes for healthcare safety. Trouble prevention is based on trouble prediction using accumulated knowledge on processes, troubles, and countermeasures. However, information on troubles has not been accumulated in hospitals in the appropriate structure, and it has not been utilized effectively to prevent troubles. In the previous study, however a detailed knowledge acquisition process for trouble prediction was proposed, the knowledgebase for countermeasures was not involved. In this paper, we aim to propose the structure of the knowledgebase for countermeasures, in the knowledge acquisition process for trouble prediction in healthcare process. We first design the structure of countermeasures and propose the knowledge representation form on countermeasures. Then, we evaluate the validity of the proposal, by applying it into an actual hospital.

Keywords: Trouble prevention, knowledge structure, structured knowledge, reusable knowledge.

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Authors: M. Pandi, K. Premalatha

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The DNA microarray technology concurrently monitors the expression levels of thousands of genes during significant biological processes and across the related samples. The better understanding of functional genomics is obtained by extracting the patterns hidden in gene expression data. It is handled by clustering which reveals natural structures and identify interesting patterns in the underlying data. In the proposed work clustering gene expression data is done through an Advanced Nelder Mead (ANM) algorithm. Nelder Mead (NM) method is a method designed for optimization process. In Nelder Mead method, the vertices of a triangle are considered as the solutions. Many operations are performed on this triangle to obtain a better result. In the proposed work, the operations like reflection and expansion is eliminated and a new operation called spread-out is introduced. The spread-out operation will increase the global search area and thus provides a better result on optimization. The spread-out operation will give three points and the best among these three points will be used to replace the worst point. The experiment results are analyzed with optimization benchmark test functions and gene expression benchmark datasets. The results show that ANM outperforms NM in both benchmarks.

Keywords: Spread out, simplex, multi-minima, fitness function, optimization, search area, monocyte, solution, genomes.

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Authors: Vasco A. P. Cadavez, Fernando C. Monteiro

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The objective of this study was to develop and compare alternative prediction equations of lean meat proportion (LMP) of lamb carcasses. Forty (40) male lambs, 22 of Churra Galega Bragançana Portuguese local breed and 18 of Suffolk breed were used. Lambs were slaughtered, and carcasses weighed approximately 30 min later in order to obtain hot carcass weight (HCW). After cooling at 4º C for 24-h a set of seventeen carcass measurements was recorded. The left side of carcasses was dissected into muscle, subcutaneous fat, inter-muscular fat, bone, and remainder (major blood vessels, ligaments, tendons, and thick connective tissue sheets associated with muscles), and the LMP was evaluated as the dissected muscle percentage. Prediction equations of LMP were developed, and fitting quality was evaluated through the coefficient of determination of estimation (R2 e) and standard error of estimate (SEE). Models validation was performed by k-fold crossvalidation and the coefficient of determination of prediction (R2 p) and standard error of prediction (SEP) were computed. The BT2 measurement was the best single predictor and accounted for 37.8% of the LMP variation with a SEP of 2.30%. The prediction of LMP of lamb carcasses can be based simple models, using as predictors the HCW and one fat thickness measurement.

Keywords: Bootstrap, Carcass, Lambs, Lean meat

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Authors: Shivakumar, G. S. Vijay, P. Srinivas Pai, B. R. Shrinivasa Rao

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In the present study, RBF neural networks were used for predicting the performance and emission parameters of a biodiesel engine. Engine experiments were carried out in a 4 stroke diesel engine using blends of diesel and Honge methyl ester as the fuel. Performance parameters like BTE, BSEC, Tex and emissions from the engine were measured. These experimental results were used for ANN modeling. RBF center initialization was done by random selection and by using Clustered techniques. Network was trained by using fixed and varying widths for the RBF units. It was observed that RBF results were having a good agreement with the experimental results. Networks trained by using clustering technique gave better results than using random selection of centers in terms of reduced MRE and increased prediction accuracy. The average MRE for the performance parameters was 3.25% with the prediction accuracy of 98% and for emissions it was 10.4% with a prediction accuracy of 80%.

Keywords: Radial Basis Function networks, emissions, Performance parameters, Fuzzy c means.

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Authors: [email protected]

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Breast cancer is one of the most common types in women. Early prediction of breast cancer helps physicians detect cancer in its early stages. Big cancer data need a very powerful tool to analyze and extract predictions. Machine learning and deep learning are two of the most efficient tools for predicting cancer based on textual data. In this study, we developed a fusion model of two machine learning and deep learning models. To obtain the final prediction, Long-Short Term Memory (LSTM), ensemble learning with hyper parameters optimization, and score-level fusion is used. Experiments are done on the Breast Cancer Surveillance Consortium (BCSC) dataset after balancing and grouping the class categories. Five different training scenarios are used, and the tests show that the designed fusion model improved the performance by 3.3% compared to the individual models.

Keywords: Machine learning, Deep learning, cancer prediction, breast cancer, LSTM, Score-Level Fusion.

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Authors: Chutimon Thitipornvanid, Siripun Sanguansintukul

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Choosing the right metadata is a critical, as good information (metadata) attached to an image will facilitate its visibility from a pile of other images. The image-s value is enhanced not only by the quality of attached metadata but also by the technique of the search. This study proposes a technique that is simple but efficient to predict a single human image from a website using the basic image data and the embedded metadata of the image-s content appearing on web pages. The result is very encouraging with the prediction accuracy of 95%. This technique may become a great assist to librarians, researchers and many others for automatically and efficiently identifying a set of human images out of a greater set of images.

Keywords: Metadata, Prediction, Multi-layer perceptron, Human facial image, Image mining.

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Authors: Wenlong Liu, Yucheng Liu

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This paper introduces the application of seismic wave method in earthquake prediction and early estimation. The advantages of the seismic wave method over the traditional earthquake prediction method are demonstrated. An example is presented in this study to show the accuracy and efficiency of using the seismic wave method in predicting a medium-sized earthquake swarm occurred in Wencheng, Zhejiang, China. By applying this method, correct predictions were made on the day after this earthquake swarm started and the day the maximum earthquake occurred, which provided scientific bases for governmental decision-making.

Keywords: earthquake prediction, earthquake swarm, seismicactivity method, seismic wave method, Wencheng earthquake

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Authors: Ahmad Ali Shahid, Muhammad Shakil Shaukat, Kamran Shehzad Bajwa, Abdul Qayyum Rao, Tayyab Husnain

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Agriculture is the backbone of economy of Pakistan and cotton is the major agricultural export and supreme source of raw fiber for our textile industry. To combat severe problems of insect and weed, combination of three genes namely Cry1Ac, Cry2A and EPSPS genes was transferred in locally cultivated cotton variety MNH-786 with the use of Agrobacterium mediated genetic transformation. The present study focused on the molecular screening of transgenic cotton plants at T3 generation in order to confirm integration and expression of all three genes (Cry1Ac, Cry2A and EPSP synthase) into the cotton genome. Initially, glyphosate spray assay was used for screening of transgenic cotton plants containing EPSP synthase gene at T3 generation. Transgenic cotton plants which were healthy and showed no damage on leaves were selected after 07 days of spray. For molecular analysis of transgenic cotton plants in the laboratory, the genomic DNA of these transgenic cotton plants were isolated and subjected to amplification of the three genes. Thus, seventeen out of twenty (Cry1Ac gene), ten out of twenty (Cry2A gene) and all twenty (EPSP synthase gene) were produced positive amplification. On the base of PCR amplification, ten transgenic plant samples were subjected to protein expression analysis through ELISA. The results showed that eight out of ten plants were actively expressing the three transgenes. Real-time PCR was also done to quantify the mRNA expression levels of Cry1Ac and EPSP synthase gene. Finally, eight plants were confirmed for the presence and active expression of all three genes at T3 generation.

Keywords: Agriculture, Cotton, Transformation, Cry Genes, ELISA and PCR.

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Authors: Chintanu K. Sarmah, Sandhya Samarasinghe, Don Kulasiri, Daniel Catchpoole

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Gene expression profiling is rapidly evolving into a powerful technique for investigating tumor malignancies. The researchers are overwhelmed with the microarray-based platforms and methods that confer them the freedom to conduct large-scale gene expression profiling measurements. Simultaneously, investigations into cross-platform integration methods have started gaining momentum due to their underlying potential to help comprehend a myriad of broad biological issues in tumor diagnosis, prognosis, and therapy. However, comparing results from different platforms remains to be a challenging task as various inherent technical differences exist between the microarray platforms. In this paper, we explain a simple ratio-transformation method, which can provide some common ground for cDNA and Affymetrix platform towards cross-platform integration. The method is based on the characteristic data attributes of Affymetrix- and cDNA- platform. In the work, we considered seven childhood leukemia patients and their gene expression levels in either platform. With a dataset of 822 differentially expressed genes from both these platforms, we carried out a specific ratio-treatment to Affymetrix data, which subsequently showed an improvement in the relationship with the cDNA data.

Keywords: Gene expression profiling, microarray, cDNA, Affymetrix, childhood leukaemia.

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Authors: Sadaf Sahar, Usman Qamar, Sadaf Ayaz

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In the software development lifecycle, the quality prediction techniques hold a prime importance in order to minimize future design errors and expensive maintenance. There are many techniques proposed by various researchers, but with the increasing complexity of the software lifecycle model, it is crucial to develop a flexible system which can cater for the factors which in result have an impact on the quality of the end product. These factors include properties of the software development process and the product along with its operation conditions. In this paper, a neural network (perceptron) based software quality prediction technique is proposed. Using this technique, the stakeholders can predict the quality of the resulting software during the early phases of the lifecycle saving time and resources on future elimination of design errors and costly maintenance. This technique can be brought into practical use using successful training.

Keywords: Software quality, fuzzy logic, perceptron, prediction.

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Authors: M. Maimunah, G.A. Froemming, H. Nawawi, M.I. Nafeeza, O. Effat, M.R. Rohayu Izanwati, M.S. Mohamed Saifulaman

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Attachment of the circulating monocytes to the endothelium is the earliest detectable events during formation of atherosclerosis. The adhesion molecules, chemokines and matrix proteases genes were identified to be expressed in atherogenesis. Expressions of these genes may influence structural integrity of the luminal endothelium. The aim of this study is to relate changes in the ultrastructural morphology of the aortic luminal surface and gene expressions of the endothelial surface, chemokine and MMP-12 in normal and hypercholesterolemic rabbits. Luminal endothelial surface from rabbit aortic tissue was examined by scanning electron microscopy (SEM) using low vacuum mode to ascertain ultrastructural changes in development of atherosclerotic lesion. Gene expression of adhesion molecules, MCP-1 and MMP-12 were studied by Real-time PCR. Ultrastructural observations of the aortic luminal surface exhibited changes from normal regular smooth intact endothelium to irregular luminal surface including marked globular appearance and ruptures of the membrane layer. Real-time PCR demonstrated differentially expressed of studied genes in atherosclerotic tissues. The appearance of ultrastructural changes in aortic tissue of hypercholesterolemic rabbits is suggested to have relation with underlying changes of endothelial surface molecules, chemokine and MMP-12 gene expressions.

Keywords: Ultrastructure of luminal endothelial surface, Macrophage metalloelastase (MMP-12), Real-time PCR.

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Authors: Li Kewen, Su Zhaoxin, Wang Xingmou, Zhu Jian Bing

Abstract:

Conventional reservoir prediction methods ar not sufficient to explore the implicit relation between seismic attributes, and thus data utilization is low. In order to improve the predictive classification accuracy of reservoir lithology, this paper proposes a deep learning lithology prediction method based on ResNet (Residual Neural Network) and SENet (Squeeze-and-Excitation Neural Network). The neural network model is built and trained by using seismic attribute data and lithology data of Shengli oilfield, and the nonlinear mapping relationship between seismic attribute and lithology marker is established. The experimental results show that this method can significantly improve the classification effect of reservoir lithology, and the classification accuracy is close to 70%. This study can effectively predict the lithology of undrilled area and provide support for exploration and development.

Keywords: Convolutional neural network, lithology, prediction of reservoir lithology, seismic attributes.

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Authors: Chunshien Li, Jhao-Wun Hu, Tai-Wei Chiang, Tsunghan Wu

Abstract:

Time series forecasting is an important and widely popular topic in the research of system modeling. This paper describes how to use the hybrid PSO-RLSE neuro-fuzzy learning approach to the problem of time series forecasting. The PSO algorithm is used to update the premise parameters of the proposed prediction system, and the RLSE is used to update the consequence parameters. Thanks to the hybrid learning (HL) approach for the neuro-fuzzy system, the prediction performance is excellent and the speed of learning convergence is much faster than other compared approaches. In the experiments, we use the well-known Mackey-Glass chaos time series. According to the experimental results, the prediction performance and accuracy in time series forecasting by the proposed approach is much better than other compared approaches, as shown in Table IV. Excellent prediction performance by the proposed approach has been observed.

Keywords: forecasting, hybrid learning (HL), Neuro-FuzzySystem (NFS), particle swarm optimization (PSO), recursiveleast-squares estimator (RLSE), time series

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Authors: Akram Khaleghei Ghosheh Balagh, Viliam Makis

Abstract:

In this paper, we investigate the residual life prediction problem for a partially observable system subject to two failure modes, namely a catastrophic failure and a failure due to the system degradation. The system is subject to condition monitoring and the degradation process is described by a hidden Markov model with unknown parameters. The parameter estimation procedure based on an EM algorithm is developed and the formulas for the conditional reliability function and the mean residual life are derived, illustrated by a numerical example.

Keywords: Partially observable system, hidden Markov model, competing risks, residual life prediction.

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