Search results for: RNA-related genomic features

Authors: Fatima Akhmedova, Simon Liao

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One of the most critical decision points in the design of a face recognition system is the choice of an appropriate face representation. Effective feature descriptors are expected to convey sufficient, invariant and non-redundant facial information. In this work, we propose a set of Hahn moments as a new approach for feature description. Hahn moments have been widely used in image analysis due to their invariance, non-redundancy and the ability to extract features either globally and locally. To assess the applicability of Hahn moments to Face Recognition we conduct two experiments on the Olivetti Research Laboratory (ORL) database and University of Notre-Dame (UND) X1 biometric collection. Fusion of the global features along with the features from local facial regions are used as an input for the conventional k-NN classifier. The method reaches an accuracy of 93% of correctly recognized subjects for the ORL database and 94% for the UND database.

Keywords: face recognition, Hahn moments, recognition-by-parts, time-lapse

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Authors: Seyed Mehdi Ghezi, Hesam Hasanpoor

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This scientific article explores enhancement methods for ensemble learning with the aim of improving the performance of classifiers in the analysis and classification of brain signals. The research approach in this field consists of two main parts, each with its own strengths and weaknesses. The choice of approach depends on the specific research question and available resources. By combining these approaches and leveraging their respective strengths, researchers can enhance the accuracy and reliability of classification results, consequently advancing our understanding of the brain and its functions. The first approach focuses on utilizing machine learning methods to identify the best features among the vast array of features present in brain signals. The selection of features varies depending on the research objective, and different techniques have been employed for this purpose. For instance, the genetic algorithm has been used in some studies to identify the best features, while optimization methods have been utilized in others to identify the most influential features. Additionally, machine learning techniques have been applied to determine the influential electrodes in classification. Ensemble learning plays a crucial role in identifying the best features that contribute to learning, thereby improving the overall results. The second approach concentrates on designing and implementing methods for selecting the best classifier or utilizing meta-classifiers to enhance the final results in ensemble learning. In a different section of the research, a single classifier is used instead of multiple classifiers, employing different sets of features to improve the results. The article provides an in-depth examination of each technique, highlighting their advantages and limitations. By integrating these techniques, researchers can enhance the performance of classifiers in the analysis and classification of brain signals. This advancement in ensemble learning methodologies contributes to a better understanding of the brain and its functions, ultimately leading to improved accuracy and reliability in brain signal analysis and classification.

Keywords: ensemble learning, brain signals, classification, feature selection, machine learning, genetic algorithm, optimization methods, influential features, influential electrodes, meta-classifiers

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Authors: Khalid Salhi, El Miloud Jaara, Mohammed Talibi Alaoui

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In this paper, we present a neural approach for unsupervised natural color-texture image segmentation, which is based on both Kohonen maps and mathematical morphology, using a combination of the texture and the image color information of the image, namely, the fractal features based on fractal dimension are selected to present the information texture, and the color features presented in RGB color space. These features are then used to train the network Kohonen, which will be represented by the underlying probability density function, the segmentation of this map is made by morphological watershed transformation. The performance of our color-texture segmentation approach is compared first, to color-based methods or texture-based methods only, and then to k-means method.

Keywords: segmentation, color-texture, neural networks, fractal, watershed

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Authors: Somaiyeh Dehghan, Mohammad Reza Kheirkhahan Haghighi

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The rapid growth of domains that have data with a large number of features, while the number of samples is limited has caused difficulty in constructing strong classifiers. To reduce the dimensionality of the feature space becomes an essential step in classification task. Random subspace method (or attribute bagging) is an ensemble classifier that consists of several classifiers that each base learner in ensemble has subset of features. In the present paper, we introduce Random Subspace Ensemble of CMAC neural network (RSE-CMAC), each of which has training with subset of features. Then we use this model for classification task. For evaluation performance of our model, we compare it with bagging algorithm on 36 UCI datasets. The results reveal that the new model has better performance.

Keywords: classification, random subspace, ensemble, CMAC neural network

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Authors: B. Ramesh Naik, T. Venugopal

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This paper presents a novel approach which improves the high-level semantics of images based on machine learning approach. The contemporary approaches for image retrieval and object recognition includes Fourier transforms, Wavelets, SIFT and HoG. Though these descriptors helpful in a wide range of applications, they exploit zero order statistics, and this lacks high descriptiveness of image features. These descriptors usually take benefit of primitive visual features such as shape, color, texture and spatial locations to describe images. These features do not adequate to describe high-level semantics of the images. This leads to a gap in semantic content caused to unacceptable performance in image retrieval system. A novel method has been proposed referred as discriminative learning which is derived from machine learning approach that efficiently discriminates image features. The analysis and results of proposed approach were validated thoroughly on WANG and Caltech-101 Databases. The results proved that this approach is very competitive in content-based image retrieval.

Keywords: CBIR, discriminative learning, region weight learning, scale invariant feature transforms

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Authors: Sreeja Shaw, Prosenjit Samanta, Asish Kumar Mukhopadhyay

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Cholera is still a global public health burden and is caused by Vibrio cholerae O1 and O139 serogroups. Evidence from recent outbreaks in Haiti and Yemen suggested that circulating V. cholerae O1 El Tor variant strains are continuously changing to cause more ruinous outbreaks worldwide, and most of them have emerged from the Indian subcontinents. Therefore, we studied the changing virulence characteristics along with the antibiotic resistance profile of V. cholerae O1strains isolated from seasonal outbreaks in three cholera endemic regions during 2018, Gujarat and Maharashtra in Western India (87 strains), and to compare those features with the isolates of West Bengal in Eastern India (48 strains) collected during the same period. All the strains from Western India were of Ogawa serotype, polymyxin B-sensitive, hemolytic, and contained a large fragment deletion in VSP-II genomic region similar with Yemen outbreak strains and carried more virulent Haitian genetic alleles of major virulence associated genes ctxB, tcpA, and rtxA. Conversely, 14.6% (7/48) of the strains from Eastern India were belong to the Inaba serotype, polymyxin B-resistant, non-hemolytic, harbored intact VSP-II region, classical ctxB, Haitian tcpA, and El Tor rtxA alleles. Interestingly, resistance to tetracycline and chloramphenicol was seen in isolates from both regions, which are not very common among V. cholerae O1 isolates in India. Therefore, this study indicated West Bengal as a diverse region where two different types of El Tor variant hypervirulent strains are co-existed, probably competing for their better environmental survival, which may result in severe irrepressible disease outcome in the future.

Keywords: cholera, vibrio cholerae, polymyxin B, Non-hemolytic, ctxB, tcpA, rtxA, VSP-II

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Authors: Nadia Akbarpour

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Pancreatic ductal adenocarcinoma is a forceful and obliterating illness, which is portrayed by intrusiveness, fast movement, and significant protection from treatment. Advances in neurotic arrangement and malignant growth hereditary qualities have worked on our illustrative comprehension of this infection; be that as it may, significant parts of pancreatic disease science remain ineffectively comprehended. A superior comprehension of pancreatic disease science should lead the way to more viable medicines. In the course of the most recent couple of years, there have been significant advances in the sub-atomic and organic comprehension of pancreatic malignancy. This included comprehension of the genomic intricacy of the illness, the job of pancreatic malignant growth undifferentiated organisms, the importance of the growth microenvironment, and the one-of-a-kind metabolic transformation of pancreas disease cells to acquire supplements under hypoxic climate. Endeavors have been made towards the advancement of the practical answer for its treatment with compelled achievement due to its complicated science. It is grounded that pancreatic malignancy undifferentiated cells (CSCs), yet present in a little count, contribute extraordinarily to PC inception, movement, and metastasis. Standard chemo and radiotherapeutic choices, notwithstanding, grow general endurance, the connected aftereffects are a huge concern. In the midst of the latest decade, our understanding with regards to atomic and cell pathways engaged with PC and the job of CSCs in its movement has expanded massively. By and by, the center is to target CSCs. The natural items have acquired a lot of thought as of late as they, generally, sharpen CSCs to chemotherapy and target atomic flagging engaged with different cancers, including PC. Some arranged investigations have demonstrated promising outcomes recommending that assessments in this course bring a ton to the table for the treatment of PC. Albeit preclinical investigations uncovered the significance of natural items in lessening pancreatic carcinoma, restricted examinations have been led to assess their part in centers. The current survey gives another knowledge to late advances in pancreatic malignancy science, treatment, and the current status of natural items in its expectation.

Keywords: pancreatic, genomic, organic, cancer

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Authors: Aishrith Rao

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Human activity recognition is an important aspect of video analytics, and many approaches have been recommended to enable action recognition. In this approach, the model is used to identify the action of the multiple people in the frame and classify them accordingly. A few approaches use RNNs and 3D CNNs, which are computationally expensive and cannot be trained with the small datasets which are currently available. Multi-person action recognition has been performed in order to understand the positions and action of people present in the video frame. The size of the video frame can be adjusted as a hyper-parameter depending on the hardware resources available. OpenPose has been used to calculate pose estimate using CNN to produce heap-maps, one of which provides skeleton features, which are basically joint features. The features are then extracted, and a classification algorithm can be applied to classify the action.

Keywords: human activity recognition, computer vision, pose estimates, convolutional neural networks

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Authors: Mahdieh Khalilinezhad, Silvana Dellepiane, Gianni Vernazza

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The aim of the present work is to build a model based on tissue characterization that is able to discriminate pathological and non-pathological regions from three-phasic CT images. Based on feature selection in different phases, in this research, we design a neural network system that has optimal neuron number in a hidden layer. Our approach consists of three steps: feature selection, feature reduction, and classification. For each ROI, 6 distinct set of texture features are extracted such as first order histogram parameters, absolute gradient, run-length matrix, co-occurrence matrix, autoregressive model, and wavelet, for a total of 270 texture features. We show that with the injection of liquid and the analysis of more phases the high relevant features in each region changed. Our results show that for detecting HCC tumor phase3 is the best one in most of the features that we apply to the classification algorithm. The percentage of detection between these two classes according to our method, relates to first order histogram parameters with the accuracy of 85% in phase 1, 95% phase 2, and 95% in phase 3.

Keywords: multi-phasic liver images, texture analysis, neural network, hidden layer

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Authors: Han Xue, Zhang Lanyue

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In order to seek more effective feature extraction technology, feature extraction method based on MFCC combined with vector hydrophone is exposed in the paper. The sound pressure signal and particle velocity signal of two kinds of ships are extracted by using MFCC and its evolution form, and the extracted features are fused by using fisher-ratio and correlated distance criterion. The features are then identified by BP neural network. The results showed that MFCC, First-Order Differential MFCC and Second-Order Differential MFCC features can be used as effective features for recognition of underwater targets, and the fusion feature can improve the recognition rate. Moreover, the results also showed that the recognition rate of the particle velocity signal is higher than that of the sound pressure signal, and it reflects the superiority of vector signal processing.

Keywords: vector information, MFCC, differential MFCC, fusion feature, BP neural network

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Authors: Kawalpreet Kalra, Alpana Goel

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The behaviour of the rotational bands should be smooth but due to large amount of inertia and decreased pairing it is not so. Many experiments have been done in the last few decades, and a large amount of data is available for comprehensive study in this region. Peculiar features like signature dependence, signature inversion, and signature reversal are observed in many two quasiparticle rotational bands of doubly odd and doubly even nuclei. At high rotational frequencies, signature and parity are the only two good quantum numbers available to label a state. Signature quantum number is denoted by α. Even-angular momentum states of a rotational band have α =0, and the odd-angular momentum states have α =1. It has been observed that the odd-spin members lie lower in energy up to a certain spin Ic; the normal signature dependence is restored afterwards. This anomalous feature is termed as signature inversion. The systematic of signature inversion in high-j orbitals for doubly odd rare earth nuclei have been done. Many unusual features like signature dependence, signature inversion and signature reversal are observed in rotational bands of even-even/odd-odd nuclei. Attempts have been made to understand these phenomena using several models. These features have been analyzed within the framework of the Two Quasiparticle Plus Rotor Model (TQPRM).

Keywords: rotational bands, signature dependence, signature quantum number, two quasiparticle

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Authors: Gong Zhilin, Jing Yang, Jian Yin

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The purpose of this paper is to develop a novel system for credit card fraud detection based on sequential modeling of data using hybrid deep learning models. The projected model encapsulates five major phases are pre-processing, imbalance-data handling, feature extraction, optimal feature selection, and fraud detection with an ensemble classifier. The collected raw data (input) is pre-processed to enhance the quality of the data through alleviation of the missing data, noisy data as well as null values. The pre-processed data are class imbalanced in nature, and therefore they are handled effectively with the K-means clustering-based SMOTE model. From the balanced class data, the most relevant features like improved Principal Component Analysis (PCA), statistical features (mean, median, standard deviation) and higher-order statistical features (skewness and kurtosis). Among the extracted features, the most optimal features are selected with the Self-improved Arithmetic Optimization Algorithm (SI-AOA). This SI-AOA model is the conceptual improvement of the standard Arithmetic Optimization Algorithm. The deep learning models like Long Short-Term Memory (LSTM), Convolutional Neural Network (CNN), and optimized Quantum Deep Neural Network (QDNN). The LSTM and CNN are trained with the extracted optimal features. The outcomes from LSTM and CNN will enter as input to optimized QDNN that provides the final detection outcome. Since the QDNN is the ultimate detector, its weight function is fine-tuned with the Self-improved Arithmetic Optimization Algorithm (SI-AOA).

Keywords: credit card, data mining, fraud detection, money transactions

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Authors: Mohammad Arabi

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The development of advanced technologies in the field of signal processing and vibration analysis has enabled more accurate analysis and fault detection in electrical systems. This research investigates the application of temporal and frequency features in detecting faults in electric motor bearings, aiming to enhance fault detection accuracy and prevent unexpected failures. The use of methods such as deep learning algorithms and neural networks in this process can yield better results. The main objective of this research is to evaluate the efficiency and accuracy of methods based on temporal and frequency features in identifying faults in electric motor bearings to prevent sudden breakdowns and operational issues. Additionally, the feasibility of using techniques such as machine learning and optimization algorithms to improve the fault detection process is also considered. This research employed an experimental method and random sampling. Vibration signals were collected from electric motors under normal and faulty conditions. After standardizing the data, temporal and frequency features were extracted. These features were then analyzed using statistical methods such as analysis of variance (ANOVA) and t-tests, as well as machine learning algorithms like artificial neural networks and support vector machines (SVM). The results showed that using temporal and frequency features significantly improves the accuracy of fault detection in electric motor bearings. ANOVA indicated significant differences between normal and faulty signals. Additionally, t-tests confirmed statistically significant differences between the features extracted from normal and faulty signals. Machine learning algorithms such as neural networks and SVM also significantly increased detection accuracy, demonstrating high effectiveness in timely and accurate fault detection. This study demonstrates that using temporal and frequency features combined with machine learning algorithms can serve as an effective tool for detecting faults in electric motor bearings. This approach not only enhances fault detection accuracy but also simplifies and streamlines the detection process. However, challenges such as data standardization and the cost of implementing advanced monitoring systems must also be considered. Utilizing temporal and frequency features in fault detection of electric motor bearings, along with advanced machine learning methods, offers an effective solution for preventing failures and ensuring the operational health of electric motors. Given the promising results of this research, it is recommended that this technology be more widely adopted in industrial maintenance processes.

Keywords: electric motor, fault detection, frequency features, temporal features

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Authors: Muhammet Baldan, Emel Timuçin

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Generally, absorption and bioavailability increase if solubility increases; therefore, it is crucial to predict them in drug discovery applications. Molecular descriptors and Molecular properties are traditionally used for the prediction of water solubility. There are various key descriptors that are used for this purpose, namely Drogan Descriptors, Morgan Descriptors, Maccs keys, etc., and each has different prediction capabilities with differentiating successes between different data sets. Another source for the prediction of solubility is structural features; they are commonly used for the prediction of solubility. However, there are little to no studies that combine three or more properties or descriptors for prediction to produce a more powerful prediction model. Unlike available models, we used a combination of those features in a random forest machine learning model for improved solubility prediction to better predict and, therefore, contribute to drug discovery systems.

Keywords: solubility, random forest, molecular descriptors, maccs keys

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Authors: Mpho Mokoatle, Darlington Mapiye, James Mashiyane, Stephanie Muller, Gciniwe Dlamini

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Great advances in high-throughput sequencing technologies have resulted in availability of huge amounts of sequencing data in public and private repositories, enabling a holistic understanding of complex biological phenomena. Sequence data are used for a wide range of applications such as gene annotations, expression studies, personalized treatment and precision medicine. However, this rapid growth in sequence data poses a great challenge which calls for novel data processing and analytic methods, as well as huge computing resources. In this work, a machine and statistical learning approach for DNA sequence classification based on $k$-mer representation of sequence data is proposed. The approach is tested using whole genome sequences of Mycobacterium tuberculosis (MTB) isolates to (i) reduce the size of genomic sequence data, (ii) identify an optimum size of k-mers and utilize it to build classification models, (iii) predict the phenotype from whole genome sequence data of a given bacterial isolate, and (iv) demonstrate computing challenges associated with the analysis of whole genome sequence data in producing interpretable and explainable insights. The classification models were trained on 104 whole genome sequences of MTB isoloates. Cluster analysis showed that k-mers maybe used to discriminate phenotypes and the discrimination becomes more concise as the size of k-mers increase. The best performing classification model had a k-mer size of 10 (longest k-mer) an accuracy, recall, precision, specificity, and Matthews Correlation coeffient of 72.0%, 80.5%, 80.5%, 63.6%, and 0.4 respectively. This study provides a comprehensive approach for resampling whole genome sequencing data, objectively selecting a k-mer size, and performing classification for phenotype prediction. The analysis also highlights the importance of increasing the k-mer size to produce more biological explainable results, which brings to the fore the interplay that exists amongst accuracy, computing resources and explainability of classification results. However, the analysis provides a new way to elucidate genetic information from genomic data, and identify phenotype relationships which are important especially in explaining complex biological mechanisms.

Keywords: AWD-LSTM, bootstrapping, k-mers, next generation sequencing

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Authors: Darlington Mapiye, Mpho Mokoatle, James Mashiyane, Stephanie Muller, Gciniwe Dlamini

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Great advances in high-throughput sequencing technologies have resulted in availability of huge amounts of sequencing data in public and private repositories, enabling a holistic understanding of complex biological phenomena. Sequence data are used for a wide range of applications such as gene annotations, expression studies, personalized treatment and precision medicine. However, this rapid growth in sequence data poses a great challenge which calls for novel data processing and analytic methods, as well as huge computing resources. In this work, a machine and statistical learning approach for DNA sequence classification based on k-mer representation of sequence data is proposed. The approach is tested using whole genome sequences of Mycobacterium tuberculosis (MTB) isolates to (i) reduce the size of genomic sequence data, (ii) identify an optimum size of k-mers and utilize it to build classification models, (iii) predict the phenotype from whole genome sequence data of a given bacterial isolate, and (iv) demonstrate computing challenges associated with the analysis of whole genome sequence data in producing interpretable and explainable insights. The classification models were trained on 104 whole genome sequences of MTB isoloates. Cluster analysis showed that k-mers maybe used to discriminate phenotypes and the discrimination becomes more concise as the size of k-mers increase. The best performing classification model had a k-mer size of 10 (longest k-mer) an accuracy, recall, precision, specificity, and Matthews Correlation coeffient of 72.0 %, 80.5 %, 80.5 %, 63.6 %, and 0.4 respectively. This study provides a comprehensive approach for resampling whole genome sequencing data, objectively selecting a k-mer size, and performing classification for phenotype prediction. The analysis also highlights the importance of increasing the k-mer size to produce more biological explainable results, which brings to the fore the interplay that exists amongst accuracy, computing resources and explainability of classification results. However, the analysis provides a new way to elucidate genetic information from genomic data, and identify phenotype relationships which are important especially in explaining complex biological mechanisms

Keywords: AWD-LSTM, bootstrapping, k-mers, next generation sequencing

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Authors: Yuanchao Sang, Zhihao Gong, Longsheng Chen, Long Chen

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Clothing fashion represents a human’s aesthetic appreciation towards everyday outfits and appetite for fashion, and it reflects the development of status in society, humanity, and economics. However, modelling fashion by machine is extremely challenging because fashion is too abstract to be efficiently described by machines. Even human beings can hardly reach a consensus about fashion. In this paper, we are dedicated to answering a fundamental fashion-related problem: what image feature best describes clothing fashion? To address this issue, we have designed and evaluated various image features, ranging from traditional low-level hand-crafted features to mid-level style awareness features to various current popular deep neural network-based features, which have shown state-of-the-art performance in various vision tasks. In summary, we tested the following 9 feature representations: color, texture, shape, style, convolutional neural networks (CNNs), CNNs with distance metric learning (CNNs&DML), AutoEncoder, CNNs with multiple layer combination (CNNs&MLC) and CNNs with dynamic feature clustering (CNNs&DFC). Finally, we validated the performance of these features on two publicly available datasets. Quantitative and qualitative experimental results on both intra-domain and inter-domain fashion clothing image retrieval showed that deep learning based feature representations far outweigh traditional hand-crafted feature representation. Additionally, among all deep learning based methods, CNNs with explicit feature clustering performs best, which shows feature clustering is essential for discriminative fashion feature representation.

Keywords: convolutional neural network, feature representation, image processing, machine modelling

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Authors: Saad M. Darwish, Mohamed A. El-Iskandarani, Guitar M. Shawkat

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Nowadays, the amount of available multimedia data is continuously on the rise. The need to find a required image for an ordinary user is a challenging task. Content based image retrieval (CBIR) computes relevance based on the visual similarity of low-level image features such as color, textures, etc. However, there is a gap between low-level visual features and semantic meanings required by applications. The typical method of bridging the semantic gap is through the automatic image annotation (AIA) that extracts semantic features using machine learning techniques. In this paper, a multi-label image annotation system guided by Firefly and Bayesian method is proposed. Firstly, images are segmented using the maximum variance intra cluster and Firefly algorithm, which is a swarm-based approach with high convergence speed, less computation rate and search for the optimal multiple threshold. Feature extraction techniques based on color features and region properties are applied to obtain the representative features. After that, the images are annotated using translation model based on the Net Bayes system, which is efficient for multi-label learning with high precision and less complexity. Experiments are performed using Corel Database. The results show that the proposed system is better than traditional ones for automatic image annotation and retrieval.

Keywords: feature extraction, feature selection, image annotation, classification

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Authors: So-Young Lee, Myoung-Won Oh, Soon-Cheol Eom, Yeon-Won Suh

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Buildings produce more than one thirds of the total energy consumption and CO₂ emissions. Korean government agency pronounced and initiated Zero Energy Buildings policy for construction as of 2025. The net zero energy design features include passive (daylight, layout, materials, insulation, finishes, etc.) and active (renewable energy sources) elements. The Zero Energy House recently built in Nowon-gu, Korea is provided for 121 households as a public rental housing complex. However most of public rental housing did not include sustainable features which can reduce housing maintaining cost significantly including energy cost. It is necessary to implement net zero design features to the obsolete public rental housing during the remodeling procedure since it can reduce housing cost in long term. The purpose of this study is to investigate sustainable design elements implemented in Net Zero Energy House in Korea and passive and active housing design features in order to apply the sustainable features to the case public rental apartment for remodeling. Housing complex cases in this study are Nowan zero Energy house, Gangnam Bogemjari House, and public rental housings built in more than 20 years in Seoul areas. As results, energy consumption in public rental housing built in 5-years can be improved by exterior surfaces. Energy optimizing in case housing built in more than 20 years can be enhanced by renovated materials, insulation, replacement of windows, exterior finishes, lightings, gardening, water, renewable energy installation, Green IT except for sunlight and layout of buildings. Further life costing analysis is needed for energy optimizing for case housing alternatives.

Keywords: affordable housing, remodeling, sustainable design, zero-energy house

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Authors: Mukolwe D. Lubembe, Odongo O. David, Githaka Naftali, Kanduma Esther, Marinda Oosthuizen, Kgomotso P. Sibeko

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Theileriosis is a tick-borne disease of cattle caused by an apicomplexan protozoan parasite of the genus Theileria. In eastern and southern Africa, Theileria infections in cattle are caused by the species Theileria parva whose natural reservoir is the African buffalo (Syncerus caffer). Currently, East Coast Fever (ECF) caused by the cattle-derived Theileria parva is still a major problem in eastern Africa and some parts of southern Africa but not in South Africa following its eradication in the 1950s. However, Corridor disease (CD) caused by the buffalo-derived Theileria parva still remains a concern in South Africa. The diversity of Theileria parva in South Africa in comparison to other affected countries is poorly defined yet its known to be the survival strategy of this parasite. We assessed the antigenic diversity of Theileria parva isolates from Buffalo and cattle at the wildlife-livestock interface comparing samples from South Africa, Zimbabwe, Kenya, Tanzania, and Uganda. Antigenic epitopes of eight schizont antigen genes (Tp1, Tp3, Tp4, Tp5, Tp6, Tp7, Tp8 and Tp10) were amplified by PCR from genomic DNA extracted from blood samples collected from cattle and buffalo at the wildlife-livestock interface. Amplicons were purified and then sequenced on NGS platform. Full length open reading frames (ORFs) of two schizont antigen genes (Tp2 and Tp9) and one sporozoite antigen gene, p67 were also amplified from genomic DNA. Amplicons were then purified and cloned for sequencing. Analysis was based on sequence differences in the genes. Preliminary results show an extensively diverse population of Theileria parva circulating in buffalo and cattle populations at the wildlife-livestock interface. Diversity of the antigen genes contributes to the evasion of the immune system of the host by Theileria parva. This possess a concern in that, some of the Theileria parva populations may re-assort and become adapted to cattle to cause a form of theileriosis that is as fatal as ECF in areas where ECF was eradicated or is absent

Keywords: Theileria parva, east coast fever, corridor diseases, antigen genes, diversity

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Authors: Baljit Singh Khehra, Amar Partap Singh Pharwaha

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Clusters of Microcalcifications (MCCs) are most frequent symptoms of Ductal Carcinoma in Situ (DCIS) recognized by mammography. Least-Square Support Vector Machine (LS-SVM) is a variant of the standard SVM. In the paper, LS-SVM is proposed as a classifier for classifying MCCs as benign or malignant based on relevant extracted features from enhanced mammogram. To establish the credibility of LS-SVM classifier for classifying MCCs, a comparative evaluation of the relative performance of LS-SVM classifier for different kernel functions is made. For comparative evaluation, confusion matrix and ROC analysis are used. Experiments are performed on data extracted from mammogram images of DDSM database. A total of 380 suspicious areas are collected, which contain 235 malignant and 145 benign samples, from mammogram images of DDSM database. A set of 50 features is calculated for each suspicious area. After this, an optimal subset of 23 most suitable features is selected from 50 features by Particle Swarm Optimization (PSO). The results of proposed study are quite promising.

Keywords: clusters of microcalcifications, ductal carcinoma in situ, least-square support vector machine, particle swarm optimization

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Authors: Tomyslav Sledevič, Artūras Serackis, Gintautas Tamulevičius, Dalius Navakauskas

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This paper presents a comparative evaluation of features extraction algorithm for a real-time isolated word recognition system based on FPGA. The Mel-frequency cepstral, linear frequency cepstral, linear predictive and their cepstral coefficients were implemented in hardware/software design. The proposed system was investigated in the speaker-dependent mode for 100 different Lithuanian words. The robustness of features extraction algorithms was tested recognizing the speech records at different signals to noise rates. The experiments on clean records show highest accuracy for Mel-frequency cepstral and linear frequency cepstral coefficients. For records with 15 dB signal to noise rate the linear predictive cepstral coefficients give best result. The hard and soft part of the system is clocked on 50 MHz and 100 MHz accordingly. For the classification purpose, the pipelined dynamic time warping core was implemented. The proposed word recognition system satisfies the real-time requirements and is suitable for applications in embedded systems.

Keywords: isolated word recognition, features extraction, MFCC, LFCC, LPCC, LPC, FPGA, DTW

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Authors: Ramy Hammady, Sylvester Arnab

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Significant attention has been directed to adopt game interventions practically to change certain behaviours in many disciplines such as health, education, psychology through many years. That’s due to the intrinsic motivation that games can cause and the substantial impact the games can leave on the player. Many review papers were induced to highlight and measure the effectiveness of the game’s interventions on changing behaviours; however, most of these studies neglected the game design process itself and the game features and elements that can stimuli changing behaviours. Therefore, this paper aims to identify the most game design mechanics and features that are the most influencing on changing behaviour during or after games interventions. This paper also sheds light on the theories of changing behaviours that clearly can led the game design process. This study gives directions to game designers to spot the most influential game features and mechanics for changing behaviour games in order to exploit it on the same manner.

Keywords: behaviour change, game design, serious gaming, gamification, review

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Authors: Lavanya Srinivasan

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Biometric identification is to identify unique features in a person like fingerprints, iris, ear, and voice recognition that need the subject's permission and physical contact. Gait biometric is used to identify the unique gait of the person by extracting moving features. The main advantage of gait biometric to identify the gait of a person at a distance, without any physical contact. In this work, the gait biometric is used for person re-identification. The person walking naturally compared with the same person walking with bag, coat, and case recorded using longwave infrared, short wave infrared, medium wave infrared, and visible cameras. The videos are recorded in rural and in urban environments. The pre-processing technique includes human identified using YOLO, background subtraction, silhouettes extraction, and synthesis Gait Entropy Image by averaging the silhouettes. The moving features are extracted from the Gait Entropy Energy Image. The extracted features are dimensionality reduced by the principal component analysis and recognised using different classifiers. The comparative results with the different classifier show that linear discriminant analysis outperforms other classifiers with 95.8% for visible in the rural dataset and 94.8% for longwave infrared in the urban dataset.

Keywords: biometric, gait, silhouettes, YOLO

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Authors: Raffaele A. Calogero

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RNAseq represents an attractive methodology for the detection of functional genomic variants. RNAseq results obtained from polyA+ RNA selection protocol (POLYA) and from exonic regions capturing protocol (ACCESS) indicate that ACCESS detects 10% more coding SNV/INDELs with respect to POLYA. ACCESS requires less reads for coding SNV detection with respect to POLYA. However, if the analysis aims at identifying SNV/INDELs also in the 5’ and 3’ UTRs, POLYA is definitively the preferred method. No particular advantage comes from ACCESS or POLYA in the detection of fusion transcripts.

Keywords: fusion transcripts, INDEL, RNA-seq, WES, SNV

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Authors: Faheema Khan

Abstract:

To investigate the ability of sensitive and tolerant genotype of Glycine max to adapt to a saline environment in a field, we examined the growth performance, water relation and activities of antioxidant enzymes in relation to photosynthetic rate, chlorophyll a fluorescence, photosynthetic pigment concentration, protein and proline in plants exposed to salt stress. Ten soybean genotypes (Pusa-20, Pusa-40, Pusa-37, Pusa-16, Pusa-24, Pusa-22, BRAGG, PK-416, PK-1042, and DS-9712) were selected and grown hydroponically. After 3 days of proper germination, the seedlings were transferred to Hoagland’s solution (Hoagland and Arnon 1950). The growth chamber was maintained at a photosynthetic photon flux density of 430 μmol m−2 s−1, 14 h of light, 10 h of dark and a relative humidity of 60%. The nutrient solution was bubbled with sterile air and changed on alternate days. Ten-day-old seedlings were given seven levels of salt in the form of NaCl viz., T1 = 0 mM NaCl, T2=25 mM NaCl, T3=50 mM NaCl, T4=75 mM NaCl, T5=100 mM NaCl, T6=125 mM NaCl, T7=150 mM NaCl. The investigation showed that genotype Pusa-24, PK-416 and Pusa-20 appeared to be the most salt-sensitive. genotypes as inferred from their significantly reduced length, fresh weight and dry weight in response to the NaCl exposure. Pusa-37 appeared to be the most tolerant genotype since no significant effect of NaCl treatment on growth was found. We observed a greater decline in the photosynthetic variables like photosynthetic rate, chlorophyll fluorescence and chlorophyll content, in salt-sensitive (Pusa-24) genotype than in salt-tolerant Pusa-37 under high salinity. Numerous primers were verified on ten soybean genotypes obtained from Operon technologies among which 30 RAPD primers shown high polymorphism and genetic variation. The Jaccard’s similarity coefficient values for each pairwise comparison between cultivars were calculated and similarity coefficient matrix was constructed. The closer varieties in the cluster behaved similar in their response to salinity tolerance. Intra-clustering within the two clusters precisely grouped the 10 genotypes in sub-cluster as expected from their physiological findings.Salt tolerant genotype Pusa-37, was further analysed by 2-Dimensional gel electrophoresis to analyse the differential expression of proteins at high salt stress. In the Present study, 173 protein spots were identified. Of these, 40 proteins responsive to salinity were either up- or down-regulated in Pusa-37. Proteomic analysis in salt-tolerant genotype (Pusa-37) led to the detection of proteins involved in a variety of biological processes, such as protein synthesis (12 %), redox regulation (19 %), primary and secondary metabolism (25 %), or disease- and defence-related processes (32 %). In conclusion, the soybean plants in our study responded to salt stress by changing their protein expression pattern. The photosynthetic, biochemical and molecular study showed that there is variability in salt tolerance behaviour in soybean genotypes. Pusa-24 is the salt-sensitive and Pusa-37 is the salt-tolerant genotype. Moreover this study gives new insights into the salt-stress response in soybean and demonstrates the power of genomic and proteomic approach in plant biology studies which finally could help us in identifying the possible regulatory switches (gene/s) controlling the salt tolerant genotype of the crop plants and their possible role in defence mechanism.

Keywords: glycine max, salt stress, RAPD, genomic and proteomic variability

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Authors: Zin Mar Lwin

Abstract:

Brain Computer Interface (BCI) Systems have developed for people who suffer from severe motor disabilities and challenging to communicate with their environment. BCI allows them for communication by a non-muscular way. For communication between human and computer, BCI uses a type of signal called Electroencephalogram (EEG) signal which is recorded from the human„s brain by means of an electrode. The electroencephalogram (EEG) signal is an important information source for knowing brain processes for the non-invasive BCI. Translating human‟s thought, it needs to classify acquired EEG signal accurately. This paper proposed a typical EEG signal classification system which experiments the Dataset from “Purdue University.” Independent Component Analysis (ICA) method via EEGLab Tools for removing artifacts which are caused by eye blinks. For features extraction, the Time and Frequency features of non-stationary EEG signals are extracted by Matching Pursuit (MP) algorithm. The classification of one of five mental tasks is performed by Multi_Class Support Vector Machine (SVM). For SVMs, the comparisons have been carried out for both 1-against-1 and 1-against-all methods.

Keywords: BCI, EEG, ICA, SVM

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Authors: Bushra Zafar, Usman Qamar

Abstract:

Large data sample size and dimensions render the effectiveness of conventional data mining methodologies. A data mining technique are important tools for collection of knowledgeable information from variety of databases and provides supervised learning in the form of classification to design models to describe vital data classes while structure of the classifier is based on class attribute. Classification efficiency and accuracy are often influenced to great extent by noisy and undesirable features in real application data sets. The inherent natures of data set greatly masks its quality analysis and leave us with quite few practical approaches to use. To our knowledge first time, we present a new approach for investigation of structure and quality of datasets by providing a targeted analysis of localization of noisy and irrelevant features of data sets. Machine learning is based primarily on feature selection as pre-processing step which offers us to select few features from number of features as a subset by reducing the space according to certain evaluation criterion. The primary objective of this study is to trim down the scope of the given data sample by searching a small set of important features which may results into good classification performance. For this purpose, a heuristic for wrapper-based feature selection using genetic algorithm and for discriminative feature selection an external classifier are used. Selection of feature based on its number of occurrence in the chosen chromosomes. Sample dataset has been used to demonstrate proposed idea effectively. A proposed method has improved average accuracy of different datasets is about 95%. Experimental results illustrate that proposed algorithm increases the accuracy of prediction of different diseases.

Keywords: data mining, generic algorithm, KNN algorithms, wrapper based feature selection

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

Abstract:

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: R. K. Chaurasiya, N. D. Londhe, S. Ghosh

Abstract:

The study of the electrical signals produced by neural activities of human brain is called Electroencephalography. In this paper, we propose an automatic and efficient EEG signal classification approach. The proposed approach is used to classify the EEG signal into two classes: epileptic seizure or not. In the proposed approach, we start with extracting the features by applying Discrete Wavelet Transform (DWT) in order to decompose the EEG signals into sub-bands. These features, extracted from details and approximation coefficients of DWT sub-bands, are used as input to Principal Component Analysis (PCA). The classification is based on reducing the feature dimension using PCA and deriving the support-vectors using Support Vector Machine (SVM). The experimental are performed on real and standard dataset. A very high level of classification accuracy is obtained in the result of classification.

Keywords: discrete wavelet transform, electroencephalogram, pattern recognition, principal component analysis, support vector machine

Procedia PDF Downloads 636