Journal Articles
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Item Two Automated Techniques for Carotid Lumen Diameter Measurement: Regional versus Boundary Approaches(Springer New York LLC barbara.b.bertram@gsk.com, 2016) Araki, T.; Kumar, P.K.; Suri, H.S.; Ikeda, N.; Gupta, A.; Saba, L.; Rajan, J.; Lavra, F.; Sharma, A.M.; Shafique, S.; Nicolaïdes, A.; Laird, J.R.; Suri, J.S.The degree of stenosis in the carotid artery can be predicted using automated carotid lumen diameter (LD) measured from B-mode ultrasound images. Systolic velocity-based methods for measurement of LD are subjective. With the advancement of high resolution imaging, image-based methods have started to emerge. However, they require robust image analysis for accurate LD measurement. This paper presents two different algorithms for automated segmentation of the lumen borders in carotid ultrasound images. Both algorithms are modeled as a two stage process. Stage one consists of a global-based model using scale-space framework for the extraction of the region of interest. This stage is common to both algorithms. Stage two is modeled using a local-based strategy that extracts the lumen interfaces. At this stage, the algorithm-1 is modeled as a region-based strategy using a classification framework, whereas the algorithm-2 is modeled as a boundary-based approach that uses the level set framework. Two sets of databases (DB), Japan DB (JDB) (202 patients, 404 images) and Hong Kong DB (HKDB) (50 patients, 300 images) were used in this study. Two trained neuroradiologists performed manual LD tracings. The mean automated LD measured was 6.35 ± 0.95 mm for JDB and 6.20 ± 1.35 mm for HKDB. The precision-of-merit was: 97.4 % and 98.0 % w.r.t to two manual tracings for JDB and 99.7 % and 97.9 % w.r.t to two manual tracings for HKDB. Statistical tests such as ANOVA, Chi-Squared, T-test, and Mann-Whitney test were conducted to show the stability and reliability of the automated techniques. © 2016, Springer Science+Business Media New York.Item Gene essentiality, conservation index and coevolution of genes in cyanobacteria(Public Library of Science plos@plos.org, 2017) Tiruveedula, G.S.S.; Wangikar, P.P.Cyanobacteria, a group of photosynthetic prokaryotes, dominate the earth with ? 1015 g wet biomass. Despite diversity in habitats and an ancient origin, cyanobacterial phylum has retained a significant core genome. Cyanobacteria are being explored for direct conversion of solar energy and carbon dioxide into biofuels. For this, efficient cyanobacterial strains will need to be designed via metabolic engineering. This will require identification of target knockouts to channelize the flow of carbon toward the product of interest while minimizing deletions of essential genes. We propose "Gene Conservation Index" (GCI) as a quick measure to predict gene essentiality in cyanobacteria. GCI is based on phylogenetic profile of a gene constructed with a reduced dataset of cyanobacterial genomes. GCI is the percentage of organism clusters in which the query gene is present in the reduced dataset. Of the 750 genes deemed to be essential in the experimental study on S. elongatus PCC 7942, we found 494 to be conserved across the phylum which largely comprise of the essential metabolic pathways. On the contrary, the conserved but non-essential genes broadly comprise of genes required under stress conditions. Exceptions to this rule include genes such as the glycogen synthesis and degradation enzymes, deoxyribose-phosphate aldolase (DERA), glucose-6-phosphate 1-dehydrogenase (zwf) and fructose-1,6-bisphosphatase class1, which are conserved but non-essential. While the essential genes are to be avoided during gene knockout studies as potentially lethal deletions, the non-essential but conserved set of genes could be interesting targets for metabolic engineering. Further, we identify clusters of co-evolving genes (CCG), which provide insights that may be useful in annotation. Principal component analysis (PCA) plots of the CCGs are demonstrated as data visualization tools that are complementary to the conventional heatmaps. Our dataset consists of phylogenetic profiles for 23,643 non-redundant cyanobacterial genes. We believe that the data and the analysis presented here will be a great resource to the scientific community interested in cyanobacteria. © 2017 Tiruveedula, Wangikar. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Item A novel feature extraction technique for pulmonary sound analysis based on EMD(Elsevier Ireland Ltd, 2018) Mondal, A.; Banerjee, P.; Tang, H.Background and objective: The stethoscope based auscultation technique is a primary diagnostic tool for chest sound analysis. However, the performance of this method is limited due to its dependency on physicians experience, knowledge and also clarity of the signal. To overcome this problem we need an automated computer-aided diagnostic system that will be competent in noisy environment. In this paper, a novel feature extraction technique is introduced for discriminating various pulmonary dysfunctions in an automated way based on pattern recognition algorithms. Method: In this work, the disease correlated relevant characteristics of lung sounds signals are identified in terms of statistical distribution parameters: mean, variance, skewness, and kurtosis. These features are extracted from selective morphological components of the mapped signal in the empirical mode decomposition domain. The feature set is fed to the classifier model to differentiate their corresponding classes. Results: The significance of features developed are validated by conducting several experiments using supervised and unsupervised classifiers. Furthermore, the discriminating power of the proposed features is compared with three types of baseline features. The experimental result is evaluated by statistical analysis and also validated with physicians inference. Conclusions: It is found that the proposed features extraction technique is superior to the baseline methods in terms of classification accuracy, sensitivity and specificity. The developed method gives better results compared to baseline methods in any circumstance. The proposed method gives a higher accuracy of 94.16, sensitivity of 100 and specificity of 93.75 for an artificial neural network classifier. © 2018 Elsevier B.V.Item T4-like Escherichia coli phages from the environment carry blaCTX-M(John Wiley and Sons Inc, 2018) Mohan Raj, J.R.; Vittal, R.; Huilgol, P.; Bhat, U.; Karunasagar, I.The resistance determinant blaCTX-M has many variants and has been the most commonly reported gene in clinical isolates of extended spectrum beta-lactamase producing Escherichia coli. Phages have been speculated as potential reservoirs of resistance genes and efficient vehicles for horizontal gene transfer. The objective of the study was to determine the prevalence and characterize bacteriophages that harbour the resistance determinant blaCTX-M. Escherichia coli specific bacteriophages were isolated from 15 samples including soil and water across Mangaluru, India using bacterial hosts that were sensitive to ?-lactams. Phenotypic and genotypic characterization based on plaque morphology, host range, restriction fragment length polymorphism (RFLP), presence of blaCTX-M and electron microscopy was performed. Of 36 phages isolated, seven were positive for Group 1 of blaCTX-M. Based on host range and RFLP pattern, the seven phages were classified into four distinct groups, each harbouring a variant of blaCTX-M. Five phages were T4-like Myoviridae by electron microscopy which was further confirmed by polymerase chain reaction (PCR) for T4 specific gp14. Generalized transduction of the CTX-M gene from these phages was also observed. The high prevalence (20%) of this gene blaCTX-M in the phage pool confirms the significant role of Myoviridae members, specifically T4-like phages in the dissemination of this resistance gene. Significance and Impact of the Study: The CTX-M gene that confers resistance to Beta-lactam class of drugs is widespread and diverse. Understanding mechanisms of antimicrobial resistance transfer is a key to devise methods for controlling it. Few studies indicate that bacteriophages are involved in the transfer of this gene but the type of phages involved and the degree of involvement remains to be explored. Our work has been able to identify the class of phages and the magnitude of involvement in the dissemination of this gene. © 2018 The Society for Applied MicrobiologyItem GPUPeP: Parallel Enzymatic Numerical P System simulator with a Python-based interface(Elsevier Ireland Ltd, 2020) Raghavan, S.; Rai, S.S.; Rohit, M.P.; Chandrasekaran, K.Membrane computing is a computational paradigm inspired by the structure and behavior of a living cell. P Systems are the computing devices that are used to realize membrane computing models. Numerous theoretical studies on many variants of P Systems have shown them to be computationally universal. There is a wide range of applications of P Systems from modeling of biological processes to image processing. Among many variants of P Systems, one of the most important is Enzymatic Numerical P System (ENPS). ENPS is a class of P System in which membranes operate on numerical values. To realize the power of ENPS there are a few simulators developed. Each and every simulator has some advantages as well as some disadvantages. Here, a GPU based simulator using Python as a user interaction language is developed. This tool is a completely parallel variant, compatible with a Python based sequential simulator (PeP) which was the first Python based work for ENPS. The developed simulator uses CUDA to interact with GPU and gives the desired speed up, while processing the membranes. There are two important case studies which show the performance of the developed tool to be far better than the other serial simulators. © 2020 Elsevier B.V.Item Enhanced protein structural class prediction using effective feature modeling and ensemble of classifiers(Institute of Electrical and Electronics Engineers Inc., 2021) Bankapur, S.; Patil, N.Protein Secondary Structural Class (PSSC) information is important in investigating further challenges of protein sequences like protein fold recognition, protein tertiary structure prediction, and analysis of protein functions for drug discovery. Identification of PSSC using biological methods is time-consuming and cost-intensive. Several computational models have been developed to predict the structural class; however, they lack in generalization of the model. Hence, predicting PSSC based on protein sequences is still proving to be an uphill task. In this article, we proposed an effective, novel and generalized prediction model consisting of a feature modeling and an ensemble of classifiers. The proposed feature modeling extracts discriminating information (features) by leveraging three techniques: (i) Embedding – features are extracted on the basis of spatial residue arrangements of the sequences using word embedding approaches; (ii) SkipXGram Bi-gram – various sets of skipped bi-gram features are extracted from the sequences; and (iii) General Statistical (GS) based features are extracted which covers the global information of structural sequences. The combined effective sets of features are trained and classified using an ensemble of three classifiers: Support Vector Machine (SVM), Random Forest (RF), and Gradient Boosting Machines (GBM). The proposed model when assessed on five benchmark datasets (high and low sequence similarity), viz. z277, z498, 25PDB, 1189, and FC699, reported an overall accuracy of 93.55, 97.58, 81.82, 81.11, and 93.93 percent respectively. The proposed model is further validated on a large-scale updated low similarity (?25%) dataset, where it achieved an overall accuracy of 81.11 percent. The proposed generalized model is robust and consistently outperformed several state-of-the-art models on all the five benchmark datasets. © 2021 Institute of Electrical and Electronics Engineers Inc.. All rights reserved.Item Physical model studies on damage and stability analysis of breakwaters armoured with geotextile sand containers(Elsevier Ltd, 2021) Elias, T.; Shirlal, K.G.; E.v, K.Harnessing the advantages of geotextile sand containers (GSCs), numerous submerged breakwaters and shoreline protection structures have been constructed worldwide. But an emerged breakwater structure with geotextile armour units, capable of replacing the conventional structures, is rarely discussed. A 1:30 scaled physical experimentation is chosen as a preliminary investigation to test the feasibility of using GSCs as breakwater armour units. Structural design is evolved based on a comprehensive literature survey. The paper focuses on the stability parameters and damage characteristics of the proposed structure. Four different configurations are subjected to waves, confining to Mangaluru's wave parameters. Effect of armour unit size and sand fill ratio on the stability of the structure is analysed and it is concluded that changing sand fill ratio from 80% to 100% shot up the structural stability to a maximum of 14%. Increasing bag size also resulted in the increased stability up to 8%. Experiments revealed that the best performing configuration could withstand wave heights up to 2.7 m. Stability curves for all tested configurations are discussed and can serve as an effective guideline for designing GSC breakwaters. © 2020 Elsevier LtdItem An automated deep learning pipeline for detecting user errors in spirometry test(Elsevier Ltd, 2024) Bonthada, S.; Pariserum Perumal, S.P.; Naik, P.P.; Mahesh, M.A.; Rajan, J.Spirometer is used as a major diagnostic tool for obstructive airway diseases and a monitoring tool for therapy response and disease staging over time. It is a sophisticated medical device employed to quantify flow and volume of air exhaled by a subject during a specific testing period. The essential metrics obtained from the spirometry test, play a crucial role in enabling healthcare professionals to thoroughly evaluate the respiratory health and condition of the individual under examination. Several spirometer measurements including Forced Vital Capacity (FVC) and Forced Expiratory Volume (FEV) serve as guidelines for diagnosis and prognosis of Chronic Obstructive Pulmonary Diseases (COPD) and asthma. However, user errors caused by different reasons, including improper handling of the equipment and poor performance during the maneuvers of the expiratory airflow, end up in incorrect treatment directions. To ensure accurate results, spirometry tests traditionally require the presence of a skilled professional to identify and address these errors promptly. A novel machine learning approach is proposed in this paper to automatically identify four such user errors based on Volume-Time and Flow-Volume graphs. By detecting specific errors and providing immediate feedback to patients, reliability and accuracy of spirometry results will be improved and the need for trained professionals will be reduced. The implementation facilitates the widespread adoption of spirometry, particularly in low-resource telemedicine settings. This work implements a binary classification model distinguishing between normal and error test samples, achieving a prediction accuracy of 93%. Additionally, a 4-way classification model is presented for identifying individual error sub-types, demonstrating a prediction accuracy of 94%. © 2023 Elsevier LtdItem Spatio-temporal classification of land use and land cover and its changes in Kerala using remote sensing and machine learning approach(Springer Science and Business Media Deutschland GmbH, 2024) Vijay, A.; Varija, K.Land use and land cover (LULC) analysis gives important information on how the region has evolved over time. Kerala, a land with an extensive and dynamic history of land-use changes, has, until now, lacked comprehensive investigations into this history. So the current study focuses on Kerala, one of the ecologically diverse states in India with complex topography, through Landsat images taken from 1990 to 2020 using two different machine learning classifications, random forest (RF) and classification and regression trees (CART) on Google Earth Engine (GEE) platform. RF and CART are versatile machine learning algorithms frequently employed for classification and regression, offering effective tools for predictive modelling across diverse domains due to their flexibility and data-handling capabilities. Normalised Difference Vegetation Index (NDVI), Normalised Differences Built-up Index (NDBI), Modified Normalised Difference Water Index (MNDWI), and Bare soil index (BSI) are integral indices utilised to enhance the precision of land use and land cover classification in satellite imagery, playing a crucial role by providing valuable insights into specific landscape attributes that may be challenging to identify using individual spectral bands alone. The results showed that the performance of RF is better than that of CART in all the years. Thus, RF algorithm outputs are used to infer the change in the LULC for three decades. The changes in the NDVI values point out the loss of vegetation for the urban area expansion during the study period. The increasing value of NDBI and BSI in the state indicates growth in high-density built-up areas and barren land. The slight reduction in the value of MNDWI indicates the shrinking water bodies in the state. The results of LULC showed the urban expansion (158.2%) and loss of agricultural area (15.52%) in the region during the study period. It was noted the area of the barren class, as well as the water class, decreased steadily from 1990 to 2020. The results of the current study will provide insight into the land-use planners, government, and non-governmental organizations (NGOs) for the necessary sustainable land-use practices. © The Author(s), under exclusive licence to Springer Nature Switzerland AG 2024.Item EffiCOVID-net: A highly efficient convolutional neural network for COVID-19 diagnosis using chest X-ray imaging(Academic Press Inc., 2025) Kumar, S.; Bhowmik, B.The global COVID-19 pandemic has drastically affected daily life, emphasizing the urgent need for early and accurate detection to provide adequate medical treatment, especially with limited antiviral options. Chest X-ray imaging has proven crucial for distinguishing COVID-19 from other respiratory conditions, providing an essential diagnostic tool. Deep learning (DL)-based models have proven highly effective in image diagnostics in recent years. Many of these models are computationally intensive and prone to overfitting, especially when trained on limited datasets. Additionally, conventional models often fail to capture multi-scale features, reducing diagnostic accuracy. This paper proposed a highly efficient convolutional neural network (CNN) called EffiCOVID-Net, incorporating diverse feature learning units. The proposed model consists of a bunch of EffiCOVID blocks that incorporate several layers of convolution containing (3×3) filters and recurrent connections to extract complex features while preserving spatial integrity. The performance of EffiCOVID-Net is rigorously evaluated using standard performance metrics on two publicly available COVID-19 chest X-ray datasets. Experimental results demonstrate that EffiCOVID-Net outperforms existing models, achieving 98.68% accuracy on the COVID-19 radiography dataset (D1), 98.55% on the curated chest X-ray dataset (D2), and 98.87% on the mixed dataset (DMix) in multi-class classification (COVID-19 vs. Normal vs. Pneumonia). For binary classification (COVID-19 vs. Normal), the model attains 99.06%, 99.78%, and 99.07% accuracy, respectively. Integrating Grad-CAM-based visualizations further enhances interpretability by highlighting critical regions influencing model predictions. EffiCOVID-Net's lightweight architecture ensures low computational overhead, making it suitable for deployment in resource-constrained clinical settings. A comparative analysis with existing methods highlights its superior accuracy, efficiency, and robustness performance. However, while the model enhances diagnostic workflows, it is best utilized as an assistive tool rather than a standalone diagnostic method. © 2025 Elsevier Inc.