•A new method i.e. sparse decomposition over a gabor dictionary is proposed.•Four different features are extracted and concatenated from the atoms of dictionary.•An optimal least-square twin SVM ...classifier model is developed using ABC technique.•The experiments are evaluated under category and personalized schemes.•A higher accuracy of proposed method outperforms the results from the literature.
As per the report of the World Health Organization (WHO), the mortalities due to cardiovascular diseases (CVDs) have increased to 50 million worldwide. Therefore, it is essential to have an efficient diagnosis of CVDs to enhance the healthcare in the clinical cardiovascular domain. The ECG signal analysis of a patient is a very popular tool to perform diagnosis of CVDs. However, due to the non-stationary nature of ECG signal and higher computational burden of the existing signal processing methods, the automated and efficient diagnosis remains a challenge.
This paper presents a new feature extraction method using the sparse representation technique to efficiently represent the different ECG signals for efficient analysis. The sparse method decomposes an ECG signal into elementary waves using an overcomplete gabor dictionary. Four features such as time delay, frequency, width parameter, and square of expansion coefficient are extracted from each of the significant atoms of the dictionary. These features are concatenated and analyzed to determine the optimal length of discriminative feature vector representing each of the ECG signal. These extracted features representing the ECG signals are further classified using machine learning techniques such as least-square twin SVM, k-NN, PNN, and RBFNN. Further, the learning parameters of the classifiers are optimized using ABC and PSO techniques. The experiments are carried out for the proposed methods (i.e. feature extraction along with all classifiers) using benchmark MIT-BIH data and evaluated under category and personalized analysis schemes.
Experimental results show that the proposed ECG signal representation using sparse decomposition technique with PSO optimized least-square twin SVM (best classifier model among k-NN, PNN and RBFNN) reported higher classification accuracy of 99.11% in category and 89.93% in personalized schemes respectively than the existing methods to the state-of-art diagnosis.
Abstract
COVID-19 pandemic has resulted in 16,114,449 cases with 646,641 deaths from the 217 countries, or territories as on July 27th 2020. Due to multifaceted issues and challenges in the ...implementation of the safety and preventive measures, inconsistent coordination between societies-governments and most importantly lack of specific vaccine to SARS-CoV-2, the spread of the virus that initially emerged at Wuhan is still uprising after taking a heavy toll on human life. In the present study, we mapped immunogenic epitopes present on the four structural proteins of SARS-CoV-2 and we designed a multi-epitope peptide based vaccine that, demonstrated a high immunogenic response with a vast application on world’s human population. On codon optimization and in-silico cloning, we found that candidate vaccine showed high expression in
E. coli
and immune simulation resulted in inducing a high level of both B-cell and T-cell mediated immunity. The results predicted that exposure of vaccine by administrating three injections significantly subsidized the antigen growth in the system. The proposed candidate vaccine found promising by yielding desired results and hence, should be validated by practical experimentations for its functioning and efficacy to neutralize SARS-CoV-2.
Nanostructure morphology originating from the self-assembly of molecules has attracted substantial attention due to its role in toxic amyloid fibril formation and immense potential in the design and ...fabrication of novel biomaterials. This study presents the role of intermolecular electrostatic interaction on the self-assembly process of l-phenylalanine (L-Phe) amino acid. We have employed attenuated total reflection Fourier transform infrared spectroscopy to probe the existence of different ionization states of the amino acid in various pH aqueous solutions. The self-assembly process of L-Phe in the aqueous phase is explored by using circular dichroism absorption and nuclear magnetic resonance spectroscopic tools. The observed spectral features have shown the signature of higher order structures and possible perturbation in the π-π stacking aromatic interactions for the cationic and anionic states of the amino acid. Scanning electron microscopy is used to probe the self-assembled morphology of the L-Phe amino acid dried samples prepared from the same pH aqueous solutions. We find that for the case of zwitterionic states the self-assembly nanostructures are dominated by the presence of fibrillar morphology, however interestingly for cationic and anionic states the morphology is dominated by the presence of flakes. Our finding demonstrates the potential influence of intermolecular electrostatic interaction over the aromatic π-π stacking interaction in hindering the fibril formation.
Different Biogeographic provinces and environmental factors are known to influence the dispersibility of long-ranging carnivores over the landscape. However, lack of empirical data on long-ranging ...carnivores may lead to erroneous decisions in formulating management plans. The Indian Grey wolf (Canis lupus pallipes) is known to be distributed in the vast areas of the Indian subcontinent. However, the actual population estimates are available only for Gujarat, Karnataka, Rajasthan and Bihar. Whereas, its distribution, population and habitat ecology is poorly known from the eastern region. Hence, this article aimed to evaluate the habitat suitability along with landscape connectivity for the species over the two major biogeographic provinces of India, i.e., Lower Gangetic Plains (7b) and Chhota Nagpur Plateau (6b). The present model with significantly higher Area under the curve (AUC) value of 0.981, indicates its accuracy in predicting the suitable habitats and identifying biological corridors by using environmental, topological and anthropogenic variables. Precipitation of the driest quarter and the precipitation of seasonality were the two best performing variables in our model, capable of explaining about 26% and 22.4% variation in the data respectively. Out of the total area i.e. 4,16,665 Km2, about 18,237 Km2 (4.37%) was found to be highly suitable area and about 3,16,803 Km2 (76.03%) areas as least suitable. The corridor analysis indicated that the habitat connectivity was highest in the border line area of the two biotic provinces located in the south-eastern zone via districts of Purba Singhbhum and Paschim Singhbhum of Jharkhand state and Bankura and West Midnapore districts of West Bengal state. Among the Protected Areas (PAs), natural corridors exist connecting the Simlipal National Park (NP)-Satkosia Wildlife Santuray (WLS), Dalma ranges of Chotta Nagpur plateau along with Badrama WLS, Khulasuni WLS and Debrigarh WLS. Differential management through landscape level planning may be helpful in securing the future of the species in the landscape.
Prior to this study, complete mitochondrial genomes from Order Thysanoptera were restricted to a single family, the Thripidae, resulting in a biased view of their evolution. Here we present the ...sequences for the mitochondrial genomes of four additional thrips species, adding three extra families and an additional subfamily, thus greatly improving taxonomic coverage. Thrips mitochondrial genomes are marked by high rates of gene rearrangement, duplications of the control region and tRNA mutations. Derived features of mitochondrial tRNAs in thrips include gene duplications, anticodon mutations, loss of secondary structures and high gene translocation rates. Duplicated control regions are found in the Aeolothripidae and the 'core' Thripinae clade but do not appear to promote gene rearrangement as previously proposed. Phylogenetic analysis of thrips mitochondrial sequence data supports the monophyly of two suborders, a sister-group relationship between Stenurothripidae and Thripidae, and suggests a novel set of relationships between thripid genera. Ancestral state reconstructions indicate that genome rearrangements are common, with just eight gene blocks conserved between any thrips species and the ancestral insect mitochondrial genome. Conversely, 71 derived rearrangements are shared between at least two species, and 24 of these are unambiguous synapomorphies for clades identified by phylogenetic analysis. While the reconstructed sequence of genome rearrangements among the protein-coding and ribosomal RNA genes could be inferred across the phylogeny, direct inference of phylogeny from rearrangement data in MLGO resulted in a highly discordant set of relationships inconsistent with both sequence-based phylogenies and previous morphological analysis. Given the demonstrated rates of genomic evolution within thrips, extensive sampling is needed to fully understand these phenomena across the order.
Highlights • A new method is proposed in this manuscript for the classification of cardiac arrhythmia beats. Algorithms used in this method are Pan-Tompkins algorithm for R-peak detection, discrete ...orthogonal stockwell transform (DOST) for feature extraction of ECG signals, support vector machines (SVMs) for classification whose parameters are tuned using particle swarm optimization (PSO) technique for automatic cardiac arrhythmia beat classification. • The best performance parameters for the SVM classifier are selected by employing PSO technique to achieve maximum accuracy. Also to the best of author's knowledge the use of discrete orthogonal stockwell transform to the cardiac arrhythmia classification is new. • The proposed methodology is evaluated under two evaluation schemes i.e class-based and patient-based schemes for real-time applications. • Performance analysis of the proposed methodology and comparison with existing methodologies under both assessment schemes are reported with improved accuracy.
The Assam Roofed Turtle, Pangshura sylhetensis is an endangered and least studied species endemic to India and Bangladesh. The present study decodes the first complete mitochondrial genome of P. ...sylhetensis (16,568 bp) by using next-generation sequencing. The assembly encodes 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one control region (CR). Most of the genes were encoded on the majority strand, except NADH dehydrogenase subunit 6 (nad6) and eight tRNAs. All PCGs start with an ATG initiation codon, except for Cytochrome oxidase subunit 1 (cox1) and NADH dehydrogenase subunit 5 (nad5), which both start with GTG codon. The study also found the typical cloverleaf secondary structures in most of the predicted tRNA structures, except for serine (trnS1) which lacks of conventional DHU arm and loop. Both Bayesian and maximum-likelihood phylogenetic inference using 13 concatenated PCGs demonstrated strong support for the monophyly of all 52 Testudines species within their respective families and revealed Batagur trivittata as the nearest neighbor of P. sylhetensis. The mitogenomic phylogeny with other amniotes is congruent with previous research, supporting the sister relationship of Testudines and Archosaurians (birds and crocodilians). Additionally, the mitochondrial Gene Order (GO) analysis indicated plesiomorphy with the typical vertebrate GO in most of the Testudines species.
Exploring the gut microbiome is an emerging tool for monitoring wildlife health and physiological conditions which often sustained under the variety of stresses and challenges. We analyzed gut ...microbiome of Arunachal macaque (Macaca munzala) of two disjunct populations from Arunachal Pradesh, India, to validate whether the geography or the feeding habits plays a principal role in shaping the gut microbiome in natural populations. We observed geography has a mere effect but feeding habits (i.e. feeding upon the leftover food and crop-raiding) significantly influenced the gut microbiome composition. The phylum Proteobacteria found to be enriched in leftover feeding group while phylum Bacteroidetes was differentially abundant in crop-raiding group. We observed predominant phyla Firmicutes followed by Proteobacteria and Bacteroidetes with the dominant classes represented by the Clostridia. Interestingly, one individual with known diarrheal/metabolic disorder exhibited complete dominance of the order Bacillales and showed 100% sequence similarity with genus Solibacillus. We raise concern that shift in diet of macaques may compel them to expose for various human diseases as two macaques feeding upon the leftover food exhibited dysbiotic gut microbiome. The present study provides the pragmatic evidences of how the alteration of food resources can harm the physiological condition of the macaques in wild and raises alarm to the forest officials/managers in strategise planting of natural food resources and monitor anthropogenic activities in the distribution of Arunachal macaques.
Deleterious somatic mutations in DNA methyltransferase 3 alpha (DNMT3A) and TET mehtylcytosine dioxygenase 2 (TET2) are associated with clonal expansion of hematopoietic cells and higher risk of ...cardiovascular disease (CVD). Here, we investigated roles of DNMT3A and TET2 in normal human monocyte-derived macrophages (MDM), in MDM isolated from individuals with DNMT3A or TET2 mutations, and in macrophages isolated from human atherosclerotic plaques. We found that loss of function of DNMT3A or TET2 resulted in a type I interferon response due to impaired mitochondrial DNA integrity and activation of cGAS signaling. DNMT3A and TET2 normally maintained mitochondrial DNA integrity by regulating the expression of transcription factor A mitochondria (TFAM) dependent on their interactions with RBPJ and ZNF143 at regulatory regions of the TFAM gene. These findings suggest that targeting the cGAS-type I IFN pathway may have therapeutic value in reducing risk of CVD in patients with DNMT3A or TET2 mutations.
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•Loss of function of DNMT3A or TET2 in human macrophages induces type I interferons•The type I interferon response is due to mitochondrial DNA release that activates cGAS•DNMT3A and TET2 maintain mitochondrial DNA integrity by regulating TFAM expression•DNMT3A and TET2 regulate TFAM expression by interacting with RBPJ and ZNF143
Clonal hematopoiesis due to mutations in DNMT3A or TET2 increases risk of cardiovascular disease, but mechanisms are presently unclear. Cobo et al. reveal that loss of function of DNMT3A and TET2 results in a type 1 interferon response in macrophages due to impaired mitochondrial DNA integrity.
Immunotherapy has revolutionized cancer treatment, yet most patients do not respond. Here, we investigated mechanisms of response by profiling the proteome of clinical samples from advanced stage ...melanoma patients undergoing either tumor infiltrating lymphocyte (TIL)-based or anti- programmed death 1 (PD1) immunotherapy. Using high-resolution mass spectrometry, we quantified over 10,300 proteins in total and ∼4,500 proteins across most samples in each dataset. Statistical analyses revealed higher oxidative phosphorylation and lipid metabolism in responders than in non-responders in both treatments. To elucidate the effects of the metabolic state on the immune response, we examined melanoma cells upon metabolic perturbations or CRISPR-Cas9 knockouts. These experiments indicated lipid metabolism as a regulatory mechanism that increases melanoma immunogenicity by elevating antigen presentation, thereby increasing sensitivity to T cell mediated killing both in vitro and in vivo. Altogether, our proteomic analyses revealed association between the melanoma metabolic state and the response to immunotherapy, which can be the basis for future improvement of therapeutic response.
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•Proteomics of 116 melanoma tumors shows the landscapes of response to immunotherapy•Immunotherapy response was associated with enriched mitochondrial lipid metabolism•High mitochondrial metabolism led to higher antigen presentation and IFN signaling•Knockout of beta-oxidation genes reduced melanoma sensitivity to T cell killing
Proteomic profiling of melanomas from patients undergoing immunotherapy reveals key mediators of tumor immunogenicity.
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