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Article ; Online: Effect of larval thermal conditions on limb regeneration in a ladybird beetle, Cheilomenes sexmaculata.

Rai, Shriza / Singh, Anupama / Omkar, Omkar / Mishra, Geetanjali

Journal of experimental zoology. Part A, Ecological and integrative physiology

2023 Volume 339, Issue 9, Page(s) 825–837

Abstract: In view of global environmental change, ecological factors especially temperature, affect development of the poikilotherms like insects. Since ladybirds are at risk of injury under mass-rearing conditions, their ability to regenerate injured limbs is ... ...

Abstract	In view of global environmental change, ecological factors especially temperature, affect development of the poikilotherms like insects. Since ladybirds are at risk of injury under mass-rearing conditions, their ability to regenerate injured limbs is highly crucial for their survival. Therefore, the effect of limb regeneration in relation to temperature forms the basis of the present study. The immature stages of insects, being more vulnerable to the surrounding temperature, were considered to study the effect of the prior thermal experience of larvae on regeneration. We exposed the early larval stages of the ladybird beetle, Cheilomenes sexmaculata, to different temperature conditions pre- and postamputation. Exposure of immature stages to extreme temperatures did not affect the ability to regenerate and regeneration occurred at given temperature conditions. However, the regenerated legs were smaller in size across given temperatures as compared to unamputated legs. Body weights in amputated treatments showed no difference and remained unchanged across temperatures when compared to unamputated treatments. Postamputation developmental duration, equivalent to recovery time postlimb amputation, was found to be affected by larval thermal conditions. Recovery was faster in larval treatments exposed to higher temperatures. Thus, larval thermal conditions though did not affect the ability to regenerate lost limbs directly, it does modulate the time taken to regenerate.
MeSH term(s)	Animals ; Coleoptera ; Larva ; Regeneration ; Temperature ; Extremities
Language	English
Publishing date	2023-07-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1474896-4
ISSN	2471-5646 ; 1932-5223 ; 2471-5646 ; 1932-5231 ; 1552-499X
ISSN (online)	2471-5646 ; 1932-5223
ISSN	2471-5646 ; 1932-5231 ; 1552-499X
DOI	10.1002/jez.2733
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Study of Correlated Motions to Detect the Conformational Transitions of the Intrinsically Disordered Sheep Prion Peptide.

Chakraborty, Debashree / Singh, Omkar / Parameswaran, Divya

Journal of chemical information and modeling

2024

Abstract: Intrinsically disordered proteins (IDPs) are known for their random structural changes throughout their sequence based on the environment. The mechanism underlying these structural changes is difficult to explain. All biological processes are known to ... ...

Abstract	Intrinsically disordered proteins (IDPs) are known for their random structural changes throughout their sequence based on the environment. The mechanism underlying these structural changes is difficult to explain. All biological processes are known to follow the direction through which they act. A study of the correlated motion can help to understand the direction of the change. Herein, we introduced the multivariate statistical analysis (MSA) technique to study the correlated motion of the peptide. The correlated motion of the sheep prion peptide was studied with the change in the temperature and solvent. These techniques helped to identify the contributing residual motions that helped to form the different secondary structures of the protein and also the triggering factors that drive these sorts of residual motions. The structural details match the experimentally reported data. It was found that the direction of the change of the secondary structure for this peptide shifted from the C-terminal to the N-terminal with an increase in the temperature. It was found that the involvement of the hydrophobic residues present at the C-terminal and the middle residues (residues 12-17) is responsible for forming a β-sheet at the normal temperature. Hydration water was found to play an important role in this change. Insights gained from this study can be used to design strategies for desirable structural changes in the IDPs.
Language	English
Publishing date	2024-04-03
Publishing country	United States
Document type	Journal Article
ZDB-ID	190019-5
ISSN	1549-960X ; 0095-2338
ISSN (online)	1549-960X
ISSN	0095-2338
DOI	10.1021/acs.jcim.4c00300
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Article ; Online: Power-line interference and baseline wander elimination in ECG using VMD and EWT.

Mir, Haroon Yousuf / Singh, Omkar

Computer methods in biomechanics and biomedical engineering

2023 , Page(s) 1–20

Abstract: Electrocardiogram (ECG) is a critical biomedical signal and plays an imperative role in diagnosing cardiovascular disorders. During ECG data acquisition in clinical environment, noise is frequently present. Various noises such as powerline interference ( ... ...

Abstract	Electrocardiogram (ECG) is a critical biomedical signal and plays an imperative role in diagnosing cardiovascular disorders. During ECG data acquisition in clinical environment, noise is frequently present. Various noises such as powerline interference (PLI) and baseline wandering (BLW) distort the ECG signal which may lead to incorrect interpretation. Consequently, substantial emphasis has been dedicated to ECG denoising for reliable diagnosis and analysis. In this study, a novel hybrid ECG denoising method based on variational mode decomposition (VMD) and the empirical wavelet transform (EWT) is presented. For effective denoising using the VMD and EWT approach, the noisy ECG signal is decomposed within narrow-band variational mode functions (VMFs). The aim is to remove noise from these narrow-band VMFs. In current approach, the centre frequency of each VMF was computed and utilized to design an adaptive wavelet filter bank using EWT. This leads to effective removal of noise components from the signal. The proposed approach was applied to ECG signals obtained from the MIT-BIH Arrhythmia database. To evaluate the denoising performance, noise sources from the MIT-BIH Noise Stress Test Database (NSTDB) are used for simulation. The assessment of denoising performance in based on two key metrics: the percentage-root-mean-square difference (PRD) and the signal-to-noise ratio (SNR). The findings of the simulation experiment demonstrate that the suggested method has lower percentage root mean square difference and higher signal-to-noise ratio as compared to existing state of the art denoising methods. An average output SNR of 24.03 was achieved, along with a 5% reduction in PRD.
Language	English
Publishing date	2023-10-27
Publishing country	England
Document type	Journal Article
ZDB-ID	2071764-7
ISSN	1476-8259 ; 1025-5842
ISSN (online)	1476-8259
ISSN	1025-5842
DOI	10.1080/10255842.2023.2271608
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Article ; Online: Exploring the Barriers in the Aggregation of a Hexadecameric Human Prion Peptide through the Markov State Model.

Das, Bratin Kumar / Singh, Omkar / Chakraborty, Debashree

ACS chemical neuroscience

2023 Volume 14, Issue 19, Page(s) 3622–3645

Abstract: The prefibrillar aggregation kinetics of prion peptides are still an enigma. In this perspective, we employ atomistic molecular dynamics (MD) simulations of the shortest human prion peptide (HPP) ( ...

Abstract	The prefibrillar aggregation kinetics of prion peptides are still an enigma. In this perspective, we employ atomistic molecular dynamics (MD) simulations of the shortest human prion peptide (HPP) (
MeSH term(s)	Humans ; Prions/metabolism ; Peptides/chemistry ; Molecular Dynamics Simulation ; Protein Conformation, beta-Strand ; Water/chemistry ; Amyloid/chemistry
Chemical Substances	Prions ; Peptides ; Water (059QF0KO0R) ; Amyloid
Language	English
Publishing date	2023-09-13
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1948-7193
ISSN (online)	1948-7193
DOI	10.1021/acschemneuro.3c00284
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Article ; Online: Are the effects of hunger stage-specific? A case study in an aphidophagous ladybird beetle.

Singh, Priya / Mishra, Geetanjali / Omkar

Bulletin of entomological research

2020 Volume 111, Issue 1, Page(s) 66–72

Abstract: Food availability is a fundamental factor determining an animal's potential fitness. Carry-over effects of food limitation from development to adulthood are known to influence reproduction, ageing, and tolerance to stress. We have examined the effect of ... ...

Abstract	Food availability is a fundamental factor determining an animal's potential fitness. Carry-over effects of food limitation from development to adulthood are known to influence reproduction, ageing, and tolerance to stress. We have examined the effect of stage-specific variation (before adult emergence or pre-emergence, post-emergence and post-mating) in food availability in Propylea dissecta (Mulsant). Larvae were reared separately on two different pre-emergence food regimes (abundant or restricted) until pupation. Newly emerged adults were further split into two groups and placed on abundant or restricted post-emergence regimes. After mating, females were split and reared on any one of two post-mating regimes. The results revealed that: (i) time to commence mating declined with increased food availability in pre- and post-emergence stages, (ii) mating duration increased with food availability post-emergence, (iii) highest reproduction output was observed in individuals who had abundant food pre- and post-emergence. However, food availability at the time of oviposition also had a strong influence on fecundity. Solo bouts of scarcity, regardless of which stage suffered them, were effectively managed in at least two of the three stages (pre-emergence, post-emergence, post-mating) had abundant food.
MeSH term(s)	Animals ; Coleoptera/growth & development ; Coleoptera/physiology ; Female ; Fertility ; Hunger ; Larva/growth & development ; Larva/physiology ; Predatory Behavior ; Reproduction ; Sexual Behavior, Animal
Language	English
Publishing date	2020-06-16
Publishing country	England
Document type	Journal Article
ZDB-ID	280516-9
ISSN	1475-2670 ; 0007-4853
ISSN (online)	1475-2670
ISSN	0007-4853
DOI	10.1017/S0007485320000309
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Article ; Online: Effect of Water Models on The Stability of RNA

Omkar Singh / Pushyaraga P Venugopal / Debashree Chakraborty

Chemical Physics Impact, Vol 7, Iss , Pp 100313- (2023)

Role of Counter-Ions

2023

Abstract: Various force fields and water model potentials influence significantly RNA conformations. The polyanionic nature of RNA attracts the water molecules and the counter ions which in turn affects their stability. The interfacial water's structural and ... ...

Abstract	Various force fields and water model potentials influence significantly RNA conformations. The polyanionic nature of RNA attracts the water molecules and the counter ions which in turn affects their stability. The interfacial water's structural and dynamic aspects affect the RNA's base-pair opening and denaturation by breaking or making inter/intra-hydrogen bonds. Herein, we employed an MD simulations study using SPC/E and modified TIP3P water models in combination with different force fields CHARMM and AMBER to find their influence on the hydration shell of the SARS-CoV-2 RNA genome at different temperatures. AMBER-mTIP3P model was found to give more dynamic and transient conformations for RNA. The lower dielectric constant of the SPC/E model helps in the formation of the ion-contact pair near the negatively charged phosphate group (Na+-PO4−) leading to strong RNA-ion interaction and strong hydration shells having higher hydrogen bond lifetime. The Na+ ion survival probability at the interface was found to be more in the SPC/E model. At lower temperatures, the water molecules inside these hydration shells were found to be inhomogeneous, with lower void space, higher-coordinated, and non-tetrahedral. The higher dielectric constant of the mTIP3P model screened out the attraction between the ion pairs leading to a more homogenous solvation shell having a lesser hydrogen bond lifetime and more diffusive water. The distribution of the ions near the RNA structure is confirmed by metadynamics simulations. Both water models were found to disrupt the base pair orientation due to the formation of water bridges between the O2ʹ group of RNA and the water molecules.
Keywords	RNA ; contact ion pair ; dihedral angles ; metadynamics ; tetrahedral order parameter ; hydrogen bond lifetime ; Physics ; QC1-999 ; Chemistry ; QD1-999
Subject code	541 ; 612
Language	English
Publishing date	2023-12-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Growth Reaction of Gold Nanorods in the Presence of Mutated Peptides and Amine-Modified Single-Stranded Nucleic Acids.

Sahu, Jitendra K / Singh, Omkar / Chakraborty, Debashree / Sadhu, Kalyan K

Chemistry, an Asian journal

2023 Volume 18, Issue 8, Page(s) e202300049

Abstract: Conformation of biomolecules like DNA, peptides and amino acids play vital role during nanoparticle growth. Herein, we have experimentally explored the effect of different noncovalent interaction between a 5'-amine modified DNA sequence ( ... ...

Abstract	Conformation of biomolecules like DNA, peptides and amino acids play vital role during nanoparticle growth. Herein, we have experimentally explored the effect of different noncovalent interaction between a 5'-amine modified DNA sequence (NH
MeSH term(s)	Amines ; Gold/chemistry ; Nucleic Acids ; Peptides/chemistry ; Amino Acids/chemistry ; Nanotubes
Chemical Substances	Amines ; Gold (7440-57-5) ; Nucleic Acids ; Peptides ; Amino Acids
Language	English
Publishing date	2023-03-20
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2233006-9
ISSN	1861-471X ; 1861-4728
ISSN (online)	1861-471X
ISSN	1861-4728
DOI	10.1002/asia.202300049
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Article ; Online: ECG denoising and feature extraction techniques - a review.

Mir, Haroon Yousuf / Singh, Omkar

Journal of medical engineering & technology

2021 Volume 45, Issue 8, Page(s) 672–684

Abstract: The electrocardiogram (ECG) is a non-invasive approach for the recording of bioelectric signals generated by the heart which is used for the examination of the electro physical state, the function of the heart, and many cardiac diseases. However, various ...

Abstract	The electrocardiogram (ECG) is a non-invasive approach for the recording of bioelectric signals generated by the heart which is used for the examination of the electro physical state, the function of the heart, and many cardiac diseases. However, various artefacts and measurement noise usually hinder providing accurate feature extraction such as power line interference, baseline wander, electromyographic noise (EMG) and electrode motion artefact. Therefore, for better analysis and interpretation ECG signals must be noise-free. Most recent and efficient techniques for ECG denoising and feature extraction techniques have been reviewed in this paper, as feature extraction and denoising of ECG are remarkably helpful in cardiology. This paper presents the review of contemporary signal processing techniques such as discrete wavelet transform (DWT), Empirical mode decomposition (EMD), Variational mode decomposition (VMD) and Empirical wavelet transform (EWT) for ECG signal denoising and feature extraction.
MeSH term(s)	Algorithms ; Artifacts ; Electrocardiography ; Signal Processing, Computer-Assisted ; Wavelet Analysis
Language	English
Publishing date	2021-08-31
Publishing country	England
Document type	Journal Article
ZDB-ID	243092-7
ISSN	1464-522X ; 0309-1902
ISSN (online)	1464-522X
ISSN	0309-1902
DOI	10.1080/03091902.2021.1955032
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Article ; Online: Modeling of carbon dioxide fixation by microalgae using hybrid artificial intelligence (AI) and fuzzy logic (FL) methods and optimization by genetic algorithm (GA).

Kushwaha, Omkar Singh / Uthayakumar, Haripriyan / Kumaresan, Karthigaiselvan

Environmental science and pollution research international

2022 Volume 30, Issue 10, Page(s) 24927–24948

Abstract: In this study, we are reporting a novel prediction model for forecasting the carbon dioxide ( ... ...

Abstract	In this study, we are reporting a novel prediction model for forecasting the carbon dioxide (CO
MeSH term(s)	Artificial Intelligence ; Fuzzy Logic ; Carbon Dioxide ; Algorithms ; Microalgae
Chemical Substances	Carbon Dioxide (142M471B3J)
Language	English
Publishing date	2022-03-29
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1178791-0
ISSN	1614-7499 ; 0944-1344
ISSN (online)	1614-7499
ISSN	0944-1344
DOI	10.1007/s11356-022-19683-0
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Article ; Online: Modeling of carbon dioxide fixation by microalgae using hybrid artificial intelligence (AI) and fuzzy logic (FL) methods and optimization by genetic algorithm (GA)

Kushwaha, Omkar Singh / Uthayakumar, Haripriyan / Kumaresan, Karthigaiselvan

Environ Sci Pollut Res. 2023 Feb., v. 30, no. 10 p.24927-24948

2023

Abstract: In this study, we are reporting a novel prediction model for forecasting the carbon dioxide (CO₂) fixation of microalgae which is based on the hybrid approach of adaptive neuro-fuzzy inference system (ANFIS) and genetic algorithm (GA). The CO₂ fixation ... ...

Abstract	In this study, we are reporting a novel prediction model for forecasting the carbon dioxide (CO₂) fixation of microalgae which is based on the hybrid approach of adaptive neuro-fuzzy inference system (ANFIS) and genetic algorithm (GA). The CO₂ fixation rate of various algal strains was collected and the cultivation conditions of the microalgae such as temperature, pH, CO₂ %, and amount of nitrogen and phosphorous (mg/L) were taken as the input variables, while the CO₂ fixation rate was taken as the output variable. The optimization of ANFIS parameters and the formation of the optimized fuzzy model structure were performed by genetic algorithm (GA) using MATLAB in order to achieve optimum prediction capability and industrial applicability. The best-fitting model was figured out using statistical analysis parameters such as root mean square error (RMSE), coefficient of regression (R²), and average absolute relative deviation (AARD). According to the analysis, GA-ANFIS model depicted a greater prediction capability over ANFIS model. The RMSE, R², and AARD for GA-ANFIS were observed to be 0.000431, 0.97865, and 0.044354 in the training phase and 0.00056, 0.98457, and 0.032156 in the testing phase, respectively, for the GA-ANFIS Model. As a result, it can be concluded that the proposed GA-ANFIS model is an efficient technique having a very high potential to accurately predict the CO₂ fixation rate.
Keywords	algorithms ; carbon dioxide ; carbon dioxide fixation ; fuzzy logic ; industrial applications ; microalgae ; nitrogen ; pH ; phosphorus ; prediction ; statistical analysis ; temperature
Language	English
Dates of publication	2023-02
Size	p. 24927-24948.
Publishing place	Springer Berlin Heidelberg
Document type	Article ; Online
ZDB-ID	1178791-0
ISSN	1614-7499 ; 0944-1344
ISSN (online)	1614-7499
ISSN	0944-1344
DOI	10.1007/s11356-022-19683-0
Database	NAL-Catalogue (AGRICOLA)

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