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Book ; Online: InBiodiv-O

Patel, Archana / Jain, Sarika / Debnath, Narayan C. / Lama, Vishal

An Ontology for Indian Biodiversity Knowledge Management

2021

Abstract: To present the biodiversity information, a semantic model is required that connects all kinds of data about living creatures and their habitats. The model must be able to encode human knowledge for machines to be understood. Ontology offers the richest ... ...

Abstract	To present the biodiversity information, a semantic model is required that connects all kinds of data about living creatures and their habitats. The model must be able to encode human knowledge for machines to be understood. Ontology offers the richest machine-interpretable (rather than just machine-processable) and explicit semantics that are being extensively used in the biodiversity domain. Various ontologies are developed for the biodiversity domain however a review of the current landscape shows that these ontologies are not capable to define the Indian biodiversity information though India is one of the megadiverse countries. To semantically analyze the Indian biodiversity information, it is crucial to build an ontology that describes all the essential terms of this domain from the unstructured format of the data available on the web. Since, the curation of the ontologies heavily depends on the domain where these are implemented hence there is no ideal methodology is defined yet to be ready for universal use. The aim of this article is to develop an ontology that semantically encodes all the terms of Indian biodiversity information in all its dimensions based on the proposed methodology. The comprehensive evaluation of the proposed ontology depicts that ontology is well built in the specified domain. Comment: This paper has been withdrawn by the author due to many grammatical errors, and inconsistent content
Keywords	Computer Science - Artificial Intelligence
Subject code	006
Publishing date	2021-08-20
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Electrochemical generation of high-valent oxo-manganese complexes featuring an anionic N5 ligand and their role in O-O bond formation.

Biswas, Sachidulal / Chowdhury, Srijan Narayan / Lepcha, Panjo / Sutradhar, Subhankar / Das, Abhishek / Paine, Tapan Kanti / Paul, Satadal / Biswas, Achintesh N

Dalton transactions (Cambridge, England : 2003)

2023 Volume 52, Issue 45, Page(s) 16616–16630

Abstract: ... compounds help in understanding the mechanism of O-O bond formation presumably occurring in the last step ...

Abstract	Generation of high-valent oxomanganese complexes through controlled removal of protons and electrons from low-valent congeners is a crucial step toward the synthesis of functional analogues of the native oxygen evolving complex (OEC). In-depth studies of the water oxidation activity of such biomimetic compounds help in understanding the mechanism of O-O bond formation presumably occurring in the last step of the photosynthetic cycle. Scarce reports of reactive high-valent oxomanganese complexes underscore the impetus for the present work, wherein we report the electrochemical generation of the non-heme oxomanganese(IV) species [(dpaq)Mn
Language	English
Publishing date	2023-11-21
Publishing country	England
Document type	Journal Article
ZDB-ID	1472887-4
ISSN	1477-9234 ; 1364-5447 ; 0300-9246 ; 1477-9226
ISSN (online)	1477-9234 ; 1364-5447
ISSN	0300-9246 ; 1477-9226
DOI	10.1039/d3dt02740f
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Chemoenzymatic o-Quinone Methide Formation

Doyon, Tyler J / Perkins, Jonathan C / Baker Dockrey, Summer A / Romero, Evan O / Skinner, Kevin C / Zimmerman, Paul M / Narayan, Alison R. H

Journal of the American Chemical Society. 2019 Dec. 16, v. 141, no. 51

2019

Abstract: ... challenge. Here, we demonstrate the utility of biocatalysis in generating o-quinone methide intermediates ... iron enzymes, CitB and ClaD, are employed to selectively modify benzylic C–H bonds of o-cresol ... a benzylic alcohol product which, under the aqueous reaction conditions, is in equilibrium with the corresponding o ...

Abstract	Generation of reactive intermediates and interception of these fleeting species under physiological conditions is a common strategy employed by Nature to build molecular complexity. However, selective formation of these species under mild conditions using classical synthetic techniques is an outstanding challenge. Here, we demonstrate the utility of biocatalysis in generating o-quinone methide intermediates with precise chemoselectivity under mild, aqueous conditions. Specifically, α-ketoglutarate-dependent non-heme iron enzymes, CitB and ClaD, are employed to selectively modify benzylic C–H bonds of o-cresol substrates. In this transformation, biocatalytic hydroxylation of a benzylic C–H bond affords a benzylic alcohol product which, under the aqueous reaction conditions, is in equilibrium with the corresponding o-quinone methide. o-Quinone methide interception by a nucleophile or a dienophile allows for one-pot conversion of benzylic C–H bonds into C–C, C–N, C–O, and C–S bonds in chemoenzymatic cascades on preparative scale. The chemoselectivity and mild nature of this platform is showcased here by the selective modification of peptides and chemoenzymatic synthesis of the chroman natural product (−)-xyloketal D.
Keywords	Lewis bases ; biocatalysis ; chemical bonding ; chemoselectivity ; enzymes ; hydroxylation ; iron ; o-cresol ; peptides ; quinones
Language	English
Dates of publication	2019-1216
Size	p. 20269-20277.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/jacs.9b10474
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Article ; Online: Neural-Network Based Modeling of I/O Buffer Predriver under Power/Ground Supply Voltage Variations.

Souilem, Malek / Tripathi, Jai Narayan / Melicio, Rui / Dghais, Wael / Belgacem, Hamdi / Rodrigues, Eduardo M G

Sensors (Basel, Switzerland)

2021 Volume 21, Issue 18

Abstract: This paper presents a neural-network based nonlinear behavioral modelling of I/O buffer ... circuit under power and ground supply voltage (PGSV) variations. Model structure and I/O device ... characterization along with extraction procedure were described. The last stage of the I/O buffer is ...

Abstract	This paper presents a neural-network based nonlinear behavioral modelling of I/O buffer that accounts for timing distortion introduced by nonlinear switching behavior of the predriver electrical circuit under power and ground supply voltage (PGSV) variations. Model structure and I/O device characterization along with extraction procedure were described. The last stage of the I/O buffer is modelled as nonlinear current-voltage (I-V) and capacitance voltage (C-V) functions capturing the nonlinear dynamic impedances of the pull-up and pull-down transistors. The mathematical model structure of the predriver was derived from the analysis of the large-signal electrical circuit switching behavior. Accordingly, a generic and surrogate multilayer neural network (NN) structure was considered in this work. Timing series data which reflects the nonlinear switching behavior of the multistage predriver's circuit PGSV variations, were used to train the NN model. The proposed model was implemented in the time-domain solver and validated against the reference transistor level (TL) model and the state-of-the-art input-output buffer information specification (IBIS) behavioral model under different scenarios. The analysis of jitter was performed using the eye diagrams plotted at different metrics values.
MeSH term(s)	Computer Simulation ; Electric Power Supplies ; Models, Theoretical ; Neural Networks, Computer ; Nonlinear Dynamics
Language	English
Publishing date	2021-09-10
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2052857-7
ISSN	1424-8220 ; 1424-8220
ISSN (online)	1424-8220
ISSN	1424-8220
DOI	10.3390/s21186074
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Article ; Online: Kaempferol 3-O-rutinoside from Antidesma acidum Retz. Stimulates glucose uptake through SIRT1 induction followed by GLUT4 translocation in skeletal muscle L6 cells.

Kashyap, Bhaswati / Saikia, Kangkon / Samanta, Suman Kumar / Thakur, Debajit / Banerjee, Sanjay Kumar / Borah, Jagat Chandra / Talukdar, Narayan Chandra

Journal of ethnopharmacology

2022 Volume 301, Page(s) 115788

Abstract: ... and spectral data analysis led us to identify the active component as Kaempferol 3-O-rutinoside (KOR ... knockdown myotubes.: Conclusion: Overall, the results of this study suggest that Kaempferol 3-O ...

Abstract	Ethnopharmacological relevance: Antidesma acidum Retz, a perennial herb is known for its anti-diabetic potential among the traditional health care providers of the tribal communities of Manipur, India. Scientific validation of the ancient knowledge on traditional use of this plant with the help of modern tools and techniques can promote further research and its use in health care. Aim of the study: Type 2 Diabetes (T2D) is a complex metabolic disorder and linked with hyperglycemia occurring from insufficiency in insulin secretion, action, or both. The aim of this study was to scientifically validate the traditional myth behind the uses of this plant material against diabetes. More specifically, it was aimed to determine the effect of methanolic extract of A. acidum leaves and/or any of its bioactive phytochemical(s), in enhancing insulin sensitization and subsequently stimulating the insulin signaling cascade of glucose metabolism. Materials and methods: Methanol was used for extraction from the leaf powder of A. acidum followed by bioactivity guided fractionation and isolation of most active component. Biological evaluation was performed to determine the glucose uptake ability against insulin resistance in skeletal muscle (L6) cells. To understand the detailed mechanism of actions of the purified compound, several molecular biology and structural biology experiments such as Western blot, siRNA transfection assay and molecular docking study were performed. Results and discussion: Bioactivity guided isolation of pure compound and spectral data analysis led us to identify the active component as Kaempferol 3-O-rutinoside (KOR) for the first time from the leaf of A. acidum. Over expression of NAD-dependent histone deacetylase, Sirtuin 1 (SIRT1) was observed following KOR treatment. SIRT1 plays an important role in the metabolic pathway and over expression of SIRT implies that it involves in insulin signaling directly or indirectly. Molecular docking and simulation study showed the strong involvement between KOR and SIRT1.Treatment with KOR resulted in significant over expression of SIRT1followed by upregulation of insulin-dependent p-IRS, AKT and AMPK signaling molecules, and stimulation of the GLUT4 translocation, which ultimately enhanced the glucose uptake in sodium palmitate-treated insulin resistant L6 myotubes. Further, the effect of KOR on IRS1, AKT and AMPK phosphorylation, GLUT4 translocation, and glucose uptake was attenuated in SIRT1-knockdown myotubes. Conclusion: Overall, the results of this study suggest that Kaempferol 3-O-rutinoside is the active component presents in the leaf of A. acidum which increases glucose consumption by inducing SIRT1 activation and consequently improves insulin sensitization. These results may find future applications in drug discovery research against T2DM.
MeSH term(s)	Humans ; Sirtuin 1/metabolism ; Diabetes Mellitus, Type 2/drug therapy ; AMP-Activated Protein Kinases/metabolism ; Proto-Oncogene Proteins c-akt/metabolism ; Kaempferols/pharmacology ; Kaempferols/therapeutic use ; Molecular Docking Simulation ; India ; Muscle Fibers, Skeletal ; Insulin/metabolism ; Glucose/metabolism ; Muscle, Skeletal ; Glucose Transporter Type 4/metabolism
Chemical Substances	Sirtuin 1 (EC 3.5.1.-) ; AMP-Activated Protein Kinases (EC 2.7.11.31) ; Proto-Oncogene Proteins c-akt (EC 2.7.11.1) ; Kaempferols ; 3-O-rutinoside ; Insulin ; Glucose (IY9XDZ35W2) ; Glucose Transporter Type 4 ; SIRT1 protein, human (EC 3.5.1.-)
Language	English
Publishing date	2022-10-09
Publishing country	Ireland
Document type	Journal Article
ZDB-ID	134511-4
ISSN	1872-7573 ; 0378-8741
ISSN (online)	1872-7573
ISSN	0378-8741
DOI	10.1016/j.jep.2022.115788
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Article ; Online: One-pot synthesized efficient molybdenum‑niobium-oxide nanocatalyst for selective C-O and C-N coupling reactions at mild conditions

Pavan Narayan Kalbande / Nittan Singh / Bhattu Swapna / Shubhangi Umbarkar / Putla Sudarsanam

Catalysis Communications, Vol 183, Iss , Pp 106766- (2023)

2023

Abstract: ... for selective C-O (glycerol ketalization) and C-N coupling (benzylamine oxidation) reactions. The catalytically ...

Abstract	An efficient molybdenum‑niobium-oxide nanomaterial was synthesized by a one-pot hydrothermal method for selective C-O (glycerol ketalization) and C-N coupling (benzylamine oxidation) reactions. The catalytically favourable properties, such as defective metal sites, truncated surfaces, and uniform metal dispersion in the MoO3-Nb2O5 nanorods, calcined at 500 °C (MoNb OPS-5), were confirmed by Raman, HR-TEM, and STEM-EDX, respectively. Because of improved Lewis/Brønsted acidic strength, the MoNb OPS-5 catalyst showed higher activity in glycerol ketalization and benzylamine oxidation at mild conditions, giving superior selectivity to solketal (97%) and dibenzylimine (99%), respectively. The MoNb OPS-5 catalyst showed high structural stability and considerable good reusability efficacy.
Keywords	Nanocatalysts ; One-pot hydrothermal synthesis ; Mo-Nb-O nanocatalyst ; C-O and C-N coupling ; Glycerol and benzylamine ; Chemistry ; QD1-999
Subject code	540
Language	English
Publishing date	2023-10-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Absence of long-range magnetic order in lithium-containing honeycombs in the Li-Cr-Sb(Te)-O phases.

Mandujano, H Cein / Gonzalez, Sandra L / Episcopo, Nathan / Sitharaman, Uma / Poudel, Narayan / Gofryk, Krzysztof / Garay, Yahir E / Lopez, Jorge A / Zhang, Qiang / Calder, Stuart / Nair, Harikrishnan S

Journal of physics. Condensed matter : an Institute of Physics journal

2021 Volume 33, Issue 29

Abstract: ... ...

Abstract	Li
Language	English
Publishing date	2021-06-04
Publishing country	England
Document type	Journal Article
ZDB-ID	1472968-4
ISSN	1361-648X ; 0953-8984
ISSN (online)	1361-648X
ISSN	0953-8984
DOI	10.1088/1361-648X/abff90
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Article: In silico discovery and evaluation of phytochemicals binding mechanism against human catechol-O-methyltransferase as a putative bioenhancer of L-DOPA therapy in Parkinson disease.

Rath, Surya Narayan / Jena, Lingaraja / Bhuyan, Rajabrata / Mahanandia, Nimai Charan / Patri, Manorama

Genomics & informatics

2021 Volume 19, Issue 1, Page(s) e7

Abstract: ... to metabolic activity of the enzyme catechol-O-methyltransferase (COMT). Although, both Entacapone and Opicapone have U ... withaphysalin O, withanolide B, withasomnine, and withaphysalin F) of plant Withania somnifera have strong ...

Abstract	Levodopa (L-DOPA) therapy is normally practised to treat motor pattern associated with Parkinson disease (PD). Additionally, several inhibitory drugs such as Entacapone and Opicapone are also cosupplemented to protect peripheral inactivation of exogenous L-DOPA (~80%) that occurs due to metabolic activity of the enzyme catechol-O-methyltransferase (COMT). Although, both Entacapone and Opicapone have U.S. Food and Drug Administration approval but regular use of these drugs is associated with high risk of side effects. Thus, authors have focused on in silico discovery of phytochemicals and evaluation of their effectiveness against human soluble COMT using virtual screening, molecular docking, drug-like property prediction, generation of pharmacophoric property, and molecular dynamics simulation. Overall, study proposed, nine phytochemicals (withaphysalin D, withaphysalin N, withaferin A, withacnistin, withaphysalin C, withaphysalin O, withanolide B, withasomnine, and withaphysalin F) of plant Withania somnifera have strong binding efficiency against human COMT in comparison to both of the drugs i.e., Opicapone and Entacapone, thus may be used as putative bioenhancer in L-DOPA therapy. The present study needs further experimental validation to be used as an adjuvant in PD treatment.
Language	English
Publishing date	2021-02-26
Publishing country	Korea (South)
Document type	Journal Article
ZDB-ID	2802682-2
ISSN	2234-0742 ; 1598-866X
ISSN (online)	2234-0742
ISSN	1598-866X
DOI	10.5808/gi.20061
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Article ; Online: Laser-Assisted Surface Lithium Fluoride Decoration of a Cobalt-Free High-Voltage Spinel LiNi₀.₅Mn₁.₅O₄ Cathode for Long-Life Lithium-Ion Batteries

Cui, Zehao / Khosla, Nayna / Lai, Tianxing / Narayan, J. / Manthiram, Arumugam

ACS Applied Materials & Interfaces. 2022 Dec. 27, v. 15, no. 1 p.1247-1255

2022

Abstract: High-voltage spinel LiNi₀.₅Mn₁.₅O₄ (LNMO) is a promising next-generation cathode material due ...

Abstract	High-voltage spinel LiNi₀.₅Mn₁.₅O₄ (LNMO) is a promising next-generation cathode material due to its structural stability, high operation voltage, and low cost. However, the cycle life of LNMO cells is compromised by detrimental electrode-electrolyte reactions, chemical crossover, and rapid anode degradation. Here, we demonstrate that the cycling stability of LNMO can be effectively enhanced by a high-energy laser treatment. Advanced characterizations unveil that the laser treatment induces partial decomposition of the polyvinylidene fluoride binder and formation of a surface LiF phase, which mitigates electrode-electrolyte side reactions and reduces the generation of dissolved transition-metal ions and acidic crossover species. As a result, the solid electrolyte interphase of the graphite counter electrode is thin and is composed of fewer electrolyte decomposition products. This work demonstrates the potential of laser treatment in tuning the surface chemistry of cathode materials for lithium-ion batteries.
Keywords	anodes ; cathodes ; chemistry ; electric potential difference ; electrolytes ; fluorides ; graphene ; lithium ; thermoplastics ; lithium-ion batteries ; high-energy laser ; high-voltage spinel cathode ; electrode−electrolyte interphases ; chemical crossover
Language	English
Dates of publication	2022-1227
Size	p. 1247-1255.
Publishing place	American Chemical Society
Document type	Article ; Online
ISSN	1944-8252
DOI	10.1021/acsami.2c18918
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Selective Interactions of O -Methylated Flavonoid Natural Products with Human Monoamine Oxidase-A and -B

Narayan D. Chaurasiya / Jacob Midiwo / Pankaj Pandey / Regina N. Bwire / Robert J. Doerksen / Ilias Muhammad / Babu L. Tekwani

Molecules, Vol 25, Iss 5358, p

2020 Volume 5358

Abstract: A set of structurally related O -methylated flavonoid natural products isolated from Senecio ... with the active-site of human MAO-A near N5 of FAD. The calculated binding free energies of the O -methylated ... than with MAO-A. The natural O -methylated flavonoid ( 1 ) with highly potent inhibition (IC 50 33 nM; Ki 37.9 ...

Abstract	A set of structurally related O -methylated flavonoid natural products isolated from Senecio roseiflorus ( 1 ), Polygonum senegalense ( 2 and 3 ), Bhaphia macrocalyx ( 4 ), Gardenia ternifolia ( 5 ), and Psiadia punctulata ( 6 ) plant species were characterized for their interaction with human monoamine oxidases (MAO-A and -B) in vitro. Compounds 1 , 2 , and 5 showed selective inhibition of MAO-A, while 4 and 6 showed selective inhibition of MAO-B. Compound 3 showed ~2-fold selectivity towards inhibition of MAO-A. Binding of compounds 1 – 3 and 5 with MAO-A, and compounds 3 and 6 with MAO-B was reversible and not time-independent. The analysis of enzyme-inhibition kinetics suggested a reversible-competitive mechanism for inhibition of MAO-A by 1 and 3 , while a partially-reversible mixed-type inhibition by 5 . Similarly, enzyme inhibition-kinetics analysis with compounds 3 , 4 , and 6 , suggested a competitive reversible inhibition of MAO-B. The molecular docking study suggested that 1 selectively interacts with the active-site of human MAO-A near N5 of FAD. The calculated binding free energies of the O -methylated flavonoids ( 1 and 4 – 6 ) and chalcones ( 2 and 3 ) to MAO-A matched closely with the trend in the experimental IC 50′ s. Analysis of the binding free-energies suggested better interaction of 4 and 6 with MAO-B than with MAO-A. The natural O -methylated flavonoid ( 1 ) with highly potent inhibition (IC 50 33 nM; Ki 37.9 nM) and >292 fold selectivity against human MAO-A (vs. MAO-B) provides a new drug lead for the treatment of neurological disorders.
Keywords	recombinant monoamine oxidase-A ; monoamine oxidase-B ; neurological disorder ; enzyme kinetics ; molecular docking ; inhibition activity ; Organic chemistry ; QD241-441
Subject code	540
Language	English
Publishing date	2020-11-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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