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Article ; Online: Environmental insults and compensative responses: when microbiome meets cancer.

Nagpal, Sunil / Mande, Sharmila S

Discover. Oncology

2023 Volume 14, Issue 1, Page(s) 130

Abstract: Tumor microenvironment has recently been ascribed a new hallmark-the polymorphic microbiome. Accumulating evidence regarding the tissue specific territories of tumor-microbiome have opened new and interesting avenues. A pertinent question is regarding ... ...

Abstract	Tumor microenvironment has recently been ascribed a new hallmark-the polymorphic microbiome. Accumulating evidence regarding the tissue specific territories of tumor-microbiome have opened new and interesting avenues. A pertinent question is regarding the functional consequence of the interface between host-microbiome and cancer. Given microbial communities have predominantly been explored through an ecological perspective, it is important that the foundational aspects of ecological stress and the fight to 'survive and thrive' are accounted for tumor-micro(b)environment as well. Building on existing evidence and classical microbial ecology, here we attempt to characterize the ecological stresses and the compensative responses of the microorganisms inside the tumor microenvironment. What insults would microbes experience inside the cancer jungle? How would they respond to these insults? How the interplay of stress and microbial quest for survival would influence the fate of tumor? This work asks these questions and tries to describe this underdiscussed ecological interface of the tumor and its microbiota. It is hoped that a larger scientific thought on the importance of microbial competition sensing vis-à-vis tumor-microenvironment would be stimulated.
Language	English
Publishing date	2023-07-15
Publishing country	United States
Document type	Journal Article ; Review
ISSN	2730-6011
ISSN (online)	2730-6011
DOI	10.1007/s12672-023-00745-9
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Article ; Online: Monitoring the lipid oxidation and fatty acid profile of oil using algorithm-assisted surface-enhanced Raman spectroscopy

Nagpal, Tanya / Yadav, Vikas / Khare, Sunil K. / Siddhanta, Soumik / Sahu, Jatindra K.

Food Chemistry. 2023 Dec., v. 428 p.136746-

2023

Abstract: Deep-fat frying of food develops lipid oxidation products that deteriorate oil and pose a health risk. This necessitates the development of a rapid and accurate oil quality and safety detection technique. Herein, surface-enhanced Raman spectroscopy (SERS) ...

Abstract	Deep-fat frying of food develops lipid oxidation products that deteriorate oil and pose a health risk. This necessitates the development of a rapid and accurate oil quality and safety detection technique. Herein, surface-enhanced Raman spectroscopy (SERS) and sophisticated chemometric techniques were used for rapid and label-free determination of peroxide value (PV) and fatty acid composition of oil in-situ. In the study, plasmon-tuned and biocompatible Ag@Au core–shell nanoparticle-based SERS substrates were used to obtain optimum enhancement despite matrix interference to efficiently detect the oil components. The potent combination of SERS and the Artificial Neural Network (ANN) method could determine the fatty acid profile and PV with upto 99% accuracy. Moreover, the SERS-ANN method could quantify the low level of trans fats, i.e., < 2%, with 97% accuracy. Therefore, the developed algorithm-assisted SERS system enabled the sleek and rapid monitoring and on-site detection of oil oxidation.
Keywords	Raman spectroscopy ; chemometrics ; fatty acid composition ; food chemistry ; lipid peroxidation ; neural networks ; oils ; oxidation ; peroxide value ; risk ; Surface-enhanced Raman spectroscopy ; Edible oil ; Lipid oxidation ; Principal component analysis ; Artificial neural network
Language	English
Dates of publication	2023-12
Publishing place	Elsevier Ltd
Document type	Article ; Online
ZDB-ID	243123-3
ISSN	1873-7072 ; 0308-8146
ISSN (online)	1873-7072
ISSN	0308-8146
DOI	10.1016/j.foodchem.2023.136746
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Article ; Online: Tracking mutational semantics of SARS-CoV-2 genomes.

Singh, Rohan / Nagpal, Sunil / Pinna, Nishal K / Mande, Sharmila S

Scientific reports

2022 Volume 12, Issue 1, Page(s) 15704

Abstract: Natural language processing (NLP) algorithms process linguistic data in order to discover the associated word semantics and develop models that can describe or even predict the latent meanings of the data. The applications of NLP become multi-fold while ... ...

Abstract	Natural language processing (NLP) algorithms process linguistic data in order to discover the associated word semantics and develop models that can describe or even predict the latent meanings of the data. The applications of NLP become multi-fold while dealing with dynamic or temporally evolving datasets (e.g., historical literature). Biological datasets of genome-sequences are interesting since they are sequential as well as dynamic. Here we describe how SARS-CoV-2 genomes and mutations thereof can be processed using fundamental algorithms in NLP to reveal the characteristics and evolution of the virus. We demonstrate applicability of NLP in not only probing the temporal mutational signatures through dynamic topic modelling, but also in tracing the mutation-associations through tracing of semantic drift in genomic mutation records. Our approach also yields promising results in unfolding the mutational relevance to patient health status, thereby identifying putative signatures linked to known/highly speculated mutations of concern.
MeSH term(s)	COVID-19/virology ; Genome, Viral ; Humans ; Mutation ; SARS-CoV-2/genetics ; Semantics
Language	English
Publishing date	2022-09-20
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-022-20000-5
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Article ; Online: Monitoring the lipid oxidation and fatty acid profile of oil using algorithm-assisted surface-enhanced Raman spectroscopy.

Nagpal, Tanya / Yadav, Vikas / Khare, Sunil K / Siddhanta, Soumik / Sahu, Jatindra K

Food chemistry

2023 Volume 428, Page(s) 136746

Abstract	Deep-fat frying of food develops lipid oxidation products that deteriorate oil and pose a health risk. This necessitates the development of a rapid and accurate oil quality and safety detection technique. Herein, surface-enhanced Raman spectroscopy (SERS) and sophisticated chemometric techniques were used for rapid and label-free determination of peroxide value (PV) and fatty acid composition of oil in-situ. In the study, plasmon-tuned and biocompatible Ag@Au core-shell nanoparticle-based SERS substrates were used to obtain optimum enhancement despite matrix interference to efficiently detect the oil components. The potent combination of SERS and the Artificial Neural Network (ANN) method could determine the fatty acid profile and PV with upto 99% accuracy. Moreover, the SERS-ANN method could quantify the low level of trans fats, i.e., < 2%, with 97% accuracy. Therefore, the developed algorithm-assisted SERS system enabled the sleek and rapid monitoring and on-site detection of oil oxidation.
MeSH term(s)	Spectrum Analysis, Raman/methods ; Fatty Acids ; Nanoparticles ; Oxidation-Reduction ; Algorithms ; Metal Nanoparticles/chemistry
Chemical Substances	Fatty Acids
Language	English
Publishing date	2023-06-26
Publishing country	England
Document type	Journal Article
ZDB-ID	243123-3
ISSN	1873-7072 ; 0308-8146
ISSN (online)	1873-7072
ISSN	0308-8146
DOI	10.1016/j.foodchem.2023.136746
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Article ; Online: MarkerML - Marker Feature Identification in Metagenomic Datasets Using Interpretable Machine Learning.

Nagpal, Sunil / Singh, Rohan / Taneja, Bhupesh / Mande, Sharmila S

Journal of molecular biology

2022 Volume 434, Issue 11, Page(s) 167589

Abstract: Identification of environment specific marker-features is one of the key objectives of many metagenomic studies. It aims to identify such features in microbiome datasets that may serve as markers of the contrasting or comparable states. Hypothesis ... ...

Abstract	Identification of environment specific marker-features is one of the key objectives of many metagenomic studies. It aims to identify such features in microbiome datasets that may serve as markers of the contrasting or comparable states. Hypothesis testing and black-box machine learnt models which are conventionally used for identification of these features are generally not exhaustive, especially because they generally do-not provide any quantifiable relevance (context) of/between the identified features. We present MarkerML web-server, that seeks to leverage the emergence of interpretable machine learning for facilitating the contextual discovery of metagenomic features of interest. It does so through a comprehensive and automated application of the concept of Shapley Additive Explanations in companionship to the compositionality accounted hypothesis testing for the multi-variate microbiome datasets. MarkerML not only helps in identification of marker-features, but also enables insights into the role and inter-dependence of the identified features in driving the decision making of the supervised machine learnt model. Generation of high quality and intuitive visualizations spanning prediction effect plots, model performance reports, feature dependency plots, Shapley and abundance informed cladograms (Sungrams), hypothesis tested violin plots along-with necessary provisions for excluding the participant bias and ensuring reproducibility of results, further seek to make the platform a useful asset for the scientists in the field of microbiome (and even beyond). The MarkerML web-server is freely available for the academic community at https://microbiome.igib.res.in/markerml/.
MeSH term(s)	Datasets as Topic ; Humans ; Internet Use ; Machine Learning ; Metagenome ; Metagenomics ; Reproducibility of Results
Language	English
Publishing date	2022-04-18
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2022.167589
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Article: Scrotal Lymphangiectasia with Penile Elephantiasis in Underlying Lymphatic Filariasis-Challenging the Diagnostic Mind! A Case Report.

Vishwanath, Tejas / Nagpal, Angela / Ghate, Sunil / Sharma, Aseem

Dermatopathology (Basel, Switzerland)

2021 Volume 8, Issue 1, Page(s) 10–16

Abstract: Background: A plethora of diseases manifest as acquired genital lymphangiectasias which clinically manifest as superficial vesicles. They range from infections such as tuberculosis to connective tissue diseases such as scleroderma and even malignancy. ... ...

Abstract	Background: A plethora of diseases manifest as acquired genital lymphangiectasias which clinically manifest as superficial vesicles. They range from infections such as tuberculosis to connective tissue diseases such as scleroderma and even malignancy. Amongst infectious etiologies, lymphatic filariasis leads as the cause for lymphatic obstruction. Despite this, acquired lymphangiectasias due to this cause are not commonly reported. An unusual case of acquired scrotal lymphangiectasia secondary to filariasis is detailed in this paper with dermoscopic and histologic findings. Methods: A 65-year-old male farmer presented with multiple, asymptomatic vesicles over the scrotum with thickened scrotal and penile skin that had occurred for six years. He gave past history of intermittent fever and milky urine, was diagnosed with filariasis and treated with diethylcarbamazine for a year, four years previously. Systemic complaints abated but the peno-scrotal lesions did not. Results: Polarized dermoscopy revealed multiple skin-colored nodules and translucent pale blue lacunae over the scrotum. A few radially arranged linear irregular vessels were noted over the nodules. On histopathology, multiple ectatic lymphatics were noted in the mid and upper dermis with acanthosis and superficial perivascular lymphocytes. Peripheral smear revealed eosinophils; however, microfilariae could not be detected despite repeated diethylcarbamazine provocation and night smears being taken. The findings were compatible with acquired scrotal lymphangiectasia secondary to treated lymphatic filariasis. Local hygiene was advised; however, procedural treatments were refused by the patient. Conclusion: Herein, we report an unusual case of acquired scrotal lymphangiectasia of the scrotum secondary to treated lymphatic filariasis. Very few similar reports exist. To the best of our knowledge, dermoscopic features of this condition have not been elucidated before. This case, detailing an uncommon manifestation of a common disease (filariasis), demonstrates the importance of careful history taking and examination. This was especially so in the present case since only circumstantial evidence of filariasis was noted in investigations. There is a need to heighten awareness of this unusual condition amongst physicians especially if the patient hails from an area endemic for filariasis.
Language	English
Publishing date	2021-01-01
Publishing country	Switzerland
Document type	Case Reports
ZDB-ID	2777118-0
ISSN	2296-3529
ISSN	2296-3529
DOI	10.3390/dermatopathology8010002
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Article: Attenuation of the BTLA/HVEM Regulatory Network in the Circulation in Primary Sjögren's Syndrome.

Small, Annabelle / Cole, Suzanne / Wang, Jing J / Nagpal, Sunil / Hao, Ling-Yang / Wechalekar, Mihir D

Journal of clinical medicine

2022 Volume 11, Issue 3

Abstract: Primary Sjögren's syndrome (SjS) is an inflammatory autoimmune disorder which targets the lacrimal and salivary glands, resulting in glandular dysfunction. Currently, the immune drivers of SjS remain poorly understood and peripheral biomarkers of disease ...

Abstract	Primary Sjögren's syndrome (SjS) is an inflammatory autoimmune disorder which targets the lacrimal and salivary glands, resulting in glandular dysfunction. Currently, the immune drivers of SjS remain poorly understood and peripheral biomarkers of disease are lacking. The present study therefore sought to investigate the immune cell constituents of the SjS peripheral blood, and to assess the role of the BTLA/HVEM/CD160 co-stimulatory network by characterizing expression within the periphery. Peripheral blood mononuclear cells (PBMCs) were isolated from whole blood of
Language	English
Publishing date	2022-01-21
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662592-1
ISSN	2077-0383
ISSN	2077-0383
DOI	10.3390/jcm11030535
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Article ; Online: Immobilization of L-asparaginase on magnetic nanoparticles: Kinetics and functional characterization and applications.

Alam, Shahenvaz / Nagpal, Tanya / Singhal, Rekha / Kumar Khare, Sunil

Bioresource technology

2021 Volume 339, Page(s) 125599

Abstract: L-asparaginase shows great potential as a food enzyme to reduce acrylamide formation in fried and baked products. But for food applications, enzymes must be stable at high temperatures and have higher catalytic efficiency. These desirable characteristics ...

Abstract	L-asparaginase shows great potential as a food enzyme to reduce acrylamide formation in fried and baked products. But for food applications, enzymes must be stable at high temperatures and have higher catalytic efficiency. These desirable characteristics are conferred by the immobilization of enzymes on a suitable matrix. The present study aimed to immobilize the L-asparaginase enzyme on magnetic nanoparticles to reduce acrylamide content in the food system. Immobilized preparations were characterized using SEM, TEM, FTIR, UV-spectrometry, and XRD diffraction analyses. These nanoparticles enhanced the thermal stability of the enzyme up to four-fold at 70 °C compared to the free enzyme. Kinetic parameters exhibited an increase in V
MeSH term(s)	Acrylamide ; Asparaginase/metabolism ; Catalysis ; Enzyme Stability ; Enzymes, Immobilized/metabolism ; Kinetics ; Magnetite Nanoparticles
Chemical Substances	Enzymes, Immobilized ; Magnetite Nanoparticles ; Acrylamide (20R035KLCI) ; Asparaginase (EC 3.5.1.1)
Language	English
Publishing date	2021-07-17
Publishing country	England
Document type	Journal Article
ZDB-ID	1065195-0
ISSN	1873-2976 ; 0960-8524
ISSN (online)	1873-2976
ISSN	0960-8524
DOI	10.1016/j.biortech.2021.125599
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Article: Effect of Psidium guajava leaves extracts on thermo-lipid oxidation and Maillard pathway born food toxicant acrylamide in Indian staple food

Nagpal, Tanya / Alam, Shahenvaz / Khare, Sunil K. / Satya, Santosh / Chaturvedi, Shivani / Sahu, Jatindra K.

Journal of food science and technology. 2022 Jan., v. 59, no. 1

2022

Abstract: Deep frying of food is a common practice that leads to the formation of lipid oxidation products. These lipid oxidation products have a role in the Maillard reaction, which ultimately leads to the formation of cancer-causing and neurotoxic substance ... ...

Abstract	Deep frying of food is a common practice that leads to the formation of lipid oxidation products. These lipid oxidation products have a role in the Maillard reaction, which ultimately leads to the formation of cancer-causing and neurotoxic substance acrylamide. In this regard, the Psidium guajava leaves extract-treated sunflower oil on oxidative stability and acrylamide content in pooris a popular deep-fried staple food in India were studied and compared with synthetic antioxidant butylated hydroxytoluene (BHT) till four frying cycles. P. guajava leaves contain 173.33 ± 1.95 mg GAE/g extract total phenolic content and 20.43 ± 0.25 mg RUE/g extract total flavonoid content. Some of the phytochemicals in the extract were identified and quantified by HPTLC. P. guajava leaves extract (1 g) contained 0.039 mg gallic acid, 0.196 mg rutin, 0.021 mg naringenin, 0.059 mg ferulic acid. The IC₅₀ values for guava leaves extract, BHT, and ascorbic acid were 61.4, 30.4, 26.6 µg/mL, respectively. The peroxide and p-anisidine values indicated that P. guajava leaves extract inhibited lipid oxidation and provided oxidative stability. Pooris fried in P. guajava leaves extract-treated, BHT treated sunflower oil contained a lower acrylamide than pooris fried in control sunflower oil.
Keywords	Maillard reaction ; Psidium guajava ; acrylamides ; antioxidants ; ascorbic acid ; butylated hydroxytoluene ; ferulic acid ; fried foods ; gallic acid ; guavas ; lipid peroxidation ; naringenin ; neurotoxicity ; oxidation ; oxidative stability ; rutin ; staple foods ; sunflower oil ; India
Language	English
Dates of publication	2022-01
Size	p. 86-94.
Publishing place	Springer India
Document type	Article
ZDB-ID	242498-8
ISSN	0975-8402 ; 0022-1155
ISSN (online)	0975-8402
ISSN	0022-1155
DOI	10.1007/s13197-021-04984-y
Database	NAL-Catalogue (AGRICOLA)

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Article: MarkerML – Marker Feature Identification in Metagenomic Datasets Using Interpretable Machine Learning

Nagpal, Sunil / Singh, Rohan / Taneja, Bhupesh / Mande, Sharmila S.

Journal of molecular biology. 2022 Apr. 12,

2022

Abstract	Identification of environment specific marker-features is one of the key objectives of many metagenomic studies. It aims to identify such features in microbiome datasets that may serve as markers of the contrasting or comparable states. Hypothesis testing and black-box machine learnt models which are conventionally used for identification of these features are generally not exhaustive, especially because they generally do-not provide any quantifiable relevance (context) of/between the identified features. We present MarkerML web-server, that seeks to leverage the emergence of interpretable machine learning for facilitating the contextual discovery of metagenomic features of interest. It does so through a comprehensive and automated application of the concept of Shapley Additive Explanations in companionship to the compositionality accounted hypothesis testing for the multi-variate microbiome datasets. MarkerML not only helps in identification of marker-features, but also enables insights into the role and inter-dependence of the identified features in driving the decision making of the supervised machine learnt model. Generation of high quality and intuitive visualizations spanning prediction effect plots, model performance reports, feature dependency plots, Shapley and abundance informed cladograms (Sungrams), hypothesis tested violin plots along-with necessary provisions for excluding the participant bias and ensuring reproducibility of results, further seek to make the platform a useful asset for the scientists in the field of microbiome (and even beyond). The MarkerML web-server is freely available for the academic community at https://microbiome.igib.res.in/markerml/.
Keywords	assets ; automation ; data collection ; metagenomics ; microbiome ; model validation ; models ; molecular biology ; prediction
Language	English
Dates of publication	2022-0412
Publishing place	Elsevier Ltd
Document type	Article
Note	Pre-press version
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2022.167589
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