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Article ; Online: Approach to fiber-based optical polarimetry for tissue assessment: system calibration and application.

Sharma, Mahima / Shaji, Chitra / Narayanan Unni, Sujatha

Applied optics

2024 Volume 63, Issue 8, Page(s) 1888–1894

Abstract: The potential of optical polarimetry is increasingly explored to unravel the tissue structure through several optical instrument configurations. Fiber-based solutions offer portability and are accommodative in an endoscopic examination environment. Here, ...

Abstract	The potential of optical polarimetry is increasingly explored to unravel the tissue structure through several optical instrument configurations. Fiber-based solutions offer portability and are accommodative in an endoscopic examination environment. Here, we address the challenges in realizing a fiber-based optical polarimetry system through an approach involving an all-fiber polarization controller. The methods of device calibration and application in bulk tissues are discussed, and results are presented.
Language	English
Publishing date	2024-04-03
Publishing country	United States
Document type	Journal Article
ISSN	1539-4522
ISSN (online)	1539-4522
DOI	10.1364/AO.501447
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Article ; Online: Skin microcirculatory responses: A potential marker for early diabetic neuropathy assessment using a low-cost portable diffuse optical spectrometry device.

Vasudevan, Vysakh / Unni, Sujatha Narayanan

Journal of biophotonics

2023 Volume 17, Issue 3, Page(s) e202300335

Abstract: Diffuse optical measurement is an evolving optical modality providing a fast and portable solution for microcirculation assessment. Diffuse optics in static and dynamic modalities are combined here in a system to assess hemodynamics in skin tissues of ... ...

Abstract	Diffuse optical measurement is an evolving optical modality providing a fast and portable solution for microcirculation assessment. Diffuse optics in static and dynamic modalities are combined here in a system to assess hemodynamics in skin tissues of control and diabetic subjects. The in-house developed system consists of a laser source, fiber optic probe, a low-cost avalanche photodiode, a finite element model (FEM) derived static optical property estimator, and a software correlator for continuous flow monitoring through microvasculature. The studies demonstrated that the system quantifies the changes in blood flow rate in the immediate skin subsurface. The system is calibrated with in vitro flow models and a proof-of-concept was demonstrated on a limited number of subjects in a clinical environment. The flow changes in response to vasoconstrictive and vasodilative stimuli were analyzed and used to classify different stages of diabetes, including diabetic neuropathy.
MeSH term(s)	Humans ; Diabetic Neuropathies/diagnosis ; Microcirculation/physiology ; Spectrum Analysis ; Skin/blood supply ; Fiber Optic Technology ; Diabetes Mellitus
Language	English
Publishing date	2023-12-20
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2390063-5
ISSN	1864-0648 ; 1864-063X
ISSN (online)	1864-0648
ISSN	1864-063X
DOI	10.1002/jbio.202300335
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Article ; Online: Fungal infection in plant leaves-A Review

Chelladurai K. / Sujatha N. / Narayanan Valli Latha

E3S Web of Conferences, Vol 399, p

2023 Volume 02010

Abstract: The primary resource of a country is agriculture and crop production. The economic development of the country also resides on the agricultural products which ultimately determines the growth of the citizen. The major crisis in food production is the ... ...

Abstract	The primary resource of a country is agriculture and crop production. The economic development of the country also resides on the agricultural products which ultimately determines the growth of the citizen. The major crisis in food production is the influence of diseases in plants. This ultimately abolish the economy of the country, as major portion of progress of the nation is dependent on agriculture and its products. The challenges faced by the farmers are the unawareness of the various diseases that affects different parts of the plants. They should be able to identify the early infection caused in plants by different pathogens like bacteria, fungi, virus etc., Main disease-causing agent is found to be the fungus which was the vital factor that produce serious loss in the agriculture. Again, the pesticides and fertilizers used by the agriculturist changes to be hazardous for human beings and wild life species. This problem should be considered as a chief calamity and an alternate measure must be found to support the cultivators. An innovative step adopted by the researchers are prompt detection of the diseases using machine learning and deep learning algorithms. These algorithms use different image processing techniques and computer vision process to classify the disease in plant parts at an earlier stage. This paper provides a detailed review on the fungal infection caused in plant leaves and its identification using deep learning methodology.
Keywords	plant diseases ; fungal infection ; machine learning ; deep learning and computer vision process ; Environmental sciences ; GE1-350
Subject code	580 ; 630
Language	English
Publishing date	2023-01-01T00:00:00Z
Publisher	EDP Sciences
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Assessment of Various Factors Contributing to Unfavourable Oral Health Care Seeking Behaviour: A Cross-Sectional Study.

Tharshini, Priya / Selvamary, Leena / Narayanan, Aswath / S G, Ramesh Kumar / A, Sujatha

Cureus

2024 Volume 16, Issue 1, Page(s) e53037

Abstract: Background: Access to effective oral health care is crucial for a good quality of life. Unfortunately, many individuals face barriers in accessing the necessary oral health care services. By examining various factors, we can gain a better understanding ...

Abstract	Background: Access to effective oral health care is crucial for a good quality of life. Unfortunately, many individuals face barriers in accessing the necessary oral health care services. By examining various factors, we can gain a better understanding of the challenges faced by the population and work towards improving oral health care outcomes. This study aims to assess the various factors contributing to unfavorable oral healthcare-seeking behavior in Chennai city. Materials and methods: A cross-sectional study was conducted in Chennai city involving six hundred and twenty-four individuals from the general population from 12 wards by lottery method. The data collection process involved interviews using a pre-designed questionnaire, through which demographic information was gathered. The Penchansky and Thomas model was employed to assess barriers in service utilization. All completed questionnaires were included in the data analysis, which was performed using SPSS version 20. Results: In the present study, among the various dimensions of access suggested by Penchansky and Thomas, the major reason for unfavorable oral healthcare-seeking behavior was accommodation (54.8%), followed by affordability (20.2%), accessibility (5.6%), acceptability (4.4%), and availability (1.1%). The other reasons that contributed were sociocultural factors (26.4%), lack of awareness (20.8%), and psychosocial factors (11.8%). Conclusion: The present study highlights lack of time as the major factor contributing to unfavourable oral healthcare-seeking behaviour in an urban population. This finding contrasts with previous studies that have focussed on the lack of awareness about dental diseases and the high cost of dental treatment in rural areas.
Language	English
Publishing date	2024-01-27
Publishing country	United States
Document type	Journal Article
ZDB-ID	2747273-5
ISSN	2168-8184
ISSN	2168-8184
DOI	10.7759/cureus.53037
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Article ; Online: Quantification of soft tissue parameters from spatially resolved diffuse reflectance finite element models.

Vasudevan, Vysakh / Narayanan Unni, Sujatha

International journal for numerical methods in biomedical engineering

2021 Volume 38, Issue 1, Page(s) e3546

Abstract: Spatially resolved diffuse reflectance spectroscopy (SRDRS) is a non-invasive optical technique that helps in clinical diagnosis of various tissue microcirculation and skin pigmentation disorders based on collected backscattered light from multi-layered ... ...

Abstract	Spatially resolved diffuse reflectance spectroscopy (SRDRS) is a non-invasive optical technique that helps in clinical diagnosis of various tissue microcirculation and skin pigmentation disorders based on collected backscattered light from multi-layered tissue. The extraction of the optical properties from the reflectance spectrum using analytical solutions is laborious. Model-based light tissue interaction studies help in quantifying the optical properties. This work presents the use of finite element models of light tissue interaction for this purpose. A bilayer model mimicking human skin was considered and the diffused reflectance spectra at multiple detector points were generated using finite element modelling for varying melanin concentration, epidermal thickness, blood volume fraction, oxygen saturation and scattering components. The reflectance value based on varying optical parameters from multiple detection points lead to the generation of a look-up table (LUT), which is further used for finding the tissue parameters that contribute to the spatially resolved reflectance values. The tissue parameters estimated after inverse modelling showed a high degree of agreement with the expected tissue parameters for a test dataset different from the training dataset.
MeSH term(s)	Diffusion ; Finite Element Analysis ; Humans ; Microcirculation ; Skin ; Spectrum Analysis/methods
Language	English
Publishing date	2021-11-14
Publishing country	England
Document type	Journal Article
ZDB-ID	2540968-2
ISSN	2040-7947 ; 2040-7939
ISSN (online)	2040-7947
ISSN	2040-7939
DOI	10.1002/cnm.3546
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Article ; Online: Characterizing colon cancer stages through optical polarimetry-assisted digital staining.

Sharma, Mahima / Unni, Sujatha Narayanan / Shaji, Chitra / Balasubramanian, Subalakshmi / Sundaram, Sandhya

Lasers in medical science

2024 Volume 39, Issue 1, Page(s) 59

Abstract: Tissue polarimetry has been gaining importance in extracting useful diagnostic information from the structural attributes of tissues, which vary in response to the tissue health status and hence find great potential in cancer diagnosis. However, the ... ...

Abstract	Tissue polarimetry has been gaining importance in extracting useful diagnostic information from the structural attributes of tissues, which vary in response to the tissue health status and hence find great potential in cancer diagnosis. However, the complexities associated with cancer make it challenging to isolate the characteristic changes as the tumor progresses using polarimetry. This study attempts to experimentally characterize the polarimetric behavior in colon cancer associated with various stages of development. Bulk and unstained sections of normal and tumor colon tissue were imaged in the reflection and transmission polarimetry configurations at low and high imaging resolutions using an in-house developed Mueller polarimeter. Through this study, we observed that the information about the major contributors of scattering in colon tissue, manifesting in depolarization and retardance, can be obtained from the bulk tissue and unstained sections. These parameters aid in characterizing the polarimetric changes as the colon tumor progresses. While the unstained colon section best indicated the depolarization contrast between normal and tumor, the contrast through the retardance parameter was more pronounced in the bulk colon tissue. The results suggest that the polarimetric "digitally stained" images obtained by Mueller polarimetry are comparable with the bulk tissue counterparts, making it useful for characterizing colon cancer tissues across different stages of development.
MeSH term(s)	Humans ; Colonic Neoplasms/diagnostic imaging ; Colonic Neoplasms/pathology ; Spectrum Analysis ; Staining and Labeling
Language	English
Publishing date	2024-02-10
Publishing country	England
Document type	Journal Article
ZDB-ID	632808-8
ISSN	1435-604X ; 0268-8921
ISSN (online)	1435-604X
ISSN	0268-8921
DOI	10.1007/s10103-024-04006-1
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Article ; Online: Evaluation of a diatom eDNA-based technique for assessing water quality variations in tropical lakes and reservoirs

Sujatha Narayanan Kutty / Rebecca K. Loh / Wayne Bannister / David Taylor

Ecological Indicators, Vol 141, Iss , Pp 109108- (2022)

2022

Abstract: Freshwater bodies, both lotic (canals, rivers) and lentic (lakes and reservoirs), in the tropics have only rarely been subjected to intense monitoring regimes owing to limited expertise and resources, despite tropical habitats being among the most ... ...

Abstract	Freshwater bodies, both lotic (canals, rivers) and lentic (lakes and reservoirs), in the tropics have only rarely been subjected to intense monitoring regimes owing to limited expertise and resources, despite tropical habitats being among the most dynamic and threatened globally. Diatoms are an important part of assessing aquatic environmental changes in parts of the world where monitoring is well-established because of their sensitivity to a range of indicators of water quality. In such cases, diatoms have traditionally been identified based on morphology. Morphological information on tropical diatom taxa and the expertise to assemble it are sparse. However, DNA-based assessment is less reliant on taxonomic expertise and has the potential to be more cost-efficient. The application of DNA-based technology could thus expedite the incorporation of diatoms into routine monitoring in the tropics. Here we evaluate an environmental DNA (eDNA) metabarcoding workflow for diatom identifications based on 109 water samples from six freshwater reservoirs in Singapore, a highly urbanised part of tropical Southeast Asia. The six reservoirs span a range of sizes and catchment settings. We generate baseline information for lentic systems by targeting planktonic assemblages and including two commonly used barcodes, rbcL and 18S, to assess detection differences. Congruence with morphological identifications is generally low and each technique reveals distinct species lists, but overall congruence between methods improves when comparisons are at the genus level. We discuss the probable methodological and analytical causes for this incongruence and conclude that both approaches be used concurrently for generating reference databases of relatively poorly-known diatom diversity in tropical freshwater habitats. More promisingly, we find that eDNA datasets were sufficient to reveal both spatial and temporal patterns in diatom assemblages across the six study sites. We also show that regardless of the detection method used, diatom ...
Keywords	Biological monitoring ; Diatom ; eDNA ; Environmental DNA ; Freshwater ; Metabarcoding ; Ecology ; QH540-549.5
Subject code	333
Language	English
Publishing date	2022-08-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Histopathological correlations of bulk tissue polarimetric images: Case study.

Sharma, Mahima / Narayanan Unni, Sujatha / Balasubramanian, Subalakshmi / Sundaram, Sandhya / Krishnamurthy, Priya / Hegde, Anoosha

Journal of biophotonics

2021 Volume 14, Issue 5, Page(s) e202000475

Abstract: Polarimetric imaging and image analysis have gained increased interest in soft tissue analysis at the cellular level. However, polarimetric imaging has widely been tested on thin tissue sections to provide reliable information correlated with ... ...

Abstract	Polarimetric imaging and image analysis have gained increased interest in soft tissue analysis at the cellular level. However, polarimetric imaging has widely been tested on thin tissue sections to provide reliable information correlated with histopathological findings. Polarimetric bulk tissue analysis always offered an overall assessment of various tissue optical properties for diagnosis. In this study, the histopathological correlation of bulk tissue polarimetry images for soft tissues is discussed. The first-hand information on the use of bulk tissue Mueller polarimetry and image analysis as an alternative to tissue histopathology is presented for surgically extracted colon and breast tissues.
Language	English
Publishing date	2021-02-13
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2390063-5
ISSN	1864-0648 ; 1864-063X
ISSN (online)	1864-0648
ISSN	1864-063X
DOI	10.1002/jbio.202000475
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Article: Evaluation of a diatom eDNA-based technique for assessing water quality variations in tropical lakes and reservoirs

Kutty, Sujatha Narayanan / Loh, Rebecca K. / Bannister, Wayne / Taylor, David

Ecological indicators. 2022 Aug., v. 141

2022

Abstract	Freshwater bodies, both lotic (canals, rivers) and lentic (lakes and reservoirs), in the tropics have only rarely been subjected to intense monitoring regimes owing to limited expertise and resources, despite tropical habitats being among the most dynamic and threatened globally. Diatoms are an important part of assessing aquatic environmental changes in parts of the world where monitoring is well-established because of their sensitivity to a range of indicators of water quality. In such cases, diatoms have traditionally been identified based on morphology. Morphological information on tropical diatom taxa and the expertise to assemble it are sparse. However, DNA-based assessment is less reliant on taxonomic expertise and has the potential to be more cost-efficient. The application of DNA-based technology could thus expedite the incorporation of diatoms into routine monitoring in the tropics. Here we evaluate an environmental DNA (eDNA) metabarcoding workflow for diatom identifications based on 109 water samples from six freshwater reservoirs in Singapore, a highly urbanised part of tropical Southeast Asia. The six reservoirs span a range of sizes and catchment settings. We generate baseline information for lentic systems by targeting planktonic assemblages and including two commonly used barcodes, rbcL and 18S, to assess detection differences. Congruence with morphological identifications is generally low and each technique reveals distinct species lists, but overall congruence between methods improves when comparisons are at the genus level. We discuss the probable methodological and analytical causes for this incongruence and conclude that both approaches be used concurrently for generating reference databases of relatively poorly-known diatom diversity in tropical freshwater habitats. More promisingly, we find that eDNA datasets were sufficient to reveal both spatial and temporal patterns in diatom assemblages across the six study sites. We also show that regardless of the detection method used, diatom assemblages correlated with similar environmental variables. Results highlight the potential feasibility of eDNA-based diatom monitoring of freshwater habitats in Southeast Asia and in the tropics more broadly.
Keywords	Bacillariophyceae ; DNA barcoding ; Singapore ; cost effectiveness ; data collection ; environmental DNA ; freshwater ; lentic systems ; lotic systems ; plankton ; urbanization ; water quality ; watersheds
Language	English
Dates of publication	2022-08
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	2036774-0
ISSN	1872-7034 ; 1470-160X
ISSN (online)	1872-7034
ISSN	1470-160X
DOI	10.1016/j.ecolind.2022.109108
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Article ; Online: Double deletion of PknI/DacB2 leads to attenuation of Mycobacterium tuberculosis for growth and virulence.

Kandasamy, Srinivasan / Palaniyandi, Kannan / Gupta, Umesh Datta / Narayanan, Sujatha

Tuberculosis (Edinburgh, Scotland)

2020 Volume 123, Page(s) 101957

Abstract: Serine/Threonine Protein Kinases (STPKs) phosphorylates target proteins thereby regulates various important cellular signal transduction pathways such as cell division and cell wall synthesis. It has been demonstrated that the STPKs regulate ... ...

Abstract	Serine/Threonine Protein Kinases (STPKs) phosphorylates target proteins thereby regulates various important cellular signal transduction pathways such as cell division and cell wall synthesis. It has been demonstrated that the STPKs regulate peptidoglycan biosynthesis by phosphorylating penicillin binding proteins (PBPs). We extensively characterized both PknI (STPK) and DacB2 (PBP) roles individually as well as combining by genetic knockout and phenotypic characterization studies. In the present study, we analyzed the role of PknI and DacB2 in cell division and virulence. The double knockout (DKO) strain growth was reduced under stress conditions like acidic pH, nutrient depletion media and low oxygen availability conditions. We also found that the DKO growth was significantly reduced in macrophage cell line and it was hypersensitive to oxidative and nitrosative stress condition. The DKO strain significantly attenuated in guinea pig model which was measured by reduced bacillary load, gross pathological and histopathological damages. Overall, these results clearly demonstrated that both PknI and DacB2 together play an important role in cell division under stress conditions, the DKO strain significantly attenuated both in vitro and in vivo models.
MeSH term(s)	Animals ; Bacterial Proteins/genetics ; Carboxypeptidases/genetics ; Disease Models, Animal ; Female ; Gene Deletion ; Genotype ; Guinea Pigs ; Host-Pathogen Interactions ; Humans ; Hydrogen-Ion Concentration ; Macrophages/metabolism ; Macrophages/microbiology ; Microbial Viability ; Mycobacterium tuberculosis/genetics ; Mycobacterium tuberculosis/growth & development ; Mycobacterium tuberculosis/pathogenicity ; Nitrosative Stress ; Oxidative Stress ; Phenotype ; Protein Serine-Threonine Kinases/genetics ; THP-1 Cells ; Tuberculosis, Pulmonary/metabolism ; Tuberculosis, Pulmonary/microbiology ; Virulence
Chemical Substances	Bacterial Proteins ; Pknk protein, Mycobacterium tuberculosis (EC 2.7.11.1) ; Protein Serine-Threonine Kinases (EC 2.7.11.1) ; Carboxypeptidases (EC 3.4.-) ; DacB2 protein, Mycobacterium tuberculosis (EC 3.4.-)
Language	English
Publishing date	2020-06-27
Publishing country	Scotland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2046804-0
ISSN	1873-281X ; 1472-9792
ISSN (online)	1873-281X
ISSN	1472-9792
DOI	10.1016/j.tube.2020.101957
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