Biology subjects

Das Gupta, S.

Publications and source records attributed to Das Gupta, S..

5 recordsLinked to original sources

bioRxiv2025

Evaluation of Iodine-Based Contrast Agents for Micro-Computed Tomography Imaging of Porcine Cardiac Conduction System

PurposeThis study compares two iodine-based contrast agents: iodine in ethanol (I2E) and aqueous solution of potassium triiodide (I2KI) in optimizing high-resolution, contrast-enhanced micro computed tomography imaging (micro-CT) of the cardiac conduction system (CCS) in porcine hearts. The study evaluates their relative efficacy in enhancing tissue contrast and anatomical delineation, aiming to improve CCS visualization for advanced cardiac research. MethodsDissected porcine hearts were stained with I2E or I2KI for contrast enhancement and scanned with micro-computed tomography. Signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR), and volumetric shrinkage were evaluated. Additionally, qualitative visualization of CCS-related anatomical landmarks, such as the sinoatrial node (SAN), atrioventricular node (AVN), and Purkinje fibres, was performed, along with assessment of artefact occurrence and sample integrity. The efficacy of the contrast agents was also determined by segmenting the regions of interest corresponding to the CCS from micro-CT images. These were then further validated against histology. ResultsI2E provided superior CNR, fewer artefacts, and preserved sample integrity, enabling smooth post-processing and histological sectioning. I2KI staining produced higher soft-tissue signal intensity and faster stain saturation (day 2) than I2E (day 3). However, I2KI exhibited leaching and introduced substantial staining artefacts. I2KI also exhibited structural disintegration, which, in turn, compromised downstream processing. ConclusionThese results suggest that I2E is a viable alternative to I2KI for CCS micro-CT imaging when sample preservation and downstream analyses are essential, whereas I2KI may be preferred for rapid, high-intensity staining where tissue integrity is less critical.

bioengineering↗

bioRxiv2025

Characterization of calcifications in posterior horn of human meniscus using micro-computed tomography

ObjectiveMeniscal calcifications are associated with meniscal degeneration and osteoarthritis (OA). We investigated micro-computed tomography ({micro}CT) imaging for identification of calcification patterns caused by basic calcium phosphate (BCP) and calcium pyrophosphate (CPP). DesignPosterior horns of human medial and lateral menisci from 19 individuals with medial compartment knee OA and 21 deceased donors were imaged with high-resolution {micro}CT. Raman spectroscopy characterized the calcification types from histological sections, adjacent to {micro}CT piece. Qualitative and quantitative analysis, visualization, and grading were performed using 3D {micro}CT images of meniscal calcifications. ResultsDifferent calcification patterns were observed with BCP and CPP. BCP was found at the borders of meniscal tissue and inside complex tears or fibrillation. In contrast, CPP accumulated as circumferential rod-like structures between collagen bundles, mainly inside the meniscal tissue, and lacked the porous 3D structure observed in BCP calcifications. Quantitatively, CPP samples had a higher calcification volume compared to BCP with a geometric mean ratio of 14 (95%CI; 3,73), and larger particle sizes with a ratio of 7 (95%CI; 2,8). Additionally, BCP calcifications had an organized porous structure with a closed porosity range of 6-19, while a similar structure was not seen in CPPs (range 1-3.5). ConclusionsWe qualitatively and quantitatively identified volumetric and morphological differences in the calcification deposition patterns between BCP and CPP calcifications in human meniscus. The calculated differences may help distinguish the calcification types with in vivo imaging modalities in the future, as well as provide a better understanding of their role in OA.

bioengineering↗

bioRxiv2023

EPINEST, an agent-based model to simulate epidemic dynamics in large-scale poultry production and distribution networks

The rapid intensification of poultry production raises important concerns about the associated risks of zoonotic infections. Here, we introduce EPINEST (EPI-demic NEtwork Simulation in poultry Transportation systems): an agent-based modelling designed to simulate pathogen transmission within realistic poultry production and distribution networks. The modular structure of the model allows for easy parameterization to suit specific countries and system configurations. Moreover, the framework enables the replication of a wide range of eco-epidemiological scenarios by incorporating diverse pathogen life-history traits, modes of transmission and interactions between multiple strains and/or pathogens. EPINEST was developed in the context of an interdisciplinary multicentre study conducted in Bangladesh, India, Vietnam and Sri Lanka, and will facilitate the investigation of the spreading patterns of various health hazards such as avian influenza, Campylobacter, Salmonella and antimicrobial resistance in these countries. Furthermore, this modelling framework holds potential for broader application in veterinary epidemiology and One Health research, extending its relevance beyond poultry to encompass other livestock species and disease systems.

bioinformatics↗

bioRxiv2021

Mineral crystal thickness in calcified cartilage and subchondral bone in healthy and osteoarthritic knees

Osteoarthritis (OA) is the most common joint disease globally. In OA, articular cartilage degradation is often accompanied with sclerosis of the subchondral bone. However, the association between OA and tissue mineralization at the nanostructural level is currently not understood. Especially, it is technically challenging to identify calcified cartilage, where relevant but poorly understood pathological processes like tidemark multiplication and advancement occur. Here, we used state-of-the-art micro-focus small-angle X-ray scattering with high 5{micro}m spatial resolution to determine mineral crystal thickness in human subchondral bone and calcified cartilage. Specimens with a wide spectrum of OA severities were acquired from the medial and lateral compartments of medial compartment knee OA patients (n=15) and cadaver knees (n=10). For the first time, we identified a well-defined layer of calcified cartilage associated with pathological tidemark multiplication, containing 0.32nm thicker crystals compared to the rest of calcified cartilage. In addition, we found 0.2nm thicker mineral crystals in both tissues of the lateral compartment in OA compared with healthy knees, indicating a loading-related disease process since the lateral compartment is typically less loaded in medial compartment knee OA. Furthermore, the crystal thickness of the subchondral bone was lower with increasing histopathological OA severity. In summary, we report novel changes in mineral crystal thickness during OA. Our data suggest that unloading in the knee is associated with the growth of mineral crystals, which is especially evident in the calcified cartilage. In the subchondral bone, mineral crystals become thinner with increasing OA severity, which indicates new bone formation with sclerosis. One Sentence SummaryMineral crystal thickness increases with osteoarthritis in the lateral condyle that is typically unloaded.

biophysics↗

bioRxiv2018

Recovery from fire affects spatial variability of nutrient availability in boreal aspen ecosystems

Fire is a key driver of nutrient biogeochemistry in boreal ecosystems. Although a significant amount of research has been conducted to understand boreal fire ecology, it is still unclear how fire affects the spatial distribution of nutrients and what mechanisms are responsible for the post-fire recovery of spatial patterns. In this study, we examined spatial variability in soil nutrient bioavailability and related aboveground (AG) and belowground (BG) properties in three boreal aspen (Populus tremuloides Michx.) stands in northern Alberta at different stages of post-fire recovery. The studied sites include a 1-year old post fire stand (PF), a 9-year old stand at canopy closure (CC), and a 72-year old mature stand (MA). Ion exchange resin was used to measure nutrient bioavailability in-situ and was related to AG (vegetation and forest floor characteristics) and BG (soil microbial and chemical) properties. Significant spatial patterns were found in all three stands. PF stand had the greatest coarse scale spatial patterns (> 23 m) and availability of major macronutrients (N, P, and K). Shorter spatial range (5 to 10 m) of nutrient availability was observed in the stand with longest time since fire. Soil microbial activity was the strongest driver of nutrient availability in the PF stand, whereas contributions from aboveground variables such as understory vegetation, tree canopy cover, coarse woody debris (CWD), distance to nearest tree, and tree size was observed only in the CC and MA stands. The findings from the current study suggest that post-fire nutrient availability follows spatially predictable patterns, and confirm the hypothesis that stand replacing fire creates uniformity in nutrient availability and that the development of post-fire heterogeneity is a product of increasing ecosystem complexity.

ecology↗