Biology subjects

Shekhar, H.

Publications and source records attributed to Shekhar, H..

4 recordsLinked to original sources

bioRxiv2026

VascFlexMap: Microvascular Ultrasound Imaging at Low Frame Rates Using Sparse Data and a Transformer-Decoder Network

ObjectiveSuper-resolution ultrasound (SR-US) reveals microvascular structures with exquisite resolution, but clinical translation remains limited by the need for ultrafast frame rates, massive data volumes, and long reconstruction times. This work proposes a deep learning framework that reconstructs microvascular maps from low-frame-rate enhanced ultrasound sequences, bypassing explicit microbubble localization and tracking. MethodsA transformer-decoder network with learned linear projections was designed to model spatiotemporal dependencies across sparse contrast-enhanced ultrasound sequences and reconstruct vessel probability maps, refined via a post-processing enhancement stage. Single-head self-attention captures temporal correlations under challenging conditions including overlapping microbubbles and low signal-to-noise ratios. Binary cross-entropy loss guided training to preserve vascular topology across synthetic and in vivo datasets. In vivo rat brain bolus data from the PALA challenge was used to evaluate this approach under up to 500 - fold data reduction (341 frames at 2 FPS vs. 170400 frames at 1000 FPS in standard ULM). ResultsDespite aggressive undersampling, the proposed pipeline recovered coherent microvascular architecture where conventional ULM pipelines applied to the same sparse data failed to produce continuous vascular networks. Major branches and higher-order microvessels remained visible with apparent vessel widths broadened by approximately three-fold relative to reference SR-US. End-to-end reconstruction completed in 28-133 seconds on an NVIDIA H100 GPU depending on the number of frames employed. ConclusionThe reported approach preserved vascular topology with fast reconstruction and low data overhead, albeit at lower resolution. The substantial reduction in frames and computation time highlights the translational potential of this SR-US-inspired microvascular imaging approach.

bioengineering↗

bioRxiv2025

Analysing a Reported Experiment That May Demonstrate the Interplay of Fluid Velocity and Pore Pressure in Bone Adaptation

Current models propose that osteogenesis occurs in regions of high mechanical stimuli such as strain, fluid velocity, or pore pressure. However, in vivo experiments on mouse tibiae under cantilever loading revealed new bone formation exclusively on the anterolateral side, despite the opposite posteromedial surface experiencing comparable magnitudes of these stimuli. This indicates that individual stimulus magnitude is insufficient and suggests an interactive mechanism among them. To investigate this, a poroelastic finite element model was developed to quantify the combined effects of load-induced fluid velocity and pore pressure. Tensile loading generated negative pore pressure, stretching osteocyte processes, while compressive loading produced positive pore pressure, compressing them. Since fluid flow exerts drag forces that also stretch osteocytes, the combined effect of flow and negative pressure on the tensile side was hypothesized to enhance mechanotransduction and trigger osteogenesis. Four potential stimuli were evaluated: dissipation energy density arising from (i) pore pressure, (ii) fluid velocity, (iii) their non-interactive sum, and (iv) their interaction. Comparison with in vivo data showed that only the interactive dissipation energy density accurately predicted both the spatial pattern and rate of new bone formation under high, low, and rest-inserted loading regimes. These results establish that the interaction between fluid velocity and pore pressure, rather than their independent contributions, governs load-induced osteogenesis. The proposed framework advances the mechanistic understanding of bone adaptation and offers a predictive basis for optimizing mechanical and clinical interventions to promote bone formation and mitigate bone loss.

bioengineering↗

bioRxiv2023

Predicting Cortical Bone Resorption in Disuse Condition Caused by Transient Muscle Paralysis

Load removal from the load-bearing bone, such as in the case of extended space travel and prolonged bed rest, harms bone health and leads to severe bone loss. However, the constitutive idea relating the quantity of bone loss to the absence of physiological loading is poorly understood. This work attempts to develop a mathematical model that predicts cortical bone loss at three sections: distal, mid-section, and proximal along the length of a mouse tibia. Load-induced interstitial fluid flow-based dissipation energy density has been adopted as a stimulus to trigger mechanotransduction. The developed model takes the loss of stimulus due to the disuse of bone as an input and predicts the quantity of bone loss with spatial accuracy. We hypothesized that the bone loss site would be the site of maximum stimulus loss due to disuse. To test the hypothesis, we calculated stimulus loss, i.e., loss of dissipation energy density due to bone disuse, based on the poroelastic analysis of the bone using a finite element method. A novel mathematical model has been then developed that successfully relates this loss of stimulus to the in-vivo bone loss data in the literature. According to the developed model, the site-specific mineral rate is found to be proportional to the square root of the loss of dissipation energy density. To the authors best knowledge, this model is the first of its kind to compute site-specific bone loss. The developed model can be extended to predict bone loss due to other disuse conditions such as long space travel, prolonged bed rest, etc.

bioengineering↗

bioRxiv2021

Ultrasound exposure enhances cellular uptake of nanoscale cargos

DNA nanotechnology utilizes DNA as a structural molecule to design palette of nanostructures with different shapes and sizes. DNA nanocages have demonstrated significant potential for drug delivery. Therefore, enhancing the delivery of DNA nanocages into cells can improve their efficacy as drug delivery agents. Numerous studies have reported the effects of ultrasound for enhancing drug delivery across biological barriers. The mechanical bioeffects caused by cell-ultrasound interaction can cause sonoporation, leading to enhanced uptake of drugs, nanoparticles, and chemotherapeutic agents through membranes. Whether ultrasound exposure can enhance the delivery of DNA nanocages has not been explored, which is the focus of this study. Specifically, we investigated the effects of ultrasound on the cellular uptake of propidium Iodide, fluorescent dextrans, and DNA nanostructures). We provide evidence of modulation of pore formation in the cell membrane by ultrasound by studying the intracellular uptake of the impermeable dye, propidium iodide. Treatment of cells with low amplitudes of ultrasound enhanced the uptake of different sizes of dextrans and DNA based nanodevices. These findings could serve as the foundation for further development ultrasound-enabled DNA nanostructure delivery and for specific understanding of underlying biological mechanisms of interaction between ultrasound parameters and cellular components; the knowledge that can be further explored for potential biological and biomedical applications.

bioengineering↗