Vineet Rakesh

Development of equine upper airway fluid mechanics model for Thoroughbred racehorses

REASON FOR PERFORMING STUDY Computational fluid dynamics (CFD) models provide the means to evaluate airflow in the upper airways without requiring in vivo experiments. HYPOTHESIS The physiological conditions of a Thoroughbred racehorses upper airway during exercise could be simulated. METHODS Computed tomography scanned images of a 3-year-old intact male Thoroughbred racehorse cadaver were used to simulate in vivo geometry. Airway pressure traces from a live Thoroughbred horse, during exercise was used to set the boundary condition. Fluid-flow equations were solved for turbulent flow in the airway during inspiratory and expiratory phases. The wall pressure turbulent kinetic energy and velocity distributions were studied at different cross-sections along the airway. This provided insight into the general flow pattern and helped identify regions susceptible to dynamic collapse. RESULTS The airflow velocity and static tracheal pressure were comparable to data of horses exercising on a high-speed treadmill reported in recent literature. The cross-sectional area of the fully dilated rima glottidis was 7% greater than the trachea. During inspiration, the area of highest turbulence (i.e. kinetic energy) was in the larynx, the rostral aspect of the nasopharynx was subjected to the most negative wall pressure and the highest airflow velocity is more caudal on the ventral aspect of the nasopharynx (i.e. the soft palate). During exhalation, the area of highest turbulence was in the rostral and mid-nasopharynx, the maximum positive pressure was observed at the caudal aspect of the soft palate and the highest airflow velocity at the front of the nasopharynx. CONCLUSIONS AND CLINICAL RELEVANCE In the equine upper airway collapsible area, the floor of the rostral aspect of the nasopharynx is subjected to the most significant collapsing pressure with high average turbulent kinetic during inhalation, which may lead to palatal instability and explain the high prevalence of dorsal displacement of the soft palate (DDSP) in racehorses. Maximal abduction of the arytenoid cartilage may not be needed for optimal performance, since the trachea cross-sectional area is 7% smaller than the rima glottidis.

Finite-element model of interaction between fungal polysaccharide and monoclonal antibody in the capsule of Cryptococcus neoformans

Many microorganisms such as bacteria and fungi possess so-called capsules made of polysaccharides which protect these microorganisms from environmental insults and host immune defenses. The polysaccharide capsule of Cryptococcus neoformans, a human pathogenic yeast, is capable of self-assembly, composed mostly of glucuronoxylomannan (GXM), a polysaccharide with a molecular weight of approximately 2,000,000, and has several layers with different densities. The objective of this study was to model pore-hindered diffusion and binding of the GXM-specific antibody within the C. neoformans capsule. Using the finite-element method (FEM), we created a model which represents the in vivo binding of a GXM-specific antibody to a C. neoformans cell taking into account the intravenous infusion time of antibody, antibody diffusion through capsular pores, and Michaelis-Menten kinetics of antibody binding to capsular GXM. The model predicted rapid diffusion of antibody to all regions of the capsule where the pore size was greater than the Stokes diameter of the antibody. Binding occurred primarily at intermediate regions of the capsule. The GXM concentration in each capsular region was the principal determinant of the steady-state antibody-GXM complex concentration, while the forward binding rate constant influenced the rate of complex formation in each region. The concentration profiles predicted by the model closely matched experimental immunofluorescence data. Inclusion of different antibody isotypes (IgG, IgA, and IgM) into the modeling algorithm resulted in similar complex formation in the outer capsular regions, but different depths of binding at the inner regions. These results have implications for the development of new antibody-based therapies.

Simulation of Turbulent Airflow Using a CT Based Upper Airway Model of a Racehorse

Computational model for airflow through the upper airway of a horse was developed. Previous flow models for human airway do not hold true for horses due to significant differences in anatomy and the high Reynolds number of flow in the equine airway. Moreover, models that simulate the entire respiratory cycle and emphasize on pressures inside the airway in relation to various anatomical diseases are lacking. The geometry of the airway was created by reconstructing images obtained from computed tomography scans of a thoroughbred racehorse. Different geometries for inhalation and exhalation were used for the model based on the difference in the nasopharynx size during the two phases of respiration. The Reynolds averaged Navier-Stokes equations were solved for the isothermal flow with the standard k-epsilon model for turbulence. Transient pressure boundary conditions for the entire breathing cycle were obtained from past experimental studies on live horses. The flow equations were solved in a commercial finite volume solver. The flow rates, computed based on the applied pressure conditions, were compared to experimentally measured flow rates for model validation. Detailed analysis of velocity, pressure, and turbulence characteristics of the flow was done. Velocity magnitudes at various slices during inhalation were found to be higher than corresponding velocity magnitudes during exhalation. The front and middle parts of the nasopharynx were found to have minimum intraluminal pressure in the airway during inhalation. During exhalation, the pressures in the soft palate were higher compared to those in the larynx, epiglottis, and nasopharynx. Turbulent kinetic energy was found to be maximum at the entry to the airway and gradually decreased as the flow moved inside the airway. However, turbulent kinetic energy increased in regions of the airway with abrupt change in area. Based on the analysis of pressure distribution at different sections of the airway, it was concluded that the front part of the nasopharynx requires maximum muscular activity to support it during inhalation. During exhalation, the soft palate is susceptible to displacements due to presence of high pressures. These can serve as critical information for diagnosis and treatment planning of diseases known to affect the soft palate and nasopharynx in horses, and can potentially be useful for human beings.

Patterns of Gene Expression Associated with Recovery and Injury in Heat-stressed Rats

BackgroundThe in vivo gene response associated with hyperthermia is poorly understood. Here, we perform a global, multiorgan characterization of the gene response to heat stress using an in vivo conscious rat model.ResultsWe heated rats until implanted thermal probes indicated a maximal core temperature of 41.8°C (Tc,Max). We then compared transcriptomic profiles of liver, lung, kidney, and heart tissues harvested from groups of experimental animals at Tc,Max, 24 hours, and 48 hours after heat stress to time-matched controls kept at an ambient temperature. Cardiac histopathology at 48 hours supported persistent cardiac injury in three out of six animals. Microarray analysis identified 78 differentially expressed genes common to all four organs at Tc,Max. Self-organizing maps identified gene-specific signatures corresponding to protein-folding disorders in heat-stressed rats with histopathological evidence of cardiac injury at 48 hours. Quantitative proteomics analysis by iTRAQ (isobaric tag for relative and absolute quantitation) demonstrated that differential protein expression most closely matched the transcriptomic profile in heat-injured animals at 48 hours. Calculation of protein supersaturation scores supported an increased propensity of proteins to aggregate for proteins that were found to be changing in abundance at 24 hours and in animals with cardiac injury at 48 hours, suggesting a mechanistic association between protein misfolding and the heat-stress response.ConclusionsPathway analyses at both the transcript and protein levels supported catastrophic deficits in energetics and cellular metabolism and activation of the unfolded protein response in heat-stressed rats with histopathological evidence of persistent heat injury, providing the basis for a systems-level physiological model of heat illness and recovery.

Computational model predicts effective delivery of 188-Re-labeled melanin-binding antibody to metastatic melanoma tumors with wide range of melanin concentrations.

Metastatic melanoma is almost always deadly and new methods of treatment are urgently needed. Recently, we established the feasibility of radioimmunotherapy (RIT) for experimental melanoma in mice using a 188-rhenium (188Re)-labeled monoclonal antibody (mAb) 6D2 (IgM) to melanin. Our objective was to determine the effects of varying tumor melanin concentration and of different diffusivities and lymphatic clearance rates of the normal tissue, on the absorbed dose to the tumor in simulated therapy, in preparation for a clinical trial of RIT for melanoma. Using finite element analysis (FEA), we created a pharmacokinetic model that describes melanin-targeting RIT of a melanoma micrometastasis (1.3-mm radius) imbedded in normal tissue (14.3-mm radius). Our method incorporates antibody plasma kinetics, transcapillary transport, interstitial diffusion, and lymphatic clearance. Michaelis–Menten kinetics was used to model mAb binding to tumor melanin for melanin concentrations of 76, 7.6, 0.76, 0.076, and 0.0076 μmol/l. An absorbed dose was calculated, after accounting for direct and crossfire irradiation, on the basis of a 7.4-GBq intravenous dose of 188Re-6D2. The results showed that penetration of mAb into the tumor was inversely proportional to tumor melanin concentration. Decreased diffusivity and increased lymphatic clearance of the surrounding normal tissue decreased the dose to the tumor. The formation of mAb–melanin complex was remarkably similar within a 1000-fold range of melanin concentration, resulting in total doses of 2840, 2820, 2710, and 1990 cGy being delivered to tumors with melanin concentrations of 76, 7.6, 0.76, and 0.076 μmol/l, respectively. In conclusion, RIT of metastatic melanoma can be effective over a wide range of tumor melanin concentrations. The results can be useful in the design of a clinical trial of melanin-targeting RIT in patients with metastatic melanoma.

Computational Study of Thrombus Formation and Clotting Factor Effects under Venous Flow Conditions.

A comprehensive understanding of thrombus formation as a physicochemical process that has evolved to protect the integrity of the human vasculature is critical to our ability to predict and control pathological states caused by a malfunctioning blood coagulation system. Despite numerous investigations, the spatial and temporal details of thrombus growth as a multicomponent process are not fully understood. Here, we used computational modeling to investigate the temporal changes in the spatial distributions of the key enzymatic (i.e., thrombin) and structural (i.e., platelets and fibrin) components within a growing thrombus. Moreover, we investigated the interplay between clot structure and its mechanical properties, such as hydraulic resistance to flow. Our model relied on the coupling of computational fluid dynamics and biochemical kinetics, and was validated using flow-chamber data from a previous experimental study. The model allowed us to identify the distinct patterns characterizing the spatial distributions of thrombin, platelets, and fibrin accumulating within a thrombus. Our modeling results suggested that under the simulated conditions, thrombin kinetics was determined predominantly by prothrombinase. Furthermore, our simulations showed that thrombus resistance imparted by fibrin was ∼30-fold higher than that imparted by platelets. Yet, thrombus-mediated bloodflow occlusion was driven primarily by the platelet deposition process, because the height of the platelet accumulation domain was approximately twice that of the fibrin accumulation domain. Fibrinogen supplementation in normal blood resulted in a nonlinear increase in thrombus resistance, and for a supplemented fibrinogen level of 48%, the thrombus resistance increased by ∼2.7-fold. Finally, our model predicted that restoring the normal levels of clotting factors II, IX, and X while simultaneously restoring fibrinogen (to 88% of its normal level) in diluted blood can restore fibrin generation to ∼78% of its normal level and hence improve clot formation under dilution.

Mathematical Modeling of the Heat-Shock Response in HeLa Cells

The heat-shock response is a key factor in diverse stress scenarios, ranging from hyperthermia to protein folding diseases. However, the complex dynamics of this physiological response have eluded mathematical modeling efforts. Although several computational models have attempted to characterize the heat-shock response, they were unable to model its dynamics across diverse experimental datasets. To address this limitation, we mined the literature to obtain a compendium of in vitro hyperthermia experiments investigating the heat-shock response in HeLa cells. We identified mechanisms previously discussed in the experimental literature, such as temperature-dependent transcription, translation, and heat-shock factor (HSF) oligomerization, as well as the role of heat-shock protein mRNA, and constructed an expanded mathematical model to explain the temperature-varying DNA-binding dynamics, the presence of free HSF during homeostasis and the initial phase of the heat-shock response, and heat-shock protein dynamics in the long-term heat-shock response. In addition, our model was able to consistently predict the extent of damage produced by different combinations of exposure temperatures and durations, which were validated against known cellular-response patterns. Our model was also in agreement with experiments showing that the number of HSF molecules in a HeLa cell is roughly 100 times greater than the number of stress-activated heat-shock element sites, further confirming the model’s ability to reproduce experimental results not used in model calibration. Finally, a sensitivity analysis revealed that altering the homeostatic concentration of HSF can lead to large changes in the stress response without significantly impacting the homeostatic levels of other model components, making it an attractive target for intervention. Overall, this model represents a step forward in the quantitative understanding of the dynamics of the heat-shock response.

Simulation as an integrator in an undergraduate biological engineering curriculum

A novel multifaceted elective course in Biological Engineering is described, along with the experience in its instruction and development over 14 years. The course introduces modeling and simulation to solve biological/biomedical problems to students with a background in transport processes but with no prior experience in modeling. The critical elements needed to introduce such modeling to less experienced students are discussed, such as simplifying a problem for problem formulation, case studies that build a clear bridge to their preparation in fundamentals, and extracting important details from a simulation. The question of a black box versus a white box approach to presenting simulations is addressed. Active learning practices such as think‐pair‐share and distributed learning are introduced as enablers for this course. Student motivation has been increased by making the course student‐centered with the students themselves selecting and executing the modeling projects. The authors describe how the same course can serve many purposes in a curriculum, including the introduction of a state‐of‐the‐art design tool, extending fundamental knowledge to solve realistic problems, enhancing the fundamentals, introducing teamwork, written and oral communication, and design concepts. Although we have discussed the course in the context of biological/biomedical engineering, it can also be extended to other engineering curricula such as Mechanical and Chemical Engineering.

Untangling the Effect of Head Acceleration on Brain Responses to Blast Waves

Multiple injury-causing mechanisms, such as wave propagation, skull flexure, cavitation, and head acceleration, have been proposed to explain blast-induced traumatic brain injury (bTBI). An accurate, quantitative description of the individual contribution of each of these mechanisms may be necessary to develop preventive strategies against bTBI. However, to date, despite numerous experimental and computational studies of bTBI, this question remains elusive. In this study, using a two-dimensional (2D) rat head model, we quantified the contribution of head acceleration to the biomechanical response of brain tissues when exposed to blast waves in a shock tube. We compared brain pressure at the coup, middle, and contre-coup regions between a 2D rat head model capable of simulating all mechanisms (i.e., the all-effects model) and an acceleration-only model. From our simulations, we determined that head acceleration contributed 36-45% of the maximum brain pressure at the coup region, had a negligible effect on the pressure at the middle region, and was responsible for the low pressure at the contre-coup region. Our findings also demonstrate that the current practice of measuring rat brain pressures close to the center of the brain would record only two-thirds of the maximum pressure observed at the coup region. Therefore, to accurately capture the effects of acceleration in experiments, we recommend placing a pressure sensor near the coup region, especially when investigating the acceleration mechanism using different experimental setups.

Experimental and analytical temperature distributions during oven-based convection heating.

Mathematical models, combined with experimental evaluation, provide an approach to understand, design, and optimize food process operations. Magnetic resonance imaging (MRI), as an experimental technique, is used extensively in both medical and engineering applications to measure and quantify transport processes. Magnetic resonance (MR) was used in this study to assess a mathematical model based on Fouriers second law. The objective was to compare analytical solutions for the prediction of internal temperature distributions in foods during oven-based convective heating to experimental temperature measurements and determine at what point during the heating process a coupled heat and mass transport process should be considered. Cylindrical samples of a model food gel, Russet potato and rehydrated mashed potato were heated in a convection oven for specified times. Experimentally measured internal temperatures were compared to the internal temperatures predicted by the analytical model. Temperatures distributions in the axial direction compared favorably for the gel and acceptably for the Russet and mashed potato samples. The MR-acquired temperatures in the radial direction for the gel resulted in a shallower gradient than predicted but followed the expected trend. For the potato samples, the MR-acquired temperatures in the radial direction were not qualitatively similar to the analytical predictions due to moisture loss during heating. If temperature resolution is required in the radial direction, moisture losses merit the use of transport models that couple heat and mass transfer.