Prediction of Neural Diameter From Morphology to Enable Accurate Simulation.

Accurate neuron morphologies are paramount for computational model simulations of realistic neural responses. Over the last decade, the online repository NeuroMorpho.Org has collected over 140,000 available neuron morphologies to understand brain function and promote interaction between experimental and computational research. Neuron morphologies describe spatial aspects of neural structure; however, many of the available morphologies do not contain accurate diameters that are essential for computational simulations of electrical activity. To best utilize available neuron morphologies, we present a set of equations that predict dendritic diameter from other morphological features. To derive the equations, we used a set of NeuroMorpho.org archives with realistic neuron diameters, representing hippocampal pyramidal, cerebellar Purkinje, and striatal spiny projection neurons. Each morphology is separated into initial, branching children, and continuing nodes. Our analysis reveals that the diameter of preceding nodes, Parent Diameter, is correlated to diameter of subsequent nodes for all cell types. Branching children and initial nodes each required additional morphological features to predict diameter, such as path length to soma, total dendritic length, and longest path to terminal end. Model simulations reveal that membrane potential response with predicted diameters is similar to the original response for several tested morphologies. We provide our open source software to extend the utility of available NeuroMorpho.org morphologies, and suggest predictive equations may supplement morphologies that lack dendritic diameter and improve model simulations with realistic dendritic diameter.

Thermosensitive Liposome-Mediated Drug Delivery in Chemotherapy: Mathematical Modelling for Spatio-temporal Drug Distribution and Model-Based Optimisation.

Thermosensitive liposome-mediated drug delivery has shown promising results in terms of improved therapeutic efficacy and reduced side effects compared to conventional chemotherapeutics. In order to facilitate our understanding of the transport mechanisms and their complex interplays in the drug delivery process, computational models have been developed to simulate the multiple steps involved in liposomal drug delivery to solid tumours. In this study we employ a multicompartmental model for drug-loaded thermosensitive liposomes, with an aim to identify the key transport parameters in determining therapeutic dosing and outcomes. The computational model allows us to not only examine the temporal and spatial variations of drug concentrations in the different compartments by utilising the tumour cord concept, but also assess the therapeutic efficacy and toxicity. In addition, the influences of key factors on systemic plasma concentration and intracellular concentration of the active drug are investigated; these include different chemotherapy drugs, release rate constants and heating duration. Our results show complex relationships between these factors and the predicted therapeutic outcome, making it difficult to identify the "best" parameter set. To overcome this challenge, a model-based optimisation method is proposed in an attempt to find a set of release rate constants and heating duration that can maximise intracellular drug concentration while minimising systemic drug concentration. Optimisation results reveal that under the operating conditions and ranges examined, the best outcome would be achieved with a low drug release rate at physiological temperature, combined with a moderate to high release rate at mild hyperthermia and 1 h heating after injection.

In vitro rumen biohydrogenation kinetics of mixed linoleic and alfa-linolenic acids / Cinética de biohidrogenación ruminal in vitro de los ácidos linoleico y alfa-linolénico mezclados / Cinética de biohidrogenação ruminal in vitro dos ácidos linoleico e alfa-linolênico misturados

Abstract Background: Dietary linoleic (LA) and alpha-linolenic (LN) acids are extensively isomerized and hydrogenated by rumen microbes, and this activity can further contribute to the fatty acid profile of ruminant- derived food products. Objective: To evaluate the effects of LA:LN ratio in lipid supplements on the rumen biohydrogenation kinetics of LA and LN, as well as on the trans-vaccenic acid (VA) production, using an in vitro system. Methods: Rumen fluid was collected from a fistulated steer, diluted with incubation buffer, and then incubated with 500 mg of kikuyu grass (Cenchrus clandestinus) supplemented with 16.3 mg of different LA:LN mixtures (100:0, 75:25, 50:50, 25:75 or 0:100). Incubations were performed in triplicate for a period of 0, 2, 4, 6, 8 or 16 hours. Differences between treatments were evaluated in a completely randomized design. Alternatively, computational chemistry was used to determine the changes in the Gibbs free energy (ΔGrxn) at 39 °C for the principal steps of LA and LN ruminal biohydrogenation. Results: Partial replacement of LA by LN decreased the VA concentration and its accumulation rate; it also increased the stearic acid concentration and the rates of transfer from LA to conjugated linoleic acid (CLA), and from CLA to VA. The conversion from CLA to VA (ΔGrxn = -2.65 kJ/mol) was more spontaneous than that from trans-11, cis-15 octadecadienoic acid (TA) to VA (ΔGrxn = -0.29 kJ/mol). Conclusion: The LA:LN ratio in lipids can modulate LA and LN biohydrogenation (BH) kinetics, as well as the VA production in the rumen.

Resumen Antecedentes: los ácidos linoleico (LA) y alfa-linolénico (LN) de la dieta son extensivamente isomerizados y biohidrogenados por los microorganismos ruminales, lo cual puede contribuir al perfil de ácidos grasos de los productos derivados de rumiantes. Objetivo: evaluar el efecto de la relación LA:LN en suplementos lipídicos sobre la cinética de biohidrogenación ruminal del LA y LN, como también sobre la producción del ácido trans-vaccénico (VA), usando un sistema in vitro. Métodos: se colectó fluido ruminal de un toro fistulado, el cual fue diluido con buffer de incubación y posteriormente incubado con 500 mg de pasto kikuyo (Cenchrus clandestinus) suplementado con 16,3 mg de diferentes mezclas de LA:LN (100:0, 75:25, 50:50, 25:75, o 0:100). Las incubaciones fueron desarrolladas en triplicado durante 0, 2, 4, 6, 8 o 16 horas. Diferencias entre tratamientos fueron evaluadas mediante un modelo completamente al azar. Alternativamente, se determinaron los cambios en energía libre de Gibbs ( Δ Grxn) a 39 °C para los pasos principales de la biohidrogenación del LA y LN, usando química computacional. Resultados: la sustitución parcial de LA por LN disminuyó la concentración de VA y su tasa de acumulación, como también incrementó la concentración de ácido esteárico y las tasas de transferencia de LA para ácido linoleico conjugado (CLA) y de CLA para VA. La conversión de CLA para VA ( Δ Grxn = -2,65 kJ/mol) fue más espontánea que la conversión del ácido trans-11, cis-15 octadecadienóico (TA) para VA ( Δ Grxn = -0,29 kJ/mol). Conclusiones: la relación LA:LN en lípidos puede modular la cinética de biohidrogenación (BH) del LA y LN y la producción de VA en el rumen.

Resumo Antecedêntes: o ácido linoleico (LA) e alfa-linolênico (LN) da dieta, são extensivamente isomerizados e biohidrogenados pelos microorganismos do rúmen, o que pode contribuir ao perfil de ácidos graxos dos produtos derivados de ruminantes. Objetivo: avaliar o efeito da relação LA:LN em suplementos lipídicos sobre a cinética de biohidrogenação ruminal do LA e LN como também sobre a produção do ácido trans- vaccênico (VA), utilizando um sistema in vitro. Métodos: coletou-se fluido ruminal de um novilho fistulado, o qual foi diluído com tampão de incubação e, em seguida, incubado com 500 mg de pasto kikuyu (Cenchrus clandestinus) suplementado com 16,3 mg de diferentes misturas LA:LN (100:0, 75:25 , 50:50, 25:75 ou 0:100). As incubações foram desenvolvidas em triplicata, durante 0, 2, 4, 6, 8 ou 16 horas. Diferenças entre tratamentos foram avaliadas utilizando-se um delineamento inteiramente casualizado. Alternativamente, foram determinadas as mudanças em energia livre de Gibbs ( Δ Grxn) a 39 °C para as principais etapas da biohidrogenação do LA e LN, utilizando-se química computacional. Resultados: a substituição parcial de LA por LN diminuiu a concentração de VA e sua taxa de acumulação, como também aumentou a concentração de ácido esteárico e as taxas de transferência do LA para o ácido linoleico conjugado (CLA) e do CLA para VA. A conversão do CLA para VA ( Δ Grxn = -2,65 kJ/ mol) foi mais espontânea que a conversão do ácido trans-11, cis-15 octadecadienóico (TA) para VA ( Δ Grxn = -0,29 kJ/mol). Conclusões: a relação LA:LN em lipídeos pode modular a cinética de biohidrogenação (BH) do LA e LN e a produção de VA no rúmen.

A Multi-Compartment Hybrid Computational Model Predicts Key Roles for Dendritic Cells in Tuberculosis Infection.

Tuberculosis (TB) is a world-wide health problem with approximately 2 billion people infected with Mycobacterium tuberculosis (Mtb, the causative bacterium of TB). The pathologic hallmark of Mtb infection in humans and Non-Human Primates (NHPs) is the formation of spherical structures, primarily in lungs, called granulomas. Infection occurs after inhalation of bacteria into lungs, where resident antigen-presenting cells (APCs), take up bacteria and initiate the immune response to Mtb infection. APCs traffic from the site of infection (lung) to lung-draining lymph nodes (LNs) where they prime T cells to recognize Mtb. These T cells, circulating back through blood, migrate back to lungs to perform their immune effector functions. We have previously developed a hybrid agent-based model (ABM, labeled GranSim) describing in silico immune cell, bacterial (Mtb) and molecular behaviors during tuberculosis infection and recently linked that model to operate across three physiological compartments: lung (infection site where granulomas form), lung draining lymph node (LN, site of generation of adaptive immunity) and blood (a measurable compartment). Granuloma formation and function is captured by a spatio-temporal model (i.e., ABM), while LN and blood compartments represent temporal dynamics of the whole body in response to infection and are captured with ordinary differential equations (ODEs). In order to have a more mechanistic representation of APC trafficking from the lung to the lymph node, and to better capture antigen presentation in a draining LN, this current study incorporates the role of dendritic cells (DCs) in a computational fashion into GranSim. RESULTS: The model was calibrated using experimental data from the lungs and blood of NHPs. The addition of DCs allowed us to investigate in greater detail mechanisms of recruitment, trafficking and antigen presentation and their role in tuberculosis infection. CONCLUSION: The main conclusion of this study is that early events after Mtb infection are critical to establishing a timely and effective response. Manipulating CD8+ and CD4+ T cell proliferation rates, as well as DC migration early on during infection can determine the difference between bacterial clearance vs. uncontrolled bacterial growth and dissemination.