Computational Oral Absorption Simulation for Low‐Solubility Compounds

Bile micelles play an important role in oral absorption of low‐solubility compounds. Bile micelles can affect solubility, dissolution rate, and permeability. For the pH–solubility profile in bile micelles, the Henderson–Hasselbalch equation should be modified to take bile‐micelle partition into account. For the dissolution rate, in the Nernst–Brunner equation, the effective diffusion coefficient in bile‐micelle media should be used instead of the monomer diffusion coefficient. The diffusion coefficient of bile micelles is 8‐ to 18‐fold smaller than that of monomer molecules. For permeability, the effective diffusion coefficient in the unstirred water layer adjacent to the epithelial membrane, and the free fraction at the epithelial membrane surface should be taken into account. The importance of these aspects is demonstrated here using several in vivo and clinical oral‐absorption data of low‐solubility model compounds. Using the theoretical equations, the food effect on oral absorption is further discussed.     

Sexual dimorphism in the visual system of flies: The divided brain of male Bibionidae (Diptera)

Summary The mapping of the compound eyes onto the visual neuropils and the cell types in the lamina and the lobula complex of Bibionidae (Diptera) were studied by means of extracellular cobalt injections and Golgi impregnations. Dorsal and ventral eyes in males map into separate dorsal-and ventral neuropils up to the level of the lobula complex. The dorsal-eye lamina is unilayered, while the ventral-eye lamina in males and the lamina in females are multilayered: layers A and C are invaded by en-passant terminals of long visual fibres, layer B by the terminals of short visual fibres. Long visual fibres have a short and a long terminal in the ventral medulla with terminal specialisations in three distinct layers. Only one type of receptor ending exists in the dorsal medulla, the terminal branches of which are restricted to one layer only. Arrays of contralateral neurones are found in the medial part of the dorsal lobula, which receives input from the zone of binocular vision of the ipsilateral dorsal eye, and in the posterior dorsal lobula and lobula plate. The dorsal lobula plate contains large tangential neurones, the dendritic arborisations of which are revealed by cobalt injection into the thoracic ganglia. The divided brain of male bibionids offers the opportunity to investigate separately the nervous systems involved in sex-specific visually guided flight behaviour and in general visually guided flight control.     

Computational Fluid Dynamics Analysis of Upper Airway Changes after Protraction Headgear and Rapid Maxillary Expansion Treatment

Clinically, it is common for Class III patients with maxillary skeletal deficiency, which may result in a variety of adverse consequences. Protraction headgear and rapid maxillary expansion (PE) is an effective treatment, but its effect on upper airway hydrodynamics has not been reported. The main purpose of this study was to evaluate the changes of the flow in the upper airway after PE by computational fluid dynamics (CFD). The sample includes fifteen patients (6 males, 9 females, age 11.00 ± 1.00) and the paired T-test was used to analyze the differences between the measured data before and after treatment. The maximum flow velocity decreased from 8.42 ± 0.16 m/s to 6.98 ± 0.36 m/s (p < 0.05), and the maximum shear force decreased from 3.72 ± 1.48 Pa to 2.13 ± 0.18 Pa. The maximum negative pressure decreased from −101.78 ± 33.60 Pa to 58.15 ± 9.16 Pa, only the changes of velopharynx and glossopharynx were statistically significant; while the maximum resistance decreased from 140.88 ± 68.68 Pa/mL/s to 45.95 ± 22.96 Pa/mL/s. PE can effectively reduce the airflow resistance of the upper airway and the probability of airway collapse, thus improving the patient’s ventilation function.     

Development and regeneration of the retinotectal map in goldfish: a computational study

We present a simple computational model to study the interplay of activity-dependent and intrinsic processes thought to be involved in the formation of topographic neural projections. Our model consists of two input layers which project to one target layer. The connections between layers are described by a set of synaptic weights. These weights develop according to three interacting developmental rules: (i) an intrinsic fibre-target interaction which generates chemospecific adhesion between afferent fibres and target cells; (ii) an intrinsic fibre-fibre interaction which generates mutual selective adhesion between the afferent fibres; and (iii) an activity-dependent fibre-fibre interaction which implements Hebbian learning. Additionally, constraints are imposed to keep synaptic weights finite. The model is applied to a set of eleven experiments on the regeneration of the retinotectal projection in goldfish. We find that the model is able to reproduce the outcome of an unprecedented range of experiments with the same set of model parameters, including details of the size of receptive and projective fields. We expect this mathematical framework to be a useful tool for the analysis of developmental processes in general. <br>     

Proximate causes and consequences of intergenerational influences of salient sensory experience

Salient sensory environments experienced by a parental generation can exert intergenerational influences on offspring. While these data provide an exciting new perspective on biological inheritance, questions remain about causes and consequences of intergenerational influences of salient sensory experience. We previously showed that exposing male mice to a salient olfactory experience, like olfactory fear conditioning, resulted in offspring demonstrating a sensitivity to the odor used to condition the paternal generation and possessing enhanced neuroanatomical representation for that odor. In this study, we first injected RNA extracted from sperm of male mice that underwent olfactory fear conditioning into naïve single‐cell zygotes and found that adults that developed from these embryos had increased sensitivity and enhanced neuroanatomical representation for the odor (Odor A) with which the paternal male had been conditioned. Next, we found that female, but not male offspring sired by males conditioned with Odor A show enhanced consolidation of a weak single‐trial Odor A + shock fear conditioning protocol. Our data provide evidence that RNA found in the paternal germline after exposure to salient sensory experiences can contribute to intergenerational influences of such experiences, and that such intergenerational influences confer an element of adaptation to the offspring. In so doing, our study of intergenerational influences of parental sensory experience adds to existing literature on intergenerational influences of parental exposures to stress and dietary manipulations and suggests that some causes (sperm RNA) and consequences (behavioral flexibility) of intergenerational influences of parental experiences may be conserved across a variety of parental experiences.     

Circadian clock effects on cellular proliferation: Insights from theory and experiments

Oscillations of the cellular circadian clock have emerged as an important regulator of many physiological processes, both in health and in disease. One such process, cellular proliferation, is being increasingly recognized to be affected by the circadian clock. Here, we review how a combination of experimental and theoretical work has furthered our understanding of the way circadian clocks couple to the cell cycle and play a role in tissue homeostasis and cancer. Finally, we discuss recently introduced methods for modeling coupling of clocks based on techniques from survival analysis and machine learning and highlight their potential importance for future studies.     

Rational design,synthesis and biological profiling of new KDM4C inhibitors

The human histone demethylases of the KDM4 family have been related to diseases such as prostate and breast cancer. Majority of currently known inhibitors suffer from the low permeability and low selectivity between the enzyme isoforms. In this study, toxoflavin motif was used to design and synthesize new KDM4C inhibitors with improved biological activity and in vitro ADME properties. Inhibitors displayed good passive cellular permeability and metabolic stability. However, diminishing of redox liability and consequently non-specific influence on cell viability still remains a challenge.     

Pressure Drops in a Distensible Model of End-to-side Anastomosis in Systemic-to-pulmonary Shunts

The modified Blalock-Taussig shunt is a surgical procedure used as a palliation to treat complex congenital heart defects. It consists of an interposing prosthetic tube between the innominate/subclavian artery and the right pulmonary artery. Previous experience indicates that the pressure drop across the shunt is affected by the pulmonary pressure at the distal anastomosis combined with the distensibility of the anastomosis. In this study, a computational fluid-structure interaction approach is presented to investigate the haemodynamic behaviour. Steady-state fluid dynamics and structural analyses were carried out using commercial codes based on the finite element method (FIDAP and ABAQUS) coupled by means of a purposely-developed procedure to transfer boundary conditions. Both prosthetic tube and artery walls were characterised by non-linear material properties. Three different pulmonary pressures (2, 5 and 15 mmHg) and two volume flow rates (0.4 and 0.8 l/min) were investigated. Results indicate that the effects of distensibility at the distal anastomosis on the shunt pressure drop are relevant only when the distal anastomosis on the shunt pressure drop are relevant only when the distal anastomosis is not fully distended, which occurs when the pulmonary pressure is lower than 5 mmHg.     

Near Infrared Optical Projection Tomography for Assessments of β-cell Mass Distribution in Diabetes Research

By adapting OPT to include the capability of imaging in the near infrared (NIR) spectrum, we here illustrate the possibility to image larger bodies of pancreatic tissue, such as the rat pancreas, and to increase the number of channels (cell types) that may be studied in a single specimen. We further describe the implementation of a number of computational tools that provide: 1/ accurate positioning of a specimen''s (in our case the pancreas) centre of mass (COM) at the axis of rotation (AR)²; 2/ improved algorithms for post-alignment tuning which prevents geometric distortions during the tomographic reconstruction² and 3/ a protocol for intensity equalization to increase signal to noise ratios in OPT-based BCM determinations³. In addition, we describe a sample holder that minimizes the risk for unintentional movements of the specimen during image acquisition. Together, these protocols enable assessments of BCM distribution and other features, to be performed throughout the volume of intact pancreata or other organs (e.g. in studies of islet transplantation), with a resolution down to the level of individual islets of Langerhans.     

Applying a multiobjective metaheuristic inspired by honey bees to phylogenetic inference

The development of increasingly popular multiobjective metaheuristics has allowed bioinformaticians to deal with optimization problems in computational biology where multiple objective functions must be taken into account. One of the most relevant research topics that can benefit from these techniques is phylogenetic inference. Throughout the years, different researchers have proposed their own view about the reconstruction of ancestral evolutionary relationships among species. As a result, biologists often report different phylogenetic trees from a same dataset when considering distinct optimality principles. In this work, we detail a multiobjective swarm intelligence approach based on the novel Artificial Bee Colony algorithm for inferring phylogenies. The aim of this paper is to propose a complementary view of phylogenetics according to the maximum parsimony and maximum likelihood criteria, in order to generate a set of phylogenetic trees that represent a compromise between these principles. Experimental results on a variety of nucleotide data sets and statistical studies highlight the relevance of the proposal with regard to other multiobjective algorithms and state-of-the-art biological methods.