Algorithms for optimization of the transport system in living and artificial cells

An optimization of the transport system in a cell has been considered from the viewpoint of the operations research. Algorithms for an optimization of the transport system of a cell in terms of both the efficiency and a weak sensitivity of a cell to environmental changes have been proposed. The switching of various systems of transport is considered as the mechanism of weak sensitivity of a cell to changes in environment. The use of the algorithms for an optimization of a cardiac cell has been considered by way of example. We received theoretically for a cell of a cardiac muscle that at the increase of potassium concentration in the environment switching of transport systems for this ion takes place. This conclusion qualitatively coincides with experiments. The problem of synthesizing an optimal system in an artificial cell has been stated.     

Use of inert gas jets to measure the forces required for mechanical gene transfection

Background

Abnormal blood glucose (BG) concentrations have been associated with increased morbidity and mortality in both critically ill adults and infants. Furthermore, hypoglycaemia and glycaemic variability have both been independently linked to mortality in these patients. Continuous Glucose Monitoring (CGM) devices have the potential to improve detection and diagnosis of these glycaemic abnormalities. However, sensor noise is a trade-off of the high measurement rate and must be managed effectively if CGMs are going to be used to monitor, diagnose and potentially help treat glycaemic abnormalities.

Aim

To develop a tool that will aid clinicians in identifying unusual CGM behaviour and highlight CGM data that potentially need to be interpreted with care.

Methods

CGM data and BG measurements from 50 infants at risk of hypoglycaemia were used. Unusual CGM measurements were classified using a stochastic model based on the kernel density method and historical CGM measurements from the cohort. CGM traces were colour coded with very unusual measurements coloured red, highlighting areas to be interpreted with care. A 5-fold validation of the model was Monte Carlo simulated 25 times to ensure an adequate model fit.

Results

The stochastic model was generated using ~67,000 CGM measurements, spread across the glycaemic range ~2-10?mmol/L. A 5-fold validation showed a good model fit: the model 80% confidence interval (CI) captured 83% of clinical CGM data, the model 90% CI captured 91% of clinical CGM data, and the model 99% CI captured 99% of clinical CGM data. Three patient examples show the stochastic classification method in use with 1) A stable, low variability patient which shows no unusual CGM measurements, 2) A patient with a very sudden, short hypoglycaemic event (classified as unusual), and, 3) A patient with very high, potentially un-physiological, glycaemic variability after day 3 of monitoring (classified as very unusual).

Conclusions

This study has produced a stochastic model and classification method capable of highlighting unusual CGM behaviour. This method has the potential to classify important glycaemic events (e.g. hypoglycaemia) as true clinical events or sensor noise, and to help identify possible sensor degradation. Colour coded CGM traces convey the information quickly and efficiently, while remaining computationally light enough to be used retrospectively or in real-time.     

Model of active transport of ions in cardiac cell

A model of the active transport of ions in a cardiac muscle cell, which takes into account the active transport of Na⁺, K⁺, Ca²⁺, Mg²⁺, HCO₃⁻ and Cl⁻ ions, has been constructed. The model allows independent calculations of the resting potential at the biomembrane and concentrations of basic ions (sodium, potassium, chlorine, magnesium and calcium) in a cell. For the analysis of transport processes in cardiac cell hierarchical algorithm “one ion-one transport system” was offered. The dependence of the resting potential on concentrations of the ions outside a cell has been established. It was shown, that ions of calcium and magnesium, despite their rather small concentration, play an essential role in maintenance of resting potential in cardiac cell. The calculated internal concentrations of ions are in good agreement with the corresponding experimental values.     

Model of active transport of ions in biomembranes based on ATP-dependent change of height of diffusion barriers to ions

A closed model of the active transport was constructed taking into account ATP-dependent opening and closing of barriers to ions and the relationship between the membrane potential and the work of ionic pumps under the condition of electroneutrality inside the cell. The internal consistency of the model was verified by the fulfillment of Onsager's reciprocity relation. It was demonstrated that at the limit of large energy barriers the operation of the system of the active transport is equivalent to the "turning segment" model, which was proposed by the authors earlier. Values of the resting potential and the intracellular concentration of ions were obtained for different types of cells. These results were in qualitative agreement with relevant experimental data.     

A model of active transport of ions in hepatocytes

A mathematical model of the transport of basic ions (K⁺, Na⁺, Cl⁻) across the hepatocyte membrane has been created using the previously constructed models of active ion transport in biomembranes. The dependence of the resting potential on extracellular ion concentration has been established. Using the model, it is possible to independently calculate the resting potential at the biomembrane and the concentrations of sodium, potassium, and chlorine ions in the cell. The calculated internal concentrations of the ions are in good agreement with the corresponding experimental values.     

Cortical potential imaging using L-curve and GCV method to choose the regularisation parameter

Background

The electroencephalography (EEG) is an attractive and a simple technique to measure the brain activity. It is attractive due its excellent temporal resolution and simple due to its non-invasiveness and sensor design. However, the spatial resolution of EEG is reduced due to the low conducting skull. In this paper, we compute the potential distribution over the closed surface covering the brain (cortex) from the EEG scalp potential. We compare two methods – L-curve and generalised cross validation (GCV) used to obtain the regularisation parameter and also investigate the feasibility in applying such techniques to N170 component of the visually evoked potential (VEP) data.

Methods

Using the image data set of the visible human man (VHM), a finite difference method (FDM) model of the head was constructed. The EEG dataset (256-channel) used was the N170 component of the VEP. A forward transfer matrix relating the cortical potential to the scalp potential was obtained. Using Tikhonov regularisation, the potential distribution over the cortex was obtained.

Results

The cortical potential distribution for three subjects was solved using both L-curve and GCV method. A total of 18 cortical potential distributions were obtained (3 subjects with three stimuli each – fearful face, neutral face, control objects).

Conclusions

The GCV method is a more robust method compared to L-curve to find the optimal regularisation parameter. Cortical potential imaging is a reliable method to obtain the potential distribution over cortex for VEP data.

     

Origin of the Directed Movement of Protocells in the Early Stages of the Evolution of Life

The origin of the directed motion of protocells during the early stages of evolution was discussed. The expenditures for movement, space orientation, and reception of information about the environment were taken into consideration, and it was shown that directed movement is evolutionarily advantageous in the following cases: when opposite gradients of different resources (for example, matter and energy) are great enough and when there is a rapid change in environmental parameters. It was also shown that the advantage of directed movement strategies depends greatly on how information about the environment is obtained by a protocell.     

Can an organism select new valuable information from environment

The process of selecting new information by the organism ("learning") was studied. To take a decision, key patterns have to be set a priori, and so knowledge accumulation (learning) based on pattern recognition is impossible. It was shown that the only physical process that, takes place during the emergence of an external signal is the triggering of a priori programmes. An equivalent biophysical scheme of pattern recognition and taking the decisions by the organism was developed in which a signal received by the receptor leads to the synthesis of one of possible catalysts. The catalyst starts up the corresponding thermodynamic process. The information contained in the organism does not change during this process.