The problem of using correlation methods in brain function]

In a series of publications, the author used the correlation hypothesis to explain the main mechanisms of functioning of bat and dolphin echo locators. A good fit of calculated parameters to experimental data was shown. In this work, by the example of generalization of the recognition problem, the use by the brain of correlation methods for solving more general problems independently on the modality of sensor signals was analyzed. In favor of the hypothesis that correlation methods are widely used in brain functioning are the data presented in the paper, which prove that an associative neuron is a suitable analog computer. It is suited for rapid "computation" of the intercorrelation function of discrete input and reference signals. The set of weighting coefficients of neuron synaptic inputs serve as such signals. The pool of associative neurons determines the values on the correlation function in the required range by changing the "numbers" of inputs from neuron to neuron at which discrete signals arrive.     

The mind body problem and the second law of thermodynamics

Cartesian mind body dualism and modern versions of this viewpoint posit a mind thermodynamically unrelated to the body but informationally interactive. The relation between information and entropy developed by Leon Brillouin demonstrates that any information about the state of a system has entropic consequences. It is therefore impossible to dissociate the mind's information from the body's entropy. Knowledge of that state of the system without an energetically significant measurement would lead to a violation of the second law of thermodynamics.     

A free energy principle for the brain.

By formulating Helmholtz's ideas about perception, in terms of modern-day theories, one arrives at a model of perceptual inference and learning that can explain a remarkable range of neurobiological facts: using constructs from statistical physics, the problems of inferring the causes of sensory input and learning the causal structure of their generation can be resolved using exactly the same principles. Furthermore, inference and learning can proceed in a biologically plausible fashion. The ensuing scheme rests on Empirical Bayes and hierarchical models of how sensory input is caused. The use of hierarchical models enables the brain to construct prior expectations in a dynamic and context-sensitive fashion. This scheme provides a principled way to understand many aspects of cortical organisation and responses. In this paper, we show these perceptual processes are just one aspect of emergent behaviours of systems that conform to a free energy principle. The free energy considered here measures the difference between the probability distribution of environmental quantities that act on the system and an arbitrary distribution encoded by its configuration. The system can minimise free energy by changing its configuration to affect the way it samples the environment or change the distribution it encodes. These changes correspond to action and perception respectively and lead to an adaptive exchange with the environment that is characteristic of biological systems. This treatment assumes that the system's state and structure encode an implicit and probabilistic model of the environment. We will look at the models entailed by the brain and how minimisation of its free energy can explain its dynamics and structure.     

Kinetic model describing the action of tryptophanyl-tRNA-synthetase]

Reaction rates for ATP-PPi isotope exchange (vex) and tryptophanyl-tRNA formation (vaa) catalysed concomitantly in one incubation mixture by beef pancreas tryptophanyl-tRNA synthetase (trsase) have been examined as a function of substrate concentrations. Comparison of the vex/vaa ratio found experimentally with the ratio predicted theoretically conforms the mechanism suggested earlier and permits to describe it in more detail. I. At least two reaction routes exist in which an ATP-PP: exchange is allowed. These routes are interconnected with each other via the stage at which tRNA binds to the enzyme. 2. In both these routes the low molecular weight substrates bind with enzyme in the order ATP first, tryptophan second. 3. Enzyme-aminoacyladenylate complex is an intermediate in the reaction of aminoacyl-tRNA formation. Pyrophosphate is detached from the enzyme prior to tRNA. 4. The enzyme releases AMP and tryptophanyl-tRNA in a random fashion. All the aformentioned properties are common both for trigger mechanism and Yarus-Berg mechanism which up to now were considered in literature independently.     

Application of the describing function to the Danziger-Elmegreen equations

The describing function method is used as a guide to the behaviour of the solutions of the equations of Danziger and Elmergreen, proposed as a model of periodic catatonia. The method suggests that whenever the equilibrium point is unstable it is surrounded by a stable closed periodic orbit. This is confirmed in specific cases by computation.     

A miniaturized technique for assessing protein thermodynamics and function using fast determination of quantitative cysteine reactivity

Protein thermodynamic stability is a fundamental physical characteristic that determines biological function. Furthermore, alteration of thermodynamic stability by macromolecular interactions or biochemical modifications is a powerful tool for assessing the relationship between protein structure, stability, and biological function. High-throughput approaches for quantifying protein stability are beginning to emerge that enable thermodynamic measurements on small amounts of material, in short periods of time, and using readily accessible instrumentation. Here we present such a method, fast quantitative cysteine reactivity, which exploits the linkage between protein stability, sidechain protection by protein structure, and structural dynamics to characterize the thermodynamic and kinetic properties of proteins. In this approach, the reaction of a protected cysteine and thiol-reactive fluorogenic indicator is monitored over a gradient of temperatures after a short incubation time. These labeling data can be used to determine the midpoint of thermal unfolding, measure the temperature dependence of protein stability, quantify ligand-binding affinity, and, under certain conditions, estimate folding rate constants. Here, we demonstrate the fQCR method by characterizing these thermodynamic and kinetic properties for variants of Staphylococcal nuclease and E. coli ribose-binding protein engineered to contain single, protected cysteines. These straightforward, information-rich experiments are likely to find applications in protein engineering and functional genomics.     

Demonstration of brain capillaries using acetyl-CoA]

The method is based on a reduced procedure for revealing cholinacetyltransferase when the stage of preincubation treatment of the material and inhibitor is omitted. The possibility to investigate the human and animal brains with a complete revealing of the capillary network, which corresponds to injection of the vessels with Indian ink, is proved.     

Structure for energy cycle: a unique status of the second law of thermodynamics for living systems

Distinguishing things from beings, or matters from lives, is a fundamental question. Extending E. Schr?dinger's neg-entropy and I. Prigogine's dissipative structure, we propose a chemical kinetic view that the earliest "live" process is embedded essentially in a special interaction between a pair of specific components under a particular, corresponding environmental conditions. The interaction exists as an inter-molecular-force-bond complex(IMFBC) that couples two separate chemical processes: one is the spontaneous formation of the IMFBC driven by a decrease of Gibbs free energy as a dissipative process; while the other is the disassembly of the IMFBC driven thermodynamically by free energy input from the environment. The two chemical processes coupled by the IMFBC originated independently and were considered non-living on Earth, but the IMFBC coupling of the two can be considered as the earliest form of metabolism: the first landmark on the path from things to a being. The dynamic formation and disassembly of the IMFBC, as a composite individual, follows a principle designated as "… structure for energy for structure for energy…", the cycle continues; and for short it will be referred to as "structure for energy cycle". With additional features derived from this starting point, the IMFBC-centered "live" process spontaneously evolved into more complex living organisms with the characteristics currently known.     

Analysis of structural motifs of proteins using sets of codes, describing local structures]

An amino acid sequence pattern conserved among a family of proteins is called motif. It is usually related to the specific function of the family. On the other hand, functions of proteins are achieved by their 3D structures. Specific local structures, called structural motifs, are considered related to their functions. However, searching for common structural motifs in different proteins is much more difficult than for common sequence motifs. We are attempting in this study to convert the information about the structural motifs into a set of one-dimensional digital strings, i.e., a set of codes, to compare them more easily by computer and to investigate their relationship to functions more quantitatively. By applying the Delaunay tessellation to a 3D structure of a protein, we can assign each local structure to a unique code that is defined so as to reflect its structural feature. Since a structural motif is defined as a set of the local structures in this paper, the structural motif is represented by a set of the codes. In order to examine the ability of the set of the codes to distinguish differences among the sets of local structures with a given PROSITE pattern that contain both true and false positives, we clustered them by introducing a similarity measure among the set of the codes. The obtained clustering shows a good agreement with other results by direct structural comparison methods such as a superposition method. The structural motifs in homologous proteins are also properly clustered according to their sources. These results suggest that the structural motifs can be well characterized by these sets of the codes, and that the method can be utilized in comparing structural motifs and relating them with function.     

Anti-ischemic protection of the brain using water-soluble form of aspirin-acelisin]

The domestic water-soluble aspirin (acelisin) has been used as an anti-ischemic brain protector. The total brain ischemia has been implemented in accordance with an original technique for 17 to 35 min. The doses of acelisin from 25 to 250 mg/kg have been tested during experiments. The infusion of solutions has been carried out before ischemia, 15 min before reperfusion and just after the beginning of reperfusion. The functional status and survival of rats have been evaluated during a week. The best result has been reached with 150 mg/kg acelisin injected 30 min before ischaemia. A positive effect was reported when acelisin was used in early postischaemic period.     

The assessment of the subjective second by using the "individual minute" test]

Correlation of the two characteristics of the "individual minute" test with age and sex of the subjects was examined in 151 persons. Close correlation was observed between the first (counting in the course of 60 s) and the second (counting time up to 60 s) modes of testing, but not between the two modes of testing and age and sex. Results are discussed from the viewpoint of the existence of the common system of time interval estimation the method of their quantum organization being used in different investigation modes.     

酒精对γ-氨基丁酸转运蛋白I（GAT1）功能调节方式的初步研究

已有报道GABA能系统参与酒精耐受和成瘾。我们实验室先前的研究表明急性和慢性酒精处理能快速增强小鼠中枢神经系统γ-氨基丁酸转运蛋白(GATs)的功能,但不影响中枢神经系统GAT1的基因表达水平;GABA转运蛋白对底物的亲和性也未发生变化。在本文中,我们用免疫荧光实验发现酒精处理后,GAT1蛋白向突触体质膜一侧聚集。蛋白磷酸化检测实验显示突触体内GAT1蛋白上丝氨酸、苏氨酸及酪氨酸的磷酸化水平降低。这些结果提示酒精通过刺激GAT1蛋白从胞内转位到突触质膜上而提高GABA重摄取的功能,GAT1蛋白去磷酸化可能在此过程中发挥了重要作用。     

On using a double-exponential model for describing faecal marker concentration curves

A mathematical and numerical appraisal of the double-exponential model is presented, with particular reference to its ability to reproduce preset values of biological measures such as rumen and whole-tract mean retention times and faecal production rate. A complete, formal mathematical derivation is provided, with consideration given to a solution to the model when the two smallest rate constants are equal. It is concluded that any error introduced by using an approximation in deriving the double-exponential form is negligible in practice, and that the double exponential in logarithmic form is able to determine the relevant biological measures quite satisfactorily and speedily.     

A computer model for describing the effect of urethral afferents on simulated lower urinary tract function

A computer model of mechanical properties of the bladder, the urethra and the rhabdosphincter, as well as their neural control is presented in this paper. The model has a rather simple design and processes sensory information from both the bladder wall tension and urethral stretch. It is assumed that afferent signals from the urethra are involved in a sacral excitatory reflex and a supraspinal inhibitory reflex. Pressure and flow signals that resemble experimentally measured normal human behaviour could be simulated with this model. From these simulations the relation between the neural control mechanisms used in the model and the neural control mechanism in vivo cannot be judged entirely because similar behaviour could be simulated with models that are bas ed on different neural control mechanisms. Also behaviour that resembles detrusor overactivity was simulated with our model after an externally induced rise in detrusor pressure was added. Detrusor overactivity, sometimes in combination with urethral relaxation, can occur during a urodynamic investigation. A possible explanation for this detrusor overactivity might be that the micturition reflex is triggered by unknown disturbances and is inhibited immediately after by the same mechanism that normally ceases voiding. The described model provides such a mechanism. Based on these simulations, therefore, it is concluded that urethral afferent signals might be important in lower urinary tract control.     

Analysis of brain chromatin subunit composition using different endonucleases]

A comparison of the processes of chromatin digestion in brain and liver nuclei by Ca, Mg-dependent and staphylococcal endonucleases demonstrates a similarity of the subunit composition of chromatin from both tissues and reveals the same type of linked DNA regions. However, a formation of low molecular weight DNP fragments during hydrolysis and the DNA spectra of soluble and insoluble DNP fragments suggest that brain chromatin contains these fragments alongside with the regions, which are specific for this particular tissue, predominate in it and are resistant to staphylococcal and, particularly, to Ca, Mg-dependent endonucleases. This is paralleled with a non-histone protein enrichment of different brain chromatin fractions and an expansion of the electrophoretic monomer band towards the fragment with a greater molecular weight. It may be assumed that brain nucleosomes are characterized by a higher size heterogeneity of linked DNA, part of which are mostly covered by non-histone proteins, and/or are characterized by a greater set variety.