Landmark learning: An illustration of associative search

In a previous paper we defined the associative search problem and presented a system capable of solving it under certain conditions. In this paper we interpret a spatial learning problem as an associative search task and describe the behavior of an adaptive network capable of solving it. This example shows how naturally the associative search problem can arise and permits the search, association, and generalization properties of the adaptive network to bee clearly illustrated.     

Improvement of seed yields under boron-limiting conditions through overexpression of BOR1, a boron transporter for xylem loading, in Arabidopsis thaliana

Soil fertilization is a common practice in modern agriculture, undertaken to prevent nutrient deficiency in crops. However, fertilization is costly and causes environmental pollution. The cultivation of plants that tolerate low nutrient supplies may circumvent this problem. Here, we report the generation of Arabidopsis thaliana plants that tolerate boron (B)-deficient conditions due to the overexpression of BOR1, an efflux B transporter that is required for efficient xylem loading of B. In several independently generated transgenic plants expressing BOR1 or BOR1-GFP under the control of the cauliflower mosaic virus 35S RNA promoter, root-to-shoot translocation of B was enhanced and shoot growth was greater under B-limiting conditions compared with wild-type plants. In addition, the transgenic plants showed increased translocation of B, especially to the shoot apex, and set seed normally under B-limiting conditions, under which wild-type plants failed to set seed. This study therefore reports plants that show improved seed yields compared with wild-type under nutrient-deficient conditions as a result of increased production of an essential mineral nutrient transporter.     

A method to combine numerical optimization and EMG data for the estimation of joint moments under dynamic conditions

To solve the problem of muscle redundancy at the level of opposing muscle groups, an alternative method to inverse dynamics must be employed. Considering the advantages of existing alternatives, the present study was aimed to compute knee joint moments under dynamic conditions using electromyographic (EMG) signals combined with non-linear constrained optimization in a single routine. The associated mathematical problems accounted for muscle behavior in an attempt to obtain accurate predictions of the resultant moment as well as physiologically realistic estimates of agonist and antagonist moments. The experiment protocol comprised (1) isometric trials to determine the most effective EMG processing for the prediction of the resultant moment and (2) stepping-in-place trials for the calculation of joint moments from processed EMG under dynamic conditions. Quantitative comparisons of the model predictions with the output of a biological-based model, showed that the proposed method (1) produced the most accurate estimates of the resultant moment and (2) avoided possible inconsistencies by enforcing appropriate constraints. As a possible solution for solving the redundancy problem under dynamic conditions, the proposed optimization formulation also led to realistic predictions of agonist and antagonist moments.     

A Mathematical Treatment of Rate Data Obtained in Biological Flow Systems under Nonsteady State Conditions

The problem of determining gas exchange rates from flow system data under nonsteady state conditions is analyzed. A correction factor is presented for obtaining constant rates under nonsteady state conditions. A general formula for obtaining any rate under nonsteady state conditions is also given. Turnover time is defined and discussed in terms of the mathematics presented. The origins of nonsteady states and steady states in flow systems are discussed, as are some of the experimental advantages of working under nonsteady state conditions.     

Structural bases of the plasticity of the nervous system

The present state of morphological study of variability in the nervous elements under conditions of adaptive change under the influence of afferent effects, age changes during different periods of ontogenesis, under conditions of de- and regeneration of synapses have been considered. A question on correlation between structure and the function of synapses during the change has been analysed. The tasks of subsequent study of this problem have been outlined.     

Physiological functions of bile acids in the body

A literary review and own data on the various physiological functions of bile acids in organism are given. The modern state of the problem on the bile salt role in lipid assimilation is reflected. The other functions of bile salts in the digestive tract are described. The regulating influence of bile acids on some metabolic processes in organism is shown. The alteration of membrane enzyme activity under the influence of bile acids possessing the detergent properties may play an important role in different pathological conditions. The significance of bile acid metabolism under physiological and pathological conditions is underlined.     

环境胁迫下植物的化感作用及其诱导机制

植物化感作用是生态学研究中一个十分活跃的领域,对植物为什么和在什么条件下释放化感物质这一重要问题有不同的认识。在对环境胁迫下植物化感作用的变化及环境胁迫因子对化感物质听诱导机制等方面进行了评述后,指出植物化感化质的产生和释放是植物在环境胁迫的选择压力下形成的,植物化感作用是植物在进化过程中产生的一种对环境的适应性机制。     

Identifying responsive functional modules from protein-protein interaction network

Proteins interact with each other within a cell, and those interactions give rise to the biological function and dynamical behavior of cellular systems. Generally, the protein interactions are temporal, spatial, or condition dependent in a specific cell, where only a small part of interactions usually take place under certain conditions. Recently, although a large amount of protein interaction data have been collected by high-throughput technologies, the interactions are recorded or summarized under various or different conditions and therefore cannot be directly used to identify signaling pathways or active networks, which are believed to work in specific cells under specific conditions. However, protein interactions activated under specific conditions may give hints to the biological process underlying corresponding phenotypes. In particular, responsive functional modules consist of protein interactions activated under specific conditions can provide insight into the mechanism underlying biological systems, e.g. protein interaction subnetworks found for certain diseases rather than normal conditions may help to discover potential biomarkers. From computational viewpoint, identifying responsive functional modules can be formulated as an optimization problem. Therefore, efficient computational methods for extracting responsive functional modules are strongly demanded due to the NP-hard nature of such a combinatorial problem. In this review, we first report recent advances in development of computational methods for extracting responsive functional modules or active pathways from protein interaction network and microarray data. Then from computational aspect, we discuss remaining obstacles and perspectives for this attractive and challenging topic in the area of systems biology.     

Studies in the mathematical biophysics of discrimination and conditioning II: Special case: Errors,trials, and number of possible responses

A special case of a problem discussed in a previous paper is treated in greater detail. An equation in the three variables, errors, trials and number of possible choices, is developed and compared with the results of an experiment performed under conditions closely approximating those required for the development of the equation. The agreement is excellent.     

Considerations of quasi-stationarity in electrophysiological systems

Conditions under which a time varying electromagnetic field problem (such as arises in electrophysiology, electrocardiography, etc.) can be reduced to the conventional quasistatic problem are summarized. These conditions are discussed for typical physiological parameters.     

Isolation of a New Root Growth-stimulating Substance from a Fungus

In the last few decades, enzymatic production of 3,4-dihydroxyphenyl-L-alanine (L-dopa) using tyrosine phenol-lyase (Tpl) has been industrialized. This method has an intrinsic problem of tyrosine contamination because Tpl is synthesized under tyrosine-induced conditions. Herein, we constructed a hyper-L-dopa-producing strain by exploiting a mutant TyrR, an activator of tpl. The highest productivity was obtained for the strain grown under non-induced conditions. It was 30-fold higher than that obtained for tyrosine-induced wild-type cells.     

Changing effective population size and the McDonald-Kreitman test

Artifactual evidence of adaptive amino acid substitution can be generated within a McDonald-Kreitman test if some amino acid mutations are slightly deleterious and there has been an increase in effective population size. Here I investigate the conditions under which this occurs. I show that fairly small increases in effective population size can generate artifactual evidence of positive selection if there is no selection upon synonymous codon use. This problem is exacerbated by the removal of low-frequency polymorphisms. However, selection on synonymous codon use restricts the conditions under which artifactual evidence of adaptive evolution is produced.     

Consequences of the non-specific binding of a protein to a linear polymer: reconciliation of stoichiometric and equilibrium titration data for the thrombin-heparin interaction

Theoretical aspects of the thermodynamic characterization of cooperative protein interactions with non-specific segments of a linear polymer lattice have been re-examined. This reconsideration has not only provided an alternative derivation of recursive expressions for the stoichiometry of random ligand binding prior to elimination of the parking problem but also extended that treatment to include binding with overlap of additional lattice units. The major obstacle to thermodynamic characterization of non-specific protein-polymer interactions is determination of the lattice capacity for ligand, which in turn defines the length of the polymer segment to which the protein binds. Although these parameters are most readily obtained from studies under conditions that ensure essentially stoichiometric interaction, the endpoint of such a titration is likely to reflect the irreversible rather than the equilibrium binding capacity of the lattice for ligand. Consideration of published results for spectrofluorometric titrations of the thrombin-heparin system under stoichiometric conditions in such terms has permitted their reconciliation with results of a later publication on the interaction under equilibrium conditions.     

Genetic analysis of post-flowering drought tolerance and components of grain development in Sorghum bicolor (L.) Moench

Drought is a serious agronomic problem and the single greatest factor contributing to crop yield loss in the world today. This problem may be alleviated by developing crops that are well adapted to dry-land environments. Sorghum (Sorghum bicolor (L.) Moench) is one of the most drought-tolerant grain crops and is an excellent crop model for evaluating mechanisms of drought tolerance. In this study, a set of 98 recombinant inbred (RI) sorghum lines was developed from a cross between two genotypes with contrasting drought reactions, TX7078 (pre-flowering-tolerant, post-flowering susceptible) and B35 (pre-flowering susceptible, post-flowering-tolerant). The RI population was characterized under drought and non-drought conditions for the inheritance of traits associated with post-flowering drought tolerance and for potentially related components of grain development. Quantitative trait loci (QTL) analysis identified 13 regions of the genome associated with one or more measures of post-flowering drought tolerance. Two QTL were identified with major effects on yield and 'staygreen under post-flowering drought. These loci were also associated with yield under fully irrigated conditions suggesting that these tolerance loci have pleiotropic effects on yield under non-drought conditions. Loci associated with rate and/or duration of grain development were also identified. QTL analysis indicated many loci that were associated with both rate and duration of grain development. High rate and short duration of grain development were generally associated with larger seed size, but only two of these loci were associated with differences in stability of performance under drought.     

Evaluation of velocity of vertical learning of the habitable space for complex behavioral experiments in rats

A selection of laboratory animals for complex behavioural experiments is of a significant importance for obtaining objective results. The problem of the selection seems to be solved by means of the proposed assessment of vertical learning of an habitable space. The assessment test is based on investigative activity of the animals under conditions of a new surrounding. The test allows to divide the rats into four types.     

Metastable balancing oscillators

The problem of an oscillator performing oscillations at the top of an oscillating potential barrier is solved exactly. The conditions under which the motion is finite, quasi-finite (metastable), or infinite are determined. Examples are presented from mechanics (a Kapitsa pendulum on a solid support that oscillates in the horizontal direction), plasma physics (Bernstein-Green-Kruskal waves), and microwave electronics (metastable electrons near an oscillating virtual cathode).     

Propagation of wave pulses in the regimes of single-particle and collective cherenkov effects during convective and absolute instabilities

Asymptotic solutions to the problem of the time evolution of delta-shaped wave pulses excited during resonant instabilities of electron beams in slowing-down electromagnetic media are found and investigated analytically. Convective and absolute instabilities developing under the conditions of collective and single-particle Cherenkov effects are considered. The results obtained apply to an arbitrary linear nonequilibrium dispersive medium that can be described by a set of first-or second-order differential transport equations.     

Aspects of cellular biology of the bacterial stationary phase: programmed cell death and regulation by guanosine tetraphosphate

The paper discusses (1) programmed cell death, the phenomenon typical of the stationary phase of bacteria occurring under unfavorable conditions, (2) its pleiotropic regulation by guanosine tetraphosphate, and (3) the conception of "addiction module," a specific genetic system responsible for the cell choice between survival and death under unfavorable conditions. The shortcomings of the proposed interpretation of the problem at hand are considered and the necessity of their further investigation is substantiated.     

Distribution of the absorbed ECRH power among the electrons in a plasma heated by an extraordinary wave

A study is made of the one-dimensional linear problem of the absorption of the energy of an extraordinary wave propagating along a nonuniform magnetic field by a plasma in the ECR region. The plasma electrons are assumed to be nonrelativistic and are described by a collisionless kinetic equation. The distribution of the absorbed power among the electrons and the distribution of the self-consistent field over the confinement system are obtained. The conditions under which the ECRH power is distributed uniformly among the bulk electrons are determined. The limits of applicability of the locally nonuniform magnetic field approximation are established. The solutions derived are compared with the solution to an analogous problem with the collisional absorption mechanism.