Use of Phase for the Detection of Hidden Periodicites

Standard tests for the detection of hidden periodicities in time series are largely ignored by applied workers. Various simple but inappropriate methods are used instead. Therefore a method is suggested which is both simple and appropriate but which requires the prior knowledge of certain characteristics of the suspected periodicity. For illustration, this method is applied to a set of data from a chronobiological study.     

Exploring simple independent action in multifactor tables of proportions

The problem of assessing synergistic or antagonistic departure from simple independent action in multifactor tables of proportions is discussed. A generalized linear model is employed in which additivity corresponds to simple independent action. Data-analytic strategies are proposed for exploring departures from simple independent action in various extensions of the 2 X 2 table of proportions. This methodology is illustrated with a series of models fitted to cellular differentiation and murine toxicity data.     

Simple sequences are ubiquitous repetitive components of eukaryotic genomes

Simple sequences are stretches of DNA which consist of only one, or a few tandemly repeated nucleotides, for example poly (dA) X poly (dT) or poly (dG-dT) X poly (dC-dA). These two types of simple sequence have been shown to be repetitive and interspersed in many eukaryotic genomes. Several other types have been found by sequencing eukaryotic DNA. In this report we have undertaken a systematical survey for simple sequences. We hybridized synthetical simple sequence DNA to genome blots of phylogenetically different organisms. We found that many, probably even all possible types of simple sequence are repetitive components of eukaryotic genomes. We propose therefore that they arise by common mechanisms namely slippage replication and unequal crossover and that they might have no general function with regards to gene expression. This latter inference is supported by the fact that we have detected simple sequences only in the metabolically inactive micronucleus of the protozoan Stylonychia, but not in the metabolically active macronucleus which is derived from the micronucleus by chromosome diminution.     

A Simple Study in Ecological Energetics using a Gall-fly and its Insect Parasites

The field ant, Lasius flavus provides an answer to the problem of demonstrating, in schools, the effect of an organism on its surroundings. There is a simple pattern of plant distribution on the anthills which is different from the surrounding meadow and the differences between anthill and undisturbed soil can be demonstrated by simple experiments. These differences modified the environment of the ant colonies in ways which were favourable to their development. The anthill is a product of social organisation which is in some ways comparable to the attempts of human societies to control their environment.     

Effect of lethality on the extinction and on the error threshold of quasispecies

In this paper the effect of lethality on error threshold and extinction has been studied in a population of error-prone self-replicating molecules. For given lethality and a simple fitness landscape, three dynamic regimes can be obtained: quasispecies, error catastrophe, and extinction. Using a simple model in which molecules are classified as master, lethal and non-lethal mutants, it is possible to obtain the mutation rates of the transitions between the three regimes analytically. The numerical resolution of the extended model, in which molecules are classified depending on their Hamming distance to the master sequence, confirms the results obtained in the simple model and shows how an error catastrophe regime changes when lethality is taken in account.     

Extensive feature detection of N-terminal protein sorting signals

MOTIVATION: The prediction of localization sites of various proteins is an important and challenging problem in the field of molecular biology. TargetP, by Emanuelsson et al. (J. Mol. Biol., 300, 1005-1016, 2000) is a neural network based system which is currently the best predictor in the literature for N-terminal sorting signals. One drawback of neural networks, however, is that it is generally difficult to understand and interpret how and why they make such predictions. In this paper, we aim to generate simple and interpretable rules as predictors, and still achieve a practical prediction accuracy. We adopt an approach which consists of an extensive search for simple rules and various attributes which is partially guided by human intuition. RESULTS: We have succeeded in finding rules whose prediction accuracies come close to that of TargetP, while still retaining a very simple and interpretable form. We also discuss and interpret the discovered rules.     

A Push-Pull CORF Model of a Simple Cell with Antiphase Inhibition Improves SNR and Contour Detection

We propose a computational model of a simple cell with push-pull inhibition, a property that is observed in many real simple cells. It is based on an existing model called Combination of Receptive Fields or CORF for brevity. A CORF model uses as afferent inputs the responses of model LGN cells with appropriately aligned center-surround receptive fields, and combines their output with a weighted geometric mean. The output of the proposed model simple cell with push-pull inhibition, which we call push-pull CORF, is computed as the response of a CORF model cell that is selective for a stimulus with preferred orientation and preferred contrast minus a fraction of the response of a CORF model cell that responds to the same stimulus but of opposite contrast. We demonstrate that the proposed push-pull CORF model improves signal-to-noise ratio (SNR) and achieves further properties that are observed in real simple cells, namely separability of spatial frequency and orientation as well as contrast-dependent changes in spatial frequency tuning. We also demonstrate the effectiveness of the proposed push-pull CORF model in contour detection, which is believed to be the primary biological role of simple cells. We use the RuG (40 images) and Berkeley (500 images) benchmark data sets of images with natural scenes and show that the proposed model outperforms, with very high statistical significance, the basic CORF model without inhibition, Gabor-based models with isotropic surround inhibition, and the Canny edge detector. The push-pull CORF model that we propose is a contribution to a better understanding of how visual information is processed in the brain as it provides the ability to reproduce a wider range of properties exhibited by real simple cells. As a result of push-pull inhibition a CORF model exhibits an improved SNR, which is the reason for a more effective contour detection.     

Dynamics of Encoding in a Population of Neurons

A simple encoder model, which is a reasonable idealization from known electrophysiological properties, yields a population in which the variation of the firing rate with time is a perfect replica of the shape of the input stimulus. A population of noise-free encoders which depart even slightly from the simple model yield a very much degraded copy of the input stimulus. The presence of noise improves the performance of such a population. The firing rate of a population of neurons is related to the firing rate of a single member in a subtle way.     

Allocation of Sample Size to Strata and Related Problems

In this paper, we shall study an alternative method of deriving Neyman's Optimum allocation of sample size to strata for simple random sampling which is intuitive and simple. In order to obtain this allocation, the within stratum standard deviations of the study variate are required which are unknown and hence are substituted by known quantities. We shall discuss the effects of deviations from the optimum allocation and other related problems.     

The use of techniques of sensory evaluation as a framework for teaching experimental methods

Several simple techniques of sensory assessment are described and the conditions for their satisfactory performance stated. The manner in which these experiments can be used to provide open-ended practical exercises for classes is discussed and its advantages as a relatively cheap and simple method of teaching experimentation is described. Experiments are described in which the diffusion of salt into potatoes after cooking them in boiling salted water is investigated using several techniques of sensory assessment, and other suitable areas ofinvestigation are suggested     

Simplified liquid nutrient media for controlling antibiotic activity, the spectrum of their antibacterial action and the sensitivity of microorganisms]

Beaf-peptone broth and some of its modifications, one of which is a simple and in expensive one to a leser extent binding to antibiotics, such as penicillin, oxytetracycline and streptomycin and providing sufficient growth of the test microbes were used to determine the antibiotic activity with the methods of serial dilutions. The simple modification was recommended for practical use. The MIC of the antibiotics in the above simple medium was less than that in the control. The results of the antibiotic activity determination on both media coincided.     

Effect of starvation on nuclear bodies and rough endoplasmic reticulum in the bovine hepatocyte

The frequency of simple nuclear bodies and the relative volume of rough endoplasmic reticulum was determined in hepatocytes of normal lactating cows and of lactating cows starved for 6 days. Starvation resulted in a highly significant decrease in frequency of simple nuclear bodies and in the relative volume of rough endoplasmic reticulum. It is suggested that simple nuclear bodies are normal nuclear organelles which can respond to physiological changes.     

Modeling water flow through arterial tissue

A simple model of, water flow through deformable porous media has been developed with emphasis on application to arterial walls. The model incorporates a strain-dependent permeability function into Darcy's Law which is coupled, to the force balance for the bulk material. A simple analytical expression relating water flux (volume flux) to pressure differential is developed which shows how strain-dependent permeability can lead to a reduction in hydraulic conductivity with increasing differential pressure as observed in experiments with arteries. The variation of permeability with position in the wall, which may influence the convective diffusion of macromolecules, is determined for both cylindrical and planar segments and a marked influence of geometry is noted.     

Photoengraving of coverslips and slides to facilitate monitoring of micromanipulated cells or chromosome spreads

A simple photolithographic technique has been developed which can be used to produce microscopic grid patterns on glass coverslips. The grid pattern is first photo-reduced onto film, and the resulting photographic negative is then used as a mask. A glass slide or coverslip, coated with a layer of photoresist, is then exposed to tungsten light through the mask. After developing and etching, the grid pattern is transferred permanently onto glass. This simple and rapid procedure allows one to mass-produce very small, high resolution grids which are useful for monitoring individual microinjected cells or chromosomal spreads under the microscope.     

The accumulation of free and phosphorylated sugars in adipocytes based on a dynamic diffusion barrier

The simple theory of a dynamic diffusion barrier is described and it is shown how this could account for the accumulation, in adipocytes, of those free sugars which are also phosphorylated. The standing concentration gradient established by this mechanism depends on the recycling of free sugar and sugar phosphate in submembrane structures which start in juxtaposition to conventional membrane hexose transporters. Although a continual expenditure of metabolic energy is involved, there can be a net gain from the potential-energy store of accumulated substrates. The hypothesis leads to a series of simple equations which can be used as the basis for computer simulations of experimental procedures.     

The distribution of membrane current in nerve with longitudinal linearly increasing applied current

The distribution of membrane current in three models of nerve, when a longitudinal, linearly increasing current is applied, is derived. For the simple core conductor model it is shown that, if the region over which such a current is applied is large compared to the space constant of the model, the membrane current in the mid-portion of the region is a constant, independent of the distance, the time following the application of the current, and the impedance of the membrane. The effect of nonlinear membrane electrical properties is discussed. It is further shown that these conclusions apply equally to the case in which the simple model is surrounded by another concentric sheath (the double cable model). In this case the impedance of the sheath does not influence the membrane current in the mid-polar region. Finally, it is shown that the form of the solution for the saltatory model, for this type of applied current, is identical with that for the simple model.     

THE SEPTAL PORES OF COPFINUS LAGOPUS IN RELATION TO NUCLEAR MIGRATION

The septal pores of homokaryotic and dikaryotic mycelia of Coprinus lagopus have the complex structure characteristic of certain Basidiomycetes. The edge of the pore is thickened and covered on either side by a dome-shaped, perforated, membranous cap. However, in heterokaryotic mycelia in which nuclear migration was believed to be taking place, in addition to the complex pores, simple pores were also observed as well as various intermediate stages interpreted as steps in the breakdown of complex to simple pores. The simple pores may facilitate nuclear migration.     

Effects of simple haemolysins in hypotonic systems

Summary Except for a small inhibition which is due to decreased electrolyte content, the lytic effect of simple lysins such as saponin and the bile salts are the same for cells in hypotonic systems as they are for cells in isotonic systems. Similarly the resistance to hypotonic solutions of cells which have been exposed to sub-lytic quantities of a variety of lysins is not less than that of untreated cells; in fact, it is often somewhat greater.The lytic effects of hypotonie solutions and of the simple lysins are accordingly non-additive, and the implications of this observation are discussed.