Evaluation of the normal equations for the analysis of diallels

Summary Analysis of diallel experiments usually requires specialised computer programs. A simple relationship between the normal equations for a diallel and the normal equations for a hypothetical model in which the general combining ability factor is viewed as two separate distinct simple factors may be useful in adapting general statistical analysis packages to the desired analysis.     

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.     

Studies of the distribution of the Z-pinch radiance during the implosion of wire arrays in the angara-5-1 facility

Results are presented from time-integrated measurements of soft X-ray emission from Z-pinches during the implosion of simple and nested wire arrays. The blackening density distribution obtained with the help of a pinhole camera is recalculated into the time-integrated Z-pinch radiance. It is found that, in the case of a simple wire array, up to 70% of the total SXR energy emitted during a discharge is radiated from the axial region, the rest of energy being radiated from plasma jets, whereas in the case of a nested wire array, more than 90% of the SXR energy is radiated from the axial region.     

Simple sequences are rare in the Protein Data Bank

A simple sequence is abundant in the proteins that have been sequenced to date. But unusual protein features, such as a simple sequence, are not present in the same high frequency within structural databases. A subset of these simple sequences, a group with a highly repetitive nature has been shown to be abundant in eukaryotes but not in prokaryotes. In this study, an examination of the eukaryotic proteins in the Protein Data Bank (PDB) has revealed a large deficiency of low complexity, highly repetitive protein repeats. Through simulated databases of similar samples of eukaryotic proteins taken from the National Center for Biotechnology Information (NCBI) database, it is shown that the PDB contains a significantly less highly repetitive, simple sequence than artificial databases of similar composition randomly derived from NCBI. When the structural data for those few PDB sequences that did contain a highly repetitive simple sequence is examined in detail, it is found that in most cases the tertiary structure is unknown for the regions consisting of a simple sequence. This lack of a simple sequence both in the PDB database and in the structural information suggests that this type of simple sequence may produce disordered structures that make structural characterization difficult.     

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.     

Theory of the EEG potential in models of the leptomeninges of the brain. IV. Radial dipoles and their double layers in the depths and on the surface of the brain]

The estimaiton of ECoG-potentials is fulfilled by means of a simple model of the isolated sphere, which is exact enough, as it was proved earlier [1]. A simple limit formula for the qualitative estimation of ECoG-potentials of a source situated in the cerebral cortex is obtained. The EEG as in [2] is obtained using the transformation of the first 20 spheric harmonics. The experimental facts of registration of the evoked potentials of comparatively little subcortical sources were explained theoretically. Numerical results of the model are used to estimate the intensity of the field induced in the brain by two electrodes placed on the scalp.     

Mathematical model of the simple cells in the visual cortex

A mathematical model for the spatial computations performed by simple cells in the mammalian visual cortex is derived. The construction uses as organizing principles the experimentally observed simple cell linearity and rotational symmetry breaking, together with the constraint that simple cell inputs must effectively be ganglion cell outputs. This leads to a closed form expression for the simple cellkernel in terms of Jacobi-functions. Using a-function identity, it is also shown how Gabor sampling arises as an approximation to this exact kernel for most cells. In addition, the model provides a natural mechanism for introducing the type of nonlinearity observed in some simple cells. The cell's responses to a variety of visual stimuli are calculated using the exact kernel and compared to single cell recordings. In all cases, the model's predictions are in agreement with available experimental data.Work supported by the National Science Foundation, grant PHYS86-20266Work supported by the Department of Energy, contract DE-AC02-76ERO2220     

On the use of the classical tests for detecting linkage.

Some drawbacks of the classical Mather's linkage text XL2 are considered, and the simple contingency analysis is suggested as an alternative method. The former test is conditional on Mendelian segregation at both loci, whereas the simple contingency test is not. Furthermore, the contingency test and the test for Mendelian segregation at each locus are orthogonal when performed using the G statistic. Simulation results show that, when the XL2 is used, the actual type I error probability (alpha a) can be dramatically perturbed. As expected, no alpha a perturbation is observed when the G contingency test is used. On the other hand, when segregation is Mendelian at both loci, the power of the XL2 method is larger than that of the contingency G test when sample size is small and strong marginal distortion is observed. Because strong marginal distortion may suggest that segregation may be non-Mendelian, the XL2 is in general discouraged in favor of the simple contingency analysis.     

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.     

A chemotactic method for the isolation of Actinoplanaceae

A simple chemotactic method for the isolation of Actinoplanaceae from soil is described. The method is based on a combination of the aerotactic behavior of the spores and the attraction to chloride ions. A simple isolation chamber is described. The method is simpler and less time-consuming than the current baiting techniques.     

Effect of anatomical fine structure on the dispersion of solutes in the spinal subarachnoid space

The dispersion of a solute bolus is calculated for cerebrospinal fluid undergoing oscillatory flow in the subarachnoid space of the spine. The fine structure of the subarachnoid space (nerves and trabeculae) enhances both longitudinal and transverse dispersions five to ten times over a simple model with an open annular space. Overall, dispersion is >10(3) times simple molecular diffusion. The result of enhanced dispersion is rapid spread and dilution of the bolus, effectively stirred by fluid movement around the fine structure.     

Distribution of the number of matches between nucleotide sequences

When two strings of symbols are aligned it is important to know whether the observed number of matches is better than that expected between two independent sequences with the same frequency of symbols. When strings are of different lengths, nulls need to be inserted in order to align the sequences. One approach is to use simple approximations of sampling for replacement. We describe an algorithm for exactly determining the frequencies of given numbers of matches, sampling without replacement. This does not lead to a simple closed form expression. However we show examples where sampling with, or without, replacement give very similar results and the simple approach may be adequate for all but the smallest cases.     

家蚕神经系统研究进展

家蚕Bombyx mori神经系统属于腹神经索型, 构造简单, 却能产生丰富的行为, 是研究神经生物学的理想实验材料。研究表明： 家蚕神经系统由中枢神经系统、 外周神经系统和交感神经系统构成, 通过信号传递在调节家蚕视觉、 嗅觉、 取食、 结茧、 交配、 排泄等生命活动中发挥作用。家蚕具有编码乙酰胆碱、 γ-氨基丁酸、 多巴胺等多种神经递质及其受体和促前胸腺激素（prothoracicotropic hormone, PTTH）、 滞育激素（diapause hormone, DH）等神经肽的基因。家蚕神经系统发育受到许多基因和bmo-miR-92等小分子RNA的调控。目前研究家蚕神经的方法主要有触角电位技术、 免疫细胞化学法、 转基因方法、 神经信息学及计算机三维重建等。对家蚕神经系统的研究有助于阐明神经系统的信号传递机制和生物神经网络的形成机制。     

A new method for the separation of the constant and the variable fluorescence of chlorophyll a in in vivo

The constant fluorescence of chlorophyll a in alga Dunaliella tertiolecta was estimated by a method of the least square regression applied to the linearized form of the equation y = axb. The value of the constant fluorescence obtained by this method was compared by the values estimated with simple linear extrapolation. Constant fluorescence, evaluated by the simple linear extrapolation of 10 ms of the initial variable fluorescence, was 50% higher than the value obtained by the method of the least square regression. We demonstrated that the estimation of constant fluorescence by the least square regression is a more correct method and provides a better comparison of results from different laboratories. This method offers a simple way to determine and separate constant fluorescence from variable fluorescence in the total yield of chlorophyll a fluorescence in "in vivo" conditions. Furthermore it facilitates the interpretation of the variable fluorescence phenomena in "in vivo".     

Speculations on the origin and evolution of metabolism

An autotrophic origin of metabolism is described, which requires clays, transition state metals, disulfide and dithiols, U.V. and cyanide ion. A general scheme is proposed, involving the fixation of CO2 and N2, for the evolution of intermediary metabolism based on the evolution of a complex system from a simple one. The basic conclusion is that metabolism could have evolved from a simple environment rather than from a complex one.     

Stochasticity in the adaptive dynamics of evolution: the bare bones

First a population model with one single type of individuals is considered. Individuals reproduce asexually by splitting into two, with a population-size-dependent probability. Population extinction, growth and persistence are studied. Subsequently the results are extended to such a population with two competing morphs and are applied to a simple model, where morphs arise through mutation. The movement in the trait space of a monomorphic population and its possible branching into polymorphism are discussed. This is a first report. It purports to display the basic conceptual structure of a simple exact probabilistic formulation of adaptive dynamics.     

Using the relationship between nucleotide sequence and codon usage for the detection of frame-shift sequencing errors in bacterial genes

Summary A simple nucleotide sequence analysis method for the detection of frame-shift sequencing errors is presented. It is based on the fact that the base content of the three positions of the codons in protein-coding. DNA-sequences varies in a predictable manner correlated to the overall G+C content. A simple computer program is needed to perform this analysis.     

Estimating the size of the dividing stem cell pool after allogeneic bone marrow transplantation

Currently the problem of estimation of the number of pluripotent stem cells reconstituting marrow grafts following bone marrow transplantation, or studies looking at questions of clonal dominance in hematopoietic cell populations, rely on indirect measurement and a simple application of the formula for the sampling variation of a binomial proportion. This approach, from a statistical viewpoint, can be seen to be flawed. It is very easily remedied though and only requires appropriate use of variance stabilizing transformations. These lead to a very simple estimator for the number of hematopoietic stem cells involved in repopulating the marrow and require little in the way of additional calculation. We give the distribution theory for this estimator as well as simple approximations for practical application. As an illustration we rework data recently gathered to address the question as to whether or not reconstitution of marrow grafts in the clinical setting is oligoclonal.     

Simulating the Entropic Collapse of Coarse-Grained Chromosomes

Depletion forces play a role in the compaction and decompaction of chromosomal material in simple cells, but it has remained debatable whether they are sufficient to account for chromosomal collapse. We present coarse-grained molecular dynamics simulations, which reveal that depletion-induced attraction is sufficient to cause the collapse of a flexible chain of large structural monomers immersed in a bath of smaller depletants. These simulations use an explicit coarse-grained computational model that treats both the supercoiled DNA structural monomers and the smaller protein crowding agents as combinatorial, truncated Lennard-Jones spheres. By presenting a simple theoretical model, we quantitatively cast the action of depletants on supercoiled bacterial DNA as an effective solvent quality. The rapid collapse of the simulated flexible chromosome at the predicted volume fraction of depletants is a continuous phase transition. Additional physical effects to such simple chromosome models, such as enthalpic interactions between structural monomers or chain rigidity, are required if the collapse is to be a first-order phase transition.