Statistical dependency as a measure to evaluate Markov properties of stochastic point processes

Neuronal spike trains are regarded as stochastic point processes. To estimate the order and value of Markov processes of the interspike interval sequences with small number of samples, we have proposed a new measure of simplified statistical dependencyd _m. This measure is derived from statistical dependencyd _m (T=) in the case of Gaussian process, and is obtained by the standard deviation and the matrices of the serial correlation coefficients. Sinced _m is a parametric measure, it is calculated from the interval sequence transformed into the aormal distribution. We designate this as normalized simplified statistical dependencyNd _m. The order and value of the maintained spike sequences recorded from the mesencephalic reticular formation, red nucleus, optic tract, and lateral geniculate nucleus neurons in cats have been estimated. It is indicated that there is a considerable correspondence between the value ofNd _m and that ofd _m (T=). This suggests thatNd _m is useful in practice to estimate the order and value of Markov process with small number of samples.     

Using the AMOVA framework to estimate a standardized genetic differentiation measure

Comparison of population structure between studies can be difficult, because the value of the often-used FST-statistic depends on the amount of genetic variation within populations. Recently, a standardized measure of genetic differentiation was developed based on GST, which addressed this problem, though no method was provided to estimate this standardized measure without bias. Here I present a method to estimate a standardized measure of population differentiation based on the analysis of molecular variance framework. One advantage of the method is that it can be readily expanded to include different hierarchical levels in the tested population structure.     

Competitive order as a measure of social dominance in dairy cattle

Three experiments were used to examine competitive orders as measures of the social hierarchy in dairy cattle. A least squares procedure, which regressed for numbers of observations, was used for obtaining dominance values, from observations of agonistic behaviour. Behavioural data were quantified by time-lapse photography at 1-min intervals. Dominance value was of little importance relative to production variables in describing the amount of time spent eating a limited amount of grain, concentrate, or hay. Likewise, production oriented variables were more important in describing time spent in free stalls or at the feed trough at five levels of competition. Individual feed intakes of group fed dairy cattle at two levels of competition were described predominantly by production variables. From these data, competitive orders are not measures of social dominance in dairy cattle. Dominance values did not describe a priority of access to feed or resting sites.     

Methods to estimate breeding values in honey bees

Background

Efficient methodologies based on animal models are widely used to estimate breeding values in farm animals. These methods are not applicable in honey bees because of their mode of reproduction. Observations are recorded on colonies, which consist of a single queen and thousands of workers that descended from the queen mated to 10 to 20 drones. Drones are haploid and sperms are copies of a drone’s genotype. As a consequence, Mendelian sampling terms of full-sibs are correlated, such that the covariance matrix of Mendelian sampling terms is not diagonal.

Results

In this paper, we show how the numerator relationship matrix and its inverse can be obtained for honey bee populations. We present algorithms to derive the covariance matrix of Mendelian sampling terms that accounts for correlated terms. The resulting matrix is a block-diagonal matrix, with a small block for each full-sib family, and is easy to invert numerically. The method allows incorporating the within-colony distribution of progeny from drone-producing queens and drones, such that estimates of breeding values weigh information from relatives appropriately. Simulation shows that the resulting estimated breeding values are unbiased predictors of true breeding values. Benefits for response to selection, compared to an existing approximate method, appear to be limited (~5%). Benefits may however be greater when estimating genetic parameters.

Conclusions

This work shows how the relationship matrix and its inverse can be developed for honey bee populations, and used to estimate breeding values and variance components.     

Markov population processes as models of primate social and population dynamics

Thanks to recently developed theory of Markov population processes, models of how an individual primate migrates from one casual social group to another or from one breeding troop to another can now deal exactly with transition rates which depend nonlinearly on the sizes of both the group (or troop) left and the group (or troop) entered. Examples of such models presented here are consistent with existing observations of primate social and population dynamics and are more plausible as explanations of these data than previous linear models.     

An unscaled parameter to measure the order of surfaces: a new surface elaboration to increase cells adhesion

We present a new parameter to quantify the order of a surface. This parameter is scale-independent and can be used to compare the organization of a surface at different scales of range and amplitude. To test the accuracy of this roughness parameter versus a hundred existing ones, we created an original statistical bootstrap method. In order to assess the physical relevance of this new parameter, we elaborated a great number of surfaces with various roughness amplitudes on titanium and titanium-based alloys using different physical processes. Then we studied the influence of the roughness amplitude on in vitro adhesion and proliferation of human osteoblasts. It was then shown that our new parameter best discriminates among the cell adhesion phenomena than others' parameters (Average roughness (Ra em leader )): cells adhere better on isotropic surfaces with a low order, provided this order is quantified on a scale that is more important than that of the cells. Additionally, on these low ordered metallic surfaces, the shape of the cells presents the same morphological aspect as that we can see on the human bone trabeculae. The method used to prepare these isotropic surfaces (electroerosion) could be undoubtedly and easily applied to prepare most biomaterials with complex geometries and to improve bone implant integration. Moreover, the new order parameter we developed may be particularly useful for the fundamental understanding of the mechanism of bone cell installation on a relief and of the formation of bone cell-material interface.     

Aerial survey as a tool to estimate whale shark abundance trends

Aerial surveys have been used to estimate population abundance of both terrestrial and marine species; in the marine environment this has largely been used for air-breathing species that spend time regularly at the surface. Whale sharks spend a large proportion of their time close to the surface and so are amenable to aerial survey techniques. This study presents the results of six years of synoptic aerial belt-surveys done nearly daily during the peak whale shark season around the island of Mahe, Seychelles. A total of 580 survey flights were flown providing 699.7 hours of survey record. A seasonal peak of shark sightings per hour was recorded in September or October in most years with the maximum on a single survey of 28.4 h^- 1 in October 2006. The aerial survey data were used to generate an estimate of relative population abundance indicating that highest mean annual relative population estimate was also in 2006, with an estimate of 38, while the lowest mean estimate was 11 in 2004. These estimates were then compared to weekly capture-mark-recapture estimates of abundance based on unique individual identification data. The results indicate that the use of aerial survey data alone may give an acceptable indication of instantaneous relative population abundance but further refinement is necessary to estimate absolute regional abundance.     

Dependency representing Markov properties of nonstationary spike trains recorded from the cat's optic tract fibers

The order and the values of Markov properties of nonstationary stochastic processes are inferred by the use of them-th order Markov value and simplified dependency, respectively: and HereK=0.5log₂ e, and is the correlation coefficient determinant obtained from the ensemble averages of sample records. When an observed value is greater than or equal to the critical value,, the null hypothesis of the (m-1)th order,, is rejected at the level of significance . Here ₁ ² () is the chi-square value with one degree of freedom at andN is sample size. With these statistics it was shown that the order and the values of Markov properties of spike trains of optic tractX- andY-fibers became higher and larger, respectively, after the light spot presentation; and that the values due to negative correlation came to increase and returned to the maintained level earlier inY-fibers than inX-fibers, while the maximum values forX-fibers continued to the light off. It is discussed that Markov properties of spike trains of optic tract fibers in the visual pathway seem to constitute a significant component of the neural information code.     

Endophenotypes as a measure of suicidality

Suicide is thought to result from the harmful interaction of multiple factors that have social, environmental, neurobiological, and genetic backgrounds. Recent studies have suggested that genetic predisposition to suicidal behavior may be independent of the risk of suicide associated to mental disorders, such as affective disorders, schizophrenia, or alcohol dependence. Given the suicidal behavior heterogeneity and its hereditary complexity, the need to find demonstrable intermediate phenotypes that may make it possible to establish links between genes and suicide behaviors (endophenotypes) seems to be necessary. The main objective of this review was to consider the candidate endophenotypes of suicidal behaviors. Due to the recent advances in neuroimaging, we also characterize brain regions implicated in vulnerability to suicide behavior that are influenced by gene polymorphisms associated with suicidal behavior.     

Puromycin dependent formation of initial peptides as a method to measure the initiation

Amino acid incorporating mitochondria, supplied with formyl-group donor, show a puromycin dependent formation of initial peptides. When the puromycin concentration is increased from 1 to 10 mM the length of the puromycin peptides formed is reduced up to the predominant formation of formyl-methionyl-puromycin. A method for measuring the total production of these peptides has been developed, allowing an assay of the initiation reaction. The number of initiation acts is higher than that of mitochondrial ribosomes present. Under suitable conditions the rate of formation of puromycin peptides is constant and largely accounts for the rate of synthesis of the polypeptide chains.     

Inversion of Markov processes to determine rate constants from single-channel data.

The determination of rate constants from single-channel data can be very difficult, in part because the single-channel lifetime distributions commonly analyzed by experimenters often have a complicated mathematical relation to the channel gating mechanism. The standard treatment of channel gating as a Markov process leads to the prediction that lifetime distributions are exponential functions. As the number of states of a channel gating scheme increases, the number of exponential terms in the lifetime distribution increases, and the weights and decay constants of the lifetime distributions become progressively more complicated functions of the underlying rate constants. In the present study a mathematical strategy for inverting these functions is introduced in order to determine rate constants from single-channel lifetime distributions. This inversion is easy for channel gating schemes with two or fewer states of a given conductance, so the present study focuses on schemes with more states. The procedure is to derive explicit equations relating the parameters of the lifetime distribution to the rate constants of the scheme. Such equations can be derived using the equality between symmetric functions of eigenvalues of a matrix and sums over principle minors, as well as expressions for the moments, derivatives, and weights of a lifetime distribution. The rate constants are then obtained as roots to this system of equations. For a gating scheme with three sequential closed states and a single gateway state, exact analytical expressions were found for each rate constant in terms of the parameters of the three-exponential closed-time distribution. For several other gating schemes, systems of equations were found that could be solved numerically to obtain the rate constants. Lifetime distributions were shown to specify a unique set of real rate constants in sequential gating schemes with up to five closed or five open states. For kinetic schemes with multiple gating pathways, the analysis of simulated data revealed multiple solutions. These multiple solutions could be distinguished by examining two-dimensional probability density functions. The utility of the methods introduced here are demonstrated by analyzing published data on nicotinic acetylcholine receptors, GABA(A) receptors, and NMDA receptors.     

Follow-up visits as a measure of adaptation process to removable prostheses

Objectives: The paper was aimed to establish the influence of some general and local factors on adaptation process to removable prostheses (RPs). The adaptation process is a complex issue, which is often associated with painful reactions. Those complaints force patients to visit a dentist who makes alterations to reduce the patient's discomfort. Material and methods: The study involved analysis of 300 dental records of patients who visited our Department for RPs. The authors analysed the influence of gender, age, condition of general health, maintenance of the prosthetic base tissues and the kind of prostheses on the process of adaptation. It was measured by means of a number of follow‐up visits of the patients to our polyclinic. The findings were analysed statistically by means of chi‐squared test. The level of significance was assumed to be p < 0.05. Results and conclusions: Adaptation to RPs without any correction was revealed by about one‐fifth of patients. Men adapted to RPs better than women. The biggest problems with adaptation to RPs were observed in patients using a complete and partial prosthesis simultaneously. The number of follow‐up visits by patients who were treated with RPs for the first time or had been treated before was almost the same. Adaptation of RPs on an atrophic muco‐osseous ridge was associated with more multiple visits than in the case of a well‐preserved ridge. Healthy patients adapt to RPs better than patients with systemic disorders. Taking into account the limitations of the study, the number of follow‐up visits may be used as a helpful indicator of the adaptation process.     

Green fluorescent protein as a novel tool to measure apoptosis and necrosis

BACKGROUND: Several apoptosis-detecting methods are currently available. Many of them are work intensive and require the additional use of antibodies, dyes, specific substrates, or enzymatic reactions. A simple, fast, and reliable method was developed to test for apoptosis or necrosis using mouse and human cell lines (e.g., Jurkat, A20.2J, and PB3c cells) stably transfected with a vector coding for green fluorescent protein (GFP) as indicator cells. METHODS: Apoptosis in GFP-transfected cell lines was induced either by soluble Fas-Ligand (sFasL), recombinant human TRAIL (rhTRAIL), or interleukin-3 (IL-3) deprivation. Necrosis was induced by polyclonal anti-A20 and complement treatment of GFP-transfected A20. Cells were analyzed by flow cytometry for GFP fluorescence. Propidium iodide and Annexin V staining were used to confirm the results obtained with the GFP-method. RESULTS: Live GFP-transfected cells show a strong fluorescence intensity, which is significantly diminished upon induction of apoptosis, whereas necrotic GFP-transfected cells almost completely lose their GFP-associated fluorescence. Apoptosis but not necrosis of GFP-transfected cells was blocked by the use of a caspase inhibitor. The results are highly comparable to conventional apoptosis-detecting methods. CONCLUSIONS: The advantage of our GFP-based assay compared with other methods is the analysis of apoptosis or necrosis without the necessity for additional staining or washing steps, making it an ideal tool for screening apoptotic or necrotic stimuli.