A method of statistical neurodynamics

A method of statistical neurodynamics is presented for treating ensembles of nets of randomly connected neuron-like elements. The concept of a macrostate plays a fundamental role in statistical neurodynamics and a criterion is given for ascertaining that given macroscopic quantities together constitute a macrostate. The activity of a nerve net is shown to be a macrostate and the equation of the dynamics of the activity is elucidated for various ensembles of random nerve nets. It is shown that the distance between two microstates can also be treated as a macrostate in a generalized sense. The equation of its dynamics represents how the distance between two states changes in the course of state transitions. The dynamics of distance reveals interesting microscopic properties of random nerve nets, such as the stability of state-transition, the transient lengths, etc.     

Comparative analysis of sensitivity of cholinesterase inhibitors by multidimensional statistical methods

Using the methods of factor and cluster analysis, the statistical treatment is performed of data on interaction of 7 cholinesterases (ChE)--human acetylcholinesterase, horse butyrylcholinesterase, cholinesterases of frog brain and of various squid species (Todarodes pacificus and Berrytheutis magister; in the latter case, individuals from three different habitats are compared)--with 141 reversible inhibitors of various structures. Statistically significant differences between ChE of squids and vertebrates are shown. The previously revealed intraspecies peculiarities of ChE in the Commander squid B. magister are statistically confirmed.     

Use of `relative-phase' analysis to assess correlation between neuronal spike trains

 We propose a new method of studying the correlation between neuronal spike trains. This technique is based on the analysis of relative phase between two point processes. Relative phase here is defined as the relative timing difference between two spike trains normalized by the associated interspike interval of one cell. This phase measurement is intended to reveal the relative timing relationship between spike trains atdifferent firing rates. We apply this method to a numerical example and an example from two cerebellar neuronal spike trains of a behaving rat. The results are compared with classical cross-correlation analysis. We show that the technique can avoid some of the limitations of cross-correlation methods, reveal certain statistical dependencies that cannot be shown by cross correlation, and provide information as to the direction of influence between two spike trains. Received: 8 November 2001 / Accepted: 30 September 2002 / Published online: 24 January 2003 Correspondence to: Y. Chen (e-mail: chen@nsi.edu, Fax: + 1-858-626-2099) Acknowledgements. Research for this paper was supported by the Alafi Family Foundation and the Neurosciences Research Foundation.     

Multimodal pressure-flow method to assess dynamics of cerebral autoregulation in stroke and hypertension

Background

This study evaluated the effects of stroke on regulation of cerebral blood flow in response to fluctuations in systemic blood pressure (BP). The autoregulatory dynamics are difficult to assess because of the nonstationarity and nonlinearity of the component signals.

Methods

We studied 15 normotensive, 20 hypertensive and 15 minor stroke subjects (48.0 ± 1.3 years). BP and blood flow velocities (BFV) from middle cerebral arteries (MCA) were measured during the Valsalva maneuver (VM) using transcranial Doppler ultrasound.

Results

A new technique, multimodal pressure-flow analysis (MMPF), was implemented to analyze these short, nonstationary signals. MMPF analysis decomposes complex BP and BFV signals into multiple empirical modes, representing their instantaneous frequency-amplitude modulation. The empirical mode corresponding to the VM BP profile was used to construct the continuous phase diagram and to identify the minimum and maximum values from the residual BP (BP_R) and BFV (BFV_R) signals. The BP-BFV phase shift was calculated as the difference between the phase corresponding to the BP_R and BFV_R minimum (maximum) values. BP-BFV phase shifts were significantly different between groups. In the normotensive group, the BFV_R minimum and maximum preceded the BP_R minimum and maximum, respectively, leading to large positive values of BP-BFV shifts.

Conclusion

In the stroke and hypertensive groups, the resulting BP-BFV phase shift was significantly smaller compared to the normotensive group. A standard autoregulation index did not differentiate the groups. The MMPF method enables evaluation of autoregulatory dynamics based on instantaneous BP-BFV phase analysis. Regulation of BP-BFV dynamics is altered with hypertension and after stroke, rendering blood flow dependent on blood pressure.

     

Rapid light curves: A new fluorescence method to assess the state of the photosynthetic apparatus

Photosynthetic electron transport rates (ETR), calculated from chlorophyll fluorescence parameters, were compared in long term light and dark adapted as well as photoinhibited Pisum sativum leaves using a novel chlorophyll fluorescence method and a new instrument: rapid light curves (RLC) generated with the MINI-PAM. RLCs are plots of ETRs versus actinic irradiances applied for 10 s. Large changes in maximum electron transport rates (ETR_max) were observed when leaves were shifted from dark to moderate light, or from dark to photoinhibitory light and vice versa. Maximum ETRs were very low following long term dark adaptation, but increased to maximum levels within 8 to 15 minutes of illumination. It took more than 3 hours, however, to return irradiance-exposed leaves to the fully dark adapted state. Quenching analysis of RLCs revealed large q_E development in long-term dark adapted leaves accounting for the low ETRs. Leaves photoinhibited for 3 hours had similarly reduced ETRs. In these leaves, however, q_I was largely responsible for this reduction. Actinic irradiance exposures and saturating flashes affected leaves with different irradiance histories differently.     

A statistical procedure to assess the significance level of barriers to gene flow

Although several methods are available to study the extent of isolation by distance （IBD） among natural populations, comparatively few exist to detect the presence of sharp genetic breaks in genetic distance datasets. In recent years, Monmonier＇s maximum-difference algorithm has been increasingly used by population geneticists. However, this method does not provide means to measure the statistical significance of such barriers, nor to determine their relative contribution to population differentiation with respect to IBD. Here, we propose an approach to assess the significance of genetic boundaries. The method is based on the calculation of a multiple regression from distance matrices, where binary matrices represent putative genetic barriers to test, in addition to geographic and genetic distances. Simulation results suggest that this method reliably detects the presence of genetic barriers, even in situations where IBD is also significant. We also illustrate the methodology by analyzing previously published datasets. Conclusions about the importance of genetic barriers can be misleading if one does not take into consideration their relative contribution to the overall genetic structure of species.     

Use of body-water content to assess the physiological state of roach Rutilus rutilus L. in natural conditions

It is shown that in natural conditions roach have two levels of water content in their organisms during their annual cycle which reflect different physiological states of the fish. During the feeding period, the body-water content is maintained at a low level of 72.6 ± 0.05%, determining the physiological state related to the growth of fishes. In winter, spring, and postspawning periods, the water content in the roach organism is high, 75 ± 0.06%, which reflects the physiological state of survival during periods of the year unfavorable for growth. The water content in the organism of fish is a convenient integrated parameter for assessing the general physiological state of fish in natural conditions.     

Using indicator species to assess the state of macrobenthic communities

Environmental impact assessments are often followed by the continuous monitoring needed to determine community change. This long-term monitoring can be time-consuming and expensive. The concept of indicator species attempts to use their presence in a sample or area to characterise a certain degree of community change or pollution effects. This approach has been widely applied to benthic monitoring studies. However, many studies develop their own list of `indicators' in cases without having a prior knowledge of the area or any long-term data. This can result in the production of circular arguments. We carry out a meta-analysis on data sets from 5 of the 20 designated United Kingdom's sewage sludge dumping grounds and the data set from the classic study of Pearson & Rosenberg (1978). We construct a number of indices to examine this robustness across studies. Having refined our criteria for an `indicator taxa' we examine the spatial and temporal changes in macrobenthic communities occurring at the Tyne sewage sludge dumpsite to examine the utility of this approach. Of the total pool of 123 taxa, 81 taxa responded in one study only. While Spio filicornis(O. F. Müller), Spiophanes bombyx(Claparède), Lagis koreni (Malmgren) and Nephtys cirrosa (Ehlers) showed directly contradictory patterns in different locations. The Spearman's rank correlation test showed a significant negative relationship between the density of macro-litter per station found at the Tyne dumping ground and the abundance of Abra alba(Wood) (r _s=0.462, n= 6, P=0.1) and Amphiura filiformis(O. F. Müller)(r _s=0.493, n= 6, P=0.1). These were the only indicator taxa, which showed a strong relationship to sewage contamination. We therefore conclude that while the concept of indicators may be widely applicable, the actual indicator taxa are not. This demonstrate that the used of indicators must be continually developed providing prior information of the study area.     

The use of different statistical methods in epidemiological analysis to assess the seasonality and territorial spread of infectious diseases

To solve the problems connected with the evaluation of the seasonal and territorial distribution of infectious diseases, indications and limitations for the use of the following statistical methods have been worked out: the calculation of the monthly morbidity level, the proportion of cases of infectious diseases falling on the months of seasonal morbidity rises, the proportion of such cases appearing due to the influence of seasonal factors, the total and partial indices, the average monthly rate of increase in seasonal morbidity, the complex evaluation of seasonal morbidity, the evaluation of the nonparallelism of two curves, the determination of the mean quadratic deviations and Shannon's entropy. The algorithms based on these methods lie in the foundation of 11 computer programs, forming the software complex "Epidanalysis" and provided with the service menu permitting an epidemiologist to proceed from the task via indications and limitations to the corresponding program. The programs are intended for different types of computers (IBM PC XT, EC-1640, Robotron 1715).     

Use of image analysis to assess the plasma membrane integrity of ram spermatozoa in different diluents

Sperm membrane integrity can be assessed by examining a large number of fluorochrome-stained sperm cells over a relative short period of time by flow cytometry or fluorimetry. However, many small laboratories lack a flow-cytometer or fluorimeter for sperm analysis. This study was designed to develop a new image analysis method to evaluate the membrane integrity of ram spermatozoa with the aid of open software, and was divided into three experiments. In the first experiment, the new computer-assisted method was validated by mixing fresh semen samples with different volumes of killed semen in order to know the proportions of damaged spermatozoa in the samples. In the second trial, the new method was compared with the traditional manual counting, and the effect of three extender media on the suitability of the new developed method was evaluated. In the third experiment, the method proposed was tested by comparing the use of milk-, citrate- or TRIS-based diluents for ram semen preservation at 15 degrees C. In all experiments, semen was assessed for plasma membrane integrity and for percentage of motile and progressive sperm by CASA. In the new computer-assisted method, two images of the sperm cells in a given microscopy field are captured and the number of total- and membrane-damaged cells counted. In the first trial, proportions of damaged sperm cells in each sample determined by the automated procedure agreed closely (r2=0.98, P<0.001) with the predicted theoretical values. In experiment 2, the results of membrane integrity obtained using the new method were highly correlated with those provided by the conventional manual counting after PI-CFDA double staining (r=0.99, P<0.001), and also correlated with sperm motility and progressive motility percentages. Viability was significantly higher after dilution with citrate-, than with Tris-based medium, but similar to PBS (70.32+/-3.93, 55.48+/-5.76 and 65.38+/-3.15, respectively), After 0, 24 and 48h of storage, significantly higher percentages of motile, progressive, and membrane-intact spermatozoa were recorded for the milk than for the Tris extenders. Our results validate the new computer-assisted method for assessing sperm membrane integrity in the sheep, and indicate that the milk extender is less damaging to the sperm of this species than citrate or Tris extenders.     

Alignment and statistical difference analysis of complex peptide data sets generated by multidimensional LC-MS

A method for high-resolution proteomics analyses of complex protein mixtures is presented using multidimensional HPLC coupled to MS (MDLC-MS). The method was applied to identify proteins that are differentially expressed during fruit ripening of tomato. Protein extracts from red and green tomato fruits were digested by trypsin. The resulting highly complex peptide mixtures were separated by strong cation exchange chromatography (SCX), and subsequently analyzed by RP nano-LC coupled to quadrupole-TOF MS. For detailed quantitative comparison, triplicate RP-LC-MS runs were performed for each SCX fraction. The resulting data sets were analyzed using MetAlign software for noise and data reduction, multiple alignment and statistical variance analysis. For each RP-LC-MS chromatogram, up to 7000 mass components were detected. Peak intensity data were compared by multivariate and statistical analysis. This revealed a clear separation between the green and red tomato samples, and a clear separation of the different SCX fractions. MS/MS spectra were collected using the data-dependent acquisition mode from a selected set of differentially detected peptide masses, enabling the identification of proteins that were differentially expressed during ripening of tomato fruits. Our approach is a highly sensitive method to analyze proteins in complex mixtures without the need of isotope labeling.     

Comparative population analysis of the variability of human neurodynamics and psychodynamics

A number of characteristics of morphological, neurodynamical, and psychodynamical levels of organization of individual personality was studied in five isolated different ethnical populations and two panmixic ones. The degree of heritability was found to decrease and that of variability to increase with the rise of organization level. Significant interpopulational differences were shown in the mean values of characteristics under study and their dispersions. The results obtained were discussed in connection with peculiarities of genetical and social structures of investigated human populations.     

Use of collateral airways to assess airway reactivity

We investigated the correlation between collateral airway reactivity and other indexes of lung reactivity in response to aerosol and intravenous (iv) challenges. In four anesthetized mongrel dogs, we measured the peripheral airway resistance (Rp) to gas flow out of a wedged lung segment in different lobes on multiple occasions. We obtained dose-response curves of peripheral airways challenged with iv histamine or aerosols through the bronchoscope. During the same iv bolus challenge, whole lung airway pressure (Paw) responses to histamine were also measured. On separate occasions, changes in lung resistance (RL) were measured after the whole lung was challenged with a histamine aerosol. Reactivity was assessed from the dose-response curves for Rp and RL as the PD50 (dose required to produce a 50% increase); for changes in Paw we calculated the PD15 (dose required to produce a 15% increase over baseline). Results for Rp showed considerably more variability among different lobes in a given animal with the aerosol challenge through the bronchoscope than with the iv challenge. With aerosol challenge there were no significant differences in the mean PD50 for Rp among any of the animals. However, with the iv challenge two of the dogs showed significant differences from the others in reactivity assessed with Rp (P less than 0.01). Moreover, the differences found in the peripheral airways with iv challenge reflected differences found in whole lung reactivity assessed with either iv challenge (Paw vs. Rp, r2 = 0.96) or whole lung aerosol challenge (RL vs. Rp, r2 = 0.84). We conclude that the measurement of the collateral resistance response to iv challenge may provide a sensitive method for assessing airway reactivity.     

SPA: Simple web tool to assess statistical significance of DNA patterns

Many statistical methods and programs are available to compute the significance of a given DNA pattern in a genome sequence. In this paper, after outlining the mathematical background of this problem, we present SPA (Statistic for PAtterns), an expert system with a simple web interface designed to be applied to two of these methods (large deviation approximations and exact computations using simple recurrences). A few results are presented, leading to a comparison between the two methods and to a simple decision rule in the choice of that to be used. Finally, future developments of SPA are discussed. This tool is available at the following address: http://stat.genopole.cnrs.fr/SPA/.     

Using soil and litter arthropods to assess the state of rainforest restoration

Summary The present study investigated recolonization patterns of selected soil and litter arthropods following replanting of pasture with rainforest species in the Mary River catchment of eastern subtropical Australia. While extensive research has been conducted in rehabilitated mined sites in Australian dry sclerophyll forests, very little attention has been paid to rainforest restoration on previously pastoral land. We examined the utility of soil and litter arthropod groups for monitoring the progress of restoration, and the relationship between arthropod assemblage patterns and environmental factors potentially under the control of those doing the replanting. Leaf litter was extracted from 20 sites: five remnant rainforest, five pasture, and 10 sites that had been revegetated (from 1 to 12 years previously) with a diversity of indigenous species. Ants (identified to genus), centipedes, millipedes, isopods, amphipods and mites were enumerated and their assemblages described with multi- and univariate methods. Ant genera alone proved unable to distinguish pasture from rainforest, and mites (identified only to oribatid or non-oribatid) proved of limited use because these two groups were present in all samples in extremely high numbers that overwhelmed the contributions of other arthropod groups. However, a coarse taxonomic approach using five arthropod groups (ants, centipedes, millipedes, isopods, amphipods) clearly discriminated between pasture and rainforest, and also arranged the revegetated sites between these two extremes. Simple frequency scores based on the presence/absence of these arthropod groups in each of three replicate subplots were sufficient to achieve this separation of site types. Habitats created by close planting of trees and mulching may accelerate invertebrate colonization and, thus, promote the rapid establishment of processes and functions characteristic of developing rainforests.