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[Estimation of the number of necessary beds for tuberculosis patients, in Japan].

OBJECTIVE: To estimate the number of necessary beds for tuberculosis patients in Japan from the view point of isolation of the source of infection. METHODS: We calculated the number of necessary beds for tuberculosis cases separately for the initial phase and for the chronic excreters. For the initial phase we calculated by multiplying the number of detected tuberculosis cases and the duration of hospitalization. The number of detected cases is based on the figures in 2002 and the duration of hospitalization is assumed to be 90 days for sputum smear positive cases and 60 days for sputum smear negative cases. We calculated the number of necessary beds using the Monte Carlo simulation for each prefecture on the assumption that the incidence and the duration of diseases will be under the effect of random fluctuation with the Poisson's distribution for the number of cases and with the log normal distribution for the duration of hospitalization. We also considered the seasonal fluctuation. RESULTS: Our calculation revealed that around 6,413 beds would be necessary for the initial phase and 200-400 beds for chronic excreters in Japan. There are several prefectures which only requires less than 30 beds. DISCUSSION: Currently, Japan has around 17,000 beds secured for tuberculosis patients. Our calculation showed that this was much more than needed. In many areas, one ward will provide more than sufficient number of tuberculosis beds. Specialist consultation system must be improved because of the reduction in the number of TB cases treated at hospitals with TB wards and TB specialists. For the treatment of non-infectious TB, ambulatory DOT system, TB shelter and nursing care facilities would be necessary to guarantee compliance to treatment.

Directly Observed Therapy↗

Detection of Cryptosporidium parvum in secondary effluents using a most probable number-polymerase chain reaction assay.

Polymerase chain reaction (PCR) was used to detect Cryptosporidium parvum oocysts in secondary effluent samples collected from activated-sludge facilities. Serial dilutions of the purified nucleic acid extracts from the samples were made and PCR was conducted to estimate the C. parvum oocyst concentration via a Poisson distribution-based most probable number (MPN). The degree of oocysts associated with wastewater particles was also evaluated. The sensitivity of the MPN-PCR assay was 20 oocysts/PCR unit. The detection limit of the concentration, extraction, and purification protocols in phosphate buffer saline spiked with a known concentration of oocysts ranged from 1.1 to 4.6 oocysts/L; the detection limit for the wastewater samples ranged from 11 to 4200 oocysts/L depending on the extent of inhibition in each sample. The recovery efficiency of the oocysts ranged from 48 to 59% in most samples. Oocysts were found in two out of seven samples with concentrations of 203 and 308 oocysts/L, as estimated by the MPN-PCR method. The oocysts were found only in the filtrate of the grab samples; particle-associated oocysts were not detected. Association of spiked C. parvum oocysts with particles in secondary effluent drawn from wastewater plants with varying operating conditions indicated a weak correlation between the degree of association and the mean cell residence time of the system.

Animals↗

Dimensionality reduction in neural models: an information-theoretic generalization of spike-triggered average and covariance analysis.

We describe an information-theoretic framework for fitting neural spike responses with a Linear-Nonlinear-Poisson cascade model. This framework unifies the spike-triggered average (STA) and spike-triggered covariance (STC) approaches to neural characterization and recovers a set of linear filters that maximize mean and variance-dependent information between stimuli and spike responses. The resulting approach has several useful properties, namely, (1) it recovers a set of linear filters sorted according to their informativeness about the neural response; (2) it is both computationally efficient and robust, allowing recovery of multiple linear filters from a data set of relatively modest size; (3) it provides an explicit "default" model of the nonlinear stage mapping the filter responses to spike rate, in the form of a ratio of Gaussians; (4) it is equivalent to maximum likelihood estimation of this default model but also converges to the correct filter estimates whenever the conditions for the consistency of STA or STC analysis are met; and (5) it can be augmented with additional constraints on the filters, such as space-time separability. We demonstrate the effectiveness of the method by applying it to simulated responses of a Hodgkin-Huxley neuron and the recorded extracellular responses of macaque retinal ganglion cells and V1 cells.

Action Potentials↗

Determination of cutoff values to detect small aneuploid clones by interphase fluorescence in situ hybridization: the Poisson model is a more appropriate approach. Should single-cell trisomy 8 be considered a clonal defect?

We applied a dual-color interphase in situ fluorescence hybridization (I-FISH) technique using centromeric probes specific to chromosomes 7 and 8 on 20 control samples in order to define the statistical model best suited to determine cutoff values for detection of small abnormal clones. We found that the Poisson model is a more appropriate approach than a Gaussian model. Then, based on the analysis of 91 samples from 80 patients with myelocytic malignant hemopathies and either clonal or nonclonal -7 or +8 as determined with conventional cytogenetics (CC), we compared the respective power of I-FISH and CC for detection of aneuploidy, with special emphasis on the potential contribution of I-FISH as a complement to CC in the case of small abnormal clones. The I-FISH results were positive in samples with clonal -7 or +8 according to CC analysis. Whereas I-FISH was negative in samples with nonclonal -7 according to CC, thus confirming the reliability of the criteria used to define the clonality of -7; the situation was different with nonclonal +8. I-FISH revealed the clonality of +8 in most samples with single-cell +8. In several cases, however, the unquestionable clonal nature of +8, as evidenced during follow-up, could not be established with either CC or I-FISH according to accepted criteria. Our data suggest that, in case of a single metaphase with +8, the general rule should be amended and the single-cell +8 should be considered and reported as potentially clonal.

Aneuploidy↗

Mean and variance of ratio estimators used in fluorescence ratio imaging.

BACKGROUND: The ratio of two measured fluorescence signals (called x and y) is used in different applications in fluorescence microscopy. Multiple instances of both signals can be combined in different ways to construct different ratio estimators. METHODS: The mean and variance of three estimators for the ratio between two random variables, x and y, are discussed. Given n samples of x and y, we can intuitively construct two different estimators: the mean of the ratio of each x and y and the ratio between the mean of x and the mean of y. The former is biased and the latter is only asymptotically unbiased. Using the statistical characteristics of this estimator, a third, unbiased estimator can be constructed. RESULTS: We tested the three estimators on simulated data, real-world fluorescence test images, and comparative genome hybridization (CGH) data. The results on the simulated and real-world test images confirm the presented theory. The CGH experiments show that our new estimator performs better than the existing estimators. CONCLUSIONS: We have derived an unbiased ratio estimator that outperforms intuitive ratio estimators.

Analysis of Variance↗

Trypanosoma cruzi: quantification in tissues of experimentally infected mice by limiting dilution analysis.

A limiting dilution assay (LDA) was developed for the quantification of Trypanosoma cruzi in the heart and blood of infected mice. Three groups of swiss mice were injected ip with "CL", "Colombiana," and "Y" strains. At 1-day intervals after infection, blood and the heart were removed. Serial blood dilutions in LIT medium were performed and distributed in four groups of 24 microplate wells. The growth of parasite was visually checked in an inverted microscope. It was found that curves of parasitemia obtained by parasite counting in a hemocytometer or estimated by LDA were similar. A similar method was used to quantify parasites in the heart of mice. The heart was cut, washed, dried, and its weight was determined. The heart pieces were disrupted by passage through a mesh stainless-steel screen into LIT. Serial dilutions of the heart homogenate were made in LIT and added to at least 24 replicate microplate wells. Parasites were detectable earlier in the heart of mouse infected with Y strain when compared to CL and Colombiana strains. Parasites were detected in the heart of mice of all strains by 6 days after infection. This LDA for quantification of T. cruzi permits a more precise evaluation of the number of living parasites in infected tissues.

Animals↗

The spike trains of inhibited pacemaker neurons seen through the magnifying glass of nonlinear analyses.

This communication describes the new information that may be obtained by applying nonlinear analytical techniques to neurobiological time-series. Specifically, we consider the sequence of interspike intervals Ti (the "timing") of trains recorded from synaptically inhibited crayfish pacemaker neurons. As reported earlier, different postsynaptic spike train forms (sets of timings with shared properties) are generated by varying the average rate and/or pattern (implying interval dispersions and sequences) of presynaptic spike trains. When the presynaptic train is Poisson (independent exponentially distributed intervals), the form is "Poisson-driven" (unperturbed and lengthened intervals succeed each other irregularly). When presynaptic trains are pacemaker (intervals practically equal), forms are either "p:q locked" (intervals repeat periodically), "intermittent" (mostly almost locked but disrupted irregularly), "phase walk throughs" (intermittencies with briefer regular portions), or "messy" (difficult to predict or describe succinctly). Messy trains are either "erratic" (some intervals natural and others lengthened irregularly) or "stammerings" (intervals are integral multiples of presynaptic intervals). The individual spike train forms were analysed using attractor reconstruction methods based on the lagged coordinates provided by successive intervals from the time-series Ti. Numerous models were evaluated in terms of their predictive performance by a trial-and-error procedure: the most successful model was taken as best reflecting the true nature of the system's attractor. Each form was characterized in terms of its dimensionality, nonlinearity and predictability. (1) The dimensionality of the underlying dynamical attractor was estimated by the minimum number of variables (coordinates Ti) required to model acceptably the system's dynamics, i.e. by the system's degrees of freedom. Each model tested was based on a different number of Ti; the smallest number whose predictions were judged successful provided the best integer approximation of the attractor's true dimension (not necessarily an integer). Dimensionalities from three to five provided acceptable fits. (2) The degree of nonlinearity was estimated by: (i) comparing the correlations between experimental results and data from linear and nonlinear models, and (ii) tuning model nonlinearity via a distance-weighting function and identifying the either local or global neighborhood size. Lockings were compatible with linear models and stammerings were marginal; nonlinear models were best for Poisson-driven, intermittent and erratic forms. (3) Finally, prediction accuracy was plotted against increasingly long sequences of intervals forecast: the accuracies for Poisson-driven, locked and stammering forms were invariant, revealing irregularities due to uncorrelated noise, but those of intermittent and messy erratic forms decayed rapidly, indicating an underlying deterministic process. The excellent reconstructions possible for messy erratic and for some intermittent forms are especially significant because of their relatively low dimensionality (around 4), high degree of nonlinearity and prediction decay with time. This is characteristic of chaotic systems, and provides evidence that nonlinear couplings between relatively few variables are the major source of the apparent complexity seen in these cases. This demonstration of different dimensions, degrees of nonlinearity and predictabilities provides rigorous support for the categorization of different synaptically driven discharge forms proposed earlier on the basis of more heuristic criteria. This has significant implications. (1) It demonstrates that heterogeneous postsynaptic forms can indeed be induced by manipulating a few presynaptic variables. (2) Each presynaptic timing induces a form with characteristic dimensionality, thus breaking up the preparation into subsystems such that the physical variables in each operate as one

Action Potentials↗

The origin of bursts and heavy tails in human dynamics.

The dynamics of many social, technological and economic phenomena are driven by individual human actions, turning the quantitative understanding of human behaviour into a central question of modern science. Current models of human dynamics, used from risk assessment to communications, assume that human actions are randomly distributed in time and thus well approximated by Poisson processes. In contrast, there is increasing evidence that the timing of many human activities, ranging from communication to entertainment and work patterns, follow non-Poisson statistics, characterized by bursts of rapidly occurring events separated by long periods of inactivity. Here I show that the bursty nature of human behaviour is a consequence of a decision-based queuing process: when individuals execute tasks based on some perceived priority, the timing of the tasks will be heavy tailed, with most tasks being rapidly executed, whereas a few experience very long waiting times. In contrast, random or priority blind execution is well approximated by uniform inter-event statistics. These finding have important implications, ranging from resource management to service allocation, in both communications and retail.

Behavior↗

The binomial nature of transmitter release at the crayfish neuromuscular junction.

1. Transmitter release at excitatory junctions on the opener muscle of the crayfish dactyl was studied by recording junctional potentials with extracellular micro-electrodes.2. At low temperatures, evoked release was dispersed sufficiently in time for potentials produced by individual quanta to be counted, and the mean (m) and variance (sigma(2)) of the quantum content distribution for a series of trials measured directly. These values were used to calculate the average probability of quantal release (p), assuming a binomial distribution.3. For all values of m and p, the observed release pattern (number of 0, 1, 2, 3,... quantal releases during a series of trials) was approximated closely by the corresponding binomial distribution. However, Poisson predictions differed significantly from the observed quantal distribution for values of p > 0.2.

Animals↗

Coding strategies in monkey V1 and inferior temporal cortices.

We would like to know whether the statistics of neuronal responses vary across cortical areas. We examined stimulus-elicited spike count response distributions in V1 and inferior temporal (IT) cortices of awake monkeys. In both areas, the distribution of spike counts for each stimulus was well described by a Gaussian distribution, with the log of the variance in the spike count linearly related to the log of the mean spike count. Two significant differences in response characteristics were found: both the range of spike counts and the slope of the log(variance) versus log(mean) regression were larger in V1 than in IT. However, neurons in the two areas transmitted approximately the same amount of information about the stimuli and had about the same channel capacity (the maximum possible transmitted information given noise in the responses). These results suggest that neurons in V1 use more variable signals over a larger dynamic range than IT neurons, which use less variable signals over a smaller dynamic range. The two coding strategies are approximately as effective in transmitting information.

Animals↗

Daily variability of equine fecal strongyle egg counts.

Fecal egg counts often are used for diagnosing equine strongyle infections and estimating the number of eggs shed in the feces. An individual egg count should be interpreted in view of the normal fluctuation of egg numbers in an individual horse. In this study, the daily variability of strongyle fecal egg counts from horses was investigated. The Cornell-McMaster egg-counting technique was used to estimate the eggs per gram of feces in repeated daily fecal samples from 39 horses. The variation of the daily egg counts across 4 days was greater than would be expected if a consistent number of eggs were produced and dispersed randomly in the feces. The means and variances of the daily counts from each horse had a logarithmic relationship. For practical purposes, however, the fluctuation of egg counts is low enough for the fecal egg count to be used to identify horses for treatment, to estimate pasture contamination, or to assess response to therapy.

Animals↗

Statistical methods for geographical surveillance in veterinary epidemiology.

Spatial clustering and cluster detection are statistical analysis developed to address relevant scientific hypothesis. The difficulty stays in the large number of alternative hypothesis due to the different mechanisms that could generate the anomalous cases aggregation. We review methods for marked point data (case/control) aimed to describe spatial intensity of disease risk, to test for randomness and to locate significant excesses. Bayesian Gaussian Spatial Exponential models are used to illustrate probabilistic aspects and the link with simpler non parametric tools are shown. We develop an informal guideline to the analysis and used data on faecal contamination and dog parasitic diseases in the city of Naples, Italy. Kernel density estimation resulted very sensitive to bandwidth choice and overemphasized localized excess, Ripley'K function and Cuzick-Edwards test were very consistent each other while the SatScan failed to detect excesses. The spatial range was around 600 meters and justifies several small clusters. Bayesian models were very powerful in reconstructing the phenomenon and allow inference on model parameters in good agreement with the non parametric analysis.

Algorithms↗

Balanced neurons: analysis of leaky integrate-and-fire neurons with reversal potentials.

A new technique is presented for analyzing leaky integrate-and-fire neurons that incorporates reversal potentials, which impose a biologically realistic lower bound to the membrane potential. The time distribution of the synaptic inputs is modeled as a Poisson process. The analysis is carried out in the Gaussian approximation, which comparison with numerical simulations confirms is most accurate in the limit of a large number of inputs. The hypothesis that the observed variability in the spike times of cortical neurons is caused by a balance of excitatory and inhibitory synaptic inputs is supported by the results for the coefficient of variation of the interspike intervals. Its value decreases with both increasing numbers and amplitude of inputs, and is consistently lower than 1.0 over a wide range of realistic parameter values. The dependence of the output spike rate upon the rate, number, and amplitude of the synaptic inputs, as well as upon the value of the inhibitory reversal potential, is given.

Action Potentials↗

Solid-fluid transition in a granular shear flow.

The rheology of a granular shear flow is studied in a quasi-2D rotating cylinder. Measurements are carried out near the midpoint along the length of the surface flowing layer where the flow is steady and nonaccelerating. Streakline photography and image analysis are used to obtain particle velocities and positions. Different particle sizes and rotational speeds are considered. We find a sharp transition in the apparent viscosity (eta) variation with rms velocity (u). Below the transition depth we find that the rms velocity decreases with depth and eta proportional to u(-1.5) for all the different cases studied. The material approaches an amorphous solidlike state deep in the layer. The velocity distribution is Maxwellian above the transition point and a Poisson velocity distribution is obtained deep in the layer. The results indicate a sharp transition from a fluid to a fluid + solid state with decreasing rms velocity.

Biophysics↗