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PubMed1995

Relationship of presaccadic activity in frontal eye field and supplementary eye field to saccade initiation in macaque: Poisson spike train analysis.

The purpose of this study was to investigate the temporal relationship between presaccadic neuronal discharges in the frontal eye fields (FEF) and supplementary eye fields (SEF) and the initiation of saccadic eye movements in macaque. We utilized an analytical technique that could reliably identify periods of neuronal modulation in individual spike trains. By comparing the observed activity of neurons with the random Poisson distribution generated from the mean discharge rate during the trial period, the period during which neural activity was significantly elevated with a predetermined confidence level was identified in each spike train. In certain neurons, bursts of action potentials were identified by determining the period in each spike train in which the activation deviated most from the expected Poisson distribution. Using this method, we related these defined periods of modulation to saccade initiation in specific cell types recorded in FEF and SEF. Cells were recorded in SEF while monkeys made saccades to targets presented alone. Cells were recorded in FEF while monkeys made saccades to targets presented alone or with surrounding distractors. There were no significant differences in the time-course of activity of the population of FEF presaccadic movement cells prior to saccades generated to singly presented or distractor-embedded targets. The discharge of presaccadic movement cells in FEF and SEF could be subdivided quantitatively into an early prelude followed by a high-rate burst of activity that occurred at a consistent interval before saccade initiation. The time of burst onset relative to saccade onset in SEF presaccadic movement cells was earlier and more variable than in FEF presaccadic movement cells. The termination of activity of another population of SEF neurons, known as preparatory set cells, was time-locked to saccade initiation. In addition, the cessation of SEF preparatory set cell activity coincided precisely with the beginning of the burst of SEF presaccadic movement cells. This finding raises the possibility that SEF preparatory set cells may be involved in saccade initiation by regulating the activation of SEF presaccadic movement cells. These results demonstrate the utility of the Poisson spike train analysis to relate periods of neuronal modulation to behavior.

Action Potentials↗

PubMed2004

Application of lot quality assurance sampling for leprosy elimination monitoring--examination of some critical factors.

BACKGROUND: The concept of elimination of an infectious disease is different from eradication and in a way from control as well. In disease elimination programmes the desired reduced level of prevalence is set up as the target to be achieved in a practical time frame. Elimination can be considered in the context of national or regional levels. Prevalence levels depend on occurrence of new cases and thus could remain fluctuating. There are no ready pragmatic methods to monitor the progress of leprosy elimination programmes. We therefore tried to explore newer methods to answer these demands. With the lowering of prevalence of leprosy to the desired level of 1 case per 10000 population at the global level, the programme administrators' concern will be shifted to smaller areas e.g. national and sub-national levels. For monitoring this situation, we earlier observed that lot quality assurance sampling (LQAS), a quality control tool in industry was useful in the initially high endemic areas. However, critical factors such as geographical distribution of cases and adoption of cluster sampling design instead of simple random sampling design deserve attention before LQAS could generally be recommended. The present exercise was aimed at validating applicability of LQAS, and adopting these modifications for monitoring leprosy elimination in Tamil Nadu state, which was highly endemic for leprosy. METHODS: A representative sample of 64000 people drawn from eight districts of Tamil Nadu state, India, with maximum allowable number of 25 cases was considered, using LQAS methodology to test whether leprosy prevalence was at or below 7 per 10000 population. Expected number of cases for each district was obtained assuming Poisson distribution. Goodness of fit for the observed and expected cases (closeness of the expected number of cases to those observed) was tested through chi(2). Enhancing factor (design effect) for sample size was obtained by computing the intraclass correlation. RESULTS: The survey actually covered a population of 62157 individuals, of whom 56469 (90.8%) were examined. Ninety-six cases were detected and this number far exceeded the critical value of 25. The number of cases for each district and the number of cases in the entire surveyed area both followed Poisson distribution. The intraclass correlation coefficients were close to zero and the design effect was observed to be close to one. CONCLUSIONS: Based on the LQAS exercises leprosy prevalence in the state of Tamil Nadu in India was above 7 per 10000. LQAS method using clusters was validated for monitoring leprosy elimination in high endemic areas. Use of cluster sampling makes this method further useful as a rapid assessment procedure. This method needs to be tested for its applicability in moderate and low endemic areas, where the sample size may need increasing. It is further possible to consider LQAS as a monitoring tool for elimination programmes with respect to other disease conditions.

Adolescent↗

PubMed2006

Utility of traditional and alternative EMG-based measures of fatigue during low-moderate level isometric efforts.

Traditional electromyographic (EMG) measures (e.g., amplitude, mean and median frequencies of the power spectra) have demonstrated inconsistent abilities in monitoring localized muscle fatigue at relatively low effort levels. In the present study, several alternative EMG-based fatigue indices were evaluated, derived using a logarithmic representation of the power spectrum, the fractal dimension of the raw signal, and a Poisson distribution fit to the power spectrum. These methods, along with traditional approaches, were applied to EMG data obtained from three separate experiments. In the first two experiments, 24 participants performed sustained isometric shoulder abductions and torso extensions at 30% of maximum voluntary strength (MVC). In the third experiment, another group of 12 participants performed similar shoulder exercises at 15% and 30% MVC, with repeatability assessed at 15% MVC. Both traditional and alternative EMG measures were analyzed for their 'utility', in terms of sensitivity to fatigue, variability, repeatability, and predictive ability. Results demonstrated that parameters derived from fractal analysis and the Poisson distribution demonstrated high utility. These alternative approaches appear promising as fatigue indices for low level isometric tasks.

Adult↗

PubMed2001

Optimal number of beds and occupancy to minimize staffing costs in an obstetrical unit?

PURPOSE: We describe how the science of analyzing patient arrival and discharge data can be used to determine the optimal number of staffed OB beds to minimize labour costs. METHODS: The number of staffed beds represents a balance between having as few staffed beds as possible to care properly for parturients vs having enough capacity to assure available staff for new admissions. The times of admission and discharge of patients from the OB unit can be used to calculate an average census. From this average census, and the properties of the Poisson distribution, the optimal number of staffed beds can be estimated. This calculation requires specification of the risk of having all in-house and on-call staff caring for patients, such that additional staff are unavailable should another parturient arrive. As an example, patient admission and discharge times were obtained for 777 successive patients cared for at an obstetrical unit. The numbers of patients present in the OB unit each two-hour period were calculated and analyzed statistically. PRINCIPAL FINDINGS: There was variation in the average census among hours of the day and days of the week. Poisson distributions fit the data for each of four periods throughout the week. Simply benchmarking the current average occupancy and comparing it to a desired occupancy would have been inadequate as this neglected consideration of the risk of being unable to appropriately care for an additional patient. CONCLUSIONS: The optimal number of beds and occupancy of an OB unit to minimize staffing costs can be determined using straightforward statistical methods.

Anesthesia, Obstetrical↗

PubMed2026

HiCPotts: An R/Bioconductor package to identify significant interactions in chromosome conformation capture data and model sources of bias.

MOTIVATION: Chromosome Conformation Capture methods, including Hi-C, micro-C or Capture-C, are used to map chromatin interactions genome-wide. Most of the existing computational methods do not account for sources of bias (such as DNA accessibility, GC content or TE content) in the data. RESULTS: We previously developed ZipHiC, a Bayesian method based on the hidden Markov random field (HMRF) model and the Approximate Bayesian Computation (ABC), that uses zero-inflated Poisson distribution to model the noise, signal and false signal of the data and showed that this approach was able to detect bias from DNA accessibility, GC content and TE content in both Hi-C and micro-C data. Here, we present HiCPotts, another Bayesian method based on the HMRF model and the ABC that uses a zero-inflated Negative Binomial distribution instead to model the noise and signal of the data. We systematically show that HiCPotts reduces false positives and increases recovery of true interactions compared to ZipHiC, but also compared to other methods such as FastHiC, Juicer and HiCExplorer. Most importantly, we provide an R/Bioconductor package that allows modelling the noise, signal and false signal using various distributions such as the zero-inflated Negative Binomial (ZINB) and the zero-inflated Poisson distribution (ZIP). AVAILABILITY AND IMPLEMENTATION: https://bioconductor.org/packages/HiCPotts/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Approximate Bayesian Computation↗

PubMed1998

[The number of beds needed for patients with infectious diseases that require hospitalization by law].

PURPOSE: Using a statistical model, a study was conducted on the number of beds that are needed for patients with infectious diseases who are required by law to be hospitalized. METHODS: Based on 1995 data, the incidence of such infectious diseases and the average duration of isolation of these patients in Japan were obtained. Using a Poisson distribution, the probability that the number of patients that exceeds a specific number over an average duration of hospitalization was computed in a finite population. The observation period was then extended to one year and the probability that the number of patients did not exceed a specific number during one year was calculated. RESULTS: In 1995, the annual incidence of infectious diseases requiring isolation by hospitalization was 1.38 per 100,000 population and the average duration of hospital confinement was 13.8 days. The estimated patient numbers calculated based on the probability of less than 0.001 that the number of patients would not exceed a specific number were: 2 for 30,000 population, 3 for 50,000 through 100,000, 5 for 200,000 and 300,000, 5 for 400,000 and 500,000, 6 for 750,000 and 1,000,000, 8 for 2,000,000, and 10 for 3,000,000. CONCLUSION: By using a Poisson distribution, a method was developed for estimating the number of beds that are needed for patients with infectious diseases when hospitalization was mandatory.

Communicable Disease Control↗

PubMed1981

[Karyotypic structure of Chinese hamster clone cell populations in prolonged culture].

The Karyotypic structure of some clones and subclones of Chinese hamster cells has been studied (CHO-KI). 60-80% of all the clonal cells demonstrated the identical karyotype (the main structural variant of karyotype - MSVK). The distribution of cells according to the number of chromosomes does not vary within 90 passages of clone cultivation (about 300 cell generations) and 35 passages of subclone cultivation (more than 100 cell generations). In two of three clones the frequencies of cells with MSVK and with additive karyotype variants do not change, while in one clone a long cultivation leads to lowering the frequency of cells with MSVK and to growing the frequency of cells with other karyotype variants. Recloning does not lead to decreasing the karyotypic heterogeneity of clonal populations. The distribution of clonal cells according to the deviation from the modal number of chromosomes is closely related to the Poisson distribution, while the distributions of cells from two clones with the stable karyotypic structure according to the number of greater structural greater deviations from MSVK are related to a degeneration Poisson distribution. Different chromosomes are involved in karyotypic changes in variable proportions, and the frequencies of cells with simultaneous deviations in various chromosome groups are in most instances higher than frequencies expected in the case of independent deviations. The reasons of stability of karyotypic structure in clonal populations is discussed.

Animals↗

PubMed1997

[Confidence of 100 per cent sensitivity and specificity].

A new strategy and four new methods are presented to calculate the limits of the confident interval for an estimate of a proportion equal to 1.0 or 0.0. A current formula which includes 1/(2n) for continuity correction leads to a confident interval which does not include the parameter estimate. Thus, it is proposed: 1) The exclusion of the factor 1/(2n) in that formula leads to correct most of its inconsistencies. The new strategy assumes that the upper limit of a confident interval when the estimates is 100%. The lower limit is calculated by assuming that there is a proportion in the population, from where the sample was taken, such as the probability of getting 100% in the sample is equal to the probability of falling into type I error of current statistics (0.05, 0.01, etc). Three methods are proposed with this strategy. 2) A combinatorial solution based in the knowledge of the number of individuals at whom the test can be applied. 3) A solution based on the binomial distribution. 4) A solution based on the Poisson distribution.

Binomial Distribution↗

PubMed2002

Simulation study for cloud detection with space lidars by use of analog detection photomultiplier tubes.

Output signal electrons from photomultiplier tubes (PMTs) have neither a Gaussian nor a Poisson distribution because of changes induced by multiplication when the number of input signal photons and dark electrons is fewer than approximately 100. Therefore the assumption of a Gaussian distribution of signal electrons cannot be used in simulations for space lidar observations with PMTs, for which the number of return signal photons is normally small. A theory is introduced for analog detection with PMTs that have Poisson-distributed secondary-electron emission at each dynode stage. The theory is validated by straightforward numerical simulations. It is shown that the multiplication in PMTs is a multiply stochastic Poisson process and that the distribution of output signal electrons can be interpreted basically as Neyman type A. Analysis by the threshold method of cloud detection with a space lidar shows considerable difference between a Gaussian approximation and the exact distribution. The result indicates that the threshold level must be optimized for the exact distribution. Return signals were simulated for a proposed space lidar, and cloud detection with the threshold method was demonstrated.

Journal Article↗

PubMed1988

Testing for a change-point in registry data with an example on hypospadias.

The Poisson distribution is often suitable for analysing non-infectious disorders with low prevalence rates. The numbers of babies born with hypospadias in the Liverpool Congenital Malformations Registry during 1960 to 1982 do not fit a Poisson distribution with constant prevalence rates, but a change-point Poisson process does fit. A significance test is described and its power is considered in two simulation studies. A small discrepancy is noted that does not diminish appreciably when Bartlett's correction is applied.

Humans↗

PubMed2006

A Markov model for interspike interval distributions of auditory cortical neurons that do not show periodic firings.

Spontaneous firing properties of individual auditory cortical neurons are interpreted in terms of local and global order present in functioning brain networks, such as alternating "up" and "down" states. A four-state modulated Markov process is used to model neuronal firings. The system alternates between a bound and an unbound state, both with Poisson-distributed lifetimes. During the unbound state, active and closed states alternate with Poisson-distributed lifetimes. Inside the active state, spikes are generated as a realization of a Poisson process. This combination of processes constitutes a four-state modulated Markov process, determined by five independent parameters. Analytical expressions for the probability density functions (pdfs) that describe the interspike interval (ISI) distribution and autocorrelation function are derived. The pdf for the ISI distribution is shown to be a linear combination of three exponential functions and is expressed through the five system parameters. Through fitting experimental ISI histograms by the theoretical ones, numerical values of the system parameters are obtained for the individual neurons. Both Monte Carlo simulations and goodness-of-fit tests are used to validate the fitting procedure. The values of the estimated system parameters related to the active-closed and bound-unbound processes and their independence on the neurons' mean firing rate suggest that the underlying quasi-periodic processes reflect properties of the network in which the neurons are embedded. The characteristic times of autocorrelations, determined by the bound-unbound and active-closed processes, are also independent of the neuron's firing rate. The agreement between experimental and theoretical ISI histograms and autocorrelation functions allows interpretation of the system parameters of the individual neurons in terms of slow and delta waves, and high-frequency oscillations observed in cortical networks. This procedure can identify and track the influence of changing brain states on the single-unit firing patterns in experimental animals.

Action Potentials↗

PubMed1983

Carbodiimide inactivation of Escherichia coli RNA polymerase promoters on supercoiled simian virus 40 and ColE1 DNAs occurs by a one-hit process at salt concentrations in the physiological range.

A previous study (Hale, P., Woodward, R. W., and Lebowitz, J. (1980) Nature 284, 640-644) showed that Escherichia coli RNA polymerase promoters on superhelical SV40 DNA are highly selective targets for chemical modification by the water-soluble carbodiimide, N-cyclohexyl-N'-beta-(4-methylmorpholinium)ethyl carbodiimide (CMC). To extend the inactivation analysis of supercoiled DNAs, we determined the number and location of RNA polymerase binding sites on the supercoiled and linear forms of ColE1 DNA. We also determined the site distribution of [3H] CMC on the superhelical form. This information, coupled with per cent inhibition of transcription versus CMC-bound curves, allowed a test of the specificity of the CMC inactivation by the Poisson equation. Curves were obtained for supercoiled SV40 DNA modified at 0 and 100 mM NaCl (2 mM NaPi, pH 7.0) and for supercoiled ColE1 DNA modified at 0, 100, and 320 mM NaCl. For supercoiled SV40 DNA, these data, coupled to our knowledge of the number of RNA polymerase binding sites from the study cited above, revealed an excellent fit to a one-hit inactivation by the Poisson equation for DNA modified at 100 mM NaCl. For ColE1 DNA, we obtained an excellent fit to a Poisson distribution when supercoiled DNA was modified at 320 mM NaCl. The Poisson distribution can be applied to [3H] CMC restriction fragment data with equivalent results. These results suggest that promoter sites can be forced into different structural conformations with variable degrees of unpairing.

Affinity Labels↗

PubMed1992

Analysis of body-length distribution of Dirofilaria immitis in the cardio-pulmonary blood vessel of naturally infected dogs in Shiga Prefecture, Japan.

Body-length frequencies of Dirofilaria immitis collected from the cardio-pulmonary blood vessel of the dogs were studied in Shiga Prefecture. Japan, in October 1983 and in January and May 1984. The frequencies were not distributed normally because they included the populations of shorter-bodied worms, probably the growing younger worms, whereas the distributions of the body length of worms collected in July 1983 were proved to fit the single normal distribution. From the results of body-length distribution analysis, the worms collected in different seasons were each composed of 1 to 3 groups with different mean body-lengths, standard deviations and composition rates and successive changes were observed in the distribution patterns. According to the analysis of population structures, the infective season was estimated to range from April or May to October or November in 1983 from the respective ages of shorter-bodied worm groups. The annual rates of first infection and re-infection in 1983 determined by the population of shorter-bodied females collected in January were 48% and 93% respectively and the number of newly infecting females per dog ranged from 1 to 27 with a geometric mean of 8.5. The numbers of newly infecting female worms were distributed following the negative binomial and Poisson distributions in newly infected and already infected dogs respectively.

Animals↗

PubMed1986

The natural variability of vital rates and associated statistics.

The first concern of this work is the development of approximations to the distributions of crude mortality rates, age-specific mortality rates, age-standardized rates, standardized mortality ratios, and the like for the case of a closed population or period study. It is found that assuming Poisson birthtimes and independent lifetimes implies that the number of deaths and the corresponding midyear population have a bivariate Poisson distribution. The Lexis diagram is seen to make direct use of the result. It is suggested that in a variety of cases, it will be satisfactory to approximate the distribution of the number of deaths given the population size, by a Poisson with mean proportional to the population size. It is further suggested that situations in which explanatory variables are present may be modelled via a doubly stochastic Poisson distribution for the number of deaths, with mean proportional to the population size and an exponential function of a linear combination of the explanatories. Such a model is fit to mortality data for Canadian females classified by age and year. A dynamic variant of the model is further fit to the time series of total female deaths alone by year. The models with extra-Poisson variation are found to lead to substantially improved fits.

Age Factors↗

PubMed1984

Non-random distribution of intraepithelial lymphoid cells in follicle-associated epithelium of Peyer's patches in mice.

The spatial distribution of intraepithelial lymphoid cells in follicle-associated and villus epithelium within Peyer's patches was studied quantitatively in Balb/C and CFW/L1 mice. The results were essentially the same for both strains. The distribution of the number of lymphoid cells per segmental length (equal to an average width of an epithelial cell) of dome epithelium was found to be non-random, since it deviated significantly from the theoretical Poisson distribution. Some segments of the dome epithelium, therefore, are lymphocyte-rich and some are lymphocyte-depleted, i.e. they contain either more, or less lymphoid cells than expected from the random distribution. This was in contrast to the distribution in the epithelial layer of the villi, in which the distribution of the number of lymphoid cells per segment followed the Poisson distribution. It was also demonstrated that segments rich in lymphocytes in the dome epithelium occurred in series or clusters. Lymphoid cell clustering was not observed in the villus epithelium. Possible mechanisms responsible for the non-random spatial distribution of lymphoid cells within the dome epithelium of the mouse Peyer's patches are discussed.

Animals↗

PubMed1986

Autoradiographic studies of chromosome replication during the cell cycle of Streptococcus faecium.

Analysis of the distribution of autoradiographic grains around cells of Streptococcus faecium which had been either continuously or pulse-labeled with tritiated thymidine (mass doubling time, 90 min) showed a non-Poisson distribution even when the distribution of cell sizes in the populations studied was taken into account. These non-Poisson distributions of grains were assumed to reflect the discontinuous nature of chromosome replication. To study this discontinuous process further, we fitted an equation to the grain distribution observed for the pulse-labeled cells that assumed that in any population of cells there were subpopulations in which there were zero, one, or two replicating chromosomes. This analysis predicted an average time for chromosome replication and for the period between completion of rounds of chromosome replication and division of 55 and 43 min, respectively, which were in excellent agreement with estimates made by other techniques. The present investigation extended past studies in indicating that the initiation and completion of rounds of chromosome replication are poorly phased with increases in cell volume and that the amount of chromosome replication may be different in different cell halves.

Autoradiography↗

PubMed2005

Statistical kinematics of axillary nodal metastases in breast carcinoma.

The number of involved lymph nodes in individuals with breast cancer is highly variable, and of both prognostic and therapeutic importance. A statistical description for the frequency distribution of the numbers of involved nodes in an affected population could potentially reveal mechanisms of axillary metastasis, and eventually facilitate predictive models for tumor control and axillary sampling. A meta-analysis of 15 studies involving 24,757 axillary dissections was performed, including conventional dissections, sentinel node dissections and studies of occult metastases. Frequency histograms for the numbers of involved axillary lymph nodes from the populations were tested for clustering and they were fitted, as a first approximation, to a negative binomial distribution. Although the number of involved nodes per individual was quite variable, some individuals sustained more involved nodes than could be expected from a random (Poisson) distribution. The negative binomial distribution, however, provided acceptable descriptions for the distributions of involved nodes in all populations studied. Two mechanisms could explain these observations: (1) an apparent contagion model, where involved nodes seeded further nodal metastases, and (2) a spurious contagion model where the number of involved nodes per individual was randomly (Poisson) distributed and population heterogeneity accounted for the more severe cases. Both models were consistent with the hypothesis that the nodal metastasis is a chance event, with the probability of involvement greatest for nodes contiguous to the primary tumor and proportioned by lymphatic flow.

Biomechanical Phenomena↗

PubMed1995

The frequencies of disease names with the natural language used in the hospital information system.

The statistical behavior of disease names referred by physicians with the natural language in a large hospital information system is little known despite the theoretical and practical interest. To address this issue, we reviewed and investigated the usage-frequencies of 18,274 disease names, 10,288 for outpatient care and 7986 for inpatient care, referred from October 1983 to June 1992 with the notation of the natural language in Japanese by the use of the registration-retrieval system of disease names at Fukui Medical School, Japan. Consequently, we found that the investigated distributions did not conform to the Poisson distribution, but conformed well to the Polya-Eggenberger distribution in both cases of outpatient and inpatient care. It implies that the disease names with the natural language are possibly referred by physicians with some interrelations.

Disease↗