SEARCH · Search PubMed

Results for “Poisson Distribution”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 541 records · Page 30Linked to original sources

PubMed2004

Shuffled antibody libraries created by in vivo homologous recombination and yeast surface display.

Homologous recombination in yeast can be exploited to reliably generate libraries of >10(7) transformants from a pool of PCR products and a linearized plasmid vector. Homology in the PCR insertion products drives shuffling of these genes in vivo by yeast homologous recombination. Two scFvs that share 89.8% homology were shuffled in vivo by homologous recombination, and chimeric genes were generated regardless of whether or not one of the scFv PCR products lacked 5' homology to the cut vector and the second scFv PCR product lacked 3' homology to the cut vector, or both PCR products had both 5' and 3' homology to the cut vector. A majority of the chimeras had single crossovers; however, double and triple crossovers were isolated. Crossover points were evenly distributed in the hybrids created and homology of as little as two nucleotides was able to produce a chimeric clone. The numbers of clones isolated with a given number of crossovers was approximated well by a Poisson distribution. Transformation efficiencies for the chimeric libraries were of the order of 10(4)-10(5) transformants per microgram of insert, which is the same order of magnitude as when a single PCR product is inserted alone into the display vector by homologous recombination. This method eliminates ligation and Escherichia coli transformation steps of previous methods for generating yeast-displayed libraries, requires fewer PCR cycles than in vitro DNA shuffling and, unlike site-specific recombination methods, allows for recombination anywhere that homology exists between the genes to be recombined. This simple technique should prove useful for protein engineering in general and antibody engineering, specifically in yeast.

DNA Shuffling↗

PubMed1996

Comorbid occurrence of cholelithiasis and gastrointestinal cancer.

OBJECTIVE: To test whether gallstone disease represents a general risk factor for gastrointestinal cancer. METHODS: The comorbid occurrences of cholelithiasis or choledocholithiasis with cancers of the biliary tract, pancreas, small and large intestine were analysed in a population of 3.41 million military veterans who were discharged from VA hospitals distributed throughout the USA between 1981 and 1993. Comorbidity was calculated as the ratio between the observed and expected number of hospitalized veterans with cholelithiasis plus cancer. A 95% confidence interval was calculated based on the Poisson distribution of the observed number of patients with comorbidity. RESULTS: In cholelithiasis, the ratio of comorbid occurrence with biliary cancer was 4.59 (4.06-5.31). In choledocholithiasis, the ratio of comorbid occurrence with biliary cancer was 9.31 (7.20-11.84) and with pancreatic cancer 4.34 (3.80-4.94). These ratios remained significant when the analyses were confined to cholelithiasis or choledocholithiasis documented before the first diagnosis of cancer. The ratios of the comorbid occurrences between cholelithiasis and cancers of the small or large intestine were only significant when total comorbid occurrences were analysed, but vanished in the analysis restricted to cholelithiasis or choledocholithiasis documented before the first diagnosis of cancer. CONCLUSION: The occurrence of gallstones represents a risk factor for pancreaticobiliary cancer, but not cancers involving other parts of the gastrointestinal tract. This association appears particularly strong in patients with choledocholithiasis.

Cholelithiasis↗

PubMed1978

Consequences of helminth aggregation for the dynamics of schistosomiasis.

The distribution of schistosome worms among their human hosts is not random but aggregated. The consequences of introducing aggregation into models of schistosomiasis transmission, especially that of Macdonald, are explored. There are two possibilities for aggregation, with the sexes distributed either independently or together. Both have profound though differing effects on the breakpoint concept, which is largely destroyed when the sexes are aggregated together, and Macdonald's epidemiological conclusions are not robust to variations from the Poisson distribution. The conclusion from his model that if schistosome densities in man are reduced appropriately the infection will spontaneously proceed to extinction even in the presence of conditions suitable for transmission, is also not therefore robust.

Humans↗

PubMed2000

Role in tumorigenesis of silent mutations in the TP53 gene.

Over 10,000 mutations in the TP53 suppressor gene have been recorded in the International Agency for Research on Cancer (IARC) tumor data base. About 4% of these mutations are silent. It is a question whether these mutations play a role in tumor development. In order to approach this question, we asked whether the reported silent mutations are randomly distributed throughout the TP53 gene. The p53 data base was searched exon by exon. From the frequency of codons with no silent mutations, the average number of silent mutations per codon for each exon was calculated using the Poisson distribution. The results indicate the distribution to be non-random. About one-third of all silent mutations occur in "hot-spots" and after subtraction of these hot-spots, the remaining silent mutations are randomly distributed. In addition, the percentage of silent mutations among the total in the silent mutation hot-spots is close to that expected for random mutation. We conclude that most of the silent mutations recorded in tumors play no role in tumor development and that the percentage of silent mutation is an indication of the amount of random mutation during tumorigenesis. Silent mutations occur to a significantly different extent in different tumor types. Tumors of the esophagus and colon have a low frequency of silent mutations, tumors of the prostate have a high frequency.

Codon↗

PubMed1964

PROBABILITY OF OCCURRENCE OF DISCRETE POTENTIAL WAVES IN THE EYE OF LIMULUS.

Discrete potential waves can be recorded from cells in the eye of Limulus both in darkness and in dim illumination. With constant illumination the frequency of these waves is linearly related to light intensity and the distribution of intervals between waves follows an exponential function. The latency of waves evoked by short flashes of light is usually long and variable and the number of waves evoked by a flash varies randomly, obeying approximately a Poisson distribution. The results of experiments with flashes of light have been compared with the predictions derived from the hypotheses that one, two, or three quanta of light are required for production of one wave. The agreement of the data with the theory can be considered acceptable for the "one quantum" hypothesis, is less satisfactory for the "two quanta" hypothesis, and is very poor for the "three quanta" hypothesis.

Adaptation, Ocular↗

PubMed1983

Frequencies of restriction sites.

Restriction sites or other sequence patterns are usually assumed to occur according to a Poisson distribution with mean equal to the reciprocal of the probability of the given site or pattern. For situations where non-overlapping occurrences of patterns, such as restriction sites, are the objects of interest, this note shows that the Poisson assumption is frequently misleading. Both the case of base composition (independent bases) and of dinucleotide frequencies (Markov chains) are treated. Moreover, a new technique is presented which allows treatment of collections of patterns, where the departure from the Poisson assumption is even more striking. This later case includes double digests, and an example of a five enzyme digest is included.

Base Sequence↗

PubMed1979

Preaggregative cell motion in Dictyostelium.

The motions of a large number (495) of preaggregative D. discoideum NC-4 cells in sparse fields are recorded on time-lapse film and analysed using a specially constructed computer graphics system. All films are produced under a standard set of conditions, so that the range of cell behaviours under given conditions can be characterized. The mean velocity of pre-aggregative D. discoideum NC-4 is 7.19 micrometers/min. The mean velocity time course has a significant early peak at about 3 h. The distribution of mean velocities is fairly broad with a long high velocity tail. A modified random walk model using the parameters diffusion constant and persistence time describes well the changes in cell direction with time. Persistence can be described as an exponentially distributed 'memory' of movement direction, with a mean of 4.89 min. High velocity cells never have long persistence times, and persistence time shows no relationship with age. A nearest neighbour model of cell spacing shows that cells are randomly (Poisson) distributed at low densities. Measurements of cell contacts are compared to a simple model of contact frequency based on the kinetic theory of gases to show that cells at low densities have an affinity for making collisions. The length of contact durations is indicative of some mechanical adhesion between cells, and cells in contact move significantly though not dramatically slower. A cross-correlation analysis shows that the various parameters of motion are significantly interrelated in numerous ways. Finally mutants and strains related to D. discoideum NC-4 exhibit a number of new behaviours, suggesting that motion is a distinctive characteristic of cell type.

Agglutination↗

PubMed2005

Reporting incidence from a surveillance system with an operational case definition of unknown predictive value positive.

When reporting incidence rate estimates for relatively rare health conditions, associated case counts are often assumed to follow a Poisson distribution. Case counts obtained from large-scale electronic surveillance systems are often inflated by the presence of false positives, however, and adjusted case counts based on the results of a validation sample will have variances which are hyper-Poisson. This paper presents a simple method for constructing interval estimates for incidence rates based on case counts that are adjusted downward using an estimate of the predictive value positive of the surveillance case definition.

Journal Article↗

PubMed2006

Correspondence patterns: mechanisms and models of human dynamics.

A stochastic queue model of human behaviour developed on the basis of the distribution of timing of tasks, as studied in a sample of e-mail messages at a university and in the written correspondence of Albert Einstein, may not be as simple as it seems. Although this model reproduces the apparently non-Poisson distribution of correspondence delays, its interpretation is more complicated than suggested by Barabási, who claims that humans execute their tasks based on some perceived priority, setting up queues that generate very uneven waiting-time distributions for different tasks. Such an explanation is intuitively appealing in the context of the queue metaphor, but does not exclude other mechanisms. By attributing delays in the correspondence to task priorities, this explanation ignores two important classes of mechanism that also contribute to the apparent distributions of task timings: the semantic content of an individual's correspondence and the social context in which this correspondence occurs.

Algorithms↗

PubMed2002

Normal value for the direct micronucleus test on peripheral blood mononuclear cells from healthy donors.

OBJECTIVE: To obtain the normal value of micronuclei in peripheral blood mononuclear cells. STUDY DESIGN: We screened 300 blood samples for micronucleated cells. Samples from donors who smoked, were ill or lived in a polluted area were excluded. From each sample, 500 swollen mononuclear leukocytes were screened with a light microscope, using 400x magnification. A frequency distribution of micronucleated cell number was made, and the mean of micronucleated cell number was calculated. Further, the data were tested for the type of probability distribution using the test of goodness of fit, and the parameters were estimated. RESULTS: Of the 300 samples, 203 were excluded and 97 analyzed. In the 97 samples, the mean of micronucleated cells (from 500 cells screened) was 0.59; the data followed a Poisson distribution. The 95% confidence limits were .45 and .76. CONCLUSION: The normal value in unexposed individuals is .59 micronucleated cells per 500 cells.

Blood Donors↗

PubMed1989

A study of ten families of transposable elements on X chromosomes from a population of Drosophila melanogaster.

Data were collected on the distribution of ten families of transposable elements among fourteen X chromosomes isolated from a natural population of Drosophila melanogaster, by means of in situ hybridization to polytene chromosomes. It was found that, with the exception of roo, the copy number per chromosome followed a Poisson distribution. There was no evidence for linkage disequilibrium, either within or between families. Some pairs of families of elements were correlated with respect to the identity of the sites that were occupied in the sample, although there was no evidence for a correlation with respect to the sites at which elements attained relatively high frequencies. Elements appeared to be distributed randomly along the distal part of the X chromosome. There was, however, a strong tendency for elements to accumulate at the base of the chromosome. Element frequencies per chromosome band were generally low, except at the base of the chromosome where bands in subdivisions 19E and 20A sometimes had high frequencies of occupation. These results are discussed in the light of models of the population dynamics of transposable elements. It is concluded that they provide strong evidence for the operation of a force or forces opposing transpositional increase in copy number. The accumulation of elements at the base of the chromosome is consistent with the idea that unequal exchange between elements at non-homologous sites is such a force, although other possibilities cannot be excluded at present. The data suggest that the rate of transposition per element per generation is of the order of 10(-4), for the elements included in this study.

Animals↗

PubMed2001

Evaluation of eight decision rules for low-level radioactivity counting.

In low-level radioactivity measurements, it is often important to decide whether a measurement differs from background. A traditional formula for decision level (DL) is given in numerous sources, including the recent ANSI/HPS N13.30-1996, Performance Criteria for Radiobioassay and the Multi-Agency Radiation Survey and Site Investigation Manual (MARSSIM). This formula, which we dub the N13.30 rule, does not adequately account for the discrete nature of the Poisson distribution for paired blank (equal count times for background and sample) measurements, especially at low numbers of counts. We calculate the actual false positive rates that occur using the N13.30 DL formula as a function of a priori false positive rate a and background Poisson mean mu = rhot, where rho is the underlying Poisson rate and t is the counting time. False positive rates exceed a by significant amounts for alpha < or = 0.2 and mu < 100 counts, peaking at 25% at mu approximately equal to 0.71, nearly independent of alpha. Monte Carlo simulations verified calculations. Currie's derivation of the N13.30 DL was based on knowing a good estimate of the mean and standard deviation of background, a case that does not hold for paired blanks and low background rates. We propose one new decision rule (simply add 1 to the number of background counts), and we present six additional decision rules from various sources. We evaluate the actual false positive rate for all eight decision rules as a function of a priori false positive rate and background mean. All of the seven alternative rules perform better than the N13.30 rule. Each has advantages and drawbacks. Given these results, we believe that many regulations, national standards, guidance documents, and texts should be corrected or modified to use a better decision rule.

Decision Making↗

PubMed1989

Intraurban physician location. New empirical evidence.

This article addresses an issue of continuing interest to social scientists: the spatial distribution of physician services. Although there have been many studies of physician distribution across urban areas and states, there have been few studies, none recent, of physician distribution within urban areas. The paper begins with a review of studies that examine the determinants of intraurban physician location. Following the review the paper offers new estimates of the determinants of intraurban physician location using a maximum-likelihood procedure based on the Poisson distribution. Contrary to previous studies, the results imply that market forces do play a significant role in the spatial distribution of physicians.

Humans↗

PubMed1982

Random distribution of the glucose transporter of human erythrocytes in reconstituted liposomes.

The glucose transporter of human erythrocytes was reconstituted with soybean phospholipids by the freeze-thaw/sonication method and the distribution of the transporter molecules in liposomes was studied. The steady state level of glucose transport in reconstituted liposomes showed saturation when increased amounts of the transporter were used for reconstitution. The saturation curve fitted well to a theoretical curve which was derived assuming a Poisson distribution of the transporter. Freeze-fracture electron micrographs showed random distribution of intramembraneous particles on liposomes, irrespective of liposome size or amount of the transporter added. A detailed study showed a parameter of the distribution (the ratio of transporter to liposome) obtained from the transport measurement can be used for the analysis of the distribution of intramembraneous particles, indicating that most of the molecules seen as particles were active in transport.

Blood Glucose↗

PubMed1993

Epidemiologic analyses of spatial clustering of bovine ephemeral fever outbreaks. I. Application of the negative binomial distribution.

An epidemic that propagates through a population results in a contagious spatial pattern. The incidence per farm of bovine ephemeral fever (BEF) outbreaks in the 22 areas of Fukuoka Prefecture in 1988 was well explained by the negative binomial distribution, which is generally considered, as the clustering of the outbreaks. Furthermore, the clustering was analyzed with three categories of vaccination rate (No. 1-40%, and 40-80%). As a result, the no vaccination and high vaccination rate (41-80%) groups tended to shift to similarly the Poisson distribution. It may be speculated that an insufficient vaccination control of the BEF was influenced with the clustering.

Animals↗

PubMed1984

The circadian distribution of interictal epileptiform EEG activity.

Eighteen continuous 48 h monitoring studies are reported from 17 patients with epilepsy. The numbers of epileptiform discharges over corresponding epochs of the 2 days were significantly positively correlated in 16 studies. However, this was explicable by masking due to the sleep/wake cycle and when waking and sleep were considered separately a minority of studies showed significant correlations. The difference in total 24 h production of discharges between the 2 days ranged from 1.3 to 30.3%, mean 15.1%. The maximum discharge rate in 75% of the studies occurred during sleep; during waking the distribution of discharges was random. Even in the waking state the 0.5 h discharge rate was extremely variable and in few patients could a single 30 min epoch be regarded as a reliable sample of the mean rate over the waking day. The intervals between events showed a Poisson distribution during 9 days and 5 nights, but there was no within-patient consistency between the first and second 24 h period. The occurrence of discharges was periodic significantly more often at night than during the day, but the periodicities did not clearly correspond to the REM cycle. Discharges increased overall during sleep in 14 studies, were unchanged in 2 and decreased in 4. The time of occurrence of maximal discharge rate during sleep was consistent from night I to night II only in patients exhibiting generalized regular spike-wave activity but random in the others. A negative correlation between antiepileptic drug levels and discharge rate was rarely observed.

Adult↗

PubMed2005

On the comparison of FROC curves in mammography CAD systems.

We present a novel method for assessing the performance of computer-aided detection systems on unseen cases at a given sensitivity level. The sampling error introduced when training the system on a limited data set is captured as the uncertainty in determining the system threshold that would yield a certain predetermined sensitivity on unseen data sets. By estimating the distribution of system thresholds, we construct a confidence interval for the expected number of false positive markings per image at a given sensitivity. We present two alternative procedures for estimating the probability density functions needed for the construction of the confidence interval. The first is based on the common assumption of Poisson distributed number of false positive markings per image. This procedure also relies on the assumption of independence between false positives and sensitivity, an assumption that can be relaxed with the second procedure, which is nonparametric. The second procedure uses the bootstrap applied to the data generated in the leave-one-out construction of the FROC curve, and is a fast and robust way of obtaining the desired confidence interval. Standard FROC curve analysis does not account for the uncertainty in setting the system threshold, so this method should allow for a more fair comparison of different systems. The resulting confidence intervals are surprisingly wide. For our system a conventional FROC curve analysis yields 0.47 false positive markings per image at 90% sensitivity. The 90% confidence interval for the number of false positive markings per image is (0.28, 1.02) with the parametric procedure and (0.27, 1.04) with the nonparametric bootstrap. Due to its computational simplicity and its allowing more fair comparisons between systems, we propose this method as a complement to the traditionally presented FROC curves.

Algorithms↗

PubMed1997

Sample size for cohort studies in pharmacoepidemiology.

OBJECT: Cohort studies in pharmacoepidemiology can result in a unique type of study, where subjects have complex types of exposure to drugs (with periods of non-exposure as well). The object of this paper is to explain how to calculate the sample size of such a study. METHOD: It is assumed that adverse events follow Poisson distributions in the two study groups. The null hypothesis is that the two groups have equal rates of disease. Formulae are provided to calculate the sample size required to significantly reject the null hypothesis. Sample size is given as the number of events, rather than the number of subjects entered. In a Poisson study, it is the ratio of the amount of person-years exposure in the two groups that is important to calculate sample size, rather than the actual amounts of exposure (or number of subjects in the study). Some examples are included.

Journal Article↗