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Random models for margins of a 2 x 2 contingency table and application to pharmacovigilance.

The identification of new adverse drug reactions is often tricky. For a given case, the relationship between drug exposure and symptom occurrence is usually questionable. It could be investigated statistically from a series of drug-event association cases with an independence test between the two variables. Analysing the related 2 x 2 contingency table obviously requires knowledge of its margins. However this information is often not available. We develop a calculation of the P-value by choosing some random models for the unknown margins. Under the hypothesis of independence, a negative binomial distribution for the frequency of the drug-event association cell is obtained, exactly or approximately. This method allows investigation of the causal relationship when some parameters, as incidence of the symptom in the population, are uncertain. An example is presented.

Anticoagulants↗

Interim analyses for monitoring clinical trials that do not materially affect the type I error rate.

Monitoring clinical trials often requires examining the interim findings to see if the sample size originally specified in the protocol will provide the required power against the null hypothesis when the alternative hypothesis is true, and to increase the sample size if necessary. This paper presents a new method, based on the overall response rate, for carrying out interim power evaluations when the observations have binomial distributions, without unblinding the treatment assignments or materially affecting the type I error rate. Simulation study results confirm the performance of the method.

Bias↗

Binary regression with continuous outcomes.

Clinical research often involves continuous outcome measures, such as blood cholesterol, that are amenable to statistical techniques of analysis based on the mean, such as the t-test or multiple linear regression. Clinical interest, however, frequently focuses on the proportion of subjects who fall below or above a clinically relevant cut-off value, as a measure of the risk of disease. The customary approach to analyse such data is to dichotomize the continuous outcome measure and use statistical techniques based on binary data and the binomial distribution. In this paper, we use a parametric approach and the framework of generalized linear models to fit various regression models, including the logistic, on the basis of the original continuous outcome. We consider the Gaussian and the three-parameter log-normal distributions for the continuous outcome, assessing both precision and bias under various conditions. In simulation analyses, we find that we are unable to fit some of the samples with the 'dichotomous' approach, but we can with the 'continuous' approach, and that the latter yields estimates between 25 and 85 per cent more efficient than the former. We illustrate the method, programmed using GLIM macros, with data from clinical studies of the risk of hypoxaemia during open thoracic surgery and the risk of nocturnal hypoglycaemia among diabetic children.

Diabetes Mellitus, Type 1↗

Differential properties of GABAergic synaptic connections in rat hippocampal cell cultures.

Based on the effect of prolonged tetanic stimulation (30 Hz, 4 sec), we divided GABAergic synaptic connections in hippocampal cell cultures into two groups: connections facilitated ( approximately 45%) and connections depressed ( approximately 55%) by the tetanic stimulation. In order to reveal possible reasons for the differential effect of the tetanization, we compared several properties of the connections belonging to both groups. We found that, on average, evoked IPSCs in the connections facilitated by the tetanization have a smaller amplitude and larger coefficient of variation (CV) of IPSC amplitude compared to connections depressed by the tetanization. We also estimated quantal parameters for both groups of connections assuming that transmitter release is reasonably described by a binomial distribution. We found that a background release probability (P) is substantially lower in the connections facilitated by the tetanization (P approximately 0.5) than in the connections depressed by the tetanization (P approximately 0.9) and suggest that this difference may underlie the differential effect of the tetanization. We also found that the tetanization induces the opposite effect on connections made by distinct presynaptic neurons with the same postsynaptic cell (convergent connections) in a fraction of postsynaptic neurons studied (3 out of 9). These results support the idea that properties of the presynaptic neuron are of primary importance for the observed differential effect of the tetanization, but they do not exclude a role of the postsynaptic neuron in this effect.

Animals↗

Protein cross-links: universal isolation and characterization by isotopic derivatization and electrospray ionization mass spectrometry.

A general method of unequivocally identifying and obtaining sequence information on cross-linked peptides derived by proteolytic digestion of cross-linked proteins has been developed. The method is based on isotopic labeling of alpha-amino groups with 2, 4-dinitrofluorobenzene (DNFB) coupled with electrospray ionization mass spectrometry. Proteins containing covalent cross-link(s) are reductively methylated to convert lysine residues to dimethyl lysine. The methylated protein is partially hydrolyzed and the liberated alpha-amino termini are derivatized with an equimolar mixture of DNFB and [(2)H(3)]DNFB. Dinitrophenyl (DNP)-labeled peptides may be fractionated into mono- and bis-DNP pools by chromatography on phenyl media. The bis-DNP peptides are further separated by reverse-phase HPLC and analyzed by electrospray ionization mass spectrometry. The molecular ions of cross-linked peptides are unambiguously identified as 1:2:1 triplets in the mass spectrum resulting from the binomial distribution of isotopic label in the bis-DNP derivative. Sequence information can be elucidated from the unique product ion patterns which are generated from in-source fragmentation at an elevated cone voltage. Analysis of the disulfide cross-linked peptide (VTCG)(2) was undertaken as a proof of concept and the generality of the method was demonstrated by isolating and sequencing the isopeptide bond of polyubiquitin.

Amino Acid Sequence↗

Dose-response assessment for developmental toxicity. III. Statistical models.

Although quantitative modeling has been central to cancer risk assessment for years, the concept of dose-response modeling for developmental effects is relatively new. The benchmark dose (BMD) approach has been proposed for use with developmental (as well as other noncancer) endpoints for determining reference doses and reference concentrations. Statistical models appropriate for representing the unique features of developmental toxicity testing have been developed and applied (K. Rai and J. Van Ryzin, 1985, Biometrics 41, 1-9; L. Kupper, C. Portier, M. Hogan, and E. Yamamoto, 1986, Biometrics 42, 85-98; R. Kodell, R. Howe, J. Chen, and D. Gaylor, 1991, Risk Anal. 11, 583-590). Generalizations of those models (designated the RVR, LOG, and NCTR models, respectively) account for the correlations among observations in individual fetuses or implant within litters; the potential for variables other than dose, such as litter size, to affect the probability of adverse outcome; and the possibility of a threshold dose below which background response rates are unaltered. The generalized models were applied to a database of 607 endpoints with significant dose-related increases in response rate. It was determined that the models were generally capable of fitting the observed dose-response patterns, with the LOG model appearing to be superior with respect to fit. A significant contributor to the ability of the LOG model to fit the data was its flexibility with respect to the representation of the dependence of response probability on litter size, a trait not shared by the other two models. Litter size appeared to be a significant covariable for predicting response rates, even when intralitter correlation was accounted for by assuming a beta-binomial distribution for the observations among individual fetuses. In contrast, a threshold dose parameter did not appear to be necessary to adequately describe the observed dose-response patterns. BMD estimates (corresponding to 5% additional risk) from all three models were similar to one another and to BMDs estimated from other, generic dose-response models (not specifically designed for developmental toxicity testing) that modeled average proportion of fetuses affected. The BMDs at the 5% level of risk were similar to no observed adverse effect levels determined by statistical tests of trend. Greater emphasis on and further examination of dose-response modeling for developmental toxicity testing are needed; biologically based approaches that consider the continuum of developmental effects induced in such tests should be encouraged.

Animals↗

Aggregation of entomopathogenic nematodes, heterorhabditis spp. and steinernema spp., among host insects at 9 and 20 degrees C and effects on efficacy

The negative binomial distribution (NBD) with density-dependent k was used to test and describe the distribution of nematodes in Otiorhynchus sulcatus, Galleria mellonella, and Spodoptera exigua at 9 and 20 degrees C. Aggregation was greater in O. sulcatus than in the other two hosts. In case of G. mellonella exposed to the heterorhabditid HF85, the distribution of nematodes in the insects was random. There was only a small effect of low temperature on aggregation; this effect was stronger for O. sulcatus than for the other two hosts. Aggregation of nematodes among insects in a population increases the infection chance of already infected insects and decreases the infection chance of uninfected insects. Consequently, more nematodes will have to penetrate O. sulcatus than G. mellonella or S. exigua to cause the same proportion of infection in a population. The relevance of aggregation of nematodes for control O. sulcatus is discussed. Copyright 1999 Academic Press.

Journal Article↗

The effects of unequal sister chromatid exchange on length of arrays of repeated sequences.

Models of homogenization of repeated sequences by unequal sister chromatid exchange (USCE) assume that no significant changes in array length occur. The effects of successive USCEs on the lengths of arrays of repeated sequences has been examined mathematically and by simulation, assuming misalignment to be greater in longer arrays, a condition necessary for homogenization. The series of duplications and deletions gives a wide, asymmetric variation in copy number. Frequencies follow a binomial distribution, but if misalignment increases with array length, lengths become logarithmically distributed, most arrays being shorter than the original, counterbalanced by a few very long arrays. The median length, which is also the modal length, decreases exponentially or asymptotically. Given a proportional misalignment of a, the median (mode) decreases by a2/2 per unequal crossover. Since drift is a random transmission of available alleles in the population, it follows that fixation of common short arrays is much more probable than fixation of rare long arrays. This process will continue inexorably until each array is too short to undergo further unequal crossing over, and no more variation is generated. The number of unequal crossovers required by some published models of homogenization would almost certainly cause dramatic reduction in number, or complete loss, of repeats. Frequent unequal sister chromatid exchanges are not compatible with survival of arrays unless counteracted by an independent amplification mechanism or selection, so are unlikely to be important as a long-term homogenization mechanism in non-essential repeated sequences.

DNA↗

A probabilistic model for ligand-cytoskeleton transmembrane adhesion: predicting the behavior of microspheres on the surface of migrating cells.

A theoretical model describing the attachment and cytoskeletal coupling of microspheres to the dorsal surface of motile cells was developed. Integral membrane receptors beneath a ligand-coated microsphere are allowed to be either free, attached to the microsphere, bound to the rearward moving actin network, or linked to both the bead and the cytoskeleton, and to switch between these four states. The binding transitions being modeled as chemical reactions governed by rate constants taken from literature, the chance for a receptor to be in each binding state over time is obtained by solving mass-balance equations for the probability functions. The population of n such receptors beneath the microsphere is accounted for by a binomial distribution for each state. Adhesion and transmembrane coupling (resulting in microsphere transport) being defined by a minimal number of ligand-receptor and receptor-cytoskeleton bonds, respectively, the probabilities of attachment and transport of the microsphere over time are expressed in terms of state probability distributions. It is found that increasing the ligand density raises the attachment and transport probabilities, in good quantitative agreement with recent experiments using optical tweezers and accurate position tracking. Increasing the bead size does not affect attachment, but raises the transport probability with a marked transition for bead diameter around 100 nm, as for experimental data. Increasing the restraining force decreases the transport probability, probably by inducing a rupture of receptor-cytoskeleton bonds. This study thus provides a framework that helps understand the process of cortical flow associated with cell locomotion.

Animals↗

Chemical modification patterns of active and inactive as well as procapsid-bound and unbound DNA-packaging RNAof bacterial virus Phi29.

During replication, the lengthy genome of dsDNA viruses is translocated with remarkable velocity into the limited space within the preformed procapsid. We previously found that a viral-encoded RNA (pRNA) played a key role in bacterial virus phi29 DNA translocation. Design of mutant pRNA sets containing two and three inactive mutant pRNAs, respectively, led to the conclusion that the stoichiometry of pRNA in DNA packaging is the common multiple of 2 and 3. Together with studies using binomial distribution of mutant and wild-type pRNA, it has been confirmed that six pRNAs of phi29 form a hexagonal complex to drive the DNA translocating machine. These findings have brought about commonality between viral DNA packaging and other universal DNA/RNA-riding processes including DNA replication and RNA transcription. Chemical modification was used to compare the structures of active and inactive as well as free and procapsid-bound pRNA. Our results explain why certain pRNA mutants are inactive in DNA packaging while remaining competent in procapsid binding, since the mutations were located in a domain involved in DNA translocation that is dispensable for procapsid binding. A mutant pRNA that had reduced procapsid binding was revealed to have a structural alteration within the procapsid-binding region that may account for the binding deficiency. Chemical probing of procapsid-bound pRNA revealed a large area of protection, while a 3-base bulge, C(18)C(19)A(20), was accessible to chemicals. A pRNA with a deletion of this 3-base bulge was fully competent to form dimers, bind procapsids, and inhibit phi29 virion assembly in vitro; however, its activity in DNA packaging and virion assembly was completely lost. The results suggest that this bulge is not involved in procapsid binding but may interact with other DNA-packaging components. A computer model showing the location of the CCA bulge was presented.

Bacillus Phages↗

Transient analysis of a chemical synaptic transmission.

The statistical dynamics of an impulse induced quanta turnover is studied by means of a nonstationary stochastic model--double barrier synapse--resulting from a previously developed mathematical theory of chemical synaptic transmission. An essential aspect of nonstationarities of the model is that the interpool quanta transfers follow binomial distribution at impulse arrival time, while in the absence of stimulation they obey Yule-Furry statistics. Under a variety of conditions, corresponding to those in actual experiments, the transient behaviour of the model is simulated and analysed in detail. As a result, the quantitative description of immediate and delayed components of synaptic action is introduced. If simulations of quantal fluctuations are performed numerically, then for the treatment of dynamic regularities, besides numerical procedures, an analytical method of envelopes is developed. It is supported by the theorems which reduce behaviour of the double-barrier synapse to the super-position of simpler solutions for single-barrier systems. With short-term facilitation quantitative analysis and simulations, the synaptic resonance phenomenon is theoretically predicted: different resonant frequencies are found at different levels of facilitation. The importance of this phenomenon treated as a clue to the information processing capabilities of a chemical synapse is discussed.

Animals↗

Properties of single- and double-barreled Cl channels of shark rectal gland in planar bilayers.

Chloride channels from the apical plasma membrane fraction of rectal gland of Squalus acanthias were characterized by incorporation into planar bilayers in the presence of cAMP-PK/ATP. In a total of 80 bilayer preparations, 21 Cl-selective channels were observed as single channels and 13 as pairs. This was a significantly greater number of double Cl channels than expected from a binomial distribution. The double Cl channels were divided into two groups based on kinetic and voltage-dependent behavior. One group had properties identical to the single channels (gb1) while the other was consistent with a double-barreled channel (gb2) with coordinated activity between proto-channels. The single-channel slope conductances of gb1 and gb2 from -60 to +20 mV with a 250/70 mM KCl gradient were 41 and 75 pS, respectively. With symmetrical 250 mM KCl, the I-V relation of gb1 showed outward rectification with 47.8 +/- 6.6 pS at cis negative potentials and 68.9 +/- 6.1 pS at cis positive potentials. gb1 was open from 70 to 95% at all electrochemical potentials from -80 to +40 mV. gb2 was steeply voltage dependent between -80 and -20 mV. Both gb1 and gb2 were insensitive to Ca (from 100 nm to 1 microM), blocked by 0.1 mM DIDS and highly selective for chloride. These data suggest that double-barreled Cl channels are related to the family of small, outwardly rectifying Cl channels of epithelial membranes.

4,4'-Diisothiocyanostilbene-2,2'-Disulfonic Acid↗

Analysis, classification, and coding of multielectrode spike trains with hidden Markov models.

It is shown that hidden Markov models (HMMs) are a powerful tool in the analysis of multielectrode data. This is demonstrated for a 30-electrode measurement of neuronal spike activity in the monkey's visual cortex during the application of different visual stimuli. HMMs with optimized parameters code the information contained in the spatiotemporal discharge patterns as a probabilistic function of a Markov process and thus provide abstract dynamical models of the pattern-generating process. We compare HMMs obtained from vector-quantized data with models in which parametrized output processes such as multivariate Poisson or binomial distributions are assumed. In the latter cases the visual stimuli are recognized at rates of more than 90% from the neuronal spike patterns. An analysis of the models obtained reveals important aspects of the coding of information in the brain. For example, we identify relevant time scales and characterize the degree and nature of the spatiotemporal variations on these scales.

Animals↗

Centromeric proteins recognized by CREST sera and meiotic chromosome segregation.

Analysis of the peptides recognized by CREST sera was carried out in different mouse tissues and cells, including spermatozoa. In all cases, a polypeptide of Mr = 18,000 was recognized by the sera and occasionally two other proteins of Mr = 80,000 and Mr = 140,000 were observed after immunoblotting of nuclear proteins. In both early and late spermatids, centromeric staining was observed after incubation and immunofluorescence with CREST sera. After detergent treatment, it was even possible to detect centromeric staining in mature spermatozoa. In spermatid cells, the immunofluorescent pattern presented a binomial distribution of the number of fluorescent spots, with a mean value around half of the haploid number of chromosomes. Since this pattern is the result of chromosome segregation after meiosis II, our data suggest that this centromeric peptide is not directly implicated in the chromosome segregation process. On the other hand, the distribution of spots after immunofluorescence suggests a different organization of centromeric components in meiosis I and meiosis II.

Animals↗

Small numbers in mutagenicity tests.

Experimental control material for statistical analysis of the results of the micronuclei test in the mouse (NMRI strain) and the Chinese hamster and for the host-mediated assay in the mouse (NMRI strain) using auxotrophic bacterial strains are presented. The binomial distribution of the micronuclei makes it possible to analyse the sample size according to the formula of Cochran and Cox (1957). For the host-mediated assay, the experimental principles are given which make it possible to evaluate the results obtained even with a weakly mutagenic, unknown substance. Critical points in comparative tests are not only the methodological questions, but also pharmacokinetic problems of the substance being tested which can only be clarified in the species used for the mutagenicity test. If this is ignored then even experimentally based findings can only be recorded as speculations.

Animals↗

Analysis of evoked and spontaneous quantal release at high pressure in crustacean excitatory synapses.

The cellular mechanisms underlying the effect of high pressure on synaptic transmission were studied in the opener muscle of the lobster walking leg. Excitatory postsynaptic currents (EPSCs) were recorded using a loose macropatch-clamp technique at normal pressure and 3.5, 6.9 MPa helium pressure. Responses of the single excitatory axon could be grouped into two types: low-yield (L) synapses exhibiting small EPSCs with a considerable number of failures, and high-yield (H) synapses having larger EPSCs with very few failures. High pressure reduced the average EPSC amplitude in all synapses and shifted their amplitude histograms to the left by decreasing the quantal content (m) without changing their quantum current (q). A binomial distribution fit of EPSC amplitudes revealed that high pressure greatly decreased n, the number of available active zones, but the effect on p, the probability of release for each zone, was not consistent. Many of the spontaneous miniature EPSCs (mEPSCs), observed only in L-type synapses, were "giant" (size = 2-5 q). High pressure increased the frequency of the giant mEPSCs but had little effect on their amplitude histogram. High pressure depressed evoked synaptic transmission by modulating the presynaptic quantal release parameters, but concomitantly enhanced spontaneous quantal release by an unknown mechanism.

Air Pressure↗

Characterization of superoxide dismutase (SOD-1 and SOD-2) activities in inbred mice: evidence for quantitative variability and possible nonallelic SOD-1 polymorphism.

Liver Cu/Zn (SOD-1) and Mn (SOD-2) superoxide dismutase activities were determined in 12 inbred mouse lines. SOD-2 activity varied from 5 to 8 U/mg protein but was never more than 5% of the total. SOD-1 activity varied from 112 (SJL/J) to 155 (RF/J) U/mg protein, with the 12 strains falling into three activity classes. No correlation between SOD-1 activity and H-2 histocompatibility phenotype was observed, i.e., these two loci do not appear linked as previously suggested [Novak, R., Bosze, Z., Matkovics, B. and Fachet, J. (1980). Science 207:86]. Several tissues in all strains exhibited three SOD-1 charge electromorphs which did not differ in relative proportions between strains or tissues. The pI values of these three isozymes were 4.0, 4.5, and 5.0, respectively. The pI value of SOD-2 was 7.7. Both SOD-1 and SOD-2 were sensitive to CHCl3/EtOH extraction, but this sensitivity was not electromorph specific. Quantitation of the SOD-1 isozymic pattern indicated that the electromorphs were present at a ratio of 1:6:23 in order of increasing pI. Fitting of these data to a binomial distribution showed that they were consistent with the presence of two SOD-1 subunits (chains) of unequal pI. The mole fractions of the two chains were calculated to be 0.14 (lower-pI chain) and 0.86 (higher-pI chain). Since the mice used were highly inbred, this pattern could be due to unequal rates of transcription of linked, nonallelic SOD-1 loci, although other explanations are possible. The activity differences between SJL/J and RF/J appear large enough and the data precise enough to make genetic studies on the control of SOD-1 expression in the mouse practicable.

Animals↗

Methodology and results of a survey of adverse reactons to a drug in private practice.

A survey of tolerance of a drug, determined in private practice under "naturalistic" conditions by 591 physicians, and involving 22277 patients is presented. The procedure used in private practice to gather systematic information about reactions to the drug involved a system of data sheets with detachable cards for optical reading and computer analysis. The survey was conducted under the responsiblity at regional level of a team of scientific coordinators-hospital pharmacologists and poison control centres. Possible side effects were noticed in 13,82% of patients, a figure similar to known nocebo reactions. Tolerance was significantly related to sex, age, weight, geographical area, duration of treatment, association with other durgs and therapeutic result. When related to individual physicians, the overall number of side effects and the frequency of three of them in particular did not follow a binomial distribution; the rate of adverse reactions was significantly related to the number of years of practice of the physicians.

Adult↗