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P53 mutations in thyroid carcinoma: tidings from an old foe.

The underlying mechanism leading to carcinogenesis involves genomic instability, likely related to aneuploidy. While p53 as a "guardian of the genome" is an appealing candidate as an initiator of genomic instability, its mutations or deletions usually occur late in the course of tumor progression. P53 may, however, become a target of events initiated by genomic instability. P53 is a transcription factor with multifaceted regulatory functions in the cell cycle, DNA repair and apoptosis. Inactivating p53 mutations have been described in some 50% of human cancers. These mutations are not only important in tumor progression but apparently also in the response of some tumors to chemotherapy and radiation treatment, thus to clinical outcome. P53 mutations are found in 14% of malignant thyroid tumors and are more frequent in poorly differentiated and anaplastic tumors. We have examined the mutation rates of p53 as a measure of genomic instability (hypermutability) of malignant thyroid tumors. We also wondered whether radiation enhances this tendency to genomic instability. To those ends we extracted all available entries from the p53 mutations database (http://www.perso@curies.fr), verified, extended where applicable, and supplemented that information from the original published reports. We were able to locate 100 entries. The distribution of the types of p53 aberrations in thyroid cancer was similar to those in the database as a whole. The silent mutation rate of 20%, not different from the expected 25%, is consistent with a random occurrence of these mutations. This silent mutation rate is 130 times that expected and is 7 times that of the p53 database. Moreover the distribution of p53 mutations is compatible with Poisson's distribution, which, when considered in the context of the silent mutation rates, indicates that p53 is particularly hypermutable in thyroid cancer. Epigenetic deamination of CpG dinucleotides at highly transforming DNA-contact residues is a feature of poorly differentiated tumors and thus associated with tumor progression. The rates of p53 mutations in radiation-related thyroid cancers (15.4%) are similar to those in spontaneously arising tumors, although there was a highly significant heterogeneity (p<0.0005) in the residues mutated in the two tumor sets. None of the residues mutated in radiation-related thyroid cancer involved CpG deamination. Based on the evidence of p53 hypermutability, thyroid cancer appears to exhibit remarkable genomic instability. Spontaneous epigenetic mutational events are involved in tumor progression. While thyroid cancer related to radiation exposure does not increase the rates of p53 mutation, they exhibit mutation at residues not involved in p53/DNA interface.

Carcinoma↗

Cardiovascular mortality focusing on socio-economic influence: the low-risk population of Halland compared to the population of Sweden as a whole.

The aim of the study was to investigate the relationship between mortality from cardiovascular diseases (CVD) and socio-economic status (SES) in Sweden and to estimate to what extent the difference between a province with low mortality and the rest of Sweden was dependent on socio-economic factors. A population-based retrospective study with a historical prospective approach was performed covering a 10-y period in the province of Halland, Sweden, as well as Sweden as a whole. Altogether 1,654,744 men and 1,592,467 women were included, of whom 45,394 men and 43,403 women were from Halland, distributed according to SES. Multivariate analysis with Poisson regression was used. Relative risks with 95% confidence intervals were calculated. Both men and women with a low SES showed a significantly higher risk of death from CVD in Sweden as a whole. The risk was 23% higher for male blue-collar workers and 44% higher for female blue-collar workers when compared to their white-collar counterparts. The level of mortality in Halland was 14% lower compared to the country as a whole when only age was taken into account. When the socio-economic variable was also included, this figure was 8%. The results show the substantial significance of social differences with respect to CVD mortality. The effect of SES seems to be more important than that of geographical conditions when the latter are isolated from socio-economic influence.

Adult↗

Interrelations between three proxies of health care need at the small area level: an urban/rural comparison.

STUDY OBJECTIVE: To examine the relations between geographical variations in mortality, morbidity, and deprivation at the small area level in the south west of England and to assess whether these relations vary between urban and rural areas. DESIGN: A geographically based cross sectional study using 1991 census data on premature limiting long term illness (LLTI) and socioeconomic characteristics, and 1991-1996 data on all cause premature mortality. The interrelations between the three widely used proxies of health care need are examined using correlation coefficients and scatterplots. The distribution of standardised LLTI residuals from a regression analysis on mortality are mapped and compared with the distribution of urban and rural areas. Multilevel Poisson modelling investigates whether customised deprivation profiles improve upon a generic deprivation index in explaining the spatial variation in morbidity and mortality after controlling for age and sex. These relations are examined separately for urban, fringe, and rural areas. SETTING: Nine counties in the south west of England. PARTICIPANTS: Those aged between 0-64 who reported having a LLTI in the 1991 census, and those who died during 1991-1996 aged 0-74. MAIN RESULTS: Relations between both health outcomes and generic deprivation indices are stronger in urban than rural areas. The replacement of generic with customised indices is an improvement in all area types, especially for LLTI in rural areas. The relation between mortality and morbidity is stronger in urban than rural areas, with levels of LLTI appearing to be greater in rural areas than would be predicted from mortality rates. Despite the weak direct relations between mortality and morbidity, there are strong relations between the customised deprivation indices computed to predict these outcomes in all area types. CONCLUSIONS: The improvement of the customised deprivation indices over the generic indices, and the similarity between the mortality and morbidity customised indices within area types highlights the importance of modelling urban and rural areas separately. Stronger relations between mortality and morbidity have been revealed at the local authority level in previous research providing empirical evidence that the inadequacy of mortality as a proxy for morbidity becomes more marked at lower levels of aggregation, especially in rural areas. Higher levels of LLTI than expected in rural areas may reflect different perceptions or differing patterns of illness. The stronger relations between the three proxies in urban than rural areas suggests that the choice of indicator will have less impact in urban than rural areas and strengthens the argument to develop better measures of health care need in rural areas.

Adolescent↗

Nosocomial infection surveillance in a surgical intensive care unit in Spain, 1996-2000: a time-trend analysis.

OBJECTIVE: To establish the occurrence, distribution, and secular time trend of nosocomial infections (NIs) in a surgical intensive care unit (ICU). DESIGN AND SETTING: Follow-up study in a teaching hospital in Spain. METHODS: In May 1995 we established an nosocomial infection surveillance system in our surgical ICU. We collected information daily for all patients who were in the ICU for at least 48 hours (546 patients from 1996 through 2000). We used the Centers for Disease Control and Prevention definitions and criteria for infections. Monthly, we determined the site-specific incidence densities of NIs, the rates of medical device use, and the Poisson probability distribution, which determined whether the case count equalled the number of expected cases (the mean number of cases during the previous year, with extreme values excluded). We compared yearly and monthly infection rates by Poisson regression, using site-specific NIs as a dependent variable and year and month as dummy variables. We tested annual trends with an alternative Poisson regression model fitting a single linear trend. RESULTS: The average rate of catheter-associated urinary tract infections was 8.4 per 1000 catheter-days; that of ventilator-associated pneumonia, 21 per 1000 ventilator-days; and that of central line-associated bloodstream infections, 30 per 1000 central line-days. The rate of urinary tract infections did not change over the study period, but there was a trend toward decreases in the rates of central line-associated bloodstream infections and ventilator-associated pneumonia. CONCLUSION: An NI surveillance and control program contributed to a progressive decrease in NI rates.

Catheterization, Central Venous↗

Determination of the carrier frequency of the common GJB2 (connexin-26) 35delG mutation in the Greek Cypriot population.

OBJECTIVE: Mutations in the GJB2 (connexin-26) gene are responsible for more than half of all cases of prelingual recessive inherited non-syndromic deafness in Europe. One specific mutation 35delG, accounts for up to 70% of the mutations detected in European populations and is one of the most frequent disease mutations identified so far. The aim of this study is to determine the percentage of carriers of this mutation in the Greek Cypriot population. METHODS: Genomic DNA was isolated from a total of 405 healthy unrelated Greek Cypriot adults. Screening for the frameshift 35delG mutation was performed by using an allele-specific PCR protocol. Moreover, using the Poisson probability distribution, we compared the carrier frequencies of the 35delG mutation of the Greek Cypriot population to the various European and Middle Eastern populations. RESULTS: The carrier frequency in the Greek Cypriot population was estimated to be 2.5% and is similar to that observed in other European populations. The variance estimate for 35delG mutation produces slightly wider intervals with the Poisson model when compared with Binomial probability variance estimate.

Adult↗

Quantitative risk assessment of noroviruses in drinking water based on qualitative data in Japan.

Noroviruses are one of the major causes of viral gastroenteritis in Japan. A quantitative risk assessment was conducted to evaluate the health risk caused by this virus in drinking water. A Monte Carlo analysis was used to calculate both the probability of infection and the disease burden using disability-adjusted life years (DALYs). The concentration of noroviruses in tap water was estimated based on qualitative data and a most probable number (MPN) method with an assumed Poisson lognormal distribution. This numerical method was evaluated using two sets of available count data of Cryptosporidium: that collected from a river and that found in tap water in Japan. The dose-response relationships for noroviruses were estimated using assumed ID50 (10 or 100). The annual risk was higher than the US-EPA acceptable level (10(-4) [infection/ person-year]) but around the WHO level (10(-6) [DALYs/ person-year]). As suggested by others, since microbial concentrations are generally lognormally distributed, the arithmetic mean was directly related to the annual risk, suggesting that the arithmetic mean is more useful in representing the degree of microbial contamination than the geometric mean.

Animals↗

A new elastographic method for estimation and imaging of lateral displacements, lateral strains, corrected axial strains and Poisson's ratios in tissues.

A major disadvantage of the current practice of elastography is that only the axial component of the strain is estimated. The lateral and elevational components are basically disregarded, yet they corrupt the axial strain estimation by inducing decorrelation noise. In this paper, we describe a new weighted interpolation method operating between neighboring RF A-lines for high precision tracking of the lateral displacement. Due to this high lateral-tracking precision, quality lateral elastograms are generated that display the lateral component of the strain tensor. These precision lateral-displacement estimates allow a fine correction for the lateral decorrelation that corrupts the axial estimation. Finally, by dividing the lateral elastogram by the axial elastogram, we are able to produce a new image that displays the distribution of Poisson's ratios in the tissue. Results are presented from finite-element simulations and phantoms as well as in vitro and in vivo experiments.

Blood Flow Velocity↗

Numerical solutions for patterns statistics on Markov chains.

We propose here a review of the methods available to compute pattern statistics on text generated by a Markov source. Theoretical, but also numerical aspects are detailed for a wide range of techniques (exact, Gaussian, large deviations, binomial and compound Poisson). The SPatt package (Statistics for Pattern, free software available at http://stat.genopole.cnrs.fr/spatt) implementing all these methods is then used to compare all these approaches in terms of computational time and reliability in the most complete pattern statistics benchmark available at the present time.

Algorithms↗

Possibility of multiquantal transmission at single inhibitory synapse in cultured rat hippocampal neurons.

Miniature, spontaneous and evoked inhibitory postsynaptic currents were studied using the whole-cell patch-clamp technique on synaptically connected cultured hippocampal neurons, at a holding potential of -75 mV. All experiments were done in tetrodotoxin-containing solution to exclude an action potential generation. Spontaneous miniature inhibitory postsynaptic currents were observed in Ca2+-free solution. The distribution of miniature inhibitory postsynaptic currents was skewed to larger current amplitudes and could be fitted reliably by one Gaussian with the mean at 10.0 +/- 1.2 pA (n = 7). Spontaneously occurring whole-cell spontaneous inhibitory postsynaptic currents were recorded in physiological solution (Ca2+ 2 mM). The average amplitude of spontaneously occurring currents depended on membrane potential and reversed at -18 +/- 5 mV (n = 5). The amplitude distribution of spontaneous inhibitory postsynaptic currents had one peak clearly detectable with the mean of 20.0 +/- 2.0 pA (n = 6) or 10.0 +/- 2.0 pA (n = 2). Inhibitory postsynaptic stimulus-evoked currents arose in responses to gradual activation of neurotransmitter release by direct extracellular electrical stimulation of a single presynaptic bouton by short depolarizing pulses. The current-voltage relation of the averaged amplitudes of evoked inhibitory postsynaptic currents was linear and reversed at potential predicted by the Nernst equation for corresponding intra- and extracellular Cl- concentrations. The time-course of decay of miniature, spontaneous and evoked inhibitory postsynaptic currents was fitted by a sum of two exponents and their time-constants were the same in the range of standard deviation. The stimulus-evoked inhibitory postsynaptic currents fluctuated with regard to the discrete aliquot values of their peak amplitudes in all the investigated synapses from a measurable minimum of about 8 pA to 200 pA. The evoked inhibitory postsynaptic currents were assumed as superimposition of statistically independent quantal events. Fitting amplitude histograms of evoked inhibitory postsynaptic currents with several Gaussian curves resulted in peaks that were equidistant with the mean space of 20 +/- 3 pA (n = 10), which was assumed as one quantum (quantum size) to construct the Poisson's distribution. A possibility of simultaneous multiquantal release at single inhibitory synapses of rat hippocampal neurons was discussed.

Algorithms↗

Modelling of discrete spatial variation in epidemiology with SAS using GLIMMIX.

SAS provides a macro GLIMMIX, which can be used for modelling of discrete spatial variation in epidemiological studies, where data are aggregated into small areas such as municipalities or postcode sectors. The purpose of these models is primary to examine to what extent unmeasured spatially correlated variables can explain the outcome of interest. Some necessary additional code is proposed for this macro implementing some of the most used models for analysing and exploring spatial variation, in for example Poisson and logistic regression: Gaussian intrinsic conditional autoregression and spatial multiple memberships models originated from multilevel models. The code is illustrated by analysing the well-known Scottish lip cancer dataset with GLIMMIX and the results are compared with a Markov chain Monte Carlo approach. The code gives epidemiologists and bio-statisticians an immediate tool for analysing discrete spatial models in a familiar statistical software package.

Biometry↗

Comparative binding energy analysis of the substrate specificity of haloalkane dehalogenase from Xanthobacter autotrophicus GJ10.

Comparative binding energy (COMBINE) analysis was conducted for 18 substrates of the haloalkane dehalogenase from Xanthobacter autotrophicus GJ10 (DhlA): 1-chlorobutane, 1-chlorohexane, dichloromethane, 1,2-dichloroethane, 1,2-dichloropropane, 2-chloroethanol, epichlorohydrine, 2-chloroacetonitrile, 2-chloroacetamide, and their brominated analogues. The purpose of the COMBINE analysis was to identify the amino acid residues determining the substrate specificity of the haloalkane dehalogenase. This knowledge is essential for the tailoring of this enzyme for biotechnological applications. Complexes of the enzyme with these substrates were modeled and then refined by molecular mechanics energy minimization. The intermolecular enzyme-substrate energy was decomposed into residue-wise van der Waals and electrostatic contributions and complemented by surface area dependent and electrostatic desolvation terms. Partial least-squares projection to latent structures analysis was then used to establish relationships between the energy contributions and the experimental apparent dissociation constants. A model containing van der Waals and electrostatic intermolecular interaction energy contributions calculated using the AMBER force field explained 91% (73% cross-validated) of the quantitative variance in the apparent dissociation constants. A model based on van der Waals intermolecular contributions from AMBER and electrostatic interactions derived from the Poisson-Boltzmann equation explained 93% (74% cross-validated) of the quantitative variance. COMBINE models predicted correctly the change in apparent dissociation constants upon single-point mutation of DhlA for six enzyme-substrate complexes. The amino acid residues contributing most significantly to the substrate specificity of DhlA were identified; they include Asp124, Trp125, Phe164, Phe172, Trp175, Phe222, Pro223, and Leu263. These residues are suitable targets for modification by site-directed mutagenesis.

Binding Sites↗

Demand for traditional medicine in Taiwan: a mixed Gaussian-Poisson model approach.

Hurdle count models are used to examine the participation and consumption decisions in Chinese medicine use. Motivated by a household production model, a second censoring mechanism is introduced into existing single-hurdle models, and the resulting specification accommodates conscientious abstainers, as well as economic non-consumers, and admits excessive zeros in the sample. In contrast to previous studies that found few predictors, empirical results based on a Taiwanese national sample suggest that Western medicine is a gross substitute to Chinese medicine, and both time price and money price play more important roles than income. Insurance, lifestyle and demographics also determine the use of Chinese medicine.

Adult↗

Noise correlation length effects on a Morris-Lecar neural network.

The role of spatially correlated stochastic perturbations on a Morris-Lecar neural network subject to an aperiodic subthreshold signal is analyzed in detail. Our results suggest that optimum signal-to-noise ratios can be obtained for two critical noise intensities due to the interplay of the subthreshold Poisson process and the correlated Gaussian forcing. For the second peak, most of the cells are periodically excited, the information transfer is enhanced, and a collective behavior develops measured in terms of the averaged activity of the network. The maximum signal-to-noise ratio increases with the correlation length, although it saturates for global coupling. It was found that there is a range of mean frequencies of the subthreshold signal that increases the signal-to-noise ratio output.

Animals↗

Neural populations can induce reliable postsynaptic currents without observable spike rate changes or precise spike timing.

Fine temporal patterns of firing in much of the brain are highly irregular. In some circuits, the precise pattern of irregularity contains information beyond that contained in mean firing rates. However, the capacity of neural circuits to use this additional information for computational purposes is not well understood. Here we employ computational methods to show that an ensemble of neurons firing at a constant mean rate can induce arbitrarily chosen temporal current patterns in postsynaptic cells. If the presynaptic neurons fire with nearly uniform interspike intervals, then current patterns are sensitive to variations in spike timing. But irregular, Poisson-like firing can drive current patterns robustly, even if spike timing varies by tens of milliseconds from trial to trial. Notably, irregular firing patterns can drive useful patterns of current even if they are so variable that several hundred repeated experimental trials would be needed to distinguish them from random firing. Together, these results describe an unrestrictive set of conditions in which postsynaptic cells might exploit virtually any information contained in spike timing. We speculate as to how this capability may underlie an extension of population coding to the temporal domain.

Algorithms↗

Changes in stability upon charge reversal and neutralization substitution in staphylococcal nuclease are dominated by favorable electrostatic effects.

Single site mutations that reverse or neutralize a surface charge were made at 22 ionizable residues in staphylococcal nuclease. Unfolding free energies were obtained by guanidine hydrochloride denaturation. These data, in conjunction with previously obtained stabilities of the corresponding alanine mutants, unequivocally show that the dominant contribution to stability for virtually all of the wild-type side chains examined is the electrostatic effect associated with each residue's charged group. With only a few exceptions, these charges stabilize the native state, with an average loss of 0.5 kcal/mol of stability upon neutralization of a charge. When the charge is reversed, the average destabilization is doubled. Structure-based calculations of electrostatic free energy with the continuum method based on the finite difference solution to the linearized Poisson-Boltzmann equation reproduce the observed energetics when the polarizability in the protein interior is represented with a dielectric constant of 20. However, in some cases, large differences are found, giving insight into possible areas for improvement of the calculations. In particular, it appears that the assumptions made in the calculations about the absence of electrostatic interactions in the denatured state and the energetic consequences of dynamic fluctuations in the native state will have to be further explored.

Amino Acid Substitution↗

Summation of spatiotemporal input patterns in leaky integrate-and-fire neurons: application to neurons in the cochlear nucleus receiving converging auditory nerve fiber input.

The response of leaky integrate-and-fire neurons is analyzed for periodic inputs whose phases vary with their spatial location. The model gives the relationship between the spatial summation distance and the degree of phase locking of the output spikes (i.e., locking to the periodic stochastic inputs, measured by the synchronization index). The synaptic inputs are modeled as an inhomogeneous Poisson process, and the analysis is carried out in the Gaussian approximation. The model has been applied to globular bushy cells of the cochlear nucleus, which receive converging inputs from auditory nerve fibers that originate at neighboring sites in the cochlea. The model elucidates the roles played by spatial summation and coincidence detection, showing how synchronization decreases with an increase in both frequency and spatial spread of inputs. It also shows under what conditions an enhancement of synchronization of the output relative to the input takes place.

Action Potentials↗

Gaussian process approach to spiking neurons for inhomogeneous Poisson inputs.

This article presents a new theoretical framework to consider the dynamics of a stochastic spiking neuron model with general membrane response to input spike. We assume that the input spikes obey an inhomogeneous Poisson process. The stochastic process of the membrane potential then becomes a gaussian process. When a general type of the membrane response is assumed, the stochastic process becomes a Markov-gaussian process. We present a calculation method for the membrane potential density and the firing probability density. Our new formulation is the extension of the existing formulation based on diffusion approximation. Although the single Markov assumption of the diffusion approximation simplifies the stochastic process analysis, the calculation is inaccurate when the stochastic process involves a multiple Markov property. We find that the variation of the shape of the membrane response, which has often been ignored in existing stochastic process studies, significantly affects the firing probability. Our approach can consider the reset effect, which has been difficult to deal with by analysis based on the first passage time density.

Action Potentials↗

An analytical framework for relating dose, risk, and incidence: an application to occupational tuberculosis infection.

An adverse health impact is often treated as a binary variable (response vs. no response), in which case the risk of response is defined as a monotonically increasing function R of the dose received D. For a population of size N, specifying the forms of R(D) and of the probability density function (pdf) for D allows determination of the pdf for risk, and computation of the mean and variance of the distribution of incidence, where the latter parameters are denoted E[SN] and Var[SN], respectively. The distribution of SN describes uncertainty in the future incidence value. Given variability in dose (and risk) among population members, the distribution of incidence is Poisson-binomial. However, depending on the value of E[SN], the distribution of incidence is adequately approximated by a Poisson distribution with parameter mu = E[SN], or by a normal distribution with mean and variance equal to E[SN] and Var[SN]. The general analytical framework is applied to occupational infection by Mycobacterium tuberculosis (M. tb). Tuberculosis is transmitted by inhalation of 1-5 microns particles carrying viable M. tb bacilli. Infection risk has traditionally been modeled by the expression: R(D) = 1 - exp(-D), where D is the expected number of bacilli that deposit in the pulmonary region. This model assumes that the infectious dose is one bacillus. The beta pdf and the gamma pdf are shown to be reasonable and especially convenient forms for modeling the distribution of the expected cumulative dose across a large healthcare worker cohort. Use of the the analytical framework is illustrated by estimating the efficacy of different respiratory protective devices in reducing healthcare worker infection risk.

Cohort Studies↗