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PubMed2004

A second life in science--working after the age of 65.

I was born in January, 1921 and was fortunate in working for a research organization that had no fixed retirement age. I was permitted to continue Science as long as there were some resources to support research that had some relevance to the organization's goals. A number of projects on which I worked were continuations of ones begun before the age of 65 (1986) and several new ones were based on both previous interests and ideas and some on new ideas. A number of the ideas arose from participation on Committees of the US National Research Council. I was able to extend my earlier interests in DNA repair to include experiments on the variations in DNA repair among apparently normal humans. In collaborations with other researchers we showed that the repair abilities following exposures to chemicals or to ionizing or ultraviolet (UV) radiation did not follow Poisson distributions. I participated in experiments, using a fish model to estimate the wavelength ranges in sunlight responsible for inducing melanoma and another fish model to estimate the germ cell mutations that might arise from exposures to the heavily ionizing particles in cosmic rays beyond low Earth orbit. A transgenic fish model was used to investigate the possibilities of using the fish to assay for mutagens in sediments in Long Island Sound. These Reflections summarize the atmosphere necessary for a second life and the scientific results of this life.

Aged↗
PubMed2006

Dose-response population analysis of levetiracetam add-on treatment in refractory epileptic patients with partial onset seizures.

In this post hoc analysis, individual seizure counts from four double-blind trials of adjunctive treatment with levetiracetam were analyzed by non-linear mixed-effects modeling (NONMEM). First, a model was fitted to the individual count data assuming a Poisson distribution, in order to classify the patients as either improving or deteriorating from baseline. In the second stage, the dose-response relationship in improving patients was determined by fitting the data to an E(max) model including a placebo effect. The percentage of improvers was 59% on placebo and 73%, 74%, 77% and 73% on levetiracetam 1, 2, 3 and 4g/day, respectively. The ED(50) of 1408mg/day was close to the current WHO Defined Daily Dose of levetiracetam (1500mg). The maximum recommended dose of 3000mg/day was predicted to reduce seizures by >or=90% in 10% of improving patients. Age, gender, body weight, race, and number of concomitant antiepileptic drugs neither affected the percentage of responders nor the extent of change in seizure frequency from baseline.

Anticonvulsants↗
PubMed2006

Reliability of multilocus sequence typing of the Burkholderia cepacia complex in cystic fibrosis.

INTRODUCTION: Infection with the Burkholderia cepacia complex is an important cause of morbidity and mortality in cystic fibrosis (CF). We investigated the molecular clock speed of the seven genes used in the multilocus sequence typing (MLST) scheme for these bacteria. METHODS: At least two isolates, separated by months to years, from each of 20 patients were typed using MLST. In total 41 isolates, providing 128 isolate-years, were analyzed. Mutation and recombination rates were estimated assuming a Poisson distribution. RESULTS: Out of 20 patients, 15 had no change in sequence type over time (mean 7.07 years, range 1.09 to 14.24). One patient had strain replacement. Three patients had evidence of recombination involving one of the seven housekeeping genes, and one patient had evidence of recombination of two genes. The mutation rate was estimated as 2.36x10(-6) per nucleotide per year (50% confidence limit) and 1.02x10(-5) per nucleotide per year (upper 95% confidence limit). The rate of nucleotide changes due to recombination events was estimated as 0.676 to 0.839 per year (95% confidence limits). CONCLUSIONS: B. cepacia complex housekeeping genes have a slow molecular clock speed and MLST provides a robust and reliable typing technique for isolates from this complex. A low rate of point mutation was found, with a higher rate of recombination events, in keeping with previous cross-sectional epidemiological data. The study also demonstrated, for the first time, recombination in a longitudinal in vivo study.

Bacterial Typing Techniques↗
PubMed2004

Quenching of fluorescence of 1-hydroxypyrene-3,6,8-trisulfonate (HPTS) by Cu2+, Co2+, Ni2+, I-, and cetylpyridinium (CP+) ions in water/AOT/heptane microemulsion.

The quenching of the fluorescence of HPTS (1-hydroxypyrene-3,6,8-trisulfonate) by Cu(2+), Ni(2+), Co(2+), I(-), and CP(+) (cetylpyridinium cation) has been studied in the w/o microemulsion medium formed with water, AOT [sodium salt of bis (2-ethylhexyl) sulfosuccinic acid], and heptane as components at two [H(2)O]/[AOT] ratios (omega), 6 and 20. The quenching process has been found to be dynamic in nature. The lifetimes of HPTS in the microemulsion medium in the absence and in the presence of quencher have been determined. The analysis of the results has been performed in terms of the Stern-Volmer equation and the quenching sphere of action model. The Poisson distribution equation has been also used in the analysis of the probability of quencher distribution in the microemulsion compartment. The quenching of HPTS has been found to be much lower in microemulsion than in bulk water.

Journal Article↗
PubMed2004

Spread of two linked social norms on complex interaction networks.

In this paper, we study the spread of social norms, such as rules and customs that are components of human cultures. We consider the spread of two social norms, which are linked through individual behaviors. Spreading social norms depend not only on the social network structure, but also on the learning system. We consider four social network structures: (1) complete mixing, in which each individual interacts with the others at random, (2) lattice, in which each individual interacts with its neighbors with some probability and with the others at random, (3) power-law network, in which a few influential people have more social contacts than the others, and (4) random graph network, in which the number of contacts follows a Poisson distribution. Using the lattice model, we also investigate the effect of the small-world phenomenon on the dynamics of social norms. In our models, each individual learns a social norm by trial and error (individual learning) and also imitates the other's social norm (social learning). We investigate how social network structure and learning systems affect the spread of two linked social norms. Our main results are: (1) Social learning does not lead to coexistence of social norms. Individual learning produces coexistence, and the dynamics of coexistence depend on which social norms are learned individually. (2) Social norms spread fastest in the power-law network model, followed by the random graph model, the complete mixing model, the two-dimensional lattice model and the one-dimensional lattice. (3) We see a "small world effect" in the one-dimensional model, but not in two dimensions.

Computer Simulation↗
PubMed2005

Floral sex ratio strategy in wind-pollinated monoecious species subject to wind-pollination efficiency and competitive sharing among male flowers as a game.

To explain the floral sex ratio strategy in wind-pollinated monoecious species, we developed four models with special reference to wind-pollination efficiency (WPE) and competitive sharing among male flowers (CSM). WPE is a function that follows a Poisson distribution and explains the frequency of seeds fertilized by an individual via wind-pollination, whereas CSM is defined by the sharing of female flowers among male flowers within the local breeding population. We argued the applicability of the results to the actual tendencies observed in wind-pollinated monoecious species and found that a game model with WPE and CSM was the most applicable. The model predicted that individuals should change their gender expression in the following order: female phase (female flowers only), male phase (male flowers only), and constant male phase (individuals constantly allocate reproductive resources to male flowers, and remaining resources to female flowers), with increasing reproductive resources. However, the trend is likely to be influenced by the variation in the reproductive investment among individuals and the degree of WPE. Thus, large variation and low pollination efficiency enable three phases to co-occur within a population. Actual trends in real populations correspond to our prediction.

Flowers↗
PubMed2005

Enumeration of bacteriophages in water by different laboratories of the European Union in two interlaboratory comparison studies.

As part of a European project on bacteriophages in bathing waters two interlaboratory comparison studies were carried out (May 1997 and March 1998). During these studies phage reference materials as well as naturally polluted standard samples were analysed in 16 European laboratories. Three groups of bacteriophages were tested using standardised methods: somatic coliphages, F-specific RNA-phages and phages of Bacteroides fragilis. Many of the participating laboratories applied one or more of the phage methods for the first time, after a one-week training session in a central laboratory. Nevertheless, the values of repeatability (r=1.35-1.38 calculated on log(10)-scale) and reproducibility (R=1.52-2.04 calculated on log(10)-scale) when analysing phage reference materials were close to the theoretical optimum for a Poisson distribution. When analysing the naturally polluted samples more variation in results within and between laboratories was found (r=1.63-2.34; R=3.10-5.72), in comparison with the results obtained with the pure phage reference materials.

Bacteriophages↗
PubMed2006

Non-linear chromosomal inversion response in prostate after low dose X-radiation exposure.

Somatic intrachromosomal recombination can result in inversions and deletions in DNA, which are important mutations in cancer. The pKZ1 chromosomal inversion assay is a sensitive assay for studying the effects of DNA damaging agents using chromosomal inversion as a mutation end-point. We have previously demonstrated that the chromosomal inversion response in pKZ1 spleen after single low doses of X-radiation exposure does not follow the linear no-threshold dose-response model. Here, we optimised a chromosomal inversion screening method to study the effect of low dose X-radiation exposure in pKZ1 prostatic tissue. In the present study, a significant induction in inversions was observed after ultra-low doses of 0.005-0.01 mGy or after a high dose of 1000 mGy, whereas a reduction in inversions to below the sham-treated frequency was observed between 1 and 10 mGy exposure. This is the first report of a reduction to below endogenous frequency for any mutation end-point in prostate. In addition, the doses of radiation studied were at least three orders of magnitude lower than have been reported in other mutation assays in prostate in vivo or in vitro. In sham-treated pKZ1 controls and in pKZ1 mice treated with low doses of 1-10 mGy the number of inversions/gland cross-section rarely exceeded three. Up to 4 and 7 inversions were observed in individual prostatic gland cross-sections after doses < or =0.02 mGy and after 1000 mGy, respectively. The number of inversions identified in individual cross-sections of prostatic glands of untreated mice and all treated mice other than the 1000 mGy treatment group followed a Poisson distribution. The dose-response curves and fold changes observed after all radiation doses studied were similar in spleen and prostate. These results suggest that the pKZ1 assay is measuring a fundamental response to DNA damage after low dose X-radiation exposure which is independent of tissue type.

Animals↗
PubMed2006

Three-dimensional maximum a posteriori (MAP) imaging with radiopharmaceuticals labeled with three Cu radionuclides.

BACKGROUND: One of the limiting factors in achieving the best spatial resolution in positron emission tomography (PET), especially in small-animal PET, is the positron range associated with the decay of nuclides, and usual PET image reconstruction algorithms do not provide a correction for the positron range. This work presents initial results obtained with the maximum a posteriori (MAP) algorithm, which has been developed to include an accurate model of the camera response, the Poisson distribution of coincidence data and the fundamental physics of positron decay including the positron range. METHODS: Phantoms were imaged with three positron emitting isotopes of Cu ((60)Cu, (61)Cu and (64)Cu), and mice and rats were imaged with two radiopharmaceuticals labeled with these isotopes in a microPET-R4 camera. These isotopes decay by positron emission with very different end-point energies resulting in wildly different spatial resolutions. Spatial resolution improvement and image quality offered by the MAP algorithm were studied with the line source phantom and a miniature Derenzo phantom. In addition, three mice and three rats were sequentially injected over a 48-h period with Cu-pyruvaldehyde bis(N(4)-methylthiosemicarbazone) (for blood flow to organs) and Cu-1,4,7,10-tetraazacyclododecane-1,4,7-tri(methanephosphonic acid) (for bone imaging) labeled with the said three isotopes of Cu. RESULTS: The line source experiment showed that comparable spatial resolution is possible with all three isotopes when using the positron range correction in MAP. The in vivo images obtained from (60)Cu and (61)Cu and reconstructed with 2D filtered back projection algorithms provided by the camera manufacturer show reduced clarity due to degraded spatial resolution arising from the extended positron ranges as compared with (64)Cu. MAP reconstructions exhibited a higher resolution with clearer organ delineation. CONCLUSION: Inclusion of a positron range model in the MAP reconstruction algorithm may potentially result in significant resolution recovery for isotopes with larger positron ranges.

Algorithms↗
PubMed2004

Estimating mutant microsatellite allele frequencies in somatic cells by small-pool PCR.

Identifying microsatellite instability (MSI) by partitioning DNA into multiple small pools containing only single genome amounts of DNA results in trapping both progenitor and low-frequency mutant alleles into pools where they can be identified and counted following PCR. Statistical approaches determining both the frequencies and the significant differences between frequencies of these Poisson-distributed alleles are presented. Results indicate a level of sensitivity and quantification not possible by standard PCR methods. Using material from colon cancer patients with high levels of MSI in their tumors, we also present the molecular and robotic methods for carrying out such studies. Validation experiments indicated mutants detectable at frequencies >0.03 above background. Frequencies obtained in tumor tissue (>0.25) met the expectations of the approach. Significant levels of MSI were detected in the constitutive tissue of the patient carrying a germ-line mutation for mismatch repair, suggesting both mechanistic and clinical applications of the procedure.

Adult↗
PubMed2003

Personality and behavioral predictors of traffic accidents: testing a contextual mediated model.

A contextual mediated model was proposed to distinguish the distal (i.e. personality factors) and proximal (i.e. aberrant driving behaviors) factors in predicting traffic accident involvement. Turkish professional drivers (N=295) answered a questionnaire including various measures of personality factors, driver behaviors, and accident history. Results of the latent variable analysis with LISREL indicated that latent variables in the distal context (i.e. psychological symptoms, sensation seeking, and aggression) predicted at least one of the proximal elements (i.e. aberrant behaviors, dysfunctional drinking, and preferred speed) with relatively high path coefficients. While aberrant driver behaviors yielded a direct effect on accident involvement, psychological symptoms yielded an indirect effect mediated by driver behaviors. Further analyses revealed that personality factors had an impact on road accidents via their effects on actual driving-related behaviors although the path coefficients in predicting accidents were relatively weaker than those predicting risky driving behaviors and habits. Results were discussed considering the implications for classifying the accident correlates in a contextual framework and binominal-poisson distribution of self-reported accidents.

Accidents, Traffic↗
PubMed1972

The frequency response, coherence, and information capacity of two neuronal models.

Two neuronal models are analyzed in which subthreshold inputs are integrated either without loss (perfect integrator) or with a decay which follows an exponential time course (leaky integrator). Linear frequency response functions for these models are compared using sinusoids, Poisson-distributed impulses, or gaussian white noise as inputs. The responses of both models show the nonlinear behavior characteristic of a rectifier for sinusoidal inputs of sufficient amplitude. The leaky integrator shows another nonlinearity in which responses become phase locked to cyclic stimuli. Addition of white noise reduces the distortions due to phase locking. Both models also show selective attenuation of high-frequency components with white noise inputs. Input, output, and cross-spectra are computed using inputs having a broad frequency spectrum. Measures of the coherence and information transmission between the input and output of the models are also derived. Steady inputs, which produce a constant "carrier" rate, and intrinsic sources, which produce variability in the discharge of neurons, may either increase or decrease coherence; however, information transmission using inputs with a broad spectrum is generally increased by steady inputs and reduced by intrinsic variability.

Mathematics↗
PubMed1981

Size and frequency of gaps in newly synthesized DNA of xeroderma pigmentosum human cells irradiated with ultraviolet light.

Native newly synthesized DNA from human cells (xeroderma pigmentosum type) irradiated with ultraviolet light releases short pieces of DNA (L-DNA) when incubated with the single-strand specific S1 nuclease. This is not observed in the case of unirradiated cells. Previous experiments had shown that the L-DNA resulted from the action of S1 nuclease upon gaps, i.e., single-stranded DNA discontinuities in larger pieces of double-stranded DNA. We verified that the duplex L-DNA, that arises from the inter-gap regions upon S1 nuclease treatment, has a size which approximates the distance between two pyrimidine dimers on the same strand; this has been observed at different fluences of ultraviolet-light and indicates that the gap is related to or opposite the dimer. A method was devised to measure the size of the gaps. A Poisson distribution analysis of the percentage of the L-DNA produced as a function of S1 nuclease concentration made this possible. 65% of the gaps corresponded to stretches of 1,250 nucleotides and 35% to stretches of 150 nucleotides. These parameters have been considered in the proposition of a model for DNA synthesis on a template containing pyrimidine dimers.

Cell Transformation, Viral↗
PubMed1983

Motility of mouse fibroblasts in tissue culture.

The growth and motion of mouse L-cells in vitro have been studied by means of time-lapse photography. In particular, the mitotic period and the motility, defined in terms of [R2], the mean square displacement of an ensemble of cells, have been measured as a function of temperature. The motility is a function of the phase of the cell cycle. For approximately the first one-eighth of the mitotic period the motility is well described as a random walk with persistence, the duration of the persistence being determined by the time of extension of the filopodic spindle. The temperature dependence of the diffusion constant follows the Arrhenius factor. The mitotic period, which varies exponentially as (1/T), exhibits a large variance, and the time difference in replication of daughter pairs follows approximately a Poisson distribution with a mean difference of 138 min at T = 37 degrees C. There is no evidence of mirror symmetry in the motion of daughter pairs for fibroblast cells plated in vitro in Corning tissue culture flasks.

Animals↗
PubMed1984

A model of dynamic quenching of fluorescence in globular proteins.

A model is presented for the quenching of a fluorophore in a protein interior. At low quencher concentration the quenching process is determined by the acquisition rate of quencher by the protein, the migration rate of quencher in the protein interior, and the exit rate of quencher from the protein. In cases where the fluorescence emission observed in the absence of quencher could be described by a single exponential decay, the presence of quencher led to doubly exponential decay times, and the aforementioned exit rates of the quencher could be determined from experimental data. At high quencher concentration, the processes became more complex, and the deterministic rate equations used at low quencher concentration had to be modified to take into account the Poisson distribution of quencher molecules throughout the protein ensemble and also by using a migration rate for quencher in the protein interior that is a function of the quencher concentration. Simulations performed for typical fluorescent probes in proteins showed good agreement with experiments.

Kinetics↗
PubMed1988

Interaction forces between red cells agglutinated by antibody. III. Micromanipulation.

In the flow studies described in two previous papers (Tha, S. P., and H. L. Goldsmith, 1986, Biophys. J. 50:1109-1116; Tha, S. P., J. Shuster, and H. L. Goldsmith, 1986, Biophys. J. 50:1117-1126), hydrodynamic forces of the order of 10(-11) N (mu dyn) were applied to measure the force of separation of doublets of hardened, sphered human red blood cells cross-linked by anti-B antibody. The same cell preparation and hyperimmune antiserum has here been used to carry out experiments with micropipet aspiration techniques. One cell of a doublet was aspirated onto a holding pipet, and a second aspiration pipet was brought into proximity of the other cell so that the two pipets and the doublet were colinear. Suction was then raised until the two cells separated. Some doublets were assembled by aspiration of a singlet, bringing a second singlet into apposition with the first, and releasing it from the pipet which was then withdrawn. Cells could be repeatedly assembled and separated. At 3.56% vol/vol antiserum, the mean normal force of separation was 0.45 +/- 0.11 nN in phosphate-buffered saline suspensions containing 2.5 x 10(4) cells/microliter; at 1.22% vol/vol antiserum, the value was 0.22 +/- 0.11 nN. The above values of the force were approximately 2.5 x greater than those from the flow studies. The data could be fitted to a Poisson distribution with 0.05 nN as the force needed to break a single cross-bridge (c.f. 0.024 nN from the previous hydrodynamic data). The forces of separation of randomly assembled doublets were lower than those of preexisting doublets. Repeated assembly and separation of doublets showed that the cell surfaces are nonuniform in adhesion strength both over the local scale less than 0.25 micron2 and the cell population.

Antibodies↗
PubMed1992

Protein dynamics and 1/f noise.

It has long been recognized that protein dynamical processes occur over a wide temporal range. However, the functionality of this spectrum of events remains unclear. In this work, a generalized noise function analysis is applied to a collection of diverse protein dynamical systems. It is shown that a power law model with an oscillatory component can adequately describe the time course of a variety of processes. These results suggest that under the appropriate conditions, proteins are in a metastable state. A microscopic, chemical kinetic model based on a Poisson distribution of activation energies is presented. From this model specific functional forms for the parameters of the generalized noise model can be derived. Additionally, a model is presented to described kinetic hole burning effects observed at low temperatures. Scaling laws are derived for these models that provide a connection with the generalized noise analysis.

Biophysics↗
PubMed1996

Kinetics and locus of failure of receptor-ligand-mediated adhesion between latex spheres. II. Protein-protein bond.

In an extension of the previous paper, we describe the force dependence of break-up of doublets of latex spheres cross-linked by protein G-IgG bonds via the Fc region of the antibody. The receptor, the monoclonal Bear-1 antibody, was either covalently linked to 4.75-microns aldehyde/sulfate (A/S) latex spheres in a one-step reaction, or physically adsorbed to the 4.63-microns carboxyl-modified latex spheres used in Part I of this paper. The spheres were suspended in 19% buffered Dextran 40 containing the ligand, the bivalent recombinant protein G (Gamma-Bind G), and observed in the counter-rotating cone and plate Rheoscope. Break-up of doublets, tracked individually under the microscope, as well as in populations of 50-150 particles, was studied over a range of normal force from 20 to 260 pN. In individual particle studies, the fraction of doublets of spheres with covalently linked IgG breaking up in the first 10 rotations, increased from 16% in the low-force to 63% in the high-force range. In population studies, the fraction broken up increased with duration and magnitude of the applied force, and decreased with increasing ligand concentration. Moreover, doublets of physically adsorbed IgG spheres required significantly lower force than doublets of covalently linked IgG spheres for the same degree of break-up, possibly because of surface detachment of IgG molecules rather than rupture of receptor-ligand bonds. Computer simulation, using the Bell stochastic model of break-up and a Poisson distribution for the number of bonds, described in Part I, showed that the parameters of the protein-protein bond differed significantly from those of the carbohydrate-protein bond studied in Part I of this paper, the former being much more responsive to force than the latter.

ABO Blood-Group System↗