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PubMed2002

Epidemiologic tools for biosecurity and biocontainment.

Quantitative models simplify reality, and therefore may misrepresent it. With that caution, models can be useful for predicting the outcomes of a variety of what-if scenarios related to biosecurity and biocontainment. Graphic representations of the models help to visualize relationships between factors that influence biosecurity that might not be obvious otherwise. The examples in this article illustrate only a few of many epidemiologic relationships relevant to biosecurity and biocontainment. Many other relationships remain to be explored.

Animal Husbandry↗

PubMed2002

Development of a short osteoporosis quality of life questionnaire by equating items from two existing instruments.

This study aimed to develop a short Osteoporosis-Specific Quality of Life Questionnaire based on the assemblage (equating) of the items of two existing questionnaires (OQLQ and QUALEFFO). For this purpose, each questionnaire was administered by random assignment to a different group of female patients (OQLQ, n = 172; QUALEFFO, n = 166) with vertebral fractures due to osteoporosis. A common anchor test (SF-36) was also given to both groups. Seven different sets of OQLQ-QUALEFFO common items were defined by inspecting their own correlation with the scores of the eight dimensions of the SF-36. Within each set, equating consisted in connecting the OQLQ and QUALEFFO through their link with the SF-36. Equating was carried out through the Rasch mathematical model. Quantitative (item statistics) and qualitative reductions (expert opinion) of the equated sets resulted in a 16-item questionnaire. Although the new instrument requires further empirical validation, it provides a promising alternative to currently existing longer questionnaires for use in clinical practice.

Activities of Daily Living↗

PubMedDate not supplied

Accurate segmentation of the breast region from digitized mammograms.

The segmentation of a digital mammogram into the breast region and the background is a necessary prerequisite in computer-assisted diagnosis of mammograms. By the exclusion of the background region, the accuracy of the analysis is increased and the running-time is decreased. The algorithm which segments the breast region from the background should be fully automated and give correct results for all kinds of digitized mammograms, including low-quality images. In this paper we present such an algorithm based on histogram thresholding, morphological filtering and contour modeling. Quantitative test results indicate that the computed boundary follows the estimated boundary accurately.

Algorithms↗

PubMed1998

Solid state NMR studies of photoinduced polarization in photosynthetic reaction centers: mechanism and simulations.

We simulate Photo-Chemically Induced Dynamic Nuclear Polarization in the 15N-solid-state NMR of 15N-labeled photosynthetic reaction centers using a Radical Pair Mechanism (RPM). According to the experimental data, the directly polarized nuclei include all eight nitrogens in the ground state of the bacteriochlorophyll special pair (P), and N-II in the bacteriopheophytin acceptor (H) [M.G. Zysmilich, A.E. McDermott, J. Am. Chem. Soc., 116 (1994) 8362-8363.] [M.G. Zysmilich, A. McDermott, J. Am. Chem. Soc., 118 (1996) 5867-5873.] [M.G. Zysmilich, A. McDermott, Proc. Natl. Acad. Sci. U.S.A., 93 (1996) 6857-6860.]; other signals are polarized in nonspecifically labeled samples, but the polarization apparently results from magnetization exchange with neighboring polarized nitrogens, and these are not treated in this work. Two quantitative models for the polarization associated with the RPM are presented and are used to test the validity of the proposal that this mechanism is cooperative in the reaction centers. The kinetic models can treat the steady state polarizations as well as the approach to steady state, and in principle could be expanded to include anisotropic effects, or pulse-probe experiments. Several features of the detailed simulations of the steady-state amplitudes and the kinetics of the approach to steady-state are compared with our data, including the signs and approximate absolute magnitudes of the polarization on the nitrogen nuclei in P and H(L), and the changes in the relative amplitudes with the change in the lifetime of the molecular triplet, photoaccumulation time, nuclear relaxation rate and illumination intensity. The simulations demonstrate that the polarization intensities are in qualitative agreement with those predicted for the RPM, including the curious observation of strong polariza-tion on the pheophytin acceptor for certain experimental conditions. However, this agreement requires efficient relaxation of the nitrogens on H(L) by 3P, due to a fortuitous low nanosecond value for the spin-lattice relaxation for the electrons in the molecular triplet of the donor, T1e of 3P. Whether this fortuitous match is valid is unproven.

Anisotropy↗

PubMed2001

Detection of lateral gene transfer among microbial genomes.

An increasingly comprehensive assessment is being developed of the extent and potential significance of lateral gene transfer among microbial genomes. Genomic sequences can be identified as being of putatively lateral origin by their unexpected phyletic distribution, atypical sequence composition, differential presence or absence in closely related genomes, or incongruent phylogenetic trees. These complementary approaches sometimes yield inconsistent results. Not only more data but also quantitative models and simulations are needed urgently.

Evolution, Molecular↗

PubMed2002

Protein folding: the free energy surface.

Quantitative models and experiments are revealing how the folding free energy surface of a protein is sculpted by sequence and environment. The sometimes conflicting demands of folding, structure and function determine which folding pathways, if any, dominate. Recent advances include experimental estimates of diffusive barrier-crossing times, the observation of ultrafast folders amenable to full-atom simulation, the use of thermodynamic tuning and nonconservative mutations to probe 'hidden' parts of the free energy surface, and a complete microscopic theory of folding.

Protein Folding↗

PubMed2003

Drosophila morphogenesis: the Newtonian revolution.

Recent quantitative modeling of dorsal closure in the fruitfly Drosophila has revealed how multiple forces drive sealing of the two symmetrical epithelial sheets. A predictive model based on the new data allows gene function to be linked to the forces that drive tissue movement.

Animals↗

PubMed2001

Computational cell biologists snowed in at Cranwell.

Cell biology is being inundated by an avalanche of data from the genomics and proteomics enterprises. The complexity and sheer volume of information threaten to overwhelm the ability of traditional cell biologists to grasp its implications and develop experimentally testable hypotheses. For this reason, some have begun to explore computational approaches towards organizing complex data into quantitative models. This requires communication and collaboration between the biological science community and and the physical and mathematical sciences communities. A recent meeting [The First International Symposium on Computational Cell Biology, Cranwell Resort, Lenox, MA, USA; 4-6 March 2001. Organizers: J.H. Carson, A. Cowan, and L.M. Loew (www.nrcam.uchc.edu/conference).] made a first attempt to bring these two communities together. Three feet of new snow fell during the meeting, but the 125 attendees, an unusual mixture of cell biologists, computer scientists, mathematicians, physicists, and engineers, were having too much fun defining the new field of computational cell biology to notice that they were literally snowed in.

Animals↗

PubMed2003

Electron-conformational study for the structure-hallucinogenic activity relationships of phenylalkylamines.

The structure-hallucinogenic activity relationships of a series of phenylethylamine and phenylisopropylamine derivatives have been investigated in the frameworks of electron-conformational method. The calculated geometry and electronic structure parameters accompanying to each atom and bond of each molecule in view were arranged as a matrix called electron-conformational matrix of contiguity (ECMC). The features that are responsible for strong and weak activity demonstrations have been found as submatrices of ECMCs belonging to some template compounds. Two electron-conformational features present in nonhallucinogenic compounds have been revealed. A quantitative model has been improved for predicting hallucinogenic activity numerically. A test series was used to verify the results obtained.

Electrons↗

PubMed2000

Quantitative dental radiography with a new photostimulable phosphor system.

OBJECTIVE: The purposes of this report are to present a quantitative model for digital oral radiography and to evaluate a new photostimulable phosphor system for bone mass measurements. STUDY DESIGN: Noise, linearity, and precision were measured from stepwedge images and blank images through use of a special least-squares calibration method. The model was used to estimate lower limits of detection for observing small changes in bone mineral content. RESULTS: The response was virtually linear, and the noise level of 2% to 3% is less than that of digitized film images. The precision of measurements averaged over a region of interest was generally better than 0.5%. CONCLUSIONS: If the scatter fraction is measured for each patient, bone loss can be measured by using only extraoral standards. Assuming a scatter fraction of 50% and considering only instrumental errors, the detection limit is <0.02 g/cm(2) for large image areas (> or =7 mm(2)) and <0.3 mg over areas of 1 mm(2) or smaller.

Artifacts↗

PubMed1998

Mutagenicity of three disinfection by-products: di- and trichloroacetic acid and chloral hydrate in L5178Y/TK +/- (-)3.7.2C mouse lymphoma cells.

The disinfection of water, required to make it safe for human consumption, leads to the presence of halogenated organic compounds. Three of these carcinogenic 'disinfection by-products', dichloroacetic acid (DCA), trichloroacetic acid (TCA) and chloral hydrate (CH) have been widely evaluated for their potential toxicity. The mechanism(s) by which they exert their activity and the steps in the etiology of the cancers that they induce are important pieces of information that are required to develop valid biologically-based quantitative models for risk assessment. Determining whether these chemicals induce tumors by genotoxic or nongenotoxic mechanisms (or a combination of both) is key to this evaluation. We evaluated these three chemicals for their potential to induce micronuclei and aberrations as well as mutations in L5178Y/TK +/- (-)3.7.2C mouse lymphoma cells. TCA was mutagenic (only with S9 activation) and is one of the least potent mutagens that we have evaluated. Likewise, CH was a very weak mutagen. DCA was weakly mutagenic, with a potency (no. of induced mutants/microgram of chemical) similar to (but less than) ethylmethanesulfonate (EMS), a classic mutagen. When our information is combined with that from other studies, it seems reasonable to postulate that mutational events are involved in the etiology of the observed mouse liver tumors induced by DCA at drinking water doses of 0.5 to 3.5 g/l, and perhaps chloral hydrate at a drinking water dose of 1 g/l. The weight-of-evidence for TCA suggest that it is less likely to be a mutagenic carcinogen. However, given the fact that DCA is a weak mutagen in the present and all of the published studies, it seems unlikely that it would be mutagenic (or possibly carcinogenic) at the levels seen in finished drinking water.

Animals↗

PubMed1998

Structure-mutagenicity relationships in 2-furylethylene derivatives. A molecular orbital study of the role of nitro groups.

An analysis of the electronic molecular structure of 2-furylethylene derivatives is carried out using a molecular orbital method. The differences in the electronic features of the nitro groups at two different positions of the furylethylene framework are well-accounted for in the present study. It is shown that nitro groups at position 5 of the furan ring of these compounds are more sensible to reduction in biological media that those at position beta of the exocyclic double bond. This greater sensitivity to reduction of 5-nitro compounds is given by the atomic and group charges on nitro group as well as for the low values of the energy of the lowest unoccupied molecular orbital. Discriminant functions able to classify 2-furylethylenes as mutagenic or not mutagenic are also obtained. These functions permitted the classification of 2-furylethylenes having or not nitro group in their structures. Finally, some quantitative models that describe the mutagenic potency of active compounds in terms of electronic molecular parameters were obtained. In all cases the models developed are in complete agreement with the experimental findings reported for this kind of compounds.

Furans↗

PubMedDate not supplied

Radiobiological principles in intravascular irradiation.

BACKGROUND: There is wide interest in the use of intravascular irradiation to control restenosis following balloon angioplasty. Part of the mechanism of restenosis appears to be the proliferation of smooth muscle cells (SMCs), triggered to divide by the damage caused by the angioplasty, and this proliferation can be inhibited by irradiation with y-rays or beta-rays. METHODS: In vitro data for the survival of smooth muscle cells exposed to radiation was used to model the likely control of restenosis by radiation. Physical and biological data were used to estimate differences in biological effectiveness of gamma-rays and beta3-rays, as well as the effect on cell killing of extending the exposure time. RESULTS: Based on the radiosensitivity of SMCs, measured in vitro, and the limited proliferative potential of these normal somatic cells, it is possible to understand and to model quantitatively how a single acute gamma-ray dose in the range of 15-20 Gy can inhibit restenosis. The few successful trials carried out to date where radiation has been shown to inhibit restenosis have all involved the gamma-emitter Iridium-192. The use of this radionuclide involves radiation safety problems and an inconveniently long treatment time. Consequently, there is much interest in developing a beta-emitting source that would solve both problems, and a number of different possibilities are being pursued. This development introduces two new problems discussed in this paper. First, beta-rays in the megavoltage range are less effective biologically than gamma-rays in the kilovoltage range, but the magnitude of the difference is not well known. Second, in the case of a single large dose, such as that proposed to inhibit restenosis, the biological effect will vary substantially as the exposure time varies from 1 to 20 min. If the clinical data are to be compared between centers using a variety of beta and y-emitting radionuclides, these factors will need to be taken into account. CONCLUSIONS: Doses of > 15 Gy are unlikely to result in elimination of the restenosis problem but should delay onset of restenosis for a significant period; the larger the dose, the longer the delay. Successful trials of endovascular radiation completed to date involve y-rays, while many systems being developed are based on beta-emitting radionuclides. Experimental data are urgently needed so that allowances can be made for the difference in dose-rate and radiation quality between gamma and beta-emitting radionuclides.

Angioplasty, Balloon↗

PubMed2003

The proliferation gene expression signature is a quantitative integrator of oncogenic events that predicts survival in mantle cell lymphoma.

We used gene expression profiling to establish a molecular diagnosis of mantle cell lymphoma (MCL), to elucidate its pathogenesis, and to predict the length of survival of these patients. An MCL gene expression signature defined a large subset of MCLs that expressed cyclin D1 and a novel subset that lacked cyclin D1 expression. A precise measurement of tumor cell proliferation, provided by the expression of proliferation signature genes, identified patient subsets that differed by more than 5 years in median survival. Differences in cyclin D1 mRNA abundance synergized with INK4a/ARF locus deletions to dictate tumor proliferation rate and survival. We propose a quantitative model of the aberrant cell cycle regulation in MCL that provides a rationale for the design of cell cycle inhibitor therapy in this malignancy.

ADP-Ribosylation Factors↗

PubMed2001

Surface Kinetics of Copper Oxidation Investigated by In Situ Ultra-high Vacuum Transmission Electron Microscopy.

We review our studies of the initial oxidation stages of Cu(001) thin films as investigated by in situ ultra-high vacuum transmission electron microscopy. We present our observations of surface reconstruction and the nucleation to coalescence of copper oxide during in situ oxidation in O2. We have proposed a semi-quantitative model, where oxygen surface diffusion is the dominant mechanism of the initial oxidation stages of Cu. We have also investigated the effect of water vapor on copper oxidation. We have observed that the presence of water vapor in the oxidizing atmosphere retards the rate of Cu oxidation and Cu2O is reduced when exposed directly to steam.

Journal Article↗

PubMed1996

Increased colonization potential of Campylobacter jejuni strain 81116 after passage through chickens and its implication on the rate of transmission within flocks.

The mechanisms by which Campylobacter jejuni rapidly spreads through large broiler flocks are unknown. Recent evidence suggests that the minimum infective oral dose for 100% caecal colonization is about 10(4) cfu, which, with such a 'fragile' organism, may limit transmissibility. However, the colonization potential of laboratory-adapted strains may be anomalous compared with fresh isolates or those passaged in vivo. The colonization potential of two chicken and one human C. jejuni isolates, which were minimally passaged, have been investigated using a quantitative model of chicken colonization. There was no detectable difference between these strains but all were more efficient colonizers than a laboratory-adapted strain 81116. In addition, the colonization potential of C. jejuni strain 81116 following a passage in vivo was also determined. The results indicated this increased c. 10000 fold following a single passage in vivo, such that a dose of only 40 cfu caused maximal colonization. Enhanced colonization potential may, therefore, account for the rapid rate of transmission within large flocks.

Animals↗

PubMed2002

A microfabrication-based dynamic array cytometer.

We have developed a microfabricated device for use in parallel luminescent single-cell assays that can sort populations upon the basis of dynamic functional responses to stimuli. This device is composed of a regular array of noncontact single-cell traps. These traps use dielectrophoresis to stably confine cells and hold them against disrupting fluid flows. Using quantitative modeling, we have designed traps with a novel asymmetric extruded-quadrupole geometry. This new trap can be physically arrayed and electrically addressed, enabling our cytometer. Situating an array of these traps in a microchannel, we have introduced cells into the array and demonstrated observation of fluorescent dynamic responses followed by sorting. Such a device has potential for use in investigating functional processes, as revealed by temporal behavior, in large numbers of single cells.

Cell Separation↗

PubMed2003

Photonic crystal aqueous metal cation sensing materials.

We developed a polymerized crystalline colloidal array photonic material that senses metal cations in water at low concentrations (PCCACS). Metal cations such as Cu2+, Co2+, Ni2+, and Zn2+ bind to 8-hydroxyquinoline groups covalently attached to the PCCACS. At low metal concentrations (<microM), the cations form bisliganded complexes with two 8-hydroxyquinolines that cross-link the hydrogel and cause it to shrink, which blue shifts the photonic crystal diffraction. These bisliganded cross-links break at higher cation concentrations due to the formation of monoliganded cation complexes. This red shifts the diffraction. We have extended hydrogel volume phase transition theory in order to quantitatively model the diffraction dependence upon metal concentration. These materials can be used as a dosimeter to sense extremely low metal cation concentrations or as a sensor material for concentrations greater than 1 microM. Metal cation concentrations can be determined visually from the color of the diffracted light or can be determined by reflectance measurements using a spectrophotometer. This sensing material could be used in the field to visually determine metal cation concentrations in drinking water. A color chart would be used to relate the diffracted color to the metal cation concentration.

Cations, Divalent↗