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PubMed1987

Development of a model to aid in reconstruction of historical silica dust exposures in the taconite industry.

The ability to reconstruct employee exposure histories would be a valuable research tool for the evaluation of occupation as a factor in disease. In many cases, however, historical environmental data are available but have not been used to compute past exposures because of differences in sampling methods. This paper describes a quantitative model to convert historical environmental data (from taconite mine and mill operations) into a form consistent with current sampling methods and results and, therefore, will enable past exposure histories to be used. (Past exposure histories are to be determined in an epidemiological study.) In this study, parallel sampling results from the environmental data base were used to obtain a coefficient for the conversion of impinger-particle counts (old sampling method) to filter-respirable mass sampling results (new sampling method). Parameters in the model were estimated using multiple regression techniques. Results show that a consistent ratio exists between impinger-particle counts and filter-respirable mass concentrations for samples collected at the same locations.

Air Pollutants, Occupational↗
PubMed2001

A conscious-rabbit model to study vardenafil hydrochloride and other agents that influence penile erection.

Experimental models to study the effect of agents on penile erection usually include electrical stimulation of peripheral nerves in anesthetized animals combined with systemic or intracavernous injection of drugs. The objective of this study was to demonstrate that conscious rabbits can be used as a simple and quantitative model for the assessment of compounds that show potential for the treatment of erectile dysfunction. Erection was assessed by measuring the length of uncovered penile mucosa before and after the intravenous (i.v.) administration of agents. Animals did not require anesthesia during the course of the study. The phosphodiesterase 5 (PDE5) inhibitors vardenafil x HCl (hereafter called vardenafil) and sildenafil were given intravenously, and measurements were taken for 0-5 h. The effects of phentolamine and milrinone were also evaluated. Vardenafil (0.1-3 mg/kg) induced dose-dependent penile erections in conscious rabbits following i.v. administration. The efficacy of vardenafil was potentiated, and the minimal effective dose was reduced significantly to 0.01 mg/kg by simultaneous administration of the nitric oxide (NO) donor sodium nitroprusside (SNP). Administration of the NO-synthase inhibitor L-NAME abolished the effect. Sildenafil was effective in this model after i.v. administration. The alpha-adrenergic receptor antagonist phentolamine (0.1, 0.3 and 1 mg/kg i.v.) induced erections with a slower t(max) compared with vardenafil and sildenafil. Intravenous administration of the PDE3 inhibitor milrinone (1 mg/kg i.v.) was less effective than the PDE5 inhibitor vardenafil. The conscious rabbit is a suitable and reliable model for the evaluation of compounds with potential for the treatment of erectile dysfunction. This was demonstrated using compounds that target different signaling pathways that induce smooth muscle relaxation in the penis.

Adrenergic alpha-Antagonists↗
PubMed1989

Cues and control strategies in visually guided tracking.

Detailed quantitative models are required to investigate the neurological basis of motor behavior. Previous studies of visually guided manual tracking have either identified a variety of control signals (cues) for planning tracking movements or analyzed how a single cue is used (i.e., one-tracking strategy). A systematic, quantitative analysis of the effects and interactions of cues in terms of human manual-tracking performance is presented here together with measurements of concomitant eye movements. These measurements help define the routes by which information reaches the CNS, and the analysis elucidates how the control signals are processed and combined. The results quantify not only the large improvement in performance observed when the target waveform being tracked is predictable but also the extent to which this improvement depends on the availability of current information about target movements and positional error. Target information is shown to provide short-term prediction independent of the error signals used in on-line negative feedback control.

Journal Article↗
PubMed2000

Meaning resolution processes for words: a parallel independent model.

Lexical ambiguity research over the last two decades is reviewed, with a focus on how that literature applies to understanding the resolution of meaning for words. Early models of ambiguity processing dealt almost exclusively with the time course of the effects of context on lexical access, in order to address the issue of modularity of lexical access. Newer models of ambiguity processing accommodate recent findings of early context effects that are contingent on both strength of context and meaning frequency. The most important contribution of these newer models of ambiguity processing is not to the modularity debate, but to investigation of the range of parameters affecting the entire meaning resolution process, including meaning access as well as the integration of meanings into context. As an example of this approach, we describe a simple quantitative model of meaning resolution that subsumes many other models as parametric variations.

Humans↗
PubMed2004

Computational model of dynein-dependent self-organization of microtubule asters.

Polar arrays of microtubules play many important roles in the cell. Normally, such arrays are organized by a centrosome anchoring the minus ends of the microtubules, while the plus ends extend to the cell periphery. However, ensembles of molecular motors and microtubules also demonstrate the ability to self-organize into polar arrays. We use quantitative modeling to analyze the self-organization of microtubule asters and the aggregation of motor-driven pigment granules in fragments of fish melanophore cells. The model is based on the observation that microtubules are immobile and treadmilling, and on the experimental evidence that cytoplasmic dynein motors associated with granules have the ability to nucleate MTs and attenuate their minus-end dynamics. The model explains the observed sequence of events as follows. Initially, pigment granules driven by cytoplasmic dynein motors aggregate to local clusters of microtubule minus ends. The pigment aggregates then nucleate microtubules with plus ends growing toward the fragment boundary, while the minus ends stay transiently in the aggregates. Microtubules emerging from one aggregate compete with any aggregates they encounter leading to the gradual formation of a single aggregate. Simultaneously, a positive feedback mechanism drives the formation of a single MT aster--a single loose aggregate leads to focused MT nucleation and hence a tighter aggregate which stabilizes MT minus ends more effectively leading to aster formation. We translate the model assumptions based on experimental measurements into mathematical equations. The model analysis and computer simulations successfully reproduce the observed pathways of pigment aggregation and microtubule aster self-organization. We test the model predictions by observing the self-organization in fragments of various sizes and in bi-lobed fragments. The model provides stringent constraints on rates and concentrations describing microtubule and motor dynamics, and sheds light on the role of polymer dynamics and polymer-motor interactions in cytoskeletal organization.

Animals↗
PubMed2006

QSAR study of mosquito repellents using Codessa Pro.

Protection times provided by 31 synthetic repellents against Aedes aegypti mosquitoes were correlated with the chemical structures of these repellents using Codessa Pro software. Two statistically significant quantitative models with R2 values of ca. 0.80 are presented and discussed.

Animals↗
PubMed1988

[Screening of immunomodulators by using the system of mononuclear phagocytes].

Immunomodulating effects of various agents can be mediated by the system of mononuclear phagocytes (SMP). Immunomodulators are able to interfere with the initial events in activation of mononuclear phagocytes (MP) on their membranes which inevitably has its impact on molecular manifestations of the MP activation: the oxidative outburst events. At the initial (tentative) stage of the screening potential immunomodulators it is expedient to use tests providing estimation of the oxidative outburst intensity by the activity of glucoso-6-phosphate dehydrogenase, the key enzyme of the hexose monophosphate shunt and by the level of superoxydanions production judged by reduction of nitroblue tetrasolium (NBTT). The use of transplantable macrophage-like lines J.744 and P 338D as the targets instead of murine peritoneal MP made it possible to increase reproducibility of the results in screening of immunomodulators. An experimental model of the mouse abdominal cavity clearance within the first hours after intraperitoneal administration of the test bacteria was used for estimating the effect of the potential immunomodulators on the barrier function of the SMP in the host. Experimentally modeled quantitative and functional defects in the SMP served as and adequate test system for study of immunostimulating agents.

Adjuvants, Immunologic↗
PubMedDate not supplied

The 1990 GP contract: modelling variation in minor surgery provision.

Logistic regression was used to determine the extent to which general medical practices undertake the maximum amount of minor surgery activity allowed for in the GP contract. Data on activity for 89 practices in the Grampian region of Scotland was available for two consecutive financial years: 1992-93 and 1993-94. Comparison of the regression models developed in each year showed that rural location and practice size were consistently associated with the maximization of minor surgery activity under the terms of 1990 GP Contract. In 1993-94 practices with a greater proportion of deprived patients were also more likely to be 'maximizers'. Quantitative modelling allows the performance of GPs to be assessed and also helps to identify factors which are a barrier to service development. It seems likely that, in Grampian, GPs who were able to exploit fully the provisions of their contract were those whose patients had the greatest capacity to benefit from minor surgery. Currently the GP contract is nationally negotiated, but in the future local negotiated remuneration is likely to become widespread. Modelling will have an important role in the design and monitoring of incentive structures, and help to ensure that service provision equates to local needs.

Contract Services↗
PubMed2002

Triage scoring systems, severity of illness measures, and mortality prediction models in pediatric trauma.

Trauma triage scores, severity of illness measures, and mortality prediction models quantitate severity of injury and stratify patients according to a specified outcome. Triage scoring systems are typically used to assist prehospital personnel determine which patients require trauma center care, but they are not recommended as the sole determinant of triage. Severity of illness measures and mortality prediction models are used in clinical and health services research for risk-adjusted outcomes analyses and institutional benchmarking. As clinicians and researchers, it is imperative that we be knowledgeable of the methodologies and applications of these scoring and risk prediction systems to ensure their quality and appropriate utilization.

Benchmarking↗
PubMed1988

Regulation of shortening velocity by cross-bridge phosphorylation in smooth muscle.

We have proposed a model that incorporates a dephosphorylated "latch bridge" to explain the mechanics and energetics of smooth muscle. Cross-bridge phosphorylation is proposed as a prerequisite for cross-bridge attachment and rapid cycling. Features of the model are 1) myosin light chain kinase and phosphatase can act on both free and attached cross bridges, 2) dephosphorylation of an attached phosphorylated cross bridge produces a noncycling "latch bridge," and 3) latch bridges have a slow detachment rate. This model quantitatively predicts the latch state: stress maintenance with reduced phosphorylation, cross-bridge cycling rates, and ATP consumption. In this study, we adapted A. F. Huxley's formulation of crossbridge cycling (A. F. Huxley, Progr. Biophys. Mol. Biol. 7: 255-318, 1957) to the latch-bridge model to predict the relationship between isotonic shortening velocity and phosphorylation. The model successfully predicted the linear dependence of maximum shortening velocity at zero external load (V0) on phosphorylation, as well as the family of stress-velocity curves determined at different times during a contraction when phosphorylation values varied. The model implies that it is unnecessary to invoke an internal load or multiple regulatory mechanisms to explain regulation of V0 in smooth muscle.

Algorithms↗
PubMed2001

Thermal modeling of snake infrared reception: evidence for limited detection range.

For more than 40 years, information has circulated with regard to the sensitivity of infrared pit organs in both boid and crotaline snakes (pythons and pit vipers, respectively). The most often quoted sensitivity is 0.003 degrees C and this value is based on the work of Bullock and co-workers (1956). Missing from previous work was a quantitative model of radiation transfer that would report sensitivity not in terms of degrees Celsius, but rather sensing distance. Since prey detection is often cited as the function of the infrared pit organ, quantification of this sensing distance seemed to be an important value that was missing from the literature. In this paper, we model the radiation transfer process from a 37 degrees C object, i.e. warm-blooded prey, to an infrared pit organ. The model tries to answer a very basic question-at what distance does the thermal signature of a 37 degrees C object blend into the background for a non-imaging biological infrared sensor? The output of the model, the sensing distance, is of particular interest in comparing biological infrared sensors to current semiconductor-based infrared (IR) detectors-largely because of inappropriate comparisons between the temperature sensitivity of IR snake reception and imaging IR cameras. The purpose of the presented work to make more appropriate comparisons, i.e. sensing distance. This sensing distance output indicates an extremely short detection distance (<5 cm)-contradictory to what is observed experimentally. This dichotomy raises further questions regarding how the biological system amplifies this weak signal.

Animals↗
PubMed2003

A topological-substructural molecular design (TOPS-MODE) approach to determining pharmacokinetics and pharmacological properties of 6-fluoroquinolone derivatives.

The topological-substructural molecular design approach was used to estimate the human bioavailability (F) and the minimum inhibitory concentration (MIC90) against Streptococcus pneumoniae from a data set of 17 and 19 fluoroquinolone derivatives, respectively. Both pharmacokinetics and pharmacological properties were well described by the present approach. The total spectral moments and local spectral moments that include the different fluoroquinolone rings, polar and non-polar areas and their interactions were calculated and weighted with the standard dipole moments and the electronegative difference between the atoms that form a bond. In order to obtain a qualitative model that permits the classification of drugs with high and moderate bioavailability, a linear discriminant analysis was carried out. The percentage of correct classification was 100% for compounds of the training set. The leave-one-out cross validation procedure showed an 88.23% of correct classification. Also, a quantitative model, by the piecewise linear regression was developed. The theoretically predicted values for human bioavailability was assessed by a correlation with in vivo rat bioavailability and the regression equation was used to predict this biopharmaceutical property for two new pre-clinical 6-fluoroquinolone derivatives. On the other hand, a linear regression model that explained the 84% of variance was developed to predict the MIC90 values. Finally, the role of a pharmacokinetic and pharmacological relationship in the design of new fluoroquinolones was evaluated in the Sitafloxacin framework, where 13 substituents were analyzed; halogens and methoxy groups had the best contributions to both properties. The present approach proved to be a good method for studying the pharmacokinetics and the pharmacological properties of new 6-fluoroquinolone candidates in drug development studies.

Animals↗
PubMed2001

Collision-induced dissociation of bradykinin ions in the interface region of an ESI-MS.

By applying different electric field strengths to the orifice-skimmer region of an electrospray ionization mass spectrometer, the rate of dissociation can be varied based on the amount of internal energy acquired by an ion through collisions with the curtain gas molecules. Both the Arrhenius equation and Rice-Ramsperger-Kassel (RRK) theory can be used to predict the rate of dissociation of internally excited molecules. A previously determined model for collision-induced dissociation is tested by comparison of predicted and experimentally observed orifice-skimmer potential differences for dissociation of ions. The rate of collision-induced dissociation of bradykinin ions is determined by monitoring the fragments produced in a mass spectrometer. The semi-quantitative model is found to yield effective predictions when accurate Arrhenius and RRK parameters are utilized.

Algorithms↗
PubMedDate not supplied

The role of molecular methods in evaluating biological treatment processes.

Methods derived from molecular biology provide powerful new tools to analyze biological treatment processes. Because molecular methods can be used to directly interrogate genetic information about the microbial community, they can provide the fine detail that is impossible with the blunt, nondiscriminating information usually obtained from more traditional measures such as biochemical oxygen demand and volatile suspended solids. Molecular methods allow tracking of critical groups of microorganisms, such as ammonia oxidizers, that comprise a small fraction of the total biomass. Molecular methods also allow tracking of specific metabolic reactions or other functions that are key to the satisfactory performance of a system. Despite their power, molecular methods do not provide sufficient information when used alone. Aggregated measures and quantitative modeling remain necessary to establish mass balances, quantify the function of the microbial community, and connect the results of molecular assays to practice. Several examples involving nitrifying bacteria in activated sludge illustrate the fine detail available with molecular methods and how they can be linked to traditional and quantitative analyses. Other manuscripts in this special issue also provide examples of the value of using molecular tools in combination with traditional methods.

Biomass↗
PubMed1991

A kinetic model for the alpha-thrombin-catalyzed conversion of plasma levels of fibrinogen to fibrin in the presence of antithrombin III.

In this study we report a kinetic model for the alpha-thrombin-catalyzed production of fibrin I and fibrin II at pH 7.4, 37 degrees C, gamma/2 0.17. The fibrin is produced by the action of human alpha-thrombin on plasma levels of human fibrinogen in the presence of the major inhibitor of alpha-thrombin in plasma, antithrombin III (AT). This model quantitatively accounts for the time dependence of alpha-thrombin-catalyzed release of fibrinopeptides A and B concurrent with the inactivation of alpha-thrombin by AT and delineates the concerted interactions of alpha-thrombin, fibrin(ogen), and AT during the production of a fibrin clot. The model also provides a method for estimating the concentration of alpha-thrombin required to produce a clot of known composition and predicts a direct relationship between the plasma concentration of fibrinogen and the amount of fibrin produced by a bolus of alpha-thrombin. The predicted relationship between the concentration of fibrinogen and the amount of fibrin produced in plasma provides a plausible explanation for the observed linkage between plasma concentrations of fibrinogen and the risk for ischemic heart disease.

Antithrombin III↗
PubMed1999

Modeling drug consumption in the clinic using simulation procedures: demand for heroin and cigarettes in opioid-dependent outpatients.

Use of a time- and cost-efficient simulation procedure to assess reinforcement efficacy in humans was explored in the present study. Opioid-dependent outpatients completed questionnaires asking how many cigarettes or bags of heroin they would purchase across a range of prices. Reported consumption patterns conformed to a quantitative model that has been successful in accounting for data obtained in studies using real rather than hypothetical consequences, suggesting the self-report data may have been a valid proxy for observations of actual consumption patterns. Simulation procedures may thus be a useful supplement to traditional operant methods for the assessment of reinforcement efficacy in humans, particularly in situations where the use of operant methods is logistically difficult or ethically questionable. The relationship between behavioral-economic and traditional measures of reinforcement efficacy is also discussed.

Adult↗
PubMed1990

Cyclic GMP and calcium: the internal messengers of excitation and adaptation in vertebrate photoreceptors.

The roles of cyclic GMP (cGMP) and calcium (Ca2+) in vertebrate rod phototransduction are reviewed, with the emphasis on developments since the discovery of the cGMP-activated conductance of the rod outer segment. The first hypothesis subjected to critical examination is that cGMP acts as the sole internal messenger of excitation. This hypothesis is evaluated with a formal, quantitative model of the biochemical actions of cGMP. Application of the model shows a remarkable agreement between independent electrophysiological and biochemical measurements of the resting dark amounts of (1) total cGMP (2) free cGMP (3) fraction of open cGMP-activated channels and (4) the rate of cGMP hydrolysis. The second hypothesis examined is that Ca2+ acts as an internal messenger in rod light adaptation. Recent electrophysiological evidence has shown minimization of the normal light-induced reduction of free Ca2+ prevents rods from exhibiting the change in sensitivity and speed characteristic of light adaptation. Physiological effects, formerly attributed to a role of calcium as an excitational messenger are shown to be consistent with a biochemical model in which Ca2+ serves as the cytoplasmic signal in a powerful feedback loop that acts to restore the concentration of cGMP both during and after exposure to light. Residual problems facing the "cGMP cascade theory of phototransduction" are reviewed. Issues are itemized that will have to be resolved quantitatively before it will be possible to develop a fully comprehensive theory of photoreceptor excitation, restoration and adaptation combining the roles of Ca2+ and cGMP.

Adaptation, Physiological↗
PubMed2004

Probing single-stranded DNA conformational flexibility using fluorescence spectroscopy.

Single-stranded DNA (ssDNA) is an essential intermediate in various DNA metabolic processes and interacts with a large number of proteins. Due to its flexibility, the conformations of ssDNA in solution can only be described using statistical approaches, such as flexibly jointed or worm-like chain models. However, there is limited data available to assess such models quantitatively, especially for describing the flexibility of short ssDNA and RNA. To address this issue, we performed FRET studies of a series of oligodeoxythymidylates, (dT)N, over a wide range of salt concentrations and chain lengths (10 < or = N < or = 70 nucleotides), which provide systematic constraints for testing theoretical models. Unlike in mechanical studies where available ssDNA conformations are averaged out during the time it takes to perform measurements, fluorescence lifetimes may act here as an internal clock that influences fluorescence signals depending on how fast the ssDNA conformations fluctuate. A reasonably good agreement could be obtained between our data and the worm-like chain model provided that limited relaxations of the ssDNA conformations occur within the fluorescence lifetime of the donor. The persistence length thus estimated ranges from 1.5 nm in 2 M NaCl to 3 nm in 25 mM NaCl.

DNA, Single-Stranded↗