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At least 1,153 records · Page 64Linked to original sources

PubMed2005

An application of model-fitting procedures for marginal structural models.

Marginal structural models (MSMs) are being used more frequently to obtain causal effect estimates in observational studies. Although the principal estimator of MSM coefficients has been the inverse probability of treatment weight (IPTW) estimator, there are few published examples that illustrate how to apply IPTW or discuss the impact of model selection on effect estimates. The authors applied IPTW estimation of an MSM to observational data from the Fresno Asthmatic Children's Environment Study (2000-2002) to evaluate the effect of asthma rescue medication use on pulmonary function and compared their results with those obtained through traditional regression methods. Akaike's Information Criterion and cross-validation methods were used to fit the MSM. In this paper, the influence of model selection and evaluation of key assumptions such as the experimental treatment assignment assumption are discussed in detail. Traditional analyses suggested that medication use was not associated with an improvement in pulmonary function--a finding that is counterintuitive and probably due to confounding by symptoms and asthma severity. The final MSM estimated that medication use was causally related to a 7% improvement in pulmonary function. The authors present examples that should encourage investigators who use IPTW estimation to undertake and discuss the impact of model-fitting procedures to justify the choice of the final weights.

Air Pollutants↗

PubMed1994

DNA modeller: an interactive program for modelling stacks of DNA base pairs on a microcomputer.

DNA Modeller is a microcomputer program for interactively manipulating up to 20 bp in a DNA double helical arrangement. It calculates the van der Waals and electrostatic energies of base-base interactions using the AMBER potential, minimizes the energy with respect to the pair (buckle, propeller, opening, shear, stretch, stagger) and step (tilt, roll, twist, shift, slide, rise) parameters, calculates lengths of the canonical hydrogen bonds between the complementary bases, and calculates interatomic distances between the successive base pairs. Input/output files are simple lists of the step and pair parameters or lists of the atom specifications (N1, C2, etc.) and their Cartesian coordinates (compatible with the Desktop Molecular Modeller*.mol files). The program is supplied with a readbrk utility which transforms PDB/NDB to the *.mol format readable by DNA Modeller. The DNA crystal structures deposited in the PDB or NDB databases can thus be analyzed, and their bases visualized and interactively manipulated. In addition, DNA Modeller can calculate the base pair and step geometrical parameters and interaction energies. A plotter utility creates wire mono or stereo pictures of the bases. This program is designed for IBM-compatible computers working under DOS or can run as a DOS application under MS Windows 3.x or Merge (SCO Unix DOS emulator).

Base Composition↗

PubMed1994

Nucleic acid modeling tool (NAMOT): an interactive graphic tool for modeling nucleic acid structures.

The helical nature of the molecule (almost all of the DNA and a significant portion of the RNA) makes the modeling of nucleic acids a unique task. Unlike other biopolymers (proteins, lipids, etc.), the integrity the structure of a nucleic acid molecule depends strongly on the maintenance of the base pairing within the molecule. Structural alterations (bending, stretching, compressing, etc.), in general, should not disturb the base pairings. A custom-made molecular modeling tool is developed taking into consideration this specific property of the molecule. Instead of Cartesian coordinates, the modeling is carried out on a set of reduced coordinates developed here in our laboratory. One of the advantages using this set of reduced coordinates is the readiness of maintaining the base pairings while altering the structure. A graphic routine is incorporated into the package to display the image of the molecule while the modeling work is being executed. The program is written in C using XView tool kit with Xlib routines to ensure portability to different workstations.

Algorithms↗

PubMed2004

Modeling T-cell activation using gene expression profiling and state-space models.

MOTIVATION: We have used state-space models to reverse engineer transcriptional networks from highly replicated gene expression profiling time series data obtained from a well-established model of T-cell activation. State space models are a class of dynamic Bayesian networks that assume that the observed measurements depend on some hidden state variables that evolve according to Markovian dynamics. These hidden variables can capture effects that cannot be measured in a gene expression profiling experiment, e.g. genes that have not been included in the microarray, levels of regulatory proteins, the effects of messenger RNA and protein degradation, etc. RESULTS: Bootstrap confidence intervals are developed for parameters representing 'gene-gene' interactions over time. Our models represent the dynamics of T-cell activation and provide a methodology for the development of rational and experimentally testable hypotheses. AVAILABILITY: Supplementary data and Matlab computer source code will be made available on the web at the URL given below. SUPPLEMENTARY INFORMATION: http://public.kgi.edu/~wild/LDS/index.htm

Computer Simulation↗

PubMed2001

Model-based administration of inhalation anaesthesia. 2. Exploring the system model.

We explored our model by displaying its new capabilities, testing its sensitivity to variations in input data and illustrating its use. Its multiple-gas character allows simulation of the mechanisms governing concentration and second gas effects. Simulating the volume of a standing bellows makes it possible to test algorithms for automated closed-circuit anaesthesia. Using desflurane, the model's sensitivity to changes in blood/gas partition coefficient (range 0.42-0.576), cardiac output and minute ventilation was analysed. The model was very sensitive to changes in blood solubility; other results agreed with those reported previously. An alveolar isoflurane tension of 1% atm was rapidly attained and maintained, even using 0.5 litres min(-1) of fresh gas, when isoflurane was 'co-administered' through a vaporizer set to 3.5 vol% and a single aliquot (1.25 ml liquid) injected into the expiratory limb. As a result of its credibility and capabilities, the model is to be tested in the clinical setting.

Algorithms↗

PubMed1993

Animal infection models and ethics -- the perfect infection model.

Experimental infection models have long been recognized as an essential part of testing anti-infective therapies. A perfect animal model would be a model that satisfied not only scientific criteria, but ethical criteria as well. In the design and execution of such experiments, scientific and ethical considerations are not mutually exclusive, but should be convergent and therefore result in the optimal model.

Animal Experimentation↗

PubMed2004

Modeling fetal adaptation to nutrient restriction: testing the fetal origins hypothesis with a supply-demand model.

The fetal origins hypothesis (FOH) posits that fetal adaptations to nutritional insufficiency elevate future risk for cardiovascular disease (CVD). Although birth weight (BW) remains the most commonly used index of fetal nutritional sufficiency in FOH research, it is a poor index of fetal nutrition because it is also influenced by genes, epigenetic effects and other nonnutritional factors. This paper uses data from the Cebu Longitudinal Health and Nutrition Survey (CLHNS) to explore an alternate strategy--the supply-demand model--as a means to model fetal nutritional sufficiency, adaptation and cardiovascular programming. Specifically, it is hypothesized that small size should be associated with elevated CVD risk, but only when there is corroborating evidence that the individual had a higher growth potential, was born to a nutritionally stressed mother, or both. Using low density lipoprotein cholesterol (LDL-C) and systolic blood pressure (SBP) as markers of CVD risk, the predictions of the model are only met for LDL-C and only in males. There is evidence for an association between maternal nutritional status and male offspring SBP, but this relationship is independent of fetal nutritional sufficiency as defined by the model. Thus, although both the LDL-C and SBP findings support the general hypothesis that the prenatal milieu has long-term implications for CVD risk in males, only the patterns observed for LDL-C are consistent with the prediction that fetal nutritional sufficiency is key to CVD programming.

Adaptation, Physiological↗

PubMed2005

An improved photo-absorption cross section model for the physics models regime in MCNPX.

The photo-nuclear physics model capabilities utilising the CEM2k model implemented in the MCNPX code were improved > 100 MeV photon energy by basing the photon transport on experimental photo-absorption cross sections of nuclides rather than on free nucleon cross sections. Below 100 MeV, the photo-nuclear physics model now uses isotope-specific giant dipole resonance (GDR) photo-absorption cross sections that are provided to the code in a parameterised form on a data file. Adjustments of the photo-fission cross sections were implemented to match the BOFOD evaluated data through a CEM2k internal parameter. The physics models with these improvements are better equipped to supplement the tabulated data based photo-nuclear MCNPX capability for isotopes with missing tabulated data evaluations especially in the GDR region, and has improved its predictive power at energies above the GDR resonances.

Absorption↗

PubMed2003

An atomic detail model for the human ATP binding cassette transporter P-glycoprotein derived from disulfide cross-linking and homology modeling.

The multidrug resistance P-glycoprotein mediates the extrusion of chemotherapeutic drugs from cancer cells. Characterization of the drug binding and ATPase activities of the protein have made it the paradigm ATP binding cassette (ABC) transporter. P-glycoprotein has been imaged at low resolution by electron cryo-microscopy and extensively analyzed by disulphide cross-linking, but a high resolution structure solved ab initio remains elusive. Homology models of P-glycoprotein were generated using the structure of a related prokaryotic ABC transporter, the lipid A transporter MsbA, as a template together with structural data describing the dimer interface of the nucleotide binding domains (NBDs). The first model, which maintained the NBD:transmembrane domain (TMD) interface of MsbA, did not satisfy previously published cross-linking data. This suggests that either P-glycoprotein has a very different structure from MsbA or that the published E. coli MsbA structure does not reflect a physiological state. To distinguish these alternatives, we mapped the interface between the two TMDs of P-glycoprotein experimentally by chemical cross-linking of introduced triple-cysteine residues. Based on these data, a plausible atomic model of P-glycoprotein could be generated using the MsbA template, if the TMDs of MsbA are reoriented with respect to the NBDs. This model will be important for understanding the mechanism of P-glycoprotein and other ABC transporters.

ATP Binding Cassette Transporter, Subfamily B, Mem↗

PubMed2000

Ingestion pathway model developed for use with an acute atmospheric dose model at the Savannah River Site.

AXAIRQ is a straight-line Gaussian plume dose model used for prospective accident assessment at the Savannah River Site and currently includes the following dose pathways: inhalation, ground shine, and plume shine. In the event of an accident, another possible pathway for dose would be through ingestion of locally produced contaminated foodstuffs. A model, AXINGST, has been developed that would incorporate this pathway. Currently available ingestion models were referenced as a basis for AXINGST. The model calculates an ingestion dose following an atmospheric release of radionuclides and includes site-specific variables where applicable. AXINGST estimates tritium vegetation concentrations that are within a factor of 20-40 of measured data during previous accidental releases at SRS.

Air Pollutants, Radioactive↗

PubMed2004

Dosimetry of metal tritide particles as evaluated by the ICRP 66 model and a biokinetic model from laboratory rats.

Internal radiation from inhalation of metal tritide aerosols may present a significant radiation protection problem for nuclear facility workers. Dose was evaluated for three metal tritides: hafnium, titanium, and zirconium. The study included in vitro and in vivo exposures. The inhalation doses for the three materials were calculated by using the ICRP 66 lung model. The doses also were evaluated by a biokinetic model, which was developed according to the results of animal studies. Results showed that the hafnium tritide particles were the most dense but they had a lower dissolution rate and a higher retention rate. Among these three tritides, hafnium was classified as a Type S material according to the ICRP 66 publication, whereas titanium and zirconium ranked between Type M and F materials. The dissolution rate of hafnium tritide appeared to agree well with the in vitro and in vivo studies. The dissolution rates of the other two materials in the in vitro studies were a little higher than those of the in vivo studies. The doses calculated by the ICRP 66 model for all materials were approximately two orders smaller than the doses obtained by the animal studies. This bias was caused by the different intake methods of the ICRP 66 model (inhalation) and in the animal study (instillation). The doses were on the same order while correcting for deposition fractions. The effective doses for hafnium, titanium, and zirconium tritides were 5.43 x 10(-10), 9.05 x 10(-11), and 6.5 x 10(-10) Sv Bq(-1), respectively, according to the animal studies.

Administration, Inhalation↗

PubMed2001

Compartmental modeling of technetium-99m-labeled teboroxime with dynamic single-photon emission computed tomography: comparison with static thallium-201 in a canine model.

UNLABELLED: Di Bella EVR, Ross SG, Kadrmas DJ, et al. Compartmental modeling of technetium-99m-labeled teboroxime with dynamic single-photon emission computed tomography: Comparison with static thallium-201 in a canine model. Invest Radiol 2001;36:178-185. RATIONALE AND OBJECTIVES: A compartmental modeling approach to deriving kinetic parameters from a time series of single-photon emission computed tomography (SPECT) images of technetium-99m-labeled (99mTc-) teboroxime may have value for semiquantitative assessment of myocardial perfusion. This study investigated the value of the kinetic parameters derived from a two-compartment model of 99mTc-teboroxime for measuring myocardial perfusion and compared it with static thallium-201 (201Tl) uptake and microsphere-measured blood flow in dogs. METHODS: Experiments were successfully conducted in 9 of 11 open-chest dogs. During adenosine stress, a single complete set of projections of 201Tl uptake was acquired. 99mTc-teboroxime was then injected during adenosine stress, and a complete set of projections was acquired every 5.7 seconds for 17 minutes. Resting studies were performed on 4 of the animals. All of the projection sets were reconstructed with an iterative algorithm and incorporated corrections for attenuation and the geometric response of the collimators. Regional kinetic parameters (washin and washout) were determined semiautomatically from the time series of reconstructed 99mTc-teboroxime images and registered with microsphere data. Regional washin estimates were compared with 201Tl intensities and myocardial blood flows determined from microspheres. RESULTS: Optimally scaled 99mTc-teboroxime washin parameters and 201Tl uptakes were correlated with microsphere-determined blood flows (r = 0.91, y = 0. 99x + 0.01, and r = 0.92, y = 0.88x + 0.28, respectively). In six of the studies, the left anterior descending coronary artery was occluded, and stress occluded-to-normal (O/N) ratios were calculated. The O/N ratios were 0.32 +/- 0.17 as determined from microspheres injected with 201Tl and 0.38 +/- 0.29 from microspheres injected with 99mTc-teboroxime (P = NS). The O/N ratios were 0.48 +/- 0.16 for static 201Tl uptake and 0.27 +/- 0.21 for 99mTc-teboroxime washin (P < 0.05). CONCLUSIONS: Both 201Tl uptake and 99mTc-teboroxime kinetic parameters were well correlated with flow. The 99mTc-teboroxime washin parameters offer semiquantitative flow values and provide greater defect contrast than can be obtained with 201Tl uptake values.

Animals↗

PubMed1999

Comparison of healing process in open osteotomy model and closed fracture model.

OBJECTIVE: Comparison of the healing process in open osteotomy and closed fracture models that were used to study fracture healing. DESIGN: Randomized, prospective study in experimental animals, with a recovery duration of two and four weeks. SETTING: Unrestricted cage activity with weight bearing as tolerated. ANIMALS: Thirty-four skeletally mature, female New Zealand White rabbits. INTERVENTIONS: Closed fractures and open osteotomies of the tibial diaphysis were reduced and immobilized with four-pin, double-bar external fixators. MAIN OUTCOME MEASUREMENTS: Callus circumference was measured with a tape measure, bridging callus was assessed on biplane radiographs and evaluated histologically, and torsional stiffness and maximum torque were measured. RESULTS: Periosteum damage was more severe and hematoma formation was smaller in the osteotomy model, resulting in a delay in biological healing and restoration of the biomechanical properties. CONCLUSIONS: Investigators should consider the difference between the closed fracture and open osteotomy models when selecting an animal model to investigate fracture healing.

Animals↗

PubMed2000

Achieving target goals most precisely using nonparametric compartmental models and "multiple model" design of dosage regimens.

Multiple model (MM) design and stochastic control of dosage regimens permit essentially full use of all the information contained in either a Bayesian prior nonparametric EM (NPEM) population pharmacokinetic model or in an MM Bayesian posterior updated parameter set, to achieve and maintain selected therapeutic goals with optimal precision (least predicted weighted squared error). The regimens are visibly more precise in the achievement of desired target goals than are current methods using mean or median population parameter values. Bayesian feedback has now also been incorporated into the MM software. An evaluation of MM dosage design using an NPEM population model versus dosage design based on conventional mean population parameter values is presented, using a population model of vancomycin. Further feedback control was also evaluated, incorporating realistic simulated uncertainties in the clinical environment such as those in the preparation and administration of doses.

Anti-Bacterial Agents↗

PubMed2002

Can the thoracic kyphosis be modeled with a simple geometric shape? The results of circular and elliptical modeling in 80 asymptomatic patients.

Many Cobb measurements have been reported at various levels for the thoracic kyphosis, but geometric models of the shape of kyphosis are rare. Thoracic vertebral bodies were digitized on 80 normal lateral full-spine radiographs to obtain the mean thoracic kyphosis. Global and segmental angles were determined. Computer iteration processes passed geometric shapes through the posterior body coordinates of the mean thoracic kyphosis to determine the best fit model in the least squares sense. The kyphosis was closely modeled with ellipses. The T1 and T12 areas tended to be flatter in curvature when compared with T2-T11, indicating these are inflection points. Mean global angles were Cobb(T1-T12) = 44.2 degrees, Cobb(T2-T11) = 39.9 degrees, and Cobb(T3-T10) = 33.3 degrees. The T2-T11 kyphotic region was closely modeled with approximately a 70-degree portion of an ellipse, with minor axis to major axis ratios of 0.6 to 0.72, and with major axis parallel to the posterior body margin of T11.

Adult↗

PubMed2002

Positron emission tomography compartmental models: a basis pursuit strategy for kinetic modeling.

A kinetic modeling approach for the quantification of in vivo tracer studies with dynamic positron emission tomography (PET) is presented. The approach is based on a general compartmental description of the tracer's fate in vivo and determines a parsimonious model consistent with the measured data. The technique involves the determination of a sparse selection of kinetic basis functions from an overcomplete dictionary using the method of basis pursuit denoising. This enables the characterization of the systems impulse response function from which values of the systems macro parameters can be estimated. These parameter estimates can be obtained from a region of interest analysis or as parametric images from a voxel-based analysis. In addition, model order estimates are returned that correspond to the number of compartments in the estimated compartmental model. Validation studies evaluate the methods performance against two preexisting data led techniques, namely, graphical analysis and spectral analysis. Application of this technique to measured PET data is demonstrated using [11C]diprenorphine (opiate receptor) and [11C]WAY-100635 (5-HT1A receptor). Although the method is presented in the context of PET neuroreceptor binding studies, it has general applicability to the quantification of PET/SPECT radiotracer studies in neurology, oncology, and cardiology.

Artifacts↗

PubMed1997

Spatial interactions between subsurface bacterial colonies in a model system: a territory model describing the inhibition of Listeria monocytogenes by a nisin-producing lactic acid bacterium.

The effect of spatial separation on interactions between subsurface bacterial colonies was tested using a model system: the inhibition of Listeria monocytogenes by nisin-producing and nisin-non-producing Lactococcus lactis subsp. lactis. Separation distance was controlled by altering the number of inoculum organisms within the agar. Mean separation distance was calculated by determining the mean volume available to each cell at the start of the experiment. Inhibition was assessed by comparing the growth of L. monocytogenes in pure culture with its growth in the presence of Lac. lactis subsp. lactis. Increasing the distance between colonies resulted in an exponential decrease in inhibition. When L. monocytogenes and Lac. lactis subsp. lactis colonies were within 100 microns of each other, the increase in cell numbers per L. monocytogenes colony was only 0.6 c.f.u. (which indicated some cells had become non-viable). This was a log reduction of 3.5 compared to the pure culture control. A separation distance of 1000 microns resulted in a L. monocytogenes colony growth increment of 2.5 x 10(2) c.f.u. per colony, a log reduction of 3.0 compared to the control. Increasing the separation distance to 3000 microns resulted in a L. monocytogenes colony growth increment of 1.3 x 10(6) c.f.u. per colony, a log reduction of 0.9 compared to the control. The effects of nisin and acidity were investigated by using a nisin-non-producing strain of Lac. lactis subsp. lactis and by buffering the medium. Data were obtained for the effect of separation on inhibition, as well as competition between colonies of the same species. The inhibition was mathematically described in terms of a simplified 'territory' model of immobilized bacterial growth. There was a strong qualitative agreement between the mathematical model and the experimental data. It was concluded that the phenomenon of propinquity is of important consideration when modeling and predicting microbial growth within solid food systems.

Antibiosis↗

PubMed1986

Comparison of abrasion model differences in heavy ion fragmentation: optical versus geometric models.

Using an abrasion-ablation collision model, which includes contributions from frictional-spectator interactions and electromagnetic dissociation, analyses of the sensitivities of predicted fragmentation cross sections to the choice of a particular abrasion formalism are made using both geometric and optical potential abrasion models. Most cross section differences obtained using the two abrasion models are less than the present experimental uncertainties, suggesting that either abrasion model is suitable for estimating isotopic and elemental fragment distributions.

Elementary Particles↗