A simple mathematical lung model for quantitative regional ventilation measurement using 81Krm.
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Krypton↗
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Results for “quantitative model”
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An in vivo quantitative angiogenesis model using tumor cells entrapped in alginate.
A new in vivo system of monitoring tumor cell induced blood vessel growth using a sodium alginate entrapment process was developed. The alginate polymer of guluronic and mannuronic acids surrounds and sequesters cells from direct contact with their immediate environment, but permits diffusible angiogenic factors to pass through to induce neovascularization in the host. The alginate beads containing tumor cells were injected subcutaneously into animals and coalesced as a point source. The tumor cells are protected from direct contact with the host's immune system, so that various tumor types may be evaluated for their angiogenic potential across histocompatibility or species barriers. C57BI/6, BALB/c and nude mice as well as squirrel monkeys were used as host animals. This provided tumor cell testing in a syngeneic, allogeneic, or xenogeneic system. We found that alginate-Lewis lung carcinoma cells were potent inducers of blood vessel growth. As few as 100 alginate-Lewis lung carcinoma cells were needed to induce macroscopically visible blood vessels by 3 days. Dose-response experiments with alginate-Lewis lung carcinoma cells showed a greater level of blood vessel induction as cell numbers increased. Neovascularization was monitored qualitatively by macroscopic photography and microscopic histologic evaluation. Also, neovascularization was monitored quantitatively by measuring the level of hemoglobin at the injection site of alginate or by measuring the amount of radioactive red blood cells pooled at the injection site of the alginate beads. Both the measured levels of hemoglobin and radiolabeled red blood cells increased at the alginate site with each log increase of tumor cells delivered, which paralleled our findings at the macroscopic and microscopic level. This in vivo angiogenesis model was relatively simple and the procedures technically easy to perform. Most importantly, this model allowed both a qualitative and quantitative assessment of tumor-induced blood vessel growth.
Alginates↗
Molecular modeling and quantitative structure-activity analysis of antibacterial sulfanilamides and sulfones.
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Anti-Bacterial Agents↗
Quantitation of model digestive mixtures by 13C NMR.
13C nuclear magnetic resonance (NMR) spectra were obtained at 50.3 and 100.5 MHz for methanolic and aqueous mixtures of sodium taurocholate, 1-monocapryloyl-rac-glycerol, and caprylic acid. Distortionless Enhancement by Polarization Transfer (DEPT) was used to improve spectral sensitivity and resolution, and to generate calibration curves for quantitative determinations of each lipid in methanol. Alternatively, the heights for nonoverlapping peaks in a 13C NMR spectrum acquired with inverse-gated decoupling provide reliable quantitative estimates for each component of the mixture, particularly when the data are obtained in methanol. These experiments also demonstrate the feasibility of detailed NMR structural investigations in model systems for glyceride digestion.
Carbon Isotopes↗
Dual β-lactam therapy against high-risk Pseudomonas aeruginosa isolates: a dynamic in-vitro infection model study integrating population genomics with quantitative systems pharmacology modelling and simulations.
BACKGROUND: Pseudomonas aeruginosa has an extraordinary capacity for resistance emergence during treatment, even with newer antipseudomonals. There is a gap in understanding how resistance mechanisms affect the time-course of bacterial response to these newer agents. Traditional approaches for predicting pathogen response to an antibiotic do not apply to combination therapy. We aimed to develop a modelling framework to predict treatment response based on resistome information, using isolates of the worldwide-disseminated high-risk clone sequence type (ST) 235 and β-lactam antibiotics as the example. METHODS: In this hollow-fibre in-vitro infection study, we used three extensively drug-resistant ST235 clinical isolates from the national collection of the Clinical Microbiology Department of the Hospital Son Espases (Palma de Mallorca, Spain) that were hospital-acquired, were isolated following routine microbiological procedures from different patients between 2017 and 2022, were susceptible to ceftolozane-tazobactam, and had different levels of meropenem resistance. The selected isolates (ST235-05, ST235-09, and ST235-10) showed classical β-lactam resistance mechanisms pre-treatment. The isolates were investigated in 240-h dynamic hollow-fibre in-vitro infection models (HFIMs). The studies exposed the isolates to pharmacokinetic profiles of ceftolozane-tazobactam (simulating 1 g of ceftolozane and 0·5 g of tazobactam as a 3-h infusion every 8 h) and meropenem (simulating 6 g per day continuous infusion) as observed in hospitalised patients, as monotherapy and in combination. Treatment response was assessed through the quantification of the time-courses of viable total and resistant bacteria. Whole-genome sequencing identified the mechanisms of emerging resistance. A quantitative systems pharmacology (QSP) approach was used to model total and resistant bacterial counts and corresponding pharmacokinetic data from the HFIM. Monte Carlo simulations were used to predict treatment responses in 1000 virtual infected patients treated with ceftolozane-tazobactam and meropenem as monotherapies or in combination over 10 days. FINDINGS: In the HFIMs, each antibiotic alone amplified resistance by approximately 48 h for all isolates; that is, monotherapies resulted in a higher concentration of resistant bacteria compared with the control treatment at the respective time, except ceftolozane-tazobactam against ST235-10. Combination of ceftolozane-tazobactam and meropenem was synergistic (bacterial counts ≥2 log10 colony forming units [CFU] per mL lower than the best performing monotherapy and initial inoculum) against all isolates and suppressed resistance. Against ST235-10, ceftolozane-tazobactam monotherapy reduced counts to less than 1 log10 CFU per mL from 192 h onwards, whereas the combination reached less than 1 log10 CFU per mL by 24 h. Across strains, population genomics confirmed monotherapy failures were associated with emerging resistance mechanisms (ceftolozane-tazobactam: ampC Ω-loop mutations; meropenem: ftsl mutation). The developed QSP model incorporated baseline resistance mechanisms and those emerging in resistant mutant subpopulations. The model explained and predicted the monotherapy failures involving amplification of these subpopulations, and synergistic killing and resistance suppression by the combination. Simulations using the model predicted bacterial regrowth above the initial inoculum for more than 90% of patients after 0 to approximately 3 days for meropenem monotherapy across all strains and for ceftolozane-tazobactam monotherapy against ST235-05 and ST235-09. For ceftolozane-tazobactam monotherapy against ST235-10, regrowth was predicted for approximately 30% of patients. In contrast, the simulations predicted sustained bacterial killing of at least 2 log10 CFU per mL compared with the initial inoculum by the combination for more than 89% of patients across all strains. INTERPRETATION: To our knowledge, this model is the first to characterise and predict the time-course of responses of clinical isolates to antibiotics only by the resistance mechanisms present and their complex interplay, representing a step towards pathogen-specific, personalised medicine. FUNDING: Australian National Health and Medical Research Council.
Pseudomonas aeruginosa↗
An immunoprecipitation-dissociation technique for large scale antibody purification and an antigen consumption electroimmunoassay for antibody quantitation. A model study with antibodies to pregnancy zone protein.
A simple immunoprecipitation--dissociation technique for large scale purification of antibodies is described, which comprises selective denaturation of the antigen and recovery of the antibody fraction by exclusion chromatography at low pH. Its use is illustrated by the purification of antibodies to pregnancy zone protein. A purification factor of about 60 was achieved. An antigen consumption electroimmunoassay was also developed which permits quantitative determination of the antigen binding activity of antibodies with a given specificity. The methods have general application.
Antibodies↗
Multifactorial genetic models for quantitative traits in humans.
Quantitative traits measured in human families can be analyzed to partition the total population variance into genetic and environmental components, or to elucidate the genetic mechanism involved. We review the estimation of variance components directly from human pedigree data, or in the form of path coefficients from correlations between pairs of relatives. To elucidate genetic mechanisms, a mixed model that allows for segregation at a major locus, a polygenic effect and a sibling environmental correlation is described for nuclear families. In each case appropriate likelihoods are derived as a basis, using numerical maximum likelihood methods, for parameter estimation and hypothesis testing. A general model is then described that allows for several familial sources of environmental variation, assortative mating, and both major gene and polygenic effects; and an algorithm for calculating the likelihood of a pedigree under this model is indicated. Finally, some of the remaining problems in this area of biometric analysis are pointed out.
Genetic Variation↗
Qualitative and quantitative experimental models to aid in risk assessment for immunotoxicology.
We have previously reported on the design and content of a screening battery using a "tier" approach for detecting potential immunosuppressive compounds in mice [1]. This battery was composed of various immune function, immunopathology and host resistance tests, the results of which could help establish the potential of chemical and biological agents to cause immunosuppression. The data from these studies, which now encompass over 50 compounds, have been analyzed in an attempt to improve future testing strategies and provide information to aid in the risk assessment process. Specifically, the following two issues will be addressed; what are the likelihood(s) for each of the individual tests and testing configurations to accurately identify immunotoxic compounds? and what are the quantitative and qualitative relationships between the immune tests and host resistance assays?
Animals↗
Interactions between K+ and ATP binding to the (Na+ + K+)-dependent ATPase.
K+ appears to decrease the affinity of the (Na+ + K+)-dependent ATPase (ATP phosphohydrolase, EC 3.6.1.3) for its substrate, Mg2+ - ATP, and Mg2+ - ATP, in turn, appears to decrease the affinity of the enzyme for K+. These antagonisms have been investigated in terms of a quantitative model defining the magnitude of the effects as well as identifying the class of K+ sites on the enzyme involved. K+ increased the apparent Km for Mg2+ - ATP, an effect that was antagonized competitively by Na+. The data can be fitted to a model in which Mg2+ - ATP binding is prevented by occupancy of alpha-sites on the enzyme by K+ (i.e. sites of moderate affinity for K+ accessible on the "free" non-phosphorylated enzyme, in situ on the external membrane surface). By contrast, occupancy of these alpha-sites by Na+ has no effect on Mg2+ - ATP binding to the enzyme. On the other hand, Mg2+ - ATP decreased the apparent affinity of the enzyme for K+ at the alpha-sites, in terms of (i) the KD for K+ measured by K+-accelerated inactivation of the enzyme by F-, and (ii) the concentration of K+ for half-maximal activation of the K+-dependent phosphatase reaction (which reflects the terminal hydrolytic steps of the overall ATPase reaction). These data fit the same quantitative model. Although this formulation does not support schemes in which ATP binding effects the release of transported K+ from discharge sites, it is consistent with observations that K+ can inhibit the enzyme at low substrate concentrations, and that Li+, which has poor efficacy when occupying these alpha-sites, can stimulate enzymatic activity at high K+ concentrations by displacing the inhibitory K+.
Adenosine Triphosphatases↗
Multivariate clinical models and quantitative dipyridamole-thallium imaging to predict cardiac morbidity and death after vascular reconstruction.
Patients with peripheral vascular disease have a high prevalence of coronary artery disease and are at increased risk for cardiac morbidity and death after vascular reconstruction. The present study was undertaken to assess the value of 18 clinical parameters, of 7 clinical scoring systems, and of quantitative dipyridamole-thallium imaging for predicting the occurrence of postoperative myocardial infarction or cardiac death. Vascular surgery was performed in 125 patients. Thirteen postoperative cardiac events occurred, including 10 cardiac deaths and 3 nonfatal infarctions. Clinical parameters were not useful in predicting postoperative outcome. All 63 patients with normal scan results or fixed perfusion defects underwent surgery uneventfully, whereas 21% (13/62) of patients with reversible defects had a postoperative cardiac complication. By use of quantitative scintigraphic indexes we found that patients with reversible defects could be stratified into intermediate and high-risk subgroups with postoperative event rates of 5% (2/47) and 85% (11/13), respectively, despite intensive postoperative monitoring and antianginal medication. Thus in patients unable to complete a standard exercise stress test, postoperative outcome cannot be predicted clinically, whereas dipyridamole-thallium imaging successfully identified all patients who had a postoperative cardiac event. By use of quantification we found that patients with reversible defects can be stratified into an intermediate risk subgroup that can undergo surgery with minimal complication rate and a high-risk subgroup that requires coronary angiography.
Canada↗
A quantitative rotational model for studying serotonergic function in the rat.
Unilateral injection of 5,7-dihydroxytryptamine (4 mug/4 mul) into the medial forebrain bundle of rats produced serotonin depletions of 65% and 70% in the ipsilateral corpus striatum and ipsilateral forebrain, respectively. These animals showed a dose-dependent increase in contralateral turning (rotational behavior) when pretreated with a peripheral decarboxylase inhibitor and then injected with L-5-hydroxytryptophan in doses ranging from 5 to 100 mg/kg i.p. Injections of p-chloroamphetamine, which releases endogenous stores of serotonin, produced ipsilateral turning which could be blocked by prior serotonin depletion. Systemic administration of the catecholamine drugs L-DOPA, apomorphine and D-amphetamine never elicited consistent turning in either direction in these animals. These data indicate that the turning response of rats with unilateral destruction of brain serotonin nerve terminals provides a sensitive tool for quantifiably studying changes in serotonergic function.
5-Hydroxytryptophan↗
Blood glucose response to stress hormone exposure in healthy man and insulin dependent diabetic patients: prediction by computer modeling.
To establish a qualitative and quantitative model of blood glucose response to stress hormone exposure, healthy subjects (HS) on and off somatostatin (250 micrograms/h) as well as insulin dependent diabetic patients were infused with either epinephrine (E), glucagon (G), cortisol (F), growth hormone (GH) or with a cocktail of these hormones raising plasma stress hormones to values seen in severe diabetic ketoacidosis. The developed input/output model consists of two submodels interconnected in series plus two additional submodels for correction of gains describing both sensitivity of tissue response and utilisation as well as provision of glucose. It was shown and confirmed experimentally that blood glucose response to stress hormones was essentially nonlinear. Furthermore, the mathematical models for healthy subjects and for insulin dependent diabetic patients proved to be of the same structure and differed only in the values of some typical parameters. The model raises the possibility to describe and in part to predict blood glucose response to stress hormone exposure in healthy man and insulin dependent diabetic patients.
Adult↗
An experimental test of two mathematical models applied to the size-weight illusion.
Two quantitative models, which make different quantitative predictions for the amount of the size-weight illusion, were tested according to the psychophysical methods employed by the respective authors (magnitude estimation versus category ratings). Both models with their corresponding method were supported. This causes uncertainty over Anderson's chaim that the validity of both a model and the applied scale used is sufficiently test by the socalled joint testing procedure.
Humans↗
A functional model of the human cardiac ventricle.
A quantitative model is presented which accurately reproduces the time activity curve of the human left ventricular blood pool. Four parameters receive numerical values and may be of clinical value.
Heart Ventricles↗
A psychophysically motivated model for two-dimensional motion perception.
A quantitative model is developed to predict the perceived direction of moving two-dimensional patterns. The model incorporates both a simple motion energy pathway and a "texture boundary motion" pathway that incorporates response squaring before the extraction of motion energy. These pathways correspond to Fourier and non-Fourier motion pathways and are hypothesized to reflect processing in the V1-MT and V1-V2-MT pathway, respectively. A cosine-weighted sum of these pathways followed by competitive feedback inhibition accurately predicts the perceived direction for patterns composed of two cosine gratings at different orientations ("plaids"). The model also predicts direction discrimination, differences between foveal and peripheral viewing, changes in perceived direction with exposure duration, motion masking, and motion transparency.
Computer Simulation↗
How membrane chain-melting phase-transition temperature is affected by the lipid chain asymmetry and degree of unsaturation: an effective chain-length model.
Hydrocarbon effects on the lipid chain-melting phase-transition temperature are analyzed. The membrane fluidization temperature is shown to increase with the effective chain length, which is proportional to the thickness of the well-packed hydrocarbon region. The latter, as a rule, increases with the length of the longest ordered and aligned segment on each chain. This conclusion is independent of the cause for the reduced chain packing in membrane interior: chain unsaturation (which effectively decouples the two hydrocarbon segments disjoined by a double bond) or chain asymmetry (which causes the terminal hydrocarbon segments to lose close contact) both affect the bilayer chain-melting phase-transition temperature comparably on the effective chain-length scale. Thermodynamic consequences of the trans unsaturation are approximately 50% smaller than the effects of the double bonds in the cis conformation, owing to the smaller membrane perturbation by the former double bonds. A simple quantitative model is introduced for the analysis of the phospholipid chain-melting phase behavior. This new model permits quantitative predictions of the chain-melting transition temperature solely on the basis of the known lipid chemical composition. It also explains lipid sensitivity to the hydrocarbon type and attachment. The model agreement with the experimental data is usually better than to within 99% and thus comparable to experimental scatter, even when only a few or no adjustable parameters are used. The membrane fluidization temperature is calculated for a number of potentially interesting, also as yet unexplored, phospholipids, and the biological significance of the effective chain-length concept is discussed.
Hydrocarbons↗
An experimental design strategy for quantitating complex pharmacokinetic models: enterohepatic circulation with time-varying gallbladder emptying as an example.
A four-step strategy is proposed for determining appropriate experimental designs for investigating the pharmacokinetics of drugs characterized by complex compartmental models and this strategy has been applied to the pharmacokinetics of enterohepatic circulation (EHC). The four steps are (1) to establish an appropriate pharmacokinetic model, (2) to complete an identifiability analysis for the model to determine the route(s) of administration and sampling compartment(s) that are theoretically adequate for the quantitation of model parameters, (3) to carry out nonlinear least-squares fitting for the proposed number and timing of simulated error-free data points, and (4) to complete nonlinear least-squares fits of the model to data obtained by adding random error to the simulated data in step 3. The four-compartment model chosen for EHC of unchanged drug contained central, peripheral, gallbladder, and intestinal compartments and an intermittent gallbladder emptying rate constant. Identifiability analysis demonstrated that three alternative experimental designs for route(s) of administration and sampling compartment(s) are adequate for quantitating all model parameters, when the gallbladder emptying rate constant as a function of time is known (using controlled emptying from an engineered gallbladder in an animal model or quantitation in humans or animals using imaging techniques). Parameter estimates from fitting error-free data matched closely with the known values for all three experimental designs, indicating an adequate number and appropriate timing of data points. Results from fitting simulated data containing +/- 10% random error indicated unacceptable coefficients of variation and a nonrandom pattern in residual plots for one of the experimental designs.(ABSTRACT TRUNCATED AT 250 WORDS)
Animals↗
Quantitative molecular cartography of emergency myelopoiesis reveals conserved modules of hematopoietic activation.
Hematopoietic stem and progenitor cells (HSPCs) respond to infections, inflammation, and regenerative challenges using emergency myelopoiesis (EM) pathways to amplify myeloid cell production. However, it remains unclear how various EM inducers regulate HSPCs using shared or distinct molecular mechanisms. Here, we generate a comprehensive and generalizable cell annotation method (HemaScribe) and a refined quantitative model of hematopoietic differentiation (HemaScape) using single-cell RNA sequencing (scRNA-seq) of murine HSPCs, which we apply to a broad range of EM modalities. We uncover multiple strategies for enhancing myelopoiesis that act at different levels of the HSPC hierarchy and are associated with both unique and shared transcriptional response modules. In particular, we identify a myeloid progenitor-based EM activation module across diverse inflammatory challenges that is conserved in humans and informs outcomes in adult and pediatric acute myeloid leukemia. Our work illuminates fundamental regulatory mechanisms in hematopoietic regeneration that have direct translational applications in disease contexts.
Animals↗