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Progress in predicting human ADME parameters in silico.

Understanding the development of a scientific approach is a valuable exercise in gauging the potential directions the process could take in the future. The relatively short history of applying computational methods to absorption, distribution, metabolism and excretion (ADME) can be split into defined periods. The first began in the 1960s and continued through the 1970s with the work of Corwin Hansch et al. Their models utilized small sets of in vivo ADME data. The second era from the 1980s through 1990s witnessed the widespread incorporation of in vitro approaches as surrogates of in vivo ADME studies. These approaches fostered the initiation and increase in interpretable computational ADME models available in the literature. The third era is the present were there are many literature data sets derived from in vitro data for absorption, drug-drug interactions (DDI), drug transporters and efflux pumps [P-glycoprotein (P-gp), MRP], intrinsic clearance and brain penetration, which can theoretically be used to predict the situation in vivo in humans. Combinatorial synthesis, high throughput screening and computational approaches have emerged as a result of continual pressure on pharmaceutical companies to accelerate drug discovery while decreasing drug development costs. The goal has become to reduce the drop-out rate of drug candidates in the latter, most expensive stages of drug development. This is accomplished by increasing the failure rate of candidate compounds in the preclinical stages and increasing the speed of nomination of likely clinical candidates. The industry now understands the reasons for clinical failure other than efficacy are mainly related to pharmacokinetics and toxicity. The late 1990s saw significant company investment in ADME and drug safety departments to assess properties such as metabolic stability, cytochrome P-450 inhibition, absorption and genotoxicity earlier in the drug discovery paradigm. The next logical step in this process is the evaluation of higher throughput data to determine if computational (in silico) models can be constructed and validated from it. Such models would allow an exponential increase in the number of compounds screened virtually for ADME parameters. A number of researchers have started to utilize in silico, in vitro and in vivo approaches in parallel to address intestinal permeability and cytochrome P-450-mediated DDI. This review will assess how computational approaches for ADME parameters have evolved and how they are likely to progress.

Catalysis↗

A mixture model with detection limits for regression analyses of antibody response to vaccine.

Antibody concentration values as determined by quantitative assays often are left-censored due to detection limits or limits established for purpose of specificity. Standard analyses which assume the data arise from a single lognormal response distribution may not be appropriate, when more observations are censored than would be expected under such a model. Interference from maternal antibodies due to vaccination at an early age, for example, could result in a high proportion of nonresponders to vaccine. A mixture model consisting of a censored lognormal distribution and a point distribution located below the detection limit is proposed for such situations. Antibody data from a study of measles vaccine are used to illustrate the utility of this approach and the interpretation of the model parameters.

Antibodies, Viral↗

Some recent developments for regression analysis of multivariate failure time data.

Cox's seminal 1972 paper on regression methods for possibly censored failure time data popularized the use of time to an event as a primary response in prospective studies. But one key assumption of this and other regression methods is that observations are independent of one another. In many problems, failure times are clustered into small groups where outcomes within a group are correlated. Examples include failure times for two eyes from one person or for members of the same family. This paper presents a survey of models for multivariate failure time data. Two distinct classes of models are considered: frailty and marginal models. In a frailty model, the correlation is assumed to derive from latent variables ("frailties") common to observations from the same cluster. Regression models are formulated for the conditional failure time distribution given the frailties. Alternatively, marginal models describe the marginal failure time distribution of each response while separately modelling the association among responses from the same cluster. We focus on recent extensions of the proportional hazards model for multivariate failure time data. Model formulation, parameter interpretation and estimation procedures are considered.

Clinical Trials as Topic↗

Algorithms for incorporating prior topological information in HMMs: application to transmembrane proteins.

BACKGROUND: Hidden Markov Models (HMMs) have been extensively used in computational molecular biology, for modelling protein and nucleic acid sequences. In many applications, such as transmembrane protein topology prediction, the incorporation of limited amount of information regarding the topology, arising from biochemical experiments, has been proved a very useful strategy that increased remarkably the performance of even the top-scoring methods. However, no clear and formal explanation of the algorithms that retains the probabilistic interpretation of the models has been presented so far in the literature. RESULTS: We present here, a simple method that allows incorporation of prior topological information concerning the sequences at hand, while at the same time the HMMs retain their full probabilistic interpretation in terms of conditional probabilities. We present modifications to the standard Forward and Backward algorithms of HMMs and we also show explicitly, how reliable predictions may arise by these modifications, using all the algorithms currently available for decoding HMMs. A similar procedure may be used in the training procedure, aiming at optimizing the labels of the HMM's classes, especially in cases such as transmembrane proteins where the labels of the membrane-spanning segments are inherently misplaced. We present an application of this approach developing a method to predict the transmembrane regions of alpha-helical membrane proteins, trained on crystallographically solved data. We show that this method compares well against already established algorithms presented in the literature, and it is extremely useful in practical applications. CONCLUSION: The algorithms presented here, are easily implemented in any kind of a Hidden Markov Model, whereas the prediction method (HMM-TM) is freely available for academic users at http://bioinformatics.biol.uoa.gr/HMM-TM, offering the most advanced decoding options currently available.

Algorithms↗

[When patients and doctors don't speak the same language-- concepts of interpretation practice].

In the Swiss Health Care System, working with an interpreter while medically treating migrants speaking a foreign language has become a common practice. However, the theoretical and conceptional framework of this practice has not yet been sufficiently elaborated. Specifically, the presence of an interpreter leads to a triadic interviewing situation that has implications for the medical treatment. Though an interpreter can improve and deepen the understanding between patient and physician, the communication can also become more complex and difficult with his or her presence. The article sheds light on the perspectives that arise from this situation by defining different role models for medical interpreters and discussing their advantages and disadvantages. The discussion focuses on the four following ideal types: word-for-word translation, cultural mediation, patient advocacy and co-therapy. The choice of interpreter's role in influenced by the institutional setting, the kind of treatment chosen as well as by the concrete interaction. To illustrate the different roles as they manifest in the therapeutic situation, examples from taped and retranslated interviews are presented. Doctor-patient interviews will illustrate the different roles interpreters take over while interpreting medical interviews with migrant patients speaking a foreign language.

Female↗

Life not lived due to disequilibrium in heterogeneous age-structured populations.

Three models of age-structured populations with demographically heterogeneous subpopulations are analyzed. In the first model, each subpopulation has its own age-specific vital rates which are fixed in time. In the second model, the vital rates of each subpopulation are uniformly inhibited by increasing total numbers of individuals. In the third, the vital rates of groups of subpopulations are inhibited by the total numbers of individuals in other groups of subpopulations with an intensity that depends on the interacting pair of groups. Three functions are defined to measure disequilibrium in the subpopulation frequencies, subpopulation age structures, and total population size. For the first model, we show that disequilibrium will shift the trajectory of the total numbers of individuals forward or backward in time by an asymptotic constant that is proportional to the sum of the disequilibrium measures. For the second model, we establish sufficient conditions for the existence of a globally stable equilibrium and we show that disequilibrium will result in a finite loss or gain in life which is proportional to the sum of the disequilibrium measures. For the last model, we show that the loss or gain in life for each group of subpopulations is a linear combination over all groups of the sums of the three disequilibrium measures. We illustrate these results with numerical examples and give possible biological interpretations of the models. We relate these new results to previous work on the cost of natural selection and measures of demographic disequilibrium.

Age Factors↗

Development of radiology prediction models using feature analysis.

RATIONALE AND OBJECTIVES: This article provides an introduction to prediction models and their application in diagnostic imaging research. Prediction models capitalize on the different degrees of association among variables to make a prediction of a health state, formulate a rule, or quantify individual contributions of various predictor variables. The purpose of this article is to elucidate the rationale, implication, and interpretation of prediction models using imaging features. MATERIALS AND METHODS: The techniques and challenges of developing, testing, and implementing prediction models are described. Prediction model development methods are similar to data-mining techniques. RESULTS: Learning objectives are to review prediction rule (model) methods, learn how prediction models may be applied to feature analysis, and understand the challenges of developing, testing, and implementing prediction models.

Decision Support Techniques↗

[The radiotherapy satellite in Kristiansand--a model for Norwegian regional hospitals?].

BACKGROUND: During the first decade of 2000, significant increase of radiotherapy capacity in Norway will take place, as the number of linear accelerators will increase from 24 to 36. In Norway, radiotherapy departments are traditionally located only in university hospitals. However, six of the new accelerators will not be installed in existing radiotherapy centres, but in small, new radiotherapy units, set up in selected county hospitals and organized as satellites of the university hospitals, in order to secure the treatment quality. The university hospital is responsible for both medical and technical standards in the satellite, while the county hospitals have the financial responsibility. RESULTS: The satellite model combines two important aspects of hospital management; treatment is geographically decentralized, while treatment quality is centralized. The first radiotherapy satellite was established in the town of Kristiansand in January 2001. We report our experience with this new concept in radiotherapy. INTERPRETATION: The satellite model should be evaluated also for other medical specialties within the university hospitals.

Health Planning↗

Lods, wrods, and mods: the interpretation of lod scores calculated under different models.

In this paper we examine the relationships among classical lod scores, "wrod" scores (lod scores calculated under the wrong genetic model), and "mod" scores (lod scores maximized over genetic model parameters). We compare the behavior of these scores when the state of nature is linkage to their behavior when the state of nature is no linkage. We describe sufficient conditions for mod scores to be valid and discuss their use to determine the correct genetic model. We show that lod scores represent a likelihood-ratio test for independence. We explain the "ascertainment-assumption-free" aspect of using mod scores to determine mode of inheritance and we set this aspect into a well-established statistical framework. Finally, we summarize practical guidelines for the use of mod scores.

Bias↗

Magnetization transfer imaging in vivo of the rat brain at 4.7 T: interpretation using a binary spin-bath model with a superLorentzian lineshape.

Proton magnetization transfer contrast (MTC) imaging, using continuous wave off-resonance irradiation, was performed on the rat brain in vivo at 4.7 Tesla. The observed MTC was studied in three different brain regions: the corpus callosum, the basal ganglia, and the temporal lobe. By systematically varying the offset frequency and the amplitude of the RF irradiation, the observed signal intensities for each region of interest were modeled using a system including free water and a pool of protons with restricted motions (R. M. Henkelman, X. Huang, Q. Xiang, G. J. Stanisz, SD Swanson, M. J. Bronskill, Magn. Res. Med. 29, 759 (1993)). Most of the relaxation parameters of both proton pools remained fairly constant for the three regions of interest, with a T2 value of about 9 micros for the immobilized protons, whereas the rate of exchange increased significantly from the temporal lobe to the corpus callosum. The optimal acquisition parameters for the improved MTC under steady-state saturation were found to be 2-10 kHz offset frequency and 500-800 Hz RF irradiation amplitude. Conversely, an irradiation amplitude of 3 kHz at an offset frequency of 12 kHz is required to minimize the direct effect of off-resonance irradiation. Such an approach could be extended to human brain imaging with the aim of characterizing tissue-specific disease.

Animals↗

Double-tracer autoradiography with Cu-ATSM/FDG and immunohistochemical interpretation in four different mouse implanted tumor models.

BACKGROUND: We studied the regional characteristics within tumor masses using PET tracers and immunohistochemical methods. METHODS: The intratumoral distribution of (64)Cu-diacetyl-bis(N4-methylthiosemicarbazone) ([(64)Cu]Cu-ATSM) and [(18)F] 2-fluoro-2-deoxyglucose ((18)F]FDG) in mice with tumors of four different origins (LLC1, Meth-A, B16 and colon26) was compared with the immunohistochemical staining of proliferating cells (Ki67), blood vessels (CD34 or von Willebrand factor), and apoptotic cells (terminal deoxynucleotidyltransferase-mediated dUTP nick end labeling method). RESULTS: With all cell lines, [(64)Cu]Cu-ATSM and [(18)F]FDG were distributed with different gradation in the tumor mass. The immunohistochemical study demonstrated that the high [(64)Cu]Cu-ATSM uptake regions were hypovascular and consisted of tumor cells arrested in the cell cycle, whereas the high [(18)F]FDG uptake regions were hypervascular and consisted of proliferating cells. CONCLUSION: In our study, it was revealed that one tumor mass contained two regions with different characteristics, which could be distinguished by [(64)Cu]Cu-ATSM and [(18)F]FDG. Because hypoxia and cell cycle arrest are critical factors to reduce tumor sensitivity to radiation and conventional chemotherapy, regions with such characteristics should be treated intensively as one of the primary targets. [(64)Cu]Cu-ATSM, which can delineate hypoxic and cell cycle-arrested regions in tumors, may provide valuable information for cancer treatment as well as possibly for treating such regions directly as an internal radiotherapy reagent.

Animals↗

Iontophoretic transport of a homologous series of ionized and nonionized model compounds: influence of hydrophobicity and mechanistic interpretation.

An in vitro study was carried out to elucidate the mechanisms controlling iontophoretic transport. The investigation focused on three areas, including the nature of the permeant (state of ionization and hydrophobicity), skin structures (hair follicle distribution and stratum corneum), and various parameters influencing iontophoresis (current, permeant concentration, and competitive ion effects). The data indicate that iontophoretic-facilitated transport is essentially pore mediated and that the transport of ionized and nonionized molecules may be enhanced through the pore-type pathway. The data presented show that iontophoresis has a detrimental effect on the lipoidal transport pathway and that the transport of more hydrophobic nonionized molecules is decreased compared with passive diffusion. The iontophoretic enhancement values decreased linearly with increasing alkyl chain length of n-alkanols. The iontophoretic permeability coefficients of ionized n-alkanoic acids was shown to decrease with increasing permeant hydrophobicity.

Administration, Cutaneous↗

Coverage dependent desorption dynamics of deuterium on Si(100) surfaces: interpretation with a diffusion-promoted desorption model.

We studied coverage dependence of time-of-flight (TOF) spectra of D2 molecules thermally desorbed from the D/Si(100) surface. The mean translational energies Et of desorbed D2 molecules were found to increase from 0.20+/-0.05 eV to 0.40+/-0.04 eV as the desorption coverage window was decreased from 1.0 ML> or =thetaD> or =0.9 ML to 0.2 ML> or =thetaD> or =0 ML, being consistent with the kinetics switch predicted in the interdimer mechanism. The measured TOF spectra were deconvoluted into 2H, 3H, and 4H components by a curve fitting method along the principle of detailed balance. As a result, it turned out that the desorption kinetics changes from the 4H to the 3H situation at high coverage above thetaD=0.9 ML, while the 2H desorption is dominant for a quite wide coverage region up to thetaD=0.8 ML. A dynamic desorption mechanism by which the desorption is promoted by D-atom diffusion to dangling bonds was proposed.

Journal Article↗

Management of individuals with Parkinson's disease: rationale and case studies.

In this article, we present a systematic approach to physical therapy management of individuals with Parkinson's disease. This approach is based on a model that relates knowledge of the underlying pathology of the disease to impairments and disability. We discuss use of the model to evaluate, interpret, and treat impairments and disabilities of the patient with Parkinson's disease. We emphasize the relative influence of impairments that arise directly from the neuroanatomical pathology and those that arise indirectly through subsequent musculoskeletal alterations. We illustrate the use of the model in setting goals and in developing a treatment program. Two case studies are presented to illustrate the application of this approach to specific patient care. These case studies suggest the efficacy of physical therapy initiated early in the disease process. The first case study illustrates improvements of balance, gait, and functional movement made by an individual who was not yet receiving medication for Parkinson's disease. The second case study illustrates improvements of balance, gait, and functional movement made by an individual who was already receiving medication for the disease. These case studies illustrate the dramatic improvements that can be achieved in the patient with Parkinson's disease.

Aged↗

Directional, regional, and layer variations of mechanical properties of esophageal tissue and its interpretation using a structure-based constitutive model.

The esophagus, like other soft tissues, exhibits nonlinear and anisotropic mechanical properties. As a composite structure, the properties of the outer muscle and inner mucosal layer are different. It is expected that the complex mechanical properties will induce nonhomogeneous stress distributions in the wall and nonuniform tissue remodeling. Both are important factors which influence the function of mechanosensitive receptor located in various layers of the wall. Hence, the characterization of the mechanical properties is essential to understand the neuromuscular motion of the esophagus. In this study, the uniaxial tensile tests were conducted along two mutually orthogonal directions of porcine esophageal tissue to identify the directional (circumferential and axial), regional (abdominal, thoracic, and cervical), and layer (muscle and mucosa) variations of the mechanical properties. A structure-based constitutive model, which took the architectures of the tissue's microstructures into account, was applied to describe the mechanical behavior of the esophagus. Results showed that the constitutive model successfully described the mechanical behavior and provided robust estimates of the material parameters. In conclusion, the model was demonstrated to be a good descriptor of the mechanical properties of the esophagus and it was able to facilitate the directional, layer, and regional comparisons of the mechanical properties in terms of the associated material parameters.

Animals↗