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PubMed1987

ISMOD: an all-subsets regression program for generalized linear models. I. Statistical and computational background.

This paper describes a system written to carry out regression analyses under certain generalized linear models that are widely used in biomedical research. These include continuous response models such as the Weibull, log-logistic, log-normal and Cox proportional hazards models used in survival analysis, and also discrete Poisson, binomial and multinomial response regression models. The system fits models, generates residuals and other diagnostic output, and has an all-subsets regression feature. This paper describes the models implemented and gives statistical background; Part II describes the ISMOD system and presents examples of its application.

Biometry↗
PubMed1991

A distributed-parameter model of the myelinated nerve fiber.

This paper presents a new model for the characterization of electrical activity in the nodal, paranodal and internodal regions of isolated amphibian and mammalian myelinated nerve fibers. It differs from previous models in the following ways: (1) in its ability to incorporate detailed anatomical and electrophysiological data; (2) in its approach to the myelinated nerve fiber as a multi-axial cable; and (3) in the numerical algorithm used to obtain distributed model equation solutions for potential and current. The morphometric properties are taken from detailed electron microscopic anatomical studies (Berthold & Rydmark, 1983a, Experientia 39, 964-976). The internodal axolemma is characterized as an excitable membrane and model-generated nodal and internodal membrane action potentials are presented. A system of describing equations for the equivalent network model is derived, based on the application of Kirchoff's Current Law, which take the form of multiple cross-coupled parabolic partial differential equations. An implicit numerical integration method is developed and the numerical solution implemented on a parallel processor. Non-uniform spatial step sizes are used, enabling detailed representation of the nodal region while minimizing the number of total segments necessary to represent the overall fiber. Conduction velocities of 20.2 m sec-1 at 20 degrees C for a 15 microns diameter amphibian fiber and 57.6 m sec-1 at 37 degrees C for a 17.5 microns diameter mammalian fiber are achieved, which agrees qualitatively with published experimental data at similar temperatures (Huxley & Stämpfli, 1949, J. Physiol., Lond. 108, 315-339; Rasminsky, 1973, Arch, Neurol. 28, 287-292). The simulation results demonstrate the ability of this model to produce detailed representations of the transaxonal, transmyelin and transfiber potentials and currents, as well as the longitudinal extra-axonal, periaxonal and intra-axonal currents. Also indicated is the potential contribution of the paranodal axolemma to nodal activity as well as the presence of significant longitudinal currents in the periaxonal space adjacent to the node of Ranvier.

Action Potentials↗
PubMed2003

The relation between depression and anxiety: an evaluation of the tripartite, approach-withdrawal and valence-arousal models.

Epidemiological studies have consistently reported that depressive and anxiety disorders co-occur frequently. This paper reviews the evidence for three models that have been proposed to explain the relation between these two conditions-the tripartite, the approach-withdrawal, and valence-arousal models. Specifically, we focus on predictions that the three models generate for cross-sectional studies, prospective and family/twin studies of personality, and EEG studies. In sum, no model was strongly supported across all types of studies, though specific aspects of each model were. Because of the heterogeneity of depression and anxiety disorders, a model with 2-4 factors or dimensions may not be sufficient to explain the relation between the two conditions.

Anxiety Disorders↗
PubMedDate not supplied

A peripartum neurologic event: shooting from the hip.

We have shown that a simplified model, generated quickly in response to an emergency consultation, may provide useful insights in certain situations. A more developed model was useful in verifying these insights. Because the more complex model considered a longer time horizon than the simple model, it allows us to consider questions regarding long-term benefits of aneurysm repair. When modeling any problem, the most important reason for performing decision analysis is to gain insight from analyzing the clinical setting and from constructing the model. The quantitative results are usually of only minor importance. However, our most important insights are sometimes gained by looking beyond the quantitative level to understand the interactions of various effects within the model. In this case, it was those insights that were of the greatest benefit to the patient in arriving at a decision to have cerebral arteriography.

Adult↗
PubMed1995

Mechanical control of swimming speed: stiffness and axial wave form in undulating fish models

The purpose of this study was to investigate the mechanical control of speed in steady undulatory swimming. The roles of body flexural stiffness, driving frequency and driving amplitude were examined; these variables were chosen because of their importance in vibration theory and their hypothesized functions in undulatory swimming. Using a mold of a pumpkinseed sunfish Lepomis gibbosus, we cast three-dimensional vinyl models of four different flexural stiffnesses. We swam the models in a flow tank and powered them via the input of an oscillating sinusoidal bending couple in the horizontal plane at the posterior margin of the neurocranium. To simulate the hydrodynamic conditions of steady swimming, drag and thrust acting on the model were balanced by adjusting flow speed. Under these conditions, the actuated models generated traveling waves of bending. At steady speeds, the motions of the ventral and lateral surfaces of the model were video-taped and analyzed to yield the following response variables: tail-beat amplitude, propulsive wavelength, wave speed and depth of the trailing edge of the caudal fin. Experimental results showed that changes in body flexural stiffness can control propulsive wavelength, wave speed, Froude efficiency and, in consequence, swimming speed. Driving frequency can control tail-beat amplitude, propulsive wavelength, Froude efficiency, relative rate of working and, in consequence, swimming speed. Although there is no significant correlation between rostral amplitude and swimming speed, rostral amplitude can control swimming speed indirectly by controlling tail-beat amplitude and relative power. Compared with live sunfish using undulatory waves at the same speed, models have a lower Froude efficiency. On the basis of the mechanical control of swimming speed in model sunfish, we predict that, in order to swim at fast speeds, live sunfish increase the flexural stiffness of their bodies by a factor of two relative to their passive body stiffness.

Journal Article↗
PubMed2001

The brain decade in debate: II. Panic or anxiety? From animal models to a neurobiological basis.

This article is a transcription of an electronic symposium sponsored by the Brazilian Society of Neuroscience and Behavior (SBNeC). Invited researchers from the European Union, North America and Brazil discussed two issues on anxiety, namely whether panic is a very intense anxiety or something else, and what aspects of clinical anxiety are reproduced by animal models. Concerning the first issue, most participants agreed that generalized anxiety and panic disorder are different on the basis of clinical manifestations, drug response and animal models. Also, underlying brain structures, neurotransmitter modulation and hormonal changes seem to involve important differences. It is also common knowledge that existing animal models generate different types of fear/anxiety. A challenge for future research is to establish a good correlation between animal models and nosological classification.

Anti-Anxiety Agents↗
PubMed1994

Modeling Alzheimer's disease in transgenic mice.

Alzheimer's disease is a common neurodegenerative disorder of unknown etiology characterized by the accumulation of beta amyloid plaques and neurofibrillary tangles in the brain. Attempts have been made to engineer an animal model of the disease using a variety of transgenic approaches. So far the models have only been partially successful. The methods used and the models generated are discussed.

Alzheimer Disease↗
PubMed2003

Consensus alignment for reliable framework prediction in homology modeling.

MOTIVATION: Even the best sequence alignment methods frequently fail to correctly identify the framework regions for which backbones can be copied from the template into the target structure. Since the underprediction and, more significantly, the overprediction of these regions reduces the quality of the final model, it is of prime importance to attain as much as possible of the true structural alignment between target and template. RESULTS: We have developed an algorithm called Consensus that consistently provides a high quality alignment for comparative modeling. The method follows from a benchmark analysis of the 3D models generated by ten alignment techniques for a set of 79 homologous protein structure pairs. For 20-to-40% of the targets, these methods yield models with at least 6 A root mean square deviation (RMSD) from the native structure. We have selected the top five performing methods, and developed a consensus algorithm to generate an improved alignment. By building on the individual strength of each method, a set of criteria was implemented to remove the alignment segments that are likely to correspond to structurally dissimilar regions. The automated algorithm was validated on a different set of 48 protein pairs, resulting in 2.2 A average RMSD for the predicted models, and only four cases in which the RMSD exceeded 3 A. The average length of the alignments was about 75% of that found by standard structural superposition methods. The performance of Consensus was consistent from 2 to 32% target-template sequence identity, and hence it can be used for accurate prediction of framework regions in homology modeling.

Algorithms↗
PubMed2000

Three-dimensional model of the extracellular domain of the type 4a metabotropic glutamate receptor: new insights into the activation process.

Metabotropic glutamate receptors (mGluRs) belong to the family 3 of G-protein-coupled receptors. On these proteins, agonist binding on the extracellular domain leads to conformational changes in the 7-transmembrane domains required for G-protein activation. To elucidate the structural features that might be responsible for such an activation mechanism, we have generated models of the amino terminal domain (ATD) of type 4 mGluR (mGlu4R). The fold recognition search allowed the identification of three hits with a low sequence identity, but with high secondary structure conservation: leucine isoleucine valine-binding protein (LIVBP) and leucine-binding protein (LBP) as already known, and acetamide-binding protein (AmiC). These proteins are characterized by a bilobate structure in an open state for LIVBP/LBP and a closed state for AmiC, with ligand binding in the cleft. Models for both open and closed forms of mGlu4R ATD have been generated. ACPT-I (1-aminocyclopentane 1,3,4-tricarboxylic acid), a selective agonist, has been docked in the two models. In the open form, ACPT-I is only bound to lobe I through interactions with Lys74, Arg78, Ser159, and Thr182. In the closed form, ACPT-I is trapped between both lobes with additional binding to Tyr230, Asp312, Ser313, and Lys317 from lobe II. These results support the hypothesis that mGluR agonists bind a closed form of the ATDs, suggesting that such a conformation of the binding domain corresponds to the active conformation.

Amino Acid Sequence↗
PubMed1995

Detection of vulnerability loci by association and sib-pair methods.

A haplotype-based haplotype relative risk (HHRR) analysis of simulated data for 200 affected offspring and their parents (Genetic Analysis Workshop 9, Problem 1) detected linkage disequilibrium at 2 of 360 marker loci. An additive model was suggested but not proven by haplotypes of affected vs. unaffected offspring. These findings were consistent with the generating model. Affected sib pair analysis failed to detect additional loci. Discussion among workshop participants suggested that the chi-square test used here (2 [transmitted vs. nontransmitted] x n [alleles] for each locus) was invalid because of the nonindependence of proportions of transmitted alleles. In post-workshop analyses, transmission disequilibrium tests (TDTs) for each allele at each locus detected only the true associations if p values were corrected by one of two methods: Bonferroni correction for 2,035 TDTs, or correcting each test for n (number of tests at the locus) minus 1 and then for the number of loci tested. Screening loci for linkage disequilibrium requires careful attention to correction for multiple comparisons.

Alleles↗
PubMed1998

Assessment of regional left ventricular wall stress after myocardial infarction by echocardiography-based structural analysis.

OBJECTIVES: The objective of this study was to determine the distribution of regional left ventricular (LV) wall stress after myocardial infarction (MI). BACKGROUND: After a large MI, structural changes occur in the heart that ultimately may lead to alterations in LV size and shape, a process generally referred to as ventricular remodeling. Regional variation in myocardial wall stress may be responsible for initiation of physiologic and cellular changes that result in myocardial hypertrophy, dilatation, and remodeling after MI. Simplified geometric analytic methods of estimating global LV wall stress cannot determine regional variation such as that occurring after MI. METHODS AND RESULTS: To assess regional LV wall stress after MI, we applied the finite element method to patient-specific end-systolic LV models generated from echocardiographic imaging. After validation by comparison with analytic solutions of LV wall stress in idealized ventricles, LV models were constructed from rotated orthogonal apical images from 13 normal volunteers, 16 patients with recent (<4 days) anterior MI, and 7 patients with recent infero-posterior MI. The mean Von Mises stress was calculated for the entire LV and for 5 separate regions of the LV. Von Mises LV wall stress was increased globally in patients with anterior MI (211 +/- 46 kdyne/cm2; P < .002) or infero-posterior MI (175 +/- 23 kdyne/cm2; P = .04) compared with normal patients (144 +/- 57 kdyne/cm2). Global wall stress correlated directly with ejection fraction (P < .0001) and inversely with wall motion index (P < .004) in patients with anterior MI. Wall stress in the apical regions was increased by a factor of 2.3 in patients with anterior MI (P < .0001), whereas other regions did not differ from normal patients. There were no individual regions that were significantly different from normal in patients with infero-posterior MI. CONCLUSIONS: Anterior MI is associated with an increase in apical end-systolic wall stress compared with normal and infero-posterior MI. This may be an important stimulus for LV remodeling after anterior MI.

Female↗
PubMed1999

Conjoint recognition.

The process-dissociation model has stimulated important advances in the study of dual-process conceptions of memory. The authors review some limiting properties of that model and consider the degree of support for its parent theory (the recollection-familiarity distinction). A 2nd-generation model (conjoint recognition) is proposed that addresses these limitations and supplies additional capabilities, such as goodness-of-fit tests, the ability to measure dual processes for false-memory responses, and statistical procedures for testing within- and between-conditions hypotheses about its parameters. The conjoint-recognition model also implements an alternative theoretical interpretation (the identity-similarity distinction of fuzzy-trace theory). Worked applications to data are provided.

Adolescent↗
PubMed2002

Experimental rodent models of brainstem tumors.

Despite recent advances in surgical technology, resection is not an option for many brainstem tumors. Experimental models have played essential roles in examining new approaches to therapy. The objective of the present study was to generate models by determining coordinates for safe inoculation into the brainstem of mice and rats, and to establish whether the implantation of heterotopic cells would create reproducible survival curves. Morbidity and survival studies were used to map stereotactic coordinates allowing successful inoculation of tumor cells. Survival studies were used to investigate the time course of tumor growth. Tumor location was examined by light microscopy and magnetic resonance imaging. Mice survived injections of 2 microL of saline at interaural, lateral, and depth coordinates of -2.5, 1.0, and 3.5 mm and -1.5, 1.0, and 3.5 mm. Rats survived injections at interaural, lateral, and depth coordinates of -2.0, 2.0, and 7.0 mm and -3.0, 0, and 7.0 mm. Median survival of mice challenged with 5 x 10(5) EMT6 and 10(4) B16 tumor cells was 11 and 10 days, respectively. Median survival for rats challenged with 10(4) 9L and F98 cells was 14 and 13 days, respectively. The present study demonstrates a feasible approach to preparing models of brainstem tumors. Limitations of these models are discussed.

Animals↗
PubMed1997

[A model for handling grievances in nursing services].

A model for management of grievances in a nursing service is described, in terms of the guidelines for model generation, based on a qualitative, exploratory, descriptive and theory generating research strategy and design. Potgieter's (1992) research served as the conceptual framework for the description of a model case. The statements derived from this description was used as basis for the description of the model. The central concepts were identified, defined and classified. The model was implemented in practice and was evaluated by means of a retrospective case study. Guidelines for the implementation of the model were consequently described and the model was positively evaluated by a panel of experts. The testing of hypothesis is recommended to validate the model.

Employee Grievances↗
PubMed1992

Alloplastic cranial implants made from computed tomographic scan-generated casts.

The complexity of cranioplasty increases with increased defect size. It is difficult to produce a symmetric, accurate implant presurgically or at the time of surgery when the defect is greater than 50 cm2. The procedure is also more difficult to perform when the defect is located in the temporal, infratemporal, or frontal areas. A new procedure generates a three-dimensional cast of the skull through computed tomography and computer-aided design reformation. This article describes the process of model generation and the production of a preprocessed cranial implant. To date, six cranial implants have been made with this technique. The whole head models are accurate and help the neurosurgeon-prosthodontist team in the creation of a symmetric, anatomically correct restoration. It is the technique of choice for large implants or where the cranial bones are thin. It is not necessary to augment or alter the implant during surgery. The technique reduces surgical time, and postsurgical complications have been minimal.

Artificial Intelligence↗
PubMedDate not supplied

Optimal synthesis of protein purification processes.

There has been an increasing interest in the development of systematic methods for the synthesis of purification steps for biotechnological products, which are often the most difficult and costly stages in a biochemical process. Chromatographic processes are extensively used in the purification of multicomponent biotechnological systems. One of the main challenges in the synthesis of purification processes is the appropriate selection and sequencing of chromatographic steps that are capable of producing the desired product at an acceptable cost and quality. This paper describes mathematical models and solution strategies based on mixed integer linear programming (MILP) for the synthesis of multistep purification processes. First, an optimization model is proposed that uses physicochemical data on a protein mixture, which contains the desired product, to select a sequence of operations with the minimum number of steps from a set of candidate chromatographic techniques that must achieve a specified purity level. Since several sequences that have the minimum number of steps may satisfy the purity level, it is possible to obtain the one that maximizes final purity. Then, a second model that may use the total number of steps obtained in the first model generates a solution with the maximum purity of the product. Whenever the sequence does not affect the final purity or more generally does not impact the objective function, alternative models that are of smaller size are developed for the optimal selection of steps. The models are tested in several examples, containing up to 13 contaminants and a set of 22 candidate high-resolution steps, generating sequences of six operations, and are compared to the current synthesis approaches.

Biotechnology↗
PubMed1993

Computer model of membrane current and intracellular Ca2+ flux in the isolated guinea pig ventricular myocyte.

This paper presents the equations and responses of a mathematical model that simulates the transmembrane current and intracellular concentrations of Ca2+ ([Ca2+]), Na+ ([Na+]), and K+ ([K+]) of an isolated guinea pig myocyte. The structure of the model is closely related to the formulation of DiFrancesco and Noble (9). Quantitative values are based on a large number of experimental constraints, taken from the literature on isolated myocytes as well as our own experimental studies, that describe the properties of individual channels and integrated responses of whole cells under a variety of conditions. The model was constructed as a homeostatic system. The equilibrium of the model corresponds to the resting potential and intracellular ionic concentrations of unstimulated myocytes. The model generates deviations from equilibrium corresponding to the behavior of cells after stimulation of action potentials at different rates, blockade of Na-K-adenosinetriphosphatase (ATPase), reduction in extracellular [K+], and injection of constant depolarizing current. Simulations from the model suggest that changes in myoplasmic [Ca2+] at different stimulation rates, the generation of restitution and postextrasystolic potentiation, and the development of intracellular [Ca2+] oscillations arise simply from different interactions between uptake of Ca2+ into the sarcoplasmic reticulum via the Ca(2+)-ATPase, Ca(2+)-induced Ca2+ release of Ca2+ into the myoplasm, flux between regions of uptake and release, and leakage between sarcoplasmic reticulum and myoplasm. The model also demonstrates that a wide variety of basic electrophysiological responses of the isolated guinea pig myocyte can be simulated with quantitative precision by a single set of equations based on experimentally measured transmembrane current and intracellular [Ca2+] and [Na+].

Action Potentials↗
PubMed1996

Non-isotopic method for quantitation of platelets and erythrocytes in experimental thrombi.

Experimental animal models of thrombosis have been established in several species to examine factors responsible for thrombotic disorders in man. One technical facet of all thrombosis models is the need to quantitate cell deposition on thrombogenic surfaces, and this is routinely accomplished with radioisotopic labeling of specific components. Data reported here demonstrate that formalin-fixed thrombi can be hydrolyzed with chymotrypsin allowing recovery and quantitation of platelets and erythrocytes incorporated within the clot. Recovery of platelets from in vitro generated, model thrombi averaged 99 +/- 10% (mean +/- 1 SD; n = 7; range 88-116%) of calculated content; recovery of erythrocytes was 94.1 +/- 1.1% (n = 6) as measured by recovery of cellular hemoglobin after chymotrypsin hydrolysis of clots. Chymotrypsin was also shown to release platelets and erythrocytes from string-bound thrombi generated in vivo with an arterio-venous shunt model in beagle dogs. Platelet recovery from these string clots after chymotrypsin hydrolysis was independently verified with a quantitative Western blot assay of platelet antigens. These data demonstrate that experimental thrombi can be hydrolyzed with chymotrypsin, thereby not only eliminating the need for radioisotopes, but also permitting flow cytometric analysis of cells comprising the thrombus.

Animals↗