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At least 721 records · Page 40Linked to original sources
PubMed2005

Mayo's older African American normative studies: confirmatory factor analysis of a core battery.

Covariance structure analyses of a core neuropsychological test battery consisting of the Wechsler Adult Intelligence Scale-Revised, Wechsler Memory Scale-Revised, and Auditory Verbal Learning Test have previously identified a 5-factor model in a sample of cognitively normal White volunteers from Mayo's Older Americans Normative Studies (MOANS). The present study sought to replicate this factor structure in a sample of 289 cognitively normal, community-dwelling African American elders from Mayo's Older African Americans Normative Studies (MOAANS). The original 5-factor model was tested against 2 alternative 4-factor models and a 6-factor model generated on a substantive basis. Confirmatory factor analysis supported the construct validity of this core battery in older African Americans by replicating the original 5-factor model of Verbal Comprehension, Perceptual Organization, Attention/Concentration, Learning, and Retention as viable in the present sample.

Black or African American↗
PubMedDate not supplied

Hierarchical PLS modeling for predicting the binding of a comprehensive set of structurally diverse protein-ligand complexes.

A new approach is presented for predicting ligand binding to proteins using hierarchical partial-least-squares regression to latent structures (Hi-PLS). Models were based on information from the 2002 release of the PDBbind database containing (after in-house refinement) high-resolution X-ray crystallography and binding affinity (Kd or Ki) data for 612 protein-ligand complexes. The complexes were characterized by four different descriptor blocks: three-dimensional (3D) structural descriptors of the proteins, protein-ligand interactions according to the Validate scoring function, binding site surface areas, and ligand 2D and 3D descriptors. These descriptor blocks were used in Hi-PLS models, generated using both linear and nonlinear terms, to relate the characterizations to pKd/i. The results show that each of the four descriptor blocks contributed to the model, and the predictions of pKd/i of the internal test set gave a root-mean-square error of prediction (RMSEP) of 1.65. The data were further divided according to the structural classification of the proteins, and Hi-PLS models were constructed for the resulting subclasses. The models for the four subclasses differed considerably in terms of both their ability to predict pKd/i (with RMSEPs ranging from 0.8 to 1.56) and the descriptor block that had the strongest influence. The models were validated with an external test set of 174 complexes from the 2003 release of the PDBbind database. The overall results show that the presented Hi-PLS methodology could facilitate the difficult task of predicting binding affinity.

Crystallography, X-Ray↗
PubMed2002

Conformational-relaxation models of single-enzyme kinetics.

Fluorescent spectroscopy experiments with single-enzyme molecules yield a large volume of statistical data that can be analyzed and interpreted using stochastic models of enzyme action. Here, we present two models, each based on the mechanism that an enzyme molecule must pass through a sequence of conformational transformations to complete its catalytic turnover cycle. In the simplest model, only one path leading to the release of product is present. In contrast to this, two different catalytic paths are possible in the second considered model. If a cycle is started from an active state, immediately after the previous product release, it follows a different conformational route and is much shorter. Our numerical investigations show that both models generate non-Markovian molecular statistics. However, their memory landscapes and distributions of cycle times are significantly different. The memory landscape of the double-path model bears strong similarity to the recent experimental data for horseradish peroxidase.

Catalysis↗
PubMed2001

Three-dimensional virtual-reality surgical planning and soft-tissue prediction for orthognathic surgery.

Complex maxillofacial malformations continue to present challenges in analysis and correction beyond modern technology. The purpose of this paper is to present a virtual-reality workbench for surgeons to perform virtual orthognathic surgical planning and soft-tissue prediction in three dimensions. A resulting surgical planning system, i.e., three-dimensional virtual-reality surgical-planning and soft-tissue prediction for orthognathic surgery, consists of four major stages: computed tomography (CT) data post-processing and reconstruction, three-dimensional (3-D) color facial soft-tissue model generation, virtual surgical planning and simulation, soft-tissue-change preoperative prediction. The surgical planning and simulation are based on a 3-D CT reconstructed bone model, whereas the soft-tissue prediction is based on color texture-mapped and individualized facial soft-tissue model. Our approach is able to provide a quantitative osteotomy-simulated bone model and prediction of postoperative appearance with photorealistic quality. The prediction appearance can be visualized from any arbitrary viewing point using a low-cost personal-computer-based system. This cost-effective solution can be easily adopted in any hospital for daily use.

Humans↗
PubMed2002

Pharmacodynamics and pharmacogenomics of methylprednisolone during 7-day infusions in rats.

An array of adverse steroid effects was examined on a whole body, tissue, and molecular level. Groups of male adrenalectomized Wistar rats were subcutaneously implanted with Alzet mini-pumps giving zero-order release rates of 0, 0.1, and 0.3 mg/kg/h methylprednisolone for 7 days. The rats were sacrificed at various times during the 7-day infusion period. A two-compartment model with a zero order input could adequately describe the kinetics of methylprednisolone upon infusion. Blood lymphocyte counts dropped to a minimum by 6 h and were well characterized by the cell trafficking model. The time course of changes in body and organ (liver, spleen, thymus, gastrocnemius muscle, and lungs) weights was described using indirect response models. Markers of gene-mediated steroid effects included hepatic cytosolic free receptor density, receptor mRNA, tyrosine aminotransferase (TAT) mRNA, and TAT levels. Our fifth-generation model of acute corticosteroid pharmacodynamics was used to predict the time course of receptor/gene-mediated effects. An excellent agreement between the expected and observed receptor dynamics suggested that receptor events and mRNA autoregulation are not altered upon 7-day methylprednisolone dosing. However, the model indicated a decoupling between the receptor and TAT dynamics with this infusion. The strong tolerance seen in TAT mRNA induction could be partly accounted for by receptor down-regulation. An amplification of translation of TAT mRNA to TAT and/or a reduction in the enzyme degradation rate could account for the observed exaggerated TAT activity. Our results exemplify the importance of biological signal transduction variables in controlling receptor/gene-mediated steroid responses during chronic dosing.

Adrenalectomy↗
PubMed2005

Deciphering structure and topology of conserved COG2042 orphan proteins.

BACKGROUND: The cluster of orthologous group COG2042 has members in all sequenced Eukaryota as well as in many Archaea. The cellular function of these proteins of ancient origin remains unknown. PSI-BLAST analysis does not indicate a possible link with even remotely-related proteins that have been functionally or structurally characterized. As a prototype among COG2042 orthologs, SSO0551 protein from the hyperthermophilic archaeon Sulfolobus solfataricus was purified to homogeneity for biophysical characterization. RESULTS: The untagged protein is thermostable and behaves as a monomeric protein in gel filtration experiment. Several mass spectrometry-based strategies were combined to obtain a set of low resolution structural information. Kinetic data from limited proteolysis with various endoproteases are concordant in pointing out that region Glu73-Arg78 is hyper-sensitive, and thus accessible and flexible. Lysine labeling with NHS-biotin and cross-linking with DTSSP revealed that the 35 amino acid RLI motif at the N terminus is solvent exposed. Cross-links between Lys10-Lys14 and Lys23-Lys25 indicate that these residues are spatially close and in adequate conformation to be cross-linked. These experimental data have been used to rank multiple three-dimensional models generated by a de novo procedure. CONCLUSION: Our data indicate that COG2042 proteins may share a novel fold. Combining biophysical, mass-spectrometry data and molecular model is a useful strategy to obtain structural information and to help in prioritizing targets in structural genomics programs.

Amino Acid Sequence↗
PubMed1992

A model for the generation of movements requiring endpoint precision.

A model is proposed in which movement accuracy is regulated by means of corrective actions taken at discrete intervals throughout the course of a movement. A movement, as represented by its tangential velocity profile, cna be decomposed into a series of one or more submovements. Each submovement consists of a prototype velocity profile which can be scaled in magnitude and duration. For planar two-joint movements, we demonstrate that these submovements can be mathematically represented either in terms of velocity profiles or in terms of the underlying joint torque profiles. In either case, the submovements superimpose linearly to produce the composite movement. The model provides a very good fit to tangential velocity profiles recorded from human subjects during three-dimensional arm movements with constraints on accuracy and speed. The model assumes that when a submovement is present, its onset is associated with a change in the direction of the hand path and/or a zero crossing or inflection in at least one of the components of the velocity vector. The model is consistent with a strategy in which precision is achieved by periodic discrete actions which redirect the moving arm in order to bring the hand closer to the target. Since submovements were also observed in slow movements where accuracy constraints had been relaxed, we hypothesize that the strategy of superimposing a series of submovements to make one composite movement may be a general one. We suggest that it would be particularly appropriate for the process of learning a new motor skill.

Adult↗
PubMedDate not supplied

Graphical and stereolithographic models of the developing human heart lumen.

Scaled physical models can be useful in analyzing stage-specific hemodynamics in the embryonic human heart to address correlations between early physical stressors and myocardial wall responses. We generated models of the cardiac blood space from reconstructions of four digitized human embryo images from Carnegie Collection at the Armed Forces Institute of Pathology. From physical scale models manufactured by stereolithography, compliant sleeves can be created for flow dynamics studies. This novel use of Carnegie collection images and graphical modeling software provides tools for broadening our understanding of normal and aberrant heart formation.

Embryonic and Fetal Development↗
PubMed1996

The within-host cellular dynamics of bloodstage malaria: theoretical and experimental studies.

The properties of a mathematical model of bloodstage infection with a single strain of malaria were investigated. Analysing the cell population dynamics in the absence of a host immune response we demonstrate a relationship between host and parasite parameters that defines a criterion for the successful invasion and persistence of the parasite. Important parameters are the rates of merozoite production and death and those of erythrocyte production, death and invasion. We present data from experiments designed to evaluate the erythrocyte invasion rate in a rodent malaria system. The model generates patterns of parasitaemia in good qualitative agreement with those seen in Plasmodium berghei infections. The sole force behind the rise and fall in parasitaemia in the model without immunity is the density of susceptible erythrocytes, suggesting that resource availability is an important determinant of the initial pattern of infection in vivo. When we incorporate a simple immune response into the model we find that immunity against the infected cell is much more effective at suppressing parasite abundance than immunity against the merozoite. Simulations reveal oscillating temporal patterns of parasite abundance similar to P. c. chabaudi infection, challenging the concept that antigenic variation is the sole mechanism behind recrudescing patterns of infection.

Animals↗
PubMed2005

Factors affecting resident performance: development of a theoretical model and a focused literature review.

PURPOSE: The clinical performances of physicians have come under scrutiny as greater public attention is paid to the quality of health care. However, determinants of physician performance have not been well elucidated. The authors sought to develop a theoretical model of physician performance, and explored the literature about factors affecting resident performance. METHOD: Using expert consensus panel, in 2002-03 the authors developed a hypothesis-generating model of resident performance. The developed model had three input factors (individual resident factors, health care infrastructure, and medical education infrastructure), intermediate process measures (knowledge, skills, attitudes, habits), and final health outcomes (affecting patient, community and population). The authors used factors from the model to focus a PubMed search (1967-2002) for all original articles related to the factors of individual resident performance. RESULTS: The authors found 52 original studies that examined factors of an individual resident's performance. They describe each study's measurement instrument, study design, major findings, and limitations. Studies were categorized into five domains: learning styles/personality, social/financial factors, practice preferences, personal health, and response to job environment. Few studies examined intermediate or final performance outcomes. Most were single-institution, cross-sectional, and survey-based studies. CONCLUSIONS: Attempting to understand resident performance without understanding factors that influence performance is analogous to examining patient adherence to medication regimens without understanding the individual patient and his or her environment. Based on a systematic review of the literature, the authors found few discrete associations between the factors of individual resident and the resident's actual job performance. Additionally, they identify and discuss major gaps in the educational literature.

Adult↗
PubMed2005

Theta oscillations by synaptic excitation in a neocortical circuit model.

Neocortical theta-band oscillatory activity is associated with cognitive tasks involving learning and memory. This oscillatory activity is proposed to originate from the synchronization of interconnected layer V intrinsic bursting (IB) neurons by recurrent excitation. To test this hypothesis, a sparsely connected spiking circuit model based on empirical data was simulated using Hodgkin-Huxley-type bursting neurons and use-dependent depressing synaptic connections. In response to a heterogeneous tonic current stimulus, the model generated coherent and robust oscillatory activity throughout the theta-band (4-12 Hz). These oscillations were not, however, self-sustaining without a driving current, and not dependent on N-methyl-D-aspartate receptor synaptic currents. At realistic connection strengths, synaptic depression was necessary to avoid instability and expanded the basin of attraction for theta oscillations by controlling the gain of recurrent excitation. These results support the hypothesis that IB neuron networks can generate robust and coherent theta-band oscillations in neocortex.

Animals↗
PubMed2006

Dynamically multilayered visual system of the multifractal fly.

We dynamically analyze our experimental results on the motion sensitive spiking H1 neuron of the fly's visual system. We find that the fly uses an alphabet composed of a few letters to encode the information contained in the stimulus. The alphabet dynamics is multifractal both with and without stimulus, though the multifractality increases with the stimulus entropy. This is in sharp contrast to models generating independent spike intervals, whose dynamics is monofractal.

Animals↗
PubMed2002

Beyond phrenology: what can neuroimaging tell us about distributed circuitry?

Unsupervised models of how the brain identifies and categorizes the causes of its sensory input can be divided into two classes: those that minimize the mutual information (i.e., redundancy) among evoked responses and those that minimize the prediction error. Although these models have the same goal, the way that goal is attained, and the functional architectures required, are fundamentally different. This review describes the differences, in the functional anatomy of sensory cortical hierarchies, implied by the two models. We then consider how neuroimaging can be used to disambiguate between them. The key distinction reduces to whether backward connections are employed by the brain to generate a prediction of sensory inputs. To ascertain whether backward influences are evident empirically requires a characterization of functional integration among brain systems. This review summarizes the approaches to measuring functional integration in terms of effective connectivity and proceeds to address the question posed by the theoretical considerations. In short, it will be shown that the conjoint manipulation of bottom-up and top-down inputs to an area can be used to test for interactions between them, in elaborating cortical responses. The conclusion, from these sorts of neuroimaging studies, points to the prevalence of top-down influences and the plausibility of generative models of sensory brain function.

Animals↗
PubMed1991

Theoretical considerations in relation to the treatment of brain tumours by means of local hyperthermia generated by ultrasound fields.

Brain tumours comprise a significant fraction of all tumours in the human body. Despite the development of technology in clinical oncology, these tumours still present a difficult challenge. The margin between destruction of tumour and damage to normal tissue is narrow in the brain. The price paid for producing tissue damage outside the tumour is high in terms of quality of survival. Results of many experiments with ultrasound hyperthermia show that this new technique is successful for treating certain types of malignant tumours. In the case of brain tumours, applying focused fields should have the advantage of selectively destroying the tumour and leaving surrounding tissues intact. Previous attempts at applying ultrasound to the field of neurosurgery are reviewed. Those factors which have effects on the generation of thermal fields in brain tissues are considered in relation to the possible treatment of human brain tumours. Calculated thermal fields in a 2-D brain model generated by an applicator built in our laboratory are also presented.

Brain↗
PubMed1983

Effects of circulating renin substrate on renal function in isolated perfused rat kidney.

The effects of two different amounts of pure rat angiotensinogen were investigated in a closed circuit isolated perfused rat kidney. In response to angiotensinogen, circulating levels of angiotensin I (AI) and angiotensin II (AII) immunoreactive materials were found to increase in a time and dose-dependent manner. Vasoconstrictor and renin inhibitory effects were observed in parallel with the increase in AII. Glomerular filtration rate decreased after administration of angiotensinogen to a greater extent than renal flow and filtration fraction. The characterization by high performance liquid chromatography of peptides generated showed the liberation of AI, des-Asp1AI, AII and des-Asp1AII (AIII). These findings demonstrate that administration of angiotensinogen in an isolated perfused kidney model generates AI and that renal converting enzyme and aminopeptidases are able to convert AI to AII, AI to des-Asp1AI, and des-Asp1AI and/or AII to AIII. Changes in circulating level of angiotensinogen influence the activity of the renin-angiotensin system and, therefore, renal function.

Angiotensin I↗
PubMed1986

On the effect of the intracellular calcium-sensitive K+ channel in the bursting pancreatic beta-cell.

Based on the observation that the calcium-activated K+ channel in the pancreatic islet cells can also be activated by the membrane potential, we have formulated a mathematical model for the electrical activity in the pancreatic beta-cell. Our model contains two types of ionic channels, which are active above the subthreshold glucose concentration in the limit-cycle region: a Ca2+-activated, voltage-gated K+ channel and voltage-gated Ca2+ channel. Numerical simulation of the model generates bursts of electrical activity in response to a variation of kCa, the rate constant for sequestration of intracellular calcium ions. The period and duration of the bursts in response to kCa are in good agreement with experiment. The model predicts that a combined spike and burst pattern can be created using only single species of inward and outward currents, the inactivation kinetics (i.e., h) in the inward current is not a necessary condition for the generation of the pattern, and a given pattern or intensity of electrical activity may produce different levels of intracellular Ca2+ depending on the set of certain electrical parameters.

Animals↗
PubMed1992

A molecular thermodynamic approach to predict the secondary structure of homopolypeptides in aqueous systems.

Under physiological conditions, many polypeptide chains spontaneously fold into discrete and tightly packed three-dimensional structures. The folded polypeptide chain conformation is believed to represent a minimum Gibbs energy of the system, governed by the weak interactions that operate between the amino acid residues and between the residues and the solvent. A semiempirical molecular thermodynamic model is proposed to represent the Gibbs energy of folding of aqueous homopolypeptide systems. The model takes into consideration both the entropy contribution and the enthalpy contribution of folding homopolypeptide chains in aqueous solutions. The entropy contribution is derived from the Flory-Huggins expression for the entropy of mixing. It accounts for the entropy loss in folding a random-coiled polypeptide chain into a specific polypeptide conformation. The enthalpy contribution is derived from a molecular segment-based Non-Random Two Liquid (NRTL) local composition model [H. Renon and J. M. Prausnitz (1968) AIChE J., Vol. 14, pp. 135-142; C.-C. Chen and L. B. Evans (1986) AIChE J., Vol. 32, pp. 444-454], which takes into consideration of the residue-residue, residue-solvent, and solvent-solvent binary physical interactions along with the local compositions of amino acid residues in aqueous homopolypeptides. The UNIFAC group contribution method [A. Fredenslund, R. L. Jones, and J. M. Prausnitz (1975) AIChE J., 21, 1086-1099; A. Fredenslund, J. Gmehling, and P. Rasmussen (1977) Vapor-Liquid Equilibrium Using UNIFAC, Elsevier Scientific Publishing Company, Amsterdam], developed originally to estimate the excess Gibbs energy of solutions of small molecules, was used to estimate the NRTL binary interaction parameters. The model yields a hydrophobicity scale for the 20 amino acid side chains, which compares favorably with established scales [Y. Nozaki and C. Tanford (1971) Journal of Biological Chemistry, Vol. 46, pp. 2211-2217; E. B. Leodidis and T. A. Hatton (1990) Journal of Physical Chemistry, Vol. 94, pp. 6411-6420]. In addition, the model generates qualitatively correct thermodynamic constants and it accurately predicts thermodynamically favorable folding of a number of aqueous homopolypeptides from random-coiled states into alpha-helices. The model further facilitates estimation of the Zimm-Bragg helix growth parameter s and the nucleation parameter sigma for amino acid residues [B. H. Zimm and J. K. Bragg (1959) Journal of Chemical Physics, Vol. 31, pp. 526-535]. The calculated values of the two parameters fall into the ranges suggested by Zimm and Bragg.

Models, Molecular↗
PubMed1995

Optimisation of transcutaneous cardiac pacing by three-dimensional finite element modelling of the human thorax.

The goal of the study is to determine by finite element analysis (FE) the optimal electrode placement, size and electrolyte resistivity that minimise the pain experienced by patients during successful transcutaneous cardiac pacing (TCP). The three-dimensional FE model generated for this purpose has 55,388 nodes, 50,913 hexahedral elements and simulated 16 different organs and tissues, as well as the properties of the electrolyte. The model uses a non-uniform mesh with an average spatial resolution of 0.8 cm in all three dimensions. To validate this model, the voltage across 3 cm2 Ag-AgCl electrodes is measured when currents of 5 mA at 50 kHz are injected into a subject's thorax through the same electrodes. For the same electrode placements and sizes and the same injected current, the FE analysis produced results in good agreement with the experimental data. The optimisation analysis tested seven different electrode placements, five different electrode sizes and six different electrolyte resistivities. The analysis indicates that the anterior-posterior electrode placement, electrode sizes of about 90 cm2 and electrolytes with resistivity of about 800 omega.cm yield the most uniform current distribution through the skin, thus having the best chances to minimise the pain delivered to the patient during successful TCP. The anterior-anterior electrode placement is the second most efficient.

Cardiac Pacing, Artificial↗