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At least 1,369 records · Page 76Linked to original sources
PubMed2004

Planning, implementation and optimization of future space missions using an immersive visualization environment (IVE) machine.

Beginning in 1995, a team of 3-D engineering visualization experts assembled at the Lockheed Martin Space Systems Company and began to develop innovative virtual prototyping simulation tools for performing ground processing and real-time visualization of design and planning of aerospace missions. At the University of Colorado, a team of 3-D visualization experts also began developing the science of 3-D visualization and immersive visualization at the newly founded British Petroleum (BP) Center for visualization, which began operations in October, 2001. BP acquired ARCO in the year 2000 and awarded the 3-D flexible IVE developed by ARCO (beginning in 1990) to the University of Colorado, CU, the winner in a competition among 6 Universities. CU then hired Dr. G. Dorn, the leader of the ARCO team as Center Director, and the other experts to apply 3-D immersive visualization to aerospace and to other University Research fields, while continuing research on surface interpretation of seismic data and 3-D volumes. This paper recounts further progress and outlines plans in Aerospace applications at Lockheed Martin and CU.

Astronauts↗
PubMed2006

Subjective visual sensation during vitrectomy under retrobulbar anesthesia.

PURPOSE: To report a precise illustrated image of patient's view during vitrectomy. DESIGN: Interventional case report. METHODS: A 56-year-old male with cystoid macular edema (CME) associated with epiretinal membrane underwent vitrectomy. The patient seemed to find gratification in being operated on because he was able to see what was going on. He was a professional artist in computer graphics, and he drew three different pictures depending on the surgical procedures. RESULTS: These pictures depicted the moving of pasty, whirling fluid during core vitrectomy, numerous black or gray spots like snowflakes by intravitrealy injected crystals of triamcinolone acetonide, and a sharp tapered instrument coming into the center and membrane-like material being peeled off. CONCLUSIONS: Patients may see a precise shape in a constant size, scale, and detailed movement as well, focused on the retina without described optics. Further investigation will be required to determine this mechanism.

Anesthesia, Local↗
PubMed2006

W3MAMCAT: a world wide web based tool for mammillary and catenary compartmental modeling and expert system distinguishability.

W(3)MAMCAT is a new web-based and interactive system for building and quantifying the parameters or parameter ranges of n-compartment mammillary and catenary model structures, with input and output in the first compartment, from unstructured multiexponential (sum-of-n-exponentials) models. It handles unidentifiable as well as identifiable models and, as such, provides finite parameter interval solutions for unidentifiable models, whereas direct parameter search programs typically do not. It also tutorially develops the theory of model distinguishability for same order mammillary versus catenary models, as did its desktop application predecessor MAMCAT+. This includes expert system analysis for distinguishing mammillary from catenary structures, given input and output in similarly numbered compartments. W(3)MAMCAT provides for universal deployment via the internet and enhanced application error checking. It uses supported Microsoft technologies to form an extensible application framework for maintaining a stable and easily updatable application. Most important, anybody, anywhere, is welcome to access it using Internet Explorer 6.0 over the internet for their teaching or research needs. It is available on the Biocybernetics Laboratory website at UCLA: www.biocyb.cs.ucla.edu.

Algorithms↗
PubMed2005

Simulating chemotherapeutic schemes in the individualized treatment context: the paradigm of glioblastoma multiforme treated by temozolomide in vivo.

A novel patient individualized, spatiotemporal Monte Carlo simulation model of tumor response to chemotherapeutic schemes in vivo is presented. Treatment of glioblastoma multiforme by temozolomide is considered as a paradigm. The model is based on the patient's imaging, histopathologic and genetic data. A discretization mesh is superimposed upon the anatomical region of interest and within each geometrical cell of the mesh the most prominent biological "laws" (cell cycling, apoptosis, etc.) in conjunction with pharmacokinetics and pharmacodynamics information are applied. A good qualitative agreement of the model's predictions with clinical experience supports the applicability of the approach to chemotherapy optimization.

Antineoplastic Agents, Alkylating↗
PubMed2005

A computer program for the simulation of fiber deposition in the human respiratory tract.

As inhaled fibers may lead to a variety of lung diseases, detailed information on their deposition in the human respiratory tract is an indispensable requirement in medical science. In the work presented here, a Visual Basic((R)) computer program, termed FIBROS, is described which enables the simulation of fibrous particle deposition in both the extrathoracic region and different parts of the lung itself, including the results of published numerical studies on inertial/interceptional as well as diffusional and gravitational deposition. The input window of FIBROS includes the selection of specific breathing conditions by variation of the tidal volume and breathing cycle. Furthermore, the user is able to determine fiber properties such as diameter, aspect ratio, specific weight, and fiber orientation with respect to the air stream in the upper and lower airways of the lungs. Besides the offer of various deposition formulae for each region of the respiratory tract, thereby also allowing a distinction between mouth and nose breathing, the user may select between different morphometric datasets of the lung and respective airway scaling procedures. Analysis routines of FIBROS include the estimation of regional deposition fractions, thereby distinguishing between extrathoracic, bronchial, and acinar compartments, and a calculation of generation-by-generation deposition probabilities within tubular and alveolar structures. Preliminary results presented here should demonstrate the effects on fiber deposition due to variations of the breathing behaviour and the particle properties.

Algorithms↗
PubMed2006

Computer systems analysis of spaceflight induced changes in left ventricular mass.

Circulatory adaptations resulting in postflight orthostasis have frequently been observed in response to space travel. It has been postulated that a decrement in left ventricular mass (LVM) found after microgravity exposure may be the central component in this cardiovascular deconditioning. However, a physiologic mechanism responsible for these changes in the myocardium has not been determined. In this study, we examined the sequential alterations in echocardiographic measured LVM from preflight to landing day and 3 days into the postflight recovery period. In a previous study in returning astronauts we found a comparative 9.1% reduction in postflight LVM that returned to preflight values by the third day of recovery. This data was further evaluated in a systems analysis approach using a well-established advanced computer model of circulatory functioning. The computer model incorporates the physiologic responses to changes in pressures, flows and hydraulics within the circulatory system as affected by gravitational forces. Myocardial muscle progression to atrophy or hypertrophy in reaction to the circulatory load conditions is also included in the model. The integrative computer analysis suggests that these variations in LVM could be explained by simple fluid shifts known to occur during spaceflight and can reverse within a few days after reentry into earth's gravity. According to model predictions, the reductions in LVM found upon exposure to microgravity are a result of a contraction of the myocardial interstitial fluid space secondary to a loss in the plasma volume. This hypothesis was additionally supported by the published ground-based study in which we followed the alterations in LVM and plasma volume in normal subjects in which hypovolemia was induced by simple dehydration. In the hypovolemic state, plasma volume was reduced in these subjects and was significantly correlated with echocardiographic measurements of LVM. Based on these experimental findings and the performance of the computer systems analysis it appears that reductions in LVM observed after spaceflight may be secondary to fluid exchanges produced by common physiologic mechanisms. Reductions in LVM observed after microgravity exposure have been previously postulated to be a central component of spaceflight-induced cardiovascular deconditioning. However, a recent study has demonstrated a return of astronauts' LVM to preflight values by the third day after landing through uncertain mechanisms. A systems analysis approach using computer simulation techniques allows for a dissection of the complex physiologic control processes and a more detailed examination of the phenomena. From the simulation studies and computer analysis it appears that microgravity induced reductions in LVM may be explained by considering physiologic fluid exchanges rather than cardiac muscle atrophy.

Adult↗
PubMed2006

Effect of the size and location of osteochondral defects in degenerative arthritis. A finite element simulation.

Physiological studies have shown that focal articular surface defects in the human knee may progress to degenerative arthritis. Although the risk of this evolutive process is multifactorial, defect size is one of the most important factors. In order to determine the influence of osteochondral defect size and location on the stress and strain concentrations around the defect rim, a finite element model of the human knee was developed. From our results, it became clear that the size and location of cartilage defects drastically affect to those variables. No stress concentration appeared around the rim of small defects, being the stress distribution mainly controlled by the meniscus contact. On the contrary, important rim stress concentration was found for large osteochondral defects. This alteration of the stress distribution has important clinical implications regarding the long-term integrity of the cartilage adjacent to osteochondral defects.

Cartilage, Articular↗
PubMed2004

PEG-Ara-C conjugates for controlled release.

The antitumour agent 1-beta-D arabinofuranosilcytosyne (Ara-C) was covalently linked to poly(ethylene glycol) (PEG) in order to improve the in vivo stability and blood residence time. Eight PEG conjugates were synthesised, with linear or branched PEG of 5000, 10000 and 20000 Da molecular weight through an amino acid spacer. Starting from mPEG-OH or HO-PEG-OH, conjugation was carried out to the one or two available hydroxyl groups at the polymer's extreme. Furthermore, to increase the drug loading of the polymer, the hydroxyl functions of PEG were functionalised with a bicarboxylic amino acid yielding a tetrafunctional derivative and, by recursive conjugation with the same bicarboxylic amino acid, products with four or eight Ara-C molecules for each PEG chain were prepared. A computer graphic investigation demonstrated that aminoadipic acid was a suitable bicarboxylic amino acid to overcome the steric hindrance between the vicinal Ara-C molecules in the dendrimeric structure. In this paper we report the optimised conditions for synthesis and purification of PEG-Ara-C products with a low amount of remaining free drug, studies toward the hydrolysis of PEG-Ara-C and the Ara-C deamination by cytidine deaminase, pharmacokinetics in mice and cytotoxicity towards HeLa human cells were also investigated. Increased stability towards degradation of the conjugated Ara-C products, in particular for the highly loaded ones, improved blood residence time in mice and a reduced cytotoxicity with respect to the free Ara-C form was demonstrated.

Animals↗
PubMed2006

PSSARD (2.0): a database server for making flexible queries relating amino acid sequences to main-chain secondary structure conformations for proteins of known three-dimensional structure and certain useful applications.

We have updated the Protein Sequence-Structure Analysis Relational Database (PSSARD) first published in the Int. J. Biol. Macromol. 36 (2005) 259-262 corresponding to 1573 representative protein chains selected from the Protein Data Bank (PDB). In this, the updated and revised PSSARD (Version 2.0), we have included all proteins in the Protein Data Bank available at the time of developing this database including the NMR PDB entries. The current database corresponds to 22,752 XRAY PDB entries and 3977 NMR PDB entries and is separated accordingly in order to facilitate the appropriate database search. The representative protein chains can also be separately accessed within the current database. We have made a provision to combine more than one field to query the database and the results of any search can be used to carry out further nested searches using a combination of queries. We have provided hyperlinks to the individual PDB entries obtained as the result of any search in PSSARD in order to obtain additional details relevant to the protein structure. Certain applications useful to identify domains and structural motifs are discussed.

Amino Acid Sequence↗
PubMed2005

Graph theoretic modeling of large-scale semantic networks.

During the past several years, social network analysis methods have been used to model many complex real-world phenomena, including social networks, transportation networks, and the Internet. Graph theoretic methods, based on an elegant representation of entities and relationships, have been used in computational biology to study biological networks; however they have not yet been adopted widely by the greater informatics community. The graphs produced are generally large, sparse, and complex, and share common global topological properties. In this review of research (1998-2005) on large-scale semantic networks, we used a tailored search strategy to identify articles involving both a graph theoretic perspective and semantic information. Thirty-one relevant articles were retrieved. The majority (28, 90.3%) involved an investigation of a real-world network. These included corpora, thesauri, dictionaries, large computer programs, biological neuronal networks, word association networks, and files on the Internet. Twenty-two of the 28 (78.6%) involved a graph comprised of words or phrases. Fifteen of the 28 (53.6%) mentioned evidence of small-world characteristics in the network investigated. Eleven (39.3%) reported a scale-free topology, which tends to have a similar appearance when examined at varying scales. The results of this review indicate that networks generated from natural language have topological properties common to other natural phenomena. It has not yet been determined whether artificial human-curated terminology systems in biomedicine share these properties. Large network analysis methods have potential application in a variety of areas of informatics, such as in development of controlled vocabularies and for characterizing a given domain.

Algorithms↗
PubMed2006

Direct classification of high-dimensional data in low-dimensional projected feature spaces--comparison of several classification methodologies.

Previously, we introduced a distance (similarity)-based mapping for the visualization of high-dimensional patterns and their relative relationships. The mapping preserves exactly the original distances from all points to any two reference patterns in a special two-dimensional coordinate system, the relative distance plane (RDP). We extend the RDP mapping's applicability from visualization to classification. Several of the classifiers use the RDP directly. These include the standard linear discriminant analysis (LDA), nearest neighbor classifiers, and a transvariation probabilities-based classification method that is natural in the RDP. Several reference directions can also be combined to create new coordinate systems in which arbitrary classifiers can be developed. We obtain increased confidence in the classification results by cycling through all possible reference pairs and computing a misclassification-based weighted accuracy. The classification results on several high-dimensional biomedical datasets are compared.

Algorithms↗
PubMed2004

Three-dimensional modeling and animation of two carpal bones: a technique.

The objectives of this study were to (a). create 3D reconstructions of two carpal bones from single CT data sets and animate these bones with experimental in vitro motion data collected during dynamic loading of the wrist joint, (b). develop a technique to calculate the minimum interbone distance between the two carpal bones, and (c). validate the interbone distance calculation process. This method utilized commercial software to create the animations and an in-house program to interface with three-dimensional CAD software to calculate the minimum distance between the irregular geometries of the bones. This interbone minimum distance provides quantitative information regarding the motion of the bones studied and may help to understand and quantify the effects of ligamentous injury.

Carpal Bones↗
PubMed2005

Report of the first virtual visualization of the reconstructed electrocardiographic display symposium.

In August 2004, a group of scientists and clinicians with a deep interest in electrocardiography met to discuss the present and future of the electrocardiogram as an imaging modality. Motivated by a set of challenges to the field, they each presented and discussed their ideas about the basic electrophysiology, the computational approaches required, and the clinical state of the art and where it might go in the future. In this paper, we present a summary of these presentations and discussions, starting with a statement of the challenges and a motivating case study that illustrates the inadequacies of electrocardiography as it is current practiced. Following this introduction are overviews of the present state of the inverse problem of electrocardiography and the underlying assumptions of this form of simulation and modeling. We conclude with a summary of the needs that we feel must be addressed to achieve the full potential of electrically based imaging of the heart.

Computer Graphics↗
PubMed2004

Molecular modeling of sigma 1 receptor ligands: a model of binding conformational and electrostatic considerations.

We have performed molecular modeling studies on several sigma 1 specific ligands, including PD144418, spipethiane, haloperidol, pentazocine, and others to develop a pharmacophore for sigma 1 receptor-ligand binding, under the assumption that all the compounds interact at the same receptor binding site. The modeling studies have investigated the conformational and electrostatic properties of the ligands. Superposition of active molecules gave the coordinates of the hypothetical 5-point sigma 1 pharmacophore, as follows: R1 (0.85, 7.26, 0.30); R2 (5.47, 2.40, -1.51); R3 (-2.57, 4.82, -7.10); N (-0.71, 3.29, -6.40); carbon centroid (3.16, 4.83, -0.60), where R1, R2 were constructed onto the aromatic ring of each compound to represent hydrophobic interactions with the receptor; and R3 represents a hydrogen bond between the nitrogen atom and the receptor. Additional analyses were used to describe secondary binding sites to electronegative groups such as oxygen or sulfur atom. Those coordinates are (2.34, 5.08, -4.18). The model was verified by fitting other sigma 1 receptor ligands. This model may be used to search conformational databases for other possibly active ligands. In conjunction with rational drug design techniques the model may be useful in design and synthesis of novel sigma 1 ligands of high selectivity and potency. Calculations were performed using Sybyl 6.5.

Binding Sites↗
PubMed2005

Inhibitor-based validation of a homology model of the active-site of tripeptidyl peptidase II.

A homology model of the active site region of tripeptidyl peptidase II (TPP II) was constructed based on the crystal structures of four subtilisin-like templates. The resulting model was subsequently validated by judging expectations of the model versus observed activities for a broad set of prepared TPP II inhibitors. The structure-activity relationships observed for the prepared TPP II inhibitors correlated nicely with the structural details of the TPP II active site model, supporting the validity of this model and its usefulness for structure-based drug design and pharmacophore searching experiments.

Amino Acid Sequence↗