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PubMed2000

Feldkamp-type cone-beam tomography in the wavelet framework.

X-ray computed tomography (CT) is in transition from fan-beam to cone-beam geometry. For cone-beam volumetric imaging, reduction of radiation exposure remains an important issue. Because the wavelet approach was shown to be effective and flexible for two-dimensional (2-D) local region reconstruction, we are motivated to perform wavelet local CT in cone-beam geometry. In this paper, we formulate the Feldkamp cone-beam reconstruction from the wavelet perspective, derive both full-scan and half-scan Feldkamp-type formulas for either global or local reconstruction, and demonstrate the feasibility and utility in synthetic and real data. It is found that using the wavelet Feldkamp approach, a three-dimensional (3-D) region of interest (ROI) can be reconstructed with neither severe image artifacts nor any significant constant bias in our simulation and experiments.

Animals↗
PubMed2004

A systematic approach to simulating metabolism in computational toxicology. I. The TIMES heuristic modelling framework.

Designing biologically active chemicals and managing their risks requires a holistic perspective on the chemical-biological interactions that form the basis of selective toxicity. The balance of therapeutic and adverse outcomes for new drugs and pesticides is managed by shaping the probabilities for transport, metabolism, and molecular initiating events. For chemicals activated as well as detoxified by metabolism, selective toxicity may be considered in terms of relative probabilities, which shift dramatically across species as well as within a population, depending on many factors. The complexity in toxicology that results from metabolism has been troublesome in QSAR research because the parent structure is less relevant to predicting ultimate effects and finding reference species/conditions for metabolic rates seems hopeless. Even the complexity of comparative xenobiotic metabolism itself seems paradoxical in light of the evidence of highly conserved catabolic processes across species. Clearly, predicting the role of metabolism in selective toxicity and adverse health outcomes requires a probabilistic framework for deterministic models as well as the many factors shaping the metabolic probability distributions under specific conditions. This paper presents a tissue metabolism simulator (TIMES), which uses a heuristic algorithm to generate plausible metabolic maps from a comprehensive library of biotransformations and abiotic reactions and estimates for system-specific transformation probabilities. The transformation probabilities can be calibrated to specific reference conditions using transformation rate information from systematic testing. In the absence of rate data, a combinatorial algorithm is used to translate known metabolic maps taken from reference systems into best-fit transformation probabilities. Finally, toxicity test data itself can be used to shape the transformation probabilities for toxicity pathways in which the metabolic activation is the rate-limiting process leading to a toxic effect. The conceptual approach for metabolic simulation will be presented along with practical uses in forecasting plausible activated metabolites.

Animals↗
PubMed1999

A pilot study on computer-assisted optimal contouring of orthopedic fixation devices.

Bending and shaping of longitudinal orthopedic fixation devices like rods and plates is often a difficult and time-consuming process to perform during surgery under sterile conditions. This study presents a novel device for implant contouring and introduces two strategies to obtain parameters necessary for the bending process. The first strategy is based on surgical navigation techniques as established within the framework of computer-assisted orthopedic surgery. Geometrical landmarks, e.g., the location of pedicle screws in a case of posterior spinal fixation, are collected with a three-dimensional pointing device. Subsequently, the final shape of the implant and the associated contouring parameters are calculated. The alternative strategy utilizes a flexible material intended to be used intra-operatively to enable the optimal shape of the implant to be modeled by hand. Contour parameters are calculated from a depth image of this model obtained using an object scanner. Bending of spinal rod systems is used to illustrate both strategies. A newly designed semi-automatic bending machine is proposed to impose the computed deformation on the implant material once parameters are obtained. Integrating the bending device into a system for computer-assisted surgery allows for the interactive control of the contouring process.

Humans↗
PubMed2006

Structure mapping and semantic integration in a construction-based neurolinguistic model of sentence processing.

The current research provides a theoretical, computational and neurophysiological framework in which particular aspects of sentence comprehension and non-linguistic sequence transformation processing are implemented by a common neural mechanism for structure mapping. The theoretical context is derived from construction grammar theory in which language is considered in terms of a structured inventory of form to meaning mappings. Computationally, the construction grammar concept is implemented in a hybrid neural network model that is derived from functional neuroanatomical studies. In particular, based on data from Hoen et al. (2006, this issue), the generalized structure mapping capability is attributed to a local cortical network that includes Brodmann's area (BA) 44, while the integration of semantic structure into this transformation mechanism relies on BA 45.

Brain↗
PubMed2005

On titanium frameworks and alternative impression techniques in implant dentistry.

PURPOSE: The objectives of this thesis were to compare the clinical and material performance of implant-supported titanium frameworks with gold-alloy frameworks in the edentulous jaw and to test a digitized impression technique to optimize material characteristics and clinical and laboratory procedures. MATERIALS AND METHODS: Two different kinds of laser-welded titanium frameworks and one type of digitized computer numeric controlled (CNC)-milled titanium framework for the edentulous jaw were evaluated and compared with gold-alloy frameworks in two clinical 5-year follow-up studies. The CNC frameworks were also evaluated and compared with gold-alloy frameworks in two experimental studies according to fit, preload, and surface roughness. Furthermore, a digitized photogrammetric technique for recording implant positions in the edentulous jaw was experimentally tested and compared with two conventional impression techniques. RESULTS: Laser-welded titanium frameworks had a lower success rate after 5 years in function than gold-alloy frameworks. The 5-year performance of CNC frameworks was similar to that of gold-alloy frameworks. The fit and precision of implant-supported CNC frameworks was significantly better compared with gold-alloy frameworks. Applications of veneering material did not significantly affect the fit of the titanium frameworks. The preload of CNC frameworks was similar to that of gold-alloy frameworks, both exhibiting significantly decreased preloads after repeated tightening. The preloads of titanium frameworks were similar before and after veneering. Unloaded milled titanium screw sites had significantly rougher surfaces than loaded sites, and loaded gold screws had rougher surfaces than unloaded. No correlation between surface of the screw joints and preload of veneered titanium frameworks was observed. The precision of photogrammetric impressions was comparable to that of conventional impression techniques. CONCLUSIONS: Implant-supported CNC-milled titanium frameworks are a viable alternative to gold-alloy castings in the edentulous jaw, and because a digital platform is used to manufacture these titanium frameworks, photogrammetric impressions can be made.

Adult↗
PubMedDate not supplied

Computers and nursing. Possibilities for transforming nursing.

The use of computers is becoming commonplace in the clinical setting. However, the impact of computer use and its implications for nursing have yet to be understood (Birckhead, 1978). The purpose of this article is to explore how computer technology may transform nursing. The discourse is guided by Burch's (1985) thesis that "the use of technology is non-neutral. It transforms experience, whether for better or worse, and ultimately shapes human thinking and being". If one values nursing as a humanizing activity, then most of the potential transformations can be viewed as negative. When viewed from an instrumental framework, however, the computer may have a positive rather than a negative impact because computer use promotes expediency, efficiency, and precision.

Humans↗
PubMed2026

Integrated computational and experimental benchmarking of Bacillus phage endolysins reveals the relationship between peptidoglycan-fragment recognition descriptors and antibacterial performance.

Protein-based antibacterials such as bacteriophage endolysins offer a targeted therapeutic strategy against Gram-positive pathogens. However, prioritizing the most effective candidates from the large sequence diversity available remains a significant challenge. Here we present a standardized computational-experimental benchmarking framework that evaluates seven phage-derived endolysin variants (E1, E2, E3, E7, E10, E12, and E15) identified from Bacillus genomes. We combined molecular docking and residue-level interaction mapping against muramyl dipeptide (MDP), a minimal conserved peptidoglycan motif, with 1000-ns molecular dynamics simulations, MM/PBSA binding free-energy estimation, and matched functional inhibition assays against Staphylococcus aureus and Micrococcus luteus. Computational analyses revealed generally favorable MDP recognition across variants, albeit with notable differences in contact patterns and complex stability profiles. Experimental screening identified E2 as the most potent antibacterial agent against both species, while E7 and E1 performed strongly in selected computational metrics. Integrated analysis showed only modest correlations between computational descriptors of fragment recognition/stability and observed antibacterial performance. This study establishes a practical comparative benchmarking platform for endolysin candidate prioritization, nominates E2 and E7 as promising candidates for further development, and highlights E1 as a potential structural scaffold for rational engineering, while explicitly demonstrating both the utility and the current limitations of using minimal peptidoglycan fragments as proxies for full cell-wall recognition in lysin benchmarking.

Endopeptidases↗
PubMed2005

Constrained geometric simulation of diffusive motion in proteins.

We describe a new computational method, FRODA (framework rigidity optimized dynamic algorithm), for exploring the internal mobility of proteins. The rigid regions in the protein are first determined, and then replaced by ghost templates which are used to guide the movements of the atoms in the protein. Using random moves, the available conformational phase space of a 100 residue protein can be well explored in approximately 10-100 min of computer time using a single processor. All of the covalent, hydrophobic and hydrogen bond constraints are maintained, and van der Waals overlaps are avoided, throughout the simulation. We illustrate the results of a FRODA simulation on barnase, and show that good agreement is obtained with nuclear magnetic resonance experiments. We additionally show how FRODA can be used to find a pathway from one conformation to another. This directed dynamics is illustrated with the protein dihydrofolate reductase.

Algorithms↗
PubMed1995

A general method for the computer simulation of biological systems interacting with fluids.

At this Symposium on Biological Fluid Dynamics, it is appropriate to ask whether there is any common theme that unites the diverse problems that arise in the study of living systems interacting with fluids. The answer that immediately comes to mind is this: biological fluid dynamics invariably involves the interaction of elastic flexible tissue with viscous incompressible fluid. (In many cases the tissue is not only elastic, it is also active, i.e. capable of doing work on the fluid). This paper describes the immersed boundary method, which is a general framework for the computer simulation of biofluid dynamic systems. This method has already been applied to blood flow in the heart (including the computer-assisted design of prosthetic cardiac valves), platelet aggregation during blood clotting, aquatic animal locomotion, wave propagation along the basilar membrane of the inner ear, and flow in collapsible tubes. In the immersed boundary method, the elastic (and possibly active) biological tissue is treated as a part of the fluid in which additional forces (derived from the tissue stresses) are applied. Because the tissue is represented in terms of its force field, the method remains straightforward, even when the geometry of the biological tissue is complicated, dynamic and not known in advance.

Animals↗
PubMed2005

Coevolutionary arms races between bacteria and bacteriophage.

We propose a computational and theoretical framework for analyzing rapid coevolutionary dynamics of bacteriophage and bacteria in their ecological context. Bacteriophage enter host cells via membrane-bound surface receptors often responsible for nutrient uptake. As such, a selective pressure will exist for the bacteria to modify its receptor configuration and, in turn, for the phage to modify its tail fiber. A mathematical model of these trait adaptations is developed by using the framework of adaptive dynamics. Host strains differ in their efficiency of resource uptake and resistance to phage, whereas phage strains differ in their host preference for adsorption. We solve the evolutionary ecology model and find the conditions for coevolutionary branching and relevant dimensionless parameters leading to distinct quasispecies. We confirm these calculations using stochastic Monte Carlo simulations of populations evolving in a chemostat with fixed washout rate and inflow resource density. We find that multiple quasispecies of bacteria and phage can coexist in a homogeneous medium with a single resource. When diversification occurs, quasispecies of phage adsorb effectively to only a limited subset of the total number of quasispecies of bacteria, i.e., functional differences between quasispecies arise endogenously within the evolutionary ecology framework. Finally, we discuss means to relate predictions of this model to experimental studies in the chemostat, using the model organisms Escherichia coli and the virulent strain of lambda phage.

Adaptation, Biological↗
PubMed1992

Preverbal and verbal counting and computation.

We describe the preverbal system of counting and arithmetic reasoning revealed by experiments on numerical representations in animals. In this system, numerosities are represented by magnitudes, which are rapidly but inaccurately generated by the Meck and Church (1983) preverbal counting mechanism. We suggest the following. (1) The preverbal counting mechanism is the source of the implicit principles that guide the acquisition of verbal counting. (2) The preverbal system of arithmetic computation provides the framework for the assimilation of the verbal system. (3) Learning to count involves, in part, learning a mapping from the preverbal numerical magnitudes to the verbal and written number symbols and the inverse mappings from these symbols to the preverbal magnitudes. (4) Subitizing is the use of the preverbal counting process and the mapping from the resulting magnitudes to number words in order to generate rapidly the number words for small numerosities. (5) The retrieval of the number facts, which plays a central role in verbal computation, is mediated via the inverse mappings from verbal and written numbers to the preverbal magnitudes and the use of these magnitudes to find the appropriate cells in tabular arrangements of the answers. (6) This model of the fact retrieval process accounts for the salient features of the reaction time differences and error patterns revealed by experiments on mental arithmetic. (7) The application of verbal and written computational algorithms goes on in parallel with, and is to some extent guided by, preverbal computations, both in the child and in the adult.

Animals↗
PubMed2006

Model-based blood glucose control for Type 1 diabetes via parametric programming.

An advanced model-based control technique for regulating the blood glucose for patients with Type 1 diabetes is presented. The optimal insulin delivery rate is obtained off-line as an explicit function of the current blood glucose concentration of the patient by using novel parametric programming algorithms, developed at Imperial College London. The implementation of the optimal insulin delivery rate, therefore, requires simple function evaluation and minimal on-line computations. The proposed framework also addresses the uncertainty in the model due to interpatient and intrapatient variability by identifying the model parameters which ensure that a feasible control law can be obtained. The developments reported in this paper are expected to simplify the insulin delivery mechanism, thereby enhancing the quality of life of the patient.

Blood Glucose↗
PubMed2003

The informatics of a C57BL/6J mouse brain atlas.

The Mouse Atlas Project (MAP) aims to produce a framework for organizing and analyzing the large volumes of neuroscientific data produced by the proliferation of genetically modified animals. Atlases provide an invaluable aid in understanding the impact of genetic manipulations by providing a standard for comparison. We use a digital atlas as the hub of an informatics network, correlating imaging data, such as structural imaging and histology, with text-based data, such as nomenclature, connections, and references. We generated brain volumes using magnetic resonance microscopy (MRM), classical histology, and immunohistochemistry, and registered them into a common and defined coordinate system. Specially designed viewers were developed in order to visualize multiple datasets simultaneously and to coordinate between textual and image data. Researchers can navigate through the brain interchangeably, in either a text-based or image-based representation that automatically updates information as they move. The atlas also allows the independent entry of other types of data, the facile retrieval of information, and the straight-forward display of images. In conjunction with centralized servers, image and text data can be kept current and can decrease the burden on individual researchers' computers. A comprehensive framework that encompasses many forms of information in the context of anatomic imaging holds tremendous promise for producing new insights. The atlas and associated tools can be found at http://www.loni.ucla.edu/MAP.

Anatomy, Artistic↗
PubMed2006

Distributed virtual experiments in water quality management.

Since the complexity of virtual experiments (VEs) and their underlying models is constantly increasing, computational performance of monolithic software solutions is rapidly becoming insufficient. Examples of VEs are probabilistic design, model calibration, optimal experimental design and scenario analysis. In order to tackle this computational bottleneck, a framework for the distributed execution of VEs on a potentially heterogeneous pool of work nodes has been implemented. This framework was named WDVE (WEST distributed virtual experimentation) and is built on top of technologies such as C++, XML and SOAP. It was designed for stability, expandability, performance, platform-independence and ease of use. Complex VEs are most often composed of mutually independent sub-experiments, which can be run concurrently. With WDVE, a complex VE that is executed on a so-called Master machine will therefore attempt to execute its sub-experiments on Slave machines that have previously registered with the Master. The process of submitting requests for the execution of sub-experiments is transparent and involves the transfer of a description of the experiment to be executed, and the resources that are needed for the execution (i.e., model and input data). WDVE is in many ways similar to the Grid Computing paradigm, which is currently receiving widespread attention. However, WDVE is more geared towards application within the scope of water quality management.

Calibration↗
PubMed1998

[Computer-assisted surgical navigation with a dynamic mobile framework for the nasal fossae, sinuses and base of the skull].

Surgery of the skull base and of the paranasal sinuses is often difficult because of the complex anatomy and the delicate structures; serious complications (loss of vision, cerebral lesion) have been reported. To improve the safety of such operations, computer-assisted navigation surgery is increasingly being put to use. We introduce the system which was developed in Berne. Our computer-assisted system is based on an intraoperative pursuit of the head and instruments which are equipped with infrared diodes and registered by an opto-electronic system-camera. The CT-acquisition of the head is accomplished framelessly without a head-holding device. This allows free movement of the head during surgery. Between March and November 1997, 35 navigation operations were performed for various pathologies at the anterior and lateral skull base. The majority of the cases were endonasal operations. No surgical complications occurred inspite of the complexity of the operations. The measured accuracy of the system between the CT and the actual instrument location in the patient was 0.5-2 mm (mean : < 1 mm) for the anterior skull base and 1-2.5 mm (mean < 1.5 mm) for the lateral skull base. The intraoperative navigation system allows identification of essential anatomical structures and permits safe and efficient surgery without additional loss of time. In addition, such a system allows minimal invasive approaches, and new operations may become possible.

Adult↗
PubMed2026

Dynamic Protein Structure Paradox: An Integrative Framework for Endpoint-Conditioned Evidentiary Sufficiency in Structure-to-Function Claims.

Accurate coordinates for a represented protein state do not, by themselves, establish activity or any other condition-specific function. This article defines the Dynamic Protein Structure Paradox (DPSP) as the apparent conflict between structural accuracy and functional underdetermination and develops it as an integrative evidentiary assessment framework rather than a new theory or paradigm. The underlying problem has been longstanding, since structural genomics, function annotation, allostery, and disorder research each established that fold does not determine function and that function does not determine fold. DPSP consolidates those results into one endpoint-conditioned rule. Once a measurable endpoint is defined, it assesses four coupled dimensions: relevant-state completeness, context completeness, ensemble or kinetic dependence, and chemical dependence. A rubric rates each dimension as adequate, uncertain, or missing, and a materiality test determines which gaps influence the stated decision. The outcome is one of three mutually exclusive modes of utilization: geometry-led, conditional, or function-measured. The deliverable is a concise evidence statement delineating what the structure supports, which decisive variable remains unmeasured, and what corroboration is necessary. DPSP complements, rather than replaces, existing structural, ensemble, and computational approaches. The framework remains unvalidated, its thresholds are provisional, and the studies necessary to confirm or refute it are specified.

Proteins↗
PubMed2005

An evaluation of contrast enhancement techniques for mammographic breast masses.

The main aim of this paper is to propose a novel set of metrics that measure the quality of the image enhancement of mammographic images in a computer-aided detection framework aimed at automatically finding masses using machine learning techniques. Our methodology includes a novel mechanism for the combination of the metrics proposed into a single quantitative measure. We have evaluated our methodology on 200 images from the publicly available digital database for screening mammograms. We show that the quantitative measures help us select the best suited image enhancement on a per mammogram basis, which improves the quality of subsequent image segmentation much better than using the same enhancement method for all mammograms.

Algorithms↗
PubMed2006

Metabolic engineering under uncertainty--II: analysis of yeast metabolism.

Yeast metabolism has been used extensively in scientific investigations and industrial applications. Understanding the properties of the yeast metabolic network is crucial, yet unaccomplished due to its high complexity, the different culture conditions, and the uncertainty associated with kinetic parameters. We recently developed a computational and mathematical framework using Monte Carlo method in which parameter uncertainty can be addressed through large-scale sampling procedure. This framework was applied on the compartmentalized central carbon pathways of Saccharomyces cerevisiae metabolism considering the growth environment of batch and chemostat reactor and integrating information from metabolic flux analysis. Statistical analysis of the results indicates that yeast cells growing in batch culture condition exhibit dramatically different control schemes from those growing in a chemostat. The difference is mainly due to the feedback introduced by the constraints of the chemostat. The control of the enzymes on the rates of the substrate uptake, product excretion, and cell growth and its practical implication are discussed. Clustering of the reaction steps according to the similarity of their responses to enzyme activity perturbations reveals functional coupling of metabolic reactions.

Bioreactors↗