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PubMed1993

Coupling of computer modeling with in vitro methodologies to reduce animal usage in toxicity testing.

The use of in vitro data to support the development of physiologically based pharmacokinetic (PBPK) models and to reduce the requirement for in vivo testing is demonstrated by three examples. In the first example, polychlorotrifluoroethylene, in vitro studies comparing metabolism and tissue response in rodents and primates made it possible to obtain definitive data for a human risk assessment without resorting to additional in vivo studies with primates. In the second example, a PBPK model for organophosphate esters was developed in which the parameters defining metabolism, tissue partitioning, and enzyme inhibition were all characterized by in vitro studies, and the rest of the model parameters were established from the literature. The resulting model was able to provide a coherent description of enzyme inhibition following both acute and chronic exposures in mice, rats, and humans. In the final example, the carcinogenic risk assessment for methylene chloride was refined by the incorporation of in vitro data on human metabolism into a PBPK model.

Animal Testing Alternatives↗

PubMed2006

Predicting protein structural class with pseudo-amino acid composition and support vector machine fusion network.

Because a priori knowledge of a protein structural class can provide useful information about its overall structure, the determination of protein structural class is a quite meaningful topic in protein science. However, with the rapid increase in newly found protein sequences entering into databanks, it is both time-consuming and expensive to do so based solely on experimental techniques. Therefore, it is vitally important to develop a computational method for predicting the protein structural class quickly and accurately. To deal with the challenge, this article presents a dual-layer support vector machine (SVM) fusion network that is featured by using a different pseudo-amino acid composition (PseAA). The PseAA here contains much information that is related to the sequence order of a protein and the distribution of the hydrophobic amino acids along its chain. As a showcase, the rigorous jackknife cross-validation test was performed on the two benchmark data sets constructed by Zhou. A significant enhancement in success rates was observed, indicating that the current approach may serve as a powerful complementary tool to other existing methods in this area.

Algorithms↗

PubMed2004

Computerized kinetic perimetry detects tubular visual fields in patients with functional visual loss.

PURPOSE: To report a novel test that uses computerized kinetic perimetry to detect tubular visual fields in patients with functional visual loss. DESIGN: Observational case series. METHODS: Ten patients who demonstrated generalized visual field constriction on prior examinations underwent testing combining computerized kinetic perimetry with a reversed Galilean telescope, used for optical visual field expansion. RESULTS: Six patients with physiologic visual field constriction demonstrated expansion of their visual fields with the use of the reversed telescope. Four patients with functional visual loss responded to the reversed telescope by demonstrating tubular visual fields, with responses equal to or smaller than their demonstrated visual fields delineated without the telescope. CONCLUSIONS: This test uses a computerized kinetic examination to reduce the subjective nature of tangent screen testing for tubular visual fields and to provide a computerized recording of visual fields. This method is a novel and easy-to-use technique to demonstrate functional visual loss.

Computing Methodologies↗

PubMed2005

Perceptions and attitudes of Canadian orthodontists regarding digital and electronic technology.

INTRODUCTION: To plan for future acceptance and implementation of computer-related technology, it is necessary to understand orthodontists' current perceptions and attitudes toward emerging technologies. METHODS: An anonymous, self-administered, mail-out survey of Canadian orthodontists was conducted. The response rate was 45.6% (304/667). RESULTS: Most orthodontists indicated that computer technology could improve current practice efficiency and quality of patient care. Only 15% reported that digital models are quite or very useful; 73.6%, 69.1%, 55%, and 37.4% agreed or strongly agreed with using digital and electronic technology to consult with other dental specialists, other orthodontists, general dentists, and the public, respectively. Cost of the technology was reported as a significant or insurmountable obstacle by 54% of the respondents. Interprovincial legislation, unclear consultation remuneration guidelines, and lack of comfort with the technology were not perceived as significant obstacles. Only 36% reported security or privacy issues as a significant or insurmountable obstacle. CONCLUSIONS: Canadian orthodontists seem to view digital and electronic technology as useful and capable of improving their offices' efficiency and production. Although they are sensitive to some potential obstacles, they are willing to overcome these and incorporate the technology into their practices.

Attitude of Health Personnel↗

PubMedDate not supplied

Parallelising a model of bacterial interaction and evolution.

Large simulations of bacterial colonies require huge amounts of computational time, the only way to achieve the necessary level of performance is with parallel computers and a suitably designed implementation that maps the problem onto the hardware. For real problems this mapping can be a non-trivial problem requiring careful consideration of the constraints in both the system being modelled and the hardware that executes that model. Here we describe an implementation of a system for modelling bacterial evolution that encompasses many physical scales. This system is composed entirely of individual entities all playing out a complex series of interactions. These individuals exist at the scale of the population of bacterial and at the gene product scale. This paper reports that it is possible to map a dynamic problem such as this onto fixed resources, for the most part making use of implicit multiplexing of resources provided by the OS and partitioning the problem to reduce communication time. Through this an efficient simulation can be created, making maximal use of the available hardware without constraining the model to require excessively specific resources.

Bacterial Physiological Phenomena↗

PubMed2004

Bio-steps beyond Turing.

Are there 'biologically computing agents' capable to compute Turing uncomputable functions? It is perhaps tempting to dismiss this question with a negative answer. Quite the opposite, for the first time in the literature on molecular computing we contend that the answer is not theoretically negative. Our results will be formulated in the language of membrane computing (P systems). Some mathematical results presented here are interesting in themselves. In contrast with most speed-up methods which are based on non-determinism, our results rest upon some universality results proved for deterministic P systems. These results will be used for building "accelerated P systems". In contrast with the case of Turing machines, acceleration is a part of the hardware (not a quality of the environment) and it is realised either by decreasing the size of "reactors" or by speeding-up the communication channels. Consequently, two acceleration postulates of biological inspiration are introduced; each of them poses specific questions to biology. Finally, in a more speculative part of the paper, we will deal with Turing non-computability activity of the brain and possible forms of (extraterrestrial) intelligence.

Cell Membrane↗

PubMed2005

A DNA solution of SAT problem by a modified sticker model.

Among various DNA computing algorithms, it is very common to create an initial data pool that covers correct and incorrect answers at first place followed by a series of selection process to destroy the incorrect ones. The surviving DNA sequences are read as the solutions to the problem. However, algorithms based on such a brute force search will be limited to the problem size. That is, as the number of parameters in the studied problem grows, eventually the algorithm becomes impossible owing to the tremendous initial data pool size. In this theoretical work, we modify a well-known sticker model to design an algorithm that does not require an initial data pool for SAT problem. We propose to build solution sequences in parts to satisfy one clause in a step, and eventually solve the whole Boolean formula after a number of steps. Accordingly, the size of data pool grows from one sort of molecule to the number of solution assignments. The proposed algorithm is expected to provide a solution to SAT problem and become practical as the problem size scales up.

Algorithms↗

PubMed2005

EXAMINE: a computational approach to reconstructing gene regulatory networks.

Reverse-engineering of gene networks using linear models often results in an underdetermined system because of excessive unknown parameters. In addition, the practical utility of linear models has remained unclear. We address these problems by developing an improved method, EXpression Array MINing Engine (EXAMINE), to infer gene regulatory networks from time-series gene expression data sets. EXAMINE takes advantage of sparse graph theory to overcome the excessive-parameter problem with an adaptive-connectivity model and fitting algorithm. EXAMINE also guarantees that the most parsimonious network structure will be found with its incremental adaptive fitting process. Compared to previous linear models, where a fully connected model is used, EXAMINE reduces the number of parameters by O(N), thereby increasing the chance of recovering the underlying regulatory network. The fitting algorithm increments the connectivity during the fitting process until a satisfactory fit is obtained. We performed a systematic study to explore the data mining ability of linear models. A guideline for using linear models is provided: If the system is small (3-20 elements), more than 90% of the regulation pathways can be determined correctly. For a large-scale system, either clustering is needed or it is necessary to integrate information in addition to expression profile. Coupled with the clustering method, we applied EXAMINE to rat central nervous system development (CNS) data with 112 genes. We were able to efficiently generate regulatory networks with statistically significant pathways that have been predicted previously.

Algorithms↗

PubMed2005

Controlled synthesis of target strings in a class of splicing systems.

This article presents an approach for synthesizing target strings in a class of computational models of DNA recombination. The computational models are formalized as splicing systems in the context of formal languages. Given a splicing system (of a restricted type) and a target string to be synthesized, we construct (i) a rule-embedded splicing automaton that recognizes languages containing strings embedded with symbols representing splicing rules, and (ii) an automaton that implicitly recognizes the target string. By manipulating these two automata, we extract all rule sequences that lead to the production of the target string (if that string belongs to the splicing language). An algorithm for synthesizing a certain type of target strings based on such rule sequences is presented.

Algorithms↗

PubMed2006

Solving satisfiability problems using a novel microarray-based DNA computer.

An algorithm based on a modified sticker model accompanied with an advanced MEMS-based microarray technology is demonstrated to solve SAT problem, which has long served as a benchmark in DNA computing. Unlike conventional DNA computing algorithms needing an initial data pool to cover correct and incorrect answers and further executing a series of separation procedures to destroy the unwanted ones, we built solutions in parts to satisfy one clause in one step, and eventually solve the entire Boolean formula through steps. No time-consuming sample preparation procedures and delicate sample applying equipment were required for the computing process. Moreover, experimental results show the bound DNA sequences can sustain the chemical solutions during computing processes such that the proposed method shall be useful in dealing with large-scale problems.

Algorithms↗

PubMed2006

An ab initio computational study of thiamin synthesis from gaseous reactants of the interstellar medium.

A set of chemical reactions is proposed to account for the formation of thiamin derivatives from gaseous reactants that have been identified in the interstellar medium, and may have been relevant to a prebiotic atmosphere. The gaseous mixture consisted of methanimine, acetonitrile, cyanoacetylene, ammonia, acetylene, allylene, hydrogen sulfide, thioformaldehyde, and hydrogen in the presence of water. Most of the reactions appear to be exothermic. The reactions have been shown to be feasible from the overall enthalpy changes in the ZKE approximation at the HF and MP2/6-31G(*) level.

Astronomical Phenomena↗

PubMed2004

Separation of low-molecular mass organic acid-metal complexes by high-performance liquid chromatography.

The solution speciation of metals is a critical parameter controlling the bioavailability, solution-solid phase distribution and transport of metals in soils. The natural metal-complexing ligands that exist in soil solution include inorganic anions, inorganic colloids, organic humic substances, amino acids (notably phytosiderophores and bacterial siderophores) and low-molecular mass organic acids. The latter two groups are of particular significance in the soil surrounding plant roots (the rhizosphere). A number of analytical methodologies, encompassing computational, spectroscopic, physico-chemical and separation techniques, have been applied to the measurement of the solution speciation of metals in the environment. However, perhaps with the exception of the determination of the free metal cation, the majority of these techniques rarely provide species specific information. High-performance liquid chromatography (HPLC) coupled to a sensitive detection system, such as inductively coupled plasma mass spectrometry (ICP-MS) or electrospray ionisation mass spectrometry (ESI-MS), offers the possibility of separating and detecting metal-organic acid complexes at the very low concentrations normally found in the soil environment. This review, therefore, critically examines the literature reporting the HPLC separation of metal-organic acid complexes with reference to thermodynamic equilibrium and kinetic considerations. The limitations of HPLC techniques (and the use of thermodynamic equilibrium calculations to validate analytical results) are discussed and the metal complex characteristics necessary for chromatographic separation are described.

Acids↗

PubMed2006

Simple multichannel system for the measurement of the net water flux across biological tissues.

This paper describes the development of a simple system for measurement of net water movement through biological membrane barriers. The system is based on the detection of a water meniscus inside a polyethylene tube, which reflects the water movement inside one hemichamber of a modified Ussing chamber containing a membrane barrier. The detection device consists of a commercial computer-controlled flat bed scanner and specifically developed software. This system allows one to perform a relatively high number of individual experiments per physical unit. It is a flexible and affordable device, which allows comparatively more information per unit to be obtained than previously described methods.

Body Water↗

PubMed2006

Optimal strategy for time-limited sequential search.

An optimal strategy is developed for maximizing the expected benefit in time limited sequential search processes with very low candidate encounter rates. We formulate a model for searches where there are k types of candidates whose benefits and encounter rates are known prior to the start of the search. The optimal strategy consists of determining the specific times during the search at which the acceptable candidate pool should be expanded by including the next lower candidate type in the pool. Results indicate that, in general, candidate types with the higher benefits dominate the optimal strategy.

Animals↗

PubMed2006

Determination of carotid disease with the application of STFT and CWT methods.

In this study, Doppler signals were recorded from the output of carotid arteries of 40 subjects and transferred to a personal computer (PC) by using a 16-bit sound card. Doppler difference frequencies were recorded from each of the subjects, and then analyzed by using short-time Fourier transform (STFT) and the continuous wavelet transform (CWT) methods to obtain their sonograms. These sonograms were then used to determine the relationships of applied methods with medical conditions. The sonograms that were obtained by CWT method gave better results for spectral resolution than the STFT method. The sonograms of CWT method offer net envelope and better imaging, so that the measurement of blood flow and brain pressure can be made more accurately. Simultaneously, receiver operating characteristic (ROC) analysis has been conducted for this study and the estimation performance of the spectral resolution for the STFT and CTW has been obtained. The STFT has shown a 80.45% success for the spectral resolution while CTW has shown a 89.90% success.

Carotid Artery Diseases↗

PubMed2006

Context awareness in health care: a review.

BACKGROUND: Health care systems will integrate new computing paradigms in the coming years. Context-awareness computing is a research field which often refers to health care as an interesting and rich area of application. AIM: Through a survey of the research literature, we intended to derive an objective view of the actual dynamism of context awareness in health care, and to identify strengths and weaknesses in this field. METHODS: After discussing definitions of context, we proposed a simple framework to analyse and characterize the use of context through three main axes. We then focused on context-awareness computing and reported on the main teams working in this area. We described some of the context-awareness projects in health care. A deeper analysis of the hospital-based projects demonstrated the gap between recommendations expressed for modelling context awareness and the actual use in a prototype. Finally, we identified pitfalls encountered in this area of research. RESULTS: A number of opportunities remain for this evolving field of research. We found relatively few groups with such a specific focus. As yet there is no consensus as to the most appropriate models or attributes to include in context awareness. We conclude that a greater understanding of which aspects of context are important in a health care setting is required; the inherent sociotechnical nature of context-aware applications in health care; and the need to draw on a number of disciplines to conduct this research.

Biomedical Technology↗

PubMed2005

Mathematical and numerical models for transfer of low-density lipoproteins through the arterial walls: a new methodology for the model set up with applications to the study of disturbed lumenal flow.

In this work we introduce and discuss several mathematical models, based on partial differential equations, devised to study the coupled transport of macromolecules as low-density lipoproteins in the blood stream and in the arterial walls. These models are accurate provided that a suitable set of physical parameters characterizing the physical properties of the molecules and of the wall layers are available. Here we turn our attention on this aspect, and propose a new methodology to compute the physical parameters needed for the model set up, starting from available in vivo measurements. Then, we focus on the study of the accumulation of low-density lipoproteins in vascular districts featuring a highly disturbed flow. Our results demonstrate that mathematical models whose set up procedure benefits from an experimental feedback provide reliable information not only qualitatively, but also quantitatively. Their application to geometrically perturbed vascular districts (as for example a severe stenosis) shows that geometrical parameters such as curvature and variations of the lumenal section strongly influence the accumulation of low-density lipoproteins within the wall. For instance, in a stenotic segment with 75% area constriction, the LDL concentration at the lumenal side of the wall is about 10% higher than for the undisturbed segment.

Arterial Occlusive Diseases↗

PubMed2006

Fundamental mechanics of aortic heart valve closure.

Stresses in a prosthetic heart valve at closure are determined by its geometrical and structural characteristics, by the mechanical support environment, and by the momentum of the valve leaflets or occluder and of the blood at the instant of closure. The mass of blood to be arrested is significantly greater than that of the leaflets or occluder, and is therefore likely to dominate the closure impulse. The kinetic energy of the blood must be transduced into potential energy in the structural components (valve leaflets, aortic root and aorta). This paper presents a methodology for computation and parameterisation of the blood momentum associated with a valve in the aortic position. It is suggested that the influence of physiological parameters, such as systolic waveform and systemic impedance, on the closure characteristics can be investigated based on the fluid dynamic implications. Detailed results are presented for a single leaflet mechanical valve (Bjork-Shiley 60 degrees Convexo-Concave). It is demonstrated that a simple analytical method can yield results that might be adequate for the purposes of valve design.

Aorta↗