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PubMed2004

A simple significance test for quantile regression.

Where OLS regression seeks to model the mean of a random variable as a function of observed variables, quantile regression seeks to model the quantiles of a random variable as functions of observed variables. Tests for the dependence of the quantiles of a random variable upon observed variables have only been developed through the use of computer resampling or based on asymptotic approximations resting on distributional assumptions. We propose an exceedingly simple but heretofore undocumented likelihood ratio test within a logistic regression framework to test the dependence of a quantile of a random variable upon observed variables. Simulated data sets are used to illustrate the rationale, ease, and utility of the hypothesis test. Simulations have been performed over a variety of situations to estimate the type I error rates and statistical power of the procedure. Results from this procedure are compared to (1) previously proposed asymptotic tests for quantile regression and (2) bootstrap techniques commonly used for quantile regression inference. Results show that this less computationally intense method has appropriate type I error control, which is not true for all competing procedures, comparable power to both previously proposed asymptotic tests and bootstrap techniques, and greater computational ease. We illustrate the approach using data from 779 adolescent boys age 12-18 from the Third National Health and Nutrition Examination Survey (NHANES III) to test hypotheses regarding age, ethnicity, and their interaction upon quantiles of waist circumference.

Adolescent↗
PubMed1995

The potential of computerized representations of anatomy in the training of health care providers.

The purpose of anatomy education is to develop the skills for anatomical reasoning, which is a requirement for performing a number of clinical tasks. Anatomical reasoning integrates an understanding of the three-dimensional (3-D) geometry of the body and its parts (the spatial domain of anatomical information) with an understanding of functional, developmental, pathological, and other relationships among anatomic entities (the symbolic domain of anatomical information). Traditional methods in anatomy have substantial shortcomings for representing and integrating these two information domains. Computer-based methods of knowledge representation have a great potential for overcoming the shortcomings and for promoting anatomical reasoning. To realize this potential, there is a need for (1) establishing 3-D electronic atlases of the human body; (2) generating models of symbolic anatomical information, and (3) developing computer programs (user interfaces) that integrate these knowledge sources and serve the needs of trainees and practitioners in different fields of the health sciences. The Digital Anatomist Program at the University of Washington has begun to build such a client-server framework for anatomical information, and its application for biomedical education is being evaluated.

Anatomy↗
PubMed2003

Modelling the world in real time: how robots engineer information.

Programming robots and other autonomous systems to interact with the world in real time is bringing into sharp focus general questions about representation, inference and understanding. These artificial agents use digital computation to interpret the data gleaned from sensors and produce decisions and actions to guide their future behaviour. In a physical system, however, finite computational resources unavoidably impose the need to approximate and make selective use of the information available to reach prompt deductions. Recent research has led to widespread adoption of the methodology of Bayesian inference, which provides the absolute framework to understand this process fully via modelling as informed, fully acknowledged approximation. The performance of modern systems has improved greatly on the heuristic methods of the early days of artificial intelligence. We discuss the general problem of real-time inference and computation, and draw on examples from recent research in computer vision and robotics: specifically visual tracking and simultaneous localization and mapping.

Artificial Intelligence↗
PubMed1990

Becoming deprofessionalized: one aspect of the staff nurse's perspective on computer-mediated nursing care plans.

Negative impacts on the professionalization of staff nurses by the development and use of computerized nursing care plans are presented as a selected finding of a qualitative study. A symbolic interaction framework, using nurses' stories as communicated in semi-structured interviews, yielded meaning and behavior in metaphorical form. The computerized system for patient care planning, and the larger system in which it is embedded, contribute to loss of autonomy, loss of individualization of care, and loss of nursing expertise. Some questions that should be addressed now are identified.

Attitude to Computers↗
PubMed2004

Simulations of the large kinetic isotope effect and the temperature dependence of the hydrogen atom transfer in lipoxygenase.

Elucidating the role of nuclear quantum mechanical (NQM) effects in enzyme catalysis is a topic of significant current interest. Despite the great experimental progress in this field it is important to have theoretical approaches capable of evaluating and analyzing nuclear quantum mechanical contributions to catalysis. In this study, we use the catalytic reaction of lipoxygenase, which is characterized by an extremely large kinetic isotope effect, as a challenging test case for our simulation approach. This is done by applying the quantum classical path (QCP) method with an empirical valence bond potential energy surface. Our computational strategy evaluates the relevant NQM corrections and reproduces the large observed kinetic isotope effect and the temperature dependence of the H atom transfer reaction while being less successful with the D atom transfer reaction. However, the main point of our study is not so much to explore the temperature dependence of the isotope effect but rather to develop and validate an approach for calculations of nuclear quantum mechanical contributions to activation free energies. Here, we find that the deviation between the calculated and observed activation free energies is small for both H and D at all investigated temperatures. The present study also explores the nature of the reorganization energy in the enzyme and solution reactions. It is found that the outer-sphere reorganization energy is extremely small. This reflects the fact that the considered reaction involves a very small charge transfer. The implication of this finding is discussed in the framework of the qualitative vibronic model. The main point of the present study is, however, that the rigorous QCP approach provides a reliable computational tool for evaluating NQM contributions to catalysis even when the given reaction includes large tunneling contributions. Interestingly, our results indicate that the NQM effects in the lipoxygenase reaction are similar in the enzyme and in the reference solution reactions, and thus do not contribute to catalysis. We also reached similar conclusions in studies of other enzymes.

Computer Simulation↗
PubMed2005

Exact family-based association tests for biallelic data.

Family-based study designs have an important role in the search for association between disease phenotypes and genetic markers. Unlike traditional case-control methods, family-based tests use within-family data to avoid identification of spurious associations that may result from population admixture. Many family-based association tests have been proposed to accommodate a variety of ascertainment schemes and patterns of missing data. In this report, we describe exact family-based association tests for biallelic data. Specifically, we discuss test of the null hypotheses "no linkage and no association" and "linkage, but no association". These tests, which are valid under various models for inheritance and patterns of missingness, utilize the procedure proposed by Rabinowitz and Laird [2000: Hum Hered 50:211-223] that provides a unified framework for family based association testing (FBAT). The conditioning approach implemented in FBAT makes an exact test conceptually straightforward, but computationally difficult since the minimum sufficient statistics upon which we condition do not have a conventional form. An exact test may be especially critical when accurate computation of the extreme area of the FBAT statistic is needed, such as when the study design necessitates multiple comparisons adjustments. We describe the exact approach as a useful alternative to the asymptotic test and show that the exact tests for biallelic data may be most useful for the recessive disease model.

Algorithms↗
PubMed2005

Multiresolution parametric estimation of transparent motions and denoising of fluoroscopic images.

We describe a novel multiresolution parametric framework to estimate transparent motions typically present in X-Ray exams. Assuming the presence if two transparent layers, it computes two affine velocity fields by minimizing an appropriate objective function with an incremental Gauss-Newton technique. We have designed a realistic simulation scheme of fluoroscopic image sequences to validate our method on data with ground truth and different levels of noise. An experiment on real clinical images is also reported. We then exploit this transparent-motion estimation method to denoise two layers image sequences using a motion-compensated estimation method. In accordance with theory, we show that we reach a denoising factor of 2/3 in a few iterations without bringing any local artifacts in the image sequence.

Algorithms↗
PubMed2001

Dynamic simulation of electromechanical systems: from Maxwell's theory to common-rail diesel injection.

This paper describes the state-of-the-art of dynamic simulation of electromechanical systems. Electromechanical systems can be split into electromagnetic and mechanical subsystems, which are described by Maxwell's equations and by Newton's law, respectively. Since such systems contain moving parts, the concepts of Lorentz and Galilean relativity are briefly addressed. The laws of physics are formulated in terms of (partial) differential equations. Numerical methods ultimately aim at linear systems of equations, which can be solved efficiently on digital computers. The various discretization methods for performing this task are discussed. Special emphasis is placed on domain decomposition as a framework for the coupling of different numerical methods such as the finite element method and the boundary element method. The paper concludes with descriptions of some applications of industrial relevance: a high performance injection valve and an electromechanical relay.

Journal Article↗
PubMedDate not supplied

Imaging and graphics in medicine: concept of an object-oriented platform for clinical research.

We present a workstation-based research platform with two major components. A turnkey application system provides a functionality kernel for a broad community of clinical users with an interest in digital imaging. A development toolbox allows efficient implementation of research ideas and consistent integration of new applications with the common framework of the turnkey system. The platform is based on an elaborate object class structure describing objects for image processing, computer graphics, study handling and user interface control. Thus expertise of computer scientists familiar with this application domain is brought into the hospital and can be readily used by clinical researchers.

Computer Graphics↗
PubMed2005

Assessing missing data assumptions in longitudinal studies: an example using a smoking cessation trial.

Due to the chaotic nature of the clinical disorder, longitudinal data analysis in substance abuse research is plagued by missing values. To obtain an unbiased estimation on intervention effects, different longitudinal modeling strategies require various assumptions on the patterns and mechanisms of missing data. By defining missingness as intermittent missingness (occasional omission) and dropout (premature withdrawal), this article demonstrates statistical ways for assessing missing data assumptions using evidence from a clinical trial. Within the framework of multiple imputation, intermittent missing data are imputed first so that dropouts can be isolated and treated specifically. A computational tool called "pattern reduction resampling" is proposed to simplify missing data methods when the number of intra-subject repeated measures is large. To test whether missingness patterns are nondifferential across treatment conditions, a formal testing approach treats indicators of missingness as a special type of repeated measures (e.g., 0: intermittent missing, 1: observed, and 2: dropout missing). After reviewing the idea of ignorability for missing data and of classifying missingness mechanisms into subcategories, the article provides an example for assessing common assumptions on missingness mechanisms and how these assumptions affect model selection for significance testing. A carbon monoxide longitudinal data set in a smoking cessation study is used for illustration.

Bias↗
PubMed2005

The context-tree kernel for strings.

We propose a new kernel for strings which borrows ideas and techniques from information theory and data compression. This kernel can be used in combination with any kernel method, in particular Support Vector Machines for string classification, with notable applications in proteomics. By using a Bayesian averaging framework with conjugate priors on a class of Markovian models known as probabilistic suffix trees or context-trees, we compute the value of this kernel in linear time and space while only using the information contained in the spectrum of the considered strings. This is ensured through an adaptation of a compression method known as the context-tree weighting algorithm. Encouraging classification results are reported on a standard protein homology detection experiment, showing that the context-tree kernel performs well with respect to other state-of-the-art methods while using no biological prior knowledge.

Algorithms↗
PubMed2026

Giants within: a new class of microbial mobile elements.

Prokaryotes harbor a diverse spectrum of extrachromosomal elements (ECEs), which are intracellular replicons maintained independently of the primary chromosome. Historically, the ECE research field has focused on relatively small ECEs, such as plasmids. However, the advent of long-read sequencing has revealed that prokaryotes also harbor various types of giant ECEs, spanning hundreds of kilobases to over 1 Mb, that were not hitherto recognized. In this review, we describe how long-read sequencing has enabled the discovery of giant ECEs and compare the genetic architectures and functional repertoires of several recently characterized examples. The functions of most genes in these ECEs remain uncharacterized, and current computational tools frequently misclassify or overlook them. We further discuss how the discovery of these giant ECEs challenges existing classification frameworks that attempt to distinguish megaplasmids, chromids, and chromosomes. Together, these findings highlight giant ECEs as a largely unexplored layer of microbial genetics, whose characterization will have broad implications for our understanding of microbial adaptation and horizontal gene transfer.

Extrachromosomal DNA↗
PubMed2003

A disaggregate approach to crash rate analysis.

This paper presents a disaggregate approach to crash rate analysis. Enumerating crash rates on a per trip-kilometer basis, the proposed method removes the linearity assumption inherent in the conventional quotient indicator of accidents per unit travel distance. The approach involves combining two disparate datasets on a geographic information systems (GIS) platform by matching accident records to a defined travel corridor. As an illustration of the methodology, travel information from the Victorian Activity and Travel Survey (VATS) and accident records contained in CrashStat were used to estimate the crash rates of Melbourne residents in different age-sex groups according to time of the day and day of the week. The results show a polynomial function of a cubic order when crash rates are plotted against age group, which contrasts distinctly with the U-shape curve generated by using the conventional aggregate quotient approach. Owing to the validity of the many assumptions adopted in the computation, this study does not claim that the results obtained are conclusive. The methodology, however, is seen as providing a framework upon which future crash risk measures could be based as the use of spatial tracking devises become prevalent in travel surveys.

Accidents, Traffic↗
PubMed2003

A model of the effects of node-link mapping on drug abuse counseling.

This paper examines the effectiveness of a promising cognitive enhancement technique called node-link mapping. Maps provide a concrete, visual, and computationally efficient means for exploring personal issues, and have received substantial empirical support. We introduce two models to provide a framework for understanding how node-link mapping improves substance abuse counseling. The TCU Process Model reviews the general process of substance abuse treatment. The second model reflects an effective treatment session. Implications of the models and node-link mapping findings are discussed, as well as future research directions.

Algorithms↗
PubMed2005

FTIR spectroscopic study of titanium-containing mesoporous silicate materials.

The surface acidity of different mesoporous titanium-silicates, such as well-organized hexagonally packed Ti-MMM, Ti-MMM-2, Ti-SBA-15, and amorphous TiO(2)-SiO(2) mixed oxides (aerogels and xerogels), was studied by means of FTIR spectroscopy of CO adsorbed at 80 K and CD(3)CN adsorbed at 293 K. The surface hydroxyl groups of mesoporous titanium-silicates with 2-7 wt % Ti revealed a Brönsted acidity slightly higher to that of pure silicate. TiO(2)-SiO(2) xerogels revealed the highest Brönsted acidity among the titanium-silicates studied. CO adsorption revealed two additional sites on the surface in comparison to pure silicate, characterized by nu(CO) from 2185 (high pressure) to 2178 (low pressure) cm(-1) and from 2174 (high pressure) to 2170 (low pressure) cm(-1). These bands are due to CO adsorbed on isolated titanium cations in the silica surrounding or having one Ti(4+) cation in their second coordination sphere and due to CO interactions with Ti-OH groups, respectively. CD(3)CN adsorption similarly revealed the existence of two additional sites, which were not detected for pure silicate: at 2289 cm(-1) due to CD(3)CN interaction with titanol groups and from 2306 (low pressure) to 2300 (high pressure) cm(-1) due to acetonitrile interaction with isolated framework titanium cations with probably one Ti(4+) cation in their second coordination shell. The spectroscopic results are compared with computational data obtained on cluster models of titanium-silicate with different titanium content. According to the IR data, the Ti accessibility on the surfaces for mesoporous titanium-silicates with similar Ti loading (2 wt %) was found to fall in the order TiO(2)-SiO(2) aerogel approximately TiO(2)-SiO(2) xerogel > Ti-MMM approximately Ti-MMM-2 > Ti-SBA-15. This order (except TiO(2)-SiO(2) xerogel) correlates with the catalytic activity found previously for titanium-silicates in 2,3,6-trimethylphenol oxidation with H(2)O(2).

Journal Article↗
PubMed1998

Measuring departures from Hardy-Weinberg: a Markov chain Monte Carlo method for estimating the inbreeding coefficient.

Many well-established statistical methods in genetics were developed in a climate of severe constraints on computational power. Recent advances in simulation methodology now bring modern, flexible statistical methods within the reach of scientists having access to a desktop workstation. We illustrate the potential advantages now available by considering the problem of assessing departures from Hardy-Weinberg (HW) equilibrium. Several hypothesis tests of HW have been established, as well as a variety of point estimation methods for the parameter which measures departures from HW under the inbreeding model. We propose a computational, Bayesian method for assessing departures from HW, which has a number of important advantages over existing approaches. The method incorporates the effects-of uncertainty about the nuisance parameters--the allele frequencies--as well as the boundary constraints on f (which are functions of the nuisance parameters). Results are naturally presented visually, exploiting the graphics capabilities of modern computer environments to allow straightforward interpretation. Perhaps most importantly, the method is founded on a flexible, likelihood-based modelling framework, which can incorporate the inbreeding model if appropriate, but also allows the assumptions of the model to he investigated and, if necessary, relaxed. Under appropriate conditions, information can be shared across loci and, possibly, across populations, leading to more precise estimation. The advantages of the method are illustrated by application both to simulated data and to data analysed by alternative methods in the recent literature.

Algorithms↗
PubMed2004

Search for organising principles: understanding in systems biology.

Due in large measure to the explosive progress in molecular biology, biology has become arguably the most exciting scientific field. The first half of the 21st century is sometimes referred to as the 'era of biology', analogous to the first half of the 20th century, which was considered to be the 'era of physics'. Yet, biology is facing a crisis--or is it an opportunity--reminiscent of the state of biology in pre-double-helix time. The principal challenge facing systems biology is complexity. According to Hood, 'Systems biology defines and analyses the interrelationships of all of the elements in a functioning system in order to understand how the system works.' With 30000+ genes in the human genome the study of all relationships simultaneously becomes a formidably complex problem. Hanahan and Weinberg raised the question as to whether progress will consist of 'adding further layers of complexity to a scientific literature that is already complex almost beyond measure' or whether the progress will lead to a 'science with a conceptual structure and logical coherence that rivals that of chemistry or physics.' At the core of the challenge is the need for a new approach, a shift from reductionism to a holistic perspective. However, more than just a pronouncement of a new approach is needed. We suggest that what is needed is to provide a conceptual framework for systems biology research. We propose that the concept of a complex system, i.e. a system of systems as defined in mathematical general systems theory (MGST), is central to provide such a framework. We further argue that for a deeper understanding in systems biology investigations should go beyond building numerical mathematical or computer models--important as they are. Biological phenomena cannot be predicted with the level of numerical precision as in classical physics. Explanations in terms of how the categories of systems are organised to function in ever changing conditions are more revealing. Non-numerical mathematical tools are appropriate for the task. Such a categorical perspective led us to propose that the core of understanding in systems biology depends on the search for organising principles rather than solely on construction of predictive descriptions (i.e. models) that exactly outline the evolution of systems in space and time. The search for organising principles requires an identification/discovery of new concepts and hypotheses. Some of them, such as coordination motifs for transcriptional regulatory networks and bounded autonomy of levccels in a hierarchy, are outlined in this article. Experimental designs are outlined to help verify the applicability of the interaction balance principle of coordination to transcriptional and posttranscriptional networks.

Cell Physiological Phenomena↗
PubMed2006

Density functional theory study of water adsorption at reduced and stoichiometric ceria (111) surfaces.

We study the structure and energetics of water molecules adsorbed at ceria (111) surfaces for 0.5 and 1.0 ML coverages using density functional theory. The results of this study provide a theoretical framework for interpreting recent experimental results on the redox properties of water at ceria (111) surfaces. In particular, we have computed the structure and energetics of various absorption geometries at the stoichiometric ceria (111) surface. We find that single hydrogen bonds between the water and the oxide surface are favored in all cases. At stoichiometric surfaces, the water adsorption energy depends rather weakly on coverage. We predict that the observed coverage dependence of the water adsorption energy at stoichiometric surfaces is likely the result of dipole-dipole interactions between adsorbed water molecules. When oxygen vacancies are introduced in various surface layers, water molecules are attracted more strongly to the surface. We find that it is very slightly energetically favorable for adsorbed water to oxidized the reduced (111) surface with the evolution of H(2). In the event that water does not oxidize the surface, we predict that the effective attractive water-vacancy interaction will result in a significant enhancement of the vacancy concentration at the surface in agreement with experimental observations. Finally, we present our results in the context of recent experimental and theoretical studies of vacancy clustering at the (111) ceria surface.

Journal Article↗