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PubMed2003

Continuum and discrete calculation of fractional contributions to solvation free energy.

Approaches to compute fractional contributions to the solvation free energy are developed in the context of continuum self consistent reaction field calculations (both classical and quantum mechanical), as well as in the framework of discrete molecular dynamics simulations. It is found that for a series of typical pharmacological drugs there is a good agreement between the different fractional descriptions. Algorithms reported here can be easily applied as molecular descriptors in the context of quantitative structure-activity relationships.

Algorithms↗
PubMed2005

Significance analysis of qualitative mammographic features, using linear classifiers, neural networks and support vector machines.

Advances in modern technologies and computers have enabled digital image processing to become a vital tool in conventional clinical practice, including mammography. However, the core problem of the clinical evaluation of mammographic tumors remains a highly demanding cognitive task. In order for these automated diagnostic systems to perform in levels of sensitivity and specificity similar to that of human experts, it is essential that a robust framework on problem-specific design parameters is formulated. This study is focused on identifying a robust set of clinical features that can be used as the base for designing the input of any computer-aided diagnosis system for automatic mammographic tumor evaluation. A thorough list of clinical features was constructed and the diagnostic value of each feature was verified against current clinical practices by an expert physician. These features were directly or indirectly related to the overall morphological properties of the mammographic tumor or the texture of the fine-scale tissue structures as they appear in the digitized image, while others contained external clinical data of outmost importance, like the patient's age. The entire feature set was used as an annotation list for describing the clinical properties of mammographic tumor cases in a quantitative way, such that subsequent objective analyses were possible. For the purposes of this study, a mammographic image database was created, with complete clinical evaluation descriptions and positive histological verification for each case. All tumors contained in the database were characterized according to the identified clinical features' set and the resulting dataset was used as input for discrimination and diagnostic value analysis for each one of these features. Specifically, several standard methodologies of statistical significance analysis were employed to create feature rankings according to their discriminating power. Moreover, three different classification models, namely linear classifiers, neural networks and support vector machines, were employed to investigate the true efficiency of each one of them, as well as the overall complexity of the diagnostic task of mammographic tumor characterization. Both the statistical and the classification results have proven the explicit correlation of all the selected features with the final diagnosis, qualifying them as an adequate input base for any type of similar automated diagnosis system. The underlying complexity of the diagnostic task has justified the high value of sophisticated pattern recognition architectures.

Analysis of Variance↗
PubMed2003

Introducing BF++: AC++ framework for cognitive bio-feedback systems design.

OBJECTIVE: This paper addressed the issue of building-up a framework for the realization of several cognitive bio-feedback (CBF) systems. It minimizes the programming effort and maximizes the efficiency and the cross-platform portability so that it can be used with many platforms (either software or hardware). METHODS: A generic CBF system was decomposed into six modules: acquisition, kernel, feedback rule, patient feedback, operator user interface and persistent storage. The way in which these modules interact was defined by immutable software interfaces in a way that allows to completely substitute a module without the need to modify the others. RESULTS: Three Brain Computer Interface engines were developed with less than 40 lines of C++ code each. They can also be used under virtually any platform that supports an ANSI C++ compiler. CONCLUSION: A framework for the implementation of a wide range of CBF systems was developed. Compared to the other approaches that are described in the literature, the proposed one is the most efficient, the most protable across different platforms, the most generic and the one that allows the realization of the cheapest final systems.

Cognition↗
PubMed2005

An examination of the structure and nomological network of trainee reactions: a closer look at "smile sheets".

Although D. L. Kirkpatrick (1959, 1996) popularized the concept of trainee reactions over 40 years ago, few studies have critically examined trainees' reactions to learning events. In this article, research on mood and emotion is used to develop a theoretical framework for research on trainee reactions. Two studies examine the factor structure of reactions and their nomological network. In Study 1, 178 undergraduate and 101 graduate students listened to a computer-delivered multimedia lecture. Results suggest that (a) reactions can be conceptualized as hierarchical, with overall satisfaction explaining associations among distinct reaction facets (enjoyment, relevance, and technology satisfaction), and (b) reactions are predicted by trainee characteristics. In Study 2, 97 undergraduates experienced the same lecture in 1 of 3 randomly assigned delivery technologies. Reactions were influenced by technology and were related to learning process (engagement) and outcomes (intentions regarding delivery technology, content, and learning). Both studies support the theoretical framework proposed.

Adult↗
PubMed2002

A computer-based OSCE station to measure competence in evidence-based medicine skills in medical students.

OBJECTIVE: To create a feasible, valid, and reliable tool to measure third-year medical students' skills in evidence-based medicine (EBM). DESCRIPTION: EBM skills-asking clinical questions, finding appropriate medical information resources, and appraising and applying them to patients-involve higher-order critical thinking abilities and are essential to being a competent physician. Students at our institution must pass a required OSCE exam at the end of their third year. As part of this exam, we developed a new 20-minute computer-based station to assess students' EBM skills. Using a specific case scenario, we asked the students to (1) ask a question using the population/intervention/comparison/outcome (PICO) framework; (2) generate appropriate search terms, given a specific question; and (3) select an appropriate abstract to answer a given question and state why two other abstracts were not appropriate. Prior to the assessment, we determined grading and passing criteria for each of the three components and for the station overall. Of the 140 students who completed the station, the percentages that passed the components were 71%, 81%, and 49% respectively, with only 29% passing all three parts. Preliminary analysis of psychometric properties of the station shows very good to excellent interrater reliability, with 65%, 67%, and 94% agreement on the scoring for the components, and kappas of.64,.82, and.94, respectively. DISCUSSION: Although there are many curricula for teaching EBM concepts, there are few tools to measure whether students are competent in applying their EBM skills. Our pilot station appears to be an innovative and promising tool to measure several EBM skills independently. By being computer-based, it is relatively simple to administer, grade, and evaluate. While preliminary data show good inter-rater reliability with our use of a single case, future work will include further testing of reliability and assessment of different types of cases. We will also use the results of this assessment to drive continuous improvement in our EBM curriculum. The students who completed this pilot station had not received an extensive formal EBM curriculum, whereas future groups will. We also will explore whether scores on our station correlate with those on other OSCE stations that also assess critical thinking skills, or if scores correlate with a student's clinical grades or overall class standing. We hope to test these hypotheses: (1) skills used in EBM are useful and valid measures of critical thinking abilities in learners and (2) tools such as ours will help to measure these essential competencies.

Clinical Competence↗
PubMed2003

DataGrid, prototype of a biomedical grid.

BACKGROUND: The availability of large amounts of data in heterogeneous formats and the rapid progress in fields such as computer based drug design, medical imaging and medical simulations have lead to a growing demand for large computational power and easy accessibility to heterogeneous data sources. OBJECTIVES: The goal is to address these needs by deploying computing grids. Grids provide both large scale and distributed storage facilities and an increased computing power. Moreover, Grids are a promising tool to foster the synergy between bioinformatics and computerised medical imaging. METHODS: A first biomedical grid is being deployed within the framework of the DataGrid IST project (http://www.edg.org). The goal of the project is to provide a novel environment to support globally distributed scientific exploration involving up to multi-Perabyte datasets. RESULTS AND CONCLUSIONS: The first biomedical applications deployed inside the project demonstrate the relevance of the grid paradigm for genomics and medical image processing. They also highlight the specific requirements of the biomedical community.

Biomedical Research↗
PubMed1995

A decision support database for nurse care planning as part of a hospital information system.

This paper, based on a doctoral thesis, describes the development and evaluation of a computerized care planning database at the Royal Hampshire County Hospital. It is part of an integrated Hospital Information System, the first to be installed in an United Kingdom. The research examines nurses' attitudes to the Nursing Process to the new care planning system before, three months after, and one year after its implementation. The quality of manual vs. computer care planning is compared in the same time periods using an existing quality assurance instrument and an audit tool, developed during the research. All data was analyzed in each time period in a framework of personal and organizational change theories. The proactive nature of the research allowed findings to be used as a basis for modifications during the process, which culminated in a further project to provide a database of standard based care plans. Results showed that an understanding of the Nursing Process was inadequate and that most nurses were ambivalent about paper care planning and the proposed computer care plans. Three months after implementation, attitudes became more unfavorable; however, after a year, attitudes showed a significant shift towards the positive pole. Conversely, the overall quality-of-care planning improved significantly.

Attitude to Computers↗
PubMed2003

Image registration via level-set motion: applications to atlas-based segmentation.

Image registration is an often encountered problem in various fields including medical imaging, computer vision and image processing. Numerous algorithms for registering image data have been reported in these areas. In this paper, we present a novel curve evolution approach expressed in a level-set framework to achieve image intensity morphing and a simple non-linear PDE for the corresponding coordinate registration. The key features of the intensity morphing model are that (a) it is very fast and (b) existence and uniqueness of the solution for the evolution model are established in a Sobolev space as opposed to using viscosity methods. The salient features of the coordinate registration model are its simplicity and computational efficiency. The intensity morph is easily achieved via evolving level-sets of one image into the level-sets of the other. To explicitly estimate the coordinate transformation between the images, we derive a non-linear PDE-based motion model which can be solved very efficiently. We demonstrate the performance of our algorithm on a variety of images including synthetic and real data. As an application of the PDE-based motion model, atlas based segmentation of hippocampal shape from several MR brain scans is depicted. In each of these experiments, automated hippocampal shape recovery results are validated via manual "expert" segmentations.

Adult↗
PubMedDate not supplied

Scalable partitioning and exploration of chemical spaces using geometric hashing.

Virtual screening (VS) has become a preferred tool to augment high-throughput screening(1) and determine new leads in the drug discovery process. The core of a VS informatics pipeline includes several data mining algorithms that work on huge databases of chemical compounds containing millions of molecular structures and their associated data. Thus, scaling traditional applications such as classification, partitioning, and outlier detection for huge chemical data sets without a significant loss in accuracy is very important. In this paper, we introduce a data mining framework built on top of a recently developed fast approximate nearest-neighbor-finding algorithm(2) called locality-sensitive hashing (LSH) that can be used to mine huge chemical spaces in a scalable fashion using very modest computational resources. The core LSH algorithm hashes chemical descriptors so that points close to each other in the descriptor space are also close to each other in the hashed space. Using this data structure, one can perform approximate nearest-neighbor searches very quickly, in sublinear time. We validate the accuracy and performance of our framework on three real data sets of sizes ranging from 4337 to 249 071 molecules. Results indicate that the identification of nearest neighbors using the LSH algorithm is at least 2 orders of magnitude faster than the traditional k-nearest-neighbor method and is over 94% accurate for most query parameters. Furthermore, when viewed as a data-partitioning procedure, the LSH algorithm lends itself to easy parallelization of nearest-neighbor classification or regression. We also apply our framework to detect outlying (diverse) compounds in a given chemical space; this algorithm is extremely rapid in determining whether a compound is located in a sparse region of chemical space or not, and it is quite accurate when compared to results obtained using principal-component-analysis-based heuristics.

Journal Article↗
PubMed1996

A psychophysical and computational analysis of intensity-based stereo.

We describe two psychophysical experiments testing predictions of the square difference mechanism we have previously proposed for intensity-based stereo. Experiment 1 assesses the relative contributions of disparity and contrast to intensity-based stereo by measuring detection thresholds. The product of disparity and contrast at threshold is shown to be constant. In experiment 2, we measure quantitatively the global depth position perceived in stereograms of curved, smoothly shaded surfaces. The results show that disparity averaging over the surface involves a contrast-dependent weighting function. The results from both experiments are consistent with predictions derived from the square difference mechanism. The relation of this mechanism to feature correspondence stereopsis and shape-from-shading is discussed and a general framework for assessing the modularity of stereopsis is presented.

Adult↗
PubMed1995

Wayfinding, displacements, and mental maps: velocity fields are not typically used to determine one's aimpoint.

When an individual moves through a cluttered environment, he or she often fixates an object relatively near his or her path in the middle distance and uses pursuit eye movements to follow it while moving forward. On the basis of previous evidence, either motion fields or displacement fields around the fixated object--two alternative representations of the same information--could be used to determine one's direction of self-movement, sometimes called heading or aimpoint. In a series of 5 experiments, the relationship between these representations was explored and it was found that the displacements of identifiable objects, not their motions, are most likely the direct inputs for wayfinding. It may be that these inputs are used in conjunction with a mental map to determine one's aimpoint. A mathematical framework for this process is proposed.

Acceleration↗
PubMed1998

Protecting patient confidentiality in hospitals.

As new methods of electronic data storage and distribution appear in hospitals, new challenges in protecting confidentiality have emerged. At the same time, demands for 'seamless' care and the desire to share information between clinicians are motivating hospitals to relax barriers to the transfer of patient information. Increasing numbers of users at multiple sites compound the difficulty of ensuring information systems security. Hospital policy may demand that requests by patients to restrict the distribution of personal information be respected, while existing electronic systems are not able to deliver on this promise. Compliance with the Information Privacy Principles of the Commonwealth Privacy Act 1988 and the Australian Standard 4400-1995 'Personal privacy protection in health care information systems' will provide a useful framework for managing these challenges. However, their implementation will require some forethought.

Australia↗
PubMed2006

Systems-based medicine approaches to understand and treat complex diseases. The example of multiple sclerosis.

Systems medicine is an emerging concept that acknowledges the complexity of a multitude of non-linear interactions among molecular and physiological variables. Under this new paradigm, rather than a collection of symptoms, diseases are seen as the product of deviations from a robust steady state compatible with life. This concept requires the incorporation of mathematics and physics to the more classical arsenal of physiology and molecular biology with which physicians are trained today. This review explores the diverse types of information that can be accumulated towards the understanding of multiple sclerosis (MS), a complex autoimmune disease that targets the central nervous system (CNS). The challenge of data integration and modeling of dynamical systems is discussed in the context of disease susceptibility and response to treatment. A theoretical framework that supports the use of combination therapy is also presented.

Animals↗
PubMed1994

Recognition and polymorphism in host-parasite genetics.

Genetic specificity occurs in many host-parasite systems. Each host can recognize and resist only a subset of parasites; each parasite can grow only on particular hosts. Biochemical recognition systems determine which matching host and parasite genotypes result in resistance or disease. Recognition systems are often associated with widespread genetic polymorphism in the host and parasite populations. I describe four systems with matching host-parasite polymorphisms: plant-pathogen interactions, nuclear-cytoplasmic conflict in plants, restriction enzymes in bacterial defence against viruses, and bacterial plasmids that compete by toxin production and toxin immunity. These systems highlight several inductive problems. For example, the observed patterns of resistance and susceptibility between samples of hosts and parasites are often used to study polymorphism. The detectable polymorphism by this method may be a poor guide to the actual polymorphism and to the underlying biochemistry of host-parasite recognition. The problem of using detectable polymorphism to infer the true nature of recognition and polymorphism is exacerbated by non-equilibrium fluctuations in allele frequencies that commonly occur in host-parasite systems. Another problem is that different matching systems may lead either to low frequencies of host resistance and common parasites, or to common resistance and rare parasites. Thus low levels of host resistance or rare parasites do not imply that parasitism is an unimportant evolutionary force on host diversity. Knowledge of biochemical recognition systems and dynamical analysis of models provide a framework for analysing the widespread polymorphisms in host-parasite genetics.

Animals↗
PubMed2006

QPath: a method for querying pathways in a protein-protein interaction network.

BACKGROUND: Sequence comparison is one of the most prominent tools in biological research, and is instrumental in studying gene function and evolution. The rapid development of high-throughput technologies for measuring protein interactions calls for extending this fundamental operation to the level of pathways in protein networks. RESULTS: We present a comprehensive framework for protein network searches using pathway queries. Given a linear query pathway and a network of interest, our algorithm, QPath, efficiently searches the network for homologous pathways, allowing both insertions and deletions of proteins in the identified pathways. Matched pathways are automatically scored according to their variation from the query pathway in terms of the protein insertions and deletions they employ, the sequence similarity of their constituent proteins to the query proteins, and the reliability of their constituent interactions. We applied QPath to systematically infer protein pathways in fly using an extensive collection of 271 putative pathways from yeast. QPath identified 69 conserved pathways whose members were both functionally enriched and coherently expressed. The resulting pathways tended to preserve the function of the original query pathways, allowing us to derive a first annotated map of conserved protein pathways in fly. CONCLUSION: Pathway homology searches using QPath provide a powerful approach for identifying biologically significant pathways and inferring their function. The growing amounts of protein interactions in public databases underscore the importance of our network querying framework for mining protein network data.

Algorithms↗
PubMed1981

On the possibility of automated scoring of pollen mutants.

Both flow cytometry and automated image analysis techniques may be useful in relieving the drudgery, increasing the speed, and adding quantitation to the scoring of pollen mutants, but practical problems related to the detection of very rare events have to be overcome. The features of flow and image cytometry instrumentation that may be useful for pollen measurements are discussed and a qualitative framework is presented from which to view the rare event problem.

Cell Count↗
PubMed1998

Insights into motion perception by observer modeling.

The statistical efficiency of human observers performing a simplified version of the motion detection task of Salzman and Newsome [Science 264, 231 (1994)] is high but not perfect. This reduced efficiency may be caused by noise internal to the observers or by the observers' using strategies that are different from that used by an ideal machine. We therefore investigated which of three simple models best accounts for the observers' performance. The models compared were a motion detector that uses the proportion of dots in the first frame that move coherently (as would an ideal machine), a model that bases its decision on the number of dots that move, and a model that differentially weights motions that occur at different locations in the visual field (for instance, differentially weights the point of fixation and the periphery). We compared these models by explicitly modeling the human observers' performance. We recorded the exact stimulus configuration on each trial together with the observer's response, and, for the different models, we found the parameters that best predicted the observer's performance in a least-squares sense. We then used N-fold cross validation to compare the models and hence the associated hypotheses. Our results show that the performance of observers is based on the proportion, not the absolute number, of dots that are moving and that there was no evidence of any differential spatial weighting. Whereas this method of modeling the observers' response is demonstrated only for one simple psychophysical paradigm, it is general and can be applied to any psychophysical framework in which the entire stimulus can be recorded.

Algorithms↗
PubMed2004

A health informatics educational framework.

There is a need to be able to define a Health Informatician by their graduate attributes. Futhermore global health informatics education that facilitates student mobility requires a common understanding of educational outcomes. An internationally agreed health informatics education framework will facilitate us to meet these needs. This chapter provides an overview of a considerable amount of work undertaken in a number of countries and by IMIA's health and medical informatics education working group. We need to make good use of these foundations as they clarify the various health informatics roles and functions together with their associated health informatics competency requirements. We are now in a good position to progress this work by developing a health informatics qualifications and educational framework. This is expected to assist educational providers with curriculum development.

Computer User Training↗