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PubMed2006

Temporal representation and reasoning in medicine: Research directions and challenges.

OBJECTIVE: The main aim of this paper is to propose and discuss promising directions of research in the field of temporal representation and reasoning in medicine, taking into account the recent scientific literature and challenging issues of current interest as viewed from the different research perspectives of the authors of the paper. BACKGROUND: Temporal representation and reasoning in medicine is a well-known field of research in the medical as well as computer science community. It encompasses several topics, such as summarizing data from temporal clinical databases, reasoning on temporal clinical data for therapeutic assessments, and modeling uncertainty in clinical knowledge and data. It is also related to several medical tasks, such as monitoring intensive care patients, providing treatments for chronic patients, as well as planning and scheduling clinical routine activities within complex healthcare organizations. METHODOLOGY: The authors jointly identified significant research areas based on their importance as for temporal representation and reasoning issues; the subjects were considered to be promising topics of future activity. Every subject was addressed in detail by one or two authors and then discussed with the entire team to achieve a consensus about future fields of research. RESULTS: We identified and focused on four research areas, namely (i) fuzzy logic, time, and medicine, (ii) temporal reasoning and data mining, (iii) health information systems, business processes, and time, and (iv) temporal clinical databases. For every area, we first highlighted a few basic notions that would permit any reader--including those who are unfamiliar with the topic--to understand the main goals. We then discuss interesting and promising directions of research, taking into account the recent literature and underlining the yet unresolved medical/clinical issues that deserve further scientific investigation. The considered research areas are by no means disjointed, because they share common theoretical and methodological features. Moreover, subjects of imminent interest in medicine are represented in many of the fields considered. CONCLUSIONS: We propose and discuss promising subjects of future research that deserve investigation to develop software systems that will properly manage the multifaceted temporal aspects of information and knowledge encountered by physicians during their clinical work. As the subjects of research have resulted from merging the different perspectives of the authors involved in this study, we hope the paper will succeed in stimulating discussion and multidisciplinary work in the described fields of research.

Artificial Intelligence↗

PubMed2005

QCM-FIA with PGMA coating for dynamic interaction study of heparin and antithrombin III.

In this work, we describe a method of constructing a film of linear poly(glycidyl methacrylate) (PGMA) polymer onto the surface of quartz crystal microbalance (QCM) electrode as a coating material that allows easy coupling of heparin molecules onto the electrode and facilitates the determination of the interaction between heparin and antithrombin III (AT III). The PGMA film was characterized with atomic force microscopy (AFM) and infra-red spectroscopy. The coupling of heparin was accomplished in one step solution reaction. A home-made quartz crystal microbalance-flow injection analysis (QCM-FIA) system with data analysis software developed in our laboratory was used to determine the interaction. The interactions between immobilized heparin and AT III were studied with various concentrations under various conditions. The obtained constants are kass=(1.49+/-0.12)x10(3)mol-1ls-1, kdiss=(3.94+/-0.63)x10(-2)s-1, KA=(3.82+/-0.33)x10(4)mol-1l.

Adsorption↗

PubMed2005

Conformation of the exopolysaccharide of Burkholderia cepacia predicted with molecular mechanics (MM3) using genetic algorithm search.

We present a computational conformational analysis of the exopolysaccharide of Burkholderia cepacia, which is believed to play a role in colonization and persistence of B. cepacia in the lungs of cystic fibrosis patients. The repeating unit of the exopolysaccharide is a heptasaccharide with three branches, which cause significant steric restraints. Conformational searches using glygal, an in-house developed software using genetic algorithm search methods, were performed on fragments as well as on the complete repeating unit with wrap-over residues. The force field used for the calculations was MM3(96). The search showed four favored conformations for an isolated repeating unit. However, for a sequence of several repeating units, the calculations indicate a single, well-defined linear conformation.

Algorithms↗

PubMed2004

Nitric oxide spatial distribution in single cultured hippocampus neurons: investigation by projection of reconstructed 3-D image and visualization technique.

Recent studies have revealed a non-homogeneous distribution of nitric oxide synthase (NOS) in neurons. However, it is not yet clear whether the intracellular distribution of NOS represents the intracellular nitric oxide (NO) distribution. In the present study, software developed in our laboratory was applied to the reconstructed image obtained from confocal slice images in order to project the 3-D reconstructed images in any direction and to cut the neuron in different sections. This enabled the spatial distribution of NO to be visualized in any direction and section. In single neurons, NO distribution was seen to be heterogeneous. After stimulation with glutamate, the spatial changes in different areas of the neuron were different. These findings are consistent with immunocytochemical data on the intracellular localization of nNOS in hippocampus neurons, and will help to elucidate the specificity of nitric oxide signaling. Finally, the administration of SNAP and L-NAME was used to examine DAF-2 distribution in the neurons. The results showed this distribution to be homogenous; therefore, it did not account for the NO distribution results.

Animals↗

PubMed2004

Automated sample preparation based on the sequential injection principle. Solid-phase extraction on a molecularly imprinted polymer coupled on-line to high-performance liquid chromatography.

A molecularly imprinted polymer (MIP) prepared using caffeine, as a template, was validated as a selective sorbent for solid-phase extraction (SPE), within an automated on-line sample preparation method. The polymer produced was packed in a polypropylene cartridge, which was incorporated in a flow system prior to the HPLC analytical instrumentation. The principle of sequential injection was utilised for a rapid automated and efficient SPE procedure on the MIP. Samples, buffers, washing and elution solvents were introduced to the extraction cartridge via a peristaltic pump and a multi-position valve, both controlled by appropriate software developed in-house. The method was optimised in terms of flow rates, extraction time and volume. After extraction, the final eluent from the extraction cartridge was directed to the injection loop and was subsequently analysed on HPLC. The overall set-up facilitated unattended operation, operation and improved both mixing fluidics and method development flexibility. This system may be readily built in the laboratory and can be further used as an automated platform for on-line sample preparation.

Automation↗

PubMed2006

Mutually suppressive interrelations of symmetric epileptic foci in bitemporal epilepsy and their inhibitory stimulation.

OBJECTIVES: The goal of this study is to analyze the suppressive interaction of symmetric temporal lobe epileptic foci, assess some failures of epilepsy surgery, and evaluate the possibility of terminating focal seizures with stimulation of symmetric epileptic foci. MATERIALS AND METHODS: One hundred and twenty-nine intractable epilepsy patients (age range 6-53 years) with bitemporal epileptiform abnormalities in multiple scalp EEGs were evaluated with chronically implanted depth and subdural electrodes. Interelectrode coherence and power spectra were studied using internally developed software. RESULTS: Bitemporal epileptic foci were found in 85/129 (66%) patients with reciprocal relations between these foci in 57/85 (67%) patients. Temporal lobectomy was performed for 67/85 patients. 12/67 patients became free of seizures (Engel's Class I), 32/67 improved (Classes II and III), and 23/67 did not improve. 14/23 patients demonstrated post-surgical activation of the contralateral temporal lobe epileptic focus. For 8/14 of these patients, the stereotactic cryoamygdalatomy was performed in the temporal lobe contralateral to the first surgery. 5/8 patients became free of seizures. It was found that stimulation of temporal lobe deep epileptic focus may terminate focal seizures in the contralateral symmetric structures. CONCLUSION: A mutually suppressive relationship is one of variants of the interaction of symmetric epileptic foci. Some epilepsy surgery failures may be a result of post-surgical activation of the intact focus. The increase of coherence between both temporal lobes before the seizure onset of the seizure suggests the establishment of functional interrelations between two epileptic foci at an early, "hidden" phase of seizures, and may predict the direction of seizure spread. Mutually suppressive interrelations of symmetric epileptic foci might be employed for chronic therapeutic stimulation.

Adolescent↗

PubMed2005

A program for the optimum design of pharmacokinetic, pharmacodynamic, drug metabolism and drug-drug interaction models.

Planning any experiment includes issues such as how many samples are to be taken and their location given some predictor variable. Often a model is used to explain these data; hence including this formally in the design will be beneficial for any subsequent parameter estimation and modelling. A number of criteria for model oriented experiments, which maximise the information content of the collected data are available. In this paper we present a program, Optdes, to investigate the optimal design of pharmacokinetic, pharmacodynamic, drug metabolism and drug-drug interaction models. Using the developed software the location of either a predetermined number of design points (exact designs) or together with the proportion of samples at each point (continuous designs) can be determined. Local as well as Bayesian designs can be optimised by either D- or A-optimality criteria. Although often the optimal design cannot be applied for practical reasons, alternative designs can be readily evaluated.

Algorithms↗

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↗

PubMed2004

Development of the cubic least squares mapping linear-kernel support vector machine classifier for improving the characterization of breast lesions on ultrasound.

An efficient classification algorithm is proposed for characterizing breast lesions. The algorithm is based on the cubic least squares mapping and the linear-kernel support vector machine (SVM(LSM)) classifier. Ultrasound images of 154 confirmed lesions (59 benign and 52 malignant solid masses, 7 simple cysts, and 32 complicated cysts) were manually segmented by a physician using a custom developed software. Texture and outline features and the SVM(LSM) algorithm were used to design a hierarchical tree classification system. Classification accuracy was 98.7%, misdiagnosing 1 malignant an 1 benign solid lesions only. This system may be used as a second opinion tool to the radiologists.

Breast Diseases↗

PubMed2006

Regional analysis of the left ventricle of the heart.

This paper presents a method to analyze the local wall motion of the left ventricle of the heart. Data are sets of points (obtained from various medical imaging modalities) corresponding to surfaces of the left ventricle, which evolve as a function of time. After re-sampling, the surfaces are segmented in order to create regions of equivalent volume. Then, the local cardiac parameters are estimated: evolution of the regional volumes as a function of time, ejection fraction, end-diastolic and end-systolic volumes, end-diastolic and end-systolic instants. The method has been validated using deformable surfaces synthesized from an ellipsoidal model. It has also been tested in vivo on a set of 59 patients using a specially developed software product, which satisfies severe constraints of robustness, real-time, interactivity and ergonomics. The results obtained are similar to those provided by a reference nuclear medicine examination, but the proposed method is faster and gives a more precise localization of the cardiac wall motion anomalies.

Algorithms↗

PubMed2006

Computer-assisted detection for CT colonography: external validation.

AIM: To externally validate a computer-assisted detection (CAD) system for computed tomography (CT) colonography, using data from a single centre uninvolved with the software development. MATERIALS AND METHODS: Twenty-five multi-detector CT colonography examinations of patients with validated polyps accumulated at a single centre were examined by two readers who used endoscopic and histopathological data to identify polyp coordinates. A CAD system that had been developed using data from elsewhere, and had not previously encountered the present data, was then applied to the data at sphericity filter settings of 0.75 and 0.50 and identified potential polyps. True-positive, false-negative, and false-positive counts were determined by comparison with the known polyp coordinates. RESULTS: Twenty-five patients had 57 polyps, median size 6mm (range 1-15mm). Per-patient sensitivity for the CAD system was 96% (24 of 25). The CAD system detected 44 (77%) polyps at sphericity setting 0.75 and 49 (86%) polyps at sphericity 0.50: the additional five polyps detected all measured 5mm or less. Sphericity of 0.75 resulted in a median of 10 (one to 34) easily dismissed false-positive prompts per patient and a median of 4 (zero to 15) that needed three-dimensional rendering before dismissal. This rose to 32 (16 to 99) and 11 (three to 35), respectively, at sphericity 0.5. CONCLUSIONS: A per-patient sensitivity of 96% was found for the CAD system (in patients with a median polyp diameter of 6mm) using external validation, a more stringent test than either internal cross-validation or temporal validation. Decreasing sphericity increases sensitivity for small polyps at the expense of decreased specificity.

Colonic Polyps↗

PubMed2005

Caco-2 permeability of weakly basic drugs predicted with the double-sink PAMPA pKa(flux) method.

The aim of this study was to analyze pH-dependent permeability of cationic drugs in Caco-2 cell monolayers using the pK(a)(flux) method and to correlate the results with those obtained in PAMPA (parallel artificial membrane permeability assay). The pH-dependent permeability of verapamil and propranolol was studied in Caco-2 cell monolayers. The data were subsequently processed using software developed for the PAMPA pK(a)(flux) method. Literature values for an additional nine cationic drugs were also analyzed. Double-Sink PAMPA data were also obtained for the same cationic drugs, to compare with the Caco-2 data. The Algorithm Builder program was then used to develop a predictive model of Caco-2 permeability based on PAMPA permeability and calculated Abraham molecular descriptors. From the relationship between permeability and pH it was shown that in PAMPA only the uncharged form of the drugs permeated across the membrane barrier, while charged and ionized forms of the drugs were significantly permeable in Caco-2. The charged-form permeability, P(i), was therefore determined and subsequently subtracted from all permeability coefficients in Caco-2 prior to the comparison with PAMPA. The resulting intrinsic permeability coefficients (P(o)) obtained in Caco-2 were successfully related to those derived from the PAMPA model. In this study we have shown that permeability coefficients obtained in PAMPA can predict the passive transcellular permeability in Caco-2.

Caco-2 Cells↗

PubMed2006

Endoscopic measurement of cardia circumference as an indicator of GERD.

BACKGROUND: It is theorized that repeated gastric distention leads to dilatation of the cardia and the development of GERD. We hypothesize that cardia circumference correlates with the presence and the severity of GERD, and we developed software to measure cardia circumference from static endoscopic images. Our aims were to validate the software and to quantify cardia circumference along the spectrum of GERD. METHODS: Software-based measurements were compared with actual measurements in animal and mechanical models. A retrospective review of an endoscopic database and patient charts produced 273 subjects, grouped as follows: controls, GERD, < or = 3-cm Barrett's esophagus, or > 3-cm Barrett's esophagus. A blinded abstractor measured cardia circumference by using images from the database. RESULTS: Software and actual measurements correlated closely and were reproducible among observers. Median cardia circumference for each group was the following: control, 31.8 mm; GERD, 37.8 mm; < or = 3-cm Barrett's esophagus, 38.4 mm; and > 3-cm Barrett's esophagus, 45.0 mm (p < 0.001). By using 34.3 mm as a cutoff, cardia circumference was 85.3% sensitive and 89.6% specific for the diagnosis of GERD. CONCLUSIONS: There was a direct relationship between cardia circumference and the presence of GERD. This finding augments our understanding of the anatomic contributions of the esophagogastric junction in the pathogenesis of GERD. Cardia measurement may prove to be a useful diagnostic tool.

Animals↗

PubMed2006

Six methodological steps to build medical data warehouses for research.

PURPOSE: We propose a simple methodology for heterogeneous data collection and central repository-style database design in healthcare. Our method can be used with or without other software development frameworks, and we argue that its application can save a relevant amount of implementation effort. Also, we believe that the method can be used in other fields of research, especially those that have a strong interdisciplinary nature. BACKGROUND: The idea emerged during a healthcare research project, which consisted among others in grouping information from heterogeneous and distributed information sources. We developed this methodology by the lessons learned when we had to build a data repository, containing information about elderly patients flows in the UK's long-term care system (LTC). DESIGN: We explain thoroughly those aspects that influenced the methodology building. The methodology is defined by six steps, which can be aligned with various iterative development frameworks. We describe here the alignment of our methodology with the RUP (rational unified process) framework. The methodology emphasizes current trends, as early identification of critical requirements, data modelling, close and timely interaction with users and stakeholders, ontology building, quality management, and exception handling. RESULTS: Of a special interest is the ontological engineering aspect, which had the effects with the highest impact after the project. That is, it helped stakeholders to perform better collaborative negotiations that brought better solutions for the overall system investigated. An insight into the problems faced by others helps to lead the negotiators to win-win situations. We consider that this should be the social result of any project that collects data for better decision making that leads finally to enhanced global outcomes.

Computer Communication Networks↗

PubMed2004

Diagnosis of liver cancer using HPLC-based metabonomics avoiding false-positive result from hepatitis and hepatocirrhosis diseases.

Metabonomics, the study of metabolites and their roles in various disease states, is a novel methodology arising from the post-genomics era. This methodology has been applied in many fields. Current metabonomics practice has relied on mass spectrometry (MS), gas chromatography-mass spectrometry (GC-MS), liquid chromatography-mass spectrometry (LC-MS) and nuclear magnetic resonance (NMR) to analyze metabolites. In this study, a novel approach of using high-performance liquid chromatography (HPLC) in conjunction with developed software was employed. Using the principal components analysis method (PCA), all (113) peaks of urinary metabolites with a cis-diol structure from patients with hepatitis and hepatocirrhosis were compared to those from liver cancer patients. The results showed that the metabonomics-PCA method might be useful to differentiate between patients with hepatocirrhosis and hepatitis from patients with liver cancer while lowering false-positive rate. These findings also suggest that a subset of the urinary nucleosides identified with metabonomics correlate better with cancer diagnosis than the traditional single tumor marker alpha-fetoprotein (AFP).

Chromatography, High Pressure Liquid↗

PubMed2004

Experimental determination of interfacial tension by different dynamical methods under simple shear flow conditions with a novel computer-controlled parallel band apparatus.

We present experimental investigations on droplet deformation under simple shear flow conditions, using a computer-controlled parallel band apparatus and an optical device which allows us to record the time dependence of the droplet shape. Several methods are applied to determine the interfacial tension from the observed shape and relaxation mechanism. Specific software developed in our laboratory allows the droplet to be fixed in a certain position for extended times, in fact, indefinite. This is an advantage over most other work done in this area, where only limited time is available. In our experiments, the transient deformation of sheared droplets can be observed to reach the steady state. The measured systems were Newtonian, both droplet and fluid phase. Droplet deformation, orientation angle and retraction were studied and compared to several models. The interfacial tension of the different systems was calculated using the theories of Taylor, Rallison, and Hinch and Acrivos. The results obtained from the analysis of the droplet deformation were in very good agreement with drop detachment experiments of Feigl and co-workers. The study of orientation angle shows qualitative agreement to the theory of Hinch and Acrivos but reveals larger quantitative discrepancies for several empirical fitting parameters of the used model. Analysis of the relaxation of sheared drops provided estimates of the interfacial tension that were in very good agreement with the steady-state measurements.

Journal Article↗

PubMed2005

Intramural activation and repolarization sequences in canine ventricles. Experimental and simulation studies.

BACKGROUND: There are no published data showing the three-dimensional sequence of repolarization and the associated potential fields in the ventricles. Knowledge of the sequence of repolarization has medical relevance because high spatial dispersion of recovery times and action potential durations favors cardiac arrhythmias. In this study we describe measured and simulated 3-D excitation and recovery sequences and activation-recovery intervals (ARIs) (measured) or action potential durations (APDs) (simulated) in the ventricular walls. METHODS: We recorded from 600 to 1400 unipolar electrograms from canine ventricular walls during atrial and ventricular pacing at 350-450 ms cycle length. Measured excitation and recovery times and ARIs were displayed as 2-D maps in transmural planes or 3-D maps in the volume explored, using specially developed software. Excitation and recovery sequences and APD distributions were also simulated in parallelepipedal slabs using anisotropic monodomain or bidomain models based on the Lou-Rudy version 1 model with homogeneous membrane properties. RESULTS: Simulations showed that in the presence of homogeneous membrane properties, the sequence of repolarization was similar but not identical to the excitation sequence. In a transmural plane perpendicular to epicardial fiber direction, both activation and recovery pathways starting from an epicardial pacing site returned toward the epicardium at a few cm distance from the pacing site. However, APDs were not constant, but had a dispersion of approximately 14 ms in the simulated domain. The maximum APD value was near the pacing site and two minima appeared along a line perpendicular to fiber directions, passing through the pacing site. Electrical measurements in dog ventricles showed that, for short cycle lengths, both excitation and recovery pathways, starting from an epicardial pacing site, returned toward the epicardium. For slower pacing rates, pathways of recovery departed from the pathway of excitation. Highest ARI values were observed near the pacing site in part of the experiments. In addition, maps of activation-recovery intervals showed mid-myocardial clusters with activation-recovery intervals that were slightly longer than ARIs closer to the epi- or endocardium, suggesting the presence of M cells in those areas. Transmural dispersion of measured ARIs was on the order of 20-25 ms. Potential distributions during recovery were less affected by myocardial anisotropy than were excitation potentials.

Action Potentials↗

PubMed2005

Development of an automated Selvester Scoring System for estimating the size of myocardial infarction from the electrocardiogram.

Although the Selvester Scoring System for estimating the size of myocardial infarction from the standard 12-lead electrocardiogram (ECG) has potential clinical value, it has found limited application because of the difficulties in making precise and reproducible measurements. The objective of this study was to develop software to automate the Selvester Scoring System, thus allowing wider application of the technique. The study was carried out using a training set consisting of ECG data recorded from 705 individuals with and without previous myocardial infarction. Algorithms for the 50 criteria in the Selvester Scoring System were iteratively improved by comparison of scores obtained by 2 experienced cardiologist investigators with those generated by the program. The final version was evaluated in a test set consisting of 60 ECGs by comparing scores derived by cardiologist investigator with those obtained by the program. The disagreements occurred only in 1.1% of the score comparisons and in 1.6% of the specific measurements. In all cases in which a disagreement occurred, it resulted from very small differences in measurements. These results indicate that the algorithm for automated application of the Selvester Scoring System is adequate for both clinical and research applications.

Algorithms↗