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PubMed2005

NASA Space Radiation Transport Code Development Consortium.

Recently, NASA established a consortium involving the University of Tennessee (lead institution), the University of Houston, Roanoke College and various government and national laboratories, to accelerate the development of a standard set of radiation transport computer codes for NASA human exploration applications. This effort involves further improvements of the Monte Carlo codes HETC and FLUKA and the deterministic code HZETRN, including developing nuclear reaction databases necessary to extend the Monte Carlo codes to carry out heavy ion transport, and extending HZETRN to three dimensions. The improved codes will be validated by comparing predictions with measured laboratory transport data, provided by an experimental measurements consortium, and measurements in the upper atmosphere on the balloon-borne Deep Space Test Bed (DSTB). In this paper, we present an overview of the consortium members and the current status and future plans of consortium efforts to meet the research goals and objectives of this extensive undertaking.

Algorithms↗

PubMed2000

An IBM PC-based system for experimental haemodynamic studies.

An IBM PC-based real-time data acquisition, monitoring and analysis system for experimental haemodynamic studies was developed. Comprehensive haemodynamic signals, such as aortic and left ventricular pressures, aortic and coronary blood flows, two segmental lengths, two segmental thicknesses, electrocardiogram and airway pressure, were acquired and monitored to assess cardiac function. The system performs computer-aided analysis and derivations on a number of haemodynamic parameters and cardiac function indices. The system has been tested and validated extensively over a number of series of experimental haemodynamic studies to investigate the effects of anaesthetic agents, cardiovascular drugs, and changes in loading on normal and critically ischaemic myocardium of anaesthetised laboratory subjects. Without this specialised and automated system, the analysis of the data acquired from the haemodynamic studies would be too time-consuming and could not be fully performed.

Blood Pressure↗

PubMed1998

Measuring resource use in the ICU with computerized therapeutic intervention scoring system-based data.

BACKGROUND AND OBJECTIVE: In this era of health-care reform, there is increasing need to monitor and control health-care resource consumption. This requires the development of measurement tools that are practical, uniform, reproducible, and of sufficient detail to allow comparison among institutions, among select groups of patients, and among individual patients. We explored the feasibility of generating an index of resource use based on the Therapeutic Intervention Scoring System (TISS) from hospital electronic billing data. Such an index is potentially comparable across institutions, allows assessment of care at many levels, is well understood by clinicians, and captures many of the resources relevant to the ICU. DESIGN: We developed an automated mapping of the hospital billing database into the different items of TISS and generated computerized active TISS scores on 1,372 ICU days. The computerized score was then validated by comparison to prospectively gathered active TISS scores by trained data collectors. SETTING: Eight ICUs within a university teaching institution. PATIENTS: We studied 1,229 general medical and surgical ICU patients. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: Active TISS scores ranged from 0 to 31 points. The two scores were well correlated (R2=0.53) and highly calibrated (as assessed by regression of active TISS on mean computerized active TISS [R2=0.85]). The scores were identical on 756 days (55.6%) and differed by < or = 3 TISS points on an additional 387 (28.2%) days. Interreliability assessment suggested substantial agreement (kappa statistic=0.71). The discriminatory power of the computerized score to identify different levels of ICU resource use was excellent as assessed by area under the receiver operating characteristics curves at four threshold points (0.91, 0.87, 0.89, and 0.88). Performance of the computerized score was similar across medical, coronary, and surgical ICU patient groups. CONCLUSION: An automated algorithm can reproduce valid TISS scores from standard hospital billing data, allowing comparison of patients and groups of patients in order to better understand ICU resource use.

Accounting↗

PubMed1999

Development of a clinical chart to compute different disease activity indices for systemic lupus erythematosus.

Between 1990 and 1995 a European Consensus Group carried out a multicenter study to reach agreement of the definition of disease activity in systemic lupus erythematosus (SLE). A new index, the European Consensus Lupus Activity Measurement (ECLAM) index, was developed. In a second phase of the study, a prospective survey aimed at validating ECLAM and 4 other scales as steady-state and transition indices for disease activity in SLE was completed. We present the results of this survey. A standardized clinical chart was developed, together with a computer program that could automatically calculate the ECLAM score, as well as the scores for some of the disease activity scales most widely used at present, i.e., the British Isles Lupus Assessment Group, Systemic Lupus Activity Measure, SLE Disease Activity Index, and the SLE Index Score (SIS). With the participation of 28 centers in 15 different European countries, data from 121 prospectively selected new lupus patients were collected. The validity of the 5 activity scales was assessed by comparing the computed scores for each patient to a gold standard, i.e., the physician's subjective judgment on disease activity measured using a semiquantitative scale. All the indices were found to be valid instruments for measuring disease activity in SLE in both the steady-state and transition phases. The results for the various indices closely correlated with one another. Thus, the computerized chart developed by the European Consensus Group offers a simple and reliable instrument to assess disease activity and could be used to monitor lupus patients both in clinical practice and in clinical trials.

Computer Simulation↗

PubMed2006

The development and validation of the Virtual Tissue Matrix, a software application that facilitates the review of tissue microarrays on line.

BACKGROUND: The Tissue Microarray (TMA) facilitates high-throughput analysis of hundreds of tissue specimens simultaneously. However, bottlenecks in the storage and manipulation of the data generated from TMA reviews have become apparent. A number of software applications have been developed to assist in image and data management; however no solution currently facilitates the easy online review, scoring and subsequent storage of images and data associated with TMA experimentation. RESULTS: This paper describes the design, development and validation of the Virtual Tissue Matrix (VTM). Through an intuitive HTML driven user interface, the VTM provides digital/virtual slide based images of each TMA core and a means to record observations on each TMA spot. Data generated from a TMA review is stored in an associated relational database, which facilitates the use of flexible scoring forms. The system allows multiple users to record their interpretation of each TMA spot for any parameters assessed. Images generated for the VTM were captured using a standard background lighting intensity and corrective algorithms were applied to each image to eliminate any background lighting hue inconsistencies or vignetting. Validation of the VTM involved examination of inter-and intra-observer variability between microscope and digital TMA reviews. Six bladder TMAs were immunohistochemically stained for E-Cadherin, beta-Catenin and PhosphoMet and were assessed by two reviewers for the amount of core and tumour present, the amount and intensity of membrane, cytoplasmic and nuclear staining. CONCLUSION: Results show that digital VTM images are representative of the original tissue viewed with a microscope. There were equivalent levels of inter-and intra-observer agreement for five out of the eight parameters assessed. Results also suggest that digital reviews may correct potential problems experienced when reviewing TMAs using a microscope, for example, removal of background lighting variance and tint, and potential disorientation of the reviewer, which may have resulted in the discrepancies evident in the remaining three parameters.

Algorithms↗

PubMed1988

A performance evaluation of the expert system ANEMIA.

This paper reports the results of an evaluation study of the current level of performance given by ANEMIA, a knowledge-based consultation system addressing the clinical problem of managing anemic patients. ANEMIA was developed on a mainframe using the AI programming scheme EXPERT and then translated into a version running on a personal computer. At present the system is able to provide assistance in the diagnosis and management of 65 disease entities. After extensive local testing of accuracy, completeness, and consistency of the knowledge base included into ANEMIA, we designed a study to evaluate whether the system is able to appropriately mirror also the reasoning of well-known hematologists other than those who provided the knowledge. We were also interested in testing whether there were conflicting opinions among hematologists. Thus, we designed a validation study in which ANEMIA's performance could be compared with that of six hematologists and the interexpert consensus evaluated. ANEMIA's overall performance was judged acceptable in 87% (26/30) of the cases, while expert evaluators agreed with their colleagues in 90% (27/30) of them. A low interexpert consensus was found: considering the ratings given by different hematologists to the same ANEMIA performance, complete agreement occurred only 47% of the time.

Adult↗

PubMed1993

Bioassay from two parabolas.

The paper deals with potency ratio estimation of parallel curve analytic dilution assays in case log dose-response relationship could be reasonably described by a parabola. It comprises: (1) testing the adequacy and validity of the quadratic model by the analysis of variance; and (2) estimation of the relative potency of an unknown in relation to a standard preparation, its standard deviation and fiducial limits for its true value. The method is applicable whenever successive doses of an unknown are a constant multiple of a standard in randomized blocks or completely randomized design. The method can be generalized to polynomial models of higher order.

Analysis of Variance↗

PubMed1998

GeneGenerator--a flexible algorithm for gene prediction and its application to maize sequences.

MOTIVATION: We developed GeneGenerator because of the need for a tool to predict gene structure without knowing in advance how to score potential exons and introns in order to obtain the best results, pertinent in particular to less well-studied organisms for which suitable training sets are small. GeneGenerator is a very flexible algorithm which for a given genomic sequence generates a number of feasible gene structures satisfying user-defined constraints. The specific implementation described in detail requires minimum scoring for translation start and donor and acceptor splice sites according to previously trained logitlinear models. In addition, potential exons and introns are required to exceed specified minimal lengths and threshold scores for coding or non-coding potential derived as log-likelihood ratios of appropriate Markov sequence models. RESULTS: A database of 46 non-redundant genomic sequences from maize is used for illustration. It is shown that the correct gene structures do not always maximize the considered target function. However, in most cases, the correct or nearly correct structures are found in a small set of high-scoring structures. A critical review of the generated structures sometimes allows the choices to be narrowed by considering additional variables such as predicted splice site strength or local optimality of splice site scores. Summary statistics for prediction accuracy over all 46 maize genes are derived under cross-validation and non-cross-validation training conditions for the Markov sequence models. The algorithm achieved exon sensitivity of 0.81 and specificity of 0.75 on an independent set of 14 novel maize genomic segments. AVAILABILITY: GeneGenerator runs under Borland-Pascal 7.0 using MS-DOS and C on UNIX work stations. The source code is available upon request. CONTACT: jkleffe@euler.grumed.fu-berlin-de

Algorithms↗

PubMed1994

An expert system for the analysis and interpretation of evoked potentials based on fuzzy classification: application to brainstem auditory evoked potentials.

EPEXS is an expert system for evoked potential analysis and interpretation (a medical examination performed in clinical neurophysiology laboratories), working from available clinical records and numerical data extracted from evoked potential traces. EPEXS integrates two formalisms of knowledge representation: rules and structured objects. The rules represent the elementary concepts (shallow knowledge) and include a model of possibility based on the Dubois and Prade default reasoning and possibility theory. The structured objects (prototypes) are organized as hierarchical taxonomies (underlying knowledge). These allow the description of both the objects and their relationships. The heuristics used to interpret knowledge are based on two hypotheses: the unicity of the pathological process leading to several given symptoms and the progression from the general to the specific, leading to the adoption or rejection of a class of diagnoses. This avoids the problem of the differential diagnosis. These sources of knowledge are used in a dynamical way that could be described as a four-step process: acquisition of clinical data in order to define the nosological frame of the pathology, production of hypotheses about the nature and topography of lesions, interpretation of data in accordance with these hypotheses, and finally evaluation of their likelihood. The validation shows that EPEXS topographic diagnoses were correct in 100% of cases and 92% of it nosologic diagnoses were correct, and no pathological record was interpreted as normal. When examined on a given pathology basis EPEXS was not significantly different from human experts as regards to performance, specificity, and sensitivity.

Computer Simulation↗

PubMed1993

An algorithm for measurement of expiratory flow rate parameters on the partial expiratory flow-volume curve.

Partial expiratory flow-volume (PEFV) curves are a useful tool in airway challenge studies, but unlike the maximal expiratory flow-volume (MEFV) curve, lung function parameters require manual calculation from the flow-volume tracing. We describe an algorithm written in QuickBASIC that analyzes a PEFV curve superimposed on a MEFV curve by (1) identifying the PEFV curve, (2) locating the maximal expiratory flow at the point on the PEFV curve that corresponds to 60% of the baseline forced vital capacity (FVC) below total lung capacity (TLC), termed MEF40%(P), and (3) identifying the size of the PEFV curve along the TLC axis. A report of these parameters is also provided. This algorithm was validated using flow-volume curves from a clinical study in which eight subjects performed two sets of MEFV and PEFV curves separated by approximately 1 hr. Paired comparison of MEF40%(P) determined by the algorithm and two independent manual calculations correlated strongly and yielded no statistically significant differences between the two methods. We conclude that this algorithm provides rapid and accurate determinations of PEFV parameters.

Algorithms↗

PubMed2005

In vivo validation of the adequacy calculator for continuous renal replacement therapies.

INTRODUCTION: The study was conducted to validate in vivo the Adequacy Calculator, a Microsoft Excel-based program, designed to assess the prescription and delivery of renal replacement therapy in the critical care setting. METHODS: The design was a prospective cohort study, set in two intensive care units of teaching hospitals. The participants were 30 consecutive critically ill patients with acute renal failure treated with 106 continuous renal replacement therapies (CRRT). Urea clearance computation was performed with the Adequacy Calculator (KCALC). Simultaneous blood and effluent urea samples were collected to measure the effectively delivered urea clearance (KDEL) at the beginning of each treatment and, during 73 treatments, between the 18th and 24th treatment hour. The correlation between 179 computed and 179 measured clearances was assessed. Fractional clearances for urea were calculated as spKt/V (where sp represents single pool, K is clearance, t is time, and V is urea volume of distribution) obtained from software prescription and compared with the delivered spKt/V obtained from empirical data. RESULTS: We found that the value of clearance predicted by the calculator was strongly correlated with the value obtained from computation on blood and dialysate determination (r = 0.97) during the first 24 treatment hours, regardless of the renal replacement modality used. The delivered spKt/V (1.25) was less than prescribed (1.4) from the Adequacy Calculator by 10.7%, owing to therapy downtime. CONCLUSION: The Adequacy Calculator is a simple tool for prescribing CRRT and for predicting the delivered dose. The calculator might be a helpful tool for standardizing therapy and for comparing disparate treatments, making it possible to perform large multi-centre studies on CRRT.

Acute Kidney Injury↗

PubMedDate not supplied

Rational selection of training and test sets for the development of validated QSAR models.

Quantitative Structure-Activity Relationship (QSAR) models are used increasingly to screen chemical databases and/or virtual chemical libraries for potentially bioactive molecules. These developments emphasize the importance of rigorous model validation to ensure that the models have acceptable predictive power. Using k nearest neighbors (kNN) variable selection QSAR method for the analysis of several datasets, we have demonstrated recently that the widely accepted leave-one-out (LOO) cross-validated R2 (q2) is an inadequate characteristic to assess the predictive ability of the models [Golbraikh, A., Tropsha, A. Beware of q2! J. Mol. Graphics Mod. 20, 269-276, (2002)]. Herein, we provide additional evidence that there exists no correlation between the values of q2 for the training set and accuracy of prediction (R2) for the test set and argue that this observation is a general property of any QSAR model developed with LOO cross-validation. We suggest that external validation using rationally selected training and test sets provides a means to establish a reliable QSAR model. We propose several approaches to the division of experimental datasets into training and test sets and apply them in QSAR studies of 48 functionalized amino acid anticonvulsants and a series of 157 epipodophyllotoxin derivatives with antitumor activity. We formulate a set of general criteria for the evaluation of predictive power of QSAR models.

Algorithms↗

PubMed1995

A computer program linking physiologically based pharmacokinetic model with cancer risk assessment for breast-fed infants.

The risk assessment process predicts the chances of adverse health effects that the toxicant possibly can do to the target organism under expected conditions of exposure. Regulators chose among several mathematical approaches to estimate the risk, but in each case it is necessary to link the dosemetrics of the toxicant with its predicted health effect. In this paper, a computer program is described that allowed us to link a physiologically based pharmacokinetic (PBPK) model for tetrachloroethylene (PCE) in the lactating mother with the estimate of extra cancer risk for breast-fed infants, according to the U.S. Environmental Protection Agency (EPA) methodology. When inhaled by a lactating woman, PCE may partition into breast milk and may be transferred to the breast-fed infant. We have developed and validated experimentally a PBPK model for lactational transfer of PCE in rats, including a quantitative description of a milk compartment and the nursing pup. Subsequently, the model has been scaled to describe human physiology, and was validated with literature data for human cases of PCE exposure. Finally, we linked the dosage predictions of the PBPK model with equations used by EPA to estimate the cancer risk from PCE. The model predictions are in good agreement with both the measured values and those reported in the literature for exposure to PCE. This comparison confirms the usefulness of PBPK modeling in risk assessments.

Air Pollutants↗

PubMed2000

Validation of ICTERUS, a knowledge-based expert system for Jaundice diagnosis.

The study aimed to describe an example of the assessment and validation of knowledge-based clinical expert systems. The paper focuses on ICTERUS, an expert system for jaundice diagnosis. It describes system design, the methodology applied for upgrading and validating the program, and the most important outcomes of the validation procedure. The clinical validation of the system on a very large European database (Euricterus Project) shows that diagnostic conclusions are reliable in about 70% of eligible cases. This figure appears acceptable for a system which provides decision support only on the basis of clinical data, assuming that the final decision is achieved under user responsibility. Expected biases, limitations and inconsistencies in the practical application of the system are discussed.

Analysis of Variance↗

PubMed1997

Computerized scoring of abnormal human sleep: a validation.

A computerized assessment of sleep staging, arousals, premature ventricular contractions (PVCs), and respiratory events in sleep, was developed. Performance of the computerized system was assessed using epoch-by-epoch comparison and two human scorers across 30 consecutive patients. Percentages of agreement and Cohen's kappa coefficients were used for comparison. All agreements between all scorers for sleep staging, arousals, PVCs and respiratory events in sleep were significant (p < 0.001). The ratios of computer-human agreement descriptors to human-human agreement descriptors indicate that computerized analysis of abnormal human sleep offers reasonable results with savings in technologist time and work, but not in physician time and work.

Electroencephalography↗

PubMed2004

Automated extraction of mutation data from the literature: application of MuteXt to G protein-coupled receptors and nuclear hormone receptors.

MOTIVATION: The amount of genomic and proteomic data that is published daily in the scientific literature is outstripping the ability of experimental scientists to stay current. Reviews, the traditional medium for collating published observations, are also unable to keep pace. For some specific classes of information (e.g. sequences and protein structures), obligatory data deposition policies have helped. However, a great deal of other valuable information is spread throughout the literature hindering coherent access. We are involved in the Molecular Class-Specific Information System (MCSIS) project, a collaborative effort to design and automate the maintenance of protein family databases. The first two databases, the GPCRDB and NucleaRDB, are focused on G protein-coupled receptors (GPCRs) and nuclear hormone receptors (NRs), respectively. The main aim of the MCSIS project is to gather heterogeneous data from across a variety of electronic and literature sources in order to draw new inferences about the target protein families. RESULTS: We present a computational method that identifies and extracts mutation data from the scientific literature. We focused on the extraction of single point mutations for the GPCR and NR superfamilies. After validation by plausibility filters, the mutation data is integrated into the corresponding MCSIS where it is combined with structural and sequence information already stored in these databases. We extracted and validated 2736 true point mutations from 914 articles on GPCRs and 785 true point mutations from 1094 articles on NRs. The current version of our automated extraction algorithm identifies 49.3% of the GPCR point mutations with a specificity of 87.9%, and 64.5% of the NR point mutations with a specificity of 85.8%. MuteXt routinely analyzes 100 electronic articles in approximately 1 h.

Algorithms↗

PubMed2006

Genome analysis of Escherichia coli promoter sequences evidences that DNA static curvature plays a more important role in gene transcription than has previously been anticipated.

We have performed a computer analysis to study the prevalence of DNA static curvature in the regulatory regions of Escherichia coli, detecting a large number of operons with curved DNA fragments in their 5' upstream regions. A statistical analysis reveals that all the global transcription factors identified so far in E. coli have a tendency to regulate operons with curved DNA sequences in their upstream regions. In addition to these global regulators, we also found that the PurR, ArgR, FruR, TyrR, and CytR specific regulators present a similar propensity. Interestingly, for these cases we found no previous reference describing a possible relationship with curved DNA regions. To validate our theoretical results, we performed site-directed mutagenesis to reduce the degree of DNA curvature in the regulatory sequences of the aroG, pyrC, and argCBH operons. The effects of these changes were measured by polyacrylamide gel electrophoresis assays and further evaluated in vivo by transcriptional fusions to a reporter gene. All our results point toward a more widespread role of curved DNA in gene transcription, a fact that has previously been underestimated.

Base Sequence↗

PubMed2006

Empirical validation of the S-Score algorithm in the analysis of gene expression data.

BACKGROUND: Current methods of analyzing Affymetrix GeneChip microarray data require the estimation of probe set expression summaries, followed by application of statistical tests to determine which genes are differentially expressed. The S-Score algorithm described by Zhang and colleagues is an alternative method that allows tests of hypotheses directly from probe level data. It is based on an error model in which the detected signal is proportional to the probe pair signal for highly expressed genes, but approaches a background level (rather than 0) for genes with low levels of expression. This model is used to calculate relative change in probe pair intensities that converts probe signals into multiple measurements with equalized errors, which are summed over a probe set to form the S-Score. Assuming no expression differences between chips, the S-Score follows a standard normal distribution, allowing direct tests of hypotheses to be made. Using spike-in and dilution datasets, we validated the S-Score method against comparisons of gene expression utilizing the more recently developed methods RMA, dChip, and MAS5. RESULTS: The S-score showed excellent sensitivity and specificity in detecting low-level gene expression changes. Rank ordering of S-Score values more accurately reflected known fold-change values compared to other algorithms. CONCLUSION: The S-score method, utilizing probe level data directly, offers significant advantages over comparisons using only probe set expression summaries.

Algorithms↗