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PubMed2006

The GIS-based SafeAirView software for the concentration assessment of radioactive pollutants after an accidental release.

The European Commission Joint Research Centre (JRC) in Ispra (Italy) has long been running nuclear installations for research purposes. The Nuclear Decommissioning and Facilities Management Unit (NDFM) is responsible for the surveillance of radioactivity levels in nuclear emergency conditions. The NDFM Unit has commissioned the implementation of a specifically developed decision support system, which can be used for quick emergency evaluation in the case of hypothetical accident and for emergency exercises. The requisites were to be a user-friendly software, able to quickly calculate and display values of air and ground radioactive contamination in the complex area around JRC, following an accidental release of radioactive substances from a JRC nuclear research installation. The developed software, named "SafeAirView", is an advanced implementation of GIS technology applied to an existing MS-DOS mode dispersion model, SAFE_AIR (Simulation of Air pollution From Emissions_Above Inhomogeneous Regions). SAFE_AIR is a numerical model which simulates transport, diffusion, and deposition of airborne pollutants emitted in the low atmosphere above complex orography at both local and regional scale, under non-stationary and inhomogeneous emission and meteorological conditions. SafeAirView makes use of user-friendly MS-Windows type interface which drives the dispersion model by a sequential and continuous input-output process, allowing a real time simulation. The GIS environment allows a direct interaction with the territory elements in which the simulation takes place, using data for the JRC Ispra region represented in geo-referenced cartography. Furthermore it offers the possibility to relate concentrations with population distribution and other geo-referenced maps, in a geographic view. Output concentration and deposition patterns can be plotted and/or exported. In spite of the selected specific databases, the SafeAirView software architecture is a general structure, therefore the decision support system could be easily modified to be applied in a region different from the JRC one. Beside the description of SafeAirView, the present paper presents a statistical evaluation of the software, which has considered three well known tracer experiments: Copenhagen, Indianapolis and Kincaid. The data sets related to these experiments are all included in the so called Model Validation Kit.

Data Interpretation, Statistical↗
PubMed2006

[Research on testing the robustness of DICOM-e-mail secure teleradiology systems].

DICOM-e-mail is a secure teleradiology protocol released by German Radiology Society and has already been applied clinically. To improve the robustness of the system, the protocol has been upgraded by adding some mechanisms such as system feedback. Moreover, a test method is also implemented by sending erroneous mails to application software that supports DICOM-e-mail. Through the tests for two different DICOM-e-mail teleradiology application, the validity of the new protocol is proved and at the same time some bugs are found. The implementation of the latest protocol and the general error tests can help to make the whole teleradiology system a better robustness. The implementation of DICOM-e-mail protocol in our country is also discussed in this paper.

Computer Communication Networks↗
PubMed2006

VICMpred: an SVM-based method for the prediction of functional proteins of Gram-negative bacteria using amino acid patterns and composition.

In this study, an attempt has been made to predict the major functions of gram-negative bacterial proteins from their amino acid sequences. The dataset used for training and testing consists of 670 non-redundant gram-negative bacterial proteins (255 of cellular process, 60 of information molecules, 285 of metabolism, and 70 of virulence factors). First we developed an SVM-based method using amino acid and dipeptide composition and achieved the overall accuracy of 52.39% and 47.01%, respectively. We introduced a new concept for the classification of proteins based on tetrapeptides, in which we identified the unique tetrapeptides significantly found in a class of proteins. These tetrapeptides were used as the input feature for predicting the function of a protein and achieved the overall accuracy of 68.66%. We also developed a hybrid method in which the tetrapeptide information was used with amino acid composition and achieved the overall accuracy of 70.75%. A five-fold cross validation was used to evaluate the performance of these methods. The web server VICMpred has been developed for predicting the function of gram-negative bacterial proteins (http://www.imtech.res.in/raghava/vicmpred/).

Bacterial Proteins↗
PubMed1990

Validation study of skull three-dimensional computerized tomography measurements.

Recent advances in imaging have led to high-resolution computerized tomography (CT) scanning with exquisitely detailed slice images of the skull and three-dimensional (3-D) surface reconstructions using computer software. It is possible to use CT scans to acquire morphologic information about the skull in a convenient digital form and to derive 3-D measurements from surface reconstruction images. Unfortunately, no effort has been made to date to test the validity of these measurements on laboratory specimens, and no compelling evidence is available from phantom studies to indicate the nature and magnitude of the errors inherent in the measurement technique. We have performed a pilot study to quantify the morphology of the skull based on surface features that can be found in CT scans and 3-D reconstructions. Comparative measurements were obtained from five skulls (two normal and three with dysmorphology) with calipers and a 3-D electromagnetic digitizer. These measurements were statistically compared with those based on original CT scan slices and reformatted 3-D images. It is concluded that 3D-CT measurement techniques are superior to those in which measurements are obtained directly from the original CT slices; 3-D CT methods, however, must be significantly improved before measurements based on these techniques can be used in studies that require a high degree of precision. The results are used to indicate the most fruitful areas of future study.

Cephalometry↗
PubMed2005

Validation of the HZETRN code for laboratory exposures with 1A GeV iron ions in several targets.

A new version of the HZETRN code capable of validation with HZE ions in either the laboratory or the space environment is under development. The computational model consists of the lowest order asymptotic approximation followed by a Neumann series expansion with non-perturbative corrections. The physical description includes energy loss with straggling, nuclear attenuation, nuclear fragmentation with energy dispersion and downshift. Measurements to test the model were performed at the Alternating Gradient Synchrotron and the NASA Space Radiation Laboratory at Brookhaven National Laboratory with iron ions. Surviving beam particles and produced fragments were measured with solid-state detectors. Beam analysis software has been written to relate the computational results to the measured energy loss spectra of the incident ions for rapid validation of modeled target transmission functions.

Aluminum↗
PubMed2004

PreSPI: a domain combination based prediction system for protein-protein interaction.

With the accumulation of protein and its related data on the Internet, many domain-based computational techniques to predict protein interactions have been developed. However, most techniques still have many limitations when used in real fields. They usually suffer from low accuracy in prediction and do not provide any interaction possibility ranking method for multiple protein pairs. In this paper, we propose a probabilistic framework to predict the interaction probability of proteins and develop an interaction possibility ranking method for multiple protein pairs. Using the ranking method, one can discern the protein pairs that are more likely to interact with each other in multiple protein pairs. The validity of the prediction model was evaluated using an interacting set of protein pairs in yeast and an artificially generated non-interacting set of protein pairs. When 80% of the set of interacting protein pairs in the DIP (Database of Interacting Proteins) was used as a learning set of interacting protein pairs, high sensitivity (77%) and specificity (95%) were achieved for the test groups containing common domains with the learning set of proteins within our framework. The stability of the prediction model was also evident when tested over DIP CORE, HMS-PCI and TAP data. In the validation of the ranking method, we reveal that some correlations exist between the interacting probability and the accuracy of the prediction.

Computational Biology↗
PubMed1999

[Therapeutic monitoring: analytic, pharmacokinetic and clinical aspects].

This paper gives an overview of present aspects and future prospects of therapeutic drug monitoring (TDM). The main aims of TDM are to avoid therapeutic failures due to bad compliance or too low dose of a given drug, as well as adverse or toxic effects due to an excessive dose. The therapeutic drugs frequently monitored depend on the country, but are generally few. For some of these drugs or for others, only patients at risk or belonging to particular sub-populations for a given drug, need TDM. A pre-analytical management is necessary, comprising a correct information of the physician, concerning the nature of the sample to collect and the clinical data necessary to the interpretation, as well as their recording; the control of the sample routing and storing conditions. Nowadays, drug analyses are essentially performed using immunochemical techniques, rapid and easy to operate but limited to a small number of drugs, and chromatographic methods, more specific and adaptable to almost any therapeutic drug and financially and technically more and more accessible. The interpretation of analytical results is a most important part of TDM, which requires knowledge of clinical data, precise collection time, co-administered treatments, and to dispose of a previously defined therapeutic range or target concentration, adapted to the population to which the patient belongs; the limitations of the analytical technique used must also be considered. Clinical pharmacokinetics is a further step in the use of analytical results, allowing the prediction of an efficient dose and administration schedule in one step, using a limited number of blood samples and generally a Bayesian estimation algorithm, readily available through commercial software dedicated to a few drugs in different reference populations. The pharmacokinetic characteristics of different populations and the validation of bayesian estimation have also been published for a number of drugs, sometimes by pharmaceutical companies following phase I and II clinical trials, even taking into account various physiopathological co-variables, but mostly by independent researchers using smaller populations. The efficiency and cost of routine TDM are questionable when it is prescribed with no clinical information or even no indication of administration and sampling times. On the contrary, several studies reported that clinical pharmacokinetics significantly improved patient outcome and were cost-saving, particularly in terms of duration of hospitalisation. The author's opinion is that TDM, in the near future, will be mainly dedicated to drugs used to treat life-threatening diseases, such as anti-HIV, anticancer and immunosuppressive drugs, and maybe also biotechnological peptides or proteins, because of cost considerations. TDM will probably also be used preferentially in target populations, characterised by higher risk or pharmacokinetic variability. Very sensitive, specific and partly automated separative techniques, such as liquid chromatography-tandem mass spectrometry, might become more common than immunochemical methods, owing to a higher flexibility and improved sample throughout. Clinical pharmacokinetics may spread to a larger number of drugs and patients, due to larger reference populations available, taking into account a number of co-variables, computerised data collection and simplified modelisation. Therefore, TDM will mainly be performed in hospitals, with an essentially clinical role for the pharmacists or pharmacologists involved and routine use of recent and efficient technologies for the TDM laboratory technical staff.

Algorithms↗
PubMed2004

Task-oriented evaluation of electronic medical records systems: development and validation of a questionnaire for physicians.

BACKGROUND: Evaluation is a challenging but necessary part of the development cycle of clinical information systems like the electronic medical records (EMR) system. It is believed that such evaluations should include multiple perspectives, be comparative and employ both qualitative and quantitative methods. Self-administered questionnaires are frequently used as a quantitative evaluation method in medical informatics, but very few validated questionnaires address clinical use of EMR systems. METHODS: We have developed a task-oriented questionnaire for evaluating EMR systems from the clinician's perspective. The key feature of the questionnaire is a list of 24 general clinical tasks. It is applicable to physicians of most specialties and covers essential parts of their information-oriented work. The task list appears in two separate sections, about EMR use and task performance using the EMR, respectively. By combining these sections, the evaluator may estimate the potential impact of the EMR system on health care delivery. The results may also be compared across time, site or vendor. This paper describes the development, performance and validation of the questionnaire. Its performance is shown in two demonstration studies (n = 219 and 80). Its content is validated in an interview study (n = 10), and its reliability is investigated in a test-retest study (n = 37) and a scaling study (n = 31). RESULTS: In the interviews, the physicians found the general clinical tasks in the questionnaire relevant and comprehensible. The tasks were interpreted concordant to their definitions. However, the physicians found questions about tasks not explicitly or only partially supported by the EMR systems difficult to answer. The two demonstration studies provided unambiguous results and low percentages of missing responses. In addition, criterion validity was demonstrated for a majority of task-oriented questions. Their test-retest reliability was generally high, and the non-standard scale was found symmetric and ordinal. CONCLUSION: This questionnaire is relevant for clinical work and EMR systems, provides reliable and interpretable results, and may be used as part of any evaluation effort involving the clinician's perspective of an EMR system.

Cooperative Behavior↗
PubMed2006

Rapid and accurate measurement of left ventricular function with a new second-harmonic fast-rotating transducer and semi-automated border detection.

Measurement of left ventricular (LV) volume and function are the most common clinical referral questions to the echocardiography laboratory. A fast, practical, and accurate method would offer important advantages to obtain this important information. To validate a new practical method for rapid measurement of LV volume and function. We developed a continuous fast-rotating transducer, with second-harmonic capabilities, for three-dimensional echocardiography (3DE). Fifteen cardiac patients underwent both 3DE and magnetic resonance imaging (reference method) on the same day. 3DE image acquisition was performed during a 10-second breath-hold with a frame rate of 100 frames/sec and a rotational speed of 6 rotations/sec. The individual images were postprocessed with Matlab software using multibeat data fusion. Subsequently, with these images, 12 datasets per cardiac cycle were reconstructed, each comprising seven equidistant cross-sectional images for analysis in the new TomTec 4DLV analysis software, which uses a semi-automated border detection (ABD) algorithm. The ABD requires an average analysis time of 15 minutes per patient. A strong correlation was found between LV end-diastolic volume (r = 0.99; y = 0.95x - 1.14 ml; SEE = 6.5 ml), LV end-systolic volume (r = 0.96; y = 0.89x + 7.91 ml; SEE = 7.0 ml), and LV ejection fraction (r = 0.93; y = 0.69x + 13.36; SEE = 2.4%). Inter- and intraobserver agreement for all measurements was good. The fast-rotating transducer with new ABD software is a dedicated tool for rapid and accurate analysis of LV volume and function.

Adult↗
PubMed2003

The use of clustering software for the classification of comparative genomic hybridization data. an analysis of 109 malignant fibrous histiocytomas.

Malignant fibrous histiocytoma (MFH) is considered the most frequent soft-tissue sarcoma of late adult life. Nevertheless, the validity of this entity has been recurrently questioned by pathologists. Preliminary analyses by comparative genomic hybridization (CGH) of series of MFH have suggested that this tumor group is heterogeneous at the genomic level, and that at least two main genetic subgroups exist. We report an analysis by CGH of a large series of 109 MFH and on the use of clustering software for an objective classification of these tumors. We confirm our preliminary CGH results and demonstrate that two main clusters of tumors are present in the series analyzed.

Cluster Analysis↗
PubMed2006

Development and preliminary validation of an index for indicating the risks of the design of working hours to health and wellbeing.

BASS 4, a computer program for the design and evaluation of workings hours, is an example of an ergonomics-based software tool that can be used by safety practitioners at the shop floor with regard to legal, ergonomic, and economic criteria. Based on experiences with this computer program, a less sophisticated Working-Hours-Risk Index for assessing the quality of work schedules (including flexible work hours) to indicate risks to health and wellbeing has been developed to provide a quick and easy applicable tool for legally required risk assessments. The results of a validation study show that this risk index seems to be a promising indicator for predicting risks of health complaints and wellbeing. The purpose of the Risk Index is to simplify the evaluation process at the shop floor and provide some more general information about the quality of a work schedule that can be used for triggering preventive interventions. Such a risk index complies with practitioners' expectations and requests for easy, useful, and valid instruments.

Employment↗
PubMed2007

Sexual dimorphism in the subadult mandible: quantification using geometric morphometrics.

There have been numerous attempts, with varying degrees of success, to differentiate males from females on the basis of the immature skeleton. We investigate here whether the mandible can discriminate immature individuals by sex; the techniques we apply are from the field of geometric morphometrics. The application of these methods in forensic anthropology is still relatively new; thus, an important aspect of this research is that it demonstrates potential applications in this discipline. The sample comprises 96 known age and sex subadult individuals; the three-dimensional coordinates of 38 landmarks are analyzed using the shape analysis software morphologika. Multivariate regressions indicated no significant sexual dimorphism in the subadult sample; this result is supported by poor cross-validated classification accuracy (59%). Our results suggest that the subadult mandible is not dimorphic (to the extent that dimorphism is not evident within the sample we studied); thus, sex determination using previously described criteria is likely to yield poor results.

Adolescent↗
PubMed2001

Low viscosity Ektacytometry and its validation tested by flow chamber.

The flow chamber was used to observe the orientation and small deformation of red blood cells (RBCs) in a shear flow of low viscosity. With the aid of computer software, the percentage of RBCs oriented to the C=0 orbit (OI)(F) and the degree of deformation (DI)(F) of such RBCs were calculated by processing the photographs. It was found that these parameters were highly correlated, respectively, to the orientation index (OI)(E) and the small deformation index (DI)(E) obtained by our low viscosity Ektacytometry (LVE). Thus, our flow chamber research has provided direct evidence to validate the use of this low viscosity Ektacytometry. Although there are relative merits for the flow chamber method using low viscosity medium, the LVE is more likely to be applied in clinic for its simplicity and convenience.

Animals↗
PubMed2004

Assessment of tremor: a new computerised tool for clinical practice.

The quantitative assessment of tremor represents the main difficulty in clinical evaluation. We developed a software package - T-Lab - for the biomechanical analysis of hyperkinetic movement disorders. This software can receive and elaborate data from an electronic device interfaced with a personal computer. The aim of our study was to verify the validity of the PC-aided method proposed in the routine assessment of tremor. We did this by a correlation (regression) analysis between the scores obtained by Webster's Amplitude Clinical Scale and the amplitude data by T-Lab and between EMG data and frequency measures of T-Lab. Forty-seven patients presenting with upper limb tremor were enrolled. Four series of data were obtained: two series for frequency and two for amplitude. A significant correlation between all sets of data compared was found. T-Lab represents a valid, objective and useful device of quantifying tremors in clinical practice.

Adolescent↗
PubMed1998

Methods of evaluation in outcomes research.

UNLABELLED: This activity is designed for pharmacists, physicians, physician assistants, nurses, and other healthcare team members; payers for health services; and healthcare executives. GOAL: To provide basic information on the methods used and computer software available for evaluating invariant factorial structures, such as those found in health status measurement tools. OBJECTIVES: 1. Discuss why comparison of mean scores may not be appropriate when interpreting humanistic outcomes results. 2. Identify alternative methods for evaluating data from health status measurement tools, such as the SF-36. 3. Define validity, reliability, and structure. 4. Understand the value of structural equation modeling when using health status measurement tools, such as the SF-36. 5. Describe the statistical software used to perform structural equation modeling.

Data Interpretation, Statistical↗
PubMedDate not supplied

[Physical workload demands: the combined use of 2 evaluation programs].

A computerized methodology is presented for the "on-site" evaluation of work-related physical activities in industrial plant workers. Subjects were videotaped during the activities while heart rate and subjective perception of effort were monitored. The videorecordings were then analyzed with two appropriate software, in order to identify activities at high risk for musculoskeletal injuries ("Vision 3000" program, Promatek Ltd., Montreal) and to evaluate energy expenditure ("Energy" program, University of Michigan). Validation of the energy expenditure indirect analysis system was done by monitoring oxygen consumption (VO2) with a portable telemetric oxygen uptake analyzer ("K2", Cosmed, Rome). No statistically significant differences were found between direct measurements of VO2 and laboratory-derived estimates of energy consumption. The utilization of these two software provides a fast and reliable profile of job requirements and associated risks of musculoskeletal injury.

Biomechanical Phenomena↗
PubMed2000

SPSS and SAS programs for determining the number of components using parallel analysis and velicer's MAP test.

Popular statistical software packages do not have the proper procedures for determining the number of components in factor and principal components analyses. Parallel analysis and Velicer's minimum average partial (MAP) test are validated procedures, recommended widely by statisticians. However, many researchers continue to use alternative, simpler, but flawed procedures, such as the eigenvalues-greater-than-one rule. Use of the proper procedures might be increased if these procedures could be conducted within familiar software environments. This paper describes brief and efficient programs for using SPSS and SAS to conduct parallel analyses and the MAP test.

Factor Analysis, Statistical↗
PubMed2006

Correlation of blood-brain penetration using structural descriptors.

Experimental blood-brain partition coefficients (logBB) for a diverse set of 113 drug molecules are correlated with computed structural descriptors using CODESSA-PRO and ISIDA programs to give statistically significant QSAR models based respectively, on molecular and on fragment descriptors. The linear correlation CODESSA-PRO five-descriptor model has correlation coefficient R2=0.781 and standard deviation s2=0.123. The 'consensus model' of ISIDA gave R2=0.872 and s2=0.047. The developed models were successfully validated using the central nervous system activity data of an external test set of 40 drug molecules.

Algorithms↗