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PubMed2006

Development and validation of a modular, extensible docking program: DOCK 5.

We report on the development and validation of a new version of DOCK. The algorithm has been rewritten in a modular format, which allows for easy implementation of new scoring functions, sampling methods and analysis tools. We validated the sampling algorithm with a test set of 114 protein-ligand complexes. Using an optimized parameter set, we are able to reproduce the crystal ligand pose to within 2 A of the crystal structure for 79% of the test cases using our rigid ligand docking algorithm with an average run time of 1 min per complex and for 72% of the test cases using our flexible ligand docking algorithm with an average run time of 5 min per complex. Finally, we perform an analysis of the docking failures in the test set and determine that the sampling algorithm is generally sufficient for the binding pose prediction problem for up to 7 rotatable bonds; i.e. 99% of the rigid ligand docking cases and 95% of the flexible ligand docking cases are sampled successfully. We point out that success rates could be improved through more advanced modeling of the receptor prior to docking and through improvement of the force field parameters, particularly for structures containing metal-based cofactors.

Algorithms↗
PubMed2004

Validation of a new ultrasound method for the measurement of carotid artery intima medial thickness and plaque dimensions.

BACKGROUND: Carotid ultrasound is an accepted method for the detection of subclinical atherosclerosis. Valid methods that allow quantitation of carotid atheroma burden may be useful for stratifying risk. OBJECTIVE: To validate the results of intima medial thickness (IMT) and plaque measurements using a newly created software algorithm by comparing them with those obtained using a previously validated method. METHODS: Carotid ultrasound videotapes (n=24) were analyzed by experienced observers using a validated method and a new method. Ultrasound parameters were compared by measuring the difference +/- SD to yield indexes of accuracy and precision. Performance was also assessed using correlation and Bland-Altman analyses. RESULTS: Average IMT (n=24), plaque area (n=46), and several indexes that integrate IMT and plaque measurements were all found to be comparable with measurements obtained using the previously validated method. For example, the plaque area showed excellent accuracy and precision (-0.17+/-2.0 mm2, P=0.56), excellent correlation (r=0.98, standard error of the estimate = 2.01 mm2, P<0.001) and no evidence of bias using Bland-Altman analyses (Spearman's rho = 0.04, P=0.82). CONCLUSIONS: A new algorithm for the quantitation of carotid atheroma burden yields results that are comparable with those of a previously validated and widely used method. Availability of valid tools for measuring carotid ultrasound should facilitate the incorporation of this procedure into clinical risk stratification paradigms.

British Columbia↗
PubMed2000

Development of normative values for resting and exercise rate pressure product.

PURPOSE: The purpose of this study was to develop multivariate models to quantify resting, submaximal, and maximal rate pressure products (RPP). METHODS: A validation sample (N = 1623) was randomly selected from a clinically healthy population, and four cross-validation samples were randomly selected from a clinical cohort. The cross-validation samples were patients who had a negative exercise ECG with (Neg-Med, N = 179) and without cardiovascular drug (Neg-NoMed, N = 350), and patients who had a positive exercise ECG with (Pos-Med, N = 60) and without cardiovascular drug (Pos-NoMed, N = 75). Men made up 83% of the validation sample (mean age = 44.2+/-8.7) and women 17% (mean age = 39.7+/-10.1). The validation sample was used to develop multiple regression equations to quantify resting, submaximal, and maximal RPP. RESULTS: Results indicated that gender, body mass index (BMI), and physical activity level (Ex-code) were significantly related with resting RPP. Gender, age, BMI, and Ex-code were significantly related with maximal RPP. Gender, age, BMI, Ex-code, and percent of maximal heart rate at submaximal exercise (%HRmax) were significantly related with submaximal RPP. The multiple correlations for the resting, submaximal, and maximal models were 0.29 (SE = 16.75 beats x min(-1) x mm Hg), 0.87 (SE = 29.04 beats x min(-1) x mm Hg), and 0.31 (SE = 42.41 beats x min(-1) x mm Hg), respectively. The accuracy of the models was confirmed when applied to the Neg-NoMed and Pos-NoMed samples but not the Neg-Med and Pos-Med samples. This result suggest that the regression models developed from this study can be generalized to other populations where patients were not taking cardiovascular medication. Microcomputer programs were suggested to evaluate RPP at rest, maximal exercise, and submaximal exercise. CONCLUSION: Normative RPP for resting and exercise relies on multiple fitness parameters. Practical regression models are developed and can be applied to patients without cardiovascular medication.

Adult↗
PubMed2005

Theoretical and experimental validation of treatment planning for narrow MLC defined photon fields.

In intensity modulated radiotherapy (IMRT), the use of small fields where electronic equilibrium does not exist is becoming more common and presents difficulties for both the measurement and calculation of dose to such fields. Pinnacle(3) (Version 6.2b) allows the user to specify a total minimum open area for each IMRT segment, which can result in sub-segments with widths of only a few millimetres. The dose for 6 MV narrow MLC defined fields between 0.1 and 3 cm in width was investigated using Kodak extended dose range film (EDR2), ionization chamber and MOSFET dosimeters and BEAMnrc Monte Carlo calculations, and these results were used to determine the accuracy of Pinnacle(3) dose calculation for narrow MLC segments. The incident fluences calculated by Pinnacle(3) and BEAMnrc were also compared. Results show that if a fluence and dose grid resolution of 0.1 cm is used, Pinnacle(3) dose agrees with the EDR2 and BEAMnrc to within 5% for field widths between 0.5 and 3.0 cm. However, Pinnacle(3) will underestimate the dose by up to 45% for the 0.1 and 0.3 cm wide fields. It is shown that the source size in the Pinnacle(3) beam model and both the fluence and dose grid resolutions have a significant effect on the accuracy of dose calculation for field widths of 1.0 cm and less. For single segment fields, Pinnacle(3) agrees with EDR2 and BEAMnrc to within 0.1 cm at the field edges and underestimates the penumbra width by up to 0.08 cm. Results for multiple segment fields showed that an MLC transmission of 1.7% and a 0.06 cm inward shift of MLCs prior to beam delivery gave the closest agreement between Pinnacle(3) and measurement. The multiple segment fields also revealed a pattern of low dose troughs of up to 7% in the Pinnacle(3) dose profiles.

Algorithms↗
PubMed2004

Validation of a noninvasive blood pressure monitoring device in normotensive and hypertensive pediatric intensive care patients.

OBJECTIVE: To evaluate the performance and to define limitations of a noninvasive blood pressure monitoring device in the critically ill pediatric population. METHOD: Patients were included in the study if they were admitted to the Pediatric Intensive Care Unit, were between the ages of 1 month and 18 years with wrist circumferences of > or =10 cm, and had an indwelling arterial line. Patients were excluded if their systolic blood pressure differed by > or =7.5% between their upper extremities. The measurements were collected simultaneously with those from an arterial line by a computer interfaced with the noninvasive blood pressure monitoring system and the patient's monitor. Heart rates were calculated from the recorded pulse waveforms of the arterial lines. Comparison analyses were performed via bias and precision plots of the blood pressure and heart rate data in addition to calculation of Pearson's correlation coefficients and concordance correlation coefficients. As a nonparametric method of comparison, the proportion of measurements that differed by greater than 10% was calculated. Results. Blood pressures and heart rates of 20 patients between the ages of 12 months and 17 years were monitored by a noninvasive blood pressure monitor for 30 min per patient. This data collection resulted in 2015 data points for each blood pressure and heart rate for comparison of methods. Concordance correlation coefficients were the following: systolic blood pressure, 0.93; diastolic blood pressure, 0.93; mean blood pressure, 0.94; and heart rate, 0.85. CONCLUSIONS: The noninvasive blood pressure monitor is capable of producing an accurate blood pressure measurement every 12-15 heartbeats in addition to providing a pulse waveform and digital display of the heart rate. Our study showed good agreement between the methods in the normotensive and hypertensive critically ill pediatric population with a wrist circumference limitation defined at > or =11 cm.

Adolescent↗
PubMed2003

SoFAR: software for fully automatic evaluation of real-time PCR data.

Quantitative real-time PCR has proven to be an extremely useful technique in life sciences for many applications. Although a lot of attention has been paid to the optimization of the assay conditions, the analysis of the data acquired is often done with software tools that do not make optimum use of the information provided by the data. Particularly, this is the case for high-throughput analysis, which requires a careful characterization and interpretation of the complete data by suitable software. Here we present a software solution for the robust, reliable, accurate, and fast evaluation of real-time PCR data, called SoFAR. The software automatically evaluates the data acquired with the LightCycler system. It applies new algorithms for an adaptive background correction of signal trends, the calculation of the effective signal noise, the automated identification of the exponential phases, the adaptive smoothing of the raw data, and the correction of melting curve data. Finally, it provides information regarding the validity of the results obtained. The SoFAR software minimizes the time required for evaluation and increases the accuracy and reliability of the results. The software is available upon request.

Algorithms↗
PubMed1998

Fast and accurate automated measurements in digitized stereophotogrammetric radiographs.

Until recently, Roentgen Stereophotogrammetric Analysis (RSA) required the manual definition of all markers using a high-resolution measurement table. To automate this tedious and time-consuming process and to eliminate observer variabilities, an analytical software package has been developed and validated for the detection, identification, and matching of markers in RSA radiographs. The digital analysis procedure consisted of the following steps: (1) the detection of markers using a variant of the Hough circle-finder technique; (2) the identification and labeling of the detected markers; (3) the reconstruction of the three-dimensional position of the bone markers and the prosthetic markers; and (4) the computation of micromotion. To assess the influence of film digitization, the measurements obtained from nine phantom radiographs using two different film scanners were compared with the results obtained by manual processing. All markers in the phantom radiographs were automatically detected and correctly labeled. The best results were obtained with a Vidar VXR-12 CCD scanner, for which the measurement errors were comparable to the errors associated with the manual approach. To assess the in vivo reproducibility, 30 patient radiographs were analyzed twice with the manual as well as with the automated procedure. Approximately, 85% of all calibration markers and bone markers were automatically detected and correctly matched. The calibration errors and the rigid-body errors show that the accuracy of the automated procedure is comparable to the accuracy of the manual procedure. The rigid-body errors had comparable mean values for both techniques: 0.05 mm for the tibia and 0.06 mm for the prosthesis. The reproducibility of the automated procedure showed to be slightly better than that of the manual procedure. The maximum errors in the computed translation and rotation of the tibial component were 0.11 mm and 0.24, compared to 0.13 mm and 0.27 for the manual RSA procedure. The total processing time is less than 10 min per radiograph, including interactive corrections, compared to approximately 1 h for the manual approach. In conclusion, a new and widely applicable, computer-assisted technique has become available to detect, identify, and match markers in RSA radiographs and to assess the micromotion of endoprostheses. This new technique will be used in our clinic for our hip, knee, and elbow studies.

Automation↗
PubMedDate not supplied

Biologically based validation of PC electrophysiology data collection systems utilizing the Good Automated Laboratory Practices.

Since there was a scientific need to conduct electrophysiology measurements to detect possible ocular (electroretinography, ERG), central neurotoxic (quantitative electroencephalography, qEEG), and cardiac (electrocardiography, ECG) effects in animals used in certain regulatory studies, the acquisition of suitable automated PC software systems were required. This article describes the process by which these systems were validated to ensure that they met the scientific requirements, while also addressing the principles of Good Automated Laboratory Practices (GALP). After a thorough search of existing commercial packages, a plan was developed specific for each PC-based collection system selected for evaluation. The common elements of each plan included consideration of both scientific and GALP elements, such as necessary biological response variables, raw data acquisition and identification, acceptance criteria, security, protection, storage media, data integrity, audit requirements and standard operating procedures. The authors' approach to validation for each electrophysiology system was to determine scientific needs for accuracy, precision, and detection limit of biological effects concurrent with GALP requirements. The selected software systems were employed in separate scientific GLP studies conducted in dogs, rats, and mini-pigs to demonstrate the ability to detect cholinesterase effects due to multiple infusions of physostigmine, based on parallel measurement of cholinesterase biomarkers. Since the systems were designed for human usage, certain adaptations were necessary. A critical assumption to be tested was the ability of the system's algorithms to adequately capture and assimilate the data in an accurate fashion. Concomitantly, the related GALP needs, such as data integrity, security, CD-ROM archive, and personnel training requirements were evaluated, implemented, and defined to accommodate the application and process needs. The biological approach to validation of these PC-based electrophysiology systems met the necessary scientific acceptance criteria as well as compliance requirements in order to be used in regulatory studies.

Algorithms↗
PubMed2002

Determination of drug concentrations in plasma by a highly automated, generic and flexible protein precipitation and liquid chromatography/tandem mass spectrometry method applicable to the drug discovery environment.

This report presents a highly automated procedure for the determination of drug concentrations in plasma samples. The method is generic, in that it has been applied without adaptation to many different drug candidate molecules, but is also flexible, in that variations in the nature and number of samples to be analyzed can be readily accommodated. The method includes preparation of dilutions of analyte stock solutions, spiking these into control plasma to generate analytical standards, and preparation of samples suitable for analysis by high-performance liquid chromatography/tandem mass spectrometry (HPLC/MS/MS) by precipitation of plasma proteins with acetonitrile, centrifugation, and dilution of the supernatants with HPLC buffer. All of these steps, apart from centrifugation, are performed without manual intervention on an automated liquid-handling workstation using 96-well plates. Analysis is by HPLC/MS/MS, using a generic HPLC gradient. Commercially available software was used for optimization of parameters for analysis by HPLC/MS/MS, integration of chromatographic peaks, and quantification of drug concentrations. The use of this methodology in our laboratory has greatly facilitated the analysis of small sample sets for a large number of analytes, a situation regularly encountered in an early drug discovery environment.

Blood Proteins↗
PubMed1992

An electronic medical record system with direct data-entry and research capabilities.

The transfer of medical records from a paper system to a computer-based system is inevitable. However, the widespread acceptance of electronic medical records has been delayed by problems such as high cost, inefficiency, data entry errors and poor physician acceptance. We have developed a database system that has overcome these difficulties and now serves as an electronic medical record. Our system has been in use for a year and a half, and currently contains information on over two thousand patients. The database provides an electronic radiation oncology chart containing patients' demographic information, technical treatment data and dictated reports. All dictated notes are captured, including consultation notes, treatment summaries, on-treatment visits, letters and follow up reports. The system provides data validation upon entry, required few additional software or hardware purchases, and allows for efficient retrieval of data. Unlike other database systems which require the hiring of data entry clerks to input the data, ours combines transcription and data entry. The database runs on a local area network of computers and uses a commercially available relational database package. It makes extensive use of mouse interface features such as pull-down menus, pop-up lists, buttons, multi-page forms, and scrolling fields, making the system easy to use with minimal training. Many custom features are built in, such as help screens, control functions, audit trails, and a system that keeps track of each patient's referring and other relevant physicians. For research purposes, the system has the capability to perform survival analyses on arbitrary user-defined subsets of patients. Data may also be exported transparently to statistical packages for other types of analyses.

Data Display↗
PubMed2005

Micropillar array chip for integrated white blood cell isolation and PCR.

We report the fabrication of silicon chips containing a row of 667 pillars, 10 by 20 microm in cross-section, etched to a depth of 80 microm with adjacent pillars being separated by 3.5 microm. The chips were used to separate white blood cells from whole blood in less than 2 min and for subsequent PCR of a genomic target (eNOS). Chip fluid dynamics were validated experimentally using CoventorWare microfluidic simulation software. The amplicon concentrations were determined using microchip capillary electrophoresis and were >40% of that observed in conventional PCR tubes for chips with and without pillars. Reproducible on-chip PCR was achieved using white blood cell preparations isolated from whole human blood pumped through the chip.

Cell Separation↗
PubMed2005

A new retrieval system for a database of 3D facial images.

A new retrieval system for a 3D facial image database was designed and its reliability was experimentally examined. This system has two steps, firstly to automatically adjust the orientation of all 3D facial images in a database to that of the 2D facial image of a target person, and then to identify the facial image of the target person from the adjusted 3D facial images in the database using a graph-matching method. From the experimental study [M. Yoshino, K. Imaizumi, T. Tanijiri, J.G. Clement, Automatic adjustment of facial orientation in 3D face image database, Jpn. J. Sci. Tech. Iden. 8 (2003) 41-47], it is concluded that the software developed for the first step will be applicable to the automatic adjustment of facial orientation in the 3D facial image database. In 28 out of 110 sets (25.5%), the 3D image of the target person was chosen as the best match (from a database of 132 3D facial images) according to the similarity of the facial image characteristics based on the graph matching. The 3D facial image of the target person was ranked in the top of 10 of the database in 75 out of 110 sets (68.2%). These results suggest that this system is inadequate for the identification level, but may be feasible for screening method in a small database. It will be necessary to further pursue the possibility of realization of a facial image retrieval system for a large database such as suspects' facial images in future.

Adult↗
PubMed2005

The detection of neurocognitive decline in schizophrenia using the Mindstreams Computerized Cognitive Test Battery.

BACKGROUND: The Mindstreams Computerized Cognitive Test Battery (Mindstreams) is a standardized computer-based battery that was designed for widespread clinical and research use. The capability of Mindstreams to test cognitive impairment in schizophrenia has yet to be evaluated. The aim of the present study was to determine the ability of Mindstreams in detecting cognitive dysfunction in schizophrenia patients and to compare it to the Cambridge Neuropsychological Test Automated Battery (CANTAB). METHOD: Fifty-five schizophrenia patients and 63 healthy subjects were enrolled in the study. The Positive and Negative Syndrome Scale (PANSS) was used to quantify symptom severity. Neurocognitive functions were assessed using Mindstreams and CANTAB. RESULTS: The schizophrenia patients scored significantly more poorly than healthy subjects on all tests comprising the Mindstreams battery. Comparable tasks of the Mindstreams and CANTAB batteries significantly correlated on raw scores and the standardized cognitive indices. The Mindstreams executive function tasks had significant correlations with the PANSS negative, autistic preoccupation and activation cluster scores, and with global functioning. Two-week test-retest reliability correlations were all significant (N=17, p<0.05-p<0.001). CONCLUSIONS: This study indicates that Mindstreams is reliable in assessing the cognitive function of patients with schizophrenia and may play a role in standardizing the cognitive assessment of these patients in clinical and research settings.

Adolescent↗
PubMed2002

RESP-24: a computer program for the investigation of 24-h breathing abnormalities in heart failure patients.

In this paper, we describe a computer program (RESP-24) specifically devised to assess the prevalence and characteristics of breathing disorders in ambulant chronic heart failure patients during the overall 24 h period. The system works on a single channel respiratory signal (RS) recorded through a Holter-like portable device. In the pre-processing stage RESP-24 removes noise, baseline drift and motion artefacts from the RS using a non-linear filter, enhances respiratory frequency components through high-pass filtering and derives an instantaneous tidal volume (ITV) signal. The core processing is devoted to the identification and classification of the breathing pattern into periodic breathing (PB), normal breathing or non-classifiable breathing using a 60 s segmentation, and to the identification and estimation of apnea and hypopnea events. Sustained episodes of PB are detected by cross analysis of both the spectral content and time behavior of the ITV signal. User-friendly interactive facilities allow all the results of the automatic analysis procedure to be edited. The final report provides a set of standard and non-standard parameters quantifying breathing abnormalities during the 24 h period, the night-time and the day-time, including the apnea/hypopnea index, the apnea index, the total time spent in apnea or in hypopnea and the prevalence of non-apneic and apneic PB. The accuracy of these measurements was appraised on a data set of 14 recordings, by comparing them with those provided by a trained analyst. The mean and standard deviation of the error of the automatic procedure were below respectively 6 and 8% of the reference value for all parameters considered and the mean total classification accuracy was 92%. In most cases, the individual error was <12%. We conclude that measurements provided automatically by the RESP-24 software are suitable for screening purposes and clinical trials, although a preventive check of signal quality should be recommended.

Apnea↗
PubMed2003

A review of data on spreading and vaporisation of cryogenic liquid spills.

This review summarises the availability and utility of experimental data on the rates of spread and vaporisation of spillages of pressure liquefied and cryogenic liquids on a variety of surfaces including: soil; sand; concrete; and water. It is intended that the paper acts as a review of those sources of information that can be used to allow the validation of current and future computer software which is to be used to predict the likely effects of such spillages, and also to extend the range of materials to which it may be applied. The majority of investigations found cover LNG or LPG, due to their widespread bulk usage, with others studying liquid nitrogen, oxygen, hydrogen, or ammonia.

Ammonia↗
PubMedDate not supplied

On the use of neural network ensembles in QSAR and QSPR.

Despite their growing popularity among neural network practitioners, ensemble methods have not been widely adopted in structure-activity and structure-property correlation. Neural networks are inherently unstable, in that small changes in the training set and/or training parameters can lead to large changes in their generalization performance. Recent research has shown that by capitalizing on the diversity of the individual models, ensemble techniques can minimize uncertainty and produce more stable and accurate predictors. In this work, we present a critical assessment of the most common ensemble technique known as bootstrap aggregation, or bagging, as applied to QSAR and QSPR. Although aggregation does offer definitive advantages, we demonstrate that bagging may not be the best possible choice and that simpler techniques such as retraining with the full sample can often produce superior results. These findings are rationalized using Krogh and Vedelsby's decomposition of the generalization error into a term that measures the average generalization performance of the individual networks and a term that measures the diversity among them. For networks that are designed to resist over-fitting, the benefits of aggregation are clear but not overwhelming.

Computer Simulation↗
PubMed2005

Pharmacophore modeling, docking, and principal component analysis based clustering: combined computer-assisted approaches to identify new inhibitors of the human rhinovirus coat protein.

The development and application of a sophisticated virtual screening and selection protocol to identify potential, novel inhibitors of the human rhinovirus coat protein employing various computer-assisted strategies are described. A large commercially available database of compounds was screened using a highly selective, structure-based pharmacophore model generated with the program Catalyst. A docking study and a principal component analysis were carried out within the software package Cerius and served to validate and further refine the obtained results. These combined efforts led to the selection of six candidate structures, for which in vitro anti-rhinoviral activity could be shown in a biological assay.

Antiviral Agents↗
PubMed2001

Developing a Bayesian belief network for the management of geriatric hospital care.

Resource management is an essential feature of hospital management. This is especially true for geriatric services, as older people often have complex medical and social needs. Hospital management should benefit from an explanatory model that provides predictions of duration of stay and destination on discharge. We describe how a Bayesian belief network models the behaviour of geriatric patients using predictive variables: personal details, admission reasons and dependency levels. This approach is illustrated using data on 4,722 patients admitted to geriatric medicine at St. George's Hospital, London; distributions of the patient outcome given typical values of the predictive variables are provided.

Aged↗