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PubMed2004

Impact of descriptor vector scaling on the classification of drugs and nondrugs with artificial neural networks.

The influence of preprocessing of molecular descriptor vectors for solving classification tasks was analyzed for drug/nondrug classification by artificial neural networks. Molecular properties were used to form descriptor vectors. Two types of neural networks were used, supervised multilayer neural nets trained with the back-propagation algorithm, and unsupervised self-organizing maps (Kohonen maps). Data were preprocessed by logistic scaling and histogram equalization. For both types of neural networks, the preprocessing step significantly improved classification compared to nonstandardized data. Classification accuracy was measured as prediction mean square error and Matthews correlation coefficient in the case of supervised learning, and quantization error in the case of unsupervised learning. The results demonstrate that appropriate data preprocessing is an essential step in solving classification tasks.

Algorithms↗

PubMedDate not supplied

Quantitative evaluation of a dual energy CT system.

We have evaluated the accuracy of CT numbers produced by a prototype dual energy system. Solutions of known composition were scanned in simple cylindrical phantoms and the observed CT values in synthetic monochromatic images were compared with the expected values computed from published cross-section data. Although accuracy varied with both the composition of the solution and the energy selected for the synthetic monoenergetic image, for the solutions used the inaccuracy was less than the uncertainty of the photon cross-section data at 80 and 100 keV. Virtually no cupping artifact was present in the monoenergetic images.

Evaluation Studies as Topic↗

PubMed1991

Effect of ionizing radiation dose, temperature, and atmosphere on the survival of Salmonella typhimurium in sterile, mechanically deboned chicken meat.

The response to gamma radiation (0 to 3.60 kGy; 100 krad = 1 kGy) of Salmonella typhimurium was tested in otherwise sterile, mechanically deboned chicken meat (MDCM) in the absence of competing microflora. Response was determined at temperatures of -20 to +20 C and when the MDCM was packaged in vacuum or in the presence of air. A central composite response-surface design was used to test the response of the pathogen to the treatments in a single experiment. Predictive equations were developed from the analyses of variances of the resulting data. The accuracy of each predictive equation was tested by further studies of the effects of gamma radiation on S. typhimurium in the presence or absence of air at -20, 0, and +20 C. All data were then analyzed to refine the predictive equations further. Both the original and the refined equations adequately predicted the response of S. typhimurium in MDCM to gamma radiation doses up to 3.60 kGy in the presence of air or in vacuo. Gamma irradiation was significantly more lethal for S. typhimurium in the presence of air and at higher temperatures. The final equations predict a reduction in the number of surviving Salmonella in MDCM irradiated to 1.50 kGy at -20 C of 2.53 logs in air or 2.12 logs if irradiated in vacuum. If the contaminated MDCM were to receive a dose of 3.0 kGy at -20 C in air, the number of Salmonella would be decreased by 4.78 logs, and if irradiated in vacuum, by 4.29 logs.(ABSTRACT TRUNCATED AT 250 WORDS)

Air↗

PubMed1978

Statistical analysis of measurement errors of binding data in the Farr technique.

A detailed statistical analysis of measurement errors in the Farr technique is performed, and approximated formulas for the error covariances are given. These formulas are then checked by means of experimental data. In particular, the analysis shows that the usually adopted linear extrapolation for the estimate of total antibody sites concentration may lead to relevant errors in the affinity distribution determination due to the low accuracy of data at high values of free hapten concentration. Conversely, this analysis may constitute the basis for implementing an optimal estimate procedure.

Animals↗

PubMed1983

A method for the calculation of renal clearance based on a single plasma sample.

A formula has been derived for the calculation of renal clearance with the use of a single plasma sample. The formula is based on a one-compartment model. A small correction for non-immediate mixing and non-uniform distribution of the tracer was calculated from empirical data. The accuracy in the calculation method depends on how exactly the distribution volume is known and at what time the blood sample is taken. The expected standard deviation in the clearance value was calculated from data of mean value and spread for the distribution volume of 99Tcm-DTPA. In an investigation of 39 subjects with 99Tcm-DTPA, a standard deviation of 5 to 6 ml/min was obtained in comparison with a standard method for clearance calculation. This value is in good agreement with the expected one.

Humans↗

PubMed2005

Systematic errors in the measurement of adsorption isotherms by frontal analysis Impact of the choice of column hold-up volume, range and density of the data points.

Besides the accuracy and the precision of the measurements of the data points, several important parameters affect the accuracy of the adsorption isotherms that are derived from the data acquired by frontal analysis (FA). The influence of these parameters is discussed. First, the effects of the width of the concentration range within which the adsorption data are measured and of the distribution of the data points in this range are investigated. Systematic elimination of parts of the data points before the calculation of the nonlinear regression of the data to the model illustrates the importance of the numbers of data points (1) within the linear range and (2) at high concentrations. The influence of the inaccuracy of the estimate of the column hold-up volume on each adsorption data point, on the selection of the isotherm model, and on the best estimates of the adsorption isotherm parameters is also stressed. Depending on the method used to measure it, the hold-up time can vary by more than 10%. The high concentration part of the adsorption isotherm is particularly sensitive to errors made on t(0,exp) and as a result, when the isotherm follows bi-Langmuir isotherm behavior, the equilibrium constant of the low-energy sites may change by a factor 2. This study shows that the agreement between calculated and experimental overloaded band profiles is a necessary condition to validate the choice of an adsorption model and the calculation of its numerical parameters but that this condition is not sufficient.

Adsorption↗

PubMed1998

Vein graft surveillance: is graft revision without angiography justified and what criteria should be used?

PURPOSE: The objective of this study was to assess the accuracy of color-flow duplex surveillance parameters to detect infrainguinal vein graft stenoses and to investigate whether graft revision without angiography is justified. METHODS: In a prospective study in which three centers participated, the data of graft surveillance in 300 patients were analyzed. For the evaluation of surveillance criteria all patients underwent a digital subtraction angiography if a graft stenosis was suspected. To create a control group, in patients with normal grafts a consented digital subtraction angiography was performed also. From these data the accuracy of seven duplex and three ankle blood pressure-derived variables was assessed. The relation between various surveillance criteria and continued graft patency was determined with life table analysis with the transient state method. RESULTS: The mean follow-up period was 20 months (range, 1 to 40 months). At univariate and multivariate analysis the peak systolic velocity (PSV) ratio provided the best correlation with angiographic stenoses > or = 70% (PSV ratio cutoff 3.0: sensitivity 80%, specificity 84%). This finding did not differ between the participating centers. With life table methods it was demonstrated that the best combination of efficacy (limitation of the number of unnecessary revisions), safety (minimal number of correctable lesions missed), and reduction of angiograms was obtained by a two-parameter surveillance algorithm. This algorithm included a PSV ratio < 2.5 to delineate patients in whom a conservative approach without angiography or revision was appropriate, a PSV ratio > or = 4.0 to indicate patients in whom vein graft revision without angiography could be scheduled, and a group with PSV ratios between 2.5 and 4.0 in whom angiography was to be performed to determine clinical management on the basis of the stenosis severity. This algorithm had a positive predictive value of 93% and a negative predictive value of 89%. In addition, it resulted in a reduction of the number of angiograms of 49% compared with a policy of angiographies in all patients with a PSV ratio > or = 2.5. CONCLUSIONS: The best criterion to identify a failing graft is the PSV ratio. With a two-parameter algorithm for vein graft surveillance, the incidence of unnecessary revisions and of missed high-grade lesions was acceptably low, whereas the number of angiograms was reduced by one half.

Adult↗

PubMed2004

Mechanisms and dynamics of the metastable decay in Ar2+.

A detailed experimental as well as theoretical investigation of the properties of the metastable dissociation Ar2+ --> Ar+ + Ar is presented. The mass-analyzed ion kinetic energy (MIKE) scan technique has been performed using a three sector field mass spectrometer. The possible mechanisms of the metastability of Ar2+ have been examined and the observed decay process is assigned to the II(1/2)(u)-->I(1/2)(g) bound to continuum radiative transition, in agreement with earlier work. The calculation of the theoretical shape of the kinetic energy release distribution of fragment ions allowed us to construct the theoretical MIKE peak and compare it with the raw experimental data. The accuracy of various sets of potential energy curves for Ar2+ is discussed, as well as the way of production of the metastable Ar2+[II(1/2)(u)] electronic state by electron impact. Excellent agreement between the experimental data and theoretical model has been observed.

Journal Article↗

PubMed1998

Evaluation of chemotherapy in advanced urinary bladder cancer with fast dynamic contrast-enhanced MR imaging.

PURPOSE: To evaluate if the failure of chemotherapy in patients with advanced urinary bladder cancer can be predicted early in the course of chemotherapy with fast dynamic contrast material-enhanced magnetic resonance (MR) imaging. MATERIALS AND METHODS: In this prospective study, 22 consecutive patients with histologically proved advanced urinary bladder cancer underwent MR imaging before and after two, four, and six cycles of chemotherapy with methotrexate, vinblastine, adriamycin, and cisplatin (MVAC). The response after two chemotherapy cycles was evaluated by using conventional tumor size parameters at unenhanced MR imaging and with changes in the time to the start of tumor or lymph node enhancement at fast dynamic contrast-enhanced MR imaging. The results obtained with these techniques were compared with the findings at histopathology in cystectomy (n = 9) or multiple transurethral resection (n = 13) specimens obtained after completion of chemotherapy. RESULTS: After two MVAC cycles, the accuracy, sensitivity, and specificity in distinguishing responders from nonresponders with conventional MR imaging were 73%, 79%, and 63%, respectively. With the dynamic technique, these were 95%, 93%, and 100%, respectively. Although the differences between these values are not significant (P = .48 for sensitivity, .25 for specificity, and .07 for accuracy), the data indicate that dynamic enhanced MR imaging performed better than unenhanced MR imaging. Dynamic imaging yielded correct results after two MVAC cycles in 21 cases, and in all cases after four cycles. After four MVAC cycles, the accuracy of dynamic MR imaging was significantly better (P < .05). Persisting early enhancement after four MVAC cycles correctly corresponded with lack of response in all nine cases, and after two cycles in eight of these cases. The unenhanced MR technique showed initial tumor size reduction in three of these cases. CONCLUSION: Conventional and dynamic enhanced MR imaging were used to evaluate chemotherapy after two, four, and six cycles of MVAC in 22 patients with bladder cancer. After two cycles, dynamic MR imaging helped detect 13 of 14 responders and eight of eight nonresponders. It helped detect five of seven lymph node responders and two of two nonresponders. Thus, it may be possible to predict after two MVAC cycles whether a patient will respond to chemotherapy.

Adult↗

PubMedDate not supplied

Liquid chromatography/electrospray ionization/isotopic dilution mass spectrometry analysis of n-(phosphonomethyl) glycine and mass spectrometry analysis of aminomethyl phosphonic acid in environmental water and vegetation matrixes.

A liquid chromatography/electrospray/mass spectrometry (LC/ES/MS) method was developed for the analysis of glyphosate (n-phosphonomethyl glycine) and its metabolite, aminomethyl phosphonic acid (AMPA) using isotope-labelled glyphosate as a method surrogate. Optimized parameters were achieved to derivatize glyphosate and AMPA using 9-fluorenylmethyl chloroformate (FMOC-Cl) in borate buffer prior to a reversed-phase LC analysis. Method spike recovery data obtained using laboratory and real world sample matrixes indicated an excellent correlation between the recovery of the native and isotope-labelled glyphosate. Hence, the first performance-based, isotope dilution MS method with superior precision, accuracy, and data quality was developed for the analysis of glyphosate. There was, however, no observable correlation between the isotope-labelled glyphosate and AMPA. Thus, the use of this procedure for the accurate analysis of AMPA was not supported. Method detection limits established using standard U.S. Environmental Protection Agency protocol were 0.06 and 0.30 microg/L, respectively, for glyphosate and AMPA in water matrixes and 0.11 and 0.53 microg/g, respectively, in vegetation matrixes. Problems, solutions, and the method performance data related to the analysis of chlorine-treated drinking water samples are discussed. Applying this method to other environmental matrixes, e.g., soil, with minimum modifications is possible, assuring accurate, multimedia studies of glyphosate concentration in the environment and the delivery of useful multimedia information for regulatory applications.

Chromatography, Liquid↗

PubMed2003

Programmed database system at the Chang Gung Craniofacial Center: part I.

BACKGROUND: A database is a system for the management of information. Databases of different forms are widely used in everyday life from telephone books to online library catalogs. The Craniofacial Center at Chang Gung Memorial Hospital has seen over 20,000 patients during the past 20 years. All of the patient records need to digitally input into a computer database. METHODS: A database was custom designed using Paradox 8. The ACDSee Photo browser and DOS linked them to the original program. The Paradox 8 was programmed to a standard mode for the diagnosis and treatment data input to prevent typographical errors. RESULTS: We collected the records of 25,200 patients from 1987 to 2002, of which 24,331 underwent operations. The data for 14,828 patients were registered as complete and/or incomplete cleft and the proportions of unilateral to bilateral and female to male are presented in Table 1. CONCLUSION: This new database system was designed to ensure the accuracy of data input using a standard model that is capable of correct data programming using the custom designed coding system for the Craniofacial Center. The system also provides easy and reliable data retrieval when using the powerful search tools.

Cleft Lip↗

PubMed2003

[Glaucoma Service Database].

We present the common problems related to clinical databases. The Glaucoma Service Database created in our clinic is an attempt of developing the optimal medical database. The system organizes our repository of clinical data. It consist of 3 modules: 1) the users list with predefined privileges and rights, 2) lists of coded data for further use, that facilitate filling in the fields, 3) clinical details of all patients. The user interface of our database is very simply, thus it is very easy to use it even by unskilled staff. The accuracy of data is protected by system's internal algorithms. It could be used to investigate clinical epidemiology, risk assessment, post-marketing surveillance of drugs, practice variation and decision analysis. Data from Glaucoma Service Database can also help in the management of health service.

Databases, Factual↗

PubMed2005

Prediction of mitochondrial proteins using support vector machine and hidden Markov model.

Mitochondria are considered as one of the core organelles of eukaryotic cells hence prediction of mitochondrial proteins is one of the major challenges in the field of genome annotation. This study describes a method, MitPred, developed for predicting mitochondrial proteins with high accuracy. The data set used in this study was obtained from Guda, C., Fahy, E. & Subramaniam, S. (2004) Bioinformatics 20, 1785-1794. First support vector machine-based modules/methods were developed using amino acid and dipeptide composition of proteins and achieved accuracy of 78.37 and 79.38%, respectively. The accuracy of prediction further improved to 83.74% when split amino acid composition (25 N-terminal, 25 C-terminal, and remaining residues) of proteins was used. Then BLAST search and support vector machine-based method were combined to get 88.22% accuracy. Finally we developed a hybrid approach that combined hidden Markov model profiles of domains (exclusively found in mitochondrial proteins) and the support vector machine-based method. We were able to predict mitochondrial protein with 100% specificity at a 56.36% sensitivity rate and with 80.50% specificity at 98.95% sensitivity. The method estimated 9.01, 6.35, 4.84, 3.95, and 4.25% of proteins as mitochondrial in Saccharomyces cerevisiae, Drosophila melanogaster, Caenorhabditis elegans, mouse, and human proteomes, respectively. MitPred was developed on the above hybrid approach.

Algorithms↗

PubMed1991

A summary measure of client level of functioning: progress and challenges for use within mental health agencies.

A summary measure of clients' level of functioning could assist mental health agencies to better document and evaluate their services. Currently, numerous state mental health authorities collect a level of functioning measure within a management information system on virtually all clients served with state resources. The uses of these data include describing the clientele, defining a priority population for services, preparing performance indicators and measuring contract obligations. However, clearer delineation of the construct of functioning, further exploration of the psychometric properties of the instruments and stricter procedures to ensure the accuracy of data would result in data that are more useful for both management and research.

Data Collection↗

PubMed2004

QA/QC: challenges and pitfalls facing the microarray community and regulatory agencies.

The scientific community has been enthusiastic about DNA microarray technology for pharmacogenomic and toxicogenomic studies in the hope of advancing personalized medicine and drug development. The US Food and Drug Administration has been proactive in promoting the use of pharmacogenomic data in drug development and has issued a draft guidance for the pharmaceutical industry on data submissions. However, many challenges and pitfalls are facing the microarray community and regulatory agencies before microarray data can be reliably applied to support regulatory decision making. Four types of factors (i.e., technical, instrumental, computational and interpretative) affect the outcome of a microarray study, and a major concern about microarray studies has been the lack of reproducibility and accuracy. Intralaboratory data consistency is the foundation of reliable knowledge extraction and meaningful crosslaboratory or crossplatform comparisons; unfortunately, it has not been seriously evaluated and demonstrated in every study. Profound problems in data quality have been observed from analyzing published data sets, and many laboratories have been struggling with technical troubleshooting rather than generating reliable data of scientific significance. The microarray community and regulatory agencies must work together to establish a set of consensus quality assurance and quality control criteria for assessing and ensuring data quality, to identify critical factors affecting data quality, and to optimize and standardize microarray procedures so that biologic interpretation and decision-making are not based on unreliable data. These fundamental issues must be adequately addressed before microarray technology can be transformed from a research tool to clinical practices.

Drug Approval↗

PubMed1995

Precision of marker heterozygosity estimates.

Sample sizes may greatly affect the accuracy of estimates of marker heterozygosities. Therefore, indicating the precision of these estimates is strongly recommended. A computer program HETMAX was written and used to obtain unbiased estimates of heterozygosity, their standard errors and unit support intervals, based on a subset of GAW9 data. The accuracy of the estimates and the associated sample sizes are presented.

Chromosome Mapping↗

PubMed2006

Assessing nonlinearity in compartment models via the relative curvature measure.

In pharmacokinetics, compartment models often play an important role in the description of the concentration of the drug in the blood over time after its administration to an individual. Statistical inference in these models can be conducted based on a linear approximation with respect to the parameter related to pharmacokinetic indices, in the same way that the usual nonlinear regression models are dealt with. Therefore, it is necessary to assess the degree of nonlinearity in a compartment model and to evaluate its effect on the linear approximation. The relative curvature measure that enables us to assess the intrinsic and parameter-effects (PE) nonlinearity can be used, but in practice it has not been applied to compartment models in pharmacokinetics. One reason may be that the relative curvature measure cannot be directly applied to blood drug concentration data that exhibit heteroscedasticity. Therefore, the relative curvature measure including the heteroscedastic variance function was utilized to assess the nonlinearity in the compartment models, and in particular, the influences of some of the reparameterizations that are empirically used in fitting the compartment models were examined. Several examples showed that the reparameterized compartment model had less PE nonlinearity than the original compartment model, but that several reparameterizations could increase the PE nonlinearity. In addition, by means of a simulation experiment with heteroscedastic blood drug concentration data, the accuracy, and precision of the relative curvature measure with the heteroscedastic variance function were evaluated and compared with those of the original relative curvature measure. The results showed that the relative curvature measure with the variance function was not affected by heteroscedastic blood drug concentration data and could be utilized for the assessment of the nonlinearity in compartment models.

Anti-Inflammatory Agents, Non-Steroidal↗

PubMedDate not supplied

Six-hour and four-hour nocturnal sampling for growth hormone.

UNLABELLED: Overnight sampling for growth hormone (GH) is a research tool for quantifying characteristics of spontaneous GH secretion. However, the study is costly in assays and blood volume, particularly that required from a small child. DESIGN AND PATIENTS: Existing overnight GH data from 126 normal children and from 227 children with GH deficiency or short stature were reanalyzed, examining 6-h and 4-h segments of this data for accuracy in representing each child's 12-h GH secretion. The goal was to see whether the test could be made shorter and more practical without losing accuracy. RESULTS: The 6-h segment 2200-0400 h consistently contained the majority of GH peaks. Correlation was high between GH values from 2200-0400 h and from the 12-h period. Normal 95% confidence limits (CL) for GH during 2200-0400 h were derived from data in normal children for gender and each pubertal stage. Data from short children were compared with the normal 6-h 95% CL. In short children, GH values low for 12-h were also low for 6-h. Only a few children with normal 12-h values (1.5% of normals, 0.5% with short stature) had GH values outside 95% CL for 6-h. CONCLUSIONS: Six-hour GH sampling (2200-0400 h) is accurate and cost-efficient compared to the 12-h overnight GH study. These studies are primarily useful in research settings.

Adolescent↗