Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Software Validation”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,351 records · Page 75Linked to original sources
PubMed2006

PLASQ: a generalized linear model-based procedure to determine allelic dosage in cancer cells from SNP array data.

Human cancer is largely driven by the acquisition of mutations. One class of such mutations is copy number polymorphisms, comprised of deviations from the normal diploid two copies of each autosomal chromosome per cell. We describe a probe-level allele-specific quantitation (PLASQ) procedure to determine copy number contributions from each of the parental chromosomes in cancer cells from single-nucleotide polymorphism (SNP) microarray data. Our approach is based upon a generalized linear model that takes advantage of a novel classification of probes on the array. As a result of this classification, we are able to fit the model to the data using an expectation-maximization algorithm designed for the purpose. We demonstrate a strong model fit to data from a variety of cell types. In normal diploid samples, PLASQ is able to genotype with very high accuracy. Moreover, we are able to provide a generalized genotype in cancer samples (e.g. CCCCT at an amplified SNP). Our approach is illustrated on a variety of lung cancer cell lines and tumors, and a number of events are validated by independent computational and experimental means. An R software package containing the methods is freely available.

Algorithms↗
PubMed1999

Gastroesophageal reflux and respiratory phenomena in infants: status of the intraluminal impedance technique.

BACKGROUND: The coincidence of recurrent respiratory symptoms and gastroesophageal reflux (GER) is a well-known phenomenon in infants. Twenty-four-hour pH metry is the presumed gold standard of diagnostic tools for this symptom complex, but with this method, only acid (pH <4) and alkaline (pH >7) GER can be detected. Gastroesophageal reflux with an esophageal pH in the physiological range (pH 5-6.8) may represent many cases of clinically relevant GER unrecognized by pH metry. In this study the intraluminal multiple electrical impedance (IMP) procedure for complete registration of GER was compared with pH metry for its diagnostic value in the presence of respiratory symptoms. METHODS: Twenty-two infants with recurrent regurgitation or pulmonary problems were investigated simultaneously with IMP, pH metry, and polygraphy during two feeding periods. Heart rate, oxygen saturation, sleep states, and oronasal flow were recorded, among other parameters. RESULTS: Three hundred sixty-four occurrences of GER were detected by IMP; only 11.4% had a pH less than 4 and were therefore recognized by pH metry. Three hundred twelve (84.8%) occurrences were associated with breathing abnormalities, and 11.9% of these were detected by pH metry. Nineteen instances were accompanied by a decrease of oxygen saturation of more than 10% of the initial value. Only three (15.8%) of these had a pH less than 4. The remaining 16 reflux episodes were recognized by IMP only. After software-aided preselection, 165 instances of apnea were visually validated, 49 of which were accompanied by GER. Thirty-eight (77.6%) of these were exclusively recorded by IMP. CONCLUSIONS: The use of pH metry alone cannot detect most GER incidents accompanied by respiratory symptoms and therefore does not appear to be suitable for this approach. The pH-independent IMP technique promises to be a reliable tool for presumably GER-associated respiratory symptoms.

Electric Impedance↗
PubMed2005

Dual-energy X-ray absorptiometry and body composition.

PURPOSE OF REVIEW: Dual-energy X-ray absorptiometry is now widely adopted for the measurement of the fat, fat-free soft tissue and bone mineral compartments of the body. Whereas it is regarded by many as a reference technique for such measurements, it is not without limitations. Inter and intra-manufacturer differences have been areas of concern. This review focuses on recent literature addressing these areas and the issue of validity. RECENT FINDINGS: Body composition measurements using newer generation dual-energy X-ray absorptiometry machines compared between different manufacturers and compared with earlier instruments continue to show differences that may be unacceptable, particularly for investigators upgrading their machines or involved in multicentre studies using different machines. In terms of validity, significant deviations at a group level are reported when compared with reference four-component models, and perhaps more importantly, wide limits of agreement are seen that are a concern for the interpretation of results at an individual level. SUMMARY: It is important that investigators recognize the limitations of dual-energy X-ray absorptiometry technology in the interpretation of their results. There is a continuing need both for inter-machine comparisons and validation studies against accepted criterion methods, particularly as new software or technological changes are introduced. Such studies permit the development of translation equations for the cross-calibration of devices, and may be vital for cross-sectional studies. For longitudinal studies in many populations, dual-energy X-ray absorptiometry is without question a valuable technique for the measurement of compositional changes, both at the total body and regional levels.

Absorptiometry, Photon↗
PubMed2004

AMON: a wearable multiparameter medical monitoring and alert system.

This paper describes an advanced care and alert portable telemedical monitor (AMON), a wearable medical monitoring and alert system targeting high-risk cardiac/respiratory patients. The system includes continuous collection and evaluation of multiple vital signs, intelligent multiparameter medical emergency detection, and a cellular connection to a medical center. By integrating the whole system in an unobtrusive, wrist-worn enclosure and applying aggressive low-power design techniques, continuous long-term monitoring can be performed without interfering with the patients' everyday activities and without restricting their mobility. In the first two and a half years of this EU IST sponsored project, the AMON consortium has designed, implemented, and tested the described wrist-worn device, a communication link, and a comprehensive medical center software package. The performance of the system has been validated by a medical study with a set of 33 subjects. The paper describes the main concepts behind the AMON system and presents details of the individual subsystems and solutions as well as the results of the medical validation.

Activities of Daily Living↗
PubMed2006

The APL test: extension to general nuclear families and haplotypes and examination of its robustness.

OBJECTIVE: The Association in the Presence of Linkage test (APL) is a powerful statistical method that allows for missing parental genotypes in nuclear families. However, in its original form, the statistic does not easily extend to mixed nuclear family structures nor to multiple-marker haplotypes. Furthermore, the robustness of APL in practice has not been examined. Here we present a generalization of the APL model and examination of its robustness under a variety of non-standard scenarios. METHODS: The generalization is made possible by incorporating a bootstrap variance estimator instead of the original robust variance estimator. This allows for use of more than two affected siblings. Haplotype analysis was accomplished by combining estimation of haplotype phase into the EM algorithm. Computer simulation was used to examine robustness of the APL to departures from test assumptions. RESULTS: The extended APL tests both single-marker and multiple-marker haplotypes and shows more power than other association methods. Simulation results showed that the single-marker APL test is robust to the departure from HWE. For the haplotype test, violation of the HWE assumption can inflate type I error. We also evaluated general guidelines for the validity of APL with rare alleles and rare haplotypes. Software for the APL test is available from http://www.chg.duke.edu/research/apl.html.

Computer Simulation↗
PubMed2001

Automatic analysis of image of surface structure of cell wall-deficient EVC.

Some computer applications for cell characterization in medicine and biology, such as analysis of surface structure of cell wall-deficient EVC (El Tor Vibrio of Cholera), operate with cell samples taken from very small areas of interest. In order to perform texture characterization in such an application, only a few texture operators can be employed: the operators should be insensitive to noise and image distortion and be reliable in order to estimate texture quality from images. Therefore, we introduce wavelet theory and mathematical morphology to analyse the cellular surface micro-area image obtained by SEM (Scanning Electron Microscope). In order to describe the quality of surface structure of cell wall-deficient EVC, we propose a fully automatic computerized method. The image analysis process is carried out in two steps. In the first, we decompose the given image by dyadic wavelet transform and form an image approximation with higher resolution, by doing so, we perform edge detection of given images efficiently. In the second, we introduce many operations of mathematical morphology to obtain morphological quantitative parameters of surface structure of cell wall-deficient EVC. The obtained results prove that the method can eliminate noise, detect the edge and extract the feature parameters validly. In this work, we have built automatic analytic software named "EVC.CELL".

Cell Membrane↗
PubMed2006

Genome-wide expression profile of human trabecular meshwork cultured cells, nonglaucomatous and primary open angle glaucoma tissue.

PURPOSE: To contrast genome-wide gene expression profiles of cultured human trabecular meshwork (HTM) cells to that of control and primary open angle glaucoma (POAG) HTM tissues. METHODS: Cultured HTM cells, HTM tissue dissected from control donors, and HTM tissue from POAG donors receiving medication for glaucoma were fixed in RNA latertrade mark. Total RNA extracted from these samples was linearly amplified with the Ovation Biotin RNA Amplification and Labeling System and individually hybridized to Affymetrix Human Genome U133 Plus 2.0 high density microarrays. Data analysis was performed using GeneSpring Software 7.0. Selected genes showing significant differential expression were validated by quantitative real-time PCR in nonamplified RNA. RESULTS: Cultured HTM cells retained the expression of some genes characteristic of HTM tissue, including chitinase 3-like 1 and matrix Gla protein, but demonstrated downregulation of physiologically important genes such as myocilin. POAG HTM tissue showed relatively small changes compared to that of control donors. These changes included the statistically significant upregulation of several genes associated with inflammation and acute-phase response, including selectin-E (ELAM-I), as well as the downregulation of the antioxidants paraoxonase 3 and ceruloplasmin. CONCLUSIONS: Downregulation in cultured HTM cells of genes potentially relevant for outflow pathway function highlights the importance of developing new conditions for the culture of TM cells capable of preserving the characteristics of TM cells in vivo. Comparative analysis between control and POAG tissues suggests that the upregulation of inflammation-associated genes might be involved in the progression of glaucoma.

Case-Control Studies↗
PubMed1991

[Evaluation of voice quality. Experimental approach and modeling of the prosthetic voice of laryngectomized patients].

The authors describe their initial results with the parametric assessment of voice quality, which still is mainly subjective. This analysis will be used both in audiology and phonology. A first approach is made on the experimental model of a laryngectomee with a Bordeaux-type phonatory implant. Such patients allow a simpler analysis of voice production both incoustics and with an electromyographic control. The analysis of the data and their statistical validation is based on the use of original computer software.

Acoustics↗
PubMed2006

Validation of GATE Monte Carlo simulations of the GE Advance/Discovery LS PET scanners.

The recently developed GATE (GEANT4 application for tomographic emission) Monte Carlo package, designed to simulate positron emission tomography (PET) and single photon emission computed tomography (SPECT) scanners, provides the ability to model and account for the effects of photon noncollinearity, off-axis detector penetration, detector size and response, positron range, photon scatter, and patient motion on the resolution and quality of PET images. The objective of this study is to validate a model within GATE of the General Electric (GE) Advance/Discovery Light Speed (LS) PET scanner. Our three-dimensional PET simulation model of the scanner consists of 12 096 detectors grouped into blocks, which are grouped into modules as per the vendor's specifications. The GATE results are compared to experimental data obtained in accordance with the National Electrical Manufactures Association/Society of Nuclear Medicine (NEMA/SNM), NEMA NU 2-1994, and NEMA NU 2-2001 protocols. The respective phantoms are also accurately modeled thus allowing us to simulate the sensitivity, scatter fraction, count rate performance, and spatial resolution. In-house software was developed to produce and analyze sinograms from the simulated data. With our model of the GE Advance/Discovery LS PET scanner, the ratio of the sensitivities with sources radially offset 0 and 10 cm from the scanner's main axis are reproduced to within 1% of measurements. Similarly, the simulated scatter fraction for the NEMA NU 2-2001 phantom agrees to within less than 3% of measured values (the measured scatter fractions are 44.8% and 40.9 +/- 1.4% and the simulated scatter fraction is 43.5 +/- 0.3%). The simulated count rate curves were made to match the experimental curves by using deadtimes as fit parameters. This resulted in deadtime values of 625 and 332 ns at the Block and Coincidence levels, respectively. The experimental peak true count rate of 139.0 kcps and the peak activity concentration of 21.5 kBq/cc were matched by the simulated results to within 0.5% and 0.1% respectively. The simulated count rate curves also resulted in a peak NECR of 35.2 kcps at 10.8 kBq/cc compared to 37.6 kcps at 10.0 kBq/cc from averaged experimental values. The spatial resolution of the simulated scanner matched the experimental results to within 0.2 mm.

Algorithms↗
PubMed1997

Ambulatory monitoring of children's activity.

One of the difficulties in clinical assessment is how to obtain accurate data in the "real world". This paper describes the Dynaport ADL Monitor, an accelerometry-based system for ambulatory monitoring of the activities of daily living (ADL). In previous studies the monitor has proved a success with adults. To validate the system for use with children, 9 h of various activities conducted by nine children were measured and videotaped at the same time. All postures and activities were divided into one of five main categories: standing, sitting, lying, locomotion and swing/seesaw. The video pictures were evaluated by an observer. Independent of this, the acceleration signals were translated by the DynaPort ADL monitor software, and were compared to the video pictures. Minimal and maximal validity percentages were calculated for each of the main classes, for each individual measurement and overall. To estimate monitoring performance the 10 sets of measurements are regarded as representative samples of children's daily activity. The overall minimal and maximal validity are 73.15 +/- 1.96 x 4.48 and 91.31 +/- 1.96 x 1.75 weighed standard deviation.

Activities of Daily Living↗
PubMed2006

New angiographic measurement tool for analysis of small cerebral vessels: application to a subarachnoid haemorrhage model in the rat.

INTRODUCTION: Exact quantification of vasospasm by angiography is known to be difficult especially in small vessels. The purpose of the study was to develop a new method for computerized analysis of small arteries and to demonstrate feasibility on cerebral angiographies of rats acquired on a clinical angiography unit. METHODS: A new software tool analysing grey values and subtracting background noise was validated on a vessel model. It was tested in practice in animals with subarachnoid haemorrhage (SAH). A total of 28 rats were divided into four groups: SAH untreated, SAH treated with local calcium antagonist, SAH treated with placebo, and sham-operated. The diameters of segments of the internal carotid, caudal cerebral, middle cerebral, rostral cerebral and the stapedial arteries were measured and compared to direct measurements of the diameters on magnified images. RESULTS: There was a direct correlation between the cross-sectional area of vessels measured in a phantom and the measurements acquired using the new image analysis method. The spread of repeated measurements with the new software was small compared to the spread of direct measurements of vessel diameters on magnified images. Application of the measurement tool to experimental SAH in rats showed a statistically significant reduction of vasospasm in the SAH groups treated with nimodipine-releasing pellets in comparison to all the other groups combined. CONCLUSION: The presented computerized method for analysis of small intracranial vessels is a new method allowing precise relative measurements. Nimodipine-releasing subarachnoidal pellets reduce vasospasm, but further testing with larger numbers is necessary. The tool can be applied to human angiography without modification and offers the promise of substantial progress in the diagnosis of vasospasm after SAH.

Animals↗
PubMedDate not supplied

LIMS user acceptance testing.

Laboratory Information Management Systems (LIMS) play a key role in the pharmaceutical industry. Thorough and accurate validation of such systems is critical and is a regulatory requirement. LIMS user acceptance testing is one aspect of this testing and enables the user to make a decision to accept or reject implementation of the system. This paper discusses key elements in facilitating the development and execution of a LIMS User Acceptance Test Plan (UATP).

Accreditation↗
PubMed1999

Considerations on the quality of medical software and information services.

Fast developments in information and communication technology have made it possible to develop new services for citizens. One of the most interesting areas is health care. Medical knowledge is usually valid all over the world that makes the market global. Information services and decision support software are becoming important tools for medical professionals but also ordinary citizens are interested in health related information. It has been estimated that by the year 2010 the turnover of health care telematics industry may be close to that of the drug industry today. The nature of this global information industry is very different from any industry in history. Since there are no frontiers, no clear products and no shops in the information market, it is difficult to develop any effective legislation. However, the history of medicine has shown that health care sector cannot be free from regulation without risking citizens' health. The huge commercial potential of the Internet has already been used to promote products and services that have no proven effect on health and that may sometimes be even dangerous. In this paper we discuss the needs and possibilities to assess the quality of medical decision support software and information services. For brevity the terms medical software and medical knowledge are used, but the issues also relate to informatics systems used by any health professional, and to computerised systems used to schedule care or to organise record systems.

Decision Support Systems, Clinical↗
PubMedDate not supplied

Validation of probabilistic predictions.

Current advances in high-speed computing and increased availability of statistical software have led to widespread use of statistical methods for the development of computerized protocols predictive of binary health outcomes. If these predictive algorithms are to be used in settings other than those for which they were developed, e.g., applied in a different geographic setting or extrapolated for use in a slightly different population, then they should be carefully validated to ensure appropriate application. Miller et al. (Stat Med. 1991) provided a comprehensive methodology for external validation of logistic prediction models, and applied these methods in a temporal validation setting. In this article, the authors emphasize how these methods can be applied to general forms of probabilistic predictions and provide several SAS macros for computation of the desired statistics.

Adolescent↗
PubMed1992

Quality control methods for data entry in pathology using a computerized data management system based on an extended data dictionary.

In pathology, computerized data management systems have been used increasingly to facilitate a more efficient supply of information. Since data entry precedes data utilization, the reliability of the information stored strongly depends on the quality of data input. Despite its potential capability, most personal computer-based database software does not provide versatile and user-friendly data validation procedures. Therefore, we developed a data dictionary-driven data management system that enables the user to perform extensive validation routines without the need for hard programming. Using examples from an existing database for endometrial carcinomas, different types of data errors and their error traps are explained. It is pointed out that data type definitions, defaults, templates, or picture clauses are suitable means to avoid formal errors. Validations on data domains and ranges test whether data fall into a predefined scope. Relational checks control data validity within a context of different data items, whereas process routines provide automatic data computation, thereby circumventing user input. By exploiting the facilities of an extended data dictionary, a powerful tool is made available to secure various aspects of data integrity simultaneously with input. In this way, computerized data quality control can improve the efficiency and reliability of data management tasks in pathology.

Medical Informatics Computing↗
PubMed1996

Automating combinatorial chemistry: a primer on benchtop robotic systems.

Benchtop robotic systems are inexpensive, flexible automation tools with potential applications in a wide array of disciplines such as combinatorial chemistry, high-throughput screening, and genomics. We explain the basic components of a benchtop system and explore factors to consider when purchasing or customizing a robot, such as automation benefits, vendor selection, and current system limitations. Issues involving system specification, software design, and hardware customization are then discussed. Additionally, system optimization, validation, and support are detailed. Given a properly designed and implemented system, the combinatorial laboratory can markedly increase compound synthesis and purification.

Computers↗
PubMed2004

Collection of white blood cell-reduced plasma by apheresis.

BACKGROUND: WBC reduction of cellular blood components has been introduced in many countries. Owing to concerns of residual WBCs in plasma, a new method to collect WBC-reduced plasma by apheresis was studied. STUDY DESIGN AND METHODS: An apheresis machine (PCS2, Haemonetics) was used, in combination with the "high-separation" core (HSC) bowl, a redesigned version of the blow-molded (BM) bowl. With the BM bowl collections as control group, various software settings were investigated applying the HSC bowl. The optimized program was validated for routine application. Results are expressed as means +/- SD. RESULTS: Plasma collected in the control group with the BM bowl (n = 25) had a volume of 622 +/- 7 mL and contained 5.3 +/- 4.6 x 10(6) WBCs per L, 11 +/- 5 x 10(9) PLTs per L, and 0.063 +/- 0.051 x 10(9) RBCs per L. The collection efficiency was 17.8 +/- 2.8 mL per minute, and the total procedure time was 36.1 +/- 6.3 minutes. The HSC bowl produced plasma that had a volume of 623 +/- 9 mL and contained 0.01 +/- 0.02 x 10(6) WBCs per L, 2 +/- 2 x 10(9) PLTs per L, and 0.00040 +/- 0.0016 x 10(9) RBCs per L (n = 134, all p < 0.001). The collection efficiency was 15.8 +/- 2.2 mL per minute, and the collection time was 40.3 +/- 6.3 minutes (both p < 0.001). CONCLUSION: The HSC bowl with the new software reliably produces WBC-reduced apheresis plasma, with a slight elongation of the procedure time.

Adult↗
PubMed2006

Validity, reliability, and reproducibility of plaster vs digital study models: comparison of peer assessment rating and Bolton analysis and their constituent measurements.

INTRODUCTION: The objective of this validation study was to compare standard plaster models (the current gold standard for cast measurements) with their digital counterparts made with emodel software (version 6.0, GeoDigm, Chanhassen, Minn) for the analysis of tooth sizes and occlusal relationships--specifically the Bolton analysis and the peer assessment rating (PAR) index and their components. METHODS: Dental casts were poured from 24 subjects with 8 malocclusion types grouped according to American Board of Orthodontics categories. Measurements were made with a digital caliper to the nearest 0.01 mm from plaster models and with the software from the digital models. A paired samples t test was used to compare reliability and validity of measurements between plaster and digital methods. RESULTS: Reproducibility of digital models via the concordance correlation coefficient was excellent in most cases and good in some. Although statistically significant differences in some measurements were found for the reliability and validity of the digital models via the average mean of the absolute differences of repeated measurements, none was clinically significant. Grouping of the measurements according to the 8 American Board of Orthodontics categories produced no significant difference (Kruskal-Wallis test). No measurement associated with Bolton analysis or PAR index made on plaster vs digital models showed a clinically significant difference. The PAR analysis and its constituent measurements were not significantly different clinically between plaster and emodel media. CONCLUSIONS: Preliminary results did not indicate that digital models would cause an orthodontist to make a different diagnosis of malocclusion compared with plaster models; digital models are not a compromised choice for treatment planning or diagnosis.

Computer Simulation↗