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At least 991 records · Page 55Linked to original sources
PubMed2001

Electrocardiographically gated blood-pool SPECT and left ventricular function: comparative value of 3 methods for ejection fraction and volume estimation.

UNLABELLED: The current major limitation to development of electrocardiographically (ECG) gated blood-pool SPECT (GBPS) for measurement of the left ventricular (LV) ejection fraction (LVEF) and volumes is the lack of availability of clinically validated automatic processing software. Recently, 2 processing software methods for quantification of the LV function have been described. Their LVEFs have been validated separately, but no validation of the LV volume measurement has been reported. METHODS: We compared 3 processing methods for evaluation of the LVEF (n = 29) and volumes (n = 58) in 29 patients: automatic geometric method (GBPS(G)), semiautomatic activity method (GBPS(M)), and 35% maximal activity manual method (GBPS(35%)). The LVEF provided by the ECG gated equilibrium planar left anterior oblique view (planar(LAO)) and the LV volumes provided by LV digital angiography (Rx) were used as gold standards. RESULTS: Whereas the GBPS(G) and GBPS(M) methods present similar low percentage variabilities, the GBPS(35%) method provided the lowest percentage variabilities for the LVEF and volume measurements (P < 0.04 and P < 0.02, respectively). The LVEF and volume provided by the 3 methods were highly correlated with the gold standard methods (r > 0.98 and r > 0.83, respectively). The LVEFs provided by the GBPS(35%) and GBPS(M) methods are similar and higher than those of the GBPS(G) method and planar(LAO) method, respectively (P < 0.0001). For the LVEF, there is no correlation between the average and paired absolute difference for the 3 GBPS methods against the planar(LAO) method, and the limits of agreement are relatively large. LV volumes are lower when calculated with the GBPS(M), GBPS(G), and Rx methods (P < 0.0001). However, the GBPS(35%) and Rx methods provide LV volumes that are similar. There is no linear correlation between the average and the paired absolute difference of volumes calculated with the GBPS(G) and GBPS(35%) methods against Rx LV volumes. However, a moderate linear correlation was found with the GBPS(M) method (r = 0.6; P = 0.0001). The 95% limits of agreement between the Rx LV volumes and the 3 GBPS methods are relatively large. CONCLUSION: GBPS is a simple, highly reproducible, and accurate technique for the LVEF and volume measurement. The reported findings should be considered when comparing results of different methods (GBPS vs. planar(LAO) LVEF; GBPS vs. Rx volume) and results of different GBPS processing methods.

Electrocardiography↗
PubMed2006

Transcription profiles of non-immortalized breast cancer cell lines.

BACKGROUND: Searches for differentially expressed genes in tumours have made extensive use of array technology. Most samples have been obtained from tumour biopsies or from established tumour-derived cell lines. Here we compare cultures of non-immortalized breast cancer cells, normal non-immortalized breast cells and immortalized normal and breast cancer cells to identify which elements of a defined set of well-known cancer-related genes are differentially expressed. METHODS: Cultures of cells from pleural effusions or ascitic fluids from breast cancer patients (MSSMs) were used in addition to commercially-available normal breast epithelial cells (HMECs), established breast cancer cell lines (T-est) and established normal breast cells (N-est). The Atlas Human Cancer 1.2 cDNA expression array was employed. The data obtained were analysed using widely-available statistical and clustering software and further validated through real-time PCR. RESULTS: According to Significance Analysis of Microarray (SAM) and AtlasImage software, 48 genes differed at least 2-fold in adjusted intensities between HMECs and MSSMs (p < 0.01). Some of these genes have already been directly linked with breast cancer, metastasis and malignant progression, whilst others encode receptors linked to signal transduction pathways or are otherwise related to cell proliferation. Fifty genes showed at least a 2.5-fold difference between MSSMs and T-est cells according to AtlasImage, 2-fold according to SAM. Most of these classified as genes related to metabolism and cell communication. CONCLUSION: The expression profiles of 1176 genes were determined in finite life-span cultures of metastatic breast cancer cells and of normal breast cells. Significant differences were detected between the finite life-span breast cancer cell cultures and the established breast cancer cell lines. These data suggest caution in extrapolating information from established lines for application to clinical cancer research.

Breast Neoplasms↗
PubMed2005

Does the use of an automated tool for self-reporting mood by patients with bipolar disorder bias the collected data?

CONTEXT: Automating data collection from patients can improve data quality, enhance compliance, and decrease costs in longitudinal studies. About half of all households in industrialized countries now have a home computer. OBJECTIVE: While we previously validated the ChronoRecord software for self-reporting mood on a home computer with patients who have bipolar disorder, this study further investigates whether this technology created a bias in the collected data. METHODS: During the validation study, 80 of 96 (83%) patients returned 8662 days of data (mean, 114.7 +/- 32.3 SD days). The patients' demographics were compared with those of similar longitudinal studies in which patients used paper-based data collection tools. In addition, because demographic characteristics may influence attitudes toward technology, observer-rated scores on the Hamilton Depression Rating Scale and Young Mania Rating Scale were used to group patients by severity of illness, and the self-reported mood ratings were analyzed for evidence of bias from the patients' gender, ethnicity, diagnosis, age, disability status, or years of education. Analysis was performed using the 2-way analysis of variance and general linear model. RESULTS: The patients' demographic characteristics were very similar to those of patients with bipolar disorder who participated in comparable longitudinal studies using paper-based tools. After grouping the patients by severity of illness, none of the demographic variables had a significant effect on the patients' self-reported mood using the automated tool. CONCLUSION: The use of a computer does not seem to bias sample data. As with studies using paper-based self-reporting, results from studies of patients using ChronoRecord software on a home computer to report mood can be generalized.

Adolescent↗
PubMed2005

Computational method for temporal pattern discovery in biomedical genomic databases.

With the rapid growth of biomedical research databases, opportunities for scientific inquiry have expanded quickly and led to a demand for computational methods that can extract biologically relevant patterns among vast amounts of data. A significant challenge is identifying temporal relationships among genotypic and clinical (phenotypic) data. Few software tools are available for such pattern matching, and they are not interoperable with existing databases. We are developing and validating a novel software method for temporal pattern discovery in biomedical genomics. In this paper, we present an efficient and flexible query algorithm (called TEMF) to extract statistical patterns from time-oriented relational databases. We show that TEMF - as an extension to our modular temporal querying application (Chronus II) - can express a wide range of complex temporal aggregations without the need for data processing in a statistical software package. We show the expressivity of TEMF using example queries from the Stanford HIV Database.

Artificial Intelligence↗
PubMed2003

Validation of the Coulter LH 750 in a hospital reference laboratory.

Validation of the Coulter LH 750 was carried out in our central hospital laboratory, which processes 1500 hemograms per day for patients admitted into the 4 hospitals of our hospital complex and their corresponding outpatient departments. It is the reference laboratory for the provincial health care area. The analytical quality and the practical use of the instrument were studied, and we obtained within- and between-run imprecision estimates with reference controls of between 0.24% and 2.56% and inaccuracies of between -1.32% and 3.07% for basic hemogram parameters. Similar results were obtained with specimens from patients, with imprecision estimates between 0.56% and 2.56%. Linearity estimates were between 0.3 x 10(9)/L and 380 x 10(9)/L for leukocytes and between 3 x 10(9)/L and 1900 x 10(9)/L for platelets. The instrument evaluation was completed with a study of interference by bilirubin, lipemia, hemolysis, platelet clumps, and heparin and an examination of other variables, including carryover, detection limits, and the correlation of results with those of the Coulter Gen-S. A special evaluation was made of the new erythroblast count feature; with reference controls, imprecision estimates for this count were 10% to 12%, and with patient specimens imprecision averaged 10.39% up to 4 erythroblasts per 100 leukocytes. We also studied the correlation of LH 750 results and interferences with those of the manual reference method. Finally, National Committee for Clinical Laboratory Standards protocols were used to test for suspect and confirmation flags in leukocyte differential counts for 258 specimens representative of our routine. The practicability of the analyzer was studied in terms of technical difficulty, speed, and cost; also evaluated were new software elements for validation by source clinic and pathology and for reference values based on age. In conclusion, we analyzed the impact and improvements that may be expected in our laboratory (a user of Technicon and Coulter instruments) from introducing the new LH 750 analyzer into our routine.

Blood Cell Count↗
PubMed2004

Three-dimensional analysis of left ventricle regional wall motion by using gated blood pool tomography.

BACKGROUND: We have elaborated a new software called ACS designed for left ventricle 3-dimensional reconstruction and quantitative analysis of regional wall motion using gated blood-pool tomography (GBPS). This paper presents the principle and the validation of this software. METHODS AND RESULTS: Blood pool tomography was reconstructed by filtered back-projection. Voxels corresponding to ventricular volumes were extracted using 3-D thresholding and 3-D elliptic mask. The auriculoventricular plane was located by phase analysis. Then, the reconstruction of the 3-D volume was initiated. First, a pre-processing based on a bi-dimensional Fourier transform re-sampled the initial points representing the wall of the left ventricle. Left ventricular contraction could be visualized in three dimensions. The points corresponding to the wall of the left ventricle were reorganized in order to obtain a regular sampling that allowed connection to the points during the cardiac cycle. Elementary volumes were defined by three adjacent wall points and the centre of the whole volume. The variation of elementary volumes during the cardiac cycle was related to the wall motion. Elementary volumes were regrouped to create regions of equivalent volume. Finally, regional and global ejection fractions could be calculated in 17 different regions. The method has been validated using a mathematical deformable ellipsoidal model. It had also been tested in vivo on a set of 59 patients in comparison to equilibrium radionuclide angiography for left ventricular ejection fraction and to echocardiography for regional wall motion evaluation. CONCLUSIONS: ACS is a new software that allows reconstruction and visualization of the left ventricle in three dimensions, and it quantified 3-dimensional regional wall motion analysis.

Algorithms↗
PubMedDate not supplied

Building quality into medical product software design.

The software engineering and quality assurance disciplines are a requisite to the design of safe and effective software-based medical devices. It is in the areas of software methodology and process that the most beneficial application of these disciplines to software development can be made. Software is a product of complex operations and methodologies and is not amenable to the traditional electromechanical quality assurance processes. Software quality must be built in by the developers, with the software verification and validation engineers acting as the independent instruments for ensuring compliance with performance objectives and with development and maintenance standards. The implementation of a software quality assurance program is a complex process involving management support, organizational changes, and new skill sets, but the benefits are profound. Its rewards provide safe, reliable, cost-effective, maintainable, and manageable software, which may significantly speed the regulatory review process and therefore potentially shorten the overall time to market. The use of a trial project can greatly facilitate the learning process associated with the first-time application of a software quality assurance program.

California↗
PubMed2005

Automation of analysis of cardiovascular autonomic function from chronic measurements of arterial pressure in conscious rats.

At present, there is no single software package that provides a comprehensive power spectral analysis of pulse interval (PI) and arterial blood pressure (BP), spontaneous cardiac baroreceptor reflex gain (sBRG) and respiratory rate. Furthermore, scientific validation of the software that is currently commercially available and employed has not been published. We introduce 'Hey-Presto' software, which fully evaluates cardiovascular autonomic function from the BP signal obtained from rats. The program performs power spectral analysis of HR and BP variability, respiratory rate and, based on a time-series method, spontaneous cardiac baroreceptor (sBRG). We have validated Hey-Presto with conventional pharmacological agents to block cardiac vagal and cardiac sympathetic transmission in conscious rats fitted with a radio-telemetery BP transducer. Following administration of atropine (1 mg kg(-1), I.V.), high-frequency (HF) power of the PI decreased (P < 0.01) and was associated with the expected increase in HR. Subsequent cardiac sympathetic blockade (atenolol, 1 mg kg(-1), I.V.) reduced the low frequency (LF) to HF ratio (LF:HF) of the PI (P < 0.01), which was consistent with the observed reduction in HR. We also found that alterations in sBRG after blockade of cardiac autonomic transmission were highly comparable to values computed manually using vasoactive drugs administered intravenously. The software also detected circadian rhythms in sBRG, HF component of the PI, LF:HF of the PI and LF component of the BP as well as BP and HR during continuous 24 h recording. By demonstrating its application to humans, we found appropriate changes in the power of PI and the LF power of the BP during postural changes. These results demonstrate that Hey-Presto allows a fully automated, reliable, fast and comprehensive evaluation of cardiovascular autonomic function based on chronic measurements of BP in rats. Moreover, we have confirmed its versatility by demonstrating its application to man.

Adrenergic beta-Antagonists↗
PubMed2002

[Criteria for management and use of instrumental techniques].

The measurement of various parameters--be it plain temperature readings or determination of pesticides, drug monitoring or measurement of contaminants in air or water--must be carried out precisely and accurately. After purchase of the instrument, the installation qualification and the operation qualification, both produced by experts in the manufacturing company, are used to ensure correct use of the instrument. The standard operating procedures for instrument management must be sufficiently detailed to allow the operator to use the instrument correctly and, above all, must contain all the information necessary for accurate and precise calibrations. From 2002, the Food and Drug Administration will no longer accept submission of paper dossiers, so that pharmaceutical companies wishing to register a product in the USA will be obliged to submit the dossier electronically. This will involve the validation of all the software used in the management and operation of all instruments. It can be assumed that the EMEA will shortly follow the FDA, so that the validation of instrument software systems will become the rule and create new responsibilities for operators and inspectors.

Calibration↗
PubMed2004

Experimental Peptide Identification Repository (EPIR): an integrated peptide-centric platform for validation and mining of tandem mass spectrometry data.

LC MS/MS has become an established technology in proteomic studies, and with the maturation of the technology the bottleneck has shifted from data generation to data validation and mining. To address this bottleneck we developed Experimental Peptide Identification Repository (EPIR), which is an integrated software platform for storage, validation, and mining of LC MS/MS-derived peptide evidence. EPIR is a cumulative data repository where precursor ions are linked to peptide assignments and protein associations returned by a search engine (e.g. Mascot, Sequest, or PepSea). Any number of datasets can be parsed into EPIR and subsequently validated and mined using a set of software modules that overlay the database. These include a peptide validation module, a protein grouping module, a generic module for extracting quantitative data, a comparative module, and additional modules for extracting statistical information. In the present study, the utility of EPIR and associated software tools is demonstrated on LC MS/MS data derived from a set of model proteins and complex protein mixtures derived from MCF-7 breast cancer cells. Emphasis is placed on the key strengths of EPIR, including the ability to validate and mine multiple combined datasets, and presentation of protein-level evidence in concise, nonredundant protein groups that are based on shared peptide evidence.

Breast Neoplasms↗
PubMed1999

[Statistically validated evaluation of clinical trials].

Data of clinical trials of medicinal products must be evaluated in statistically valid models. The statistical validity criteria are defined. Statistically invalid models will result in biased parameter and confidence interval estimations, erroneous statistical inferences and clinical interpretations. Finally, wrong decisions will call forth deleterious consequences in the judgement of the therapeutic effect and the frequency and severity of the adverse reactions of the tested new medicinal, and generic products. Statistically validated analyses will promote the international harmonization of the scientific evaluation of medicinal products according to the idea of the evidence-based-medicine. The study presents examples of clinical trials evaluated with a software checking statistical validity assumptions while performing evaluation of data.

Clinical Trials as Topic↗
PubMed2004

CONFAC: automated application of comparative genomic promoter analysis to DNA microarray datasets.

The advent of DNA microarray technology and the sequencing of multiple vertebrate genomes has provided a unique opportunity for the integration of comparative genomics with high-throughput gene expression analysis. Here we describe the conserved transcription factor binding site (CONFAC) software that enables the high-throughput identification of conserved transcription factor binding sites (TFBSs) in the regulatory regions of hundreds of genes at a time (http://morenolab.whitehead.emory.edu/cgi-bin/confac/login.pl). The CONFAC software compares non-coding regulatory sequences between human and mouse genomes to enable identification of conserved TFBSs that are significantly enriched in promoters of gene clusters from microarray analyses compared to sets of unchanging control genes using a Mann-Whitney U-test. Analysis of random gene sets demonstrated that using our approach, over 98% of TFBSs had false positive rates below 5%. As a proof-of-principle, we have validated the CONFAC software using gene sets from four separate microarray studies and identified TFBSs known to be functionally important for regulation of each of the four gene sets.

Animals↗
PubMedDate not supplied

New statistical software for intralaboratory and interlaboratory quality control in clinical cytology. Validation in a simulation study on clinical samples.

OBJECTIVE: To design a statistical software package to provide automated calculations of normal and weighted and 3 indices. STUDY DESIGN: Prompted by the lack of commonly available software to compute weighted kappa and the nonproportionate workload needed to calculate our 3 variability indices manually, the new statistical software package was designed. To demonstrate the performance of the new CONQUISTADOR software, a simulation study (both intralaboratory and interlaboratory) was designed using 5,000 clinical samples randomly selected from a data file of > or = 200,000 conventional Pap smears and programmed to become "analyzed" by 12 cytologists in 5 imaginary laboratories. RESULTS: A representative set of both complete and partial outputs provided by the software, in Excel format (Microsoft, Redmond, Washington, U.S.A.) are shown to illustrate the different functions of the program. In the interlaboratory mode, the software calculates accuracy indicators (sensitivity, specificity, positive and negative predictive value, and their 95% CI), which are not common features of regular statistical packages; kappa and weighted kappa; and their 95% CI (comparison of single laboratories to all laboratories and pairwise comparisons between single laboratories). The 3 diagnostic variability indices can be computed separately for all samples or for only the positive samples. In the intralaboratory mode, the software calculates the same indices for individual cytologists. CONCLUSION: The CONQUISTADOR statistical package has properties that are useful in monitoring cytologic laboratory quality in both intralaboratory and interlaboratory settings. The software will be distributed by the National Institute of Health, Rome, for the delivery costs only.

Clinical Laboratory Techniques↗
PubMed2002

Comparison of four artificial neural network software programs used to predict the in vitro dissolution of controlled-release tablets.

The purpose of this study was to evaluate four commercially available artificial neural network (ANN) software programs: NeuroShell2 v3.0, BrainMaker v3.7, CAD/Chem v5.0, and NeuralWorks Professional II/Plus for prediction of in vitro dissolution-time profiles of controlled-release tablets containing a model sympathomimetic drug. Seven independent formulation variables and three other tablet variables (moisture content of granules, granule particle size, and tablet hardness), for 22 tablet formulations, were used as the ANN model input. In vitro dissolution time-profiles at 10 different sampling times were used as the output. The models' optimum architectures were determined for each ANN software by varying the number of hidden layers and number of nodes in hidden layer(s). The ANN developed from the four software programs were validated by predicting the in vitro dissolution time-profiles of each of the 19 formulations, which were excluded from the training process. Although the same data set was used, the optimum ANN architectures generated from the four software programs were different. Using the four optimum ANN models, the plots of predicted vs. observed percentage of drug dissolved gave slopes ranging from 0.95 to 1.01 and r2 values ranging from 0.95 to 0.99 for all 190 dissolution data points for the 19 training formulations. The difference factors (f1) and similarity factors (f2) between the ANN predicted and the observed in vitro dissolution profiles were also used to compare the predictions for the four software programs. It was concluded that the four programs provided reasonable predictions of in vitro dissolution profiles for the data set employed in this study, with NeuralShell2 showing the best overall prediction.

Delayed-Action Preparations↗
PubMed2006

Novel fast semi-automated software to segment cartilage for knee MR acquisitions.

OBJECTIVE: Validation of a new fast software technique to segment the cartilage on knee magnetic resonance (MR) acquisitions. Large studies of knee osteoarthritis (OA) will require fast and reproducible methods to quantify cartilage changes for knee MR data. In this report we document and measure the reproducibility and reader time of a software-based technique to quantify the volume and thickness of articular cartilage on knee MR images. METHODS: The software was tested on a set of duplicate sagittal three-dimensional (3D) dual echo steady state (DESS) acquisitions from 15 (8 OA, 7 normal) subjects. The repositioning, inter-reader, and intra-reader reproducibility of the cartilage volume (VC) and thickness (ThC) were measured independently as well as the reader time for each cartilage plate. The root-mean square coefficient of variation (RMSCoV) was used as metric to quantify the reproducibility of VC and mean ThC. RESULTS: The repositioning RMSCoV was as follows: VC=2.0% and ThC=1.2% (femur), VC=2.9% and ThC=1.6% (medial tibial plateau), VC=5.5% and ThC=2.4% (lateral tibial plateau), and VC=4.6% and ThC=2.3% (patella). RMSCoV values were higher for the inter-reader reproducibility (VC: 2.5-8.6%) (ThC: 1.9-5.2%) and lower for the intra-reader reproducibility (VC: 1.6-2.5%) (ThC: 1.2-1.9%). The method required an average of 75.4min per knee. CONCLUSIONS: We have documented a fast reproducible semi-automated software method to segment articular cartilage on knee MR acquisitions.

Cartilage, Articular↗
PubMed2001

[Spectral interference correction software and its application in ICP-4 spectroscopic instrument].

In this paper, the spectral interference correction software based on Kalman filtering and its application in ICP-4 spectroscopic instrument are introduced. The principle, algorithm and experimental results of the software are discussed. The three analyte lines P (213.618 nm), P(214.914 nm) and Mo(268.323 nm) interforced by Cu(213.598 nm), Cu(214.897 nm) and V(268.309 nm) respectively were chosen as typical examples. The experiment results prove the validity of the software.

Algorithms↗
PubMed1994

Postmortem validation of the automated coronary analysis (ACA) software package.

Goal of this study was to compare the quantitative coronary arteriographic (QCA) results obtained with the Philips DCI/ACA analytical software package with those from postmortem casts in an animal experimental setting. Standard digital coronary arteriograms were obtained from 6 mongrel dogs. After the imaging procedure, the dogs were sacrificed and casts were made of the coronary trees by filling the vessels with a mixture of radio-opaque barium and silicone gel at a fixed pressure of 100 mmHg. Vessel diameters were measured from the digital arteriograms at a total of 118 selected locations with the ACA package. Thin slices were cut from the casts at these same measurement locations and the areas of the cross sections were obtained by manual tracing of the outline of each slice in an approximately 40 x magnified image. From these cross-sectional areas, cast diameters were derived using the formula for circular cross-sections. Cast diameters ranged in size from 0.69 to 3.30 mm. The systematic error between the measurements was found to be 0.058 mm; (p < 0.015) and the standard deviation of the signed difference 0.255 mm; the correlation coefficient was r = 0.91. The largest error sources are supposed to be the slight differences in the selection of identical positions in the X-ray images and on the casts, and the 'out-of-plane' magnification for a number of vessel locations. This postmortem study demonstrates that the diameters of coronary vessels can be measured from digital arteriograms with the DCI/ACA package with a high degree of accuracy and precision.

Animals↗
PubMed2002

[Specific parameters for the calculation of dose after aerosol inhalation of transuranium elements].

A review on specific parameter measurements to calculate doses per unit of incorporation according to recommendations of the International Commission of Radiological Protection has been performed for inhaled actinide oxides. Alpha activity distribution of the particles can be obtained by autoradiography analysis using aerosol sampling filters at the work places. This allows us to characterize granulometric parameters of "pure" actinide oxides, but complementary analysis by scanning electron microscopy is needed for complex aerosols. Dissolution parameters with their standard deviation are obtained after rat inhalation exposure, taking into account both mechanical lung clearance and actinide transfer to the blood estimated from bone retention. In vitro experiments suggest that the slow dissolution rate might decrease as a function of time following exposure. Dose calculation software packages have been developed to take into account granulometry and dissolution parameters as well as specific physiological parameters of exposed individuals. In the case of poorly soluble actinide oxides, granulometry and physiology appear as the main parameters controlling dose value, whereas dissolution only alters dose distribution. Validation of these software packages are in progress.

Actinoid Series Elements↗