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At least 1,135 records · Page 63Linked to original sources
PubMed2006

Automated PCR setup for forensic casework samples using the Normalization Wizard and PCR Setup robotic methods.

Human genome, pharmaceutical and research laboratories have long enjoyed the application of robotics to performing repetitive laboratory tasks. However, the utilization of robotics in forensic laboratories for processing casework samples is relatively new and poses particular challenges. Since the quantity and quality (a mixture versus a single source sample, the level of degradation, the presence of PCR inhibitors) of the DNA contained within a casework sample is unknown, particular attention must be paid to procedural susceptibility to contamination, as well as DNA yield, especially as it pertains to samples with little biological material. The Virginia Department of Forensic Science (VDFS) has successfully automated forensic casework DNA extraction utilizing the DNA IQ(trade mark) System in conjunction with the Biomek 2000 Automation Workstation. Human DNA quantitation is also performed in a near complete automated fashion utilizing the AluQuant Human DNA Quantitation System and the Biomek 2000 Automation Workstation. Recently, the PCR setup for casework samples has been automated, employing the Biomek 2000 Automation Workstation and Normalization Wizard, Genetic Identity version, which utilizes the quantitation data, imported into the software, to create a customized automated method for DNA dilution, unique to that plate of DNA samples. The PCR Setup software method, used in conjunction with the Normalization Wizard method and written for the Biomek 2000, functions to mix the diluted DNA samples, transfer the PCR master mix, and transfer the diluted DNA samples to PCR amplification tubes. Once the process is complete, the DNA extracts, still on the deck of the robot in PCR amplification strip tubes, are transferred to pre-labeled 1.5 mL tubes for long-term storage using an automated method. The automation of these steps in the process of forensic DNA casework analysis has been accomplished by performing extensive optimization, validation and testing of the software methods.

Automation↗
PubMed2004

Chemometric and derivative methods as flexible spectrophotometric approaches for dissolution and assaying tests in multicomponent tablets.

Two derivative spectrophotometric (ratio derivative spectra and algorithm bivariate calibration) and a chemometric methods (partial least squares, PLS) are proposed for the simultaneous determination of binary mixtures in tablet analysis and dissolutions tests, without prior separation. These approaches are successfully applied to quantify trimethoprim (TMP) combined with sulfamethoxazole (SMX) or sulfamethazine (SMZ) or sulfafurazole (SFZ) using the information in the absorption spectra of appropriate solutions. Beer's law was obeyed in the concentration range of 0.98-17.5 microg/ml for TMP, 0.95-17.2 microg/ml for SMX, 1.16-17.5 microg/ml for SMZ and 0.97-17.4 microg/ml for SFZ. The first derivative (1D) bivariate algorithm method involves the use of four calibration curves: two for each compound at two different wavelengths, selected by Kaiser's method. Similarly, the first derivative ratio spectrophotometry employs the linear relationship between the ratio spectra of the analytes and the concentration range. The results were compared with those obtained by PLS multivariate calibration. The calibration models from PLS were pre-treated by orthogonal signal correction and evaluated by cross-validation using the 'SIMCA-P 9' software. Synthetic mixtures of TMP and sulfonamides were used in five different sets for the validity of the calibrations. Mean recoveries for derivative ratio, derivative bivariate and PLS methods were found to be between 99.7% and 102.0% for TMP, 99.4% and 100.2% for SMX, 99.3% and 101.0% for SMZ and 98.1% and 102.3% for SFZ. The calibrations of the three methods were successfully applied to the assaying and dissolution of placebo and commercial tablets without any prior separation. More than 85% of TMP, SMX and SMZ were dissolved within 15 min. For SFZ, only 85% of the compound was dissolved after 60 min. In this study, the three spectrophotometric methods can be satisfactorily used for the quantitative analysis and for dissolution tests of multicomponent dosage forms.

Algorithms↗
PubMed2005

Validation of physics improvements for IMRT with a commercial treatment-planning system.

A new Pinnacle 3D treatment-planning system software release has recently become available (v7.4, Philips Radiation Oncology Systems, Milpitas, CA), which supports modeling of rounded multileaf collimator (MLC) leaf ends; it also includes a number of other software enhancements intended to improve the overall dose calculation accuracy. In this report, we provide a general discussion of the dose calculation algorithm and new beam-modeling parameters. The accuracy of a diode dosimeter was established for measurement of MLC-shaped beam profiles required by the new software version by comparison with film and ion chamber measurements in various regions of the field. The results suggest that a suitable diode or other small volume dosimeter with appropriate energy sensitivity should be used to obtain profiles for commissioning the planning system. Film should be used with caution, especially for larger field profile measurements. The dose calculation algorithm and modeling parameters chosen were validated through various test field measurements including a bar pattern, a strip pattern, and a clinical head and neck IMRT field. For the bar and strip patterns, the agreement between Pinnacle calculations and diode measurements was generally very good. These tests were helpful in establishing the new model parameter values, especially tongue-and-groove width, additional interleaf leakage, rounded leaf tip radius, and MLC transmission. For the clinical head and neck field, the comparison between Pinnacle and film measurements showed regions of approximately 2 cGy under- or overdose. However, the Pinnacle calculations agreed with diode measurements at all points to within 1 cGy or 1% of the maximum dose for the field (67 cGy). The greatest discrepancy between film and diode measurements for the clinical field (maximum of 2.8%) occurred in low-dose regions in the central part of the field. The disagreement may be due to the overresponse of film to scattered radiation in the low-dose regions, which have significant shielding by the MLCs.

Algorithms↗
PubMed1998

Validation of computer systems: practical testing of a standard LIMS.

In recent years the introduction of computer systems for data handling in the pharmaceutical industry has increased. A standard LIMS (laboratory information management system) is software commercially available from different suppliers not only to facilitate data handling in laboratories but also to cover GMP-requirements. Computer systems introduced in GMP-areas of pharmaceutical companies have to be validated. For a standard LIMS, the general validation of the program is performed by the supplier. Nevertheless, the user is always required to cover all phases of a validation. The objective of this paper is to discuss suitable test procedures for the most critical functions of a standard LIMS needed during the verification step of the validation process.

Clinical Laboratory Information Systems↗
PubMed1996

Determination of sleep and wakefulness with the actigraph data analysis software (ADAS).

Current evidence has shown that, overall, actigraphy is an excellent tool for unobtrusive documentation of sleep/wake activity in normal individuals. However, a number of methodological issues remain to be resolved to warrant its use in clinical research. In this paper, we report the results of a study aimed at the development of a new scoring software that can accurately identify sleep and wakefulness. Using total sleep time as an index of comparison, the software was optimized on a calibration sample and prospectively tested on a validation sample. A strong correlation coefficient (r = 0.93, p < 0.008), with an average discrepancy value of 10 minutes, was observed for the calibration sample. The application of the optimal software to the validation sample revealed an even higher correlation coefficient (r = 0.97, p < 0.0001), with an average discrepancy value of 12 minutes.

Adult↗
PubMed2000

Variance and confidence limits in validation studies based on comparison between three different types of measurements.

BACKGROUND: The methods used in epidemiological studies to assess exposure are often affected by a conspicuous amount of measurement error. Exposure-measurement error is recognised to cause attenuation in the association between exposure and disease. Among different possible approaches, the validity coefficient of a measurement can be estimated by a comparison of three types of measurements, using either structural equation models or factor analysis (the triads method). These approaches assume that the measurements are linearly related to true intake and have independent random errors. METHODS: In this paper we present an estimator of the variance of the estimated validity coefficient to compute the associated confidence intervals. Standard error for the validity coefficient allows the efficiency of validation studies to be evaluated. Our work was motivated by the fact that existing software does not provide correct standard errors for the estimated validity coefficient. The approach is illustrated using selected examples from dietary validation studies. RESULTS: The accuracy of our formula is evaluated by comparison with the results of a simulation study, which shows that our variance estimator provides good results for sample sizes of at least n = 100 and when the expected value of the validity coefficient is not too close to 1.0, independent of the sample size. Our estimator formula performs better than either a naïve approach, that computes the standard error for a validity coefficient as if it is a straightforward correlation coefficient, or the SAS-CALIS procedure, which uses a maximum likelihood method. CONCLUSIONS: In evaluating the validity of the type of measurement chosen to assess exposure in an epidemiological study, it is important to provide an estimate of the precision of the validity coefficient of the measurement. Our variance estimator may help calculate sample size requirements for validation studies.

Analysis of Variance↗
PubMed2004

Quantitative coronary arteriography on digital flat-panel system.

On images acquired with a digital flat-panel (DFP) detector, known for its better image quality, the performance of a validated quantitative coronary arteriography (QCA) software, CAASII (Cardiovascular Angiography Analysis System or CAAS), and a DFP-dedicated QCA algorithm (flat-panel analysis software or FPAS) was compared in a phantom and a patient study. On phantom, FPAS performed with higher accuracy the quantification of the smallest tubes and the calibration of an empty catheter. The overall accuracy and precision for the quantification procedure was better for FPAS (0.07 +/- 0.04 mm) than for the CAAS (0.19 +/- 0.06 mm; P = 0.03 and P < 0.01, respectively). In the patient study, the main difference between the two algorithms was found in the small diameters: CAAS almost always gave higher values than FPAS for the minimal luminal diameter (P < 0.001) and could only give values up to 70% for diameter stenosis. In conclusion, the FPAS can be considered more appropriate for assessing severe stenoses on digital flat-panel images.

Algorithms↗
PubMed2004

The benefits of stereoscopic vision in robotic-assisted performance on bench models.

BACKGROUND: Previous studies have failed to establish clear advantages for the use of stereoscopic visualization systems in minimal-access surgery. The aim of this study was to objectively assess whether stereoscopic visualization improves performance on bench models using the da Vinci robotic system. METHODS: Eleven surgeons carried out a series of four tasks. Positional data streamed from the da Vinci system was analyzed by means of a previously validated custom-designed software-package. An independent blinded observer scored errors. Statistical analysis included the Wilcoxon signed rank test. A p < 0.05 was deemed significant. RESULTS: We found significant improvements in all tasks and for all parameters (p < 0.05). In addition, a significantly lower number of errors was scored using the stereoscopic mode as compared to the standard two-dimensional image (p < 0.001). CONCLUSION: Robotic-assisted performance on bench models is more efficient and accurate using stereoscopic visualization.

Data Display↗
PubMed1995

Quantitation of human cytomegalovirus glycoprotein H gene in cells using competitive PCR and a rapid fluorescence-based detection system.

A technique is described for quantitation of the human cytomegalovirus (HCMV) glycoprotein H (gH) gene in cells using a quantitative-competitive polymerase chain reaction (QC-PCR). Two recombinant DNA molecules, differing in size due to a 92-bp deletion within the HCMV gH sequence, were used in co-amplification studies to construct a standard curve from which the copy number of the gH gene present in clinical samples could be interpolated. The use of primers labeled with a fluorescent dye allowed direct detection of the amplified products by measuring the amount of fluorescence emitted by each specific PCR fragment with an automated DNA sequencer coupled to a software program. This system was validated subsequently using bronchoalveolar lavage cells obtained from immunocompromised patients and found to be highly sensitive and reproducible over a range of 5-50,000 HCMV gH copies. This rapid procedure could easily be applied to study the pathogenesis of HCMV infection, identify the patients at high risk of developing HCMV disease, and monitor the effects of antiviral therapy at the molecular level.

Base Sequence↗
PubMedDate not supplied

Development and transferability of near-infrared methods for determination of moisture in a freeze-dried injection product.

Near-infrared reflectance (NIR) methods for non-invasive and non-destructive measurement of moisture in a lyophilized product were developed independently at two sites. NIR spectra were collected with the same model instrument at each site. The spectra were scanned through the bases of unopened glass vials using a horizontal instrument accessory. The primary reference data for moisture content were generated using Karl-Fischer titration on the same individual vials. The NIR calibration equations were developed with second derivative spectral data using regression programs within the NIR software. These calibration equations were validated using independent test data from additional vials of product from the original site, and cross tested against similar data from the other site to check their robustness. This cross comparison demonstrated that a calibration equation from one site could satisfactorily be used for predicting moisture contents in product manufactured at the other site. Expected variations arising from differences in vial material, manufacturing process, analysts and instruments appeared to be satisfactorily accommodated. Finally, two test data sets were obtained by scanning a set of samples on two spectrometers at one site. The results from these data sets were comparable using the calibration equation developed solely on one of the two instruments. The results from all calibration and test sets are presented and discussed, and an assessment of the method transferability between instruments and sites is given.

Calibration↗
PubMed2006

Biomechanical comparison between fusion of two vertebrae and implantation of an artificial intervertebral disc.

Surgical treatments for lower back pain can be distributed into two main groups: fusion (arthrodesis) and disc replacement (arthroplasty). The objective of this study was to compare, under severe loading conditions, the biomechanics of the lumbar spine treated either by fusion or total disc replacement (TDR). A three-dimensional model of a two-level ligamentous lumbar segment was created and simulated through static analyses with the finite-element method (FEM) software ABAQUS. The model was validated by comparing mobility, pressure on the facets, force in the ligaments, maximum stresses, disc bulge, and endplate deflection with measured data given in the literature. The FEM analysis predicted that the mobility of the model after arthrodesis on the upper level was reduced in all rotational degrees of freedom by an average of approximately 44%, relative to healthy normal discs. Conversely, the mobility of the model after TDR on the upper level was increased in all rotational degrees of freedom by an average of approximately 52%. The level implanted with the artificial disc showed excessive ligament tensions (greater than 500 N), high facet pressures (greater than 3 MPa), and a high risk of instability. The mobility and the stresses in the level adjacent to the arthroplasty were also increased. In conclusion, the model for an implanted movable artificial disc illustrated complications common to spinal arthroplasty and showed greater risk of instability and further degeneration than predicted for the fused model. This modeling technique provides an accurate means for assessing potential biomechanical risks and can be used to improve the design of future artificial intervertebral discs.

Biomechanical Phenomena↗
PubMed2006

The ABCs of computerized naming: equivalency, reliability, and predictive validity of a computerized rapid automatized naming (RAN) task.

Population-based studies indicate dual routes to disabled reading in adolescence and adulthood: slowed acquisition of single word reading and ADHD (particularly inattention) in early childhood. Impairments in rapid serial naming may be a factor common to both problems. The gold-standard measure of this ability, the Rapid Automatized Naming Task (RAN; [Denckla MB, Rudel R. Rapid automatized naming of pictured objects, colors, letters and numbers by normal children. Cortex 1974;10:186-202]), has traditionally been administered in a paper-pencil format. Recently however, researchers [Neuhaus GF, Carlson CD, Jeng WM, Post Y, Swank PR. The reliability and validity of rapid automatized scoring software ratings for the determination of pause and articulation component durations. Educ Psychol Meas 2001;61:490-504] have begun to use computerized versions of the RAN. Here a slightly modified computerized version of the RAN was created and the equivalency between the computerized RAN and the conventional version was investigated using a university student sample. Naming times on the conventional and computerized RAN were highly correlated, overall, and for each of the four RAN stimulus types (letters, digit, colors, objects). Conventional and computerized RAN times predicted reading rate and reading comprehension scores equally well and both showed very high test-retest reliability. With our university student sample, findings indicate equivalency between the two testing mediums in all areas examined.

Adult↗
PubMed2006

Regulation of chemokine production in response to pro-inflammatory cytokines in first trimester decidual cells.

OBJECTIVE: Chemokines initiate the immune response by controlling leukocyte migration and lymphocyte development. Macrophage infiltration of the decidua has been implicated in the genesis of recurrent miscarriage and preeclampsia. Therefore, we determined whether cultured human decidual cells produce monocyte/macrophage-recruiting chemokines in response to a potent pro-inflammatory cytokine, interleukin-1beta (IL-1beta), and whether decidual cell-conditioned medium contains monocyte- and macrophage-chemoattractant activity. METHODS: Leukocyte-free first trimester decidual cells were treated for 6h with estradiol (E(2)) and medroxyprogesterone acetate (MPA) to mimic the steroidal milieu of pregnancy, or E(2) and MPA and IL-1beta (1 ng/ml) to mimic inflamed decidua. Total RNA was used for cDNA synthesis. Biotinylated cRNAs were generated and chemically fragmented for hybridization on Affymetrix HG_U133 Plus 2.0 chips followed by fluorescence labeling and optical scanning. Raw data generated from Affymetrix GCOS 1.2 (GeneChip Operating Software) were analyzed by GeneSpring 7.2 software. Subsequently microarray results were validated by real time RT-PCR and Western blotting. A functional study of monocyte migration was carried out also using conditioned media from culture. RESULTS: Five chemokines responsible for monocyte/macrophage chemoattraction and activation, including C-C motif ligand 2 (CCL2), CCL5, C-X-C motif ligand 2 (CXCL2), CXCL3 and CXCL8, were markedly elevated from 29- to 975-fold after exposure to IL-1beta in cultured first trimester decidual cells. The results of real-time RT-PCR (up-regulation from 43- to 3069-fold) and Western blotting (up-regulation from 15- to 300-fold) confirmed the microarray findings. Monocyte migration was significantly induced by the conditioned medium from IL-1beta-treated decidual cells. CONCLUSIONS: Treatment of first trimester decidual cells with IL-1beta induces secretion of monocyte/macrophage recruiting-chemokines and promotes monocyte migration. Extrapolation of these in vitro results to the milieu of implantation site suggests a mechanism whereby IL-1beta could mediate excessive macrophage infiltration of the decidua.

Blotting, Western↗
PubMed2000

Use of automated solid-phase extraction equipment for the determination of isoniazid in milk.

The possibility of using automated equipment for solid phase extraction of isoniazid from milk has been investigated. This equipment provides two noteworthy advantages: it shortens the time of analysis and avoids SPE column plugging, stabilizing flow rates. After setting the correct programme on software controlling the equipment, some validation parameters have been determined to obtain recovery and repeatability data. The mean recovery for spiked samples resulted in the range 75-95%, the standard error ranged from -5 to -20% while the RSD varied from 2 to 22%. Therefore the method can be considered reliable and fast.

Animals↗
PubMed2004

PARIS: a proteomic analysis and resources indexation system.

UNLABELLED: We developed a system for managing data from two-dimensional electrophoresis-based proteomic experiments. Named PARIS, the system stores gel image and information about experiments and analysis procedures, allows the user to search and navigate in genomic and proteomic data, supports visual verification and validation of the analysis results, and provides tools for cross multi-experiment and multi-experimenter data validation and exploration. AVAILABILITY: The software is freely available from http://www.inra.fr/bia/J/imaste/Projets/PARIS/index.html

Abstracting and Indexing↗
PubMed2026

Elucidating the mechanism of Buyang Huanwu Decoction in the treatment of ischemic stroke: A network pharmacology and molecular docking study.

A large number of functional disorders and uncomfortable symptoms often remain following ischemic stroke (IS). Existing drug therapy is not ideal for the direct improvement of symptoms, which often leads to poor patient compliance with physical rehabilitation therapy. Buyang Huanwu Decoction (BYHWD) is a famous prescription that is effective in treating IS, especially during the sequela stage of IS. We analyzed the therapeutic mechanism of BYHWD through network pharmacology. This study aims to investigate the potential active ingredients, targets, and signaling pathways of BYHWD for the treatment of IS, utilizing network pharmacology and molecular docking technology. The active ingredients of 7 Chinese herbs in BYHWD were obtained from the Traditional Chinese Medicine Systems Pharmacology and HERB databases, and IS-related disease targets were searched in the DisGeNET, GeneCards, and OMIM databases. The protein-protein interaction network was constructed using the STRING database and analyzed by Cytoscape 3.10.2 software. Additionally, the target genes were uploaded to the Database for Annotation, Visualization, and Integrated Discovery website for Gene Ontology alongside Kyoto Encyclopedia of Genes and Genomes analyses. With the assistance of AutoDockTools and PyMOL software (Schr&#xf6;dinger, Inc.), a validation of molecular docking results and a visualization of the results were performed. The results showed that there were 190 intersection targets between the active drug components and IS, corresponding to 61 active components, among which the top 5 target genes were tumor suppressor protein 53, Jun proto-oncogene, AKT serine/threonine kinase 1, mitogen-activated protein kinase 1, and estrogen receptor alpha. The PI3K-Akt signaling pathway is one of the top 10 pathways. The molecular docking results indicated that most of the top 5 targets had good affinities for the 8 core compounds. This computational analysis suggests that BYHWD may treat IS through multiple targets and pathways. It may play a neuroprotective role by regulating the inflammatory response, oxidative stress, apoptosis, autophagy, and vascular endothelial homeostasis. The identification of core effective components provides a theoretical foundation and candidate compounds for further investigation into new drugs for the treatment of sequelae after IS.

Drugs, Chinese Herbal↗
PubMed2006

Sixteen-channel multidetector row computed tomography versus coronary angiography in a surgical view.

BACKGROUND: Invasive coronary angiography (ICA) is the gold standard for the diagnosis of coronary artery disease and also for imaging procedures for preoperative planning of coronary artery bypass grafting (CABG). Sixteen-multidetector row computed tomography (MDCT) represents an alternative depiction of coronary vessels. METHODS: Preoperative exams included ICA and MDCT in 50 patients. Two blinded surgical readers independently investigated both diagnostic modalities regarding location, severity, and morphology of the stenoses. The right coronary artery, left anterior descending branch, and circumflex branch--each divided in 3 sections--and the left main artery with a diameter (3) 1.5 mm were rated in both procedures, and the percentage of complete evaluations by MDCT was assessed. RESULTS: Heart rate was 72 +/- 8 bpm. Forty-six percent of patients received a complete MDCT evaluation, and 54% received an incomplete MDCT evaluation. In 62% of these incompletely examined patients, 1 branch was not completely analyzable, in 31% 2 branches; and in 7% all 3 branches. In total, 9% of all segments were incompletely assessed. Investigators detected coronary stenoses in complete evaluations with a sensitivity of 94% and a specificity of 95%. Positive predictive value was 87% and negative predictive value was 98%. Plaque classification in soft and hard plaques was possible. CONCLUSION: Sixteen-MDCT is not a viable alternative diagnostic tool at present. However, although the percentage of incomplete evaluated patients is more then 50%, only 9% of all segments were incompletely assessable. If this technology can be further improved, especially its software, it will become a valid diagnostic tool for coronary artery disease.

Coronary Angiography↗