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 1,531 records · Page 85Linked to original sources
PubMed1993

Development of intelligent design associates: a case study.

A number of human factors data sets provides guidelines and recommendations for the system design process. Much of this information is available to the human factors engineer in design handbooks, textbooks, and periodicals. While human factors design information is both available and abundant, it is not necessarily readily accessible or in a format that is easily assimilated into a particular design scenario. This paper discusses the feasibility of incorporating human factors design data into intelligent, knowledge-based systems referred to as design associates. Successful implementation of any design associate is dependent upon two key issues: conversion of human factors data into a valid knowledge base, and overcoming the knowledge representation constraints imposed by an intelligent software tool. Detailed results of a recent effort to address these issues, and subsequently implement a design associate on a commercially available intelligent software tool, are presented. This particular associate, implemented in a rule-based tool environment, aids in the selection of visual display technologies.

Journal Article↗
PubMed2006

Histone proteins determined in a human colon cancer by high-performance liquid chromatography and mass spectrometry.

The application of reversed-phase high-pressure liquid chromatography under gradient conditions and electrospray ion trap mass spectrometry (LC-ESI-MS) to the analysis of global modification levels of core histones is described. The optimised LC-ESI-MS method was applied for the first time to the characterisation of histones extracted from HT29, a human colon cancer cell line. Eight histones (H1-1, H1-2, H2A-1, H2A-2, H2B, H3-1, H3-2, H4) were separated on a C4 stationary phase with complete resolution, never reached in previous HPLC-MS methods, by using a gradient elution with the combined presence of heptafluorobutyric acid and formic acid as acidic modifiers in the mobile phase. Heptafluorobutyric acid was found to improve selectivity, whereas the presence of formic acid decreased ion suppression. Histones eluted from the column were detected with an ion trap mass spectrometer with an electrospray source. The peak averaged mass spectra were reconstructed by Mag Tran 1.0 software and the mass of the various isoforms of histones were derived. Method validation was conducted by performing the same sample analysis by coupling LC-ESI to a quadrupole-time-of-flight mass spectrometer (Q-TOF). The number of histone forms and their mass were found to differ not significantly from those obtained by ion trap mass spectrometer. Also the relative modifications abundance within the same histone type was found following the same trend as the two mass analysers. This method was then applied to the characterisation of changes in histone modification in HT29, never analysed by LC-MS before, treated with histone deacetylase inhibitors such as valproate and sodium butyrate, also used in preclinical trials as anticancer drugs. In particular, both the inhibitors produced a significant increase in H4 histone acetylated forms: 89% increase of the diacetyl dimethyl H4 form was observed with 1mM valproate supplementation, whereas 5 mM butyrate led to a 68% increase of the same form. Triacetyl monomethyl H4 (11,377 Da) and triacetyl dimethyl H4 (11,390 Da) were found only in cells treated with butyrate. Selective changes of H3 histone were detected with butyrate, in agreement with recently reported western blotting studies. Modifications in the H2A histone degree of acetylation were revealed by treatment of the cells with butyrate (H2A-1, H2A-2) and valproate (H2A-2). The results of the proposed methodology confirmed that inhibition of histone deacetylases caused histone hyperacetylation, responsible for decondensation and reorganization of interphase dynamic chromatin. This method resulted in selective and sensitive method to monitor variations in the acetylation and methylation state of histones after treatment of HT29 with inhibitors, and is therefore suitable for further application in new drug discovery for tumour therapy.

Acetylation↗
PubMed2003

Docking experiments showing similar recognition patterns of paclitaxel when interacting with different macromolecular targets.

Using the Protein Data Bank crystallographic model of paclitaxel with tubulin as reference, a comparative interaction study of the antitumor drug with known macromolecular targets such as beta-cyclodextrin and Dickerson's DNA dodecamer was carried out by molecular modeling techniques. AMBER* united atoms was found to be the most appropriate force field for our study. Conformational search of paclitaxel was performed using a water environment. A large set of conformers was selected for automatic "quasi-flexible" docking calculations performed by the "in-house" software MOLINE. A proper docking protocol was based on a crystallographic model and validated by a remarkable low atomic coordinate deviation. Using this method, a similar pattern via benzamide interaction was established for molecular recognition of paclitaxel cyclodextrin and DNA. The results are supported by our previous observations and other author's experimental data.

Antineoplastic Agents, Phytogenic↗
PubMed2001

A dynamic simulator to evaluate distal radio-ulnar joint kinematics.

In order to perform cadaveric biomechanical studies of the human forearm and distal radio-ulnar joint, a dynamic simulator has been constructed. The device is based upon a Plexiglas frame, to which the ulna is secured in a vertical orientation and the humerus in a horizontal orientation. The hand is secured in a sliding bar linkage to a stepper-motor that is used to rotate the forearm. The tendons to be loaded are connected to pneumatic actuators that provide agonist and antagonist muscle loading resulting in torque along the forearm axis. The muscle loading profiles and magnitudes are programmable as a function of the pronation-supination position and direction. A magnetic tracking system is used to collect three-dimensional kinematics data of up to four segments, in conjunction with the muscle tendon loads, forearm torque and other prescribed experimental measures. All functions are under PC control using custom software written with LabVIEW (National Instruments, Austin, TX). For the DRUJ testing, the validity of the tendon loading protocol to produce physiologic torque/rotation patterns was verified using in vivo data. The relationship of individual muscle forces to forearm torque was determined by a cadaveric study.

Biomechanical Phenomena↗
PubMed1998

A testing system for implantable cardioverter defibrillators.

Implantable cardioverter defibrillator (ICD) testing during the implantation process is important in order to avoid repeated induction of arrhythmias, which extends the implantation procedure and poses a risk to the patient. Hence, an in vitro testing system has been designed to assist optimal device programming and avoid repetitive inductions. The system includes a high-speed computer with A/D and D/A subsystems. Software has been designed to eliminate repeated arrhythmia induction by real-time capture and storage of the electrogram. Subsequently, the electrogram can be replayed into ICD software simulators at a variety of settings to determine candidate programming parameters. To validate the simulation system, signals were fed directly to an ICD via an attenuator. Output event markers were captured simultaneously with the signal into a digital file to assess the device performance. Four ventricular tachycardia (VT), three supraventricular tachycardia, (SVT), three atrial flutter (AFL), three atrial fibrillation (AF), and ten ventricular fibrillation (VF) passages were used to verify the system. Test settings were 110-160 beats/min for detection rate and 5 seconds for shock delay. The simulator and ICD detected the episodes for all passages at the 110 beats/min setting. For the setting of 160 beats/min, two VTs, two SVTs, three AFLs, and nine VFs were detected by the device, but no Afb triggered a shock. The simulator detection criteria were met by two VTs, two SVTs, three AFLs, ten VFs, and one AF. The mean detection time was 6,869-7,330 ms (110-160 beats/min) for the simulator and 7,840-8,170 ms for device. Comparison of results showed general agreement between simulator and device. Results demonstrated that device behavior at a variety of settings can be elucidated by the simulator for selection of optimal performance. The automated system can also function as a test bed for evaluation of new algorithms during device development and design.

Algorithms↗
PubMedDate not supplied

Left ventricular ejection fraction and volumes from gated single photon emission tomographic myocardial perfusion images: comparison between two algorithms working in three-dimensional space.

OBJECTIVE: Two different algorithms operating in three-dimensional space, one dependent on surface detection developed at Cedars-Sinai Medical Center (CS) and another dependent on statistical parameters and developed at Stanford University Medical School (SU), were compared in the same patients to assess the left ventricular volumes and the left ventricular ejection fractions (LVEFs) from gated single-photon emission tomography (SPECT) myocardial perfusion images. METHODS: Perfusion SPECT images gated in eight time bins were recorded in 40 patients with coronary artery disease 60 minutes after the injection of 925 MBq 99mTc-labeled tetrofosmin at rest. The LVEF values were validated against planar gated 99mTc-labeled blood pool studies (ERNA). RESULTS: The software success rates were 95% (38/40 patients) for CS and 100% for SU. Agreement between LVEFs measured with CS and SU and agreement between both methods and ERNA were excellent (LVEF[CS] = 0.89LVEF[SU] + 6.21, r = 0.93; LVEF[SU] = 0.92LVEF[ERNA] + 0.99, r = 0.94; and LVEF[CS] = 0.88LVEF[ERNA] + 4.58, r = 0.93). Bland-Altman plots showed that differences between LVEFs from SU and CS and from ERNA were similar across a wide range (20% to 80%) of LVEF values. No relationship between these differences and the severity of perfusion defects was observed. For left ventricular volumes, linear regression analysis showed an excellent correlation between both methods (end-diastolic volume r = 0.97 end-systolic volume r = 0.98), but systematically higher values were obtained with SU (p = 0.013). CONCLUSION: Measurements of LVEF obtained with CS and SU correspond well with those from the standard, ERNA, even in patients with severe perfusion defects. A close relationship is observed between SU and CS when left ventricular volumes are considered. Measurements of LVEF (and left ventricular volumes) should be considered as an integral part of myocardial perfusion studies whenever possible.

Adult↗
PubMed2006

Efficient and sensitive method for quantitative analysis of alkaloids in hardinggrass (Phalaris aquatica L.).

An efficient high-performance thin-layer chromatography (HPTLC) method for the analysis of alkaloids in hardinggrass (Phalaris aquatica L.) was developed. The method employed HPTLC glass plates precoated with silica gel 60F-254 as the stationary phase. The solvent system consisted of ethyl acetate/chloroform/7 N NH4OH in methanol (8:2:1, v/v/v). Using unidimensional double-development, bands were well separated for 10 alkaloid standards as well as alkaloids observed in hardinggrass plant extracts. Identities of compounds observed using HPTLC were validated by high-performance liquid chromatography-mass spectrometry (HPLC-MS). Software was used to quantify individual alkaloids in plant samples based on HPTLC retention factors and intensities relative to standards of known concentration. Correlation coefficients of 0.99 were obtained between estimated and actual concentrations for four standards (methyltyramine, hordenine, gramine, and 5-methoxydimethyltryptamine), with linearity in the range of 120-3840 ng/spot. The HPTLC method is repeatable and specific for beta-carboline, tryptamine, gramine, and tyramine type alkaloids in mixed standard and plant extracts. Initial results indicate substantial variation in alkaloid composition among and within hardinggrass populations.

Alkaloids↗
PubMed2004

Dual energy X-ray absorptiometry measurements in small subjects: conditions affecting clinical measurements.

OBJECTIVE: To document the clinical and experimental situations that may affect DXA measurements in small subjects. METHODS: 49 piglets (886g to 21100g) had measurements with either of two pencil beam densitometers (QDR 1000W and QDR 2000 Plus, Hologic Inc, Waltham, MA) using commercial infant (IWB) and adult whole body (AWB) software v5.71p and v5.71 respectively. AWB scans were analyzed with three additional software versions. 35 infants (2115 to 11564g) had IWB measurements. RESULTS: DXA measurements of total weight, bone mineral content, bone area, bone mineral density, fat and lean mass from IWB scans (all piglets) and from AWB scans (piglets >12 kg) were highly reproducible (p < 0.001). A statistically significant change occurred in at least one of the DXA measurements from the use of different platforms, variations in the amount and placement of covering (e.g., blanket), placement of the external calibration standard, presence of radiographic contrast material, presence of movement artifact, delivery of an intravenous fluid bolus prior to scanning or improper delineation of external calibration standard during analysis. Additionally, results varied amongst different versions of software as well as between IWB and AWB softwares. CONCLUSION: In small subjects, consistency in the DXA techniques is paramount for valid and meaningful comparison of DXA data in bone mass and body composition.

Absorptiometry, Photon↗
PubMed1998

Distinguishing the effects of maternal and offspring genes through studies of "case-parent triads".

A gene variant that increases disease risk will be overrepresented among diseased persons, even compared with their own biologic parents. This insight has led to tests based solely on the asymmetric distribution of a variant allele among cases and their parents (e.g., the transmission/disequilibrium test). Existing methods focus on effects of alleles that operate through the offspring genotype. Alleles can also operate through the mother's genotype, particularly for conditions such as birth defects that have their origins in fetal life. An allele working through the mother would have higher frequency in case-mothers than in case-fathers. The authors develop a log-linear method for estimating relative risks for alleles in the context of case-parent triads. This method is able to detect the effects of genes working through the offspring, the mother, or both. The authors assume Mendelian inheritance, but Hardy-Weinberg equilibrium is unnecessary. Their approach uses standard software, and simulations demonstrate satisfactory power and confidence interval coverage. This method is valid with a self-selected or hospital-based series of cases and helps to protect against misleading inference that can result when cases and controls are randomly sampled from a population not in Hardy-Weinberg equilibrium.

5,10-Methylenetetrahydrofolate Reductase (FADH2)↗
PubMed1996

A new concept for Cochlear implant speech processing.

OBJECTIVE: A new speech processing concept and its implementation cochlear implant neural net, simulation and stimulation (CINSTIM), for cochlear implant systems is currently under investigation. The main objectives of this new strategy are to improve speech perception within the early rehabilitation period for prelingually deaf cochlear implant users and to improve speech perception in noise for all implant users. The advantage of this approach is the capability to assess and compare entirely different speech processing methods within the existing implant hardware. DESIGN: The processing concept is based on discrete sequences of distinguishable stimulus patterns, robust speech processing, and a classifier. The embedded Kohonen classifier employs unsupervised neural net algorithms. RESULTS: Initial experimental results have validated the general processing scheme as well as the development of this complex software. In addition, a limited alphabet of distinguishable stimulus patterns was achieved and assessed with experienced users of a conventional cochlear implant system. Test subjects were able to learn and recognize up to 60% of these artificial patterns after a few training sessions. Currently this speech processing strategy is being evaluated through the Cochlear MSP system; however, it is compatible with the other computer driven digital cochlear implant systems.

Cochlear Implants↗
PubMed2002

Progress of capillary electrophoresis in therapeutic drug monitoring and clinical and forensic toxicology.

During the past decade, capillary electrophoresis (CE) emerged as a promising, effective, and economical approach for the analysis of licit and illicit drugs and their metabolites in biologic samples. This review provides an overview of the principles of CE, the features of CE instrumentation, and the key aspects of CE-based drug assays that were developed for therapeutic drug monitoring (TDM), clinical and forensic toxicology, and assessment of drug metabolism and pharmacokinetics. CE performed in fused-silica capillaries has sufficiently matured and can thus be applied routinely, whereas chip-based instrumentation comprising fully integrated assays is still in development. Despite the attractive advantages of electrokinetic capillary technology, relatively few CE-based assays for TDM and for drug screening of clinical and forensic interest have been adopted in the routine arena. The lack of complete systems designed for unattended operation, the reluctance of bioanalysts to replace a satisfactory existing method, and tight budgets are believed to have hindered the widespread replacement of older (mainly chromatographic) technology. Another limitation of CE is that this technique is somewhat less sensitive than other analytic techniques used for drug analysis in biologic fluids. New instrumental developments featuring user-friendly software and the introduction of assay kits, however, should increase the number of validated CE drug tests becoming used on a routine basis.

Drug Monitoring↗
PubMed2000

Comparison of an integral equation on energy and the ray-tracing technique in room acoustics.

This paper deals with a comparison of two room acoustic models. The first one is an integral formulation stemming from power balance and the second is the ray-tracing technique with a perfectly diffuse reflection law. The common assumptions to both models are the uncorrelated wave hypothesis and the perfectly diffuse reflection law. The latter allows the use of these methods for nondiffuse fields beyond the validity domain of Sabine's formula. Comparisons of numerical simulations performed with the softwares RAYON and CeReS point out that these results are close to each other and finally, a formal proof is proposed showing that both methods are actually equivalent.

Acoustics↗
PubMed2026

[Analysis of a Chinese pedigree affected with Townes-Brocks syndrome due to a novel variant of SALL1 gene and a literature review].

OBJECTIVE: To analyze a novel exonic variant of the SALL1 gene and its impact on the binding site of SALL protein. METHODS: Clinical data of three children diagnosed with Townes-Brocks syndrome and their family members who had presented at the First Affiliated Hospital of Shandong First Medical University in April 2022 were retrospectively collected. The pathogenic variant was identified through whole-genome sequencing (WGS) and validated by Sanger sequencing. Protein structural prediction was performed using AlphaFold and PyMOL software to construct three-dimensional models of the wild-type and mutant proteins. Additionally, previously reported cases were systematically reviewed. This study was approved by the Medical Ethics Committee of the hospital (Ethics No.: 2023-386). RESULTS: The proband was one of triplet sisters born at 34+4 gestational weeks. All three cases had presented with anal atresia and rectovaginal fistula, and case 3 also had toe malformation of left foot. WGS revealed a novel heterozygous c.757C>T (p.Gln253*) variant in the SALL1 gene, which was predicted to be pathogenic. Sanger sequencing confirmed co-segregation of the variant with the disease within the family. Protein structural modeling demonstrated that the variant has introduced a premature stop codon at position 253, resulting in a truncated protein. CONCLUSION: Above finding has enriched the mutation spectrum of the SALL1 gene in association with Townes-Brocks syndrome, which also represented a rare case of anal atresia in triplets, and provided a basis for molecular diagnosis, genetic counseling, and further research.

Humans↗
PubMed2002

Cytoarchitecture of the retinal ganglion cells in the rat.

PURPOSE: To determine the number and cytoarchitecture of retinal ganglion cells (RGCs) in the female Wistar rat, by using a newly devised procedure for rapid RGC counting in the entire retina that avoids assumptions about RGC spatial arrangement. METHODS: RGCs of normal female Wistar rats were retrogradely labeled with a fluorescent tracer. Automated counting was accomplished by applying standard imaging software to analysis of all labeled cells in retinal flatmounts. The method was validated by comparison of automated and manual counts of 70,000 RGCs in frames covering the density range in the normal rat retina of 600 to 3600 RGC/mm(2). RGC numbers were determined for each retina and compared with the contralateral retina of the same animal. RGC density maps were constructed for each retina. RGC size distribution was determined. RESULTS: Automated RGC counting showed a good linear correlation with manual counting (R(2) = 0.9416). Mean total RGC count in 10 rat eyes was 97,609 +/- 3,930 (SEM) per eye. Contralateral eyes differed by an average of 4.1% (3983 plus minus 5098 RGCs). Size analysis calculated from cell areas confirmed that the majority of rat RGCs are between 7 and 21.5 microm in equivalent diameter. The RGC counts for all frames at the same eccentricity in all 10 of the retinas showed that variability increased with eccentricity and increased further as the fractional area of the retina sampled at each eccentricity was reduced. There was also significant variability in the spatial density of the RGCs at the same eccentricity location between different eyes. Comparison of total RGC counts between left and right eyes estimated from RGC counts in sectors of the retina (hemiretinas or quadrants) showed increased variability compared with counting all the RGCs in a retina. CONCLUSIONS: RGCs in the Wistar rat display significant variability in their cytoarchitecture. Such variability can make quantification by sampling problematic for diffuse, and particularly, for focal RGC losses resulting from experimental interventions, unless virtually the entire RGC population is counted.

Animals↗
PubMed2006

Gene expression changes in the retina following optic nerve transection.

PURPOSE: To obtain and analyze the gene expression profiles of the retina following optic nerve transection (ONT). METHODS: An axotomy animal model was generated by taking a cross section of the optic nerve with care not to damage the adjacent blood supply. The extent of cell loss was evaluated by counting cells in the ganglion cell layer (GCL) of flat-mounted retinas stained with cresyl violet. Gene expression profiles of control and ONT retinas were analyzed with Agilent's rat oligo microarray slides. Differentially expressed genes were identified from three independent experiments and clustered based on their functions with expression analysis systematic explorer software. Real-time quantitative and semiquantitative RT-PCR were used to validate changes in gene expression levels. RESULTS: Gene expression changes in axotomized retinas were analyzed with rat oligo microarray slides containing 22,575 oligonucleotide probes that represent over 20,000 genes and expressed sequence tags (ESTs). The expression of 493 genes was increased more than 1.5 fold, including 85 that were upregulated more than 2 fold, and the expression of 113 genes was decreased 1.5 fold or more, including 21 that were downregulated more than 2 fold. Differentially expressed genes were clustered based on their functions. Several novel genes expressed in the GCL have been identified and their expression patterns in different tissues were analyzed. Among the genes differentially regulated in retinas with induced retinal ganglion cell (RGC) death, we have identified 13 genes that are mapped to known glaucoma loci and can be considered for mutation screening in patients with inherited forms of glaucoma. CONCLUSIONS: The gene expression profiles of the ONT retinas can be used to identify RGC-expressed genes, which may be essential for the morphological and physiological characteristics of RGCs. The results of this study can also be used to evaluate the molecular changes taking place in the retina in response to RGC loss.

Animals↗
PubMed1988

[Use of an expert system as a tool to carry out urinary cyto-bacteriologic tests].

An expert system for urine examinations was developed. Its validation was performed in a routine work, by comparison of expert decisions with software conclusions. Results of finished examinations or in progress were taken into account. The agreement was satisfactory. In addition to reliability, advantages constituted by availability, flexibility and adaptability were notified. Repeatability and reproducibility were also emphasized.

Algorithms↗
PubMed1995

[Endothelial keratopathy in pseudoexfoliation syndrome: quantitative and qualitative morphometry using automated video image analysis].

UNLABELLED: This prospective study intended to quantify and classify morphological changes of the corneal endothelium in pseudoexfoliation syndrome (PSX) after having tested reproducibility and validity of a new automated technique for analysing corneal endothelium. PATIENTS AND METHODS: We used a contact specular microscope combined with a video camera (Tomey EM-1000) and a computer (IBM compatible PC, 486DX33) with suitable software (Tomey EM-1100, version 0.94). Video images of corneal endothelium (area: 0.312 mm2) are passed directly into the computer input by means of a frame grabber and are automatically processed. Missing or falsely recognized cell borders are corrected using the mouse. We examined 85 eyes with PSX and 33 healthy control eyes. At first, retest-stability and validity of the cell density measurements were assessed in the PSX-eyes. A qualitative analysis of the corneal endothelium followed. RESULTS: The cell density measurements showed a high retest-stability (reliability coefficient r = 0.974). The values of the automated method (2040 +/- 285 cells/mm2) and those of manual cell counting (2041 +/- 275 cells/mm2) did not differ significantly (p = 0.441). The mean difference was 3.1 +/- 2.4%. Comparing the 85 PSX-eyes (2052 +/- 264 cells/mm2) to the 33 control eyes (2372 +/- 276 cells/mm2), there was a significant reduction of cell density (p < 0.001). The cell density of the 69 PSX-eyes with glaucoma (2014 +/- 254 cells/mm2) was significantly lower than that of the 16 PSX-eyes without glaucoma (2214 +/- 251 cells/mm2) (p = 0.008). Eighty-five percent of the 85 PSX-eyes showed polymegalism, 77% pleomorphism; 68% had white deposits and 42% guttae. White deposits and guttae were significantly more frequent and more intensive in PSX-eyes than in control eyes. PSX-eyes with and those without glaucoma showed no significant differences concerning the four qualitative parameters. CONCLUSION: The automated method for analysing corneal endothelium quickly provides reproducible and valid results using the correction mode of the software. Semiquantitative analysis of qualitative parameters permits a more differentiated assessment of keratopathy in pseudoexfoliation syndrome than does mere consideration of endothelial cell density. Both evaluations are recommended to assess the risk of a diffuse endothelial decompensation before intraocular surgery.

Aged↗
PubMed1998

A software program to calculate Goodman and Kruskal's gamma: a method to monitor surgical-site infection rates.

Several studies have described a need for a valid statistical methodology to facilitate interhospital and intrahospital infection rates for their operative procedures. Physician awareness of postoperative surgical-site infection rates has been demonstrated as an effective means to reduce infection rates in both high- and low-risk surgical patients. This article presents a new software program that allows for simple data entry and provides results including the gamma statistic, sample size, variance, standard error, and Z value and P value of the gamma result. This software also provides a data interpretation table, allowing infectious disease department physicians or staff to determine if a significant relation exists between operative procedure infection rates and patient risk factors.

Hospitals↗