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At least 1,117 records · Page 62Linked to original sources
PubMed1999

Analysis of helminth genetic data: comparative examples with Haemonchus contortus isozymes using exact tests or resampling procedures.

Population genetic data on helminths are scarce and it is important to fine tune analyses of these data, the interpretation of which is based on between-(Fst) and within-(Fis) population variability. Several computer programs are available and confidence intervals of each index are based on different procedures. These programs (Genetix, Diploid, Genepop) were compared with a classical program (Biosys-1) using a large set of Haemonchus contortus isozyme data. The results were identical for all softwares for large differences when natural populations were studied (Fst > 0.25 and Fis > 0.15 or <-0.15). When small Fst were investigated in laboratory-reared populations, the significance of differences was often related to the software used. As a rule of thumb, it is suggested that at least two out of three software packages (based on different calculation procedures) should give similar results before differences are validated.

Animals↗
PubMed1999

Continuous thermodilution cardiac output: clinical validation against a reference technique of known accuracy.

OBJECTIVE: To evaluate the accuracy and precision of continuous thermodilution (CCO) by using a validated bolus thermodilution (BCO) reference technique as criterion standard. DESIGN: Under circulatory steady state conditions, a CCO system (Vigilance, software versions 4.35 and 4.39) was validated with regard to CCO as well as iced and room temperature BCO. SETTING: Intensive care unit at a university hospital. PATIENTS: Method comparison was conducted in 56 cardiac surgical patients, 28 patients being allocated to one of the two software versions, and 14 within each group to either iced or room temperature BCO. MEASUREMENTS AND RESULTS: CCO readings were registered in duplicate before and after three to five bolus injections conducted with both the Vigilance and reference systems. Iced BCO showed excellent agreement between the Vigilance and reference systems, yielding SDs of bias of 0.41 and 0.37 l/min and linear correlation coefficients (r) of 0.97 and 0.96. With room temperature BCO, agreement was significantly less. CCO, irrespective of software version, showed higher SDs of bias (0.90 and 0.84 l/min) and lower r values (0.84 and 0.81) than iced BCO (p < 0.0001). CCO measurements with software version 4.39 yielded a similar SD of bias to that with room temperature BCO. CONCLUSION: Decreased precision of CCO as compared to iced BCO may, in clinical settings, be outweighed by the advantages of automated and continuous monitoring. Under research conditions, however, iced BCO remains the method of choice.

Adolescent↗
PubMed1997

Experimental validation of dose distributions predicted by a treatment planning system for complex models.

The trend towards dose escalation in radiation therapy creates the need for non-coplanar beam arrangements to help minimize healthy tissue morbidity in the proximity of treatment volumes. Treatment planning software packages are able to generate external beam non-coplanar isodose distributions and this must be validated before use in a clinical setting. Kodak XV film was used to measure the relative dose within various tissue equivalent phantoms for comparison with the distributions predicted by the G.E. Target ("Target") treatment planning software. The results confirm that Target is able to predict the isodose distribution for coplanar and non-coplanar beams incident on patient equivalent phantoms containing relatively large, semi-infinite inhomogeneities well enough to warrant its implementation into routine clinical use. However, we have found that Target may not be able to adequately predict dose distributions around smaller inhomogeneous inclusions. Further work will be required to investigate this potential problem.

Film Dosimetry↗
PubMed1996

A methodology for solving physiologically based pharmacokinetic models without the use of simulation softwares.

The objective of the present study was to develop and validate a methodology for solving physiologically based pharmacokinetic (PBPK) models without the use of simulation software. The approach involves keying the parameter values and model equations into Microsoft Excel spreadsheets, and conducting simulations by solving the model equations according to Euler's method of numerical integration. This approach was applied to simulate the pharmacokinetics of styrene in rats exposed to 80 and 600 ppm for 6 h. The simulation results were plotted along with experimental data using the regular graphic features available in Excel, and validated by comparing them with simulation results obtained using a commercially available software (Advanced Continuous Simulation Language, ACSL). The simulations obtained with ACSL and Excel, in general, differed by <1%. The methodology developed in the present study should help informed individuals understand and solve PBPK models, without having to use "black-box' kind of computer programs and simulation softwares.

Algorithms↗
PubMed1998

Isolated U-fiber involvement in MS: preliminary observations.

We studied the frequency and location of isolated U-fiber involvement in MS and correlated these findings exploratively with physical disability and neuropsychological impairment. Fifty-three MS patients were examined. Three-millimeter-thick, fast spin-echo T2-weighted MR images and spin-echo postgadolinium T1-weighted images were obtained. Computer software that which had been validated previously for quantitation of MS lesions was used to detect lesions on the T2-weighted images. The Expanded Disability Status Scale (EDSS), Ambulation Index (AI), and a battery of neurocognitive tests were performed on each patient. Forty-two arcuate hyperintensities along the U-fiber were detected by the software in 28 patients (53%). Twenty-seven lesions (64.3%) were seen in the frontal lobe, eight (19.0%) in the temporal lobe, three (7.1%) in the parietal lobe, three (7.1%) in the occipital lobe, and one (2.4%) in both frontal and parietal lobes. Four lesions (9.5%) showed gadolinium enhancement. Seventeen lesions (40%) were hypointense on the T1-weighted images. Scores of three of the 11 neuropsychological tests reflecting performance in executive control and memory were significantly different at least at the p = 0.05 level between the eight patients with multiple, isolated U-fiber lesions and the 45 patients without any or with only a single U-fiber lesion. No significant difference was noted for EDSS or AI. Isolated U-fiber involvement is an underappreciated MR finding in MS. Our preliminary hypothesis is that U-fiber lesions may contribute to neuropsychological impairment, although our observation requires confirmation.

Adult↗
PubMed2001

Quantitative assessment of motion artifacts and validation of a new motion-correction program for myocardial perfusion SPECT.

UNLABELLED: Patient motion during myocardial perfusion SPECT can produce images that show artifactual perfusion defects. The relationship between the degree of motion and the extent of artifactual perfusion defects is not clear for either single- or double-head detectors. Using both single- and double-head detectors and quantitative perfusion SPECT (QPS) software, we studied the pattern and extent of defects induced by simulated motion and validated a new automatic motion-correction program for myocardial perfusion SPECT. METHODS: Vertical motion was simulated by upward shifting of the raw projection datasets in a returning pattern (bounce) and in a nonreturning pattern at 3 different phases of the SPECT acquisition (early, middle, and late), whereas upward creep was simulated by uniform shifting throughout the acquisition. Lateral motion was similarly simulated by left shifting of the raw projection datasets in a returning pattern and in a nonreturning pattern. Simulations were performed using single- and double-head detectors, and simulated motion was applied to projection images from 8 patients who had normal 99mTc-sestamibi SPECT findings. Additionally, images from 130 patients with actual clinical motion were assessed before and after motion correction. The extent of perfusion defects was assessed by QPS, and a 20-segment, 5-point scoring system was used to assess the effect of motion on the presence and extent of perfusion defects. RESULTS: Of 12 bounce simulations, the bouncing motion failed to produce significant (>3%) perfusion defects with either the single- or the double-head detector. With the single-head detector, early shifting created the largest defect, whereas with the double-head detector, shifting during the middle of the acquisition created the largest defect. With regard to upward creep, defects were of larger extent with the double- than the single-head detector. With the single-head detector, 8 of 20 simulated motion patterns yielded significant perfusion defects of the left ventricle, 7 (88%) of which were significantly improved after motion correction. With the double-head detector, 12 of 20 patterns yielded significant defects, all of which improved significantly after correction. Of 2,600 segments in the 130 patients with actual clinical motion, only 1.3% (30/2,259) of segments that were considered normal (score = 0 or 1) changed to abnormal (score = 2-4) after motion correction, whereas 27% (92/341) of abnormal segments were reclassified as normal after motion correction. CONCLUSION: Artifactual perfusion defects created by simulated motion are a function of the time, degree, and type of motion and the number of camera detectors. Application of an automatic motion-correction algorithm effectively decreases motion artifacts on myocardial perfusion SPECT images.

Aged↗
PubMed2005

[Study of serum proteome biomarkers with relation to the formation of portal vein tumor thrombi in hepatocellular carcinoma patients].

OBJECTIVE: To screen serum proteome biomarkers and establish predictive model with relation to the formation of portal vein tumor thrombi (PVTT) in hepatocellular carcinoma (HCC) patients. METHODS: Serum samples were collected from 135 HCC patients, which were divided, into training set (including 33 HCC patients with PVTT and 62 HCC patients without PVTT) and blind testing set (including 18 HCC patients with PVTT and 22 HCC patients without PVTT). Special serum protein or peptide pattern was determined by SELDI-TOF-MS measurement after treating the sample onto WCX2 protein chip for each case. The obtained data were analyzed by BioMarker Wizard software to screen serum proteome biomarkers with relation to the formation of PVTT, while decision tree classification algorithm and blind validation were determined by Biomarker Patterns Software. RESULTS: Ranging from 1100 to 30 000 at the m/z value, 100 protein features were detected in the serum protein pattern stably. Among them, 6 protein peaks with the m/z value of 3478, 1314, 1744, 1725, 2022 and 3380 were upregulated, 10 proteins peaks with the m/z value of 8901, 9353, 9415, 8773, 2766, 2745, 8697, 7773, 8569 and 1373 were downregulated respectively in the group of HCC with PVTT. The 7 candidate protein peaks with the m/z value of 3478, 2022, 8901, 9415, 8773, 2766 and 2745 were selected to establish predictive model by BPS with a sensitivity of 75.8% (25/33) and specificity of 82.3% (51/62). An accuracy of 87.5% (35/40), sensitivity of 100% (18/18), specificity of 77.3% (17/22), positive predictive value of 78.3% (18/23), and negative predictive value of 100% (17/17) were validated in blind testing set. CONCLUSION: Sixteen candidate proteome biomarkers may be related with the formation of PVTT in HCC patients. Decision tree classification algorithm may have great clinical significance in predicting the formation of PVTT.

Adult↗
PubMed2006

User-guided 3D active contour segmentation of anatomical structures: significantly improved efficiency and reliability.

Active contour segmentation and its robust implementation using level set methods are well-established theoretical approaches that have been studied thoroughly in the image analysis literature. Despite the existence of these powerful segmentation methods, the needs of clinical research continue to be fulfilled, to a large extent, using slice-by-slice manual tracing. To bridge the gap between methodological advances and clinical routine, we developed an open source application called ITK-SNAP, which is intended to make level set segmentation easily accessible to a wide range of users, including those with little or no mathematical expertise. This paper describes the methods and software engineering philosophy behind this new tool and provides the results of validation experiments performed in the context of an ongoing child autism neuroimaging study. The validation establishes SNAP intrarater and interrater reliability and overlap error statistics for the caudate nucleus and finds that SNAP is a highly reliable and efficient alternative to manual tracing. Analogous results for lateral ventricle segmentation are provided.

Brain↗
PubMed1988

Development and validation of an automated method of the Selvester QRS scoring system for myocardial infarct size.

The Selvester QRS score for estimation of myocardial infarct (MI) size from the standard 12-lead electrocardiogram (ECG) has not yet achieved wide recognition as a valuable tool in the routine assessment of the MI patient, primarily because of the practical limitations inherent to manual application. This study examined the ECGs of 438 patients (105 normal subjects, 161 with "possible" MI and 172 with "definite" MI based on data from cardiac catheterization) to develop software for an automated method of the Selvester system in attempts to overcome the manual constraints. After a comprehensive validation process involving extensive interactions between the manual scorer and the software developer, an automated method of the Selvester system was generated that had a high correlation with manual application (r = 0.94) and was superior regarding time, training, reader bias, reproducibility and precision of measurement. These results indicate that an automated version of the Selvester QRS scoring system would resolve many of the limitations of manual application and would provide a reliable, technically accurate estimate of MI size that could be incorporated into ECG diagnostic programs and used in standard digital ECG machines.

Cardiac Catheterization↗
PubMed2004

Software approach to merging molecular with anatomic information.

Software image registration is a powerful and versatile tool that allows the fusion of molecular and anatomic information. Image registration can be applied to compare anatomic information with function, localize organs and lesions, and plan radiation therapy, biopsy, or surgery. Automatic volume-based image registration techniques have been devised for both linear and nonlinear image alignment. Challenges remain in the validation of the accuracy of software registration. Image registration has been applied clinically in neurology and oncology and may be particularly practical in radiotherapy applications. Potential new applications in cardiology could allow the combination of CT angiography with perfusion and viability images obtained by PET, SPECT, or MRI. Software methods allow versatility in the choice of modalities and facilitate retrospective and selective application. Fully automatic registration algorithms are needed for routine clinical applications. Connectivity, compatibility, and cooperation between various clinical departments are essential for the successful application of software-based image fusion in a hospital setting.

Algorithms↗
PubMedDate not supplied

Probabilistic linkage of large public health data files.

Probabilistic linkage technology makes it feasible and efficient to link large public health databases in a statistically justifiable manner. The problem addressed by the methodology is that of matching two files of individual data under conditions of uncertainty. Each field is subject to error which is measured by the probability that the field agrees given a record pair matches (called the m probability) and probabilities of chance agreement of its value states (called the u probability). Fellegi and Sunter pioneered record linkage theory. Advances in methodology include use of an EM algorithm for parameter estimation, optimization of matches by means of a linear sum assignment program, and more recently, a probability model that addresses both m and u probabilities for all value states of a field. This provides a means for obtaining greater precision from non-uniformly distributed fields, without the theoretical complications arising from frequency-based matching alone. The model includes an iterative parameter estimation procedure that is more robust than pre-match estimation techniques. The methodology was originally developed and tested by the author at the U.S. Census Bureau for census undercount estimation. The more recent advances and a new generalized software system were tested and validated by linking highway crashes to Emergency Medical Service (EMS) reports and to hospital admission records for the National Highway Traffic Safety Administration (NHTSA).

Adult↗
PubMed2004

Self-validating presentation and response timing in cognitive paradigms: how and why?

With the proliferation of commercial experiment generators and custom software within cognitive psychology and the behavioral sciences, many have assumed that issues regarding millisecond timing accuracy have been largely solved. However, through empirical investigation of a variety of paradigms, we have discovered numerous sources of timing error. These can range from poor scripting practices, to incorrect timing specifications, to hardware variability. Building upon earlier research, we have developed a commercial device and associated software that enables researchers to benchmark most computer-based paradigms in situ and without modification. This gives them the opportunity to correct timing errors where practicable, increase replicability, and reduce variability by altering onset times for stimuli, by replacing inaccurate hardware, or by post hoc statistical manipulation should the source of error be constant. We outline the features of the device and accompanying software suite, stress the importance of such independent validation, and highlight typical areas that can be subject to error.

Benchmarking↗
PubMedDate not supplied

Software requirements: definition and specification.

The software requirements specification is the single most important document in the software development process. It provides the basis for development as well as for validation. The SRS needs to include adequate definition of all requirements without specifying implementation or project management issues. The SRS should be completed early in the development process. However, it is very likely that changes will occur during the development life cycle. This is not an excuse for approving and releasing the current version of the SRS. When changes occur, the SRS must be revised. In any case, the concept is to deal with the current, approved version of the SRS. Ultimately, the SRS should include all the information needed to proceed into the design phase of software development.

Software↗
PubMed2006

[A preliminary study on the extraction method of velocity pulsated signals in the velocity spectrum image of pulsed Doppler ultrasounds in vitro].

Focus on the defects of the extraction method of velocity pulsated signals in the velocity spectrum image of pulsed Doppler ultrasounds (such as the limited data, great amount of work and low reproducibility), we combine the earlier research results and the basic rules of the velocity spectrum image, and employing the visual basics plateau, to design and develop a software to extract the velocity signals from the spectrum image automatically. Compare the mean velocity and RNS between the PIV and the PDU resulting from the method, the correlations are r = 0.93 and r = 0.78 respectively. The study reveals the software increase the amount of valid data, decrease the amount of work and increase reproducibility of the signals extraction. The method may be an effective way to analyse the velocity spectrum image of PDU in clinic.

Arteries↗
PubMedDate not supplied

[Estimate of potential health benefits of the reduction of air pollution with PM10 in Trieste, Italy].

OBJECTIVES: Estimate of the possible benefits, in Trieste, of a reduction of PM10 to values not over 60, 50, 40, 30, 20, 10 microg/mc, utilizing data of PM10 of the year 2002 as cause specific deaths and admissions. DESIGN: Cause specific deaths and admissions attributable to short term effects of PM10 calculated by software AirQ, utilizing Relative Risk from MISA 1 study (as published in 2002). SETTING: Trieste (Italy). MAIN OUTCOMES MEASURES: Cause specific deaths and admissions. RESULTS: Using air pollution data for 2002, 1.8% (CI 95% 0.6%; 2.9%) of natural deaths, 2.2% (CI 95% 0.6%; 3.7%) of cardiovascular deaths and 2.5% (CI 95% 0; 7.3%) of respiratory deaths, 1.5% (CI 95% 0.6; 2.4%) of cardiovascular admissions and 1.6% (CI 95% 0; 3.3%) of respiratory admissions were attributable to PM10 concentrations over 20 microg/mc. CONCLUSIONS: AirQ software proved to be a valid and reliable tool to estimate the potential short term effects of air pollution. Special attention is required to choose the relative risks to be utilized.

Air Pollutants↗
PubMed2001

Optical analysis of displacement and strain fields on human skin.

BACKGROUND/AIMS: The aim of this article is to propose a new way to measure the mechanical behaviour of skin by using optical analysis software. Some examples on scars and stretch marks show the validity and the prospects of such a method. METHODS: Software is used to compare two states of deformation. The user takes two photos of the skin surface he wants to study, before and after the deformation is applied. The software is used to process the data. RESULTS: The software gives a mapping of the displacement, and strain fields of the area studied. Investigations can be realised in vitro or in vivo, and it is possible to study, for example, cutaneous lesions like scars and stretch marks. CONCLUSIONS: The method presented gives convincing results, which open many prospects in dermatology, surgery and cosmetology.

Cicatrix↗
PubMed1987

Electric and magnetic fields of the brain computed by way of a discrete systems analytical approach: theory and validation.

It is shown how the stationary volume conduction phenomena in the brain, namely the electric and magnetic fields can be described in discrete terms. The volume conductor is sampled in space by introducing a sampling distance corresponding to the uncertainty in the measurements. In this way, a three-dimensional lattice is needed with equidistantly spaced nodes. The electric and magnetic properties of such a lattice are assumed to be equivalent to that of brain and other tissues. The electric and magnetic potential fields are calculated for each node as the output of a linear feedback system which has the impressed currents as the input. By way of the feedback loop the reflection phenomena at the boundaries between media of different conductivity can be taken into account. This discrete formalism has been implemented in a software system. To demonstrate the validity and accuracy of this system a number of analytically tractable problem in volume conduction has been evaluated.

Animals↗