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PubMedDate not supplied

Direct memory access of diffraction patterns from striated muscle--a software view.

Complete software support has been developed for a direct memory access microprocessor system used to store and analyze diffraction data from striated muscle. These studies are based on the premise that the regularly alternating light and dark regions of the fiber behave like a phase grating to incident laser light. A knowledge of the position of a diffracted order can thus be used to determine striation spacing. Since these striations are directly associated with the force generating components of the muscle, diffraction data can provide insights into the mechanism of force generation in muscle. In our system, a charge-coupled device (CCD) is used to detect diffracted order, position, and intensity. In addition, a high speed muscle puller and tension transducer are used to characterize or alter the mechanical state of the muscle. The software has been designed to allow the inexperienced user to perform sophisticated diffraction experiments. The user may present several experimental parameters: magnitude and direction of puller movement; number of frames of data to be taken; and delay of puller or scan. This has been accomplished by interleaving DMA and control loop cycles. System performance indicates that the full 256 point analog output of the CCD can be digitized and stored in about 2 ms. The data can be transferred directly from the CCD to memory leaving the CPU free for experimental control or closed-loop processing.

Animals↗

PubMed2004

Assessment of donor liver steatosis: pathologist or automated software?

Steatosis in donor liver biopsy specimens has been shown to correlate with graft dysfunction after orthotopic liver transplantation. This 2-part (laboratory pilot, clinical retrospective) study compared the traditional interpretation of steatosis by a pathologist with an automated measurement determined by an image analysis system. In our pilot study, Sprague-Dawley rats were studied prospectively by feeding them a choline-deficient diet for up to 7 days. In our clinical group, data from 49 consecutive recipients of cadaveric liver transplantation were reviewed retrospectively. In both studies, the percentages of microvesicular fat, macrovesicular fat, and total fat content within liver biopsy specimens were determined by an automated image analysis software program and a pathologist using the same set of slides. The association between fat content of the donor liver and patient survival and graft survival, along with levels of aspartate aminotransferase, alanine aminotransferase, prothrombin time, and total bilirubin after transplantation, were also examined in the clinical study. A direct correlation was observed between levels of macrovesicular fat determined by a pathologist and the automated software using livers from rats fed a choline-deficient diet and livers from deceased donors. A significant association was observed between macrovesicular fat content in the donor liver biopsy and graft survival by both techniques. We conclude that an image analysis system can be used to automate the determination of fat content in liver biopsy specimens, and that its findings correlate with both the visual interpretation by a pathologist and graft survival. Further study is needed to determine the role of an automated technique in the evaluation of donor livers for transplantation.

Animals↗

PubMed2004

The use of a 3D laser scanner using superimpositional software to assess the accuracy of impression techniques.

OBJECTIVE: Several studies have made comparisons in the dimensional accuracy of different elastomeric impression materials. Most have used two-dimensional measuring devices, which neglect to account for the dimensional changes that exist along a three-dimensional surface. PURPOSE: The aim of this study was to compare the dimensional accuracy of an impression technique using a polyether material (Impregum) and a vinyl poly siloxane material (President) using a laser scanner with three-dimensional superimpositional software. MATERIALS AND METHODS: Twenty impressions, 10 with a polyether and 10 with addition silicone, of a stone master model that resembled a dental arch containing three acrylic posterior teeth were cast in orthodontic stone. One plastic tooth was prepared for a metal crown. The master model and the casts were digitised with the non-contacting laser scanner to produce a 3D image. 3D surface viewer software superimposed the master model to the stone replica and the difference between the images analysed. RESULTS: The mean difference between the model and the stone replica made from Impregum was 0.072mm (SD 0.006) and that for the silicone 0.097mm (SD 0.005) and this difference was statistically significantly, p=0.001. CONCLUSIONS: Both impression materials provided an accurate replica of the prepared teeth supporting the view that these materials are highly accurate.

Dental Impression Materials↗

PubMed2004

XSophe-Sophe-XeprView. A computer simulation software suite (v. 1.1.3) for the analysis of continuous wave EPR spectra.

The XSophe-Sophe-XeprView computer simulation software suite enables scientists to easily determine spin Hamiltonian parameters from isotropic, randomly oriented and single crystal continuous wave electron paramagnetic resonance (CW EPR) spectra from radicals and isolated paramagnetic metal ion centers or clusters found in metalloproteins, chemical systems and materials science. XSophe provides an X-windows graphical user interface to the Sophe programme and allows: creation of multiple input files, local and remote execution of Sophe, the display of sophelog (output from Sophe) and input parameters/files. Sophe is a sophisticated computer simulation software programme employing a number of innovative technologies including; the Sydney OPera HousE (SOPHE) partition and interpolation schemes, a field segmentation algorithm, the mosaic misorientation linewidth model, parallelization and spectral optimisation. In conjunction with the SOPHE partition scheme and the field segmentation algorithm, the SOPHE interpolation scheme and the mosaic misorientation linewidth model greatly increase the speed of simulations for most spin systems. Employing brute force matrix diagonalization in the simulation of an EPR spectrum from a high spin Cr(III) complex with the spin Hamiltonian parameters g(e) = 2.00, D=0.10 cm(-1), E/D = 0.25, A(x) = 120.0, A(y) = 120.0, A(z) = 240.0 x 10 (-4) cm(-1) requires a SOPHE grid size of N = 400 (to produce a good signal to noise ratio) and takes 229.47 s. In contrast the use of either the SOPHE interpolation scheme or the mosaic misorientation linewidth model requires a SOPHE grid size of only N = 18 and takes 44.08 and 0.79 s, respectively. Results from Sophe are transferred via the Common Object Request Broker Architecture (CORBA) to XSophe and subsequently to XeprView where the simulated CW EPR spectra (1D and 2D) can be compared to the experimental spectra. Energy level diagrams, transition roadmaps and transition surfaces aid the interpretation of complicated randomly oriented CW EPR spectra and can be viewed with a web browser and an OpenInventor scene graph viewer.

Journal Article↗

PubMed2006

Klusters, NeuroScope, NDManager: a free software suite for neurophysiological data processing and visualization.

Recent technological advances now allow for simultaneous recording of large populations of anatomically distributed neurons in behaving animals. The free software package described here was designed to help neurophysiologists process and view recorded data in an efficient and user-friendly manner. This package consists of several well-integrated applications, including NeuroScope (http://neuroscope.sourceforce.net), an advanced viewer for electrophysiological and behavioral data with limited editing capabilities, Klusters (http://klusters.sourceforge.net), a graphical cluster cutting application for manual and semi-automatic spike sorting, NDManager (GPL,see http://www.gnu.org/licenses/gpl.html), an experimental parameter and data processing manager. All of these programs are distributed under the GNU General Public License (GPL, see ), which gives its users legal permission to copy, distribute and/or modify the software. Also included are extensive user manuals and sample data, as well as source code and documentation.

Animals↗

PubMed2006

Prediction of bone mass gain by bone turnover parameters after parathyroidectomy for primary hyperparathyroidism: neural network software statistical analysis.

BACKGROUND: Primary hyperparathyroidism (pHPT) is the most frequent endocrine hypersecretion disease, and parathyroidectomy is the only curative option, since pharmacologic therapy reduces hypercalcemia but does not impede parathyroid hormone hypersecretion. According to guidelines from the National Institutes of Health, parathyroidectomy is associated with bone mass increase in some asymptomatic patients, while in others bone mass is not changed after surgery. Therefore, we performed the present study in an attempt to elucidate whether a preoperative biochemical bone parameter can be predictive of a significant vertebral bone mass increase in patients with pHPT. METHODS: For each patient we analyzed the following preoperative parameters: parathyroid hormone, urinary calcium excretion, urinary type I collagen cross-linked N-telopeptide (NTX), osteocalcin, and vertebral computerized bone mineralography. All patients underwent vertebral computerized bone mineralography 12 months after the operation. Statistical analysis was carried out by a neural network program, an event-predicting software modeled on human brain neuronal connections, which is able to examine independent statistical parameters. RESULTS: The patients presenting with high preoperative bone turnover (especially high NTX levels) will have a 5% vertebral bone mass gain in 83.33% of cases after surgery, independently of the National Institutes of Health guidelines. CONCLUSIONS: A high preoperative NTX level seems to be the best predictor parameter for postoperative vertebral bone mass gain in patients with pHPT. Our study also illustrates that neural network software may be a valuable method to help elucidate which pHPT patients should undergo surgical treatment.

Aged↗

PubMed2004

The regulatory software of cellular metabolism.

Understanding the regulation of metabolic pathways in the cell is like unraveling the 'software' that is running on the 'hardware' of the metabolic network. Transcriptional regulation of enzymes is an important component of this software. A recent systematic analysis of metabolic gene-expression data in Saccharomyces cerevisiae reveals a complex modular organization of co-expressed genes, which could increase our ability to understand and engineer cellular metabolic functions.

Algorithms↗

PubMed2001

Evaluation of Spartan semi-empirical molecular modeling software for calculations of molecules on surfaces: CO adsorption on Ni(111).

This paper reports the use of the PM3(tm) semi-empirical method in the Spartan molecular modeling software to optimize geometries and calculate vibrational frequencies for increasingly complex transition metal- and carbon monoxide (CO)-containing systems, culminating in calculations of CO adsorbed on a Ni(111) surface. Mononuclear and dinuclear transition metal carbonyl molecular species were used to establish the level of accuracy that could be expected for vibrational frequencies to provide a context for the results from the adsorbed molecule calculations. One to four CO molecules adsorbed on the (111) face of a 22-atom-nickel crystal were then modeled, and the accuracy of the adsorption geometry and vibrational frequency was evaluated. The calculated CO stretching vibrational frequencies were within 8% larger than the gas phase experimental values for the molecular species and were approximately 10% larger than the range of experimental values for CO on the nickel surface. The geometry optimization predicted that the CO molecules on the Ni(111) surface occupy three-fold hollow sites with no preference for sites over Ni atoms, in agreement with recent structural data and other theoretical calculations. The software was less successful in calculating the CO bond angle to the surface and the distance of the CO molecules from the surface, but the calculation did produce a reasonable distance between CO molecules on the surface. In general, the PM3(tm) method in Spartan shows promise for predicting adsorption sites and vibrational frequencies of molecules on metal surfaces.

Journal Article↗

PubMed2002

Automation of a procedure to find the polynomial which best fits (kappa, c1, c2, T) data of electrolyte solutions by non-linear regression analysis using MATHEMATICA software.

A MATHEMATICA package, 'CONDU.M', has been developed to find the polynomial in concentration and temperature which best fits conductimetric data of the type (kappa, c, T) or (kappa, c1, c2, T) of electrolyte solutions (kappa: specific conductivity; ci: concentration of component i; T: temperature). In addition, an interface, 'TKONDU', has been written in the TCL/Tk language to facilitate the use of CONDU.M by an operator not familiarised with MATHEMATICA. All this software is available on line (UPV/EHU, 2001). 'CONDU.M' has been programmed to: (i) select the optimum grade in c1 and/or c2; (ii) compare models with linear or quadratic terms in temperature; (iii) calculate the set of adjustable parameters which best fits data; (iv) simplify the model by elimination of 'a priori' included adjustable parameters which after the regression analysis result in low statistical significance; (v) facilitate the location of outlier data by graphical analysis of the residuals; and (vi) provide quantitative statistical information on the quality of the fit, allowing a critical comparison among different models. Due to the multiple options offered the software allows testing different conductivity models in a short time, even if a large set of conductivity data is being considered simultaneously. Then, the user can choose the best model making use of the graphical and statistical information provided in the output file. Although the program has been initially designed to treat conductimetric data, it can be also applied for processing data with similar structure, e.g. (P, c, T) or (P, c1, c2, T), being P any appropriate transport, physical or thermodynamic property.

Journal Article↗

PubMed2003

Evaluating dissolution profiles of an anti-HIV agent using ANOVA and non-linear regression models in JMP software.

A powerful statistical method was designed using JMP software to detect factors contributing to differences in the dissolution process of an antiviral drug delivered in an oral dosage form. Due to the large number of dissolution media available for solid dosage forms, a statistical method to choose the appropriate medium is critical for testing solid dosage forms. We have developed an analysis of variance model to analyze the overall dissolution profile obtained from the various media. In vitro tests were performed using a standard USP basket apparatus (Vankel Inc., Cary, NC), and the analysis used the restricted/residual maximum likelihood method (JMP software) to partition the variance due to media (pH 1.2 and 6.8, +SDS, water alone and at pH 1.2 with pepsin), time (repeated measure) and capsule (random effect). This allowed correct standard error estimates to be used to compare dissolution in different media using planned linear contrasts. The model provided us with statistically powerful criteria to identify significant differences in capsule dissolution across time and to quantify capsule-to-capsule population variance estimate. The time specific linear contrasts showed the largest sum of square values (SS) occurred at 180 min (SS=0.268) for the simulated SIF (pH 6.8) versus SGF (pH 1.2) comparison (DF=166, MSE=3.92 x 10(-3)). The dissolution processes were further characterized using a non-linear regression fit of a power law function to the data for each capsule. This resulted in a method to statistically differentiate between the dissolution processes of the capsules in different media.

Analysis of Variance↗

PubMed2003

The effect of noise on computer-aided measures of voice: a comparison of CSpeechSP and the Multi-Dimensional Voice Program software using the CSL 4300B Module and Multi-Speech for Windows.

The effect of noise on computer-derived samples of voice was compared across three different hardware/software configurations. The hardware/software systems included a stand-alone A/D converter (CSL Module 4300B) coupled to a custom Pentium PC used in conjunction with the Multi-Dimensional Voice Program (MDVP) software, and a Creative Labs A/D converter coupled to the same custom PC under software control of MDVP/Multispeech and CSpeechSP. Voice samples were taken from 10 female subjects, then mixed with computer fan noise creating three different signal-to-noise (S/N) levels. Mixed signals were analyzed on the three hardware/software systems. Results revealed that fundamental frequency was most resistant to the degradation effect of noise across systems; jitter and shimmer values, however, were more variable across all configurations. Jitter and shimmer values were significantly higher under certain S/N levels for the MDVP 4300B based system as compared to MDVP for Multi-Speech and CSpeechSP. The findings punctuate the need for sensitivity to recording environments, careful selection of hardware/software equipment arrays, and the establishment of minimal recording conditions (>25 dBA S/N) for voice sampling and analysis using computer-assisted methods.

Adult↗

PubMedDate not supplied

Software coincidence counting.

A system designed for absolute activity measurement is described using a digital method. The system is based on data recording from a coincidence measurement and subsequent software processing of the data records. The data acquisition device collects amplitudes of individual pulses from analogue-to-digital converters and supplies them with time information. Software processing of data records from this system offers many benefits in comparison to conventional coincidence counting, for example it enables to perform time and pulse height analysis and setting of coincidence parameters by using a wide variety of evaluation methods to one data record. The digital system was tested with a 4pi beta-gamma coincidence detectors arrangement consisting of a proportional counter and two NaI(Tl) scintillation detectors. The results obtained with a 60Co source are presented.

Journal Article↗

PubMedDate not supplied

Cage: software for a critical analysis of (2)H spin-lattice relaxation in liquid crystals.

A software package of Mathematica, aimed at the analysis of (2)H NMR Zeeman (T(1Z)) and quadrupolar (T(1Q)) spin-lattice relaxation times in liquid crystals in terms of diffusional models, is presented. The models most commonly used to describe internal, overall, and collective motions in liquid-crystalline phases are considered, and dynamic parameters are obtained by means of either single point or global target approaches using simulation or fitting procedures. The use of the software as a tool for highlighting the problems encountered in this kind of analysis as well as for dealing with such problems following suitable strategies is illustrated by means of applications to experimental (2)H relaxation times of three different calamitic liquid crystals.

Journal Article↗

PubMed2002

Software techniques for EELS to realize about 0.3 eV energy resolution using 300 kV FEG-TEM.

In this short communication we describe some software techniques for electron energy-loss spectrum measurement. We prepared DigitalMicrograph (Gatan) scripts for multiple spectrum acquisitions, quasi-simultaneous acquisition of low-loss and core-loss spectra, energy drift correction, and other operations. Narrow zero-loss spread of 0.27 eV is demonstrated using a 300 kV field-emission transmission electron microscope (TEM) (Hitachi, HF-3000) and a post-column energy filter (Gatan, GIF2002). The core-loss spectrum is acquired with an energy resolution of 0.36 eV with high reproducibility. The present software techniques effectively achieve the intrinsic energy resolution of electron sources. Sample scripts are provided in the Appendix.

Journal Article↗

PubMed2001

Voice recognition software versus a traditional transcription service for physician charting in the ED.

This study was conducted to compare real-time voice recognition software to a traditional transcription service. Two emergency department (ED) physicians dictated 47 charts using a voice dictation software program and a traditional transcription service. Accuracy, word per minute dictation time and turnaround time were calculated from the data. The transcription service used in our study was more accurate than the voice recognition program with an accuracy of 99.7 percent versus 98.5 percent for the voice recognition program. The average number of corrections per chart was 2.5 for the voice recognition program and 1.2 for the traditional transcription service. Turnaround time was much better using the computer voice recognition program with an average turnaround time of 3.65 minutes versus a turnaround time of 39.6 minutes for the traditionally transcribed charts. The charts dictated using the voice recognition program were considerably less costly than the manually transcribed charts. In summary, computer voice recognition is nearly as accurate as traditional transcription, it has a much shorter turnaround time and is less expensive than traditional transcription. We recommend its use as a tool for physician charting in the ED.

Confidence Intervals↗

PubMed2002

Determination of melting temperature for variant detection using dHPLC: a comparison between an empirical approach and DNA melting prediction software.

Detection of DNA sequence variants by the use of denaturing high-performance liquid chromatography (dHPLC) is a relatively new method (Underhill et al., 1997) and has distinct advantages over other methods such as single-strand conformation polymorphism (SSCP), direct sequencing, and DNA chip hybridization. The dHPLC-based single-nucleotide polymorphism (SNP) screening relies on different DNA thermodynamic properties between perfectly matched base pairs in homoduplex molecules and single base-pair mismatches in heteroduplex DNAs. Separation of the two forms of duplex DNAs by dHPLC is based on ionic forces between the negatively charged DNA and the hydrophobic stationary phase, which consists of C(18) chains on PSDVB (polystyrene-divinylbenzene) beads coated with a positively charged ion-pairing agent (TEAA, triethylammonium acetate). Removal of the DNA from the TEAA-coated beads is dependent upon a mobile organic phase, in the form of a linear acetonitrile gradient. The major factor that influences the success of dHPLC to detect sequence variation is the thermal stability of the duplex DNA, which is determined by the melting temperature (TM(50)), where 50% of the DNA strand is single stranded and 50% is double stranded. The TM(50) predicts the best probability of detecting a single base-pair change based on the altered thermodynamics it imparts to the DNA duplex. Generally, there are two ways to determine this melting temperature, either empirically or with the aid of predictive DNA melting analysis software. Such programs include the DNAMelt program located on the Stanford University DNA Sequencing and Technology Center website, MeltCalc (Schutz and von Ahsen 1999), and WAVEMAKER, the proprietary melting analysis software provided with the Transgenomic WAVE dHPLC system. The goal of the current study was to determine whether currently available predictive DNA melting programs could be used to increase efficiency and throughput of SNP detection. A wide range of amplicons, differing in both size and GC composition, were selected for analysis to simulate the broad spectrum of PCR products that may be encountered during a large-scale dHPLC screening project.

Chromatography, High Pressure Liquid↗

PubMed2002

Using the AIDA--www.2aida.org--diabetes simulator. Part 1: recommended guidelines for health-carers planning to teach with the software.

AIDA is a novel diabetes-computing program freely available from www.2aida.org on the Web. The software is intended to serve as an educational support tool and can be used by anyone-patient with diabetes, relative of patient, health-care professional, or student-who has a minimal knowledge of the pathophysiology of diabetes. However, to obtain maximum benefit from the program, a teacher or demonstrator may be helpful. How much (or little) experience should the potential teacher have prior to giving formal lessons with the program? There is no hard or fast "rigid" answer to this. However, one of the aims of this article is to try and encourage people to consider these issues. In this respect it is important to make clear that health-carers cannot just download the program and start teaching with it the next day (or week) if they want their patients to get the most out of lessons with the program. As with many teaching interventions, the rewards of education-"what one gets out of it"-are in part dependent on the effort that one is willing to put in. Therefore teachers have to invest some time and effort into finding out how they can best work with the program to teach their patients in their particular local hospital/clinic setting. A further purpose of this article, and the one that follows in a future issue, is to generate some guidelines and provide some minimum recommendations for small group teaching sessions using AIDA. Previous experience of the authors has revealed a number of ways to improve the outcome of lessons that make use of the software. Among the most important points seem to be the preparation of the teacher, consideration of how to impart preliminary information to help patients understand the pathophysiology of diabetes, the optimum selection of topics to be covered, the arrangement of the lessons, how to involve each of the participants, and how to deal with questions. Other important topics include how to spot and deal with some of the difficulties that may be encountered by participants who apparently seem disinterested, obtaining feedback from the lessons, and practical ideas on how to lead a class.

Communication↗

PubMed2000

Reproducibility of assessment of myocardial function using gated 99Tc(m)-MIBI SPECT and quantitative software.

PURPOSE: We investigated the reproducibility of the quantification of left ventricular volumes and ejection fraction, and grading of myocardial wall motion and systolic thickening with gated myocardial single-photon emission computed tomography (SPECT) and Cedars quantification software. PATIENTS, MATERIALS AND METHODS: We performed post-stress gated myocardial SPECT in 33 consecutive patients twice sequentially in situ. Sixteen frames per cycle were used for gating. Using Cedars quantitative gated SPECT software ventricular volumes and ejection fraction (EF) were calculated. Wall motion and thickening was graded using 5- and 4-point scores, respectively. Coefficients of variation for re-examination of volumes and EF were calculated. Kappa values for assessing reproducibility of wall motion or wall thickening were calculated. RESULTS: Root mean square of errors was 5.0 ml for end-diastolic volume, 3.9 ml for end-systolic volume and 1.9% for EF. No bias or difference was found between the first and second acquisition by Bland-Altman analysis. Kappa values for wall motion and thickening of repeated acquisition was 0.76 and 0.87, respectively. The value of 2 SD from Bland-Altman analysis was 14.4 ml for EDV, 11.2 ml for ESV and 5.3% for EF. CONCLUSION: We conclude that quantification of functional indices and assessment of wall motion or thickening using gated 99Tc(m)-sestamibi (MIBI) SPECT was reproducible and we found that their ranges of physiological fluctuation were narrow enough.

Aged↗