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PubMed1988

Development of stereological analysis software for the calculation of volume, number and surface density.

COSAS, an acronym for COmputerized Stereological Analysis System, is software designed to facilitate the process of quantitative morphological analysis. It is a flexible, reliable, and easy to use software system which provides the biologist with a simple means for performing stereological analysis. It provides for estimation of volume and surface density and allows for direct calculation of diameter information from planimetric data. The latter capability is unique to COSAS and provides the ability to calculate longest and shortest diameters for convex profiles, enabling calculation of number density. Access to all intermediate calculations is possible, so the process of transformation of raw data into the stereological descriptors can be completely exposed. This serves two purposes: (1) it provides a means for tracing results; (2) the intermediate values can be utilized independently. This system was used to analyze peroxisomes in tissues from patients with Zellweger's disease and neonatal-onset adrenoleukodystrophy. The system was also used to facilitate an immunocytochemical analysis of cytochrome P450 topology in the endoplasmic reticulum membrane.

Algorithms↗
PubMed2002

[The St. Gallen digital ophthalmological imaging system].

BACKGROUND: Digital photography has many advantages over the conventional method. At present commercially available digital ophthalmological imaging systems utilise only a fraction of the advantages of this technique and some of them have fundamental conceptional problems. METHODS: Images of a fundus camera, a slit lamp and a scanning laser ophthalmoscope were digitised using digital and video cameras and/or frame grabber cards. Digital images and movies were recorded via a personal computer. The image recording software was developed using an imaging library and open source software. The recorded images and video sequences were processed with three different commercially available programme packages. The images were archived in a around-the-clock accessible database. RESULT: Our digital imaging system is capable to record normal and high resolution slit lamp images, colour fundus images in normal resolution, Fluorescein angiography images in normal and high resolution, digital simultaneous ICG and Fluorescein videoangiograms (without compression) and high resolution macro images. Different functions, e.g., contrast enhancement are integrated in the image capture software. Most of the parameters of the image acquisition are individually adaptable. The digital image archive supports multiple image and video formats. CONCLUSIONS: Using standard software and hardware components an imaging system can be constructed featuring functions usually not available in commercial ones. Since the system is adaptable, recording of images with a wide variety of parameters, e.g., for measurements for scientific experiments, is possible.

Computer Systems↗
PubMed2000

Coupled electromagnetic and thermal modeling of microwave oven heating of foods.

Temperature distributions from heating in a domestic microwave oven were studied by considering the coupling between the electromagnetics and heat transfer through changes in dielectric properties during heating. Maxwell's equations for electromagnetics and the thermal energy equations are solved numerically using two separate finite-element softwares. The coupling between the softwares was developed by writing special modules that interfaced these softwares at the system level. Experimentally measured temperature profiles were compared with the numerical predictions. The importance of coupling was evident when the properties changed significantly with temperature for low and high dielectric loss materials and more so for the high loss materials. For moderate loss materials, when the properties do not change as much with temperature, coupled solutions lead to results very close to the results for the uncoupled solution.

Algorithms↗
PubMed2004

Analysis of red blood cell aggregation in cardio-pulmonary bypass (CPB) surgery.

Not much is known about red cell aggregation during cardio-pulmonary bypass surgery (CPB). Blood samples from 19 patients undergoing CPB were anticoagulated with EDTA. Hematocrit was adjusted to 40%. A red blood cell aggregometer (LORCA) measured changes in light reflection from each blood sample after cessation of the rotation, and calculated an aggregation index (AI). Reflection measurements were stored. Because LORCA software failed for 87 of 171 samples, we developed new software, and applied it to the stored reflection measurements. This software failed only in 7 out of 171 cases and showed that all LORCA failures occurred for AI < 40%. The new calculations revealed that the aggregation index significantly decreased from 46.6 +/- 10.1 (mean +/- standard deviation) baseline to 22.8 +/- 8.3 at the end of CPB and recovered to 37.1 +/- 13.5 at day 1. It is concluded that the new software can be used to study decreased red cell aggregation during CPB.

Coronary Artery Bypass↗
PubMed1999

Calculation of signal detection theory measures.

Signal detection theory (SDT) may be applied to any area of psychology in which two different types of stimuli must be discriminated. We describe several of these areas and the advantages that can be realized through the application of SDT. Three of the most popular tasks used to study discriminability are then discussed, together with the measures that SDT prescribes for quantifying performance in these tasks. Mathematical formulae for the measures are presented, as are methods for calculating the measures with lookup tables, computer software specifically developed for SDT applications, and general purpose computer software (including spreadsheets and statistical analysis software).

Discrimination, Psychological↗
PubMed2000

Breast cancer patterns and lifetime risk of developing breast cancer among Puerto Rican females.

OBJECTIVES: The purpose of this study was to evaluate the epidemiologic patterns of breast cancer and to estimate the lifetime risk probability of developing breast cancer among Hispanic females using cancer data from Puerto Rico. BACKGROUND: The age-adjusted breast cancer incidence rate (per 100,000) in Puerto Rico increased from 15.3 in 1960-1964 to 43.3 in 1985-1989. The age-adjusted breast cancer mortality rate (per 100,000) increased from 5.7 to 10.6 comparing the same two time periods (1960-1964 vs 1985-1989). Nevertheless, in 1985-1989 breast cancer incidence rate was higher in US White females (110.8 per 100,000) compared to Puerto Rican females (51.4 per 100,000; age-adjusted to the 1970 US standard population). The breast cancer mortality rate was also higher in US White females (27.4 per 100,000) than in Puerto Rican females (15.1 per 100,000; age-adjusted to the 1970 US standard population) during 1985-1989. METHODS: A multiple decrement life table was constructed applying age-specific incidence and mortality rates from cross-sectional data sets (1980-1984 and 1985-1989 data for Puerto Rican females and 1987-1989 SEER data sets for US White and Black females) to a hypothetical cohort of 10,000,000 women. The probability of developing invasive breast cancer was computed for the three groups using the long version of DEVCAN: Probability of DEVeloping CANcer software, version 3.3. RESULTS: The lifetime risk of developing breast cancer was 5.4% for Puerto Rican females, compared to 8.8% for US Black females and 13.0% for US White females. Lifetime risk for Puerto Rican females increased from 4.5% in 1980-1984 to 5.4% in 1985-1989. CONCLUSIONS: Lifetime risk of breast cancer appears to be increasing in Puerto Rico, but remains lower than the probability for US White females. Therefore, the application of lifetime probability of developing invasive breast cancer estimated for the US female population will overestimate the risk for the Puerto Rican female population.

Adolescent↗
PubMed2001

High-Pressure Synthesis of gamma-P(3)N(5) at 11 GPa and 1500 degrees C in a Multianvil Assembly: A Binary Phosphorus(V) Nitride with a Three-Dimensional Network Structure from PN(4) Tetrahedra and Tetragonal PN(5) Pyramids This work was supported by the Fonds der Chemischen Industrie and the Deutsche Forschungsgemeinschaft (Gottfried-Wilhelm-Leibniz-Programm). The authors thank Dr. D. Frost and Prof. Dr. D. C. Rubie, Bayerisches Geoinstitut, Universität Bayreuth, as well as Dr. P. Ulmer, ETH Zürich, for help in adapting the multianvil-technique. Also many thanks to W. Wünschheim, Department Chemie, LMU München for the development and programming of software for the high-pressure experiments.

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Journal Article↗
PubMedDate not supplied

[Development of an integrated software program to analyze statistically the results of complex investigations in space biology and medicine].

A concept of implementing the problem-oriented statistical software based on an application of expert systems is presented. The shortcomings of existing statistical software for personal computers and trends of their improvements are analyzed. Recommendations on designing of statistical expert systems can be used by the statisticians, mathematicians, programmers and users not being professionals in these fields. Integrated statistical software will make it possible to perform additional retrospective analysis and to check up the large arrays of previously gained data and to obtain supplementary scientific information and to find new regularities in the previous experimental findings.

Aerospace Medicine↗
PubMed2000

Structure and content of 400 CT reports in four teaching hospitals using a new, Windows-based software tool.

PURPOSE: To test a new software tool developed for analysis of radiology reports and to compare CT reports from four different teaching hospitals. MATERIAL AND METHODS: Four hundred CT reports were randomly collected from four Finnish university hospitals. A Windows 3.1-based software tool was developed to make a comparative analysis of the information content of CT reports. The structure of the reports was partly analyzed manually. RESULTS: The new software tool greatly facilitated semiquantitative analysis of the information content of residents' and radiologists' reports. There were some local differences in the length and structure of the reports, the choice of vocabulary and the number of differential diagnoses given, and large differences in the use of an "impression" section. Thorough description of focal lesions was included in less than 50% of the reports from each of the four institutions. CONCLUSION: The variation in well-structured CT reports indicates considerable geographic differences in radiology reporting, which may reflect the long-term influences of a few teachers. Rational application of the communication standards should improve the quality of written radiology reports. Such standards should be emphasized, particularly in teaching hospitals.

Hospitals, Teaching↗
PubMed2006

New softwares for automated microsatellite marker development.

Microsatellites are repeated small sequence motifs that are highly polymorphic and abundant in the genomes of eukaryotes. Often they are the molecular markers of choice. To aid the development of microsatellite markers we have developed a module that integrates a program for the detection of microsatellites (TROLL), with the sequence assembly and analysis software, the Staden Package. The module has easily adjustable parameters for microsatellite lengths and base pair quality control. Starting with large datasets of unassembled sequence data in the form of chromatograms and/or text data, it enables the creation of a compact database consisting of the processed and assembled microsatellite containing sequences. For the final phase of primer design, we developed a program that accepts the multi-sequence 'experiment file' format as input and produces a list of primer pairs for amplification of microsatellite markers. The program can take into account the quality values of consensus bases, improving success rate of primer pairs in PCR. The software is freely available and simple to install in both Windows and Unix-based operating systems. Here we demonstrate the software by developing primer pairs for 427 new candidate markers for peanut.

Arachis↗
PubMed2002

Characteristics of educational software use in 106 clinical laboratories.

The University of Washington, Seattle, has developed educational software for clinical laboratories. We used a 32-question survey to study software implementation. Of 106 clinical laboratories (response rate, 60%) that purchased the software and completed the survey, 89 laboratories (84%) that reported using the software formed the basis for the study. The most common software users were laboratory personnel, followed by medical technologist or medical laboratory technician students, residents, and medical students; the mean (SD) number of personnel categories using the software per laboratory was 1.8 (0.8). The most common reasons for use were initial instruction, cross-training, and competency assessment. The most frequent setting for software use was an area where laboratory testing occurred, followed by a dedicated training location, a location chosen by the employee, a classroom, and a distance learning mode. On a scale of 1 (poor) to 5 (excellent), the average satisfaction rating as an instructional tool was 4.4 and as a competency assessment tool, 4.2. Compared with laboratories in hospitals with 400 beds or fewer, laboratories in hospitals with more than 400 beds used the software for more categories of users (P = .008), had a higher proportion of laboratories using it for residents (P = .003), and had a higher proportion of laboratories with dedicated training areas (P = .02).

Clinical Laboratory Techniques↗
PubMed2004

Quantification methodology for peripheral quantitative computed tomography (PQCT) data using public domain software.

OBJECTIVE: To develop a method for viewing, processing and acquiring 3-dimensional volumetric data from existing ovine spinal peripheral quantitative computed tomography (PQCT) scans of posterior lateral fusion. DESIGN: An image processing development study. BACKGROUND: Existing medical image viewing software can be expensive and difficult to adapt to meet specific research needs. The goals of this study were to produce volume rendering of PQCT scans through processing, masking, and segmentation using public domain software with established source code. METHODS: Raw data files (DICOM format) of 32 PQCT scans from animals receiving spine fusion were obtained. Metal hardware was removed from the images by masks and image segmentation. Calculation of bone macro-architecture volumetric data was performed on right and left sides of spines to quantify fusion volume in normalized segments between transverse processes. RESULTS: Images were acquired and opened. Application of image processing techniques made it possible to remove surgical hardware from original images with minimal loss of original PQCT data. Volumes were calculated and normalized to gray-scale of total bone throughout individual selected segments. CONCLUSION: Using public domain software is a cost effective means to view, process, and manipulate PQCT data. Bone macro-architecture can provide quantitative volumetric contributions to ascertain the role of structure on mechanical function.

Algorithms↗
PubMed2003

Fiswidgets: a graphical computing environment for neuroimaging analysis.

Current fMRI neuroimaging software programs offer the researcher a wealth of analysis methods and tools. However, the incompatibilities in user interface, data format, and computing environment in these tools make it difficult if not impossible for most researchers to take advantage of the full set of resources available for neuroimaging analyses. We describe a graphical computing environment, Functional Imaging Software Widgets (fiswidgets), which was developed to address these interoperability and usability problems. This environment provides a desktop style framework into which 100 subcomponents from a number of widely used fMRI analysis software packages (e.g., AFNI, AIR) are incorporated. It is an open-source, extensible environment available for reuse and modification by other software developers. A discussion of the design criteria (open architecture, modularity, wrapper technology, commercial utilities) that support such loosely integrative computing environments, and the problems entailed in maintaining them (development overhead, distribution logistics, format incompatibilities, graphics vs scripting tradeoffs, and appropriate acknowledgment of software developers) follows.

Computer Graphics↗
PubMed1996

An analysis of the dynamic range and linearity of an infrared DNA sequencer.

We are currently developing genotyping software and protocols for use on the Li-Cor model 4000(L) infrared fluorescence DNA sequencers. During the development of the genotyping software it became apparent that the potential dynamic range of the instrument was not being realized when the data collection parameters were optimized to produce a high-contrast image on the computer screen. In particular, we were unable to obtain peaks with signal to noise (S/N) greater than about 30:1 and the stronger peaks often saturated the detector. Because the numerical dynamic range available in 16-bit data collection mode exceeds 65000, our limited dynamic range of about 30 in actual data was somewhat puzzling. Hence, we undertook a study to explore the dynamic range and linearity of the Li-Cor DNA sequencer in order to minimize background fluorescence and noise as well as maximize the available S/N. Data is presented on the background and noise using different polyacrylamide gel mixes with various signal gain and offset values, and the relative contribution of the glass, gel and instrumentation to the background fluorescence is discussed. Based on these results, optimum gain and offset values were determined that maintain the background fluorescence at approximately 1-2% of the maximum dynamic range with a minimum amount of noise. Using these optimized values, we determined the detection system is linear over three orders of magnitude by titrating known quantities of an infrared fluorophore-labeled primer. In addition, we were able to detect approximately 15.2 amoles of labeled primer. The results provided by this study establish a set of guidelines for evaluating how to set the signal gain and offset in order to minimize the background and maximize the S/N and dynamic range of the Li-Cor sequencer.

DNA↗
PubMedDate not supplied

Combinatorial electrochemical screening of fuel cell electrocatalysts.

Combinatorial methods have been applied to the preparation and screening of fuel cell electrocatalysts. Hardware and software have been developed for fast sequential measurements of cyclic voltammetric and steady-state currents in 64-element half-cell arrays. The arrays were designed for the screening of high-surface-area supported electrocatalysts. Analysis software developed allowed the semiautomated processing of the large quantities of data, applying filters that defined figures of merit relevant to fuel cell catalyst activity and tolerance. Results are presented on the screening of carbon-supported platinum catalysts of varying platinum metal loading on carbon (and thus, particle size) in order to demonstrate the speed and sensitivity of the screening methodology. CO electro-oxidation, oxygen reduction, and methanol oxidation on a series of such catalysts reveal clear trends in characteristics and activities. Catalysts with smaller particle sizes reveal structure in the CO stripping voltammetry that can be associated with edge sites in addition to the closely packed planes, and this is concomitantly reduced as particle size is increased. Specific activity for steady-state methanol oxidation and oxygen reduction at room temperature in H(2)SO(4) electrolyte is found to be a maximum for the largest particle sizes, in agreement with the literature. These trends in activity are significantly smaller than the differences in activities of promoted platinum-based alloy catalysts for the same reaction.

Journal Article↗
PubMed1995

Renal function tests for windows--a model for the development and distribution of medical software on the Internet.

A computer application (Renal Function Tests for Windows) was developed to calculate and sort data for quantitative renal function testing using the Microsoft Visual Basic for Windows programming language. The following diagnostic indices are computed: Measured creatinine clearance--The rate at which serum is cleared of creatinine. Standardized clearance--Creatinine clearance scaled by body surface area. Estimated creatinine clearance--Renal creatinine clearance estimated from serum creatinine Renal failure index--To distinguish prerenal azotemia from oliguric acute renal failure. Renal free water clearance--Net volume per min of free water excreted by the kidneys. Fractional excretion of filtered sodium--To distinguish prerenal azotemia from acute renal failure. Renal Function Tests for Windows (RFT) allows the user to choose to enter only the data that is available. The program will then calculate all the possible results from the given data. Upon request, the program will also inform the user of data that is missing for those results that cannot be calculated. The flexibility of this program allows the user to perform 'what if' analysis through the manipulation of input data. Distribution of this program was accomplished using the Internet File Transfer Protocol (FTP) service. The effectiveness of mode of distributing medical software awaits feedback from users on the Internet.

Acute Kidney Injury↗