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PubMed1993

Establishment of a computerized biodiversity/biotechnology network: the Brazilian effort.

Information technology plays an increasingly vital role in bioindustrial development and in the establishment of biodiversity conservation and sustainable management of the environment. Recognizing the need and importance of local and regional database developments, the Tropical Data Base is establishing an interactive biodiversity/biotechnology information resource. The system is linked to major international networks and information centres, and is based on a workstation system and personal computers. All software was developed to attend specific needs and to cope with hardware limitations, making the system adequate to other developing countries.

Biotechnology↗

PubMed1992

Developing computer training programs for blood bankers.

Two surveys were conducted in July 1991 to gather information about computer training currently performed within American Red Cross Blood Services Regions. One survey was completed by computer trainers from software developer-vendors and regional centers. The second survey was directed to the trainees, to determine their perception of the computer training. The surveys identified the major concepts, length of training, evaluations, and methods of instruction used. Strengths and weaknesses of training programs were highlighted by trainee respondents. Using the survey information and other sources, recommendations (including those concerning which computer skills and tasks should be covered) are made that can be used as guidelines for developing comprehensive computer training programs at any blood bank or blood center.

Journal Article↗

PubMed2005

A software solution for the control of visual behavioral experimentation.

Psychophysical and neurophysiological research requires precise control of experimental devices for the purpose of delivering stimuli and monitoring behavioral and neural responses. This has previously been accomplished by complex, often proprietary, programmable systems, interfacing with a limited range of hardware. We have developed a software solution entirely within the Matlab environment that can achieve high-speed control of experimental and behavioral variables. We make this Wake-Forest Visual Experimentation (WaVE) software freely available under the GNU public license, and demonstrate how to customize it to individual laboratory needs. WaVE takes advantage of existing Matlab libraries and toolboxes to present visual stimuli, collect experimental data, update behavioral variables, and communicate with other computers. Although we have developed it for use in a Windows-based Personal Computer, the portability of the Matlab code makes possible its customization for use in a variety of other systems. We present simulation results showing sub-millisecond sampling rate and updating precision, running on single-processor, desktop PCs. The WaVE software offers a simple, flexible and powerful solution that compares favorably with many of its costly alternatives.

Animals↗

PubMed2001

[Computer-assisted surgical planning. 3-D software for the PC].

A potent software was developed for virtual planning in orthopedic surgery with complex spatial relationships, that runs on a standard PC with Windows 98/NT/2000. This voxel-based 3D-software creates data from tomographic images (CT, MRI, 3D-Sono, PET) in Dicom-III-format, that are visualized in near real-time as 2D-reconstructions or 3D-images. For three-dimensional analysis interactive tools, geometric rulers and an anatomic coordinate-system are available. Multiplanar osteotomies are carried out with a virtual saw. Selected segments are moved freely to mimic fracture reduction and deformity correction. Three-dimensional movement coordination is supported by problem-oriented movement features and a 3D-mouse. User defined objects in CAD-format like implants or anatomical templates can be inserted and moved. Matching of two volume data sets is possible as well as simultaneous processing of different data sets. All 3D-reconstructions can be calculated as virtual radiographs and viewed stereoscopically with LCD-shutter glasses. Export features in various data formats allow further processing of all volume data in CAD applications and rapid prototyping. An intra-operative navigation system can be integrated via an interface. This universally applicable software allows thorough three-dimensional analysis and processing of volume data sets from tomographic images and can be used in various applications through its flexible modular setup.

Diagnostic Imaging↗

PubMed2003

Key-string algorithm--novel approach to computational analysis of repetitive sequences in human centromeric DNA.

AIM: To use a novel computational approach, Key-string Algorithm (KSA), for the identification and analysis of arbitrarily large repetitive sequences and higher-order repeats (HORs) in noncoding DNA. This approach is based on the use of key string that plays a role of an arbitrarily constructed "computer enzyme". METHOD: A cluster of novel KSA-related methods was introduced and developed on the basis of a combination of computations on a very modest scale, by eye inspection and graphical display of results of analysis. Sequence analysis software was developed, containing seven programs for KSA-related analyses. This approach was demonstrated in the case study of alpha satellites and HORs in the human genetic sequence AC017075.8 (193277 bp) from the centromeric region of human chromosome 7. The KSA segmentation method was applied by using DCCGTTT, GTA, and TTTC key strings. RESULTS: Fifty-five copies of 2734-bp 16mer HORs were identified and investigated, and a start-string TTTTTTAAAAA was identified. The HOR-matrix was constructed and employed for graphical display of mutations. KSA identification of HORs in AC017075.8 was compared with that of RepeatMasker and Tandem Repeat Finder, which identified alpha monomers in AC017075.8, but not the HORs. On the basis of KSA study, the centromere folding was described as an effect of HORs and super-HORs (3 x 2734 bp) in AC017075.8. The following novel computational KSA-based methods, easy-to-use and intended for computational "pedestrians", were demonstrated: color-HOR diagram, KSA-divergence method, 171-bp subsequence-convergence diagram, and total frequency distribution of the key-string subsequence lengths. The results were supplemented by Fast Fourier Transform, employing a novel mapping of symbolic genomic sequence into a numerical sequence. CONCLUSION: The KSA approach offers a simple and robust framework for a wide range of investigations of large repetitive sequences and HORs, involving a very modest scope of computations that can be carried out by using a PC. As the KSA method is HOR-oriented, the identification of HORs is even easier than the identification of underlying alpha monomer itself. This approach provides an easy identification of point mutations, insertions, and deletions, with respect to consensus. This may be useful in a wide range of investigations and applied in forensic medicine, medical diagnosis of malignant diseases, biological evolution, and paleontology.

Algorithms↗

PubMed2004

A relation-centric query engine for the Foundational Model of Anatomy.

The Foundational Model of Anatomy (FMA), a detailed representation of the structural organization of the human body, was constructed to support the development of software applications requiring knowledge of anatomy. The FMA's focus on the structural relationships between anatomical entities distinguishes it from other current anatomical knowledge sources. We developed Emily, a query engine for the FMA, to enable users to explore the richness and depth of these relationships. Preliminary analysis suggests that Emily is capable of correctly processing real world anatomical queries provided they have been translated into a constrained form suitable for processing by the query engine.

Anatomy↗

PubMed1999

Implementation of three-dimensional EEG brain mapping.

The electroencephalogram (EEG) visualization software was developed containing two-dimensional (2D) and three-dimensional (3D) brain mapping modules. The input to the program is standard clinical individual patient data recorded using digital EEG and magnetic resonance imaging (MRI). The software utilizes several techniques, such as heuristic triangulation, ray casting, Gouraud shading, and image fusion to form multimodal 3D images. The program has been applied to the 3D visualization of various EEG signals, "cortical" EEG signals, and potential fields generated by a computer model. The developed program appears to operate efficiently and intuitively in PC/Windows environment.

Algorithms↗

PubMed1995

A practical tool for community-oriented primary care community diagnosis using a personal computer.

BACKGROUND AND OBJECTIVES: Community-oriented primary care (COPC) is considered an attractive concept by many but has had limited implementation due to a lack of practical methodology. An important step in COPC is assessment of a community's health status, using health indicators as one means of assessment. Currently, there is no easy way to combine these indicators and examine their distribution over a community. This study analyzed a process for doing that by using a personal computer. METHODS: For the community studied, all available community-based health indicators were identified. A process for combining these indicators, using commonly available database and spreadsheet software, was developed and analyzed for cost, clinical utility, and problems encountered. RESULTS: Problems were encountered with collecting and combining some data, but a clinically useful tool was produced. Costs, including purchase of all software (with mapping software), were $1,500-$2,000. CONCLUSIONS: With efforts to reduce the initial costs, this is a practical and clinically useful tool for viewing the geographic distribution of community health indicators. Such practical methodology is essential for COPC development.

Community Health Planning↗

PubMed1990

Development of automated immunoassays for immune status screening and serodiagnosis of rubella virus infection.

The fully automated IMx immunoassay analyzer was used to develop a system for the detection of IgG and IgM antibodies to rubella virus for immune status screening and diagnosis of primary infections. Reagents and assay protocol software were developed using rubella virus sensitized microparticles as the solid phase to capture specific antibodies from serum samples. Anti-human IgG or IgM antibody coupled to alkaline phosphatase enzyme followed by methylumbelliferyl phosphate substrate was used to detect the presence or absence of antibodies specific to the antigens on the solid phase. To evaluate the efficacy of the IMx rubella IgG assay, immune status screening was performed with a clinical patient population of 501 sera. When compared to an IgG specific enzyme immunoassay and passive hemagglutination assay the agreement was greater than 99%. The IMx rubella IgM assay was utilized to determine the presence of rubella specific IgM antibodies in 462 sera. These results were compared to IgM specific enzyme immunoassay results and also demonstrated greater than 99% agreement. Seroconversion following rubella vaccination of susceptible individuals was demonstrated by IgG and IgM antibody responses as early as two weeks postvaccination. In addition to automation, the IMx system offers rapid assay times and calibration curve storage without sacrificing clinical efficacy.

Antibodies, Viral↗

PubMed2002

Nanosecond fluorescence resonance energy transfer-fluorescence lifetime imaging microscopy to localize the protein interactions in a single living cell.

Visualizing and quantifying protein-protein interactions is a recent trend in biomedical imaging. The current advances in fluorescence microscopy, coupled with the development of new fluorescent probes such as green fluorescent proteins, allow fluorescence resonance energy transfer (FRET) to be used to study protein interactions in living specimens. Intensity-based FRET microscopy is limited by spectral bleed-through and fluorophore concentration. Fluorescence lifetime imaging (FLIM) microscopy and lifetime measurements are independent of change in fluorophore concentration or excitation intensity, and the combination of FRET and FLIM provides high spatial (nanometre) and temporal (nanoseconds) resolution. Because only the donor fluorophore lifetime is measured, spectral bleed-through is not an issue in FRET-FLIM imaging. In this paper we describe the development of a nanosecond FRET-FLIM microscopy instrumentation to acquire the time-resolved images of donor in the presence and the absence of the acceptor. Software was developed to process the acquired images for single and double exponential decays. Measurement of donor lifetime in two different conditions allowed us to calculate accurately the distance between the interacting proteins. We used this approach to quantify the dimerization of the transcription factor CAATT/enhancer binding protein alpha in living pituitary cells. The one- and two-component analysis of the donor molecule lifetime in the presence of acceptor demonstrates the distance distribution between interacting proteins.

CCAAT-Enhancer-Binding Protein-alpha↗

PubMed1999

A computer generated interactive transurethral prostatic resection simulator.

PURPOSE: We developed a computer generated model of the prostate gland and an interactive simulator for use in training urologists in transurethral resection of the prostate. MATERIALS AND METHODS: Software was developed on a standard personal computer which allowed images of the lumen of the prostatic urethra and resectoscope loop to be generated and interacted with using a magnetic position sensor input device attached to a dummy resectoscope. RESULTS: An anatomically accurate computer model of the prostate was generated at low cost which permitted user interaction and which simulated key elements of transurethral prostatic resection. CONCLUSIONS: Although not a substitute for learning transurethral prostatic resection on patients, the simulator enabled the user to become familiar with the technique of transurethral prostatic resection in the absence of time constraints and without risk to patients. The simulator may become an important tool in training and assessing surgeon competency, and may reduce the costs of training. Further development is needed to refine the transurethral prostatic resection simulator and expand its surgical range.

Computer Simulation↗

PubMedDate not supplied

Design of a DSP controller for an innovative ventricular assist system.

The design and development of the digital signal processor controller for an innovative ventricular assist system is presented. A DSP56005 is used as the central processor, with other peripheral components. System hardware and software were developed through the advanced development system, and stand alone operation of the system was also accomplished. Two different control modes--current control mode and speed control mode--were developed and investigated. Performance of efficiency and dynamic response were examined through experimental testing.

Biomedical Engineering↗

PubMed1986

The AAHA Computer Program. American Animal Hospital Association.

The American Animal Hospital Association Computer Program should benefit all small animal practitioners. Through the availability of well-researched and well-developed certified software, veterinarians will have increased confidence in their purchase decisions. With the expansion of computer applications to improve practice management efficiency, veterinary computer systems will further justify their initial expense. The development of the Association's veterinary computer network will provide a variety of important services to the profession.

Animals↗

PubMed2003

[Automatic classification of liver segments according to Couinaud: development of a new algorithm and evaluation spiral CT data].

PURPOSE: To develop a software tool that analyzes the anatomy of the portal vein branches and assigns segmental and subsegmental branches according to Couinaud's classification system and to evaluate its accuracy. MATERIALS AND METHODS: The algorithm was developed in C++ on a PC. The algorithm recognizes the three major branching patterns of the portal vein. Segmental and subsegmental branches are assigned to 8 segments following Couinaud and encoded by 8 colors. The software was evaluated using CT data sets of 39 patients. After the individual segmental anatomy of each patient was determined by an experienced radiologist, automatic classification was performed and the results were compared on a branch by branch basis. RESULTS: The numbering was accurate according to Couinaud's system in 358 of 409 segmental and subsegmental branches (88 %). The assignment failed in 51 of 409 branches due to unexpected anatomy or software problems. CONCLUSION: Automatic classification of portal vein branches and their appendant parenchyma is possible. The automatic designation of liver segments enables the three-dimensional visualization of the segmental anatomy. In the future, automatic analysis might facilitate the reporting and communication of CT findings.

Algorithms↗

PubMed2007

[Electronic documentation of injuries of the hand with a semantic network: effective and efficient methods for the documentation of clinical and administrative processes].

BACKGROUND: An efficient medical documentation is mandatory for a trauma-oriented department in the DRG environment. Besides the continuously increasing clinical/administrative demands, the additional documentation for quality assurance, clinical studies, and research requires additional efforts. Standard solutions are only partially effective. Especially in hand surgery there is a high demand for sophisticated clinical documentation, represented by a wide variety of classifications in diagnosis and therapy. The standard documentation tools lack accuracy. The development of a software tool that defines administrative/business processes and simultaneously generates clinical and administrative information was the goal of this project. METHODS AND RESULTS: With a standard medical terminology, an innovative semantic network, and a completely new graphical user interface, it was possible to develop and introduce a software program specifically adjusted for hand surgery. This program facilitated for the first time a single-stage acquisition of clinically relevant scientific data and the simultaneous generation of DRG, quality assurance, and administrative data relevant for the hospital's revenues. CONCLUSIONS: The newly developed software tool is a step forward into a new dimension of medical software, obviating the need for multi/documentation and significantly improving the quality of clinically relevant medical data.

Computer Graphics↗

PubMed1985

Multiwell chamber chemotaxis assays: improved experimental design and data analysis.

The chemotaxis assay using the Boyden transfilter technique has become widely used in recent years for assessing migratory responses of a wide variety of cell types. In the study reported here we examined the migratory responses of mouse peritoneal macrophages using a multiwell chamber. The experiments were designed to analyze the components of variance in the assay method, to optimize the experimental design, and to develop objective statistical criteria for choosing among experiments with disparate results. Cell counts were obtained with the aid of an image analyzer coupled to a light microscope. Microcomputer software was developed to drive the image analyzer, collect data and conduct statistical analyses. Nested analysis of variance (ANOVA, either 2- or 3-level) was employed to partition the components of variance and F-tests were used to determine their significance. Significant sources of experimental error were identified both within and among wells and were attributed mostly to variability in the chamber/filter assembly and counting procedure. Statistical analyses demonstrated that there was significant variation among assays conducted in different multiwell chambers on the same day, among assays where the same agent was tested on different days in the same chamber, and among replicate counts of the same assay. The following recommendations were made: use ANOVA to distinguish differences due to biological effects from those due to experimental error, design experiments so that all relevant comparisons are included in the same chamber and the same assay, avoid pooling data from different assays unless ANOVA treatment variances are comparable, and when replicate assays yield disparate results choose the assay with the lowest percentage of variation due to experimental error.

Animals↗

PubMed2004

Subtle modification of isotope ratio proteomics; an integrated strategy for expression proteomics.

Use of minor modification of isotope ratio to code samples for expression proteomics is being investigated. Alteration of (13)C abundance to approximately 2% yields a measurable effect on peptide isotopic distribution and inferred isotope ratio. Elevation of (13)C abundance to 4% leads to extension of isotopic distribution and background peaks across every unit of the mass range. Assessment of isotope ratio measurement variability suggests substantial contributions from natural measurement variability. A better understanding of this variable will allow assessment of the contribution of sequence dependence. Both variables must be understood before meaningful mixing experiments for relative expression proteomics are performed. Subtle modification of isotope ratio ( approximately 1-2% increase in (13)C) had no effect upon either the ability of data-dependent acquisition software or database searching software to trigger tandem mass spectrometry or match MSMS data to peptide sequences. More severe modification of isotope ratio caused a significant drop in performance of both functionalities. Development of software for deconvolution of isotope ratio concomitant with protein identification using LC-MSMS, or any other proteomics strategy, is underway (Isosolv). The identified peptide sequence is then be used to provide elemental composition for accurate isotope ratio decoding and the potential to control for specific amino acid biases should these prove significant. It is suggested that subtle modification of isotope ratio proteomics (SMIRP) offers a convenient approach to in vivo isotope coding of plants and might ultimately be extended to mammals including humans.

Carbon Isotopes↗

PubMedDate not supplied

Developing an evaluation tool for instructional software programs.

The use of instructional software is predominant in many nursing programs. The need for cost-effective, quality programs requires faculty to evaluate instructional software before its purchase and use. The purpose of this work was to develop a tool for evaluating instructional software programs. The tool was based on data from the literature, as well as input and feedback from nurse educators and multimedia specialists. The evaluation tool assists faculty to ensure proper evaluation and selection of instructional software.

Choice Behavior↗