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PubMed2005

Roles for software technologies in advancing research and theory in educational psychology.

While reviews abound on theoretical topics in educational psychology, it is rare that we examine our field's instrumentation development, and what effects this has on educational psychology's evolution. To repair this gap, this paper investigates and reveals the implications of software technologies for researching and theorizing about core issues in educational psychology. From a set of approximately 1,500 articles published between 1999 and 2004, we sampled illustrative studies and organized them into four broad themes: (a) innovative ways to operationalize variables, (b) the changing nature of instructional interventions, (c) new fields of research in educational psychology, and (d) new constructs to be examined. In each area, we identify novel uses of these technologies and suggest how they may advance, and, in some instances, reshape theory and methodology. Overall, we demonstrate that software technologies hold significant potential to elaborate research in the field.

Anxiety↗
PubMed2006

[Studies of methods and exploitation of computer software for mapping interactive genes].

There are six possible types of gene interaction in qualitative traits, namely, complementary, duplicate, cumulative, dominant epistasis, recessive epistasis and inhibiting. In genetic studies, the problem of mapping interactive genes may be met sometimes, but no systematic researches on the methodology and computer software for the mapping of interactive genes have been reported up to date. In this paper, methods for the mapping of interactive genes based on maximum-likelihood estimation and corresponding computer software (IGMapping 1.0) are presented. Computer simulations have shown that the methods proposed can unbiasedly estimate the recombination frequency or linkage distance between a codominant marker and an interactive gene.

Chromosome Mapping↗
PubMed2004

A new technique for endobronchial ultrasonography and comparison of two ultrasonic probes: analysis with a plot profile of the image analysis software NIH Image.

STUDY OBJECTIVES: Endobronchial ultrasonography (EBUS) is currently the sole clinical method available for delineating the bronchial wall structure; however, the image resolution is inadequate. Thus, an improved image analysis system is needed for both a more accurate and more readily interpretable endobronchial ultrasonogram. MATERIALS AND METHODS: A total of 10 patients underwent pulmonary resection for lung cancer. EBUS was performed on the bronchi of the resected lungs, which had been immersed in physiologic saline solution. The same bronchial lesion in each specimen was imaged with two probes: 20 MHz and 30 MHz. The images were analyzed using the plot profile derived from freeware image analysis software: NIH Image (National Institutes of Health; Bethesda, MD). The measured echo intensity of the bronchial wall was statistically analyzed. RESULTS: A normal bronchial wall image consists of five layers, and the plot profile shows a W-shaped curve. The mean value of the echo intensity of each peak or trough of the W-shaped curve was calculated and compared for both probes. The differences in the mean echo intensity between both the third and fourth layer and the second and fourth layer were found to be significantly greater with the 30-MHz probe than with the 20-MHz probe. The echo intensity curve of a central-type lung cancer was not W shaped, indicating that the bronchial wall was not composed of the normal five layers. CONCLUSION: We employed image analysis software and drew a plot to obtain a W-shaped curve from the EBUS image data. This enabled us to make an objective assessment of the laminar structure of the bronchial wall. In order to clearly recognize the laminar structure of the bronchial wall, the 30-MHz probe was found to be more useful than the 20-MHz probe.

Bronchi↗
PubMed2005

Computerized image analysis software for the comet assay.

Single-cell gel electrophoresis (SCGE) or the comet assay is a powerful tool for the detection of DNA single- and double-strand breaks and base damage and for investigating the kinetics of DNA strand break rejoining in human and animal model systems. It is a versatile technique that can be applied in various areas of biomedical research. This chapter highlights the importance of computerized analysis and data processing for the comet assay and describes the criteria used for manual evaluation of comets and their limitations compared with the computer-based analysis. It describes in detail SCGE-Pro, a semiautomatic software developed in our laboratory for comet evaluation and data processing. For comparison, some of the commercially available software for analysis of data from the comet assay is also described.

Animals↗
PubMed2007

Crystallographic software: a sustainable resource for the community.

Virtually all software is constantly changing and evolving (and crystallographic software is no exception), which makes it nearly impossible to write a chapter that will remain current. In this chapter, we introduce CRYSTAL, a website (http://crystal.uvm.edu) where a comprehensive list of available crystallographic packages for each step of macromolecular structure determination will be maintained. Additionally, we provide links to books, journals, and a number of educational sites on crystallography. For each program/site included at CRYSTAL, a detailed description will include: the most current version, the authors, and appropriate operating systems to host the program. Links to download the programs, available tutorials, and references to cite when using the program/site are also provided.

Crystallography↗
PubMed2004

Accuracy and precision of PIXImus densitometry for ex vivo mouse long bones: comparison of technique and software version.

Many densitometric studies in mice assess bone mineral density (BMD) at specified regions of interest, often using ex vivo specimens. In the present study, we sought to determine the precision and accuracy of ex vivo densitometry of mouse bones, comparing two software versions and two data acquisition techniques. The newer software allows manual adjustment of the threshold value for bone, improving the ability to analyze bone edges correctly. Root mean square standard deviations were 2-3 mg/cm2, with coefficients of variation ranging between 3% and 5% for femora and humeri and between 6% and 7% for radii. The regression coefficients for bone mineral content as a function of ash mass were near 1 for femora and humeri, but considerably lower for radii. Coefficients of determination were inversely related to bone size, with R2 values exceeding 0.9 at the femur, 0.8 at the humerus, and ranging between 0.3 and 0.6 at the radius. We found that our instrument has a position artifact, with BMD and bone mineral content dependent on the specimen's coordinates in the scanned field. Our findings establish the limitations of ex vivo densitometry with the PIXImus and support our recommendation that investigators seek position artifacts in their instruments.

Absorptiometry, Photon↗
PubMed2000

[A modular software concept for individual numerical simulation (FEM) of the human mandible].

A new modular software concept for individual numerical simulation of the human mandible using the finite element method (FEM) is presented. The main task is an individual analysis of regional stress and stress-compatibility on the basis of computed tomographic data in individual patients. Simulation should, however, also be possible in parallel with biomechanical experiments, or for further research projects. For this purpose, rapid and uncomplicated generation of the FEM model, easy modification of input data, and short computation times are required. Practical use in the clinical setting makes appreciable additional demands on the individual software components.

Biomechanical Phenomena↗
PubMed2002

Julius--a software framework for computer-aided-surgery.

In the paper we introduce Julius--an extendable cross-platform software framework for medical visualization and surgical planning. Julius features a modular, cross-platform design using Qt and Vtk libraries and comes with a set of image analysis components, like semi-automatic segmentation, registration, visualization and navigation. We also present a 3D surface generation pipeline used in Julius for generating surfaces from volume data. The pipeline consists of image based filtering, marching cubes surface extraction algorithm, surface decimation and surface smoothing steps. We use this approach within different medical applications like craniofacial surgical planning and will also show the overall software framework within the paper.

Computer Graphics↗
PubMed2002

[HeiDATAProViT--a universal software tool for evaluating biomedical data].

Evaluation of large sets of biomedical data can be divided into three universal stages: 1. archiving of clinical data together with data obtained from measurements, 2. processing of numerical data using signal processing algorithms and 3. visualizing the results. In this paper a software is presented which tightly integrates a data base under MS Access and the possibilities for data processing and visualization offered by Matlab. This software tool provides an interface between a data base containing large sets of biomedical data and an extensible pool of evaluation and visualization procedures. It can serve both as an instrument for data processing in clinical routine and an important component for evaluation of measurement data in any medical research project.

Algorithms↗
PubMed2006

Clinical and education workload measurements using personal digital assistant-based software.

OBJECTIVE: There are no accepted and practical measures of the relative clinical and educational activities of pediatricians who work in an academic health science center. Such measures are necessary for justification of existing and future human resource plans and evaluation of the activities and performance of physicians. The limited literature on the measurement of physician workload usually focuses on a specific subspecialty group and does not account for such issues as indirect patient care, such as telephone calls or e-mail consultations; variables that affect the delivery of clinical care, including patient acuity and complexity; and the presence of students during the patient care activities. After completing a pilot study that assessed the educational workload of faculty members, we adapted existing personal digital assistant technology and software to document clinical and educational activities. METHODS: Twenty full-time physicians from 4 subspecialty pediatric divisions participated in a 2-week evaluation project in May through June 2005. Clinical activities, with and without trainees, and educational activities were collected with the use of personal digital assistants. Software allowed an individualized division-specific drop-down menu. Information that was collected included clinical (location of activity, diagnosis, and time requirement) and educational activities. After completion of a 2-week data collection period, each physician was asked to complete a 5-question evaluation form. RESULTS: The project was completed successfully with capture of additional clinical and educational activities. A 5-question evaluation form was completed by 70% of the participants at the end of the 2-week data collection. Data on clinical and educational activities were analyzed qualitatively and graphed. CONCLUSIONS: This method of workload data collection added significant information in capturing activities that are not measured in traditional workload evaluations for either clinical activities, such as e-mail, telephone, and patient information review, or educational endeavors, including mentoring and educational lectures and presentations.

Academic Medical Centers↗
PubMed2006

[Nursing care planning: proposal for a software prototype].

This study aims to develop a software prototype to help hospital nurses plan nursing care, and carry out nursing interventions and all documentation in a computerized way. The methodology is based on the life cycle of system development, particularly the prototype concept, involving two phases: definition and development. The definition phase began with the planning stage, followed by the definition and analysis of requirements for the construction, and culminated with the specification of the software requirements. The development phase translated the group of requirements into a computerized model, structured in 10 modules, regarding the nursing care system process. The performance of this innovative resource in the different stages of the nursing care system process will be analyzed in future studies.

Health Planning↗
PubMed2006

[Nursing physical examination of the full-term neonate: self-instructional software].

The purpose of this research is to elaborate software about the physical examination of full-term newborns (TNB) for neonatal nursing teaching at undergraduate level. The software was developed according to the phases of planning, content development and evaluation. The construction of the modules was based on Gagné's modern learning theory and structured on the Keller Plan, in line with the systemic approach. The objectives were to elaborate and evaluate the contents of the self-instructional modules, to be used as a teaching strategy in the undergraduate course. After being structured, the material was reviewed and analyzed by 11 neonatal nursing experts, who rated the 42 exposed items as good or excellent.

Humans↗
PubMed2002

Drug-information software for Palm operating system personal digital assistants: breadth, clinical dependability, and ease of use.

STUDY OBJECTIVE: To examine the breadth, clinical dependability, and ease of use of drug-information software programs for personal digital assistants that incorporate the Palm operating system. DESIGN: Prospective evaluation with descriptive analysis. METHODS: Nine drug-information software programs were evaluated for breadth, clinical dependability, and ease of use, based on responses to 56 questions. RESULTS: Breadth of information (percentage of questions that could be answered) was 32-75%; LexiComp Platinum was the leader in this category. Clinical dependability (factual completeness) of information was 66.7-100%; LexiComp Platinum led this category as well. MobileMicromedex provided the narrowest breadth of information and the least clinically dependable information. Time to locate an answer to posed questions averaged 17.5 +/- 4.98 seconds. The fastest retrieval time was achieved by Davis's Drug Guide for Physicians (12.1 sec). Tarascon's Pharmacopoeia required the fewest viewed PDA screens to locate the requested information (3.3 screens). Cost of programs ranged from free to $129.95. Cost was not related to breadth or clinical dependability. CONCLUSIONS: LexiComp Platinum offered the greatest breadth of information and the most clinically dependable content. MobileMicromedex was the least helpful of these products for answering straightforward drug-information questions.

Costs and Cost Analysis↗
PubMed2004

Applications of computer-based instruction: using specialized software to aid letter-name and letter-sound recognition.

We evaluated computerized training and testing programs with children who were having difficulties learning prereading skills. The programs were derived from equivalence research and were written in authoring software designed for educators. After learning to match uppercase and lowercase printed letters to the corresponding letter names (Tasks 1 and 2), the children matched the letters to one another (Tasks 4 and 5). Then, after learning to match uppercase letters to sounds (Task 3), they also matched lowercase letters to sounds (Task 6) and matched printed to spoken words (Tasks 7 and 8). The results recommend equivalence-based protocols and user-friendly software in further development of prereading instruction.

Child, Preschool↗
PubMed2003

Evaluation of contemporary software methods used to quantify polyethylene wear after total hip arthroplasty.

BACKGROUND: Radiographic measurements of the wear of total hip arthroplasty implants are indirect measurements based on radiographic determinations of the location of the femoral head relative to the acetabular component. Using the simplest case of zero wear, we assessed the reproducibility and accuracy of two software applications designed to quantify wear from clinical radiographs. METHODS: After a cobalt-chromium head was glued into the polyethylene liner of a titanium shell, one cross-table lateral radiograph and three anteroposterior pelvic radiographs were made for twelve permutations of acetabular component angulation. The three anteroposterior radiographs differed only with regard to the cephalocaudal positioning of the prosthesis relative to the x-ray tube. To assess method reproducibility, each anteroposterior radiograph was assumed to be both the initial and the latest follow-up radiograph of a wear analysis. To assess method accuracy, each anteroposterior radiograph was paired in a wear analysis with each of the two anteroposterior radiographs made when the component was in the same angulation but at a different cephalocaudal position relative to the tube (one radiograph was the initial follow-up radiograph while the second was the latest follow-up radiograph). The analyses of reproducibility and accuracy were performed both with and without inclusion of the lateral radiograph made with the component in the same angulation. RESULTS: Both methods fared well in the reproducibility analyses, with mean linear and volumetric wear values of 0.00 to 0.07 mm and 0 to 24 mm(3), respectively. In the accuracy analyses, the mean linear and volumetric wear values derived with the two methods were 0.26 to 0.40 mm and 78 to 126 mm(3), respectively. CONCLUSIONS: Whereas the results of the reproducibility analyses showed that the methods were consistent in determining the relative positions of the head and shell from a given anteroposterior radiograph or pair of anteroposterior and lateral radiographs, the non-zero wear results obtained in the accuracy analyses proved that these positional determinations were often inaccurate. Thus, while contemporary software methods may yield reproducible results, their accuracy is limited by their inability to correctly determine the position of the head relative to the acetabular component.

Analysis of Variance↗
PubMed2001

Electrophoresis gel image processing and analysis using the KODAK 1D software.

The present article reports on the performance of the KODAK 1D Image Analysis Software for the acquisition of information from electrophoresis experiments and highlights the utility of several mathematical functions for subsequent image processing, analysis, and presentation. Digital images of Coomassie-stained polyacrylamide protein gels containing molecular weight standards and ethidium bromide stained agarose gels containing DNA mass standards are acquired using the KODAK Electrophoresis Documentation and Analysis System 290 (EDAS 290). The KODAK 1D software is used to optimize lane and band identification using features such as isomolecular weight lines. Mathematical functions for mass standard representation are presented, and two methods for estimation of unknown band mass are compared. Given the progressive transition of electrophoresis data acquisition and daily reporting in peer-reviewed journals to digital formats ranging from 8-bit systems such as EDAS 290 to more expensive 16-bit systems, the utility of algorithms such as Gaussian modeling, which can correct geometric aberrations such as clipping due to signal saturation common at lower bit depth levels, is discussed. Finally, image-processing tools that can facilitate image preparation for presentation are demonstrated.

Algorithms↗
PubMed2004

GeneX Va: VBC open source microarray database and analysis software.

Developed by the Virginia Bioinformatics Consortium (VBC), GeneX Va is an open source, freeware database and bioinformatics analysis software for archiving and analyzing Affymetrix GeneChip data. It provides an integrated framework for management, documentation, and analysis of microarray experiments and data to support a range of users, from individual research laboratories to institutional microarray facilities. GeneX Va also provides web-based access to a PostgreSQL relational database system with a comprehensive security system. Data can be extracted from the database and delivered to interactive or scriptable statistical analysis protocols. The security system allows each investigator to manage their own array data and analysis output files and also provides custom access privileges for other users, groups, and internal/external collaborators. The analysis interface uses "Analysis Trees," an innovative user interface that allows researchers to interactively create a tree-structured flow chart of analysis routines. The latest GeneX Va software is available from and can be freely downloaded at the Sourceforge web site http://va-genex.sourceforge.net. To allow researchers to access the database and analysis capabilities of the GeneX Va system, microarray data from many VBC GeneChip experiments have been deposited into a public section of the GeneX Va system at the University of Virginia. The VBC GeneX Va sites, which include documentation, are at http://genes.med.virginia.edu/ of the University of Virginia and at http://genex.csbc.vcu.edu/ of the Virginia Commonwealth University.

Computer Security↗