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PubMed2005

Building research administration applications for the academic health center: a case study.

The academic health center information environment is saturated with information of varying quality and overwhelming quantity. The most significant challenge is transforming data and information into knowledge. The University of Cincinnati Medical Center's (UCMC) focus is to develop an information architecture comprising data structures, Web services, and user interfaces that enable individuals to manage the information overload so that they can create new knowledge. UCMC has accomplished much of what is reported in this article with the help of a four-year Integrated Advanced Information Management Systems (IAIMS) operation grant awarded by the National Library of Medicine in 2003. In the UCMC vision for knowledge management, individuals have reliable, secure access to information that is filtered, organized, and highly relevant for specific tasks and personal needs. Current applications and tool sets will evolve to become the next generation knowledge management applications or smart digital services. When smart digital services are implemented, silo applications will disappear. A major focus of UCMC's IAIMS grant is research administration. Testing and building out existing and new research administration applications and digital services is underway. The authors review UCMC's progress and results in developing a software architecture, tools, and services for research administration. Included are sections on the evolution to full integration, the impact of the work at UCMC to date, lessons learned during this research and development process, and future plans and needs.

Academic Medical Centers↗

PubMed2006

3D geometry of a normal tricuspid annulus during systole: a comparison study with the mitral annulus using real-time 3D echocardiography.

AIM: This study was done to explore the 3D geometry of the normal tricuspid annulus and compare it with the mitral annulus (MA), using real-time 3D echocardiography (RT3DE) and newly developed 3D computer software. METHODS: Thirteen left ventricular (LV) and 13 right ventricular (RV) volumetric images were obtained using RT3DE from normal subjects. LV and RV volumetric data were segmented into 16 rotational apical planes (angle increment=11.25 degrees ) around the rotational axis from the apex through the center of two annuli, using newly developed 3D software (TomTec, Co., Munich, Germany). Two hinge points of the MA and the TA were traced in each plane during early and late systole. The MA and the TA were then automatically reconstructed with those 32 traced points. 3D surface (3DMAA, 3DTAA) and 2D projected areas (2DMAA, 2DTAA) of the annuli were calculated automatically as well, from those fitted data. For a comparison between the two annuli, the 3D and 2D area measurements of both annuli were corrected (c) according to the height of each patient (c2DMAA, c2DTAA, c3DMAA, and c3DTAA). Non-planarity of the annuli was estimated by their non-planar angles (MA: the angle between the anterior and posterior parts of the annulus; TA: the angle between the septal and free wall parts of the annulus). RESULTS: The TA revealed a less non-planar saddle shape than did the MA, which had a significantly wider non-planar angle (167.7+/-3.2 vs 145.5+/-6.1 degrees , p<0.01) and a round or oval appearance on the projected view. The c2DTAA was significantly larger than the c2DMAA during early systole (p<0.01). However, there was no significant difference between the c3DTAA and c3DMAA during early and late systole (p>0.01). CONCLUSION: We assessed the 3D geometry of the MA and the TA by 3D reconstruction using RT3DE and newly developed computer software. The TA had a less non-planar shape compared with the MA, with either a round or oval appearance on the projected view.

Adult↗

PubMed1989

(PLOT79): a comprehensive portable Fortran scientific line graphics system, as applied to biomedical research.

Scientific results are often most succinctly presented in graphical form. We describe a system for computer-generated scientific line graphics known as (PLOT79), named to commemorate the SIGGRAPH CORE graphics standard proposal of 1979. (PLOT79) is a widely used and actively evolving graphics system, written primarily in SFTRAN3, a structured procedural computer language which can be translated readily into Fortran. The package embodies concepts of sound software engineering, having been designed from the outset to be portable, maintainable and hardware-independent; much of the effort required to implement the system was directed toward the development of software engineering tools to ensure these goals. A modular design strategy has allowed a wide variety of graphics output devices to be supported. (PLOT79) has been installed under numerous operating systems, and software tools provided by UNIX have allowed particularly efficient installation and use of the system. Access to (PLOT79) is available through three avenues: (1) linking (PLOT79) routines with a user-written high-level program; (2) use of pre-written high-level applications programs which perform certain frequently-required tasks such as the plotting of simple two or three-dimensional data; or (3) the use of an interactive graphics command parser known as slides. (PLOT79) has proven popular among workers in the physical sciences and engineering both for its easy availability, openness (all source code is provided), and powerful capability. The system presents an equally important (though lesser known) resource for biomedical research, as demonstrated by examples from ongoing biomedical research projects. It also provides a focus for discussion of the practical limitations inherent in existing graphics standards and programming languages.

Computer Graphics↗

PubMed1996

Use of notebook computers for third-year surgical students.

BACKGROUND: Computer-aided instruction has become increasingly popular in medical education. Notebook computers (NCs) are attractive, convenient microcomputers. We hypothesized that use of NCs by third-year surgical students would enhance their performance of educational activities. METHODS: During the 1994-1995 academic year 25 student volunteers used NCs during the surgery clerkship. NC software included questions for self-examination, anatomy self-instruction program, word processing and electronic mail (e-mail) for recording and sending history and physicals (H & Ps) to faculty for review, and MEDLINE search software. Identical software was available to all students at on-campus computer centers. All students were asked to record the number of hours that they used the self-examination and anatomy programs, number of H & Ps performed and reviewed by faculty, and number of literature searches performed. NC users were interviewed regarding the value of NC use and their rating of software programs. RESULTS: NC users (n = 25) used the self-examination and anatomy programs more often, performed more literature searches, and had a greater percentage of their H & Ps reviewed by faculty compared with non-NC users (n = 143) (p < 0.05 for all outcomes). Most NC users agreed that NC use was enjoyable and valuable, and they believed that all students should have NCs during the surgery clerkship. Students rated software in order of preference: e-mail > self-examination > MEDLINE search > anatomy program. CONCLUSIONS: NC use enhanced performance of educational activities in the surgery clerkship. Effort toward developing educational software for surgical students is warranted because students are likely to use such programs.

Anatomy↗

PubMedDate not supplied

[Digital photography as an object of forensic medical examination].

The possibility of diagnosing skin lesions by means of digital pictures was investigated. A "Zenit ET" film camera, HP flatbed scanner, amateur "'Panasonic" and "Sony" videocameras, miniature USB camera and digital photocameras were used to obtain images. Above 1000 images were studied. Criteria were fixed for the required quality of images. A method was developed to formalize images by means of a color etalon and mathematical assessment of formalized skin lesions. Stages were suggested for the computer-based analysis of images. Computer software was developed for the automated formalization of images and for the statistical processing of values of image elements. It was demonstrated that digital photography can be an independent informative object of forensic medical examination.

Forensic Pathology↗

PubMed2006

Evaluating kriging as a tool to improve moderate resolution maps of forest biomass.

The USDA Forest Service, Forest Inventory and Analysis program (FIA) recently produced a nationwide map of forest biomass by modeling biomass collected on forest inventory plots as nonparametric functions of moderate resolution satellite data and other environmental variables using Cubist software. Efforts are underway to develop methods to enhance this initial map. We explored the possibility of modeling spatial structure to make such improvements. Spatial structure in the field biomass data as well as in residuals from the map was investigated across 18 ecological zones in the Interior Western U.S. Exploratory tools included directional graphs of summary statistics, three dimensional maps, Moran's I correlograms, and variograms. Where spatial pattern was present, field and residual biomass were kriged, and predictions made for an independent test set were evaluated for improvement over predictions in the initial biomass map. While kriging has some potential benefit when analyzing the field data and exploring spatial structure, kriging residuals resulted in little or no improvement in the initial biomass map developed using Cubist software. Stationarity assumptions, variogram behavior, and appropriate model fitting strategies are discussed.

Biomass↗

PubMed2007

CT colonography: techniques, indications, findings.

Computed tomographic colonography (CTC) is a minimally invasive technique for imaging the entire colon. Based on a helical thin-section CT of the cleansed and air-distended colon, two-dimensional and three-dimensional projections are used for image interpretation. Several clinical improvements in patient preparation, technical advances in CT, and new developments in evaluation software have allowed CTC to develop into a powerful diagnostic tool. It is already well established as a reliable diagnostic tool in symptomatic patients. Many experts currently consider CTC a comparable alternative to conventional colonoscopy, although there is still debate about its sensitivity for the detection of colonic polyps in a screening population. This article summarizes the main indications, the current techniques in patient preparation, data acquisition and data analysis as well as imaging features for common benign and malignant colorectal lesions.

Colonic Polyps↗

PubMed2006

GenePro: a Cytoscape plug-in for advanced visualization and analysis of interaction networks.

MOTIVATION: Analyzing the networks of interactions between genes and proteins has become a central theme in systems biology. Versatile software tools for interactively displaying and analyzing these networks are therefore very much in demand. The public-domain open software environment Cytoscape has been developed with the goal of facilitating the design and development of such software tools by the scientific community. RESULTS: We present GenePro, a plugin to Cytoscape featuring a set of versatile tools that greatly facilitates the visualization and analysis of protein networks derived from high-throughput interactions data and the validation of various methods for parsing these networks into meaningful functional modules. AVAILABILITY: The GenePro plugin is available at the website http://genepro.ccb.sickkids.ca.

Algorithms↗

PubMed1997

Average age at first occurrence as an alternative occurrence parameter in epidemiology.

BACKGROUND: Current epidemiological methods focus mostly on incidence rates and their ratios as measures of occurrence and effect. Incidence rates and rate ratios can be hard to interpret when the outcome disease is common. METHODS: The possibilities of using an alternative measure, average age at first occurrence of the disease, are discussed. RESULTS: Methods for the analysis of average age at first occurrence are illustrated in a study of occupation and disability pension. We estimate that the average age at pension among crane drivers is only about 0.8 that of maintenance workers, regardless of the method, although the confidence intervals depend on the method. CONCLUSIONS: Average age at first occurrence is easier to interpret than the incidence rate for a very common disease. Because estimates are not readily available in software packages, we encourage further development of packaged software for this measure.

Adolescent↗

PubMed2006

Impact of physician gender on sexual history taking in a multispecialty practice.

INTRODUCTION: Identification of sexual dysfunction may help physicians diagnose problems such as diabetes, pituitary tumors, atherosclerosis, and depression. Sexual concerns are common among patients; however, there is evidence to suggest that these concerns are not appropriately investigated by clinicians. AIM: To examine the impact of physician gender on sexual history taking. METHODS: One hundred and thirty-one study questionnaires were sent to OB/Gyns, family practitioners, internists, pediatricians, and surgeons. Physicians were asked to rank their discomfort during interviews with patients of different ages, races, marital status, sexual preference, religious beliefs, and academic achievement, and they were asked to rank their perception of patient discomfort. MAIN OUTCOME MEASURES: A cross-sectional descriptive analysis was generated, Fisher's exact test was performed utilizing SPSS software, and confidence intervals were developed utilizing SAS software. RESULTS: Of the 78 questionnaires (59%) returned, 69 (88%) reported taking sexual histories. Characteristics identified by physicians as causing discomfort included patient's age younger than 18 and greater than 65, patient's academic achievement below college level, and patient's divorced or single marital status. Moreover, there was a statistically significant difference (P < 0.05) between male and female physicians reporting their discomfort when interviewing males (19% and 50%, respectively) and females (35% and 12%, respectively). CONCLUSION: Although a high percentage of practitioners report taking a sexual history, physicians reported and perceived greatest discomfort when interviewing opposite gender patients as well as patients of very young and old ages. It is clear that not only is there a need for physician education on the topic of sexual history taking, but also consideration of the impact of physician and patient gender.

Adult↗

PubMedDate not supplied

Use of three-dimensional sonomicrometry to study the motion of the mitral valve.

To develop an anatomically correct mitral valve prosthesis, one needs to study the dynamics of the mitral valve apparatus in vivo. The authors used three-dimensional (3D) sonomicrometry and custom visualization software to develop a system to study the mitral valve. Sixteen ultrasonic transducers each were implanted into the hearts of pigs under cardiopulmonary bypass. Four of these crystals were affixed to the base and apex of both papillary muscles, four were attached to the free edge of the anterior and posterior leaflets where the main chordae attach, six were placed around the mitral annulus, and two were affixed to the epicardial wall. The digital sonomicrometer system sequentially fired each transducer and listened for an ultrasound signal at the other 15. This process was repeated so that all 16 transducers were sequentially fired, and each cycle of 16 was repeated 200 times/sec. The matrix of distances obtained between all the combinations of pairs of the 16 transducers was converted to x, y, z coordinates, the shape of the mitral valve apparatus was reconstructed in 3D on a graphics computer, and the valve's motion was analyzed over several cardiac cycles. The authors conclude that mapping of the mitral valve apparatus in pigs by 3D sonomicrometry provides quantitative measurements that can aid in the design of a mitral valve prosthesis that closely replicates the anatomy and function of the natural valve.

Animals↗

PubMed1999

E-CELL: software environment for whole-cell simulation.

MOTIVATION: Genome sequencing projects and further systematic functional analyses of complete gene sets are producing an unprecedented mass of molecular information for a wide range of model organisms. This provides us with a detailed account of the cell with which we may begin to build models for simulating intracellular molecular processes to predict the dynamic behavior of living cells. Previous work in biochemical and genetic simulation has isolated well-characterized pathways for detailed analysis, but methods for building integrative models of the cell that incorporate gene regulation, metabolism and signaling have not been established. We, therefore, were motivated to develop a software environment for building such integrative models based on gene sets, and running simulations to conduct experiments in silico. RESULTS: E-CELL, a modeling and simulation environment for biochemical and genetic processes, has been developed. The E-CELL system allows a user to define functions of proteins, protein-protein interactions, protein-DNA interactions, regulation of gene expression and other features of cellular metabolism, as a set of reaction rules. E-CELL simulates cell behavior by numerically integrating the differential equations described implicitly in these reaction rules. The user can observe, through a computer display, dynamic changes in concentrations of proteins, protein complexes and other chemical compounds in the cell. Using this software, we constructed a model of a hypothetical cell with only 127 genes sufficient for transcription, translation, energy production and phospholipid synthesis. Most of the genes are taken from Mycoplasma genitalium, the organism having the smallest known chromosome, whose complete 580 kb genome sequence was determined at TIGR in 1995. We discuss future applications of the E-CELL system with special respect to genome engineering. AVAILABILITY: The E-CELL software is available upon request. SUPPLEMENTARY INFORMATION: The complete list of rules of the developed cell model with kinetic parameters can be obtained via our web site at: http://e-cell.org/.

Adenosine Triphosphate↗

PubMed2001

Progress in aberration-corrected scanning transmission electron microscopy.

A new corrector of spherical aberration (C(S)) for a dedicated scanning transmission electron microscope (STEM) is described and its results are presented. The corrector uses strong octupoles and increases C(C) by only 0.2 mm relative to the uncorrected microscope. Its overall stability is greatly improved compared to our previous design. It has achieved a point-to-point resolution of 1.23 A in high-angle annular dark field images at 100 kV. It has also increased the current available in a 1.3 A-sized probe by about a factor of ten compared to existing STEMs. Its operation is greatly assisted by newly developed autotuning software which measures all the aberration coefficients up to fifth order in less than one minute. We conclude by discussing the present limits of aberration-corrected STEM, and likely future developments.

Journal Article↗

PubMed2005

TERMTrial--terminology-based documentation systems for cooperative clinical trials.

Within cooperative groups of multi-center clinical trials a standardized documentation is a prerequisite for communication and sharing of data. Standardizing documentation systems means standardizing the underlying terminology. The management and consistent application of terminology systems is a difficult and fault-prone task, which should be supported by appropriate software tools. Today, documentation systems for clinical trials are often implemented as so-called Remote-Data-Entry-Systems (RDE-systems). Although there are many commercial systems, which support the development of RDE-systems there is none offering a comprehensive terminological support. Therefore, we developed the software system TERMTrial which consists of a component for the definition and management of terminology systems for cooperative groups of clinical trials and two components for the terminology-based automatic generation of trial databases and terminology-based interactive design of electronic case report forms (eCRFs). TERMTrial combines the advantages of remote data entry with a comprehensive terminological control.

Clinical Trials as Topic↗

PubMed1994

BIOESTIM: software for automatic design of estimators in bioprocess engineering.

This paper describes BIOESTIM, a software package devoted to on-line estimation in bioprocess engineering. BIOESTIM enables bioengineers automatically to design state and parameter estimators from a minimal knowledge of the process kinetics. Such estimators allow development of software sensors capable of coping with the lack of reliable instrumentation suited to real-time monitoring. The estimator building procedure through BIOESTIM starts up from a dynamical material balance model of the bioprocess. This model, supplied by the user, is next completed by other information with no requirement for numerical values: the user has only to specify available measurements, coupled reactions and the known yield coefficients. On the base of this knowledge, BIOESTIM proceeds to symbolic algebraic manipulations on the model in order to study estimation possibilities and check identifiability of yield coefficients. When the design of an estimator is possible, the corresponding equations are automatically generated. Moreover, these estimators are stored in a user-specified file which is automatically interfaced with a specialized simulation software including data treatment and numerical integration packages. Thus, the user can simulate the estimator performances under various operational conditions using available experimental measurements. A typical example dealing with microbial growth and biosynthesis reactions is given in order to illustrate the main functional capabilities of BIOESTIM. BIOESTIM has been designed and written in a modular fashion. The module dealing with estimators design makes use of symbolic computation; it is written in Mathematica and runs on every computer on which this language is available.

Algorithms↗

PubMed2002

Noncontact three-dimensional laser measuring device for tracheoscopy.

Luminal dimension measurements are still an unsolved problem in endoscopy. The goal of our study was to develop a 3-dimensional (3-D) measuring device for endoscopic applications. For this purpose, a fiber probe projecting a ring of laser light (laser diode, 675 nm) was integrated in a position registration system. Software was developed for image analysis, distortion correction, and export of data for 3-D display. Experimental evaluation of measuring accuracy employing plastic tubes and 15 postmortem pig trachea preparations with artificial stenosis indicated a high level of method precision (Pearson's correlation coefficients, r = 0.99 for normal tracheal lumen and r = 0.97 for high-grade stenosis; p < .0001). Our clinical experience with the technique in 10 patients with tracheal stenosis revealed no side effects and encourages us to recommend this method for other endoscopic applications. The method enhances our 3-D grasp of endoscopically examined lesions.

Animals↗

PubMed1992

Analysis of beat-to-beat cardiovascular hemodynamic variables obtained from long-term biotelemetry.

Manual methods of large volume data storage, retrieval, and analysis are difficult, time consuming, and present numerous opportunities for calculation errors. We have designed and implemented a comprehensive computer-based system for performing these functions. Development of this system was necessary since left ventricular (LV) blood pressure and two regional LV wall thickness measurements were obtained during long-term extracorporeal biotelemetry of miniswine for 24-h periods. During a single recording period over 100,000 individual cardiac cycles were recorded on analog tape and later analysed for determination of global myocardial oxygen demand and regional myocardial function. In addition, custom designed software was developed to determine the extent and duration of myocardial dysfunction. Batch file commands enabled the customized software to operate without prompting by the user thus optimizing the time usage of the computer, and the computer based data acquisition and analysis system. Although this system was designed specifically for analysing cardiovascular hemodynamic variables, it is flexible and can be applied to other experimental applications.

Analog-Digital Conversion↗

PubMed2001

Open Source Software meets gene expression.

Use of the Open Source Software (OSS) development model has been crucial in a number of recent technological areas, including operating systems, applications and bioinformatics. The rationale for why OSS is often a better development model than proprietary development and some of the results of this model in the field of Gene Expression are reviewed. The paper concludes with a discussion of why funding agencies should endorse OSS and require funded software projects to be released Open Source.

Access to Information↗