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Cardiovascular physiology teaching: computer simulations vs. animal demonstrations.

The roots of physiology lie in laboratory observation, and physiology courses continue to rely on laboratory observation to provide students with practical information to correlate with their developing base of conceptual knowledge. To this end, animal laboratories provide a functioning example of interactions among organ systems and a source of data for student analysis. However, there are continuing objections to using animals for teaching, and animal labs are costly in time and effort. As an alternative laboratory tool, computer software can simulate the operation of multiple organ systems: responses to interventions illustrate intrinsic organ behavior and integrated systems physiology. Advantages of software over animal studies include alteration of variables that are not easily changed in vivo, repeated interventions, and cost-effective hands-on student access. Nevertheless, simulations miss intangible aspects of experimental physiology, and results depend critically on the assumptions of the model. We used both computer and animal demonstrations in teaching cardiovascular physiology to first-year medical students. The students rated both highly, but the computer-based session received a higher rating. We believe that both forms of teaching have educational merit. At the introductory level, the computer appears to provide an effective alternative.

Animals↗

Integrated functional visualization of eukaryotic genomes.

BACKGROUND: Increasing amounts of data from large scale whole genome analysis efforts demands convenient tools for manipulation, visualization and investigation. Whole genome plots offer an intuitive window to the analysis. We describe two applications that enable users to easily plot and explore whole genome data from their own or other researchers' experiments. RESULTS: STRIPE and GFFtool (General Feature Format Tool) are softwares designed to support integration, visualization and exploration of whole genome data from eukaryotic genomes. STRIPE, in addition to providing a highly customizable and interactive data plot, provides access to numerous well-selected databases with updated information on all genes of a genome. GFFtool provides a user-friendly solution to integrating experimental data with the genomic information available in public databases. They also obviate the need for users to maintain large annotation resources, as they link to well-known resources using standard gene and protein identifiers. CONCLUSION: The programs provide the user with broad genomic overviews of data distribution, fast access to data of interest, and the ability to navigate speedily from one resource to another, and gain a better understanding of result of whole genome analysis experiments.

Algorithms↗

BayGO: Bayesian analysis of ontology term enrichment in microarray data.

BACKGROUND: The search for enriched (aka over-represented or enhanced) ontology terms in a list of genes obtained from microarray experiments is becoming a standard procedure for a system-level analysis. This procedure tries to summarize the information focussing on classification designs such as Gene Ontology, KEGG pathways, and so on, instead of focussing on individual genes. Although it is well known in statistics that association and significance are distinct concepts, only the former approach has been used to deal with the ontology term enrichment problem. RESULTS: BayGO implements a Bayesian approach to search for enriched terms from microarray data. The R source-code is freely available at http://blasto.iq.usp.br/~tkoide/BayGO in three versions: Linux, which can be easily incorporated into pre-existent pipelines; Windows, to be controlled interactively; and as a web-tool. The software was validated using a bacterial heat shock response dataset, since this stress triggers known system-level responses. CONCLUSION: The Bayesian model accounts for the fact that, eventually, not all the genes from a given category are observable in microarray data due to low intensity signal, quality filters, genes that were not spotted and so on. Moreover, BayGO allows one to measure the statistical association between generic ontology terms and differential expression, instead of working only with the common significance analysis.

Bacteria↗

Computerized protocol for anatomical and functional studies of joints.

This chapter describes a new methodology for the acquisition and computer elaboration of joint anatomy and motion data and the study of their correlation. The method uses a commercial industrial electrogoniometer, custom tools, and software designed and developed by the authors for interactive display of the anatomical structures during joint motion, numerical interpolations of the articular geometries, and kinematic analysis of motion. The original data acquisition protocol and computer elaboration software are described in detail, and a final subheading describes briefly previous studies and future developments.

Biomechanical Phenomena↗

Biomedical informatics methods in pharmacogenomics.

Pharmacogenomics is the study of the genetic basis of individual variation in response to therapeutic agents. Pharmacogenomics may potentially affect on every step of health care and every drug treatment protocol. The optimal approach to pharmacogenomics in hypertension requires the integration of different disciplines, in which biomedical informatics plays an essential role. This chapter describes biomedical informatics methods used in dealing with key issues in pharmacogenomics. These key issues include the association between structure and function, the interaction between gene and drug, and the correlation between genotype and phenotype. Heterogeneous resources, including web sites, databases, and software analysis tools, are selected, organized, and integrated in practical methods to support these studies. Bioinformatics methods described in this chapter include genetic sequence searching, comparison, structural modeling, functional analysis, and systems biology studies, with emphasis on single-nucleotide polymorphism (SNP) analysis. Medical informatics methods such as disease and drug information and clinical terminology are also embraced in this chapter. This combination of both biological and medical informatics provides comprehensive methodologies to resolve complex problems in pharmacogenomics.

Computational Biology↗

Global approach to perinatal medicine: functional genomics and proteomics.

Functional genomics (transcriptomics and proteomics) is a global, systematic and comprehensive approach to the identification and description of the processes and pathways involved in normal and abnormal physiological states. The functional genomics methods most applied today are DNA microarrays and proteomics methods, primarily two-dimensional gel electrophoresis coupled with mass spectrometry. To date, interesting research has been carried out, representing milestones for future implementation of functional genomics/proteomics in perinatal medicine. For instance, possible biomarkers of pre-eclampsia, preterm labor and gestational trophoblastic diseases have been discovered. Further systematic examination of differentially regulated genes and proteins in maternal and fetal tissues and fluids will be required. However, high-throughput technologies reflect biological fluctuations and methodological errors. Large amounts of such different data challenge the performance and capacity of the statistical tools and software available at present. Further major developments in this field are pending and the intellectual investment will certainly result in clinical advances.

Female↗

Dentin penetrability evaluation of three different dyes in root-end cavities filled with mineral trioxide aggregate (MTA).

The purpose of this study was to evaluate the penetration of three dyes in MTA root-end fillings. In 30 single-rooted teeth, cavities for retrofilling were prepared with an ultrasound appliance and filled with MTA. The specimens were randomly assigned to three groups (n = 10) and immersed in the following solutions: 2% methylene blue (MET), 50% silver nitrate (NIT) and 0.2% rhodamine B (ROD). Two transversal slices (1 mm) of the retrofilling region were obtained and evaluated using the Image Tool 3.0 software to obtain a quantitative evaluation (in mm2) of the dye penetration around the retrofillings. Data were submitted to statistical analysis using Students t-test. The lowest degree of dye penetration was observed for the NIT group, in both slices (p < 0.05). Dye penetration was significantly larger in the ROD group when compared to the NIT group, in both slices (p < 0.05), and to the MET group, only in slice 1 (p < 0.05). Within the limitations of this study, it was concluded that the choice of dye could influence the penetration evaluation in root-end filling studies, and that the NIT had the lowest penetration capacity in the apical dentine.

Aluminum Compounds↗

[Contribution to the anatomical-morphological study of the pelvic floor in the asymptomatic female: the use of MRI imaging].

OBJECTIVES: To confirm the results of previous studies demonstrating the morphology of the levator ani muscle in the living subject is different to that described in classic anatomical works; to evaluate the anatomical-morphological differences of the pelvic floor between nulliparous and multiparous women in order to analyze the influence of pregnancy and delivery. METHODS: Comparative study of the morphological variations of the iliococcigeous fascicle of the levator ani muscle between two groups of females using T2 MRI.: the first group included 11 nulliparous women and the second group 9 multiparous women. The curvature radium of the fascicles was calculated in the frontal projections. The differences in height were also calculated. The anterior limit of the iliococcygeal muscle dome was determined in the sagittal plane. The software Image Tool 3.0 was employed for the measurements. The Kolmogorov-Smirnov test was employed to analyze the distribution of the study populations; mean value comparisons between groups were performed by the Student's t test. Finally, the various morphological measurements were compared in relation to various parameters: parity, side, body mass index (BMI), sports practice, menstrual cycle phase, and presence or absence of episiotomy. Data obtained were analyzed using the Fisher's exact test, with a statistical significance of p < 0.05. RESULTS: Morphological measurements: We observed that the concavity of the iliococcygeal fascicle dome is larger in nulliparous women (p = 0.03 for the right side and p = 0.04 for the left). Moreover, these women have the domes significantly more anterior (p < 0.001 for both sides). Comparisons between other variables: an association between nulliparous status and the presence of a higher and more anterior left dome, and multiparous status and a higher and more anterior right dome were (p = 0.02). CONCLUSIONS: The hypothesis of the pelvic floor morphology being a double dome with inferior-posterior concavity in the living asymptomatic female is confirmed. We also demonstrate the existence of anatomical-morphological differences in the iliococcygeal muscle of the levator ani between nulliparous and multiparous females, which seems to confirm a relationship with pregnancy and/or delivery.

Adult↗

QMHC interview: Alan C. Brewster, M.D.. Interview by Marie E. Sinioris.

Information systems for severity-of-illness measurement and case mix adjustment are at the cutting edge of health care quality technology. The rapid rise of these systems in the past decade has paralleled hospital needs for better data on clinical processes and the burgeoning need among health care customers for better data on clinical outcomes and the relative performance of providers. The dual nature of the demand is fueling what promises to be a decade of growth for the developers of severity systems. To get a better handle on the status of these software-based tools, QMHC interviewed Alan C. Brewster, M.D., Vice Chairman and cofounder of MediQual Systems, Inc., and a principal developer of the widely used MedisGroups system.

Diagnosis-Related Groups↗

[Evidence-based medicine and medical databases in obstetrics and gynecology].

Evidence-based medicine is a new trend in both teaching medicine and supporting the clinical decisive process, answering the clinical questions. The basis of the evidence-based medicine comprises of analysing and interpreting current and reliable medical publications concerning certain subject. The important condition, which has to be fulfilled is a possibility of an easy access to current medical information--via internet, medical publications' databases and publications themselves. It is crucial to use the proper hardware system (local net) and proper software system--tools for using evidence-based medicine. Regarding the medical research, nowadays, database systems became unavoidable. By using such a programs process of data collection, control and analysis became both easier and more reliable thanks to eliminating many "human based" errors. In following paper own experience in introducing evidence-based medicine and medical databases in the field of obstetrics and gynaecology will be presented.

Evidence-Based Medicine↗

Computerised coordinated care system in the RISE project.

It is a fact that elderly peoples' life is characterized by problems such as deteriorating health and physical condition, feelings of loneliness, isolation, and of being dependent on others, in many aspects of their everyday lives. The objective of the RISE project is to provide an efficient vehicle for Health Care Professionals for improving Health Care, quality of life and integration of the elderly and disabled people with society by implementing Information technology applications. In particular, RISE project aims in developing a distributed network of service providers across the European Union, which will provide integrated types of services to the elderly and disabled population. The purpose of this paper is to present the impact of this project concerning the Health Informatics sector. It will describe the issues regarding, the needs for education and training of the professionals that arise by the introduction of this concept, and, the possible ways that such a concept forms an efficient vehicle for Health Professionals in assisting these particular groups of users. The longer perspective seeks to redefine and reshape the Health Care services' larger purpose, i.e. to make those comport with elementary individual needs of the elderly and disabled by introducing new methods of efficient health service provision. To achieve this there is an increased need for the training of the professionals. The outcome of RISE will be a set of specialised software components, tools and training methodologies designed to assist the Health Professionals achieving the aforementioned tasks.

Aged↗

Optical properties of hair--detailed examination of specular reflection patterns in various hair types.

Details of the specular reflection of curved hair tresses, resulting from illumination with a collimated incident light source, were examined both qualitatively and quantitatively using high-resolution photography and image analysis. The reflections were found to consist of a multitude of light dots aligned with the fibers and typically separated by a distance of 81-145 microm. The contrast between the dots (specular reflection) and the darker regions (diffuse reflection) of the entire reflection band was found to increase with increasing pigmentation of hair. Highly pigmented Oriental hair provided more contrast within the specular reflection band than unpigmented natural white hair. A quantitative description of the light reflection patterns within the specular reflection band included two-dimensional distribution of luminosity, histograms of the frequency of appearance for peak maxima and minima in luminosity distribution plots, and histograms of absolute maxima and minima of luminosity along the length of the fibers. Specular reflection from African hair, which consists of many curls that provide multiple and randomly distributed reflection centers, have also been investigated. Using microscopy software, Image Tool 2.0, and a method termed image threshold, the number of reflection sites and their shapes could be quantified. For example, treatment of African hair with synthetic sebum was shown to significantly affect the reflection patterns, resulting in a decrease in the overall hair luster. Comparison of reflection patterns from Caucasian frizzy, very curly, and curly hair is also discussed.

Hair↗

Teaming up for medical necessity compliance.

Healthcare finance professionals and other employees from departments involved with a hospital's revenue cycle can work together in many ways to minimize denials, delays, and write-offs: Verifying medical necessity when a patient is first seen, rather than when the patient arrives for service, so that an advance beneficiary notice can be issued and signed at the time of service. Ensuring that the proper codes and modifiers are assigned before a claim is submitted. Augmenting software compliance tools with human expertise in compliance and internal education programs to reduce errors over time before they reach the billing department.

Cooperative Behavior↗

Automated analysis of muscle fibre images.

A technique for studying the distribution and size of different fibre types in muscles is proposed for automated analysis of individual fibres in optical density images from ATPase-stained muscle sections. After delineation, fibres may be classified into different histological types (1, 2A, 2B and 2C) using the measurement of their mean optical density (mOD). The densitometric measurements were obtained from three serial histological slides stained under different conditions. The delineation procedure is performed on one of the images: the resulting mask is fitted to the other images using a linear coordinate transform. Along with densitometric measurements, the lesser diameter of the fibres is computed. Both in processing and in analysis, extensive use was made of mathematical morphology tools. All software was implemented on a VICOM digital image processor, extended with a VISIOMORPH morphoprocessor board.

Adenosine Triphosphatases↗

[Measuring signal processing by analog/digital conversion using personal computers. I: General principles].

Sampling rate, quantization noise and the number of channels to be acquired, the main concepts of computerized data acquisition, are discussed as regards their relevance to clinical research. Different setups of analog/digital conversion and signal processing, such as real-time and post-acquisition mode, are contrasted with respect to performance and installation effort. Additionally, continuous analog recording on FM coded tape is presented as a useful tool for software testing, re-evaluation and backup purposes.

Analog-Digital Conversion↗

[Data and quality assurance tools from a new cardiac center in Denmark].

Open heart surgery was established at Aalborg Hospital in 1992. In the time period March to December 1992 cardiac anaesthesia was administered in 98 operations utilizing extracorporeal circulation and cardiopulmonary bypass. Mortality in coronary artery surgery was 1.6%. All patients were prospectively registered using a new dataform allowing registration of 228 patients related variables concerning preoperative status, course of anaesthesia and perfusion, surgery and postoperative intensive care. Quality assurance in cardiac surgery requires risk factor analysis, and registration of numerous data is a necessary tool. The software for our database system has been developed and programmed using the database programme dBASE IV from the Ashton/Tate Corporation.

Adult↗

A study of the effectiveness of an interactive computer classroom.

This study examined the use of an interactive computer classroom (ICC) compared with a traditional lecture/discussion format (LD) for a nursing management course taught from fall semester 1994 through fall semester 1996. The ICC was structured around a group systems support software, a tool previously used in business settings for group decision-making activities. Structured learning activities allowed all students to participate simultaneously and anonymously. Data were collected during the second and final semesters of the study. The outcomes included academic performance, measured by course exams; class participation, measured by direct observation; and attendance records. The control group was a concurrent management course taught with the same objectives and evaluated by identical examinations. The examination scores and the frequency of class participation of the ICC group were significantly higher than those measures of the LD group. There was no significant difference in class attendance. Evaluation forms with open-ended questions were completed by the ICC students and revealed that the students believed that the process enhanced application and understanding. The negative aspects of the ICC experience were the need for increased preparation time for faculty and the students' lack of tolerance when technical difficulties caused delays.

Computer-Assisted Instruction↗

Use of project ontologies and terminology servers to support software engineering.

Complex medical software imposes new requirements on the methods and tools used for maintenance. Appropriate maintenance tools can increase software reliability and quality by providing means to trace dependencies among software artifacts for reducing unexpected impacts in software caused by software changes. We have used the GRAIL concept-representation language for medical terminologies to build a project ontology that models relationships among software artifacts. Our approach involves modeling of the terminology used in software projects, which enables us to describe, classify and relate individual software artifacts. A networked repository accessible to the entire software development staff stores the conceptual model, source code and associated documents. We present an architecture for a maintenance tool, and show how developers can use GRAIL to build a project ontology.

Databases as Topic↗