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PubMedDate not supplied

Virtual microscopes in podiatric medical education.

In many medical schools, microscopes are being replaced as teaching tools by computers with software that emulates the use of a light microscope. This article chronicles the adoption of "virtual microscopes" by a podiatric medical school and presents the results of educational research on the effectiveness of this adoption in a histology course. If the trend toward virtual microscopy in education continues, many 21st-century physicians will not be trained to operate a light microscope. The replacement of old technologies by new is discussed. The fundamental question is whether all podiatric physicians should be trained in the use of a particular tool or only those who are likely to use it in their own practice.

Computer-Assisted Instruction↗
PubMed1998

Evaluation of low density spine software for the assessment of bone mineral density in children.

Pediatric dual-energy X-ray absorptiometry spine scans often cannot be analyzed with standard software due to a failure to identify the bone edges of low density vertebrae. Low density spine (LDS) software improves bone detection compared with standard software. The objective of this study was to compare bone mineral density (BMD) measurements obtained with the standard and LDS software in 27 healthy nonobese, 32 obese, and 41 chronically ill children, ages 2-18 years. Lumbar spine (L1-L4) BMD, measured by standard analysis, ranged from 0.531-1.244 gm/cm2. Reanalysis with the LDS software resulted in a systematic increase (mean +/- SD) in estimated bone area of 17.0+/-5.0%, an increase in bone mineral content of 6.1+/-6.3%, and a mean decrease in BMD of 8.7+/-1.7% (all p < 0.001). This resulted in a mean decrease in BMD Z score of 0.7+/-0.2. Linear regression models, predicting standard BMD from LDS BMD, were fit for the three subject groups (R2 = 0.993-0.995). Small differences in slopes were detected across groups (p = 0.07); LDS BMD predicted higher standard BMD in obese subjects. In conclusion, LDS analysis resulted in a clinically significant decrease in measured BMD. The association between analysis methods was exceptionally high (R2 > 0.99), indicating that LDS BMD accurately predicts standard BMD. Although LDS BMD in obese subjects predicts higher standard BMD results than in nonobese subjects, the small difference is of questionable clinical significance. LDS software is a useful tool for the assessment of BMD in children.

Absorptiometry, Photon↗
PubMed2007

Requirements, features, and performance of high content screening platforms.

High content screening (HCS) platforms integrate fluorescence microscopy with image analysis algorithms and informatics to automate cell analysis. The initial applications of HCS to secondary screening in drug discovery have spread throughout the discovery pipeline, and now into the expanding research field of systems cell biology, in which new manipulation tools enable the use of large scale screens to understand cellular pathways, and cell functions. In this chapter we discuss the requirements for HCS and the systems that have been designed to meet these application needs. The number of HCS systems available in the market place, and the range of features available, has grown considerably in the past 2 yr. Of the two general optical designs, the confocal systems have dominated the high-throughput HCS market, whereas the more cost effective wide-field systems have dominated all other market segments, and have a much larger market share. The majority of available systems have been optimized for fixed cell applications; however, there is growing interest in live cell kinetic assays, and four systems have successfully penetrated this application area. The breadth of applications for these systems continues to expand, especially with the integration of new technologies. New applications, improved software, better data visualization tools, and new detection methods such as multispectral imaging and fluorescence lifetime are predicted to drive the development of future HCS platforms.

Animals↗
PubMed2005

htSNPer1.0: software for haplotype block partition and htSNPs selection.

BACKGROUND: There is recently great interest in haplotype block structure and haplotype tagging SNPs (htSNPs) in the human genome for its implication on htSNPs-based association mapping strategy for complex disease. Different definitions have been used to characterize the haplotype block structure in the human genome, and several different performance criteria and algorithms have been suggested on htSNPs selection. RESULTS: A heuristic algorithm, generalized branch-and-bound algorithm, is applied to the searching of minimal set of haplotype tagging SNPs (htSNPs) according to different htSNPs performance criteria. We develop a software htSNPer1.0 to implement the algorithm, and integrate three htSNPs performance criteria and four haplotype block definitions for haplotype block partitioning. It is a software with powerful Graphical User Interface (GUI), which can be used to characterize the haplotype block structure and select htSNPs in the candidate gene or interested genomic regions. It can find the global optimization with only a fraction of the computing time consumed by exhaustive searching algorithm. CONCLUSION: htSNPer1.0 allows molecular geneticists to perform haplotype block analysis and htSNPs selection using different definitions and performance criteria. The software is a powerful tool for those focusing on association mapping based on strategy of haplotype block and htSNPs.

Algorithms↗
PubMed2003

Automated biofilm morphology quantification from confocal laser scanning microscopy imaging.

In spite of the immediate visual appeal of confocal laser scanning microscopy images, the extraction of accurate reconstitutions of biofilm morphology requires a lengthy and computational intensive succession of processing steps. However, once performed, it provides ample reward by enabling the quantitative study of biofilm structure. A software suite of image processing tools for full automation of biofilm morphology quantification was developed by integrating preprocessing, segmentation and morphology quantification operations. This software toolbox was implemented in a web server and a user friendly interface was developed to facilitate image submission, storage and sharing, its access being unrestricted for scientific applications. The image bioinformatics tool which results from the integration of the processing operations can be accessed at http://www.itqb.unl.pt:111/clsmip/. Its use is described in this paper and is illustrated with an example of processing of experimental data describing the growth of a mixed species dentrifying biofilm.

Automation↗
PubMed1999

On-line computer system to minimize laser injuries during surgery: preliminary system layout and proposal of the key features.

The aim of this paper is to investigate some new user interface ideas and related application packages which aim to improve the degree of safety in an operating room during surgical operations in which an invasive laser beam is deployed. The overall value of the proposition is that a means is provided which ensures the successful completion of the surgical case while minimizing the risk of thermal and mechanical injuries to healthy tissues adjacent to the surgical field. According to surgeons operating with a variety of CO2 lasers available at both the National Cancer Institute in Milan, Italy, and the Sackler School of Medicine, Tel Aviv University, Israel, each laser device presents different cutting and coagulation properties. In order to identify which 'ideal' procedure might corroborate the subjective impression of each surgeon and also to provide one common tool to ensure procedures with a high level of safety, the author has worked for several months with surgeons and technicians of both Institutions to define the general design of a new on-line surgical operation planning and design system to be used during the pre-operative briefing activities and also as a consultation tool during operation. This software package will be developed and tested on both 'C' and FORTRAN compilers running on a commercially available PC which is driving a continuous wave (CW) CO2 laser device via its Instrument Bus interface. The present proposal describes the details of a software package called LCA (Laser-beam Controller and Adviser) which performs several controls in parallel on the key output parameters of a laser beam device during its utilization in delicate surgical operations. The required performances of this device needed during a given surgical operation are pre-simulated and compared against the well-known safety limits, which are stored in the computer's mass storage. If the surgeon's decision about the laser device set-up are considered to be too close to the required physiological safety limits, then the SW alerts the surgeon and proposes alternatives based on other combinations of both HW and SW configurations. An additional application of LCA uses this SW as a warning tool during the operation itself. If a wrong set-up of the laser device is accidentally used, an alarm will be generated and the laser beam automatically switched-off prior to an 'incident report' printout. The operation will continue only when the surgeon validates the choices that the SW suggests for implementation. If necessary, the surgeon can switch off the device and continue to operate it manually. In this case, the surveillance mode will be totally excluded.

Bone Cements↗
PubMed2006

Rapid and accurate measurement of left ventricular function with a new second-harmonic fast-rotating transducer and semi-automated border detection.

Measurement of left ventricular (LV) volume and function are the most common clinical referral questions to the echocardiography laboratory. A fast, practical, and accurate method would offer important advantages to obtain this important information. To validate a new practical method for rapid measurement of LV volume and function. We developed a continuous fast-rotating transducer, with second-harmonic capabilities, for three-dimensional echocardiography (3DE). Fifteen cardiac patients underwent both 3DE and magnetic resonance imaging (reference method) on the same day. 3DE image acquisition was performed during a 10-second breath-hold with a frame rate of 100 frames/sec and a rotational speed of 6 rotations/sec. The individual images were postprocessed with Matlab software using multibeat data fusion. Subsequently, with these images, 12 datasets per cardiac cycle were reconstructed, each comprising seven equidistant cross-sectional images for analysis in the new TomTec 4DLV analysis software, which uses a semi-automated border detection (ABD) algorithm. The ABD requires an average analysis time of 15 minutes per patient. A strong correlation was found between LV end-diastolic volume (r = 0.99; y = 0.95x - 1.14 ml; SEE = 6.5 ml), LV end-systolic volume (r = 0.96; y = 0.89x + 7.91 ml; SEE = 7.0 ml), and LV ejection fraction (r = 0.93; y = 0.69x + 13.36; SEE = 2.4%). Inter- and intraobserver agreement for all measurements was good. The fast-rotating transducer with new ABD software is a dedicated tool for rapid and accurate analysis of LV volume and function.

Adult↗
PubMed2004

Sedimentation equilibrium analysis of protein interactions with global implicit mass conservation constraints and systematic noise decomposition.

Sedimentation equilibrium is a powerful tool for the characterization of protein self-association and heterogeneous protein interactions. Frequently, it is applied in a configuration with relatively long solution columns and with equilibrium profiles being acquired sequentially at several rotor speeds. The present study proposes computational tools, implemented in the software SEDPHAT, for the global analysis of equilibrium data at multiple rotor speeds with multiple concentrations and multiple optical detection methods. The detailed global modeling of such equilibrium data can be a nontrivial computational problem. It was shown previously that mass conservation constraints can significantly improve and extend the analysis of heterogeneous protein interactions. Here, a method for using conservation of mass constraints for the macromolecular redistribution is proposed in which the effective loading concentrations are calculated from the sedimentation equilibrium profiles. The approach is similar to that described by Roark (Biophys. Chem. 5 (1976) 185-196), but its utility is extended by determining the bottom position of the solution columns from the macromolecular redistribution. For analyzing heterogeneous associations at multiple protein concentrations, additional constraints that relate the effective loading concentrations of the different components or their molar ratio in the global analysis are introduced. Equilibrium profiles at multiple rotor speeds also permit the algebraic determination of radial-dependent baseline profiles, which can govern interference optical ultracentrifugation data, but usually also occur, to a smaller extent, in absorbance optical data. Finally, the global analysis of equilibrium profiles at multiple rotor speeds with implicit mass conservation and computation of the bottom of the solution column provides an unbiased scale for determining molar mass distributions of noninteracting species. The properties of these tools are studied with theoretical and experimental data sets.

Macromolecular Substances↗
PubMed2006

A tool for selecting SNPs for association studies based on observed linkage disequilibrium patterns.

The design of genetic association studies using single-nucleotide polymorphisms (SNPs) requires the selection of subsets of the variants providing high statistical power at a reasonable cost. SNPs must be selected to maximize the probability that a causative mutation is in linkage disequilibrium (LD) with at least one marker genotyped in the study. The HapMap project performed a genome-wide survey of genetic variation with about a million SNPs typed in four populations, providing a rich resource to inform the design of association studies. A number of strategies have been proposed for the selection of SNPs based on observed LD, including construction of metric LD maps and the selection of haplotype tagging SNPs. Power calculations are important at the study design stage to ensure successful results. Integrating these methods and annotations can be challenging: the algorithms required to implement these methods are complex to deploy, and all the necessary data and annotations are deposited in disparate databases. Here, we present the SNPbrowser Software, a freely available tool to assist in the LD-based selection of markers for association studies. This stand-alone application provides fast query capabilities and swift visualization of SNPs, gene annotations, power, haplotype blocks, and LD map coordinates. Wizards implement several common SNP selection workflows including the selection of optimal subsets of SNPs (e.g. tagging SNPs). Selected SNPs are screened for their conversion potential to either TaqMan SNP Genotyping Assays or the SNPlex Genotyping System, two commercially available genotyping platforms, expediting the set-up of genetic studies with an increased probability of success.

Computational Biology↗
PubMed2002

DNA array analysis in a Microsoft Windows environment.

Microsoft Windows-based computers have evolved to the point that they provide sufficient computational and visualization power for robust analysis of DNA array data. In fact, smaller laboratories might prefer to carry out some or all of their analyses and visualization in a Windows environment, rather than alternative platforms such as UNIX. We have developed a series of manually executed macros written in Visual Basic for Microsoft Excel spreadsheets, that allows for rapid and comprehensive gene expression data analysis. The first macro assigns gene names to spots on the DNA array and normalizes individual hybridizations by expressing the signal intensity for each gene as a percentage of the sum of all gene intensities. The second macro streamlines statistical consideration of the confidence in individual gene measurements for sets of experimental replicates by calculating probability values with the Student's t test. The third macro introduces a threshold value, calculates expression ratios between experimental conditions, and calculates the standard deviation of the mean of the log ratio values. Selected columns of data are copied by a fourth macro to create a processed data set suitable for entry into a Microsoft Access database. An Access database structure is described that allows simple queries across multiple experiments and export of data into third-party data visualization software packages. These analysis tools can be used in their present form by others working with commercial E. coli membrane arrays, or they may be adapted for use with other systems. The Excel spreadsheets with embedded Visual Basic macros and detailed instructions for their use are available at http://www.ou.edu/microarray.

Databases, Nucleic Acid↗
PubMed2007

Counting colonies of clonogenic assays by using densitometric software.

Clonogenic assays are a useful tool to test whether a given cancer therapy can reduce the clonogenic survival of tumour cells. A colony is defined as a cluster of at least 50 cells which can often only be determined microscopically. The process of counting colonies is very extensive work and so we developed software that is able to count the colonies automatically from scanned flasks. This software is made freely available by us with a detailed description how to use and install the necessary features.

Algorithms↗
PubMed2002

VEGA: a versatile program to convert, handle and visualize molecular structure on Windows-based PCs.

We here propose the program VEGA, that was developed to create a bridge between the most popular molecular software packages. In this tool some features are implemented some features to analyze, display and manage the three dimensional (3D) structure of the molecules. The most important features are (1) file format conversion (with assignment of the atom types and atomic charges), (2) surface calculation and (3) trajectory analysis. The executable and the source code can be free downloaded from [URL: see text].

Bacterial Toxins↗
PubMed2026

miRNA Target Prediction: An Overview of the Past and Current Tools.

MicroRNAs (miRNAs) are among the most studied molecules in recent years, and since their discovery, many miRNAs have been identified across various species. As members of the non-coding RNA family, miRNAs are key players in post-transcriptional gene regulation. These molecules can inhibit translation or promote degradation of messenger RNA (mRNA) by binding to the 3' untranslated region (UTR) of mRNA, thereby influencing almost all biological processes. To identify a miRNA's biological role, it is essential to predict the target sites to which it binds, a goal made possible through bioinformatics tools. This chapter discusses the bioinformatics tools commonly used for this purpose. Also, it analyzes the main factors considered in target prediction, such as seed match, free energy, conservation, site accessibility, multiple binding site contribution, and machine learning and deep learning approaches. Understanding the principles underlying these predictive methodologies is crucial for advancing one's biological research on miRNAs.

MicroRNAs↗
PubMed1999

Virtual network computing: cross-platform remote display and collaboration software.

VNC (Virtual Network Computing) is a computer program written to address the problem of cross-platform remote desktop/application display. VNC uses a client/server model in which an image of the desktop of the server is transmitted to the client and displayed. The client collects mouse and keyboard input from the user and transmits them back to the server. The VNC client and server can run on Windows 95/98/NT, MacOS, and Unix (including Linux) operating systems. VNC is multi-user on Unix machines (any number of servers can be run are unrelated to the primary display of the computer), while it is effectively single-user on Macintosh and Windows machines (only one server can be run, displaying the contents of the primary display of the server). The VNC servers can be configured to allow more than one client to connect at one time, effectively allowing collaboration through the shared desktop. I describe the function of VNC, provide details of installation, describe how it achieves its goal, and evaluate the use of VNC for molecular modelling. VNC is an extremely useful tool for collaboration, instruction, software development, and debugging of graphical programs with remote users.

Chemistry↗
PubMed1999

Considerations on the quality of medical software and information services.

Fast developments in information and communication technology have made it possible to develop new services for citizens. One of the most interesting areas is health care. Medical knowledge is usually valid all over the world that makes the market global. Information services and decision support software are becoming important tools for medical professionals but also ordinary citizens are interested in health related information. It has been estimated that by the year 2010 the turnover of health care telematics industry may be close to that of the drug industry today. The nature of this global information industry is very different from any industry in history. Since there are no frontiers, no clear products and no shops in the information market, it is difficult to develop any effective legislation. However, the history of medicine has shown that health care sector cannot be free from regulation without risking citizens' health. The huge commercial potential of the Internet has already been used to promote products and services that have no proven effect on health and that may sometimes be even dangerous. In this paper we discuss the needs and possibilities to assess the quality of medical decision support software and information services. For brevity the terms medical software and medical knowledge are used, but the issues also relate to informatics systems used by any health professional, and to computerised systems used to schedule care or to organise record systems.

Decision Support Systems, Clinical↗
PubMed2004

Supporting clinical practice at the bedside using wireless technology.

OBJECTIVES: Despite studies that show improvements in both standards of care and outcomes with the judicious application of clinical practice guidelines (CPGs), their clinical utilization remains low. This randomized controlled trial examined the use of a wirelessly networked mobile computer (MC) by physicians at the bedside with access to an emergency department information system, decision support tools (DSTs), and other software options. METHODS: Each of ten volunteer emergency physicians was randomized using a matched-pair design to work five shifts in standard fashion (desktop computer [DC] access) and five shifts with a wirelessly networked MC. Work pattern issues and electronic CPG/DST use were compared using end-of-shift satisfaction questionnaires and review of a CPG/DST database. Repeated-measures analysis of variance was used to examine between-shift differences. RESULTS: A total of 100 eight-hour shifts were evaluated; 99% compliance with postshift questionnaires was achieved. Using a seven-point Likert scale (MC values first), MCs were rated as being as fast (5.04 vs. 4.54; p=0.13) and convenient (5.08 vs. 4.14; p=0.07) as DCs. Overall, physicians rated MCs to be less efficient (3.18 vs. 4.30; p=0.02) but encouraged more frequent use of DSTs (4.10 vs. 3.47; p=0.03) without impacting doctor-patient communication (2.78 vs. 2.96; p=0.51). During the study period, physician use of an intranet Web application (eCPG) was more frequent during shifts assigned to the MC when compared with the DC (eCPG uses/shift, 3.6 vs. 2.0; p=0.033). CONCLUSIONS: The MC technology permitted physicians to access information at the bedside and increased the use of CPG/DST tools. According to physicians, patients appeared to accept their use of information technology to assist in decision making. Development of improved computer technology may address the major limitation of MC portability.

Computers↗
PubMed2005

The Chemnitz LogAnalyzer: a tool for analyzing data from hypertext navigation research.

Computer-based studies usually produce log files as raw data. These data cannot be analyzed adequately with conventional statistical software. The Chemnitz LogAnalyzer provides tools for quick and comfortable visualization and analyses of hypertext navigation behavior by individual users and for aggregated data. In addition, it supports analogous analyses of questionnaire data and reanalysis with respect to several predefined orders of nodes of the same hypertext. As an illustration of how to use the Chemnitz LogAnalyzer, we give an account of one study on learning with hypertext. Participants either searched for specific details or read a hypertext document to familiarize themselves with its content. The tool helped identify navigation strategies affected by these two processing goals and provided comparisons, for example, of processing times and visited sites. Altogether, the Chemnitz LogAnalyzer fills the gap between log files as raw data of Web-based studies and conventional statistical software.

Adult↗
PubMed1993

Countering advanced HIS marketing tactics.

An explosion of technological advances and system developments in the information systems industry pushes the envelope in both hardware and software design. Equipment breakthroughs--reduced instruction set computing chips, or RISC, and DEC's 64-bit Alpha chip--herald an exciting new era in price-performance computing. And object-oriented programming systems, or OOPS, and computer-assisted software engineering, or CASE tools, both promise a golden age in programming productivity. At the same time however, marketing mavens at healthcare information system, or HIS, vendors keep pace with their cohorts in Research and Development by blazing new trails in the science of sales and marketing. To help healthcare executives keep pace with new developments in selling, let's review a few infamous breakthroughs in marketing. They put a new twist on the old saw: "caveat emptor." Following each marketing "advance" are counters to new marketing tricks, each recommended to keep savvy CIOs a step ahead.

Computer Systems↗