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PANORAMA: an integrated Web-based sequence analysis tool and its role in gene discovery.

As the exponential growth of DNA sequence information in databases continues, the task of converting this deposited information into knowledge becomes more dependent on integrative sequence analysis and visualization tools. PANORAMA is an Internet-accessible software package that performs a variety of informatics analyses on a given DNA sequence and returns a visual and interactive representation of the results. Its design is modular, so that further sequence analysis tools can be integrated with minimal effort. The utility of PANORAMA is demonstrated in the analysis of 650 kb of human genomic DNA from chromosome region 3p21.3, a region of potential tumor suppressor genes involved in lung cancer, breast cancer, and other forms of cancer. PANORAMA aided in the discovery of genes and alternate splice forms of known exons, in the demarcation of intron-exon boundaries, and in the identification of promoter regions and polymorphisms, all of which contributed to a better understanding of the region. PANORAMA is available on the World Wide Web at http://atlas.swmed.edu.

Animals↗

A modeling environment with three-dimensional morphology, A-Cell-3D, and Ca2+ dynamics in a spine.

A-Cell-3D was developed to model and simulate a neuron with three-dimensional (3D) morphology utilizing graphic user interface (GUI)-based operations. A-Cell-3D generates and compartmentalizes 3D morphologies of a whole cell or a part of a cell based on a small number of parameters. A-Cell-3D has functions for embedding biochemical reactions and electrical equivalent circuits in the generated 3D morphology, automatically generating a simulation program for spatiotemporal numerical integration, and for visualizing the simulation results. A-Cell-3D is a free software and will be a powerful tool for both experimental and theoretical researchers in modeling and simulating neurons. The Ca2+ dynamics in a dendritic spine and its parent dendrite were modeled and simulated to demonstrate the capabilities of A-Cell-3D. The constructed reaction-diffusion model comprised Ca2+ entry at the spine head, Ca2+ buffering by endogenous buffers, Ca2+ extrusion, and Ca2+ diffusion with or without exogenous Ca2+ indicator dyes. A simulation program was generated by A-Cell-3D, and differential equations were numerically integrated by the fourth-order Runge-Kutta method.

Calcium↗

WinArrhythmia: a Windows based application for studying cardiac arrhythmias.

We have developed Windows-based software for ECG training as a tool in teaching physiology. A standard user interface allows the user to choose which arrhythmia to review. The arrhythmia is drawn in real time with sound beeps synchronized to R waves. The system also presents a brief summary or multiple choice question corresponding to the arrhythmia. A ladder diagram shows how simulate the conduction system, which consisted of 4 modules characterized by 4 parameters: automaticity, refractory period, antegrade- and retrograde-conduction time. This system has proved both useful and effective for training medical students in ECG interpretation of arrhythmias.

Arrhythmias, Cardiac↗

Melanie II--a third-generation software package for analysis of two-dimensional electrophoresis images: II. Algorithms.

After two generations of software systems for the analysis of two-dimensional electrophoresis (2-DE) images, a third generation of such software packages has recently emerged that combines state-of-the-art graphical user interfaces with comprehensive spot data analysis capabilities. A key characteristic common to most of these software packages is that many of their tools are implementations of algorithms that resulted from research areas such as image processing, vision, artificial intelligence or machine learning. This article presents the main algorithms implemented in the Melanie II 2-D PAGE software package. The applications of these algorithms, embodied as the feature of the program, are explained in an accompanying article (R. D. Appel et al.; Electrophoresis 1997, 18, 2724-2734).

Algorithms↗

Localizing complex neural circuits with MEG data.

During cognitive processing, the various cortical areas, with specialized functions, supply for different tasks. In most cases then, the information flows are processed in a parallel way by brain networks which work together integrating the single performances for a common goal. Such a step is generally performed at higher processing levels in the associative areas. The frequency range at which neuronal pools oscillate is generally wider than the one which is detectable by bold changes in fMRI studies. A high time resolution technique like magnetoencephalography or electroencephalography is therefore required as well as new data processing algorithms for detecting different coherent brain areas cooperating for one cognitive task. Our experiments show that no algorithm for the inverse problem solution is immune from bias. We propose therefore, as a possible solution, our software LOCANTO (LOcalization and Coherence ANalysis TOol). This new package features a set of tools for the detection of coherent areas. For such a task, as a default, it employs the algorithm with best performances for the neural landscape to be detected. If the neural landscape under attention involves more than two interacting areas the SLoreta algorithm is used. Our study shows in fact that SLoreta performance is not biased when the correlation among multiple sources is high. On the other hand, the Beamforming algorithm is more precise than SLoreta at localizing single or double sources but it gets a relevant localization bias when the sources are more than three and are highly correlated.

Bias↗

Scenario-based simulation of runoff-related pesticide entries into small streams on a landscape level.

The prediction of runoff-related pesticide entry into surface waters on a landscape level usually requires considerable efforts with regard to input data, time, and personnel. Therefore, the need for an easy to use simulation tool with easily accessible input data, for example from already existing public sources, is obvious. In this paper, we present a simulation tool for the simulation of pesticide entry from arable land into adjacent streams. Our aim was to develop a tool applicable on the landscape level using "real world data" from numerous sites and for the simulation of parameter case studies concerning particular parameters at single sites. We used the ratio of exposure to toxicity (REXTOX) model proposed by the OECD, which had been successfully validated in the study area as part of a previous study and which was extended to calculate pesticide concentrations in adjacent streams. We simulated the pesticide entry on the landscape level at 737 sites in small streams situated in the central lowland of Germany with winter wheat, barley, and sugar beat as the main agricultural crops. A sensitivity analysis indicated that the most significant model parameters were the width of the no-application zone and the degree of plant interception. The simulation was carried out for the 15 most frequently detected substances found in the study area using eight different environmental scenarios, covering variation of the width of the no-application zone, climate, and seasonal scenarios. The highest in-stream concentrations were predicted for a scenario using no (0m) buffer zone in conjunction with increased precipitation. According to the predicted concentrations, the risk for the aquatic communities was estimated based on standard toxicity tests and the application of a safety factor. The simulation results are presented both by means of risk maps for the study area showing the simulated pesticide concentration and the resulting ecological risk for numerous sites under varying scenarios and by case study diagrams with focus on the model behavior under the influence of single parameters. Risk maps confirmed the importance of no-application (buffer) zones for the levels of pesticide input. They also indicated the importance of the existing no-application zones for certain compounds and in some cases the need for a further evaluation of these regulations. The simulation tool was implemented as a standard PC software combining the REXTOX model with a geographical information system and can be used on any current personal computer. All input data was taken from public sources of German authorities. With little effort the tool should be applicable for other areas with similar data quality.

Computer Simulation↗

Critical care medicine in cyperspace: Internet resources and techniques for the intensivist.

The internet, is an informational tool of impressive proportions and capabilities. New software developments puts the use of this informational technology into the hands of all physicians. The use of Internet informational resources allows the intensivist to stay abreast of new developments in critical care medicine, communicate in a matter of seconds with colleagues half a world away, acquire medically related software, access remote database structures, obtain continuing medical education, and in the near future to "see' patients and obtain physiological data in real time. This tutorial will introduce the Internet and it's current tool suite.

Computer Communication Networks↗

Scientific inventory planning in materials management.

This is all just one example of how computer and appropriate analytical software routines can improve the fiscal and physical efficiency of the hospital materials management department. Together, they can provide logical, unemotional guidelines for purchase quantities, reorder points and safety stocks. Once a computer based materials management tool is in place and the materials manager has appropriate software at his or her disposal, a whole array of other possibilities can open up. For example, with appropriate analytical software and about six months of data, materials managers can estimate the performance of a current inventory system, comparing it to the expected results of upgrading current software. In effect, you can predetermine the cost-effectiveness of embedding economic order quantities, reorder points and service level policy routines before committing to such a course. Another valuable tool for materials management is "cost/use variance" software, which can pinpoint quickly and by line item whether inventory costs are rising due to higher vendor costs or to expanded use of products, and what percent each represents. A natural extension of this is an ABC analysis to identify groups of line items deserving more or less intense management. Continuous vendor performance tracking is another candidate for analytical software. The cost consequences of partial, late or missed deliveries can be severe, and delivery documentation becomes critical if the hospital has a performance liability agreement with the vendor. Other analytical software may permit dramatic improvement in storeroom labor efficiency through logical stock location schemes. In short, the basic formulas for scientific inventory management are only the beginning of a complex materials management story.

Costs and Cost Analysis↗

Proteome informatics I: bioinformatics tools for processing experimental data.

Bioinformatics tools for proteomics, also called proteome informatics tools, span today a large panel of very diverse applications ranging from simple tools to compare protein amino acid compositions to sophisticated software for large-scale protein structure determination. This review considers the available and ready to use tools that can help end-users to interpret, validate and generate biological information from their experimental data. It concentrates on bioinformatics tools for 2-DE analysis, for LC followed by MS analysis, for protein identification by PMF, by peptide fragment fingerprinting and by de novo sequencing and for data quantitation with MS data. It also discloses initiatives that propose to automate the processes of MS analysis and enhance the quality of the obtained results.

Algorithms↗

An interactive visualization tool to explore the biophysical properties of amino acids and their contribution to substitution matrices.

BACKGROUND: Quantitative descriptions of amino acid similarity, expressed as probabilistic models of evolutionary interchangeability, are central to many mainstream bioinformatic procedures such as sequence alignment, homology searching, and protein structural prediction. Here we present a web-based, user-friendly analysis tool that allows any researcher to quickly and easily visualize relationships between these bioinformatic metrics and to explore their relationships to underlying indices of amino acid molecular descriptors. RESULTS: We demonstrate the three fundamental types of question that our software can address by taking as a specific example the connections between 49 measures of amino acid biophysical properties (e.g., size, charge and hydrophobicity), a generalized model of amino acid substitution (as represented by the PAM74-100 matrix), and the mutational distance that separates amino acids within the standard genetic code (i.e., the number of point mutations required for interconversion during protein evolution). We show that our software allows a user to recapture the insights from several key publications on these topics in just a few minutes. CONCLUSION: Our software facilitates rapid, interactive exploration of three interconnected topics: (i) the multidimensional molecular descriptors of the twenty proteinaceous amino acids, (ii) the correlation of these biophysical measurements with observed patterns of amino acid substitution, and (iii) the causal basis for differences between any two observed patterns of amino acid substitution. This software acts as an intuitive bioinformatic exploration tool that can guide more comprehensive statistical analyses relating to a diverse array of specific research questions.

Amino Acid Sequence↗

Design methods and architectural issues of integrated medical image data base systems.

The past 20 years have seen tremendous changes in medical imaging techniques. New modalities and protocols are expanding the available digital image data at a rapid rate. Yet a framework for gathering, managing, and using multimodal image information is an integrated database environment is missing. The purpose of this paper is to present the experience of implementing an integrated medical image database system at UCSF. We discuss the general system architecture, software design methods, and specific database tools and illustrate them with application examples. Two immediate issues conforming the building of medical image database systems are: lack of supporting infrastructure and inability to index images by contest. To circumvent these problems, the evolutionary medical image database system being implemented at UCSF is based on a three-tiered client-server architecture: client medical workstations, database application servers, and a hospital-integrated picture archiving and communication system (HIP-PACS). The approach used to integrate content-based retrieval and knowledge base techniques within the existing HI-PACS to make the whole database system useful in medicine.

Adult↗

Italian Society of Cardiovascular Echography (SIEC) Consensus Conference on the state of the art of contrast echocardiography.

Part 1: Technical and methodological issues. Contrast echocardiography is based on the use of gas microbubbles. The size, gas composition and shell structure of the microbubbles modify their stability, resistance to pressure and scattering behavior. A proposed classification of contrast agents is based on the modalities of production of microbubbles (galenic or industrial); the industrial agents are divided into three generations depending on their characteristics. Following venous administration, the industrial microbubbles behave as intravascular free-flowing tracers and this is fundamental for their use in perfusion studies. When insonated at a low acoustic pressure, microbubbles show a linear behavior and can be used for signal amplification. At intermediate acoustic pressures microbubbles resonate and produce a harmonic signal that is detectable by new scanners. Higher acoustic pressures cause microbubble disruption with emission of a transient acoustic signal. The available contrast agents behave differently in an ultrasound field. Part 2: Safety of contrast echocardiography. Galenic contrast agents were tested in many studies for intracoronary and intravenous injection and no clinically relevant side effects were detected. The intravenous injection of industrial contrast agents is safe in all conditions, even in acute coronary syndromes. The interaction between ultrasound and microbubbles produces energy with potential effects on tissue for inertial cavitation and acoustic current production. These effects seem particularly interesting for the therapeutic applications of contrast echocardiography, but they do not appear to have clinically relevant effects. Part 3: Experimental studies. Experimental studies in contrast echocardiography are designed to induce, in animal models, acute myocardial infarction and coronary artery stenosis and to evaluate the differences in blood flow. The risk area and infarct area are well visualized with serial contrast agent infusion. No-reflow after coronary occlusion is a well-known phenomenon and is detectable at contrast echocardiography. Different degrees of induced coronary stenosis cause differences in the regional flow rate. The results of contrast echocardiographic studies are comparable with those of other invasive flow measurements. Caution must be used to transfer the knowledge acquired from animal studies to the clinical arena, owing to both methodological and anatomical differences. Part 4: Enhancement of Doppler signal and coronary flow study. The anterior descending coronary artery flow is detectable in almost all patients, and the posterior descending coronary artery in about 70%. The coronary flow reserve can be measured by injection of a vasodilator agent (dipyridamole or preferably adenosine) with a success rate of almost 100 % for the anterior descending but only 50 % for the posterior descending coronary artery. Data from transthoracic studies are comparable with those of Doppler flow wire. The fields of application presently include the evaluation of acute myocardial infarction, the short- and long-term results of percutaneous coronary interventions and coronary grafts, and the study of the microcirculation in several clinical conditions where the coronary flow reserve may be reduced, such as in syndrome X, hypertension, hypercholesterolemia or diabetes. Part 5: Endocardial border enhancement. Opacification of the left ventricle is the main indication to contrast echocardiography that, in this setting, is principally used to improve endocardial border delineation. This allows accurate evaluation of left ventricular volumes and function, increasing the role of echocardiography for the quantitative study of the left ventricle. Other indications for left ventricular opacification are the identification of intraventricular thrombosis, non-compaction of the left ventricle and heart rupture. In this respect, industrial second-generation contrast agents are more useful. The most appropriate patients for contrast echocardiography are those with a poor or suboptimal acoustic window, in whom a predictable diagnostic and prognostic usefulness of the procedure is expected. If appropriately used, contrast echocardiography is a cost-effective technique, although lack of reimbursement presently limits its use. Part 6: Use of contrast agents during stress echocardiography. Contrast agents during stress echocardiography may be used to improve the diagnostic accuracy of the test and to study myocardial perfusion. The diagnosis of ischemia in stress echo relies on the operator's visual assessment of changes in contractility during stress. Contrast agents must be considered an important tool that improve image quality especially in patients with an intermediate or poor acoustic window and their use has been reported to be cost-effective in the few studies designed to this end. The evaluation of myocardial perfusion during stress is certainly one of the most important goals of contrast echocardiography. Preliminary data are interesting but there is still a number of methodological problems that currently hamper clinical application. Part 7: Myocardial perfusion. Echocardiography has the potential of visualizing microbubbles in the microcirculation by detecting stimulated acoustic emission, produced by high-energy applied ultrasound, or by detecting the harmonic signal produced by resonance of the microbubbles in a low-energy ultrasound field. In the first case images are triggered at increasing end-systolic intervals (intermittent imaging), whereas in the second case entire cardiac cycles are analyzed (real-time imaging). Continuous infusion is the preferred method of maintaining a large and constant microbubble concentration inside the microcirculation. Analysis of the perfusion signal may be made in the qualitative, semi-quantitative or quantitative mode. Quantitative analysis is based on the construction of videointensity-time curves to study the refilling phase after complete microbubble destruction. There are not enough data in the literature showing the additional role of quantitative analysis for clinical purposes. Thus, at present, quantitative softwares should be considered as research tools. Conversely, there is a general consensus based on experimental and clinical studies on the use of myocardial contrast echo in patients with acute myocardial infarction by means of qualitative or semi-quantitative analysis. Important information on the infarct area extension, on the efficacy of reperfusion therapy, on the presence and extension of the no-reflow phenomenon and on the extent of residual tissue viability may be derived from the routine use of myocardial contrast echo. The reference technique still remains myocardial scintigraphy even though many theoretical problems are being discussed. Part 8: Implementing ultrasound contrast in the echocardiography laboratory. Contrast echocardiography should be considered an extension of the existing echocardiographic examination. Standard laboratory equipment is sufficient to run a contrast echocardiography program. However, cultural and technological upgrading is mandatory to obtain good results in contrast echocardiography. Intravenous infusion is easier during stress echocardiography than during rest study, because the time and cost for the venous line are comprised. In this setting, the cost-effectiveness for the addition of contrast agent is optimal, but patient selection is a critical point. The economic issue (contrast agent and personnel costs, and time needed) of contrast echocardiography determines the fact that without adequate reimbursement there is no incentive to perform the procedure.

Animals↗

Identification of organ-specific T cell populations by analysis of multiparameter flow cytometry data using DNA-chip analysis software.

BACKGROUND: The analysis of cells from multiple experimental groups by multiparameter flow cytometry leads to the generation of complex data sets, for which adequate analysis tools are not commonly available. We report here that software designed for transcriptomics applications can be used in multiparameter flow cytometry. METHODS: Lymphocytes isolated from nine different mouse organs were stained and subjected to 10-parameter flow cytometry. The resulting data set contained 594 different T cell subsets per organ per mouse and was organized into a so-called flow cytometry array (FCA). RESULTS: Computation of a hierarchical tree revealed that lymph nodes and spleen were populated by similar T cell subsets, while T cells from peripheral organs displayed a diverse subset composition. Furthermore, organ-specific T cell subsets were identified. CONCLUSIONS: This new FCA concept in flow cytomics proved to be a valuable tool for the fast and unbiased analysis of complex multiparameter flow cytometry data sets. It can be used for assessing disease progression and therapeutic intervention, and for the association of disease-related biomarkers on the protein level.

Animals↗

[Multimedia teaching software in university education].

This article is aimed at developing of multimedia teaching programs. Authoring tool Authorware Professional for Windows is briefly described as a suited system for the developing of didactic applications. Author presents own application based on Authorware--Biophysics of perception of sound and light. At the end are also disscused benefits of multimedia teaching tools.

Biophysics↗

P-Mod: an algorithm and software to map modifications to peptide sequences using tandem MS data.

The discovery of unanticipated protein modifications is one of the most challenging problems in proteomics. Whereas widely used algorithms such as Sequest and Mascot enable mapping of modifications when the mass and amino acid specificity are known, unexpected modifications cannot be identified with these tools. We have developed an algorithm and software called P-Mod, which enables discovery and sequence mapping of modifications to target proteins known to be represented in the analysis or identified by Sequest. P-Mod matches MS/MS spectra to peptide sequences in a search list. For spectra of modified peptides, P-Mod calculates mass differences between search peptide sequences and MS/MS precursors and localizes the mass shift to a sequence position in the peptide. Because modifications are detected as mass shifts, P-Mod does not require the user to guess at masses or sequence locations of modifications. P-Mod uses extreme value statistics to assign p value estimates to sequence-to-spectrum matches. The reported p values are scaled to account for the number of comparisons, so that error rates do not increase with the expanded search lists that result from incorporating potential peptide modifications. Combination of P-Mod searches from multiple LC-MS/MS analyses and multiple samples revealed previously unreported BSA modifications, including a novel decarboxymethylation or D-->G substitution at position 579 of the protein. P-Mod can serve a unique role in the identification of protein modifications both from exogenous and endogenous sources and may be useful for identifying modified protein forms as biomarkers for toxicity and disease processes.

Algorithms↗

Theoretical and experimental investigation of the thermal effects within body cavities during transendoscopical CO2 laser-based surgery.

BACKGROUND AND OBJECTIVES: The recent development of flexible hollow waveguides for MID-IR lasers may be utilized transendoscopically to ablate selectively neoplastic, superficial tissues within body cavities. Study goals are to investigate theoretically and experimentally heat distribution and thermal response of cavity lining, during CO2 laser minimally invasive surgery (MIS), and to thermally optimize the procedure under practical conditions. STUDY DESIGN/MATERIALS AND METHODS: Mathematical model was developed to predict temperature distribution along cavity lining. Experimental setup was built, including all the necessary components for a fully feedback-controlled MIS, i.e., laser generator, gas insufflating system, surgical suction, and infrared imaging feedback mechanism, all controlled by central PC-based program. Thermal images of cavity lining were recorded and analyzed throughout varying conditions. RESULTS: Thermal gradients along the cavity lining, during and after the laser irradiation, were obtained mathematically and experimentally. Diverse modes of heat dispersions were observed, as well as the relative contributions of user-controlled parameters to the maximal heat of cavity lining. The software-controlled setup has demonstrated the capacity to instantly manage varying conditions, by which it automatically protects cavity lining from getting overheated. CONCLUSIONS: Analytical predictions and experimental measurements were highly correlated. The software-controlled system may serve a powerful tool to control thermal side effects during MIS within body cavities.

Carbon Dioxide↗

"Non-trivial pursuit of physiology".

This article describes a novel way to conduct a review session that combines interactivity, team learning, and peer-to-peer instruction. It uses the format of the familiar game "Trivial Pursuit." To facilitate the game process and to encourage its use by others, we have developed custom software. It allows an instructor to run the game from the podium and to input questions/answers for a particular block or other area to be reviewed. In addition to the software itself, the online supplement (http://advan.physiology.org/cgi/content/full/00031.2004/DC1) contains 100 sample questions and answers written for the cardiovascular physiology review session. The developed game format and its software add to the arsenal of educational tools that can be used to enrich students' learning experiences.

Cardiology↗

Quantitative immunohistochemistry of fluorescence labelled probes using low-cost software.

This paper describes simple procedures to process digital images in quantitative immunofluorescence microscopy. Monoclonal antibodies directed against the sarcoplasmic myosin heavy chain isoforms and against laminin, located on the basement membranes, were applied to sections of human skeletal muscle. The localisation and staining intensity of a fluorescent secondary antibody were recorded using an indirect histochemical method. The digitised images were pre-processed and the luminosities of appropriate structures were determined using existing tools in the widely used image processing software Photoshop from Adobe. Procedures to obtain a quantitative measure for the specific fluorescence signal (the background corrected fluorescence in the object) were developed. In addition, antibody binding to individual cells could be quantified whether these cells are well separated or not. The relation between the specific fluorescence signal and the dilution factor of the primary antibody could be measured to determine a suitable concentration of the antibody for incubation of the sections. The potential fading of the fluorescence signal with time and prolonged exposure to light from the microscope was explored and analysed. With the tools described in the present report it is thus possible also to optimize the topical immunohistochemical protocol in order to quantify the fluorescence signal.

Adenosine Triphosphatases↗