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At least 397 records · Page 22Linked to original sources
PubMed1996

A simulation of microbial competition in the human colonic ecosystem.

Many investigations of the interactions of microbial competitors in the gastrointestinal tract used continuous-flow anaerobic cultures. The simulation reported here was a deterministic 11-compartment model coded by using the C programming language and based on parameters from published in vitro studies and assumptions were data were unavailable. The resource compartments were glucose, lactose and sucrose, starch, sorbose, and serine. Six microbial competitors included indigenous nonpathogenic colonizers of the human gastrointestinal tract (Escherichia coli, Enterobacter aerogenes, Bacteroids ovatus, Fusobacterium varium, and Enterococcus faecalis) and the potential human enteropathogen Salmonella typhimurium. Flows of carbon from the resources to the microbes were modified by resource and space controls. Partitioning of resources to the competitors that could utilize them was calculated at each iteration on the basis of availability of all resources by feeding preference functions. Resources did not accumulate during iterations of the model. The results of the computer simulation of microbial competition model and for various modifications of the model. The results were based on few measured parameters but may be useful in the design of user-friendly software to aid researchers in defining and manipulating the microbial ecology of colonic ecosystems as relates to food-borne disease.

Carbohydrates↗
PubMed1994

Model-based compartmental analyses in nutrition research.

Kinetic tracer studies have been used extensively in understanding digestion, absorption, and whole-body metabolism of nutrients. Optimal interpretation of changes in tracer levels over time and movement across body pools often requires sophisticated data analysis. The use of model-based compartmental analysis (MCA) can yield more detailed quantitative and predictive information concerning system dynamics, compared with direct stochastic approaches. With MCA, tracer and tracee data from both experimental and literature values are fit to a model that best approximates the system on the basis of experimental data at hand. The number of compartments of the model is determined by the shape of the curve fit to the tracee and tracer data and by literature information. On this basis, MCA can yield information about compartment numbers and sizes, fractional and net turnover, as well as catabolic and synthetic rates. PC-based MCA programs are now available. Whereas earlier editions required use of a programming language, the most recent versions being developed are completely menu driven. Model-based compartmental analyses thus represent important biotechnological advances permitting maximal interpretation of kinetic data in nutrition research.

Animal Nutritional Physiological Phenomena↗
PubMed2000

The Ensemble/Legacy Chimera extension: standardized user and programmer interface to molecular Ensemble data and Legacy modeling programs.

Ensemble/Legacy is a toolkit extension of the Object Technology Framework (OTF) that exposes an object oriented interface for accessing and manipulating ensembles (collections of molecular conformations that share a common chemical topology) and driving Legacy programs (such as MSMS, AMBER, X-PLOR, CORMA/MARDIGRAS, Dials and Windows, and CURVES). Ensemble/Legacy provides a natural programming interface for running Legacy programs on ensembles of molecules and accessing the resulting data. Using the OTF reduces the time cost of developing a new library to store and manipulate molecular data and also allows Ensemble/Legacy to integrate into the Chimera visualization program. The extension to Chimera exposes the Legacy functionality using a graphical user interface that greatly simplifies the process of modeling and analyzing conformational ensembles. Furthermore, all the C++ functionality of the Ensemble/Legacy toolkit is "wrapped" for use in the Python programming language. More detailed documentation on using Ensemble/Legacy is available online (http:¿picasso.nmr.ucsf.edu/dek/ensemble. html).

Computer Graphics↗
PubMedDate not supplied

Collaboration system for radiology workstations.

Consultation between radiologists and referring physicians is part of routine medical practice. Nevertheless, a typical picture archiving and communication system contains no provision that will allow this critical interaction to occur on-line. The authors describe an image viewing system designed for real-time interactive consultation over the Internet. The system has two main components: an image viewer and a collaboration server. The image viewer connects to the collaboration server over an Internet-compatible network. Once the image viewer is connected, its display can be synchronized with that of another connected image viewer, so that radiologists can point out image findings and diagnoses in real time to remotely located physicians. The image viewer can retrieve images from any DICOM-compatible archive. In addition to standard image manipulation functions, the image viewer contains a new user interface for image annotation. Developed specifically for medical imaging, this user interface is activated by mouse actions instead of conventional on-screen controls, greatly improving the ease with which annotations can be created. The collaboration system is based on a simple yet flexible programming interface that can be readily generalized to other types of collaborative applications. The system was developed with the Java programming language because of Java's integrated support of Internet-compatible networking capabilities.

Humans↗
PubMedDate not supplied

The quick machine--a mathematical model for the extrinsic activation of coagulation.

The present paper describes a mathematical model of the kinetics of the extrinsic coagulation cascade in vitro. The coagulation factors FI, FII, FV, FVII, FX, heparin and antithrombin III (ATIII) as well as soluble fibrin polymers are considered. The effect of single-factor deficiencies of the factors II, V, VII and X, diseases like hypo- and dysfibrinogenaemia, hepatic insufficiency, inhibited polymerisation by degradation products, heparin therapy with and without ATIII deficiency and coumarin therapy on prothrombin time can be portrayed. Physiology of coagulation is represented in a dynamic mathematical model as a differential equation system. The model is based on three reaction types: enzymatic cleavage, complex formation and polymerisation. The model was implemented in a continuous simulation program on a personal computer using the Pascal programming language. Unknown rate constants were estimated by chi 2 fit. Prothrombin time calculated by the model was compared to the training set of 20 plasma samples. In most but not all cases the model harmonized quite well with the coagulometric data.

Blood Coagulation↗
PubMed1999

Visualizing evolutionary activity of genotypes.

We introduce a method for visualizing evolutionary activity of genotypes. Following a proposal of Bedau and Packard [11], we define a genotype's evolutionary activity in terms of the history of its concentration in the evolving population. To visualize this evolutionary activity we graph the distribution of evolutionary activity in the population of genotypes as a function of time. Adaptively significant genotypes trace a salient line or "wave" in these graphs. The quality of these waves indicates a variety of neutral variation, and random genetic drift. We apply this method in an evolutionary model of self-replicating assembly language programs competing for room in a two-dimensional space. Comparison with fitness graphs and with a nonadaptive analogue of this model shows how this method highlights adaptively significant events.

Biological Evolution↗
PubMed2000

Accessing and distributing EMBL data using CORBA (common object request broker architecture).

BACKGROUND: The EMBL Nucleotide Sequence Database is a comprehensive database of DNA and RNA sequences and related information traditionally made available in flat-file format. Queries through tools such as SRS (Sequence Retrieval System) also return data in flat-file format. Flat files have a number of shortcomings, however, and the resources therefore currently lack a flexible environment to meet individual researchers' needs. The Object Management Group's common object request broker architecture (CORBA) is an industry standard that provides platform-independent programming interfaces and models for portable distributed object-oriented computing applications. Its independence from programming languages, computing platforms and network protocols makes it attractive for developing new applications for querying and distributing biological data. RESULTS: A CORBA infrastructure developed by EMBL-EBI provides an efficient means of accessing and distributing EMBL data. The EMBL object model is defined such that it provides a basis for specifying interfaces in interface definition language (IDL) and thus for developing the CORBA servers. The mapping from the object model to the relational schema in the underlying Oracle database uses the facilities provided by PersistenceTM, an object/relational tool. The techniques of developing loaders and 'live object caching' with persistent objects achieve a smart live object cache where objects are created on demand. The objects are managed by an evictor pattern mechanism. CONCLUSIONS: The CORBA interfaces to the EMBL database address some of the problems of traditional flat-file formats and provide an efficient means for accessing and distributing EMBL data. CORBA also provides a flexible environment for users to develop their applications by building clients to our CORBA servers, which can be integrated into existing systems.

Computational Biology↗
PubMed1981

A pharmacokinetic analysis program (multi) for microcomputer.

A nonlinear least squares program (MULTI) for microcomputers was developed. The program is written in BASIC programming language. Four algorithms, (1) Gauss-Newton method, (2) damping Gauss-Newton method, (3) modified Marquardt method and (4) simplex method, can be used for nonlinear curve fitting in MULTI. Up to five pharmacokinetic equations, which are voluntarily defined by the user, are simultaneously fitted to observed time courses. The executions of MULTI are demonstrated for time courses of ampicillin and oxacillin in man.

Ampicillin↗
PubMed1998

A remote collaboration system for telemedicine using the Internet.

We have developed a still-image telemedicine system for the Internet. It was implemented with the Java programming language and enables remote collaboration between two or more client computers located anywhere on the Internet. Each client requires only a PC or workstation and a popular Internet browser--no special hardware or software is required. We carried out both local-area and wide-area tests of the system. On a local network, JPEG images at a resolution of 640 x 480 pixels took 2-5 s to display on four different clients (PCs or workstations); at 1000 x 1000 pixels, the images took 10-65 s. We also tested the system between two universities in Japan, one in Italy and one in the USA, using the Internet for communications. Images required 4-20 s for display. The exchange of remote collaboration commands between the four locations was good and the maximum lag in mouse pointer movement was less than 1 s. The system has the potential to solve three problems of conventional telemedicine systems: their cost, the need for high-bandwidth telecommunication and the low compatibility between them.

Computer Communication Networks↗
PubMed1998

The integrated exposure uptake biokinetic model for lead in children: independent validation and verification.

The U.S. Environmental Protection Agency employs a model, the integrated exposure biokinetic (IEUBK) model for lead in children, for the assessment of risks to children posed by environmental lead at hazardous waste sites. This paper describes results of an effort to verify the consistency of the documentation with the computer model and to test the computer code using a group that is independent from those involved in the model development. This review concluded that the IEUBK model correctly calculates the equations specified in the IEUBK model theory documentation. However, several issues were identified on model documentation, model performance, and the C++ programming language code (i.e., IEUBK model source code) documentation. These issues affect the ability of an independent reviewer to understand the workings of the IEUBK model but not the model's reliability. As a result of these findings, recommendations have been provided for updating documentation to the model as well as associated adjustments to the model documentation.

Child↗
PubMed1987

Application of a general database manager in a clinical medical librarian program.

The morning report reference file was automated at the Stollerman Library because the manual system was time-intensive to maintain and cumbersome to search. A general database management system (DBMS) was chosen so that it could be used in the future for other data management functions in the library. DBMS features that should be examined before use with a bibliographic application include size limitations, data entry forms, data types, search options, index files, sort options, report generation, query and programming languages, command and/or menu files, file interaction, interface with other software, and documentation. Desired requirements for this application are discussed. It is noted that a general database manager probably will not meet all of the desired requirements. For some bibliographic applications, software specifically designed for bibliographic information management and retrieval should be used. A database for the purposes of searching the morning report reference file and producing a weekly reference list and a yearly index was developed using CONDOR 3. The structure of the database is described, and examples of the reports are given. The system has been in operation since December 1984 and has been well-received by staff and patrons.

Database Management Systems↗
PubMedDate not supplied

Design of an EEG-based brain-computer interface (BCI) from standard components running in real-time under Windows.

An EEG-based brain-computer interface (BCI) is a direct connection between the human brain and the computer. Such a communication system is needed by patients with severe motor impairments (e.g. late stage of Amyotrophic Lateral Sclerosis) and has to operate in real-time. This paper describes the selection of the appropriate components to construct such a BCI and focuses also on the selection of a suitable programming language and operating system. The multichannel system runs under Windows 95, equipped with a real-time Kernel expansion to obtain reasonable real-time operations on a standard PC. Matlab controls the data acquisition and the presentation of the experimental paradigm, while Simulink is used to calculate the recursive least square (RLS) algorithm that describes the current state of the EEG in real-time. First results of the new low-cost BCI show that the accuracy of differentiating imagination of left and right hand movement is around 95%.

Amyotrophic Lateral Sclerosis↗
PubMed2000

Useful Microsoft Word Macros for molecular biologists and protein chemists.

Biologists today make extensive use of word processing programs for the production of research reports, literature reviews and grant proposals. Frequently, such programs become the default platform for viewing and the later publication of protein and nucleic acid sequence data. Thus, researchers often switch between their word processor and more specialized programs designed to analyze protein and nucleic acid sequences. It would be more convenient to perform these simple sequence analyses using the word processor without switching to another program. The focus here is on the use of the Visual Basic programming language, which is built into all recent versions of Microsoft Word to generate surprisingly complex and useful macros that can conveniently analyze several important features of protein and nucleic acid sequences. The standard Word interface can also be easily modified to display and run these macros from a pull-down menu. Several examples of this approach are provided.

Amino Acid Sequence↗
PubMed2026

Identification of NR4A2 as a Potential Predictive Biomarker for Atherosclerosis.

INTRODUCTION/OBJECTIVE: Atherosclerosis, a leading cause of death globally, is characterized by the buildup of immune cells and lipids in medium to large-sized arteries. However, its precise mechanism remains unclear. The purpose of this study is to explore innovative and reliable biomarkers as a viable approach for the identification and management of atherosclerosis. METHODS: The atherosclerosis-related datasets GSE100927 and GSE66360 were retrieved from the Gene Expression Omnibus (GEO) database. The Limma package in the R programming language was utilized, applying the criteria of |logFC| > 1 and P < 0.05. Subsequently, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed on the 127 identified DEGs using R. Machine learning techniques were then applied to these data to explore and pinpoint potential biomarkers. The diagnostic potential of these markers was assessed via Receiver Operating Characteristic (ROC) curve analysis. Finally, western blot, real-time quantitative PCR (qRT-PCR), and immunohistochemistry (IHC) were employed to confirm the key biomarkers. RESULTS: Our research indicated that a total of 127 DEGs linked to atherosclerosis were successfully identified. Through the application of machine learning methods, eight critical genes were highlighted. Among these, Nuclear Receptor Subfamily 4 Group A Member-2 (NR4A2) emerged as the most promising marker for further investigation. CIBERSORT analysis revealed that NR4A2 expression levels were significantly correlated with multiple immune cell types, including B cells, plasma cells, and macrophages. Additional validation experiments confirmed that NR4A2 expression was indeed elevated in atherosclerotic plaques, supporting its potential as a biomarker for atherosclerosis. CONCLUSION: Our study identified NR4A2 as a potential immune-related biomarker for the diagnosis and treatment of atherosclerosis.

Atherosclerosis↗
PubMedDate not supplied

Borderless teleradiology with CHILI.

Teleradiology is one of the most evolved areas of telemedicine, but one of the basic problems which remains unsolved concerns system compatibility. The DICOM (Digital Imaging and Communications in Medicine) standard is a prerequisite, but it is not sufficient in all aspects. Examples of other currently open issues are security and cooperative work in synchronous teleconferences. Users without a DICOM radiological workstation would benefit from the ability to join a teleradiology network without any special tools. Drawbacks of many teleradiology systems are that they are monolithic in their software design and cannot be adapted to the actual user's environment. Existing radiological systems currently cannot be extended with additional software components. Consequently, every new application usually needs a new workstation with a different look and feel, which must be connected and integrated into the existing infrastructure. This paper introduces the second generation teleradiology system CHILI. The system has been designed to match both the teleradiology requirements of the American College of Radiology (ACR), and the functionality and usability needs of the users. The experiences of software developers and teleradiology users who participated in the first years of the clinical use of CHILI's predecessor MEDICUS have been integrated into a new design. The system has been designed as a component-based architecture. The most powerful communication protocol for data exchange and teleconferencing is the CHILI protocol, which includes a strong data security concept. The system offers, in addition to its own secure protocol, several different communication Methods: DICOM, classic e-mail, Remote Copy functions (RCP), File Transfer Protocol (FTP), the internet protocols HTTP (HyperText Transfer Protocol) and HTTPS (HyperText Transfer Protocol Secure),and CD-ROMs for off-line communication. These transfer METHODS allow the user to send images to nearly anyone with a computer and a network. The drawbacks of the non-CHILI protocols are that teleconferences are not possible, and that the user must take reasonable precautions for data privacy and security. The CHILI PlugIn mechanism enables the users or third parties to extend the system capabilities by adding powerful image postprocessing functions or interfaces to other information systems. Suitable PlugIns can be either existing programs, or dedicated applications programmed with interfaces to the CHILI components. The developer may freely choose programming languages and interface toolkits. The CHILI architecture is a powerful and flexible environment for Picture Archiving and Communications Systems (PACS)and teleradiology. More than 40 systems are currently running in clinical routine in Germany. More than 300,000 images have been distributed among the communication partners in the last two years. Feedback and suggestions from the users influenced the system architecture by a great extent. The proposed and implemented system has been optimized to be as platform independent, open, and secure as possible.

Radiology Information Systems↗
PubMed1996

A computer utility for automated retrieval of radiology reports.

OBJECTIVE: Many radiology information systems (RISs) installed during the 1980s have a user interface that is crude by today's standards. We explored improving this user interface by using the local processing power of the personal computer. In this article we describe a computer program that significantly enhances the ease of report retrieval by automating much of the interaction with our RIS, which is IDXrad. MATERIALS AND METHODS: The program, named DERVISH, runs under DOS on International Business Machines-compatible personal computers having an 80286 or faster processor, an enhanced graphics adapter or video gate array display, two serial ports, a mouse, and a bar code wand. It is written in the C++ programming language. Input may be keyboard, mouse, or bar code wand, and reports may be displayed singly or multiply and printed to a local printer or an RIS printer or copied to a disk file. DERVISH not only performs many of the routine tasks of an RIS session such a logging on and off but also provides a menu-driven environment for report display, including optional restriction of the report list to related prior reports. Keyboard use is minimized in favor of a mouse and a bar code wand. DERVISH emulates a standard RIS terminal for functions other than report retrieval. RESULTS: Originally intended to help retrieve the prior radiology reports of a patient at hand, DERVISH has found use in our quality management effort as well, simplifying comparison of reports from related radiologic techniques. An early version suffered poor acceptance because of its nonstandard interface and frequent malfunctions. The current version is presently in use in our emergency radiology department. CONCLUSION: DERVISH serves not only as a useful utility in itself but also as a demonstration of the ability of the local processing power of a desktop computer to improve the user interface of an aging RIS and to extend its functional life.

Computer Graphics↗
PubMed1993

Teaching medical diagnosis: a rule-based approach.

This paper discusses the design of a diagnostic process simulator which teaches medical students to think clinically. This was possible to achieve due to the application of a rule-based approach to represent diagnosis and treatments. Whilst using the simulator, as a result of the student's incorrect and correct decisions, the clinical situation changes accordingly. New diagnostic options result in the ability to choose further clinical and laboratory tests. The simulator is being implemented on Sun workstations and Macintosh computers using Prolog programming language.

Clinical Competence↗