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PubMed2006

Gene expression omnibus: microarray data storage, submission, retrieval, and analysis.

The Gene Expression Omnibus (GEO) repository at the National Center for Biotechnology Information archives and freely distributes high-throughput molecular abundance data, predominantly gene expression data generated by DNA microarray technology. The database has a flexible design that can handle diverse styles of both unprocessed and processed data in a Minimum Information About a Microarray Experiment-supportive infrastructure that promotes fully annotated submissions. GEO currently stores about a billion individual gene expression measurements, derived from over 100 organisms, submitted by over 1500 laboratories, addressing a wide range of biological phenomena. To maximize the utility of these data, several user-friendly web-based interfaces and applications have been implemented that enable effective exploration, query, and visualization of these data at the level of individual genes or entire studies. This chapter describes how data are stored, submission procedures, and mechanisms for data retrieval and query. GEO is publicly accessible at http://www.ncbi.nlm.nih.gov/projects/geo/.

Animals↗

PubMed2002

A knowledge-driven agent-centred framework for data mining in EMG.

In this paper, we present a multi-agent framework for data mining in electromyography. This application, based on a web interface, provides a set of functionalities allowing to manipulate 1000 medical cases and more than 25,000 neurological tests stored in a medical database. The aim is to extract medical information using data mining algorithms and to supply a knowledge base with pertinent information. The multi-agent platform gives the possibility to distribute the data management process between several autonomous entities. This framework provides a parallel and flexible data manipulation.

Data Collection↗

PubMed2006

Laryngeal cancer after topical mitomycin C application.

Mitomycin C is part of the mitomycin group of antibiotics and has found use in medicine in the treatment of various cancers, including those of the head and neck. In recent years, it has gained popularity as a topical treatment to prevent scar formation in the larynx and choanae in paediatric and adult inflammatory processes. Also, this alkylating agent is potentially a potent carcinogen. We report the first case in the world literature of laryngeal carcinoma in a non-smoking adult, which may have been induced by topical mitomycin C application to a glottic web. We discuss the mechanism of action of this drug, and we advise caution on its use for benign laryngeal pathologies.

Administration, Topical↗

PubMedDate not supplied

PASS biological activity spectrum predictions in the enhanced open NCI database browser.

The application of the program PASS (Prediction of Activity Spectra for Substances) to about 250 000 compounds of the NCI Open Database and the incorporation of over 64 million PASS predictions in the Enhanced NCI Database Browser are described. A total of 565 different types of activity are included, encompassing general pharmacological effects, specific mechanisms of action, known toxicities, and others. Application of this Web-based service to prediction of activities of the kinds "Angiogenesis inhibitor," "Antiviral (HIV)", and a set of activities that can be associated with antineoplastic action are reported. For this latter data set, a very substantial enrichment over random selection was found in the PASS predictions. It is shown how the user can conduct complex searches by combining ranges of PASS-predicted probabilities of compounds to be active or to be inactive, respectively, with, e.g., value ranges of physicochemical parameters, presence or absence of particular substructural fragment, and other search criteria.

Antineoplastic Agents↗

PubMed2005

Potentials and pitfalls for nutrition counselling in general practice.

This paper was based on collaborative research efforts from Wageningen University and the University Medical Centre St Radboud in The Netherlands and describes the rationale for web-based nutrition counselling applications in general practice as well as some of the frequently used models and theories (predominantly the Stages of Change Model). General practitioners can play an important role in cardiovascular risk reduction by giving nutrition counselling to patients at elevated cardiovascular risk. Unfortunately, general practitioners perceive barriers that may limit their nutrition counselling practices. Some of these barriers may be overcome using computer and Internet technologies. Computerized reminders for preventive services, and websites with reliable high-quality information may prove to be valuable additions to usual care. Cooperation with dietitians may also lead to improvements in nutrition counselling in general practice. For example, general practitioners could use their unique position to create awareness and motivation among patients. They could subsequently refer motivated patients to dietitians for detailed personal dietary advice.

Counseling↗

PubMed2002

Wireless and Web-based medical monitoring in the home.

A remote medical monitoring system is described, which continuously monitors patients' state of health. The system uses the services provided by intranets and the Internet to allow remote supervision of patients, who may be domiciled in their own home. A hardware/software prototype system has been constructed to demonstrate the use of non-invasive and minimally intrusive sensors attached to patients. Continuous real-time data is acquired, stored and processed. A wireless system or wires connect these monitor devices to the World Wide Web and, on request, information is delivered to authorized medical staff via a web browser or Wireless Application Protocol-enabled mobile telephones. Medical staff may examine real-time data or graphical information and make comparisons with historical data. Parameters may be set to select and control the data acquisition devices. The potential exists for augmentation of patient health by development of novel sensors and low-power electronic circuitry, and this research continues.

Aged↗

PubMed2004

Efficacy and safety of the Healthtronics LithoTron lithotripter.

PURPOSE: To evaluate our experience with the LithoTron lithotripter (Healthtronics, Atlanta, GA), a dry portable system that utilizes a spark-gap electrode as an energy source. PATIENTS AND METHODS: We prospectively evaluated the first 312 treatments performed on 199 men and 99 women with an average age of 43.5 years (range 4 months-80 years), over a 25-month period between May 1999 and June 2001. Of the 468 stones treated, 136 were located in the ureter, 52 in the renal pelvis or ureteropelvic junction, and 230 in the kidney; the sites of 50 were not specified in our database. The average stone size was 8.0 mm (range 1-40 mm). Follow-up included a plain (KUB) film, CT scan, or intravenous urogram (IVU) and was available for 256 patients. "Stone free" was defined as no fragments visible on postoperative images. The mean radiographic follow-up was 74 days (range 0-866 days). Data collection was initially done manually by data sheets, but a Web-based medical database application was developed in order to enter, store, retrieve, and analyze the data more efficiently. RESULTS: The average number of shocks delivered per renal unit was 2689 at 25.8 kV. Seventy-five percent of the procedures were performed with intravenous sedation. Two thirds (169/256) of the patients were rendered stone free with one treatment. According to size, 71% (209/294) of stones <1 cm, 57% (39/68) of stones between 1.0 and 1.5 cm, and 22% (8/36) of stones >1.5 cm were eliminated. There were 23 patients who required further treatment; from the available data, 18 of them are currently stone free. Perioperative complications occurred in 6 patients (2%). No patient had worsening renal function or new-onset hypertension. The effectiveness quotient was 59.3%. CONCLUSION: The LithoTron lithotripter is satisfactory for stones <1 cm.

Adolescent↗

PubMed2000

The microarray explorer tool for data mining of cDNA microarrays: application for the mammary gland.

The Microarray Explorer (MAExplorer) is a versatile Java-based data mining bioinformatic tool for analyzing quantitative cDNA expression profiles across multiple microarray platforms and DNA labeling systems. It may be run as either a stand-alone application or as a Web browser applet over the Internet. With this program it is possible to (i) analyze the expression of individual genes, (ii) analyze the expression of gene families and clusters, (iii) compare expression patterns and (iv) directly access other genomic databases for clones of interest. Data may be downloaded as required from a Web server or in the case of the stand-alone version, reside on the user's computer. Analyses are performed in real-time and may be viewed and directly manipulated in images, reports, scatter plots, histograms, expression profile plots and cluster analyses plots. A key feature is the clone data filter for constraining a working set of clones to those passing a variety of user-specified logical and statistical tests. Reports may be generated with hypertext Web access to UniGene, GenBank and other Internet databases for sets of clones found to be of interest. Users may save their explorations on the Web server or local computer and later recall or share them with other scientists in this groupware Web environment. The emphasis on direct manipulation of clones and sets of clones in graphics and tables provides a high level of interaction with the data, making it easier for investigators to test ideas when looking for patterns. We have used the MAExplorer to profile gene expression patterns of 1500 duplicated genes isolated from mouse mammary tissue. We have identified genes that are preferentially expressed during pregnancy and during lactation. One gene we identified, carbonic anhydrase III, is highly expressed in mammary tissue from virgin and pregnant mice and in gene knock-out mice with underdeveloped mammary epithelium. Other genes, which include those encoding milk proteins, are preferentially expressed during lactation.

Animals↗

PubMed2006

NCBI GEO: mining tens of millions of expression profiles--database and tools update.

The Gene Expression Omnibus (GEO) repository at the National Center for Biotechnology Information (NCBI) archives and freely disseminates microarray and other forms of high-throughput data generated by the scientific community. The database has a minimum information about a microarray experiment (MIAME)-compliant infrastructure that captures fully annotated raw and processed data. Several data deposit options and formats are supported, including web forms, spreadsheets, XML and Simple Omnibus Format in Text (SOFT). In addition to data storage, a collection of user-friendly web-based interfaces and applications are available to help users effectively explore, visualize and download the thousands of experiments and tens of millions of gene expression patterns stored in GEO. This paper provides a summary of the GEO database structure and user facilities, and describes recent enhancements to database design, performance, submission format options, data query and retrieval utilities. GEO is accessible at http://www.ncbi.nlm.nih.gov/geo/

Computer Graphics↗

PubMed2005

Munich information center for protein sequences plant genome resources: a framework for integrative and comparative analyses 1(W).

With several plant genomes sequenced, the power of comparative genome analysis can now be applied. However, genome-scale cross-species analyses are limited by the effort for data integration. To develop an integrated cross-species plant genome resource, we maintain comprehensive databases for model plant genomes, including Arabidopsis (Arabidopsis thaliana), maize (Zea mays), Medicago truncatula, and rice (Oryza sativa). Integration of data and resources is emphasized, both in house as well as with external partners and databases. Manual curation and state-of-the-art bioinformatic analysis are combined to achieve quality data. Easy access to the data is provided through Web interfaces and visualization tools, bulk downloads, and Web services for application-level access. This allows a consistent view of the model plant genomes for comparative and evolutionary studies, the transfer of knowledge between species, and the integration with functional genomics data.

Computational Biology↗

PubMed2006

Selecting biological data sources and tools with XPR, a path language for RDF.

As the number, richness and diversity of biological sources grow, scientists are increasingly confronted with the problem of selecting appropriate sources and tools. To address this problem, we have designed BioGuidel, a user-centric framework that helps scientists choose sources and tools according to their preferences and strategy, by specifying queries through a user-friendly visual interface. In this paper, we provide a complete RDF representation of BioGuide and introduce XPR (eXtensible Path language for RDF), an extension of FSL2 that is expressive enough to model all BioGuide queries. BioGuide queries modeled as XPR expressions can then be saved, compared, evaluated and exchanged through the Web between users and applications.

Computational Biology↗

PubMed2005

MARS: microarray analysis, retrieval, and storage system.

BACKGROUND: Microarray analysis has become a widely used technique for the study of gene-expression patterns on a genomic scale. As more and more laboratories are adopting microarray technology, there is a need for powerful and easy to use microarray databases facilitating array fabrication, labeling, hybridization, and data analysis. The wealth of data generated by this high throughput approach renders adequate database and analysis tools crucial for the pursuit of insights into the transcriptomic behavior of cells. RESULTS: MARS (Microarray Analysis and Retrieval System) provides a comprehensive MIAME supportive suite for storing, retrieving, and analyzing multi color microarray data. The system comprises a laboratory information management system (LIMS), a quality control management, as well as a sophisticated user management system. MARS is fully integrated into an analytical pipeline of microarray image analysis, normalization, gene expression clustering, and mapping of gene expression data onto biological pathways. The incorporation of ontologies and the use of MAGE-ML enables an export of studies stored in MARS to public repositories and other databases accepting these documents. CONCLUSION: We have developed an integrated system tailored to serve the specific needs of microarray based research projects using a unique fusion of Web based and standalone applications connected to the latest J2EE application server technology. The presented system is freely available for academic and non-profit institutions. More information can be found at http://genome.tugraz.at.

Algorithms↗

PubMed2000

DiasNet--an Internet tool for communication and education in diabetes.

Although studies have shown that intensive diabetes treatment with the goal of maintaining blood glucose concentrations close to the normal range lead to a substantial reduction of the rate of the complications (e.g. blindness, kidney failure, amputations and circulatory diseases), this can be difficult to achieve using conventional means. It is recognised that a number of patients may have poor control despite specialist care, and this along with devolution of care to non-specialists suggests that alternative interventions should be developed. DiasNet, which is used by patients as a tool for education and communication, is based on a well documented decision support system used by clinicians to give advise on insulin dose. In DiasNet the patients can experiment with their own data, adjusting insulin doses or meals sizes, and thereby learning how to cope with various situations. The system can run both as an ordinary application on a standard PC, and as an Internet application using a standard web browser. The latter enables a new way of communication between patient and clinician. DiasNet is currently being tested on a small group of diabetes patients.

Blood Glucose↗

PubMed2002

Data warehouse implementation with clinical pharmacokinetic/pharmacodynamic data.

OBJECTIVES: We have created a data warehouse for human pharmacokinetic (PK) and pharmacodynamic (PD) data generated primarily within the Clinical PK Group of the Drug Metabolism and Pharmacokinetics (DM&PK) Department of DuPont Pharmaceuticals. METHODS: Data which enters an Oracle-based LIMS directly from chromatography systems or through files from contract research organizations are accessed via SAS/PH.Kinetics, GLP-compliant data analysis software residing on individual users' workstations. Upon completion of the final PK or PD analysis, data are pushed to a predefined location. Data analyzed/created with other software (i.e., WinNonlin, NONMEM, Adapt, etc.) are added to this file repository as well. The warehouse creates views to these data and accumulates metadata on all data sources defined in the warehouse. The warehouse is managed via the SAS/Warehouse Administrator product that defines the environment, creates summarized data structures, and schedules data refresh. RESULTS: The clinical PK/PD warehouse encompasses laboratory, biometric, PK and PD data streams. Detailed logical tables for each compound are created/updated as the clinical PK/PD data warehouse is populated. The data model defined to the warehouse is based on a star schema. Summarized data structures such as multidimensional data bases (MDDB), infomarts, and datamarts are created from detail tables. Data mining and querying of highly summarized data as well as drill-down to detail data is possible via the creation of exploitation tools which front-end the warehouse data. Based on periodic refreshing of the warehouse data, these applications are able to access the most current data available and do not require a manual interface to update/populate the data store. Prototype applications have been web-enabled to facilitate their usage to varied data customers across platform and location. The warehouse also contains automated mechanisms for the construction of study data listings and SAS transport files for eventual incorporation into an electronic submission. CONCLUSIONS: This environment permits the management of online analytical processing via a single administrator once the data model and warehouse configuration have been designed. The expansion of the current environment will eventually connect data from all phases of research and development ensuring the return on investment and hopefully efficiencies in data processing unforeseen with earlier legacy systems.

Adult↗

PubMed2003

Development and successful pilot of a web-based scaleable, distributed curriculum development and management system for medical education.

In response to a need for a comprehensive online curriculum development and management system for medical education at the University of Pittsburgh the author, the Lab for Educational Technology (the Lab), students and faculty developed the Pitt Med Navigator website (Navigator). This completely web-based, distributed, personalized application is used by students and faculty to: 1) create, manage, and rapidly access online course resources; 2) author teaching cases, interactive multimedia presentations, and quizzes; and 3) manage a personal education portal. Four pilot courses and objective evaluations have revealed high student and faculty utilization and a high degree of perceived educational value.

Computer-Assisted Instruction↗

PubMed2005

[National public health information system].

Information production and its communication being a key public health activity, developing modern information systems is a precondition for its fulfilling these assignments. A national public health information system (NPHIS) is a set of human resources combined with computing and communication technologies. It enables data linkage and data coverage as well as undertaking information production and dissemination in an effective, standardized and safe way. The Croatian Institute of Public Health LAN/WAN modules are under development. Health Safety System, Health Workers Registry, and Digital Library are among the Institute's developmental priorities. Communication between NPHIS participants would unfold over the Internet by using every relevant data protection method. Web technology-based applications would be run on special servers. Between individual applications, use would be made of the transaction module of communication through an exchange of the HL7 standard-based xml messages. In the conditions of transition, the health system must make an optimal use of the resources, which is not feasible without applying modern information and communication technologies.

Croatia↗

PubMed1998

[A method for ordering CT examinations on the Intranet].

We have created a method for ordering CT examinations on the Intranet. Using user-friendly, free software for Web browsers and server applications, this method is easy to operate and inexpensive to install. The database engine, originally developed with Perl (Practical Extraction and Report Language), performed quickly. Equipped with security and access control functions, the method prevents not only illegal access, but also multiple orders placed simultaneously. This method enables personal computer users to order CT examinations quickly and with assurance.

Computer Communication Networks↗

PubMed2002

Email recruitment to use web decision support tools for pneumonia.

Application of guidelines to improve clinical decisions for Community Acquired Pneumonia (CAP) patients depends on accurate information about specific facts of each case and on presenting guideline support at the time decisions are being made. We report here on a system designed to solicit information from physicians about their CAP patients in order to classify CAP and present appropriate guidelines for type of care, length of stay, and use of antibiotics. We used elements of three existing information systems to create a achieve these goals: professionals coding diagnoses captured by the existing clinical information system (CIS), email, and web-based decision support tools including a pneumonia severity evaluation tool (SET). The non-secure IS components (email and web) were able to link to information in the CIS using tokens that do not reveal confidential patient-identifiable information. We examined their response to this strategy and the accuracy of pneumonia classification using this approach compared to chart review as a gold standard. On average physicians responded to email solicitations 50% of the time over the 14 month study. Also using this standard, we examined various information triggers for case finding. Professional coding of the primary reason for admission as pneumonia was fairly sensitive as an indicator of CAP. Physician use of the web SET was insensitive but fairly specific. Pneumonia classification using the SET was very reliable compared to experts' chart review using the same algorithm. We examined the distribution of severity of pneumonia for cases of pneumonia found by the various information triggers and for each severity the average length of stay. The distribution found by both chart review and by SET has demonstrated a shift toward more severe cases being admitted compared to only 3 years ago. The length of stay for level of severity is above expectations published by guidelines even for cases of true CAP by chart review. We suggest that the Fine classification system may not adequately describe patients in this setting. Physicians frequently responded that the guidelines presented did not fit their patients.

Algorithms↗