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At least 199 records · Page 11Linked to original sources

PubMed2001

Atlas-assisted localization analysis of functional images.

OBJECTIVE: This paper introduces a method for localization analysis of functional images assisted by a brain atlas. The usefulness of the system developed, based on this method, is analyzed for human brain mapping and neuroradiology. MATERIALS AND METHODS: We use an enhanced and extended electronic Talairach-Tournoux brain atlas, containing segmented and labeled subcortical structures, Brodmann's areas, and gyri. The brain atlas serves as a tool for anatomy referencing, segmentation, labeling, registration, and providing 3D anatomical relationships. The process of localization analysis is decomposed into five steps: data loading, feature extraction, data normalization, identification and editing of loci, and getting labels and values. This analysis is supported by near real-time data-to-atlas warping based on the Talairach transformation. Metanalysis is enabled by merging the current and external lists of activation loci. RESULTS: We have designed, developed, tested, and deployed a commercial system for atlas-assisted localization analysis of functional images. This is the first system where an electronic version of the Talairach-Tournoux brain atlas is used interactively for analysis of functional images. This system runs on personal computers and provides functions for a rapid normalization of anatomical and functional volumetric data, data segmentation and labeling, readout of Talairach coordinates, and data display. It also is empowered with several unique features including: interactive warping facilitating fine tuning of the data-to-atlas fit, a backtracking mechanism to compensate for missing landmarks and enhancing the outcome of the overall process of data analysis, navigation on the triplanar formed by the data and the atlas, multiple-images-in-one display with atlas-anatomy-function blending, a fast locus-controlled generation of results, editing of loci, multiple label display, and saving and reading of loci. The system normalizes a single image in near real-time (0.7 s), so analysis of anatomical and functional datasets can be done on-the-fly regardless of the number of slices. The same task performed by the state-of-the-art non-linear registration methods may require up to several days. CONCLUSIONS: The system is a useful tool for atlas-assisted localization analysis and a helpful adjunct to function/location metanalysis in human brain mapping research. It is also a step forward in bringing the atlas and the clinical data together within a practical and powerful solution that is fast and flexible, yet low-cost and affordable.

Anatomy, Artistic↗

PubMed2002

EMBL-Align: a new public nucleotide and amino acid multiple sequence alignment database.

UNLABELLED: The submission of multiple sequence alignment data to EMBL has grown 30-fold in the past 10 years, creating a problem of archiving them. The EBI has developed a new public database of multiple sequence alignments called EMBL-Align. It has a dedicated web-based submission tool, Webin-Align. Together they represent a comprehensive data management solution for alignment data. Webin-Align accepts all the common alignment formats and can display data in CLUSTALW format as well as a new standard EMBL-Align flat file format. The alignments are stored in the EMBL-Align database and can be queried from the EBI SRS (Sequence Retrieval System) server. AVAILABILITY: Webin-Align: http://www.ebi.ac.uk/embl/Submission/align_top.html, EMBL-Align: ftp://ftp.ebi.ac.uk/pub/databases/embl/align, http://srs.ebi.ac.uk/

Amino Acid Sequence↗

PubMed2004

CEBS object model for systems biology data, SysBio-OM.

MOTIVATION: To promote a systems biology approach to understanding the biological effects of environmental stressors, the Chemical Effects in Biological Systems (CEBS) knowledge base is being developed to house data from multiple complex data streams in a systems friendly manner that will accommodate extensive querying from users. Unified data representation via a single object model will greatly aid in integrating data storage and management, and facilitate reuse of software to analyze and display data resulting from diverse differential expression or differential profile technologies. Data streams include, but are not limited to, gene expression analysis (transcriptomics), protein expression and protein-protein interaction analysis (proteomics) and changes in low molecular weight metabolite levels (metabolomics). RESULTS: To enable the integration of microarray gene expression, proteomics and metabolomics data in the CEBS system, we designed an object model, Systems Biology Object Model (SysBio-OM). The model is comprehensive and leverages other open source efforts, namely the MicroArray Gene Expression Object Model (MAGE-OM) and the Proteomics Experiment Data Repository (PEDRo) object model. SysBio-OM is designed by extending MAGE-OM to represent protein expression data elements (including those from PEDRo), protein-protein interaction and metabolomics data. SysBio-OM promotes the standardization of data representation and data quality by facilitating the capture of the minimum annotation required for an experiment. Such standardization refines the accuracy of data mining and interpretation. The open source SysBio-OM model, which can be implemented on varied computing platforms is presented here. AVAILABILITY: A universal modeling language depiction of the entire SysBio-OM is available at http://cebs.niehs.nih.gov/SysBioOM/. The Rational Rose object model package is distributed under an open source license that permits unrestricted academic and commercial use and is available at http://cebs.niehs.nih.gov/cebsdownloads. The database and interface are being built to implement the model and will be available for public use at http://cebs.niehs.nih.gov.

Database Management Systems↗

PubMed2006

Construction of a nasopharyngeal carcinoma 2D/MS repository with Open Source XML database--Xindice.

BACKGROUND: Many proteomics initiatives require integration of all information with uniformcriteria from collection of samples and data display to publication of experimental results. The integration and exchanging of these data of different formats and structure imposes a great challenge to us. The XML technology presents a promise in handling this task due to its simplicity and flexibility. Nasopharyngeal carcinoma (NPC) is one of the most common cancers in southern China and Southeast Asia, which has marked geographic and racial differences in incidence. Although there are some cancer proteome databases now, there is still no NPC proteome database. RESULTS: The raw NPC proteome experiment data were captured into one XML document with Human Proteome Markup Language (HUP-ML) editor and imported into native XML database Xindice. The 2D/MS repository of NPC proteome was constructed with Apache, PHP and Xindice to provide access to the database via Internet. On our website, two methods, keyword query and click query, were provided at the same time to access the entries of the NPC proteome database. CONCLUSION: Our 2D/MS repository can be used to share the raw NPC proteomics data that are generated from gel-based proteomics experiments. The database, as well as the PHP source codes for constructing users' own proteome repository, can be accessed at http://www.xyproteomics.org/.

Carcinoma↗

PubMed1995

Understanding the dynamics of information technology implementation: a study of clinical information systems.

Health care institutions are considering a variety of emerging information technologies (ITs) in the hope of increasing efficiency, reducing costs, re-engineering work processes, and improving quality of care. The recent, rapid advances made in the use of innovative ITs in the health care field can present a plethora of problems to the administrative staff. Perhaps the most pressing of these concerns is the ability of today's hospitals to effectively create and utilize computer-based information systems. IT implementation has long been of great interest for information systems researchers. This branch of information system study seeks to identify those factors that are integral to optimizing the usage of IT. For example, researchers have advised practitioners that managerial support, high quality system design, commitment to advancing with the field, and extensive project planning are all key elements of successful system. In sum, previous research has produced a set of managerial proscriptions which, taken as a whole, constitute the "ideal" way to implement an IT system. Yet despite these normative principles and proscriptions, many health care institutions continue to find their attempts to make use of IT fraught with difficulty. Therefore, the objective of this study is to broaden and edify our understanding of IT implementation. More specifically, we seek to dispel the myth of the "ideal" system setup by exploring some of the alternative systems in use. We wish to investigate how and why the components of these alternative systems interact to produce utilization success (or failure). The study investigates the establishment and subsequent use of three clinical information systems (CIS) in a large tertiary care teaching hospital. The first case study is that of the hospital-wide implementation of a computer system that allows physicians to sign their medical records electronically. The second case examines the use of an electronic patient chart used to support the work of a variety of clinicians. Finally, we study a nursing assessment system used by two groups of nurses (intensive care unit and resuscitation unit) at a state-of-the-art, newly established Trauma Center. Qualitative was gathered through semi-structured interviews with people involved in the implementation process as well as a sample of user representatives. More than 90 interviews were conducted over a period of six months. Observational data completed our qualitative assessment. Quantitative evidence was gathered through questionnaires administered to a small sample of key informants. Three techniques of qualitative data analysis are being used in combination, namely, coding, analytical memos and displays. Data analysis is still in its infancy at this point. Regarding its relevance to the role of the administrator, this study will allow general and health care management as well as IT professionals to gain insight into the dynamics of the implementation of innovative technologies. In other words, results from this study will provide clear and relevant answers to the questions of how and why the outcome of the information system project is influenced by the way in which the technology is introduced.

Attitude to Computers↗

PubMed2000

A Web-based, secure, light weight clinical multimedia data capture and display system.

Computer-based patient records are traditionally composed of textual data. Integration of multimedia data has been historically slow. Multimedia data such as image, audio, and video have been traditionally more difficult to handle. An implementation of a clinical system for multimedia data is discussed. The system implementation uses Java, Secure Socket Layer (SSL), and Oracle 8i. The system is on top of the Internet so it is architectural independent, cross-platform, cross-vendor, and secure. Design and implementations issues are discussed.

Computer Security↗

PubMed1996

Analysis of neuro-behavioral Discovery data on the Macintosh computer.

This paper describes a suite of routines using IgorPro, a powerful analysis and graphing software package for the Macintosh computer, to enhance the ability to analyze, manipulate, and display data recorded with the Discovery acquisition software marketed by DataWave Technologies. The routines are able to time-align fast and slow data channels, and are especially useful for analyses that involve both neural and behavioral data. The software was designed for eyeblink conditioning and vocalization experiments, but it can easily be used for analyzing other types of neurobehavioral data. The data are first prepared on the PC with routines that inspect the header of the data file and translate the data file into a compact binary format that can be read by IgorPro. An option is also available to splice out data from unnecessary portions of an intertrial interval. The new file is then put on the Macintosh computer for display and analysis by IgorPro. These routines enable both neural and behavioral data to be quickly and easily reduced, manipulated, and statistically and graphically summarized.

Analysis of Variance↗

PubMed1987

Creation of a three-dimensional atlas by interpolation from Schaltenbrand-Bailey's atlas.

A 0.5-mm step atlas was interpolated from Schaltenbrand-Bailey's atlas. By serial display of the atlas with the desired rotation on a three-dimensional axis, a three-dimensional atlas was created. The newly created atlas can be used for computer-processed stereotactic data display. Any three-dimensionally located point can be displayed within 0.25 mm distance from the point, and spatial understanding of anatomical structures and stereotactic data is facilitated by the three-dimensional display.

Brain↗

PubMed1987

Managing research data with self-documenting files.

Processing biomedical research data is frequently complex due to the evolutionary nature of experiments and the requisite modification of analysis software. For the past several years we have been evolving a set of software tools designed to improve our ability to respond to evolving experimental designs. These tools allow the investigator to easily manipulate the research data and specify desired data transformations at run time. Coupling of analysis software to research data files is dependent on data files that are commented in a manner similar to that used in programming languages. The resulting annotated data files are self-documenting, and their use facilitates visual interpretation of displayed data as well as automatic processing of subsets of data. Here we present a formal description of a self-documenting file and describe several software tools that facilitate processing of biomedical research data.

Electronic Data Processing↗

PubMed1985

A computerized system for the identification of alloimmune neutropenia in neonates.

In an attempt to determine the incidence of alloimmune neonatal neutropenia, a systematic study was initiated during a period of six months. Complete blood count, differential and absolute neutrophil count of all the newborns were determined to identify the newborns with neutropenia and those with persistent neutropenia were evaluated for the presence of maternal neutrophil antibodies. This resulted in the design and use of a computerized system which was successfully employed to identify several neonates born with this disorder. The system includes a main program and eight functional options, and is operated under a secret authority code so that patients' data are accessible only to the investigators. The major functional options are: create, display, update and delete a record for the newborn; display most recent neutropenic babies; search all records and display name and ID number; search all records for a given year and display data; and perform statistics. The statistical analysis includes the total number of babies, both normal and those with neutropenia, the total number of babies with neutropenia and with/without sepsis, and those with persistent neutropenia. Also included are the hematological data consisting of complete blood count and differential of all of the newborns. Several possibilities exist to expand and extend the program for additional research-related purposes.

Agranulocytosis↗

PubMed2000

Setting thresholds for quality indicators derived from MDS data for nursing home quality improvement reports: an update.

BACKGROUND: Determining meaningful thresholds to reinforce excellent performance and flag potential problem areas in nursing home care is critical for preparing reports for nursing homes to use in their quality improvement programs. This article builds on the work of an earlier panel of experts that set thresholds for quality indicators (QIs) derived from Minimum Data Set (MDS) assessment data. Thresholds were now set for the revised MDS 2.0 two-page quarterly form and Resource Utilization Groups III (RUGS III) quarterly instrument. SETTING THRESHOLDS: In a day-long session in October 1998, panel members individually determined lower (good) and upper (poor) threshold scores for each QI, reviewed statewide distributions of MDS QIs, and completed a follow-up Delphi of the final results. REPORTING MDS QIS FOR QUALITY IMPROVEMENT: The QI reports compiled longitudinal data for all residents in the nursing home during each quarter and cumulatively displayed data for five quarters for each QI. A resident roster was provided to the nursing home so that the quality improvement team could identify the specific residents who developed the problems defined by each QI during the last quarter. Quality improvement teams found the reports helpful and easy to interpret. SUMMARY AND CONCLUSIONS: As promised in an earlier report, to ensure that thresholds reflect current practice, research using experts in a panel to set thresholds was repeated as needed. As the MDS instrument or recommended calculations for the MDS QIs change, thresholds will be reestablished to ensure a fit with the instrument and data.

Activities of Daily Living↗

PubMed1992

Temperature effects on the MgATP-induced electron transfer between the nitrogenase proteins from Azotobacter vinelandii.

The temperature dependence of the pre-steady-state MgATP-dependent electron transfer from the MoFe protein to the Fe protein of the nitrogenase from Azotobacter vinelandii has been investigated between 6 degrees C and 31 degrees C by stopped-flow spectrophotometry. Below 14 degrees C, the data are consistent with a model in which interaction of MgATP with nitrogenase is fast and irreversible, and is followed by reversible electron transfer. From the extent and from the rate of the absorbance change, the rate constants for electron transfer from Fe protein to MoFe protein and of the reverse reaction were calculated. The direct rate constant increases with temperature (6-14 degrees C) from about 1 s-1 to about 26 s-1. The rate constant for the reverse reaction was found to be approximately 4 s-1 and invariant with the reaction temperature. Analysis of the data obtained in the temperature range between 6 degrees C and 12 degrees C within the framework of the transition-state theory show that electron transfer from the Fe protein to the MoFe protein occurs via a highly disordered transition state with activation parameters delta H(0) ++ = 289 kJ.mol-1 and delta S(0) ++ = 792 J.K-1.mol-1. The Eyring plot of the stopped-flow data displays an inflection point around 14 degrees C. From the stopped-flow data obtained between 18 degrees and 27 degrees C the activation parameters delta H(0) ++ and delta S(0) ++ for the reduction of the MoFe protein by Fe protein are calculated to be 90 kJ.mol-1 and 99 J.K-1.mol-1 respectively. A second inflection point in the Eyring plot could exist around 28 degrees C.

Adenosine Triphosphate↗

PubMed2003

Generic design of Web-based clinical databases.

BACKGROUND: The complexity and the rapid evolution and expansion of the domain of clinical information make development and maintenance of clinical databases difficult. Whenever new data types are introduced or existing types are modified in a conventional relational database system, the physical design of the database must be changed accordingly. For this reason, it is desirable that a clinical database be flexible and allow for modifications and for addition of new types of data without having to change the physical database schema. The ideal clinical database would therefore implement a highly-detailed logical database schema in a completely-generic physical schema that stores the wide variety of clinical data in a small and constant number of tables. OBJECTIVE: The objective was to review the medical literature regarding generic design of clinical databases. METHODS: A search strategy was devised for PubMed and Google to get the best match of peer-reviewed articles and free Web resources on the subject. RESULTS: Eight peer reviewed articles and a Web tutorial were found. All the resources described the so-called Entity-Attribute-Value (EAV) design as a means of simplifying the physical layout of data tables in a clinical database. In Entity-Attribute-Value design all data can be stored in a single generic table with conceptually 3 columns: 1 for entity (eg, patient identification), 1 for attribute (eg, name), and 1 for value (eg, "Jens Hansen"). To add more descriptive fields to the entity class, all that is necessary is to add attribute values to be stored in the attribute field. The main advantages of the Entity-Attribute-Value design are flexibility and effective entity-centered data retrieval. The main disadvantages are complicated front-end programming needed to display data in a conventional layout that the user understands and less-efficient attribute-centered queries. The Internet offers unique opportunities for database deployment, eliminating problems of user-interface deployment. Furthermore, Web forms may be generated in a completely-generic fashion during run time from metadata describing the semantic structure of clinical information stored in the database. CONCLUSIONS: The Entity-Attribute-Value model is useful for generic design of clinical databases. Depending on the specific requirements of the application, more or less complex metadata models may be applied.

Databases, Factual↗

PubMed1998

MHCWeb: converting a WWW database into a knowledge-based collaborative environment.

The World Wide Web (WWW) is useful for distributing scientific data. Most existing web data resources organize their information either in structured flat files or relational databases with basic retrieval capabilities. For databases with one or a few simple relations, these approaches are successful, but they can be cumbersome when there is a data model involving multiple relations between complex data. We believe that knowledge-based resources offer a solution in these cases. Knowledge bases have explicit declarations of the concepts in the domain, along with the relations between them. They are usually organized hierarchically, and provide a global data model with a controlled vocabulary. We have created the OWEB architecture for building online scientific data resources using knowledge bases. OWEB provides a shell for structuring data, providing secure and shared access, and creating computational modules for processing and displaying data. In this paper, we describe the translation of the online immunological database MHCPEP into an OWEB system called MHCWeb. This effort involved building a conceptual model for the data, creating a controlled terminology for the legal values for different types of data, and then translating the original data into the new structure. The OWEB environment allows for flexible access to the data by both users and computer programs.

Artificial Intelligence↗

PubMed2004

Interleaved echo-planar imaging for fast multiplanar magnetic resonance temperature imaging of ultrasound thermal ablation therapy.

PURPOSE: To develop a multiplanar magnetic resonance temperature imaging (MRTI) technique based on interleaved gradient-echo echo-planar imaging (EPI), verify in phantom, develop software tools to process and display data on a clinical scanner in near real-time, and demonstrate feasibility to monitor ultrasound thermal ablation therapy in vivo. MATERIALS AND METHODS: Temperature estimation used complex phase-difference subtraction of the EPI MRTI data to indirectly measure the temperature-dependent water proton-resonance-frequency shift. Software tools were developed to run on a clinical 1.5-T MR scanner that processed and displayed relevant temperature and thermal dosimetry data during the course of thermal ablation treatments in canine brain and prostate in vivo. RESULTS: EPI MRTI provided multi-planar acquisitions and increased temperature sensitivity and lipid suppression. Relative to a single-plane fast gradient-echo MRTI sequence at comparable spatial and temporal resolutions in phantom, EPI MRTI demonstrated a three-fold increase in sensitivity and slice coverage per TR. In vivo monitoring of ultrasound thermal ablation therapy in canine brain and prostate demonstrated the usefulness of the temperature and thermal dose information. CONCLUSION: Multi-planar MRTI allowed progression of thermal damage to be monitored and treatment parameters adjusted in near real-time (less than five second delay). EPI MRTI is an effective multi-planar monitoring method during ultrasound thermal ablation procedures.

Animals↗

PubMed2003

Using a geographical information system to plan a malaria control programme in South Africa.

INTRODUCTION: Sustainable control of malaria in sub-Saharan Africa is jeopardized by dwindling public health resources resulting from competing health priorities that include an overwhelming acquired immunodeficiency syndrome (AIDS) epidemic. In Mpumalanga province, South Africa, rational planning has historically been hampered by a case surveillance system for malaria that only provided estimates of risk at the magisterial district level (a subdivision of a province). METHODS: To better map control programme activities to their geographical location, the malaria notification system was overhauled and a geographical information system implemented. The introduction of a simplified notification form used only for malaria and a carefully monitored notification system provided the good quality data necessary to support an effective geographical information system. RESULTS: The geographical information system displays data on malaria cases at a village or town level and has proved valuable in stratifying malaria risk within those magisterial districts at highest risk, Barberton and Nkomazi. The conspicuous west-to-east gradient, in which the risk rises sharply towards the Mozambican border (relative risk = 4.12, 95% confidence interval = 3.88-4.46 when the malaria risk within 5 km of the border was compared with the remaining areas in these two districts), allowed development of a targeted approach to control. DISCUSSION: The geographical information system for malaria was enormously valuable in enabling malaria risk at town and village level to be shown. Matching malaria control measures to specific strata of endemic malaria has provided the opportunity for more efficient malaria control in Mpumalanga province.

Databases, Factual↗

PubMed2002

Pitch and loudness interact in auditory displays: can the data get lost in the map?

Many auditory displays use acoustic attributes such as frequency, intensity, and spectral content to represent different characteristics of multidimensional data. This study demonstrated a perceptual interaction between dynamic changes in pitch and loudness, as well as perceived asymmetries in directional acoustic change, that distorted the data relations represented in an auditory display. Three experiments showed that changes in loudness can influence pitch change, that changes in pitch can influence loudness change, and that increases in acoustic intensity are judged to change more than equivalent decreases. Within a sonification of stock market data, these characteristics created perceptual distortions in the data set. The results suggest that great care should be exercised when using lower level acoustic dimensions to represent multidimensional data.

Adult↗

PubMed1999

Telemedicine: the new must for surgery.

The vision of telesurgery comprises a multitude of new communicative elements influencing the way surgeons will treat their patients in the future. The first prerequisite for effective telecommunication is to digitize surgical data. Many medical imaging modalities provide primarily digital data sets, and digital image communication is already entering clinical practice under the labels of teleradiology and telepathology. However, for any surgical purpose, images must refer to tissues. Three-dimensional image reconstruction is warranted, and if such data shall be useful during surgery, different image sources must be combined into some virtual, multiparametric body model and matched to an intraoperatively distorted organ contour. A multitude of detail problems arise, beginning with image standards, data interfaces, data transport, image fusion, registering, contour matching, and, once the data are integrated, all the aspects of surgery-suitable data display and interaction. We refer here to several demonstration projects illustrating such a complex surgical data set and its interactive telecommunication. In all instances, telecommunication was to enable a concentration of distributed medical intelligence at the site where the patient was treated. With further technological development, such telesurgical applications will have a growing influence on patient management and surgical decision making. In the very near future, computer-aided navigation and robotic assistance, based on the same surgical data sets, will be available to all fields of surgery. How decisive the role these methods will play for specific procedures or diseases needs to be determined.

Computer Simulation↗