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PubMed2003

JXP4BIGI: a generalized, Java XML-based approach for biological information gathering and integration.

MOTIVATION: In the post-genomic era, biologists interested in systems biology often need to import data from public databases and construct their own system-specific or subject-oriented databases to support their complex analysis and knowledge discovery. To facilitate the analysis and data processing, customized and centralized databases are often created by extracting and integrating heterogeneous data retrieved from public databases. A generalized methodology for accessing, extracting, transforming and integrating the heterogeneous data is needed. RESULTS: This paper presents a new data integration approach named JXP4BIGI (Java XML Page for Biological Information Gathering and Integration). The approach provides a system-independent framework, which generalizes and streamlines the steps of accessing, extracting, transforming and integrating the data retrieved from heterogeneous data sources to build a customized data warehouse. It allows the data integrator of a biological database to define the desired bio-entities in XML templates (or Java XML pages), and use embedded extended SQL statements to extract structured, semi-structured and unstructured data from public databases. By running the templates in the JXP4BIGI framework and using a number of generalized wrappers, the required data from public databases can be efficiently extracted and integrated to construct the bio-entities in the XML format without having to hard-code the extraction logics for different data sources. The constructed XML bio-entities can then be imported into either a relational database system or a native XML database system to build a biological data warehouse. AVAILABILITY: JXP4BIGI has been integrated and tested in conjunction with the IKBAR system (http://www.ikbar.org/) in two integration efforts to collect and integrate data for about 200 human genes related to cell death from HUGO, Ensembl, and SWISS-PROT (Bairoch and Apweiler, 2000), and about 700 Drosophila genes from FlyBase (FlyBase Consortium, 2002). The integrated data has been used in comparative genomic analysis of x-ray induced cell death. Also, as explained later, JXP4BIGI is a middleware and framework to be integrated with biological database applications, and cannot run as a stand-alone software for end users. For demonstration purposes, a demonstration version is accessible at (http://www.ikbar.org/jxp4bigi/demo.html).

Database Management Systems↗

PubMed2002

Carbon - the first frontier of information processing.

Information is often encoded as an aperiodic chain of building blocks. Modern digital computers use bits as the building blocks, but in general the choice of building blocks depends on the nature of the information to be encoded. What are the optimal building blocks to encode structural information? This can be analysed by substituting the operations of addition and multiplication of conventional arithmetic with translation and rotation. It is argued that at the molecular level, the best component for encoding discretized structural information is carbon. Living organisms discovered this billions of years ago, and used carbon as the back-bone for constructing proteins that function according to their structure. Structural analysis of polypeptide chains shows that an efficient and versatile structural language of 20 building blocks is needed to implement all the tasks carried out by proteins. Properties of amino acids indicate that the present triplet genetic code was preceded by a more primitive one, coding for 10 amino acids using two nucleotide bases.

Amino Acid Sequence↗

PubMed2005

Review of the Australian incident monitoring system.

BACKGROUND: A survey was conducted to assess the benefits and limitations of the Australian Incident Monitoring System (AIMS) as a programme to improve patient safety. METHODS: A 12-point questionnaire was sent to 12 current users of AIMS in November 2002. RESULTS: The AIMS provides a consistent system of coding, trending and monitoring of incident data. It promotes a patient safety culture and an awareness of system error. Other benefits include the building of teamwork and the implementation of strategies to reduce the prevalence and severity of incidents. The majority of respondents (83%) reported that AIMS investigations resulted in significant changes to equipment usage, medication prescribing or administration, clinical protocols, training programmes and falls risk assessment tools. Although 75% of users reported improvements in patient outcomes, these were difficult to measure. A major limitation of AIMS was the low rate of incident reporting by medical staff. Voluntary reporting systems did not capture all incident data and the information was often too generic for root cause analysis. There were difficulties benchmarking data and concerns were raised regarding the ownership of information. The programme requires ongoing resources to implement change strategies and to maintain incident reporting levels. On a scale of 1 (poor rating) to 10 (excellent rating) the mean benefit rating was 7.6. CONCLUSION: The Australian Incident Monitoring System is beneficial as a component of a clinical risk management strategy. Usefulness could be improved by increased participation by medical staff. The level of resources required should not be underestimated if the programme is to demonstrate improvements to patient outcomes. More recent versions of AIMS promise improved capabilities and will require similar evaluation.

Australia↗

PubMed2002

Towards a semantic medical Web: HealthCyberMap's tool for building an RDF metadata base of health information resources based on the Qualified Dublin Core Metadata Set.

BACKGROUND: HealthCyberMap (http://healthcybermap.semanticweb.org/) aims at mapping Internet health information resources in novel ways for enhanced retrieval and navigation. This is achieved by collecting appropriate resource metadata in an unambiguous form that preserves semantics. MATERIAL/METHODS: We modelled a qualified Dublin Core (DC) metadata set ontology with extra elements for resource quality and geographical provenance in Prot g -2000. A metadata collection form helps acquiring resource instance data within Prot g . The DC subject field is populated with UMLS terms directly imported from UMLS Knowledge Source Server using UMLS tab, a Prot g -2000 plug-in. The project is saved in RDFS/RDF. RESULTS: The ontology and associated form serve as a free tool for building and maintaining an RDF medical resource metadata base. The UMLS tab enables browsing and searching for concepts that best describe a resource, and importing them to DC subject fields. The resultant metadata base can be used with a search and inference engine, and have textual and/or visual navigation interface(s) applied to it, to ultimately build a medical Semantic Web portal. Different ways of exploiting Prot g -2000 RDF output are discussed. CONCLUSIONS: By making the context and semantics of resources, not merely their raw text and formatting, amenable to computer 'understanding,' we can build a Semantic Web that is more useful to humans than the current Web. This requires proper use of metadata and ontologies. Clinical codes can reliably describe the subjects of medical resources, establish the semantic relationships (as defined by underlying coding scheme) between related resources, and automate their topical categorisation.

Humans↗

PubMedDate not supplied

[A new computer-assisted possibility for evaluating the evidence value of textile fiber traces].

This paper deals with the possibility of coding synthetic textile fibers. Using a small data bank the efficiency of a computer aided data search is demonstrated. It is intended to build up a large collection of textile fibers and to determine at least approximately the frequency of a certain fiber type. If this can be achieved the forensic scientist who has to examine textile fibers in case work will be able for the first time to answer the question about the frequency of an incriminating fiber, a question which is often asked in court.

Computers↗

PubMed2006

Monte Carlo simulation of the photon beam characteristics from medical linear accelerators.

The MCNPX code has been employed on a personal computer to calculate the dosimetric characteristics of the photon beams from the 6 MV Siemens MX2 and the 10 MV Varian Clinac 2100C linear accelerators. A model of the treatment head includes the major geometric structure within the beam path. The model was used to calculate the energy spectra of the photon beam, percentage depth dose and the dose profiles. The accuracy of the calculated results is examined by comparing them with the measured dose distributions for the two machines. The computed and measured depth dose curves agree to within 2% for all the depths beyond the build-up region for both treatment machines. The calculations agree to within 2% of the measured profiles within the 100-50% dose level. It has been found that the MCNPX code is an effective tool for simulating the clinical photon beam.

Body Burden↗

PubMed1995

A local alignment tool for very long DNA sequences.

This paper presents a practical program, called sim2, for building local alignments of two sequences, each of which may be hundreds of kilobases long. sim2 first constructs n best non-intersecting chains of 'fragments', such as all occurrences of identical 5-tuples in each of two DNA sequences, for any specified n > or = 1. Each chain is then refined by delivering an optimal alignment in a region delimited by the chain. sim2 requires only space proportional to the size of the input sequences and the output alignments, and the same source code runs on Unix machines, on Macintoshes, on PCs, and on DEC Alpha PCs. We also describe an application of sim2 for aligning long DNA sequences from Escherichia coli. sim2 facilitates contig-building by providing a complete view of the related sequences, so differences can be analyzed and inconsistencies resolved. Examples are shown using the alignment display and editing functions from the software tool ChromoScope.

Amino Acid Sequence↗

PubMed2004

Temporal codes and computations for sensory representation and scene analysis.

This paper considers a space of possible temporal codes, surveys neurophysiological and psychological evidence for their use in nervous systems, and presents examples of neural timing networks that operate in the time-domain. Sensory qualities can be encoded temporally by means of two broad strategies: stimulus-driven temporal correlations (phase-locking) and stimulus-triggering of endogenous temporal response patterns. Evidence for stimulus-related spike timing patterns exists in nearly every sensory modality, and such information can be potentially utilized for representation of stimulus qualities, localization of sources, and perceptual grouping. Multiple strategies for temporal (time, frequency, and code-division) multiplexing of information for transmission and grouping are outlined. Using delays and multiplications (coincidences), neural timing networks perform time-domain signal processing operations to compare, extract and separate temporal patterns. Separation of synthetic double vowels by a recurrent neural timing network is used to illustrate how coherences in temporal fine structure can be exploited to build up and separate periodic signals with different fundamentals. Timing nets constitute a time-domain scene analysis strategy based on temporal pattern invariance rather than feature-based labeling, segregation and binding of channels. Further potential implications of temporal codes and computations for new kinds of neural networks are explored.

Action Potentials↗

PubMed2002

Regional similarities in polymorphism in the human genome extend over many megabases.

The human genome exhibits extensive regional variation both in base composition and in the synonymous and nonsynonymous substitution rates of protein-coding genes. If such regional variation is due to variation in mutation rates, then levels of polymorphism should also vary across the human genome. Building on recent advances in mapping the human genome, we demonstrate regional variation in single nucleotide polymorphism density extending over many megabases. The range of local similarity in polymorphism shown by our genome-wide study is similar to the range of local similarity in base composition, and occurs over much longer distances than the variation in polymorphism revealed by studies of linkage disequilibrium.

GC Rich Sequence↗

PubMed2003

Uranium transport around the reactor zone at Bangombé and Okélobondo (Oklo): examples of hydrogeological and geochemical model integration and data evaluation.

The sites at Bangombé and Okélobondo (Oklo) in Gabon provide a unique opportunity to study the behaviour of products from natural nuclear reactions in the vicinity of reactor zones which were active around two billion years ago. The Commission of the European Communities initiated the Oklo Natural Analogue Programme. One of the principal aims was to study indications of present time migration of elements from the reactor zones under ambient conditions. The hydrogeological and hydrochemical data from the Oklo sites were modelled in order to better understand the geochemical behaviour of radionuclides in the natural system, by using independent models and by comparing the modelling outcome. Two modelling approaches were used: M3 code (hydrochemical mixing and mass balance model), developed by the Swedish Nuclear Fuel and Waste Management Company (SKB) and HYTEC (reactive transport model) developed by Ecole des Mines de Paris. Two different reactor zones were studied: Bangombé, a shallow site, the reactor being at 11 m depth, and OK84 at Okélobondo, situated at about 450 m depth, more comparable with a real repository location. This allowed the validation of modelling tools in two different sedimentary environments: one shallow, with a more homogeneous layering situated in an area of meteoric alteration, and the other offering the opportunity to study radionuclide migration from the reaction zone over a distance of 450 m through very heterogeneous sedimentary layers. The modeling results indicate that the chemical reactions retarding radionuclide transport are very different at the two sites. At Bangombé, the decomposition of organic material consumes oxygen and at Okélobondo the oxygen is consumed by inorganic reactions resulting, in both cases, in uranium retardation. Both modelling approaches (statistic with M3 code and deterministic with HYTEC code) could describe this situation. The goal of this exercise is to test codes which can help to describe and understand the processes taking place at the sites, validate the models with in situ data, and thus build confidence in the tools used for future site characterization. Ultimately, this allows identifying and selecting processes and parameters that can be used as input into repository performance assessment calculations and modelling exercises.

Environmental Monitoring↗

PubMed2005

Single-nucleotide polymorphisms in genes relating to homocysteine metabolism: how applicable are public SNP databases to a typical European population?

To facilitate the association studies in complex diseases characterized by hyperhomocysteinemia, we collected structural and frequency data on single-nucleotide polymorphism (SNPs) in 24 genes relating to homocysteine metabolism. Firstly, we scanned approximately 1.2 Mbp of sequence in the NCBI SNP database (dbSNP) build 110 and we detected 1353 putative SNPs with an average in silico genic density of 1:683. Out of 112 putative SNPs in coding regions (cSNPs), we selected a subset of 42 cSNPs and we assessed the applicability of the NCBI dbSNP to the Czech population - a typical representative of European Caucasians - by determining the frequency of the putative cSNPs experimentally by PCR-RFLP or ARMS-PCR in at least 110 control Czech chromosomes. As only 25 of the 42 analyzed cSNPs met the criterion of >/=1% frequency, the positive predictive value of the NCBI data set for our population reached 60%, which is similar to other studies. The correlation of SNP frequency between Czechs and other Caucasians - obtained from NCBI and/or literature - was stronger (r(2)=0.90 for 20 cSNPs) than between Czechs and general NCBI database entries (r(2)=0.73 for 27 cSNPs). Moreover, frequencies of all 20 putative cSNPs, for which data in Caucasians were available, were congruently below or above the 1% frequency criterion both in Czechs and in other Caucasians. In summary, our study shows that the NCBI dbSNP is a useful tool for selecting cSNPs for genetic studies of hyperhomocysteinemia in European populations, although experimental validation of SNPs should be performed, especially if the cSNP entry lacks any frequency data in Caucasians.

Czechoslovakia↗

PubMed2002

The new World Health Organization classification of haematopoietic and lymphoid tumours: a dermatopathological perspective.

The World Health Organization (WHO) has published a new consensus classification of tumours of haematopoietic and lymphoid tissue, based on recognizable disease entities defined by clinical and scientific criteria. The WHO does not support the use of stand-alone organ-related classifications, such as for skin. The Royal College of Pathologists (London) has adopted the WHO classification in its minimum dataset for the histopathological reporting of lymphoma and this will be used in the National Health Service Skin Cancer Dataset. The purpose of this review is to highlight the principal primary and secondary cutaneous haematopoietic and lymphoid tumours that are defined in the WHO classification. The review also discusses selected problematical areas in the WHO classification relevant to the skin and contains suggestions to encourage a unified approach in the use of the WHO coded summary. These represent an attempt to facilitate future progress and research in the field of cutaneous lymphoma. They are perceived as possible building-blocks for wider discussion and not as alterations to the classification. The WHO classification has been compared with a road map that indicates directions for future clinical and scientific research.

Hematologic Neoplasms↗

PubMed2005

Large-scale profiling of Rab GTPase trafficking networks: the membrome.

Rab GTPases and SNARE fusion proteins direct cargo trafficking through the exocytic and endocytic pathways of eukaryotic cells. We have used steady state mRNA expression profiling and computational hierarchical clustering methods to generate a global overview of the distribution of Rabs, SNAREs, and coat machinery components, as well as their respective adaptors, effectors, and regulators in 79 human and 61 mouse nonredundant tissues. We now show that this systems biology approach can be used to define building blocks for membrane trafficking based on Rab-centric protein activity hubs. These Rab-regulated hubs provide a framework for an integrated coding system, the membrome network, which regulates the dynamics of the specialized membrane architecture of differentiated cells. The distribution of Rab-regulated hubs illustrates a number of facets that guides the overall organization of subcellular compartments of cells and tissues through the activity of dynamic protein interaction networks. An interactive website for exploring datasets comprising components of the Rab-regulated hubs that define the membrome of different cell and organ systems in both human and mouse is available at http://www.membrome.org/.

Animals↗

PubMed1986

The collective dose equivalent due to the naturally occurring radionuclides in building materials in the German Democratic Republic. Part 1: External exposure.

The 226Ra, 232Th and 40K concentrations of building materials have been investigated by gamma spectrometry. The results demonstrate that 90% of bricks and concrete have 226Ra concentrations less than 85 mBq g-1 or less than 50 mBq g-1, respectively. In some waste products of mining and industry especially, the 226Ra concentrations are high compared to those of common building materials. Based on the results, the mean gamma dose equivalent to individuals and the collective dose equivalent have been calculated using the computer code ZYLIA-3. The mean indoor gamma dose equivalent to individuals is 510 mu Sv y-1 and the collective dose equivalent 8.5 X 10(3) man-Sv y-1. The outdoor values range from 60 to 81 mu Sv y-1 and 1.0 X 10(3) to 1.4 X 10(3) man-Sv y-1, respectively.

Construction Materials↗

PubMedDate not supplied

Determinants of physical activity and low-fat diet among low income African American and Hispanic middle school students.

African Americans, Hispanics, and those with low income experience disproportionate health problems that can be prevented by physical activity and a lower fat diet. In this descriptive cross-sectional study, antecedents of diet and exercise within the Health Promotion/Transtheoretical Model were examined among low-income African American and Hispanic seventh-grade students (n = 127). Total support was associated with higher physical activity for girls. African Americans perceived greater social support for activity than Hispanics. Family models and support for physical activity and low-fat diet were greater as family income increased. However, higher family role models and lower dietary fat were found among the lowest income Hispanic students' residing ZIP code with a higher concentration of Hispanics and greater availability of Hispanic foods and culture. A school-based approach may be useful to build peer support for physical activity and lower dietary fat. Parish nurse or clinic settings may be most appropriate for building family role models and support. Living in a neighborhood with traditional Hispanic culture and foods appears to have ameliorated the harmful effects of lower income, although further study with larger samples followed over time is needed.

Adolescent↗

PubMed2006

Medication administration practices in Pennsylvania schools.

As a result of various health concerns, children are receiving an increased number of medications while at school. In Pennsylvania, the School Code mandates a ratio of 1 certified school nurse to 1,500 students, which may mean that 1 school nurse is covering 3-5 buildings. This implies that unlicensed personnel are administering medications, a violation of licensing laws in Pennsylvania. The purpose of this study was to determine the policies and practices that Pennsylvania public schools have in place regarding medication administration. The sample consisted of 314 state-certified school nurses who returned a 71-question survey. Findings indicated that school nurses are very concerned about issues related to medication administration. Additional findings identified the lack of standing orders to administer over-the-counter medications, the increase in medication errors when the school nurse had responsibility for multiple buildings, and the lack of understanding of the ramifications of the Nurse Practice Act on school nursing practice in regard to delegation. Recommendations for practice include development of detailed policies and procedures and collaboration among all stakeholders in the development of policies that address legal issues.

Adult↗

PubMed2004

The University of Connecticut Biomedical Engineering Mentoring Program for high school students.

For the past four years, the Biomedical Engineering Program at the University of Connecticut has offered a summer mentoring program for high school students interested in biomedical engineering. To offer this program, we have partnered with the UConn Mentor Connection Program, the School of Engineering 2000 Program and the College of Liberal Arts and Sciences Summer Laboratory Apprentice Program. We typically have approximately 20-25 high school students learning about biomedical engineering each summer. The mentoring aspect of the program exists at many different levels, with the graduate students mentoring the undergraduate students, and these students mentoring the high school students. The program starts with a three-hour lecture on biomedical engineering to properly orient the students. An in-depth paper on an area in biomedical engineering is a required component, as well as a PowerPoint presentation on their research. All of the students build a device to record an EKG on a computer using LabView, including signal processing to remove noise. The students learn some rudimentary concepts on electrocardiography and the physiology and anatomy of the heart. The students also learn basic electronics and breadboarding circuits, PSpice, the building of a printed circuit board, PIC microcontroller, the operation of Multimeters (including the oscilloscope), soldering, assembly of the EKG device and writing LabView code to run their device on a PC. The students keep their EKG device, LabView program and a fully illustrated booklet on EKG to bring home with them, and hopefully bring back to their high school to share their experiences with other students and teachers. The students also work on several other projects during this summer experience as well as visit Hartford Hospital to learn about Clinical Engineering.

Biomedical Engineering↗

PubMed1996

A Web-based repository manager for brain mapping data.

The Web provides a rapid prototyping environment for building platform-independent graphical user interfaces. A Web-based console can be implemented as a suite of CGI scripts that generate HTML code, manipulate files, execute system commands, and invoke external tools. Often these tools share data by reading and writing flat files, which must be explicitly maintained by the CGI programmer. In a repository system, meta-data about each file object are maintained in a database, and access to all data is regulated by a layer of control services. This paper describes the design and implementation of a Web-based Repository Manager (WRM), which provides an application programmer's interface for controlling applications, generating HTML documents, handling Web forms, and managing multi-media data. The WRM is being used to develop a console for the Brain Mapping Framework, a system for visualizing cortical stimulation data obtained during neurosurgery.

Brain Mapping↗