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At least 1,549 records · Page 86Linked to original sources
PubMed2005

Mobilization of vacuolar iron by AtNRAMP3 and AtNRAMP4 is essential for seed germination on low iron.

Iron (Fe) is necessary for all living cells, but its bioavailability is often limited. Fe deficiency limits agriculture in many areas and affects over a billion human beings worldwide. In mammals, NRAMP2/DMT1/DCT1 was identified as a major pathway for Fe acquisition and recycling. In plants, AtNRAMP3 and AtNRAMP4 are induced under Fe deficiency. The similitude of AtNRAMP3 and AtNRAMP4 expression patterns and their common targeting to the vacuole, together with the lack of obvious phenotype in nramp3-1 and nramp4-1 single knockout mutants, suggested a functional redundancy. Indeed, the germination of nramp3 nramp4 double mutants is arrested under low Fe nutrition and fully rescued by high Fe supply. Mutant seeds have wild type Fe content, but fail to retrieve Fe from the vacuolar globoids. Our work thus identifies for the first time the vacuole as an essential compartment for Fe storage in seeds. Our data indicate that mobilization of vacuolar Fe stores by AtNRAMP3 and AtNRAMP4 is crucial to support Arabidopsis early development until efficient systems for Fe acquisition from the soil take over.

Arabidopsis↗
PubMed2001

[Confidentiality within the scope of secondary data research--approaches to a solution of the problem of data concentration].

In order to implement general data protection requirements and internationally recognised ethical requirements, research with personal health and social data demands a specific framework for the secure handling of confidential data. In the process of transferring data from the health service providers to the place where they are analysed, an important role is played by a so-called trust centre, responsible for pseudonymisation of personal and institutional identifiers. An undesirable concentration of data in the trust centre can be avoided by early separation of data in the data transfer institution: the trust centre receives only the identifier to be pseudonymised, while the health provision data are sent direct to the analysing institution, where they can be matched with the pseudonyms from the trust centre, with the help of a unique case number. The possibility of reidentification, which exists mainly in large (pseudonymised) data sets, can be reduced by use of an appropriate pseudonymisation process (e.g. insuree-based pseudonymisation by health service providers for sampling of insurees). The measures described here are suitable for protecting confidentiality and for further improving data security in the handling of confidential personal and institutional data.

Computer Security↗
PubMed2005

BioIE: extracting informative sentences from the biomedical literature.

SUMMARY: BioIE is a rule-based system that extracts informative sentences relating to protein families, their structures, functions and diseases from the biomedical literaturE. Based on manual definition of templates and rules, it aims at precise sentence extraction rather than wide recall. After uploading source text or retrieving abstracts from MEDLINE, users can extract sentences based on predefined or user-defined template categories. BioIE also provides a brief insight into the syntactic and semantic context of the source-text by looking at word, N-gram and MeSH-term distributions. Important Applications of BioIE are in, for example, annotation of microarray data and of protein databases. AVAILABILITY: http://umber.sbs.man.ac.uk/dbbrowser/bioie/

Database Management Systems↗
PubMed2006

A genetic algorithm using hyper-quadtrees for low-dimensional K-means clustering.

The k-means algorithm is widely used for clustering because of its computational efficiency. Given n points in d-dimensional space and the number of desired clusters k, k-means seeks a set of k cluster centers so as to minimize the sum of the squared Euclidean distance between each point and its nearest cluster center. However, the algorithm is very sensitive to the initial selection of centers and is likely to converge to partitions that are significantly inferior to the global optimum. We present a genetic algorithm (GA) for evolving centers in the k-means algorithm that simultaneously identifies good partitions for a range of values around a specified k. The set of centers is represented using a hyper-quadtree constructed on the data. This representation is exploited in our GA to generate an initial population of good centers and to support a novel crossover operation that selectively passes good subsets of neighboring centers from parents to offspring by swapping subtrees. Experimental results indicate that our GA finds the global optimum for data sets with known optima and finds good solutions for large simulated data sets.

Algorithms↗
PubMed2006

Building k-connected neighborhood graphs for isometric data embedding.

Isometric data embedding using geodesic distance requires the construction of a connected neighborhood graph so that the geodesic distance between every pair of data points can be estimated. This paper proposes an approach for constructing k-connected neighborhood graphs. The approach works by applying a greedy algorithm to add each edge, in a nondecreasing order of edge length, to a neighborhood graph if end vertices of the edge are not yet k-connected on the graph. The k-connectedness between vertices is tested using a network flow technique by assigning every vertex a unit flow capacity. This approach is applicable to a wide range of data. Experiments show that it gives better estimation of geodesic distances than other approaches, especially when the data are undersampled or nonuniformly distributed.

Algorithms↗
PubMed2005

Fisher sequential classifiers.

This paper presents further discussion and development of the two-parameter Fisher criterion and describes its two modifications (weighted criterion and another multiclass form). The criteria are applied in two algorithms for training linear sequential classifiers. The main idea of the first algorithm is separating the outermost class from the others. The second algorithm, which is a generalization of the first one, is based on the idea of linear division of classes into two subsets. As linear division of classes is not always satisfactory, a piecewise-linear version of the sequential algorithm is proposed as well. The computational complexity of different algorithms is analyzed. All methods are verified on artificial and real-life data sets.

Algorithms↗
PubMed1991

Toxic chemical release inventory information.

As part of a U.S. government effort to inform the public about toxic or hazardous chemicals released into the environment, the National Library of Medicine (NLM) and the Environmental Protection Agency (EPA) are jointly producing the TRI (Toxic Chemical Release Inventory) databanks which consist of two separate files, TRI87 and TRI88. Both files reside on NLM's TOX-NET system. The files contain geographic information about reporting facilities and land, air, and water release data for approximately 300 listed chemicals.

Databases, Factual↗
PubMed2001

Chemiluminescence microscopy as a tool in biomedical research.

Chemiluminescence has become a standard tool in biomedical research. Chemiluminescent probes are used for immunoassays, nucleic acid identification, reporter gene assays, measuring enzyme activity, and the detection of ions and small molecules such as Ca2+, ATP, NO, O2- and H2O2. Along with the development of new chemiluminescent probes, significant progress has been made in techniques to measure chemiluminescence. Ultra-sensitive photometers or luminometers have become widely available and can be obtained with automatic injectors and microplate readers. In addition, imaging photon detectors have been developed that allow the imaging of chemiluminescence from gels, blots, and microplates. Imaging photon detectors have also been attached to microscopes and allow imaging of chemiluminescent probes and reporter genes in cells and tissues. Specific methods of photon collection, storage, and analysis have been developed for microscopic imaging of chemiluminescence. Two of these methods are discussed in detail. The first is a method of data storage that allows days of continuous imaging without creating oversized files. The second is a method for calibrating photon imaging microscopes using a low-light standard. Such calibration will be helpful for comparing the performance of various photon imaging systems and for comparing data obtained in different laboratories.

Animals↗
PubMed1998

UMLS-based access to CPR data.

This paper describes the results of a project that explores the use the Unified Medical Language System (UMLS) for knowledge-driven tasks, such as browsing a computer-based patient record (CPR). The project consisted of a number of steps: the mapping between CPR terms and UMLS concepts, the development of an algorithm that explores the CPR data using this mapping, and the implementation of a first prototype browser that visualizes "found" data. A second task addressed in this project has been the direct access to online medical literature (MEDLINE) using the UMLS concepts found in the CPR data. In this project, we used a preliminary version of the Open Records for Patient Care (ORCA) CPR that consisted only of the history and physical examination data of patient suffering from heart failure.

Algorithms↗
PubMed2001

Uses of internet technology in clinical practice.

The practice of medicine has extended itself to vast areas and requires active clinicians to systematize and organize their workload through the use of the most up-to-date digital and computer communication technologies. Computerization and worldwide accessibility of information has especially provided great assistance in this regard. The explosive growth of medical information increases the need for the use of these new methods of organizing and accessing data. This article briefly summarizes a few of the vital tools that internet technology has provided clinical practice, with the aid of basic concepts of internet, database systems, hospital systems and data security and reliability.

Clinical Medicine↗
PubMed2002

NLP-based information extraction for managing the molecular biology literature.

We present research aimed at devising a tool for using natural language processing to identify and extract biomedical information from text for the purpose of assisting researchers in molecular biology manage large amounts of information. A pilot project based on the molecular genetics of diabetes demonstrates our ability to explore the interaction of genomic phenomena and clinical findings. We suggest the cooperation of this extracted information with systems for clustering text and constructing labeled networks of data.

Diabetes Mellitus↗
PubMed2003

Building an application framework for integrative genomics.

The accelerated pace of biological research and the current availability of whole-genome data sets provides significant new sources of functional insight. We designed an architecture and framework for software to query and explore such data in an orderly and iterative fashion. The architecture is intended to provide an extensible platform for developing web based bioinformatics applications and to offer a flexible and end-user-extensible software environment to explore and integrate disparate biological data sources. This will enable the user to explore existing relationships and discover new functional relationships among these data.

Computational Biology↗
PubMed2005

Applying Hybrid-Asbru clinical guidelines using the Spock system.

Clinical Guidelines are a major tool for improving the quality of medical care. Currently, a major research direction is automating the application of guidelines at the point of care. To support that automation, several requirements must be fulfilled, such as specification in a machine-interpretable format, and connection to an electronic patent record. We propose an innovative approach to guideline application, which capitalizes on our Digital electronic Guidelines Library (DeGeL). The DeGeL framework includes a new hybrid model for incremental specification of free-text guidelines, using several intermediate representations. The new approach was implemented, in the case of the Asbru guideline ontology, as the Spock system. Spock's hybrid application engine supports application of guideline represented at an intermediate format. Spock was evaluated in a preliminary fashion by applying several guidelines to sample patient data.

Decision Making, Computer-Assisted↗
PubMed1991

Work coding: beyond SIC and SOC, BOC and DOT.

Traditional coding schemes for occupational health related factors (eg, SIC, SOC, CAS) are structured similarly as hierarchical, exclusive, and exhaustive systems. Each is limited to information of one particular type (eg, industry) and, therefore, the relationships implicit in the coding scheme are limited. This study empirically determined that "natural" coding schemes used by occupational health professionals do not share these characteristics but are more akin to semantic network data bases. There is therefore a need to re-evaluate how occupational data are to be coded.

Databases, Factual↗
PubMed1995

A clinical data repository implementation progress report.

In late 1992, the 161 bed Grace Hospital of Morganton, North Carolina, USA, entered into a prototype agreement with a major vendor of hospital information systems software to help develop remote delivery of a Clinical Data Repository system. A process for planning and designing the implementation of this system was instituted by the Hospital. As of June 1994, several types of patient data are being collected for storage in the repository; interfaces to existing systems have been created, and progress is being made on designing clinical user presentation formats for long-term, on-line clinical data.

Computer Communication Networks↗
PubMed1996

Integrating data from natural language processing into a clinical information system.

Demographic data extracted from discharge summaries by natural language processing was compared to data gathered by a conventional hospital admitting system. Discrepancies in data were noted in names, age, sex, race, and ethnicity. Some differences are attributable to errors in collection: interaction with patient, dictation, transcription, and data entry. Very few differences were due to errors in natural language processing. Other differences can be used to critique existing data, or to enhance data with more detailed information. Discrepancies in data as elementary as patient demographics raise the issue of resolving conflicts when neither source of data is known to be more reliable. Clinical repositories can represent conflicting data from multiple sources, but clinical information systems must bear the cost of increased complexity in the application programs that will use the data.

Evaluation Studies as Topic↗
PubMed1998

Platform independent implementation of DICOM-based miniPACS.

Platform independence is an important issue for a software designed to run across a hospital environment which is practically always heterogeneous one. This paper presents a simple miniPACS solution designed over an existing Intranet (Internet limited to a local area network). Platform independence is achieved with Java programming language which allows resulting code to be executed on virtually all machines. System consists of a server application providing DICOM (Digital Imaging and Communications in Medicine) services and clients that can use these services over a TCP/IP connection. The server application is capable of an image storage and supports a query mechanism to allow access to stored data, thus the clients may perform two major functions: providing image data for archiving or image retrieval for viewing. Presented client application provides both these functions. It retrieves stored images for further processing and returns calculated results to the archive. The parts of the system are connected through a DICOM interface. Consequently the system architecture is open and any devices like scanners or viewing stations supporting specific DICOM services may be attached.

Humans↗
PubMed2004

[Effective literature searching. Focusing the question and using PubMed queries].

Apart from clinical and social expertise, the availability of contemporary knowledge is a key component in organisations within the health system that aim for excellence and competitiveness. Efficient literature searching is within this context a core business of evidence-based medicine. In addition to the need for valid data, the retrieval of information based on published literature has so far constituted a critical hurdle. Based on these requirements, two core issues for success with respect to literature searching are described: First, the generation of a structured question to form the basis of the most promising search terms. Second, a new feature of the web service of the national library of medicine, called "clinical queries", that allows the application of predefined filters to allocate clinically relevant data in terms of published clinical trials and systematic reviews.

Evidence-Based Medicine↗