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At least 721 records · Page 40Linked to original sources

PubMed2005

Extracorporeal shock wave lithotripsy with a transportable electrohydraulic lithotripter: experience with >300 patients.

OBJECTIVE: To review a multicentre experience of using a transportable lithotripter (STS-T, Medstone, Inc, Aliso Viejo, CA. USA) for treating patients with urolithiasis in all parts of the urinary tract. PATIENTS AND METHODS: In all, 326 patients with a total of 370 stones were treated as outpatients with the STS-T lithotripter. All patients received a single shock wave lithotripsy treatment and were followed after 4-6 weeks in the outpatient clinic, the primary endpoint being to determine the efficacy (as defined by the stone-free rate). Secondary objectives included establishing a database of patient demographic information, stone characteristics, stone location, procedural endpoints, and complication rates. RESULTS: In all there were 370 procedures, with a mean of 2394 shocks administered at an energy level of 24 kV. The mean treatment time was 51 min, excluding anaesthesia-induction time. The mean stone aggregate size was 8.2 mm; 62% of the stones were in the kidney while 38% were in various locations in the ureter. Of the treated stones, 90% had definite or probable evidence of fragmentation. The overall stone-free rate after one treatment with the STS-T was 52.8%. Of patients with residual fragments, most (61%) had fragments of <4 mm in aggregate diameter. The overall complication rate was 3.8%, the most common complication being postoperative pain. CONCLUSION: The Medstone STS-T lithotripter was an effective device for treating urolithiasis in all parts of the urinary tract. This system had a high margin of safety, as shown by the low complication rate. With no apparent sacrifice of efficacy compared to first-generation or fixed (not transportable) second-generation devices, the Medstone STS-T represents an important advance in the development of a truly transportable lithotripter.

Adult↗

PubMed2005

Using co-occurrence network structure to extract synonymous gene and protein names from MEDLINE abstracts.

BACKGROUND: Text-mining can assist biomedical researchers in reducing information overload by extracting useful knowledge from large collections of text. We developed a novel text-mining method based on analyzing the network structure created by symbol co-occurrences as a way to extend the capabilities of knowledge extraction. The method was applied to the task of automatic gene and protein name synonym extraction. RESULTS: Performance was measured on a test set consisting of about 50,000 abstracts from one year of MEDLINE. Synonyms retrieved from curated genomics databases were used as a gold standard. The system obtained a maximum F-score of 22.21% (23.18% precision and 21.36% recall), with high efficiency in the use of seed pairs. CONCLUSION: The method performs comparably with other studied methods, does not rely on sophisticated named-entity recognition, and requires little initial seed knowledge.

Algorithms↗

PubMed2005

Knowledge discovery and system biology in molecular medicine: an application on neurodegenerative diseases.

The possibility to study an organism in terms of system theory has been proposed in the past, but only the advancement of molecular biology techniques allow us to investigate the dynamical properties of a biological system in a more quantitative and rational way than before . These new techniques can gave only the basic level view of an organisms functionality. The comprehension of its dynamical behaviour depends on the possibility to perform a multiple level analysis. Functional genomics has stimulated the interest in the investigation the dynamical behaviour of an organism as a whole. These activities are commonly known as System Biology, and its interests ranges from molecules to organs. One of the more promising applications is the 'disease modeling'. The use of experimental models is a common procedure in pharmacological and clinical researches; today this approach is supported by 'in silico' predictive methods. This investigation can be improved by a combination of experimental and computational tools. The Machine Learning (ML) tools are able to process different heterogeneous data sources, taking into account this peculiarity, they could be fruitfully applied to support a multilevel data processing (molecular, cellular and morphological) that is the prerequisite for the formal model design; these techniques can allow us to extract the knowledge for mathematical model development. The aim of our work is the development and implementation of a system that combines ML and dynamical models simulations. The program is addressed to the virtual analysis of the pathways involved in neurodegenerative diseases. These pathologies are multifactorial diseases and the relevance of the different factors has not yet been well elucidated. This is a very complex task; in order to test the integrative approach our program has been limited to the analysis of the effects of a specific protein, the Cyclin dependent kinase 5 (CDK5) which relies on the induction of neuronal apoptosis. The system has a modular structure centred on a textual knowledge discovery approach. The text mining is the only way to enhance the capability to extract ,from multiple data sources, the information required for the dynamical simulator. The user may access the publically available modules through the following site: http://biocomp.ge.ismac.cnr.it.

Biomedical Research↗

PubMed2004

Design and implementation of a mosquito database through an entomological ontology.

There have been constant changes in the biology and behavior of the vector and parasite involved in the transmission of malaria. There is limited interest in developing new technologies and procedures for controlling the underlying factors of this threat, which poses an enormous challenge to health systems. To understand the various vector species and their interrelations is of prime importance in understanding the transmission mechanisms of malaria in order to react efficiently. To attain this objective, we have used an ontological approach to producing a database that we consider to be our own contribution in helping to control malaria vectors if eradication has been unsuccessful in the previous control campaign.

Animals↗

PubMed2005

Design and implementation of a mosquito database through an entomological ontology.

There have been constant changes in the biology and behavior of the vector and parasite involved in the transmission of malaria. There is limited interest in developing new technologies and procedures for controlling the underlying factors of this threat, which poses an enormous challenge to health systems. To understand the various vector species and their interrelations is of prime importance in understanding the transmission mechanisms of malaria in order to react efficiently. To attain this objective, we have used an ontological approach to produce a database that we consider to be our own contribution in helping to control malarial vectors if eradication has been unsuccessful in the previous control campaign.

Animals↗

PubMed2003

Concept-match medical data scrubbing. How pathology text can be used in research.

CONTEXT: In the normal course of activity, pathologists create and archive immense data sets of scientifically valuable information. Researchers need pathology-based data sets, annotated with clinical information and linked to archived tissues, to discover and validate new diagnostic tests and therapies. Pathology records can be used for research purposes (without obtaining informed patient consent for each use of each record), provided the data are rendered harmless. Large data sets can be made harmless through 3 computational steps: (1) deidentification, the removal or modification of data fields that can be used to identify a patient (name, social security number, etc); (2) rendering the data ambiguous, ensuring that every data record in a public data set has a nonunique set of characterizing data; and (3) data scrubbing, the removal or transformation of words in free text that can be used to identify persons or that contain information that is incriminating or otherwise private. This article addresses the problem of data scrubbing. OBJECTIVE: To design and implement a general algorithm that scrubs pathology free text, removing all identifying or private information. METHODS: The Concept-Match algorithm steps through confidential text. When a medical term matching a standard nomenclature term is encountered, the term is replaced by a nomenclature code and a synonym for the original term. When a high-frequency "stop" word, such as a, an, the, or for, is encountered, it is left in place. When any other word is encountered, it is blocked and replaced by asterisks. This produces a scrubbed text. An open-source implementation of the algorithm is freely available. RESULTS: The Concept-Match scrub method transformed pathology free text into scrubbed output that preserved the sense of the original sentences, while it blocked terms that did not match terms found in the Unified Medical Language System (UMLS). The scrubbed product is safe, in the restricted sense that the output retains only standard medical terms. The software implementation scrubbed more than half a million surgical pathology report phrases in less than an hour. CONCLUSIONS: Computerized scrubbing can render the textual portion of a pathology report harmless for research purposes. Scrubbing and deidentification methods allow pathologists to create and use large pathology databases to conduct medical research.

Computing Methodologies↗

PubMed2002

An overview of Electronic Document Management System product offerings.

The goal of this article is to provide insight in the evaluation of Electronic Document Management Systems (EDMSs) and the current EDMS vendors and their product offerings. Comparisons are made between the vendors and the products over the past decade. Appendix A and Appendix B outline many of today's key vendor offerings. Issues such as HIPAA and medical errors are discussed as it becomes clearer that the quality of patient care can be positively impacted with the application of information technology such as EDMSs.

Commerce↗

PubMed2005

pFind: a novel database-searching software system for automated peptide and protein identification via tandem mass spectrometry.

SUMMARY: Research in proteomics requires powerful database-searching software to automatically identify protein sequences in a complex protein mixture via tandem mass spectrometry. In this paper, we describe a novel database-searching software system called pFind (peptide/protein Finder), which employs an effective peptide-scoring algorithm that we reported earlier. The pFind server is implemented with the C++ STL, .Net and XML technologies. As a result, high speed and good usability of the software are achieved.

Algorithms↗

PubMed2006

SNP Function Portal: a web database for exploring the function implication of SNP alleles.

MOTIVATION: Finding the potential functional significance of SNPs is a major bottleneck in understanding genome-wide SNP scanning results, as the related functional data are distributed across many different databases. The SNP Function Portal is designed to be a clearing house for all public domain SNP functional annotation data, as well as in-house functional annotations derived from different data sources. It currently contains SNP functional annotations in six major categories including genomic elements, transcription regulation, protein function, pathway, disease and population genetics. Besides extensive SNP functional annotations, the SNP Function Portal includes a powerful search engine that accepts different types of genetic markers as input and identifies all genetically related SNPs based on the HapMap Phase II data as well as the relationship of different markers to known genes. As a result, our system allows users to identify the potential biological impact of genetic markers and complex relationships among genetic markers and genes, and it greatly facilitates knowledge discovery in genome-wide SNP scanning experiments. AVAILABILITY: http://brainarray.mbni.med.umich.edu/Brainarray/Database/SearchSNP/snpfunc.aspx.

Alleles↗

PubMed2003

An integrated genetic data environment (GDE)-based LINUX interface for analysis of HIV-1 and other microbial sequences.

MOTIVATION: Sequence databases encode a wealth of information needed to develop improved vaccination and treatment strategies for the control of HIV and other important pathogens. To facilitate effective utilization of these datasets, we developed a user-friendly GDE-based LINUX interface that reduces input/output file formatting. DESIGN AND RESULTS: GDE was adapted to the Linux operating system, bioinformatics tools were integrated with microbe-specific databases, and up-to-date GDE menus were developed for several clinically important viral, bacterial and parasitic genomes. Each microbial interface was designed for local access and contains Genbank, BLAST-formatted and phylogenetic databases. AVAILABILITY: GDE-Linux is available for research purposes by direct application to the corresponding author. Application-specific menus and support files can be downloaded from (http://www.bioafrica.net).

Database Management Systems↗

PubMed2006

Model storage, exchange and integration.

The field of Computational Systems Neurobiology is maturing quickly. If one wants it to fulfil its central role in the new Integrative Neurobiology, the reuse of quantitative models needs to be facilitated. The community has to develop standards and guidelines in order to maximise the diffusion of its scientific production, but also to render it more trustworthy. In the recent years, various projects tackled the problems of the syntax and semantics of quantitative models. More recently the international initiative BioModels.net launched three projects: (1) MIRIAM is a standard to curate and annotate models, in order to facilitate their reuse. (2) The Systems Biology Ontology is a set of controlled vocabularies aimed to be used in conjunction with models, in order to characterise their components. (3) BioModels Database is a resource that allows biologists to store, search and retrieve published mathematical models of biological interests. We expect that those resources, together with the use of formal languages such as SBML, will support the fruitful exchange and reuse of quantitative models.

Animals↗

PubMed1998

Representing metabolic pathway information: an object-oriented approach.

MOTIVATION: The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) is a website providing information and dynamic links for microbial metabolic pathways, enzyme reactions, and their substrates and products. The Compound, Organism, Reaction and Enzyme (CORE) object-oriented database management system was developed to contain and serve this information. RESULTS: CORE was developed using Java, an object-oriented programming language, and PSE persistent object classes from Object Design, Inc. CORE dynamically generates descriptive web pages for reactions, compounds and enzymes, and reconstructs ad hoc pathway maps starting from any UM-BBD reaction. AVAILABILITY: CORE code is available from the authors upon request. CORE is accessible through the UM-BBD at: http://www. labmed.umn.edu/umbbd/index.html.

Databases, Factual↗

PubMed2005

Applying GIFT, a Gene Interactions Finder in Text, to fly literature.

UNLABELLED: A number of freely available text mining tools have been put together to extract highly reliable Drosophila gene interaction data from text. The system has been tested with The Interactive Fly, showing low recall (27-34%), but very high precision (93-97%). AVAILABILITY: The extracted data and a web interface for submission of texts to GIFT analysis are available at http://gift.cryst.bbk.ac.uk/gift CONTACT: n.domedel_puig@cryst.bbk.ac.uk SUPPLEMENTARY INFORMATION: Additional documentation, such as the dictionaries and the reference sets, are available at the GIFT website.

Artificial Intelligence↗

PubMed2005

ASRP: the Arabidopsis Small RNA Project Database.

Eukaryotes produce functionally diverse classes of small RNAs (20-25 nt). These include microRNAs (miRNAs), which act as regulatory factors during growth and development, and short-interfering RNAs (siRNAs), which function in several epigenetic and post-transcriptional silencing systems. The Arabidopsis Small RNA Project (ASRP) seeks to characterize and functionally analyze the major classes of endogenous small RNAs in plants. The ASRP database provides a repository for sequences of small RNAs cloned from various Arabidopsis genotypes and tissues. Version 3.0 of the database contains 1920 unique sequences, with tools to assist in miRNA and siRNA identification and analysis. The comprehensive database is publicly available through a web interface at http://asrp.cgrb.oregonstate.edu.

Arabidopsis↗

PubMed2002

PheGe, the platform for exploring genotype-phenotype relations on cellular and organism level.

One major challenge of bioinformatics is to extract biological information into a form that gives access to analyses and predictive models and that sheds new light on cellular and organism function. In order to approach automated network analysis on organism level the relational platform PheGe was generated. PheGe enables a) presentation of cell-specific regulatory and metabolic pathways, b) sorting and coordination of the various molecules, genes and reactions to their particular signaling systems, c) visualization of signaling par distance, d) organization of downstream events on a multi-cellular level, e) recording and evaluation of pathological relevant data, f) coordination of the aberrant genes and gene products into the various regulatory pathways balancing phenotypic patterns g) modeling of cellular differentiation and finally h) tracing of network components that balance differentiation programs.

Algorithms↗

PubMed1994

Safety assessment of data management in a clinical laboratory.

This paper briefly reviews work undertaken within the DTI-sponsored MORSE project. The Clinical Biochemistry Department of the West Middlesex University Hospital, one of the five project partners, provides clinical and laboratory services to a wide range of users. The Laboratory Information Management System used within the department has been developed using a range of commercially available hardware and software together with software that has been designed and developed within the laboratory. This paper reports on the first stages of safety analysis of the overall operations in the laboratory. This is a pre-cursor to the systematic re-development of the information system in the light of the findings of the safety analysis.

Clinical Laboratory Information Systems↗

PubMed2005

Extraction of biological interaction networks from scientific literature.

Biology can be regarded as a science of networks: interactions between various biological entities (eg genes, proteins, metabolites) on different levels (eg gene regulation, cell signalling) can be represented as graphs and, thus, analysis of such networks might shed new light on the function of biological systems. Such biological networks can be obtained from different sources. The extraction of networks from text is an important technique that requires the integration of several different computational disciplines. This paper summarises the most important steps in network extraction and reviews common approaches and solutions for the extraction of biological networks from scientific literature.

Abstracting and Indexing↗

PubMed2003

Evaluation of annotation strategies using an entire genome sequence.

MOTIVATION: Genome-wide functional annotation either by manual or automatic means has raised considerable concerns regarding the accuracy of assignments and the reproducibility of methodologies. In addition, a performance evaluation of automated systems that attempt to tackle sequence analyses rapidly and reproducibly is generally missing. In order to quantify the accuracy and reproducibility of function assignments on a genome-wide scale, we have re-annotated the entire genome sequence of Chlamydia trachomatis (serovar D), in a collaborative manner. RESULTS: We have encoded all annotations in a structured format to allow further comparison and data exchange and have used a scale that records the different levels of potential annotation errors according to their propensity to propagate in the database due to transitive function assignments. We conclude that genome annotation may entail a considerable amount of errors, ranging from simple typographical errors to complex sequence analysis problems. The most surprising result of this comparative study is that automatic systems might perform as well as the teams of experts annotating genome sequences.

Amino Acid Sequence↗