Height-based equations as screening tools for high blood pressure in pediatric practice, the GENOBOX study.

Due to the absence of easily applicable cut-off points to determine high blood pressure or hypertension in children, as in the adult population, blood pressure is rarely measured in the pediatrician's clinical routine. This has led to an underdiagnosis of high blood pressure or hypertension in children. For this reason, the present study evaluate the utility of five equations for the screening of high blood pressure in children: blood pressure to height ratio, modified blood pressure to height ratio, new modified blood pressure to height ratio, new simple formula and height-based equations.

A method and software framework for enriching private biomedical sources with data from public online repositories.

Modern biomedical research relies on the semantic integration of heterogeneous data sources to find data correlations. Researchers access multiple datasets of disparate origin, and identify elements-e.g.

A machine learning approach to identify clinical trials involving nanodrugs and nanodevices from ClinicalTrials.gov.

Background: Clinical Trials (CTs) are essential for bridging the gap between experimental research on new drugs and their clinical application. Just like CTs for traditional drugs and biologics have helped accelerate the translation of biomedical findings into medical practice, CTs for nanodrugs and nanodevices could advance novel nanomaterials as agents for diagnosis and therapy. Although there is publicly available information about nanomedicine-related CTs, the online archiving of this information is carried out without adhering to criteria that discriminate between studies involving nanomaterials or nanotechnology-based processes (nano), and CTs that do not involve nanotechnology (non-nano).

Toward a view-oriented approach for aligning RDF-based biomedical repositories.

Introduction: This article is part of the Focus Theme of METHODS of Information in Medicine on "Managing Interoperability and Complexity in Health Systems".

Background: The need for complementary access to multiple RDF databases has fostered new lines of research, but also entailed new challenges due to data representation disparities. While several approaches for RDF-based database integration have been proposed, those focused on schema alignment have become the most widely adopted.

Usability on the p-medicine infrastructure: an extended usability concept.

Usability testing methods are nowadays integrated into the design and development of health-care software, and the need for usability in health-care information technology (IT) is widely accepted by clinicians and researchers. Usability assessment starts with the identification of specific objectives that need to be tested and continues with the definition of evaluation criteria and monitoring procedures before usability tests are performed to assess the quality of all services and tasks. Such a process is implemented in the p-medicine environment and gives feedback iteratively to all software developers in the project.

p-medicine: A Medical Informatics Platform for Integrated Large Scale Heterogeneous Patient Data.

Secure access to patient data is becoming of increasing importance, as medical informatics grows in significance, to both assist with population health studies, and patient specific medicine in support of treatment. However, assembling the many different types of data emanating from the clinic is in itself a difficulty, and doing so across national borders compounds the problem. In this paper we present our solution: an easy to use distributed informatics platform embedding a state of the art data warehouse incorporating a secure pseudonymisation system protecting access to personal healthcare data.

Improving the implementation of clinical decision support systems.

Clinical decision support (CDS) systems promise to improve the quality of clinical care by helping physicians to make better, more informed decisions efficiently. However, the design and testing of CDS systems for practical medical use is cumbersome. It has been recognized that this may easily lead to a problematic mismatch between the developers' idea of the system and requirements from clinical practice.

NCBI2RDF: enabling full RDF-based access to NCBI databases.

RDF has become the standard technology for enabling interoperability among heterogeneous biomedical databases. The NCBI provides access to a large set of life sciences databases through a common interface called Entrez. However, the latter does not provide RDF-based access to such databases, and, therefore, they cannot be integrated with other RDF-compliant databases and accessed via SPARQL query interfaces.

Fostering ontology alignment sharing: a general-purpose RDF mapping format.

RDF has established in the last years as the language for describing, publishing and sharing biomedical resources. Following this trend, a great amount of RDF-based data sources, as well as ontologies, have appeared. Using a common language as RDF has provided a unified syntactic for sharing resources, but the semantics remain as the main cause of heterogeneity, hampering data integration and homogenization efforts.

RDFBuilder: a tool to automatically build RDF-based interfaces for MAGE-OM microarray data sources.

This paper presents RDFBuilder, a tool that enables RDF-based access to MAGE-ML-compliant microarray databases. We have developed a system that automatically transforms the MAGE-OM model and microarray data stored in the ArrayExpress database into RDF format. Additionally, the system automatically enables a SPARQL endpoint.

ACGT: advancing clinico-genomic trials on cancer - four years of experience.

The challenges regarding seamless integration of distributed, heterogeneous and multilevel data arising in the context of contemporary, post-genomic clinical trials cannot be effectively addressed with current methodologies. An urgent need exists to access data in a uniform manner, to share information among different clinical and research centers, and to store data in secure repositories assuring the privacy of patients. Advancing Clinico-Genomic Trials (ACGT) was a European Commission funded Integrated Project that aimed at providing tools and methods to enhance the efficiency of clinical trials in the -omics era.

PubDNA Finder: a web database linking full-text articles to sequences of nucleic acids.

Summary: PubDNA Finder is an online repository that we have created to link PubMed Central manuscripts to the sequences of nucleic acids appearing in them. It extends the search capabilities provided by PubMed Central by enabling researchers to perform advanced searches involving sequences of nucleic acids. This includes, among other features (i) searching for papers mentioning one or more specific sequences of nucleic acids and (ii) retrieving the genetic sequences appearing in different articles.

The ACGT Master Ontology and its applications--towards an ontology-driven cancer research and management system.

Objective: This paper introduces the objectives, methods and results of ontology development in the EU co-funded project Advancing Clinico-genomic Trials on Cancer-Open Grid Services for Improving Medical Knowledge Discovery (ACGT). While the available data in the life sciences has recently grown both in amount and quality, the full exploitation of it is being hindered by the use of different underlying technologies, coding systems, category schemes and reporting methods on the part of different research groups. The goal of the ACGT project is to contribute to the resolution of these problems by developing an ontology-driven, semantic grid services infrastructure that will enable efficient execution of discovery-driven scientific workflows in the context of multi-centric, post-genomic clinical trials.

An ontology-based and distributed KDD model for biomedical sources.

Knowledge discovery approaches in modern biomedical research usually require to access heterogeneous and remote data sources in a distributed environment. Traditional KDD models assumed a central repository, lacking mechanisms to access decentralized databases. In such distributed environment, ontologies can be used in all the KDD phases.

Semantic data integration in the European ACGT project.

ACGT is an IST-FP6 Integrated Project, funded by the European Commission, for the development of services to support clinico-genomic trials on cancer in a grid-based environment. In these trials, physicians and researchers need to access heterogeneous and disparate data sources. Semantic access to these data and the possibility to integrate them seamlessly are issues that ACGT aim to solve.

An ontology based method to solve query identifier heterogeneity in post-genomic clinical trials.

The increasing amount of information available for biomedical research has led to issues related to knowledge discovery in large collections of data. Moreover, Information Retrieval techniques must consider heterogeneities present in databases, initially belonging to different domains-e.g.

Comparison of a dipstick assay for detection of Brucella-specific immunoglobulin M antibodies with other tests for serodiagnosis of human brucellosis.

A dipstick assay for the detection of Brucella-specific immunoglobulin M (IgM) antibodies was evaluated by studying the serological response of 133 cultures and or serologically confirmed patients with brucellosis in its different stages along with those of 34 healthy controls. As regards patients with illness less than 3 months in duration, 93.1% tested positive by the dipstick assay, a percentage similar to that obtained in the standard serum agglutination test (SAT) (92.

[Temporal evolution of tuberculosis and human immunodeficiency virus infection in a population cared for in a hospital in Málaga].

Background: We have studied the incidence of tuberculosis++ disease, HIV infection and their association during a period of 6 years using samples analysed in a third level hospital laboratory.

Material And Method: 21,242 samples for mycobacteria and 63,425 for HIV antibodies were analysed between 1993 and 1998. The protocol used for mycobacteria consisted of Lowenstein-Jensen, hemoculture, biochemical tests for identification and DNA probe.

Metabolic acidosis and coma due to an overdose of nalidixic acid.

A case of severe metabolic acidosis and coma after taking 28 g of nalidixic acid is described. After administration of 600 mEq of sodium bicarbonate the patient developed a respiratory alkalosis with secondary tetany. She recovered her state of consciousness nine hours later and the acid-base disturbance resolved after sixty hours.

[Acute abdomen due to hemoperitoneum as the first manifestation of a liver tumor. Report of four cases (author's transl)].

Four cases of spontaneous acute hemoperitoneum due to rupture of a liver tumor are presented. The resulting acute abdomen was the first manifestation of the neoplasia. The four tumors corresponded histopathologically to a cavernous hemangioma, a bening adenoma related to anabolizing androgens, and two hepatocarcinomas in cirrhotic livers.