Use of pulse oximetry as an investigative test for paediatric respiratory sleep disorders.

The article covers the following elements: practical and technological considerations for optimising data collection and output; reference ranges for oximetry parameters across the ages; things to consider when interpreting a pulse oximetry study (eg, sleep/wake times); the ability of pulse oximetry to predict obstructive sleep apnoea; using oximetry as a screening tool for sleep disordered breathing in children with Down syndrome; things to consider when setting up a home oximetry service; and a case of an infant being weaned from oxygen using pulse oximetry studies.

Development, implementation and evaluation of Altered States of Consciousness: an immersive art exhibition designed to increase public awareness of psychotic experiences.

Background: The arts can increase public awareness of mental health. Stigma about psychosis remains high despite common occurrences of psychotic experiences in the general population (e.g.

Altered States of Consciousness: Evaluation of a voice-hearing simulation during an immersive art exhibition.

Aim: To improve public understanding of the subjective experience of auditory hallucinations and increase empathy towards individuals who hear voices and have other unusual sensory experiences.

Methods: This pilot study developed a new immersive art exhibition, Altered States of Consciousness, which gave members of the public an individualized voice-hearing simulation experience in 2 real-world settings-an art gallery and the London Underground. A total of 150 visitors completed visual analogue scales immediately before and after their experience of the exhibition.

An atlas of genetic influences on human blood metabolites.

Genome-wide association scans with high-throughput metabolic profiling provide unprecedented insights into how genetic variation influences metabolism and complex disease. Here we report the most comprehensive exploration of genetic loci influencing human metabolism thus far, comprising 7,824 adult individuals from 2 European population studies. We report genome-wide significant associations at 145 metabolic loci and their biochemical connectivity with more than 400 metabolites in human blood.

A CTD-Pfizer collaboration: manual curation of 88,000 scientific articles text mined for drug-disease and drug-phenotype interactions.

Improving the prediction of chemical toxicity is a goal common to both environmental health research and pharmaceutical drug development. To improve safety detection assays, it is critical to have a reference set of molecules with well-defined toxicity annotations for training and validation purposes. Here, we describe a collaboration between safety researchers at Pfizer and the research team at the Comparative Toxicogenomics Database (CTD) to text mine and manually review a collection of 88,629 articles relating over 1,200 pharmaceutical drugs to their potential involvement in cardiovascular, neurological, renal and hepatic toxicity.

Cataloging the biomedical world of pain through semi-automated curation of molecular interactions.

The vast collection of biomedical literature and its continued expansion has presented a number of challenges to researchers who require structured findings to stay abreast of and analyze molecular mechanisms relevant to their domain of interest. By structuring literature content into topic-specific machine-readable databases, the aggregate data from multiple articles can be used to infer trends that can be compared and contrasted with similar findings from topic-independent resources. Our study presents a generalized procedure for semi-automatically creating a custom topic-specific molecular interaction database through the use of text mining to assist manual curation.

An overview of the BioCreative 2012 Workshop Track III: interactive text mining task.

In many databases, biocuration primarily involves literature curation, which usually involves retrieving relevant articles, extracting information that will translate into annotations and identifying new incoming literature. As the volume of biological literature increases, the use of text mining to assist in biocuration becomes increasingly relevant. A number of groups have developed tools for text mining from a computer science/linguistics perspective, and there are many initiatives to curate some aspect of biology from the literature.

BioCreative III interactive task: an overview.

Background: The BioCreative challenge evaluation is a community-wide effort for evaluating text mining and information extraction systems applied to the biological domain. The biocurator community, as an active user of biomedical literature, provides a diverse and engaged end user group for text mining tools. Earlier BioCreative challenges involved many text mining teams in developing basic capabilities relevant to biological curation, but they did not address the issues of system usage, insertion into the workflow and adoption by curators.

Identifying and classifying biomedical perturbations in text.

Molecular perturbations provide a powerful toolset for biomedical researchers to scrutinize the contributions of individual molecules in biological systems. Perturbations qualify the context of experimental results and, despite their diversity, share properties in different dimensions in ways that can be formalized. We propose a formal framework to describe and classify perturbations that allows accumulation of knowledge in order to inform the process of biomedical scientific experimentation and target analysis.

Information needs and the role of text mining in drug development.

Drug development generates information needs from groups throughout a company. Knowing where to look for high-quality information is essential for minimizing costs and remaining competitive. Using 1131 research requests that came to our library between 2001 and 2007, we show that drugs, diseases, and genes/proteins are the most frequently searched subjects, and journal articles, patents, and competitive intelligence literature are the most frequently consulted textual resources.

Mining literature for systems biology.

Currently, literature is integrated in systems biology studies in three ways. Hand-curated pathways have been sufficient for assembling models in numerous studies. Second, literature is frequently accessed in a derived form, such as the concepts represented by the Medical Subject Headings (MeSH) and Gene Ontologies (GO), or functional relationships captured in protein-protein interaction (PPI) databases; both of these are convenient, consistent reductions of more complex concepts expressed as free text in the literature.

Enhancing access to the Bibliome: the TREC 2004 Genomics Track.

Background: The goal of the TREC Genomics Track is to improve information retrieval in the area of genomics by creating test collections that will allow researchers to improve and better understand failures of their systems. The 2004 track included an ad hoc retrieval task, simulating use of a search engine to obtain documents about biomedical topics. This paper describes the Genomics Track of the Text Retrieval Conference (TREC) 2004, a forum for evaluation of IR research systems, where retrieval in the genomics domain has recently begun to be assessed.

Advances in text analytics for drug discovery.

The automated extraction of biological and chemical information has improved over the past year, with advances in access to content, entity extraction of genes, chemicals, kinetic data and relationships, and algorithms for generating and testing hypotheses. As the systems for reading and understanding scientific literature grow more powerful, so must the infrastructure in which to assemble information. Advances in infrastructure systems are discussed in this review.