BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains

The application of semantic technologies to the integration of biological data and the interoperability of bioinformatics analysis and visualization tools has been the common theme of a series of annual BioHackathons hosted in Japan for the past five years. Here we provide a review of the activities and outcomes from the BioHackathons held in 2011 in Kyoto and 2012 in Toyama. In order to efficiently implement semantic technologies in the life sciences, participants formed various sub-groups and worked on the following topics: Resource Description Framework (RDF) models for specific domains, text mining of the literature, ontology development, essential metadata for biological databases, platforms to enable efficient Semantic Web technology development and interoperability, and the development of applications for Semantic Web data. In this review, we briefly introduce the themes covered by these sub-groups. The observations made, conclusions drawn, and software development projects that emerged from these activities are discussed

Estimating Forest Age and Site Productivity using Time Series of 3D Remote Sensing Data

Three-dimensional (3D) data about forest captured by airborne laser scanning (ALS) have revolutionized forest management planning. Accurate, updated large-scale maps of forest variables produced with low costs today support greatly improved decisions about silvicultural treatments compared to the past practice based on field surveyed data only. These maps usually lack important information about forest age and site productivity, as this cannot be accurately assessed from the available ALS data. In Sweden, ALS has recently been performed nation-wide, except the mountainous area, to produce a new and accurate digital terrain model (DTM). This DTM enables extremely costefficient extraction of 3D data about the forest from other sources than ALS, such as automatic stereo-matching of aerial images as well as from single-pass spaceborne interferometric synthetic aperture radar (InSAR). In contrast to ALS, these data sources can provide low-cost time-series of 3D data. Aerial images of Sweden are often available in archives back to approximately 1960, and the TanDEM-X SAR system has the potential to provide new data every second week over large areas. These data have a potentially high value for forest management planning, since they may provide missing and highly important information -forest site productivity, Site Index (SI) and forest age. This pilot study explores a least-squares minimization approach to estimate forest age and SI from time series of 3D data produced by 1) image matching of DMC aerial images, and 2) TanDEM-X SAR data

Prevalence of Subclinical Coronary Artery Atherosclerosis in the General Population

Background: Early detection of coronary atherosclerosis using coronary computed tomography angiography (CCTA), in addition to coronary artery calcification (CAC) scoring, may help inform prevention strategies. We used CCTA to determine the prevalence, severity, and characteristics of coronary atherosclerosis and its association with CAC scores in a general population. Methods: We recruited 30 154 randomly invited individuals age 50 to 64 years to SCAPIS (the Swedish Cardiopulmonary Bioimage Study). The study includes individuals without known coronary heart disease (ie, no previous myocardial infarctions or cardiac procedures) and with high-quality results from CCTA and CAC imaging performed using dedicated dual-source CT scanners. Noncontrast images were scored for CAC. CCTA images were visually read and scored for coronary atherosclerosis per segment (defined as no atherosclerosis, 1% to 49% stenosis, or ≥50% stenosis). External validity of prevalence estimates was evaluated using inverse probability for participation weighting and Swedish register data. Results: In total, 25 182 individuals without known coronary heart disease were included (50.6% women). Any CCTA-detected atherosclerosis was found in 42.1%; any significant stenosis (≥50%) in 5.2%; left main, proximal left anterior descending artery, or 3-vessel disease in 1.9%; and any noncalcified plaques in 8.3% of this population. Onset of atherosclerosis was delayed on average by 10 years in women. Atherosclerosis was more prevalent in older individuals and predominantly found in the proximal left anterior descending artery. Prevalence of CCTA-detected atherosclerosis increased with increasing CAC scores. Among those with a CAC score >400, all had atherosclerosis and 45.7% had significant stenosis. In those with 0 CAC, 5.5% had atherosclerosis and 0.4% had significant stenosis. In participants with 0 CAC and intermediate 10-year risk of atherosclerotic cardiovascular disease according to the pooled cohort equation, 9.2% had CCTA-verified atherosclerosis. Prevalence estimates had excellent external validity and changed marginally when adjusted to the age-matched Swedish background population. Conclusions: Using CCTA in a large, random sample of the general population without established disease, we showed that silent coronary atherosclerosis is common in this population. High CAC scores convey a significant probability of substantial stenosis, and 0 CAC does not exclude atherosclerosis, particularly in those at higher baseline risk