The NCBO OBOF to OWL Mapping

Two of the most significant formats for biomedical ontologies are the Open Biomedical Ontologies Format (OBOF) and the Web Ontology Language (OWL). To make it possible to translate ontologies between these two representation formats, the National Center for Biomedical Ontology (NCBO) has developed a mapping between the OBOF and OWL formats as well as inter-conversion software. The goal was to allow the sharing of tools, ontologies, and associated data between the OBOF and Semantic Web communities.

OBOF does not have a formal grammar, so the NCBO had to capture its intended semantics to map it to OWL.

This official NCBO mapping was used to make all OBO Foundry ontologies available in OWL. 

Availability: This mapping functionality can be embedded into OBO-Edit and Protégé-OWL ontology editors. This software is available at: http://bioontology.org/wiki/index.php/OboInOwl:Main_Pag

Contemporary forest loss in Ireland; quantifying rare deforestation events in a fragmented forest landscape

Accurate quantification of forest loss is required to meet international reporting requirements, even in countries where deforestation rates are low. In Ireland, recent evidence has suggested the rate of gross annual deforestation is increasing. However, no spatially explicit data on the extent and character of contemporary deforestation exists. Here, we quantify deforestation in a region where forest loss is rare. Deforestation estimates derived from wall-to-wall photointerpretation, official records (e.g. felling licences), the CORINE land-use/land cover changes dataset and a combined approach (hereafter termed “the Deforestation Map”) are compared in two regions in Ireland for the period 2000 to 2012. Deforestation area based on the Deforestation Map (1497 ha) was greater than estimates derived from using photo-interpretation (730 ha), official records (908 ha) and CORINE (139 ha) alone. Independent accuracy assessment highlighted high errors of omission for photo-interpretation (68.9%), official records (66.7%) and CORINE (91.84%) estimates compared to the Deforestation Map (20%). No general increase in the deforestation rate during the study period was recorded, despite regional variations. Post deforestation land-use transitions were principally to wetland, grassland and settlement although the magnitude and proportion of change varied regionally. Gross annual deforestation was higher in older broadleaf forests than in conifer plantation forests, a surprising finding considering the small area and conservation status of many broadleaf forests in Ireland. For countries with small forest area and/or low rates of deforestation, the use of methodologies employed herein can provide a valuable record of forest loss and be used to validate sample-based or remotely sensed deforestation estimates

Intravenous omega-3, a technique to prevent an excessive innate immune response to cardiac surgery in a rodent gut ischemia model

ObjectivesNeutrophil infiltration of tissues as part of the inflammatory response to cardiac surgery is one of the major mediators of postoperative multiple-organ dysfunction. Omega-3 fatty acids markedly attenuate endothelial cell inflammatory responses, including upregulation of neutrophil adhesion molecules. The efficacy of a clinically safe form of omega-3 to produce this effect in vivo was examined.MethodsRat gut intravital microscopic analysis was used to visualize neutrophil transmigration from the microcirculation into the tissues of the gut. Inflammatory activation was in the form of 30 minutes of ischemia and 90 minutes of reperfusion. Sham, control (0.9% saline infusion over 4 hours), and omega-3 (Omegaven [Fresenius Kabi, Bad Homburg, Germany] infusion over 4 hours) pretreatments were compared.ResultsIschemia–reperfusion resulted in a 4-fold increase in neutrophil adherence to the endothelium (baseline: 4.3 ± 0.2 vs control group: 19.2 ± 3.5 adherent neutrophils per 100 μm, P < .01), which intravenous omega-3 suppressed (7.8 ± 1.7 adherent neutrophils per 100 μm, P < .01). Omega-3 pretreatment also reduced neutrophil transmigration into the tissues after reperfusion (sham group: 6.3 ± 0.8 vs control group: 13.2 ± 1.4 vs omega-3 group: 9.4 ± 0.9 neutrophils per field, P = .037). Gut tissue levels of the neutrophil-released enzyme myeloperoxidase were similarly markedly reduced with omega-3 pretreatment (sham group: 10.5 ± 1.6 vs control group: 19.0 ± 3.3 vs omega-3 group: 10.1 ± 1.2 U/g, P = .03).ConclusionsFour hours' pretreatment with a relatively safe form of intravenous omega-3 suppressed neutrophil adherence and tissue infiltration, resulting in lower levels of the tissue-damaging enzyme myeloperoxidase. This suggests a possible strategy for diminishing postoperative multiple-organ dysfunction

Deforestation in Ireland 2000 – 2012

Although Ireland’s national forest area continues to expand, recent evidence has suggested that the gross annual rate of deforestation is also increasing. Heretofore, no spatially explicit characterisation of contemporary deforestation areas in Ireland exists. Given uncertainties associated with current deforestation estimates, investigation of new methodologies is required to inform future land-use change accounting approaches. This paper presents a summary of the DEFORMAP project, which investigated the extent and nature of deforestation in Ireland for the 2000 – 2012 period. A combination of high resolution aerial photography, satellite imagery and ancillary datasets was used to quantify forest loss in the Republic of Ireland. In total, 5,457 ha of deforested land was identified which, following accuracy assessment, was error-adjusted to 7,465 ±785 ha. The error-adjusted gross annual national deforestation rate for the period of study was 0.103%. The deforestation rate increased from the first time interval investigated (2000-2005) to the second (2005-2010), followed by a reduction during the 2010 – 2012 period. High inter-county variation in gross annual deforestation was identified, with the highest level of deforestation occurring in Co. Monaghan (0.25% yr-1) and the lowest in Co. Limerick (0.02% yr-1). Principal post-deforestation land-use transitions were to agricultural grassland, built-land and wetland. Patterns of post-deforestation land-use transitions varied widely between counties indicating changing regional pressures on forest land. This paper presents an important development in our understanding of contemporary land-use change in Ireland by developing the first national deforestation map. The Deforestation Map presented here will provide a valuable record of forest loss, which can be used to validate any future earth observation based deforestation monitoring approaches, such as automated radar remote sensing techniques

Can we spot deleterious ageing in two waves of data? The Lothian Birth Cohort 1936 from ages 70 to 73

‘Younger ’ old age (the late 60s through early 70s) is, for many, a period of stability of lifestyle and considerable freedom to pursue leisure activities. Despite the stability that many enjoy, the mortality rate is about 2 % per year in western nations. This increases to about 5 % by age 80. It would be useful to know if those most vulnerable can be identified through patterns of deleterious ageing, and especially if this could be accomplished with just two waves of data. The Lothian Birth Cohort 1936 was surveyed on a host of individual difference variables including cognition, personality, biomarkers of physical health, and activities at ages 70 and 73 years. Overall, the group showed the expected basic stability in mean levels for these variables, but some individuals had died and others did show substantial changes that could be considered statistically reliable. These presumably reliable changes were at least as likely to be positive (reflecting improved condition/ability) as negative (reflecting decline/ageing). Moreover, limitations in the estimated reliabilities of the measures meant that most of the observed changes could not be considered reliable. The changes clustered only weakly around general health to predict death over the next approximately two years. We concluded that two waves of longitudinal data were not sufficient to assess meaningful patterns of ageing, despite often being used to do so

Uncovering the Neural Signature of Lapsing Attention: Electrophysiological Signals Predict Errors up to 20 s before They Occur

The extent to which changes in brain activity can foreshadow human error is uncertain yet has important theoretical and practical implications. The present study examined the temporal dynamics of electrocortical signals preceding a lapse of sustained attention. Twenty-one participants performed a continuous temporal expectancy task, which involved continuously monitoring a stream of regularly alternating patterned stimuli to detect a rarely occurring target stimulus whose duration was 40% longer. The stimulus stream flickered at a rate of 25 Hz to elicit a steady-state visual-evoked potential (SSVEP), which served as a continuous measure of basic visual processing. Increasing activity in the band (8 –14 Hz) was found beginning20 s before a missed target. This was followed by decreases in the amplitude of two event-related components over a short pretarget time frame: the frontal P3 (3– 4 s) and contingent-negative variation (during the target interval). In contrast, SSVEP amplitude before hits and misses was closely matched, suggesting that the efficacy of ongoing basic visual processing was unaffected. Our results show that the specific neural signatures of attentional lapses are registered in the EEG up to 20 s before an error

The epigenetic clock is correlated with physical and cognitive fitness in the Lothian Birth Cohort 1936

Background: The DNA methylation-based 'epigenetic clock' correlates strongly with chronological age, but it is currently unclear what drives individual differences. We examine cross-sectional and longitudinal associations between the epigenetic clock and four mortality-linked markers of physical and mental fitness: lung function, walking speed, grip strength and cognitive ability. Methods: DNA methylation-based age acceleration (residuals of the epigenetic clock estimate regressed on chronological age) were estimated in the Lothian Birth Cohort 1936 at ages 70 (n=920), 73 (n=299) and 76 (n=273) years. General cognitive ability, walking speed, lung function and grip strength were measured concurrently. Cross-sectional correlations between age acceleration and the fitness variables were calculated. Longitudinal change in the epigenetic clock estimates and the fitness variables were assessed via linear mixed models and latent growth curves. Epigenetic age acceleration at age 70 was used as a predictor of longitudinal change in fitness. Epigenome-wide association studies (EWASs) were conducted on the four fitness measures. Results: Cross-sectional correlations were significant between greater age acceleration and poorer performance on the lung function, cognition and grip strength measures (r range: -0.07 to -0.05, P range: 9.7 x 10 to 0.024). All of the fitness variables declined over time but age acceleration did not correlate with subsequent change over 6 years. There were no EWAS hits for the fitness traits. Conclusions: Markers of physical and mental fitness are associated with the epigenetic clock (lower abilities associated with age acceleration). However, age acceleration does not associate with decline in these measures, at least over a relatively short follow-up

Peripheral Nerve Activation Evokes Machine-Learnable Signals in the Dorsal Column Nuclei

The brainstem dorsal column nuclei (DCN) are essential to inform the brain of tactile and proprioceptive events experienced by the body. However, little is known about how ascending somatosensory information is represented in the DCN. Our objective was to investigate the usefulness of high-frequency (HF) and low-frequency (LF) DCN signal features (SFs) in predicting the nerve from which signals were evoked. We also aimed to explore the robustness of DCN SFs and map their relative information content across the brainstem surface. DCN surface potentials were recorded from urethane-anesthetized Wistar rats during sural and peroneal nerve electrical stimulation. Five salient SFs were extracted from each recording electrode of a seven-electrode array. We used a machine learning approach to quantify and rank information content contained within DCN surface-potential signals following peripheral nerve activation. Machine-learning of SF and electrode position combinations was quantified to determine a hierarchy of information importance for resolving the peripheral origin of nerve activation. A supervised back-propagation artificial neural network (ANN) could predict the nerve from which a response was evoked with up to 96.8 ± 0.8% accuracy. Guided by feature-learnability, we maintained high prediction accuracy after reducing ANN algorithm inputs from 35 (5 SFs from 7 electrodes) to 6 (4 SFs from one electrode and 2 SFs from a second electrode). When the number of input features were reduced, the best performing input combinations included HF and LF features. Feature-learnability also revealed that signals recorded from the same midline electrode can be accurately classified when evoked from bilateral nerve pairs, suggesting DCN surface activity asymmetry. Here we demonstrate a novel method for mapping the information content of signal patterns across the DCN surface and show that DCN SFs are robust across a population. Finally, we also show that the DCN is functionally asymmetrically organized, which challenges our current understanding of somatotopic symmetry across the midline at sub-cortical levels