When one Logic is Not Enough: Integrating First-order Annotations in OWL Ontologies

In ontology development, there is a gap between domain ontologies which mostly use the web ontology language, OWL, and foundational ontologies written in first-order logic, FOL. To bridge this gap, we present Gavel, a tool that supports the development of heterogeneous 'FOWL' ontologies that extend OWL with FOL annotations, and is able to reason over the combined set of axioms. Since FOL annotations are stored in OWL annotations, FOWL ontologies remain compatible with the existing OWL infrastructure. We show that for the OWL domain ontology OBI, the stronger integration with its FOL top-level ontology BFO via our approach enables us to detect several inconsistencies. Furthermore, existing OWL ontologies can benefit from FOL annotations. We illustrate this with FOWL ontologies containing mereotopological axioms that enable new meaningful inferences. Finally, we show that even for large domain ontologies such as ChEBI, automatic reasoning with FOL annotations can be used to detect previously unnoticed errors in the classification

Acute Beneficial Hemodynamic Effects of a Novel 3D-Echocardiographic Optimization Protocol in Cardiac Resynchronization Therapy

Post-implantation therapies to optimize cardiac resynchronization therapy (CRT) focus on adjustments of the atrio-ventricular (AV) delay and ventricular-to-ventricular (VV) interval. However, there is little consensus on how to achieve best resynchronization with these parameters. The aim of this study was to examine a novel combination of doppler echocardiography (DE) and three-dimensional echocardiography (3DE) for individualized optimization of device based AV delays and VV intervals compared to empiric programming.25 recipients of CRT (male: 56%, mean age: 67 years) were included in this study. Ejection fraction (EF), the primary outcome parameter, and left ventricular (LV) dimensions were evaluated by 3DE before CRT (baseline), after AV delay optimization while pacing the ventricles simultaneously (empiric VV interval programming) and after individualized VV interval optimization. For AV delay optimization aortic velocity time integral (AoVTI) was examined in eight different AV delays, and the AV delay with the highest AoVTI was programmed. For individualized VV interval optimization 3DE full-volume datasets of the left ventricle were obtained and analyzed to derive a systolic dyssynchrony index (SDI), calculated from the dispersion of time to minimal regional volume for all 16 LV segments. Consecutively, SDI was evaluated in six different VV intervals (including LV or right ventricular preactivation), and the VV interval with the lowest SDI was programmed (individualized optimization).EF increased from baseline 23±7% to 30±8 (p<0.001) after AV delay optimization and to 32±8% (p<0.05) after individualized optimization with an associated decrease of end-systolic volume from a baseline of 138±60 ml to 115±42 ml (p<0.001). Moreover, individualized optimization significantly reduced SDI from a baseline of 14.3±5.5% to 6.1±2.6% (p<0.001).Compared with empiric programming of biventricular pacemakers, individualized echocardiographic optimization with the integration of 3-dimensional indices into the optimization protocol acutely improved LV systolic function and decreased ESV and can be used to select the optimal AV delay and VV interval in CRT

A Mississippian black shale record of redox oscillation in the Craven Basin, UK

Early diagenetic redox oscillation processes have been rarely recognised in the ancient rock record but potentially exert an important control on mineral authigenesis, hydrocarbon prospectivity and supply of metals and/or reduced S as part of associated mineral systems. The upper unit of the Mississippian Bowland Shale Formation is a candidate record of diagenetic redox oscillation processes because it was deposited under a relatively high sediment accumulation rate linked to a large delta system, and under dominantly anoxic and intermittently sulphidic bottom-water conditions. In order to characterise the syngenetic and early diagenetic processes, sedimentological and geochemical data were integrated through the Upper Bowland Shale at three sites in the Craven Basin (Lancashire, UK). Organic matter (OM) comprises a mixture of Type II, II-S, II/III and III OM. ‘Redox zones’ are defined by patterns of Fe-speciation and redox-sensitive trace element enrichment and split into two groups. ‘Sulphidic’ zones (EUX, AN-III, AN-I and AN-IT) represent sediments deposited under conditions of at least intermittently active sulphate-reduction in bottom-waters. ‘Non-sulphidic’ zones (OX-RX, OX-F and OX) represent sediments deposited under non-sulphidic (oxic to ferruginous anoxic) bottom-waters. Operation of a shelf-to-basin ‘reactive Fe’ (FeHR) shuttle, moderated by sea level fluctuation and delta proximity, controlled the position and stability of redoxclines between zones of Fe and sulphate reduction, and methanogenesis. Early diagenetic redoxclines were capable of migration through the shallow sediment column relatively quickly, in response to sea level fluctuation. Preservation of syngenetic and early diagenetic geochemical signals shows redoxclines between Fe and sulphate reduction, and the upper boundary of sulphate-methane transition zone, were positioned within decimetres (i.e., 10 s cm) of seabed. Falling sea level and increasing FeHR supply is recognised as a switch from zones EUX (high sea level), AN-III and ultimately AN-I and AN-IT (low sea level). Zone AN-I defines the operation of ‘redox oscillation’, between zones of Fe and sulphate reduction in shallow porewaters, associated with enhanced degradation of OM and complete dissolution of primary carbonate. Preservation of OM and carbonate, in this system, was a function of changing bottom and pore water redox processes. Redox oscillation operated in a siliciclastic, prodeltaic environment associated with a relatively high sediment accumulation rate and high loadings of labile organic matter and metal oxides. These findings are important for understanding Late Palaeozoic black shales in the context of hydrocarbon and mineral systems

Geobiology of a lower Cambrian carbonate platform, Pedroche Formation, Ossa Morena Zone, Spain

The Cambrian Pedroche Formation comprises a mixed siliciclastic-carbonate succession recording subtidal deposition on a marine platform. Carbonate carbon isotope chemostratigraphy confirms previous biostratigraphic assignment of the Pedroche Formation to the Atdabanian regional stage of Siberia, correlative to Cambrian Series 2. At the outcrop scale, thrombolitic facies comprise ~. 60% of carbonate-normalized stratigraphy and coated-grains another ~. 10%. Petrographic point counts reveal that skeletons contribute at most 20% to thrombolitic inter-reef and reef-flank lithologies; on average, archaeocyath clasts make up 68% of skeletal materials. In contrast, petrographic point counts show that skeletons comprise a negligible volume of biohermal and biostromal thrombolite, associated nodular carbonate facies, and ooid, oncoid and peloid grainstone facies. As such, archaeocyathan reefal bioconstructions represent a specific and limited locus of skeletal carbonate production and deposition. Consistent with data from coeval, globally dispersed lower Cambrian successions, our analysis of the Pedroche Formation supports the view that lower Cambrian carbonates have more in common with earlier, Neoproterozoic deposits than with younger carbonates dominated by skeletal production and accumulation. © 2013 Elsevier B.V.Jessica R. Creveling, David Fernández-Remolar, Marta Rodríguez-Martínez, Silvia Menéndez, Kristin D. Bergmann, Benjamin C. Gill, John Abelson, Ricardo Amils, Bethany L. Ehlmann, Diego C. García-Bellido, John P. Grotzinger, Christian Hallmann, Kathryn M. Stack, Andrew H. Knol

Baseline characteristics.

<p>Values are shown as means ± standard deviation or count (percentage).</p><p>NYHA, New York Heart Association; CMP, cardiomyopathy; ACE, Angiotensin-converting enzyme; ARB, Angiotensin receptor blocker; LV, left ventricle; SDI, systolic dyssynchrony index.</p

Echocardiographic parameters at baseline and after AV delay and VV interval optimization.

<p>SDI, systolic dyssynchrony index; AV, atrio-ventricular; VV, ventriculo-ventricular; LV, left ventricular; VTI, velocity-time integral.</p><p>Shown are means ± standard deviation.</p>†<p>p<0.001: for comparison of AV optimization vs baseline.</p>¶<p>p<0.05: for comparison of complete optimization vs AV optimization only.</p><p>*p<0.05: for comparison of complete optimization vs baseline.</p

Acute hemodynamic effects of 3D-echocardiography guided optimization.

<p>Hemodynamic variables for each timestep of the optimization protocol: A) systolic dyssynchrony index, B) ejection fraction, and C) left-ventricular end-diastolic and end-systolic volumes. Shown are means ± standard deviation. * p<0.05 vs. baseline values.</p