Remarks on logic for process descriptions in ontological reasoning: A Drug Interaction Ontology case study

We present some ideas on logical process descriptions, using relations from the DIO (Drug Interaction Ontology) as examples and explaining how these relations can be naturally decomposed in terms of more basic structured logical process descriptions using terms from linear logic. In our view, the process descriptions are able to clarify the usual relational descriptions of DIO. In particular, we discuss the use of logical process descriptions in proving linear logical theorems. Among the types of reasoning supported by DIO one can distinguish both (1) basic reasoning about general structures in reality and (2) the domain-specific reasoning of experts. We here propose a clarification of this important distinction between (realist) reasoning on the basis of an ontology and rule-based inferences on the basis of an expert’s view

Systematic Detection of Short‐Term Slow Slip Events in Southcentral Alaska

Slow slip events (SSEs) are important for the slip budget along a megathrust fault. Although the recurrence of weeks-long short-term SSEs (S-SSEs) in southcentral Alaska has been suggested, a large amount of noise prevented us from detecting discrete events. We applied a systematic detection method to Global Navigation Satellite System data and detected 31 S-SSEs during the 14-year analysis period. The events mainly occurred at a depth from 35 to 45 km at a down-dip extension of the 1964 Alaska earthquake, and the active clusters correlated with the region of the subducting Yakutat microplate. A large cumulative slip of S-SSEs indicated a significant contribution to stress transfer along the plate interface, and its source area spatially coincided with that of the long-term SSEs and the afterslip of the 1964 earthquake. Large and recurrent S-SSEs are key phenomena for understanding interplate slip kinematics in this region

Earthquake Swarm Detection Along the Hikurangi Trench, New Zealand: Insights Into the Relationship Between Seismicity and Slow Slip Events

Earthquake swarms, which are anomalous increases in the seismicity rate without a distinguishable mainshock, often accompany transient aseismic processes, such as fluid migration and episodic aseismic slip along faults. Investigations of earthquake swarm activity can provide insights into the causal relationship between aseismic processes and seismicity. Slow slip events (SSEs) along the plate interface in the Hikurangi Trench, New Zealand, are often accompanied by intensive earthquake swarms. However, the detailed spatiotemporal distribution of these earthquake swarms is still unclear. Here, we use the epidemic-type aftershock-sequence (ETAS) model to detect earthquake swarms (M ≥ 3) and create a new earthquake swarm catalog (1997–2015) along the Hikurangi Trench. We compare the earthquake swarm catalog with Global Navigation Satellite System (GNSS) time series data, and existing SSE and tectonic tremor catalogs. Most of the detected (119) earthquake swarm sequences were intraplate events, and their epicenters were mainly concentrated along the east coast of the North Island, whereas many tectonic tremors were located inland. Twenty-five of the detected earthquake swarms occurred within 25 days before and after transient eastward GNSS displacements due to known or newly detected SSEs. We find that the earthquake swarms sometimes preceded the GNSS displacements by more than several days. SSE-induced stress loading is therefore not a plausible triggering mechanism for these pre-SSE earthquake swarms. We propose that high fluid pressure within the slab, which accumulated before the SSEs, may have caused intraplate fluid migration, which in turn triggered the pre-SSE earthquake swarms

Cellular response of Parachlorella kessleri to a solid surface culture environment

Attached culture allows high biomass productivity and is a promising biomass cultivating system because neither a huge facility area nor a large volume of culture medium are needed. This study investigates photosynthetic and transcriptomic behaviors in Parachlorella kessleri cells on a solid surface after their transfer from liquid culture to elucidate the physiological and gene-expression regulatory mechanisms that underlie their vigorous proliferation. The chlorophyll content shows a decrease at 12 h after the transfer; however, it has fully recovered at 24 h, suggesting temporary decreases in the amounts of light harvesting complexes. On PAM analysis, it is demonstrated that the effective quantum yield of PSII decreases at 0 h right after the transfer, followed by its recovery in the next 24 h. A similar changing pattern is observed for the photochemical quenching, with the PSII maximum quantum yield remaining at an almost unaltered level. Non-photochemical quenching was increased at both 0 h and 12 h after the transfer. These observations suggest that electron transfer downstream of PSII but not PSII itself is only temporarily damaged in solid-surface cells just after the transfer, with light energy in excess being dissipated as heat for PSII protection. It thus seems that the photosynthetic machinery acclimates to high-light and/or dehydration stresses through its temporal size-down and functional regulation that start right after the transfer. Meanwhile, transcriptomic analysis by RNA-Seq demonstrates temporary upregulation at 12 h after the transfer as to the expression levels of many genes for photosynthesis, amino acid synthesis, general stress response, and ribosomal subunit proteins. These findings suggest that cells transferred to a solid surface become stressed immediately after transfer but can recover their high photosynthetic activity through adaptation of photosynthetic machinery and metabolic flow as well as induction of general stress response mechanisms within 24 h