RL Profile Research Articles

Functional harmony ontology: Musical harmony analysis with Description Logics

Symbolic representations of music are emerging as an important data domain both for the music industry and for computer science research, aiding in the organization of large collections of music and facilitating the development of creative and interactive AI. An aspect of symbolic representations of music, which differentiates them from audio representations, is their suitability to be linked with notions from music theory that have been developed over the centuries. One core such notion is that of functional harmony, which involves analyzing progressions of chords. This paper proposes a description of the theory of functional harmony within the OWL 2 RL profile and experimentally demonstrates its practical use.

OWL 2 learn profile: an ontology sublanguage for the learning domain.

Many experimental ontologies have been developed for the learning domain for use at different institutions. These ontologies include different OWL/OWL 2 (Web Ontology Language) constructors. However, it is not clear which OWL 2 constructors are the most appropriate ones for designing ontologies for the learning domain. It is possible that the constructors used in these learning domain ontologies match one of the three standard OWL 2 profiles (sublanguages). To investigate whether this is the case, we have analysed a corpus of 14 ontologies designed for the learning domain. We have also compared the constructors used in these ontologies with those of the OWL 2 RL profile, one of the OWL 2 standard profiles. The results of our analysis suggest that the OWL 2 constructors used in these ontologies do not exactly match the standard OWL 2 RL profile, but form a subset of that profile which we call OWL 2 Learn.

The bioactivity and fractionation of peptide hydrolysates in cultures of CHO cells.

Peptide hydrolysate supplements in mammalian cell cultures provide enhanced growth and productivity. The objective of this study was to compare the bioactivity of ten different commercially available hydrolysates from plant, microbial, and animal sources. The peptide hydrolysates were tested as supplements to cultures of Chinese hamster ovary (CHO) cells that produce human beta interferon (β-IFN). A soy hydrolysate was shown to support high cell growth but not protein productivity compared to an animal component hydrolysate (Primatone RL). On the other hand, a yeast hydrolysate showed lower cell growth, but comparable productivity of the recombinant protein. Glycosylation analysis showed that the glycan profile of β-IFN produced in yeast hydrolysate supplemented cultures was equivalent to that from Primatone RL-supplemented cultures. Fractionation of the yeast hydrolysate and Primatone RL produced a similar protein-assayed pattern except for one extra peak at around 1 kDa in the Primatone RL profile. A fraction taken at a molecular weight range of 1.5-1.7 kDa showed the highest growth promoting activity in both samples. However, four other fractions in yeast hydrolysate and two in Primatone RL at lower molecular weights showed some growth promoting activity. In conclusion, the yeast hydrolysates provided a good alternative to the animal sourced Primatone RL for high productivity of β-IFN from CHO cells with equivalent glycosylation.

Comparison of Rule based Semantic Web Reasoners for Ontologies in OWL2 Profile

The Semantic Web is a vision for the future of the Web in which information is given explicit meaning, making it easier for machines to automatically process and integrate information available on the Web[1]. In semantic web, Knowledge can be encoded using a formal language termed as OWL (Ontology Web Language). To keep this language alive Progression of OWL2 from OWL is one such major step. OWL2 is a strong Modeling language and extends the W3C OWL with a small but useful set of features. The objective of this study is an attempt to highlight those features and to provide and indepth analysis on: a. Introduction to three profiles of OWL2 with a particular focus on how these profiles differ and why the differences are important. b. Comparison of OWL Profiles on the basis of Usage, Reasoning Time, Complexity and Algorithms. c. Reasoning in OWL RL Profile and comparison of Reasoners in OWL RL Profiles. Keywords: OWL – Ontology Web Language, OWL axioms – Inference rules

Acyclicity Notions for Existential Rules and Their Application to Query Answering in Ontologies

Answering conjunctive queries (CQs) over a set of facts extended with existential rules is a prominent problem in knowledge representation and databases. This problem can be solved using the chase algorithm, which extends the given set of facts with fresh facts in order to satisfy the rules. If the chase terminates, then CQs can be evaluated directly in the resulting set of facts. The chase, however, does not terminate necessarily, and checking whether the chase terminates on a given set of rules and facts is undecidable. Numerous acyclicity notions were proposed as sufficient conditions for chase termination. In this paper, we present two new acyclicity notions called model-faithful acyclicity (MFA) and model-summarising acyclicity (MSA). Furthermore, we investigate the landscape of the known acyclicity notions and establish a complete taxonomy of all notions known to us. Finally, we show that MFA and MSA generalise most of these notions. Existential rules are closely related to the Horn fragments of the OWL 2 ontology language; furthermore, several prominent OWL 2 reasoners implement CQ answering by using the chase to materialise all relevant facts. In order to avoid termination problems, many of these systems handle only the OWL 2 RL profile of OWL 2; furthermore, some systems go beyond OWL 2 RL, but without any termination guarantees. In this paper we also investigate whether various acyclicity notions can provide a principled and practical solution to these problems. On the theoretical side, we show that query answering for acyclic ontologies is of lower complexity than for general ontologies. On the practical side, we show that many of the commonly used OWL 2 ontologies are MSA, and that the number of facts obtained by materialisation is not too large. Our results thus suggest that principled development of materialisation-based OWL 2 reasoners is practically feasible.

DLEJena: A Practical Forward-Chaining OWL 2 RL Reasoner Combining Jena and Pellet

This paper describes DLEJena, a practical reasoner for the OWL 2 RL profile that combines the forward-chaining rule engine of Jena and the Pellet DL reasoner. This combination is based on rule templates, instantiating at run-time a set of ABox OWL 2 RL/RDF Jena rules dedicated to a particular TBox that is handled by Pellet. The goal of DLEJena is to handle efficiently, through instantiated rules, the OWL 2 RL ontologies under direct semantics, where classes and properties cannot be at the same time individuals. The TBox semantics are treated by Pellet, reusing in that way efficient and sophisticated TBox DL reasoning algorithms. The experimental evaluation shows that DLEJena achieves more scalable ABox reasoning than the direct implementation of the OWL 2 RL/RDF rule set in the Jena's production rule engine, which is the main target of the system. DLEJena can be also used as a generic framework for applying an arbitrary number of entailments beyond the OWL 2 RL profile.

DLEJena: A practical forward-chaining OWL 2 RL reasoner combining Jena and Pellet

This paper describes DLEJena, a practical reasoner for the OWL 2 RL profile that combines the forward-chaining rule engine of Jena and the Pellet DL reasoner. This combination is based on rule templates, instantiating at run-time a set of ABox OWL 2 RL/RDF Jena rules dedicated to a particular TBox that is handled by Pellet. The goal of DLEJena is to handle efficiently, through instantiated rules, the OWL 2 RL ontologies under direct semantics, where classes and properties cannot be at the same time individuals. The TBox semantics are treated by Pellet, reusing in that way efficient and sophisticated TBox DL reasoning algorithms. The experimental evaluation shows that DLEJena achieves more scalable ABox reasoning than the direct implementation of the OWL 2 RL/RDF rule set in the Jena’s production rule engine, which is the main target of the system. DLEJena can be also used as a generic framework for applying an arbitrary number of entailments beyond the OWL 2 RL profile.

Distribution, morphology, and synaptic targets of corticothalamic terminals in the cat lateral posterior-pulvinar complex that originate from the posteromedial lateral suprasylvian cortex

The lateral posterior (LP) nucleus is a higher order thalamic nucleus that is believed to play a key role in the transmission of visual information between cortical areas. Two types of cortical terminals have been identified in higher order nuclei, large (type II) and smaller (type I), which have been proposed to drive and modulate, respectively, the response properties of thalamic cells (Sherman and Guillery [1998] Proc. Natl. Acad. Sci. U. S. A. 95:7121-7126). The aim of this study was to assess and compare the relative contribution of driver and modulator inputs to the LP nucleus that originate from the posteromedial part of the lateral suprasylvian cortex (PMLS) and area 17. To achieve this goal, the anterograde tracers biotinylated dextran amine (BDA) or Phaseolus vulgaris leucoagglutinin (PHAL) were injected into area 17 or PMLS. Results indicate that area 17 injections preferentially labelled large terminals, whereas PMLS injections preferentially labelled small terminals. A detailed analysis of PMLS terminal morphology revealed at least four categories of terminals: small type I terminals (57%), medium-sized to large singletons (30%), large terminals in arrangements of intermediate complexity (8%), and large terminals that form arrangements resembling rosettes (5%). Ultrastructural analysis and postembedding immunocytochemical staining for gamma-aminobutyric acid (GABA) distinguished two types of labelled PMLS terminals: small profiles with round vesicles (RS profiles) that contacted mostly non-GABAergic dendrites outside of glomeruli and large profiles with round vesicles (RL profiles) that contacted non-GABAergic dendrites (55%) and GABAergic dendritic terminals (45%) in glomeruli. RL profiles likely include singleton, intermediate, and rosette terminals, although future studies are needed to establish definitively the relationship between light microscopic morphology and ultrastructural features. All terminals types appeared to be involved in reciprocal corticothalamocortical connections as a result of an intermingling of terminals labelled by anterograde transport and cells labelled by retrograde transport. In conclusion, our results indicate that the origin of the driver inputs reaching the LP nucleus is not restricted to the primary visual cortex and that extrastriate visual areas might also contribute to the basic organization of visual receptive fields of neurons in this higher order nucleus.

Relative distribution of synapses in the pulvinar nucleus of the cat: implications regarding the "driver/modulator" theory of thalamic function.

To provide a quantitative comparison of the synaptic organization of "first-order" and "higher-order" thalamic nuclei, we followed bias-corrected sampling methods identical to a previous study of the cat dorsal lateral geniculate nucleus (dLGN; Van Horn et al. [2000] J. Comp. Neurol. 416:509-520) to examine the distribution of terminal types within the cat pulvinar nucleus. We observed the following distribution of synaptic contacts: large terminals that contain loosely packed round vesicles (RL profiles), 3.5%; presynaptic profiles that contain densely packed pleomorphic vesicles (F1 profiles), 7.3%; profiles that could be both presynaptic and postsynaptic that contain loosely packed pleomorphic vesicles (F2 profiles), 5.0%; and small terminals that contain densely packed round vesicles (RS profiles), 84.2%. Postembedding immunocytochemistry for gamma-aminobutyric acid (GABA) was used to distinguish the postsynaptic targets as thalamocortical cells or interneurons. The distribution of synaptic contacts on thalamocortical cells was as follows: RL profiles, 2.1%; F1 profiles, 6.9%; F2 profiles, 5.4%; and RS profiles, 85.6%. The distribution of synaptic contacts on interneurons was as follows: RL profiles, 11.8%; F1 profiles, 9.7%; F2 profiles, 2.8%; and RS profiles, 75.6%. These distributions are similar to that found within the dLGN in that the RS inputs (the presumed "modulators") far outnumber the RL inputs (the presumed "drivers"). However, in comparison to the dLGN, the pulvinar nucleus receives significantly fewer numbers of RL, F1, and F2 contacts and significantly higher numbers of RS contacts. Thus, the RS/RL synapse ratio in the pulvinar nucleus is 24:1, in contrast to the 5:1 RS/RL synapse ratio in the dLGN (Van Horn et al., 2000). In first-order nuclei, the lower RS/RL synapse ratio may result in the transfer of visual information that is largely unmodified. In contrast, in higher-order nuclei, the higher RS/RL synapse ratio may allow for a finer modulation of driving inputs.

Synaptic inputs of class III and class V interneurons in the cat pulvinar nucleus: differential integration of RS and RL inputs.

We previously reported that two types of visual thalamic interneurons (class III and class V) could be distinguished by the presence or absence of the enzyme brain nitric oxide synthase (bNOS; Bickford et al., 1999). In the present study, we found that further immunocytochemical characterization can be used to isolate class V and class III neurons: class V neurons express GABA and bNOS but not the calcium binding protein calbindin, whereas class III neurons express GABA and calbindin, but not bNOS. By pairing staining for bNOS or calbindin with staining for GABA, we were able to distinguish class III and class V neurons, thereby allowing us to characterize the synaptic inputs to these two interneuron populations within the cat pulvinar nucleus. We found class III and class V interneurons participate in distinctly different circuitries. Class III cells receive the majority of their input from large terminals with round vesicles (RL profiles, that presumably originate from cortical layer V) while class V cells receive all of their input from small terminals with round vesicles (RS profiles, that presumably originate from cortical layer VI). These two types of interneurons also target different regions of the dendritic arbors of thalamocortical cells; class III cells contact large caliber (presumably proximal) thalamocortical dendrites within glomeruli, while class V cells contact the small caliber (presumably distal) thalamocortical cell dendrites within the extraglomerular neuropil. Thus, a dual inhibitory system exists within the visual thalamus that integrates different types of corticothalamic input and targets distinct regions of thalamocortical cell dendritic arbors.

Thalamic projections of the superior colliculus in the rhesus monkey, Macaca mulatta. A light and electron microscopic study

The projections of the superior colliculus to the thalamus have been studied in the monkey, Macaca mulatta, with anterograde degeneration techniques. The superior colliculus has been shown to project to the inferior nucleus of the pulvinar in a topographical manner with the lower visual field represented dorsomedially and the upper field ventrolaterally. The peripheral zone is located along the medial border and the fovea at the dorsolateral angle adjacent to the lateral geniculate nucleus. The superior colliculus also sends a dense projection to the ipsilateral intralaminar complex, i.e., to the parafascicular, central lateral and paracentral nuclei, and a lesser projection to the same contralateral nuclei. Degenerating tectal fibers were also found in the lateral geniculate nuclei. Four types of vesicle containing profiles were observed in the inferior pulvinar and paracentral nucleus. The large RL and small RS terminals contain round vesicles of uniform size and form asymmetric contacts mainly with large and small dendrites respectively. The F terminal contains a mixture of small round and flat vesicles. It forms symmetric contacts with dendrites and cell somata. The P profile is very pale and contains a relatively sparse population of vesicles showing a great variation in size. It forms symmetric contacts with medium to large dendrites. It is frequently found postsynaptic to the other types, especially the RL terminal, and is regularly seen as the intermediate element of serial and triadic synaptic arrangements. The experimental electron microscopic study has shown that many fibers from the superior colliculus terminate as RL profiles, undergoing direct dense degeneration, in both the inferior pulvinar and the paracentral nucleus. Others probably end as smaller RS terminals.