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Papers by Keiichi Oyamada
Journal of the Japan Association for Philosophy of Science
Annals of the Japan Association For Philosophy of Science, Mar 25, 2007
Concepts can be arranged in a taxonomical order by means of a partial ordering relation, and a ta... more Concepts can be arranged in a taxonomical order by means of a partial ordering relation, and a taxonomical structure of concepts is usually supposed to have a linkage to reality. However, here is a logico-ontological jump of significant theoretical importance: a taxonomical structure of concepts does not include in itself any logical ability to relate concepts to objects. That is to say, a mere arrangement of concepts does not logically require at all of any linkage between concepts and reality. There can logically be no direct jump from concepts to reality. The partial ordering relation required to describe a conceptual taxonomy is in close logical relation to the particle known historically as copula in syllogistic systems. By and large the copula corresponds to the relation IS-A that is today widely used in describing a conceptual taxonomy. We use the symbol '•¼' for IS-A relation. Another relation that relates concepts to objects often called today 'an-instance-of relation' will be introduced by definition. This relation will be expressed by the symbol 'ƒÃ'. To define this relation we shall use the functor of (non-reflexive) identity to which we assign the symbol '='. We aim in this paper to construct a logical system that is appropriate to describing the logical relations between a taxonomy of concepts and reality, which is tantamount to constructing a version of logical Ontology (first constructed by Lesniewski in 1920) on the basis of two primitive functors, i.e. •¼ and =.
Proteomics, 2005
Protein ubiquitylation contributes to the regulation of many cellular processes including protein... more Protein ubiquitylation contributes to the regulation of many cellular processes including protein degradation, receptor internalization, and repair of DNA damage. We now present a comprehensive characterization of ubiquitin-conjugated and ubiquitin-associated proteins in human cells. The proteins were purified by immunoaffinity chromatography under denaturing or native conditions. They were then digested with trypsin, and the resulting peptides were analyzed by 2-D LC and MS/MS. A total of 670 distinct proteins were identified; 345 proteins (51%) were classified as Urp-D (ubiquitin-related proteome under the denaturing condition) and comprised ubiquitin-conjugated molecules, whereas 325 proteins (49%) were classified as Urp-N (ubiquitin-related proteome only under the native condition) and included molecules that associated with ubiquitylated proteins. The proportions of proteins in various functional categories differed substantially between Urp-D and Urp-N. Many ribosomal subunits were detected in the Urp-D group of proteins and several of these subunits were directly shown to be ubiquitylated by mass spectrometric analysis, suggesting that ubiquitylation might play an important role in the regulation and/or quality control of ribosomal proteins. Our results demonstrate the potential of proteomics analysis of protein ubiquitylation to provide important insight into the regulation of protein stability and other ubiquitin-related cellular functions.
Journal of the Japan Association for Philosophy of Science
Annals of the Japan Association For Philosophy of Science, Mar 25, 2007
Concepts can be arranged in a taxonomical order by means of a partial ordering relation, and a ta... more Concepts can be arranged in a taxonomical order by means of a partial ordering relation, and a taxonomical structure of concepts is usually supposed to have a linkage to reality. However, here is a logico-ontological jump of significant theoretical importance: a taxonomical structure of concepts does not include in itself any logical ability to relate concepts to objects. That is to say, a mere arrangement of concepts does not logically require at all of any linkage between concepts and reality. There can logically be no direct jump from concepts to reality. The partial ordering relation required to describe a conceptual taxonomy is in close logical relation to the particle known historically as copula in syllogistic systems. By and large the copula corresponds to the relation IS-A that is today widely used in describing a conceptual taxonomy. We use the symbol '•¼' for IS-A relation. Another relation that relates concepts to objects often called today 'an-instance-of relation' will be introduced by definition. This relation will be expressed by the symbol 'ƒÃ'. To define this relation we shall use the functor of (non-reflexive) identity to which we assign the symbol '='. We aim in this paper to construct a logical system that is appropriate to describing the logical relations between a taxonomy of concepts and reality, which is tantamount to constructing a version of logical Ontology (first constructed by Lesniewski in 1920) on the basis of two primitive functors, i.e. •¼ and =.
Proteomics, 2005
Protein ubiquitylation contributes to the regulation of many cellular processes including protein... more Protein ubiquitylation contributes to the regulation of many cellular processes including protein degradation, receptor internalization, and repair of DNA damage. We now present a comprehensive characterization of ubiquitin-conjugated and ubiquitin-associated proteins in human cells. The proteins were purified by immunoaffinity chromatography under denaturing or native conditions. They were then digested with trypsin, and the resulting peptides were analyzed by 2-D LC and MS/MS. A total of 670 distinct proteins were identified; 345 proteins (51%) were classified as Urp-D (ubiquitin-related proteome under the denaturing condition) and comprised ubiquitin-conjugated molecules, whereas 325 proteins (49%) were classified as Urp-N (ubiquitin-related proteome only under the native condition) and included molecules that associated with ubiquitylated proteins. The proportions of proteins in various functional categories differed substantially between Urp-D and Urp-N. Many ribosomal subunits were detected in the Urp-D group of proteins and several of these subunits were directly shown to be ubiquitylated by mass spectrometric analysis, suggesting that ubiquitylation might play an important role in the regulation and/or quality control of ribosomal proteins. Our results demonstrate the potential of proteomics analysis of protein ubiquitylation to provide important insight into the regulation of protein stability and other ubiquitin-related cellular functions.