Aiming to build a complete benchmark for better evaluation of existing ontology systems, we exten... more Aiming to build a complete benchmark for better evaluation of existing ontology systems, we extend the well-known Lehigh University Benchmark in terms of inference and scalability testing. The extended benchmark, named University Ontology Benchmark (UOBM), includes both OWL Lite and OWL DL ontologies covering a complete set of OWL Lite and DL constructs, respectively. We also add necessary properties to construct effective instance links and improve instance generation methods to make the scalability testing more convincing. Several well-known ontology systems are evaluated on the extended benchmark and detailed discussions on both existing ontology systems and future benchmark development are presented.
Reasoning on OWL ontologies is known to be intractable in the worst-case, which is a serious prob... more Reasoning on OWL ontologies is known to be intractable in the worst-case, which is a serious problem because in practice, most OWL ontologies have large Aboxes, i.e., numerous assertions about individuals and their relations. We propose a technique that uses a summary of the ontology (summary Abox) to reduce reasoning to a small subset of the original Abox, and prove that our techniques are sound and complete. We demonstrate the scalability of this technique for consistency detection in 4 ontologies, the largest of which has 6.5 million role assertions.
Adult-onset type II citrullinemia (CTLN2) is characterized by a liver-specific deficiency of argi... more Adult-onset type II citrullinemia (CTLN2) is characterized by a liver-specific deficiency of argininosuccinate synthetase (ASS) protein. We have recently identified the gene responsible for CTLN2, viz., SLC25A13, which encodes a calcium-binding mitochondrial carrier protein, designated citrin, and found five mutations of the SLC25A13 gene in CTLN2 patients. In the present study, we have identified two novel mutations, 1800ins1 and R605X, in SLC25A13 mRNA and the SLC25A13 gene. Diagnostic analysis for the seven mutations in 103 CTLN2 patients diagnosed by biochemical and enzymatic studies has revealed that 102 patients had one or two of the seven mutations and 93 patients were homozygotes or compound heterozygotes. These results indicate that CTLN2 is caused by an abnormality in the SLC25A13 gene, and that our criteria for CTLN2 before DNA diagnosis are correct. Five of 22 patients from consanguineous unions have been shown to be compound heterozygotes, suggesting a high frequency of the mutated genes. The frequency of homozygotes is calculated to be more than 1 in 20,000 from carrier detection (6 in 400 individuals tested) in the Japanese population. We have detected no cross-reactive immune materials in the liver of CTLN2 patients with any of the seven mutations by Western blot analysis with anti-human citrin antibody. From these findings, we hypothesize that CTLN2 is caused by a complete deletion of citrin, although the mechanism of ASS deficiency is still unknown.
Abstract— A 2 × 5 factorial experiment was conducted using practical-type extruded feeds containi... more Abstract— A 2 × 5 factorial experiment was conducted using practical-type extruded feeds containing 20, 24, 28, 32, or 36% crude protein with or without animal protein. The animal protein supplement consisted of 4% menhaden fish meal and 4% meat, bone and blood meal. Channel catfish fingerlings (average size: 26.3 g/fish) were stocked into 50 0.04-ha ponds at a rate of 24,700 fishha. Five ponds were used for each dietary treatment. Fish were fed once daily to satiation for 202 d. There were no differences in feed conversion ratio (FCR), percentage fillet moisture, and survival among treatments. In fish fed diets containing no animal protein, feed consumption, weight gain, and percentage dressout were lower for fish fed the 20% protein diet than those fed diets containing 28% and 32% protein. Fish fed 28, 32, or 36% protein diets without animal protein did not differ in respect to percentage dressout and percentage visceral fat; fish fed the 36% protein diet had higher percentage fillet protein and a lower percentage fillet fat than fish fed other diets with the exception of fish fed the 28% protein diet. In fish fed diets containing animal protein, feed consumption, weight gain, percentage fillet protein and ash, and percentage dressout were lower and visceral fat was higher for fish fed the 20% protein diet than those fed other diets. Fish fed diets containing 24% protein and above with animal protein were not different in respect to weight gain and feed consumption, but fish fed the 24% protein diet had a higher percentage fillet fat than fish fed a 32% or 36% protein diet. Fish fed the 32% protein diet had a lower visceral fat. Considering animal protein vs non-animal protein with the data pooled across all diets without regard to dietary protein level, weight gain and FCR of fish fed diets containing animal protein were higher than those fed diets containing no animal protein. However, weight gain of fish fed diets containing 20, 28, or 32% protein with or without animal protein did not differ. Dressout percentage and fillet protein were higher and fillet fat was lower for fish fed diets containing no animal protein than those fed diets containing animal protein. Data from this study indicated that animal protein may not be a necessary dietary ingredient for fish fed 28% or 32% protein diets typically used for grow out of pond-raised channel catfish under satiation feeding conditions. Whether animal protein should be included in catfish diets containing less than 28% protein is unclear, since fish fed the 24% protein diet benefited from animal protein but those fed the 20% protein diet did not benefit from animal protein. Additional studies to provide more information on low-protein, all-plant diets are currently being conducted.
The CBP protein (cAMP response element binding protein (CREB) binding protein) is a co-activator ... more The CBP protein (cAMP response element binding protein (CREB) binding protein) is a co-activator for several transcription factors with a wide range of important biological functions, such as sterol regulatory element binding proteins (SREBPs), CCAAT/enhancer-binding proteins (C/EBPs), nuclear receptors (including peroxisome proliferator-activated receptors, PPARs), and signal transducers and activators of transcription (STATs). In contrast to these individual transcription factors, the biological roles of CBP are poorly understood. CBP enhances transcriptional activities via histone acetylation and the recruitment of additional co-activators such as SRC (steroid coactivator)-1 (ref. 9). To identify its physiological functions using a loss-of-function mutant, we analyzed CBP-deficient mice. As Crebbp null mice (Crebbp-/-) died during embryogenesis, we used Crebbp+/- mice. Unexpectedly, Crebbp+/- mice showed markedly reduced weight of white adipose tissue (WAT) but not of other tissues. Despite this lipodystrophy, Crebbp+/- mice showed increased insulin sensitivity and glucose tolerance and were completely protected from body weight gain induced by a high-fat (HF) diet. We observed increased leptin sensitivity and increased serum adiponectin levels in Crebbp+/- mice. These increased effects of insulin-sensitizing hormones secreted from WAT may explain, at least in part, the phenotypes of Crebbp+/- mice. This study demonstrates that CBP may function as a 'master-switch' between energy storage and expenditure.
The motility of gastrointestinal tract is regulated by classical neurotransmitters, neuropeptides... more The motility of gastrointestinal tract is regulated by classical neurotransmitters, neuropeptides, and humoral agents. Two novel human cDNAs have been cloned based on their sequence similarity to a frog skin secretion protein, Bv8, and a nontoxic protein of mamba snake venom. These human cDNAs encode two secreted proteins of 86 and 81 amino acids. Northern blot hybridization has revealed that these cDNAs are expressed in gastrointestinal tract, particularly the stomach. Recombinant proteins with authentic N-terminal sequences have been produced in Escherichia coli and refolded into functional proteins by careful control of protein aggregation. Mass spectrometry has confirmed the formation of five pairs of disulfide bonds. The refolded recombinant proteins potently contract gastrointestinal smooth muscle with EC(50) values in the subnanomolar range. The contractile effects of the recombinant proteins are specific for gastrointestinal smooth muscle, because they have no effect on vascular or respiratory smooth muscle. To reflect their potent and specific effects on gastrointestinal smooth muscle cells, we have named these recombinant proteins prokineticins. Ligand binding studies with iodinated prokineticin revealed the presence of a high-affinity site in ileal smooth muscle. The displacement of specific binding by GTP gamma S suggests that the prokineticin receptor may belong to the family of G protein-coupled receptors. Experiments with verapamil and nifedipine revealed that calcium influx is essential for the contractile activity of prokineticins on gastrointestinal smooth muscle. In summary, we have identified two novel endogenous regulators of gastrointestinal motility. The availability of recombinant prokineticins should provide novel therapeutic agents for disorders involving impaired gastrointestinal motility.
Plant protein sources were evaluated in 32% protein grow-out feeds for channel catfish (initial w... more Plant protein sources were evaluated in 32% protein grow-out feeds for channel catfish (initial weight: 180 g/fish) stocked at high densities (24,700 fish/ha) in 0.04 ha earthen ponds. Each of the eight practical-type feeds was assigned for five replicate ponds. The fish were fed to satiation once daily for 170 d. Specifically, cottonseed meal and cottonseed meal plus supplemental lysine were evaluated as replacements for soybean meal. Soybean meal, a combination of soybean meal and cottonseed meal, or a combination of soybean meal and cottonseed meal plus supplemental lysine were evaluated as a substitute for animal protein sources. Based on weight pin, feed conversion ratio, body composition, percentage visceral fat, and dressed yield, the data indicated that cottonseed meal plus lysine can be used as a total substitute for soybean meal in catfish feeds. However, it is not recommended that more than 30% cottonseed meal be used in catfish feeds until additional data are available on the effects of gossypol on reproduction in catfish. Also, data indicated that plant proteins can be used as a total replacement for animal protein without detrimental effects. Reduced weight gain was observed in fish fed a feed that contained 68% of the established available lysine requirement. However, fish fed feeds estimated to contain only 76 or 82% of the available lysine requirement did not show reduced weight gain. This suggests that lysine may be more highly available from cottonseed meal than previously estimated, or that natural food organisms in the pond contributed nutrients including lysine, or that fish were able to consume enough of the marginally deficient feeds to meet their requirement for lysine. This study was conducted with large catfish fed a 32% protein feed to satiation once daily. If smaller fish, a lower protein fed, or a restricted feeding regimen had been used, the results may have been different.
This paper deals with the conceptual design and optimal dimensional synthesis of a novel 2-DOF tr... more This paper deals with the conceptual design and optimal dimensional synthesis of a novel 2-DOF translational parallel robot for pick-and-place operations. In a conceptual design phase, the conditions for generating such kinds of parallel robots are investigated, ...
Aiming to build a complete benchmark for better evaluation of existing ontology systems, we exten... more Aiming to build a complete benchmark for better evaluation of existing ontology systems, we extend the well-known Lehigh University Benchmark in terms of inference and scalability testing. The extended benchmark, named University Ontology Benchmark (UOBM), includes both OWL Lite and OWL DL ontologies covering a complete set of OWL Lite and DL constructs, respectively. We also add necessary properties to construct effective instance links and improve instance generation methods to make the scalability testing more convincing. Several well-known ontology systems are evaluated on the extended benchmark and detailed discussions on both existing ontology systems and future benchmark development are presented.
Reasoning on OWL ontologies is known to be intractable in the worst-case, which is a serious prob... more Reasoning on OWL ontologies is known to be intractable in the worst-case, which is a serious problem because in practice, most OWL ontologies have large Aboxes, i.e., numerous assertions about individuals and their relations. We propose a technique that uses a summary of the ontology (summary Abox) to reduce reasoning to a small subset of the original Abox, and prove that our techniques are sound and complete. We demonstrate the scalability of this technique for consistency detection in 4 ontologies, the largest of which has 6.5 million role assertions.
Adult-onset type II citrullinemia (CTLN2) is characterized by a liver-specific deficiency of argi... more Adult-onset type II citrullinemia (CTLN2) is characterized by a liver-specific deficiency of argininosuccinate synthetase (ASS) protein. We have recently identified the gene responsible for CTLN2, viz., SLC25A13, which encodes a calcium-binding mitochondrial carrier protein, designated citrin, and found five mutations of the SLC25A13 gene in CTLN2 patients. In the present study, we have identified two novel mutations, 1800ins1 and R605X, in SLC25A13 mRNA and the SLC25A13 gene. Diagnostic analysis for the seven mutations in 103 CTLN2 patients diagnosed by biochemical and enzymatic studies has revealed that 102 patients had one or two of the seven mutations and 93 patients were homozygotes or compound heterozygotes. These results indicate that CTLN2 is caused by an abnormality in the SLC25A13 gene, and that our criteria for CTLN2 before DNA diagnosis are correct. Five of 22 patients from consanguineous unions have been shown to be compound heterozygotes, suggesting a high frequency of the mutated genes. The frequency of homozygotes is calculated to be more than 1 in 20,000 from carrier detection (6 in 400 individuals tested) in the Japanese population. We have detected no cross-reactive immune materials in the liver of CTLN2 patients with any of the seven mutations by Western blot analysis with anti-human citrin antibody. From these findings, we hypothesize that CTLN2 is caused by a complete deletion of citrin, although the mechanism of ASS deficiency is still unknown.
Abstract— A 2 × 5 factorial experiment was conducted using practical-type extruded feeds containi... more Abstract— A 2 × 5 factorial experiment was conducted using practical-type extruded feeds containing 20, 24, 28, 32, or 36% crude protein with or without animal protein. The animal protein supplement consisted of 4% menhaden fish meal and 4% meat, bone and blood meal. Channel catfish fingerlings (average size: 26.3 g/fish) were stocked into 50 0.04-ha ponds at a rate of 24,700 fishha. Five ponds were used for each dietary treatment. Fish were fed once daily to satiation for 202 d. There were no differences in feed conversion ratio (FCR), percentage fillet moisture, and survival among treatments. In fish fed diets containing no animal protein, feed consumption, weight gain, and percentage dressout were lower for fish fed the 20% protein diet than those fed diets containing 28% and 32% protein. Fish fed 28, 32, or 36% protein diets without animal protein did not differ in respect to percentage dressout and percentage visceral fat; fish fed the 36% protein diet had higher percentage fillet protein and a lower percentage fillet fat than fish fed other diets with the exception of fish fed the 28% protein diet. In fish fed diets containing animal protein, feed consumption, weight gain, percentage fillet protein and ash, and percentage dressout were lower and visceral fat was higher for fish fed the 20% protein diet than those fed other diets. Fish fed diets containing 24% protein and above with animal protein were not different in respect to weight gain and feed consumption, but fish fed the 24% protein diet had a higher percentage fillet fat than fish fed a 32% or 36% protein diet. Fish fed the 32% protein diet had a lower visceral fat. Considering animal protein vs non-animal protein with the data pooled across all diets without regard to dietary protein level, weight gain and FCR of fish fed diets containing animal protein were higher than those fed diets containing no animal protein. However, weight gain of fish fed diets containing 20, 28, or 32% protein with or without animal protein did not differ. Dressout percentage and fillet protein were higher and fillet fat was lower for fish fed diets containing no animal protein than those fed diets containing animal protein. Data from this study indicated that animal protein may not be a necessary dietary ingredient for fish fed 28% or 32% protein diets typically used for grow out of pond-raised channel catfish under satiation feeding conditions. Whether animal protein should be included in catfish diets containing less than 28% protein is unclear, since fish fed the 24% protein diet benefited from animal protein but those fed the 20% protein diet did not benefit from animal protein. Additional studies to provide more information on low-protein, all-plant diets are currently being conducted.
The CBP protein (cAMP response element binding protein (CREB) binding protein) is a co-activator ... more The CBP protein (cAMP response element binding protein (CREB) binding protein) is a co-activator for several transcription factors with a wide range of important biological functions, such as sterol regulatory element binding proteins (SREBPs), CCAAT/enhancer-binding proteins (C/EBPs), nuclear receptors (including peroxisome proliferator-activated receptors, PPARs), and signal transducers and activators of transcription (STATs). In contrast to these individual transcription factors, the biological roles of CBP are poorly understood. CBP enhances transcriptional activities via histone acetylation and the recruitment of additional co-activators such as SRC (steroid coactivator)-1 (ref. 9). To identify its physiological functions using a loss-of-function mutant, we analyzed CBP-deficient mice. As Crebbp null mice (Crebbp-/-) died during embryogenesis, we used Crebbp+/- mice. Unexpectedly, Crebbp+/- mice showed markedly reduced weight of white adipose tissue (WAT) but not of other tissues. Despite this lipodystrophy, Crebbp+/- mice showed increased insulin sensitivity and glucose tolerance and were completely protected from body weight gain induced by a high-fat (HF) diet. We observed increased leptin sensitivity and increased serum adiponectin levels in Crebbp+/- mice. These increased effects of insulin-sensitizing hormones secreted from WAT may explain, at least in part, the phenotypes of Crebbp+/- mice. This study demonstrates that CBP may function as a 'master-switch' between energy storage and expenditure.
The motility of gastrointestinal tract is regulated by classical neurotransmitters, neuropeptides... more The motility of gastrointestinal tract is regulated by classical neurotransmitters, neuropeptides, and humoral agents. Two novel human cDNAs have been cloned based on their sequence similarity to a frog skin secretion protein, Bv8, and a nontoxic protein of mamba snake venom. These human cDNAs encode two secreted proteins of 86 and 81 amino acids. Northern blot hybridization has revealed that these cDNAs are expressed in gastrointestinal tract, particularly the stomach. Recombinant proteins with authentic N-terminal sequences have been produced in Escherichia coli and refolded into functional proteins by careful control of protein aggregation. Mass spectrometry has confirmed the formation of five pairs of disulfide bonds. The refolded recombinant proteins potently contract gastrointestinal smooth muscle with EC(50) values in the subnanomolar range. The contractile effects of the recombinant proteins are specific for gastrointestinal smooth muscle, because they have no effect on vascular or respiratory smooth muscle. To reflect their potent and specific effects on gastrointestinal smooth muscle cells, we have named these recombinant proteins prokineticins. Ligand binding studies with iodinated prokineticin revealed the presence of a high-affinity site in ileal smooth muscle. The displacement of specific binding by GTP gamma S suggests that the prokineticin receptor may belong to the family of G protein-coupled receptors. Experiments with verapamil and nifedipine revealed that calcium influx is essential for the contractile activity of prokineticins on gastrointestinal smooth muscle. In summary, we have identified two novel endogenous regulators of gastrointestinal motility. The availability of recombinant prokineticins should provide novel therapeutic agents for disorders involving impaired gastrointestinal motility.
Plant protein sources were evaluated in 32% protein grow-out feeds for channel catfish (initial w... more Plant protein sources were evaluated in 32% protein grow-out feeds for channel catfish (initial weight: 180 g/fish) stocked at high densities (24,700 fish/ha) in 0.04 ha earthen ponds. Each of the eight practical-type feeds was assigned for five replicate ponds. The fish were fed to satiation once daily for 170 d. Specifically, cottonseed meal and cottonseed meal plus supplemental lysine were evaluated as replacements for soybean meal. Soybean meal, a combination of soybean meal and cottonseed meal, or a combination of soybean meal and cottonseed meal plus supplemental lysine were evaluated as a substitute for animal protein sources. Based on weight pin, feed conversion ratio, body composition, percentage visceral fat, and dressed yield, the data indicated that cottonseed meal plus lysine can be used as a total substitute for soybean meal in catfish feeds. However, it is not recommended that more than 30% cottonseed meal be used in catfish feeds until additional data are available on the effects of gossypol on reproduction in catfish. Also, data indicated that plant proteins can be used as a total replacement for animal protein without detrimental effects. Reduced weight gain was observed in fish fed a feed that contained 68% of the established available lysine requirement. However, fish fed feeds estimated to contain only 76 or 82% of the available lysine requirement did not show reduced weight gain. This suggests that lysine may be more highly available from cottonseed meal than previously estimated, or that natural food organisms in the pond contributed nutrients including lysine, or that fish were able to consume enough of the marginally deficient feeds to meet their requirement for lysine. This study was conducted with large catfish fed a 32% protein feed to satiation once daily. If smaller fish, a lower protein fed, or a restricted feeding regimen had been used, the results may have been different.
This paper deals with the conceptual design and optimal dimensional synthesis of a novel 2-DOF tr... more This paper deals with the conceptual design and optimal dimensional synthesis of a novel 2-DOF translational parallel robot for pick-and-place operations. In a conceptual design phase, the conditions for generating such kinds of parallel robots are investigated, ...
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