29 results on '"Thomas Bittner"'
Search Results
2. Assessing the effect of topography on Cs-137 concentrations within forested soils due to the Fukushima Daiichi Nuclear Power Plant accident, Japan
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Taku Nishimura, Sean J. Bennett, Jared Aldstadt, Thomas Bittner, and Misa Yasumiishi
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010504 meteorology & atmospheric sciences ,business.industry ,Elevation ,QE500-639.5 ,Soil science ,010501 environmental sciences ,Nuclear power ,01 natural sciences ,Bulk density ,law.invention ,Plume ,Dynamic and structural geology ,Geophysics ,law ,Nuclear power plant ,Soil water ,Environmental science ,business ,Digital elevation model ,Water content ,0105 earth and related environmental sciences ,Earth-Surface Processes - Abstract
Topographic effects on Cs-137 concentrations in a forested area were quantitatively examined using 58 soil core samples collected in a village in Fukushima, Japan, which was directly impacted by the radioactive plume emitted during the 2011 Fukushima Daiichi Nuclear Power Plant (FDNPP) accident. In this study, five topographic parameters and two soil properties were evaluated as controls on the soil Cs-137 concentration using generalized additive models (GAMs), a flexible statistical method for evaluating the functional dependencies of multiple parameters. GAMs employing soil dry bulk density, mass water content, and elevation explained 54 % of the observed concentrations of Cs-137 within this landscape, whereas GAMs employing elevation, slope, and upslope distance explained 47 % of the observed concentrations, which provide strong evidence of topographic effects on Cs-137 concentrations in soils. The model fit analysis confirmed that the topographic effects are strongest when multiple topographic parameters and soil properties are included. The ability of each topographic feature to predict Cs-137 concentrations was influenced by the resolution of the digital elevation models. The movement of Cs-137 into the subsurface in this area near Fukushima was faster in comparison to regions affected by the Chernobyl Nuclear Power Plant accident. These results suggest that the effects of topographic parameters should be considered carefully in the use of anthropogenic radionuclides as environmental tracers and in the assessment of current and future environmental risks due to nuclear power plant accidents.
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- 2021
3. The effects of topography and soil properties on radiocesium concentrations in forest soils in Fukushima, Japan
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Sean J. Bennett, Thomas Bittner, Misa Yasumiishi, Jared Aldstadt, and Taku Nishimura
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Fukushima daiichi ,Physical model ,Soil test ,Soil water ,Environmental science ,Soil science ,Soil properties ,Contamination ,Bulk density ,Vegetation cover - Abstract
This research collected forest soil samples from Fukushima, Japan, where the 2011 Fukushima Daiichi Nuclear Power Plant (FDNPP) accident contaminated the land. The purpose of this study was to examine how the local topography influenced the radiocesium (Cs-137) accumulation patterns in soils over the years since the accident. As an analytical method, the general additive model (GAM) was used to determine at what percentages the topographic parameters explain Cs-137 contamination levels down to a depth of 30 cm. For comparison, topographic parameters were extracted from both 1 m and 10 m digital evaluation models (DEMs). The effects of topography were compared with the effects of the soil water content and dry soil bulk density. An additional Tukey’s honestly significant difference (HSD) test was conducted to determine the significance of the hillslope aspect and vegetation cover differences on concentration predictions. The results showed that, at this study site, topographic parameters extracted from the 10 m DEM better predicted Cs-137 levels. The models with a single topographic parameter did not explain Cs-137 levels higher than 30 %. However, combining the parameters improved the explanation percentages. The relative influences of topographic parameters and soil properties were similar throughout the soil depth, showing their subsurface co-functionalities for Cs-137 concentration levels. Tukey’s HSD test results showed the inter-effects of topography and vegetation cover differences. The results of this study indicate that the selection of topographic parameters, as well as the chosen methods of their extractions, have implications for physical models assessing radionuclide contamination levels.
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- 2020
4. Vague distance predicates
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Thomas Bittner
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0301 basic medicine ,business.industry ,Theory ,Object language ,Geography, Planning and Development ,Axiomatic system ,Context (language use) ,Vagueness ,Semantic property ,computer.software_genre ,03 medical and health sciences ,030104 developmental biology ,Formal ontology ,Logical conjunction ,Computer Science::Logic in Computer Science ,Computer Science::Programming Languages ,Data mining ,Artificial intelligence ,business ,computer ,Natural language processing ,Information Systems ,Mathematics - Abstract
A formal theory of vague distance predicates is presented which combines a crisp region-based geometry with a theory of vague size predicates in a supervaluation-based formal framework. In the object language of the axiomatic theory, logical and semantic properties of vague distance predicates that are context- and domain-independent are formalized. Context and domain-dependent aspects are addressed in the meta-language of the theory by incorporating context- and domain-specific restrictions on the canonical interpretations. This allows to relate the ontological and qualitative analysis in the object language to numeric values as they are commonly used in scientific discourses.
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- 2016
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5. Why Classificatory Information of Geographic Regions Is Quantum Information (Vision Paper)
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Thomas Bittner, Bittner, Thomas, Thomas Bittner, and Bittner, Thomas
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This paper gives an information - theoretic argument in support of the claim that there is geographic quantum information. Quantum information is information in the sense of Shannon’s information theory, that, in addition, satisfies two characteristic postulates. The paper aims to show that if the density of information (bits per unit of space) that is possible for classificatory geographic qualities is limited, then it follows that the two characteristic postulates of quantum information are satisfied for information about those geographic qualities.
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- 2019
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6. A spatio-temporal ontology for geographic information integration
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Thomas Bittner, Maureen Donnelly, and Barry Smith
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Theoretical computer science ,Relation (database) ,Geography, Planning and Development ,Ontology ,Information processing ,Axiomatic system ,Library and Information Sciences ,Mathematical proof ,Problem of universals ,Axiom ,Information Systems ,Information integration ,Mathematics - Abstract
This paper presents an axiomatic formalization of a theory of top-level relations between three categories of entities: individuals, universals, and collections. We deal with a variety of relations between entities in these categories, including the sub-universal relation among universals and the parthood relation among individuals, as well as cross-categorial relations such as instantiation and membership. We show that an adequate understanding of the formal properties of such relations-in particular their behavior with respect to time-is critical for geographic information processing. The axiomatic theory is developed using Isabelle, a computational system for implementing logical formalisms. All proofs are computer verified and the computational representation of the theory is available online.
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- 2009
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7. Punishment for Criminal Attempts: A Legal Perspective on the Problem of Moral Luck
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Thomas Bittner
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Philosophy ,Contemporary philosophy ,Moral luck ,Moral philosophy ,General interest ,Luck ,Punishment ,media_common.quotation_subject ,Perspective (graphical) ,Sociology ,Criminology ,media_common - Abstract
In the criminal law, the law of attempts is of comparatively recent vintage. It is part of an important contemporary legal trend towards early intervention in the criminal process. There are now a substantial number of crimes on the books that, like the crime of attempt, only require that the perpetrator start down the road to carrying out his criminal intentions and do not require him actually to have harmed (or, in some cases, even identified) his victim. Besides the law of attempts, these new crimes include conspiracy and solicitation, forgery and counterfeiting, the possession offences (drugs, burglary tools, counterfeit money, automobile master keys, etc.), even corruption of youth (children). In all these cases, the law is stepping in to forestall harm, rather than waiting until a harm has already happened.
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- 2008
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8. Summation relations and portions of stuff
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Thomas Bittner and Maureen Donnelly
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Philosophy of mind ,Philosophy of language ,Philosophy ,Modal ,Metaphysics ,Composition (combinatorics) ,Mereology ,Epistemology - Abstract
According to the prevalent 'sum view' of stuffs, each portion of stuff is a mereological sum of its subportions. The purpose of this paper is to re-examine the sum view in the light of a modal temporal mereology which distinguishes between different varieties of summation relations. While admitting David Barnett's recent counter-example to the sum view (Barnett, Philos Rev 113:89-100, 2004), we show that there is nonetheless an important sense in which all portions of stuff are sums of their subportions. We use our summation relations to develop, as an alternative to the sum view, an analysis of stuffs that distinguishes between the ways in which different sorts of stuffs are sums of their subportions.
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- 2008
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9. Funktions- und Risikoanalyse
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Thomas Bittner
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Die Vergleichbarkeitsanalyse ist ein zentraler Teil jeder Verrechnungspreisanalyse, denn in jeder Verrechnungspreisanalyse wird die Fremdublichkeit eines konzerninternen Verrechnungspreises durch einen Vergleich mit Markttransaktionen gepruft. Fur einen Vergleich sind jedoch die relevanten Vergleichskriterien zu definieren und dann auf die entsprechende Transaktion anzuwenden.
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- 2016
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10. Two homolog wheat Glycogen Synthase Kinase 3/SHAGGY--like kinases are involved in brassinosteroid signaling
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Thomas, Bittner, Sabine, Nadler, Eija, Schulze, and Christiane, Fischer-Iglesias
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GSK-3/SHAGGY-like kinases ,Sequence Homology, Amino Acid ,Arabidopsis Proteins ,Arabidopsis ,Triticum aestivum ,Aminopyridines ,Succinates ,Triazoles ,Embryonic patterning ,Plants, Genetically Modified ,Glycogen Synthase Kinase 3 ,Phenotype ,Gene Expression Regulation, Plant ,Seedlings ,Brassinosteroids ,Mutation ,Seedling growth response ,Triticum ,Plant Proteins ,Signal Transduction ,Research Article - Abstract
Background Glycogen Synthase Kinase 3/SHAGGY-like kinases (GSKs) are multifunctional non-receptor ser/thr kinases. Plant GSKs are involved in hormonal signaling networks and are required for growth, development, light as well as stress responses. So far, most studies have been carried out on Arabidopsis or on other eudicotyledon GSKs. Here, we evaluated the role of TaSK1 and TaSK2, two homolog wheat (Triticum aestivum) GSKs, in brassinosteroid signaling. We explored in addition the physiological effects of brassinosteroids on wheat growth and development. Results A bin2-1 like gain-of-function mutation has been inserted respectively in one of the homoeologous gene copies of TaSK1 (TaSK1-A.2-1) and in one of the homoeologous gene copies of TaSK2 (TaSK2-A.2-1). Arabidopsis plants were transformed with these mutated gene copies. Severe dwarf phenotypes were obtained closely resembling those of Arabidopsis bin2-1 lines and Arabidopsis BR-deficient or BR-signaling mutants. Expression of BR downstream genes, SAUR-AC1, CPD and BAS1 was deregulated in TaSK1.2-1 and TaSK2.2-1 transgenic lines. Severe dwarf lines were partially rescued by Bikinin beforehand shown to inhibit TaSK kinase activity. This rescue was accompanied with changes in BR downstream gene expression levels. Wheat embryos and seedlings were treated with compounds interfering with BR signaling or modifying BR levels to gain insight into the role of brassinosteroids in wheat development. Embryonic axis and scutellum differentiation were impaired, and seedling growth responses were affected when embryos were treated with Epibrassinolides, Propiconazole, and Bikinin. Conclusions In view of our findings, TaSKs are proposed to be involved in BR signaling and to be orthologous of Arabidopsis Clade II GSK3/SHAGGY-like kinases. Observed effects of Epibrassinolide, Propiconazole and Bikinin treatments on wheat embryos and seedlings indicate a role for BR signaling in embryonic patterning and seedling growth. Electronic supplementary material The online version of this article (doi:10.1186/s12870-015-0617-z) contains supplementary material, which is available to authorized users.
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- 2015
11. Ontological Investigation of a Multiscale Ecosystem Classification Using the 'National Hierarchical Framework of Ecological Units' as an Example
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Chris S. Renschler, Thomas Bittner, and Alexandre Sorokine
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Set (abstract data type) ,Earth surface ,Predicate logic ,Data processing ,Ecosystem classification ,Geography ,Relation (database) ,Ecology ,Geography, Planning and Development ,Interoperability ,Axiom ,Information Systems - Abstract
This paper presents a formalized ontological framework for the analysis of multiscale classifications of geographic objects. We propose a set of logical principles that guide such geographic classifications. These principles are represented as definitions and axioms of the first-order predicate logic. Then we demonstrate an application of these principles with a practical example of the "National Hierarchical Framework of Ecological Units." The study presents a minimal set of entities and relation need for such formalizations and emphasizes the need to distinguish clearly between classes of ecosystems and ecosystems-individuals physically located on the Earth surface. The ontological framework proposed in the paper has the potential to be used to facilitate interoperability between such geographic classifications.
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- 2006
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12. A formal theory for spatial representation and reasoning in biomedical ontologies
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Thomas Bittner, Cornelius Rosse, and Maureen Donnelly
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Informatics ,Theoretical computer science ,Knowledge representation and reasoning ,Logic ,Computer science ,Theory ,business.industry ,Foundational Model of Anatomy ,Computational Biology ,Medicine (miscellaneous) ,Spatial intelligence ,Ontology (information science) ,computer.software_genre ,Open Biomedical Ontologies ,Spatial relation ,Vocabulary, Controlled ,Artificial Intelligence ,Humans ,Artificial intelligence ,Anatomy ,business ,computer ,Natural language processing ,Mereology - Abstract
Objective: The objective of this paper is to demonstrate how a formal spatial theory can be used as an important tool for disambiguating the spatial information embodied in biomedical ontologies and for enhancing their automatic reasoning capabilities. Method and materials: This paper presents a formal theory of parthood and location relations among individuals, called Basic Inclusion Theory (BIT). Since biomedical ontologies are comprised of assertions about classes of individuals (rather than assertions about individuals), we define parthood and location relations among classes in the extended theory Basic Inclusion Theory for Classes (BIT+Cl). We then demonstrate the usefulness of this formal theory for making the logical structure of spatial information more precise in two ontologies concerned with human anatomy: the Foundational Model of Anatomy (FMA) and GALEN. Results: We find that in both the FMA and GALEN, class-level spatial relations with different logical properties are not always explicitly distinguished. As a result, the spatial information included in these biomedical ontologies is often ambiguous and the possibilities for implementing consistent automatic reasoning within or across ontologies are limited. Conclusion: Precise formal characterizations of all spatial relations assumed by a biomedical ontology are necessary to ensure that the information embodied in the ontology can be fully and coherently utilized in a computational environment. This paper can be seen as an important beginning step toward achieving this goal, but much more work along these lines is required.
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- 2006
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13. Towards a Quantum Theory of Geographic Fields
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Thomas Bittner, Bittner, Thomas, Thomas Bittner, and Bittner, Thomas
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This paper proposes a framework that that allows for the possibility that multiple classically incompatible states are expressed simultaneously at a given point of a geographic field. The admission of such superposition states provides the basis for a new understanding of indeterminacy and ontological vagueness in the geographic world.
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- 2017
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14. An event study of the Rhenish-Westphalian Coal Syndicate
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Thomas Bittner
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History ,business.industry ,Economics, Econometrics and Finance (miscellaneous) ,Cartel ,Event study ,Risk–return spectrum ,Syndicate ,Westphalian sovereignty ,language.human_language ,German ,Market economy ,Economics ,language ,Coal ,business ,Economic consequences - Abstract
This article applies event-study methodology to explore the economic consequences of cartelisation in Imperial Germany. By combining qualitative and quantitative sources it discusses the risk and return effects of the establishment of the allegedly most powerful cartel, the Rhenish-Westphalian Coal Syndicate (RWKS). Its findings cast doubts on the importance of the RWKS for the development of the German coal industry. The cartel did not affect the major part of a typical mine's risk-the firm-specific risk – and its moderate return effects were mostly confined to larger mines. Cartelisation did not seem to be an important pillar of ‘organised capitalism’.
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- 2005
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15. A MEREOLOGICAL THEORY OF FRAMES OF REFERENCE
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Thomas Bittner
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Theoretical computer science ,Artificial Intelligence ,Computer science ,Semantics (computer science) ,Metric (mathematics) ,Hierarchical organization ,Vagueness ,Rough set ,Granularity ,Algorithm ,Frame of reference ,Mereology - Abstract
In this paper a mereological theory of frames of reference is presented. It shows that mereology extended by the notion of granularity and approximation is sufficient to provide a theory for location based features of frames of reference. More complex theories, taking also into account orientation and metric properties can be built as extensions of the presented theory. In order to take the hierarchical organization of frames of reference into account we introduce the notion of stratified approximation to facilitate transformations between different levels of granularity. This paper shows that the ontological grounding of the theory of frames of reference into mereology allows us to give a clear semantics to the notion 'degree of parthood' which is central to the notion of approximation. It also shows how epistemic aspects which affect the use of frames of reference help us to understand the feature of epistemic vagueness and the way it affects the notions of approximation and of degree of parthood.
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- 2004
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16. [Untitled]
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Thomas Bittner and John G. Stell
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Theoretical computer science ,Geographic information system ,business.industry ,Geography, Planning and Development ,Vagueness ,Ontology (information science) ,Formal methods ,Indeterminacy (literature) ,Formal ontology ,Intersection ,Artificial intelligence ,Representation (mathematics) ,business ,Information Systems ,Mathematics - Abstract
This paper deals with the representation and the processing of information about spatial objects with indeterminate location like valleys or dunes (objects subject to vagueness). The indeterminacy of the location of spatial objects is caused by the vagueness of the unity condition provided by the underlying human concepts valley and dune. We propose the notion of rough, i.e., approximate, location for representing and processing information about indeterminate location of objects subject to vagueness. We provide an analysis of the relationships between vagueness of concepts, indeterminacy of location of objects, and rough approximations using methods of formal ontology. In the second part of the paper we propose an algebraic formalization of rough location, and hence, a formal method for the representation of objects subject to vagueness on a computer. We further define operations on those representations, which can be interpreted as union and intersection operations between those objects. The discussion of vagueness of concepts, indeterminacy of location, rough location and the relationships between these notions contributes to the theory about the ontology of geographic space. The formalization presented can provide the foundation for the implementation of vague objects and their location indeterminacy in GIS.
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- 2002
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17. Consciousness and the act of will
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Thomas Bittner
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Philosophy of mind ,Philosophy of language ,Philosophy ,media_common.quotation_subject ,Intentionality ,Metaphysics ,Consciousness ,Humanities ,Motion (physics) ,Conscience ,media_common - Abstract
L'A. propose une explication des experiences sur la conscience entreprises par B. Libet qui va dans le sens de l'idee selon laquelle la decision consciente de bouger entraine un processus neurophysiologique qui provoque le mouvement physique. Cette explication necessite une revision de la conception ordinaire de la conscience, a la lumiere de la theorie de la perception d'un ordre superieur (HOP) developpee par D. M. Armstrong
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- 1996
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18. Identification and characterization of two wheat Glycogen Synthase Kinase 3/ SHAGGY-like kinases
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Thomas, Bittner, Sarah, Campagne, Gunther, Neuhaus, Stefan A, Rensing, and Christiane, Fischer-Iglesias
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Homoeologs ,Phylogenetic analysis ,fungi ,Molecular Sequence Data ,food and beverages ,Homologs ,Plants ,Poaceae ,Brassinosteroid signaling ,GSK-3-like kinase ,Evolution, Molecular ,Glycogen Synthase Kinase 3 ,Multigene Family ,SHAGGY-like kinase ,Wheat ,Amino Acid Sequence ,Sequence Alignment ,Phylogeny ,Triticum ,Plant Proteins ,Research Article - Abstract
Background Plant Glycogen Synthase Kinase 3/ SHAGGY-like kinases (GSKs) have been implicated in numerous biological processes ranging from embryonic, flower, stomata development to stress and wound responses. They are key regulators of brassinosteroid signaling and are also involved in the cross-talk between auxin and brassinosteroid pathways. In contrast to the human genome that contains two genes, plant GSKs are encoded by a multigene family. Little is known about Liliopsida resp. Poaceae in comparison to Brassicaceae GSKs. Here, we report the identification and structural characterization of two GSK homologs named TaSK1 and TaSK2 in the hexaploid wheat genome as well as a widespread phylogenetic analysis of land plant GSKs. Results Genomic and cDNA sequence alignments as well as chromosome localization using nullisomic-tetrasomic lines provided strong evidence for three expressed gene copies located on homoeolog chromosomes for TaSK1 as well as for TaSK2. Predicted proteins displayed a clear GSK signature. In vitro kinase assays showed that TaSK1 and TaSK2 possessed kinase activity. A phylogenetic analysis of land plant GSKs indicated that TaSK1 and TaSK2 belong to clade II of plant GSKs, the Arabidopsis members of which are all involved in Brassinosteroid signaling. Based on a single ancestral gene in the last common ancestor of all land plants, paralogs were acquired and retained through paleopolyploidization events, resulting in six to eight genes in angiosperms. More recent duplication events have increased the number up to ten in some lineages. Conclusions To account for plant diversity in terms of functionality, morphology and development, attention has to be devoted to Liliopsida resp Poaceae GSKs in addition to Arabidopsis GSKs. In this study, molecular characterization, chromosome localization, kinase activity test and phylogenetic analysis (1) clarified the homologous/paralogous versus homoeologous status of TaSK sequences, (2) pointed out their affiliation to the GSK multigene family, (3) showed a functional kinase activity, (4) allowed a classification in clade II, members of which are involved in BR signaling and (5) allowed to gain information on acquisition and retention of GSK paralogs in angiosperms in the context of whole genome duplication events. Our results provide a framework to explore Liliopsida resp Poaceae GSKs functions in development.
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- 2012
19. The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data
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Thomas Bittner, Jane S. Richardson, Colin Batchelor, Jesse Stombaugh, Rob Knight, Christopher J. Mungall, Neocles B. Leontis, Eric Westhof, Karen Eilbeck, and Craig L. Zirbel
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Structure (mathematical logic) ,Computer science ,Bioinformatics ,RNA ,Computational biology ,Ontology (information science) ,Genetics & Genomics ,Open Biomedical Ontologies ,Annotation ,Chemistry ,Data file ,RNA Sequence ,General Materials Science ,Sequence (medicine) - Abstract
Biomedical Ontologies are intended to integrate diverse biomedical data to enable intelligent data-mining and facilitate translation of basic research into useful clinical knowledge. We present the first version of RNAO, an ontology for integrating RNA 3D structural, biochemical and sequence data. While each 3D data file depicts the structure of a specific molecule, such data have broader significance as representatives of classes of homologous molecules, which, while differing in sequence, generally share core structural features of functional importance. Thus, 3D structure data gain value by being linked to homologous sequences in genomic data and databases of sequence alignments. Likewise genomic data can increase in value by annotation of shared structural features, especially when these can be linked to specific functions. The RNAO is being developed in line with the developing standards of the Open Biomedical Ontologies (OBO) Consortium.
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- 2009
20. Chapter 6: A Theory of Granular Partitions
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Thomas Bittner and Barry Smith
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Computer science - Published
- 2008
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21. Biomedical ontologies: what part-of is and isn't
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Stefan Schulz, Thomas Bittner, and Anand Kumar
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Knowledge representation and reasoning ,Computer science ,Partonomies ,Information Storage and Retrieval ,Health Informatics ,(Bio)medical ontologies ,Pattern Recognition, Automated ,Open Biomedical Ontologies ,Terminology as Topic ,Animals ,Humans ,Relation (history of concept) ,Biology ,Natural Language Processing ,Structure (mathematical logic) ,business.industry ,Computational Biology ,Epistemology ,Computer Science Applications ,Vocabulary, Controlled ,Knowledge representation ,Artificial intelligence ,Terminological standards ,Anatomy ,business ,Mereology ,Medical Informatics - Abstract
Mereological relations such as part-of and its inverse has-part are fundamental to the description of the structure of living organisms. Whereas classical mereology focuses on individual entities, mereological relations in biomedical ontologies are generally asserted between classes of individuals. In general, this practice leaves some basic issues unanswered: type constraints of mereological relations, e.g., concerning artifacts and biological entities, the relation between parthood and time, inferred parts and wholes as well as a delimitation of parthood against spatial inclusion. Furthermore, mereological relations can be asserted not only between physical objects but also between biological processes and medical procedures. We analyze these ambiguities and make suggestions for a standardization of mereological relations in biomedical ontologies.
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- 2005
22. Granularity, scale and collectivity: when size does and does not matter
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Alan L. Rector, Jeremy Rogers, and Thomas Bittner
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Theoretical computer science ,Knowledge representation and reasoning ,Databases, Factual ,Computer science ,Health Informatics ,Models, Biological ,Motion (physics) ,Terminology ,Bridging (programming) ,Key (music) ,Crowds ,Terminology as Topic ,Ontologies ,Animals ,Humans ,Computer Simulation ,Medical Informatics Applications ,Biology ,Transitive relation ,Scale (chemistry) ,Computational Biology ,Epistemology ,Computer Science Applications ,Knowledge representation ,Part–whole relations ,Medical Informatics - Abstract
Bridging levels of “granularity” and “scale” are frequently cited as key problems for biomedical informatics. However, detailed accounts of what is meant by these terms are sparse in the literature. We argue for distinguishing two notions: “size range,” which deals with physical size, and “collectivity,” which deals with aggregations of individuals into collections, which have emergent properties and effects. We further distinguish these notions from “specialisation,” “degree of detail,” “density,” and “connectivity.” We argue that the notion of “collectivity”—molecules in water, cells in tissues, people in crowds, stars in galaxies—has been neglected but is a key to representing biological notions, that it is a pervasive notion across size ranges—micro, macro, cosmological, etc.—and that it provides an account of a number of troublesome issues including the most important cases of when the biomedical notion of parthood is, or is not, best represented by a transitive relation. Although examples are taken from biomedicine, we believe these notions to have wider application.
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- 2005
23. A Theory of Granular Partitions
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Thomas Bittner and Barry Smith
- Published
- 2003
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24. Scale in Object and Process Ontologies
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Thomas Bittner and Femke Reitsma
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Cognitive science ,Hierarchy ,business.industry ,Computer science ,Process (engineering) ,Scale (chemistry) ,Ontology (information science) ,Object (philosophy) ,Formal ontology ,Hierarchy theory ,Ontology ,Artificial intelligence ,business ,Mereology - Abstract
Scale is of great importance to the analysis of real world phenomena, be they enduring objects or perduring processes. This paper presents a new perspective on the concept of scale by considering it within two complementary ontological views. The first, called SNAP, recognizes enduring entities or objects, the other, called SPAN, perduring entities or processes. Within the meta-theory provided by the complementary SNAP and SPAN ontologies, we apply different theories of formal ontology such as mereology and granular partitions, and ideas derived from hierarchy theory. These theories are applied to objects and processes and form the framework within which we present tentative definitions of scale, which are found to differ between the two ontologies.
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- 2003
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25. Removal of PCR Inhibitors by Silica Membranes: Evaluating the Amplicor Mycobacterium tuberculosis Kit
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Thomas Bittner, Boris Böddinghaus, Thomas A. Wichelhaus, and Volker Brade
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Microbiology (medical) ,DNA, Bacterial ,Tuberculosis ,Polymerase Chain Reaction ,Sensitivity and Specificity ,Microbiology ,law.invention ,Mycobacterium tuberculosis ,law ,medicine ,Humans ,Polymerase chain reaction ,biology ,Mycobacteriology and Aerobic Actinomycetes ,Membranes, Artificial ,biology.organism_classification ,medicine.disease ,Silicon Dioxide ,Molecular biology ,DNA extraction ,Culture Media ,Silica membrane ,Reagent Kits, Diagnostic ,Bacteria ,Filtration - Abstract
The effectiveness of PCR inhibitor removal by silica membranes in combination with the Amplicor Mycobacterium tuberculosis kit was analyzed for 655 respiratory and nonrespiratory specimens. The overall inhibition rate was reduced from 12.5%, when applying the Amplicor kit alone, to 1.1% with the addition of silica membrane DNA purification.
- Published
- 2001
26. Rough Sets in Approximate Spatial Reasoning
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Thomas Bittner and John G. Stell
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Spatial relation ,Qualitative reasoning ,Computer science ,Partition (number theory) ,Spatial intelligence ,Rough set ,Set theory ,Algorithm ,Equivalence (measure theory) - Abstract
In spatial reasoning the qualitative description of relations between spatial regions is of practical importance and has been widely studied. Examples of such relations are that two regions may meet only at their boundaries or that one region is a proper part of another. This paper shows how systems of relations between regions can be extended from precisely known regions to approximate ones. One way of approximating regions with respect to a partition of the plane is that provided by rough set theory for approximating subsets of a set. Relations between regions approximated in this way can be described by an extension of the RCC5 system of relations for precise regions. Two techniques for extending RCC5 are presented, and the equivalence between them is proved. A more elaborate approximation technique for regions (boundary sensitive approximation) takes account of some of the topological structure of regions. Using this technique, an extension to the RCC8 system of spatial relations is presented.
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- 2001
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27. A Taxonomy of Granular Partitions
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Barry Smith and Thomas Bittner
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Pure mathematics ,Theoretical computer science ,Theory ,Computer science ,Partition (number theory) ,Attribute domain ,Set theory ,Categorical variable ,Spatial analysis ,Mereology - Abstract
In this paper we propose a formal theory of granular partitions (ways of dividing up or sorting or mapping reality) and we show how the theory can be applied in the geospatial domain. We characterize granular partitions at two levels: as systems of cells, and in terms of their projective relation to reality. We lay down conditions of well-formedness for granular partitions, and we define what it means for partitions to project transparently onto reality in such a way as to be structure-preserving. We continue by classifying granular partitions along three axes, according to: (a) the degree to which a partition represents the mereological structure of the domain it is projected onto; (b) the degree of completeness and exhaustiveness with which a partition represents reality; and (c) the degree of redundancy in the partition structure. This classification is used to characterize three types of granular partitions that play an important role in spatial information science: cadastral partitions, categorical coverages, and the partitions involved in folk categorizations of the geospatial domain.
- Published
- 2001
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28. Modeling surface hydrology concepts with endurance and perdurance
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Thomas Bittner, Chen-Chieh Feng, and Douglas M. Flewelling
- Subjects
Surface (mathematics) ,Hydrology ,Geographic information system ,business.industry ,Computer science ,Semantics (computer science) ,Hydrological modelling ,Aggregate (data warehouse) ,Set (abstract data type) ,Hydrology (agriculture) ,Entity–relationship model ,business ,Surface runoff ,Surface water - Abstract
Integration of GIS and hydrologic models has been a common approach for monitoring our ever-changing hydrologic system. One important issue in adapting such an approach is to ensure the right correspondence of data across databases. To reach this goal, it is necessary to develop a description of the surface hydrology concepts that is internally consistent and semantically rich. In this paper, we apply the notions of endurance and perdurance to model the semantics of hydrologic processes in surface hydrology. Three hydrologic models were examined to identify concepts used in surface hydrology. The paper demonstrates the usefulness of applying the notions of endurance and perdurance to surface hydrology. The result is a set of primitive entities, aggregate entities, and relations between these entities that are necessary to cover surface hydrology concepts.
29. The qualitative and time-dependent character of spatial relations in biomedical ontologies.
- Author
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Thomas Bittner and Louis J. Goldberg
- Subjects
- *
SPATIAL analysis (Statistics) , *WHOLE & parts (Philosophy) , *TEMPOROMANDIBULAR joint , *MEDICAL scientists - Abstract
Motivation: The formal representation of mereological aspects of canonical anatomy (parthood relations) is relatively well understood. The formal representation of other aspects of canonical anatomy, such as connectedness and adjacency relations between anatomical parts, their shape and size as well as the spatial arrangement of anatomical parts within larger anatomical structures are, however, much less well understood and represented in existing computational anatomical and bio-medical ontologies only insufficiently. Results: In this article, we provide a methodology of how to incorporate this kind of information into anatomical and bio-medical ontologies by applying techniques of representing qualitative spatial information from Artificial Intelligence. In particular, we focus on how to explicitly take into account the qualitative and time-dependent character of these relations. As a running example, we use the human temporomandibular joint (TMJ). Availability: Using the presented methodology, a formal ontology was developed which is accessible on http://www.ifomis.org/bfo/fol. This ontology may help to improve the logical and ontological rigor of bio-medical ontologies such as the OBO relation ontology. Contact: bittner3@buffalo.edu [ABSTRACT FROM AUTHOR]
- Published
- 2007
- Full Text
- View/download PDF
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