51 research outputs found
Comparing organisms on the level of metabolism
No full textOehm S. Comparing organisms on the level of metabolism. Bielefeld (Germany): Bielefeld University; 2009.With the accumulation of gene and protein sequence data in publicly available databases and the development of computational methods for their comparison, sequence analysis has become an extremely powerful tool to uncover functional properties of these molecules. In general, however, the biological function is a result of many interacting molecules forming large interaction networks such as regulatory networks or metabolic pathways. To improve our understanding of the phenotype of organisms it is of great value to analyze not only individual genes, but also these interaction networks. In particular the growing amount of publicly available data on metabolic pathways as well as of functional annotation data for sequenced organisms enables the comparison of organisms based on their metabolic reaction networks on a large scale.
In this thesis a fully automated approach for comparative analysis of organisms on the functional level of metabolism is developed that yields a classification of the analyzed organisms according to their individual metabolic pathway variants. In contrast to gene sequence-based comparison techniques, this approach is based on the functional annotation of genes, namely metabolic reactions. Moreover, instead of comparing individual reactions one at a time, metabolic pathways are compared, which are sets of reactions that are jointly involved in the same cellular process.
As an application example, five Corynebacteria are compared against each other using the newly developed approach and the results are discussed in light of their biological relevance. This example demonstrates the benefit of the developed approach for improving knowledge on habitat and lifestyle of organisms and the respective metabolic prerequisites, for detecting potential drug targets, as well as for improving the functional annotation of the respective genomes.
A web frontend called CPA (Comparative Pathway Analyzer), which is available at http://cpa.cebitec.uni-bielefeld.de, can be used free of charge to apply the developed approach on genome and pathway data from the KEGG database or on data provided by the user
A Knowledge-Based System for the Diagnosis of Alzheimer`s Disease
No full textOehm S, Siessmeier T, Buchholz HG, Bartenstein P, Uthmann T. A Knowledge-Based System for the Diagnosis of Alzheimer`s Disease. In: Dojat M, Keravnou E, Barahona P, eds. Artificial intelligence in medicine. Lecture Notes in Computer Science. Vol 2780. Berlin: Springer; 2003: 117-121
Comparative Analysis of Plasmids in the Genus Listeria
No full textKuenne C, Voget S, Pischimarov J, et al. Comparative Analysis of Plasmids in the Genus Listeria. PLOS ONE. 2010;5(9): e12511.Background: We sequenced four plasmids of the genus Listeria, including two novel plasmids from L. monocytogenes serotype 1/2c and 7 strains as well as one from the species L. grayi. A comparative analysis in conjunction with 10 published Listeria plasmids revealed a common evolutionary background. Principal Findings: All analysed plasmids share a common replicon-type related to theta-replicating plasmid pAMbeta1. Nonetheless plasmids could be broadly divided into two distinct groups based on replicon diversity and the genetic content of the respective plasmid groups. Listeria plasmids are characterized by the presence of a large number of diverse mobile genetic elements and a commonly occurring translesion DNA polymerase both of which have probably contributed to the evolution of these plasmids. We detected small non-coding RNAs on some plasmids that were homologous to those present on the chromosome of L. monocytogenes EGD-e. Multiple genes involved in heavy metal resistance (cadmium, copper, arsenite) as well as multidrug efflux (MDR, SMR, MATE) were detected on all listerial plasmids. These factors promote bacterial growth and survival in the environment and may have been acquired as a result of selective pressure due to the use of disinfectants in food processing environments. MDR efflux pumps have also recently been shown to promote transport of cyclic diadenosine monophosphate (c-di-AMP) as a secreted molecule able to trigger a cytosolic host immune response following infection. Conclusions: The comparative analysis of 14 plasmids of genus Listeria implied the existence of a common ancestor. Ubiquitously-occurring MDR genes on plasmids and their role in listerial infection now deserve further attention
Selbstlernende Assistenzsysteme für Maschinenbediener
No full textTechnische Entwicklungen sowie Elemente der Automatisierung führen im Maschinen- und Anlagenbau zu einer steigenden Komplexität, welche mit einem gesteigerten Gesamtwirkungsgrad (nach (DIN 8743:2014-01) der Endprodukte einhergeht. In der Bedienung kann jedoch, bspw. in der Lebensmittelverarbeitungs- und -verpackungsindustrie, eine Diskrepanz des technisch möglichen und real erzielten Wirkungsgrades im zweistelligen Prozentbereich festgestellt werden (Schult, Oehm, Klaeger & Carsch 2018). Mit den Ironies of automation wurde bereits in den 1980er Jahren eine Ursache dafür identifiziert. Die fehlende Erfahrung sowie fehlendes Prozessverständnis im Umgang mit komplexen Systemen auf Bedienenden-Seite führen zu Problemen im Umgang mit ebenjenen (Bainbridge 1983). Insbesondere bei biogenen Rohstoffen mit volatilen Eigenschaften können weit verzweigte Ursache-Wirkungs-Kausalitäten im Störungsfall weder verstanden noch nachhaltig behoben werden. Diese theoretische Annahme wird auch durch Analysen am Fraunhofer Institut für Verfahrenstechnik und Verpackung (IVV) in Dresden bestätigt. Seit 1995 konnte in über 6.000 Stunden Maschineneffizienzanalysen in der Lebensmittelverarbeitung und -verpackung festgestellt werden, dass die Prozesse von so genannten Mikrostörungen, also Unterbrechungen kürzer als 2 Minuten, geprägt sind (Schult, Beck & Majschak 2015). Ein für die nachhaltige Problemlösung notwendiger Erfahrungsaustausch und -aufbau unter den Mitarbeitenden wird dabei häufig durch Personalfluktuation, Fachkräftemangel und Kommunikationsbarrieren behindert. [...aus der Einleitung
Comparative Pathway Analyzer - a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms
No full textOehm S, Gilbert D, Tauch A, Stoye J, Goesmann A. Comparative Pathway Analyzer - a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms. NUCLEIC ACIDS RESEARCH. 2008;36(Web Server):W433-W437.In order to understand the phenotype of any living system, it is essential to not only investigate its genes, but also the specific metabolic pathway variant of the organism of interest, ideally in comparison with other organisms. The Comparative Pathway Analyzer, CPA, calculates and displays the differences in metabolic reaction content between two sets of organisms. Because results are highly dependent on the distribution of organisms into these two sets and the appropriate definition of these sets often is not easy, we provide hierarchical clustering methods for the identification of significant groupings. CPA also visualizes the reaction content of several organisms simultaneously allowing easy comparison. Reaction annotation data and maps for visualizing the results are taken from the KEGG database. Additionally, users can upload their own annotation data. This website is free and open to all users and there is no login requirement. It is available at https://www.cebitec.uni-bielefeld.de/groups/brf/software/cpa/index.html
The governing bodies of a cooperative
No full textThis diploma thesis deals with cooperatives and closely focuses on their bodies. Czech legal order gives only superficial legislation which causes many questions and imperfections to arise. The aim of this thesis is to find solutions to these problems and create an ideal model of cooperative. Following that, the author bases his thoughts on the legal doctrine and Czech court jurisdiction. The introductory part focuses on general questions, i.e. history of cooperatives, legislation and legal characteristics of cooperatives. The author refers to the negative impact of the Communistic Party of Czechoslovakia on cooperativeness between years 1948 - 1989. Such impacts are still present in nowadays legislation. Another imperfections are seen in the starkness and fragmentation of the legislation itself. All these imperfections may be removed by the future law about business cooperatives. The main body of the thesis follows as this describes the cooperative body legislation. Current legislation brings three obligatory bodies - assembly, board and control committee. Next to these, every cooperative may establish optional bodies. The chapter on assembly deals with its status and scope. In connection with assembly's scope the author describes in detail the process of assembly's decisions approving, together..
The Transfers of Cooperative Apartments from Housing Cooperatives to Their Members
No full textV ANGLICKÉM JAZYCE The thesis deals with the issue of transfer of cooperative apartments to the ownership of the members of housing cooperatives. After the initial definition of the object and subjects of transfer, the author in order to find the reasons why the members of housing cooperatives consider to transfer cooperative apartment to their property compares the legal regimes of cooperative apartment lease and condominium. The largest part of the thesis is devoted to the issue of transfers of cooperative apartments to the ownership of the members of housing cooperatives whose accomplishment is entailed by law, without allowing housing cooperatives to request for transferring apartment into ownership consideration in the form of property purchase price. The author examines the reasons which let the legislators to take the measures seriously affecting the property right of housing cooperatives, he evaluates it in terms of its adequacy and ability to achieve the persued aim. In this context, he analyzes the development in the years 1948-1991, both in terms of interference with rights of the members of housing cooperatives and cooperative housing tenants. Another part of the thesis focuses on already effective legal modification. The author tries mainly to draw attention to significant problems of..
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Musical rhetoric in J S Bach's two-part inventions and implications for their performance on the modern piano
No full textMusical rhetoric, the application of the art of speech to music, is a basic principle of German Baroque composition. J. S. Bach had a close relationship to rhetoric, as well as musical rhetoric, and he followed the Baroque ideal of rhetorical structuring and affective content in his compositions. As shown by other scholars, he also employed musical rhetoric in his purely instrumental compositions. The author investigates the elements of musical rhetoric in J. S. Bach's Two-part Inventions and provides suggestions for their performance on the modern piano, as implied by the analysis.</p
Data Science on Industrial Data—Today’s Challenges in Brown Field Applications
No full textMuch research is done on data analytics and machine learning for data coming from industrial processes. In practical approaches, one finds many pitfalls restraining the application of these modern technologies especially in brownfield applications. With this paper, we want to show state of the art and what to expect when working with stock machines in the field. The paper is a review of literature found to cover challenges for cyber-physical production systems (CPPS) in brownfield applications. This review is combined with our own personal experience and findings gained while setting up such systems in processing and packaging machines as well as in other areas. A major focus in this paper is on data collection, which tends be more cumbersome than most people might expect. In addition, data quality for machine learning applications is a challenge once leaving the laboratory and its academic data sets. Topics here include missing ground truth or the lack of semantic description of the data. A last challenge covered is IT security and passing data through firewalls to allow for the cyber part in CPPS. However, all of these findings show that potentials of data driven production systems are strongly depending on data collection to build proclaimed new automation systems with more flexibility, improved human–machine interaction and better process-stability and thus less waste during manufacturing
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