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Base pair interactions and hybridization isotherms of matched and mismatched oligonucleotide probes on microarrays
Hans Binder,Stephan Preibisch,Toralf Kirsten
Quantitative Biology , 2005,
Abstract: The lack of specificity in microarray experiments due to non-specific hybridization raises a serious problem for the analysis of microarray data because the residual chemical background intensity is not related to the expression degree of the gene of interest. We analyzed the concentration dependence of the signal intensity of perfect match (PM) and mismatch (MM) probes in terms using a microscopic binding model using a combination of mean hybridization isotherms and single base related affinity terms. The signal intensities of the PM and MM probes and their difference are assessed with regard to their sensitivity, specificity and resolution for gene expression measures. The presented theory implies the refinement of existing algorithms of probe level analysis to correct microarray data for non-specific background intensities.
OnEX: Exploring changes in life science ontologies
Michael Hartung, Toralf Kirsten, Anika Gross, Erhard Rahm
BMC Bioinformatics , 2009, DOI: 10.1186/1471-2105-10-250
Abstract: We present OnEX (Ontology Evolution EXplorer) a system for exploring ontology changes. Currently, OnEX provides access to about 560 versions of 16 well-known life science ontologies. The system is based on a three-tier architecture including an ontology version repository, a middleware component and the OnEX web application. Interactive workflows allow a systematic and explorative change analysis of ontologies and their concepts as well as the semi-automatic migration of out-dated annotations to the current version of an ontology.OnEX provides a user-friendly web interface to explore information about changes in current life science ontologies. It is available at http://www.izbi.de/onex webcite.Ontologies have become increasingly important in life sciences [1,2]. They consist of a set of concepts denoted by terms describing and structuring a domain of interest. Concepts are interconnected by different relationship types such as is_a and part_of relationships. A heavily used ontology is the Gene Ontology (GO) [3] providing sub-ontologies for molecular functions (MF), biological processes (BP) and cellular components (CC). A wide range of life science ontologies is made available by the OBO (Open Biomedical Ontologies) Foundry [4]. The ontologies cover various life science disciplines, such as anatomy, health, biochemistry or phenotype. Other biomedical ontologies consider clinical and disease-related issues (for instance the NCI Thesaurus [5], SNOMED CT [6] or OMIM [7]). Due to their different focus and usage the developed ontologies vary in their size and complexity. For example, some OBO ontologies consist of only a few hundred concepts while others, such as the GO possess up to several ten thousand concepts.There are different kinds of applications of life science ontologies. They are used for the annotation of biological objects, such as gene products and proteins. Particularly, biological objects are associated ("annotated") with ontology concepts to consistentl
GOMMA: a component-based infrastructure for managing and analyzing life science ontologies and their evolution
Toralf Kirsten, Anika Gross, Michael Hartung, Erhard Rahm
Journal of Biomedical Semantics , 2011, DOI: 10.1186/2041-1480-2-6
Abstract: We present GOMMA, a generic infrastructure for managing and analyzing life science ontologies and their evolution. GOMMA utilizes a generic repository to uniformly and efficiently manage ontology versions and different kinds of mappings. Furthermore, it provides components for ontology matching, and determining evolutionary ontology changes. These components are used by analysis tools, such as the Ontology Evolution Explorer (OnEX) and the detection of unstable ontology regions. We introduce the component-based infrastructure and show analysis results for selected components and life science applications. GOMMA is available at http://dbs.uni-leipzig.de/GOMMA webcite.GOMMA provides a comprehensive and scalable infrastructure to manage large life science ontologies and analyze their evolution. Key functions include a generic storage of ontology versions and mappings, support for ontology matching and determining ontology changes. The supported features for analyzing ontology changes are helpful to assess their impact on ontology-dependent applications such as for term enrichment. GOMMA complements OnEX by providing functionalities to manage various versions of mappings between two ontologies and allows combining different match approaches.Ontologies and taxonomies have become increasingly important especially in the life sciences [1,2]. They are predominantly utilized to structure and uniformly describe the entities of a domain of interest such as molecular functions or the anatomy of species [3,4]. Ontologies consist of a set of concepts that are usually interrelated by "is-a", "part-of" or other semantically meaningful relationships (e.g., "regulated-by") [5]. Ontologies enable a consistent annotation of biological objects, experiments, publications or clinical documents by describing their properties. For instance, the Molecular Function ontology of the Gene Ontology [6] is used to specify the functions of genes and proteins on the molecular level. Biomedical ontol
Data Partitioning for Parallel Entity Matching
Toralf Kirsten,Lars Kolb,Michael Hartung,Anika Gro?,Hanna K?pcke,Erhard Rahm
Computer Science , 2010,
Abstract: Entity matching is an important and difficult step for integrating web data. To reduce the typically high execution time for matching we investigate how we can perform entity matching in parallel on a distributed infrastructure. We propose different strategies to partition the input data and generate multiple match tasks that can be independently executed. One of our strategies supports both, blocking to reduce the search space for matching and parallel matching to improve efficiency. Special attention is given to the number and size of data partitions as they impact the overall communication overhead and memory requirements of individual match tasks. We have developed a service-based distributed infrastructure for the parallel execution of match workflows. We evaluate our approach in detail for different match strategies for matching real-world product data of different web shops. We also consider caching of in-put entities and affinity-based scheduling of match tasks.
Genomic organization of eukaryotic tRNAs
Clara Bermudez-Santana, Camille Attolini, Toralf Kirsten, Jan Engelhardt, Sonja J Prohaska, Stephan Steigele, Peter F Stadler
BMC Genomics , 2010, DOI: 10.1186/1471-2164-11-270
Abstract: In line with previous reports, we find that tRNA complements evolve rapidly and tRNA gene and pseudogene locations are subject to rapid turnover. At phylum level, the distributions of the number of tRNA genes and pseudogenes numbers are very broad, with standard deviations on the order of the mean. Even among closely related species we observe dramatic changes in local organization. For instance, 65% and 87% of the tRNA genes and pseudogenes are located in genomic clusters in zebrafish and stickleback, resp., while such arrangements are relatively rare in the other three sequenced teleost fish genomes. Among basal metazoa, Trichoplax adhaerens has hardly any duplicated tRNA gene, while the sea anemone Nematostella vectensis boasts more than 17000 tRNA genes and pseudogenes. Dramatic variations are observed even within the eutherian mammals. Higher primates, for instance, have 616 ± 120 tRNA genes and pseudogenes of which 17% to 36% are arranged in clusters, while the genome of the bushbaby Otolemur garnetti has 45225 tRNA genes and pseudogenes of which only 5.6% appear in clusters. In contrast, the distribution is surprisingly uniform across plant genomes. Consistent with this variability, syntenic conservation of tRNA genes and pseudogenes is also poor in general, with turn-over rates comparable to those of unconstrained sequence elements. Despite this large variation in abundance in Eukarya we observe a significant correlation between the number of tRNA genes, tRNA pseudogenes, and genome size.The genomic organization of tRNA genes and pseudogenes shows complex lineage-specific patterns characterized by an extensive variability that is in striking contrast to the extreme levels of sequence-conservation of the tRNAs themselves. The comprehensive analysis of the genomic organization of tRNA genes and pseudogenes in Eukarya provides a basis for further studies into the interplay of tRNA gene arrangements and genome organization in general.Transfer RNAs (tRNAs) are am
Spectral Analysis of a Discrete Metastable System Driven by Lévy Flights
Toralf Burghoff,Ilya Pavlyukevich
Mathematics , 2015,
Abstract: In this paper we consider a finite state time discrete Markov chain that mimics the behaviour of solutions of the stochastic differential equation $dX=-U'(X)dt+\epsilon dL$, where $U$ is a multi-well potential with $n\geq 2$ local minima and L is a symmetric \alpha-stable L\'evy process (L\'evy flights process). We investigate the spectrum of the generator of this Markov chain in the limit $\epsilon\to 0$ and localize the top n eigenvalues $\lambda^\epsilon_1,\dots, \lambda^\epsilon_n$. These eigenvalues turn out to be of the same algebraic order $O(\epsilon^\alpha)$ and are well separated from the rest of the spectrum by a spectral gap. We also determine the limits $\lim_{\epsilon\to 0}\epsilon^{-\alpha} \lambda^\epsilon_i$, $1\leq i\leq n$, and show that the corresponding eigenvectors are approximately constant over the domains which correspond to the potential wells of $U$.
Water and the Configuration of Social Worlds: An Anthropological Perspective  [PDF]
Kirsten Hastrup
Journal of Water Resource and Protection (JWARP) , 2013, DOI: 10.4236/jwarp.2013.54A009

From an anthropological perspective, water is not only the sine qua non of life in general, it is also seen to configure societies in particular ways, and to generate particular values. This will be substantiated in four moves. First, the hydrological cycle and other elementals of water will be discussed. Second, we shall zoom in on rivers, transforming natural resources and social communities as they bend and twist. Third, we shall discuss artificially established canals, emulating natural flows, but having their own long-term social and political implications. Fourth, we shall focus on wells, providing nodal points of social life and potential conflict. The article ends with some observations on water as a theory-machine.

Orchestrating neuronal networks: sustained after-effects of transcranial alternating current stimulation depend upon brain states
Toralf Neuling,Stefan Rach,Christoph S. Herrmann
Frontiers in Human Neuroscience , 2013, DOI: 10.3389/fnhum.2013.00161
Abstract: The interest in transcranial alternating current stimulation (tACS) has significantly increased in the past decade. It has potential to modulate brain oscillations in a frequency specific manner, offering the possibility to demonstrate a causal nature of oscillation behavior relationships. TACS is a strong candidate as a tool for clinical applications, however, to fulfill this potential, certain parameters have yet to be evaluated. First, little is known about long-lasting after-effects of tACS with respect to the modulations of rhythmic brain activity. Second, the power of endogenous brain oscillations might play a crucial role in the efficacy of tACS. We hypothesize that the after-effects of tACS depend on the endogenous power of oscillations. To this end, we modulated the power of endogenous occipital alpha oscillations via tACS. In two experiments, participants either had their eyes open or closed to keep endogenous alpha power either low or high while they were stimulated for 20 min with their individual alpha frequency (IAF) and simultaneously performing a vigilance task. After-effects on IAF power were evaluated over a course of 30 min with a pre stimulation period serving as baseline. After-effects were strongly dependent on IAF power. Enhanced IAF power was observed for at least 30 min after tACS under conditions of low endogenous IAF power, whereas, IAF power could not be further enhanced by tACS under conditions of high IAF power. The current study demonstrates, for the first time, a long lasting effect after tACS on endogenous EEG power in the range of the stimulation frequency. Additionally, we present conclusive evidence that the power of the endogenous oscillations has a critical impact on tACS efficacy. Long lasting after-effects foster the role of tACS as a tool for non-invasive brain stimulation and demonstrate the potential for therapeutic application to reestablish the balance of altered brain oscillations.
Photon tunneling through absorbing dielectric barriers
Toralf Gruner,Dirk-Gunnar Welsch
Physics , 1996, DOI: 10.1016/S0030-4018(96)00584-6
Abstract: Using a recently developed formalism of quantization of radiation in the presence of absorbing dielectric bodies, the problem of photon tunneling through absorbing barriers is studied. The multilayer barriers are described in terms of multistep complex permittivities in the frequency domain which satisfy the Kramers--Kronig relations. From the resulting input--output relations it is shown that losses in the layers may considerably change the photon tunneling times observed in two-photon interference experiments. It is further shown that for sufficiently large numbers of layers interference fringes are observed that cannot be related to a single traversal time.
Normal Human Cell Conversion to 3-D Cancer-like Growth: Genome Damage, Endopolyploidy, Senecence Escape, and Cell Polarity Change/Loss  [PDF]
Kirsten H. Walen
Journal of Cancer Therapy (JCT) , 2011, DOI: 10.4236/jct.2011.22023
Abstract: In cell cultures monolayered cell growth is controlled by contact inhibition which again is controlled by the cell polarity system by always being positioned in accord with the cytoskeleton axis. Presently, cycling endopolyploid cells (tetraploidy) were shown to undergo perpendicular divisions relative to the cytoskeleton axis which disrupted to some degree contact inhibition in the near-senescent phase of human primary cells. These experiments included genome damage-induced endopolyploidization (TAS-treated) to simulate as a model system the state of in vivo accelerated cell senescence (ACS) which is induced by therapy-associated genomic damage. From ACS delayed tumor re-growth (re-lapse) occurs from “robust” cell propagation, but mechanisms for such cell escape from senescence are unknown. For TAS-treated a karyoplast bud-off process with change to limited mitotic activity occurred in young senescent cultures. In old, deep senescent (5 - 8 weeks) cultures, unexpectedly escape cell-growth showed three dimensional (3-D) tumor-like spheres from growths of morphologically different cells as compared to the fibroblastic phenotype. These cells expressed cell polarity change, and very condensed nuclei were variously perpendicularly oriented to what-ever cell polarity was present. These results were discussed in regard to in vivo relapse and, to the importance of cell polarity change in tumorigenesis. Induced senescence as an anti-tumor mechanism in therapy treatment becomes a questionable procedure from the present experimental results.
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