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  • 1
    Electronic Resource
    Electronic Resource
    Springer
    European biophysics journal 23 (1994), S. 29-38 
    ISSN: 1432-1017
    Keywords: Activation energy landscape ; RNA folding ; RNA melting ; RNA secondary structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Physics
    Notes: Abstract We present and study the behavior of a simple kinetic model for the melting of RNA secondary structures, given that those structures are known. The model is then used as a map that. assigns structure dependent overall rate constants of melting (or refolding) to a sequence. This induces a “landscape” of reaction rates, or activation energies, over the space of sequences with fixed length. We study the distribution and the correlation structure of these activation energies.
    Type of Medium: Electronic Resource
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  • 2
    ISSN: 1432-1017
    Keywords: Key words Kinetic folding ; Minimun free energy structures ; RNA secondary structures ; Sequence structure relations
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Physics
    Notes: Abstract Algorithms predicting RNA secondary structures based on different folding criteria – minimum free energies (mfe), kinetic folding (kin), maximum matching (mm) – and different parameter sets are studied systematically. Two base pairing alphabets were used: the binary GC and the natural four-letter AUGC alphabet. Computed structures and free energies depend strongly on both the algorithm and the parameter set. Statistical properties, such as mean number of base pairs, mean numbers of stacks, mean loop sizes, etc., are much less sensitive to the choice of parameter set and even of algorithm. Some features of RNA secondary structures, such as structure correlation functions, shape space covering and neutral networks, seem to depend only on the base pairing logic (GC or AUGC alphabet).
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    Springer
    Bulletin of mathematical biology 52 (1990), S. 485-508 
    ISSN: 1522-9602
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Mathematics
    Notes: Abstract Catalysis in replication networks has become an important issue in biophysics and other areas of biology. Examples are RNA catalysis, idiotype recognition in the immune response and dynamical models of Maynard-Smith games in sociobiology. Chemical reaction networks describing catalysed, template-induced reproduction of three species are analysed in full generality. The nine-dimensional parameter space is reduced to three relevant angular coordinates which determine completely the phase portraits (PPs) and the bifurcation patterns. All cases are classified and all generic as well as most of the nongeneric transitions are listed and described.
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    Springer
    Bulletin of mathematical biology 58 (1996), S. 877-905 
    ISSN: 1522-9602
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Mathematics
    Notes: Abstract We consider the kinetics of an autocatalytic reaction network in which replication and catalytic actions are separated by a translation step. We find that the behaviour of such a system is closely related to second-order replicator equations, which describe the kinetics of autocatalytic reaction networks in which the replicators act also as catalysts. In fact, the qualitative dynamics seems to be described almost entirely be the second-order reaction rates of the replication step. For two species we recover the qualitative dynamics of the replicator equations. Larger networks show some deviations, however. A hypercyclic system consisting of three interacting species can converge toward a stable limit cycle in contrast to the replicator equation case. A singular perturbation analysis shows that the replication-translation system reduces to a second-order replicator equation if translation is fast. The influence of mutations on replication-translation networks is also very similar to the behavior of selection-mutation equations.
    Type of Medium: Electronic Resource
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  • 5
    ISSN: 1439-099X
    Keywords: Schlüsselwörter: p53-Überexpression ; Hypoxie ; Kopf-Hals-Karzinome ; Key Words: p53 ; Hypoxia ; Head and neck carcinomas
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Description / Table of Contents: Purpose: Clinical investigation of a potential relationship between the polarographically measured tumor oxygenation and the p53 status in patients with squamous cell carcinoma of the head and neck. Patients and Methods: In 99 patients with mostly advanced, histologically proven squamous cell carcinoma of the head and neck were estimated the classical tumor parameters (TNM stage, histological grading) the immunohistochemical p53-overexpression (DO-7) and the tumor oxygenation status (Eppendorf pO2 Histograph). The tumor volume and the hemoglobin concentration were evaluated simultaneously. Results: No statistically significant difference could be detected between immunohistological p53-positive (p53 ≥ 10% stained cells) and p53-negative tumors (p53 〈 10% stained cells) regarding both the median pO2 and the relative frequency of values ≤ 5 mm Hg. Moreover, no statistically relevant differences could be seen between both p53-groups considering the hemoglobin concentration, the TNM stag, the histological grading and the tumor volume. Conclusion: Our data imply that there is no association between p53-overexpression and tumor hypoxia in head and neck carcinomas. However, this is not necessarily in contradiction to experimental or clinical data that confirmed a relationship between hypoxia and p53-mediated increased malignancy of tumor cells in other tumor entities. The comparable oxygenation status of p53-positive and p53-negative tumors in our study is associated with an analogous clinical tumor aggressiveness of both groups. That could be caused by hypoxia related but p53-independent selection of tumor cells with a more malignant phenotype in head and neck carcinomas. However, further research is needed to prove this possible relationship.
    Notes: Ziel: Klinische Prüfung einer potentiellen Beziehung zwischen polarographisch gemesener Tumoroxygenierung und p53-Status bei Patienten mit Plattenepithelkarzinomen der Kopf-Hals-Region. Patienten und Methode: Bei 99 Patienten mit überwiegend fortgeschrittenen, histologisch gesicherten Plattenepithelkarzinomen der Kopf-Hals-Region wurden neben den klassischen Tumorparametern (TNM-Stadium, histologisches Grading) die immunhistochemische p53-Überexpression (DO-7) und der Tumoroxygenierungsstatus ermittelt (Eppendorf-pO2-Histograph). Simultan erfolgte die Bestimmung des Tumorvolumens und der Hämoglobinkonzentration. Ergebnisse: Zwischen immunhistochemisch p53-positiven (≥ 10% angefärbte Zellen) und p53-negativen (〈 10% angefärbte Zellen) Tumoren fand sich weder für den pO2-Median noch für die relative Anzahl von Werten ≤ 5 mm Hg ein statistisch signifikanter Unterschied. Auch bei der Betrachtung der Hämoglobinkonzentration, der TNM-Klassifikation, des histologischen Gradings und des Tumorvolumens fanden sich zwischen beiden p53-Gruppen keine statistisch relevanten Differenzen. Schlussfolgerung: Unsere Daten sprechen gegen eine Assoziation von p53-Überexpression und Tumorhypoxie bei Kopf-Hals-Karzinomen. Zu experimentellen und klinischen Ergebnissen, die bei anderen Tumorentitäten zeigen, dass Hypoxie zu einer p53-vermittelten Steigerung der Malignität führt, ergibt sich trotzdem kein prinzipieller Widerspruch. Die in unserer Studie adäquate Oxygenierung von p53-positiven und p53-negativen Tumoren reflektiert sich in einer vergleichbaren klinischen Tumoraggressivität beider Gruppen. Dies könnte dadurch bedingt sein, dass bei Kopf-Hals-Karzinomen hypoxieassoziierte, aber p53-unabhängiger Formen der Selektion von Tumorzellen mit malignerem Phänotyp zum Tragen kommen. Es bedarf jedoch weiterführender Untersuchungen, um einen solchen möglichen Zusammenhang zu belegen.
    Type of Medium: Electronic Resource
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  • 6
    ISSN: 1522-9602
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Mathematics
    Notes: Abstract Mutation is introduced into autocatalytic reaction networks. The differential equations obtained are neither of repliator-type nor can they be transformed straightway into a linear equation. Examples of low dimensional dynamical systems —n=2, 3 and 4 — are discussed and complete qualitative analysis is presented. Error thresholds known from simple replication-mutation kinetics with frequency independent replication rates occur here as well. Instead of cooperative transitions or higher order phase transitions the thresholds appear here as supercritical or subcritical bifurcations being analogous to first-order phase transitions.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    Bradford : Emerald
    The @electronic library 17 (1999), S. 23-26 
    ISSN: 0264-0473
    Source: Emerald Fulltext Archive Database 1994-2005
    Topics: Information Science and Librarianship
    Notes: For some time, the central library at Boehringer Mannheim, a company in the research-based pharmaceutical industry, has placed the majority of its book orders using EDIFACT. This article describes the situation before the introduction of the system, the technical and organisational preconditions, and the changes that were necessary to DP systems. The results are presented and the new situation of EDI versus the Internet is discussed.
    Type of Medium: Electronic Resource
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  • 8
    ISSN: 1546-1696
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: [Auszug] In contrast to the fairly reliable and complete annotation of the protein coding genes in the human genome, comparable information is lacking for noncoding RNAs (ncRNAs). We present a comparative screen of vertebrate genomes for structural noncoding RNAs, which evaluates conserved genomic DNA ...
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    Springer
    Journal of mathematical biology 30 (1992), S. 597-632 
    ISSN: 1432-1416
    Keywords: Autocatalysis ; Mutation ; Perturbation theory ; Qualitative analysis ; Replication dynamics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Mathematics
    Notes: Abstract A class of kinetic equations describing catalysed and template induced replication, and mutation is introduced. This ODE in its most general form is split into two vector fields, a replication and a mutation field. The mutation field is considered as a perturbation of the replicator equation. The perturbation expansion is a Taylor series in a mutation parameter λ. First, second and higher order contributions are computed by means of the conventional Rayleigh-Schrödinger approach. Qualitative shifts in the positions of rest points and limit cycles on the boundary of the physically meaningful part of concentration space are predicted from flow topologies. The results of the topological analysis are summarized in two theorems which turned out to be useful in applications: the rest point migration theorem (RPM) and the limit cycle migration theorem (LCM). Quantitative expressions for the shifts of rest points are computed directly from the perturbation expansion. The concept is applied to a collection of selected examples from biophysical chemistry and biology.
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    Springer
    Journal of mathematical biology 30 (1992), S. 597-631 
    ISSN: 1432-1416
    Keywords: Autocatalysis ; Mutation ; Perturbation theory ; Qualitative analysis ; Replication dynamics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Mathematics
    Notes: Abstract A class of kinetic equations describing catalysed and template induced replication, and mutation is introduced. This ODE in its most general form is split into two vector fields, a replication and a mutation field. The mutation field is considered as a perturbation of the replicator equation. The perturbation expansion is a Taylor series in a mutation parameter λ. First, second and higher order contributions are computed by means of the conventional Rayleigh-Schrödinger approach. Qualitative shifts in the positions of rest points and limit cycles on the boundary of the physically meaningful part of concentration space are predicted from flow topologies. The results of the topological analysis are summarized in two theorems which turned out to be useful in applications: the rest point migration theorem (RPM) and the limit cycle migration theorem (LCM). Quantitative expressions for the shifts of rest points are computed directly from the perturbation expansion. The concept is applied to a collection of selected examples from biophysical chemistry and biology.
    Type of Medium: Electronic Resource
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