1,726,371 research outputs found
HPLC raw data related to Koeppl et al.: Structure, function and substrate preferences of archaeal S-adenosyl-L-homocysteine hydrolases
No full textIn this study, synthesis and cleavage reactions catalysed by S-adenosyl-L-homocysteine hydrolases originating from different domains of life were investigated. The reactions were studied using S-adenosyl-L-homocysteine or S-inosyl-L-homocysteine as substrate for the cleavage reaction, and L-homocysteine together with inosine or adenosine as substrates for the synthesis reaction.
The data contains the underlying HPLC chromatograms shown in Figures 3b and 3c as well as the Supplementary Figures S4-S24.
All chromatograms are stored within the .xlsx file. The retention times (in min) are given in column A and the absorption values (in mAU) are given in column B. Additionally, the csv folder contains all data sheets of the excel file as individual .csv files
Judith Koeppl : Alma Mater Award
No full textJudith Koeppl ’63 won the Alma Mater Award in 2020, her bio is archived here from the SNC website
Stochastic Semantics of Signaling as a Composition of Agent-view Automata
No full textAbstractIn this paper we present a formalism based on stochastic automata to describe the stochastic dynamics of signal transduction networks that are specified by rule-sets. Our formalism gives a modular description of the underlying stochastic process, in the sense that it is a composition of smaller units, agent-views. The view of an agent is an automaton that identifies all local modification changes of that agent (internal state modifications, binding and unbinding), but also those of interacting agents, which are tested within the same rule. We show how to represent the generator matrix of the underlying Markov process of the whole rule-set as Kronecker sums of the rate matrices belonging to individual view-automata. In the absence of birth the automata are finite, since the number of different contexts in which one agent can appear in
Analysis and Design of Biological Circuits and Systems
No full textSystems and synthetic biology are two emerging disciplines that hold promise to revolutionize our understanding of biological systems and to herald a new era of programmable hardware, respectively. Mathematical abstraction and today's abundance of quantitative biological data enables the up-scaling of analysis and design methodologies. In this tutorial paper we provide an engineering-centered introduction to those disciplines. Biological key concepts such as the central dogma of molecular biology are discussed, descriptions of bio-molecular reaction networks in terms of continuous-time Markov processes and ordinary differential equations are reviewed. Topological analysis of networks is introduced and the methods of metabolic flux balance analysis and elementary flux modes or extreme pathways are discussed.LANO
Approximate model reductions for combinatorial reaction systems
No full textThe paper considers a model reduction technique that is well-suited for biochemical reaction systems giving rise to the assembly of a large number of different molecular species. The reduction is performed by grouping species with common properties, directly from the model specification in terms of a rule-based language. In recent works, general algorithms for the exact reductions of rule-based models were established, but the state space often remains combinatorial. We extend this line of research by introducing approximate reductions, and an error measure which allows us to quantitatively study the effect of approximate model reductions
Self-assembly and Self-organization in Computer Science and Biology (Dagstuhl Seminar 15402)
No full textThis report documents the program and the outcomes of Dagstuhl Seminar 15402 "Self-assembly and Self-organization in Computer Science and Biology". With the trend of technological systems to become more distributed they tend to resemble closer biological systems. Biological systems on all scale are distributed and most often operate without central coordination. Taking the morphogenesis as an example, it is clear that the complexity and precision of distributed mechanisms in biology supersedes our current design attempts to distributed systems.
The seminar assembled together researchers from computer science, engineering, physics and molecular biology working on the problem of decentralized coordination of distributed systems. Within every domain different terms have been coined, different analysis methods have been developed and applied and the seminar aims to foster the exchange of methods and the instantiation and alignment of important problem statements that can span across the disciplines. A representative example for a problem that is studied across domains through different methods is self-assembly. For example, computer scientists consider abstract self-assembly models such as Wang tiles to bound shape complexities while polymer physicists and biologists use molecular dynamics simulations to characterize self-assembly by means of energy and entropy. Because of its well-definedness, we deliberately placed emphasis on self-assembly that is otherwise entailed in the more general term self-organization. Within the domain of self-organization various research threads were represented at the seminar and a certain convergence of underlying concepts was possible. The seminar helped to exchange techniques from different domains and to agree on certain problem statements for future collaborations
Going Beyond Counting First Authors in Author Co-citation Analysis
No full textThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Model Decomposition and Stochastic Fragments
No full textAbstractIn this paper, we discuss a method for decomposition, abstraction and reconstruction of the stochastic semantics of rule-based systems with conserved number of agents. Abstraction is induced by counting fragments instead of the species, which are the standard entities of information in molecular signaling. The rule-set can be decomposed to smaller rule-sets, so that the fragment-based dynamics of the whole rule-set is exactly a composition of species-based dynamics of smaller rule-sets. The reconstruction of the transient species-based dynamics is possible for certain initial distributions. We show that, if all the rules in a rule set are reversible, the reconstruction of the species-based dynamics is always possible at the stationary distribution. We use a case study of colloidal aggregation to demonstrate that the method can reduce the state space exponentially with respect to the standard, species-based description
Variations on the Author
No full text“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
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