1,721,153 research outputs found
Source code release for: Gaussian distributed codon frequencies of genomes
No full text<p>Source code to accompany the publication:</p>
<p>Khomtchouk BB, Nonner W: "Gaussian-distributed codon frequencies of genomes", <em>G3 (Bethesda)</em>, 2019 (in press).</p>
Optimal Algorithms for Train Shunting and Relaxed List Update Problems
Full text linkThis paper considers a Train Shunting problem which occurs in cargo train organizations: We have a locomotive travelling along a track segment and a collection of n cars, where each car has a source and a target. Whenever the train passes the source of a car, it needs to be added to the train, and on the target, the respective car needs to be removed. Any such operation at the end of the train incurs low shunting cost, but adding or removing truly in the interior requires a more complex shunting operation and thus yields high cost. The objective is to schedule the adding and removal of cars as to minimize the total cost. This problem can also be seen as a relaxed version of the well-known List Update problem, which may be of independent interest.
We derive polynomial time algorithms for Train Shunting by reducing this problem to finding independent sets in bipartite graphs. This allows us to treat several variants of the problem in a generic way. Specifically, we obtain an algorithm with running time O(n^{5/2}) for the uniform case, where all low costs and all high costs are identical, respectively. Furthermore, for the non-uniform case we have running time of O(n^3). Both versions translate to a symmetric variant, where it is also allowed to add and remove cars at the front of the train at low cost. In addition, we formulate a dynamic program with running time O(n^4), which exploits the special structure of the graph. Although the running time is worse, it allows us to solve many extensions, e.g., prize-collection, economies of scale, and dependencies between consecutive stations
Membrane properties of Ranvier nodes from South American toads frogs (Bufo marinus ictericus and Leptodactylus ocellatus)
No full textEstudaram-se propriedades eletrofisiológicas de membranas excitáveis em algusn anfíbios do Brasil. O presente trabalho refere-se aos resultados obtidos em nódulos de Ranvier de fibras motoras e sensoriais isoladas de Bufo marinus ictericus e Leptodactylus ocellatus. Empregou-se o método desenvolvido por Nonner (1969).</jats:p
Theoretical predictions of gating behavior for mutants of Shaker-type Kv channels from inter-domain energetics
Full text linkA multiscale physical model of Shaker-type Kv channels is used to span from atomic-scale interactions to macroscopic experimental measures such as charge/voltage (QV) and conductance/voltage (GV) relations. The model [1] comprises the experimentally well-characterized voltage sensor (VS) domains described by four replications of an independent continuum electrostatic model under voltage clamp conditions [2, 3] and a hydrophobic gate controlling the flow of ions by a vapor lock mechanism [4], connected by a simple coupling principle derived from known experimental results and trial-and-error. The total Hamiltonian of the system is calculated from the computed configurational energy for each components as a function of applied voltage, VS positions andg ate radius, allowing us to produce statistical-mechanical expectation values for macroscopic laboratory observables over the full range of physiological membrane potentials (|V| ≤ 100 mV, in 1 mV steps). The Shaker QV and GV relations seen in Seoh et al. [5] are predicted by this model. With this approach, functional energetic relations can be decomposed in terms of physical components, and thus the effects of modifications in those elements can be quantified. We find that the total work required to operate the gate is an order of magnitude larger than the work available to the VS, and that the the experimentally observed bistable gating is due to the VS slide-and-interlock behavior. The same model was systematically applied to VS charge mutants (Seoh et al. [5]). The QV and GV relations can be qualitatively predicted and the associated effects on functional domains determined. Additional features such as surface charges become significant for the pathological cases. Our engineering approach clearly elucidates that both normal function and mutant changes are electrostatic in nature.[1] Alexander Peyser, Dirk Gillespie, Roland Roth, and Wolfgang Nonner. Domain and inter-domain energetics underlying gating in Shaker-type Kv channels. Accepted: Biophys J,2014. doi:10.1016/j.bpj.2014.08.015.[2] Alexander Peyser and Wolfgang Nonner. Voltage sensing in ion channels: Mesoscale simulations of biological devices. Phys Rev E StatNonlin Soft Matter Phys, 86: 011910, Jul 2012. doi:10.1103/PhysRevE.86.011910.[3] Alexander Peyser and Wolfgang Nonner. The sliding-helix voltage sensor: mesoscale views of a robust structure-function relationship. Eur Biophys J, 41:705–721,2012. doi:10.1007/s00249-012-0847-z.[4] Roland Roth, Dirk Gillespie, Wolfgang Nonner, and Robert E. Eisenberg. Bubbles, gating, and anesthetics in ion channels. Biophys J, 94(11):4282–4298,2008. doi:10.1529/biophysj.107.120493.[5] Sang-Ah Seoh, Daniel Sigg, Diane M. Papazian, and Francisco Bezanilla. Voltage-sensing residues in the S2 and S4 segments of the Shaker K+ channel. Neuron, 16 (6):1159–1167, 1 June1996. doi:10.1016/S0896-6273(00)80142-7.[6] Stephen B. Long, Xiao Tao, Ernest B. Campbell, and Roderick MacKinnon. Atomic structure of a voltage-dependent K+ channel in a lipid membrane-like environment. Nature, 450(7168):376–382,2007. doi:10.1038/nature06265
Shortest Path with Alternatives for Uniform Arrival Times: Algorithms and Experiments
Full text linkThe Shortest Path with Alternatives (SPA) policy differs from classical shortest path routing in the following way: instead of providing an exact list of means of transportation to follow, this policy gives such a list for each stop, and the traveler is supposed to pick the first option from this list when waiting at some stop. First, we show that an optimal policy of this type can be computed in polynomial time for uniform arrival times under reasonable assumptions. A similar result was so far only known for Poisson arrival times, which are less realistic for frequency-based public transportation systems. Second, we experimentally evaluate such policies. In this context, our main finding is that SPA policies are surprisingly competitive compared to traditional shortest paths, and moreover yield a significant reduction of waiting times, and therefore improvement of user experience, compared to similar greedy approaches. Specifically, for roughly 25% of considered cases, we could decrease the expected waiting time by at least 20%. To run our experiments, we also describe a tool-chain to derive the necessary information from the popular GTFS-format, therefore allowing the application of SPA policies to a wide range of public transportation systems
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe 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
Variations on the Author
Full text link“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
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
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