1,721,115 research outputs found
Multiscale modelling of cellular calcium signalling
No full textThe ability to design effective medicines that treat disease requires a detailed knowledge of the associated natural processes. These natural processes operate on a range of complex spatio-temporal scales. Computational modelling allows us to investigate such processes, however these often provide detail only at a single spatiotemporal scale. Multiscale modelling aims to combine or link these scales represented by computational models, such that information is passed between different types of simulation. The aim of this investigation is to develop a multiscale model of cellular calcium signalling through extension of existing models. The pancreatic acinar cell was chosen for this treatment, owing to the polarised structure, range of signalling events, and disease states that are characteristic of this cell type.Published models, that use networks of Ordinary Differential Equations (ODE), were implemented to gain understanding of the complex dynamics exhibited by cellular systems. ODE-based biological network models reduce the complexity of a system by making assumptions about the spatio-temporal properties. A model of the calcium dynamics of the pancreatic acinar cell was coupled to a model of the mitochondria, and the resulting collection of ODEs was extended to hypothetically simulate the onset of acute pancreatitis; a disease state whose mechanism is not yet fully understood. The entire model was then reformulated into one that uses the Finite Element Method (FEM) to solve the diffusion equation of species around the system, as well as to distribute spatially the contributing factors to cellular calcium signalling, such as associated calcium pumps. This provided a more physical representation of the cell, compared to the ODE model.However, some of the results found in the original published material relating to model behaviour could not be reproduced fully in the FEM implementation. The issues encountered during this study highlight the challenges faced when modelling complex systems that have incomplete data, and instead rely on heavily fitted parameters. Despite this, the results demonstrate behaviour consistent with many experimental observations, due to the sophistication of FEM over ODE models. These include insight into the distribution of mitochondria, calcium tunnelling in the endoplasmic reticulum (ER), and mitochondrial calcium accumulation as a mechanism of acute pancreatitis onset. These findings represent the unique paths that may be followed while constructing a multiscale model, and a platform from which further research may continue
Data related to: Simulated TEM imaging of a heavily irradiated metal
No full text<p>Data set related to article "Simulated TEM imaging of a heavily irradiated metal"</p>
<p>The data is the output of a simulation of single-crystal tungsten with periodic boundary conditions evolving under irradiation up to high dose (1 dpa). The simulation was done in LAMMPS, only every 100th snapshot in LAMMPS Dump format is uploaded here. A frame corresponds to a dose increment of 0.000167 dpa, i.e. frame 1000 corresponds to a dose of 0.167 dpa. The files are zipped. A finer resolution can be supplied upon request.</p>
<p>The simulations were performed for the article: <a href="https://doi.org/10.1103/PhysRevMaterials.6.063601" target="_blank" rel="noopener">10.1103/PhysRevMaterials.6.063601</a>, where more details on the simulations are found. The data is here made available for the article: <a href="https://doi.org/10.48550/arXiv.2401.14781" target="_blank" rel="noopener">10.48550/arXiv.2401.14781</a>.</p>
<p>The TEM simulation software is available at: <a href="https://github.com/mason-daniel/simulated_tem">https://github.com/mason-daniel/simulated_tem</a>.</p>
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
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
Unusual Otto excitation dynamics and enhanced coupling of light to TE plasmons in graphene
No full textTransverse-electric (TE) plasmons are a unique and unusual aspect of graphene's plasmonic response that are predicted to manifest when the sign of imaginary part of conductivity changes to negative near the spectral onset of interband transitions. Although thus far, a feasible platform for the direct experimental detection of TE plasmons at finite temperature is yet to be suggested. Here we analyze the dynamics of Otto-Kretschmann excitation of TE plasmons in graphene. We show that TE plasmons supported by graphene in an Otto configuration unusually exhibit a cutoff thickness between the coupling prism and the graphene layer that forbids their efficient coupling to an incident wave in the case of a singlelayer graphene at typical finite temperatures. In contrast, significantly increased coupling in the case of an N-layer graphene insulator stack, owing to an N-fold increase of the effective graphene conductivity as the insulator thickness approaches zero, is predicted to provide a TE plasmon resonance that is easily detectable at room temperature.
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