1,720,953 research outputs found
Approximation methods and inference for stochastic biochemical kinetics
Full text linkRecent experiments have shown the fundamental role that random fluctuations play
in many chemical systems in living cells, such as gene regulatory networks. Mathematical
models are thus indispensable to describe such systems and to extract relevant
biological information from experimental data. Recent decades have seen a considerable
amount of modelling effort devoted to this task. However, current methodologies
still present outstanding mathematical and computational hurdles. In particular,
models which retain the discrete nature of particle numbers incur necessarily severe
computational overheads, greatly complicating the tasks of characterising statistically
the noise in cells and inferring parameters from data. In this thesis we study analytical
approximations and inference methods for stochastic reaction dynamics.
The chemical master equation is the accepted description of stochastic chemical
reaction networks whenever spatial effects can be ignored. Unfortunately, for most
systems no analytic solutions are known and stochastic simulations are computationally
expensive, making analytic approximations appealing alternatives. In the case
where spatial effects cannot be ignored, such systems are typically modelled by means
of stochastic reaction-diffusion processes. As in the non-spatial case an analytic treatment
is rarely possible and simulations quickly become infeasible. In particular, the
calibration of models to data constitutes a fundamental unsolved problem.
In the first part of this thesis we study two approximation methods of the chemical
master equation; the chemical Langevin equation and moment closure approximations.
The chemical Langevin equation approximates the discrete-valued process described
by the chemical master equation by a continuous diffusion process. Despite being frequently
used in the literature, it remains unclear how the boundary conditions behave
under this transition from discrete to continuous variables. We show that this boundary
problem results in the chemical Langevin equation being mathematically ill-defined if
defined in real space due to the occurrence of square roots of negative expressions.
We show that this problem can be avoided by extending the state space from real to
complex variables. We prove that this approach gives rise to real-valued moments and
thus admits a probabilistic interpretation. Numerical examples demonstrate better accuracy
of the developed complex chemical Langevin equation than various real-valued
implementations proposed in the literature.
Moment closure approximations aim at directly approximating the moments of a
process, rather then its distribution. The chemical master equation gives rise to an
infinite system of ordinary differential equations for the moments of a process. Moment
closure approximations close this infinite hierarchy of equations by expressing
moments above a certain order in terms of lower order moments. This is an ad hoc
approximation without any systematic justification, and the question arises if the resulting
equations always lead to physically meaningful results. We find that this is
indeed not always the case. Rather, moment closure approximations may give rise to
diverging time trajectories or otherwise unphysical behaviour, such as negative mean
values or unphysical oscillations. They thus fail to admit a probabilistic interpretation
in these cases, and care is needed when using them to not draw wrong conclusions.
In the second part of this work we consider systems where spatial effects have to be
taken into account. In general, such stochastic reaction-diffusion processes are only defined
in an algorithmic sense without any analytic description, and it is hence not even
conceptually clear how to define likelihoods for experimental data for such processes.
Calibration of such models to experimental data thus constitutes a highly non-trivial
task. We derive here a novel inference method by establishing a basic relationship
between stochastic reaction-diffusion processes and spatio-temporal Cox processes,
two classes of models that were considered to be distinct to each other to this date.
This novel connection naturally allows to compute approximate likelihoods and thus
to perform inference tasks for stochastic reaction-diffusion processes. The accuracy
and efficiency of this approach is demonstrated by means of several examples.
Overall, this thesis advances the state of the art of modelling methods for stochastic
reaction systems. It advances the understanding of several existing methods by elucidating
fundamental limitations of these methods, and several novel approximation and
inference methods are developed
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
Author-wise bibliometric analysis based on entropy.
No full textAuthor-wise bibliometric analysis based on entropy.</p
Author Under Sail The Imagination of Jack London, 1893-1902
No full textIn Author Under Sail, Jay Williams offers the first complete literary biography of Jack London as a professional writer engaged in the labor of writing. It examines the authorial imagination in London's work, the use of imagination in both his fiction and nonfiction, and the ways he defined imagination in the creative process in his business dealings with his publishers, editors, and agents. In this first volume of a two-volume biography, Williams traverses the years 1893 to 1902, from London's "Story of a Typhoon" to The People of the Abyss. The Jack London who emerges in the pages of Author Under Sail is a writer whose partnership with publishers, most notably his productive alliance with George Brett of Macmillan, was one of the most formative in American literary history. London pioneered many author models during the heyday of realism and naturalism, blurring the boundaries of these popular genres by focusing on absorption and theatricality and the representation of the seen and unseen. London created an impassioned, sincere, and extremely personal realism unlike that of other American writers of the time. Author Under Sail is a literary tour de force that reveals the full range of London as writer, creative citizen, and entrepreneur at the same time it sheds light on the maverick side of machine-age literature.Intro -- Title Page -- Copyright Page -- Dedication -- Contents -- Acknowledgments -- Introduction -- 1. Spirit Truth -- 2. From Absorption to Theatricality and Back Again -- 3. "I Will Build a New Present" -- 4. Sons as Authors -- 5. Fathers as Publishers -- 6. The Daughter as Author -- 7. Lovers as Authors -- 8. At Sea with the Family -- 9. Yellow News, Yellow Stories -- 10. The Return Home -- Notes -- Bibliography -- Index -- About Jay WilliamsIn Author Under Sail, Jay Williams offers the first complete literary biography of Jack London as a professional writer engaged in the labor of writing. It examines the authorial imagination in London's work, the use of imagination in both his fiction and nonfiction, and the ways he defined imagination in the creative process in his business dealings with his publishers, editors, and agents. In this first volume of a two-volume biography, Williams traverses the years 1893 to 1902, from London's "Story of a Typhoon" to The People of the Abyss. The Jack London who emerges in the pages of Author Under Sail is a writer whose partnership with publishers, most notably his productive alliance with George Brett of Macmillan, was one of the most formative in American literary history. London pioneered many author models during the heyday of realism and naturalism, blurring the boundaries of these popular genres by focusing on absorption and theatricality and the representation of the seen and unseen. London created an impassioned, sincere, and extremely personal realism unlike that of other American writers of the time. Author Under Sail is a literary tour de force that reveals the full range of London as writer, creative citizen, and entrepreneur at the same time it sheds light on the maverick side of machine-age literature.Description based on publisher supplied metadata and other sources.Electronic reproduction. Ann Arbor, Michigan : ProQuest Ebook Central, YYYY. Available via World Wide Web. Access may be limited to ProQuest Ebook Central affiliated libraries
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