1,720,956 research outputs found
Dynamical analysis of mushroom bifurcations: deterministic and stochastic approaches
No full textTreballs Finals de Grau de Matemàtiques, Facultat de Matemàtiques, Universitat de Barcelona, Any: 2023, Director: Àlex Haro i Josep Sardanyés i Cayuela[en] Bifurcation theory has found contemporary applications in synthetic biology, particularly in the field of biosensors [43]. The aim of this thesis is to expand upon the framework presented in the referenced paper, which introduces a model depicting the behavior of mushroom bifurcations. The mushroom bifurcation diagram exhibits four saddle-node bifurcations and involves bistability. Our goal is to develop a comprehensive mathematical formalism that can effectively describe this behavior, both deterministically and stochastically. By doing so, we seek to uncover additional properties regarding the transients exhibited by these biosensors, specifically focusing on optimizing their timer-effect, memory properties, and signaling capabilities.
We will introduce stochastic dynamics by considering intrinsic noise in the molecular processes, allowing us to investigate the slowing-down effects in the vicinity of the saddle-nodes and transcritical bifurcations. To conduct this study, we will use three fundamental mathematical tools, which can be regarded as the backbone of our analysis. These mathematical vertebrae include the Lemma of Morse, the Weierstrass Preparation Theorem and, most notably, the Implicit Function Theorem. Through this rigorous analysis, we aim to enhance our understanding of the underlying dynamics of these biosensors and facilitate their further improvement and utilization in various applications
Dynamical analysis of mushroom bifurcations: deterministic and stochastic approaches
Get PDFTreballs Finals de Grau de Matemàtiques, Facultat de Matemàtiques, Universitat de Barcelona, Any: 2023, Director: Àlex Haro i Josep Sardanyés i Cayuela[en] Bifurcation theory has found contemporary applications in synthetic biology, particularly in the field of biosensors [43]. The aim of this thesis is to expand upon the framework presented in the referenced paper, which introduces a model depicting the behavior of mushroom bifurcations. The mushroom bifurcation diagram exhibits four saddle-node bifurcations and involves bistability. Our goal is to develop a comprehensive mathematical formalism that can effectively describe this behavior, both deterministically and stochastically. By doing so, we seek to uncover additional properties regarding the transients exhibited by these biosensors, specifically focusing on optimizing their timer-effect, memory properties, and signaling capabilities.
We will introduce stochastic dynamics by considering intrinsic noise in the molecular processes, allowing us to investigate the slowing-down effects in the vicinity of the saddle-nodes and transcritical bifurcations. To conduct this study, we will use three fundamental mathematical tools, which can be regarded as the backbone of our analysis. These mathematical vertebrae include the Lemma of Morse, the Weierstrass Preparation Theorem and, most notably, the Implicit Function Theorem. Through this rigorous analysis, we aim to enhance our understanding of the underlying dynamics of these biosensors and facilitate their further improvement and utilization in various applications
A mathematical study of combined bacteriophage and antibiotic therapies
No full textThe rise of antimicrobial resistance poses a major global health threat, requiring innovative treatment strategies beyond conventional antibiotics. Among the most promising alternatives is the combined use of bacteriophages (phages) and antibiotics—a synergy that can potentially suppress or reverse bacterial resistance. In this work, we develop and analyze several mathematical models to study the population dynamics of bacteria under antibiotic and phage pressure, focusing on \textit{in vitro} systems involving \textit{Klebsiella pneumoniae}, a clinically relevant pathogen. We begin by analyzing a reduced antibiotic–bacteria model, characterizing its equilibria, stability, and bifurcations. Through the use of the variational equations, we identify the system's sensitivity to parameters—particularly the antibiotic-induced mutation rate and bacterial death rate—that govern extinction times and transient behaviors. We then extend the model to incorporate phage dynamics, resulting in a coupled system that allows the study of phage-antibiotic synergies. We investigate scenarios such as the temporary near-disappearance and subsequent re-emergence of bacterial populations, and study the role of pseudo-equilibria, where the phage population may not be at equilibrium.
Our findings suggest that system behavior is highly sensitive to specific parameters such as antibiotic concentration, mutation rate (from resistant to sensitive), growth rate, and mortality rate. This modeling framework lays the groundwork for future experimental calibration and optimization of phage–antibiotic strategies, and opens up new questions regarding the influence of additional variables, such as temperature and pH causing both phage and bacteria decays, and the existence of scaling laws near bifurcations
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe 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
Get PDF“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
Get PDFWe 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
Get PDFWe 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
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