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Full text linkMathematical model of competence regulation circuit
No full textGene expression regulatory networks are molecular networks which describe interactions among gene products in terms of biochemical reactions. This helps us understand the molecular mechanisms underlying important biological processes as well as cell functioning as a whole. For instance, the phenomenon of bacterial competence, whereby a bacterium enters a transiently differentiated state, incorporating DNA fragments from its environment into its genome, has been studied with the help of such gene regulatory circuits (Suel et al., 2006; Maamar and Dubnau, 2005). As a result, a genetic circuit has been taken into account in order to describe the transition from a vegetative state to a transient state of competence and vice versa. In this work, we are going to study a genetic circuit presented by Suel et al. (2007) to describe this dynamical behaviour. The authors introduce model reduction techniques to study the behaviour of stochastic chemical system of X species by means of an adiabatic two dimensional model. While the adiabatic model helps us understand about the dynamics near the steady state, it gives an incorrect description of the time-scales of the competent state. For this reason, it is necessary to build up a model which better describes the system realistically. In the thesis, I propose an approximate two-dimensional model of the full high-dimensional system and from that, the dynamics of the system can be simulated more accurately compared to that of Suel et al. (2007). I then show how to put the noise back into the approximate model to be able come up with a stochastic model which can mathematically describe the dynamical behaviour of the original high dimensional system. I also found out that the evolution of the system is not well approximated by a Langevin process. This leads to a gap between the real behavior which is described by Gillespie's stochastic simulation and the Langevin approximation. To overcome this, I have fixed the stochastic Langevin model by incorporating empirically tunable noise into the model so as to obtain a similar behaviour as observed in the original system. I also introduce the chemical Fokker-Planck equation aimed to estimate the probability density function of species concentrations which are involved in the biochemical system
A low dimensional approximation for competence in Bacillus subtilis
No full textThe behaviour of a high dimensional stochastic system described by a chemical master equation (CME) depends on many parameters, rendering explicit simulation an inefficient method for exploring the properties of such models. Capturing their behaviour by low-dimensional models makes analysis of system behaviour tractable. In this paper, we present low dimensional models for the noise-induced excitable dynamics in Bacillus subtilis, whereby a key protein ComK, which drives a complex chain of reactions leading to bacterial competence, gets expressed rapidly in large quantities (competent state) before subsiding to low levels of expression (vegetative state). These rapid reactions suggest the application of an adiabatic approximation of the dynamics of the regulatory model that, however, lead to competence durations that are incorrect by a factor of 2. We apply a modified version of an iterative functional procedure that faithfully approximates the time-course of the trajectories in terms of a two-dimensional model involving proteins ComK and ComS. Furthermore, in order to describe the bimodal bivariate marginal probability distribution obtained from the Gillespie simulations of the CME, we introduce a tunable multiplicative noise term in a two-dimensional Langevin model whose stationary state is described by the time-independent solution of the corresponding Fokker-Planck equation
BASIC CHARACTERISTICS OF NGUYEN AN NINH’S POLITICAL IDEOLOGY AND THE MEANING OF THAT IDEOLOGY
Full text linkThe late 19th and early 20th century was a special historical period for the Vietnamese people, a period of transformation that changed the nature of society. Our country was invaded by the French colonialists and became a semi-feudal, colonial country. It can be said that Nguyen An Ninh was a typical thinker of Vietnam in the late 19th and early 20th centuries. He introduced political ideas consistent with the reality of the Vietnamese revolution in this historical period. Based on an overview of the basic contents of Nguyen An Ninh’s political ideology, this study aims to clarify the basic characteristics of Nguyen An Ninh’s political ideology such as (i) Deep nationality in Nguyen An Ninh’s political ideology; (ii) Vivid practicality in Nguyen An Ninh’s political ideology; (iii) Nguyen An Ninh’s political ideology represents the transition from bourgeois-democratic ideology to Marxism-Leninism. On that basis, clarify the values of that characteristic in Vietnam’s revolutionary process. Article visualizations
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
Source and Pathway of the Western Arctic Upper Halocline in a Data-Constrained Coupled Ocean and Sea Ice Model
No full textA coupled ocean and sea ice model is used to investigate dense water (DW) formation in the Chukchi and Bering shelves and the pathways by which this water feeds the upper halocline. Two 1992–2008 data-constrained solutions at 9- and 4-km horizontal grid spacing show that 1) winter sea ice growth results in brine rejection and DW formation; 2) the DW flows primarily down Barrow and Central–Herald Canyons in the form of bottom-trapped, intermittent currents to depths of 50–150 m from the late winter to late summer seasons; and 3) eddies with diameters ~ 30 km carry the cold DW from the shelf break into the Canada Basin interior at depths of 50–150 m. The 4-km data-constrained solution does not show eddy transport across the Chukchi Shelf at shallow depths; instead, advection of DW downstream of polynya regions is driven by a strong (~0.1 m s[superscript −1]) mean current on the Chukchi Shelf. Upper halocline water (UHW) formation rate was obtained from two methods: one is based on satellite data and on a simple parameterized approach, and the other is computed from the authors’ model solution. The two methods yield 5740 ±1420 km[superscript 3] yr[superscript −1] and 4190–4860 ±1440 km[superscript 3] yr[superscript −1], respectively. These rates imply a halocline replenishment period of 10–21 yr. Passive tracers also show that water with highest density forms in the Gulf of Anadyr and along the eastern Siberian coast immediately north of the Bering Strait. These results provide a coherent picture of the seasonal development of UHW at high spatial and temporal resolutions and serve as a guide for improving understanding of water-mass formation in the western Arctic Ocean.National Science Foundation (U.S.) (Grant NSF ARC-1023499)United States. National Aeronautics and Space Administration (ECCO2 Project
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
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