1,721,004 research outputs found
Going Beyond Counting First Authors in Author Co-citation Analysis
No full textThe 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
Stochastic Modelling of Gene Expression: From Single Molecules to Populations
No full textGene expression constitutes a vital life process through which pieces of genetic information stored in the nucleotide sequence of DNA are transformed into functional molecules, namely proteins and RNA chains. These molecules and the intricate network of interactions among them are the driving force behind most cellular processes, including gene expression itself. Also, of particular importance is the regulation of gene expression. By modulating the levels of proteins they produce, cells manage to synchronise their internal workings and adapt to various environmental conditions. Moreover, in this manner cells manage to coordinate their genetically prescribed behaviour when present in populations, such as a developing embryo or a bacterial colony. This thesis presents a theoretical study of gene expression within the context of different organisational levels from the molecular to the cell population level.
On the single molecule level special emphasis is given on the dynamics of the RNA polymerase, the enzyme that carries out the transcription of DNA into RNA. Recent single molecule experiments have shed light on the dynamical behaviour of this molecule as it transcribes DNA. Of particular importance is the direct observation of transient pauses in the process of transcription, induced by the he backward translocation of the enzyme along the DNA template, a phenomenon dubbed backtracking. Motivated by this finding and the implications transcriptional pausing has for the regulation of DNA transcription, our work aims at providing a quantitative characterisation of backtracking and the effect of such pauses on the temporal dynamics of the process. Our results indicate that the lifetime of such pauses should obey a wide distribution and can have dramatic effects on the temporal statistics of the transcription process.
A particularly interesting function of backtracking is transcriptional error correction. Indeed, RNAP does not copy the genetic information accurately; thermal fluctuations introduce errors to the process that must be corrected on the fly. A proposed mechanism of transcriptional error correction involves backtracking of the RNA polymerase and the subsequent cleavage of the the erroneous RNA segment. Based on the picture of DNA transcription provided by singlemolecule experimentswe propose a putativemodel of this editing process. Our work offers a quantitative picture of transcriptional error correction, predicting the error rate in terms of microscopic rates parameters and allowing one to assess the role of backtracking in transcriptional fidelity. Furthermore, our model puts the specific mechanism of error correction into context by linking it to kinetic proofreading, a general principle of biological accuracy.
On a different level, the microscopic dynamics of the DNA transcription ought to have direct implications regarding fluctuations in the numbers of RNA species observed within the cell. These fluctuations have on their turn far-reaching implications regarding cell fate, behaviour and function. To study the effect transcriptional pauses have on the statistics of RNA production we propose an integrated model of DNA transcription. A key element of our model is that several RNAP molecules can transcribe DNA at the same time, moving in tandem on the template. Our results indicate that transcriptional pauses and exclusive interactions between the RNAP molecules, lead to bursts of RNA production and therefore make the process appear more random. Interestingly such pattern of mRNA production has been observed experimentally and hence our model provides a possible explanations of the phenomenon. It also demonstrates how interactions between molecules can affect behaviour at cellular level by introducing fluctuations in the process of gene expression.
At an even higher level, one should appreciate the fact that cells rarely exist in isolation. At this level of description we are interested in how intra-cellular fluctuations of molecular species affect the behaviour of populations of cells. In particular, motivated by the complex social behaviour observed in certain bacterial species, we propose an insilico paradigm of bacterial communication. In a nutshell, the circuit enables cells to communicate and choose between two antagonistic social behaviours. We find that owing to intra-cellular fluctuations the population can exist in two states: for low values of intra-cellular coupling the population appears mixed (disordered), with approximately one half of the cells adopting each behaviour. As the coupling is increased the population a consensus state starts to appear. We study the transition between the two regimes of behaviour and find that intra-cellular fluctuations as well as the size of the population affect the steepness of this transition
Variations on the Author
No full text“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
No full textWe 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
No full textWe 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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