1,720,955 research outputs found
DNA Capture and Translocation through Nanopore
Full text linkThis thesis investigates DNA dynamics and translocation through nanopores using Brownian dynamics (BD) simulations, offering insights into sequencing technologies, DNA marker detection, and accurate barcoding utilizing solid-state nanopore platforms. First, we in silico study the intricate process of capture and translocation in a single nanopore. Our simulation reveals a high probability of hairpin loop formation during the capture process. However, attaching a charged tag to one end of DNA improves multi-scan rates and enhances unidirectional translocations. We use modulating voltage biases to multi-scan a lambda-phage dsDNA with oligonucleotide flap markers (tags) through a single and double nanopore system. Our study shows that the bulkier tags introduce velocity variations along the chain length that lead to potential inaccuracies in genetic distance (barcode) estimations. We introduce an interpolation scheme that incorporates both the tag velocities and the average velocity of the chain to improve barcode precision. Subsequently, we include bead and side-chain tags to explain asymmetric dwell time distributions as observed in double nanopore experiments. Our findings indicate that local charge interactions between tags and the nanopore\u27s electric field introduce dwell time asymmetries that can be used for discriminating tags based on their net charges. Finally, we obtain the current blockades of the molecular motifs attached to a dsDNA using electrokinetic Brownian dynamics (EKBD) simulation. Our simulation demonstrates that divalent salt reduces the translocation speed, facilitating precise measurement of the motif\u27s dwell time. Finally, we formulate a volumetric ansatz to construct current blockade diagrams from the ordinary BD simulation in a computationally efficient way and show that using simple scale factors, these volumetric blockades can be mapped accurately to the ionic current blockades obtained from more expensive EKBD simulation. Our studies present comprehensive explorations of DNA translocation and barcoding methods in solid-state nanopores, demonstrating their utility in nanopore sequencing and nanobiotechnolog
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
How capture affects polymer translocation in a solitary nanopore
Full text linkDNA capture with high fidelity is an essential part of nanopore
translocation. We report several important aspects of the capture process and
subsequent translocation of a model DNA polymer through a solid-state nanopore
in presence of an extended electric field using the Brownian dynamics
simulation that enables us to record statistics of the conformations at every
stage of the translocation process. By releasing the equilibrated DNAs from
different equipotentials, we observe that the capture time distribution depends
on the initial starting point and follows a Poisson process. The field gradient
elongates the DNA on its way towards the nanopore and favors a successful
translocation even after multiple failed threading attempts. Even in the limit
of an extremely narrow pore, a fully flexible chain has a finite probability of
hairpin-loop capture while this probability decreases for a stiffer chain and
promotes single file translocation. Our in silico studies identify and
differentiate characteristic distributions of the mean first passage time due
to single file translocation from those due to translocation of different types
of folds and provide direct evidences of the interpretation of the
experimentally observed folds [M. Gershow et al., Nat. Nanotech. 2, 775 (2007)
and M. Mihovilovic et al. Phys. Rev. Letts. 110, 028102 (2013)] in a solitary
nanopore. Finally, we show a new finding, - that a charged tag attached at the
end of the DNA enhances both the multi-scan rate as well as the
uni-directional translocation () probability
that would benefit the genomic barcoding and sequencing experiments
Author-wise bibliometric analysis based on entropy.
No full textAuthor-wise bibliometric analysis based on entropy.</p
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