1,721,034 research outputs found
Code for the simulations of rupture steps in "megaprimer" DNA constructs in magnetic tweezers
No full textCode to predict first label positions in DNA constructs obtained by "mega primer" PCR assembly, convert the label positions to step size distributions, and to fit experimental step size data using simulated step size distributions.
The code is first described by
Yi-Yun Lin, Tine Brouns, Pauline J. Kolbeck, Willem Vanderlinden, and Jan Lipfert
"High-yield, ligation-free assembly of DNA constructs with nucleosome
positioning sequence repeats for single molecule manipulation assays"
Submitted
Preprint available at
https://www.biorxiv.org/content/10.1101/2023.01.05.522917v1
There are two Matlab scripts:
- Lin_etal_predict_steps.m is used to generate the step size distribution. It can be run stand alone. Simulation parameters are specified in the script.
It outputs a plot of the simulated step size distribution and also writes the simulated steps to a text file.
- Lin_etal_fit_step_distribution.m reads in simulated steps for different values of the label probability from files in the sub-directory "simulated_distributions".
An example set of simulated step sizes is included in the package. More steps (e.g. for different label probabilities, different sequences, etc.) can readily be computed using the first script Lin_etal_predict_steps.m.
The script Lin_etal_fit_step_distribution.m then reads in experimental data, an example of which is provided as Experimental_Steps_45pN.txt.
The script then compared the simulated distributions to the experimental data using both a chi-squared criterion and the mean step size.
The output are plots that are also exported to png and eps files. Example outputs are included in the package
Data for "DNA fluctuations reveal the size and dynamics of topological domains"
No full textThese are the data for the manuscript
"DNA fluctuations reveal the size and dynamics of topological domains"
Willem Vanderlinden, Enrico Skoruppa, Pauline Kolbeck, Enrico Carlon, and Jan Lipfert
PNAS Nexus (2022)
Please cite this reference when using or referring to these data.
The data sets contain experimental data and data from Monte Carlo simulations
- The data are organized by which figure in the main text they are presented in.
- The experimental data were generated by single-molecule magnetic tweezers measurements of DNA under defined forces and torques. The consist both of raw extension vs. time traces (both for bare DNA and in the presence of enzymes) and of analyzed data based on these extension time traces.
For Figure 1 and 4 we provide magnetic tweezers traces as text files with 6 columns, in the following format:
Column 1: Time in ms
Column 2: X position in µm
Column 3: Y position in µm
Column 4: Z position in µm
Column 5: Magnet Height (above the flow cell) in mm
Column 6: Magnet Rotation in turns
- The simulation data were generated by Monte Carlo simulations of DNA treated as an elastic rod
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
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