1,721,007 research outputs found
Mathematical model of stem and differentiated cell population size and depth dynamics
No full textMulticellular tissues are generally maintained and regenerated by populations of stem cells that undergo cell division and differentiation into specific cell types. In order to gain a quantitative understanding of the architecture of such tissues, it is important to characterize them according to the parameters governing the stem and differentiated cell population dynamics, such as division rates, death rates, and population sizes. Here we present a mathematical framework for quantitatively characterizing any such tissue. The framework consists of an analytically solvable model that captures the dynamics of stem and differentiated cell populations and an estimator of cell depth – the number of cell divisions undergone since the zygote – based on microsatellite mutation data. By fitting the model’s solution to data on average cell population depth obtained using the estimator and data on cell population size, one can obtain estimates of the biological parameters of interest. We exemplify this framework by applying it to data on mouse oocyte population size and average depth
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
cellanneal - a user-friendly deconvolution software for omics data
No full textcellanneal is a python-based software for deconvolving bulk RNA sequencing data. cellanneal relies on the optimisation of Spearman's rank correlation coefficient between experimental and computational mixture gene expression vectors using simulated annealing.
cellanneal can be used as a python package or via a command line interface, but importantly also provides a simple graphical user interface which is distributed as a single executable file for user convenience. The python package is available at https://github.com/LiBuchauer/cellanneal, the graphical software for MacOS and Microsoft Windows can be downloaded from this zenodo repository. Each zip archive contains an executable, an example mixture data file and an example signature data file.
Please notice that the there is delay of up to one minute between clicking the executable and the opening of the cellanneal graphical user interface.
macOS: Under most security settings, macOS does not allow to open software from unidentified developers via double-click. To circumvent this, right-click (secondary click) onto the cellanneal executable and choose "Open" at the top of the emerging context menu. This primes a dialogue in which you can then press "Open". Subsequently, the software will also be accessible via double-click.
Windows: Antiviral software may inhibit the launching of the software - it may be necessary to set an exception or click "Allow" when asked whether to procede.
For instructions on how to use cellanneal, please visit https://github.com/LiBuchauer/cellanneal
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
The spatio-temporal program of liver zonal regeneration
No full textWe performed mouse bulk liver mRNA sequencing (mcSCRBseq, Bagnoli et al., 2018), single-cell RNA seq (Feature Barcode 10x) and spatial transcriptomics (10x Visium) of hepatocytes and non-parenchymal cells (NPCs) at several time points along the time course of Acetaminophen (APAP)-induced liver damage and regeneration to identify spatio-temporal dynamics of liver regeneration.see README file for experiment detail
Visium datasets of mouse liver in different time points after APAP injection
No full text<p>The datasets were used to analyse the spatial trascriptomics for the manuscript "The spatiotemporal program of zonal liver regeneration following acute injury" (DOI https://doi.org/10.1016/j.stem.2022.04.008). Mice were injected a single dose of 300 mg/kg APAP, and livers were harvested 24, 48 and 72 hours after injection. livers were sectioned for Visium spatial transcirpomics (N = 2 mice per time point). see article's methods section for more detail. </p>
<p>other datasets used in the study are deposited in https://zenodo.org/records/6035873</p>
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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
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