1,721,106 research outputs found
Leaf Vein CNN Software
No full textSoftware to extract and analyse leaf vein networks using convolutional neural networks.
LeafVeinCNN.mlappinstall - installs the software and trained CNN models as a matlab app (requires Matlab 2020a or later)
LeafVeinCNN.exe - installs the software and trained CNN models as a standalone package for Windows 10. This will automatically download the Matlab runtime library from the web during installation.
LeafVeinCNN_Manual.pdf - A user manual describing installation and use of the software
AnalyzER v1: Network analysis of the endoplasmic reticulum
Full text linkThe AnalyzER program provides quantitative analysis of the morphology and dynamics of the Endoplasmic Reticulum (ER) from confocal time-series. The tubular network and cisternae are automatically segmented and converted to graph representation with nodes at junctions connected by edges along the tubules. The program measures:
(i) The length, width, morphology and protein distribution along the ER tubules;
(ii) The degree and branch angles at junctions (nodes) in the tubular network;
(iii) The size, shape, and protein distribution in cisternal sheets and around the perimeter of the cisternae;
(iv) The topological organisation of the tubular and cisternal network determined using graph-theoretic metrics;
(v) The distribution of immobile nodes, tubules and cisternae using persistency mapping;
(vi) The local speed and direction of movement of tubules and cisternae using optical flow;
(vii) The size and shape of the polygonal regions enclosed by the network.
The AnalyzER package is implemented in MatLab (2017a) and can be downloaded as a MatLab app, or as a standalone *.exe package for Windows 10.
A full manual, tutorial and test data sets can also be downloaded.
All aspects of the analyses are handled through a single graphical user interface (GUI) to provide an integrated platform. An additional GUI is provided to facilitate statistical analysis by concatenating results from multiple experiments. The endoplasmic reticulum (ER) is a highly dynamic polygonal membrane network composed of interconnected tubules and sheets (cisternae) that forms the first compartment in the secretory pathway involved in protein translocation, folding, glycosylation, quality control, lipid synthesis, calcium signalling, and metabolon formation. Despite its central role in this plethora of biosynthetic, metabolic and physiological processes, there is little quantitative information on ER structure, morphology or dynamics. Here we describe a software package (AnalyzER) to automatically extract ER tubules and cisternae from multi-dimensional fluorescence images of plant ER. The structure, topology, protein-localisation patterns, and dynamics are automatically quantified using spatial, intensity and graph-theoretic metrics. We validate the method against manually-traced ground-truth networks, and calibrate the sub-resolution width estimates against ER profiles identified in serial block-face SEM images. We apply the approach to quantify the effects on ER morphology of drug treatments, abiotic stress and over-expression of ER tubule-shaping and cisternal-modifying proteins
Transcriptome of bacterial pathogens of common bean exposed to hydrogen peroxide at 21°C and 28°C.
No full textNB: This dataset is currently under embargo while the data is being verified.
For more details, please see my thesis "Investigating the effects of temperature on bacterial pathogens of common bean".
Aim: Determine which genes are transcriptionally affected by temperature and oxidative stress in plant pathogenic Pseudomonas (Pseudomonas savastanoi pv phaseolicola 1302A and Pseudomonas syringae pv syringae B728a)
(Description continued in ReadMe.txt file
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
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