1,720,971 research outputs found
A framework for image-based, automated, multilevel analysis of the cytoskeletal morphology
Full text linkAim: The aim of this thesis is to create an integrated bioinformatic framework for the quantitative assessment of cytoskeleton (CSK) morphology. In this research, we demonstrated the validity of this approach by applying computational biology in two cases: Cytospace images and neurite images. I used these 2 dataset of images as reference dataset to build the computational biology framework and to verify its functionality. To accomplish this, I have analyzed Cytospace optical and confocal microscope images by Image J and MATLAB programming.
I have analyzed the neurite number and length of PC 12 cells by using the following software and tools: (a) custom made tool MATLAB, (b) Cell profiler, (c) Image J, and (d) Filopodyan. Outside this goal of CSK analysis I have also analysed the microcalcification and parenchyma images through my framework to verify the capability of the framework to operate on a different scenario.
Methods: We have developed various algorithms and protocols for the analysis of nuclei, tubulin and microtubules. Each component of the cytoskeleton plays a very essential role in understanding the behaviour of the cell. Moreover, the confocal images were processed properly to extract the information regarding the cytoskelton.
Finally, we also studied PC 12 cells and selected / designed useful algorithms to analyze changes in the number and length of neurites.
Results: In the first part of this thesis we presented an in-silico model constructed by using measurable parameters obtained from microscope images of cells. We use image analysis software Image J to identify cell shape parameters – including surface area, roundness, fractal dimension, such as entropy and coherency.
In the second part of thesis, we also analysed area, perimeter, major and minor axis, circularity, the solidity of the nuclei and tubulin by MATLAB programming. In the third part of the thesis, we anlayzed the dynamics of neurites by developing MATLAB scripts, using also other analysis tools such as Image J, Neuron J.
Conclusion: I have build a computational framework to analyse in quantitative manner images from optical and confocal microscopy.
During the first two years of PhD course I select, develop and integrated bioinformatics protocols and algorithms to define optimized operational pipelines. I used two datasets of image as reference to tuning the computational pipeline.
In the last period of phd course I can apply my optimised framework on microscopy images for detection and analysis of neurites. By means of the application of the framework was possible reduce considerable time of biologist to analyse the images
Microcalcification morphological descriptors and parenchyma fractal dimension hierarchically interact in breast cancer: a diagnostic perspective
No full textIntroduction
Herein, we propose a Systems Biology approach aimed at identifying quantitative morphological parameters useful in discriminating benign from malignant breast microcalcifications at digital mammography.
Materials and Methods
The study includes 31 patients in which microcalcifications had been detected during XR mammography and were further confirmed by stereotactic (XR-guided) biopsies. Patients were classified according to the BIRADS (Breast Imaging-Reporting and Data System), along with their parenchyma fractal dimension and biopsy size. A geometrical-topological characterization of microcalcifications was obtained as well.
Results
The ‘size of biopsy’ was the parameter endowed with the highest discriminant power between malignant and benign lesions thus confirming the reliability of surgeon judgment. The quantitative shape evaluation of both lesions and parenchyma allowed for a promising prediction of the BIRADS score. The area of lesions and parenchyma fractal dimension show a complex distribution for malignant breast calcifications that are consistent with their qualitative morphological pattern. Fractal dimension analysis enables the user to obtain reliable results as proved by its efficiency in the prediction of the morphology of breast cancer.
Conclusion
By reconstructing a phase-space distribution of biophysical parameters, different patterns of aggregation are recognized corresponding to different calcium deposition patterns, while the combination of tissue and microcalcification morphological descriptors provide a statistically significant prediction of tumour grade.
Clinical Relevance
The development of an automated morphology evaluation system can help during clinical evaluation while also sketching mechanistic hypotheses of microcalcification generation
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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