1,720,960 research outputs found
Identification of novel miRNAs as diagnostic and prognostic biomarkers for prostate cancer using an in silico approach
Get PDFMagister Scientiae - MSc (Biotechnology)Cancer is known as uncontrollable cell growth which results in the formation of
tumours in the areas that are affected by the cancer. There are two types of tumours:
benign and malignant. This study focus is on prostate cancer (PCa) as one of the most
common cancers in men around the world. A previous study has reported that there
were 27,132 new cases of cancer in South Africa in 2010. Out of those, 4652 were
prostate cancer cases, which make it a considerable issue. The prostate is a gland that
forms part of the male reproductive system. Prostate cancer is more apparent in men
over the age of 65 years however it can be present in men of a lower age. However it
is rare in men under 45 years of age. Prostate cancer start as a small group of cancer
cells that can grow into a mature tumour. In the advanced stages, the tumour cells can
spread to other tissue by metastases and can lead to death. Current diagnostic tools
include Digital Rectal Examination (DRE), the Prostate-Specific Antigen test (PSA)
ultra sound, and biopsy
Identification of novel miRNAs as diagnostic and prognostic biomarkers for prostate cancer using an in silico approach
No full textMagister Scientiae - MSc (Biotechnology)Cancer is known as uncontrollable cell growth which results in the formation of
tumours in the areas that are affected by the cancer. There are two types of tumours:
benign and malignant. This study focus is on prostate cancer (PCa) as one of the most
common cancers in men around the world. A previous study has reported that there
were 27,132 new cases of cancer in South Africa in 2010. Out of those, 4652 were
prostate cancer cases, which make it a considerable issue. The prostate is a gland that
forms part of the male reproductive system. Prostate cancer is more apparent in men
over the age of 65 years however it can be present in men of a lower age. However it
is rare in men under 45 years of age. Prostate cancer start as a small group of cancer
cells that can grow into a mature tumour. In the advanced stages, the tumour cells can
spread to other tissue by metastases and can lead to death. Current diagnostic tools
include Digital Rectal Examination (DRE), the Prostate-Specific Antigen test (PSA)
ultra sound, and biopsy
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
Prediction of antimicrobial peptides using hyperparameter optimized support vector machines
No full textPhilosophiae Doctor - PhDAntimicrobial peptides (AMPs) play a key role in the innate immune response. They can be ubiquitously found in a wide range of eukaryotes including mammals, amphibians, insects, plants, and protozoa. In lower organisms, AMPs function merely as antibiotics by permeabilizing cell membranes and lysing invading microbes. Prediction of antimicrobial peptides is important because experimental methods used in characterizing AMPs are costly, time consuming and resource intensive and identification of AMPs in insects can serve as a template for the design of novel antibiotic. In order to fulfil this, firstly, data on antimicrobial peptides is extracted from UniProt, manually curated and stored into a centralized database called dragon antimicrobial peptide database (DAMPD). Secondly, based on the curated data, models to predict antimicrobial peptides are created using support vector machine with optimized hyperparameters. In particular, global optimization methods such as grid search, pattern search and derivative-free methods are utilised to optimize the SVM hyperparameters. These models are useful in characterizing unknown antimicrobial peptides. Finally, a webserver is created that will be used to predict antimicrobial peptides in haemotophagous insects such as Glossina morsitan and Anopheles gambiae.South Afric
Simulated annealing driven pattern search algorithms for global optimization
No full textThis dissertation is concerned with the unconstrained global optimization of nonlinear problems. These
problems are not easy to solve because of the multiplicity of local and global minima. In this dissertation,
we first study the pattern search method for local optimization. We study the pattern search method
numerically and provide a modification to it. In particular, we design a new pattern search method for
local optimization. The new pattern search improves the efficiency and reliability of the original pattern
search method. We then designed two simulated annealing algorithms for global optimization based on
the basic features of pattern search. The new methods are therefore hybrid. The first hybrid method is the
hybrid of simulated annealing and pattern search. This method is denoted by MSA. The second hybrid
method is a combination of MSA and the multi-level single linkage method. This method is denoted
by SAPS. The performance of MSA and SAPS are reported through extensive experiments on 50 test
problems. Results indicate that the new hybrids are efficient and reliable
Prediction of antimicrobial peptides using hyperparameter optimized support vector machines
Get PDFPhilosophiae Doctor - PhDAntimicrobial peptides (AMPs) play a key role in the innate immune response. They can be ubiquitously found in a wide range of eukaryotes including mammals, amphibians, insects, plants, and protozoa. In lower organisms, AMPs function merely as antibiotics by permeabilizing cell membranes and lysing invading microbes. Prediction of antimicrobial peptides is important because experimental methods used in characterizing AMPs are costly, time consuming and resource intensive and identification of AMPs in insects can serve as a template for the design of novel antibiotic. In order to fulfil this, firstly, data on antimicrobial peptides is extracted from UniProt, manually curated and stored into a centralized database called dragon antimicrobial peptide database (DAMPD). Secondly, based on the curated data, models to predict antimicrobial peptides are created using support vector machine with optimized hyperparameters. In particular, global optimization methods such as grid search, pattern search and derivative-free methods are utilised to optimize the SVM hyperparameters. These models are useful in characterizing unknown antimicrobial peptides. Finally, a webserver is created that will be used to predict antimicrobial peptides in haemotophagous insects such as Glossina morsitan and Anopheles gambiae.South Afric
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
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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