1,720,962 research outputs found
Application of cloning in the detection of HIV-1 and drug resistant minority populations
No full textMSc (Microbiology)Department of MicrobiologyHuman immunodeficiency virus (HIV) is the causative agent of acquired immunodeficiency syndrome (AIDS). The virus is genetically highly diversified with different genetic strains infecting different populations worldwide. Highly active antiretroviral therapy (HAART) reduces the morbidity and mortality due to AIDS. Unfortunately, the efficiency of these drugs is limited by the development of drug resistance usually caused by mutations in the protease and reverse transcriptase genes which complicates patient management.
Sequencing direct PCR products reveals the properties of major viral populations but has the potential to miss minority viral populations. This clearly means that resistant strains of minority populations may not be detected in direct sequencing of PCR products. Furthermore, if multiple drug resistance mutations are detected as mixtures in a given sample, it is not possible to determine whether the individual drug resistance mutations are present together on a single virus or exist in different viral sub-populations. Therefore, the general objective of this study was to design and evaluate a single genome sequencing protocol for the detection of HIV-1 drug resistance mutations in the protease and reverse transcriptase genes.
In this study the HIV Pol gene ( for protease and reverse transcriptase genes respectively) was amplified from 8 samples of HIV-1 infected individuals (7 treatment experienced and 1 treatment na·ive). Subsequent cloning was done on all 8 samples using the Topo TA cloning vector, 35 and 33 clones were obtained for protease and reverse transcriptase respectively. Sequencing of purified PCR products and viral clones was done using a BigDye terminator sequencer. A comparison of sequences obtained from direct sequencing of PCR products and cloned PCR sequences was done. Phylogenetic analysis confirmed that all sequences were of HIV-1 subtype C and amino acid determination helped revealed amino acid substitutions in comparison to the HIV-1 subtype B and C global consensus.
Using the Stanford drug resistance interpretation program, sequences obtained by direct sequencing of PCR products revealed mutations V11I (a minor resistant mutation for the protease region) and M184V (a NRTI resistant mutation), K101E and Y181C (NNRTI resistant mutations) from samples MARBB14 and MARBB73. Viral clones of samples MARBB14 and MARBB73 revealed the same mutations as those observed by direct sequencing of PCR products. In addition viral clones of sample MARBB73 also revealed reverse transcriptase mutations T215Y (a NRTI resistant mutation) and Y181V (a NNRTI resistant Mutation).
Polymorphisms such as K20R, M361, M36V, L63P, H69K, V771 and V821 selected by protease inhibitors were also observed in the protease region from both direct sequences of PCR products and cloned PCR sequences. Using the student t-test, p values of 0.03 and 0.0002 for protease and reverse transcriptase respectively were obtained from comparisons of resistant mutations observed in sequences of PCR products and clone sequences for both protease and reverse transcriptase genes and the difference was considered significant.
The cloning technique was used as an approach to detect minority variants. Important resistant mutations were detected in clone sequences and not in sequences of PCR products. This suggests that mutations of interest could be missed in the direct sequencing of PCR products which is currently the norm in many settings.Technology Innovation Agency and University of Venda Research and Publication Committe
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
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
Serologic markers and molecular pidemiology of HBV in an HIV infected cohort from Cameroon
No full textMSc (Microbiology)Department of MicrobiologySee the attached abstract belo
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
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
- …
