1,721,000 research outputs found
Statistical methods for biomarker discovery in proteomics
No full textSurface-Enhanced Laser Desorption and Ionization (SELDI) is a promising proteomic technique for discovering biomarkers. However, the pre-processing of the raw data is still problematic. Integrating transcriptomic and proteomic data may enhance the search for biomarkers, but the current data integration approach results in the loss of large amounts of data.In this thesis, we made improvements to the peak detection step in SELDI by developing the Annotated Regions of Signicance (ARS) method. It uses a multi-spectral signal detection method, `Region of Signicance' (RS), to identify regions with potential biomarkers. RS had better operating characteristics (OC) than existing methods in identifying peaks. Using lung cell line data, at 80% sensitivity, the False Discovery Rates (FDRs) of existing methods were around 25% to 50%, compared to around 8% for RS. ARS extracts a peak template from all spectra in the peak region via Principal Component Analysis (PCA) and ts the template to the spectra. A renement was made to the estimation of the amplitude via a mixture model. Using patient samples from a clinical study, we showed that ARS detected more peaks and gave more accurate peak quantications than the standard method. We implemented ARS as an R package, ProSpect, and also developed a graphical user interface, ProSpectGUI.Motivated by the performance of ARS in SELDI, we extended ARS to MALDI data with isotopic resolution. The extended ARS utilizes the isotopic pattern to lter out peaks which do not adhere to the expected isotopic pattern. Using the spike-in data, we validated the use of the log-transformed intensities for ARS in MALDI. Compared to the standard method, extended ARS generally had better specicity and was better in quantifying the peaks. At low FDR, extended ARS had higher sensitivity than the standard method.We also contributed to the integration of proteomic and transcriptomic information from the same samples by investigating the use of Maximum Covariance Analysis (MCA). The estimates of the gene and protein pattern-pairs from MCA were consistent and biologically congruent, compared to Generalized Singular Value Decomposition (gSVD). Therefore MCA has the potential to enhance biomarker discovery and our understanding of the interplay between genes and proteins.List of scientific papersI. Tan CS, Ploner A, Quandt A, Lehtiö J, Pawitan Y (2006). "Finding regions of significance in SELDI measurements for identifying protein biomarkers." Bioinformatics 22(12): 1515-23. Epub 2006 Mar 27 https://pubmed.ncbi.nlm.nih.gov/16567365II. Tan CS, Ploner A, Quandt A, Lehtiö J, Pernemalm M, Lewensohn R, Pawitan Y (2006). "Annotated regions of significance of SELDI-TOF-MS spectra for detecting protein biomarkers." Proteomics 6(23): 6124-33 https://pubmed.ncbi.nlm.nih.gov/17072907III. Quandt A, Ploner A, Tan CS, Lehtio J, Pawitan Y (2005). "ProSpect: An R package for analyzing SELDI measurements identifying protein biomarkers." Lecture Notes in Computer Science 3695: 140-150IV. Tan CS, Salim, A, Ploner A, Lehtio J, Chia KS, Pawitan Y (2008). "Correlating gene and protein expression data using Maximum Covariance Analysis." (Submitted)V. Tan CS, Lehtio J, Forshed J, Pernemalm M, Ploner A, Chia KS, Pawitan Y (2008). "Identifying peaks and isotopic patterns in MALDI data." (Submitted)</p
Supplemental Material, ECMO_manuscript_supplementary_JICM - Extracorporeal Membrane Oxygenation in Pregnant and Postpartum Women: A Systematic Review and Meta-Regression Analysis
No full textSupplemental Material, ECMO_manuscript_supplementary_JICM for Extracorporeal Membrane Oxygenation in Pregnant and Postpartum Women: A Systematic Review and Meta-Regression Analysis by John J. Y. Zhang, Jamie Ann-Hui Ong, Nicholas L. Syn, Roberto Lorusso, Chuen Seng Tan, Graeme MacLaren and Kollengode Ramanathan in Journal of Intensive Care Medicine</p
Supplemental material for Handling ties in continuous outcomes for confounder adjustment with rank-ordered logit and its application to ordinal outcomes
No full textSupplemental Material for Handling ties in continuous outcomes for confounder adjustment with rank-ordered logit and its application to ordinal outcomes by Yilin Ning, Chuen Seng Tan, Angeliki Maraki, Peh Joo Ho, Sheilagh Hodgins, Erika Comasco, Kent W Nilsson, Philippe Wagner, Eric YH Khoo, E-Shyong Tai, Shih Ling Kao, Mikael Hartman, Marie Reilly and Nathalie C Støer in Statistical Methods in Medical Research</p
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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