1,721,037 research outputs found
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
NEXT GENERATION SEQUENCING: EEN TOOL OM DE GENETISCHE OORZAAK VAN MENSELIJKE ZIEKTES TE ACHTERHALEN
No full textAs a PhD student, I studied the potential of whole-genome sequencing data to assess various types of genetic variability (i.e. point mutations, insertions and deletions, copy number alterations, fusion genes, expression and methylation changes) and studied how each of them could contribute to a specific human disease. For this purpose, I developed, used, combined and adapted numerous different bioinformatical approaches and applied them to several whole-genome sequencing datasets (e.g., Complete Genomics and Illumina) in order to answer biological and clinical relevant questions. In particular, I studied sequencing data of familial amyotrophic lateral sclerosis (ALS), mismatch repair (MMR)-deficient cancers, uterine leiomyosarcoma (uLMS) and lung tumors.
First, I demonstrated that depth of coverage from WGS can be used to reveal repeat expansions. In combination with a tagging variant in a shared haplotype, this method confirmed the involvement of the (GGGGCC)n repeat expansions in C9orf72 as a cause of familial ALS.
In a second project, I performed whole-genome and whole-exome sequencing of MMR-deficient tumours. These tumours are characterized by very high mutation rates, requiring optimized variant filtering techniques to increase the number of true-positive and reduce false-negative variants. Furthermore, I demonstrated that MMR-deficient tumors carry a mutation signature distinct from other tumor genomes, but similar to germline DNA. This suggests that human genetic variation arises through mutations escaping MMR. Furthermore, I developed an MSI test based on these WGS data to detect MMR-deficient tumors. This MSI test has been patented and is being further developed by Biocartis into a clinical diagnostic test.
After sequencing uLMS cancer patients, characterized by genetic heterogeneity and a complex karyotype, I developed a novel method to uncover tumor driver genes. This model was successful in confirming the known involvement of the tumor suppressor gene RB1 and PTEN-pathway genes in uLMS. Furthermore by analysing copy number profiles of additional uLMSs, I identified additional genomic regions of prognostic relevance, i.e., deletion of 5q15, 7q36.3 (VIPR2) and 9q34.13.
Finally, I embarked on a computationally challenging project, in which I developed a strategy to integrate DNA methylation and gene expression data obtained from genome wide 450K Illumina methylation chips and transcriptome sequencing data. In this project, I studied the link between two respiratory diseases: COPD and lung cancer. This revealed that lung tumors that develop in a COPD environment differ from those that develop in patients without COPD. In particular, DNA methylation, gene expression and histological data all pointed to an altered anti-tumor immune response in COPD patients. Given the impaired immune response present in COPD lungs, these epigenetic events provide a biologically plausible and relevant link to lung cancer in COPD patients.status: Publishe
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
Induction and recovery of CpG site specific methylation changes in human bronchial cells after long-term exposure to carbon nanotubes and asbestos
No full textINTRODUCTION: Inhalation of asbestos induces lung cancer via different cellular mechanisms. Together with the increased production of carbon nanotubes (CNTs) grows the concern about adverse effects on the lungs given the similarities with asbestos. While it has been established that CNT and asbestos induce epigenetic alterations, it is currently not known whether alterations at epigenetic level remain stable after withdrawal of the exposure. Identification of DNA methylation changes after a low dose of CNT and asbestos exposure and recovery can be useful to determine the fibre/particle toxicity and adverse outcome. METHODS: Human bronchial epithelial cells (16HBE) were treated with a low and non-cytotoxic dose (0.25 µg/ml) of multi-walled carbon nanotubes (MWCNTs-NM400) or single-walled carbon nanotubes (SWCNTs-SRM2483) and 0.05 µg/ml amosite (brown) asbestos for the course of four weeks (sub-chronic exposure). After this treatment, the cells were further incubated (without particle/fibre) for two weeks, allowing recovery from the exposure (recovery period). Nuclear depositions of the CNTs were assessed using femtosecond pulsed laser microscopy in a label-free manner. DNA methylation alterations were analysed using microarrays that assess more than 850 thousand CpG sites in the whole genome. RESULTS: At non-cytotoxic doses, CNTs were noted to be incorporated with in the nucleus after a four weeks period. Exposure to MWCNTs induced a single hypomethylation at a CpG site and gene promoter region. No change in DNA methylation was observed after the recovery period for MWCNTs. Exposure to SWCNTs or amosite induced hypermethylation at CpG sites after sub-chronic exposure which may involve in 'transcription factor activity' and 'sequence-specific DNA binding' gene ontologies. After the recovery period, hypermethylation and hypomethylation were noted for both SWCNTs and amosite. Hippocalcinlike 1 (HPCAL1), protease serine 3 (PRSS3), kallikrein-related peptidase 3 (KLK3), kruppel like factor 3 (KLF3) genes were hypermethylated at different time points in either SWCNT-exposed or amosite-exposed cells. CONCLUSION: These results suggest that the specific SWCNT (SRM2483) and amosite fibres studied induce hypo- or hypermethylation on CpG sites in DNA after very low-dose exposure and recovery period. This effect was not seen for the studied MWCNT (NM400).sponsorship: This project was granted by Stichting Tegen Kanker (agreement no: 2012-218, project no: 3M150270). Manosij Ghosh would like to acknowledge Fwo Post-Doctoral Fellowship (12W7718N) and European Respiratory Society RESPIRE Postdoctoral Fellowship (RESPIRE2-2014-7310). Hannelore Bove acknowledges FWO for her post-doctoral fellowship (12P6819N). The authors thank Thomas Van Brussel for the technical assistance. (Stichting Tegen Kanker|2012-218, Stichting Tegen Kanker|3M150270, Fwo Post-Doctoral Fellowship|12W7718N, European Respiratory Society RESPIRE Postdoctoral Fellowship|RESPIRE2-2014-7310, FWO|12P6819N)status: Publishe
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
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