1,721,182 research outputs found
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
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Plasticity of extrachromosomal and intrachromosomal BRAF amplifications in overcoming targeted therapy dosage challenges
Full text linkFocal amplifications (FAs) resulting in copy number gain of short genomic regions, can mediate targeted therapy resistance. Understanding the structure, plasticity and vulnerability of FAs is critical for designing treatments that overcome such resistance. Here we developed a combined BRAF plus MEK inhibitor resistance melanoma model that bears high mutant BRAF amplifications through two modes of FAs: extrachromosomal double minutes (ecDNA/DMs) and intrachromosomal homogenously staining regions (HSRs), and investigated FA structure and dynamics in the context of drug resistance plasticity. We found that cells harboring BRAF FAs displayed mode switching between DMs and HSRs, from both de novo genetic changes and selection of pre-existing subpopulations. Plasticity is not exclusive to ecDNAs, as cells harboring HSRs also exhibit copy number and length changes through structural loss of amplicon repeats that allow them to respond to dose reduction and recover from drug addiction. DM and HSR mechanisms can couple with other BRAF genomic changes, such as kinase domain duplications and alternative splicing, to enhance therapy resistance. Amplicon plasticity is observed in other MAPK pathway genes, such as RAF1 and NRAS, and occurs in clinical cases of therapy resistance. We found that BRAF FA-induced dual MAPKi-resistant cells are more sensitive to pro-ferroptotic drugs, which extends the spectrum of melanoma resistance-derived ferroptosis sensitivity beyond cases of dedifferentiation
Characterizing the transcriptomic and genomic signatures of immune cell infiltration in undifferentiated sarcoma
Full text linkThere is a critical need for more effective systemic therapies for the treatment of soft tissue sarcoma and, specifically, undifferentiated sarcoma. Immunotherapy has shown signs of efficacy for the treatment of soft tissue sarcoma, particularly in undifferentiated sarcoma, though selecting the patients who will benefit from immunotherapy remains difficult and unclear. Further studies are needed to characterize the immune landscape of soft tissue sarcoma and to develop strategies to identify patients that are likely to benefit from immunotherapy.In this study, I investigated the immunologic heterogeneity and identify transcriptomic and genomic correlates of immune cell infiltration in undifferentiated sarcoma. In doing so, I determined the immune cell landscape, the optimal high-throughput tools, and the transcriptomic and genomic changes associated with high and low immune cell infiltration in soft tissue sarcoma. This study synthesized many datasets and data types for a comprehensive analysis of the immune landscape in soft tissue sarcoma. I first characterized the immune cell landscape in soft tissue sarcoma using flow cytometry data from fresh operative samples (n=105) of multiple soft tissue sarcoma subtypes. I then generated a tissue microarray with matched RNA sequencing data from 60 samples of untreated undifferentiated sarcoma to determine the optimal method of in-silico immune deconvolution, which allows for the expansion of this analysis to other next generation sequencing data. Finally, I synthesized multiple publicly available datasets containing next generation sequencing data (RNA sequencing and whole exome sequencing) from undifferentiated sarcoma samples. This data is combined with data from the aforementioned samples for a total of 193 samples and is used to determine the transcriptomic and genomic correlates of immune cell infiltration in undifferentiated sarcoma.In the analysis of the flow cytometry data, I found that undifferentiated sarcoma tumors are characterized by a myeloid predominance and a relative abundance of suppressor cells, such as Treg cells and CD11b cells. I additionally found that the immune composition of peripheral blood was associated with intratumoral leukocyte infiltration, and specifically that myeloid-predominant tumor and lymphocyte-predominant blood are mutually exclusive. I then determined the optimal in-silico immune deconvolution tool in undifferentiated sarcoma by determining the correlation between mIF and in-silico immune deconvolution scores. Based on these findings, I suggest the following practices when applying in-silico immune deconvolution tools to undifferentiated sarcoma: (1) Use TIMER to define overall immune cell infiltration. (2) Use MCP counter to define monocyte infiltration or use CIBERSORTx, EPIC, quanTIseq, TIMER, or xCell to define macrophage infiltration. (3) Use caution when using in-silico immune deconvolution tools to define CD8+ T cell infiltration. CIBERSORTx most accurately defines CD8+ T cell immune infiltration, however, there are still many instances when tumors with high CD8+ T cell infiltration will be missed using this technique. (4) Avoid applying in-silico immune deconvolution results to define B cell or CD4+ T cell immune infiltration. Finally, I found that increased copy number changes were associated with low immune cell infiltration in undifferentiated sarcoma. These findings were suggested in both transcriptomic and genomic analyses. Interestingly, this association between CNA and immune invasion were unique to the UPS and DDLPS subtypes of STS, but it was not seen in other subtypes of STS. The mechanisms underlying this association are not clear and warrant further study. These insights provide necessary information to understand which patients may benefit from immunotherapy and guide future studies to further the treatment of soft tissue sarcoma. These studies provide the groundwork for further investigation in this study of immune cell infiltration in soft tissue sarcoma and provide insights into how we may be able to improve outcomes in this rare and devastating disease. The mechanisms underlying these findings remain unclear and warrant further investigation. A deeper understanding of the drivers of immune cell infiltration, the unique tumor microenvironment in soft tissue sarcoma, and role that chromosomal instability plays in soft tissue sarcoma will hopefully ultimately lead to insights to new, and much-needed, treatments for this disease
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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