1,721,019 research outputs found
Unipept Desktop 2.0 : construction of targeted reference protein databases for metaproteogenomics analyses
No full textUnipept Desktop 2.0 is the most recent iteration of theUnipeptDesktop tool that adds support for the analysis of metaproteogenomicsdatasets. Unipept Desktop now supports the automatic constructionof targeted protein reference databases that only contain proteins(originating from the UniProtKB resource) associated with a predeterminedlist of taxa. This improves both the taxonomic and functional resolutionof a metaproteomic analysis and yields several technical advantages.By limiting the proteins present in a reference database, it is alsopossible to perform (meta)proteogenomics analyses. Since the proteinreference database resides on the user's local machine, theyhave complete control over the database used during an analysis. Datano longer need to be transmitted over the Internet, decreasing thetime required for an analysis and better safeguarding privacy-sensitivedata. As a proof of concept, we present a case study in which a humangut metaproteome dataset is analyzed with Unipept Desktop 2.0 usingdifferent targeted databases based on matched 16S rRNA gene sequencingdata
Research culture : science from bench to society
Full text linkResearch is a long process in which the collaboration between stakeholders involved in academia, industry and governments is crucial. Ideally, these stakeholders should work together to better align the innovation process with the values, needs and expectations of the research community. Reflecting on how we perform research and how our discoveries can benefit society is therefore of the utmost importance. The complete system of shared values concerning the research process is embedded in the concept of research culture, which has been gaining more attention in recent years. With the hope of increasing awareness of research culture among established scientists and early-career professionals, in this manuscript we discuss what research culture is, what it consists of and how it can positively influence scientific developments
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
Prediction-based reduction of the search space in metaproteomics
No full textMetaproteomics search databases typically take on enormous sizes since the a priori unknown composition of metaproteomics samples requires the inclusion of proteomes of hundreds to thousands of species that could potentially be found in the samples. A major consequence is that the identification rate in metaproteomics experiments remains drastically below the identification rate in single-species proteomics. Therefore, reducing the database size will not only decrease computation time, but can simultaneously increase identification rate.
To reduce database size, I used predictions from the machine learning algorithm CP-DT. This algorithm, originally intended to predict likely tryptic cleavage sites based on an ensemble of decision trees, has been shown to also be a useful predictor of the likelihood of observing a given peptide in a proteomics experiment. Indeed, if a large database (1.85 million protein sequences) is in silico digested using CP-DT, most peptides are marked as highly unlikely to be observed by the mass spectrometer. Moreover, if the peptide search space is reduced to only the top-35% scoring peptides according to CP-DT, more than 95% of the peptides that were actually observed by the mass spectrometer, are recovered.
From these results I can conclude that the search space can be drastically reduced using CP-DT. Ongoing work will show if this reduction in search space will lead to an increased identification rate, while keeping the false discovery rate (FDR) under control
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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