1,720,974 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
Accurate modeling of protein structures by homology
Full text linkProteins are macromolecules which play a crucial role in virtually any process in the living cell. The determination of the 3-dimensional structure of a protein is a key component in understanding its function and mode of action. Preferably, the structure is solved by an experimental technique such as X-ray crystallography, nuclear magnetic resonance (NMR), or electron microscopy (EM). In many instances, experimental structures are unavailable or can not be readily determined. To the rescue come computational modeling techniques, e.g. comparative modeling, which are producing structures at a fast pace. State of the art methods are capable of generating accurate models down to the level of sidechains. These models are a useful tool in designing experiments, e.g. site-directed mutagenesis, virtual screening and identifying proteins of similar function. Despite the recent advancements, comparative modeling still has substantial room for improvement in many areas. In the course of this thesis, we aim at developing techniques which address some of the shortcomings of today's methods. As a solid foundation for this work, the OpenStructure software framework is developed, which allows to conveniently implement new methods and seamlessly integrate them with existing programs.
Computational modeling often requires comparisons of models and/or template structures. Standard structure similarity measures, such as RMSD and GDT are based on global superposition of structures, and their results are not meaningful when applied to structures exhibiting domain movements. For unsupervised comparison of structures on a large scale, a similarity measure based on internal distances was developed, which, to a large extent, is insensitive to domain movements. In analogy to the global distance test, the similarity measure is referred to as local distance difference test (lDDT).
A critical step of template-based modeling is the selection of suitable template structure information. For well characterized protein families, often 20 or more alternative experimental template structures are available. While all templates may share a similar overall topology, the relative orientation of sub-domains often differs significantly. Such intrinsic movements limit the assignment of consistent structural constraints for the comparative modeling step. An efficient and robust procedure to identify stable structural building blocks in ensembles of structures using contact-overlap map consistency (COM) is proposed.
The ability of a structural model to answer a particular biological research question is determined by its accuracy. Since models may contain substantial errors, reliable quality estimates are fundamental to determine their usefulness. We will develop techniques to assign quality estimates to models, which expand on the typical potential of mean force (PMF) formalism used in the field. By relating the protein's PMF energy to energy of experimental structures, we obtain a Z-score of the model's structure being of comparable quality to experimentally determined structures. In a second scoring function, the PMF scores are complemented with distance restraints from evolutionary related experimental structures. These restraints are helpful in discriminating between correct and incorrect folds and greatly improve the accuracy of the scoring function.
A novel modeling pipeline for the SWISS-MODEL expert system for comparative modeling is presented. For template and model selection, the pipeline builds on scoring functions developed in this thesis, and combines them with probability-based reliability estimates. The pipeline is embedded into a new web-interface, leveraging on capabilities of modern web browsers to perform the modeling in an interactive manner.
Finally, computational models are often improved by incorporating experimental restraints, e.g. from electron density maps, proteomics cross-links, mutation studies etc. Likewise, at resolutions below 2.5 A, X-ray density maps are often insufficiently defined to allow completely automated model building and can benefit from the incorporation of computational techniques. We explore the application of computational sampling techniques to the automated model building with ARP/wARP at low resolution with the aim to improve model completeness and to reduce fragmentation
Subjective sleep quality evolution in patients starting or switching to dolutegravir or cabotegravir: A real-world longitudinal study
No full textSubjective sleep quality evolution in patients starting or switching to dolutegravir or cabotegravir: A real-world longitudinal study
No full textVariations 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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