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Electronic appendix to thesis: "Multiscale approximations of integral equation-based solvation models"
No full textElectronic supplementary material to the doctoral thesis "Multiscale approximations of integral equation-based solvation models" by Lennart Eisel
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
Multiscale approximations of integral equation-based solvation models
No full textDie Anwendbarkeit und Kosten quantenchemischer Solvatationsmodelle, wie dem "embedded cluster reference interaction site model" (EC-RISM) werden vor allem durch die Berechnungskosten der Elektronenstruktur, sowie des elektrostatischen Potentials bestimmt, bedingt durch die iterative Lösung dieser Verfahren und der damit einhergehenden Wiederholung der teuren Elektronenstrukturrechnung.
Hierdurch wird ihre Anwendung auf chemische Systeme geringer Größe beschränkt. In dieser Arbeit wird ein neues Solvatationsmodell, ONIOM-EC-RISM, präsentiert mit dem dieser Rechenaufwand für das bisherige EC-RISM Verfahren, durch die Einführung einer multiskalen Approximation der Elektronenstruktur, drastisch reduziert werden kann. Hierdurch erschließt sich die Möglichkeit das EC-RISM-Solvatationsmodell auch auf größere chemische Systeme, wie z.B. Proteinsysteme, anzuwenden.
Neben den für das Verständnis des ONIOM-EC-RISM-Modells relevanten theoretischen Grundlagen additiver und subtraktiver Multiskalenapproximationen, des statistisch-thermodynamischen RISM-Solvatationsmodells, sowie des methodisch verwandten ONIOM-PCM-Solvatationsmodells, werden die Theorie und technische Implementation des neuen Modells umfangreich dargestellt. Darüber hinaus wird aufgezeigt wie zuvor für das EC-RISM-Referenzmodell verwendete empirische Korrekturen in den ONIOM-EC-RISM-Kontext übertragen werden können. Hierbei wird das Größenextrapolationslimit der ONIOM-Methode ausgenutzt, wodurch Korrekturen erhalten werden, die frei von jeglichen Partitionierungsfehlern sind.
Die resultierenden Modelle sind in der Lage, die \pKa-Vorhersagequalität des EC-RISM-Referenzmodells für den pKa-Datensatz der SAMPL6-Challenge, einem "blind prediction" Wettbewerb zur Vorhersage thermodynamischer Größen, zu reproduzieren und teilweise zu übertreffen, während gleichzeitig die Gesamtkosten des EC-RISM-Verfahrens drastisch reduziert werden können.
Neben der Validierung des ONIOM-EC-RISM-Verfahrens anhand von pKa-Werten wird demonstriert, wie das ONIOM-EC-RISM-Modell zusätzlich zur Vorhersage chemischer Verschiebungen eines Pentapeptidsystem verwendet werden kann. In diesem Zusammenhang wird ein neuartiger Ansatz vorgestellt der es erlaubt, pH-abhängige chemische Verschiebungen direkt aus spektroskopischen sowie pKa-Vorhersagen zu berechnen. Dies eröffnet erstmalig die Möglichkeit der direkten Modellierung von NMR-Titrationsexperimenten auf Grundlage des EC-RISM-Solvatationsmodells.The applicability and costs of quantum chemical solvation models, such as the "embedded cluster reference interaction site model" (EC-RISM), are mainly determined by the calculation costs of the electronic structure and the electrostatic potential, due to the iterative solution of these methods and the associated repetition of the expensive electronic structure calculation.
This limits their application to chemical systems of small size. In this work, a new solvation model, ONIOM-EC-RISM, is presented which drastically reduces the computational cost of the previous EC-RISM method by introducing a multiscale approximation of the electronic structure. This opens up the possibility of applying the EC-RISM solvation model to larger chemical systems, such as protein systems.
In addition to the relevant theoretical foundations of additive and subtractive multiscale approximations, required for the understanding of the ONIOM-EC-RISM model, the statistical-thermodynamical RISM solvation model and the methodologically related ONIOM-PCM solvation model, as well as the theory and technical implementation of the new model are presented in detail. In addition, it is shown how empirical corrections previously used for the EC-RISM reference model can be transferred to the ONIOM-EC-RISM context. Here, the size extrapolation limit of the ONIOM method is utilised, whereby corrections are obtained that are free of any partitioning errors.
The resulting models are able to reproduce and partially exceed the pKa prediction quality of the EC-RISM reference model for the pKa dataset of the SAMPL6 challenge, a blind prediction challenge for thermodynamic quantities, while at the same time drastically reducing the overall cost of the EC-RISM method.
In addition to the validation of the ONIOM-EC-RISM method on the basis of pKa values, it will be demonstrated how the ONIOM-EC-RISM model can additionally be used to predict chemical shifts of a pentapeptide system. In this context, a novel approach is presented that allows pH-dependent chemical shifts to be calculated directly from spectroscopic and pKa predictions. This opens up for the first time the possibility to directly model NMR titration experiments on the basis of the EC-RISM solvation model
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
Author-wise bibliometric analysis based on entropy.
No full textAuthor-wise bibliometric analysis based on entropy.</p
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