1,720,977 research outputs found
Far red fluorescent proteins: Where is the limit of the Acylimine Chromophore?
No full textThe search for new near-infrared probes for fluorescence imaging applications is a rapidly growing field of research. Monomeric fluorescent proteins that autocatalyze their chromophore are the most versatile markers for in vivo applications, but the development of bright far-red fluorescent proteins (RFPs) has proven difficult. In this contribution, we search for the theoretical limit of the red shift and how it can be reached without sacrificing the fluorescence quantum yield. Through extensive excited-state pathway calculations, molecular dynamics sampling, and statistical modeling using QM/MM schemes, we provide a new understanding of the chromophore's photophysics including the role of its acylimine extension, which is the main difference from other families of fluorescent proteins. The excited-state dynamics of the mPlum RFP and its mutants provide an ideal basis due to mPlum's flexible binding pocket and extended dynamic Stokes shift. We found a large number of structural species with red-shifted emission that differ in rotamer states and H-bonds between key amino acid residues in the binding pocket. By analyzing their spectral and structural features, we derive guidelines for future rational genetic design strategies.The authors acknowledge financial support from the European Research Council Advanced Grant DYNamo (ERC-2010- AdG-267374), Spanish Grant (FIS2013-46159-C3-1-P), and Grupos Consolidados UPV/EHU del Gobierno Vasco (IT578-13
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
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
Optische Anregungen in Biologischen Systemen: Multiskalen-Simulations-Strategien und Anwendungen an Rhodopsinen
Get PDFIn this work, novel computational approaches are developed for the quantitative calculation of optical properties of chromophores in biologic systems. To investigate the influence of interactions between a chromophore and its molecular environment (protein, membrane, solvent), different theoretical approaches, which describe the matter at different length- and timescales, in a "multi-scale approach", which is tested on proteins of the rhodopsin family. In these proteins, acting as visual pigments or light-driven proton pumps in halobacteria, the optical absorbtion maximum of retinal is shifted over a wide spectral range.
For the quantum mechanical (QM) description of the chromophore, appropriate approximations are found, which correctly describe its response (geometry, optical spectrum) to steric and electrostatic interactions. Here, shortcomings of time-dependent density functional theory and the role of static and dynamic correlation are analyzed.
The conventional QM/MM scheme, which combines the QM description of the chromophore with a molecular-mechanical (MM) description of the environment, is extended to achieve a self-consistent mutual polarization of QM and MM fragments. For this purpose, an interacting atomic induced dipole model is implemented and assessed for application in polypeptides. This polarization model is integrated in a multi-state QM/MM scheme for the calculation of excitation energies, which
incorporates the instantaneous polarization response of the protein/solvent environment to the excitation-induced charge redistribution on the chromophore. Moreover, the effects of charge transfer and dispersive interactions on the optical spectrum is investigated, and simple tests are proposed to predict the relevance of these effects and make an optimal choice for the QM region in a particular system.In dieser Arbeit werden neue computergestützte Ansätze für die quantitative Berechnung der optischen Eigenschaften von Chromophoren (CHR) in biologischen Systemen entwickelt. Um den Einfluss der Wechselwirkungen (WW) zwischen CHR und dessen molekularer Umgebung (Protein, Membran, Solvent) zu untersuchen, werden verschiedene theoretische Ansätze, welche die Materie auf unterschiedlicher Längen- und Zeitskala beschreiben, in einem "Multiskalen-Ansatz" kombiniert, der an Proteinen der Rhodopsin Familie getestet wird. In diesen Proteinen, die als Sehpigmente oder Licht-getriebene Ionenpumpen in Halobakterien dienen, wird das Absorptionsmaximum des Retinals im optischen Spektrum über einen weiten Wellenlängenbereich verschoben.
Für die quantenmechanische (QM) Beschreibung des CHR werden Näherungen gesucht, welche die Reaktion des CHR (Geometrie, Absorptionsspektrum) auf sterische und elektrostatische WW korrekt beschreiben. Dabei werden u.a. Defizite der zeitabhängigen Dichtefunktionaltheorie und die Rolle statischer und dynamischer Elektronenkorrelation analysiert.
Das übliche QM/MM-Schema, welches die QM Beschreibung des CHR mit einer molekular-mechanischen (MM) Beschreibung der Umgebung verbindet, wird erweitert, um eine selbst-konsistente gegenseitige Polarisation von QM und MM Fragment zu erreichen. Zu diesem Zweck wird ein Modell wechselwirkender atomarer induzierter Dipole implementiert und für die Anwendung an Polypeptiden getestet. Dieses Polarisationsmodell wird in ein QM/MM-Schema zur Berechnung vertikaler Anregungsenergien integriert, welches die instantane Polarisations-Antwort des Protein-Solvent-Systems auf die anregungsinduzierte Ladungsumverteilung auf dem CHR einbezieht. Ferner wird der Einfluss von Ladungstransfer und dispersiven WW auf das optische Spektrum untersucht und einfache Tests vorgeschlagen, um die Relevanz dieser Effekte vorherzusagen und die optimale Wahl der QM-Zone für das zu untersuchende System zu finden
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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