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Author Correction: Lysogenic control of Bacillus subtilis morphology and fitness by Spbetavirus phi3T
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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
Dynamics of the Min system in Bacillus subtilis
Full text linkCell division is an essential process and thus under tight spatio-temporal control, which includes identification of the divisional plane. In most bacterial cells, the divisional plane is positioned at the geometrical cell center and its localization is indicated by the tubulin homologue FtsZ. After polymerizing into a ring-like structure (Z-ring), FtsZ will eventually recruit a multi-enzyme complex responsible for cell division, termed “divisome”. Similar to Escherichia coli, the Min system of the Gram-positive soil bacterium Bacillus subtilis was thought to aid in confining FtsZ polymerization to midcell by inhibiting the process close to the poles. Consisting of MinCDJ and the curvature sensing protein DivIVA, the protein network was expected to form a stable, bipolar gradient, in contrast to the oscillating Min system in E. coli. Since the B. subtilis Min system was later also observed to dynamically relocalize to the divisional septum before cytokinesis, we set out to re-characterize the Min system and the dynamic behavior of the individual components MinD, MinJ and DivIVA.
In this work, we first constructed functional fluorescent fusions for the Min proteins, encoded in their native, genomic loci. Using fluorescence recovery after photobleaching (FRAP) studies, we show that all components of the Min system display fast protein recovery at divisional septa, and further affect each other in their dynamics. Moreover, individual protein copy numbers were determined through in-gel fluorescence. Using photoactivated localization microscopy (PALM), we found a majority of Min proteins associated in large protein clusters, occurring frequently along lateral cell membrane, besides the expected polar and septal regions. Based on these data, a minimal reaction-diffusion model was built, confirming the experimental observations during simulations. In conclusion, we propose a new model of the B. subtilis Min system as cell cycle regulator, where a majority of Min proteins resides in dynamic clusters that constantly probe the cell for curvature. Upon septum formation, they partially relocalize to the site of division to aid in disassembly of the divisome and the FtsZ-ring downstream of division.
Additionally, a single-particle tracking (SPT) PALM workflow was established for routine usage. This technique was then utilized to analyze and dissect dynamic subpopulations of MinD and DivIVA, where both exhibited an immobile, a slow- and a fast-diffusive subpopulation.
Finally, we present an optimized workflow for employing mNeonGreen in bacterial PALM. By controlled and stepwise enhancement of sample-preparation, imaging conditions and post-processing, we demonstrate that mNeonGreen can even be used to resolve dense structures with a localization precision of 25 nm, exemplified by use of DivIVA-mNeonGreen.Da Zellteilung einen für Bakterien lebensnotwendigen Prozess darstellt, wird dieser räumlich und zeitlich streng kontrolliert, was die Identifizierung der korrekten Zellteilungsebene miteinschließt. In Bakterien ist diese Teilungsebene für gewöhnlich in der geometrischen Zellmitte positioniert. Das bakterielle Tubulin-Homolog FtsZ lokalisiert als erstes Protein an dieser zukünftigen Teilungsebene. Dort bildet sie eine aus FtsZ-Filamenten bestehende, ringförmige Struktur (Z-Ring), die hauptverantwortlich für die Rekrutierung des Divisoms ist, ein Multienzymkomplex der die Zellteilung orchestriert. Ähnlich wie Escherichia coli verfügt das Gram-positive Bakterium Bacillus subtilis über Min Proteine. In E. coli verhindert das oszillierende Min System eine Polymerisierung von FtsZ-Filamenten in den polaren Regionen der Zelle und sorgt damit für die korrekte Positionierung des Z-Rings. In B. subtilis besteht das Min Netzwerk aus MinCDJ und DivIVA, einem Protein das in der Lage ist Membrankrümmung zu detektieren. Auch wenn das System in B. subtilis nicht oszilliert, sondern einen scheinbar stabilen, bipolaren Gradienten bildet, wurde dort eine ähnliche Funktion vermutet. Später wurde allerdings beobachtet, dass sich Min Proteine in Bacillus dynamisch zum Teilungsseptum bewegen, sobald sich dieses bildet, was die genannte Rolle in Frage stellte. Aus diesem Grund haben wir in dieser Studie die einzelnen Min Proteine und ihre Dynamik erneut beobachtet und charakterisiert.
Zu diesem Zweck wurden zuerst funktionale, fluoreszente Proteinfusionen konstruiert, welche im nativen Genlocus kodiert sind. Diese Fusionen wurden für „fluorescence recovery after photobleaching” (FRAP) Experimente genutzt. Dabei konnten wir zeigen, dass sich alle Min Proteine dynamisch verhalten und dabei gegenseitig beeinflussen. Weiterhin konnten wir durch in-Gel-Fluoreszenz Proteinmengen der einzelnen Min Protein bestimmen. Mithilfe von photoaktivierter Lokalisationsmikroskopie (PALM) konnten wir im nächsten Schritt erkennen, dass sich die Mehrheit der Min Proteine in dynamischen Proteinclustern befindet. Neben der erwarteten Lokalisation nahe der Pole und des Septums wurden diese auch vermehrt an der lateralen Zellwand und im Cytosol beobachtet. Basierend auf diesen Daten wurde ein mathematisches Modell erstellt, welches die experimentellen Beobachtungen simulierte und bestätigte. Aufgrund dieser Erkenntnisse vermuten wir, dass das Min System in B. subtilis die Aufgabe eines Zellzyklus Regulators hat, und eine Neuinitiation der Teilung neben der genutzten Teilungsebene verhindert. Dabei befindet sich die Mehrzahl der Min Proteine in dynamischen Clustern, welche die Zelle nach Membrankrümmung absuchen, und sich in entsprechenden Regionen stabilisieren. Nach der Bildung eines Septums verlagert sich eine Mehrzahl dieser Cluster zur Mitte der Zelle, um nach erfolgter Teilung den Abbau des Zellteilungsapparates und des Z-Ringes zu unterstützen und voranzutreiben.
Darüber hinaus wurde ein Protokoll für die Routineanwendung von Einzelpartikelverfolgung (single-particle tracking, SPT) in PALM Experimenten entwickelt und optimiert. Dieses wurde dann zur Analyse und Unterscheidung der dynamischen Subpopulationen von MinD und DivIVA herangezogen. Diese konnten in jeweils drei Untergruppen unterteilt werden: immobile, langsam diffundierende und schnell diffundierende Proteine, wobei MinD das deutlich schnellere der beiden Proteine war.
Abschließend wurden im Rahmen dieser Arbeit ein Protokoll für den optimierten Einsatz des fluoreszenten Proteins mNeonGreen in der bakteriellen PAL Mikroskopie erarbeitet. Durch kontrollierte, schrittweise Verbesserung von Probenaufbereitung, Mikroskopie- und Belichtungsparametern sowie kontrolliertem Filtern der Bilddaten konnten wir demonstrieren, dass mNeonGreen sogar für die Rekonstruktion von dichten, zellulären Strukturen in Bakterien geeignet ist. Dabei erreichten wir bei Aufnahmen von DivIVA-mNeonGreen eine Lokalisationspräzision von 25 nm
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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