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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
Dynamics and molecular mechanisms aiding symbiont establishment in Lagria villosa beetles
No full textMany animals live in a symbiotic relationship with microbial partners. Among them, beneficial host-associated microorganisms may provide nutritional benefits, protect the host from antagonists, or help in detoxifying harmful compounds. To maintain a stable association, animal hosts vertically transmit symbionts to the offspring, acquire them horizontally from an external source, or carry out both transmission modes. In horizontal and mixed transmission modes, host molecular factors are necessary to screen for the right microbial partners from the environment, and microbial machineries help the symbionts gain entry and establish in the host. However, we know little about molecular factors that mediate symbiont establishment in invertebrates harbouring ectosymbionts. To expand our knowledge, I studied the defensive symbiotic association between Lagria villosa beetles and Burkholderia bacteria. Here, the female Lagria beetles smear symbionts on the egg surface during oviposition. The symbionts colonize three specialized cuticular invaginations on the dorsal surface of the larvae. On eggs and in the larvae, the symbionts produce antifungal compounds and protect the beetle from antagonists. Furthermore, the larvae can occasionally acquire symbionts from the external environment; therefore, they maintain a mixed transmission mode. Among the multiple strains of Burkholderia usually found in an individual, Burkholderia Lv-StB is the most dominant strain, but is uncultivable in the lab. However, Burkholderia gladioli Lv-StA that is occasionally found in the beetles, is cultivable. The ability to rear the beetles in the lab and cultivate one of the symbionts in vitro gives us the opportunity to study host and symbiont molecular factors involved in symbiont establishment. In this dissertation, first, I provide details on the dynamics and mechanisms of symbiont colonization. Symbionts colonize the dorsal structures of the larvae during hatching and a colonization time-window may restrict microbial entry into the host. Further, a transposon-insertion directed sequencing (Tn-seq) method was established in the lab using which 271 potential colonization factors in Lv-StA were identified, including motility, biofilm formation, cell wall structures, lipopeptides, oxidative stress response factors and iron scavenging molecules. Additionally, targeted mutagenesis and colonization assays with Lv-StA reveal that non-motile strains can still colonize the host, and this likely explains the loss of flagellar motility genes in Lv-StB, which has a more reduced genome than Lv-StA. Finally, by performing gene expression analysis across multiple developmental time points in symbiotic and aposymbiotic beetles, the host molecular responses in the presence of Lv-StB was investigated. It reveals that the host may not recognise symbiont presence, likely due to compartmentalization, or may have a constitutive response to the symbionts. Thus, combining our understanding of both host and symbiont molecular factors involved in establishment, interesting questions regarding how partner specificity is achieved in ectosymbioses, are revealed. This study gives us the opportunity to understand the mechanistic details of host – symbiont interactions and further to compare emerging patterns across other model and non-model systems.xii, 181 Seiten ; Illustrationen, Diagramm
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
Blanking on blanks: few insect microbiota studies control for contaminants.
Get PDFResearch on insect-microbe relationships is booming, with DNA sequencing being the most commonly used method to describe insect microbiota. However, sequencing is vulnerable to contamination, especially when the sample has low microbial biomass. Such low-biomass samples are common across insect taxa, developmental stages, and tissue types. Identifying putative contaminants is essential to distinguish between true microbiota and introduced contaminant DNA. It is therefore important that studies control for contamination, but how often this is done is unknown. To investigate the status quo of contamination control, we undertook a systematic literature review to quantify the prevalence of negative control usage and contamination control across the literature on insect microbiota (specifically bacterial communities) over a 10 year period. Two-thirds of the 243 insect microbiota studies evaluated had not included blanks (negative controls), and only 13.6% of the studies sequenced these blanks and controlled for contamination in their samples. Our findings highlight a major lack of contamination control in the field of insect microbiota research. This result suggests that a number of microbes reported in the literature may be contaminants as opposed to insect-associated microbiota and that more rigorous contamination control is needed to improve research reliability, validity, and reproducibility. Based on our findings, we recommend the previously developed guidelines outlined in the RIDE checklist, with the addition of one more guideline. We refer to this as the RIDES checklist, which stands for Report methodology, Include negative controls, Determine the level of contamination, Explore contamination downstream, and State the amount of off-target amplification.IMPORTANCEOur systematic review reveals a major lack of methodological rigor within the field of research on insect-associated microbiota. The small percentage of studies that control for contamination suggests that an unknown but potentially considerable number of bacteria reported in the literature could be contaminants. The implication of this finding is that true microbiota may be masked or misrepresented, especially in insects with low microbial biomass
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
Host adaptation protects a defensive symbiont during vertical transmission in beewolf wasps (Hymenoptera: Crabronidae)
Get PDFMicrobial symbioses are ubiquitous in insects, and present key drivers of evolutionary innovation. To
stabilize a symbiosis over long evolutionary timescales, the symbiont must be reliably transmitted to
the next host generation. Vertically transmitted extracellular symbionts commonly face prolonged
periods outside of the stable host environment during transmission, entailing exposure to diverse
biotic and abiotic threats. These threats should be exacerbated in insect symbionts of evolutionary
ancient associations, which generally possess eroded genomes with reduced genetic inventories.
While external transmission is widespread among the Hemiptera, Hymenoptera, Coleoptera and
Diptera, the mechanism protecting the symbionts from environmental threats during transmission
remain poorly studied.
In this dissertation, I employ the defensive symbiosis of the European beewolf Philanthus triangulum
(Hymneoptera: Crabronidae) and the Actinobacterium ‘Candidatus Streptomyces philanthi’
(henceforth S. philanthi) to investigate how a symbiont with an eroded genome copes with a host-derived exogenous challenge during vertical transmission in an evolutionary ancient symbiosis. Female
beewolves provide their brood cells with a symbiont-containing secretion, from which S. philanthi is
later transferred to the cocoon to protect the offspring from microbial opportunists by producing
antibiotics. In the brood cell, this secretion is exposed to extremely high concentrations of toxic nitric
oxide (NO) emitted by the beewolf egg, which effectively kills antagonistic microbes. How S. philanthi
withstands the lethal burst of NO remained unknown.
I show that the symbiont’s global stress response to NO is not sufficient to survive NO concentrations
mimicking brood cell-level concentrations in vitro. Instead, I demonstrate that the symbiont-
containing secretion consisting of long-chain hydrocarbons (HCs) forms an effective NO diffusion
barrier around S. philanthi, and additionally contains host-derived protective enzymes. While different
functions of an insect’s HC profile can exert conflicting selection pressures on its composition, in vitro
assays with beewolf-derived and synthetic HCs reveal that the NO diffusion barrier function of HCs in
P. triangulum does not constrain the insect’s multifunctional HC profile. My comparisons of HC profiles
across different beewolf hosts suggest their suitability for NO protection, and in vitro assays with their
respective symbionts indicate a widespread NO sensitivity. Given the shared ecology among
beewolves, as well as additional reports on NO defense in P. gibbosus and P. basilaris, NO fumigation
and the concomitant HC-mediated protection of the symbiont from NO is likely crucial across
beewolves.
My findings add a novel dimension to the plethora of functions of insect HCs, and constitute one of
the few examples of a host adaptation protecting a symbiont from a lethal threat during external
vertical transmission. I therefore illustrate a mechanism by which a symbiotic association can be
stabilized over long evolutionary timescales, an aspect essential to our general understanding of
microbial symbiosis.Mikrobielle Symbiosen sind allgegenwärtig in Insekten und stellen eine treibende Kraft für
evolutionäre Innovationen dar. Um eine Symbiose über lange evolutionäre Zeiträume zu stabilisieren
ist es erforderlich, dass der Symbiont zuverlässig auf die nächste Wirtsgeneration übertragen wird.
Vertikal übertragene extrazelluläre Symbionten verbringen während der Transmission oftmals längere
Zeiträume außerhalb des stabilen Wirtsmilieus, wobei sie mit diversen biotischen und abiotischen
Bedrohungen konfrontiert sind. Insektensymbionten in evolutionär alten Assoziationen sind aufgrund
ihrer erodierten Genome besonders anfällig gegenüber diesen Bedrohungen. Die externe
Symbiontentransmission ist zwar innerhalb der Ordnungen Hemiptera, Hymenoptera, Coleoptera und
Diptera weit verbreitet, dennoch sind die Mechanismen, die die Symbionten während dieser
Transmission vor Bedrohungen schützen, weitgehend unerforscht.
In dieser Dissertation untersuche ich anhand der evolutionär alten Verteidigungssymbiose des
Europäischen Bienenwolfes Philanthus triangulum (Hymenoptera: Crabronidae) mit dem
Actinobakterium ‘Candidatus Streptomyces philanthi’ (nachfolgend S. philanthi), wie ein Symbiont mit
einem erodierten Genom mit einer vom Wirt ausgehenden externen Bedrohung während der
vertikalen Transmission umgeht. Weibchen versehen ihre Brutzellen mit einem Sekret, das die
Symbionten beinhaltet. Die Symbionten werden zu einem späteren Zeitpunkt in den Kokon integriert,
wo sie Antibiotika zum Schutz der Brut vor opportunistischen Mikroben produzieren. Das Sekret ist in
der Brutzelle sehr hohen Konzentrationen toxischen Stickstoffmonoxids (NO) ausgesetzt, welches vom
Bienenwolf-Ei freigesetzt wird und antagonistische Mikroorganismen effektiv abtötet. Bisher war
unbekannt, wie die Symbionten den lethalen NO-Konzentrationen in der Brutzelle standhalten.
Ich zeige, dass die eigene Stressreaktion des Symbionten auf NO nicht ausreicht, um die in vitro
simulierten NO-Konzentrationen der Brutzelle zu überleben. Jedoch bildet das aus langkettigen
Kohlenwasserstoffen (KWs) bestehende Sekret, das die Symbionten umgibt, eine effektive NO-
Diffusionsbarriere um S. philanthi. Weiterhin enthält das Sekret vom Wirt produzierte Schutzenzyme.
Verschiedene Funktionen eines KW-Profils können gegensätzliche Selektionsdrücke auf seine
Komposition ausüben; allerdings zeigten in vitro-Experimente mit Bienenwolf- und synthetischen
KWs, dass die Fähigkeit, eine NO-Diffusionbarriere zu bilden, die Komposition des multifunktionalen
KW-Profils des Bienenwolfes nicht einschränkt. Vergleiche von KW-Profilen verschiedener
Bienenwolf-Wirte legen deren Eignung für eine NO-Barrierefunktion nahe, und in vitro-Experimente
mit den zugehörigen Symbionten weisen auf eine weit verbreitete NO-Sensitivität hin. Angesichts der
vergleichbaren Ökologie aller Bienenwölfe, sowie zusätzlicher Berichte über die Freisetzung von NO
in P. gibbosus und P. basilaris, ist der Einsatz von NO zu Verteidigungszwecken und der damit
einhergehende KW-vermittelte Symbiontenschutz wahrscheinlich von großer Bedeutung für alle
Bienenwölfe.
Meine Ergebnisse erweitern die Fülle an Funktionen von KWs in Insekten um eine neue Dimension,
und beschreiben eine der wenigen bekannten Wirtsadaptationen zum Schutz eines Symbionten vor
einer lethalen Bedrohung während der externen vertikalen Transmission. Sie illustrieren damit einen
Mechanismus, mithilfe dessen eine symbiotische Beziehung über lange evolutionäre Zeiträume
stabilisiert werden kann. Dieser Aspekt ist wesentlich für unser Verständnis von mikrobiellen
Symbiosen.VI, 126 Seiten; Illustrationen, Diagramme, Tabelle
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
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