1,720,980 research outputs found
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
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
Bioinformatical analysis of RNA - protein interactions in AU-rich element mediated decay
No full textIn dieser Arbeit wird die Interaktion von RNA bindenden Proteinen
(RBPS) mit ihren Ziel-RNAs untersucht. Das Hauptaugenmerk liegt
dabei auf Proteinen, die mit so genannten AU-reichen Elementen
(ARE) interagieren, so genannte AU-reich bindende Proteine (ABPs).
Der Interaktionspartner, AREs, sind cis-regulatorische Elemente welche
entlang vieler Gene in höheren Organismen zu finden sind. Ihre Funk-
tion im so genannten AU-rich element mediated decay (AMD), also
dem gezielten Abbau von mRNA, und Faktoren mit denen aktive (gebundene) von inaktiven (ungebundenen) Elementen voneinander
unterscheidbar werden, sind Teil dieser Studie.
Zu den behandelten Themen gehört die Analyse von PAR-iCLIP Daten,
bei der primäre Ziele von Tristetraprolin (TTP) und HuR (ELAVL1)
in LPS induzierten, primären "bonemarrow derived" Makrophagen
(BMDMs) aus Maus identifiziert werden. Des weiteren befasst sich
diese Arbeit mit dem Einfluss von RNA Sekundärstrukturen auf Bindung,
kooperatives bzw. kompetitives Bindungsverhalten von RBPs, Korre-
lation mit mRNA Abbauraten, überrepräsentierte Bindemotife und
Unterschiede in der frühen und späten Phase der Immunantwort.
Ein Vergleich unseres Datensets mit einem Überexpressions Datenset
und die Untersuchung des Potentials Ergebnisse von Maus auf Men-
sch zu übertragen sind weitere Punkte dieser Arbeit. AREsite, eine
von uns publizierte Datenbank wurde im Verlauf dieser Arbeit über-
arbeitet und durch eine neue Version, AREsite2 ersetzt. Diese neue
Datenbank enthält Annotationen von AU-/GU-/U- reichen Elementen
in allen genischen Regionen (exons, introns, UTRs) von kodieren-
den und nicht-kodierenden Genen in Mensch, Maus, Fruchtfliege, Ze-
brafisch und Bandwurm.
Zusammen mit der Integration experimenteller Ergebnisse in ARE-
site2 präsentiert diese Arbeit eine umfassende Analyse von RNA Ele-
menten und deren Sequenz- und Struktureigenschaften die für funk-
tionelle RNA-RBP Interaktion eine Rolle spielen.This work is concerned with the interaction of RNA binding proteins
(RPBs) and their RNA target sites. The main focus lies on proteins
interacting with AU-rich elements (AREs), so called AU-rich binding
proteins (ABPs). Their targets, AREs, are cis-acting RNA motifs found
throughout genes in many higher organisms. Their function in AU-
rich element mediated decay and the factors discriminating between
active (bound) and inactive (unbound) status of such RNA elements
is subject to this study.
We analyzed PAR-iCLIP data, identifying main targets of tristetrapro-
lin (TTP) and HuR (ELAVL1) in LPS induced, primary bonemarrow
derived marcophages (BMDMs) in mouse. The influence of RNA sec-
ondary structure on binding, cooperative vs. competitive behavior of
RBPs, correlation with mRNA decay rates, over-represented binding
motifs and differences between early and late immune-response bind-
ing of TTP are part of this thesis.
Furthermore, we compare our dataset to an over-expression study
and investigate the potential of our predictions in mouse for their
portability to human. Our previously published database for AREs
in human and mouse (AREsite) was updated during this thesis and
replaced by a new version (AREsite2), which contains annotations of
AU-/GU- and U-rich elements in all genic regions (exons, introns,
UTRs) of coding and non-coding genes in human, mouse, fruit fly,
zebrafish and bandworm.
Together with an example analysis of AREsite2 derived data, this the-
sis presents a comprehensive analysis of RNA elements and their se-
quence and structure features crucial for functional RNA-RBP inter-
action
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
Investigation and prediction of interactions between AU-rich binding proteins and AU rich elements and the generation of the "AREsite" webserver
No full textDiese Diplomarbeit beschäftigt sich mit der Rolle von AU-reichen Elementen (ARE) und an sie bindende Proteine (AUBPs). AU-reiche Elemente finden sich in der 3’ untranslatierten Region von messenger RNAs(mRNAs). Sie sind RNA Sequenz Motife und die mit ihnen interagierenden AUBPs spielen eine wichtige Rolle in der Regulation der Stabilität von mRNA. In einem Organismus finden sich viele Möglichkeiten die Expression von Genen in Abhaengigkeit des Bedarfs
zu regulieren. Eine sehr schnelle und effektive Möglichkeiten stellt die genannte Regulation der mRNA Stabilität dar. Unter den bekannten Mechanismen für diese Art der Regulation finden sich die Interaktionen von AUBPs mit der zu regulierenden mRNA. Diese Proteine binden an AU-reiche Sequenzabschnitte in der 3’ untranslatierten Region von mRNAs und kõnnen ihre Stabilität in Abhängigkeit ihrer Art und Anzahl, sowie agonistischer oder antagonistischer Effekte von weiteren AUBPs oder RNA bindenden Faktoren, regulieren.
Die Tatsache der schnellen und effektiven Regulation der Genexpression durch mRNA De-/Stabilisierung lässt diese Proteine und durch sie regulierte mRNAs vermehrt in den Fokus wissenschaftlicher Arbeiten in Bereichen von der Krebsforschung bis hin zur synthetischen Biologie rücken. Das entwickeln eines besseren Verständnisses von ARE Motifen die tatsächlich von AUBPs gebunden werden sowie im Folgenden die Vorhersage neuer durch AUBP regulierter mRNAs mit Hilfe bioinformatischer Methoden waren Ziele dieser Diplomarbeit.
Zu diesem Zwecke wurde eine Datenbank generiert, die Transkripte von Maus und Mensch mit von uns annotierten ARE Motifen beinhaltet. Des weiteren enthält die Datenbank Informationen über die Zugänglichkeit und Überrepresentation dieser Motife, sowie phylogenetische Information, welche Allesamt durch das Anwenden von in silico Methoden wie RNA Faltung, der Erstellung multipler Alignments und der Analyse der Nukleotidanreicherung mittels Markov Modellen der Ordnung 0 und 1, erzeugt wurden. Eine zweite Datenbank die Literatur bezüglich der Effekte von AUPBs auf experimentell untersuchte Ziele dieser Proteine enthält wurde ebenfalls aufgebaut. Beide
Datenbanken wurden anschliessend vereint um einen Webserver namens ’AREsite’ herzustellen.Dieser Webserver wurde bereits publiziert (1) und ist ein frei zugängliches Werkzeug zur Untersuchung von bekannten sowie der Vorhersage bisher unbekannter mRNAs unter AUPB Regulation. Die Analyse der über den Webserver verfügbaren Information zur Vorhersage neuer AUPB Ziele war Teil dieser Diplomarbeit und die Resultate dieser Analyse sind im Bereich 5 beschrieben. Der Webserver ’AREsite’ ist unter der
Adresse http://rna.tbi.univie.ac.at/AREsite erreichbar und wurde bere-
its erfolgreich zur Analyse von AUPB Zielen herangezogen (2).This thesis is focused on AU-rich elements (ARE) and AU-rich binding proteins (AUBPs). AU-rich elements can be found in the 3’ untranslated region of messenger RNAs (mRNAs). They are RNA sequence motifs and their interacting proteins play a a major role for regulation of mRNA stability. Various layers of regulation exist in an organism that allow it to regulate the level of gene expression according to it’s needs. One of those layers is the regulation of mRNA stability, which allows an organism to regulate the amount of protein levels very fast and effective. A well known example for this type of control is the interaction of AU-rich binding proteins and their target mRNA.
This proteins can bind to ARE sequence motifs in the mRNAs 3’ untranslated region and stabilize or destabilize their target as a function of the type and amount of AUBPs bound and agonistic or antagonistic effects by other AUBPs or RNA binding factors.
As regulation of gene expression via mRNA stability is a very fast and precise method, these proteins and their targets are attracting the attention of researchers in various fields, from cancer research to synthetic biology. The main goal of this thesis is a better understanding of ARE motifs that mark mRNAs as AUBP targets and in the following the prediction of novel AUBP targets with bioinformatical analysis. To analyze these RNA binding proteins, a database was generated, that contains human and mouse transcripts which where annotated for the presence of ARE motifs. Information on the accessibility and fold-enrichment, as well as on phylogenetic conservation of this motifs
in known one-to-one orthologs was added by in silico folding of the mRNA 3’ UTRs, the generation of multiple alignments and analyzation of the nucleotide composition in the 3’ UTR with an order-0 and an order-1 markov model . A second database containing literature about the effects of AUBPs on experimentally validated AUBP targets was produced as well. The webserver ’AREsite’ has been built and published (1), combining both databases as backends and making the generated information freely accessible, thereby presenting a tool
that can be used to examine known, or to predicted novel AUBP targets.
Part of this thesis was the analyzation of information provided by this webserver for the prediction of novel AUBP targets.
The results of this analysis are presented in the section 5. The generated webserver ’AREsite’ is avaliable at http://rna.tbi.univie.ac.at/AREsite and has already been used as tool for the analysis of AUBP targets (2)
Author-wise bibliometric analysis based on entropy.
No full textAuthor-wise bibliometric analysis based on entropy.</p
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