1,720,958 research outputs found
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
Methodological Advances in the Field of Cross-linking Mass Spectrometry Data Acquisition and Analysis
Full text linkProtein-protein interactions (PPIs) are the drivers of most biological processes. Cross-linking mass spectrometry (XL-MS) allows the detection of PPIs from complex biological systems and even in vivo scenarios by combining chemical cross-linking with small reactive molecules, proteolytic digestion and LC-MS (liquid chromatography coupled to mass spectrometry) analyses. However, as the abundance and physicochemical properties of cross-linked peptides differ from those of unmodified peptides, the reliable identification and accurate quantification of cross-linked peptides requires tailored protocols, efficient acquisition strategies and dedicated data analysis pipelines. Throughout my doctoral studies, I focused on advancing different steps of the XL-MS pipeline, including (1) the optimization of acquisition parameters for the detection and quantification of isobarically labeled cross-linked peptides, (2) the development of novel methods for the targeted detection of cross-linked peptides over less wanted species, and (3) the introduction of a ground truth dataset for benchmarking existing cross-linking database search engines and the development of new computational tools.
Firstly, I described a speedy MS2-based acquisition strategy with an optimized stepped collision energy of 42% ± 6 and a perfect balance between sensitivity and accurate quantification of TMT-labeled cross-linked peptides from complex samples. Previously described MS2-MS3-based methods were shown to have exhaustive duty cycles, hampering the identification of cross-linked peptides, although their quantification capabilities overcame MS2-based methods.
Secondly, utilizing a real-time library search (RTLS) algorithm was shown to increase cross-link identifications by 45% as the instrument was able to partially distinguish cross-links from other peptide species based on the unique relative intensity pattern of a set of four diagnostic peaks. This was achieved by performing a fast scan on each precursor and comparing it on-the-fly to a library of theoretical spectra for cross-links and other species. Exhaustive identification scans were only triggered when the previous survey scan matched to the theoretical cross-link spectrum. Lastly, I generated a dataset with known PPIs by mixing purified proteins according to a defined scheme and heat-induced interactions. The dataset was used to monitor the empirical false-discovery rate of various existing database search algorithms. Multiple features of spectral quality from this dataset have been used to develop Scout, a machine-learned cross-link search engine that greatly outperforms other software in terms of usability, sensitivity, reliability and speed. Taken together, these methodological achievements display a considerable progress for the XL-MS community by providing versatile tools that will promote the research on PPIs across various biological models.Protein-Protein Interaktionen (PPIs) bilden die Grundlage vieler biologischer Prozesse. Cross-Linking Massenspektrometrie (XL-MS) ermöglicht das Detektieren von PPIs aus komplexen biologischen Systemen und sogar in vivo Szenarios. Dies wird erreicht durch die Kombination der Quervernetzung von Organellen, Zellen oder Geweben mittels kleiner, reaktiver Moleküle mit proteolytischem Verdau und LC-MS (Flüssigchromatografie gekoppelt mit Massenspektrometrie) Analyse. Da sich jedoch ihre Abundanz und physikalisch-chemischen Eigenschaften von denen unmodifizierter Peptide unterscheiden, sind für ihre zuverlässige Identifikation und genaue Quantifizierung spezielle Protokolle, effiziente Messmethoden und Datenanalyseverfahren notwendig. Im Verlauf dieser Arbeit wurden mehrere Schritte des XL-MS Arbeitsvorgangs optimiert, darunter (1) die Optimierung der Messparameter für den Nachweis und die Quantifizierung isobar markierter vernetzter Peptide, (2) die Entwicklung neuartiger Methoden für die gezielte Identifikation vernetzter statt unvernetzter Peptide und (3) die Bereitstellung eines kontrollierten Datensatzes für die Validierung bestehender oder die Entwicklung neuer Software für die Analyse von XL-MS Daten. Zuerst habe ich eine schnelle MS2-basierte Methode mit einer optimierten gestuften Kollisionsenergie von 42% ± 6 für die optimale Balance zwischen Sensitivität und akkurater Quantifizierung TMT-markierter, vernetzter Peptide aus komplexen Proben konzipiert. Zuvor entwickelte MS2-MS3-basierte Methoden haben nachweislich ausgelastete Laufzyklen, was den Nachweis vernetzter Peptide erschwert, obwohl ihre Quantifizierungskapazitäten die von MS2-basierten Methoden übertreffen. Zweitens habe ich gezeigt, dass die Verwendung eines Echtzeit-Suchalgorithmus die Anzahl identifizierter vernetzter Peptide um 45% erhöht, da das Instrument mithilfe eines einzigartigen Musters relativer Intensitäten von vier diagnostischen Peaks vernetzte Peptide von unvernetzten unterscheiden konnte. Dies wurde erreicht, indem für jeden Precursor ein schneller Abfragescan durchgeführt wurde, der während der Messung mit theoretischen Spektren vernetzter und unvernetzter Peptide verglichen wurde. Ausgiebige Identifikations-Scans wurden nur dann ausgelöst, wenn der Abfragescan mit dem theoretischen Spektrum vernetzter Peptide übereinstimmte. Und schließlich generierte ich einen Datensatz mit kontrollierten PPIs, indem ich aufgereinigte Proteine nach einem bestimmten Schema zusammengab und Interaktionen durch Hitze induzierten. Der Datensatz wurde verwendet um die empirische Falscherkennungsrate verschiedener bestehender Datenbanksuchalgorithmen zu überprüfen. Mehrere spektrale Merkmale wurden zudem verwendet, um Scout zu entwickeln, eine neuartige maschinen-gelernte Suchmaschine für vernetzte Peptide, die andere Programme in Benutzerfreundlichkeit, Sensitivität, Zuverlässigkeit und Geschwindigkeit übertrifft. Zusammenfassend lässt sich sagen, dass diese methodischen Fortschritte einen bedeutenden Nutzen für die XL-MS Gemeinschaft darstellen, da sie Werkzeuge bereitstellen, die die Erforschung von PPIs aus verschiedenen biologischen Modellen erleichtern werden
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
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
Author Under Sail The Imagination of Jack London, 1893-1902
No full textIn Author Under Sail, Jay Williams offers the first complete literary biography of Jack London as a professional writer engaged in the labor of writing. It examines the authorial imagination in London's work, the use of imagination in both his fiction and nonfiction, and the ways he defined imagination in the creative process in his business dealings with his publishers, editors, and agents. In this first volume of a two-volume biography, Williams traverses the years 1893 to 1902, from London's "Story of a Typhoon" to The People of the Abyss. The Jack London who emerges in the pages of Author Under Sail is a writer whose partnership with publishers, most notably his productive alliance with George Brett of Macmillan, was one of the most formative in American literary history. London pioneered many author models during the heyday of realism and naturalism, blurring the boundaries of these popular genres by focusing on absorption and theatricality and the representation of the seen and unseen. London created an impassioned, sincere, and extremely personal realism unlike that of other American writers of the time. Author Under Sail is a literary tour de force that reveals the full range of London as writer, creative citizen, and entrepreneur at the same time it sheds light on the maverick side of machine-age literature.Intro -- Title Page -- Copyright Page -- Dedication -- Contents -- Acknowledgments -- Introduction -- 1. Spirit Truth -- 2. From Absorption to Theatricality and Back Again -- 3. "I Will Build a New Present" -- 4. Sons as Authors -- 5. Fathers as Publishers -- 6. The Daughter as Author -- 7. Lovers as Authors -- 8. At Sea with the Family -- 9. Yellow News, Yellow Stories -- 10. The Return Home -- Notes -- Bibliography -- Index -- About Jay WilliamsIn Author Under Sail, Jay Williams offers the first complete literary biography of Jack London as a professional writer engaged in the labor of writing. It examines the authorial imagination in London's work, the use of imagination in both his fiction and nonfiction, and the ways he defined imagination in the creative process in his business dealings with his publishers, editors, and agents. In this first volume of a two-volume biography, Williams traverses the years 1893 to 1902, from London's "Story of a Typhoon" to The People of the Abyss. The Jack London who emerges in the pages of Author Under Sail is a writer whose partnership with publishers, most notably his productive alliance with George Brett of Macmillan, was one of the most formative in American literary history. London pioneered many author models during the heyday of realism and naturalism, blurring the boundaries of these popular genres by focusing on absorption and theatricality and the representation of the seen and unseen. London created an impassioned, sincere, and extremely personal realism unlike that of other American writers of the time. Author Under Sail is a literary tour de force that reveals the full range of London as writer, creative citizen, and entrepreneur at the same time it sheds light on the maverick side of machine-age literature.Description based on publisher supplied metadata and other sources.Electronic reproduction. Ann Arbor, Michigan : ProQuest Ebook Central, YYYY. Available via World Wide Web. Access may be limited to ProQuest Ebook Central affiliated libraries
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