196,486 research outputs found
Solving the multi-class problem of protein secondary structure prediction
No full textDie Sekundärstrukturvorhersage von Proteinen als erster Schritt zur Aufklärung
ihrer 3D-Strukturen und Funktionen ist eine wichtige Fragestellung der
modernen Molekularbiologie. In dieser Arbeit wird mit dem Programm *SPARROW
eine neue Methode zur Vorhersage der Sekundärstruktur von Proteinen
vorgestellt, die auf einem neuartigen Lernverfahren basiert. Dieses als
vektorwertiger Klassifikator bezeichnete Verfahren verwendet eine
Klassifikatorfunktion um hochdimensionale Eingangsvektoren in einen
niederdimensionalen Ausgangsraum zu projizieren um mit Hilfe der Orientierung
dieser Ausgangsvektoren die Sekundärstrukturen zu klassifizieren. Um eine
möglichst hohe Genauigkeit dieser Klassifikationen zu gewährleisten wird die
Klassifikatorfunktion mittels empirischer Risikominimierung, einem Verfahren
der statistischen Lerntheorie, optimiert. Das *SPARROW zugrunde liegende
Verfahren besteht aus drei Stufen, von denen die ersten beiden vektorwertige
Klassifikatoren verwenden, während die dritte aus einem künstlichen neuronalen
Netz besteht. Die erste Stufe korreliert die Sekundärstruktur von Residuen,
die durch Sequenzausschnitte in Form von PSI-BLAST-Profilen repräsentiert
werden, mit der Primärstruktur. Dabei wird die von DSSP vorhergesagte
Sekundärstruktur als Referenz verwendet. Die Vorhersage der ersten Stufe wird
von der zweiten Stufe weiterverarbeitet, die damit eine Struktur-Struktur-
Korrelation darstellt. Die dritte Stufe stellt eine weitere Struktur-Struktur-
Korrelation dar, die aufgrund der nichtlinearen Natur des verwendeten
neuronalen Netzes Korrelationen höherer Ordnung in die Vorhersage einbezieht.
Durch diesen hierarchischen Aufbau verbessert jede Stufe effektiv die
Vorhersage der vorherigen Stufe. Zudem macht es diese Architektur von *SPARROW
möglich, über eine Änderung der Anzahl der berücksichtigten Klassen, in den
einzelnen Stufen Einfluss auf den Informationsfluss durch das System zu
nehmen. Tests auf dem ASTRAL40-Datensatz zeigen, dass *SPARROW bei der
Vorhersage dreier Sekundärstrukturklassen (Helices, β-Stränge und strukturlose
Regionen) eine Genauigkeit von 81,53% erreicht und somit mit existierenden
Vorhersageprogrammen vergleichbar ist. Zudem zeigt dieser Wert, dass *SPARROW
eine Verbesserung von ungefähr 0,5% gegenüber seinem Vorgänger SPARROW
erreicht. Aus den durchgeführten Untersuchungen geht weiterhin hervor, dass
*SPARROW das beste Programm zur Vorhersage kurzer Proteine ist. In Kombination
mit anderen Vorhersageprogrammen erweist sich *SPARROW als wichtiger Beitrag
zur Aufstellung kombinierter Vorhersageverfahren, die die Korrektheit der
vorhergesagten Sekundärstruktur drastisch verbessern können. So kann in der
Kombination mit PSIPRED bereits mittels einer einfachen Kombinationsmethode
eine Genauigkeit von 82,54% erreicht werden. Ein weiterer Vorteil von *SPARROW
äußert sich in der Möglichkeit der Vorhersage der acht von DSSP vorhergesagten
Sekundärstrukturklassen, was potentiell mit einer Genauigkeit von 68,28%
möglich ist.The prediction of the secondary structure of proteins as a first step towards
elucidating their 3D structure and function is an important issue of modern
molecular biology. In this thesis a new method for the prediction of protein
secondary structure is presented in form of the program *SPARROW, which is
based on a newly developed learning machine. This learning machine, denoted as
vector valued classifier, uses a vector valued function to project high
dimensional input data into a lower dimensional output space and uses the
orientation of these projections within the output space to perform the
classification of the input data into secondary structure classes. To maximize
the accuracy of classifications the vector valued classifier is optimized by
means of empirical risk minimization, a technique of statistical learning
theory. The prediction scheme underlying *SPARROW consists of three stages,
the first two of which are realized by vector valued classifiers while the
third consists of an artificial neural network. The first stage correlates the
secondary structure of residues, represented by sequence windows encoded in
form of PSI-BLAST profiles, with the primary structure (sequence). The
reference secondary structure is provided by DSSP. The prediction of the first
stage is further processed by the second stage, which thus performs a
structure-structure correlation. The final stage, being another structure-
structure correlation, makes use of the nonlinear nature of the neural network
to allow for higher order correlations in the prediction. For this hierarchic
composition each stage effectively improves the prediction of the previous
stages. Furthermore the architecture of *SPARROW allows to influence the flow
of information through the system by changing the number of classes that each
stage distinguishes. In benchmark tests on predicting three secondary
structure classes (helices, β-strands and random coils) performed on the
ASTRAL40 dataset *SPARROW achieved an accuracy of 81,53% and is thus
comparable to established programs for secondary structure prediction. In
addition *SPARROW improves the accuracy achieved by its predecessor SPARROW by
0,5%. Another result of the aforementioned investigations is that *SPARROW
outperforms other programs in the prediction of short proteins. Considering
the creation of combined prediction methods *SPARROW proofs to be an important
contribution. For example in combination with PSIPRED using a simple
combination method an accuracy of 82,54% can be measured. Another advantage of
the concept of *SPARROW is the possibility to predict the eight secondary
structure classes provided by DSSP, which yields a potential accuracy of
68,28%
Dr. Duane M. Jackson, Morehouse College, July 2011
No full textThis video is a conversation with Dr. Duane M. Jackson. Dr. Jackson talks about his paper, "Recall and the Serial Position Effect: The Role of Primacy and Recency on Accounting Students' Performance." Jackie Daniel, AUC Woodruff Library, is the interviewer
"Reflections on the subject of Emigration from Europe with a view to Settlement in the United States" By M. Carey.
No full text"Reflections on the subject of Emigration from Europe with a view to Settlement in the United States: containing bried sketches of the moral and political character of those states.
By M. Carey, member of the American philosophical, and of the American Antiquarian Society, and author of The Olive Branch, Cindiciae Hibernicae, essays on banking, on political economy, and on internal improvement.
To which are now added the English editor's comments on the subject; together with Important Advice to Emigrants, and Cautions Against Impositions Practiced in the Outports
Dispelling the Myths Behind First-author Citation Counts
No full textWe 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
Dr. Glendon Swarthout
No full textHosted by Roger M. Busfield, MSU Assistant Professor of Speech and Theater, Meet the Author is designed to introduce a general audience to a contemporary author and their work through in-depth interviews. This episode features a conversation between Dr. Glendon Swarthout, prolific author and English professor at MSU, and assistant professors Sam S. Baskett and Theodore B. Strandness
Simulation of thermal plant optimization and hydraulic aspects of thermal distribution loops for large campuses
No full textFollowing an introduction, the author describes Texas A&M University and its utilities system. After that, the author presents how to construct simulation models for chilled water and heating hot water distribution systems. The simulation model was used in a $2.3 million Ross Street chilled water pipe replacement project at Texas A&M University. A second project conducted at the University of Texas at San Antonio was used as an example to demonstrate how to identify and design an optimal distribution system by using a simulation model. The author found that the minor losses of these closed loop thermal distribution systems are significantly higher than potable water distribution systems. In the second part of the report, the author presents the latest development of software called the Plant Optimization Program, which can simulate cogeneration plant operation, estimate its operation cost and provide optimized operation suggestions. The author also developed detailed simulation models for a gas turbine and heat recovery steam generator and identified significant potential savings. Finally, the author also used a steam turbine as an example to present a multi-regression method on constructing simulation models by using basic statistics and optimization algorithms. This report presents a survey of the author??s working experience at the Energy Systems Laboratory (ESL) at Texas A&M University during the period of January 2002 through March 2004. The purpose of the above work was to allow the author to become familiar with the practice of engineering. The result is that the author knows how to complete a project from start to finish and understands how both technical and nontechnical aspects of a project need to be considered in order to ensure a quality deliverable and bring a project to successful completion. This report concludes that the objectives of the internship were successfully accomplished and that the requirements for the degree of Degree of Engineering have been satisfied
Intern experience at CH���M Hill, Inc.: an internship report
No full textIncludes author's vita"Submitted to the College of Engineering of Texas A&M University in partial
fulfillment of the requirement for the degree of Doctor of Engineering."Includes bibliographical referencesA review of the author's internship experience with CH���M HILL, Inc.
during the period September 1975 through May 1976 is presented. During this nine month
internship the author worked as an Engineer II in the Industrial Processes discipline of this
large consulting engineering firm... The author's prime responsibility was as one of three
lead design engineers on the design of a large wastewater treatment facility for a pulp mill
in Hoquiam, Washington owned by ITT Rayonier Inc. The work generally consisted of the design
of individual treatment units and associated piping and pumping. The purpose of the project
was to provide wastewater treatment capabilities that would satisfy the effluent limitations
(standards) imposed upon the mill by the State of Washington Department of Ecology and the
U.S. Environmental Protection Agency. The author's assignment also entailed necessary
interaction with the project manager and other CH���M HILL design engineers and support staff
members, the client's representatives, and representatives of two other consulting engineering
firms working on the project. Thus, the internship position at CH���M HILL provided considerable
experience coordinating the author's work with the work of other engineers, guiding the design
and administrative efforts of a support staff, and interacting regularly with the client and
other consulting firms. This broad exposure to a variety of engineering and organizational
problems provided a valuable educational experience
Transition to turbulence in a qblique shock-wave/boundary-layer interaction at M=15
No full textDirect numerical simulations are carried out for different forcing techniques to trigger transition during the interaction between an oblique shock-wave and a laminar boundary-layer at M = 1.5. Three forcing methods are used: a) forcing of oblique unstable modes, whose shape and behaviour are determined by the local linear stability theory, b) broadband free-stream acoustic disturbances, and c) a cold plasma flow control device. While the oblique-mode breakdown is dominant for low-amplitude forcing, long streaky structures drive the transition process in a high-amplitude disturbance environment. LES are also performed on the experimental setup by the Institute of Theoretical and Applied Mechanics (ITAM) from Novosibirsk State University with cold plasma actuation. As well as the disturbance type, the effect of Reynolds number and forcing amplitude will be investigated
Letter from Cedrick M. Shimo to the Office of Redress Administration, June 4, 1991
No full textA letter from Cedrick M. Shimo to the Office of Redress Administration arguing that John Y. Udaka is entitled to a redress payment.These materials are from box 73 and 74 of the Frank Chin Papers. The Frank Chin Papers contain personal and professional correspondence between Frank Chin and Michi Weglyn relating to particular projects on which either author was working as well as files related to the Day of Remembrance Tribute to Michi Weglyn
The construction of Karen Karnak: The multi-author-function
No full textThis thesis is situated within the comparatively recent developments of Web 2.0 and the emergence of interactive WikiMedia, and explores the mode of authorship within a Read/Write culture compared to that of a Read/Only tradition. The hypothesis of this study is that the role of the audience has become merged with the author, and as such, represents new functions and attributes, distinct from a more conventional concept of authorship, in which the roles of audience and author are more separate. Read/Write and participatory culture, as defined by this study, is focused on collaboration, and includes the influences of D.I.Y. culture, Open-Source practices and the production of text by multiple authors. Multi-authorship presents a re-thinking of several concepts which support the notion of the individual author, since the focus of multi-authorship is not on attribution and ownership of a finished text, but on the continued malleability of a text. Modes of multi-authorship, demonstrated in the use of the pseudonyms Alan Smithee and Karen Eliot, represent declarative authors whose names signify multiple origins, whilst concurrently indicating a distinct body of work. The function of these names form an important context to this study, since primary research involves the construction of an experimental mode of multi-authorship utilising WikiMedia technology and the interaction of thirty nine participants, who are invited to create a body of work under the collective pseudonym Karen Karnak. The data generated by this experiment is analysed using aspects of Michel Foucault's author-function to identify and determine power structures inherent in the WikiMedia context. The interplay of power structures, including concepts such as identity, ownership and the body of work, affect the resulting mode of authorship and contribute to the construction of Karen Karnak, suggesting further areas of research into the emerging multi-author
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