101,082 research outputs found
Biosynthetic investigations of the v-type ATPase inhibitors bafilomycin A(1), B-1 and concanamycin A
No full textThe plecomacrolides bafilornycin A(1) and B-1 (1, 2) and concanamycin A (3), produced by different Streptomyces species, show a unique macrolactone structure with characteristic side chains and exhibit striking biological activities including distinct V-type ATPase inhibition. The biosynthesis of 1 and 2 has been established by feeding experiments with C-13-labelled precursors. Both, bafilomycin (1, 2) and concanamycin. (3) feature an "unusual C-2 chain extension unit" of as yet unknown origin which was addressed by feeding labelled 2-hydroxy- and 2-methoxymalonyl-derivatives
Letter, [Author unclear] to Paulina T. Merritt
No full textHandwritten letter to Paulina Merritt from an unknown author, October 1, 1876.
Improving classification in protein structure databases using text mining
Get PDFBackground: The classification of protein domains in the CATH resource is primarily based on structural comparisons, sequence similarity and manual analysis. One of the main bottlenecks in the processing of new entries is the evaluation of 'borderline' cases by human curators with reference to the literature, and better tools for helping both expert and non-expert users quickly identify relevant functional information from text are urgently needed. A text based method for protein classification is presented, which complements the existing sequence and structure-based approaches, especially in cases exhibiting low similarity to existing members and requiring manual intervention. The method is based on the assumption that textual similarity between sets of documents relating to proteins reflects biological function similarities and can be exploited to make classification decisions.Results: An optimal strategy for the text comparisons was identified by using an established gold standard enzyme dataset. Filtering of the abstracts using a machine learning approach to discriminate sentences containing functional, structural and classification information that are relevant to the protein classification task improved performance. Testing this classification scheme on a dataset of 'borderline' protein domains that lack significant sequence or structure similarity to classified proteins showed that although, as expected, the structural similarity classifiers perform better on average, there is a significant benefit in incorporating text similarity in logistic regression models, indicating significant orthogonality in this additional information. Coverage was significantly increased especially at low error rates, which is important for routine classification tasks: 15.3% for the combined structure and text classifier compared to 10% for the structural classifier alone, at 10(-3) error rate. Finally when only the highest scoring predictions were used to infer classification, an extra 4.2% of correct decisions were made by the combined classifier.Conclusion: We have described a simple text based method to classify protein domains that demonstrates an improvement over existing methods. The method is unique in incorporating structural and text based classifiers directly and is particularly useful in cases where inconclusive evidence from sequence or structure similarity requires laborious manual classification
Handwritten biographical information on Paulina T. McClung Merritt
No full textA handwritten biography of Paulina T. McClung Merritt by an unknown author, 1892.
Heterogeneous and tissue-specific regulation of effector T cell responses by IFN-gamma during Plasmodium berghei ANKA infection.
Get PDFIFN-γ and T cells are both required for the development of experimental cerebral malaria during Plasmodium berghei ANKA infection. Surprisingly, however, the role of IFN-γ in shaping the effector CD4(+) and CD8(+) T cell response during this infection has not been examined in detail. To address this, we have compared the effector T cell responses in wild-type and IFN-γ(-/-) mice during P. berghei ANKA infection. The expansion of splenic CD4(+) and CD8(+) T cells during P. berghei ANKA infection was unaffected by the absence of IFN-γ, but the contraction phase of the T cell response was significantly attenuated. Splenic T cell activation and effector function were essentially normal in IFN-γ(-/-) mice; however, the migration to, and accumulation of, effector CD4(+) and CD8(+) T cells in the lung, liver, and brain was altered in IFN-γ(-/-) mice. Interestingly, activation and accumulation of T cells in various nonlymphoid organs was differently affected by lack of IFN-γ, suggesting that IFN-γ influences T cell effector function to varying levels in different anatomical locations. Importantly, control of splenic T cell numbers during P. berghei ANKA infection depended on active IFN-γ-dependent environmental signals--leading to T cell apoptosis--rather than upon intrinsic alterations in T cell programming. To our knowledge, this is the first study to fully investigate the role of IFN-γ in modulating T cell function during P. berghei ANKA infection and reveals that IFN-γ is required for efficient contraction of the pool of activated T cells
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
BioLexicon: A Lexical Resource for the Biology Domain
Get PDFNatural language processing technologies have advanced remarkably in the past two decades. However, biological terminology is a frequent cause of analysis errors when processing literature written in the biology domain. The BOOTStrep BioLexicon is a linguistic resource tailored for the domain to cope with these problems. It contains the following types of entries: (1) a set of terminological verbs; (2) a set of derived forms of the terminological verbs; (3) general English words frequently used in the biology domain; (4) domain terms. This comprehensive coverage of biological terms makes the lexicon a unique linguistic resource within the domain. This paper focuses on the linguistic aspects of the lexicon
Pelevin’s Trinity in the novel “t”: author – protagonist – reader
No full textThe article attempts to interpret Pelevin's artistic strategy in the novel "T" by exploring its subject organization and addressing the key problems of the author, the protagonist, and the reader as they are seen by the researcher. The article analyzes the peculiarities of constructing the narrative reality in the novel "T", and goes on to discuss Pelevin's philosophic models of the development of the humankind, and the emergence of his new anthropology
ElKowmGIS : ein neues System zur Dokumentation archäologischer Fundstellen
Get PDFSeit dem Jahr 2005 beruht die Dokumentation der paläolithischen Grabung Hummal (El Kowm, Syrien) auf der Dokumentation mittels Computer. Hierfür wurde, speziell für die Vermessung, die Software AutoCAD mit den Applikationen TachyCAD und Photoplan angeschafft. Hierbei handelt es sich um eine kommerzielle Lösung, welche in vielen archäologischen Institutionen zum Einsatz kommt. Während der Arbeit mit diesem System fiel jedoch auf, dass nicht alle Belange, welche ein Archäologe haben kann, berücksichtigt werden (können). Eine Anpassung der Software auf die individuelle Grabung ist nicht ohne weiteres möglich, da es sich hierbei um Lösungen handelt, die nicht frei veränderbar sind. Aus der Notwendigkeit, eine anpassbare Lösung zu haben, entstand die Idee, eine eigene Softwarelösung zu produzieren, welche von Archäologen für Archäologen geschaffen wurde. Hierbei handelt es sich um ElKowmGIS, einem archäologischen Dokumentationssystem, welches im Wesentlichen die drei Bestandteile CAD, GIS und Datenbank in einem Paket vereint. Für die Entwicklung von ElKowmGIS wurden im Rahmen einer Doktorarbeit folgende Grundregeln definiert:
- Plattformunabhängigkeit: Der User soll die Software auf “seinem“ Computer nutzen können, egal welches Betriebssystem installiert ist.
- Modularer Aufbau: Das System soll so aufgebaut sein, dass für jede Aufgabenstellung Module zur Verfügung gestellt werden. Fehlt ein Modul, so kann es ohne weiteres nachträglich erstellt werden.
- Adaption der Software: Die Software soll auf die Dokumentationsstruktur anpassbar sein, nicht umgekehrt.
- “Künstliche Intelligenz“: Das Programm soll gewisse Aufgaben, z.B. Weiterführung der Laufnummer, Sortieren der Bilder, etc., selbstständig ausführen. Der Benutzer muss lediglich die Regeln hierfür vorgeben.
- Dokumentstruktur und Dateigrößen: Die verwendete Datenbank im Hintergrund soll es ermöglichen, mit kleinstmöglichem Platzbedarf und Zeitaufwand die erhobenen Daten zu sichern und auch zu verwenden.
- Anwenderfreundlichkeit: Das Programm soll selbsterklärend sein, d.h. der User soll sich alleine zurechtfinden, ohne tagelang ein Handbuch wälzen zu müssen.
Für die Implementierung wurde die Kombination aus JAVA, für die Programmierung der Benutzeroberfläche, und PostgreSQL als Datenbankserver gewählt. Zum einen bietet sich hier die Möglichkeit, die Plattformunabhängigkeit zu implementieren. Zum anderen lässt sich dadurch das ganze System modular aufbauen
Measuring industry-science links through inventor-author relations: A profiling method
Get PDFIn this pilot study we examine the performance of text-based profiling in recovering a set of validated inventor-author links. In a first step we match patents and publications solely based on their similarity in content. Next, we compare inventor and author names on the highest ranked matches for the occurrence of name matches. Finally, we compare these candidate matches with the names listed in a validated set of inventor-author names. Our text-based profile methodology performs significantly better than a random matching of patents and publications, suggesting that text-based profiling is a valuable complementary tool to the name searches used in previous studies.innovation; industry-science links; text-based profiling;
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