Search, Reading and the Rise of Database

Over the past decade large, searchable collections of primary texts have been embraced by virtually all literary scholars and this has led to changes in how scholarship is conducted. This article offers a partial history of the introduction of search to large collections of primary texts, and explores its effects. It did not come automatically or easily, but when it did search broke down barriers to access (no longer requiring background knowledge in history and bibliography), offering a new means of discovering and selecting texts to read. This change was more than a convenience. It was transformative. Database represents a new form of textuality, and scholars have come to rely on database’s affordances to develop new ways of reading. In addition to content analysis of claims made about data- base in various fora, modest bibliometric analysis of two journals (American Literature and English Literary History) suggests trends: more and more diverse primary texts are being read and cited. Interviews with authors of journal articles and journal editors are used to characterize how the databases are used and the effect on scholarship.Ope

Combining in silico prediction and ribosome profiling in a genome-wide search for novel putatively coding sORFs

Background: It was long assumed that proteins are at least 100 amino acids (AAs) long. Moreover, the detection of short translation products (e. g. coded from small Open Reading Frames, sORFs) is very difficult as the short length makes it hard to distinguish true coding ORFs from ORFs occurring by chance. Nevertheless, over the past few years many such non-canonical genes (with ORFs < 100 AAs) have been discovered in different organisms like Arabidopsis thaliana, Saccharomyces cerevisiae, and Drosophila melanogaster. Thanks to advances in sequencing, bioinformatics and computing power, it is now possible to scan the genome in unprecedented scrutiny, for example in a search of this type of small ORFs. Results: Using bioinformatics methods, we performed a systematic search for putatively functional sORFs in the Mus musculus genome. A genome-wide scan detected all sORFs which were subsequently analyzed for their coding potential, based on evolutionary conservation at the AA level, and ranked using a Support Vector Machine (SVM) learning model. The ranked sORFs are finally overlapped with ribosome profiling data, hinting to sORF translation. All candidates are visually inspected using an in-house developed genome browser. In this way dozens of highly conserved sORFs, targeted by ribosomes were identified in the mouse genome, putatively encoding micropeptides. Conclusion: Our combined genome-wide approach leads to the prediction of a comprehensive but manageable set of putatively coding sORFs, a very important first step towards the identification of a new class of bioactive peptides, called micropeptides

N-terminal proteomics assisted profiling of the unexplored translation initiation landscape in Arabidopsis thaliana

Proteogenomics is an emerging research field yet lacking a uniform method of analysis. Proteogenomic studies in which N-terminal proteomics and ribosome profiling are combined, suggest that a high number of protein start sites are currently missing in genome annotations. We constructed a proteogenomic pipeline specific for the analysis of N-terminal proteomics data, with the aim of discovering novel translational start sites outside annotated protein coding regions. In summary, unidentified MS/MS spectra were matched to a specific N-terminal peptide library encompassing protein N termini encoded in the Arabidopsis thaliana genome. After a stringent false discovery rate filtering, 117 protein N termini compliant with N-terminal methionine excision specificity and indicative of translation initiation were found. These include N-terminal protein extensions and translation from transposable elements and pseudogenes. Gene prediction provided supporting protein-coding models for approximately half of the protein N termini. Besides the prediction of functional domains (partially) contained within the newly predicted ORFs, further supporting evidence of translation was found in the recently released Araport11 genome re-annotation of Arabidopsis and computational translations of sequences stored in public repositories. Most interestingly, complementary evidence by ribosome profiling was found for 23 protein N termini. Finally, by analyzing protein N-terminal peptides, an in silico analysis demonstrates the applicability of our N-terminal proteogenomics strategy in revealing protein-coding potential in species with well-and poorly-annotated genomes

Accessing and understanding research in education

Introductory comments This chapter describes the range of evidence that exists relevant to educational studies, and discusses how to locate, read, and use such evidence. The evidence exists in publicly available datasets as well as in the writings of others. The chapter introduces some generic methods of assessing the quality and usefulness of evidence, including a key quality control principle. The chapter ends by outlining some ideas for future research

Visualization of database structures for information retrieval

This paper describes the Book House system, which is designed to support children's information retrieval in libraries as part of their education. It is a shareware program available on CD‐ROM or floppy disks, and comprises functionality for database searching as well as for classifying and storing book information in the database. The system concept is based on an understanding of children's domain structures and their capabilities for categorization of information needs in connection with their activities in schools, in school libraries or in public libraries. These structures are visualized in the interface by using metaphors and multimedia technology. Through the use of text, images and animation, the Book House encourages children ‐ even at a very early age ‐ to learn by doing in an enjoyable way, which plays on their previous experiences with computer games. Both words and pictures can be used for searching; this makes the system suitable for all age groups. Even children who have not yet learned to read properly can, by selecting pictures, search for and find those books they would like to have read aloud. Thus, at the very beginning of their school life, they can learn to search for books on their own. For the library community, such a system will provide an extended service which will increase the number of children's own searches and also improve the relevance, quality and utilization of the book collections in the libraries. A market research report on the need for an annual indexing service for books in the Book House format is in preparation by the Danish Library Centre A/S

Design and Development of a User Specific Dynamic E-Magazine

Internet and electronic media gaining more popularity due to ease and speed, the count of Internet users has increased tremendously. The world is moving faster each day with several events taking place at once and the Internet is flooded with information in every field. There are categories of information ranging from most relevant to user, to the information totally irrelevant or less relevant to specific users. In such a scenario getting the information which is most relevant to the user is indispensable to save time. The motivation of our solution is based on the idea of optimizing the search for information automatically. This information is delivered to user in the form of an interactive GUI. The optimization of the contents or information served to him is based on his social networking profiles and on his reading habits on the proposed solution. The aim is to get the user's profile information based on his social networking profile considering that almost every Internet user has one. This helps us personalize the contents delivered to the user in order to produce what is most relevant to him, in the form of a personalized e-magazine. Further the proposed solution learns user's reading habits for example the news he saves or clicks the most and makes a decision to provide him with the best contents.Comment: 19 pages, 6 figure

eRes: Innovative E-learning with E-resources

There has been an explosion in the use of electronic resources by students; this existing high usage of e-resources will be intensified as virtual learning environments (VLEs) become the primary means of interaction between students and universities. The challenge facing academic libraries is to provide appropriate resources in electronic form and through interfaces meeting the expectations of the Digital Natives. This paper examines the marketplace for e-books and reports on Bournemouth University’s innovative response to this challenge: leading a national tender not only for general collections of e-books, but also for bespoke subject collections; integrating existing resources into the VLE and creating new resources; exploiting the VLE and federated search technology. It also reports on Bournemouth’s current Higher Education Academy-funded pathfinder project, Innovative E-Learning with E-Resources (eRes), to develop innovative pedagogic frameworks and an e-reading strategy