The “Double Dean”: Embracing the Unexpected Opportunities of a Non-librarian Interim Dean

Serving as an interim administrator is never an easy thing to do. Walking into an interim administrator position when it is not in your area of expertise… well, that is just crazy. Or is it? A University of Arkansas practice is to fill vacant dean positions with an interim leader who is a current sitting dean from another college. When our former dean announced his departure, the university appointed the dean of the Honors College to serve as interim dean of libraries. For the senior library leadership group, all relatively new associate deans from other academic organizations, this practice at first seemed a bit bizarre. Many libraries struggle with maintaining organizational momentum on key initiatives in the vacuum of interim leadership. How would this work with someone whose field of expertise was so unrelated? As we quickly learned, having an experienced administrator with already established campus relationships to advise us became an immediate asset for the libraries. A neutral advocate at the table for campus decisions meant more exposure for the libraries, more access to decision-makers, and greater opportunities to build and advance our core programs and services across campus with key stakeholders. This relationship is also not one-sided, as our new double dean was very candid about what she saw as an investment in a long-term relationship between her home college and the libraries. This chapter will explore, from the perspectives of two associate deans and the interim dean, what those advantages were and why this arrangement served academic libraries well

Ribo-seQC: comprehensive analysis of cytoplasmic and organellar ribosome profiling data

Summary: Ribosome profiling enables genome-wide analysis of translation with unprecedented resolution. We present Ribo-seQC, a versatile tool for the comprehensive analysis of Ribo-seq data, providing in-depth insights on data quality and translational profiles for cytoplasmic and organelle ribosomes. Ribo-seQC automatically generates platform-independent HTML reports, offering a detailed and easy-to-share basis for collaborative Ribo-seq projects. Availability: Ribo-seQC is available at https://github.com/ohlerlab/RiboseQC and submitted to Bioconductor. Contact: uwe.ohler{at}mdc-berlin.d

Canceling the Big Deal: Three R1 Libraries Compare Data, Communication, and Strategies

Canceling the Big Deal is becoming more common, but there are still many unanswered questions about the impact of this change and the fundamental shift in the library collections model that it represents. Institutions like Southern Illinois University Carbondale and the University of Oregon were some of the first institutions to have written about their own experience with canceling the Big Deal several years ago, but are those experiences the norm in terms of changes in budgets, collection development, and interlibrary loan activity? Within the context of the University of California system’s move to cancel a system-wide contract with Elsevier, how are libraries managing the communication about Big Deals both internally with library personnel as well as externally with campus stakeholders? Three R1 libraries (University of Maryland, University of Oklahoma, and Kansas State University) will compare their data, discuss both internal and external communication strategies, and examine the impact these decisions have had on their collections in terms of interlibrary loan and collection development strategies. The results of a brief survey measuring the status of the audience members with respect to Big Deals, communication efforts with campus stakeholders, and impacts on collections will also be discussed

PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data

Crosslinking and immunoprecipitation (CLIP) protocols have made it possible to identify transcriptome-wide RNA-protein interaction sites. In particular, PAR-CLIP utilizes a photoactivatable nucleoside for more efficient crosslinking. We present an approach, centered on the novel PARalyzer tool, for mapping high-confidence sites from PAR-CLIP deep-sequencing data. We show that PARalyzer delineates sites with a high signal-to-noise ratio. Motif finding identifies the sequence preferences of RNA-binding proteins, as well as seed-matches for highly expressed microRNAs when profiling Argonaute proteins. Our study describes tailored analytical methods and provides guidelines for future efforts to utilize high-throughput sequencing in RNA biology. PARalyzer is available at http://www.genome.duke.edu/labs/ohler/research/PARalyzer/

Ebook Collection Development in Academic Libraries: Examining Preference, Management, and Purchasing Patterns.

The practice of acquiring ebooks and managing them within the collection is complex. Through survey results and a review of the literature, this report attempts to measure the significance of the ebook format within the collection, the procedures and preferences academic libraries have for acquiring ebooks, and the perceptions librarians have of the acquisition and management workflows. This survey and white paper aim to provide empirical context around the factors that are having the most influence on the way academic libraries acquire and integrate ebooks into their collections.Overdriv

Character building in childrens’ online information behaviours: applying a virtue epistemology perspective to information literacy.

This paper advances our understanding of the theoretical and practical challenges of developing intellectual character in children’s online information behaviours. We argue that widely reported issues such as misinformation and disinformation extend IL education beyond considerations of ability to considerations of disposition, and highlight this as an understudied topic within IL education. We introduce the classical concept of intellectual character and discuss virtues traits in the IL context. Applying Baehr’s nine intellectual virtues to two commonly cited IL models, we evidence limited presence of virtues in IL models, and propose an important agenda for future research

Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity

BACKGROUND: Epigenetic mechanisms such as chromatin accessibility impact transcription factor binding to DNA and transcriptional specificity. The androgen receptor (AR), a master regulator of the male phenotype and prostate cancer pathogenesis, acts primarily through ligand-activated transcription of target genes. Although several determinants of AR transcriptional specificity have been elucidated, our understanding of the interplay between chromatin accessibility and AR function remains incomplete. RESULTS: We used deep sequencing to assess chromatin structure via DNase I hypersensitivity and mRNA abundance, and paired these datasets with three independent AR ChIP-seq datasets. Our analysis revealed qualitative and quantitative differences in chromatin accessibility that corresponded to both AR binding and an enrichment of motifs for potential collaborating factors, one of which was identified as SP1. These quantitative differences were significantly associated with AR-regulated mRNA transcription across the genome. Base-pair resolution of the DNase I cleavage profile revealed three distinct footprinting patterns associated with the AR-DNA interaction, suggesting multiple modes of AR interaction with the genome. CONCLUSIONS: In contrast with other DNA-binding factors, AR binding to the genome does not only target regions that are accessible to DNase I cleavage prior to hormone induction. AR binding is invariably associated with an increase in chromatin accessibility and, consequently, changes in gene expression. Furthermore, we present the first in vivo evidence that a significant fraction of AR binds only to half of the full AR DNA motif. These findings indicate a dynamic quantitative relationship between chromatin structure and AR-DNA binding that impacts AR transcriptional specificity

Electric fields and valence band offsets at strained [111] heterojunctions

[111] ordered common atom strained layer superlattices (in particular the common anion GaSb/InSb system and the common cation InAs/InSb system) are investigated using the ab initio full potential linearized augmented plane wave (FLAPW) method. We have focused our attention on the potential line-up at the two sides of the homopolar isovalent heterojunctions considered, and in particular on its dependence on the strain conditions and on the strain induced electric fields. We propose a procedure to locate the interface plane where the band alignment could be evaluated; furthermore, we suggest that the polarization charges, due to piezoelectric effects, are approximately confined to a narrow region close to the interface and do not affect the potential discontinuity. We find that the interface contribution to the valence band offset is substantially unaffected by strain conditions, whereas the total band line-up is highly tunable, as a function of the strain conditions. Finally, we compare our results with those obtained for [001] heterojunctions.Comment: 18 pages, Latex-file, to appear in Phys.Rev.

Features of mammalian microRNA promoters emerge from polymerase II chromatin immunoprecipitation data

Background: MicroRNAs (miRNAs) are short, non-coding RNA regulators of protein coding genes. miRNAs play a very important role in diverse biological processes and various diseases. Many algorithms are able to predict miRNA genes and their targets, but their transcription regulation is still under investigation. It is generally believed that intragenic miRNAs (located in introns or exons of protein coding genes) are co-transcribed with their host genes and most intergenic miRNAs transcribed from their own RNA polymerase II (Pol II) promoter. However, the length of the primary transcripts and promoter organization is currently unknown. Methodology: We performed Pol II chromatin immunoprecipitation (ChIP)-chip using a custom array surrounding regions of known miRNA genes. To identify the true core transcription start sites of the miRNA genes we developed a new tool (CPPP). We showed that miRNA genes can be transcribed from promoters located several kilobases away and that their promoters share the same general features as those of protein coding genes. Finally, we found evidence that as many as 26% of the intragenic miRNAs may be transcribed from their own unique promoters. Conclusion: miRNA promoters have similar features to those of protein coding genes, but miRNA transcript organization is more complex. © 2009 Corcoran et al