Innovations in Discovery Systems: User Studies and the Bento Approach

Over the past 30 years, library discovery services have evolved through expanded OPACs, federated search systems employing broadcast searching; Web-scale discovery systems (WSDS) that aggregate metadata and full-text content into a single integrated index; and, currently, hybrid bento-style systems that use federated techniques over WSDS, OPACs, and local information content. The bento systems partition search results into separate zoned screen displays grouped by content format type and/or local service results. Recent studies on Web-scale discovery systems have identified a number of user access issues centering on problems with blended result displays, problematical relevancy rankings of search results, full-text search problems, and the inability of WSDS to adequately provide access to local library services and resources. The concept of “full library discovery,” a phrase first coined by Lorcan Dempsey, has been introduced to refer to discovery approaches that move beyond the retrieval of collection materials to also include local information services and local content and links. The bento-based systems are an attempt to address the identified problems with WSDS and also provide discovery services that address user needs, in particular known item search and streamlined full-text access. This presentation will provide an analysis of the 38 libraries presently employing the bento approach and will look at identified user needs and search behaviors, as revealed in detailed search and clickthrough transaction log analyses. There is a clear need for an evidence-based analysis of user search behaviors in retrieval environments characterized by access to distributed information resources

An Analysis of Data Management Plans in University of Illinois National Science Foundation Grant Proposals

The University of Illinois at Urbana-Champaign (UIUC) Library conducted an analysis of 1,260 Data Management Plans (DMPs) submitted in National Science Foundation (NSF) proposals from July 2011 through November 2013. Each DMP was assigned controlled vocabulary and keyword terms which summarized the proposed data management mechanisms for storing and sharing data. A database composed of the proposal’s title, PI (Principal Investigator), PI’s department and college, NSF grant number, funded status, assigned DMP vocabulary, and keyword terms was constructed. As of May 2014, a total of 298 of these UIUC proposals had been funded by the NSF. Our analysis of this sample revealed no significant statistical differences in proposed data storage and reuse venues between funded and unfunded proposals. However, there was a statistically higher frequency of use of the campus institutional repository and disciplinary repositories in proposals submitted after October 2012

Hodgkin's lymphoma in remission after first-line therapy: which patients need FDG-PET/CT for follow-up?

Background: The purpose of the study was to evaluate the impact of 2-[fluorine-18]fluoro-2-deoxy-D-glucose-positron emission tomography (FDG-PET)/computed tomography (CT) during follow-up of patients with Hodgkin's lymphoma. Patients and methods: Patients in complete remission or an unconfirmed complete remission after first-line therapy who received FDG-PET/CT during their follow-up were analyzed retrospectively. Confirmatory biopsy was mandatory in case of recurrence. Results: Overall, 134 patients were analyzed. Forty-two (31.3%) patients had a recurrence. The positive predictive value of FDG-PET/CT was 0.98. Single-factor analysis identified morphological residual mass [P = 0.0005, hazard ratio (HR) 3.4, 95% confidence interval (CI) 1.7-6.6] and symptoms (P 24 months). Conclusions: Asymptomatic patients without morphological residues and an early stage of disease do not need a routine FDG-PET/CT for follow-up. Asymptomatic patients with morphological residues should receive routine follow-up FDG-PET/CT for the first 24 months. Only patients with advanced initial stage do need a routine follow-up FDG-PET/CT beyond 24 month

Strength of bacterial adhesion on nanostructured surfaces quantified by substrate morphometry

Microbial adhesion and the subsequent formation of resilient biofilms at surfaces are decisively influenced by substrate properties, such as the topography. To date, studies that quantitatively link surface topography and bacterial adhesion are scarce, as both are not straightforward to quantify. To fill this gap, surface morphometry combined with single-cell force spectroscopy was performed on surfaces with irregular topographies on the nano-scale. As surfaces, hydrophobized silicon wafers were used that were etched to exhibit surface structures in the same size range as the bacterial cell wall molecules. The surface structures were characterized by a detailed morphometric analysis based on Minkowski functionals revealing both qualitatively similar features and quantitatively different extensions. We find that as the size of the nanostructures increases, the adhesion forces decrease in a way that can be quantified by the area of the surface that is available for the tethering of cell wall molecules. In addition, we observe a bactericidal effect, which is more pronounced on substrates with taller structures but does not influence adhesion. Our results can be used for a targeted development of 3D-structured materials for/against bio-adhesion. Moreover, the morphometric analysis can serve as a future gold standard for characterizing a broad spectrum of material structures. © The Royal Society of Chemistry 2019

Risk-adapted FDG-PET/CT-based follow-up in patients with diffuse large B-cell lymphoma after first-line therapy

Background: The purpose of this study was to evaluate the impact of 2-[fluorine-18]fluoro-2-deoxy-D-glucose-positron emission tomography/computed tomography (FDG-PET/CT) during follow-up of patients with diffuse large B-cell lymphoma (DLBCL) being in complete remission or unconfirmed complete remission after first-line therapy. Patients and methods: DLBCL patients receiving FDG-PET/CT during follow-up were analyzed retrospectively. Confirmatory biopsy was mandatory in cases of suspected disease recurrence. Results: Seventy-five patients were analyzed and 23 (30%) had disease recurrence. The positive predictive value (PPV) of FDG-PET/CT was 0.85. Patients >60 years [P = 0.036, hazard ratio (HR) = 3.82, 95% confidence interval (CI) 1.02-7.77] and patients with symptoms indicative of a relapse (P = 0.015; HR = 4.1; 95% CI 1.20-14.03) had a significantly higher risk for relapse. A risk score on the basis of signs of relapse, age >60 years, or a combination of these factors identified patients at high risk for recurrence (P = 0.041). Conclusions: FDG-PET/CT detects recurrent DLBCL after first-line therapy with high PPV. However, it should not be used routinely and if only in selected high-risk patients to reduce radiation burden and costs. On the basis of our retrospective data, FDG-PET/CT during follow-up is indicated for patients 60 years with and without clinical signs of relaps

The PolyA tail length of yeast histone mRNAs varies during the cell cycle and is influenced by Sen1p and Rrp6p

Yeast histone mRNAs are polyadenylated, yet factors such as Rrp6p and Trf4p, required for the 3′-end processing of non-polyadenylated RNAs, contribute to the cell cycle regulation of these transcripts. Here, we investigated the role of other known 3′-end processing/transcription termination factors of non-polyadenylated RNA in the biogenesis of histone mRNAs, specifically the Nab3p/Nrd1p/Sen1p complex. We also re-evaluated the polyadenylation status of these mRNAs during the cell cycle. Our analysis reveals that yeast histone mRNAs have shorter than average PolyA tails and the length of the PolyA tail varies during the cell cycle; S-phase histone mRNAs possess very short PolyA tails while in G1, the tail length is relatively longer. Inactivation of either Sen1p or Rrp6p leads to a decrease in the PolyA tail length of histone mRNAs. Our data also show that Sen1p contributes to 3′-end processing of histone primary transcripts. Thus, histone mRNAs are distinct from the general pool of yeast mRNAs and 3′-end processing and polyadenylation contribute to the cell cycle regulation of these transcripts

The conserved C-terminus of the PcrA/UvrD helicase interacts directly with RNA polymerase

Copyright: © 2013 Gwynn et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was supported by a Wellcome Trust project grant to MD (Reference: 077368), an ERC starting grant to MD (Acronym: SM-DNA-REPAIR) and a BBSRC project grant to PM, NS and MD (Reference: BB/I003142/1). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer reviewedPublisher PD

A Participant Agreement for Minting DOIs for Data Not in a Repository

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Researching shadow education: Methodological challenges and directions

Research on shadow education has considerably increased in volume and has helped to improve understanding of the scale, nature, and implications of the phenomenon. However, the field is still in its infancy. Literature on shadow education reflects confusion over terms and parameters, and data suffer from challenges in securing evidence from actors who may be unwilling or unable to respond to enquiries in a clear manner. Particular care is needed in cross-national and cross-cultural comparisons. Nevertheless, the trajectory of improvement in both conceptualisation and instrumentation gives ground for confidence that shadow education will be progressively better documented and better understood. © Education Research Institute, Seoul National University, Seoul, Korea 2010.published_or_final_versionSpringer Open Choice, 01 Dec 201

Transcriptome-Wide Binding Sites for Components of the Saccharomyces cerevisiae Non-Poly(A) Termination Pathway: Nrd1, Nab3, and Sen1

RNA polymerase II synthesizes a diverse set of transcripts including both protein-coding and non-coding RNAs. One major difference between these two classes of transcripts is the mechanism of termination. Messenger RNA transcripts terminate downstream of the coding region in a process that is coupled to cleavage and polyadenylation reactions. Non-coding transcripts like Saccharomyces cerevisiae snoRNAs terminate in a process that requires the RNA–binding proteins Nrd1, Nab3, and Sen1. We report here the transcriptome-wide distribution of these termination factors. These data sets derived from in vivo protein–RNA cross-linking provide high-resolution definition of non-poly(A) terminators, identify novel genes regulated by attenuation of nascent transcripts close to the promoter, and demonstrate the widespread occurrence of Nrd1-bound 3′ antisense transcripts on genes that are poorly expressed. In addition, we show that Sen1 does not cross-link efficiently to many expected non-coding RNAs but does cross-link to the 3′ end of most pre–mRNA transcripts, suggesting an extensive role in mRNA 3′ end formation and/or termination