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Open Access
A 212-nt long RNA structure in the Tobacco necrosis virus-D RNA genome is resistant to Xrn degradation
(Oxford University Press, 2019) White, K. Andrew; Chaminda, Gunawardene D.; Newburn, Laura R.
Plus-strand RNA viruses can accumulate viral RNA degradation products during infections. Some of these decay intermediates are generated by the cytosolic 5′-to-3′ exoribonuclease Xrn1 (mammals and yeast) or Xrn4 (plants) and are formed when the enzyme stalls on substrate RNAs upon encountering inhibitory RNA structures. Many Xrn-generated RNAs correspond to 3′-terminal segments within the 3′-UTR of viral genomes and perform important functions during infections. Here we have investigated a 3′-terminal small viral RNA (svRNA) generated by Xrn during infections with Tobacco necrosis virus-D (family Tombusviridae). Our results indicate that (i) unlike known stalling RNA structures that are compact and modular, the TNV-D structure encompasses the entire 212 nt of the svRNA and is not functionally transposable, (ii) at least two tertiary interactions within the RNA structure are required for effective Xrn blocking and (iii) most of the svRNA generated in infections is derived from viral polymerase-generated subgenomic mRNA1. In vitro and in vivo analyses allowed for inferences on roles for the svRNA. Our findings provide a new and distinct addition to the growing list of Xrn-resistant viral RNAs and stalling structures found associated with different plant and animal RNA viruses.
Open Access
ABCDEF - The 6 key features behind scalable, multi-tenant web archive processing with ARCH: Archive, Big Data, Concurrent, Distributed, Efficient, Flexible
(ACM, 2022-06-20) Holzmann, Helge; Ruest, Nick; Bailey, Jefferson; Dempsey, Alex; Fritz, Samantha; Lee, Peggy; Milligan, Ian
Over the past quarter-century, web archive collection has emerged as a user-friendly process thanks to cloud-hosted solutions such as the Internet Archive’s Archive-It subscription service. Despite advancements in collecting web archive content, no equivalent has been found by way of a user-friendly cloud-hosted analysis system. Web archive processing and research require significant hardware resources and cumbersome tools that interdisciplinary researchers find difficult to work with. In this paper, we identify six principles - the ABCDEFs (Archive, Big data, Concurrent, Distributed, Efficient, and Flexible) - used to guide the development and design of a system. These make the transformation of, and working with, web archive data as enjoyable as the collection process. We make these objectives – largely common sense – explicit and transparent in this paper. They can be employed by every computing platform in the area of digital libraries and archives and adapted by teams seeking to implement similar infrastructures. Furthermore, we present ARCH (Archives Research Compute Hub), the first cloud-based system designed from scratch to meet all of these six key principles. ARCH is an interactive interface, closely connected with Archive-It, engineered to provide analytical actions, specifically generating datasets and in-browser visualizations. It efficiently streamlines research workflows while eliminating the burden of computing requirements. Building off past work by both the Internet Archive (Archive-It Research Services) and the Archives Unleashed Project (the Archives Unleashed Cloud), this merged platform achieves a scalable processing pipeline for web archive research. It will be made open-source shortly and can be considered a reference implementation of the ABCDEF, which we have evaluated and discussed in terms of feasibility and compliance as a benchmark for similar platforms.
Open Access
Academic Ableism and Open Access(ibility)
(2019-01-29) Dolmage, Jay
In this presentation, we will address the ableist attitudes, policies, and practices that are built into higher education. We will also interrogate the minimal and temporary means we have been given to address inequities and provide accessibility, and the cost such an approach has for disabled students and faculty. Finally, we will explore our own ableist biases, apologies and defenses in an effort to build tools for anti-ableist education.
Open Access
Academic Blogging: Promoting your Research on the Web
(2009-03-25) Dupuis, John
In a world of information overload, lightning fast news cycles, proliferating journals, declining traditional media outlets and short attention spans, how do we make sure our research has all the impact we want? How do we advance our agenda and create opportunities? How do we explain our research to the general public and get our peers' attention? We blog, of course! Come to this session and see how others have used blogs to engage the public in their research agenda, explore new ideas and join a worldwide community of scholars in every field. At the end of the session, those that are interested will have the chance to set up their own blogs.
Open Access
Academic Success Challenges Faced by International Graduate Students: Final Report
(2013-07-10) Olshen, Toni
This is the report and recommendations resulting from a research project exploring the academic success challenges faced by non-English speaking international graduate students as they pursue their graduate studies at York. It includes research findings and offers recommendations for changes for a more proactive approach to removing the academic challenges for York international students which have been identified. This report includes examples of best that may serve as models for improvements in this arena.
Open Access
Accessible Copying and Copyright: Section 32 and the Copyright Act Review
(2019-01-29) Martin, Heather
Copyright concerns often present an obstacle when providing content in accessible formats. Even with a specific Copyright Act exception intended to enable the provision of accessible material to those who need it, there are still restrictions on when, how, and what kinds of copies can be made. This presentation examines the finer points of Section 32 of the Copyright Act, and the ways in which it facilitates (or doesn’t!) accessible copying. It also looks at Canada’s recent Copyright Act review, which provided an opportunity to raise awareness of the problems that Section 32 presents, and to advocate for changes that would remove barriers for persons with disabilities as well as for those who provide accessible services.
Open Access
Active Digital Preservation and Data/Metadata Migration
(2017-04-04) Estlund, Karen; Ruest, Nick
Digital preservation activities increasingly focus on the movement of data and metadata between systems. This panel will present case studies in moving content through preservation activities with APTrust, the Digital Preservation Network, MetaArchive, and local applications. The presentations will highlight common methodologies and elicit group discussion on strategic and sustainable planning for active digital preservation. As the pace of evolution of repository systems continues to increase and new opportunities for digital preservation systems continue to emerge, the nature of active movement of repository objects and metadata has become a growing concern. The focus of content stewardship is shifting from being application-centric to data-centric, with the understanding that content must move through time. In order to provide effective mechanisms to move repository data during repository migrations and to these preservation systems, significant efforts are needed for various import, export, and verification services. The Fedora and MetaArchive communities have begun collaborative efforts to create tools that using the BagIt standard will enable preservation and system profiles that allow for ease of digital object transfer. Essential to these discussions is the role of metadata, file integrity, and size of transfers to actively manage digital objects.
Open Access
Addressing Open Access in Your Grant Application
(2014-04-17) Friskney, Janet
Open Access
Addressing Student Needs By Offering Customized RSS Feeds: TRY 2007
(2007-05) Nariani, Rajiv
Using RSS feeds from STM databases to keep on top of current research. These new tools can saves time valuable research time.
Open Access
An adiponectin-S1P axis protects against lipid induced insulin resistance and cardiomyocyte cell death via reduction of oxidative stress
(Biomed Central, 2019-02-21) Botta, Amy; Liu, Ying; Wannaiampikul, Sivaporn; Tungtrongchitr, Rungsunn; Dadson, Keith; Park, Tae-Sik; Sweeney, Gary
Background: Adiponectin exerts several beneficial cardiovascular effects, however their specific molecular mechanisms require additional understanding. This study investigated the mechanisms of adiponectin action in the heart during high fat diet (HFD) feeding or in palmitate (PA) treated H9c2 cardiomyoblasts. Methods: 6-week-old male adiponectin knock out (Ad-KO) mice were fed chow or 60% HFD for 6 weeks then received saline or recombinant adiponectin (3μg/g body weight) for an additional 2 weeks. After acute insulin stimulation (4 U/kg), tissue and serum samples were collected for analysis. H9c2 cardiomyocytes were treated ±0.1 mM PA, the adiponectin receptor agonist AdipoRon, or the antioxidant MnTBAP then assays to analyze reactive oxygen species (ROS) production and cell death were conducted. To specifically determine the mechanistic role of S1P, gain and loss of function studies were conducted with adding S1P to cells or the inhibitors THI and SKI-II, respectively. Results: HFD feeding induced cardiac insulin resistance in Ad-KO mice, which was reversed following replenishment of normal circulating adiponectin levels. In addition, myocardial total triglyceride was elevated by HFD and lipidomic analysis showed increased levels of ceramides and sphingosine-1 phosphate (S1P), with only the latter being corrected by adiponectin administration. Similarly, treatment of H9C2 cardiomyoblasts with PA led to a significant increase of intracellular S1P but not in conditioned media whereas AdipoRon significantly increased S1P production and secretion from cells. AdipoRon or the antioxidant MnTBAP significantly reduced PA-induced cell death. Gain and loss of function studies suggested S1P secretion and autocrine receptor activation mediated the effect of AdipoRon to attenuate PA-induced ROS production and cell death. Conclusion: Our data establish adiponectin signaling-mediated increase in S1P secretion as a mechanism via which HFD or PA induced cardiomyocyte lipotoxicity, leading to insulin resistance and cell death, is attenuated. Keywords: Adiponectin, Sphingosine-1-phosphate, Ceramide, Cardiomyocyte apoptosis, High fat diet, Palmitate, ROS
Open Access
Advancing and Promoting your Research on the Web
(2010-03-17T20:34:36Z) Dupuis, John
Open Access
Advancing Research Data Management: A Social Capital Perspective on Functional Librarianship
(Facet Publishing, 2022-12-22) Kosavic, Andrea; Wang, Minglu
This chapter investigates librarianship in the area of Research Data Management (RDM) through the lens of social capital theory. If social capital theories and concepts have the potential to bring to light the invisible or non-quantifiable value of academic library services (Bracke 2016; Corrall 2015), we postulate that they will lend a generative lens to explore the symbolic, network, and normative effects of engagement within the academic library. Using librarian and archivist-authored RDM literature as a case study, we will explore the dynamic relationships between network structures and the effects of functional librarianship on the social capital of academic libraries. User studies of scientists and case studies of library RDM programs (Perrier et al. 2017) are common in the literature, but their underlying theoretical frameworks are limited to “individual behaviourism” (Fecher, Friesike, and Hebing 2015), normative and historical institutionalism (Akers et al. 2014; Zenk-Möltgen et al. 2018), “wicked problem” theory (Cox, Pinfield, and Smith 2014) and organizational subculture theory (Cox and Verbaan 2016). Insights about the unique positionality of libraries within the academic community (Gold 2007) and potential leadership opportunities (Flores et al. 2015) have been mentioned but have yet to be clearly theorized to the level of a useful framework for deeper analysis or practical application of RDM research. A social capital perspective will offer a theoretical framework which contextualizes the potential benefits borne of functional engagement, including access to information attributed to network positionality and bridging connections, mutual supports found in communities with dense ties and group cohesion, and agency for enhancing reputation (Lin et al. 2001). As the presence of social capital can be used as a predictor of healthier institutional, disciplinary and departmental climates, this examination will highlight opportunities for strengthening social capital in libraries. We will also suggest modalities for libraries and related organizations to more consciously transform themselves using identified relationship building strategies. We provide a review of current RDM literature which summarizes the existing theoretical assumptions applied in the research to describe the development of RDM services and solutions in light of existing challenges. This is followed by an introduction of classic symbolic, normative, and network views of social capital theory, which are synthesized and applied to our sample during our coding exercise. Several essential themes surface in our axial coding exercise and they are summarized in our results and findings.
Open Access
Affective Labor, Resistance, and the Academic Librarian
(Johns Hopkins University Press, 2016) Sloniowski, Lisa
The affective turn in the humanities and social sciences seeks to theorize the social through examining spheres of experience, particularly bodily experience and the emotions, not typically explored in dominant theoretical paradigms of the twentieth century. Affective or immaterial labor is work that is intended to produce or alter emotional experiences in people. Although it has a long history, affective labor has been of increasing importance to modern economies since the nineteenth century. This paper will explore the gendered dimensions of affective labor and offer a feminist reading of the production of academic subjectivities through affective labor by specifically examining the pink-collar immaterial labor of academic reference and liaison librarians. It will end by exploring how the work of the academic librarian may also productively subvert the neoliberal goals of the corporate university.
Open Access
After Launching Search and Discovery, Who Is Mission Control?
(2010-10-15T05:20:31Z) Denton, William; Taves, Adam
Reference librarians are whiny and demanding. Systems librarians are arrogant and rude. Users are clueless and uninformed. A new discovery layer means that they need to collaborate to build it and then — the next step — integrate it into teaching and learning. How should we (reference librarians, systems people, and users) work together to better exploit the possibilities of open source systems so we can focus on discovery and understanding instead of the mechanics of searching?
Open Access
Age- and sex- specific all-cause mortality risk greatest in metabolic syndrome combinations with elevated blood pressure from 7 U.S. cohorts
(PLoS One, 2019) Yu, Winnie; Randhawa, Arshdeep K.; Blair, Steven N.; Sui, Xuemei; Kuk, Jennifer
Background The association between metabolic syndrome (MetS) and all-cause mortality is well established but it is unclear if there are differences in mortality risk among the 32 possible MetS combinations. Hence, the purpose of this study is to evaluate the associations between different MetS combinations and its individual components with all-cause mortality, and to examine differences in the association by age and sex. Methods A merged sample of 82,717 adults from 7 U.S. cohorts was used. Results In our sample, MetS was present in 32% of men, 34% of women, 28% of younger adults (18–65 years) and 62% of older adults (>65 years) with 14,989 deaths over 14.6 ± 7.4 years of follow-up. Risk of all-cause mortality was higher in younger individuals with a greater number of MetS factors present, but in older adults having all 5 MetS factors was the only combination significantly associated with mortality. Regardless of age or sex, elevated blood pressure was the MetS factor most consistently present in MetS combinations that were significantly and most strongly associated with mortality. In fact, elevated blood pressure in the absence of other risk factors was significantly associated with mortality in men (HR, 95% CI = 1.56, 1.33–1.84), women (HR = 1.62, 1.44–1.81) and younger adults (HR = 1.61, 1.45–1.79). Conversely, waist circumference, glucose and triglycerides in isolation were not associated with mortality (p>0.05). Conclusion In a large U.S. population, different combinations of MetS components vary substantially in their associations with all-cause mortality. Men, women and younger individuals with MetS combinations including elevated blood pressure had stronger associations with greater mortality risk, with minimal associations between MetS and mortality risk in older adults. Thus, we suggest that future algorithms may wish to consider differential weighting of these common metabolic risk factors, particularly in younger populations.
Open Access
Already Enough Ghosts:The Invisibility of Emotional Labour in Archives
(2016-06-12) St.Onge, Anna
Presented as part of a roundtable intended to provide a glimpse into the emotional and affective labour required to do archival work. Though many traditional archival theorists have suggested that professional archivists should remain objective and at an emotional "arms length" from the records and people with and for whom they work, failing to acknowledge the at times intensely emotional impact of archival work can negatively impact the mental and psychic wellness of the archivist - thereby affecting the archivist's professional output and professional relationships.
Open Access
Altered anterior visual system development following early monocular enucleation
(Elsevier Inc., 01/11/2013) Kelly, Krista; McKetton, Larissa; Schneider, Keith; Gallie, Brenda; Steeves, Jennifer
Purpose Retinoblastoma is a rare eye cancer that generally occurs before 5 years of age and often results in enucleation (surgical removal) of the cancerous eye. In the present study, we sought to determine the consequences of early monocular enucleation on the morphological development of the anterior visual pathway including the optic chiasm and lateral geniculate nucleus. Methods A group of adults who had one eye enucleated early in life due to retinoblastoma was compared to binocularly intact controls. Although structural changes have previously been reported in late enucleation, we also collected data from one late enucleated participant to compare to our early enucleated participants. Measurements of the optic nerves, optic chiasm, optic tracts and lateral geniculate nuclei were evaluated from T1 weighted and proton density weighted images collected from each participant. Results The early monocular enucleation group exhibited overall degeneration of the anterior visual system compared to controls. Surprisingly, however, optic tract diameter and geniculate volume decreases were less severe contralateral to the remaining eye. Consistent with previous research, the late enucleated participant showed no asymmetry and significantly larger volume decreases in both geniculate nuclei compared to controls. Conclusions The novel finding of an asymmetry in morphology of the anterior visual system following long-term survival from early monocular enucleation indicates altered postnatal visual development. Possible mechanisms behind this altered development include recruitment of deafferented cells by crossing nasal fibres and/or geniculate cell retention via feedback from primary visual cortex. These data highlight the importance of balanced binocular input during postnatal maturation for typical anterior visual system morphology.
Open Access
Altered white matter connectivity associated with visual hallucinations following occipital stroke
(Wiley, 2018-05-21) Rafique, Sara; Richards, John R.; Steeves, Jennifer
Introduction: Visual hallucinations that arise following vision loss stem from aberrant functional activity in visual cortices and an imbalance of activity across associated cortical and subcortical networks subsequent to visual pathway damage. We sought to determine if structural changes in white matter connectivity play a role in cases of chronic visual hallucinations associated with visual cortical damage. Methods: We performed diffusion tensor imaging (DTI) and probabilistic fiber tractography to assess white matter connectivity in a patient suffering from continuous and disruptive phosphene (simple) visual hallucinations for more than 2 years following right occipital stroke. We compared these data to that of healthy age-matched controls. Results: Probabilistic tractography to reconstruct white matter tracts suggests regeneration of terminal fibers of the ipsilesional optic radiations in the patient. However, arrangement of the converse reconstruction of these tracts, which were seeded from the ipsilesional visual cortex to the intrahemispheric lateral geniculate body, remained disrupted. We further observed compromised structural characteristics, and changes in diffusion (measured using diffusion tensor indices) of white matter tracts in the patient connecting the visual cortex with frontal and temporal regions, and also in interhemispheric connectivity between visual cortices. Conclusions: Cortical remapping and the disruption of communication between visual cortices and remote regions are consistent with our previous functional magnetic resonance imaging (fMRI) data showing imbalanced functional activity of the same regions in this patient (Rafique et al, 2016, Neurology, 87, 1493–1500). Long-term adaptive and disruptive changes in white matter connectivity may account for the rare nature of cases presenting with chronic and continuous visual hallucinations.
Open Access
Altered white matter structure in auditory tracts following early monocular enucleation
(Elsevier, 2019) Wong, Nikita; Rafique, Sara; Moro, Stefania S.; Kelly, Krista; Steeves, Jennifer
Purpose: Similar to early blindness, monocular enucleation (the removal of one eye) early in life results in crossmodal behavioral and morphological adaptations. Previously it has been shown that partial visual deprivation from early monocular enucleation results in structural white matter changes throughout the visual system (Wong et al., 2018). The current study investigated structural white matter of the auditory system in adults who have undergone early monocular enucleation compared to binocular control participants. Methods: We reconstructed four auditory and audiovisual tracts of interest using probabilistic tractography and compared microstructural properties of these tracts to binocularly intact controls using standard diffusion indices. Results: Although both groups demonstrated asymmetries in indices in intrahemispheric tracts, monocular enucleation participants showed asymmetries opposite to control participants in the auditory and A1-V1 tracts. Monocularenucleation participants also demonstrated significantly lower fractional anisotropy in the audiovisual projections contralateral to the enucleated eye relative to control participants. Conclusions: Partial vision loss from early monocular enucleation results in altered structural
Open Access
Amino acid-induced impairment of insulin sensitivity in healthy and obese rats is reversible
(Physiological Reports, 2014-07-04) Jeganathan, Senthure; Abdullahi, Abdikarim; Zargar, Sana; Maeda, Naomi; Riddell, Michael; ADEGOKE, OLASUNKANMI
High-protein diets (HPDs) promote weight loss but other studies implicate these diets and their constituent amino acids (AAs) in insulin resistance. We hypothesized that AA-induced insulin resistance is a temporal and reversible metabolic event. L6 myotubes were serum deprived for 4 h and then incubated in AA and/or insulin (100 nmol/L). Another group of cells was incubated overnight in AA + insulin, starved again, and then reincubated with AA and insulin. Mammalian (mechanistic) target of rapamycin complex 1 (mTORC1) signaling and glucose uptake were then measured. Healthy or insulin-resistant rats were gavaged with leucine (0.48 g/kg) and insulin sensitivity was examined. In myotubes, incubation with AA and insulin significantly (P < 0.05) increased the phosphorylation of the mTORC1 substrate ribosomal protein S6 kinase 1 (S6K1, T389) and of insulin receptor substrate 1 (IRS-1, serine residues), but suppressed insulinstimulated glucose uptake by 40% (P < 0.01). These modifications were mTORC1-dependent and were reversible. In vivo, leucine gavage reversibly increased S6K1 phosphorylation and IRS-1 serine phosphorylation 5- to 12- fold in skeletal muscle and impaired insulin tolerance of glucose (P < 0.05) in lean rats. In insulin-resistant rats, the impairment of whole blood glucose and AA metabolism induced by leucine gavage (0.001 < P < 0.05) was more severe than that observed in lean rats; however, the impairment was reversible within 24 h of treatment. If these data are confirmed in long-term studies, it would imply that the use of leucine/HPD in treating metabolic diseases is unlikely to have lasting negative effects on insulin sensitivity.

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