14 research outputs found
Large expert-curated database for benchmarking document similarity detection in biomedical literature search
Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe
\u27By seeing with our own eyes, it can remain in our mind\u27: qualitative evaluation findings suggest the ability of participatory video to reduce gender-based violence in conflict-affected settings.
\u27By seeing with our own eyes, it can remain in our mind\u27: Qualitative evaluation findings suggest the ability of participatory video to reduce gender-based violence in conflict-affected settings
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Gle1 Regulates RNA Binding of the DEAD-Box Helicase Ded1 in Its Complex Role in Translation Initiation
DEAD-box proteins (DBPs) are required in gene expression to facilitate changes to ribonucleoprotein complexes, but the cellular mechanisms and regulation of DBPs are not fully defined. Gle1 is a multifunctional regulator of DBPs with roles in mRNA export and translation. In translation, Gle1 modulates Ded1, a DBP required for initiation. However, DED1 overexpression causes defects, suggesting that Ded1 can promote or repress translation in different contexts. Here we show that GLE1 expression suppresses the repressive effects of DED1 in vivo and Gle1 counteracts Ded1 in translation assays in vitro. Furthermore, both Ded1 and Gle1 affect the assembly of preinitiation complexes. Through mutation analysis and binding assays, we show that Gle1 inhibits Ded1 by reducing its affinity for RNA. Our results are consistent with a model wherein active Ded1 promotes translation but inactive or excess Ded1 leads to translation repression. Gle1 can inhibit either role of Ded1, positioning it as a gatekeeper to optimize Ded1 activity to the appropriate level for translation. This study suggests a paradigm for finely controlling the activity of DEAD-box proteins to optimize their function in RNA-based processes. It also positions the versatile regulator Gle1 as a potential node for the coordination of different steps of gene expression.American Cancer Society [13-263-01-RMC]6 month embargo; accepted manuscript posted online 7 August 2017This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]
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The dementia-inclusive choices in exercise project: using participatory action research to improve physical activity supports for persons with dementia
Persons with dementia have the right to equal inclusion in rehabilitation, including physical activity. However, the perspectives of persons with dementia are rarely integrated into decision-making related to physical activity programming, services, and supports. Here, we describe the participatory action research (PAR) approach used to develop the Dementia-Inclusive Choices for Exercise (DICE) toolkit, which aims to increase the quality and number of physical activity opportunities available to persons with dementia. The DICE Research Team included persons with dementia, a family care partner, exercise professionals, community and dementia service providers, health care professionals, and researchers who worked to: 1) Engage/maintain the Research Team; 2) Set/ navigate ways of engagement; 3) Understand barriers to physical activity; 4) Prioritize the audience and actions; 5) Develop the toolkit; 6) Conduct usability testing; and 7) Implement and evaluate. Guided by the Behaviour Change Wheel, and informed by interviews, focus groups, and existing research, our PAR Team chose to prioritize training exercise providers; exercise providers can enable exercise for persons with dementia if they understand common changes with dementia and how to support persons with dementia in exercise. The content and format of the toolkit was co- developed: drafted by our Research Team, adapted through a stakeholder workshop, and refined through iterative development and usability testing. The product of our PAR process, the DICE toolkit, includes videos meant to destigmatize dementia, training modules and a training manual for exercise providers, a physical activity handout for persons with dementia, and wallet cards to help persons with dementia communicate their abilities, needs, and preferences. Our usability study indicated that the toolkit could be used by exercise providers and may improve attitudes about dementia. Our vision is that our co-developed DICE toolkit will empower exercise providers to improve physical activity opportunities and support for persons with dementia