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

The role of AMP-activated protein kinase in the coordination of metabolic suppression in the common goldfish

Cell survival in conditions of severe oxygen deprivation depends on a wide variety of biochemical modifications, which result in a large-scale suppression of metabolism, preventing [ATP] from falling to fatally low levels. We investigated whether AMP-activated protein kinase (AMPK) has a role in the coordination of cellular modification during hypoxia, which leads to a regulated state of metabolic suppression in the goldfish (Carassius auratus). Energy charge, AMPK activity, protein and gene expression, as well as the translational capacity and phosphorylation state of a downstream target were measured in goldfish tissues during exposure to hypoxia (-0.3 mg 02/L) for up to 12 h. AMPK activity in the goldfish liver increased by 4-fold at 0.5 h hypoxia and was temporally associated with a —11-fold increase in calculated AMPfree/ATP. No change was observed in total AMPK protein or relative gene expression of identified AMPK isoforms. Changes in AMPK activity were also associated with a decreased rate of protein synthesis and an increase in the phosphorylated form of eukaryotic elongation factor-2 (eEF2; relative to total eEF2). Increases in AMPK activity were not seen in hypoxic goldfish muscle, brain, heart or gill, nor was a significant alteration in cellular energy charge seen in muscle. Still, the present study is the first to show that AMPK activity increases in liver in response to short-term severe hypoxia exposure in a hypoxia-tolerant fish. The decreased rates of protein synthesis, a well known component of metabolic suppression, combined with increased phosphorylation of eEF2, a downstream target of AMPK, potentially implicate the kinase in the cellular effort to suppress metabolism in hypoxia-tolerant species during oxygen deprivation.Science, Faculty ofZoology, Department ofGraduat

Assessment and Management of Pain in Juvenile Idiopathic Arthritis

Juvenile idiopathic arthritis (JIA) is a common chronic childhood illness. Pain is the most common and distressing symptom of JIA. Pain has been found to negatively impact all aspects of functioning, including physical, social, emotional and role functions. Children with arthritis continue to experience clinically significant pain despite adequate doses of disease-modifying antirheumatic drugs and anti-inflammatory agents. The present article reviews the prevalence and nature of pain in JIA, the biopsychosocial factors that contribute to the pain experience, current approaches to assessing pain in this population, and ways of managing both acute and persistent pain using pharmacological, physical and psychological therapies. Finally, new approaches to delivering disease self-management treatment for youth with JIA using the Internet will be outlined

Assessment and Management of Pain in Juvenile Idiopathic Arthritis

Juvenile idiopathic arthritis (JIA) is a common chronic childhood illness. Pain is the most common and distressing symptom of JIA. Pain has been found to negatively impact all aspects of functioning, including physical, social, emotional and role functions. Children with arthritis continue to experience clinically significant pain despite adequate doses of disease-modifying antirheumatic drugs and anti-inflammatory agents. The present article reviews the prevalence and nature of pain in JIA, the biopsychosocial factors that contribute to the pain experience, current approaches to assessing pain in this population, and ways of managing both acute and persistent pain using pharmacological, physical and psychological therapies. Finally, new approaches to delivering disease self-management treatment for youth with JIA using the Internet will be outlined.Peer Reviewe

Top reaching post during social media campaign duration.

Top reaching post during social media campaign duration.</p

Recommendations for future research-based social media campaign.

Recommendations for future research-based social media campaign.</p

Overview of website traffic sources.

Social media is increasingly used to engage persons with lived experience and healthcare professionals in research, however, there remains sparse guidance on how to effectively use social media to engage these groups in research agenda-setting. Here we report our process and experience utilizing a social media campaign to engage Canadians within the pediatric cancer community in a research priority-setting exercise. Following the James Lind Alliance method, we launched a priority-setting partnership (PSP) to develop a child with cancer-, survivor-, family member-, and healthcare professional-based Canadian pediatric cancer research agenda. Social media-based strategies were implemented to recruit participants for two PSP surveys, including preparatory activities, developing a website, launching graphics and advertisements, and engaging internal and external networks. Descriptive statistics of our data and analytics provided by the platforms are used presently to report our process. The framework we implemented involved preparing for social media use, identifying a target audience, developing campaign content, conducting the campaign, refining the campaign as needed, and evaluating its success. Our process resulted in a substantial social media-based reach, good survey completion rates, and a successfully developed pediatric cancer community-specified research agenda. Social media may represent a useful approach to engage persons with lived experience and healthcare professionals in research agenda development. Based on our experience, we present strategies to increase social media campaign engagement that may be useful to those seeking to conduct health research priority-setting exercises.</div

Impact of engagement strategies on survey response rates during initial survey period.

Impact of engagement strategies on survey response rates during initial survey period.</p