A History of Aboriginal Sydney…digitally delivering the past to the present

For more than two centuries, the history of the Indigenous people of the Sydney region has remained locked away in archives, held within families, or obliterated by the dominant culture. Now, with community approval and co-operation, our project, A history of Aboriginal Sydney, is beginning to use digital tools to restore Sydney's Aboriginal history in forms which can be appreciated and shared by the families themselves, by high school students and by everyone who values the history and culture of Australia's first peoples. Our project is based on the developing knowledge management platform, which integrates historical records, methods and tools of e-scholarship, and solutions for delivering research data for different uses. The project team employs methods such as marking of topic threads, and linking data with interactive timelines and digital maps to enable online learning and information discovery on the website . The project itself is based in the Department of History, University of Sydney and is funded by an Australia Research Council, Australian Professorial Fellowship and Discovery Grant. The research data are archived in ATSIDA (Aboriginal and Torres Strait Islander Data Archive), which provides long-term preservation and manages appropriate access to the data.ARC, ATSID

Significant correlation between the infant gut microbiome and rotavirus vaccine response in rural Ghana

Contains fulltext : 162913.pdf (publisher's version ) (Open Access)Background. Rotavirus (RV) is the leading cause of diarrhea-related death in children worldwide and ninety-five percent of RV deaths occur in Africa and Asia where rotavirus vaccines (RVV) have lower efficacy. We hypothesize that differences in intestinal microbiome composition correlate with the decreased RVV efficacy observed in poor settings. Methods. We conducted a nested, case-control study comparing pre-vaccination, fecal microbiome compositions between 6-week old, matched RVV-responders and non-responders in rural Ghana. These infants' microbiomes were then compared to 154 age-matched, healthy Dutch infants' microbiomes, assumed to be RVV-responders. Fecal microbiota analysis was performed in all groups using the Human Intestinal Tract Chip (HITChip). Results. 78 Ghanaian infants, equalling 39 RVV responder and non-responder pairs, were analysed. The overall microbiome composition was significantly different between RVV-responders and non-responders (FDR=0.12), and Ghanaian responders were more similar to Dutch infants than non-responders (p=0.002). RVV-response correlated with an increased abundance of Streptococcus bovis and a decreased abundance of the Bacteroidetes phylum in comparisons between Ghanaian RVV-responders and non-responders (FDR=0.008, FDR=0.003) as well as between Dutch infants and Ghanaian non-responders (FDR=0.002, FDR=0.009). Conclusions. The intestinal microbiome composition correlates significantly with RVV immunogenicity and may contribute to the diminished RVV immunogenicity observed in developing countries.8 p

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 science. © The Author(s) 2019. Published by Oxford University Press

Genetic studies of body mass index yield new insights for obesity biology

Note: A full list of authors and affiliations appears at the end of the article. Obesity is heritable and predisposes to many diseases. To understand the genetic basis of obesity better, here we conduct a genome-wide association study and Metabochip meta-analysis of body mass index (BMI), a measure commonly used to define obesity and assess adiposity, in up to 339,224 individuals. This analysis identifies 97 BMI-associated loci (P 20% of BMI variation. Pathway analyses provide strong support for a role of the central nervous system in obesity susceptibility and implicate new genes and pathways, including those related to synaptic function, glutamate signalling, insulin secretion/action, energy metabolism, lipid biology and adipogenesis.</p