652 research outputs found

    Large expert-curated database for benchmarking document similarity detection in biomedical literature search

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    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

    Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

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    Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

    A COMMON GENETIC ETIOLOGY FOR IMPULSIVITY AND OVEREATING

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    10.3153/fh18024Food and Health44247-25

    Location of School Lunch Salad Bars in Cafeterias: Design and Analysis Issues

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    10.1016/j.jand.2016.04.020JOURNAL OF THE ACADEMY OF NUTRITION AND DIETETICS11671077-107

    Preferences and willingness-to-pay for a blood pressure telemonitoring program using a discrete choice experiment

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    Abstract This study aimed to elicit the preferences and willingness-to-pay for blood pressure (BP) telemonitoring programs. This study also investigated the different factors or participant characteristics that could influence preferences and choice behaviors. Participants with hypertension were identified from an online survey panel demographically representative of Singapore’s general population. Participants completed a discrete choice experiment (DCE) with 12 choice sets, selecting their preferred BP monitoring program differing on five attributes: mode of consultation, BP machine type (with Bluetooth or not), BP machine price, monthly fee, and program duration. The base reference population (male, married, higher income, more formal education years, full-time worker, aged 55 to <65 years, and digital skills score of 36) preferred teleconsultation over in-person consultation, Bluetooth feature, lower machine price, lower monthly fee, and shorter program duration. A subgroup of participants can be considered teleconsultation-resistant, and three demographic factors were associated with lower preference for teleconsultation: female, fewer formal education years, and lower income. Considering the reference population and Bluetooth attribute, participants were willing to pay 66 SGD (~49 USD) additional for the machine to obtain the Bluetooth feature. Considering the reference population and teleconsultation attribute, participants were willing to pay 6.80 SGD (~5.10 USD) extra monthly fee for a program using teleconsultation. Here we report that amongst participants with hypertension, there is strong preference for the use of teleconsultation and a BP machine with Bluetooth feature in a BP monitoring program. However, a subgroup of participants are teleconsultation-resistant and would prefer in-person consultation
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