37 research outputs found

    Capturing Emerging Realities in Citizen Engagement in Science in Social Media : A Social Media Analytics Protocol for the Allinteract Study

    Get PDF
    In the digital era, social media has become a space for the socialization and interaction of citizens, who are using social networks to express themselves and to discuss scientific advances with citizens from all over the world. Researchers are aware of this reality and are increasingly using social media as a source of data to explore citizens' voices. In this context, the methods followed by researchers are mainly based on the content analysis using manual, automated or combined tools. The aim of this article is to share a protocol for Social Media Analytics that includes a Communicative Content Analysis (CCA). This protocol has been designed for the Horizon 2020 project Allinteract, and it includes the social impact in social media methodology. The novel contribution of this protocol is the detailed elaboration of methods and procedures to capture emerging realities in citizen engagement in science in social media using a Communicative Content Analysis (CCA) based on the contributions of Communicative Methodology (CM).Peer reviewe

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

    Get PDF
    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

    No full text
    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

    Ibero-American Society of Interventionism (SIDI) and the Spanish Society of Vascular and Interventional Radiology (SERVEI) Standard of Practice (SOP) for the Management of Inferior Vena Cava Filters in the Treatment of Acute Venous Thromboembolism

    No full text
    Objectives: to present an interventional radiology standard of practice on the use of inferior vena cava filters (IVCFs) in patients with or at risk to develop venous thromboembolism (VTE) from the Iberoamerican Interventional Society (SIDI) and Spanish Vascular and Interventional Radiology Society (SERVEI). Methods: a group of twenty-two interventional radiologist experts, from the SIDI and SERVEI societies, attended online meetings to develop a current clinical practice guideline on the proper indication for the placement and retrieval of IVCFs. A broad review was undertaken to determine the participation of interventional radiologists in the current guidelines and a consensus on inferior vena cava filters. Twenty-two experts from both societies worked on a common draft and received a questionnaire where they had to assess, for IVCF placement, the absolute, relative, and prophylactic indications. The experts voted on the different indications and reasoned their decision. Results: a total of two-hundred-thirty-three articles were reviewed. Interventional radiologists participated in the development of just two of the eight guidelines. The threshold for inclusion was 100% agreement. Three absolute and four relative indications for the IVCF placement were identified. No indications for the prophylactic filter placement reached the threshold. Conclusion: interventional radiologists are highly involved in the management of IVCFs but have limited participation in the development of multidisciplinary clinical practice guidelines

    Stromal oncostatin M cytokine promotes breast cancer progression by reprogramming the tumor microenvironment.

    Get PDF
    The tumor microenvironment (TME) is reprogrammed by cancer cells and participates in all stages of tumor progression. The contribution of stromal cells to the reprogramming of the TME is not well understood. Here, we provide evidence of the role of the cytokine oncostatin M (OSM) as central node for multicellular interactions between immune and nonimmune stromal cells and the epithelial cancer cell compartment. OSM receptor (OSMR) deletion in a multistage breast cancer model halted tumor progression. We ascribed causality to the stromal function of the OSM axis by demonstrating reduced tumor burden of syngeneic tumors implanted in mice lacking OSMR. Single-cell and bioinformatic analysis of murine and human breast tumors revealed that OSM expression was restricted to myeloid cells, whereas OSMR was detected predominantly in fibroblasts and, to a lower extent, cancer cells. Myeloid-derived OSM reprogrammed fibroblasts to a more contractile and tumorigenic phenotype and elicited the secretion of VEGF and proinflammatory chemokines CXCL1 and CXCL16, leading to increased myeloid cell recruitment. Collectively, our data support the notion that the stromal OSM/OSMR axis reprograms the immune and nonimmune microenvironment and plays a key role in breast cancer progression

    Discovering HIV related information by means of association rules and machine learning

    Get PDF
    Acquired immunodeficiency syndrome (AIDS) is still one of the main health problems worldwide. It is therefore essential to keep making progress in improving the prognosis and quality of life of affected patients. One way to advance along this pathway is to uncover connections between other disorders associated with HIV/AIDS-so that they can be anticipated and possibly mitigated. We propose to achieve this by using Association Rules (ARs). They allow us to represent the dependencies between a number of diseases and other specific diseases. However, classical techniques systematically generate every AR meeting some minimal conditions on data frequency, hence generating a vast amount of uninteresting ARs, which need to be filtered out. The lack of manually annotated ARs has favored unsupervised filtering, even though they produce limited results. In this paper, we propose a semi-supervised system, able to identify relevant ARs among HIV-related diseases with a minimal amount of annotated training data. Our system has been able to extract a good number of relationships between HIV-related diseases that have been previously detected in the literature but are scattered and are often little known. Furthermore, a number of plausible new relationships have shown up which deserve further investigation by qualified medical experts

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

    Get PDF
    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.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 (VAFPeer reviewe
    corecore