Search

Background: Global DNA methylation has been reported to be associated with urothelial cell carcinoma (UCC) by studies using blood samples collected at diagnosis. Using the Illumina HumanMethylation450 assay, we derived genome-wide measures of blood DNA methylation and assessed them for their prospective association with UCC risk. Methods: We used 439 case–control pairs from the Melbourne Collaborative Cohort Study matched on age, sex, country of birth, DNA sample type, and collection period. Conditional logistic regression was used to compute odds ratios (OR) of UCC risk per s.d. of each genome-wide measure of DNA methylation and 95% confidence intervals (CIs), adjusted for potential confounders. We also investigated associations by disease subtype, sex, smoking, and time since blood collection. Results: The risk of superficial UCC was decreased for individuals with higher levels of our genome-wide DNA methylation measure (OR=0.71, 95% CI: 0.54–0.94; P=0.02). This association was particularly strong for current smokers at sample collection (OR=0.47, 95% CI: 0.27–0.83). Intermediate levels of our genome-wide measure were associated with decreased risk of invasive UCC. Some variation was observed between UCC subtypes and the location and regulatory function of the CpGs included in the genome-wide measures of methylation. Conclusions: Higher levels of our genome-wide DNA methylation measure were associated with decreased risk of superficial UCC and intermediate levels were associated with reduced risk of invasive disease. These findings require replication by other prospective studies.

O presente artigo tem por objetivo divulgar os resultados obtidos com o mapeamento geomorfológico na bacia do ribeirão Santa Bárbara (MG) e elaboração da carta geomorfológica correspondente, editada na escala de 1/50.000, em consonância ao plano metodológico estabelecido pelo Instituto Brasileiro de Geografia e Estatística. O trabalho deu conta de mapear unidades geomorfológicas ordenadas em padrões de formas semelhantes segundo os modelados de dissecação e agradação identificados e seus aspectos morfométricos fundamentais (declividade, profundidade de dissecação e dimensão interfluvial). Em um segundo nível de abordagem, foi empreendida a inserção de símbolos representativos de feições morfológicas e processos atuais (escarpas de falha, ravinas, focos de arenização, capturas), permitindo uma interpretação abrangente do relevo da área de estudo em suas formas e processos, pretéritos e atuais.

Background: The automation of data analysis in the form of scientific workflows has become a widely adopted practice in many fields of research. Computationally driven data-intensive experiments using workflows enable Automation, Scaling, Adaption and Provenance support (ASAP). However, there are still several challenges associated with the effective sharing, publication, understandability and reproducibility of such workflows due to the incomplete capture of provenance and lack of interoperability between different technical (software) platforms. Results: Based on best practice recommendations identified from literature on workflow sharing and publishing, we define four hierarchical levels of provenance that collectively result in comprehensive and fully re-executable workflows when used with domain-specific information. To realise these levels, we present CWLProv, a standard-based format to represent any workflow-based computational analysis to produce workflow output artefacts that satisfy the various levels of provenance. We utilise open source community-driven standards; interoperable workflow definitions in Common Workflow Language (CWL), structured provenance representation using the W3C PROV model, and resource aggregation and sharing as workflow-centric Research Objects (RO) generated along with the final outputs of a given workflow enactment. We illustrate this approach through a practical demonstration of CWLProv applied to real-life genomic workflows developed by independent groups. Conclusions: Our approach to workflow sharing and publication mitigates workflow decay. The underlying principles of the standards utilised by CWLProv enable semantically-rich and executable Research Objects that capture computational workflows with retrospective provenance such that any platform supporting CWL will be able to understand the analysis, re-use the methods for partial re-runs, or reproduce the analysis to validate the published findings.

We present our ongoing work on integrating Research Object practices with Common Workflow Language, capturing and describing prospective and retrospective provenance with the CWL Viewer and CWLProv. Full abstract: http://s11.no/2018/cwl.html Online slides: http://slides.com/soilandreyes/2018-10-29-cwlprov, Accepted Talk at RO2018

This interdisciplinary thesis advances existing debates regarding the importance of understanding the complex and contradictory nature of young women’s engagement with an increasingly mediatised and celebritised political landscape. Based on interviews with young women aged between 18-30 years and living in either London or Sydney in 2015, the thesis demonstrates how the changing media sphere – in terms of both medium and message – has reshaped young women’s political engagement (as it can be broadly understood). For these women, evolving interaction with various new media platforms, as well as the deployment and influence of a diverse range of celebrified politicians and politically-engaged celebrities, has played a significant role in redefining that engagement. The primacy of new media and celebrity to understanding young women’s political activities – both in terms of their own characterisations, and my subjective reading – also emphasises how these two factors are thoroughly, and increasingly, intertwined. By demonstrating the (often complementary) relationship between parliamentary-based and online forms of political engagement, the cross-platform circulation of pervasive ideologies regarding gender, race and sexuality, as well as the enduring relevance of characteristics associated with post-feminism (and within a climate of a "renewed" feminist movement), this thesis also disrupts the traditional, stereotypical and largely redundant binaries of "old" and "new" politics, "old" and "new" media and, similarly, "old" and "new" conceptions of feminism. Drawing on the interrelated fields of gender studies, media studies, youth studies and celebrity studies, this thesis clearly emphasises that the nexus between politics, media and celebrity not only increasingly dictates how politics is (quite literally) performed among this particular demographic, but also how feminist activism and identification are generally expressed and enacted in contemporary Western contexts.

Presented at Bioinformatics Open Source Conference (BOSC) 2018 Source Code snapshot:https://github.com/common-workflow-language/cwltool/tree/921fc1d387930a0a5fede332c43f039697f6a4de License: https://www.apache.org/licenses/LICENSE-2.0 Research Object: https://doi.org/10.5281/zenodo.1215611 Abstract(accepted for poster and talk at BOSC2018) The automation of data analysis in the form of scientific workflows is a widely adopted practice in many fields of research nowadays. Computationally driven data-intensive experiments using workflows enable Automation, Scaling, Adaption and Provenance support (ASAP). However, there are still a number of challenges associated with the effective sharing, publication, understandability and reproducibility of such workflows due to the incomplete capture of provenance and the dependence on the particular technical (software) platforms. We present CWLProv, an approach for retrospective provenance-capture utilizing open source community-driven standards involving application and customization of workflow-centric Research Objects (ROs). The ROs are produced as an output of a workflow enactment defined in the Common Workflow Language (CWL) using reference implementation cwltool. The approach aggregates and annotates all the resources involved in the scientific investigation including inputs, outputs, workflow specification, command line tool specifications and input parameter settings. The resources are linked within the RO to enable re-enactment of an analysis without depending on external resources. The workflow provenance profile is represented in W3C standardized PROV-N and PROV-JSON format and captures retrospective provenance of the workflow enactment. The workflow-centric RO produced as an output of a CWL workflow enactment is expected to be interoperable, reusable, shareable and portable across different platforms. Our work describes the need and motivation for CWLProv and the lessons learned in applying it for ROs using CWL in the bioinformatics domain. The complete capture of provenance along with the aggregated resources used in a workflow enactment will mitigate the workflow decay and allow applications of provenance to make experiments transparent, reproducible and authentic. We believe that underlying principles of the standards utilized to implement CWLProv will result in a semantically rich executable workflow objects such that any platform supporting CWL and CWLProv will be able to reproduce them. We ultimately aim to achieve a solution that is compliant with all four dimensions of FAIR principles. Currently CWLProv is implemented using the reference implementation, cwltool. This study can further be extended to support Provenance Capture on other platforms supporting CWL to demonstrate interoperability of analysis methods.

Masses described as having indistinct margins lack a clear demarcation of a portion or the entire margin from the surrounding tissues. The indistinctness of the margin raises the possibility of infiltration; therefore, this descriptor implies suspicion for malignancy. “Indistinct” differs from “obscured.” A mass with obscured margins insinuates that the surrounding tissues masks or covers the presence of the lesion. This chapter, appearing in the section on asymmetry, mass, and distortion, reviews the key imaging and clinical features, imaging protocols and pitfalls, differential diagnoses, and management recommendations for masses with indistinct margins. Topics discussed include differentiation of the mass with indistinct margins from an obscured mass and focal asymmetry, and how the presence of adjacent features can increase the suspicion of the mass with indistinct margins.

© 2018 Elsevier Inc. In any given year approximately 34% of the 130 million adults in the United States suffer from a mental health condition or disorder. Anxiety and depressive disorders are the most common followed by substance use disorder. Many people who suffer from a mental illness do not seek help. Studies have shown that the stigma of being perceived as having a mental illness prevents many adults from seeking help. Mental Health First Aid ™ (MHFA) is an educational program geared towards educating MHFA responders to assist those who may be experiencing a mental health condition or disorder. Pharmacists are the most accessible healthcare professionals, and many are trained in delivering MHFA. The literature on MHFA suggests that it is an effective educational program for those that take the training course. What is lacking is evidence that MHFA interventions positively affect help-seeking behaviours after an intervention has occurred between a mental health first air responder and an individual requiring MHFA. This paper highlights this issue and provides suggestions for future research.

This chapter explores approaches to evaluation and measurement in community music, within a policy environment increasingly focused on establishing the impact of public investment on individuals, communities, and society as a whole. It seeks to critically engage with terminology and appraise common models of evaluation and measurement advocated by a range of funders of community music by reviewing policy documents and evaluation approaches promoted across the public and third sectors, using recent history in the United Kingdom as a case study. Drawing on published examples of community music evaluations, a variety of methods are discussed including quantitative studies, interpretative and qualitative approaches, and standardized tools. These are examined in relation to their ability to convey project learnings, as well as the extent to which ‘impact’ can be attributed and claimed. The findings are then discussed in relation to the broader literature relating to the impact of community music, and an emerging field of applicable methods is proposed.

With decreasing indication for abdominoperineal resection and an increase in sphincter preserving surgery, there is a growing population of patients who suffer from low anterior resection syndrome (LARS). The aim of this study is to use the LARS score to determine the prevalence of LARS at a regional centre in Australia and determine the effect of short- and long-course neoadjuvant therapy, anastomotic technique and interval from surgery will also be assessed.Patients who had undergone an anterior resection (high, low or ultralow) at a regional centre over an 11-year period were identified. Eligible patients were contacted to complete a LARS score questionnaire. Results were analysed to determine the rate of major LARS and possible causative roles of certain patient and treatment-related variables.A total of 64 of 76 patients (84%) returned completed questionnaires. The prevalence of major LARS was 37.5%. Short-course neoadjuvant therapy appeared to be more likely to be associated with major LARS compared to long course (odds ratio (OR) = 2.4, 95% confidence interval (CI) 0.37-15.3, P = 0.35); however, this did not reach statistical significance. Rates of major LARS appear to decrease slowly over time and J-pouch colonic anastomosis appears to be slightly protective against major LARS (OR = 0.7, 95% CI 0.12-3.9, P = 0.70); however, neither results were statistically significant.The rate of major LARS at this regional centre is 37.5%. Larger prospective multicentre studies are required to determine impact of variables such as type of neoadjuvant therapy, anastomotic techniques and progression of LARS over time.

Several techniques have been described for the percutaneous treatment of trigeminal neuralgia; however, each has significant drawbacks. We propose a new technique for percutaneous balloon compression of the trigeminal ganglion and distal trigeminal nerve using electromagnetic (EM) neuronavigation. The procedure was performed in 17 consecutive patients with trigeminal neuralgia. Patients were then followed up with telephone interview. We also performed a cadaveric validation study to further investigate the accuracy of the technique using dye. Excellent clinical outcomes were achieved with a reduction in the median pain score from 10 out of 10 to 0 out of 10 following the procedure. The cadaveric study also demonstrated a high rate of foramen ovale cannulation. EM-based targeting of the foramen ovale and balloon inflation within Meckel’s cave is a quick, reproducible and straightforward technique for the percutaneous treatment of trigeminal neuralgia.

Côte d’Ivoire has the world’s largest cocoa sector, producing over 1.4 million metric tons of raw cocoa per year, accounting for thirty two percent of world production. Harvest payments often arrive late due to the complex logistics of cash-based payments and, it is not uncommon for the amount farmers receive to be somewhat below market value due to high commissions taken by chains of intermediary middlemen. Cognizant of these costs and inefficiencies, many actors in the cocoa value chain are exploring alternatives. One such alternative is paying farmers through Digital financial services (DFS). This research focuses specifically on mobile money accounts and discusses, first, how these have already expanded financial inclusion in Côte d’Ivoire and, secondly, how mobile money could help deliver products to cocoa farmers that meet their needs. The study is a knowledge product of the Partnership for Financial Inclusion, a joint initiative of IFC and The MasterCard Foundation to expand microfinance and advance digital financial services in Sub-Saharan Africa. It is organized as follows: The first section reviews the financial inclusion landscape in Côte d’Ivoire, revealing that DFS has unusually high penetration in rural areas. The second section analyzes the specific financial behavior of cocoa farmers based on new data collected by IFC,and is followed by a third section presenting a framework for how DFS could help improve farmers’ lives. The report concludes with a call to stakeholders to keep piloting and innovating with products and payment channels that cater to the financial needs of rural communities in Côte d’Ivoire and beyond.