HEALTH GeoJunction: place-time-concept browsing of health publications

<p>Abstract</p> <p>Background</p> <p>The volume of health science publications is escalating rapidly. Thus, keeping up with developments is becoming harder as is the task of finding important cross-domain connections. When geographic location is a relevant component of research reported in publications, these tasks are more difficult because standard search and indexing facilities have limited or no ability to identify geographic foci in documents. This paper introduces <it><smcaps>HEALTH</smcaps> GeoJunction</it>, a web application that supports researchers in the task of quickly finding scientific publications that are relevant geographically and temporally as well as thematically.</p> <p>Results</p> <p><it><smcaps>HEALTH</smcaps> GeoJunction </it>is a geovisual analytics-enabled web application providing: (a) web services using computational reasoning methods to extract place-time-concept information from bibliographic data for documents and (b) visually-enabled place-time-concept query, filtering, and contextualizing tools that apply to both the documents and their extracted content. This paper focuses specifically on strategies for visually-enabled, iterative, facet-like, place-time-concept filtering that allows analysts to quickly drill down to scientific findings of interest in PubMed abstracts and to explore relations among abstracts and extracted concepts in place and time. The approach enables analysts to: find publications without knowing all relevant query parameters, recognize unanticipated geographic relations within and among documents in multiple health domains, identify the thematic emphasis of research targeting particular places, notice changes in concepts over time, and notice changes in places where concepts are emphasized.</p> <p>Conclusions</p> <p>PubMed is a database of over 19 million biomedical abstracts and citations maintained by the National Center for Biotechnology Information; achieving quick filtering is an important contribution due to the database size. Including geography in filters is important due to rapidly escalating attention to geographic factors in public health. The implementation of mechanisms for iterative place-time-concept filtering makes it possible to narrow searches efficiently and quickly from thousands of documents to a small subset that meet place-time-concept constraints. Support for a <it>more-like-this </it>query creates the potential to identify unexpected connections across diverse areas of research. Multi-view visualization methods support understanding of the place, time, and concept components of document collections and enable comparison of filtered query results to the full set of publications.</p

Breast cancer management pathways during the COVID-19 pandemic: outcomes from the UK ‘Alert Level 4’ phase of the B-MaP-C study

Abstract: Background: The B-MaP-C study aimed to determine alterations to breast cancer (BC) management during the peak transmission period of the UK COVID-19 pandemic and the potential impact of these treatment decisions. Methods: This was a national cohort study of patients with early BC undergoing multidisciplinary team (MDT)-guided treatment recommendations during the pandemic, designated ‘standard’ or ‘COVID-altered’, in the preoperative, operative and post-operative setting. Findings: Of 3776 patients (from 64 UK units) in the study, 2246 (59%) had ‘COVID-altered’ management. ‘Bridging’ endocrine therapy was used (n = 951) where theatre capacity was reduced. There was increasing access to COVID-19 low-risk theatres during the study period (59%). In line with national guidance, immediate breast reconstruction was avoided (n = 299). Where adjuvant chemotherapy was omitted (n = 81), the median benefit was only 3% (IQR 2–9%) using ‘NHS Predict’. There was the rapid adoption of new evidence-based hypofractionated radiotherapy (n = 781, from 46 units). Only 14 patients (1%) tested positive for SARS-CoV-2 during their treatment journey. Conclusions: The majority of ‘COVID-altered’ management decisions were largely in line with pre-COVID evidence-based guidelines, implying that breast cancer survival outcomes are unlikely to be negatively impacted by the pandemic. However, in this study, the potential impact of delays to BC presentation or diagnosis remains unknown

The contribution of X-linked coding variation to severe developmental disorders

Abstract: Over 130 X-linked genes have been robustly associated with developmental disorders, and X-linked causes have been hypothesised to underlie the higher developmental disorder rates in males. Here, we evaluate the burden of X-linked coding variation in 11,044 developmental disorder patients, and find a similar rate of X-linked causes in males and females (6.0% and 6.9%, respectively), indicating that such variants do not account for the 1.4-fold male bias. We develop an improved strategy to detect X-linked developmental disorders and identify 23 significant genes, all of which were previously known, consistent with our inference that the vast majority of the X-linked burden is in known developmental disorder-associated genes. Importantly, we estimate that, in male probands, only 13% of inherited rare missense variants in known developmental disorder-associated genes are likely to be pathogenic. Our results demonstrate that statistical analysis of large datasets can refine our understanding of modes of inheritance for individual X-linked disorders

Geography

*Signatures are on file in the Graduate School. ii This thesis presents a conceptual and computational framework for the Semantic Geospatial Problem Solving Environment, an enabling technology for geographical problem solving under today’s open, heterogeneous environment. The framework adopts an open software architecture to integrate different geospatial information technologies, employs the dataflow-based visual programming interface to facilitate front-end user task construction, and most importantly, utilizes structurally represented semantic knowledge to assist and automate the construction of geographical applications. The major contribution of this thesis is the development of a semantic model of geographical problem solving, which synthesizes aspects of knowledge representation and reasoning to capture and model the meanings of geospatial information technologies and geographical applications. Three levels of semantics are addressed according to C. S. Peirce’s theory of pragmatism, including the first level semantics about individual resources, the secon

Breast implant-associated anaplastic large cell lymphoma (BIA-ALCL):an overview of presentation and pathogenesis and guidelines for pathological diagnosis and management

AIMS: Breast implant-associated anaplastic large cell lymphoma (BIA-ALCL) is an uncommon complication associated largely with textured implants. It is important that the symptoms associated with BIA-ALCL are recognised and that robust pathways are in place to establish the diagnosis. The aim of this paper is to review what is known of the incidence of the disease, current thoughts on pathogenesis, patterns of presentation and pathological features to provide standard guidelines for its diagnosis. METHODS AND RESULTS: Systematic review of the literature via PubMed covering cases series, modes of presentation, cytological, histological and immunohistochemical features and disease outcome. Since 1997, 518 cases throughout 25 countries have been registered on the American Society of Plastic Surgeons PROFILE registry, with an estimated risk for women with an implant of one to three per million per year. It most frequently presents as a late-onset accumulation of seroma fluid, sometimes as a mass lesion. The neoplastic cells are highly atypical, consistently strongly positive for CD30, with 43-90% also positive for EMA, and all are ALK-negative. Behaviour is best predicted using a staging system for solid tumours. CONCLUSION: BIA-ALCL is a rare but important complication of breast implants. While characterised by CD30-positive neoplastic cells this must be interpreted with care, and we provide pathological guidelines for the robust diagnosis of this lesion as well as the most appropriate staging system and management strategies. Finally, in order to generate more accurate data on incidence, we recommend mechanisms for the routine central reporting of all cases