Combining data mining and text mining for detection of early stage dementia:the SAMS framework

In this paper, we describe the open-source SAMS framework whose novelty lies in bringing together both data collection (keystrokes, mouse movements, application pathways) and text collection (email, documents, diaries) and analysis methodologies. The aim of SAMS is to provide a non-invasive method for large scale collection, secure storage, retrieval and analysis of an individual’s computer usage for the detection of cognitive decline, and to infer whether this decline is consistent with the early stages of dementia. The framework will allow evaluation and study by medical professionals in which data and textual features can be linked to deficits in cognitive domains that are characteristic of dementia. Having described requirements gathering and ethical concerns in previous papers, here we focus on the implementation of the data and text collection components

SemEHR:A general-purpose semantic search system to surface semantic data from clinical notes for tailored care, trial recruitment, and clinical research

Objective: Unlocking the data contained within both structured and unstructured components of electronic health records (EHRs) has the potential to provide a step change in data available for secondary research use, generation of actionable medical insights, hospital management, and trial recruitment. To achieve this, we implemented SemEHR, an open source semantic search and analytics tool for EHRs.Methods: SemEHR implements a generic information extraction (IE) and retrieval infrastructure by identifying contextualized mentions of a wide range of biomedical concepts within EHRs. Natural language processing annotations are further assembled at the patient level and extended with EHR-specific knowledge to generate a timeline for each patient. The semantic data are serviced via ontology-based search and analytics interfaces.Results: SemEHR has been deployed at a number of UK hospitals, including the Clinical Record Interactive Search, an anonymized replica of the EHR of the UK South London and Maudsley National Health Service Foundation Trust, one of Europe's largest providers of mental health services. In 2 Clinical Record Interactive Search-based studies, SemEHR achieved 93% (hepatitis C) and 99% (HIV) F-measure results in identifying true positive patients. At King's College Hospital in London, as part of the CogStack program (github.com/cogstack), SemEHR is being used to recruit patients into the UK Department of Health 100 000 Genomes Project (genomicsengland.co.uk). The validation study suggests that the tool can validate previously recruited cases and is very fast at searching phenotypes; time for recruitment criteria checking was reduced from days to minutes. Validated on open intensive care EHR data, Medical Information Mart for Intensive Care III, the vital signs extracted by SemEHR can achieve around 97% accuracy.Conclusion: Results from the multiple case studies demonstrate SemEHR's efficiency: weeks or months of work can be done within hours or minutes in some cases. SemEHR provides a more comprehensive view of patients, bringing in more and unexpected insight compared to study-oriented bespoke IE systems. SemEHR is open source, available at https://github.com/CogStack/SemEHR.</p

CogStack:Experiences of deploying integrated information retrieval and extraction services in a large National Health Service Foundation Trust hospital

BackgroundTraditional health information systems are generally devised to support clinical data collection at the point of care. However, as the significance of the modern information economy expands in scope and permeates the healthcare domain, there is an increasing urgency for healthcare organisations to offer information systems that address the expectations of clinicians, researchers and the business intelligence community alike. Amongst other emergent requirements, the principal unmet need might be defined as the 3R principle (right data, right place, right time) to address deficiencies in organisational data flow while retaining the strict information governance policies that apply within the UK National Health Service (NHS). Here, we describe our work on creating and deploying a low cost structured and unstructured information retrieval and extraction architecture within King’s College Hospital, the management of governance concerns and the associated use cases and cost saving opportunities that such components present.ResultsTo date, our CogStack architecture has processed over 300 million lines of clinical data, making it available for internal service improvement projects at King’s College London. On generated data designed to simulate real world clinical text, our de-identification algorithm achieved up to 94% precision and up to 96% recall.ConclusionWe describe a toolkit which we feel is of huge value to the UK (and beyond) healthcare community. It is the only open source, easily deployable solution designed for the UK healthcare environment, in a landscape populated by expensive proprietary systems. Solutions such as these provide a crucial foundation for the genomic revolution in medicine

Late survival of Neanderthals at the southernmost extreme of Europe

4 pages, 1 table, 1 figure.The late survival of archaic hominin populations and their long contemporaneity with modern humans is now clear for southeast Asia1. In Europe the extinction of the Neanderthals, firmly associated with Mousterian technology, has received much attention, and evidence of their survival after 35 kyr BP has recently been put in doubt2. Here we present data, based on a high-resolution record of human occupation from Gorham’s Cave, Gibraltar, that establish the survival of a population of Neanderthals to 28 kyr BP. These Neanderthals survived in the southernmost point of Europe, within a particular physiographic context, and are the last currently recorded anywhere. Our results show that the Neanderthals survived in isolated refuges well after the arrival of modern humans in Europe.We thank all those who have participated in this project. The project Palaeomed was co-funded by the Government of Gibraltar and the European Union Interreg IIIB Programme Medocc. Palynological and geochemical investigations were funded by Fundación Séneca, Murcia, Spain, and Ministerio de Educación y Ciencia, DGI, Spain, respectively. Geomorphological work was funded by Ministerio de Educación y Ciencia, DGI, Spain.Peer reviewe

Duration of androgen deprivation therapy with postoperative radiotherapy for prostate cancer: a comparison of long-course versus short-course androgen deprivation therapy in the RADICALS-HD randomised trial

Background Previous evidence supports androgen deprivation therapy (ADT) with primary radiotherapy as initial treatment for intermediate-risk and high-risk localised prostate cancer. However, the use and optimal duration of ADT with postoperative radiotherapy after radical prostatectomy remains uncertain. Methods RADICALS-HD was a randomised controlled trial of ADT duration within the RADICALS protocol. Here, we report on the comparison of short-course versus long-course ADT. Key eligibility criteria were indication for radiotherapy after previous radical prostatectomy for prostate cancer, prostate-specific antigen less than 5 ng/mL, absence of metastatic disease, and written consent. Participants were randomly assigned (1:1) to add 6 months of ADT (short-course ADT) or 24 months of ADT (long-course ADT) to radiotherapy, using subcutaneous gonadotrophin-releasing hormone analogue (monthly in the short-course ADT group and 3-monthly in the long-course ADT group), daily oral bicalutamide monotherapy 150 mg, or monthly subcutaneous degarelix. Randomisation was done centrally through minimisation with a random element, stratified by Gleason score, positive margins, radiotherapy timing, planned radiotherapy schedule, and planned type of ADT, in a computerised system. The allocated treatment was not masked. The primary outcome measure was metastasis-free survival, defined as metastasis arising from prostate cancer or death from any cause. The comparison had more than 80% power with two-sided α of 5% to detect an absolute increase in 10-year metastasis-free survival from 75% to 81% (hazard ratio [HR] 0·72). Standard time-to-event analyses were used. Analyses followed intention-to-treat principle. The trial is registered with the ISRCTN registry, ISRCTN40814031, and ClinicalTrials.gov , NCT00541047 . Findings Between Jan 30, 2008, and July 7, 2015, 1523 patients (median age 65 years, IQR 60–69) were randomly assigned to receive short-course ADT (n=761) or long-course ADT (n=762) in addition to postoperative radiotherapy at 138 centres in Canada, Denmark, Ireland, and the UK. With a median follow-up of 8·9 years (7·0–10·0), 313 metastasis-free survival events were reported overall (174 in the short-course ADT group and 139 in the long-course ADT group; HR 0·773 [95% CI 0·612–0·975]; p=0·029). 10-year metastasis-free survival was 71·9% (95% CI 67·6–75·7) in the short-course ADT group and 78·1% (74·2–81·5) in the long-course ADT group. Toxicity of grade 3 or higher was reported for 105 (14%) of 753 participants in the short-course ADT group and 142 (19%) of 757 participants in the long-course ADT group (p=0·025), with no treatment-related deaths. Interpretation Compared with adding 6 months of ADT, adding 24 months of ADT improved metastasis-free survival in people receiving postoperative radiotherapy. For individuals who can accept the additional duration of adverse effects, long-course ADT should be offered with postoperative radiotherapy. Funding Cancer Research UK, UK Research and Innovation (formerly Medical Research Council), and Canadian Cancer Society

In search of the neanderthals: solving the puzzle of human origins

Ever since the first discovery of their bones, the Neanderthals have provoked controversy. Who were they? How were they related to modern people? What caused their disappearance 35,000 years ago? The Neanderthals have become the archetype of all that is primitive. But what is their true story? Today Neanderthal specialists are locked in one of the fiercest debates in modern science. One side, the "multiregional" school, argues that the Neanderthals and their contemporaries evolved semi-independently into modern humans. Christopher Stringer leads the "out of Africa" school, which believes that the Neanderthals were replaced by modern people from Africa. Here he sets out his views for the first time, with the archaeologist Clive Gamble. Step by step the authors put forward their case. The Neanderthals had an anatomy crucially different from our own, adapted to Ice Age Europe. Neanderthal behaviour similarly points to fundamental differences. New genetic evidence strongly suggests a single origin for modern humans in Africa. The authors argue that, capable and intelligent as the Neanderthals were, they proved no match for the better-organized, better-equipped newcomers, and died out

Network analysis of patient flow in two UK acute care hospitals identifies key sub-networks for A&amp;E performance

AbstractThe topology of the patient flow network in a hospital is complex, comprising hundreds of overlapping patient journeys, and is a determinant of operational efficiency. To understand the network architecture of patient flow, we performed a data-driven network analysis of patient flow through two acute hospital sites of King’s College Hospital NHS Foundation Trust. Administration databases were queried for all intra-hospital patient transfers in an 18- month period and modelled as a dynamic weighted directed graph. A ‘core’ subnetwork containing only 13-17% of all edges channelled 83-90% of the patient flow, while an ‘ephemeral’ network constituted the remainder. Unsupervised cluster analysis and differential network analysis identified sub-networks where traffic is most associated with A&amp;E performance the following day. Increased flow to clinical decision units was associated with the best A&amp;E performance in both sites. The component analysis also detected a weekend effect on patient transfers which was not associated with performance. We have performed the first data-driven hypothesis-free analysis of patient flow which can enhance understanding of whole healthcare systems. Such analysis can drive transformation in healthcare as it has in industries such as manufacturing.</jats:p