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

No ocean acidification effects on shell growth and repair in the New Zealand brachiopod Calloria inconspicua (Sowerby, 1846)

AbstractSurface seawaters are becoming more acidic due to the absorption of rising anthropogenic CO2. Marine calcifiers are considered to be the most vulnerable organisms to ocean acidification due to the reduction in the availability of carbonate ions for shell or skeletal production. Rhychonelliform brachiopods are potentially one of the most calcium carbonate-dependent groups of marine organisms because of their large skeletal content. Little is known, however, about the effects of lowered pH on these taxa. A CO2 perturbation experiment was performed on the New Zealand terebratulide brachiopod Calloria inconspicua to investigate the effects of pH conditions predicted for 2050 and 2100 on the growth rate and ability to repair shell. Three treatments were used: an ambient pH control (pH 8.16), a mid-century scenario (pH 7.79), and an end-century scenario (pH 7.62). The ability to repair shell was not affected by acidified conditions with >80% of all damaged individuals at the start of the experiment completing shell repair after 12 weeks. Growth rates in undamaged individuals >3 mm in length were also not affected by lowered pH conditions, whereas undamaged individuals <3 mm grew faster at pH 7.62 than the control. The capability of C. inconspicua to continue shell production and repair under acidified conditions suggests that this species has a robust control over the calcification process, where suitable conditions at the site of calcification can be generated across a range of pH conditions.The authors would like to thank the science support staff at the Portobello Marine Laboratory, University of Otago, for their help in the set up and maintenance of the ocean acidification experimental system. Thanks also to Kim Currie at National Institute of Water and Atmospheric Research for the DIC and total alkalinity measurements. ELC is supported by the NERC PhD Studentship (NE/T/A/ 2011).This is the final version of the article. It first appeared from Oxford University Press via http://dx.doi.org/10.1093/icesjms/fsv03

The RESET project: constructing a European tephra lattice for refined synchronisation of environmental and archaeological events during the last c. 100 ka

This paper introduces the aims and scope of the RESET project (. RESponse of humans to abrupt Environmental Transitions), a programme of research funded by the Natural Environment Research Council (UK) between 2008 and 2013; it also provides the context and rationale for papers included in a special volume of Quaternary Science Reviews that report some of the project's findings. RESET examined the chronological and correlation methods employed to establish causal links between the timing of abrupt environmental transitions (AETs) on the one hand, and of human dispersal and development on the other, with a focus on the Middle and Upper Palaeolithic periods. The period of interest is the Last Glacial cycle and the early Holocene (c. 100-8 ka), during which time a number of pronounced AETs occurred. A long-running topic of debate is the degree to which human history in Europe and the Mediterranean region during the Palaeolithic was shaped by these AETs, but this has proved difficult to assess because of poor dating control. In an attempt to move the science forward, RESET examined the potential that tephra isochrons, and in particular non-visible ash layers (cryptotephras), might offer for synchronising palaeo-records with a greater degree of finesse. New tephrostratigraphical data generated by the project augment previously-established tephra frameworks for the region, and underpin a more evolved tephra 'lattice' that links palaeo-records between Greenland, the European mainland, sub-marine sequences in the Mediterranean and North Africa. The paper also outlines the significance of other contributions to this special volume: collectively, these illustrate how the lattice was constructed, how it links with cognate tephra research in Europe and elsewhere, and how the evidence of tephra isochrons is beginning to challenge long-held views about the impacts of environmental change on humans during the Palaeolithic. © 2015 Elsevier Ltd.RESET was funded through Consortium Grants awarded by the Natural Environment Research Council, UK, to a collaborating team drawn from four institutions: Royal Holloway University of London (grant reference NE/E015905/1), the Natural History Museum, London (NE/E015913/1), Oxford University (NE/E015670/1) and the University of Southampton, including the National Oceanography Centre (NE/01531X/1). The authors also wish to record their deep gratitude to four members of the scientific community who formed a consultative advisory panel during the lifetime of the RESET project: Professor Barbara Wohlfarth (Stockholm University), Professor Jørgen Peder Steffensen (Niels Bohr Institute, Copenhagen), Dr. Martin Street (Romisch-Germanisches Zentralmuseum, Neuwied) and Professor Clive Oppenheimer (Cambridge University). They provided excellent advice at key stages of the work, which we greatly valued. We also thank Jenny Kynaston (Geography Department, Royal Holloway) for construction of several of the figures in this paper, and Debbie Barrett (Elsevier) and Colin Murray Wallace (Editor-in-Chief, QSR) for their considerable assistance in the production of this special volume.Peer Reviewe

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&E performance

The 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&E performance. Increased flow to clinical decision units was associated with the best A&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

Summary of A&E performance and arrivals per site.

<p>Summary of A&E performance and arrivals per site.</p

Representative topology of two of Kings’ major hospital sites over a 6-month period.

<p>Green nodes are in Denmark Hill (DH), turquoise nodes are in Princess Royal University Hospital (PRUH), purple nodes are External to King’s, red nodes are Orpington Hospital. Edge thickness represents the relative flow of the patients (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0185912#sec002" target="_blank">Methods</a> below). The A&E entry points are on the lower right of the diagram. The network is directed, but for clarity at this scale direction is not represented here.</p

Distribution of input and output weight variability scores.

<p>The input and output weight variability scores were calculated for every node each month. Counts are over all nodes and months. DH = Denmark Hill, PRUH = Princess Royal University Hospital.</p