Full Metadata Object profiling for flexible geoprocessing workflows

The design and running of complex geoprocessing workflows is an increasingly common geospatial modelling and analysis task. The Business Process Model and Notation (BPMN) standard, which provides a graphical representation of a workflow, allows stakeholders to discuss the scientific conceptual approach behind this modelling while also defining a machine-readable encoding in XML. Previous research has enabled the orchestration of Open Geospatial Consortium (OGC) Web Processing Services (WPS) with a BPMN workflow engine. However, the need for direct access to pre-defined data inputs and outputs results in a lack of flexibility during composition of the workflow and of efficiency during execution. This article develops metadata profiling approaches, described as two possible configurations, which enable workflow management at the meta-level through a coupling with a metadata catalogue. Specifically, a WPS profile and a BPMN profile are developed and tested using open-source components to achieve this coupling. A case study in the context of an event mapping task applied within a big data framework and based on analysis of the Global Database of Event Language and Tone (GDELT) database illustrates the two different architectures

Rapid flood inundation mapping using social media, remote sensing and topographic data

Flood events cause substantial damage to urban and rural areas. Monitoring water extent during large-scale flooding is crucial in order to identify the area affected and to evaluate damage. During such events, spatial assessments of floodwater may be derived from satellite or airborne sensing platforms. Meanwhile, an increasing availability of smartphones is leading to documentation of flood events directly by individuals, with information shared in real-time using social media. Topographic data, which can be used to determine where floodwater can accumulate, are now often available from national mapping or governmental repositories. In this work, we present and evaluate a method for rapidly estimating flood inundation extent based on a model that fuses remote sensing, social media and topographic data sources. Using geotagged photographs sourced from social media, optical remote sensing and high-resolution terrain mapping, we develop a Bayesian statistical model to estimate the probability of flood inundation through weights-of-evidence analysis. Our experiments were conducted using data collected during the 2014 UK flood event and focus on the Oxford city and surrounding areas. Using the proposed technique, predictions of inundation were evaluated against ground-truth flood extent. The results report on the quantitative accuracy of the multisource mapping process, which obtained area under receiver operating curve values of 0.95 and 0.93 for model fitting and testing, respectively

Predicting residential building age from map data

The age of a building influences its form and fabric composition and this in turn is critical to inferring its energy performance. However, often this data is unknown. In this paper, we present a methodology to automatically identify the construction period of houses, for the purpose of urban energy modelling and simulation. We describe two major stages to achieving this – a per-building classification model and post-classification analysis to improve the accuracy of the class inferences. In the first stage, we extract measures of the morphology and neighbourhood characteristics from readily available topographic mapping, a high-resolution Digital Surface Model and statistical boundary data. These measures are then used as features within a random forest classifier to infer an age category for each building. We evaluate various predictive model combinations based on scenarios of available data, evaluating these using 5-fold cross-validation to train and tune the classifier hyper-parameters based on a sample of city properties. A separate sample estimated the best performing cross-validated model as achieving 77% accuracy. In the second stage, we improve the inferred per-building age classification (for a spatially contiguous neighbourhood test sample) through aggregating prediction probabilities using different methods of spatial reasoning. We report on three methods for achieving this based on adjacency relations, near neighbour graph analysis and graph-cuts label optimisation. We show that post-processing can improve the accuracy by up to 8 percentage points

Automated classification metrics for energy modelling of residential buildings in the UK with open algorithms

Estimating residential building energy use across large spatial extents is vital for identifying and testing effective strategies to reduce carbon emissions and improve urban sustainability. This task is underpinned by the availability of accurate models of building stock from which appropriate parameters may be extracted. For example, the form of a building, such as whether it is detached, semi-detached, terraced etc and its shape may be used as part of a typology for defining its likely energy use. When these details are combined with information on building construction materials or glazing ratio, it can be used to infer the heat transfer characteristics of different properties. However, these data are not readily available for energy modelling or urban simulation. Although this is not a problem when the geographic scope corresponds to a small area and can be hand-collected, such manual approaches cannot be easily applied at the city or national scale. In this paper, we demonstrate an approach that can automatically extract this information at the city scale using off-the-shelf products supplied by a National Mapping Agency. We present two novel techniques to create this knowledge directly from input geometry. The first technique is used to identify built form based upon the physical relationships between buildings. The second technique is used to determine a more refined internal/external wall measurement and ratio. The second technique has greater metric accuracy and can also be used to address problems identified in extracting the built form. A case study is presented for the City of Nottingham in the United Kingdom using two data products provided by the Ordnance Survey of Great Britain (OSGB): MasterMap and AddressBase. This is followed by a discussion of a new categorisation approach for housing form for urban energy assessment

Earth observation for citizen science validation, or citizen science for earth observation validation? The role of quality assurance of volunteered observations

Environmental policy involving citizen science (CS) is of growing interest. In support of this open data stream of information, validation or quality assessment of the CS geo-located data to their appropriate usage for evidence-based policy making needs a flexible and easily adaptable data curation process ensuring transparency. Addressing these needs, this paper describes an approach for automatic quality assurance as proposed by the Citizen OBservatory WEB (COBWEB) FP7 project. This approach is based upon a workflow composition that combines different quality controls, each belonging to seven categories or “pillars”. Each pillar focuses on a specific dimension in the types of reasoning algorithms for CS data qualification. These pillars attribute values to a range of quality elements belonging to three complementary quality models. Additional data from various sources, such as Earth Observation (EO) data, are often included as part of the inputs of quality controls within the pillars. However, qualified CS data can also contribute to the validation of EO data. Therefore, the question of validation can be considered as “two sides of the same coin”. Based on an invasive species CS study, concerning Fallopia japonica (Japanese knotweed), the paper discusses the flexibility and usefulness of qualifying CS data, either when using an EO data product for the validation within the quality assurance process, or validating an EO data product that describes the risk of occurrence of the plant. Both validation paths are found to be improved by quality assurance of the CS data. Addressing the reliability of CS open data, issues and limitations of the role of quality assurance for validation, due to the quality of secondary data used within the automatic workflow, are described, e.g., error propagation, paving the route to improvements in the approach

Data driven estimation of building interior plans

This work investigates constructing plans of building interiors using learned building measurements. In particular, we address the problem of accurately estimating dimensions of rooms when measurements of the interior space have not been captured. Our approach focuses on learning the geometry, orientation and occurrence of rooms from a corpus of real-world building plan data to form a predictive model. The trained predictive model may then be queried to generate estimates of room dimensions and orientations. These estimates are then integrated with the overall building footprint and iteratively improved using a two-stage optimisation process to form complete interior plans. The approach is presented as a semi-automatic method for constructing plans which can cope with a limited set of known information and constructs likely representations of building plans through modelling of soft and hard constraints. We evaluate the method in the context of estimating residential house plans and demonstrate that predictions can effectively be used for constructing plans given limited prior knowledge about the types of rooms and their topology

Global patient outcomes after elective surgery: prospective cohort study in 27 low-, middle- and high-income countries.

BACKGROUND: As global initiatives increase patient access to surgical treatments, there remains a need to understand the adverse effects of surgery and define appropriate levels of perioperative care. METHODS: We designed a prospective international 7-day cohort study of outcomes following elective adult inpatient surgery in 27 countries. The primary outcome was in-hospital complications. Secondary outcomes were death following a complication (failure to rescue) and death in hospital. Process measures were admission to critical care immediately after surgery or to treat a complication and duration of hospital stay. A single definition of critical care was used for all countries. RESULTS: A total of 474 hospitals in 19 high-, 7 middle- and 1 low-income country were included in the primary analysis. Data included 44 814 patients with a median hospital stay of 4 (range 2-7) days. A total of 7508 patients (16.8%) developed one or more postoperative complication and 207 died (0.5%). The overall mortality among patients who developed complications was 2.8%. Mortality following complications ranged from 2.4% for pulmonary embolism to 43.9% for cardiac arrest. A total of 4360 (9.7%) patients were admitted to a critical care unit as routine immediately after surgery, of whom 2198 (50.4%) developed a complication, with 105 (2.4%) deaths. A total of 1233 patients (16.4%) were admitted to a critical care unit to treat complications, with 119 (9.7%) deaths. Despite lower baseline risk, outcomes were similar in low- and middle-income compared with high-income countries. CONCLUSIONS: Poor patient outcomes are common after inpatient surgery. Global initiatives to increase access to surgical treatments should also address the need for safe perioperative care. STUDY REGISTRATION: ISRCTN5181700

Comprehensive Cancer-Predisposition Gene Testing in an Adult Multiple Primary Tumor Series Shows a Broad Range of Deleterious Variants and Atypical Tumor Phenotypes.

Multiple primary tumors (MPTs) affect a substantial proportion of cancer survivors and can result from various causes, including inherited predisposition. Currently, germline genetic testing of MPT-affected individuals for variants in cancer-predisposition genes (CPGs) is mostly targeted by tumor type. We ascertained pre-assessed MPT individuals (with at least two primary tumors by age 60 years or at least three by 70 years) from genetics centers and performed whole-genome sequencing (WGS) on 460 individuals from 440 families. Despite previous negative genetic assessment and molecular investigations, pathogenic variants in moderate- and high-risk CPGs were detected in 67/440 (15.2%) probands. WGS detected variants that would not be (or were not) detected by targeted resequencing strategies, including low-frequency structural variants (6/440 [1.4%] probands). In most individuals with a germline variant assessed as pathogenic or likely pathogenic (P/LP), at least one of their tumor types was characteristic of variants in the relevant CPG. However, in 29 probands (42.2% of those with a P/LP variant), the tumor phenotype appeared discordant. The frequency of individuals with truncating or splice-site CPG variants and at least one discordant tumor type was significantly higher than in a control population (χ2 = 43.642; p ≤ 0.0001). 2/67 (3%) probands with P/LP variants had evidence of multiple inherited neoplasia allele syndrome (MINAS) with deleterious variants in two CPGs. Together with variant detection rates from a previous series of similarly ascertained MPT-affected individuals, the present results suggest that first-line comprehensive CPG analysis in an MPT cohort referred to clinical genetics services would detect a deleterious variant in about a third of individuals.JW is supported by a Cancer Research UK Cambridge Cancer Centre Clinical Research Training Fellowship. Funding for the NIHR BioResource – Rare diseases project was provided by the National Institute for Health Research (NIHR, grant number RG65966). ERM acknowledges support from the European Research Council (Advanced Researcher Award), NIHR (Senior Investigator Award and Cambridge NIHR Biomedical Research Centre), Cancer Research UK Cambridge Cancer Centre and Medical Research Council Infrastructure Award. The University of Cambridge has received salary support in respect of EM from the NHS in the East of England through the Clinical Academic Reserve. The views expressed are those of the authors and not necessarily those of the NHS or Department of Health. DGE is an NIHR Senior Investigator and is supported by the all Manchester NIHR Biomedical Research Centre

Prevalence and architecture of de novo mutations in developmental disorders.

The genomes of individuals with severe, undiagnosed developmental disorders are enriched in damaging de novo mutations (DNMs) in developmentally important genes. Here we have sequenced the exomes of 4,293 families containing individuals with developmental disorders, and meta-analysed these data with data from another 3,287 individuals with similar disorders. We show that the most important factors influencing the diagnostic yield of DNMs are the sex of the affected individual, the relatedness of their parents, whether close relatives are affected and the parental ages. We identified 94 genes enriched in damaging DNMs, including 14 that previously lacked compelling evidence of involvement in developmental disorders. We have also characterized the phenotypic diversity among these disorders. We estimate that 42% of our cohort carry pathogenic DNMs in coding sequences; approximately half of these DNMs disrupt gene function and the remainder result in altered protein function. We estimate that developmental disorders caused by DNMs have an average prevalence of 1 in 213 to 1 in 448 births, depending on parental age. Given current global demographics, this equates to almost 400,000 children born per year

Differential cross section measurements for the production of a W boson in association with jets in proton–proton collisions at √s = 7 TeV

Measurements are reported of differential cross sections for the production of a W boson, which decays into a muon and a neutrino, in association with jets, as a function of several variables, including the transverse momenta (pT) and pseudorapidities of the four leading jets, the scalar sum of jet transverse momenta (HT), and the difference in azimuthal angle between the directions of each jet and the muon. The data sample of pp collisions at a centre-of-mass energy of 7 TeV was collected with the CMS detector at the LHC and corresponds to an integrated luminosity of 5.0 fb[superscript −1]. The measured cross sections are compared to predictions from Monte Carlo generators, MadGraph + pythia and sherpa, and to next-to-leading-order calculations from BlackHat + sherpa. The differential cross sections are found to be in agreement with the predictions, apart from the pT distributions of the leading jets at high pT values, the distributions of the HT at high-HT and low jet multiplicity, and the distribution of the difference in azimuthal angle between the leading jet and the muon at low values.United States. Dept. of EnergyNational Science Foundation (U.S.)Alfred P. Sloan Foundatio