The benefits of a compute cluster approach to high spatial resolution biodiversity richness modelling: projecting the impact of climate change on Mediterranean flora

High spatial resolution environmental data gives us a better understanding of the environmental factors affecting plant distributions at fine spatial scales. However, large environmental datasets dramatically increase compute times and output species model size stimulating the need for an alternative computing solution. Cluster computing offers such a solution, by allowing both multiple plant species Environmental Niche Models (ENMs) and individual tiles of high spatial resolution models to be computed concurrently on the same compute cluster. We apply our methodology to a case study of 4,209 species of Mediterranean flora (around 17% of species believed present in the biome). We demonstrate a 16 times speed-up of ENM computation time when 16 CPUs were used on the compute cluster. Our custom Java ‘Merge’ and ‘Downsize’ programs reduce ENM output files sizes by 94%. The median 0.98 test AUC score of species ENMs is aided by various species occurrence data filtering techniques. Finally, by calculating the percentage change of individual grid cell values, we map the projected percentages of plant species vulnerable to climate change in the Mediterranean region between 1950–2000 and 2020.

Exploring the role of reanalysis data in simulating regional wind generation variability over Northern Ireland

As wind generation increases, system impact studies rely on predictions of future generation and effective representation of wind variability. A well-established approach to investigate the impact of wind variability is to simulate generation using observations from 10 m meteorological mast-data. However, there are problems with relying purely on historical wind-speed records or generation histories: mast-data is often incomplete, not sited at a relevant wind generation sites, and recorded at the wrong altitude above ground (usually 10 m), each of which may distort the generation profile. A possible complimentary approach is to use reanalysis data, where data assimilation techniques are combined with state-of-the-art weather forecast models to produce complete gridded wind time-series over an area. Previous investigations of reanalysis datasets have placed an emphasis on comparing reanalysis to meteorological site records whereas this paper compares wind generation simulated using reanalysis data directly against historic wind generation records. Importantly, this comparison is conducted using raw reanalysis data (typical resolution ∼50 km), without relying on a computationally expensive “dynamical downscaling” for a particular target region. Although the raw reanalysis data cannot, by nature of its construction, represent the site-specific effects of sub-gridscale topography, it is nevertheless shown to be comparable to or better than the mast-based simulation in the region considered and it is therefore argued that raw reanalysis data may offer a number of significant advantages as a data source.

An integrated view of data quality in Earth observation

Data quality is a difficult notion to define precisely, and different communities have different views and understandings of the subject. This causes confusion, a lack of harmonization of data across communities and omission of vital quality information. For some existing data infrastructures, data quality standards cannot address the problem adequately and cannot fulfil all user needs or cover all concepts of data quality. In this study, we discuss some philosophical issues on data quality. We identify actual user needs on data quality, review existing standards and specifications on data quality, and propose an integrated model for data quality in the field of Earth observation (EO). We also propose a practical mechanism for applying the integrated quality information model to a large number of datasets through metadata inheritance. While our data quality management approach is in the domain of EO, we believe that the ideas and methodologies for data quality management can be applied to wider domains and disciplines to facilitate quality-enabled scientific research.

The integration of proteomics and systems approaches to map regulatory mechanisms underpinning platelet function.

Platelets in the circulation are triggered by vascular damage to activate, aggregate and form a thrombus that prevents excessive blood loss. Platelet activation is stringently regulated by intracellular signalling cascades, which when activated inappropriately lead to myocardial infarction and stroke. Strategies to address platelet dysfunction have included proteomics approaches which have lead to the discovery of a number of novel regulatory proteins of potential therapeutic value. Global analysis of platelet proteomes may enhance the outcome of these studies by arranging this information in a contextual manner that recapitulates established signalling complexes and predicts novel regulatory processes. Platelet signalling networks have already begun to be exploited with interrogation of protein datasets using in silico methodologies that locate functionally feasible protein clusters for subsequent biochemical validation. Characterization of these biological systems through analysis of spatial and temporal organization of component proteins is developing alongside advances in the proteomics field. This focused review highlights advances in platelet proteomics data mining approaches that complement the emerging systems biology field. We have also highlighted nucleated cell types as key examples that can inform platelet research. Therapeutic translation of these modern approaches to understanding platelet regulatory mechanisms will enable the development of novel anti-thrombotic strategies.

The distribution of London residential property prices and the role of spatial lock-in

Much of mainstream economic analysis assumes that markets adjust smoothly, through prices, to changes in economic conditions. However, this is not necessarily the case for local housing markets, whose spatial structures may exhibit persistence, so that conditions may not be those most suited to the requirements of modern-day living. Persistence can arise from the existence of transaction costs. The paper tests the proposition that housing markets in Inner London exhibit a degree of path dependence, through the construction of a three-equation model, and examines the impact of variables constructed for the 19th and early 20th centuries on modern house prices. These include 19th-century social structures, slum clearance programmes and the 1908 underground network. Each is found to be significant. The tests require the construction of novel historical datasets, which are also described in the paper.

Robust abandoned object detection integrating wide area visual surveillance and social context

This paper presents a video surveillance framework that robustly and efficiently detects abandoned objects in surveillance scenes. The framework is based on a novel threat assessment algorithm which combines the concept of ownership with automatic understanding of social relations in order to infer abandonment of objects. Implementation is achieved through development of a logic-based inference engine based on Prolog. Threat detection performance is conducted by testing against a range of datasets describing realistic situations and demonstrates a reduction in the number of false alarms generated. The proposed system represents the approach employed in the EU SUBITO project (Surveillance of Unattended Baggage and the Identification and Tracking of the Owner).

ATD: a multiplatform for semiautomatic 3-D detection of kidneys and their pathology in real time

This research presents a novel multi-functional system for medical Imaging-enabled Assistive Diagnosis (IAD). Although the IAD demonstrator has focused on abdominal images and supports the clinical diagnosis of kidneys using CT/MRI imaging, it can be adapted to work on image delineation, annotation and 3D real-size volumetric modelling of other organ structures such as the brain, spine, etc. The IAD provides advanced real-time 3D visualisation and measurements with fully automated functionalities as developed in two stages. In the first stage, via the clinically driven user interface, specialist clinicians use CT/MRI imaging datasets to accurately delineate and annotate the kidneys and their possible abnormalities, thus creating “3D Golden Standard Models”. Based on these models, in the second stage, clinical support staff i.e. medical technicians interactively define model-based rules and parameters for the integrated “Automatic Recognition Framework” to achieve results which are closest to that of the clinicians. These specific rules and parameters are stored in “Templates” and can later be used by any clinician to automatically identify organ structures i.e. kidneys and their possible abnormalities. The system also supports the transmission of these “Templates” to another expert for a second opinion. A 3D model of the body, the organs and their possible pathology with real metrics is also integrated. The automatic functionality was tested on eleven MRI datasets (comprising of 286 images) and the 3D models were validated by comparing them with the metrics from the corresponding “3D Golden Standard Models”. The system provides metrics for the evaluation of the results, in terms of Accuracy, Precision, Sensitivity, Specificity and Dice Similarity Coefficient (DSC) so as to enable benchmarking of its performance. The first IAD prototype has produced promising results as its performance accuracy based on the most widely deployed evaluation metric, DSC, yields 97% for the recognition of kidneys and 96% for their abnormalities; whilst across all the above evaluation metrics its performance ranges between 96% and 100%. Further development of the IAD system is in progress to extend and evaluate its clinical diagnostic support capability through development and integration of additional algorithms to offer fully computer-aided identification of other organs and their abnormalities based on CT/MRI/Ultra-sound Imaging.

A survey of human motion analysis using depth imagery

Analysis of human behaviour through visual information has been a highly active research topic in the computer vision community. This was previously achieved via images from a conventional camera, but recently depth sensors have made a new type of data available. This survey starts by explaining the advantages of depth imagery, then describes the new sensors that are available to obtain it. In particular, the Microsoft Kinect has made high-resolution real-time depth cheaply available. The main published research on the use of depth imagery for analysing human activity is reviewed. Much of the existing work focuses on body part detection and pose estimation. A growing research area addresses the recognition of human actions. The publicly available datasets that include depth imagery are listed, as are the software libraries that can acquire it from a sensor. This survey concludes by summarising the current state of work on this topic, and pointing out promising future research directions.

Testing for significance of phase synchronisation dynamics in the EEG

A number of tests exist to check for statistical significance of phase synchronisation within the Electroencephalogram (EEG); however, the majority suffer from a lack of generality and applicability. They may also fail to account for temporal dynamics in the phase synchronisation, regarding synchronisation as a constant state instead of a dynamical process. Therefore, a novel test is developed for identifying the statistical significance of phase synchronisation based upon a combination of work characterising temporal dynamics of multivariate time-series and Markov modelling. We show how this method is better able to assess the significance of phase synchronisation than a range of commonly used significance tests. We also show how the method may be applied to identify and classify significantly different phase synchronisation dynamics in both univariate and multivariate datasets.

Assessment of a 1 hour gridded precipitation dataset to drive a hydrological model: a case study of the summer 2007 floods in the Upper Severn, UK

In this study a gridded hourly 1-km precipitation dataset for a meso-scale catchment (4,062 km2) of the Upper Severn River, UK was constructed using rainfall radar data to disaggregate a daily precipitation (rain gauge) dataset. The dataset was compared to an hourly precipitation dataset created entirely from rainfall radar data. Results found that when assessed against gauge readings and as input to the Lisflood-RR hydrological model, the rain gauge/radar disaggregated dataset performed the best suggesting that this simple method of combining rainfall radar data with rain gauge readings can provide temporally detailed precipitation datasets for calibrating hydrological models.

Some challenges of middle atmosphere data assimilation

The assimilation of measurements from the stratosphere and mesosphere is becoming increasingly common as the lids of weather prediction and climate models rise into the mesosphere and thermosphere. However, the dynamics of the middle atmosphere pose specific challenges to the assimilation of measurements from this region. Forecast-error variances can be very large in the mesosphere and this can render assimilation schemes very sensitive to the details of the specification of forecast error correlations. An example is shown where observations in the stratosphere are able to produce increments in the mesosphere. Such sensitivity of the assimilation scheme to misspecification of covariances can also amplify any existing biases in measurements or forecasts. Since both models and measurements of the middle atmosphere are known to have biases, the separation of these sources of bias remains a issue. Finally, well-known deficiencies of assimilation schemes, such as the production of imbalanced states or the assumption of zero bias, are proposed explanations for the inaccurate transport resulting from assimilated winds. The inability of assimilated winds to accurately transport constituents in the middle atmosphere remains a fundamental issue limiting the use of assimilated products for applications involving longer time-scales.

Statistical characterization of arctic polar-night jet oscillation events

A novel diagnostic tool is presented, based on polar-cap temperature anomalies, for visualizing daily variability of the Arctic stratospheric polar vortex over multiple decades. This visualization illustrates the ubiquity of extended-time-scale recoveries from stratospheric sudden warmings, termed here polar-night jet oscillation (PJO) events. These are characterized by an anomalously warm polar lower stratosphere that persists for several months. Following the initial warming, a cold anomaly forms in the middle stratosphere, as does an anomalously high stratopause, both of which descend while the lower-stratospheric anomaly persists. These events are characterized in four datasets: Microwave Limb Sounder (MLS) temperature observations; the 40-yr ECMWF Re-Analysis (ERA-40) and Modern Era Retrospective Analysis for Research and Applications (MERRA) reanalyses; and an ensemble of three 150-yr simulations from the Canadian Middle Atmosphere Model. The statistics of PJO events in the model are found to agree very closely with those of the observations and reanalyses. The time scale for the recovery of the polar vortex following sudden warmings correlates strongly with the depth to which the warming initially descends. PJO events occur following roughly half of all major sudden warmings and are associated with an extended period of suppressed wave-activity fluxes entering the polar vortex. They follow vortex splits more frequently than they do vortex displacements. They are also related to weak vortex events as identified by the northern annular mode; in particular, those weak vortex events followed by a PJO event show a stronger tropospheric response. The long time scales, predominantly radiative dynamics, and tropospheric influence of PJO events suggest that they represent an important source of conditional skill in seasonal forecasting.

A comprehensive benchmarking system for evaluating global vegetation models.

We present a benchmark system for global vegetation models. This system provides a quantitative evaluation of multiple simulated vegetation properties, including primary production; seasonal net ecosystem production; vegetation cover, composition and 5 height; fire regime; and runoff. The benchmarks are derived from remotely sensed gridded datasets and site-based observations. The datasets allow comparisons of annual average conditions and seasonal and inter-annual variability, and they allow the impact of spatial and temporal biases in means and variability to be assessed separately. Specifically designed metrics quantify model performance for each process, 10 and are compared to scores based on the temporal or spatial mean value of the observations and a “random” model produced by bootstrap resampling of the observations. The benchmark system is applied to three models: a simple light-use efficiency and water-balance model (the Simple Diagnostic Biosphere Model: SDBM), and the Lund-Potsdam-Jena (LPJ) and Land Processes and eXchanges (LPX) dynamic global 15 vegetation models (DGVMs). SDBM reproduces observed CO2 seasonal cycles, but its simulation of independent measurements of net primary production (NPP) is too high. The two DGVMs show little difference for most benchmarks (including the interannual variability in the growth rate and seasonal cycle of atmospheric CO2), but LPX represents burnt fraction demonstrably more accurately. Benchmarking also identified 20 several weaknesses common to both DGVMs. The benchmarking system provides a quantitative approach for evaluating how adequately processes are represented in a model, identifying errors and biases, tracking improvements in performance through model development, and discriminating among models. Adoption of such a system would do much to improve confidence in terrestrial model predictions of climate change 25 impacts and feedbacks.

Femto-chemometrics: the signal processing of fast pulse transients

Traditional chemometrics techniques are augmented with algorithms tailored specifically for the de-noising and analysis of femtosecond duration pulse datasets. The new algorithms provide additional insights on sample responses to broadband excitation and multi-moded propagation phenomena.

The world at one's fingertips: interactive interpretation of environmental data

This chapter introduces the latest practices and technologies in the interactive interpretation of environmental data. With environmental data becoming ever larger, more diverse and more complex, there is a need for a new generation of tools that provides new capabilities over and above those of the standard workhorses of science. These new tools aid the scientist in discovering interesting new features (and also problems) in large datasets by allowing the data to be explored interactively using simple, intuitive graphical tools. In this way, new discoveries are made that are commonly missed by automated batch data processing. This chapter discusses the characteristics of environmental science data, common current practice in data analysis and the supporting tools and infrastructure. New approaches are introduced and illustrated from the points of view of both the end user and the underlying technology. We conclude by speculating as to future developments in the field and what must be achieved to fulfil this vision.