Spatio-temporal analysis of an invasive plant pathogen (Phytophthora ramorum) in England and Wales

Phytophthora ramorum is a damaging invasive plant pathogen and was first discovered in the UK in 2002. Spatial point analyses were applied to the occurrence of this disease in England and Wales during the period of 2003-2006 in order to assess its spatio-temporal spread. Out of the 4301 garden centres and nurseries (GCN) surveyed, there were 164, 105, 123 and 41 sites with P. ramorum in 2003, 2004, 2005 and 2006, respectively. Spatial analysis of the observed point patterns of GCN outbreaks suggested that these sites were significantly clumped within a radius of ca 60 km in 2003, but not in later years. Further analyses were conducted to determine the relationship of GCN outbreak sites over two consecutive years and thus to infer possible disease spread over time. This analysis suggested that disease spread among GCN sites was most likely to have occurred within a distance of 60 km for 2003-2004, but not for the later years. There were 35, 63, 81 and 58 sites with P. ramorum in the semi-natural environment (SNE). Analyses were carried out to assess whether infected GCN sites could act as an inoculum source of infected SNE plants or vice versa. In all years, there was a significant spatial closeness among GCN and SNE outbreak sites within a distance of 1 km. But a significant relationship over a longer distance (within 60 km) was only observed between cases in 2003 and 2004. These analyses suggest that statutory actions taken so far appear to have reduced the extent of long-distance spread of P. ramorum among garden centres and nurseries, but not the disease spread at a shorter distance between GCN and SNE sites.

TRCM: a methodology for temporal analysis of evolving concepts in Twitter

The Twitter network has been labelled the most commonly used microblogging application around today. With about 500 million estimated registered users as of June, 2012, Twitter has become a credible medium of sentiment/opinion expression. It is also a notable medium for information dissemination; including breaking news on diverse issues since it was launched in 2007. Many organisations, individuals and even government bodies follow activities on the network in order to obtain knowledge on how their audience reacts to tweets that affect them. We can use postings on Twitter (known as tweets) to analyse patterns associated with events by detecting the dynamics of the tweets. A common way of labelling a tweet is by including a number of hashtags that describe its contents. Association Rule Mining can find the likelihood of co-occurrence of hashtags. In this paper, we propose the use of temporal Association Rule Mining to detect rule dynamics, and consequently dynamics of tweets. We coined our methodology Transaction-based Rule Change Mining (TRCM). A number of patterns are identifiable in these rule dynamics including, new rules, emerging rules, unexpected rules and ?dead' rules. Also the linkage between the different types of rule dynamics is investigated experimentally in this paper.

Process analysis of trauma-focused cognitive behavioural therapy for individuals with schizophrenia

Objective. Therapeutic alliance, modality, and ability to engage with the process of therapy have been the main focus of research into what makes psychotherapy successful. Individuals with complex trauma histories or schizophrenia are suggested to be more difficult to engage and may be less likely to benefit from therapy. This study aimed to track the in-session ‘process’ of working alliance and emotional processing of trauma memories for individuals with schizophrenia. Design. The study utilized session recordings from the treatment arm of an open randomized clinical trial investigating trauma-focused cognitive behavioural therapy (TF-CBT) for individuals with schizophrenia (N = 26). Method. Observer measures of working alliance, emotional processing, and affect arousal were rated at early and late phases of therapy. Correlation analysis was undertaken for process measures. Temporal analysis of expressed emotions was also reported. Results. Working alliance was established and maintained throughout the therapy; however, agreement on goals reduced at the late phase. The participants appeared to be able to engage in emotional processing, but not to the required level for successful cognitive restructuring. Conclusion. This study undertook novel exploration of process variables not usually explored in CBT. It is also the first study of process for TF-CBT with individuals with schizophrenia. This complex clinical sample showed no difficulty in engagement; however, they may not be able to fully undertake the cognitive–emotional demands of this type of therapy. Clinical and research implications and potential limitations of these methods are considered.

Fundamental deficits of auditory perception in Wernicke’s aphasia

Objective: This work investigates the nature of the comprehension impairment in Wernicke’s aphasia, by examining the relationship between deficits in auditory processing of fundamental, non-verbal acoustic stimuli and auditory comprehension. Wernicke’s aphasia, a condition resulting in severely disrupted auditory comprehension, primarily occurs following a cerebrovascular accident (CVA) to the left temporo-parietal cortex. Whilst damage to posterior superior temporal areas is associated with auditory linguistic comprehension impairments, functional imaging indicates that these areas may not be specific to speech processing but part of a network for generic auditory analysis. Methods: We examined analysis of basic acoustic stimuli in Wernicke’s aphasia participants (n = 10) using auditory stimuli reflective of theories of cortical auditory processing and of speech cues. Auditory spectral, temporal and spectro-temporal analysis was assessed using pure tone frequency discrimination, frequency modulation (FM) detection and the detection of dynamic modulation (DM) in “moving ripple” stimuli. All tasks used criterion-free, adaptive measures of threshold to ensure reliable results at the individual level. Results: Participants with Wernicke’s aphasia showed normal frequency discrimination but significant impairments in FM and DM detection, relative to age- and hearing-matched controls at the group level (n = 10). At the individual level, there was considerable variation in performance, and thresholds for both frequency and dynamic modulation detection correlated significantly with auditory comprehension abilities in the Wernicke’s aphasia participants. Conclusion: These results demonstrate the co-occurrence of a deficit in fundamental auditory processing of temporal and spectrotemporal nonverbal stimuli in Wernicke’s aphasia, which may have a causal contribution to the auditory language comprehension impairment Results are discussed in the context of traditional neuropsychology and current models of cortical auditory processing.

Identification of micro-scale anthropogenic CO2, heat and moisture sources – processing eddy covariance fluxes for a dense urban environment

Anthropogenic emissions of heat and exhaust gases play an important role in the atmospheric boundary layer, altering air quality, greenhouse gas concentrations and the transport of heat and moisture at various scales. This is particularly evident in urban areas where emission sources are integrated in the highly heterogeneous urban canopy layer and directly linked to human activities which exhibit significant temporal variability. It is common practice to use eddy covariance observations to estimate turbulent surface fluxes of latent heat, sensible heat and carbon dioxide, which can be attributed to a local scale source area. This study provides a method to assess the influence of micro-scale anthropogenic emissions on heat, moisture and carbon dioxide exchange in a highly urbanized environment for two sites in central London, UK. A new algorithm for the Identification of Micro-scale Anthropogenic Sources (IMAS) is presented, with two aims. Firstly, IMAS filters out the influence of micro-scale emissions and allows for the analysis of the turbulent fluxes representative of the local scale source area. Secondly, it is used to give a first order estimate of anthropogenic heat flux and carbon dioxide flux representative of the building scale. The algorithm is evaluated using directional and temporal analysis. The algorithm is then used at a second site which was not incorporated in its development. The spatial and temporal local scale patterns, as well as micro-scale fluxes, appear physically reasonable and can be incorporated in the analysis of long-term eddy covariance measurements at the sites in central London. In addition to the new IMAS-technique, further steps in quality control and quality assurance used for the flux processing are presented. The methods and results have implications for urban flux measurements in dense urbanised settings with significant sources of heat and greenhouse gases.

Spatial-temporal aspects of cost-benefit analysis for park management: an example from Khao Yai National Park, Thailand

Using a model calibrated to Khao Yai National Park in Thailand, this paper highlights the importance of generating explicitly spatial and temporal data for developing management plans for tropical protected forests. Spatial and temporal cost-benefit analysis should account for the interactions between different land uses – such as the benefits of contiguous areas of preserved land and edge effects – and the realities of villagers living near forests who rely on extracted resources. By taking a temporal perspective, this paper provides a rare empirical assessment of the importance of quasi-option values when determining optimal management plans.

Sensitivity of feature-based analysis methods of storm tracks to the form of background field removal

For the tracking of extrema associated with weather systems to be applied to a broad range of fields it is necessary to remove a background field that represents the slowly varying, large spatial scales. The sensitivity of the tracking analysis to the form of background field removed is explored for the Northern Hemisphere winter storm tracks for three contrasting fields from an integration of the U. K. Met Office's (UKMO) Hadley Centre Climate Model (HadAM3). Several methods are explored for the removal of a background field from the simple subtraction of the climatology, to the more sophisticated removal of the planetary scales. Two temporal filters are also considered in the form of a 2-6-day Lanczos filter and a 20-day high-pass Fourier filter. The analysis indicates that the simple subtraction of the climatology tends to change the nature of the systems to the extent that there is a redistribution of the systems relative to the climatological background resulting in very similar statistical distributions for both positive and negative anomalies. The optimal planetary wave filter removes total wavenumbers less than or equal to a number in the range 5-7, resulting in distributions more easily related to particular types of weather system. For the temporal filters the 2-6-day bandpass filter is found to have a detrimental impact on the individual weather systems, resulting in the storm tracks having a weak waveguide type of behavior. The 20-day high-pass temporal filter is less aggressive than the 2-6-day filter and produces results falling between those of the climatological and 2-6-day filters.

Analysis of convectively-generated gravity waves in mesoscale model simulations and wind profiler observations

The characteristics of convectively-generated gravity waves during an episode of deep convection near the coast of Wales are examined in both high resolution mesoscale simulations [with the (UK) Met Oce Unified Model] and in observations from a Mesosphere-Stratosphere-Troposphere (MST) wind profiling Doppler radar. Deep convection reached the tropopause and generated vertically propagating, high frequency waves in the lower stratosphere that produced vertical velocity perturbations O(1 m/s). Wavelet analysis is applied in order to determine the characteristic periods and wavelengths of the waves. In both the simulations and observations, the wavelet spectra contain several distinct preferred scales indicated by multiple spectral peaks. The peaks are most pronounced in the horizontal spectra at several wavelengths less than 50 km. Although these peaks are most clear and of largest amplitude in the highest resolution simulations (with 1 km horizontal grid length), they are also evident in coarser simulations (with 4 km horizontal grid length). Peaks also exist in the vertical and temporal spectra (between approximately 2.5 and 4.5 km, and 10 to 30 minutes, respectively) with good agreement between simulation and observation. Two-dimensional (wavenumber-frequency) spectra demonstrate that each of the selected horizontal scales contains peaks at each of preferred temporal scales revealed by the one- dimensional spectra alone.

Independent component analysis of climate data: A new look at EOF rotation

The complexity inherent in climate data makes it necessary to introduce more than one statistical tool to the researcher to gain insight into the climate system. Empirical orthogonal function (EOF) analysis is one of the most widely used methods to analyze weather/climate modes of variability and to reduce the dimensionality of the system. Simple structure rotation of EOFs can enhance interpretability of the obtained patterns but cannot provide anything more than temporal uncorrelatedness. In this paper, an alternative rotation method based on independent component analysis (ICA) is considered. The ICA is viewed here as a method of EOF rotation. Starting from an initial EOF solution rather than rotating the loadings toward simplicity, ICA seeks a rotation matrix that maximizes the independence between the components in the time domain. If the underlying climate signals have an independent forcing, one can expect to find loadings with interpretable patterns whose time coefficients have properties that go beyond simple noncorrelation observed in EOFs. The methodology is presented and an application to monthly means sea level pressure (SLP) field is discussed. Among the rotated (to independence) EOFs, the North Atlantic Oscillation (NAO) pattern, an Arctic Oscillation–like pattern, and a Scandinavian-like pattern have been identified. There is the suggestion that the NAO is an intrinsic mode of variability independent of the Pacific.

Farm-level performance of genetically modified cotton - A frontier analysis of cotton production in Maharashtra

In this paper, the yield increases resulting from the cultivation of Bt cotton in Maharashtra, India, are analysed. The study relies on commercial farm, rather than trial, data and is among the first of its kind to be based on real farm and market conditions. Findings show that since its commercial release in 2002, Bt cotton has had a significant positive impact on yields and on the economic performance of cotton growers in Maharashtra. This difference remains even after controlling for different soil and insecticide inputs in the production of Bt cotton. There is also significant spatial and temporal variation in this 'benefit', and much depends upon where production is taking place and on the season.

Cost-benefit analysis model of badger (Meles meles) culling to reduce cattle herd tuberculosis breakdowns in Britain, with particular reference to badger perturbation

Bovine tuberculosis (TB)is an important economic disease. Badgers (Meles meles) are the wildlife source implicated in many cattle outbreaks of TB in Britain, and extensive badger control is a controversial option to reduce the disease. A badger and cattle population model was developed, simulating TB epidemiology; badger ecology, including postcull social perturbation; and TB-related farm management. An economic cost-benefit module was integrated into the model to assess whether badger control offers economic benefits. Model results strongly indicate that although, if perturbation were restricted, extensive badger culling could reduce rates in cattle, overall an economic loss would be more likely than a benefit. Perturbation of the badger population was a key factor determining success or failure of control. The model highlighted some important knowledge gaps regarding both the spatial and temporal characteristics of perturbation that warrant further research.

From dichotic listening to the irrelevant sound effect: a behavioural and neuroimaging analysis of the processing of unattended speech

The assumption that ignoring irrelevant sound in a serial recall situation is identical to ignoring a non-target channel in dichotic listening is challenged. Dichotic listening is open to moderating effects of working memory capacity (Conway et al., 2001) whereas irrelevant sound effects (ISE) are not (Beaman, 2004). A right ear processing bias is apparent in dichotic listening, whereas the bias is to the left ear in the ISE (Hadlington et al., 2004). Positron emission tomography (PET) imaging data (Scott et al., 2004, submitted) show bilateral activation of the superior temporal gyrus (STG) in the presence of intelligible, but ignored, background speech and right hemisphere activation of the STG in the presence of unintelligible background speech. It is suggested that the right STG may be involved in the ISE and a particularly strong left ear effect might occur because of the contralateral connections in audition. It is further suggested that left STG activity is associated with dichotic listening effects and may be influenced by working memory span capacity. The relationship of this functional and neuroanatomical model to known neural correlates of working memory is considered.

Geostatistical analysis of rainfall

Rainfall can be modeled as a spatially correlated random field superimposed on a background mean value; therefore, geostatistical methods are appropriate for the analysis of rain gauge data. Nevertheless, there are certain typical features of these data that must be taken into account to produce useful results, including the generally non-Gaussian mixed distribution, the inhomogeneity and low density of observations, and the temporal and spatial variability of spatial correlation patterns. Many studies show that rigorous geostatistical analysis performs better than other available interpolation techniques for rain gauge data. Important elements are the use of climatological variograms and the appropriate treatment of rainy and nonrainy areas. Benefits of geostatistical analysis for rainfall include ease of estimating areal averages, estimation of uncertainties, and the possibility of using secondary information (e.g., topography). Geostatistical analysis also facilitates the generation of ensembles of rainfall fields that are consistent with a given set of observations, allowing for a more realistic exploration of errors and their propagation in downstream models, such as those used for agricultural or hydrological forecasting. This article provides a review of geostatistical methods used for kriging, exemplified where appropriate by daily rain gauge data from Ethiopia.