Analysis of Three-Dimensional Protein Images

A fundamental goal of research in molecular biology is to understand protein structure. Protein crystallography is currently the most successful method for determining the three-dimensional (3D) conformation of a protein, yet it remains labor intensive and relies on an expert's ability to derive and evaluate a protein scene model. In this paper, the problem of protein structure determination is formulated as an exercise in scene analysis. A computational methodology is presented in which a 3D image of a protein is segmented into a graph of critical points. Bayesian and certainty factor approaches are described and used to analyze critical point graphs and identify meaningful substructures, such as alpha-helices and beta-sheets. Results of applying the methodologies to protein images at low and medium resolution are reported. The research is related to approaches to representation, segmentation and classification in vision, as well as to top-down approaches to protein structure prediction.Comment: See http://www.jair.org/ for any accompanying file

Modeling the sustainability and economics of stacked herbicide-tolerant traits and early weed management strategy for waterhemp (Amaranthus tuberculatus) control

Diversity is key for sustainable weed management and can be achieved via both chemical and nonchemical control tactics. Genetically modified crops with two-way or three-way stacked herbicide-tolerant traits allow use of herbicide mixtures that would otherwise be phytotoxic to the crop. Early weed management(EWM)strategies promote the use of PRE herbicides with residual activity to keep the field free of weeds early in the season for successful crop establishment. To evaluate the respective sustainability and practicality of the two chemical-based management tactics(i.e.,stacked traits and EWM),we used a population model of waterhemp, Amaranthus tuberculatus (Moq.) Sauer (syn. rudis), to simulate the evolution of resistance in this key weed species in midwestern U.S.soybean [Glycinemax(L.)Merr.] agroecosystems. The model tested scenarios with a varying number of herbicide sites of action (SOAs), application timings (PRE and POST), and preexisting levels of resistance. Results showed that both tactics provided opportunity for controlling resistant A.tuberculatus populations. In general,each pass over the field should include at least two effective herbicide SOAs. Nevertheless, the potential evolution of cross-resistance may void the weed control programs embraced by stacked traits and diverse herbicide SOAs. Economic calculations suggested that the diversified programs could double long-term profitability when compared to the conventional system, because of improved yield and grain quality. Ultimately, the essence of a sustainable herbicide resistance management strategy is to be proactive. Although a herbicide-dominated approach to diversifying weed management has been prevalent, the increasing presence of weed populations with multiple resistance means that finding herbicides to which weed populations are still susceptible is becoming increasingly difficult, and thus the importance of reintroducing cultural and mechanical practices to support herbicides must be recognized

Investigation of Statistical and Imaging Methods for Luminescence Detection of Irradiated Ingredients

This project investigated two potential approaches to improving the reliability of lumines-cence methods for detecting minor irradiated ingredients in foods. Whereas in the 1980’s there were no validated methods for laboratory detection of irradiated foods, work conducted in the UK and elsewhere by the mid 1990’s had resulted in the development of a series of physical, chemical and biological methods capable of detecting a range of irradiated food classes. Of these the luminescence methods embodied in EN1788 (Thermoluminescence) and EN13751 (Photostimulated luminescence) standards have been applied to detection of a vari-ety of products including herbs and spices, and seafood. In common with the other EN stan-dard methods almost all validation work had been originally conducted using pure irradiated or unirradiated ingredients. Yet application experience had shown the presence of mixed products containing both irradiated and unirradiated ingredients. A short study was commis-sioned by MAFF to investigate the impact of blending on standard EN1788 methods, and on the provisional draft EN13751 (the standard having been published in the meantime) method. This showed the impact of dilution of irradiated material between 10% and 0.1% concentra-tions on detection rates, which unsurprisingly are reduced by extreme dilution. UK labelling regulation, both before and after adoption of the European Directive on Food Irradiation, call for labelling of all irradiated ingredients regardless of concentration or origin within the final product. This study was therefore motivated by the recognition of the long term need for im-proved methods to improve reliability at low concentrations. Two complementary approaches were investigated. The project first examined whether TL data collected using the EN1788 method could be enhanced using advanced statistical proce-dures. Data sets from the SURRC TL archive, and from project CSA4790 were used both to define the characteristics of irradiated and unirradiated end members, and to assess classifica-tion methods using the controlled blending experimental data sets of CSA 4790. Multivariate analyses, based on principal components analysis and discriminant analysis of glow curve data; kinetic deconvolution approaches coupled to PCA and DA, and neural analyses were investigated and compared with detection rates achieved using expert visual classification. To complement this experiments were undertaken to explore the potential of using focussed laser stimulation to produce spatially resolved measurements from mineral grains separated from foods. Two systems were evaluated based on IR and visible band lasers. Work was under-taken to explore sample presentation and to assess the ability of this approach to distinguish mixtures of irradiated and unirradiated grains. The statistical work was successful in developing three approaches which could be used for objective identification of irradiated materials. Pure irradiated and unirradiated data sets from 150 sample pairs were obtained having searched the SUERC archive of more than 3500 lu-minescence analyses. These were used to set up multivariate analyses based on the ap-proaches outlined above. Performance in recognising irradiated ingredients using these meth-ods was then assessed with data drawn from the MAFF blending investigation, comprising 160 permutations of irradiated and unirradiated herbs and spices at 10%, 1% and 0.1% con-centrations. It was possible to achieve good detection rates with alatistical approaches, the best approaches inigated being the use of glow curve deconvolution coupwith li discrimination, and the use of neural appros. The absolute performance achieved matched that opert visual clfication utilising the revised EN1788 criterwhich were adopted within the international standauring course of this project. The use of ad-vancedtistical methods, while not adding performance, can pde objective support to visual classifications. During performance assessment it was aloted that theformance of all methods wasficiently close to infer that detections rates are most dependent on the statistical presence or absence of irradiated grains within the extracted samples used for TL analysis. This raises practical suggestions for improving detection rates at low concentrations based on the use of larger samples and more specific mineral separation approaches. These may be worth investigating further. Laser scanning approaches were also investigated using highly focussed laser beams to stimulated luminescence sequentially from different parts of separated mineral samples. Work was conducted using a system which had been developed in earlier work at SUERC, and then followed by additional investigation using an improved instrument built during the project. Initial work confirmed the feasibility of using laser scanning approaches to obtain spatially resolved luminescence data at or near the dimensions of individual mineral grains. Practical obstacles included the recognition that laser scattering from surfaces coated with mineral grains introduced an element of cross-talk between different parts of the sample, and difficulties in accurate re-positioning of the sample using the first generation prototype in-strument. Work was conducted to investigate a series of different sample presentation media to improve the former, and to incorporate high precision mechanical and optoelectronic means of re-positioning samples between initial measurements, external irradiation, and sub-sequent re-measurement. Both IR and visible band semiconductor lasers were investigated with successful production of single grain images. The short and medium term reliability of the lasers used was acceptable. The lasers used both however eventually failed, which sug-gests that long term lifetime may be an issue for further work. Of the two lasers the IR laser in particular gave a good signal to background ratio for discriminating between irradiated and unirradiated grains. Quantitative analysis of the grain resolved images confirms the potential of this approach in identifying minor irradiated components. The overall conclusions of the work are that both statistical approaches and imaging instru-ments are able to enhance current methods. The observation that visual classification can match the performance even of deconvolution or neural approaches suggests that future effort should be directed more towards improvement of grain statistics in conventional measure-ments, and in further development and investigation of imaging approaches. In these ways it can anticipated that the performance of standard luminescence methods for detecting dilute mixtures of irradiated and unirradiated food ingredients could be significantly improved. To do so would further enhance work conducted by FSA and other bodies to ensure that regula-tions governing the use of irradiation in food processing and the labelling of imported foods are followed

Notorious places: image, reputation, stigma: the role of newspapers in area reputations for social housing estates

This paper reviews work in several disciplines to distinguish between image, reputation and stigma. It also shows that there has been little research on the process by which area reputations are established and sustained through transmission processes. This paper reports on research into the portrayal of two social housing estates in the printed media over an extended period of time (14 years). It was found that negative and mixed coverage of the estates dominated, with the amount of positive coverage being very small. By examining the way in which dominant themes were used by newspapers in respect of each estate, questions are raised about the mode of operation of the press and the communities' collective right to challenge this. By identifying the way regeneration stories are covered and the nature of the content of positive stories, lessons are drawn for programmes of area transformation. The need for social regeneration activities is identified as an important ingredient for changing deprived-area reputations

Assessing Organizational Readiness for Depression Care Quality Improvement: Relative Commitment and Implementation Capability

Background: Depression is a major cause of morbidity and cost in primary care patient populations. Successful depression improvement models, however, are complex. Based on organizational readiness theory, a practice’s commitment to change and its capability to carry out the change are both important predictors of initiating improvement. We empirically explored the links between relative commitment (i.e., the intention to move forward within the following year) and implementation capability. Methods: The DIAMOND initiative administered organizational surveys to medical and quality improvement leaders from each of 83 primary care practices in Minnesota. Surveys preceded initiation of activities directed at implementation of a collaborative care model for improving depression care. To assess implementation capability, we developed composites of survey items for five types of organizational factors postulated to be collaborative care barriers and facilitators. To assess relative commitment for each practice, we averaged leader ratings on an identical survey question assessing practice priorities. We used multivariable regression analyses to assess the extent to which implementation capability predicted relative commitment. We explored whether relative commitment or implementation capability measures were associated with earlier initiation of DIAMOND improvements. Results: All five implementation capability measures independently predicted practice leaders’ relative commitment to improving depression care in the following year. These included the following: quality improvement culture and attitudes (p = 0.003), depression culture and attitudes (p \u3c0.001), prior depression quality improvement activities (p \u3c0.001), advanced access and tracking capabilities (p = 0.03), and depression collaborative care features in place (p = 0.03). Higher relative commitment (p = 0.002) and prior depression quality improvement activities appeared to be associated with earlier participation in the DIAMOND initiative. Conclusions: The study supports the concept of organizational readiness to improve quality of care and the use of practice leader surveys to assess it. Practice leaders’ relative commitment to depression care improvement may be a useful measure of the likelihood that a practice is ready to initiate evidence-based depression care changes. A comprehensive organizational assessment of implementation capability for depression care improvement may identify specific barriers or facilitators to readiness that require targeted attention from implementers

Crocodiles and grey nomads: a deadly combination?

Increasing numbers of retirees seek individual, extended, unstructured activities in remote, non-commercial locations. Travel is predominantly by self-drive 4WD vehicle towing a caravan/campervan. These ‘grey nomads’ often prefer remote bush camping sites/caravan parks to commercial resorts. The tropics – a popular destination – are inhabited by Australia’s only large semi-terrestrial carnivore, the estuarine crocodile Crocodylus porosus. Conservation programmes of recent decades have resulted in a substantial increase in numbers. With naive grey nomads increasingly encroaching on crocodile territory, attacks are expected to increase. Review of conservation programmes to incorporate awareness education targeting grey nomads is therefore required