Radar studies of the vertical distribution of insects migrating over southern Britain: the influence of temperature inversions on nocturnal layer concentrations

Insects migrating over two sites in southern UK (Malvern in Worcestershire, and Harpenden in Hertfordshire) have been monitored continuously with nutating vertical-looking radars (VLRs) equipped with powerful control and analysis software. These observations make possible, for the first time, a systematic investigation of the vertical distribution of insect aerial density in the atmosphere, over temporal scales ranging from the short (instantaneous vertical profiles updated every 15 min) to the very long (profiles aggregated over whole seasons or even years). In the present paper, an outline is given of some general features of insect stratification as revealed by the radars, followed by a description of occasions during warm nights in the summer months when intense insect layers developed. Some of these nocturnal layers were due to the insects flying preferentially at the top of strong surface temperature inversions, and in other cases, layering was associated with higher-altitude temperature maxima, such as those due to subsidence inversions. The layers were formed from insects of a great variety of sizes, but peaks in the mass distributions pointed to a preponderance of medium-sized noctuid moths on certain occasions.

Comparison of survival rates of captive-reared and wild-bred Mauritius kestrels (Falco punctatus) in a re-introduced population

Re-introduction is a technique widely used in the conservation of threatened bird species. With advances in aviculture the use of captive-produced individuals as the release stock is becoming more commonplace, and ideally, survival of captive-produced, released individuals should be no different from their wild-bred counterparts. During the late 1980s the Critically Endangered Mauritius kestrel (Falco punctatus) was successfully re-introduced into the Bambous mountain range, Mauritius, some 30 years after its local extinction. Between 1987 and 2001 the developing population was closely monitored enabling us to construct re-sighting histories for 88 released and 284 wild-bred kestrels. We used age-structured models in the survival analysis software program MARK to determine if an individual's origin influenced its subsequent survival. Our analysis indicated no compelling evidence for reduced survival among juvenile captive-reared and released individuals, relative to their wild-bred counterparts, across the majority of cohorts and only limited evidence of a cohort-specific effect. This study illustrates that despite the lack of a formal experimental approach it is still feasible to conduct an assessment of re-introduction outcomes and techniques.

Stress-induced changes in the Schizosaccharomyces pombe proteome using two-dimensional difference gel electrophoresis, mass spectrometry and a novel integrated robotics platform

Robotic and manual methods have been used to obtain identification of significantly changing proteins regulated when Schizosaccharomyces pombe is exposed to oxidative stress. Differently treated S. pombe cells were lysed, labelled with CyDye and analysed by two-dimensional difference gel electrophoresis. Gel images analysed off-line, using the DeCyder image analysis software [GE Healthcare, Amersham, UK] allowed selection of significantly regulated proteins. Proteins displaying differential expression were excised robotically for manual digestion and identified by matrix-assisted laser desorption/ionisation - mass spectrometry (MALDI-MS). Additionally the same set of proteins displaying differential expression were automatically cut and digested using a prototype robotic platform. Automated MALDI-MS, peak label assignment and database searching were utilised to identify as many proteins as possible. The results achieved by the robotic system were compared to manual methods. The identification of all significantly altered proteins provides an annotated peroxide stress-related proteome that can be used as a base resource against which other stress-induced proteomic changes can be compared.

Comparison of survival rates of captive-reared and wild-bred Mauritius kestrels (falco punctatus) in a re-introduced population

Re-introduction is a technique widely used in the conservation of threatened bird species. With advances in aviculture the use of captive-produced individuals as the release stock is becoming more commonplace, and ideally, survival of captive-produced, released individuals should be no different from their wild-bred counterparts. During the late 1980s the Critically Endangered Mauritius kestrel (Falco punctatus) was successfully re-introduced into the Bambous mountain range, Mauritius, some 30 years after its local extinction. Between 1987 and 2001 the developing population was closely monitored enabling us to construct re-sighting histories for 88 released and 284 wild-bred kestrels. We used age-structured models in the survival analysis software program MARK to determine if an individual's origin influenced its subsequent survival. Our analysis indicated no compelling evidence for reduced survival among juvenile captive-reared and released individuals, relative to their wild-bred counterparts, across the majority of cohorts and only limited evidence of a cohort-specific effect. This study illustrates that despite the lack of a formal experimental approach it is still feasible to conduct an assessment of re-introduction outcomes and techniques. (C) 2003 Elsevier Ltd. All rights reserved.

Stress-induced changes in the Schizosaccharomyces pombe proteome using two-dimensional difference gel electrophoresis, mass spectrometry and a novel integrated robotics platform

Robotic and manual methods have been used to obtain identification of significantly changing proteins regulated when Schizosaccharomyces pombe is exposed to oxidative stress. Differently treated S. pombe cells were lysed, labelled with CyDye (TM) and analysed by two-dimensional difference gel. electrophoresis. Gel images analysed off-line, using the DeCyder (TM) image analysis software [GE Healthcare, Amersham, UK] allowed selection of significantly regulated proteins. Proteins displaying differential expression were excised robotically for manual digestion and identified by matrix-assisted laser desorption/ionisation - mass spectrometry (MALDI-MS). Additionally the same set of proteins displaying differential expression were automatically cut and digested using a prototype robotic platform. Automated MALDI-MS, peak label assignment and database searching were utilised to identify as many proteins as possible. The results achieved by the robotic system were compared to manual methods. The identification of all significantly altered proteins provides an annotated peroxide stress-related proteome that can be used as a base resource against which other stress-induced proteomic changes can be compared.

A molecular and structural characterization of senescing Arabidopsis siliques and comparison of transcriptional profiles with senescing petals and leaves

Senescence of plant organs is a genetically controlled process that regulates cell death to facilitate nutrient recovery and recycling, and frequently precedes, or is concomitant with, ripening of reproductive structures. In Arabidopsis thaliana, the seeds are contained within a silique, which is itself a photosynthetic organ in the early stages of development and undergoes a programme of senescence prior to dehiscence. A transcriptional analysis of the silique wall was undertaken to identify changes in gene expression during senescence and to correlate these events with ultrastructural changes. The study revealed that the most highly up-regulated genes in senescing silique wall tissues encoded seed storage proteins, and the significance of this finding is discussed. Global transcription profiles of senescing siliques were compared with those from senescing Arabidopsis leaf or petal tissues using microarray datasets and metabolic pathway analysis software (MapMan). In all three tissues, members of NAC and WRKY transcription factor families were up-regulated, but components of the shikimate and cell-wall biosynthetic pathways were down-regulated during senescence. Expression of genes encoding ethylene biosynthesis and action showed more similarity between senescing siliques and petals than between senescing siliques and leaves. Genes involved in autophagy were highly expressed in the late stages of death of all plant tissues studied, but not always during the preceding remobilization phase of senescence. Analyses showed that, during senescence, silique wall tissues exhibited more transcriptional features in common with petals than with leaves. The shared and distinct regulatory events associated with senescence in the three organs are evaluated and discussed.

Final report on research project PS2010, proof of concept of automated mapping of weeds in arable fields

Many weeds occur in patches but farmers frequently spray whole fields to control the weeds in these patches. Given a geo-referenced weed map, technology exists to confine spraying to these patches. Adoption of patch spraying by arable farmers has, however, been negligible partly due to the difficulty of constructing weed maps. Building on previous DEFRA and HGCA projects, this proposal aims to develop and evaluate a machine vision system to automate the weed mapping process. The project thereby addresses the principal technical stumbling block to widespread adoption of site specific weed management (SSWM). The accuracy of weed identification by machine vision based on a single field survey may be inadequate to create herbicide application maps. We therefore propose to test the hypothesis that sufficiently accurate weed maps can be constructed by integrating information from geo-referenced images captured automatically at different times of the year during normal field activities. Accuracy of identification will also be increased by utilising a priori knowledge of weeds present in fields. To prove this concept, images will be captured from arable fields on two farms and processed offline to identify and map the weeds, focussing especially on black-grass, wild oats, barren brome, couch grass and cleavers. As advocated by Lutman et al. (2002), the approach uncouples the weed mapping and treatment processes and builds on the observation that patches of these weeds are quite stable in arable fields. There are three main aspects to the project. 1) Machine vision hardware. Hardware component parts of the system are one or more cameras connected to a single board computer (Concurrent Solutions LLC) and interfaced with an accurate Global Positioning System (GPS) supplied by Patchwork Technology. The camera(s) will take separate measurements for each of the three primary colours of visible light (red, green and blue) in each pixel. The basic proof of concept can be achieved in principle using a single camera system, but in practice systems with more than one camera may need to be installed so that larger fractions of each field can be photographed. Hardware will be reviewed regularly during the project in response to feedback from other work packages and updated as required. 2) Image capture and weed identification software. The machine vision system will be attached to toolbars of farm machinery so that images can be collected during different field operations. Images will be captured at different ground speeds, in different directions and at different crop growth stages as well as in different crop backgrounds. Having captured geo-referenced images in the field, image analysis software will be developed to identify weed species by Murray State and Reading Universities with advice from The Arable Group. A wide range of pattern recognition and in particular Bayesian Networks will be used to advance the state of the art in machine vision-based weed identification and mapping. Weed identification algorithms used by others are inadequate for this project as we intend to collect and correlate images collected at different growth stages. Plants grown for this purpose by Herbiseed will be used in the first instance. In addition, our image capture and analysis system will include plant characteristics such as leaf shape, size, vein structure, colour and textural pattern, some of which are not detectable by other machine vision systems or are omitted by their algorithms. Using such a list of features observable using our machine vision system, we will determine those that can be used to distinguish weed species of interest. 3) Weed mapping. Geo-referenced maps of weeds in arable fields (Reading University and Syngenta) will be produced with advice from The Arable Group and Patchwork Technology. Natural infestations will be mapped in the fields but we will also introduce specimen plants in pots to facilitate more rigorous system evaluation and testing. Manual weed maps of the same fields will be generated by Reading University, Syngenta and Peter Lutman so that the accuracy of automated mapping can be assessed. The principal hypothesis and concept to be tested is that by combining maps from several surveys, a weed map with acceptable accuracy for endusers can be produced. If the concept is proved and can be commercialised, systems could be retrofitted at low cost onto existing farm machinery. The outputs of the weed mapping software would then link with the precision farming options already built into many commercial sprayers, allowing their use for targeted, site-specific herbicide applications. Immediate economic benefits would, therefore, arise directly from reducing herbicide costs. SSWM will also reduce the overall pesticide load on the crop and so may reduce pesticide residues in food and drinking water, and reduce adverse impacts of pesticides on non-target species and beneficials. Farmers may even choose to leave unsprayed some non-injurious, environmentally-beneficial, low density weed infestations. These benefits fit very well with the anticipated legislation emerging in the new EU Thematic Strategy for Pesticides which will encourage more targeted use of pesticides and greater uptake of Integrated Crop (Pest) Management approaches, and also with the requirements of the Water Framework Directive to reduce levels of pesticides in water bodies. The greater precision of weed management offered by SSWM is therefore a key element in preparing arable farming systems for the future, where policy makers and consumers want to minimise pesticide use and the carbon footprint of farming while maintaining food production and security. The mapping technology could also be used on organic farms to identify areas of fields needing mechanical weed control thereby reducing both carbon footprints and also damage to crops by, for example, spring tines. Objective i. To develop a prototype machine vision system for automated image capture during agricultural field operations; ii. To prove the concept that images captured by the machine vision system over a series of field operations can be processed to identify and geo-reference specific weeds in the field; iii. To generate weed maps from the geo-referenced, weed plants/patches identified in objective (ii).

Root phenomics of crops: opportunities and challenges

Reliable techniques for screening large numbers of plants for root traits are still being developed, but include aeroponic, hydroponic and agar plate systems. Coupled with digital cameras and image analysis software, these systems permit the rapid measurement of root numbers, length and diameter in moderate ( typically <1000) numbers of plants. Usually such systems are employed with relatively small seedlings, and information is recorded in 2D. Recent developments in X-ray microtomography have facilitated 3D non-invasive measurement of small root systems grown in solid media, allowing angular distributions to be obtained in addition to numbers and length. However, because of the time taken to scan samples, only a small number can be screened (typically<10 per day, not including analysis time of the large spatial datasets generated) and, depending on sample size, limited resolution may mean that fine roots remain unresolved. Although agar plates allow differences between lines and genotypes to be discerned in young seedlings, the rank order may not be the same when the same materials are grown in solid media. For example, root length of dwarfing wheat ( Triticum aestivum L.) lines grown on agar plates was increased by similar to 40% relative to wild-type and semi-dwarfing lines, but in a sandy loam soil under well watered conditions it was decreased by 24-33%. Such differences in ranking suggest that significant soil environment-genotype interactions are occurring. Developments in instruments and software mean that a combination of high-throughput simple screens and more in-depth examination of root-soil interactions is becoming viable.

Ever decreasing circles: speech production in semantic dementia

We explored the impact of a degraded semantic system on lexical, morphological and syntactic complexity in language production. We analysed transcripts from connected speech samples from eight patients with semantic dementia (SD) and eight age-matched healthy speakers. The frequency distributions of nouns and verbs were compared for hand-scored data and data extracted using text-analysis software. Lexical measures showed the predicted pattern for nouns and verbs in hand-scored data, and for nouns in software-extracted data, with fewer low frequency items in the speech of the patients relative to controls. The distribution of complex morpho-syntactic forms for the SD group showed a reduced range, with fewer constructions that required multiple auxiliaries and inflections. Finally, the distribution of syntactic constructions also differed between groups, with a pattern that reflects the patients’ characteristic anomia and constraints on morpho-syntactic complexity. The data are in line with previous findings of an absence of gross syntactic errors or violations in SD speech. Alterations in the distributions of morphology and syntax, however, support constraint satisfaction models of speech production in which there is no hard boundary between lexical retrieval and grammatical encoding.

Massive Science with VO and Grids

There is a growing need for massive computational resources for the analysis of new astronomical datasets. To tackle this problem, we present here our first steps towards marrying two new and emerging technologies; the Virtual Observatory (e.g, AstroGrid) and the computa- tional grid (e.g. TeraGrid, COSMOS etc.). We discuss the construction of VOTechBroker, which is a modular software tool designed to abstract the tasks of submission and management of a large number of compu- tational jobs to a distributed computer system. The broker will also interact with the AstroGrid workflow and MySpace environments. We discuss our planned usages of the VOTechBroker in computing a huge number of n–point correlation functions from the SDSS data and mas- sive model-fitting of millions of CMBfast models to WMAP data. We also discuss other applications including the determination of the XMM Cluster Survey selection function and the construction of new WMAP maps.

Teachers as researchers and teachers as software developers: how use-case analysis helps build better educational software

A series of government initiatives has raised both the profile of ICT in the curriculum and the expectation that high quality teaching and learning resources will be accessible across electronic networks. In order for e-learning resources such as websites to have the maximum educational impact, teachers need to be involved in their design and development. Use-case analysis provides a means of defining user requirements and other constraints in such a way that software developers can produce e-learning resources which reflect teachers' professional knowledge and support their classroom practice. It has some features in common with the participatory action research used to develop other aspects of classroom practice. Two case-studies are presented: one involves the development of an on-line resource centred on transcripts of original historical documents; the other describes how 'Learning how to Learn', a major, distributed research project funded under the ESRC Teaching and Learning Research Programme is using use-case analysis to develop web resources and services.

Case-based analysis in user requirements modelling for knowledge construction

Context: Learning can be regarded as knowledge construction in which prior knowledge and experience serve as basis for the learners to expand their knowledge base. Such a process of knowledge construction has to take place continuously in order to enhance the learners’ competence in a competitive working environment. As the information consumers, the individual users demand personalised information provision which meets their own specific purposes, goals, and expectations. Objectives: The current methods in requirements engineering are capable of modelling the common user’s behaviour in the domain of knowledge construction. The users’ requirements can be represented as a case in the defined structure which can be reasoned to enable the requirements analysis. Such analysis needs to be enhanced so that personalised information provision can be tackled and modelled. However, there is a lack of suitable modelling methods to achieve this end. This paper presents a new ontological method for capturing individual user’s requirements and transforming the requirements onto personalised information provision specifications. Hence the right information can be provided to the right user for the right purpose. Method: An experiment was conducted based on the qualitative method. A medium size of group of users participated to validate the method and its techniques, i.e. articulates, maps, configures, and learning content. The results were used as the feedback for the improvement. Result: The research work has produced an ontology model with a set of techniques which support the functions for profiling user’s requirements, reasoning requirements patterns, generating workflow from norms, and formulating information provision specifications. Conclusion: The current requirements engineering approaches provide the methodical capability for developing solutions. Our research outcome, i.e. the ontology model with the techniques, can further enhance the RE approaches for modelling the individual user’s needs and discovering the user’s requirements.

A lightweight technique for assessing risks in requirements analysis

A simple and practical technique for assessing the risks, that is, the potential for error, and consequent loss, in software system development, acquired during a requirements engineering phase is described. The technique uses a goal-based requirements analysis as a framework to identify and rate a set of key issues in order to arrive at estimates of the feasibility and adequacy of the requirements. The technique is illustrated and how it has been applied to a real systems development project is shown. How problems in this project could have been identified earlier is shown, thereby avoiding costly additional work and unhappy users.