Fast training of self organizing maps for the visual exploration of molecular compounds

Visual exploration of scientific data in life science area is a growing research field due to the large amount of available data. The Kohonen’s Self Organizing Map (SOM) is a widely used tool for visualization of multidimensional data. In this paper we present a fast learning algorithm for SOMs that uses a simulated annealing method to adapt the learning parameters. The algorithm has been adopted in a data analysis framework for the generation of similarity maps. Such maps provide an effective tool for the visual exploration of large and multi-dimensional input spaces. The approach has been applied to data generated during the High Throughput Screening of molecular compounds; the generated maps allow a visual exploration of molecules with similar topological properties. The experimental analysis on real world data from the National Cancer Institute shows the speed up of the proposed SOM training process in comparison to a traditional approach. The resulting visual landscape groups molecules with similar chemical properties in densely connected regions.

The effects of landscape modifications on the long-term persistence of animal populations

Background: The effects of landscape modifications on the long-term persistence of wild animal populations is of crucial importance to wildlife managers and conservation biologists, but obtaining experimental evidence using real landscapes is usually impossible. To circumvent this problem we used individual-based models (IBMs) of interacting animals in experimental modifications of a real Danish landscape. The models incorporate as much as possible of the behaviour and ecology of four species with contrasting life-history characteristics: skylark (Alauda arvensis), vole (Microtus agrestis), a ground beetle (Bembidion lampros) and a linyphiid spider (Erigone atra). This allows us to quantify the population implications of experimental modifications of landscape configuration and composition. Methodology/Principal Findings: Starting with a real agricultural landscape, we progressively reduced landscape complexity by (i) homogenizing habitat patch shapes, (ii) randomizing the locations of the patches, and (iii) randomizing the size of the patches. The first two steps increased landscape fragmentation. We assessed the effects of these manipulations on the long-term persistence of animal populations by measuring equilibrium population sizes and time to recovery after disturbance. Patch rearrangement and the presence of corridors had a large effect on the population dynamics of species whose local success depends on the surrounding terrain. Landscape modifications that reduced population sizes increased recovery times in the short-dispersing species, making small populations vulnerable to increasing disturbance. The species that were most strongly affected by large disturbances fluctuated little in population sizes in years when no perturbations took place. Significance: Traditional approaches to the management and conservation of populations use either classical methods of population analysis, which fail to adequately account for the spatial configurations of landscapes, or landscape ecology, which accounts for landscape structure but has difficulty predicting the dynamics of populations living in them. Here we show how realistic and replicable individual-based models can bridge the gap between non-spatial population theory and non-dynamic landscape ecology. A major strength of the approach is its ability to identify population vulnerabilities not detected by standard population viability analyses.

Interactive learning in UK construction practice: examining the role of BIM process standards

From a construction innovation systems perspective, firms acquire knowledge from suppliers, clients, universities and institutional environment. Building information modelling (BIM) involves these firms using new process standards. To understand the implications on interactive learning using BIM process standards, a case study is conducted with the UK operations of a multinational construction firm. Data is drawn from: a) two workshops involving the firm and a wider industry group, b) observations of practice in the BIM core team and in three ongoing projects, c) 12 semi-structured interviews; and d) secondary publications. The firm uses a set of BIM process standards (IFC, PAS 1192, Uniclass, COBie) in its construction activities. It is also involved in a pilot to implement the COBie standard, supported by technical and management standards for BIM, such as Uniclass and PAS1192. Analyses suggest that such BIM process standards unconsciously shapes the firm's internal and external interactive learning processes. Internally standards allow engineers to learn from each through visualising 3D information and talking around designs with operatives to address problems during construction. Externally, the firm participates in trial and pilot projects involving other construction firms, government agencies, universities and suppliers to learn about the standard and access knowledge to solve its specific design problems. Through its BIM manager, the firm provides feedback to standards developers and information technology suppliers. The research contributes by articulating how BIM process standards unconsciously change interactive learning processes in construction practice. Further research could investigate these findings in the wider UK construction innovation system.

On the development of horizontal CEN standards supporting the implementation of EU directives on sludge, soil and biowaste - Project HORIZONTAL

We give an overview on the development of "horizontal" European Committee for Standardisation (CEN) standards for characterising soils, sludges and biowaste in the context of environmental legislation in the European Union (EU). We discuss the various steps in the development of a horizontal standard (i.e. assessment of the possibility of such a standard, review of existing normative documents, pre-normative testing and validation) and related problems. We also provide a synopsis of European and international standards covered by the so-called Project HORIZONTAL. (C) 2004 Elsevier Ltd. All rights reserved.

Longitudinal investigation of the role of temperament and stressful life events in childhood anxiety

The current study investigated the longitudinal relationships between BI, life events, and anxiety in a sample of 102 behaviourally inhibited (BI) and 100 uninhibited (BUI) children aged 3 to 4 years. Children’s parents completed questionnaires on BI, stressful life events, and anxiety symptoms, and were administered a diagnostic interview three times in a 5-year period. In line with our hypotheses, negative life events, and negative behaviour- dependent life events (i.e. life events that are related to the children’s own behaviours) in particular, and the impact of negative life events, were predictive of increases in subsequent anxiety symptoms, the likelihood of having an anxiety disorder, and increased number of anxiety diagnoses over the five year follow-up period. Experiencing more positive, behaviour-independent life events decreased the risk of being diagnosed with an anxiety disorder. Furthermore, differences were found in life events between BI and BUI children. That is, BI children experienced fewer positive and specifically positive behaviour-dependent life events, and the impact of these positive life events was also lower in BI children than in BUI children. However, BI did not interact with life events in the prediction of anxiety problems as hypothesized. Therefore, this study seems to indicate that BI and life events act as additive risk factors in the development of anxiety problems.

The population dynamics of disease on short and long time-scales

Observational evidence is scarce concerning the distribution of plant pathogen population sizes or densities as a function of time-scale or spatial scale. For wild pathosystems we can only get indirect evidence from evolutionary patterns and the consequences of biological invasions.We have little or no evidence bearing on extermination of hosts by pathogens, or successful escape of a host from a pathogen. Evidence over the last couple of centuries from crops suggest that the abundance of particular pathogens in the spectrum affecting a given host can vary hugely on decadal timescales. However, this may be an artefact of domestication and intensive cultivation. Host-pathogen dynamics can be formulated mathematically fairly easily–for example as SIR-type differential equation or difference equation models, and this has been the (successful) focus of recent work in crops. “Long-term” is then discussed in terms of the time taken to relax from a perturbation to the asymptotic state. However, both host and pathogen dynamics are driven by environmental factors as well as their mutual interactions, and both host and pathogen co-evolve, and evolve in response to external factors. We have virtually no information about the importance and natural role of higher trophic levels (hyperpathogens) and competitors, but they could also induce long-scale fluctuations in the abundance of pathogens on particular hosts. In wild pathosystems the host distribution cannot be modelled as either a uniform density or even a uniform distribution of fields (which could then be treated as individuals). Patterns of short term density-dependence and the detail of host distribution are therefore critical to long-term dynamics. Host density distributions are not usually scale-free, but are rarely uniform or clearly structured on a single scale. In a (multiply structured) metapopulation with coevolution and external disturbances it could well be the case that the time required to attain equilibrium (if it exists) based on conditions stable over a specified time-scale is longer than that time-scale. Alternatively, local equilibria may be reached fairly rapidly following perturbations but the meta-population equilibrium be attained very slowly. In either case, meta-stability on various time-scales is a more relevant than equilibrium concepts in explaining observed patterns.

Clonal expansion of early to mid-life mitochondrial DNA point mutations drives mitochondrial dysfunction during human ageing

Age-related decline in the integrity of mitochondria is an important contributor to the human ageing process. In a number of ageing stem cell populations, this decline in mitochondrial function is due to clonal expansion of individual mitochondrial DNA (mtDNA) point mutations within single cells. However the dynamics of this process and when these mtDNA mutations occur initially are poorly understood. Using human colorectal epithelium as an exemplar tissue with a well-defined stem cell population, we analysed samples from 207 healthy participants aged 17-78 years using a combination of techniques (Random Mutation Capture, Next Generation Sequencing and mitochondrial enzyme histochemistry), and show that: 1) non-pathogenic mtDNA mutations are present from early embryogenesis or may be transmitted through the germline, whereas pathogenic mtDNA mutations are detected in the somatic cells, providing evidence for purifying selection in humans, 2) pathogenic mtDNA mutations are present from early adulthood (<20 years of age), at both low levels and as clonal expansions, 3) low level mtDNA mutation frequency does not change significantly with age, suggesting that mtDNA mutation rate does not increase significantly with age, and 4) clonally expanded mtDNA mutations increase dramatically with age. These data confirm that clonal expansion of mtDNA mutations, some of which are generated very early in life, is the major driving force behind the mitochondrial dysfunction associated with ageing of the human colorectal epithelium.

Student teachers’ perceptions of reading and the teaching of reading: the implications for teacher education

This article reports on research which identified perceptions of reading and the teaching of reading held by trainee teachers and the impact on my provision as a teacher educator. It found that students’ past and present experiences of learning to read and being a reader influenced their perceptions of what reading is and of what it means to teach reading. As a teacher educator, I am not able to give students long experience of seeing children becoming readers, but I am able to give them richer experiences of reading in personally and culturally relevant contexts. This has implications for the nature of subject knowledge required by a student teacher of reading and the curriculum and practice of teacher education.