Context-aware visual exploration of molecular databases

Facilitating the visual exploration of scientific data has received increasing attention in the past decade or so. Especially in life science related application areas the amount of available data has grown at a breath taking pace. In this paper we describe an approach that allows for visual inspection of large collections of molecular compounds. In contrast to classical visualizations of such spaces we incorporate a specific focus of analysis, for example the outcome of a biological experiment such as high throughout screening results. The presented method uses this experimental data to select molecular fragments of the underlying molecules that have interesting properties and uses the resulting space to generate a two dimensional map based on a singular value decomposition algorithm and a self organizing map. Experiments on real datasets show that the resulting visual landscape groups molecules of similar chemical properties in densely connected regions.

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.

Personal status laws in Morocco and Tunisia: A comparative exploration of the possibilities for equality-enhancing reform in Bangladesh

This paper focuses on successful reform strategies invoked in parts of the Muslim world to address issues of gender inequality in the context of Islamic personal law. It traces the development of personal status laws in Tunisia and Morocco, exploring the models they offer in initiating equality-enhancing reforms in Bangladesh, where a secular and equality-based reform approach conflicts with Islamic-based conservatism. Recent landmark family law reforms in Morocco show the possibility of achieving ‘women-friendly’ reforms within an Islamic legal framework. Moreover, the Tunisian Personal Status Code, with its successive reforms, shows that a gender equality-based model of personal law can be successfully integrated into the Muslim way of life. This study examines the response of Muslim societies to equality-based reforms and differences in approach in initiating them. The paper maps these sometimes competing approaches, locating them within contemporary feminist debates related to gender equality in the East and West.

The influence of age and gender on food choice: a focus group exploration

With 25% of the UK population predicted to be obese by 2010, the costs to individuals and society are set to rise. Due to the extra economic and social pressures obesity causes, there is an increasing need to understand what motivates and prevents consumers from eating a healthy diet so as to be able to tailor policy interventions to specific groups in society. In so doing, it is important to explore potential variations in attitudes, motivation and behaviour as a function of age and gender. Both demographic factors are easily distinguished within society and a future intervention study which targets either, or both, of these would likely be both feasible and cost-effective for policy makers. As part of a preliminary study, six focus groups (total n = 43) were conducted at the University of Reading in November 2006, with groups segmented on the basis of age and gender. In order to gather more sensitive information, participants were also asked to fill out a short anonymous questionnaire before each focus group began, relating to healthy eating, alcohol consumption and body dissatisfaction. Making use of thematic content analysis, results suggested that most participants were aware of the type of foods that contribute to a healthy diet and the importance of achieving a healthy balance within a diet. However, they believed that healthy eating messages were often conflicting, and were uncertain about where to find information on the topic. Participants believed that the family has an important role in educating children about eating habits. Despite these similarities, there were a number of key differences among the groups in terms of their reasons for making food choices. Older participants (60+ years old) were more likely to make food choices based on health considerations. Participants between the ages of 18–30 were less concerned with this link, and instead focused on issues of food preparation and knowledge, prices and time. Younger female participants said they had more energy when they ate healthier diets; however, very often their food choices related to concern with their appearance. Older female participants also expressed this concern within the questionnaire, rather than in the group discussions. Overall, these results suggest that consumer motivations for healthy eating are diverse and that this must be considered by government, retailers and food producers.

An exploration of the drivers to bio-security collective action among a sample of UK cattle and sheep farmers

At present, collective action regarding bio-security among UK cattle and sheep farmers is rare. Despite the occurrence of catastrophic livestock diseases such as bovine spongiform encephalopathy (BSE) and foot and mouth disease (FMD), within recent decades, there are few national or local farmer-led animal health schemes. To explore the reasons for this apparent lack of interest, we utilised a socio-psychological approach to disaggregate the cognitive, emotive and contextual factors driving bio-security behaviour among cattle and sheep farmers in the United Kingdom (UK). In total, we interviewed 121 farmers in South-West England and Wales. The main analytical tools included a content, cluster and logistic regression analysis. The results of the content analysis illustrated apparent 'dissonance' between bio-security attitudes and behaviour.(1) Despite the heavy toll animal disease has taken on the agricultural economy, most study participants were dismissive of the many measures associated with bio-security. Justification for this lack of interest was largely framed in relation to the collective attribution or blame for the disease threats themselves. Indeed, epidemic diseases were largely related to external actors and agents. Reasons for outbreaks included inadequate border control, in tandem with ineffective policies and regulations. Conversely, endemic livestock disease was viewed as a problem for 'bad' farmers and not an issue for those individuals who managed their stock well. As such, there was little utility in forming groups to address what was largely perceived as an individual problem. Further, we found that attitudes toward bio-security did not appear to be influenced by any particular source of information per se. While strong negative attitudes were found toward specific sources of bio-security information, e.g. government leaflets, these appear to simply reflect widely held beliefs. In relation to actual bio-security behaviours, the logistic regression analysis revealed no significant difference between in-scheme and out of scheme farmers. We concluded that in order to support collective action with regard to bio-security, messages need to be reframed and delivered from a neutral source. Efforts to support group formation must also recognise and address the issues relating to perceptions of social connectedness among the communities involved. (c) 2008 Elsevier B.V. All rights reserved.

What is poverty? A diachronic exploration of the discourse on poverty from the 1970s to the 2000s

Poverty is central to the concept of development. However, the relevance given to particular aspects of poverty has changed over the years and with it the manner in which poverty has been represented. The following paper explores how concepts of poverty within the 'poverty discourse' have altered over a 30-year period. A diachronic analysis is performed to explore changes in the topical and thematic composition of the definitions, in addition to the manner in which poverty has been 'framed'. The results illustrated that poverty was variably framed across the decades ranging from a 'neutral' fact to a highly contested state with little agreement over causes and consequences. Nevertheless, the relational analysis revealed the de-problematization of poverty over time. The finding has clear implications for development praxis: poverty needs to be 'attacked', but the root causes, at least from a discursive perspective, may be ignored.

Metabolic changes of rhizobia in legume nodules

Bacteria have evolved a wide variety of metabolic strategies to cope with varied environments. Some are specialists and only able to survive in restricted environments; others are generalists and able to cope with diverse environmental conditions. Rhizolbia (e.g. Rhizobium, Sinorhizobium, Bradyrhizobium, Mesorhizobium and Azorhizobium species) can survive and compete for nutrients in soil and the plant rhizosphere but can also form a beneficial symbiosis with legumes in a highly specialized plant cell environment. Inside the legume-root nodule, the bacteria (bacteroids) reduce dinitrogen to ammonium, which is secreted to the plant in exchange for a carbon and energy source. A new and challenging aspect of nodule physiology is that nitrogen fixation requires the cycling of amino acids between the bacteroid and plant. This review aims to summarize the metabolic plasticity of rhizobia and the importance of amino acid cycling.

De novo alanine synthesis by bacteroids of Mesorhizobium loti is not required for nitrogen transfer in the determinate nodules of Lotus corniculatus

Deletion of both alanine dehydrogenase genes (aldA) in Mesorhizobium loti resulted in the loss of AldA enzyme activity from cultured bacteria and bacteroids but had no effect on the symbiotic performance of Lotus corniculatus plants. Thus, neither indeterminate pea nodules nor determinate L. corniculatus nodules export alanine as the sole nitrogen secretion product.

Regulation of L-alanine dehydrogenase in Rhizobium leguminosarum bv. viciae and its role in pea nodules

Alanine dehydrogenase (AldA) is the principal enzyme with which pea bacteroids synthesize alanine de novo. In free-living culture, AMA activity is induced by carboxylic acids (succinate, malate, and pyruvate), although the best inducer is alanine. Measurement of the intracellular concentration of alanine showed that AldA contributes to net alanine synthesis in laboratory cultures. Divergently transcribed from aldA is an AsnC type regulator, aldR. Mutation of aldR prevents induction of AldA activity. Plasmid-borne gusA fusions showed that aldR is required for transcription of both aldA and aldR; hence, AldR is autoregulatory. However, plasmid fusions containing the aldA-aldR intergenic region could apparently titrate out AldR, sometimes resulting in a complete loss of AldA enzyme activity. Therefore, integrated aldR::gusA and aldA::gusA fusions, as well as Northern blotting, were used to confirm the induction of aldA activity. Both aldA and aldR were expressed in the II/III interzone and zone III of pea nodules. Overexpression of aldA in bacteroids did not alter the ability of pea plants to fix nitrogen, as measured by acetylene reduction, but caused a large reduction in the size and dry weight of plants. This suggests that overexpression of aldA impairs the ability of bacteroids to donate fixed nitrogen that the plant can productively assimilate. We propose that the role of AldA may be to balance the alanine level for optimal functioning of bacteroid metabolism rather than to synthesize alanine as the sole product of N-2 reduction.

Nanosized polymetallic resorcinarene-based host assemblies that strongly bind fullerenes

Polymetallic nanodimensional assemblies have been prepared via metal directed assembly of dithiocarbamate functionalized cavitand structural frameworks with late transition metals (Ni, Pd, Cu, Au, Zn, and Cd). The coordination geometry about the metal centers is shown to dictate the architecture adopted. X-ray crystallographic studies confirm that square planar coordination geometries result in "cagelike" octanuclear complexes, whereas square-based pyramidal metal geometries favor hexanuclear "molecular loop" structures. Both classes of complex are sterically and electronically complementary to the fullerenes (C-60 and C-70). The strong binding of these guests occurred via favorable interactions with the sulfur atoms of multiple dithiocarbamate moieties of the hosts. In the case of the tetrameric copper(II) complexes, the lability of the copper(II)-dithiocarbamate bond enabled the fullerene guests to be encapsulated in the electron-rich cavity of the host, over time. The examination of the binding of fullerenes has been undertaken using spectroscopic and electrochemical methods, electrospray mass spectrometry, and molecular modeling.

Soluble redox-active polymetallic chains [{Ru-0(CO)(L)(bpy)}(m)](n) (bpy=2,2 '-bipyridine, L = PrCN, Cl-; m=0,-1): electrosynthesis and characterization

Electrochemical and spectroelectrochemical techniques were employed to study in detail the formation and so far unreported spectroscopic properties of soluble electroactive molecular chains with nonbridged metal-metal backbones, namely, [{Ru-0(CO)(PrCN)(bpy)}(m)](n) (m = 0, -1) and [{Ru-0(CO)(bpy)Cl}(m)](n) (m = -1, -2; bpy = 2,2'-bipyridine). The precursors cis-(Cl)-[Ru-II(CO)(MeCN)(bpy)Cl-2] (in PrCN) and mer-[Ru-II(CO)(bpy)Cl-3](-) (in tetrahydrofuran (THF) and PrCN) undergo one-electron reductions to reactive radicals [Ru-II(CO)(MeCN)(bpy(center dot-))Cl-2](-) and [Ru-II(CO)(bpy(center dot-))Cl-3](2-), respectively. Both [bpy(center dot-)]-containing species readily electropolymerize on concomitant dissociation of two chloride ligands and consumption of a second electron. Along this path, mer-to-fac isomerization of the bpy-reduced trichlorido complex (supported by density functional theory calculations) and a concentration-dependent oligomerization process contribute to the complex reactivity pattern. In situ spectroelectrochemistry (IR, UV/vis a has revealed that the charged polymer [{Ru-0(CO)(bpy)Cl}(-)](n) is stable in THF, but in PrCN it converts readily to [Ru-0(CO)(PrCN)(bpy)](n). An excess of chloride ions retards this substitution at low temperatures. Both polymetallic chains are completely soluble in the electrolyte solution and can be reduced reversibly to the corresponding [bpy(center dot-)]-containing species.

'Anxious cognitions' in children: an exploration of associations and mediators

To investigate sources of influences connecting mothers' and their children's anxious cognitions, 65 children (aged 10 to 11 years) completed self-report measures of anxiety. Children and mothers responded to an ambiguous scenario questionnaire and measures of parenting style and life events. Mothers also reported expectations about their child's reaction to ambiguous situations. Mothers' and children's threat cognitions were significantly correlated (r = .31), and partially mediated by mothers' expectations about their child. Mothers' anticipated distress was associated with expectations for their child's distress, which was associated with the child's own anticipated distress. Parenting and life events were significantly associated with children's interpretative bias, but did not mediate the intergenerational association in interpretative bias. The results suggest influences on children's 'anxious cognitive style' and potential targets for preventing and reducing maladaptive cognitions in children.