Image analysis methods for quantifying structural variation in cluster molecular dynamics

Inspired by methods of remote sensing image analysis, we analyze structural variation in cluster molecular dynamics (MD) simulations through a unique application of the principal component analysis (PCA) and Pearson Correlation Coefficient (PCC). The PCA analysis characterizes the geometric shape of the cluster structure at each time step, yielding a detailed and quantitative measure of structural stability and variation at finite temperature. Our PCC analysis captures bond structure variation in MD, which can be used to both supplement the PCA analysis as well as compare bond patterns between different cluster sizes. Relying only on atomic position data, without requirement for a priori structural input, PCA and PCC can be used to analyze both classical and ab initio MD simulations for any cluster composition or electronic configuration. Taken together, these statistical tools represent powerful new techniques for quantitative structural characterization and isomer identification in cluster MD

Integrating norms, knowledge and social ties into the deterrence model of cartels: A survey study of business executives

We expand the rational choice theory of crime, as applied to cartels, with three psychological factors—personal norms, social norms and social ties—and knowledge of competition law. Through a survey of Dutch businesses, we find that adding psychological factors substantially increases the explanatory power of the model: All predict attitudes toward future cartel behavior, with personal norms as the strongest (negative) predictor. Better knowledge of competition law relates to stronger deterrence and norms against collusion. We conclude that psychological factors and knowledge of the law are likely necessary to understand and prevent potential cartel behavior

Gene conversion in human rearranged immunoglobulin genes

Over the past 20 years, many DNA sequences have been published suggesting that all or part of the V<sub>H</sub> segment of a rearranged immunoglobulin gene may be replaced in vivo. Two different mechanisms appear to be operating. One of these is very similar to primary V(D)J recombination, involving the RAG proteins acting upon recombination signal sequences, and this has recently been proven to occur. Other sequences, many of which show partial V<sub>H</sub> replacements with no addition of untemplated nucleotides at the V<sub>H</sub>–V<sub>H</sub> joint, have been proposed to occur by an unusual RAG-mediated recombination with the formation of hybrid (coding-to-signal) joints. These appear to occur in cells already undergoing somatic hypermutation in which, some authors are convinced, RAG genes are silenced. We recently proposed that the latter type of V<sub>H</sub> replacement might occur by homologous recombination initiated by the activity of AID (activation-induced cytidine deaminase), which is essential for somatic hypermutation and gene conversion. The latter has been observed in other species, but not in human Ig genes, so far. In this paper, we present a new analysis of sequences published as examples of the second type of rearrangement. This not only shows that AID recognition motifs occur in recombination regions but also that some sequences show replacement of central sections by a sequence from another gene, similar to gene conversion in the immunoglobulin genes of other species. These observations support the proposal that this type of rearrangement is likely to be AID-mediated rather than RAG-mediated and is consistent with gene conversion

A theory of scaling for community-based fisheries management

AbstractCommunity-based approaches to fisheries management has emerged as a mainstream strategy to govern dispersed, diverse and dynamic small scale fisheries. However, amplifying local community led sustainability outcomes remains an enduring challenge. We seek to fill a theoretical gap in the conceptualization of ‘scaling up community-based fisheries management’. We draw on literature of agriculture innovations to provide a framework that takes into account process-driven and structural change occurring across multiple levels of governance, as well as different phases of scaling. We hypothesize that successful scaling requires engagement with all aspects of a governing regime, coalescing a range of actors, and therefore, is an enterprise that is larger than its parts. To demonstrate where the framework offers value, we illustrate the development of community-based fisheries management in Vanuatu according to the framework’s main scaling dimensions.</jats:p

A new purple sulfur bacterium from saline littoral sediments, Thiorhodotvibrio winogradskyi gen. nov. and sp. nov.

Two strains of a new purple sulfur bacterium were isolated in pure culture from the littoral sediment of a saline lake (Mahoney Lake, Canada) and a marine microbial mat from the North Sea island of Mellum, respectively. Single cells were vibrioid-to spirilloid-shaped and motile by means of single polar flagella. Intracellular photosynthetic membranes were of the vesicular type. As photosynthetic pigments, bacteriochlorophyll a and the carotenoids lycopene, rhodopin, anhydrorhodovibrin, rhodovibrin and spirilloxanthin were present. Hydrogen sulfide and elemental sulfur were used under anoxic conditions for phototrophic growth. In addition one strain (06511) used thiosulfate. Carbon dioxide, acetate and pyruvate were utilized by both strains as carbon sources. Depending on the strain propionate, succinate, fumarate, malate, tartrate, malonate, glycerol or peptone may additionally serve as carbon sources in the light. Optimum growth rates were obtained at pH 7.2, 33 °C, 50 mol m-2 s-1 intensity of daylight fluorescent tubes and a salinity of 2.2–3.2% NaCl. During growth on sulfide, up to ten small sulfur globules were formed inside the cells. The strains grew microaerophilic in the dark and exhibited high specific respiration rates. No vitamins were required for growth. The DNA base composition was 61.0–62.4 mol% G+C. The newly isolated bacterium belongs to the family chromatiaceae and is described as a member of a new genus and species, Thiorhodovibrio winogradskyi gen. nov. and sp. nov. with the type strain SSP1, DSM No. 6702

Linking transitions to sustainability: A study of the societal effects of transition management

Sustainability transitions as processes of fundamental change in societal systems are open-ended, nonlinear and uncertain. Respective research and governance approaches, e.g., transition management, propose a reflexive way of governing, aiming for a number of societal effects to help facilitating a transition. Effects include empowerment, social learning and social capital development. Jointly mentioned effects shall allow for reflexivity and innovation in developing socially robust and contextualized solutions to sustainability challenges that work in practice. But, understanding the mentioned societal effects and their interplay in more depth is necessary to design and assess transition management processes. While such understanding and related assessment framework is under development in the transition management literature, transdisciplinary sustainability research can provide a rich body of tools and experiences. Building on a review of the literature, this article develops an evaluation framework focusing on social learning, empowerment and social capital as important and hitherto under-conceptualised aspects of the sustainability transition literature. This framework is used to empirically investigate the effects of two specific transition management processes at the local scale. In doing so, the article provides a conceptual and empirical understanding of how social learning, empowerment and social capital contribute to a transition towards sustainability. The three effects are shown to be interrelated, mutually supportive and bridging different scale levels from individuals to groups, niches and beyond. Results highlight possibilities to facilitate and assess societal effects, addressing sustainability as their inherent quality

Developing sustainable small-scale fisheries livelihoods in Indonesia: Trends, enabling and constraining factors, and future opportunities

Small-scale fisheries (SSF) provide crucial contributions to livelihoods, food and nutrition security, and the well-being of coastal communities worldwide. In Indonesia, 2.5 million households are involved in SSF production, yet these households are characterised by high poverty rates and vulnerability due to declining ecosystem health and climatic change. In this study we applied the Sustainable Livelihoods Framework to analyse the characteristics and immediate and longer-term outcomes of 20 SSF livelihood-focused intervention programs implemented in coastal communities across the Indonesian Archipelago over the last two decades. Projects covered a wide range of spatial scales, funding providers and key participants. Factors supporting positive program outcomes included application of inclusive and holistic approaches to sustainable livelihoods, implemented and supported over appropriate time frames; use of participatory capacity development methodologies and locally-situated project facilitators; and collaborative engagement with local government, non-government organisations and private-sector actors. However, it was impossible to identify evidenced successes from a longer-term sustainability perspective. Short project timeframes, absence of baseline or monitoring data, pressure for satisfactory reports to donors, and limited post-project evaluation, together with invisibility of women’s work and non-commercial exchanges, affected the adequacy of assessments. Given the lack of post-project assessment among projects studied, a thorough review of longer-term project impacts is recommended, guided by the Sustainable Livelihoods Framework, to evaluate sustained improvements in livelihoods outcomes and environmental sustainability. This would support best-practice design and implementation of SSF livelihood-focused interventions, disseminated beyond academia, to influence policy and development to achieve socio-economic equity and environmental goals

A global climatology of total columnar water vapour from SSM/I and MERIS

A global time series of total columnar water vapour from combined data of the Medium Resolution Imaging Spectrometer (MERIS) onboard ESA's Environmental Satellite (ENVISAT) and the Special Sensor Microwave/Imager (SSM/I) onboard the satellite series of the US Defense Meteorological Satellite Program (DMSP) is presented. The unique data set, generated in the framework of the ESA Data User Element (DUE) GlobVapour project, combines atmospheric water vapour observations over land and ocean, derived from measurements in the near- infrared and the microwave range, respectively. Daily composites and monthly means of total columnar water vapour are available as global maps on rectangular latitude–longitude grids with a spatial resolution of 0.05° × 0.05° over land and 0.5° × 0.5° over ocean for the years 2003 to 2008. The data are stored in NetCDF files and is fully compliant with the NetCDF Climate Forecast convention. Through the combination of high-quality microwave observations and near-infrared observations over ocean and land surfaces, respectively, the data set provides global coverage. The combination of both products is carried out such that the individual properties of the microwave and near-infrared products, in particular their uncertainties, are not modified by the merging process and are therefore well defined. Due to the global coverage and the provided uncertainty estimates this data set is potentially of high value for climate research. The SSM/I-MERIS TCWV data set is freely available via the GlobVapour project web page (www.globvapour.info) with associated doi:10.5676/DFE/WV_COMB/FP. In this paper, the details of the data set generation, i.e. the satellite data used, the retrieval techniques and merging approaches, are presented. The derived level 3 products are compared to global radiosonde data from the GCOS upper air network (GUAN), showing a high agreement with a root-mean-square deviation of roughly 4.4 kg m−2 and a small wet bias well below 1 kg m−2. Furthermore, the data set is shown to be free of seasonal biases. The consistency of the MERIS and SSM/I retrievals is demonstrated by applying the MERIS retrieval to sun glint areas over ocean

A global climatology of total columnar water vapour from SSM/I and MERIS

A global time series of total columnar water vapour from combined data of the Medium Resolution Imaging Spectrometer (MERIS) onboard ESA's Environmental Satellite (ENVISAT) and the Special Sensor Microwave/Imager (SSM/I) onboard the satellite series of the US Defense Meteorological Satellite Program (DMSP) is presented. The unique data set, generated in the framework of the ESA Data User Element (DUE) GlobVapour project, combines atmospheric water vapour observations over land and ocean, derived from measurements in the near- infrared and the microwave range, respectively. Daily composites and monthly means of total columnar water vapour are available as global maps on rectangular latitude–longitude grids with a spatial resolution of 0.05° × 0.05° over land and 0.5° × 0.5° over ocean for the years 2003 to 2008. The data are stored in NetCDF files and is fully compliant with the NetCDF Climate Forecast convention. Through the combination of high-quality microwave observations and near-infrared observations over ocean and land surfaces, respectively, the data set provides global coverage. The combination of both products is carried out such that the individual properties of the microwave and near-infrared products, in particular their uncertainties, are not modified by the merging process and are therefore well defined. Due to the global coverage and the provided uncertainty estimates this data set is potentially of high value for climate research. The SSM/I-MERIS TCWV data set is freely available via the GlobVapour project web page (www.globvapour.info) with associated doi:10.5676/DFE/WV_COMB/FP. In this paper, the details of the data set generation, i.e. the satellite data used, the retrieval techniques and merging approaches, are presented. The derived level 3 products are compared to global radiosonde data from the GCOS upper air network (GUAN), showing a high agreement with a root-mean-square deviation of roughly 4.4 kg m−2 and a small wet bias well below 1 kg m−2. Furthermore, the data set is shown to be free of seasonal biases. The consistency of the MERIS and SSM/I retrievals is demonstrated by applying the MERIS retrieval to sun glint areas over ocean