Finding our way through phenotypes.

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility.

The origin and evolution of synaptic proteins - choanoflagellates lead the way.

The origin of neurons was a key event in evolution, allowing metazoans to evolve rapid behavioral responses to environmental cues. Reconstructing the origin of synaptic proteins promises to reveal their ancestral functions and might shed light on the evolution of the first neuron-like cells in metazoans. By analyzing the genomes of diverse metazoans and their closest relatives, the evolutionary history of diverse presynaptic and postsynaptic proteins has been reconstructed. These analyses revealed that choanoflagellates, the closest relatives of metazoans, possess diverse synaptic protein homologs. Recent studies have now begun to investigate their ancestral functions. A primordial neurosecretory apparatus in choanoflagellates was identified and it was found that the mechanism, by which presynaptic proteins required for secretion of neurotransmitters interact, is conserved in choanoflagellates and metazoans. Moreover, studies on the postsynaptic protein homolog Homer revealed unexpected localization patterns in choanoflagellates and new binding partners, both which are conserved in metazoans. These findings demonstrate that the study of choanoflagellates can uncover ancient and previously undescribed functions of synaptic proteins.

The role of economics in ecosystem based management: The case of the EU Marine Strategy Framework Directive, First lessons learnt and way forward

The EU Marine Strategy Framework Directive (MSFD) sets out a plan of action relating to marine environmental policy and in particular to achieving ‘good environmental status’ (GES) in European marine waters by 2020. Article 8.1 (c) of the Directive calls for ‘an economic and social analysis of the use of those waters and of the cost of degradation of the marine environment’. The MSFD is ‘informed’ by the Ecosystem Approach to management, with GES interpreted in terms of ecosystem functioning and services provision. Implementation of the Ecosystem Approach is expected to be by adaptive management policy and practice. The initial socio-economic assessment was made by maritime EU Member States between 2011 and 2012, with future updates to be made on a regular basis. For the majority of Member States, this assessment has led to an exercise combining an analysis of maritime activities both at national and coastal zone scales, and an analysis of the non-market value of marine waters. In this paper we examine the approaches taken in more detail, outline the main challenges facing the Member States in assessing the economic value of achieving GES as outlined in the Directive and make recommendations for the theoretically sound and practically useful completion of the required follow-up economic assessments specified in the MSFD.

The role of economics in ecosystem based management: The case of the EU Marine Strategy Framework Directive, First lessons learnt and way forward

The EU Marine Strategy Framework Directive (MSFD) sets out a plan of action relating to marine environmental policy and in particular to achieving ‘good environmental status’ (GES) in European marine waters by 2020. Article 8.1 (c) of the Directive calls for ‘an economic and social analysis of the use of those waters and of the cost of degradation of the marine environment’. The MSFD is ‘informed’ by the Ecosystem Approach to management, with GES interpreted in terms of ecosystem functioning and services provision. Implementation of the Ecosystem Approach is expected to be by adaptive management policy and practice. The initial socio-economic assessment was made by maritime EU Member States between 2011 and 2012, with future updates to be made on a regular basis. For the majority of Member States, this assessment has led to an exercise combining an analysis of maritime activities both at national and coastal zone scales, and an analysis of the non-market value of marine waters. In this paper we examine the approaches taken in more detail, outline the main challenges facing the Member States in assessing the economic value of achieving GES as outlined in the Directive and make recommendations for the theoretically sound and practically useful completion of the required follow-up economic assessments specified in the MSFD.

Ocean Virtual Laboratory: A new way to explore multi-sensor synergy demonstrated over the Agulhas region

Ocean Virtual Laboratory is an ESA-funded project to prototype the concept of a single point of access for all satellite remote-sensing data with ancillary model output and in situ measurements for a given region. The idea is to provide easy access for the non-specialist to both data and state-of-the-art processing techniques and enable their easy analysis and display. The project, led by OceanDataLab, is being trialled in the region of the Agulhas Current, as it contains signals of strong contrast (due to very energetic upper ocean dynamics) and special SAR data acquisitions have been recorded there. The project also encourages the take up of Earth Observation data by developing training material to help those not in large scientific or governmental organizations make the best use of what data are available. The website for access is: http://ovl-project.oceandatalab.com/

Simulation of the Unsteady Gas Flow through a Three-way Automotive Catalyst

This paper describes a model of a 1.8-litre four-cylinder four-stroke gasoline engine fitted with a close-coupled three-way catalyst (TWC). Designed to meet EURO 3 emissions standards, the engine includes some advanced emission control features in addition to the TWC, namely: variable valve timing (VVT), swirl control plates, and exhaust gas recirculation (EGR). Gas flow is treated as one-dimensional (1D) and unsteady in the engine ducting and in the catalyst. Reflection and transmission of pressure waves at the boundaries of the catalyst monolith are modelled. In-cylinder combustion is represented by a two-zone burn model with dissociation and reaction kinetics. A single Wiebe analysis of measured in-cylinder pressure data is used to determine the mass fraction burned as a function of crank angle (CA) at each engine speed. Measured data from steady-state dynamometer tests are presented for operation at wide open throttle (WOT) over a range of engine speeds. These results include CA-resolved traces of pressure at various locations throughout the engine together with cycle-averaged traces of gas composition entering the catalyst as indicated by a fast-response emissions analyser. Simulated engine performance and pressure wave action throughout the engine are well validated by the measured data.

Effects of tip structure on the generation of metal clusters by an STM tip: a way to control the orientation of nanocrystallites?

The role of the crystalline orientation of the STM tip in the generation of metal clusters is studied by atom dynamics simulations. When a (111) facet is facing the surface, the process is accompanied by a perturbation of the surface stronger than that observed for more open tip structures. This implies a technological application: the possibility of orienting a nanocrystallite deposited on a tip according to the changes observed in the force on the tip.