References

www.biogeosciences-discuss.net/11/8373/2014/ doi:10.5194/bgd-11-8373-2014 © Author(s) 2014. CC Attribution 3.0 License. This discussion paper is/has been under review for the journal Biogeosciences (BG). Please refer to the corresponding final paper in BG if available. Wind-induced upwelling in the Kerguele

Decadal timescale shift in the ^14C record of a central equatorial Pacific coral

Coral skeletal radiocarbon records reflect seawater Δ^14C and are useful for reconstructing the history of water mass movement and ventilation in the tropical oceans. Here, we reconstructed the inter-annual variability in central equatorial Pacific surface water Δ^14C from 1922–1956 using near-monthly 14C measurements in a Porites sp. coral skeleton (FI5A) from the windward side of Fanning Island (3°54'32"N, 159°18'88"W). The most pronounced feature in this record is a large, positive shift in the Δ^14C between 1947 and 1956 that coincides with the switch of the Pacific Decadal Oscillation (PDO) from a positive to a negative phase in the mid-1940s. Although the absolute Δ^14C values from 1950–1955 in FI5A differ from the Δ^14C values of another coral core collected from the opposite side of the island, both records show a large, positive shift in their Δ^14C records at that time. The relative increase in the Δ^14C of each record is consistent with the premise that a common mechanism is controlling the Δ^14C records within each coral record. Overall, the Fanning Δ^14C data support the notion that a significant amount of subtropical seawater is arriving at the Equator, but does not allow us to determine the mechanism for its transport

Spin properties of dense near-surface ensembles of nitrogen-vacancy centres in diamond

We present a study of the spin properties of dense layers of near-surface nitrogen-vacancy (NV) centres in diamond created by nitrogen ion implantation. The optically detected magnetic resonance contrast and linewidth, spin coherence time, and spin relaxation time, are measured as a function of implantation energy, dose, annealing temperature and surface treatment. To track the presence of damage and surface-related spin defects, we perform in situ electron spin resonance spectroscopy through both double electron-electron resonance and cross-relaxation spectroscopy on the NV centres. We find that, for the energy ($4-30$~keV) and dose ($5\times10^{11}-10^{13}$~ions/cm$^2$) ranges considered, the NV spin properties are mainly governed by the dose via residual implantation-induced paramagnetic defects, but that the resulting magnetic sensitivity is essentially independent of both dose and energy. We then show that the magnetic sensitivity is significantly improved by high-temperature annealing at $\geq1100^\circ$C. Moreover, the spin properties are not significantly affected by oxygen annealing, apart from the spin relaxation time, which is dramatically decreased. Finally, the average NV depth is determined by nuclear magnetic resonance measurements, giving $\approx10$-17~nm at 4-6 keV implantation energy. This study sheds light on the optimal conditions to create dense layers of near-surface NV centres for high-sensitivity sensing and imaging applications.Comment: 12 pages, 7 figure

LINEARISATION D’UN MODELE DE REACTEUR A BOUES ACTIVEES

Cet article présente une stratégie de linéarisation d’un modèle non linéaire de réacteur à boues activées. Cette stratégie a pour but d’obtenir un modèle linéaire simplifié, pour des fins d’estimation, de commande et d’analyse de stabilité. En appuyant sur un modèle initiale comportant trois variables d’états représentant respectivement : la concentration du substrat biodégradable, la concentration de la biomasse hétérotrophe et la concentration de l’oxygène dissous, une approche systématique de réduction de complexité du modèle est envisagée. Cette approche comprend essentiellement trois étapes. Dans la première étape, une analyse de sensibilité est effectuée dont le but est d’hiérarchiser les variables d’états selon leurs effets sur la réponse du modèle. Par la suite, une procédure de linéarisation est appliquée, basée sur une combinaison linéaire pondérée des termes présentant des non-linéarités dans le système. Les variables identifiées comme non influentes peuvent être ignorées, le modèle s’en trouve avantageusement simplifié. Dans la dernière étape, les paramètres inconnus des termes linéaires trouvés sont identifiés en utilisant un algorithme évolutionnaire. L’avantage principal de la méthode proposée est de conserver la structure générale ainsi que l’ordre du modèle original

METANNOGEN: compiling features of biochemical reactions needed for the reconstruction of metabolic networks

BACKGROUND: One central goal of computational systems biology is the mathematical modelling of complex metabolic reaction networks. The first and most time-consuming step in the development of such models consists in the stoichiometric reconstruction of the network, i. e. compilation of all metabolites, reactions and transport processes relevant to the considered network and their assignment to the various cellular compartments. Therefore an information system is required to collect and manage data from different databases and scientific literature in order to generate a metabolic network of biochemical reactions that can be subjected to further computational analyses. RESULTS: The computer program METANNOGEN facilitates the reconstruction of metabolic networks. It uses the well-known database of biochemical reactions KEGG of biochemical reactions as primary information source from which biochemical reactions relevant to the considered network can be selected, edited and stored in a separate, user-defined database. Reactions not contained in KEGG can be entered manually into the system. To aid the decision whether or not a reaction selected from KEGG belongs to the considered network METANNOGEN contains information of SWISSPROT and ENSEMBL and provides Web links to a number of important information sources like METACYC, BRENDA, NIST, and REACTOME. If a reaction is reported to occur in more than one cellular compartment, a corresponding number of reactions is generated each referring to one specific compartment. Transport processes of metabolites are entered like chemical reactions where reactants and products have different compartment attributes. The list of compartmentalized biochemical reactions and membrane transport processes compiled by means of METANNOGEN can be exported as an SBML file for further computational analysis. METANNOGEN is highly customizable with respect to the content of the SBML output file, additional data-fields, the graphical input form, highlighting of project specific search terms and dynamically generated Web-links. CONCLUSION: METANNOGEN is a flexible tool to manage information for the design of metabolic networks. The program requires Java Runtime Environment 1.4 or higher and about 100 MB of free RAM and about 200 MB of free HD space. It does not require installation and can be directly Java-webstarted from

Spatiotemporal Characteristics of the Near-Surface Turbulent Cascade at the Submesoscale in the Drake Passage.

Submesoscale currents and internal gravity waves achieve an intense turbulent cascade near the ocean surface [depth of 0–O(100) m], which is thought to give rise to significant energy sources and sinks for mesoscale eddies. Here, we characterize the contributions of nonwave currents (NWCs; including eddies and fronts) and internal gravity waves (IGWs; including near-inertial motions, lee waves, and the internal wave continuum) to near-surface submesoscale turbulence in the Drake Passage. Using a numerical simulation, we combine Lagrangian filtering and a Helmholtz decomposition to identify NWCs and IGWs and to characterize their dynamics (rotational versus divergent). We show that NWCs and IGWs contribute in different proportions to the inverse and forward turbulent kinetic energy cascades, based on their dynamics and spatiotemporal scales. Purely rotational NWCs cause most of the inverse cascade, while coupled rotational–divergent components of NWCs and coupled NWC–IGWs cause the forward cascade. The cascade changes direction at a spatial scale at which motions become increasingly divergent. However, the forward cascade is ultimately limited by the motions’ spatiotemporal scales. The bulk of the forward cascade (80%–95%) is caused by NWCs and IGWs of small spatiotemporal scales (L < 10 km; T < 6 h), which are primarily rotational: submesoscale eddies, fronts, and the internal wave continuum. These motions also cause a significant part of the inverse cascade (30%). Our results highlight the requirement for high spatiotemporal resolutions to diagnose the properties and large-scale impacts of near-surface submesoscale turbulence accurately, with significant implications for ocean energy cycle study strategies

The precautions of clinical waste: disposable medical sharps in the United Kingdom

This article deals with recent changes in UK guidance on clinical waste, in particular a shift to disposable, single-use instruments and sharps. I use interviews conducted with nurses from a GP practice and two clinical waste managers at alternative treatment and incineration sites as a springboard for reflection on the relationship between the legislation on clinical waste management and its implementation. Scrutinizing the UK guidance, European legislation and World Health Organization principles, I draw out interviewees’ concerns that the changed practices lead to an expansion of the hazardous waste category, with an increased volume going to incineration. This raises questions regarding the regulations’ environmental and health effects, and regarding the precautionary approach embedded in the regulations. Tracing the diverse reverberations of the term ‘waste’ in different points along the journeys made by sharps in particular, and locating these questions in relation to existing literature on waste, I emphasize that public health rationales for the new practices are not made clear in the guidance. I suggest that this relative silence on the subject conceals both the uncertainties regarding the necessity for these means of managing the risks of infectious waste, and the tensions between policies of precautionary public health and environmental sustainability