A general framework for aquatic biogeochemical models

One of the most of challenging steps in the development of coupled hydrodynamic-biogeochemical models is the combination of multiple, often incompatible computer codes that describe individual physical, chemical, biological and geological processes. This “coupling” is time-consuming, error-prone, and demanding in terms of scientific and programming expertise. The open source, Fortran-based Framework for Aquatic Biogeochemical Models addresses these problems by providing a consistent set of programming interfaces through which hydrodynamic and biogeochemical models communicate. Models are coded once to connect to FABM, after which arbitrary combinations of hydrodynamic and biogeochemical models can be made. Thus, a biogeochemical model code works unmodified within models of a chemostat, a vertically structured water column, and a three-dimensional basin. Moreover, complex biogeochemistry can be distributed over many compact, self-contained modules, coupled at run-time. By enabling distributed development and user-controlled coupling of biogeochemical models, FABM enables optimal use of the expertise of scientists, programmers and end-users

Scoping report on the potential impact of on-board desulphurisation on the water quality in SOx emission control areas

The input of acid substances (like SO2) into the sea has been recognized as an environmental issue that needs to be considered in terms of ocean acidification; acid inputs and techniques to deal with them have implications for member states' obligations under the Water Framework Directive and Marine Strategy Framework Directive. This study provides an initial assessment on the potential impact of on-board desulphurisation equipment (open loop scrubbers) on the seawater quality with focus on SOx Emission Control Areas (SECAs). The study focuses on the potential impact of shipborne SO2 on acidification (pH) of seawater in comparison to the impact from climate change. The report comprises a literature study and a dedicated modelling exercise covering the North Sea region. Most available studies and the peer reviewed literature found only a small additional impact from SO2 emissions on acidification in the various investigated parts of the world ocean. However these studies generally assessed spatially averaged effects and regional and coastal oriented studies are mostly lacking from the literature, which means that potential effects to vulnerable ecosystems in such areas have not previously been considered. A coupled hydrodynamic-chemistry model was employed to assess the impact of adding SO2 and CO2 on the complex carbonate system in sea water. The impact on the pH decrease in the open North Sea region from discharging the acid wash water into the seawater was found to be small, but not insignificant, and regionally varying. The calculated annual mean decrease of pH due to SO2 injection for the North Sea total water column is 0.00011; when considering only the change in the surface layer (0-20m), the annual decrease is 0.00024. The total annual impact from increasing atmospheric CO2 concentrations on the acidification of the North Sea surface area is about 8 times stronger (0.001) than the impact from wash water injection. However because of the pronounced spatial variations the mean impact does not reflect the overall situation well. Consequently we find critical regions with high ship traffic intensity, for example along the shipping lanes and in the larger Rotterdam port area. Here, the contribution from SO2 injection can be double the impact from increasing CO2 concentrations and 20 times larger than the North Sea mean value. These critical regions indicate potential problems related to the surface water quality in ports, estuaries and coastal waters that are subject to regulation under the Water Framework Directive (WFD). In addition, the problem of decreasing pH caused by SO2 input from ship exhaust gases in regional seas (North Sea) is relevant to the obligation of the Member States to assess the environmental state of their marine areas and to establish a Good Environmental Status (GES) under the Marine Strategy Framework Directive (MFSD), as pH value is one of the GES criteria

FABM-PCLake – linking aquatic ecology with hydrodynamics

This study presents FABM-PCLake, a redesigned structure of the PCLake aquatic ecosystem model, which we implemented in the Framework for Aquatic Biogeochemical Models (FABM). In contrast to the original model, which was designed for temperate, fully mixed freshwater lakes, the new FABM-PCLake represents an integrated aquatic ecosystem model that can be linked with different hydrodynamic models and allows simulations of hydrodynamic and biogeochemical processes for zero-dimensional, one-dimensional as well as three-dimensional environments. FABM-PCLake describes interactions between multiple trophic levels, including piscivorous, zooplanktivorous and benthivorous fish, zooplankton, zoobenthos, three groups of phytoplankton and rooted macrophytes. The model also accounts for oxygen dynamics and nutrient cycling for nitrogen, phosphorus and silicon, both within the pelagic and benthic domains. FABM-PCLake includes a two-way communication between the biogeochemical processes and the physics, where some biogeochemical state variables (e.g., phytoplankton) influence light attenuation and thereby the spatial and temporal distributions of light and heat. At the same time, the physical environment, including water currents, light and temperature influence a wide range of biogeochemical processes. The model enables studies on ecosystem dynamics in physically heterogeneous environments (e.g., stratifying water bodies, and water bodies with horizontal gradients in physical and biogeochemical properties), and through FABM also enables data assimilation and multi-model ensemble simulations. Examples of potential new model applications include climate change impact studies and environmental impact assessment scenarios for temperate, sub-tropical and tropical lakes and reservoirs

Online Social Networking Technologies, HIV Knowledge, and Sexual Risk and Testing Behaviors Among Homeless Youth

This study evaluates associations between online social networking and sexual health behaviors among homeless youth in Los Angeles. We analyzed survey data from 201 homeless youth accessing services at a Los Angeles agency. Multivariate (regression and logistic) models assessed whether use of (and topics discussed on) online social networking technologies affect HIV knowledge, sexual risk behaviors, and testing for sexually transmitted infections (STIs). One set of results suggests that using online social networks for partner seeking (compared to not using the networks for seeking partners) is associated with increased sexual risk behaviors. Supporting data suggest that (1) using online social networks to talk about safe sex is associated with an increased likelihood of having met a recent sex partner online, and (2) having online sex partners and talking to friends on online social networks about drugs and partying is associated with increased exchange sex. However, results also suggest that online social network usage is associated with increased knowledge and HIV/STI prevention among homeless youth: (1) using online social networks to talk about love and safe sex is associated with increased knowledge about HIV, (2) using the networks to talk about love is associated with decreased exchange sex, and (3) merely being a member of an online social network is associated with increased likelihood of having previously tested for STIs. Taken together, this study suggests that online social networking and the topics discussed on these networks can potentially increase and decrease sexual risk behaviors depending on how the networks are used. Developing sexual health services and interventions on online social networks could reduce sexual risk behaviors

EAT v1.0.0: a 1D test bed for physical–biogeochemical data assimilation in natural waters

Data assimilation (DA) in marine and freshwater systems combines numerical models and observations to deliver the best possible characterization of a waterbody's physical and biogeochemical state. DA underpins the widely used 3D ocean state reanalyses and forecasts produced operationally by, e.g., the Copernicus Marine Service. The use of DA in natural waters is an active field of research, but testing new developments in realistic setting can be challenging as operational DA systems are demanding in terms of computational resources and technical skill. There is a need for test beds that are sufficiently realistic but also efficient to run and easy to operate. Here, we present the Ensemble and Assimilation Tool (EAT), a flexible and extensible software package that enables data assimilation of physical and biogeochemical variables in a one-dimensional water column. EAT builds on established open-source components for hydrodynamics (GOTM), biogeochemistry (FABM), and data assimilation (PDAF). It is easy to install and operate and is flexible through support for user-written plugins. EAT is well suited to explore and advance the state of the art in DA in natural waters thanks to its support for (1) strongly and weakly coupled data assimilation, (2) observations describing any prognostic and diagnostic element of the physical–biogeochemical model, and (3) the estimation of biogeochemical parameters. Its range of capabilities is demonstrated with three applications: ensemble-based coupled physical–biogeochemical assimilation, the use of variational methods (3D-Var) to assimilate sea surface chlorophyll, and the estimation of biogeochemical parameters.</p

HIV in East London: ethnicity, gender and risk. Design and methods

BACKGROUND: While men who have sex with men remain the group at greatest risk of acquiring HIV infection in the UK, the number of new diagnoses among heterosexuals has risen steadily over the last five years. In the UK, three-quarters of heterosexual men and women diagnosed with HIV in 2004 probably acquired their infection in Africa. This changing epidemiological pattern is particularly pronounced in East London because of its ethnically diverse population. DESIGN AND METHODS: The objective of the study was to examine the social, economic and behavioural characteristics of patients with HIV infection currently receiving treatment and care in hospitals in East London. The research focused on ethnicity, gender, sexuality, education, employment, housing, HIV treatment, stigma, discrimination, religion, migration and sexual risk behaviour. People diagnosed with HIV infection attending outpatient treatment clinics at St Bartholomew's, the Royal London, Whipp's Cross, Homerton, Newham and Barking hospitals (all in East London) over a 4–6 month period were invited to participate in the study in 2004–2005. Those who agreed to participate completed a confidential, self-administered pen-and-paper questionnaire. During the study period, 2680 patients with HIV attended the outpatient clinics in the six participating hospitals, of whom 2299 were eligible for the study and 1687 completed a questionnaire. The response rate was 73% of eligible patients and 63% of all patients attending the clinics during the survey period. DISCUSSION: A clinic-based study has allowed us to survey nearly 1700 patients with HIV from diverse backgrounds receiving treatment and care in East London. The data collected in this study will provide valuable information for the planning and delivery of appropriate clinical care, social support and health promotion for people living with HIV not only in East London but in other parts of the capital as well as elsewhere in the UK

Magic Numbers of Silicon Clusters

A structural model for intermediate sized silicon clusters is proposed that is able to generate unique structures without any dangling bonds. This structural model consists of bulk-like core of five atoms surrounded by fullerene-like surface. Reconstruction of the ideal fullerene geometry results in the formation of crown atoms surrounded by $\pi$-bonded dimer pairs. This model yields unique structures for \Si{33}, \Si{39}, and \Si{45} clusters without any dangling bonds and hence explains why these clusters are least reactive towards chemisorption of ammonia, methanol, ethylene, and water. This model is also consistent with the experimental finding that silicon clusters undergo a transition from prolate to spherical shapes at \Si{27}. Finally, reagent specific chemisorption reactivities observed experimentally is explained based on the electronic structures of the reagents.Comment: 4 pages + 3 figures (postscript files after \end{document}

The Neuromelanin-related T2* Contrast in Postmortem Human Substantia Nigra with 7T MRI

High field magnetic resonance imaging (MRI)-based delineation of the substantia nigra (SN) and visualization of its inner cellular organization are promising methods for the evaluation of morphological changes associated with neurodegenerative diseases; however, corresponding MR contrasts must be matched and validated with quantitative histological information. Slices from two postmortem SN samples were imaged with a 7 Tesla (7T) MRI with T1 and T2* imaging protocols and then stained with Perl???s Prussian blue, Kluver-Barrera, tyrosine hydroxylase, and calbindin immunohistochemistry in a serial manner. The association between T2* values and quantitative histology was investigated with a co-registration method that accounts for histology slice preparation. The ventral T2* hypointense layers between the SNr and the crus cerebri extended anteriorly to the posterior part of the crus cerebri, which demonstrates the difficulty with an MRI-based delineation of the SN. We found that the paramagnetic hypointense areas within the dorsolateral SN corresponded to clusters of neuromelanin (NM). These NM-rich zones were distinct from the hypointense ventromedial regions with high iron pigments. Nigral T2* imaging at 7T can reflect the density of NM-containing neurons as the metal-bound NM macromolecules may decrease T2* values and cause hypointense signalling in T2* imaging at 7T.ope

African farmer-led irrigation development: re-framing agricultural policy and investment?

The past decade has witnessed an intensifying focus on the development of irrigation in sub-Saharan Africa. It follows a 20-year hiatus in the wake of disappointing irrigation performance during the 1970s and 1980s. Persistent low productivity in African agriculture and vulnerability of African food supplies to increasing instability in international commodity markets are driving pan-African agricultural investment initiatives, such as the Comprehensive Africa Agricultural Development Programme (CAADP), that identify as a priority the improvement in reliability of water control for agriculture. The paper argues that, for such initiatives to be effective, there needs to be a re-appraisal of current dynamics of irrigation development in sub-Saharan Africa, particularly with respect to the role of small-scale producers’ initiatives in expanding irrigation. The paper reviews the principal forms such initiatives take and argues that official narratives and statistics on African irrigation often underestimate the extent of such activities. The paper identifies five key characteristics which, it argues, contradict widely held assumptions that inform irrigation policy in Africa. The paper concludes by offering a definition of ‘farmer-led irrigation’ that embraces a range of interaction between producers and commercial, government and non-government agencies, and identifies priority areas for research on the growth potential and impact of such interactions and strategies for their future development

Exploring, exploiting and evolving diversity of aquatic ecosystem models: A community perspective

Here, we present a community perspective on how to explore, exploit and evolve the diversity in aquatic ecosystem models. These models play an important role in understanding the functioning of aquatic ecosystems, filling in observation gaps and developing effective strategies for water quality management. In this spirit, numerous models have been developed since the 1970s. We set off to explore model diversity by making an inventory among 42 aquatic ecosystem modellers, by categorizing the resulting set of models and by analysing them for diversity. We then focus on how to exploit model diversity by comparing and combining different aspects of existing models. Finally, we discuss how model diversity came about in the past and could evolve in the future. Throughout our study, we use analogies from biodiversity research to analyse and interpret model diversity. We recommend to make models publicly available through open-source policies, to standardize documentation and technical implementation of models, and to compare models through ensemble modelling and interdisciplinary approaches. We end with our perspective on how the field of aquatic ecosystem modelling might develop in the next 5–10 years. To strive for clarity and to improve readability for non-modellers, we include a glossary