An objective, niche-based approach to indicator species selection

1. Species-based indices are frequently employed as surrogates for wider biodiversity health and measures of environmental condition. Species selection is crucial in determining an indicators metric value and hence the validity of the interpretation of ecosystem condition and function it provides, yet an objective process to identify appropriate indicator species is frequently lacking. 2. An effective indicator needs to (i) be representative, reflecting the status of wider biodiversity; (ii) be reactive, acting as early-warning systems for detrimental changes in environmental conditions; (iii) respond to change in a predictable way. We present an objective, niche-based approach for species' selection, founded on a coarse categorisation of species' niche space and key resource requirements, which ensures the resultant indicator has these key attributes. 3. We use UK farmland birds as a case study to demonstrate this approach, identifying an optimal indicator set containing 12 species. In contrast to the 19 species included in the farmland bird index (FBI), a key UK biodiversity indicator that contributes to one of the UK Government's headline indicators of sustainability, the niche space occupied by these species fully encompasses that occupied by the wider community of 62 species. 4. We demonstrate that the response of these 12 species to land-use change is a strong correlate to that of the wider farmland bird community. Furthermore, the temporal dynamics of the index based on their population trends closely matches the population dynamics of the wider community. However, in both analyses, the magnitude of the change in our indicator was significantly greater, allowing this indicator to act as an early-warning system. 5. Ecological indicators are embedded in environmental management, sustainable development and biodiversity conservation policy and practice where they act as metrics against which progress towards national, regional and global targets can be measured. Adopting this niche-based approach for objective selection of indicator species will facilitate the development of sensitive and representative indices for a range of taxonomic groups, habitats and spatial scales.

Application of the BRAFO-tiered approach for benefit-risk assessment to case studies on natural foods

There is evidence that consumption of fish, especially oily fish, has substantial beneficial effects on health. In particular an inverse relationship of oily fish intake to coronary heart disease incidence has been established. These beneficial effects are ascribed to fish oil components including long chain ω-3 polyunsaturated fatty acids. On the other hand it should be noted that oily fish also contains hazardous substances such as dioxins, PCBs and methylmercury. Soy consumption has been associated with potential beneficial and adverse effects. The claimed benefits include reduced risk of cardiovascular disease; osteoporosis, breast and prostate cancer whereas potential adverse effects include impaired thyroid function, disruption of sex hormone levels, changes in reproductive function and increased breast cancer risk The two cases of natural foods highlight the need to consider both risks and benefits in order to establish the net health impact associated to the consumption of specific food products. Within the Sixth Framework programme of the European Commission, the BRAFO project was funded to develop a framework that allows for the quantitative comparison of human health risks and benefits in relation to foods and food compounds. This paper describes the application of the developed framework to two natural foods, farmed salmon and soy protein. We conclude that the BRAFO methodology is highly applicable to natural foods. It will help the benefit-risk managers in selecting the appropriate dietary recommendations for the population.

The Natural History of Slapton Ley Nature Reserve XVIII: nitrogen and phosphorus losses from the catchment - an export coefficient modelling approach

Nitrogen and phosphorus losses from the catchment of Slapton Ley, a small coastal lake in SW England, were calculated using an adaptation of a model developed by Jorgensen (1980). A detailed survey of the catchment revealed that its land use is dominated by both permanent and temporary grassland (respectively 38 and 32% of its total area), and that the remainder is made up of the cultivation of cereals and field vegetables, and market gardening. Livestock numbers in the catchment constitute ca. 6600 head of cattle, 10,000 sheep, 590 pigs, 1700 poultry and 58 horses. The permanent human population of the area is ca. 2000, served by two small gravity-fed sewage treatment works (STWs). Inputs to, and losses from, farmland in the catchment were computed using Jorgensen’s model, and coefficients derived from the data of Cooke (1976), Gostick (1982), Rast and Lee (1983) and Vollenweider (1968). Allowing for outputs from STWs, the total annual external load of N and P upon Slapton Ley is 160 t (35 kg ha-1) a-1 N, and 4.8 t (1.05 kg ha-1) a-1 P. Accordingly to Vollenweider (1968, 1975), such loadings exceed OECD permissible level by a factor of ca. 50 in the case of N, and ca. 5 in that of P. In order to reduce nutrient loads, attention would need to be paid to both STW and agricultural sources.

Passive and active hybrid approach to buildings design in Saudi Arabia

The building sector is one of the highest consumers of energy in the world. This has led to high dependency on using fossil fuel to supply energy without due consideration to its environmental impact. Saudi Arabia has been through rapid development accompanied by population growth, which in turn has increased the demand for construction. However, this fast development has been met without considering sustainable building design. General design practices rely on using international design approaches and features without considering the local climate and aspects of traditional passive design. This is by constructing buildings with a large amount of glass fully exposed to solar radiation. The aim of this paper is to investigate the development of sustainability in passive design and vernacular architecture. Furthermore, it compares them with current building in Saudi Arabia in terms of making the most of the climate. Moreover, it will explore the most sustainable renewable energy that can be used to reduce the environmental impact on modern building in Saudi Arabia. This will be carried out using case studies demonstrating the performance of vernacular design in Saudi Arabia and thus its benefits in terms of environmental, economic and social sustainability. It argues that the adoption of a hybrid approach can improve the energy efficiency as well as reduce the carbon footprint of buildings. This is by combining passive design, learning from the vernacular architecture and implementing innovative sustainable technologies.

An effective approach for land-cover classification from airborne lidar fused with co-registered data

Airborne lidar provides accurate height information of objects on the earth and has been recognized as a reliable and accurate surveying tool in many applications. In particular, lidar data offer vital and significant features for urban land-cover classification, which is an important task in urban land-use studies. In this article, we present an effective approach in which lidar data fused with its co-registered images (i.e. aerial colour images containing red, green and blue (RGB) bands and near-infrared (NIR) images) and other derived features are used effectively for accurate urban land-cover classification. The proposed approach begins with an initial classification performed by the Dempster–Shafer theory of evidence with a specifically designed basic probability assignment function. It outputs two results, i.e. the initial classification and pseudo-training samples, which are selected automatically according to the combined probability masses. Second, a support vector machine (SVM)-based probability estimator is adopted to compute the class conditional probability (CCP) for each pixel from the pseudo-training samples. Finally, a Markov random field (MRF) model is established to combine spatial contextual information into the classification. In this stage, the initial classification result and the CCP are exploited. An efficient belief propagation (EBP) algorithm is developed to search for the global minimum-energy solution for the maximum a posteriori (MAP)-MRF framework in which three techniques are developed to speed up the standard belief propagation (BP) algorithm. Lidar and its co-registered data acquired by Toposys Falcon II are used in performance tests. The experimental results prove that fusing the height data and optical images is particularly suited for urban land-cover classification. There is no training sample needed in the proposed approach, and the computational cost is relatively low. An average classification accuracy of 93.63% is achieved.

The coevolution of two phytoplankton species on a single resource: allelopathy as a pseudo-mixotrophy

Without the top-down effects and the external/physical forcing, a stable coexistence of two phytoplankton species under a single resource is impossible — a result well known from the principle of competitive exclusion. Here I demonstrate by analysis of a mathematical model that such a stable coexistence in a homogeneous media without any external factor would be possible, at least theoretically, provided (i) one of the two species is toxin producing thereby has an allelopathic effect on the other, and (ii) the allelopathic effect exceeds a critical level. The threshold level of allelopathy required for the coexistence has been derived analytically in terms of the parameters associated with the resource competition and the nutrient recycling. That the extra mortality of a competitor driven by allelopathy of a toxic species gives a positive feed back to the algal growth process through the recycling is explained. And that this positive feed back plays a pivotal role in reducing competition pressures and helping species succession in the two-species model is demonstrated. Based on these specific coexistence results, I introduce and explain theoretically the allelopathic effect of a toxic species as a ‘pseudo-mixotrophy’—a mechanism of ‘if you cannot beat them or eat them, just kill them by chemical weapons’. The impact of this mechanism of species succession by pseudo-mixotrophy in the form of alleopathy is discussed in the context of current understanding on straight mixotrophy and resource-species relationship among phytoplankton species.

Synbiotic approach restores intestinal homeostasis and prolongs survival in leukaemia mice with cachexia

Cancer cachexia is a multifactorial syndrome that includes muscle wasting and inflammation. As gut microbes influence host immunity and metabolism, we investigated the role of the gut microbiota in the therapeutic management of cancer and associated cachexia. A community-wide analysis of the caecal microbiome in two mouse models of cancer cachexia (acute leukaemia or subcutaneous transplantation of colon cancer cells) identified common microbial signatures, including decreased Lactobacillus spp. and increased Enterobacteriaceae and Parabacteroides goldsteinii/ASF 519. Building on this information, we administered a synbiotic containing inulin-type fructans and live Lactobacillus reuteri 100-23 to leukaemic mice. This treatment restored the Lactobacillus population and reduced the Enterobacteriaceae levels. It also reduced hepatic cancer cell proliferation, muscle wasting and morbidity, and prolonged survival. Administration of the synbiotic was associated with restoration of the expression of antimicrobial proteins controlling intestinal barrier function and gut immunity markers, but did not impact the portal metabolomics imprinting of energy demand. In summary, this study provided evidence that the development of cancer outside the gut can impact intestinal homeostasis and the gut microbial ecosystem and that a synbiotic intervention, by targeting some alterations of the gut microbiota, confers benefits to the host, prolonging survival and reducing cancer proliferation and cachexia.

Neural population models and cortical field theory: overview

The term neural population models (NPMs) is used here as catchall for a wide range of approaches that have been variously called neural mass models, mean field models, neural field models, bulk models, and so forth. All NPMs attempt to describe the collective action of neural assemblies directly. Some NPMs treat the densely populated tissue of cortex as an excitable medium, leading to spatially continuous cortical field theories (CFTs). An indirect approach would start by modelling individual cells and then would explain the collective action of a group of cells by coupling many individual models together. In contrast, NPMs employ collective state variables, typically defined as averages over the group of cells, in order to describe the population activity directly in a single model. The strength and the weakness of his approach are hence one and the same: simplification by bulk. Is this justified and indeed useful, or does it lead to oversimplification which fails to capture the pheno ...

Effects of agricultural management practices on earthworm populations and crop yield: validation and application of a mechanistic modelling approach

There is little consensus on how agriculture will meet future food demands sustainably. Soils and their biota play a crucial role by mediating ecosystem services that support agricultural productivity. However, a multitude of site-specific environmental factors and management practices interact to affect the ability of soil biota to perform vital functions, confounding the interpretation of results from experimental approaches. Insights can be gained through models, which integrate the physiological, biological and ecological mechanisms underpinning soil functions. We present a powerful modelling approach for predicting how agricultural management practices (pesticide applications and tillage) affect soil functioning through earthworm populations. By combining energy budgets and individual-based simulation models, and integrating key behavioural and ecological drivers, we accurately predict population responses to pesticide applications in different climatic conditions. We use the model to analyse the ecological consequences of different weed management practices. Our results demonstrate that an important link between agricultural management (herbicide applications and zero, reduced and conventional tillage) and earthworms is the maintenance of soil organic matter (SOM). We show how zero and reduced tillage practices can increase crop yields while preserving natural ecosystem functions. This demonstrates how management practices which aim to sustain agricultural productivity should account for their effects on earthworm populations, as their proliferation stimulates agricultural productivity. Synthesis and applications. Our results indicate that conventional tillage practices have longer term effects on soil biota than pesticide control, if the pesticide has a short dissipation time. The risk of earthworm populations becoming exposed to toxic pesticides will be reduced under dry soil conditions. Similarly, an increase in soil organic matter could increase the recovery rate of earthworm populations. However, effects are not necessarily additive and the impact of different management practices on earthworms depends on their timing and the prevailing environmental conditions. Our model can be used to determine which combinations of crop management practices and climatic conditions pose least overall risk to earthworm populations. Linking our model mechanistically to crop yield models would aid the optimization of crop management systems by exploring the trade-off between different ecosystem services.

Targeting medication non-adherence behavior in selected autoimmune diseases: a systematic approach to digital health program development

Background 29 autoimmune diseases, including Rheumatoid Arthritis, gout, Crohn’s Disease, and Systematic Lupus Erythematosus affect 7.6-9.4% of the population. While effective therapy is available, many patients do not follow treatment or use medications as directed. Digital health and Web 2.0 interventions have demonstrated much promise in increasing medication and treatment adherence, but to date many Internet tools have proven disappointing. In fact, most digital interventions continue to suffer from high attrition in patient populations, are burdensome for healthcare professionals, and have relatively short life spans. Objective Digital health tools have traditionally centered on the transformation of existing interventions (such as diaries, trackers, stage-based or cognitive behavioral therapy programs, coupons, or symptom checklists) to electronic format. Advanced digital interventions have also incorporated attributes of Web 2.0 such as social networking, text messaging, and the use of video. Despite these efforts, there has not been little measurable impact in non-adherence for illnesses that require medical interventions, and research must look to other strategies or development methodologies. As a first step in investigating the feasibility of developing such a tool, the objective of the current study is to systematically rate factors of non-adherence that have been reported in past research studies. Methods Grounded Theory, recognized as a rigorous method that facilitates the emergence of new themes through systematic analysis, data collection and coding, was used to analyze quantitative, qualitative and mixed method studies addressing the following autoimmune diseases: Rheumatoid Arthritis, gout, Crohn’s Disease, Systematic Lupus Erythematosus, and inflammatory bowel disease. Studies were only included if they contained primary data addressing the relationship with non-adherence. Results Out of the 27 studies, four non-modifiable and 11 modifiable risk factors were discovered. Over one third of articles identified the following risk factors as common contributors to medication non-adherence (percent of studies reporting): patients not understanding treatment (44%), side effects (41%), age (37%), dose regimen (33%), and perceived medication ineffectiveness (33%). An unanticipated finding that emerged was the need for risk stratification tools (81%) with patient-centric approaches (67%). Conclusions This study systematically identifies and categorizes medication non-adherence risk factors in select autoimmune diseases. Findings indicate that patients understanding of their disease and the role of medication are paramount. An unexpected finding was that the majority of research articles called for the creation of tailored, patient-centric interventions that dispel personal misconceptions about disease, pharmacotherapy, and how the body responds to treatment. To our knowledge, these interventions do not yet exist in digital format. Rather than adopting a systems level approach, digital health programs should focus on cohorts with heterogeneous needs, and develop tailored interventions based on individual non-adherence patterns.

Regulation of early steps of GPVI signal transduction by phosphatases: a systems biology approach

We present a data-driven mathematical model of a key initiating step in platelet activation, a central process in the prevention of bleeding following Injury. In vascular disease, this process is activated inappropriately and causes thrombosis, heart attacks and stroke. The collagen receptor GPVI is the primary trigger for platelet activation at sites of injury. Understanding the complex molecular mechanisms initiated by this receptor is important for development of more effective antithrombotic medicines. In this work we developed a series of nonlinear ordinary differential equation models that are direct representations of biological hypotheses surrounding the initial steps in GPVI-stimulated signal transduction. At each stage model simulations were compared to our own quantitative, high-temporal experimental data that guides further experimental design, data collection and model refinement. Much is known about the linear forward reactions within platelet signalling pathways but knowledge of the roles of putative reverse reactions are poorly understood. An initial model, that includes a simple constitutively active phosphatase, was unable to explain experimental data. Model revisions, incorporating a complex pathway of interactions (and specifically the phosphatase TULA-2), provided a good description of the experimental data both based on observations of phosphorylation in samples from one donor and in those of a wider population. Our model was used to investigate the levels of proteins involved in regulating the pathway and the effect of low GPVI levels that have been associated with disease. Results indicate a clear separation in healthy and GPVI deficient states in respect of the signalling cascade dynamics associated with Syk tyrosine phosphorylation and activation. Our approach reveals the central importance of this negative feedback pathway that results in the temporal regulation of a specific class of protein tyrosine phosphatases in controlling the rate, and therefore extent, of GPVI-stimulated platelet activation.

The Léger ruling as another example of the ECJ’s disappointingly reticent approach to the protection of the rights of LGB persons under EU law

In the 1980s, in the midst of the AIDS epidemic, many countries introduced lifetime bans on blood donations by men who had sexual relations with men (MSM). These blanket bans have, recently, begun to be challenged and, as a result, many countries have either relaxed them or completely abolished them. The case under examination (Léger ) is another instance of questioning the legality of such a ban. In particular, in this case, the European Court of Justice was called on to rule on whether a measure such as the French lifetime exclusion from blood donation of the MSM population that was at issue before the referring court is contrary to EU law. The Court ruled that although discriminatory on the ground of sexual orientation, such a ban may be justified in certain circumstances, and left it to the national court to make the final decision. This article seeks to analyse the case and to explain why, in the author’s view, the Court can be accused of—once more—not going far enough in the protection of lesbian, gay and bisexual (LGB) rights.