Using learning networks to understand complex systems: a case study of biological, geophysical and social research in the Amazon

Developing high-quality scientific research will be most effective if research communities with diverse skills and interests are able to share information and knowledge, are aware of the major challenges across disciplines, and can exploit economies of scale to provide robust answers and better inform policy. We evaluate opportunities and challenges facing the development of a more interactive research environment by developing an interdisciplinary synthesis of research on a single geographic region. We focus on the Amazon as it is of enormous regional and global environmental importance and faces a highly uncertain future. To take stock of existing knowledge and provide a framework for analysis we present a set of mini-reviews from fourteen different areas of research, encompassing taxonomy, biodiversity, biogeography, vegetation dynamics, landscape ecology, earth-atmosphere interactions, ecosystem processes, fire, deforestation dynamics, hydrology, hunting, conservation planning, livelihoods, and payments for ecosystem services. Each review highlights the current state of knowledge and identifies research priorities, including major challenges and opportunities. We show that while substantial progress is being made across many areas of scientific research, our understanding of specific issues is often dependent on knowledge from other disciplines. Accelerating the acquisition of reliable and contextualized knowledge about the fate of complex pristine and modified ecosystems is partly dependent on our ability to exploit economies of scale in shared resources and technical expertise, recognise and make explicit interconnections and feedbacks among sub-disciplines, increase the temporal and spatial scale of existing studies, and improve the dissemination of scientific findings to policy makers and society at large. Enhancing interaction among research efforts is vital if we are to make the most of limited funds and overcome the challenges posed by addressing large-scale interdisciplinary questions. Bringing together a diverse scientific community with a single geographic focus can help increase awareness of research questions both within and among disciplines, and reveal the opportunities that may exist for advancing acquisition of reliable knowledge. This approach could be useful for a variety of globally important scientific questions.

Identification of potential mechanisms of toxicity after di-(2-ethylhexyl)-phthalate (DEHP) adult exposure in the liver using a systems biology approach

Phthalates are industrial additives widely used as plasticizers. In addition to deleterious effects on male genital development, population studies have documented correlations between phthalates exposure and impacts on reproductive tract development and on the metabolic syndrome in male adults. In this work we investigated potential mechanisms underlying the impact of DEHP on adult mouse liver in vivo. A parallel analysis of hepatic transcript and metabolic profiles from adult mice exposed to varying DEHP doses was performed. Hepatic genes modulated by DEHP are predominantly PPARalpha targets. However, the induction of prototypic cytochrome P450 genes strongly supports the activation of additional NR pathways, including Constitutive Androstane Receptor (CAR). Integration of transcriptomic and metabonomic profiles revealed a correlation between the impacts of DEHP on genes and metabolites related to heme synthesis and to the Rev-erbalpha pathway that senses endogenous heme level. We further confirmed the combined impact of DEHP on the hepatic expression of Alas1, a critical enzyme in heme synthesis and on the expression of Rev-erbalpha target genes involved in the cellular clock and in energy metabolism. This work shows that DEHP interferes with hepatic CAR and Rev-erbalpha pathways which are both involved in the control of metabolism. The identification of these new hepatic pathways targeted by DEHP could contribute to metabolic and endocrine disruption associated with phthalate exposure. Gene expression profiles performed on microdissected testis territories displayed a differential responsiveness to DEHP. Altogether, this suggests that impacts of DEHP on adult organs, including testis, could be documented and deserve further investigations.

Hospital catering systems and their impact on the sensorial profile of foods provided to older patients in the UK

Impaired sensorial perception is very common in older people and low sensorial quality of foods is associated with decreased appetite and dietary intake. Hospital undernutrition in older patients could be linked to sensorial quality of hospital food if the quality were low or inappropriate for older people. The aim of this study was to examine changes in the sensorial quality of different foods that occur as a result of the food journey (i.e. freezing, regeneration, etc.) in the most common hospital catering systems in the UK. A trained sensory panel assessed sensorial descriptors of certain foods with and without the hospital food journey as it occurs in the in-house and cook/freeze systems. The results showed effects of the food journey on a small number of sensorial descriptors related to flavour, appearance and mouthfeel. The majority of these effects were due to temperature changes, which caused accumulation of condensation. A daily variation in sensorial descriptors was also detected and in some cases it was greater than the effect of the food journey. This study has shown that changes occur in the sensory quality of meals due to hospital food journeys, however these changes were small and are not expected to substantially contribute to acceptability or have a major role in hospital malnutrition.

Modelling phosphorus dynamics in multi-branch river systems: A study of the Black River, Lake Simcoe, Ontario, Canada

High rates of nutrient loading from agricultural and urban development have resulted in surface water eutrophication and groundwater contamination in regions of Ontario. In Lake Simcoe (Ontario, Canada), anthropogenic nutrient contributions have contributed to increased algal growth, low hypolimnetic oxygen concentrations, and impaired fish reproduction. An ambitious programme has been initiated to reduce phosphorus loads to the lake, aiming to achieve at least a 40% reduction in phosphorus loads by 2045. Achievement of this target necessitates effective remediation strategies, which will rely upon an improved understanding of controls on nutrient export from tributaries of Lake Simcoe as well as improved understanding of the importance of phosphorus cycling within the lake. In this paper, we describe a new model structure for the integrated dynamic and process-based model INCA-P, which allows fully-distributed applications, suited to branched river networks. We demonstrate application of this model to the Black River, a tributary of Lake Simcoe, and use INCA-P to simulate the fluxes of P entering the lake system, apportion phosphorus among different sources in the catchment, and explore future scenarios of land-use change and nutrient management to identify high priority sites for implementation of watershed best management practises.

TIGGE: comparison of the prediction of Southern Hemisphere extratropical cyclones by different ensemble prediction systems.

The prediction of Northern Hemisphere (NH) extratropical cyclones by nine different ensemble prediction systems(EPSs), archived as part of The Observing System Research and Predictability Experiment (THORPEX) Interactive Grand Global Ensemble (TIGGE), has recently been explored using a cyclone tracking approach. This paper provides a continuation of this work, extending the analysis to the Southern Hemisphere (SH). While the EPSs have larger error in all cyclone properties in the SH, the relative performance of the different EPSs remains broadly consistent between the two hemispheres. Some interesting differences are also shown. The Chinese Meteorological Administration (CMA) EPS has a significantly lower level of performance in the SH compared to the NH. Previous NH results showed that the Centro de Previsao de Tempo e Estudos Climaticos (CPTEC) EPS underpredicts cyclone intensity. The results of this current study show that this bias is significantly larger in the SH. The CPTEC EPS also has very little spread in both hemispheres. As with the NH results, cyclone propagation speed is underpredicted by all the EPSs in the SH. To investigate this further, the bias was also computed for theECMWFhigh-resolution deterministic forecast. The bias was significantly smaller than the lower resolution ECMWF EPS.

Duality, observability, and controllability for linear time-varying descriptor systems

A characterization of observability for linear time-varying descriptor systemsE(t)x(t)+F(t)x(t)=B(t)u(t), y(t)=C(t)x(t) was recently developed. NeitherE norC were required to have constant rank. This paper defines a dual system, and a type of controllability so that observability of the original system is equivalent to controllability of the dual system. Criteria for observability and controllability are given in terms of arrays of derivatives of the original coefficients. In addition, the duality results of this paper lead to an improvement on a previous fundamental structure result for solvable systems of the formE(t)x(t)+F(t)x(t)=f(tt).

Eigenstructure assignment in descriptor systems

Coordinate free conditions are given for pole assignment by feedback in linear descriptor (singular) systems which guarantee closed-loop regularity. These conditions are shown to be both necessary and sufficient for assignment of the maximum possible number of finite poles. Transformation to special coordinates are not used and the results provide a robust algorithm for the computation of the required feedback.

In vitro evaluation of the fermentation properties and potential prebiotic activity of caprine cheese whey oligosaccharides in batch culture systems

The prebiotic effect of oligosaccharides recovered and purified from caprine whey, was evaluated by in vitro fermentation under anaerobic conditions using batch cultures at 37ºC with human faeces. Effects on key gut bacterial groups were monitored over 24h by fluorescence in situ hybridisation (FISH), which was used to determine a quantitative prebiotic index score. Production of short-chain fatty acids (SCFAs) as fermentation end products was analysed by high-performance liquid chromatography (HPLC). Growth of Bifidobacterium spp was significantly higher (p ≥ 0.05) with the purified oligosaccharides compared to the negative control. Lactic and propionic acids were the main SCFAs produced. Antimicrobial activity of the oligosaccharides was also tested, revealing no inhibition though a decrease in Staphylococcus aureus and Escherichia coli growth. These findings indicate that naturally extracted oligosaccharides from caprine whey could be used as new and valuable source of prebiotics.

On the growth of errors in data assimilation systems

Considerable progress has taken place in numerical weather prediction over the last decade. It has been possible to extend predictive skills in the extra-tropics of the Northern Hemisphere during the winter from less than five days to seven days. Similar improvements, albeit on a lower level, have taken place in the Southern Hemisphere. Another example of improvement in the forecasts is the prediction of intense synoptic phenomena such as cyclogenesis which on the whole is quite successful with the most advanced operational models (Bengtsson (1989), Gadd and Kruze (1988)). A careful examination shows that there are no single causes for the improvements in predictive skill, but instead they are due to several different factors encompassing the forecasting system as a whole (Bengtsson, 1985). In this paper we will focus our attention on the role of data-assimilation and the effect it may have on reducing the initial error and hence improving the forecast. The first part of the paper contains a theoretical discussion on error growth in simple data assimilation systems, following Leith (1983). In the second part we will apply the result on actual forecast data from ECMWF. The potential for further forecast improvements within the framework of the present observing system in the two hemispheres will be discussed.

Soil food web properties explain ecosystem services across European land use systems

Intensive land use reduces the diversity and abundance of many soil biota, with consequences for the processes that they govern and the ecosystem services that these processes underpin. Relationships between soil biota and ecosystem processes have mostly been found in laboratory experiments and rarely are found in the field. Here, we quantified, across four countries of contrasting climatic and soil conditions in Europe, how differences in soil food web composition resulting from land use systems (intensive wheat rotation, extensive rotation, and permanent grassland) influence the functioning of soils and the ecosystem services that they deliver. Intensive wheat rotation consistently reduced the biomass of all components of the soil food web across all countries. Soil food web properties strongly and consistently predicted processes of C and N cycling across land use systems and geographic locations, and they were a better predictor of these processes than land use. Processes of carbon loss increased with soil food web properties that correlated with soil C content, such as earthworm biomass and fungal/bacterial energy channel ratio, and were greatest in permanent grassland. In contrast, processes of N cycling were explained by soil food web properties independent of land use, such as arbuscular mycorrhizal fungi and bacterial channel biomass. Our quantification of the contribution of soil organisms to processes of C and N cycling across land use systems and geographic locations shows that soil biota need to be included in C and N cycling models and highlights the need to map and conserve soil biodiversity across the world.

Complex dynamics in simple systems with periodic parameter oscillations

We study systems with periodically oscillating parameters that can give way to complex periodic or nonperiodic orbits. Performing the long time limit, we can define ergodic averages such as Lyapunov exponents, where a negative maximal Lyapunov exponent corresponds to a stable periodic orbit. By this, extremely complicated periodic orbits composed of contracting and expanding phases appear in a natural way. Employing the technique of ϵ-uncertain points, we find that values of the control parameters supporting such periodic motion are densely embedded in a set of values for which the motion is chaotic. When a tiny amount of noise is coupled to the system, dynamics with positive and with negative nontrivial Lyapunov exponents are indistinguishable. We discuss two physical systems, an oscillatory flow inside a duct and a dripping faucet with variable water supply, where such a mechanism seems to be responsible for a complicated alternation of laminar and turbulent phases.