Global climate change and soil carbon stocks: predictions from two contrasting models for the turnover of organic carbon in soil

Enhanced release of CO2 to the atmosphere from soil organic carbon as a result of increased temperatures may lead to a positive feedback between climate change and the carbon cycle, resulting in much higher CO2 levels and accelerated lobal warming. However, the magnitude of this effect is uncertain and critically dependent on how the decomposition of soil organic C (heterotrophic respiration) responds to changes in climate. Previous studies with the Hadley Centre’s coupled climate–carbon cycle general circulation model (GCM) (HadCM3LC) used a simple, single-pool soil carbon model to simulate the response. Here we present results from numerical simulations that use the more sophisticated ‘RothC’ multipool soil carbon model, driven with the same climate data. The results show strong similarities in the behaviour of the two models, although RothC tends to simulate slightly smaller changes in global soil carbon stocks for the same forcing. RothC simulates global soil carbon stocks decreasing by 54 GtC by 2100 in a climate change simulation compared with an 80 GtC decrease in HadCM3LC. The multipool carbon dynamics of RothC cause it to exhibit a slower magnitude of transient response to both increased organic carbon inputs and changes in climate. We conclude that the projection of a positive feedback between climate and carbon cycle is robust, but the magnitude of the feedback is dependent on the structure of the soil carbon model.

Spatio-temporal dependencies in functional connectivity in rodent cortical cultures

Models of functional connectivity in cortical cultures on multi-electrodes arrays may aid in understanding how cognitive pathways form and improve techniques that aim to interface with neuronal systems. To enable research on such models, this study uses both data- and model-driven approaches to determine what dependencies are present in and between functional connectivity networks derived from bursts of extracellularly recorded activity. Properties of excitation in bursts were analysed using correlative techniques to assess the degree of linear dependence and then two parallel techniques were used to assess functional connectivity. Three models presenting increasing levels of spatio-temporal dependency were used to capture the dynamics of individual functional connections and their consistencies were verified using surrogate data. By comparing network-wide properties between model generated networks and functional networks from data, complex interdependencies were revealed. This indicates the persistent co-activation of neuronal pathways in spontaneous bursts, as can be found in whole brain structures.

The middle-atmosphere Hadley circulation and equatorial inertial adjustment

In the tropical middle atmosphere the climatological radiative equilibrium temperature is inconsistent with gradient-wind balance and the available angular momentum, especially during solstice seasons. Adjustment toward a balanced state results in a type of Hadley circulation that lies outside the “downward control” view of zonally averaged dynamics. This middle-atmosphere Hadley circulation is reexamined here using a zonally symmetric balance model driven through an annual cycle. It is found that the inclusion of a realistic radiation scheme leads to a concentration of the circulation near the stratopause and to its closing off in the mesosphere, with no need for relaxational damping or a rigid lid. The evolving zonal flow is inertially unstable, leading to a rapid process of inertial adjustment, which becomes significant in the mesosphere. This short-circuits the slower process of angular momentum homogenization by the Hadley circulation itself, thereby weakening the latter. The effect of the meridional circulation associated with extratropical wave drag on the Hadley circulation is considered. It is shown that the two circulations are independent for linear (quasigeostrophic) zonal-mean dynamics, and interact primarily through the advection of temperature and angular momentum. There appears to be no significant coupling in the deep Tropics via temperature advection since the wave-driven circulation is unable to alter meridional temperature gradients in this region. However, the wave-driven circulation can affect the Hadley circulation by advecting angular momentum out of the Tropics. The validity of the zonally symmetric balance model with parameterized inertial adjustment is tested by comparison with a three-dimensional primitive equations model. Fields from a middle-atmosphere GCM are also examined for evidence of these processes. While many aspects of the GCM circulation are indicative of the middle-atmosphere Hadley circulation, particularly in the upper stratosphere, it appears that the circulation is obscured in the mesosphere and lower stratosphere by other processes.

ERA-Interim/Land: a global land surface reanalysis data set

ERA-Interim/Land is a global land surface reanalysis data set covering the period 1979–2010. It describes the evolution of soil moisture, soil temperature and snowpack. ERA-Interim/Land is the result of a single 32-year simulation with the latest ECMWF (European Centre for Medium-Range Weather Forecasts) land surface model driven by meteorological forcing from the ERA-Interim atmospheric reanalysis and precipitation adjustments based on monthly GPCP v2.1 (Global Precipitation Climatology Project). The horizontal resolution is about 80 km and the time frequency is 3-hourly. ERA-Interim/Land includes a number of parameterization improvements in the land surface scheme with respect to the original ERA-Interim data set, which makes it more suitable for climate studies involving land water resources. The quality of ERA-Interim/Land is assessed by comparing with ground-based and remote sensing observations. In particular, estimates of soil moisture, snow depth, surface albedo, turbulent latent and sensible fluxes, and river discharges are verified against a large number of site measurements. ERA-Interim/Land provides a global integrated and coherent estimate of soil moisture and snow water equivalent, which can also be used for the initialization of numerical weather prediction and climate models.

Recent lake-level and outflow variations at Lake Viljandi, Estonia: validation of a coupled lake-catchment modelling scheme for climate change studies

Changes in the depth of Lake Viljandi between 1940 and 1990 were simulated using a lake water and energy-balance model driven by standard monthly weather data. Catchment runoff was simulated using a one-dimensional hydrological model, with a two-layer soil, a single-layer snowpack, a simple representation of vegetation cover and similarly modest input requirements. Outflow was modelled as a function of lake level. The simulated record of lake level and outflow matched observations of lake-level variations (r = 0.78) and streamflow (r = 0.87) well. The ability of the model to capture both intra- and inter-annual variations in the behaviour of a specific lake, despite the relatively simple input requirements, makes it extremely suitable for investigations of the impacts of climate change on lake water balance.

The synergies between goal sketching and enterprise architecture

This paper introduces a pragmatic and practical method for requirements modeling. The method is built using the concepts of our goal sketching technique together with techniques from an enterprise architecture modeling language. Our claim is that our method will help project managers who want to establish early control of their projects and will also give managers confidence in the scope of their project. In particular we propose the inclusion of assumptions as first class entities in the ArchiMate enterprise architecture modeling language and an extension of the ArchiMate Motivation Model principle to allow radical as well as normative analyses. We demonstrate the usefulness of this method using a simple university library system as an example.

Precipitation and floodiness

There are a number of factors that lead to non-linearity between precipitation anomalies and flood hazard; this non-linearity is a pertinent issue for applications that use a precipitation forecast as a proxy for imminent flood hazard. We assessed the degree of this non-linearity for the first time using a recently developed global-scale hydrological model driven by the ERA-Interim Land precipitation reanalysis (1980–2010). We introduced new indices to assess large-scale flood hazard, or floodiness, and quantified the link between monthly precipitation, river discharge and floodiness anomalies at the global and regional scales. The results show that monthly floodiness is not well correlated with precipitation, therefore demonstrating the value of hydrometeorological systems for providing floodiness forecasts for decision-makers. A method is described for forecasting floodiness using the Global Flood Awareness System, building a climatology of regional floodiness from which to forecast floodiness anomalies out to two weeks.

Sea ice production and water mass modification in the eastern Laptev Sea

A simple polynya flux model driven by standard atmospheric forcing is used to investigate the ice formation that took place during an exceptionally strong and consistent western New Siberian (WNS) polynya event in 2004 in the Laptev Sea. Whether formation rates are high enough to erode the stratification of the water column beneath is examined by adding the brine released during the 2004 polynya event to the average winter density stratification of the water body, preconditioned by summers with a cyclonic atmospheric forcing (comparatively weakly stratified water column). Beforehand, the model performance is tested through a simulation of a well‐documented event in April 2008. Neglecting the replenishment of water masses by advection into the polynya area, we find the probability for the occurrence of density‐driven convection down to the bottom to be low. Our findings can be explained by the distinct vertical density gradient that characterizes the area of the WNS polynya and the apparent lack of extreme events in the eastern Laptev Sea. The simple approach is expected to be sufficiently rigorous, since the simulated event is exceptionally strong and consistent, the ice production and salt rejection rates are likely to be overestimated, and the amount of salt rejected is distrusted over a comparatively weakly stratified water column. We conclude that the observed erosion of the halocline and formation of vertically mixed water layers during a WNS polynya event is therefore predominantly related to wind‐ and tidally driven turbulent mixing processes.

Prototype Generation from Ontology Charts

Semantic Analysis is a business analysis method designed to capture system requirements. While these requirements may be represented as text, the method also advocates the use of Ontology Charts to formally denote the system's required roles, relationships and forms of communication. Following model driven engineering techniques, Ontology Charts can be transformed to temporal Database schemas, class diagrams and component diagrams, which can then be used to produce software systems. A nice property of these transformations is that resulting system design models lend themselves to complicated extensions that do not require changes to the design models. For example, resulting databases can be extended with new types of data without the need to modify the database schema of the legacy system. Semantic Analysis is not widely used in software engineering, so there is a lack of experts in the field and no design patterns are available. This make it difficult for the analysts to pass organizational knowledge to the engineers. This study describes an implementation that is readily usable by engineers, which includes an automated technique that can produce a prototype from an Ontology Chart. The use of such tools should enable developers to make use of Semantic Analysis with minimal expertise of ontologies and MDA.

Geração automática de interfaces com o utilizador: uma abordagem baseada em MDA para a plataforma PHP

Os modelos e as técnicas de modelação são, hoje em dia, fundamentais na engenharia de software, devido à complexidade e sofisticação dos sistemas de informação actuais.A linguagem Unified Modeling Language (UML) [OMG, 2005a] [OMG, 2005b] tornou-se uma norma para modelação, na engenharia de software e em outras áreas e domínios, mas é reconhecida a sua falta de suporte para a modelação da interactividade e da interface com o utilizador [Nunes and Falcão e Cunha, 2000].Neste trabalho, é explorada a ligação entre as áreas de engenharia de software e de interacção humano-computador, tendo, para isso, sido escolhido o processo de desenvolvimento Wisdom [Nunes and Falcão e Cunha, 2000] [Nunes, 2001]. O método Wisdom é conduzido por casos de utilização essenciais e pelo princípio da prototipificação evolutiva, focando-se no desenho das interfaces com o utilizador através da estrutura da apresentação, com a notação Protótipos Abstractos Canónicos (PAC) [Constantine and Lockwood, 1999] [Constantine, 2003], e do comportamento da interacção com a notação ConcurTaskTrees (CTT) [Paternò, 1999] [Mori, Paternò, et al., 2004] em UML.É proposto, também, neste trabalho um novo passo no processo Wisdom, sendo definido um modelo específico, construído segundo os requisitos da recomendação Model Driven Architecture (MDA) [Soley and OMG, 2000] [OMG, 2003] elaborada pela organização Object Managent Group (OMG). Este modelo específico será o intermediário entre o modelo de desenho e a implementação da interface final com o utilizador. Esta proposta alinha o método Wisdom com a recomendação MDA, tornando possível que sejam gerados, de forma automática, protótipos funcionais de interfaces com o utilizador a partir dos modelos conceptuais de análise e desenho.Foi utilizada a ferramenta de modelação e de metamodelação MetaSketch [Nóbrega, Nunes, et al., 2006] para a definição e manipulação dos modelos e elementos propostos. Foram criadas as aplicações Model2Model e Model2Code para suportar as transformações entre modelos e a geração de código a partir destes. Para a plataforma de implementação foi escolhida a framework Hydra, desenvolvida na linguagem PHP [PHP, 2006], que foi adaptada com alguns conceitos de modo a suportar a abordagem defendida neste trabalho.

Meta, tracer - MOF with traceability

The following document proposes a traceability solution for model-driven development. There as been already previous work done in this area, but so far there has not been yet any standardized way for exchanging traceability information, thus the goal of this project developed and documented here is not to automatize the traceability process but to provide an approach to achieve traceability that follows OMG standards, making traceability information exchangeable between tools that follow the same standards. As such, we propose a traceability meta-model as an extension of MetaObject Facility (MOF)1. Using MetaSketch2 modeling language workbench, we present a modeling language for traceability information. This traceability information then can be used for tool cooperation. Using Meta.Tracer (our tool developed for this thesis), we enable the users to establish traceability relationships between different traceability elements and offer a visualization for the traceability information. We then demonstrate the benefits of using a traceability tool on a software development life cycle using a case study. We finalize by commenting on the work developed.

A outra face dos modelos: técnicas de visualização para explorar modelos

Os modelos são tradicionalmente utilizados na engenharia de software para documentar aspetos do desenho e, em alguns casos, como base para a geração de parte ou a totalidade dos sistemas informáticos que descrevem. Embora subsista o debate sobre este tipo de abordagens e sobre o papel e qualidades que os modelos devem possuir nesta área de engenharia, a existência de modelos que estejam em conformidade com linguagens de modelação bem definidas permite outro tipo de utilizações que vão além das anteriormente referidas. Assente no conhecimento existente sobre a visualização de dados, nesta dissertação irá ser demonstrado a utilização de técnicas de visualização que permitem extrair informação sobre os modelos numa perspetiva inovadora e que contribui favoravelmente para uma melhor compreensão, análise e validação dos mesmos.

Integrating eye tracking in virtual reality for stroke rehabilitation

This thesis reports on research done for the integration of eye tracking technology into virtual reality environments, with the goal of using it in rehabilitation of patients who suffered from stroke. For the last few years, eye tracking has been a focus on medical research, used as an assistive tool  to help people with disabilities interact with new technologies  and as an assessment tool  to track the eye gaze during computer interactions. However, tracking more complex gaze behaviors and relating them to motor deficits in people with disabilities is an area that has not been fully explored, therefore it became the focal point of this research. During the research, two exploratory studies were performed in which eye tracking technology was integrated in the context of a newly created virtual reality task to assess the impact of stroke. Using an eye tracking device and a custom virtual task, the system developed is able to monitor the eye gaze pattern changes over time in patients with stroke, as well as allowing their eye gaze to function as an input for the task. Based on neuroscientific hypotheses of upper limb motor control, the studies aimed at verifying the differences in gaze patterns during the observation and execution of the virtual goal-oriented task in stroke patients (N=10), and also to assess normal gaze behavior in healthy participants (N=20). Results were found consistent and supported the hypotheses formulated, showing that eye gaze could be used as a valid assessment tool on these patients. However, the findings of this first exploratory approach are limited in order to fully understand the effect of stroke on eye gaze behavior. Therefore, a novel model-driven paradigm is proposed to further understand the relation between the neuronal mechanisms underlying goal-oriented actions and eye gaze behavior.

Uma estratégia dirigida a modelos e baseada em linguagem de descrição arquitetural para linhas de produtos de software

Model-oriented strategies have been used to facilitate products customization in the software products lines (SPL) context and to generate the source code of these derived products through variability management. Most of these strategies use an UML (Unified Modeling Language)-based model specification. Despite its wide application, the UML-based model specification has some limitations such as the fact that it is essentially graphic, presents deficiencies regarding the precise description of the system architecture semantic representation, and generates a large model, thus hampering the visualization and comprehension of the system elements. In contrast, architecture description languages (ADLs) provide graphic and textual support for the structural representation of architectural elements, their constraints and interactions. This thesis introduces ArchSPL-MDD, a model-driven strategy in which models are specified and configured by using the LightPL-ACME ADL. Such strategy is associated to a generic process with systematic activities that enable to automatically generate customized source code from the product model. ArchSPLMDD strategy integrates aspect-oriented software development (AOSD), modeldriven development (MDD) and SPL, thus enabling the explicit modeling as well as the modularization of variabilities and crosscutting concerns. The process is instantiated by the ArchSPL-MDD tool, which supports the specification of domain models (the focus of the development) in LightPL-ACME. The ArchSPL-MDD uses the Ginga Digital TV middleware as case study. In order to evaluate the efficiency, applicability, expressiveness, and complexity of the ArchSPL-MDD strategy, a controlled experiment was carried out in order to evaluate and compare the ArchSPL-MDD tool with the GingaForAll tool, which instantiates the process that is part of the GingaForAll UML-based strategy. Both tools were used for configuring the products of Ginga SPL and generating the product source code

A Methodology for Building Service-Oriented Applications in the Presence of Non-Functional Properties

This thesis presents ⇡SOD-M (Policy-based Service Oriented Development Methodology), a methodology for modeling reliable service-based applications using policies. It proposes a model driven method with: (i) a set of meta-models for representing non-functional constraints associated to service-based applications, starting from an use case model until a service composition model; (ii) a platform providing guidelines for expressing the composition and the policies; (iii) model-to-model and model-to-text transformation rules for semi-automatizing the implementation of reliable service-based applications; and (iv) an environment that implements these meta-models and rules, and enables the application of ⇡SOD-M. This thesis also presents a classification and nomenclature for non-functional requirements for developing service-oriented applications. Our approach is intended to add value to the development of service-oriented applications that have quality requirements needs. This work uses concepts from the service-oriented development, non-functional requirements design and model-driven delevopment areas to propose a solution that minimizes the problem of reliable service modeling. Some examples are developed as proof of concepts