Software framework for inverse modeling and uncertainty characterization

Estimation of spatial random fields (SRFs) is required for predicting groundwater flow, subsurface contaminant movement, and other areas of environmental and earth sciences modeling. This paper presents an inverse modeling framework called MAD# for characterizing SRFs, which is an implementation of the Bayesian inverse modeling technique Method of Anchored Distributions (MAD). MAD# allows modelers to “wrap” simulation models using an extensible driver architecture that exposes model parameters to the inversion engine. MAD# is implemented in an open source software package with the goal of lowering the barrier to using inverse modeling in education, research, and resource management. MAD# includes an intentionally simple user interface for simulation configuration, external software integration, spatial domain and model output visualization, and evaluation of model convergence. Four test cases are presented demonstrating the novel functionality of this framework to apply inversion in order to calibrate the model parameters characterizing a groundwater aquifer.     

Agro-ecosystem modeling can aid in the optimization of biomass feedstock supply

Recent European Directives promoted the development of biofuels, requesting mandatory limits to their emissions ot greenhouse gases (GHG). Second-generation biofuels based on lignocellulosic biomass are prime candidates but their GHG emissions are variable and uncertain. Agro-ecosystem modeling can capture them and the performance of biofuel feedstocks.This study aimed at optimizing feedstock supply for a bioethanol unit in France, from agricultural residues, annual and perennial crops. Their productivity and environmental impacts were modelled on a regional scale using geo-referenced data on soil properties, crop management, land-use and future weather data. Several supply scenarios were tested. Cereal straw was the most efficient feedstock but had a low availability, and only miscanthus could meet the bioethanol plant's demand. Sorghum combined poor yields and high GHG emissions compared by miscanthus and triticale. A mix of three biomass sources used less than 3% of the regional agricultural land while abating GHG emissions by 60%.     

Narrowband signal detection techniques in shallow ocean by acoustic vector sensor array

This paper presents the formulation and performance analysis of four techniques for detection of a narrowband acoustic source in a shallow range-independent ocean using an acoustic vector sensor (AVS) array. The array signal vector is not known due to the unknown location of the source. Hence all detectors are based on a generalized likelihood ratio test (GLRT) which involves estimation of the array signal vector. One non-parametric and three parametric (model-based) signal estimators are presented. It is shown that there is a strong correlation between the detector performance and the mean-square signal estimation error. Theoretical expressions for probability of false alarm and probability of detection are derived for all the detectors, and the theoretical predictions are compared with simulation results. It is shown that the detection performance of an AVS array with a certain number of sensors is equal to or slightly better than that of a conventional acoustic pressure sensor array with thrice as many sensors.     

Global parameter optimization for biokinetic modeling of simple batch experiments

Environmental process modeling is challenged by the lack of high quality data, stochastic variations, and nonlinear behavior. Conventionally, parameter optimization is based on stochastic sampling techniques to deal with the nonlinear behavior of the proposed models. Despite widespread use, such tools cannot guarantee globally optimal parameter estimates. It can be especially difficult in practice to differentiate between lack of algorithm convergence, convergence to a non-global local optimum, and model structure deficits. For this reason, we use a deterministic global optimization algorithm for kinetic model identification and demonstrate it with a model describing a typical batch experiment. A combination of interval arithmetic, reformulations, and relaxations allows globally optimal identification of all (six) model parameters. In addition, the results suggest that further improvements may be obtained by modification of the optimization problem or by proof of the hypothesized pseudo-convex nature of the problem suggested by our results.     

Electric vehicles charging control in a smart grid: A model predictive control approach

The paper presents an event driven model predictive control (MPC) framework for managing charging operations of electric vehicles (EV) in a smart grid. The objective is to minimize the cost of energy consumption, while respecting EV drivers' preferences, technical bounds on the control action (in compliance with the IEC 61851 standard) and both market and grid constraints (by seeking the tracking of a reference load profile defined by the grid operator). The proposed control approach allows “flexible” EV users to participate in demand side management (DSM) programs, which will play a crucial role in improving stability and efficiency of future smart grids. Further, the natural MPC formulation of the problem can be recast into a mixed integer linear programming problem, suitable for implementation on a calculator. Simulation results are provided and discussed in detail.     

A real time experimental setup for classification of epilepsy risk levels

The objective of this paper is to analyze the performance of singular value decomposition, expectation maximization, and Elman Neural Networks in optimization of code converter outputs in the classification of epilepsy risk levels from EEG (electroencephalogram) signals. The signal parameters such as the total number of positive and negative peaks, spikes and sharp waves, their duration etc., were extracted using morphological operators and wavelet transforms. Code converters were considered as a level one classifier. Code converters were found to have a performance index and quality value of 33.26 and 12.74, respectively, which is low. Consequently, for the EEG signals of 20 patients, the post classifiers were applied across 3 epochs of 16 channels. After having made a comparative study of different architectures, SVD was found to be the best post classifier as it marked a performance index of 89.48 and a quality value of 20.62. Elman neural network also exhibits good performance metrics than SVD in the morphological operator based feature extraction method.     

Activity theory as a framework for building adaptive e-learning systems: A case to provide empirical evidence

We apply activity theory (AT) to design adaptive e-learning systems (AeLS). AT is a framework to study human’s behavior at learning; whereas, AeLS enhance students’ apprenticeship by the personalization of teaching–learning experiences. AeLS depict users’ traits and predicts learning outcomes. The approach was successfully tested: Experimental group took lectures chosen by the anticipation AT principle; whilst, control group received randomly selected lectures. Learning achieved by experimental group reveals a correlation quite significant and high positive; but, for control group the correlation it is not significant and medium positive. We conclude: AT is a useful framework to design AeLS and provide student-centered education.     

Individual-based modeling of soil organic matter in NetLogo: Transparent,user-friendly,and open

Soil organic matter dynamics are essential for terrestrial ecosystem functions as they affect biogeochemical cycles and, thus, the provision of plant nutrients or the release of greenhouse gases to the atmosphere. Most of the involved processes are driven by microorganisms. To investigate and understand these processes, individual-based models allow analyzing complex microbial systems' behavior based on rules and conditions for individual entities within these systems, taking into account local interactions and individual variations. Here, we present a streamlined, user-friendly and open version of the individual-based model INDISIM-SOM, which describes the mineralization of soil carbon and nitrogen. It was implemented in NetLogo, a widely used and easily accessible software platform especially designed for individual-based simulation models. Including powerful means to observe the model behavior and a standardized documentation, this increases INDISIM-SOM's range of potential uses and users, and facilitates the exchange among soil scientists as well as between different modeling approaches.     

Effect of handle design on movement dynamics and muscle co-activation in a wrist flexion task

Arm and wrist manipulanda are commonly used as input devices in teleoperation and gaming applications, establish a physical interface to patients in several rehabilitation robots, and are applied as advanced research tools in biomechanics and neuroscience. Despite the fact that the physical interface, i.e. the handle through which the wrist/hand is attached to the manipulator, may influence interaction and movement behavior, the effects of handle design on these parameters has received little attention. Yet, a poor handle design might lead to overexertion and altered movement dynamics, or result in misinterpretation of results in research studies. In this study, twelve healthy subjects performed repetitions of a wrist flexion task against a dynamic load generated by a 1-DOF robotic wrist manipulandum. Three different handle designs were qualitatively and quantitatively evaluated based on wrist movement kinematics and dynamics, patterns of finger and wrist muscle activity, and ergonomics criteria such as perceived comfort and fatigue. The three proposed designs were further compared to a conventional joystick-like handle. Task performance as well as kinematic and kinetic parameters were found to be unaffected by handle design. Nevertheless, differences were found in perceived task difficulty, comfort and levels of muscle activation of wrist and finger muscles, with significantly higher muscle activation when using a joystick-like design, where the handle is completely enclosed by the hand. Comfort was rated high for the flat handle, adapted to the natural curvature of the hand with the fingers extended. These results may inform for the design of handles serving as physical interface in teleoperation applications, robot-assisted rehabilitation and biomechanics/neuroscience research.     

An extended systematic literature review on provision of evidence for safety certification

ContextCritical systems in domains such as aviation, railway, and automotive are often subject to a formal process of safety certification. The goal of this process is to ensure that these systems will operate safely without posing undue risks to the user, the public, or the environment. Safety is typically ensured via complying with safety standards. Demonstrating compliance to these standards involves providing evidence to show that the safety criteria of the standards are met.ObjectiveIn order to cope with the complexity of large critical systems and subsequently the plethora of evidence information required for achieving compliance, safety professionals need in-depth knowledge to assist them in classifying different types of evidence, and in structuring and assessing the evidence. This paper is a step towards developing such a body of knowledge that is derived from a large-scale empirically rigorous literature review.MethodWe use a Systematic Literature Review (SLR) as the basis for our work. The SLR builds on 218 peer-reviewed studies, selected through a multi-stage process, from 4963 studies published between 1990 and 2012.ResultsWe develop a taxonomy that classifies the information and artefacts considered as evidence for safety. We review the existing techniques for safety evidence structuring and assessment, and further study the relevant challenges that have been the target of investigation in the academic literature. We analyse commonalities in the results among different application domains and discuss implications of the results for both research and practice.ConclusionThe paper is, to our knowledge, the largest existing study on the topic of safety evidence. The results are particularly relevant to practitioners seeking a better grasp on evidence requirements as well as to researchers in the area of system safety. As a major finding of the review, the results strongly suggest the need for more practitioner-oriented and industry-driven empirical studies in the area of safety certification.     

Simulating agricultural land rental markets by combining agent-based models with traditional economics concepts: The case of the Argentine Pampas

Land exchange through rental transactions is a central process in agricultural systems. The land tenure regimes emerge from land transactions and structural and land use changes are tied to the dynamics of the land market. We introduce LARMA, a LAnd Rental MArket model embedded within the Pampas Model (PM), an agent-based model of Argentinean agricultural systems. LARMA produces endogenous formation of land rental prices. LARMA relies on traditional economic concepts for LRP formation but addresses some drawbacks of this approach by being integrated into an agent-based model that considers heterogeneous agents interacting with one another. PM-LARMA successfully reproduced the agricultural land tenure regimes and land rental prices observed in the Pampas. Including adaptive, heterogeneous and interacting agents was critical to this success. We conclude that agent-based and traditional economic models can be successfully combined to capture complex emergent land tenure and market price patterns while simplifying the overall model design.     

Integrated watershed modeling for simulation of spatiotemporal redistribution of post-fallout radionuclides: Application in radiocesium fate and transport processes derived from the Fukushima accidents

Simulation of the watershed-scale fate and transport of radionuclides is required in order to predict the consequences of contamination redistribution. Integrated watershed modeling is a suitable technique for this task, but it requires fully coupled investigation of radionuclide behavior in surface water, suspended sediment and subsurface aquifers. We developed a novel simulator for computing the spatiotemporal redistribution of fallout radionuclides in watersheds. The simulator was applied to an actual reservoir basin contaminated by fallout radionuclides from the Fukushima Dai-Ichi Nuclear Power Plant accident in 2011. As a result, the simulated ¹³⁷Cs concentration in bottom sediment showed a reasonably close match with the measurement data. The distribution coefficient of ¹³⁷Cs consistent with the latest measurement data was identified as being at least 400,000 L/kg, and it was estimated that more than 90% of the total ¹³⁷Cs distributed in the fallout remains in the catchment area.     

Use of freely available datasets and machine learning methods in predicting deforestation

The range and quality of freely available geo-referenced datasets is increasing. We evaluate the usefulness of free datasets for deforestation prediction by comparing generalised linear models and generalised linear mixed models (GLMMs) with a variety of machine learning models (Bayesian networks, artificial neural networks and Gaussian processes) across two study regions. Freely available datasets were able to generate plausible risk maps of deforestation using all techniques for study zones in both Mexico and Madagascar. Artificial neural networks outperformed GLMMs in the Madagascan (average AUC 0.83 vs 0.80), but not the Mexican study zone (average AUC 0.81 vs 0.89). In Mexico and Madagascar, Gaussian processes (average AUC 0.89, 0.85) and structured Bayesian networks (average AUC 0.88, 0.82) performed at least as well as GLMMs (average AUC 0.89, 0.80). Bayesian networks produced more stable results across different sampling methods. Gaussian processes performed well (average AUC 0.85) with fewer predictor variables.     

Continuum electrostatic approach for evaluating positions and interactions of proteins in a bilayer membrane

Orientations of proteins in the membranes are crucial to their function and stability. Unfortunately the exact positions of these proteins in the lipid bilayer are mostly undetermined. Here, the spatial orientation of membrane proteins within the lipid membrane was evaluated using a Poisson–Boltzmann solvent continuum approach to calculate the electrostatic free energy of the protein solvation at various orientations in an implicit bilayer. The solvation energy was obtained by computing the difference in electrostatic energies of the protein in water and in lipid/water environments, treating each as an implicit solvent model. The optimal position of transmembrane proteins (TMP) in a lipid bilayer is identified by the minimum in the “downhill” pathway of the solvation energy landscape. The energy landscape pattern was considerably conserved in various TMP classes. Evaluation of the position of 1060 membrane proteins from the orientations of proteins in membranes (OPM) database revealed that most of the polytopic and β-barrel proteins were in good agreement with those of the OPM database. The study provides a useful scheme for estimating the membrane solvation energy made by lipid-exposed amino acids in membrane proteins. In addition, our results tested with the bacterial potassium channel model demonstrated the potential usefulness of the approach in assessing the quality of membrane protein models. The present approach should be applicable for constructing transmembrane proteins–lipid configuration suitable for membrane protein simulations and will have utility for the structural modeling of membrane proteins.     

Combining fuzzy cognitive maps with agent-based modeling: Frameworks and pitfalls of a powerful hybrid modeling approach to understand human-environment interactions

Agent-based modeling (ABM) is an established technique to capture human-environment interactions in socio-ecological systems. As a micro-model, it explicitly represents each agent, such that heterogeneous decision-making processes (e.g. based on the beliefs and experiences of stakeholders) can anticipate the socio-environmental consequences of aggregated individual behaviors. In contrast to ABM, Fuzzy Cognitive Mapping takes a macro-level view of the world that represents causal connections between concepts rather than individual entities. Researchers have expressed interest in reconciling the two, i.e. taking a hybrid approach and drawing of the strengths of each to more accurately model socio-ecological interactions. The intuition is to take FCMs, which can be quickly developed using participatory modeling tools and use them to create a virtual population of agents with sophisticated decision-making processes. In this paper, we detail two ways in which this combination can be done, and highlight the key questions that modelers need to be mindful of.     

A new method for trust and reputation evaluation in the cloud environments using the recommendations of opinion leaders' entities and removing the effect of troll entities

Trust in the cloud environment is not written into an agreement and is something earned. In any trust evaluation mechanism, opinion leaders are the entities influencing the behaviors or attitudes of others, this makes them to be trustworthy, valid among other characteristics. On the other hand, trolls are the entities posting incorrect and unreal comments; therefore, their effect must be removed. This paper evaluates the trust by considering the influence of opinion leaders on other entities and removing the troll entities’ effect in the cloud environment. Trust value is evaluated using five parameters; availability, reliability, data integrity, identity and capability. Also, we propose a method for opinion leaders and troll entity identification using three topological metrics, including input-degree, output-degree and reputation measures. The method being evaluated in various situation where shows the results of accuracy by removing the effect of troll entities and the advice of opinion leaders.     

Effect of body-borne equipment on injury of military pilots and aircrew during a simulated helicopter crash

Military helicopter pilots are expected to wear a variety of items of body-borne equipment during flight so as to be prepared for any situation that may arise in combat. Helicopter seats are designed to a specified weight range for an occupant with equipment. This paper investigates how distributing the equipment on the body affects injury potential during a helicopter crash. A finite element model representing a helicopter seat with a fully deformable 50th percentile Hybrid III carrying equipment was developed. The model was subjected to a standard military certification crash test. Various equipment configurations were investigated and analysed to determine its influence on the risk of injury. It was found that placing the equipment low on the torso, i.e. near the thighs, not only reduces the likelihood of injury in the lumbar, spinal region but also provides favourable results in neck and head injury risk when compared to other configurations investigated. In contrast, placing equipment high on the torso, i.e. close to the chin, increases the lumbar load and implicitly, the risk of head injury. A statistical analysis is carried out using the Wilcoxon Signed Rank Test to deliver probability of loads experienced within a certain interval. This study recommends an equipment configuration that improves survivability for an occupant seated on a fixed load energy absorbing seat which is subjected to Military Standard 58095A Test 4.     

Designing new surfactant peptides for binding to carbon nanotubes via computational approaches

The non-covalent interaction between single-walled carbon nanotube and surfactant peptides makes them soluble in biological media to be used in nano-medicine, drug delivery and gene therapy. Pervious study has shown that two important parameters in binding peptides into nanotubes are hydrophobic effect and the number of aromatic amino acids. Ten surfactant peptides with the length of eight residue, including Lys, Trp, Tyr, Phe and Val, were designed to investigate the important parameters in binding peptides to a (6, 6) carbon nanotube. 500 ns MD simulation was performed for free surfactant peptides in water or near to a nanotube. Our results have indicated that the binding affinity of peptides to nanotube increases with the increase of aromatic residue content. Also, among aromatic residues, the peptides containing Trp residues have higher binding affinity to nanotube compared to the peptides with Phe or Tyr residue. Steric hindrance between bulky aromatic residues in peptide sequence has negative influence in binding peptide to nanotube, and in designing a surfactant peptide, the number and distance of aromatic residue and polarity of them should be taken into account. Our results also show that in docking peptides to nanotube, full-flexible docking leads to incorrect results.     

Iterative augmentation of a medical training simulator: Effects of affective metacognitive scaffolding

Experiential training simulators are gaining increasing popularity for job-related training due to their potential to engage and motivate adult learners. They are designed to provide learning experiences that are directly connected to users' work environments and support self-regulated learning. Nevertheless, learners often fail to transfer the knowledge gained in the simulated environment to real-world contexts. The EU-funded ImREAL project aimed to bridge that gap by developing a suite of intelligent services designed to enhance existing training simulators. This paper presents work that was a subset of this research project, reporting the iterative development and evaluation of a scaffolding service, which was integrated into a simulator for training medical students to perform diagnostic interviews. The study comprises three evaluation phases, comparing the pure simulator to a first version with metacognitive scaffolding and then to a final version with affective metacognitive scaffolding and enriched user modelling. The scaffolding service provides the learner with metacognitive prompts; affective elements are realized by an integrated affect reporting tool and affective prompts. Using a mixed-method approach by analysing questionnaires (N = 106) and log-data (N = 426), the effects of the services were investigated with respect to real-world relevance, self-regulated learning support, learning experience, and integration. Despite some limitations, the outcomes of this study demonstrate the usefulness of affective metacognitive scaffolding in the context of experiential training simulators; significant post-simulation increases in perceived relevance of the simulator, reflective note-taking, overall motivation, and feeling of success could be identified. Perceived usability and flow of the simulation increased, whereas overall workload and frustration decreased. However, low response rates to specific functions of the simulation point to a need to further investigate how to raise users' awareness and understanding of the provided tools, to encourage interaction with the services, and to better convey the benefits of using them. Thus, future challenges concern not so much technological developments for personalizing learning experiences, but rather new ways to change user attitudes towards an open approach to learning systems that enables them to benefit from all offered features.