Ribosomal frameshifting and transcriptional slippage: from genetic steganography and cryptography to adventitious use

Genetic decoding is not ‘frozen’ as was earlier thought, but dynamic. One facet of this is frameshifting that often results in synthesis of a C-terminal region encoded by a new frame. Ribosomal frameshifting is utilized for the synthesis of additional products, for regulatory purposes and for translational ‘correction’ of problem or ‘savior’ indels. Utilization for synthesis of additional products occurs prominently in the decoding of mobile chromosomal element and viral genomes. One class of regulatory frameshifting of stable chromosomal genes governs cellular polyamine levels from yeasts to humans. In many cases of productively utilized frameshifting, the proportion of ribosomes that frameshift at a shift-prone site is enhanced by specific nascent peptide or mRNA context features. Such mRNA signals, which can be 5′ or 3′ of the shift site or both, can act by pairing with ribosomal RNA or as stem loops or pseudoknots even with one component being 4 kb 3′ from the shift site. Transcriptional realignment at slippage-prone sequences also generates productively utilized products encoded trans-frame with respect to the genomic sequence. This too can be enhanced by nucleic acid structure. Together with dynamic codon redefinition, frameshifting is one of the forms of recoding that enriches gene expression.

Age and alkenone-derived Holocene sea-surface temperature records of sediment core M40-4-SL78

This Special Issue of The Holocene contains 16 research papers based on a symposium at the 11th International Meeting of the European Union of Geosciences held in Strasbourg in April 2001. The aim of the symposium was a state-of-the-art assessment of empirical studies of postglacial marine and terrestrial climatic archives and their integration with numerical climate models. This editorial places the individual papers in the broader context of natural climate variability and anthropogenic impacts on the global climate system, regional differences in climate between maritime and continental areas, and the need for an improved theoretical basis for understanding the underlying causes of environmental change. The focus of the Special Issue is the dynamic and relatively well-understood climate of the North Atlantic and the European realm, where, in relation to the steepest offshore temperature gradient on Earth, observational data are abundant and many recent advances have been made in climate reconstruction from proxy archives. The editorial also contains a summary and overview of the papers included in the four main sections of the Special Issue, which emphasize: (1) numerical modelling experiments; (2) models of glacier buildup and equilibrium-line altitude; (3) marine and terrestrial proxy records of climatic change; and (4) multiproxy palaeoenvironmental reconstruction of a Portuguese lagoonal system.

A Proposed Framework for Simulation Based Learning of Inheritance

Different types of serious games have been used in elucidating computer science areas such as computer games, mobile games, Lego-based games, virtual worlds and webbased games. Different evaluation techniques have been conducted like questionnaires, interviews, discussions and tests. Simulation have been widely used in computer science as a motivational and interactive learning tool. This paper aims to evaluate the possibility of successful implementation of simulation in computer programming modules. A framework is proposed to measure the impact of serious games on enhancing students understanding of key computer science concepts. Experiments will be held on the EEECS of Queen’s University Belfast students to test the framework and attain results.

Model reduction for nonlinear aerodynamics and aeroelasticity using a Discrete Empirical Interpolation Method

A novel surrogate model is proposed in lieu of Computational Fluid Dynamics (CFD) solvers, for fast nonlinear aerodynamic and aeroelastic modeling. A nonlinear function is identified on selected interpolation points by
a discrete empirical interpolation method (DEIM). The flow field is then reconstructed using a least square approximation of the flow modes extracted
by proper orthogonal decomposition (POD). The aeroelastic reduce order
model (ROM) is completed by introducing a nonlinear mapping function
between displacements and the DEIM points. The proposed model is investigated to predict the aerodynamic forces due to forced motions using
a N ACA 0012 airfoil undergoing a prescribed pitching oscillation. To investigate aeroelastic problems at transonic conditions, a pitch/plunge airfoil
and a cropped delta wing aeroelastic models are built using linear structural models. The presence of shock-waves triggers the appearance of limit
cycle oscillations (LCO), which the model is able to predict. For all cases
tested, the new ROM shows the ability to replicate the nonlinear aerodynamic forces, structural displacements and reconstruct the complete flow
field with sufficient accuracy at a fraction of the cost of full order CFD
model.

Methods, Models & Systems for Dealing with Some Business, Management & Engineering Problems

This keynote presentation will report some of our research work and experience on the development and applications of relevant methods, models, systems and simulation techniques in support of different types and various levels of decision making for business, management and engineering. In particular, the following topics will be covered. Modelling, multi-agent-based simulation and analysis of the allocation management of carbon dioxide emission permits in China (Nanfeng Liu & Shuliang Li Agent-based simulation of the dynamic evolution of enterprise carbon assets (Yin Zeng & Shuliang Li) A framework & system for extracting and representing project knowledge contexts using topic models and dynamic knowledge maps: a big data perspective (Jin Xu, Zheng Li, Shuliang Li & Yanyan Zhang) Open innovation: intelligent model, social media & complex adaptive system simulation (Shuliang Li & Jim Zheng Li) A framework, model and software prototype for modelling and simulation for deshopping behaviour and how companies respond (Shawkat Rahman & Shuliang Li) Integrating multiple agents, simulation, knowledge bases and fuzzy logic for international marketing decision making (Shuliang Li & Jim Zheng Li) A Web-based hybrid intelligent system for combined conventional, digital, mobile, social media and mobile marketing strategy formulation (Shuliang Li & Jim Zheng Li) A hybrid intelligent model for Web & social media dynamics, and evolutionary and adaptive branding (Shuliang Li) A hybrid paradigm for modelling, simulation and analysis of brand virality in social media (Shuliang Li & Jim Zheng Li) Network configuration management: attack paradigms and architectures for computer network survivability (Tero Karvinen & Shuliang Li)

A signaling visualization toolkit to support rational design of combination therapies and biomarker discovery: SiViT

Targeted cancer therapy aims to disrupt aberrant cellular signalling pathways. Biomarkers are surrogates of pathway state, but there is limited success in translating candidate biomarkers to clinical practice due to the intrinsic complexity of pathway networks. Systems biology approaches afford better understanding of complex, dynamical interactions in signalling pathways targeted by anticancer drugs. However, adoption of dynamical modelling by clinicians and biologists is impeded by model inaccessibility. Drawing on computer games technology, we present a novel visualisation toolkit, SiViT, that converts systems biology models of cancer cell signalling into interactive simulations that can be used without specialist computational expertise. SiViT allows clinicians and biologists to directly introduce for example loss of function mutations and specific inhibitors. SiViT animates the effects of these introductions on pathway dynamics, suggesting further experiments and assessing candidate biomarker effectiveness. In a systems biology model of Her2 signalling we experimentally validated predictions using SiViT, revealing the dynamics of biomarkers of drug resistance and highlighting the role of pathway crosstalk. No model is ever complete: the iteration of real data and simulation facilitates continued evolution of more accurate, useful models. SiViT will make accessible libraries of models to support preclinical research, combinatorial strategy design and biomarker discovery.

Dynamic load balancing of distributed memory parallel computational mechanics using unstructured meshes for multi-physical modelling

As the complexity of parallel applications increase, the performance limitations resulting from computational load imbalance become dominant. Mapping the problem space to the processors in a parallel machine in a manner that balances the workload of each processors will typically reduce the run-time. In many cases the computation time required for a given calculation cannot be predetermined even at run-time and so static partition of the problem returns poor performance. For problems in which the computational load across the discretisation is dynamic and inhomogeneous, for example multi-physics problems involving fluid and solid mechanics with phase changes, the workload for a static subdomain will change over the course of a computation and cannot be estimated beforehand. For such applications the mapping of loads to process is required to change dynamically, at run-time in order to maintain reasonable efficiency. The issue of dynamic load balancing are examined in the context of PHYSICA, a three dimensional unstructured mesh multi-physics continuum mechanics computational modelling code.

Big data: appearance and disappearance

The mainstay of Big Data is prediction in that it allows practitioners, researchers, and policy analysts to predict trends based upon the analysis of large and varied sources of data. These can range from changing social and political opinions, patterns in crimes, and consumer behaviour. Big Data has therefore shifted the criterion of success in science from causal explanations to predictive modelling and simulation. The 19th-century science sought to capture phenomena and seek to show the appearance of it through causal mechanisms while 20th-century science attempted to save the appearance and relinquish causal explanations. Now 21st-century science in the form of Big Data is concerned with the prediction of appearances and nothing more. However, this pulls social science back in the direction of a more rule- or law-governed reality model of science and away from a consideration of the internal nature of rules in relation to various practices. In effect Big Data offers us no more than a world of surface appearance and in doing so it makes disappear any context-specific conceptual sensitivity.

Navegação de um robô móvel baseado em um modelo de consciência artificial

This work presents a study about a the Baars-Franklin architecture, which defines a model of computational consciousness, and use it in a mobile robot navigation task. The insertion of mobile robots in dynamic environments carries a high complexity in navigation tasks, in order to deal with the constant environment changes, it is essential that the robot can adapt to this dynamism. The approach utilized in this work is to make the execution of these tasks closer to how human beings react to the same conditions by means of a model of computational consci-ousness. The LIDA architecture (Learning Intelligent Distribution Agent) is a cognitive system that seeks tomodel some of the human cognitive aspects, from low-level perceptions to decision making, as well as attention mechanism and episodic memory. In the present work, a computa-tional implementation of the LIDA architecture was evaluated by means of a case study, aiming to evaluate the capabilities of a cognitive approach to navigation of a mobile robot in dynamic and unknown environments, using experiments both with virtual environments (simulation) and a real robot in a realistic environment. This study concluded that it is possible to obtain benefits by using conscious cognitive models in mobile robot navigation tasks, presenting the positive and negative aspects of this approach.

Mobile Platforms and monetising the Second Screen.

Discussion paper commissioned by the RSE for its official working group on BBC Charter Renewal. The paper sought to investigate evolving mobile digital platforms and audience habits. Beyond this the research was intended to highlight areas where the BBC might develop a more commercial strategy in the new charter period. The paper fed into the discussions around the RSE response to the government consultation on BBC Charter renewal. The paper is significant to measure the impact of research around interactive Second Screen activity in the media landscape.

Introduction to Multi-Agent Simulation

When designing systems that are complex, dynamic and stochastic in nature, simulation is generally recognised as one of the best design support technologies, and a valuable aid in the strategic and tactical decision making process. A simulation model consists of a set of rules that define how a system changes over time, given its current state. Unlike analytical models, a simulation model is not solved but is run and the changes of system states can be observed at any point in time. This provides an insight into system dynamics rather than just predicting the output of a system based on specific inputs. Simulation is not a decision making tool but a decision support tool, allowing better informed decisions to be made. Due to the complexity of the real world, a simulation model can only be an approximation of the target system. The essence of the art of simulation modelling is abstraction and simplification. Only those characteristics that are important for the study and analysis of the target system should be included in the simulation model. The purpose of simulation is either to better understand the operation of a target system, or to make predictions about a target system’s performance. It can be viewed as an artificial white-room which allows one to gain insight but also to test new theories and practices without disrupting the daily routine of the focal organisation. What you can expect to gain from a simulation study is very well summarised by FIRMA (2000). His idea is that if the theory that has been framed about the target system holds, and if this theory has been adequately translated into a computer model this would allow you to answer some of the following questions: · Which kind of behaviour can be expected under arbitrarily given parameter combinations and initial conditions? · Which kind of behaviour will a given target system display in the future? · Which state will the target system reach in the future? The required accuracy of the simulation model very much depends on the type of question one is trying to answer. In order to be able to respond to the first question the simulation model needs to be an explanatory model. This requires less data accuracy. In comparison, the simulation model required to answer the latter two questions has to be predictive in nature and therefore needs highly accurate input data to achieve credible outputs. These predictions involve showing trends, rather than giving precise and absolute predictions of the target system performance. The numerical results of a simulation experiment on their own are most often not very useful and need to be rigorously analysed with statistical methods. These results then need to be considered in the context of the real system and interpreted in a qualitative way to make meaningful recommendations or compile best practice guidelines. One needs a good working knowledge about the behaviour of the real system to be able to fully exploit the understanding gained from simulation experiments. The goal of this chapter is to brace the newcomer to the topic of what we think is a valuable asset to the toolset of analysts and decision makers. We will give you a summary of information we have gathered from the literature and of the experiences that we have made first hand during the last five years, whilst obtaining a better understanding of this exciting technology. We hope that this will help you to avoid some pitfalls that we have unwittingly encountered. Section 2 is an introduction to the different types of simulation used in Operational Research and Management Science with a clear focus on agent-based simulation. In Section 3 we outline the theoretical background of multi-agent systems and their elements to prepare you for Section 4 where we discuss how to develop a multi-agent simulation model. Section 5 outlines a simple example of a multi-agent system. Section 6 provides a collection of resources for further studies and finally in Section 7 we will conclude the chapter with a short summary.

Sorghum Crop Modeling and Its Utility in Agronomy and Breeding

Crop models are simplified mathematical representations of the interacting biological and environmental components of the dynamic soil–plant–environment system. Sorghum crop modeling has evolved in parallel with crop modeling capability in general, since its origins in the 1960s and 1970s. Here we briefly review the trajectory in sorghum crop modeling leading to the development of advanced models. We then (i) overview the structure and function of the sorghum model in the Agricultural Production System sIMulator (APSIM) to exemplify advanced modeling concepts that suit both agronomic and breeding applications, (ii) review an example of use of sorghum modeling in supporting agronomic management decisions, (iii) review an example of the use of sorghum modeling in plant breeding, and (iv) consider implications for future roles of sorghum crop modeling. Modeling and simulation provide an avenue to explore consequences of crop management decision options in situations confronted with risks associated with seasonal climate uncertainties. Here we consider the possibility of manipulating planting configuration and density in sorghum as a means to manipulate the productivity–risk trade-off. A simulation analysis of decision options is presented and avenues for its use with decision-makers discussed. Modeling and simulation also provide opportunities to improve breeding efficiency by either dissecting complex traits to more amenable targets for genetics and breeding, or by trait evaluation via phenotypic prediction in target production regions to help prioritize effort and assess breeding strategies. Here we consider studies on the stay-green trait in sorghum, which confers yield advantage in water-limited situations, to exemplify both aspects. The possible future roles of sorghum modeling in agronomy and breeding are discussed as are opportunities related to their synergistic interaction. The potential to add significant value to the revolution in plant breeding associated with genomic technologies is identified as the new modeling frontier.

Contributions to 3D Data Registration and Representation

Nowadays, new computers generation provides a high performance that enables to build computationally expensive computer vision applications applied to mobile robotics. Building a map of the environment is a common task of a robot and is an essential part to allow the robots to move through these environments. Traditionally, mobile robots used a combination of several sensors from different technologies. Lasers, sonars and contact sensors have been typically used in any mobile robotic architecture, however color cameras are an important sensor due to we want the robots to use the same information that humans to sense and move through the different environments. Color cameras are cheap and flexible but a lot of work need to be done to give robots enough visual understanding of the scenes. Computer vision algorithms are computational complex problems but nowadays robots have access to different and powerful architectures that can be used for mobile robotics purposes. The advent of low-cost RGB-D sensors like Microsoft Kinect which provide 3D colored point clouds at high frame rates made the computer vision even more relevant in the mobile robotics field. The combination of visual and 3D data allows the systems to use both computer vision and 3D processing and therefore to be aware of more details of the surrounding environment. The research described in this thesis was motivated by the need of scene mapping. Being aware of the surrounding environment is a key feature in many mobile robotics applications from simple robotic navigation to complex surveillance applications. In addition, the acquisition of a 3D model of the scenes is useful in many areas as video games scene modeling where well-known places are reconstructed and added to game systems or advertising where once you get the 3D model of one room the system can add furniture pieces using augmented reality techniques. In this thesis we perform an experimental study of the state-of-the-art registration methods to find which one fits better to our scene mapping purposes. Different methods are tested and analyzed on different scene distributions of visual and geometry appearance. In addition, this thesis proposes two methods for 3d data compression and representation of 3D maps. Our 3D representation proposal is based on the use of Growing Neural Gas (GNG) method. This Self-Organizing Maps (SOMs) has been successfully used for clustering, pattern recognition and topology representation of various kind of data. Until now, Self-Organizing Maps have been primarily computed offline and their application in 3D data has mainly focused on free noise models without considering time constraints. Self-organising neural models have the ability to provide a good representation of the input space. In particular, the Growing Neural Gas (GNG) is a suitable model because of its flexibility, rapid adaptation and excellent quality of representation. However, this type of learning is time consuming, specially for high-dimensional input data. Since real applications often work under time constraints, it is necessary to adapt the learning process in order to complete it in a predefined time. This thesis proposes a hardware implementation leveraging the computing power of modern GPUs which takes advantage of a new paradigm coined as General-Purpose Computing on Graphics Processing Units (GPGPU). Our proposed geometrical 3D compression method seeks to reduce the 3D information using plane detection as basic structure to compress the data. This is due to our target environments are man-made and therefore there are a lot of points that belong to a plane surface. Our proposed method is able to get good compression results in those man-made scenarios. The detected and compressed planes can be also used in other applications as surface reconstruction or plane-based registration algorithms. Finally, we have also demonstrated the goodness of the GPU technologies getting a high performance implementation of a CAD/CAM common technique called Virtual Digitizing.

Probability and Common-Sense: Tandem Towards Robust Robotic Object Recognition in Ambient Assisted Living

The suitable operation of mobile robots when providing Ambient Assisted Living (AAL) services calls for robust object recognition capabilities. Probabilistic Graphical Models (PGMs) have become the de-facto choice in recognition systems aiming to e ciently exploit contextual relations among objects, also dealing with the uncertainty inherent to the robot workspace. However, these models can perform in an inco herent way when operating in a long-term fashion out of the laboratory, e.g. while recognizing objects in peculiar con gurations or belonging to new types. In this work we propose a recognition system that resorts to PGMs and common-sense knowledge, represented in the form of an ontology, to detect those inconsistencies and learn from them. The utilization of the ontology carries additional advantages, e.g. the possibility to verbalize the robot's knowledge. A primary demonstration of the system capabilities has been carried out with very promising results.

DATA DRIVEN INTELLIGENT AGENT NETWORKS FOR ADAPTIVE MONITORING AND CONTROL

To analyze the characteristics and predict the dynamic behaviors of complex systems over time, comprehensive research to enable the development of systems that can intelligently adapt to the evolving conditions and infer new knowledge with algorithms that are not predesigned is crucially needed. This dissertation research studies the integration of the techniques and methodologies resulted from the fields of pattern recognition, intelligent agents, artificial immune systems, and distributed computing platforms, to create technologies that can more accurately describe and control the dynamics of real-world complex systems. The need for such technologies is emerging in manufacturing, transportation, hazard mitigation, weather and climate prediction, homeland security, and emergency response. Motivated by the ability of mobile agents to dynamically incorporate additional computational and control algorithms into executing applications, mobile agent technology is employed in this research for the adaptive sensing and monitoring in a wireless sensor network. Mobile agents are software components that can travel from one computing platform to another in a network and carry programs and data states that are needed for performing the assigned tasks. To support the generation, migration, communication, and management of mobile monitoring agents, an embeddable mobile agent system (Mobile-C) is integrated with sensor nodes. Mobile monitoring agents visit distributed sensor nodes, read real-time sensor data, and perform anomaly detection using the equipped pattern recognition algorithms. The optimal control of agents is achieved by mimicking the adaptive immune response and the application of multi-objective optimization algorithms. The mobile agent approach provides potential to reduce the communication load and energy consumption in monitoring networks. The major research work of this dissertation project includes: (1) studying effective feature extraction methods for time series measurement data; (2) investigating the impact of the feature extraction methods and dissimilarity measures on the performance of pattern recognition; (3) researching the effects of environmental factors on the performance of pattern recognition; (4) integrating an embeddable mobile agent system with wireless sensor nodes; (5) optimizing agent generation and distribution using artificial immune system concept and multi-objective algorithms; (6) applying mobile agent technology and pattern recognition algorithms for adaptive structural health monitoring and driving cycle pattern recognition; (7) developing a web-based monitoring network to enable the visualization and analysis of real-time sensor data remotely. Techniques and algorithms developed in this dissertation project will contribute to research advances in networked distributed systems operating under changing environments.