Transient Pulse Formation in Jasmonate Signaling Pathway

The jasmonate (JA) signaling pathway in plants is activated as defense response to a number of stresses like attacks by pests or pathogens and wounding by animals. Some recent experiments provide significant new knowledge on the molecular detail and connectivity of the pathway. The pathway has two major components in the form of feedback loops, one negative and the other positive. We construct a minimal mathematical model, incorporating the feedback loops, to study the dynamics of the JA signaling pathway. The model exhibits transient gene expression activity in the form of JA pulses in agreement with experimental observations. The dependence of the pulse amplitude, duration and peak time on the key parameters of the model is determined computationally. The deterministic and stochastic aspects of the pathway dynamics are investigated using both the full mathematical model as well as a reduced version of it. We also compare the mechanism of pulse formation with the known mechanisms of pulse generation in some bacterial and viral systems

Functional connectivity in relation to motor performance and recovery after stroke.

Plasticity after stroke has traditionally been studied by observing changes only in the spatial distribution and laterality of focal brain activation during affected limb movement. However, neural reorganization is multifaceted and our understanding may be enhanced by examining dynamics of activity within large-scale networks involved in sensorimotor control of the limbs. Here, we review functional connectivity as a promising means of assessing the consequences of a stroke lesion on the transfer of activity within large-scale neural networks. We first provide a brief overview of techniques used to assess functional connectivity in subjects with stroke. Next, we review task-related and resting-state functional connectivity studies that demonstrate a lesion-induced disruption of neural networks, the relationship of the extent of this disruption with motor performance, and the potential for network reorganization in the presence of a stroke lesion. We conclude with suggestions for future research and theories that may enhance the interpretation of changing functional connectivity. Overall findings suggest that a network level assessment provides a useful framework to examine brain reorganization and to potentially better predict behavioral outcomes following stroke

Quantification of flow impairment in faulted sandstone reservoirs.

Abstract unavailable please refer to PD

Brain network mechanisms in learning behavior

The study of learning has been a central focus of psychology and neuroscience since their inception. Cognitive neuroscience’s traditional approach to understanding learn-ing has been to decompose it into discrete cognitive processes with separable and localized underlying neural systems. While this focus on modular cognitive functions for individual brain areas has led to considerable progress, there is increasing evidence that much of learn-ing behavior relies on overlapping cognitive and neural systems, which may be harder to disentangle than previously envisioned. This is not surprising, as the processes underlying learning must involve widespread integration of information from sensory, affective, and motor sources. The standard tools of cognitive neuroscience limit our ability to describe processes that rely on widespread coordination of brain activity. To understand learning, it will be necessary to characterize dynamic co-activation at the circuit level. In this dissertation, I present three studies that seek to describe the roles of distrib-uted brain networks in learning. I begin by giving an overview of our current understand-ing of multiple forms of learning, describing the neural and computational mechanisms thought to underlie incremental feedback-based learning and flexible episodic memory. I will focus in particular on the difficulties in separating these processes at the cognitive level and in localizing them to individual regions at the neural level. I will then describe recent findings that have begun to characterize the brain’s large-scale network structure, emphasiz-ing the potential roles that distributed networks could play in understanding learning and cognition more generally. I will end the introduction by reviewing current attempts to char-acterize the dynamics of large-scale brain networks, which will be essential for providing a mechanistic link to learning behavior. Chapter 2 is a study demonstrating that intrinsic connectivity between the hippo-campus and the ventromedial prefrontal cortex, as well as between these regions and dis-tributed brain networks, is related to individual differences in the transfer of learning on a sensory preconditioning task. The hippocampus and ventromedial prefrontal cortex have both been shown to be involved in this type of learning, and this study represents an early attempt to link connectivity between individual regions and broader networks to learning processes. Chapter 3 is a study that takes advantage of recent developments in mathematical modeling of temporal networks to demonstrate a relationship between large-scale network dynamics and reinforcement learning within individuals. This study shows that the flexibil-ity of network connectivity in the striatum is related to learning performance over time, as well as to individual differences in parameters estimated from computational models of re-inforcement learning. Notably, connectivity between the striatum and visual as well as or-bitofrontal regions increased over the course of the task, which is consistent with an inte-grative role for the region in learning value-based associations. Network flexibility in a dis-tinct set of regions is associated with episodic memory for object images presented during the learning task. Chapter 4 examines the role of dopamine, a neurotransmitter strongly linked to val-ue updating in reinforcement learning, in the dynamic network changes occurring during learning. Patients with Parkinson’s disease, who experience a loss of dopaminergic neu-rons in the substantia nigra, performed a reversal-learning task while undergoing functional magnetic resonance imaging. Patients were scanned on and off of a dopamine precursor medication (levodopa) in a within-subject design in order to examine the impact of dopa-mine on brain network dynamics during learning. The reversal provided an experimental manipulation of dynamic connectivity, and patients on medication showed greater modula-tion of striatal-cortical connectivity. Similar results were found in a number of regions re-ceiving midbrain projections including the prefrontal cortex and medial temporal lobe. This study indicates that dopamine inputs from the midbrain modulate large-scale network dy-namics during learning, providing a direct link between reinforcement learning theories of value updating and network neuroscience accounts of dynamic connectivity. Together, these results indicate that large-scale networks play a critical role in multi-ple forms of learning behavior. Each highlights the potential importance of understanding dynamic routing and integration of information across large-scale circuits for our concep-tion of learning and other cognitive processes. Understanding the when, where, and how of this information flow in the brain may provide an alternative or compliment to traditional theories of distinct learning systems. These studies also illustrate challenges in integrating this perspective with established theories in cognitive neuroscience. Chapter 5 will situate the studies in a broader discussion of how brain activity relates to cognition in general, while pointing out current roadblocks and potential ways forward for a cognitive network neuroscience of learning

Critical Infrastructures: Enhancing Preparedness & Resilience for the Security of Citizens and Services Supply Continuity: Proceedings of the 52nd ESReDA Seminar Hosted by the Lithuanian Energy Institute & Vytautas Magnus University

Critical Infrastructures Preparedness and Resilience is a major societal security issue in modern society. Critical Infrastructures (CIs) provide vital services to modern societies. Some CIs’ disruptions may endanger the security of the citizen, the safety of the strategic assets and even the governance continuity. The European Safety, Reliability and Data Association (ESReDA) as one of the most active EU networks in the field has initiated a project group on the “Critical Infrastructure/Modelling, Simulation and Analysis – Data”. The main focus of the project group is to report on the state of progress in MS&A of the CIs preparedness & resilience with a specific focus on the corresponding data availability and relevance. In order to report on the most recent developments in the field of the CIs preparedness & resilience MS&A and the availability of the relevant data, ESReDA held its 52nd Seminar on the following thematic: “Critical Infrastructures: Enhancing Preparedness & Resilience for the security of citizens and services supply continuity”. The 52nd ESReDA Seminar was a very successful event, which attracted about 50 participants from industry, authorities, operators, research centres, academia and consultancy companies.JRC.G.10-Knowledge for Nuclear Security and Safet

Scalable attack modelling in support of security information and event management

Includes bibliographical referencesWhile assessing security on single devices can be performed using vulnerability assessment tools, modelling of more intricate attacks, which incorporate multiple steps on different machines, requires more advanced techniques. Attack graphs are a promising technique, however they face a number of challenges. An attack graph is an abstract description of what attacks are possible against a specific network. Nodes in an attack graph represent the state of a network at a point in time while arcs between nodes indicate the transformation of a network from one state to another, via the exploit of a vulnerability. Using attack graphs allows system and network configuration information to be correlated and analysed to indicate imminent threats. This approach is limited by several serious issues including the state-space explosion, due to the exponential nature of the problem, and the difficulty in visualising an exhaustive graph of all potential attacks. Furthermore, the lack of availability of information regarding exploits, in a standardised format, makes it difficult to model atomic attacks in terms of exploit requirements and effects. This thesis has as its objective to address these issues and to present a proof of concept solution. It describes a proof of concept implementation of an automated attack graph based tool, to assist in evaluation of network security, assessing whether a sequence of actions could lead to an attacker gaining access to critical network resources. Key objectives are the investigation of attacks that can be modelled, discovery of attack paths, development of techniques to strengthen networks based on attack paths, and testing scalability for larger networks. The proof of concept framework, Network Vulnerability Analyser (NVA), sources vulnerability information from National Vulnerability Database (NVD), a comprehensive, publicly available vulnerability database, transforming it into atomic exploit actions. NVA combines these with a topological network model, using an automated planner to identify potential attacks on network devices. Automated planning is an area of Artificial Intelligence (AI) which focuses on the computational deliberation process of action sequences, by measuring their expected outcomes and this technique is applied to support discovery of a best possible solution to an attack graph that is created. Through the use of heuristics developed for this study, unpromising regions of an attack graph are avoided. Effectively, this prevents the state-space explosion problem associated with modelling large scale networks, only enumerating critical paths rather than an exhaustive graph. SGPlan5 was selected as the most suitable automated planner for this study and was integrated into the system, employing network and exploit models to construct critical attack paths. A critical attack path indicates the most likely attack vector to be used in compromising a targeted device. Critical attack paths are identifed by SGPlan5 by using a heuristic to search through the state-space the attack which yields the highest aggregated severity score. CVSS severity scores were selected as a means of guiding state-space exploration since they are currently the only publicly available metric which can measure the impact of an exploited vulnerability. Two analysis techniques have been implemented to further support the user in making an informed decision as to how to prevent identified attacks. Evaluation of NVA was broken down into a demonstration of its effectiveness in two case studies, and analysis of its scalability potential. Results demonstrate that NVA can successfully enumerate the expected critical attack paths and also this information to establish a solution to identified attacks. Additionally, performance and scalability testing illustrate NVA's success in application to realistically sized larger networks

Road network recovery from concurrent capacity-reducing incidents : model development and optimisation

Local and regional economies are highly dependent on the road network. The concurrent closure of multiple sections of the network following a hazardous event is likely to have significant negative consequences for those using the network. In situations such as these, infrastructure managers must decide how best to restore the network to protect users, maximise connectivity and minimise overall disruption. Furthermore, many hazardous events are forecast to become more frequent and extreme in the future as a result of climate change. Extensive research has been undertaken to understand how to improve the resilience of degraded transport networks. Whilst network robustness (that is, the ability of a network to withstand stress) has been considered in numerous studies, the recovery of the network has captured less attention among researchers. Methodologies developed to date are overly simplistic, especially when simulating the dynamics of traffic demand and drivers’ decision-making in multi-day situations where there is considerable interplay between actual and perceived network states and behaviour. This thesis presents a decision-support tool that optimises the recovery of road transport networks after major day-to-day disruptions, maximising network connectivity and minimising total travel costs. This work expands upon previous efforts by introducing a new approach that models the damage-capacity-time relationship and improves the existing reinforcement-learning traffic-assignment models to be applicable to disrupted scenarios. An efficient metaheuristic approach (NSGA-II) is proposed to find optimal solutions for the recovery problem. The model is also applied to a real-world scenario based on the Scottish road network. Results from this case study clearly highlight the potential applicability of this model to evaluate different recovery strategies and optimise the recovery of road networks after multi-day major disruptions.Local and regional economies are highly dependent on the road network. The concurrent closure of multiple sections of the network following a hazardous event is likely to have significant negative consequences for those using the network. In situations such as these, infrastructure managers must decide how best to restore the network to protect users, maximise connectivity and minimise overall disruption. Furthermore, many hazardous events are forecast to become more frequent and extreme in the future as a result of climate change. Extensive research has been undertaken to understand how to improve the resilience of degraded transport networks. Whilst network robustness (that is, the ability of a network to withstand stress) has been considered in numerous studies, the recovery of the network has captured less attention among researchers. Methodologies developed to date are overly simplistic, especially when simulating the dynamics of traffic demand and drivers’ decision-making in multi-day situations where there is considerable interplay between actual and perceived network states and behaviour. This thesis presents a decision-support tool that optimises the recovery of road transport networks after major day-to-day disruptions, maximising network connectivity and minimising total travel costs. This work expands upon previous efforts by introducing a new approach that models the damage-capacity-time relationship and improves the existing reinforcement-learning traffic-assignment models to be applicable to disrupted scenarios. An efficient metaheuristic approach (NSGA-II) is proposed to find optimal solutions for the recovery problem. The model is also applied to a real-world scenario based on the Scottish road network. Results from this case study clearly highlight the potential applicability of this model to evaluate different recovery strategies and optimise the recovery of road networks after multi-day major disruptions