Large Scale Simulations of Hippocampal-Neocortical Interactions in a Parallel Version of Genesis

A hippocampal-CA3 memory model was constructed with PGENESIS, a recently developed version of GENESIS that allows for distributed processing of a neural network simulation. A number of neural models of the human memory system have identified the CA3 region of the hippocampus as storing the declarative memory trace. However, computational models designed to assess the viability of the putative mechanisms of storage and retrieval have generally been too abstract to allow comparison with empirical data. Recent experimental evidence has shown that selective knock-out of NMDA receptors in the CA1 of mice leads to reduced stability of firing specificity in place cells. Here a similar reduction of stability of input specificity is demonstrated in a biologically plausible neural network model of the CA3 region, under conditions of Hebbian synaptic plasticity versus an absence of plasticity. The CA3 region is also commonly associated with seizure activity. Further simulations of the same model tested the response to continuously repeating versus randomized nonrepeating input patterns. Each paradigm delivered input of equal intensity and duration. Non-repeating input patterns elicited a greater pyramidal cell spike count. This suggests that repetitive versus non-repeating neocortical inpus has a quantitatively different effect on the hippocampus. This may be relevant to the production of independent epileptogenic zones and the process of encoding new memories.

In search of Nirvana : why Nirvana : the True Story could never be "true"

In my book Nirvana: The True Story (2006), I undertake an autoethnographical approach to biography, attempting to impart an understanding of my chosen subject - the rock band Nirvana - via discussion of my own experiences. On numerous occasions, I veer off into tangential asides, frequently using extensive footnotes to explain obscure musical references. Personal anecdotes are juxtaposed with "insider" information; at crucial points in the story (notable concerts, the first meeting of singer Kurt Cobain with his future wife Courtney Love, the news of Cobain's suicide), the linear thread of the narrative spills over into a multi-faceted approach, with several different (and sometimes opposing) voices given equal prominence. Despite my firsthand experience of the band, however, Nirvana: The True Story is not considered authoritative, even within its own field. This article considers the reasons why this may be the case.In my book Nirvana: The True Story (2006), I undertake an autoethnographical approach to biography, attempting to impart an understanding of my chosen subject - the rock band Nirvana - via discussion of my own experiences. On numerous occasions, I veer off into tangential asides, frequently using extensive footnotes to explain obscure musical references. Personal anecdotes are juxtaposed with "insider" information; at crucial points in the story (notable concerts, the first meeting of singer Kurt Cobain with his future wife Courtney Love, the news of Cobain's suicide), the linear thread of the narrative spills over into a multi-faceted approach, with several different (and sometimes opposing) voices given equal prominence. Despite my firsthand experience of the band, however, Nirvana: The True Story is not considered authoritative, even within its own field. This article considers the reasons why this may be the case.

Optimizing search strategies for invasive pests: Learn before you leap

Strategic searching for invasive pests presents a formidable challenge for conservation managers. Limited funding can necessitate choosing between surveying many sites cursorily, or focussing intensively on fewer sites. While existing knowledge may help to target more likely sites, e.g. with species distribution models (maps), this knowledge is not flawless and improving it also requires management investment. 2.In a rare example of trading-off action against knowledge gain, we combine search coverage and accuracy, and its future improvement, within a single optimisation framework. More specifically we examine under which circumstances managers should adopt one of two search-and-control strategies (cursory or focussed), and when they should divert funding to improving knowledge, making better predictive maps that benefit future searches. 3.We use a family of Receiver Operating Characteristic curves to reflect the quality of maps that direct search efforts. We demonstrate our framework by linking these to a logistic model of invasive spread such as that for the red imported fire ant Solenopsis invicta in south-east Queensland, Australia. 4.Cursory widespread searching is only optimal if the pest is already widespread or knowledge is poor, otherwise focussed searching exploiting the map is preferable. For longer management timeframes, eradication is more likely if funds are initially devoted to improving knowledge, even if this results in a short-term explosion of the pest population. 5.Synthesis and applications. By combining trade-offs between knowledge acquisition and utilization, managers can better focus - and justify - their spending to achieve optimal results in invasive control efforts. This framework can improve the efficiency of any ecological management that relies on predicting occurrence. © 2010 The Authors. Journal of Applied Ecology © 2010 British Ecological Society.

Using internet search queries for infectious disease surveillance: screening diseases for suitability

Background Internet-based surveillance systems provide a novel approach to monitoring infectious diseases. Surveillance systems built on internet data are economically, logistically and epidemiologically appealing and have shown significant promise. The potential for these systems has increased with increased internet availability and shifts in health-related information seeking behaviour. This approach to monitoring infectious diseases has, however, only been applied to single or small groups of select diseases. This study aims to systematically investigate the potential for developing surveillance and early warning systems using internet search data, for a wide range of infectious diseases. Methods Official notifications for 64 infectious diseases in Australia were downloaded and correlated with frequencies for 164 internet search terms for the period 2009–13 using Spearman’s rank correlations. Time series cross correlations were performed to assess the potential for search terms to be used in construction of early warning systems. Results Notifications for 17 infectious diseases (26.6%) were found to be significantly correlated with a selected search term. The use of internet metrics as a means of surveillance has not previously been described for 12 (70.6%) of these diseases. The majority of diseases identified were vaccine-preventable, vector-borne or sexually transmissible; cross correlations, however, indicated that vector-borne and vaccine preventable diseases are best suited for development of early warning systems. Conclusions The findings of this study suggest that internet-based surveillance systems have broader applicability to monitoring infectious diseases than has previously been recognised. Furthermore, internet-based surveillance systems have a potential role in forecasting emerging infectious disease events, especially for vaccine-preventable and vector-borne diseases

Diagnose this if you can: On the effectiveness of search engines in finding medical self-diagnosis information

An increasing amount of people seek health advice on the web using search engines; this poses challenging problems for current search technologies. In this paper we report an initial study of the effectiveness of current search engines in retrieving relevant information for diagnostic medical circumlocutory queries, i.e., queries that are issued by people seeking information about their health condition using a description of the symptoms they observes (e.g. hives all over body) rather than the medical term (e.g. urticaria). This type of queries frequently happens when people are unfamiliar with a domain or language and they are common among health information seekers attempting to self-diagnose or self-treat themselves. Our analysis reveals that current search engines are not equipped to effectively satisfy such information needs; this can have potential harmful outcomes on people’s health. Our results advocate for more research in developing information retrieval methods to support such complex information needs.

In silico biology : making the most of parallel computing

Biological systems are typically complex and adaptive, involving large numbers of entities, or organisms, and many-layered interactions between these. System behaviour evolves over time, and typically benefits from previous experience by retaining memory of previous events. Given the dynamic nature of these phenomena, it is non-trivial to provide a comprehensive description of complex adaptive systems and, in particular, to define the importance and contribution of low-level unsupervised interactions to the overall evolution process. In this chapter, the authors focus on the application of the agent-based paradigm in the context of the immune response to HIV. Explicit implementation of lymph nodes and the associated lymph network, including lymphatic chain structure, is a key objective, and requires parallelisation of the model. Steps taken towards an optimal communication strategy are detailed.

A parallel approach to social network generation and agent-based epidemic simulation

Understanding the dynamics of disease spread is essential in contexts such as estimating load on medical services, as well as risk assessment and interven- tion policies against large-scale epidemic outbreaks. However, most of the information is available after the outbreak itself, and preemptive assessment is far from trivial. Here, we report on an agent-based model developed to investigate such epidemic events in a stylised urban environment. For most diseases, infection of a new individual may occur from casual contact in crowds as well as from repeated interactions with social partners such as work colleagues or family members. Our model therefore accounts for these two phenomena. Given the scale of the system, efficient parallel computing is required. In this presentation, we focus on aspects related to paralllelisation for large networks generation and massively multi-agent simulations.

Performance evaluation of cloud-based parallel computing

As computational models in fields such as medicine and engineering get more refined, resource requirements are increased. In a first instance, these needs have been satisfied using parallel computing and HPC clusters. However, such systems are often costly and lack flexibility. HPC users are therefore tempted to move to elastic HPC using cloud services. One difficulty in making this transition is that HPC and cloud systems are different, and performance may vary. The purpose of this study is to evaluate cloud services as a means to minimise both cost and computation time for large-scale simulations, and to identify which system properties have the most significant impact on performance. Our simulation results show that, while the performance of Virtual CPU (VCPU) is satisfactory, network throughput may lead to difficulties.

Parallel attentive visual tracking

The research reported here addresses the problem of detecting and tracking independently moving objects from a moving observer in real-time, using corners as object tokens. Corners are detected using the Harris corner detector, and local image-plane constraints are employed to solve the correspondence problem. The approach relaxes the restrictive static-world assumption conventionally made, and is therefore capable of tracking independently moving and deformable objects. Tracking is performed without the use of any 3-dimensional motion model. The technique is novel in that, unlike traditional feature-tracking algorithms where feature detection and tracking is carried out over the entire image-plane, here it is restricted to those areas most likely to contain-meaningful image structure. Two distinct types of instantiation regions are identified, these being the “focus-of-expansion” region and “border” regions of the image-plane. The size and location of these regions are defined from a combination of odometry information and a limited knowledge of the operating scenario. The algorithms developed have been tested on real image sequences taken from typical driving scenarios. Implementation of the algorithm using T800 Transputers has shown that near-linear speedups are achievable, and that real-time operation is possible (half-video rate has been achieved using 30 processing elements).

Approximate nearest-neighbour search with inverted signature slice lists

In this paper we present an original approach for finding approximate nearest neighbours in collections of locality-sensitive hashes. The paper demonstrates that this approach makes high-performance nearest-neighbour searching feasible on Web-scale collections and commodity hardware with minimal degradation in search quality.

Sectionalizing strategies for minimizing outage durations of critical loads in parallel power system restoration with bi-level programming

Fast restoration of critical loads and non-black-start generators can significantly reduce the economic losses caused by power system blackouts. In a parallel power system restoration scenario, the sectionalization of restoration subsystems plays a very important role in determining the pickup of critical loads before synchronization. Most existing research mainly focuses on the startup of non-black-start generators. The restoration of critical loads, especially the loads with cold load characteristics, has not yet been addressed in optimizing the subsystem divisions. As a result, sectionalized restoration subsystems cannot achieve the best coordination between the pickup of loads and the ramping of generators. In order to generate sectionalizing strategies considering the pickup of critical loads in parallel power system restoration scenarios, an optimization model considering power system constraints, the characteristics of the cold load pickup and the features of generator startup is proposed in this paper. A bi-level programming approach is employed to solve the proposed sectionalizing model. In the upper level the optimal sectionalizing problem for the restoration subsystems is addressed, while in the lower level the objective is to minimize the outage durations of critical loads. The proposed sectionalizing model has been validated by the New-England 39-bus system and the IEEE 118-bus system. Further comparisons with some existing methods are carried out as well.

Selection criteria in the search for a sperm donor: Behavioural traits versus physical appearance

Despite extensive literature on female mate choice, empirical evidence on women’s mating preferences in the search for a sperm donor is scarce, even though this search, by isolating a male’s genetic impact on offspring from other factors like paternal investment, offers a naturally ”controlled” research setting. In this paper, we work to fill this void by examining the rapidly growing online sperm donor market, which is raising new challenges by offering women novel ways to seek out donor sperm. We not only identify individual factors that influence women’s mating preferences but find strong support for the proposition that behavioural traits (inner values) are more important in these choices than physical appearance (exterior values). We also report evidence that physical factors matter more than resources or other external cues of material success, perhaps because the relevance of good character in donor selection is part of a female psychological adaptation throughout evolutionary history. The lack of evidence on a preference for material resources, on the other hand, may indicate the ability of peer socialization and better access to resources to rapidly shape the female decision process. Overall, the paper makes useful contributions to both the literature on human behaviour and that on decision-making in extreme and highly important situations.

A Monte-Carlo tree search in argumentation

Monte-Carlo Tree Search (MCTS) is a heuristic to search in large trees. We apply it to argumentative puzzles where MCTS pursues the best argumentation with respect to a set of arguments to be argued. To make our ideas as widely applicable as possible, we integrate MCTS to an abstract setting for argumentation where the content of arguments is left unspecified. Experimental results show the pertinence of this integration for learning argumentations by comparing it with a basic reinforcement learning.

A hybrid of modified PSO and local search on a multi-robot search system

Particle swarm optimization (PSO), a new population based algorithm, has recently been used on multi-robot systems. Although this algorithm is applied to solve many optimization problems as well as multi-robot systems, it has some drawbacks when it is applied on multi-robot search systems to find a target in a search space containing big static obstacles. One of these defects is premature convergence. This means that one of the properties of basic PSO is that when particles are spread in a search space, as time increases they tend to converge in a small area. This shortcoming is also evident on a multi-robot search system, particularly when there are big static obstacles in the search space that prevent the robots from finding the target easily; therefore, as time increases, based on this property they converge to a small area that may not contain the target and become entrapped in that area.Another shortcoming is that basic PSO cannot guarantee the global convergence of the algorithm. In other words, initially particles explore different areas, but in some cases they are not good at exploiting promising areas, which will increase the search time.This study proposes a method based on the particle swarm optimization (PSO) technique on a multi-robot system to find a target in a search space containing big static obstacles. This method is not only able to overcome the premature convergence problem but also establishes an efficient balance between exploration and exploitation and guarantees global convergence, reducing the search time by combining with a local search method, such as A-star.To validate the effectiveness and usefulness of algorithms,a simulation environment has been developed for conducting simulation-based experiments in different scenarios and for reporting experimental results. These experimental results have demonstrated that the proposed method is able to overcome the premature convergence problem and guarantee global convergence.

Exhaustive search of the SNP-sNP interactome identifies epistatic effects on brain volume in two cohorts

The SNP-SNP interactome has rarely been explored in the context of neuroimaging genetics mainly due to the complexity of conducting approximately 10(11) pairwise statistical tests. However, recent advances in machine learning, specifically the iterative sure independence screening (SIS) method, have enabled the analysis of datasets where the number of predictors is much larger than the number of observations. Using an implementation of the SIS algorithm (called EPISIS), we used exhaustive search of the genome-wide, SNP-SNP interactome to identify and prioritize SNPs for interaction analysis. We identified a significant SNP pair, rs1345203 and rs1213205, associated with temporal lobe volume. We further examined the full-brain, voxelwise effects of the interaction in the ADNI dataset and separately in an independent dataset of healthy twins (QTIM). We found that each additional loading in the epistatic effect was associated with approximately 5% greater brain regional brain volume (a protective effect) in both the ADNI and QTIM samples.