Non-coding RNAs: the architects of eukaryotic complexity

Around 98% of all transcriptional output in humans is noncoding RNA. RNA-mediated gene regulation is widespread in higher eukaryotes and complex genetic phenomena like RNA interference, co-suppression, transgene silencing, imprinting, methylation, and possibly position-effect variegation and transvection, all involve intersecting pathways based on or connected to RNA signaling. I suggest that the central dogma is incomplete, and that intronic and other non-coding RNAs have evolved to comprise a second tier of gene expression in eukaryotes, which enables the integration and networking of complex suites of gene activity. Although proteins are the fundamental effectors of cellular function, the basis of eukaryotic complexity and phenotypic variation may lie primarily in a control architecture composed of a highly parallel system of trans-acting RNAs that relay state information required for the coordination and modulation of gene expression, via chromatin remodeling, RNA-DNA, RNA-RNA and RNA-protein interactions. This system has interesting and perhaps informative analogies with small world networks and dataflow computing.

Analysis of the mouse transcriptome for genes involved in the function of the nervous system

We analyzed the mouse Representative Transcript and Protein Set for molecules involved in brain function. We found full-length cDNAs of many known brain genes and discovered new members of known brain gene families, including Family 3 G-protein coupled receptors, voltage-gated channels, and connexins. We also identified previously unknown candidates for secreted neuroactive molecules. The existence of a large number of unique brain ESTs suggests an additional molecular complexity that remains to be explored. A list of genes containing CAG stretches in the coding region represents a first step in the potential identification of candidates for hereditary neurological disorders.

Independent contribution of plaque complexity to myocardial ischemia during Dobutamine stress echocardiography

The influence of complex plaque morphology on the extent of demand-induced ischemia in unselected patients is not well defined. We sought to investigate the functional significance of lesion morphology in patients who underwent coronary angiography and dobutamine stress echocardiography (DSE).,Angiography and DSE were performed within a 6-month period (mean 1 +/- 1 month) in 196 patients. Angiographic assessments involved quantification of stenosis severity, assessment of the extent of jeopardized myocardium, and categorization of plaque morphology according to the Ambrose classification. DSE was interpreted by separate investigators with respect to wall motion score index (WMSI) and number of coronary territories involved. A general linear model was constructed to assess,the independent contribution of patient characteristics and angiographic and DSE results with respect to extent of ischemic myocardium. Complex lesion morphology was seen in 62 patients (32%). Patients with complex lesions were more likely to have had prior myocardial infarction (p < 0.001) and be current smokers (p = 0.03). During angiography, they exhibited a trend toward a greater number of diseased vessels, had a greater coronary jeopardy score (p < 0.001) and more frequent collateral flow (p = 0.03). During echocardiography, patients had a higher stress WMSI (p < 0.001) and were more likely to show ischemia in all 3 arterial territories (p < 0.01). On multivariate regression, the coronary artery jeopardy score and the presence of complex plaque morphology were independent predictors of the extent of ischemic myocardium (R 2 = 34%, p < 0.001). Thus, patients with complex plaque morphology are older, more likely to smoke, and more likely to have had prior myocardial. infarction. They exhibit more extensive disease with higher coronary jeopardy scores and a higher resting and peak stress WMSI. Despite these differences, complex plaque morphology remains an independent predictor of the extent of ischemia during stress. (C) 2003 by Excerpta Medica, Inc.

Trait physiology and crop modelling as a framework to link phenotypic complexity to underlying genetic systems

New tools derived from advances in molecular biology have not been widely adopted in plant breeding for complex traits because of the inability to connect information at gene level to the phenotype in a manner that is useful for selection. In this study, we explored whether physiological dissection and integrative modelling of complex traits could link phenotype complexity to underlying genetic systems in a way that enhanced the power of molecular breeding strategies. A crop and breeding system simulation study on sorghum, which involved variation in 4 key adaptive traits-phenology, osmotic adjustment, transpiration efficiency, stay-green-and a broad range of production environments in north-eastern Australia, was used. The full matrix of simulated phenotypes, which consisted of 547 location-season combinations and 4235 genotypic expression states, was analysed for genetic and environmental effects. The analysis was conducted in stages assuming gradually increased understanding of gene-to-phenotype relationships, which would arise from physiological dissection and modelling. It was found that environmental characterisation and physiological knowledge helped to explain and unravel gene and environment context dependencies in the data. Based on the analyses of gene effects, a range of marker-assisted selection breeding strategies was simulated. It was shown that the inclusion of knowledge resulting from trait physiology and modelling generated an enhanced rate of yield advance over cycles of selection. This occurred because the knowledge associated with component trait physiology and extrapolation to the target population of environments by modelling removed confounding effects associated with environment and gene context dependencies for the markers used. Developing and implementing this gene-to-phenotype capability in crop improvement requires enhanced attention to phenotyping, ecophysiological modelling, and validation studies to test the stability of candidate genetic regions.

Low-complexity low-PAR transmission for MIMO-DSL

This letter considers clip-limited transmission over multiple-input multiple-output digital subscriber lines (MIMO-DSL). We show that a recent low complexity, low peak-to-average-ratio (PAR) single-input modulation technique can be applied to the case of multiple cross-talking channels in a bonded-DSL system. Unfortunately however the direct initialization procedure is computationally infeasible. In this paper, we provide a novel low-complexity initialization procedure. Simulations confirm that the proposed approach has superior performance in clip-limited conditions, compared with both discrete matrix multitone and vectored discrete multitone.

A cognitive genetic algorithm for power distribution system planning

Power systems are large scale nonlinear systems with high complexity. Various optimization techniques and expert systems have been used in power system planning. However, there are always some factors that cannot be quantified, modeled, or even expressed by expert systems. Moreover, such planning problems are often large scale optimization problems. Although computational algorithms that are capable of handling large dimensional problems can be used, the computational costs are still very high. To solve these problems, in this paper, investigation is made to explore the efficiency and effectiveness of combining mathematic algorithms with human intelligence. It had been discovered that humans can join the decision making progresses by cognitive feedback. Based on cognitive feedback and genetic algorithm, a new algorithm called cognitive genetic algorithm is presented. This algorithm can clarify and extract human's cognition. As an important application of this cognitive genetic algorithm, a practical decision method for power distribution system planning is proposed. By using this decision method, the optimal results that satisfy human expertise can be obtained and the limitations of human experts can be minimized in the mean time.

The effects of task complexity and practice on dual-task interference in visuospatial working memory

Although the n-back task has been widely applied to neuroimagery investigations of working memory (WM), the role of practice effects on behavioural performance of this task has not yet been investigated. The current study aimed to investigate the effects of task complexity and familiarity on the n-back task. Seventy-seven participants (39 male, 38 female) completed a visuospatial n-back task four times, twice in two testing sessions separated by a week. Participants were required to remember either the first, second or third (n-back) most recent letter positions in a continuous sequence and to indicate whether the current item matched or did not match the remembered position. A control task, with no working memory requirements required participants to match to a predetermined stimulus position. In both testing sessions, reaction time (RT) and error rate increased with increasing WM load. An exponential slope for RTs in the first session indicated dual-task interference at the 3-back level. However, a linear slope in the second session indicated a reduction of dual-task interference. Attenuation of interference in the second session suggested a reduction in executive demands of the task with practice. This suggested that practice effects occur within the n-back ask and need to be controlled for in future neuroimagery research using the task.

Development of a web-service-agents-based family wealth management system

The roiling financial markets, constantly changing tax law and increasing complexity of planning transaction increase the demand of aggregated family wealth management (FWM) services. However, current trend of developing such advisory systems is mainly focusing on financial or investment side. In addition, these existing systems lack of flexibility and are hard to be integrated with other organizational information systems, such as CRM systems. In this paper, a novel architecture of Web-service-agents-based FWM systems has been proposed. Multiple intelligent agents are wrapped as Web services and can communicate with each other via Web service protocols. On the one hand, these agents can collaborate with each other and provide comprehensive FWM advices. On the other hand, each service can work independently to achieve its own tasks. A prototype system for supporting financial advice is also presented to demonstrate the advances of the proposed Webservice- agents-based FWM system architecture.

Tracking the states of a nonlinear system in the weight-space of a feed-forward neural network

Nonlinear, non-stationary signals are commonly found in a variety of disciplines such as biology, medicine, geology and financial modeling. The complexity (e.g. nonlinearity and non-stationarity) of such signals and their low signal to noise ratios often make it a challenging task to use them in critical applications. In this paper we propose a new neural network based technique to address those problems. We show that a feed forward, multi-layered neural network can conveniently capture the states of a nonlinear system in its connection weight-space, after a process of supervised training. The performance of the proposed method is investigated via computer simulations.

The programming language python in earth system simulations

-scale vary from a planetary scale and million years for convection problems to 100km and 10 years for fault systems simulations. Various techniques are in use to deal with the time dependency (e.g. Crank-Nicholson), with the non-linearity (e.g. Newton-Raphson) and weakly coupled equations (e.g. non-linear Gauss-Seidel). Besides these high-level solution algorithms discretization methods (e.g. finite element method (FEM), boundary element method (BEM)) are used to deal with spatial derivatives. Typically, large-scale, three dimensional meshes are required to resolve geometrical complexity (e.g. in the case of fault systems) or features in the solution (e.g. in mantel convection simulations). The modelling environment escript allows the rapid implementation of new physics as required for the development of simulation codes in earth sciences. Its main object is to provide a programming language, where the user can define new models and rapidly develop high-level solution algorithms. The current implementation is linked with the finite element package finley as a PDE solver. However, the design is open and other discretization technologies such as finite differences and boundary element methods could be included. escript is implemented as an extension of the interactive programming environment python (see www.python.org). Key concepts introduced are Data objects, which are holding values on nodes or elements of the finite element mesh, and linearPDE objects, which are defining linear partial differential equations to be solved by the underlying discretization technology. In this paper we will show the basic concepts of escript and will show how escript is used to implement a simulation code for interacting fault systems. We will show some results of large-scale, parallel simulations on an SGI Altix system. Acknowledgements: Project work is supported by Australian Commonwealth Government through the Australian Computational Earth Systems Simulator Major National Research Facility, Queensland State Government Smart State Research Facility Fund, The University of Queensland and SGI.

A synchronous multimedia annotation system for secure collaboratories

In this paper, we describe the Vannotea system - an application designed to enable collaborating groups to discuss and annotate collections of high quality images, video, audio or 3D objects. The system has been designed specifically to capture and share scholarly discourse and annotations about multimedia research data by teams of trusted colleagues within a research or academic environment. As such, it provides: authenticated access to a web browser search interface for discovering and retrieving media objects; a media replay window that can incorporate a variety of embedded plug-ins to render different scientific media formats; an annotation authoring, editing, searching and browsing tool; and session logging and replay capabilities. Annotations are personal remarks, interpretations, questions or references that can be attached to whole files, segments or regions. Vannotea enables annotations to be attached either synchronously (using jabber message passing and audio/video conferencing) or asynchronously and stand-alone. The annotations are stored on an Annotea server, extended for multimedia content. Their access, retrieval and re-use is controlled via Shibboleth identity management and XACML access policies.

All in Good Time: Exploring Change in Neanderthal Behavioural Complexity

Since their discovery 150 years ago, Neanderthals have been considered incapable of behavioural change and innovation. Traditional synchronic approaches to the study of Neanderthal behaviour have perpetuated this view and shaped our understanding of their lifeways and eventual extinction. In this thesis I implement an innovative diachronic approach to the analysis of Neanderthal faunal extraction, technology and symbolic behaviour as contained in the archaeological record of the critical period between 80,000 and 30,000 years BP. The thesis demonstrates patterns of change in Neanderthal behaviour which are at odds with traditional perspectives and which are consistent with an interpretation of increasing behavioural complexity over time, an idea that has been suggested but never thoroughly explored in Neanderthal archaeology. Demonstrating an increase in behavioural complexity in Neanderthals provides much needed new data with which to fuel the debate over the behavioural capacities of Neanderthals and the first appearance of Modern Human Behaviour in Europe. It supports the notion that Neanderthal populations were active agents of behavioural innovation prior to the arrival of Anatomically Modern Humans in Europe and, ultimately, that they produced an early Upper Palaeolithic cultural assemblage (the Châtelperronian) independent of modern humans. Overall, this thesis provides an initial step towards the development of a quantitative approach to measuring behavioural complexity which provides fresh insights into the cognitive and behavioural capabilities of Neanderthals.

Exploring Change in Neanderthal Behavioural Complexity: An Innovative Approach to the Study of Neanderthal Behaviour

Diachronic approaches provide potential for a more sophisticated framework within which to examine change in Neanderthal behavioural complexity using archaeological proxies such as symbolic artefacts, faunal assemblages and technology. Analysis of the temporal appearance and distribution of such artefacts and assemblages provide the basis for identifying changes in Neanderthal behavioural complexity in terms of symbolism, faunal extraction and technology respectively. Although changes in technology and faunal extraction were examined in the wider study, only the results of the symbolic study are presented below to illustrate the potential of the approach.

Two times three little pigs: Dysfluency, cognitive complexity and autism

This paper presents an analysis of dysfluencies in two oral tellings of a familiar children's story by a young boy with autism. Thurber & Tager-Flusberg (1993) postulate a lower degree of cognitive and communicative investment to explain a lower frequency of non-grammatical pauses observed in elicited narratives of children with autism in comparison to typically developing and intellectually disabled controls. we also found a very low frequency of non-grammatical pauses in our data, but indications of high engagement and cognitive and communicative investment. We point to a wider range of disfluencies as indicators of cognitive load, and show that the kind and location of dysfluencies produced may reveal which aspects of the narrative task are creating the greatest cognitive demand: here, mental state ascription, perspectivization, and adherence to story schema. This paper thus generates analytical options and hypotheses that can be explored further in a larger population of children with autism and typically developing controls.