Novel non-linear elastic structural analysis with generalised transverse element loads using a refined finite element

In the finite element modelling of structural frames, external loads such as wind loads, dead loads and imposed loads usually act along the elements rather than at the nodes only. Conventionally, when an element is subjected to these general transverse element loads, they are usually converted to nodal forces acting at the ends of the elements by either lumping or consistent load approaches. In addition, it is especially important for an element subjected to the first- and second-order elastic behaviour, to which the steel structure is critically prone to; in particular the thin-walled steel structures, when the stocky element section may be generally critical to the inelastic behaviour. In this sense, the accurate first- and second-order elastic displacement solutions of element load effect along an element is vitally crucial, but cannot be simulated using neither numerical nodal nor consistent load methods alone, as long as no equilibrium condition is enforced in the finite element formulation, which can inevitably impair the structural safety of the steel structure particularly. It can be therefore regarded as a unique element load method to account for the element load nonlinearly. If accurate displacement solution is targeted for simulating the first- and second-order elastic behaviour on an element on the basis of sophisticated non-linear element stiffness formulation, the numerous prescribed stiffness matrices must indispensably be used for the plethora of specific transverse element loading patterns encountered. In order to circumvent this shortcoming, the present paper proposes a numerical technique to include the transverse element loading in the non-linear stiffness formulation without numerous prescribed stiffness matrices, and which is able to predict structural responses involving the effect of first-order element loads as well as the second-order coupling effect between the transverse load and axial force in the element. This paper shows that the principle of superposition can be applied to derive the generalized stiffness formulation for element load effect, so that the form of the stiffness matrix remains unchanged with respect to the specific loading patterns, but with only the magnitude of the loading (element load coefficients) being needed to be adjusted in the stiffness formulation, and subsequently the non-linear effect on element loadings can be commensurate by updating the magnitude of element load coefficients through the non-linear solution procedures. In principle, the element loading distribution is converted into a single loading magnitude at mid-span in order to provide the initial perturbation for triggering the member bowing effect due to its transverse element loads. This approach in turn sacrifices the effect of element loading distribution except at mid-span. Therefore, it can be foreseen that the load-deflection behaviour may not be as accurate as those at mid-span, but its discrepancy is still trivial as proved. This novelty allows for a very useful generalised stiffness formulation for a single higher-order element with arbitrary transverse loading patterns to be formulated. Moreover, another significance of this paper is placed on shifting the nodal response (system analysis) to both nodal and element response (sophisticated element formulation). For the conventional finite element method, such as the cubic element, all accurate solutions can be only found at node. It means no accurate and reliable structural safety can be ensured within an element, and as a result, it hinders the engineering applications. The results of the paper are verified using analytical stability function studies, as well as with numerical results reported by independent researchers on several simple frames.

Biophysical correlates of intrinsic and stress-induced morphological variability in lateral amygdaloid neurons: A computational study

Morphological and physiological characteristics of neurons located in the dorsolateral and two ventral subdivisions of the lateral amygdala (LA) have been compared in order to differentiate their roles in the formation and storage of fear memories (Alphs et al, SfN abs 623.1, 2003). Briefly, in these populations, significant differences are observed in input resistance, membrane time constant, firing frequency, dendritic tortuosity, numbers of primary dendrites, dendritic segments and dendritic nodes...

Quantification of the total neuronal structure of the fear conditioning circuit of the lateral amygdala of the rat

During Pavlovian auditory fear conditioning a previously neutral auditory stimulus (CS) gains emotional significance through pairing with a noxious unconditioned stimulus (US). These associations are believed to be formed by way of plasticity at auditory input synapses on principal neurons in the lateral nucleus of the amygdala (LA). In order to begin to understand how fear memories are stored and processed by synaptic changes in the LA, we have quantified both the entire neural number and the sub-cellular structure of LA principal neurons.We first used stereological cell counting methods on Gimsa or GABA immunostained rat brain. We identified 60,322+/-1408 neurons in the LA unilaterally (n=7). Of these 16,917+/-471 were GABA positive. The intercalated nuclei were excluded from the counts and thus GABA cells are believed to represent GABAergic interneurons. The sub-nuclei of the LA were also independently counted. We then quantified the morphometric properties of in vitro electrophysiologically identified principal neurons of the LA, corrected for shrinkage in xyz planes. The total dendritic length was 9.97+/-2.57mm, with 21+/-4 nodes (n=6). Dendritic spine density was 0.19+/-0.03 spines/um (n=6). Intra-LA axon collaterals had a bouton density of 0.1+/-0.02 boutons/um (n=5). These data begin to reveal the finite cellular and sub-cellular processing capacity of the lateral amygdala, and should facilitate efforts to understand mechanisms of plasticity in LA.

Prior and posterior linear pooling for combining expert opinions: Uses and impact on Bayesian Networks

The use of expert knowledge to quantify a Bayesian Network (BN) is necessary when data is not available. This however raises questions regarding how opinions from multiple experts can be used in a BN. Linear pooling is a popular method for combining probability assessments from multiple experts. In particular, Prior Linear Pooling (PrLP), which pools opinions then places them into the BN is a common method. This paper firstly proposes an alternative pooling method, Posterior Linear Pooling (PoLP). This method constructs a BN for each expert, then pools the resulting probabilities at the nodes of interest. Secondly, it investigates the advantages and disadvantages of using these pooling methods to combine the opinions of multiple experts. Finally, the methods are applied to an existing BN, the Wayfinding Bayesian Network Model, to investigate the behaviour of different groups of people and how these different methods may be able to capture such differences. The paper focusses on 6 nodes Human Factors, Environmental Factors, Wayfinding, Communication, Visual Elements of Communication and Navigation Pathway, and three subgroups Gender (female, male),Travel Experience (experienced, inexperienced), and Travel Purpose (business, personal) and finds that different behaviors can indeed be captured by the different methods.

Formal modelling and analysis of DNP3 secure authentication

Supervisory Control and Data Acquisition (SCADA) systems are one of the key foundations of smart grids. The Distributed Network Protocol version 3 (DNP3) is a standard SCADA protocol designed to facilitate communications in substations and smart grid nodes. The protocol is embedded with a security mechanism called Secure Authentication (DNP3-SA). This mechanism ensures that end-to-end communication security is provided in substations. This paper presents a formal model for the behavioural analysis of DNP3-SA using Coloured Petri Nets (CPN). Our DNP3-SA CPN model is capable of testing and verifying various attack scenarios: modification, replay and spoofing, combined complex attack and mitigation strategies. Using the model has revealed a previously unidentified flaw in the DNP3-SA protocol that can be exploited by an attacker that has access to the network interconnecting DNP3 devices. An attacker can launch a successful attack on an outstation without possessing the pre-shared keys by replaying a previously authenticated command with arbitrary parameters. We propose an update to the DNP3-SA protocol that removes the flaw and prevents such attacks. The update is validated and verified using our CPN model proving the effectiveness of the model and importance of the formal protocol analysis.

Two-dimensional bow and stern flows in a finite-depth fluid with constant vorticity

This thesis is concerned with two-dimensional free surface flows past semi-infinite surface-piercing bodies in a fluid of finite-depth. Throughout the study, it is assumed that the fluid in question is incompressible, and that the effects of viscosity and surface tension are negligible. The problems considered are physically important, since they can be used to model the flow of water near the bow or stern of a wide, blunt ship. Alternatively, the solutions can be interpreted as describing the flow into, or out of, a horizontal slot. In the past, all research conducted on this topic has been dedicated to the situation where the flow is irrotational. The results from such studies are extended here, by allowing the fluid to have constant vorticity throughout the flow domain. In addition, new results for irrotational flow are also presented. When studying the flow of a fluid past a surface-piercing body, it is important to stipulate in advance the nature of the free surface as it intersects the body. Three different possibilities are considered in this thesis. In the first of these possibilities, it is assumed that the free surface rises up and meets the body at a stagnation point. For this configuration, the nonlinear problem is solved numerically with the use of a boundary integral method in the physical plane. Here the semi-infinite body is assumed to be rectangular in shape, with a rounded corner. Supercritical solutions which satisfy the radiation condition are found for various values of the Froude number and the dimensionless vorticity. Subcritical solutions are also found; however these solutions violate the radiation condition and are characterised by a train of waves upstream. In the limit that the height of the body above the horizontal bottom vanishes, the flow approaches that due to a submerged line sink in a $90^\circ$ corner. This limiting problem is also examined as a special case. The second configuration considered in this thesis involves the free surface attaching smoothly to the front face of the rectangular shaped body. For this configuration, nonlinear solutions are computed using a similar numerical scheme to that used in the stagnant attachment case. It is found that these solution exist for all supercritical Froude numbers. The related problem of the cusp-like flow due to a submerged sink in a corner is also considered. Finally, the flow of a fluid emerging from beneath a semi-infinite flat plate is examined. Here the free surface is assumed to detach from the trailing edge of the plate horizontally. A linear problem is formulated under the assumption that the elevation of the plate is close to the undisturbed free surface level. This problem is solved exactly using the Wiener-Hopf technique, and subcritical solutions are found which are characterised by a train of sinusoidal waves in the far field. The nonlinear problem is also considered. Exact relations between certain parameters for supercritical flow are derived using conservation of mass and momentum arguments, and these are confirmed numerically. Nonlinear subcritical solutions are computed, and the results are compared to those predicted by the linear theory.

Development of brain structural connectivity between ages 12 and 30: A 4-Tesla diffusion imaging study in 439 adolescents and adults

Understanding how the brain matures in healthy individuals is critical for evaluating deviations from normal development in psychiatric and neurodevelopmental disorders. The brain's anatomical networks are profoundly re-modeled between childhood and adulthood, and diffusion tractography offers unprecedented power to reconstruct these networks and neural pathways in vivo. Here we tracked changes in structural connectivity and network efficiency in 439 right-handed individuals aged 12 to 30 (211 female/126 male adults, mean age=23.6, SD=2.19; 31 female/24 male 12 year olds, mean age=12.3, SD=0.18; and 25 female/22 male 16 year olds, mean age=16.2, SD=0.37). All participants were scanned with high angular resolution diffusion imaging (HARDI) at 4 T. After we performed whole brain tractography, 70 cortical gyral-based regions of interest were extracted from each participant's co-registered anatomical scans. The proportion of fiber connections between all pairs of cortical regions, or nodes, was found to create symmetric fiber density matrices, reflecting the structural brain network. From those 70 × 70 matrices we computed graph theory metrics characterizing structural connectivity. Several key global and nodal metrics changed across development, showing increased network integration, with some connections pruned and others strengthened. The increases and decreases in fiber density, however, were not distributed proportionally across the brain. The frontal cortex had a disproportionate number of decreases in fiber density while the temporal cortex had a disproportionate number of increases in fiber density. This large-scale analysis of the developing structural connectome offers a foundation to develop statistical criteria for aberrant brain connectivity as the human brain matures.

Development of the 'rich club' in brain connectivity networks from 438 adolescents & adults aged 12 to 30

The 'rich club' coefficient describes a phenomenon where a network's hubs (high-degree nodes) are on average more intensely interconnected than lower-degree nodes. Networks with rich clubs often have an efficient, higher-order organization, but we do not yet know how the rich club emerges in the living brain, or how it changes as our brain networks develop. Here we chart the developmental trajectory of the rich club in anatomical brain networks from 438 subjects aged 12-30. Cortical networks were constructed from 68×68 connectivity matrices of fiber density, using whole-brain tractography in 4-Tesla 105-gradient high angular resolution diffusion images (HARDI). The adult and younger cohorts had rich clubs that included different nodes; the rich club effect intensified with age. Rich-club organization is a sign of a network's efficiency and robustness. These concepts and findings may be advantageous for studying brain maturation and abnormal brain development.

Hierarchical topological network analysis of anatomical human brain connectivity and differences related to sex and kinship

Modern non-invasive brain imaging technologies, such as diffusion weighted magnetic resonance imaging (DWI), enable the mapping of neural fiber tracts in the white matter, providing a basis to reconstruct a detailed map of brain structural connectivity networks. Brain connectivity networks differ from random networks in their topology, which can be measured using small worldness, modularity, and high-degree nodes (hubs). Still, little is known about how individual differences in structural brain network properties relate to age, sex, or genetic differences. Recently, some groups have reported brain network biomarkers that enable differentiation among individuals, pairs of individuals, and groups of individuals. In addition to studying new topological features, here we provide a unifying general method to investigate topological brain networks and connectivity differences between individuals, pairs of individuals, and groups of individuals at several levels of the data hierarchy, while appropriately controlling false discovery rate (FDR) errors. We apply our new method to a large dataset of high quality brain connectivity networks obtained from High Angular Resolution Diffusion Imaging (HARDI) tractography in 303 young adult twins, siblings, and unrelated people. Our proposed approach can accurately classify brain connectivity networks based on sex (93% accuracy) and kinship (88.5% accuracy). We find statistically significant differences associated with sex and kinship both in the brain connectivity networks and in derived topological metrics, such as the clustering coefficient and the communicability matrix.

Discovery of genes that affect human brain connectivity: A genome-wide analysis of the connectome

Human brain connectivity is disrupted in a wide range of disorders from Alzheimer's disease to autism but little is known about which specific genes affect it. Here we conducted a genome-wide association for connectivity matrices that capture information on the density of fiber connections between 70 brain regions. We scanned a large twin cohort (N=366) with 4-Tesla high angular resolution diffusion imaging (105-gradient HARDI). Using whole brain HARDI tractography, we extracted a relatively sparse 70×70 matrix representing fiber density between all pairs of cortical regions automatically labeled in co-registered anatomical scans. Additive genetic factors accounted for 1-58% of the variance in connectivity between 90 (of 122) tested nodes. We discovered genome-wide significant associations between variants and connectivity. GWAS permutations at various levels of heritability, and split-sample replication, validated our genetic findings. The resulting genes may offer new leads for mechanisms influencing aberrant connectivity and neurodegeneration. © 2012 IEEE.

Genetics of path lengths in brain connectivity networks: HARDI-based maps in 457 adults

Brain connectivity analyses are increasingly popular for investigating organization. Many connectivity measures including path lengths are generally defined as the number of nodes traversed to connect a node in a graph to the others. Despite its name, path length is purely topological, and does not take into account the physical length of the connections. The distance of the trajectory may also be highly relevant, but is typically overlooked in connectivity analyses. Here we combined genotyping, anatomical MRI and HARDI to understand how our genes influence the cortical connections, using whole-brain tractography. We defined a new measure, based on Dijkstra's algorithm, to compute path lengths for tracts connecting pairs of cortical regions. We compiled these measures into matrices where elements represent the physical distance traveled along tracts. We then analyzed a large cohort of healthy twins and show that our path length measure is reliable, heritable, and influenced even in young adults by the Alzheimer's risk gene, CLU.

The evolutionary history of termites as inferred from 66 mitochondrial genomes

Termites have colonized many habitats and are among the most abundant animals in tropical ecosystems, which they modify considerably through their actions. The timing of their rise in abundance and of the dispersal events that gave rise to modern termite lineages is not well understood. To shed light on termite origins and diversification, we sequenced the mitochondrial genome of 48 termite species and combined them with 18 previously sequenced termite mitochondrial genomes for phylogenetic and molecular clock analyses using multiple fossil calibrations. The 66 genomes represent most major clades of termites. Unlike previous phylogenetic studies based on fewer molecular data, our phylogenetic tree is fully resolved for the lower termites. The phylogenetic positions of Macrotermitinae and Apicotermitinae are also resolved as the basal groups in the higher termites, but in the crown termitid groups, including Termitinae + Syntermitinae + Nasutitermitinae + Cubitermitinae, the position of some nodes remains uncertain. Our molecular clock tree indicates that the lineages leading to termites and Cryptocercus roaches diverged 170 Ma (153-196 Ma 95% confidence interval [CI]), that modern Termitidae arose 54 Ma (46-66 Ma 95% CI), and that the crown termitid group arose 40 Ma (35-49 Ma 95% CI). This indicates that the distribution of basal termite clades was influenced by the final stages of the breakup of Pangaea. Our inference of ancestral geographic ranges shows that the Termitidae, which includes more than 75% of extant termite species, most likely originated in Africa or Asia, and acquired their pantropical distribution after a series of dispersal and subsequent diversification events.

A life cycle assessment approach to quantifying greenhouse gas emissions from land-use change for beef production in eastern Australia

In life cycle assessment studies, greenhouse gas (GHG) emissions from direct land-use change have been estimated to make a significant contribution to the global warming potential of agricultural products. However, these estimates have a high uncertainty due to the complexity of data requirements and difficulty in attribution of land-use change. This paper presents estimates of GHG emissions from direct land-use change from native woodland to grazing land for two beef production regions in eastern Australia, which were the subject of a multi-impact life cycle assessment study for premium beef production. Spatially- and temporally consistent datasets were derived for areas of forest cover and biomass carbon stocks using published remotely sensed tree-cover data and regionally applicable allometric equations consistent with Australia's national GHG inventory report. Standard life cycle assessment methodology was used to estimate GHG emissions and removals from direct land-use change attributed to beef production. For the northern-central New South Wales region of Australia estimates ranged from a net emission of 0.03 t CO2-e ha-1 year-1 to net removal of 0.12 t CO2-e ha-1 year-1 using low and high scenarios, respectively, for sequestration in regrowing forests. For the same period (1990-2010), the study region in southern-central Queensland was estimated to have net emissions from land-use change in the range of 0.45-0.25 t CO2-e ha-1 year-1. The difference between regions reflects continuation of higher rates of deforestation in Queensland until strict regulation in 2006 whereas native vegetation protection laws were introduced earlier in New South Wales. On the basis of liveweight produced at the farm-gate, emissions from direct land-use change for 1990-2010 were comparable in magnitude to those from other on-farm sources, which were dominated by enteric methane. However, calculation of land-use change impacts for the Queensland region for a period starting 2006, gave a range from net emissions of 0.11 t CO2-e ha-1 year-1 to net removals of 0.07 t CO2-e ha-1 year-1. This study demonstrated a method for deriving spatially- and temporally consistent datasets to improve estimates for direct land-use change impacts in life cycle assessment. It identified areas of uncertainty, including rates of sequestration in woody regrowth and impacts of land-use change on soil carbon stocks in grazed woodlands, but also showed the potential for direct land-use change to represent a net sink for GHG.

A preconditioned numerical solver for stiff nonlinear reaction-diffusion equations with fractional Laplacians that avoids dense matrices

The numerical solution of fractional partial differential equations poses significant computational challenges in regard to efficiency as a result of the spatial nonlocality of the fractional differential operators. The dense coefficient matrices that arise from spatial discretisation of these operators mean that even one-dimensional problems can be difficult to solve using standard methods on grids comprising thousands of nodes or more. In this work we address this issue of efficiency for one-dimensional, nonlinear space-fractional reaction–diffusion equations with fractional Laplacian operators. We apply variable-order, variable-stepsize backward differentiation formulas in a Jacobian-free Newton–Krylov framework to advance the solution in time. A key advantage of this approach is the elimination of any requirement to form the dense matrix representation of the fractional Laplacian operator. We show how a banded approximation to this matrix, which can be formed and factorised efficiently, can be used as part of an effective preconditioner that accelerates convergence of the Krylov subspace iterative solver. Our approach also captures the full contribution from the nonlinear reaction term in the preconditioner, which is crucial for problems that exhibit stiff reactions. Numerical examples are presented to illustrate the overall effectiveness of the solver.

Tissue requirements for establishing long-term CD4+ T cell-mediated immunity following Leishmania donovani infection

Organ-specific immunity is a feature of many infectious diseases, including visceral leishmaniasis caused by Leishmania donovani. Experimental visceral leishmaniasis in genetically susceptible mice is characterized by an acute, resolving infection in the liver and chronic infection in the spleen. CD4+ T cell responses are critical for the establishment and maintenance of hepatic immunity in this disease model, but their role in chronically infected spleens remains unclear. In this study, we show that dendritic cells are critical for CD4+ T cell activation and expansion in all tissue sites examined. We found that FTY720-mediated blockade of T cell trafficking early in infection prevented Ag-specific CD4+ T cells from appearing in lymph nodes, but not the spleen and liver, suggesting that early CD4+ T cell priming does not occur in liver-draining lymph nodes. Extended treatment with FTY720 over the first month of infection increased parasite burdens, although this associated with blockade of lymphocyte egress from secondary lymphoid tissue, as well as with more generalized splenic lymphopenia. Importantly, we demonstrate that CD4+ T cells are required for the establishment and maintenance of antiparasitic immunity in the liver, as well as for immune surveillance and suppression of parasite outgrowth in chronically infected spleens. Finally, although early CD4+ T cell priming appeared to occur most effectively in the spleen, we unexpectedly revealed that protective CD4+ T cell-mediated hepatic immunity could be generated in the complete absence of all secondary lymphoid tissues.