Towards a Unified Theory of Neocortex: Laminar Cortical Circuits for Vision and Cognition

A key goal of computational neuroscience is to link brain mechanisms to behavioral functions. The present article describes recent progress towards explaining how laminar neocortical circuits give rise to biological intelligence. These circuits embody two new and revolutionary computational paradigms: Complementary Computing and Laminar Computing. Circuit properties include a novel synthesis of feedforward and feedback processing, of digital and analog processing, and of pre-attentive and attentive processing. This synthesis clarifies the appeal of Bayesian approaches but has a far greater predictive range that naturally extends to self-organizing processes. Examples from vision and cognition are summarized. A LAMINART architecture unifies properties of visual development, learning, perceptual grouping, attention, and 3D vision. A key modeling theme is that the mechanisms which enable development and learning to occur in a stable way imply properties of adult behavior. It is noted how higher-order attentional constraints can influence multiple cortical regions, and how spatial and object attention work together to learn view-invariant object categories. In particular, a form-fitting spatial attentional shroud can allow an emerging view-invariant object category to remain active while multiple view categories are associated with it during sequences of saccadic eye movements. Finally, the chapter summarizes recent work on the LIST PARSE model of cognitive information processing by the laminar circuits of prefrontal cortex. LIST PARSE models the short-term storage of event sequences in working memory, their unitization through learning into sequence, or list, chunks, and their read-out in planned sequential performance that is under volitional control. LIST PARSE provides a laminar embodiment of Item and Order working memories, also called Competitive Queuing models, that have been supported by both psychophysical and neurobiological data. These examples show how variations of a common laminar cortical design can embody properties of visual and cognitive intelligence that seem, at least on the surface, to be mechanistically unrelated.

The Synthesis of Arbitrary Stable Dynamics in Non-linear Neural Networks II: Feedback and Universality

We wish to construct a realization theory of stable neural networks and use this theory to model the variety of stable dynamics apparent in natural data. Such a theory should have numerous applications to constructing specific artificial neural networks with desired dynamical behavior. The networks used in this theory should have well understood dynamics yet be as diverse as possible to capture natural diversity. In this article, I describe a parameterized family of higher order, gradient-like neural networks which have known arbitrary equilibria with unstable manifolds of known specified dimension. Moreover, any system with hyperbolic dynamics is conjugate to one of these systems in a neighborhood of the equilibrium points. Prior work on how to synthesize attractors using dynamical systems theory, optimization, or direct parametric. fits to known stable systems, is either non-constructive, lacks generality, or has unspecified attracting equilibria. More specifically, We construct a parameterized family of gradient-like neural networks with a simple feedback rule which will generate equilibrium points with a set of unstable manifolds of specified dimension. Strict Lyapunov functions and nested periodic orbits are obtained for these systems and used as a method of synthesis to generate a large family of systems with the same local dynamics. This work is applied to show how one can interpolate finite sets of data, on nested periodic orbits.

Shear effects on the properties and separation characteristics of whey protein precipitates

Selective isoelectric whey protein precipitation and aggregation is carried out at laboratory scale in a standard configuration batch agitation vessel. Geometric scale-up of this operation is implemented on the basis of constant impeller power input per unit volume and subsequent clarification is achieved by high speed disc-stack centrifugation. Particle size and fractal geometry are important in achieving efficient separation while aggregates need to be strong enough to resist the more extreme levels of shear that are encountered during processing, for example through pumps, valves and at the centrifuge inlet zone. This study investigates how impeller agitation intensity and ageing time affect aggregate size, strength, fractal dimension and hindered settling rate at laboratory scale in order to determine conditions conducive for improved separation. Particle strength is measured by observing the effects of subjecting aggregates to moderate and high levels of process shear in a capillary rig and through a partially open ball-valve respectively. The protein precipitate yield is also investigated with respect to ageing time and impeller agitation intensity. A pilot scale study is undertaken to investigate scale-up and how agitation vessel shear affects centrifugal separation efficiency. Laboratory scale studies show that precipitates subject to higher impeller shear-rates during the addition of the precipitation agent are smaller but more compact than those subject to lower impeller agitation and are better able to resist turbulent breakage. They are thus more likely to provide a better feed for more efficient centrifugal separation. Protein precipitation yield improves significantly with ageing, and 50 minutes of ageing is required to obtain a 70 - 80% yield of α-lactalbumin. Geometric scale-up of the agitation vessel at constant power per unit volume results in aggregates of broadly similar size exhibiting similar trends but with some differences due to the absence of dynamic similarity due to longer circulation time and higher tip speed in the larger vessel. Disc stack centrifuge clarification efficiency curves show aggregates formed at higher shear-rates separate more efficiently, in accordance with laboratory scale projections. Exposure of aggregates to highly turbulent conditions, even for short exposure times, can lead to a large reduction in particle size. Thus, improving separation efficiencies can be achieved by the identification of high shear zones in a centrifugal process and the subsequent elimination or amelioration of such.

Variability in north temperate dung beetle assemblages at different spatial and temporal scales

This study examined the spatial and temporal variability of dung beetle assemblages across a variety of scales e.g. from the between-pad scale (examining the effects of dung size and type) to larger spatial scales encompassing southern Ireland. Dung beetle assemblage structure as sampled by dung pad cohort samples and dung baited pitfall trapping were compared. Generally, the rank order of abundance of dung beetle species was significantly correlated between pitfall catches and cohort pad samples. Across different dung sizes, in both pitfall catches and cohort pad samples, the relative abundance of species was frequently significantly different, but the rank order of abundance of dung beetle was usually significantly correlated. Considerable variations in pitfall catches at temporal scales of a few days appeared to be closely related to weather conditions and rotational grazing. However, despite considerable variation in absolute abundances between consecutive days of sampling, assemblage structure typically remained very similar. The relationship between dung pad size and dung beetle colonisation was investigated. In field experiments in which pads of different sizes (0.25 L, 0.5 L, 1.0 L and 1.5 L) were artificially deposited, there was a positive relationship between pad size and both biomass and number of beetles colonising dung pads and pitfall traps. In addition, with one exception, the field experiments indicated a general positive relationship between dung pad size and biomass density (dung beetle biomass per unit dung volume). A laboratory experiment indicated that pat residence times of A. rufipes were significantly correlated with dung pad size. Investigation of naturally-deposited cow dung pads in the field also indicated that both larval numbers and densities were significantly correlated with dung pad size. These results were discussed in the context of theory related to aggregation and coexistence of species, and resource utilisation by organisms in ephemeral, patchy resources. The colonisation by dung beetles of dung types from native herbivores (sheep, horse and cow) was investigated in field experiments. There were significant differences between the dung types in the chemical parameters measured, and there were significant differences in abundances of dung beetles colonising the dung types. Sheep dung was typically the preferred dung type. Data from these field experiments, and from published literature, indicated that dung beetle species can display dung type preferences, in terms of comparisons of both absolute and relative abundances. In addition, data from laboratory experiments indicate that both Aphodius larval production and pat residence times tended to be higher in those dung types which were preferred by adult Aphodius in the colonisation experiments. Data from dung-baited pitfall trapping (from this and another study) at several sites (up to 180 km distant) and over a number of years (between 1991 and 1996) were used to investigate spatial and temporal variation in dung beetle assemblage structure and composition (Aphodius, Sphaeridium and Geotrupes) across a range of scales in southern Ireland. Species richness levels, species composition and rank order of abundances were very similar between the assemblages. The temporal variability between seasons within any year exceeded temporal variability between years. DCA ordinations indicated that there was a similar level of variability between assemblage structure from the between-field (~1km) to regional (~180 km) spatial scales, and between year (6 years) temporal scales. At the biogeographical spatial scale, analysis of data from the literature indicated that there was considerable variability at this scale, largely due to species turnover.

Reasoning about trust, entrepreneurial services, and the virtual team

This Portfolio of Exploration (PoE) tracks a transformative learning developmental journey that is directed at changing meaning making structures and mental models within an innovation practice. The explicit purpose of the Portfolio is to develop new and different perspectives that enable the handling of new and more complex phenomena through self transformation and increased emotional intelligence development. The Portfolio provides a response to the question: ‘What are the key determinants that enable a Virtual Team (VT) to flourish where flourishing means developing and delivering on the firm’s innovative imperatives?’ Furthermore, the PoE is structured as an investigation into how higher order meaning making promotes ‘entrepreneurial services’ within an intra-firm virtual team, with a secondary aim to identify how reasoning about trust influence KGPs to exchange knowledge. I have developed a framework which specifically focuses on the effectiveness of any firms’ Virtual Team (VT) through transforming the meaning making of the VT participants. I hypothesized it is the way KGPs make meaning (reasoning about trust) which differentiates the firm as a growing firm in the sense of Penrosean resources: ‘inducement to expand and a limit of expansion’ (1959). Reasoning about trust is used as a higher order meaning-making concept in line with Kegan’s (1994) conception of complex meaning making, which is the combining of ideas and data in ways that transform meaning and implicates participants to find new ways of knowledge generation. Simply, it is the VT participants who develop higher order meaning making that hold the capabilities to transform the firm from within, providing a unique competitive advantage that enables the firm to grow.

Development and characterization of novel transgenic techniques for the study of neuronal circuitry

Modern neuroscience relies heavily on sophisticated tools that allow us to visualize and manipulate cells with precise spatial and temporal control. Transgenic mouse models, for example, can be used to manipulate cellular activity in order to draw conclusions about the molecular events responsible for the development, maintenance and refinement of healthy and/or diseased neuronal circuits. Although it is fairly well established that circuits respond to activity-dependent competition between neurons, we have yet to understand either the mechanisms underlying these events or the higher-order plasticity that synchronizes entire circuits. In this thesis we aimed to develop and characterize transgenic mouse models that can be used to directly address these outstanding biological questions in different ways. We present SLICK-H, a Cre-expressing mouse line that can achieve drug-inducible, widespread, neuron-specific manipulations in vivo. This model is a clear improvement over existing models because of its particularly strong, widespread, and even distribution pattern that can be tightly controlled in the absence of drug induction. We also present SLICK-V::Ptox, a mouse line that, through expression of the tetanus toxin light chain, allows long-term inhibition of neurotransmission in a small subset (<1%) of fluorescently labeled pyramidal cells. This model, which can be used to study how a silenced cell performs in a wildtype environment, greatly facilitates the in vivo study of activity-dependent competition in the mammalian brain. As an initial application we used this model to show that tetanus toxin-expressing CA1 neurons experience a 15% - 19% decrease in apical dendritic spine density. Finally, we also describe the attempt to create additional Cre-driven mouse lines that would allow conditional alteration of neuronal activity either by hyperpolarization or inhibition of neurotransmission. Overall, the models characterized in this thesis expand upon the wealth of tools available that aim to dissect neuronal circuitry by genetically manipulating neurons in vivo.

Fabrication and characterisation of semiconductor nanowires and metal interconnects

One-dimensional semiconductor nanowires are considered to be promising materials for future nanoelectronic applications. However, before these nanowires can be integrated into such applications, a thorough understanding of their growth behaviour is necessary. In particular, methods that allow the control over nanowire growth are deemed especially important as it is these methods that will enable the control of nanowire dimensions such as length and diameter (high aspect ratios). The production of nanowires with high-aspect ratios is vital in order to take advantage of the unique properties experienced at the nanoscale, thus allowing us to maximise their use in devices. Additionally, the development of low-resistivity interconnects is desirable in order to connect such nanowires in multi-nanowire components. Consequently, this thesis aims to discuss the synthesis and characterisation of germanium (Ge) nanowires and platinum (Pt) interconnects. Particular emphasis is placed on manipulating the nanowire growth kinetics to produce high aspect ratio structures. The discussion of Pt interconnects focuses on the development of low-resistivity devices and the electrical and structural analysis of those devices. Chapter 1 reviews the most critical aspects of Ge nanowire growth which must be understood before they can be integrated into future nanodevices. These features include the synthetic methods employed to grow Ge nanowires, the kinetic and thermodynamic aspects of their growth and nanowire morphology control. Chapter 2 outlines the experimental methods used to synthesise and characterise Ge nanowires as well as the methods used to fabricate and analyse Pt interconnects. Chapter 3 discusses the control of Ge nanowire growth kinetics via the manipulation of the supersaturation of Ge in the Au/Ge binary alloy system. This is accomplished through the use of bi-layer films, which pre-form Au/Ge alloy catalysts before the introduction of the Ge precursor. The growth from these catalysts is then compared with Ge nanowire growth from standard elemental Au seeds. Nanowires grown from pre-formed Au/Ge alloy seeds demonstrate longer lengths and higher growth rates than those grown from standard Au seeds. In-situ TEM heating on the Au/Ge bi-layer films is used to support the growth characteristics observed. Chapter 4 extends the work of chapter 3 by utilising Au/Ag/Ge tri-layer films to enhance the growth rates and lengths of Ge nanowires. These nanowires are grown from Au/Ag/Ge ternary alloy catalysts. Once again, the supersaturation is influenced, only this time it is through the simultaneous manipulation of both the solute concentration and equilibrium concentration of Ge in the Au/Ag/Ge ternary alloy system. The introduction of Ag to the Au/Ge binary alloy lowers the equilibrium concentration, thus increasing the nanowire growth rate and length. Nanowires with uniform diameters were obtained via synthesis from AuxAg1-x alloy nanoparticles. Manifestation of the Gibbs-Thomson effect, resulting from the dependence of the mean nanowire length as a function of diameter, was observed for all of the nanowires grown from the AuxAg1-x nanoparticles. Finally, in-situ TEM heating was used to support the nanowire growth characteristics. Chapter 5 details the fabrication and characterisation of Pt interconnects deposited by electron beam induced deposition of two different precursors. The fabrication is conducted inside a dual beam FIB. The electrical and structural characteristics of interconnects deposited from a standard organometallic precursor and a novel carbon-free precursor are compared. The electrical performance of the carbon-free interconnects is shown to be superior to that of the organometallic devices and this is correlated to the structural composition of both interconnects via in-situ TEM heating and HAADF-STEM analysis. Annealing of the interconnects is carried out under two different atmospheres in order to reduce the electrical resistivity even further. Finally, chapter 6 presents some important conclusions and summarises each of the previous chapters.

Development of inversion-mode and junctionless Indium-Gallium-Arsenide MOSFETs

This PhD covers the development of planar inversion-mode and junctionless Al2O3/In0.53Ga0.47As metal-oxidesemiconductor field-effect transistors (MOSFETs). An implant activation anneal was developed for the formation of the source and drain (S/D) of the inversionmode MOSFET. Fabricated inversion-mode devices were used as test vehicles to investigate the impact of forming gas annealing (FGA) on device performance. Following FGA, the devices exhibited a subthreshold swing (SS) of 150mV/dec., an ION/IOFF of 104 and the transconductance, drive current and peak effective mobility increased by 29%, 25% and 15%, respectively. An alternative technique, based on the fitting of the measured full-gate capacitance vs gate voltage using a selfconsistent Poisson-Schrödinger solver, was developed to extract the trap energy profile across the full In0.53Ga0.47As bandgap and beyond. A multi-frequency inversion-charge pumping approach was proposed to (1) study the traps located at energy levels aligned with the In0.53Ga0.47As conduction band and (2) separate the trapped charge and mobile charge contributions. The analysis revealed an effective mobility (μeff) peaking at ~2850cm2/V.s for an inversion-charge density (Ninv) = 7*1011cm2 and rapidly decreasing to ~600cm2/V.s for Ninv = 1*1013 cm2, consistent with a μeff limited by surface roughness scattering. Atomic force microscopy measurements confirmed a large surface roughness of 1.95±0.28nm on the In0.53Ga0.47As channel caused by the S/D activation anneal. In order to circumvent the issue relative to S/D formation, a junctionless In0.53Ga0.47As device was developed. A digital etch was used to thin the In0.53Ga0.47As channel and investigate the impact of channel thickness (tInGaAs) on device performance. Scaling of the SS with tInGaAs was observed for tInGaAs going from 24 to 16nm, yielding a SS of 115mV/dec. for tInGaAs = 16nm. Flat-band μeff values of 2130 and 1975cm2/V.s were extracted on devices with tInGaAs of 24 and 20nm, respectively

Nonlinear piezoelectricity in electroelastic energy harvesters: Modeling and experimental identification

We propose and experimentally validate a first-principles based model for the nonlinear piezoelectric response of an electroelastic energy harvester. The analysis herein highlights the importance of modeling inherent piezoelectric nonlinearities that are not limited to higher order elastic effects but also include nonlinear coupling to a power harvesting circuit. Furthermore, a nonlinear damping mechanism is shown to accurately restrict the amplitude and bandwidth of the frequency response. The linear piezoelectric modeling framework widely accepted for theoretical investigations is demonstrated to be a weak presumption for near-resonant excitation amplitudes as low as 0.5 g in a prefabricated bimorph whose oscillation amplitudes remain geometrically linear for the full range of experimental tests performed (never exceeding 0.25% of the cantilever overhang length). Nonlinear coefficients are identified via a nonlinear least-squares optimization algorithm that utilizes an approximate analytic solution obtained by the method of harmonic balance. For lead zirconate titanate (PZT-5H), we obtained a fourth order elastic tensor component of c1111p =-3.6673× 1017 N/m2 and a fourth order electroelastic tensor value of e3111 =1.7212× 108 m/V. © 2010 American Institute of Physics.

Cysteine proteinase-1 and cut protein isoform control dendritic innervation of two distinct sensory fields by a single neuron.

Dendrites often exhibit structural changes in response to local inputs. Although mechanisms that pattern and maintain dendritic arbors are becoming clearer, processes regulating regrowth, during context-dependent plasticity or after injury, remain poorly understood. We found that a class of Drosophila sensory neurons, through complete pruning and regeneration, can elaborate two distinct dendritic trees, innervating independent sensory fields. An expression screen identified Cysteine proteinase-1 (Cp1) as a critical regulator of this process. Unlike known ecdysone effectors, Cp1-mutant ddaC neurons pruned larval dendrites normally but failed to regrow adult dendrites. Cp1 expression was upregulated/concentrated in the nucleus during metamorphosis, controlling production of a truncated Cut homeodomain transcription factor. This truncated Cut, but not the full-length protein, allowed Cp1-mutant ddaC neurons to regenerate higher-order adult dendrites. These results identify a molecular pathway needed for dendrite regrowth after pruning, which allows the same neuron to innervate distinct sensory fields.

The past, present, and future of human centromere genomics.

The centromere is the chromosomal locus essential for chromosome inheritance and genome stability. Human centromeres are located at repetitive alpha satellite DNA arrays that compose approximately 5% of the genome. Contiguous alpha satellite DNA sequence is absent from the assembled reference genome, limiting current understanding of centromere organization and function. Here, we review the progress in centromere genomics spanning the discovery of the sequence to its molecular characterization and the work done during the Human Genome Project era to elucidate alpha satellite structure and sequence variation. We discuss exciting recent advances in alpha satellite sequence assembly that have provided important insight into the abundance and complex organization of this sequence on human chromosomes. In light of these new findings, we offer perspectives for future studies of human centromere assembly and function.

Creating a suitable and successful solution for the integration of podcasting and vidcasting in a higher education e-learning environment

A small research project is currently taking place within a department of the University of Greenwich. The project involves using current technology (Apple’s xServe, iPhones, iPod touch, Podcast Producer application and some 3rd party capture software) with the intention to provide a solution for quick and simple podcasting. This paper also aims to investigate the use of podcasting to help promote and extend the e-learning provision within the school. In short this project aims to justify the use of podcasting as a teaching and learning tool to help enhance student learning while identifying the most appropriate manner to integrate podcasting within an e-learning environment.

Estimation of atmospheric nutrient inputs to the Atlantic Ocean from 50°N to 50°S based on large-scale field sampling: Iron and other dust-associated elements

Atmospheric inputs of mineral dust supply iron and other trace metals to the remote ocean and can influence the marine carbon cycle due to iron's role as a potentially limiting micronutrient. Dust generation, transport, and deposition are highly heterogeneous, and there are very few remote marine locations where dust concentrations and chemistry (e.g., iron solubility) are routinely monitored. Here we use aerosol and rainwater samples collected during 10 large-scale research cruises to estimate the atmospheric input of iron, aluminum, and manganese to four broad regions of the Atlantic Ocean over two 3 month periods for the years 2001–2005. We estimate total inputs of these metals to our study regions to be 4.2, 17, and 0.27 Gmol in April–June and 4.9, 14, and 0.19 Gmol in September–November, respectively. Inputs were highest in regions of high rainfall (the intertropical convergence zone and South Atlantic storm track), and rainfall contributed higher proportions of total input to wetter regions. By combining input estimates for total and soluble metals for these time periods, we calculated overall percentage solubilities for each metal that account for the contributions from both wet and dry depositions and the relative contributions from different aerosol types. Calculated solubilities were in the range 2.4%–9.1% for iron, 6.1%–15% for aluminum, and 54%–73% for manganese. We discuss sources of uncertainty in our estimates and compare our results to some recent estimates of atmospheric iron input to the Atlantic.

Shark personalities? Repeatability of social network traits in a widely distributed predatory fish. Behavioral Ecology and Sociobiology, 68, 1995-2003.

Interest in animal personalities has generated a burgeoning literature on repeatability in individual traits such as boldness or exploration through time or across different contexts. Yet, repeatability can be influenced by the interactive social strategies of individuals, for example, consistent inter-individual variation in aggression is well documented. Previous work has largely focused on the social aspects of repeatability in animal behaviour by testing individuals in dyadic pairings. Under natural conditions, individuals interact in a heterogeneous polyadic network. However, the extent to which there is repeatability of social traits at this higher order network level remains unknown. Here, we provide the first empirical evidence of consistent and repeatable animal social networks. Using a model species of shark, a taxonomic group in which repeatability in behaviour has yet to be described, we repeatedly quantified the social networks of ten independent shark groups across different habitats, testing repeatability in individual network position under changing environments. To understand better the mechanisms behind repeatable social behaviour, we also explored the coupling between individual preferences for specific group sizes and social network position. We quantify repeatability in sharks by demonstrating that despite changes in aggregation measured at the group level, the social network position of individuals is consistent across treatments. Group size preferences were found to influence the social network position of individuals in small groups but less so for larger groups suggesting network structure, and thus, repeatability was driven by social preference over aggregation tendency.

Comparison of mass transfer effects in the heterogeneously catalysed hydrogenation of phenyl acetylene in heptane and an ionic liquid

The selective heterogeneous catalytic reduction of phenyl acetylene to styrene over palladium supported on calcium carbonate is reported in both an ionic liquid and a molecular solvent. By using a rotating disc reactor in conjunction with results from a stirred tank reactor it is possible, for the first time, to disentangle the mass transfer contributions in the ionic liquid system. For both heptane and 1-butyl-3-methyl imidazolium bis{(trifluoromethyl)sulfonyl}imide, the reaction in the rotating disc reactor is dominated by reaction in the entrained film on the disc compared with very limited reaction in the bulk liquid. The lower reaction rate obtained in the ionic liquid compared with the organic solvent is shown to be due to the slow transport of the hydrogen dissolved in the liquid. It is clear from the results presented herein that, although the hydrodynamics of similar reactors used for biological treatment of wastewater are well understood, on using a more viscous fluid and higher rotation speeds necessary for fine chemical catalysis these simple relationships breakdown.