Orientational Harmonic Model for Rotation, Translation, and Scale Invariant Pattern Representation in Biological Vision

An extension to the orientational harmonic model is presented as a rotation, translation, and scale invariant representation of geometrical form in biological vision.

Orientational Harmonic Model for Rotation, Translation, and Scale Invariant Pattern Representation in Biological Vision

The proposed model, called the combinatorial and competitive spatio-temporal memory or CCSTM, provides an elegant solution to the general problem of having to store and recall spatio-temporal patterns in which states or sequences of states can recur in various contexts. For example, fig. 1 shows two state sequences that have a common subsequence, C and D. The CCSTM assumes that any state has a distributed representation as a collection of features. Each feature has an associated competitive module (CM) containing K cells. On any given occurrence of a particular feature, A, exactly one of the cells in CMA will be chosen to represent it. It is the particular set of cells active on the previous time step that determines which cells are chosen to represent instances of their associated features on the current time step. If we assume that typically S features are active in any state then any state has K^S different neural representations. This huge space of possible neural representations of any state is what underlies the model's ability to store and recall numerous context-sensitive state sequences. The purpose of this paper is simply to describe this mechanism.

Laminar Cortical Dynamics of Visual Form and Motion Interactions During Coherent Object Motion Perception

How do visual form and motion processes cooperate to compute object motion when each process separately is insufficient? Consider, for example, a deer moving behind a bush. Here the partially occluded fragments of motion signals available to an observer must be coherently grouped into the motion of a single object. A 3D FORMOTION model comprises five important functional interactions involving the brain’s form and motion systems that address such situations. Because the model’s stages are analogous to areas of the primate visual system, we refer to the stages by corresponding anatomical names. In one of these functional interactions, 3D boundary representations, in which figures are separated from their backgrounds, are formed in cortical area V2. These depth-selective V2 boundaries select motion signals at the appropriate depths in MT via V2-to-MT signals. In another, motion signals in MT disambiguate locally incomplete or ambiguous boundary signals in V2 via MT-to-V1-to-V2 feedback. The third functional property concerns resolution of the aperture problem along straight moving contours by propagating the influence of unambiguous motion signals generated at contour terminators or corners. Here, sparse “feature tracking signals” from, e.g., line ends, are amplified to overwhelm numerically superior ambiguous motion signals along line segment interiors. In the fourth, a spatially anisotropic motion grouping process takes place across perceptual space via MT-MST feedback to integrate veridical feature-tracking and ambiguous motion signals to determine a global object motion percept. The fifth property uses the MT-MST feedback loop to convey an attentional priming signal from higher brain areas back to V1 and V2. The model's use of mechanisms such as divisive normalization, endstopping, cross-orientation inhibition, and longrange cooperation is described. Simulated data include: the degree of motion coherence of rotating shapes observed through apertures, the coherent vs. element motion percepts separated in depth during the chopsticks illusion, and the rigid vs. non-rigid appearance of rotating ellipses.

The Perception of Globally Coherent Motion

How do human observers perceive a coherent pattern of motion from a disparate set of local motion measures? Our research has examined how ambiguous motion signals along straight contours are spatially integrated to obtain a globally coherent perception of motion. Observers viewed displays containing a large number of apertures, with each aperture containing one or more contours whose orientations and velocities could be independently specified. The total pattern of the contour trajectories across the individual apertures was manipulated to produce globally coherent motions, such as rotations, expansions, or translations. For displays containing only straight contours extending to the circumferences of the apertures, observers' reports of global motion direction were biased whenever the sampling of contour orientations was asymmetric relative to the direction of motion. Performance was improved by the presence of identifiable features, such as line ends or crossings, whose trajectories could be tracked over time. The reports of our observers were consistent with a pooling process involving a vector average of measures of the component of velocity normal to contour orientation, rather than with the predictions of the intersection-of-constraints analysis in velocity space.

Coherent wavelength division multiplexing: a novel transmission format for high spectral density optical communication networks

In this thesis a novel transmission format, named Coherent Wavelength Division Multiplexing (CoWDM) for use in high information spectral density optical communication networks is proposed and studied. In chapter I a historical view of fibre optic communication systems as well as an overview of state of the art technology is presented to provide an introduction to the subject area. We see that, in general the aim of modern optical communication system designers is to provide high bandwidth services while reducing the overall cost per transmitted bit of information. In the remainder of the thesis a range of investigations, both of a theoretical and experimental nature are carried out using the CoWDM transmission format. These investigations are designed to consider features of CoWDM such as its dispersion tolerance, compatibility with forward error correction and suitability for use in currently installed long haul networks amongst others. A high bit rate optical test bed constructed at the Tyndall National Institute facilitated most of the experimental work outlined in this thesis and a collaboration with France Telecom enabled long haul transmission experiments using the CoWDM format to be carried out. An amount of research was also carried out on ancillary topics such as optical comb generation, forward error correction and phase stabilisation techniques. The aim of these investigations is to verify the suitability of CoWDM as a cost effective solution for use in both current and future high bit rate optical communication networks

Photonic integrated circuits for the generation of coherent optical signals

The demand for optical bandwidth continues to increase year on year and is being driven primarily by entertainment services and video streaming to the home. Current photonic systems are coping with this demand by increasing data rates through faster modulation techniques, spectrally efficient transmission systems and by increasing the number of modulated optical channels per fibre strand. Such photonic systems are large and power hungry due to the high number of discrete components required in their operation. Photonic integration offers excellent potential for combining otherwise discrete system components together on a single device to provide robust, power efficient and cost effective solutions. In particular, the design of optical modulators has been an area of immense interest in recent times. Not only has research been aimed at developing modulators with faster data rates, but there has also a push towards making modulators as compact as possible. Mach-Zehnder modulators (MZM) have proven to be highly successful in many optical communication applications. However, due to the relatively weak electro-optic effect on which they are based, they remain large with typical device lengths of 4 to 7 mm while requiring a travelling wave structure for high-speed operation. Nested MZMs have been extensively used in the generation of advanced modulation formats, where multi-symbol transmission can be used to increase data rates at a given modulation frequency. Such nested structures have high losses and require both complex fabrication and packaging. In recent times, it has been shown that Electro-absorption modulators (EAMs) can be used in a specific arrangement to generate Quadrature Phase Shift Keying (QPSK) modulation. EAM based QPSK modulators have increased potential for integration and can be made significantly more compact than MZM based modulators. Such modulator designs suffer from losses in excess of 40 dB, which limits their use in practical applications. The work in this thesis has focused on how these losses can be reduced by using photonic integration. In particular, the integration of multiple lasers with the modulator structure was considered as an excellent means of reducing fibre coupling losses while maximising the optical power on chip. A significant difficultly when using multiple integrated lasers in such an arrangement was to ensure coherence between the integrated lasers. The work investigated in this thesis demonstrates for the first time how optical injection locking between discrete lasers on a single photonic integrated circuit (PIC) can be used in the generation of coherent optical signals. This was done by first considering the monolithic integration of lasers and optical couplers to form an on chip optical power splitter, before then examining the behaviour of a mutually coupled system of integrated lasers. By operating the system in a highly asymmetric coupling regime, a stable phase locking region was found between the integrated lasers. It was then shown that in this stable phase locked region the optical outputs of each laser were coherent with each other and phase locked to a common master laser.

Photonic integrated circuit for the manipulation of coherent optical combs

Photonic integration has become an important research topic in research for applications in the telecommunications industry. Current optical internet infrastructure has reached capacity with current generation dense wavelength division multiplexing (DWDM) systems fully occupying the low absorption region of optical fibre from 1530 nm to 1625 nm (the C and L bands). This is both due to an increase in the number of users worldwide and existing users demanding more bandwidth. Therefore, current research is focussed on using the available telecommunication spectrum more efficiently. To this end, coherent communication systems are being developed. Advanced coherent modulation schemes can be quite complex in terms of the number and array of devices required for implementation. In order to make these systems viable both logistically and commercially, photonic integration is required. In traditional DWDM systems, arrayed waveguide gratings (AWG) are used to both multiplex and demultiplex the multi-wavelength signal involved. AWGs are used widely as they allow filtering of the many DWDM wavelengths simultaneously. However, when moving to coherent telecommunication systems such as coherent optical frequency division multiplexing (OFDM) smaller FSR ranges are required from the AWG. This increases the size of the device which is counter to the miniaturisation which integration is trying to achieve. Much work was done with active filters during the 1980s. This involved using a laser device (usually below threshold) to allow selective wavelength filtering of input signals. By using more complicated cavity geometry devices such as distributed feedback (DFB) and sampled grating distributed Bragg gratings (SG-DBR) narrowband filtering is achievable with high suppression (>30 dB) of spurious wavelengths. The active nature of the devices also means that, through carrier injection, the index can be altered resulting in tunability of the filter. Used above threshold, active filters become useful in filtering coherent combs. Through injection locking, the coherence of the filtered wavelengths with the original comb source is retained. This gives active filters potential application in coherent communication system as demultiplexers. This work will focus on the use of slotted Fabry-Pérot (SFP) semiconductor lasers as active filters. Experiments were carried out to ensure that SFP lasers were useful as tunable active filters. In all experiments in this work the SFP lasers were operated above threshold and so injection locking was the mechanic by which the filters operated. Performance of the lasers under injection locking was examined using both single wavelength and coherent comb injection. In another experiment two discrete SFP lasers were used simultaneously to demultiplex a two-line coherent comb. The relative coherence of the comb lines was retained after demultiplexing. After showing that SFP lasers could be used to successfully demultiplex coherent combs a photonic integrated circuit was designed and fabricated. This involved monolithic integration of a MMI power splitter with an array of single facet SFP lasers. This device was tested much in the same way as the discrete devices. The integrated device was used to successfully demultiplex a two line coherent comb signal whilst retaining the relative coherence between the filtered comb lines. A series of modelling systems were then employed in order to understand the resonance characteristics of the fabricated devices, and to understand their performance under injection locking. Using this information, alterations to the SFP laser designs were made which were theoretically shown to provide improved performance and suitability for use in filtering coherent comb signals.

Infrared spectra of C2H2 under jet-cooled and para-H2 matrix conditions

In spectra of jet-cooled C2H2 recorded with an FTIR spectrometer, the ν5, ν4 + ν5, ν3 and ν2 + ν4 + ν5 bands all exhibit an intensity distribution corresponding to ∼6 K for rotation, with no evidence of nuclear spin conversion. Spectra of C2H2 isolated in solid p-H2 show no evidence of rotation of C2H2. The strong interaction between ν3 and ν2 + ν4 + ν5 in the gas phase is diminished in solid p-H2. Lines associated with dimer, trimer and tetramer of C2H2 are identified. Spectral features characteristic of solid state acetylene are observed under jet-cooled conditions. © 2007 Elsevier B.V. All rights reserved.

Nuclear ingredients for cross section calculation of exotic nuclei

The increasing need for cross sections far from the valley of stability, especially for applications such as nuclear astrophysics, poses a challenge for nuclear reaction models. So far, predictions of cross sections have relied on more or less phenomenological approaches, depending on parameters adjusted to available experimental data or deduced from systematic relations. While such predictions are expected to be reliable for nuclei not too far from the experimentally known regions, it is clearly preferable to use more fundamental approaches, based on sound physical bases, when dealing with very exotic nuclei. Thanks to the high computer power available today, all major ingredients required to model a nuclear reaction can now be (and have been) microscopically (or semi-microscopically) determined starting from the information provided by an effective nucleon-nucleon interaction. All these microscopic ingredients have been included in the latest version of the TALYS nuclear reaction code (http://www.talys.eu/).

Latest development of the combinatorial model of nuclear level densities

The combinatorial model of nuclear level densities has now reached a level of accuracy comparable to that of the best global analytical expressions without suffering from the limits imposed by the statistical hypothesis on which the latter expressions rely. In particular, it provides, naturally, non-Gaussian spin distribution as well as non-equipartition of parities which are known to have an impact on cross section predictions at low energies [1, 2, 3]. Our previous global models developed in Refs. [1, 2] suffered from deficiencies, in particular in the way the collective effects - both vibrational and rotational - were treated. We have recently improved this treatment using simultaneously the single-particle levels and collective properties predicted by a newly derived Gogny interaction [4], therefore enabling a microscopic description of energy-dependent shell, pairing and deformation effects. In addition for deformed nuclei, the transition to sphericity is coherently taken into account on the basis of a temperature-dependent Hartree-Fock calculation which provides at each temperature the structure properties needed to build the level densities. This new method is described and shown to give promising results with respect to available experimental data.

Co-regulation of nuclear respiratory factor-1 by NFkappaB and CREB links LPS-induced inflammation to mitochondrial biogenesis.

The nuclear respiratory factor-1 (NRF1) gene is activated by lipopolysaccharide (LPS), which might reflect TLR4-mediated mitigation of cellular inflammatory damage via initiation of mitochondrial biogenesis. To test this hypothesis, we examined NRF1 promoter regulation by NFκB, and identified interspecies-conserved κB-responsive promoter and intronic elements in the NRF1 locus. In mice, activation of Nrf1 and its downstream target, Tfam, by Escherichia coli was contingent on NFκB, and in LPS-treated hepatocytes, NFκB served as an NRF1 enhancer element in conjunction with NFκB promoter binding. Unexpectedly, optimal NRF1 promoter activity after LPS also required binding by the energy-state-dependent transcription factor CREB. EMSA and ChIP assays confirmed p65 and CREB binding to the NRF1 promoter and p65 binding to intron 1. Functionality for both transcription factors was validated by gene-knockdown studies. LPS regulation of NRF1 led to mtDNA-encoded gene expression and expansion of mtDNA copy number. In cells expressing plasmid constructs containing the NRF-1 promoter and GFP, LPS-dependent reporter activity was abolished by cis-acting κB-element mutations, and nuclear accumulation of NFκB and CREB demonstrated dependence on mitochondrial H(2)O(2). These findings indicate that TLR4-dependent NFκB and CREB activation co-regulate the NRF1 promoter with NFκB intronic enhancement and redox-regulated nuclear translocation, leading to downstream target-gene expression, and identify NRF-1 as an early-phase component of the host antibacterial defenses.

Cytokinesis proteins Tum and Pav have a nuclear role in Wnt regulation.

Wg/Wnt signals specify cell fates in both invertebrate and vertebrate embryos and maintain stem-cell populations in many adult tissues. Deregulation of the Wnt pathway can transform cells to a proliferative fate, leading to cancer. We have discovered that two Drosophila proteins that are crucial for cytokinesis have a second, largely independent, role in restricting activity of the Wnt pathway. The fly homolog of RacGAP1, Tumbleweed (Tum)/RacGAP50C, and its binding partner, the kinesin-like protein Pavarotti (Pav), negatively regulate Wnt activity in fly embryos and in cultured mammalian cells. Unlike many known regulators of the Wnt pathway, these molecules do not affect stabilization of Arm/beta-catenin (betacat), the principal effector molecule in Wnt signal transduction. Rather, they appear to act downstream of betacat stabilization to control target-gene transcription. Both Tum and Pav accumulate in the nuclei of interphase cells, a location that is spatially distinct from their cleavage-furrow localization during cytokinesis. We show that this nuclear localization is essential for their role in Wnt regulation. Thus, we have identified two modulators of the Wnt pathway that have shared functions in cell division, which hints at a possible link between cytokinesis and Wnt activity during tumorigenesis.

Inline holographic coherent anti-Stokes Raman microscopy.

We demonstrate a simple approach for inline holographic coherent anti-Stokes Raman scattering (CARS) microscopy, in which a layer of uniform nonlinear medium is placed in front of a specimen to be imaged. The reference wave created by four-wave mixing in the nonlinear medium can interfere with the CARS signal generated in the specimen to result in an inline hologram. We experimentally and theoretically investigate the inline CARS holography and show that it has chemical selectivity and can allow for three-dimensional imaging.

Delimiting species without nuclear monophyly in Madagascar's mouse lemurs.

BACKGROUND: Speciation begins when populations become genetically separated through a substantial reduction in gene flow, and it is at this point that a genetically cohesive set of populations attain the sole property of species: the independent evolution of a population-level lineage. The comprehensive delimitation of species within biodiversity hotspots, regardless of their level of divergence, is important for understanding the factors that drive the diversification of biota and for identifying them as targets for conservation. However, delimiting recently diverged species is challenging due to insufficient time for the differential evolution of characters--including morphological differences, reproductive isolation, and gene tree monophyly--that are typically used as evidence for separately evolving lineages. METHODOLOGY: In this study, we assembled multiple lines of evidence from the analysis of mtDNA and nDNA sequence data for the delimitation of a high diversity of cryptically diverged population-level mouse lemur lineages across the island of Madagascar. Our study uses a multi-faceted approach that applies phylogenetic, population genetic, and genealogical analysis for recognizing lineage diversity and presents the most thoroughly sampled species delimitation of mouse lemur ever performed. CONCLUSIONS: The resolution of a large number of geographically defined clades in the mtDNA gene tree provides strong initial evidence for recognizing a high diversity of population-level lineages in mouse lemurs. We find additional support for lineage recognition in the striking concordance between mtDNA clades and patterns of nuclear population structure. Lineages identified using these two sources of evidence also exhibit patterns of population divergence according to genealogical exclusivity estimates. Mouse lemur lineage diversity is reflected in both a geographically fine-scaled pattern of population divergence within established and geographically widespread taxa, as well as newly resolved patterns of micro-endemism revealed through expanded field sampling into previously poorly and well-sampled regions.

Nuclear import of Cdk/cyclin complexes: identification of distinct mechanisms for import of Cdk2/cyclin E and Cdc2/cyclin B1.

Reversible phosphorylation of nuclear proteins is required for both DNA replication and entry into mitosis. Consequently, most cyclin-dependent kinase (Cdk)/cyclin complexes are localized to the nucleus when active. Although our understanding of nuclear transport processes has been greatly enhanced by the recent identification of nuclear targeting sequences and soluble nuclear import factors with which they interact, the mechanisms used to target Cdk/cyclin complexes to the nucleus remain obscure; this is in part because these proteins lack obvious nuclear localization sequences. To elucidate the molecular mechanisms responsible for Cdk/cyclin transport, we examined nuclear import of fluorescent Cdk2/cyclin E and Cdc2/cyclin B1 complexes in digitonin-permeabilized mammalian cells and also examined potential physical interactions between these Cdks, cyclins, and soluble import factors. We found that the nuclear import machinery recognizes these Cdk/cyclin complexes through direct interactions with the cyclin component. Surprisingly, cyclins E and B1 are imported into nuclei via distinct mechanisms. Cyclin E behaves like a classical basic nuclear localization sequence-containing protein, binding to the alpha adaptor subunit of the importin-alpha/beta heterodimer. In contrast, cyclin B1 is imported via a direct interaction with a site in the NH2 terminus of importin-beta that is distinct from that used to bind importin-alpha.