ATPase cycle and DNA unwinding kinetics of RecG helicase

The superfamily 2 bacterial helicase, RecG, is a monomeric enzyme with a role in DNA repair by reversing stalled replication forks. The helicase must act specifically and rapidly to prevent replication fork collapse. We have shown that RecG binds tightly and rapidly to four-strand oligonucleotide junctions, which mimic a stalled replication fork. The helicase unwinds such DNA junctions with a step-size of approximately four bases per ATP hydrolyzed. To gain an insight into this mechanism, we used fluorescent stopped-flow and quenched-flow to measure individual steps within the ATPase cycle of RecG, when bound to a DNA junction. The fluorescent ATP analogue, mantATP, was used throughout to determine the rate limiting steps, effects due to DNA and the main states in the cycle. Measurements, when possible, were also performed with unlabeled ATP to confirm the mechanism. The data show that the chemical step of hydrolysis is the rate limiting step in the cycle and that this step is greatly accelerated by bound DNA. The ADP release rate is similar to the cleavage rate, so that bound ATP and ADP would be the main states during the ATP cycle. Evidence is provided that the main structural rearrangements, which bring about DNA unwinding, are linked to these states

Adaptation to implied tilt: extensive spatial extrapolation of orientation gradients

To extract the global structure of an image, the visual system must integrate local orientation estimates across space. Progress is being made toward understanding this integration process, but very little is known about whether the presence of structure exerts a reciprocal influence on local orientation coding. We have previously shown that adaptation to patterns containing circular or radial structure induces tilt-aftereffects (TAEs), even in locations where the adapting pattern was occluded. These spatially “remote” TAEs have novel tuning properties and behave in a manner consistent with adaptation to the local orientation implied by the circular structure (but not physically present) at a given test location. Here, by manipulating the spatial distribution of local elements in noisy circular textures, we demonstrate that remote TAEs are driven by the extrapolation of orientation structure over remarkably large regions of visual space (more than 20°). We further show that these effects are not specific to adapting stimuli with polar orientation structure, but require a gradient of orientation change across space. Our results suggest that mechanisms of visual adaptation exploit orientation gradients to predict the local pattern content of unfilled regions of space

Gloucester Marine Station: Future Development Feasibility Study

The study commenced in July 2009 with historical research about the site and its context, site analysis, including the existing conditions and development regulations. This analysis included: topography, soils, vegetation, structures, utilities, easements, property deed, and city, state, and federal regulations. From this analysis an assessment of future development potentials was made based on the existing data/documents from UMass files, public records, Mass GIS data, site visits, and interviews with Gloucester, Commonwealth of Massachusetts, and other officials and stakeholders. From the assessment we identified potential future uses, building locations, and feasible alternative layouts of the site. These alternatives were summarily analyzed to support continuing discussions among committed and potential partners regarding shared space and facilities, development costs and timing of future needs

MIRACLE: MIcRo-ArChitectural Leakage Evaluation

In this paper, we describe an extensible experimental infrastructure for evaluating the micro-architectural leakage, based on power consumption, that stems from a physical device. Building on existing literature, we use it to systematically study 14 different devices, which span 4 different instruction set architectures and 4 different vendors. The study allows a characterisation of each device with respect to any leakage effects stemming from sources within the micro-architectural implementation. We use it, for example, to identify and document several novel leakage effects (e.g., due to speculative instruction execution), and scenarios where an assumption about leakage is non-portable between different yet compatible devices. Ours is the widest study of its kind we are aware of, and highlights a range of challenges with respect to 1) the design, implementation, and evaluation of, e.g., masking schemes, 2) construction of accurate leakage models, and 3) selection of suitable devices for experimental research. For example, in relation to 1), we cast further doubt on whether a given device upholds the assumptions required by a given masking scheme; in relation to 2), we conclude that (statistical or formal) device leakage models must include information about the micro-architecture being modelled; in relation to 3), we claim the near mono-culture of devices that dominates existing literature is insufficient to support general claims regarding leakage. This is particularly important in the context of the FIPS 140-3 standard for non-invasive side-channel evaluation

Visual motion integration is mediated by directional ambiguities in local motion signals

The output of primary visual cortex (V1) is a piecemeal representation of the visual scene and the response of any one cell cannot unambiguously guide sensorimotor behavior. It remains unsolved how subsequent stages of cortical processing combine (“pool”) these early visual signals into a coherent representation. We (Webb et al., 2007, 2011) have shown that responses of human observers on a pooling task employing broadband, random dot motion can be accurately predicted by decoding the maximum likelihood direction from a population of motion-sensitive neurons. Whereas Amano et al. (2009) found that the vector average velocity of arrays of narrowband, two-dimensional (2-d) plaids predicts perceived global motion. To reconcile these different results, we designed two experiments in which we used 2-d noise textures moving behind spatially distributed apertures and measured the point of subjective equality between pairs of global noise textures. Textures in the standard stimulus moved rigidly in the same direction, whereas their directions in the comparison stimulus were sampled from a set of probability distributions. Human observers judged which noise texture had a more clockwise (CW) global direction. In agreement with Amano and colleagues, observers' perceived global motion coincided with the vector average stimulus direction. To test if directional ambiguities in local motion signals governed perceived global direction, we manipulated the fidelity of the texture motion within each aperture. A proportion of the apertures contained texture that underwent rigid translation and the remainder contained dynamic (temporally uncorrelated) noise to create locally ambiguous motion. Perceived global motion matched the vector average when the majority of apertures contained rigid motion, but with increasing levels of dynamic noise shifted toward the maximum likelihood direction. A class of population decoders utilizing power-law non-linearities can accommodate this flexible pooling

Criterion-free measurement of motion transparency perception at different speeds

Transparency perception often occurs when objects within the visual scene partially occlude each other or move at the same time, at different velocities across the same spatial region. Although transparent motion perception has been extensively studied, we still do not understand how the distribution of velocities within a visual scene contribute to transparent perception. Here we use a novel psychophysical procedure to characterize the distribution of velocities in a scene that give rise to transparent motion perception. To prevent participants from adopting a subjective decision criterion when discriminating transparent motion, we used an ‘‘oddone-out,’’ three alternative forced-choice procedure. Two intervals contained the standard—a random-dotkinematogram with dot speeds or directions sampled from a uniform distribution. The other interval contained the comparison—speeds or directions sampled from a distribution with the same range as the standard, but with a notch of different widths removed. Our results suggest that transparent motion perception is driven primarily by relatively slow speeds, and does not emerge when only very fast speeds are present within a visual scene. Transparent perception of moving surfaces is modulated by stimulus-based characteristics, such as the separation between the means of the overlapping distributions or the range of speeds presented within an image. Our work illustrates the utility of using objective, forced-choice methods to reveal the mechanisms underlying motion transparency perception