Alignment of cryo-EM movies of individual particles by optimization of image translations

Direct detector device (DDD) cameras have revolutionized single particle electron cryomicroscopy (cryo-EM). In addition to an improved camera detective quantum efficiency, acquisition of DDD movies allows for correction of movement of the specimen, due both to instabilities in the microscope specimen stage and electron beam-induced movement. Unlike specimen stage drift, beam-induced movement is not always homogeneous within an image. Local correlation in the trajectories of nearby particles suggests that beam-induced motion is due to deformation of the ice layer. Algorithms have already been described that can correct movement for large regions of frames and for > 1 MDa protein particles. Another algorithm allows individual < 1 MDa protein particle trajectories to be estimated, but requires rolling averages to be calculated from frames and fits linear trajectories for particles. Here we describe an algorithm that allows for individual < 1 MDa particle images to be aligned without frame averaging or linear trajectories. The algorithm maximizes the overall correlation of the shifted frames with the sum of the shifted frames. The optimum in this single objective function is found efficiently by making use of analytically calculated derivatives of the function. To smooth estimates of particle trajectories, rapid changes in particle positions between frames are penalized in the objective function and weighted averaging of nearby trajectories ensures local correlation in trajectories. This individual particle motion correction, in combination with weighting of Fourier components to account for increasing radiation damage in later frames, can be used to improve 3-D maps from single particle cryo-EM.Comment: 11 pages, 4 figure

Current Measurements in the York River near the Coleman Bridge

In support of Tidewater Construction Corporation\u27s project to widen the George P. Coleman Bridge, current measurements were conducted in the York River between Gloucester Point and Yorktown, Virginia, along both sides of the bridge. The objective was to sample the currents at approximately 10 feet below the water surface during maximum ebb and flood flow, at enough locations to resolve cross-river variations in the flow field. This objective was well satisfied with multiple surveys conducted during ebb, slack, and flood phases of the tidal flow, each survey providing current data at multiple depths. Significant cross-river variability was documented

Field study of currents at Norfolk Naval Shipyard, Portsmouth, Virginia

As a component of an investigation into biofouling problems near the Norfolk Naval Shipyard, a field study of currents was conducted in the Southern Branch of the Elizabeth River in the vicinity of the shipyard\u27s aircraft carrier slips. The objective of this study was to determine the magnitude and direction of currents in an area encompassing the turning basin adjacent to the slips, and the transitional regions to the north and south where the river tapers from a width of approximately 600 m in the turning basin to its more typical width of 150 m. To the north, the transition is gradual; to the south it is abrupt

A Realistic Critique of Freedom of Contract in Labor Law Negotiations: Creating More Optimal and Just Outcomes

This Note initially discusses fundamental problems created by the “freedom of contract” principle that arise in an era where the imbalance of both wealth and political power are at their highest rates seen in years. This Note also discusses the principles at work in current labor law: (1) how it is influenced by neoclassical economics and, (2) how, in the alternative, both the related legal doctrine and practice of collective bargaining can improve by incorporating behavioral economics, neuroeconomics, and game theory. Labor law practitioners and shapers should recognize neoclassical economics’ shortcomings and adopt a more efficient contractual process that leads to more just and efficient outcomes

Flow convergence and stability at a tidal estuarine front: Acoustic Doppler current observations

Characteristics of the flow field in an estuarine frontal zone have been investigated in a field study in the lower James River estuary. Underway sampling with an acoustic Doppler current profiler (ADCP) on repeated transects across the front provided information on the structure of the flow field near the front and its evolution in time. As this tidal intrusion front advanced up the estuary during the flooding tide, prominent and consistent features in the velocity field included a localized zone of convergent flow beneath the visible surface line and a stratified shear layer just upriver of the front. Within the shear layer between the buoyant surface water and the faster, higher-salinity undercurrent, gradient Richardson number estimates suggest that the flow was at or near the threshold for sheer instability. Another shear-type gradient in the flow field, the across-front variation of the along-front velocity component, strengthened over a sequence of transects, with intensity increasing toward the surface. Tracking of the front was then interrupted when the identifying line of foam and accumulated material on the surface, previously sharp and well defined, broke up and dispersed to such an extent that the visible signature of the front was lost temporarily. A visible frontal expression later reappeared, and propagation upriver continued. Lower bound estimates of downwelling flow in the frontal zone were determined by continuity considerations

The formation of longitudinal fronts in a coastal plain estuary

Longitudinal estuarine fronts, aligned parallel to the axis of the estuary, are characteristic of the York River. Their time scale for genesis and decay is of the order of hours; they are usually located at the inner edge of the shoals or over the main channel. Field measurements have shown marked intratidal differences in density and current speeds across this estuary. These can be correlated with changes in depth and the strength of the advective processes. Differential advection between the channel and shoal regions, when acting upon a constant longitudinal density gradient, is shown to be of sufficient magnitude to generate strong lateral density gradients, and thus fronts, at particular times within the tidal cycle

Chesapeake Bay Land Subsidence and Sea Level Change : an evaluation of past and present trends and future outlook

Ten Chesapeake Bay water level stations presently have a combined total of 647 years of water level measurements with record lengths varying between 35 years (1975-2009) at the Chesapeake Bay Bridge Tunnel, VA, and 107 years (1903-2009) at Baltimore, MD. All ten stations, with the exception of Gloucester Point, VA, are active stations in the National Water Level Observation Network of water level stations maintained by the U.S. National Oceanic and Atmospheric Administration, Center for Operational Oceanographic Products and Services. New technologies such as sea surface range measurements from earth-orbiting satellites now provide a global assessment of absolute sea level (ASL) trends relative to the center of a reference ellipsoid rather than fixed points on the earth’s surface to which relative sea level (RSL) measurements refer. New methodologies have also been applied to derive spatial averages of ASL trends over large regions with greater accuracy. Notwithstanding these advances, there is still no substitute for an accurate time series of water level measurements obtained locally, preferably one spanning several decades, when assessing RSL trends that will affect a specific community or township in the coming decades. RSL trends will determine local inundation risk whether due to vertical land movement (emergence or subsidence) or the ASL trend found as the sum of RSL trend and land movement when both are measured positive upward. In Chesapeake Bay, RSL trends are consistently positive (rising) while land movement is negative (subsiding). By choosing a common time span for the ten bay stations evaluated in this report, we are able to compare differences in RSL rise rates with approximately the same degree of confidence at each station. Uncertainty has been reduced by extracting the decadal signal present at all ten stations before using linear regression to obtain new RSL rise rates with smaller than usual confidence intervals, permitting both temporal and spatial comparisons to be made

Cross-shoreface Suspended Sediment Transport : A Response to the Interaction of Nearshore and Shelf Processes, Fall 1994 Duck, NC Field Experiment

Deployment : The tripods were assembled, tested and secured onboard the RIV Sea Diver, which left the Little Creek Amphibious Base in Norfolk, Virginia early on 26 September. While underway to the deployment site, the continuous surface water conductivity and temperature survey was run and several CTD casts were made. The tripods were deployed on 26 September and secured to the sea floor with sand anchors by VIMS divers. The R/V Sea Diver then began the series of on/off shore transects at the tripod deployment site for approximately 12 hours. The vessel returned to port on 27 September . Recovery: The tripod recovery cruise began late on 21 October and repeated the underway data collection scheme of the September cruise. On October 22 divers removed the sand anchors and the tripods were recovered without incident. The on/off shore transects were repeated and transit to port occurred on 23 October