How to Measure Molecular Forces in Cells: A Guide to Evaluating Genetically-Encoded FRET-Based Tension Sensors

The ability of cells to sense and respond to mechanical forces is central to a wide range of biological processes and plays an important role in numerous pathol- ogies. The molecular mechanisms underlying cellular mech- anotransduction, however, have remained largely elusive because suitable methods to investigate subcellular force propagation were missing. Here, we review recent advances in the development of biosensors that allow molecular force measurements. We describe the underlying principle of currently available techniques and propose a strategy to systematically evaluate new Fo ̈ rster resonance energy trans- fer (FRET)-based biosensor

Solving the primitive equations on a spherical geodesic grid: a technical report to a new class of dynamical cores

November 1998.Includes bibliographical references.This report documents the development and testing of a new type of dynamical core. Toe· model uses the invariant form of the primitive equations, solving the vorticity and divergence equations in place of the momentum equation. In the horizontal directions the model is discretized on a geodesic grid which is nearly uniform over the entire globe. In the vertical direction the model can use a variety of coordinate systems, including the generalized sigma coordinate of Suarez et al. (1983) and the Phillips (1957) sigma coordinate. By integrating the vorticity and divergence equations, terms related to gravity wave propagation are isolated and an efficient semi-implicit time stepping scheme is implemented. The model is tested using the idealized forcing proposed by Held and Suarez (1994). Results are presented for a variety of vertical coordinate systems with horizontal resolutions using 2562 polygons (approximately 4.5° x 4.5°) and using 10242 polygons (approximately 2.25° x 2.25° ). The results are compared to standard spectral model simulations truncated at T30 and T63. In terms of averages and variances of state variables, e geodesic grid model results using 2562 polygons are comparable to those of a spectral model truncated at slightly less than TIO, while a simulation with 10242 polygons is comparable to a spectral model simulation truncated at slightly less than T63. In terms of computational efficiency, further development of this geodesic grid model is required. Model timings completed on an SGI Origin 2000 indicate that the geodesic grid model with 10242 polygons is 2.7 times slower than the spectral model truncated at T63. At these resolutions, the MFlop rate of the geodesic grid model is 15% faster than the spectral model, so the differences in model speed are due to differences in the number of floating point operations required per day of simulation. The geodesic grid model is more competitive at higher resolution than at lower resolution, so further optimization and future trends toward higher resolution should benefit the geodesic grid model.Sponsored by the U.S. Department of Energy DE-FG03-98ER62611 and DE-FG03-94ER61929

Impairing the useful field of view in natural scenes: Tunnel vision versus general interference

Citation: Ringer, R. V., Throneburg, Z., Johnson, A. P., Kramer, A. F., & Loschky, L. C. (2016). Impairing the useful field of view in natural scenes: Tunnel vision versus general interference. Journal of Vision, 16(2), 25. doi:10.1167/16.2.7A fundamental issue in visual attention is the relationship between the useful field of view (UFOV), the region of visual space where information is encoded within a single fixation, and eccentricity. A common assumption is that impairing attentional resources reduces the size of the UFOV (i. e., tunnel vision). However, most research has not accounted for eccentricity-dependent changes in spatial resolution, potentially conflating fixed visual properties with flexible changes in visual attention. Williams (1988, 1989) argued that foveal loads are necessary to reduce the size of the UFOV, producing tunnel vision. Without a foveal load, it is argued that the attentional decrement is constant across the visual field (i. e., general interference). However, other research asserts that auditory working memory (WM) loads produce tunnel vision. To date, foveal versus auditory WM loads have not been compared to determine if they differentially change the size of the UFOV. In two experiments, we tested the effects of a foveal (rotated L vs. T discrimination) task and an auditory WM (N-back) task on an extrafoveal (Gabor) discrimination task. Gabor patches were scaled for size and processing time to produce equal performance across the visual field under single-task conditions, thus removing the confound of eccentricity-dependent differences in visual sensitivity. The results showed that although both foveal and auditory loads reduced Gabor orientation sensitivity, only the foveal load interacted with retinal eccentricity to produce tunnel vision, clearly demonstrating task-specific changes to the form of the UFOV. This has theoretical implications for understanding the UFOV

Effect of pre-straining and bake hardening on the microstructure and mechanical properties of CMnSi trip steels

The effects of pre-straining and bake hardening on the mechanical behaviour and microstructural changes were studied in two CMnSi TRansformation-Induced Plasticity (TRIP) steels with different microstructures after intercritical annealing. The TRIP steels before and after pre-straining and bake hardening were characterised by X-ray diffraction, optical microscopy, transmission electron microscopy, three dimensional atom probe and tensile tests. Both steels exhibited discontinuous yielding behaviour and a significant strength increase with some reduction in ductility after pre-straining and bake hardening treatment. The following main microstructural changes are responsible for the observed mechanical behaviours: a decrease in the volume fraction of retained austenite, an increase in the dislocation density and the formation of cell substructure in the polygonal ferrite, higher localized dislocation density in the polygonal ferrite regions adjacent to martensite or retained austenite, and the precipitation of fine iron carbides in bainite and martensite. The mechanism for the observed yield point phenomenon in both steels after treatment was analysed.<br /

Embracing Uncertainty in "Small Data" Problems: Estimating Earthquakes from Historical Anecdotes

We apply the Bayesian inversion process to make principled estimates of the magnitude and location of a pre-instrumental earthquake in Eastern Indonesia in the mid 19th century, by combining anecdotal historical accounts of the resultant tsunami with our modern understanding of the geology of the region. Quantifying the seismic record prior to modern instrumentation is critical to a more thorough understanding of the current risks in Eastern Indonesia. In particular, the occurrence of such a major earthquake in the 1850s provides evidence that this region is susceptible to future seismic hazards on the same order of magnitude. More importantly, the approach taken here gives evidence that even "small data" that is limited in scope and extremely uncertain can still be used to yield information on past seismic events, which is key to an increased understanding of the current seismic state. Moreover, sensitivity bounds indicate that the results obtained here are robust despite the inherent uncertainty in the observations