Numerical simulations are used to consider several problems relevant to the turbulent oceanic bottom boundary layer. In the first study, stratified open channel flow is considered with thermal boundary conditions chosen to approximate a shallow sea. Specifically, a constant heat flux is applied at the free surface and the lower wall is assumed to be adiabatic. When the surface heat flux is strong, turbulent upwellings of low speed fluid from near the lower wall are inhibited by the stable stratification. Subsequent studies consider a stratified bottom Ekman layer over a non-sloping lower wall. The influence of the free surface is removed by using an open boundary condition at the top of the computational domain. Particular attention is paid to the influence of the outer layer stratification on the boundary layer structure. When the density field is initialized with a linear profile, a turbulent mixed layer forms near the wall, which is separated from the outer layer by a strongly stable pycnocline. It is found that the bottom stress is not strongly affected by the outer layer stratification. However, stratification reduces turbulent transport to the outer layer and strongly limits the boundary layer height. The mean shear at the top of the boundary layer is enhanced when the outer layer is stratified, and this shear is strong enough to cause intermittent instabilities above the pycnocline. Turbulence-generated internal gravity waves are observed in the outer layer with a relatively narrow frequency range. An explanation for frequency content of these waves is proposed, starting with an observed broad-banded turbulent spectrum and invoking linear viscous decay to explain the preferential damping of low and high frequency waves. During the course of this work, an open-source computational fluid dynamics code has been developed with a number of advanced features including scalar advection, subgrid-scale models for large -eddy simulation, and distributed memory parallelism

Structural genomics programs and drug discovery efforts that investigate large sets of crystalline samples are placing increased demands on synchrotron beamlines. To facilitate high-throughput work, beamlines 5.0.1, 5.0.2, and 5.0.3 at the ALS have been equipped with robotic arms [Structure (2004) 12:537-545] to transfer cryocooled samples to the goniometer. High-level graphical controls allow the user to conduct experiments with minimal input, while much of the work is performed by underlying software modules. The AutoScreen module rapidly evaluates 96 samples, centering each cryoloop on the beam position by analyzing videomicrographs. Two diffraction snapshots are acquired for each crystal, and then the Lawrence Berkeley Indexing Toolbox (LABELIT) autoindexes the diffraction pattern and determines the Bravais symmetry. LABELIT implements new methods to treat three common failure modes experienced during indexing: 1) non-primitive basis, 2) incorrect beam center, and 3) faulty symmetry. Correcting these problems allows images to be indexed rapidly without the need for interactive visual inspection. An AutoCollect module is now under development to deduce and set the optimal data collection parameters, while an AutoProcess module will reduce the diffraction data in real time and determine the space group. We anticipate that these tools will increase experimental efficiency for both individual users and large-scale efforts alike.

Background

Diet may substantially alter prostate cancer initiation and progression. However, large-scale clinical trials of diet modification have yet to be performed for prostate cancer. The Men's Eating and Living (MEAL) Study (CALGB 70807 [Alliance]) is investigating the effect of increased vegetable consumption on clinical progression in men with localized prostate cancer.

Study design

MEAL is a randomized, phase III clinical trial designed to test whether an intervention that increases vegetable intake will decrease the incidence of clinical progression in men with clinically localized prostate cancer on active surveillance. We are randomizing 464 patients to either a validated telephone-based diet counseling intervention or a control condition in which patients receive a published diet guideline. The intervention will continue for two years. The primary outcome variable is clinical progression defined by serum prostate-specific antigen (PSA) and pathological findings on follow-up prostate biopsy. Secondary outcome variables include incidence of surgical and non-surgical treatments for prostate cancer, prostate-cancer related patient anxiety and health-related quality of life.

Conclusion

The MEAL Study is assessing the effectiveness of a high-vegetable diet intervention for preventing clinical progression in men with localized prostate cancer on active surveillance.