Measurement of turbulence spectra using scanning pulsed wind lidars

Turbulent velocity spectra, as measured by a scanning pulsed wind lidar (WindCube), are analyzed. The relationship between ordinary velocity spectra and lidar derived spectra is mathematically very complex, and deployment of the three-dimensional spectral velocity tensor is necessary. The resulting scanning lidar spectra depend on beam angles, line-of-sight averaging, sampling rate, and the full three-dimensional structure of the turbulence being measured, in a convoluted way. The model captures the attenuation and redistribution of the spectral energy at high and low wave numbers very well. The model and measured spectra are in good agreement at two analyzed heights for the u and w components of the velocity field. An interference phenomenon is observed, both in the model and the measurements, when the diameter of the scanning circle divided by the mean wind speed is a multiple of the time between the beam measurements. For the v spectrum, the model and the measurements agree well at both heights, except at very low wave numbers, k1 < 0.005 m?1. In this region, where the spectral tensor model has not been verified, the model overestimates the spectral energy measured by the lidar. The theoretical understanding of the shape of turbulent velocity spectra measured by scanning pulsed wind lidar is given a firm foundation.Aerodynamics, Wind Energy, Flight Performance and PropulsionAerospace Engineerin

Transition phenomena in unstably stratified turbulent flows

We study experimentally and theoretically transition phenomena caused by the external forcing from Rayleigh-Benard convection with the large-scale circulation (LSC) to the limiting regime of unstably stratified turbulent flow without LSC whereby the temperature field behaves like a passive scalar. In the experiments we use the Rayleigh-B\'enard apparatus with an additional source of turbulence produced by two oscillating grids located nearby the side walls of the chamber. When the frequency of the grid oscillations is larger than 2 Hz, the large-scale circulation (LSC) in turbulent convection is destroyed, and the destruction of the LSC is accompanied by a strong change of the mean temperature distribution. However, in all regimes of the unstably stratified turbulent flow the ratio $\big[(\ell_x \nabla_x T)^2 + (\ell_y \nabla_y T)^2 + (\ell_z \nabla_z T)^2\big] /$ varies slightly (even in the range of parameters whereby the behaviour of the temperature field is different from that of the passive scalar). Here $\ell_i$ are the integral scales of turbulence along x, y, z directions, T and \theta are the mean and fluctuating parts of the fluid temperature. At all frequencies of the grid oscillations we have detected the long-term nonlinear oscillations of the mean temperature. The theoretical predictions based on the budget equations for turbulent kinetic energy, turbulent temperature fluctuations and turbulent heat flux, are in agreement with the experimental results.Comment: 14 pages, 14 figures, REVTEX4-1, revised versio

GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs

Transcriptional cis-regulatory control regions frequently are found within non-coding DNA segments conserved across multi-species gene orthologs. Adopting a systematic gene-centric pipeline approach, we report here the development of a web-accessible database resource—GenomeTraFac ()—that allows genome-wide detection and characterization of compositionally similar cis-clusters that occur in gene orthologs between any two genomes for both microRNA genes as well as conventional RNA-encoding genes. Each ortholog gene pair can be scanned to visualize overall conserved sequence regions, and within these, the relative density of conserved cis-element motif clusters form graph peak structures. The results of these analyses can be mined en masse to identify most frequently represented cis-motifs in a list of genes. The system also provides a method for rapid evaluation and visualization of gene model-consistency between orthologs, and facilitates consideration of the potential impact of sequence variation in conserved non-coding regions to impact complex cis-element structures. Using the mouse and human genomes via the NCBI Reference Sequence database and the Sanger Institute miRBase, the system demonstrated the ability to identify validated transcription factor targets within promoter and distal genomic regulatory regions of both conventional and microRNA genes

Direct estimation of the Reynolds stress vertical structure in the nearshore

Author Posting. © American Meteorological Society, 2007. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Atmospheric and Oceanic Technology 24 (2007): 102-116, doi:10.1175/JTECH1953.1.Measurements of the vertical Reynolds stress components in the wave-dominated nearshore are required to diagnose momentum and turbulence dynamics. Removing wave bias from Reynolds stress estimates is critical to a successful diagnosis. Here two existing Reynolds stress estimation methods (those of Trowbridge, and Shaw and Trowbridge) for wave-dominated environments and an extended method (FW) that is a combination of the two are tested with a vertical array of three current meters deployed in 3.2-m water depth off an ocean beach. During the 175-h-long experiment the instruments were seaward of the surfzone and the alongshore current was wind driven. Intercomparison of Reynolds stress methods reveals that the Trowbridge method is wave bias dominated. Tests of the integrated cospectra are used to reject bad Reynolds stress estimates, and the Shaw and Trowbridge estimates are rejected more often than FW estimates. With the FW method, wave bias remains apparent in the cross-shore component of the Reynolds stress. However, the alongshore component of Reynolds stress measured at the three current meters are related to each other with a vertically uniform first EOF containing 73% of the variance, indicating the presence of a constant stress layer. This is the first time the vertical structure of Reynolds stress has been measured in a wave-dominated environment. The Reynolds stress is, albeit weakly, related to the wind stress and a parameterized bottom stress. Using derived wave bias and bottom stress parameterizations, the effect of wave bias on Reynolds stress estimates is shown to be weaker for more typical surfzone conditions (with both stronger waves and currents than those observed here).Funded by NSF, ONR, and NOPP

Turbulent flow at 190 m height above London during 2006-2008: A climatology and the applicability of similarity theory

Flow and turbulence above urban terrain is more complex than above rural terrain, due to the different momentum and heat transfer characteristics that are affected by the presence of buildings (e.g. pressure variations around buildings). The applicability of similarity theory (as developed over rural terrain) is tested using observations of flow from a sonic anemometer located at 190.3 m height in London, U.K. using about 6500 h of data. Turbulence statistics—dimensionless wind speed and temperature, standard deviations and correlation coefficients for momentum and heat transfer—were analysed in three ways. First, turbulence statistics were plotted as a function only of a local stability parameter z/Λ (where Λ is the local Obukhov length and z is the height above ground); the σ_i/u_* values (i = u, v, w) for neutral conditions are 2.3, 1.85 and 1.35 respectively, similar to canonical values. Second, analysis of urban mixed-layer formulations during daytime convective conditions over London was undertaken, showing that atmospheric turbulence at high altitude over large cities might not behave dissimilarly from that over rural terrain. Third, correlation coefficients for heat and momentum were analyzed with respect to local stability. The results give confidence in using the framework of local similarity for turbulence measured over London, and perhaps other cities. However, the following caveats for our data are worth noting: (i) the terrain is reasonably flat, (ii) building heights vary little over a large area, and (iii) the sensor height is above the mean roughness sublayer depth

Staging of biliary atresia at diagnosis by molecular profiling of the liver

Abstract Background Young age at portoenterostomy has been linked to improved outcome in biliary atresia, but pre-existing biological factors may influence the rate of disease progression. In this study, we aimed to determine whether molecular profiling of the liver identifies stages of disease at diagnosis. Methods We examined liver biopsies from 47 infants with biliary atresia enrolled in a prospective observational study. Biopsies were scored for inflammation and fibrosis, used for gene expression profiles, and tested for association with indicators of disease severity, response to surgery, and survival at 2 years. Results Fourteen of 47 livers displayed predominant histological features of inflammation (N = 9) or fibrosis (N = 5), with the remainder showing similar levels of both simultaneously. By differential profiling of gene expression, the 14 livers had a unique molecular signature containing 150 gene probes. Applying prediction analysis models, the probes classified 29 of the remaining 33 livers into inflammation or fibrosis. Molecular classification into the two groups was validated by the findings of increased hepatic population of lymphocyte subsets or tissue accumulation of matrix substrates. The groups had no association with traditional markers of liver injury or function, response to surgery, or complications of cirrhosis. However, infants with an inflammation signature were younger, while those with a fibrosis signature had decreased transplant-free survival. Conclusions Molecular profiling at diagnosis of biliary atresia uncovers a signature of inflammation or fibrosis in most livers. This signature may relate to staging of disease at diagnosis and has implications to clinical outcomes.http://deepblue.lib.umich.edu/bitstream/2027.42/112492/1/13073_2010_Article_154.pd

Airborne measurements of the vertical flux of ozone in the boundary layer

A fast-response chemiluminescent ozone sensor was mounted in an aircraft instrumented for air motion and temperature measurements. Measurements of the vertical flux of ozone by the eddy correlation technique were obtained after correcting for time delay and pressure sensitivity in the ozone sensor output. The observations were taken over eastern Colorado for two days in April, one a morning and the other an afternoon flight. Since the correlation coefficient of ozone and vertical velocity is small compared to, for example, temperature and vertical velocity in the lower part of the convective boundary layer, an averaging length of the order of 100 km was required to obtain a reasonably accurate estimate of the ozone flux. The measured variance of ozone appeared to be too large, probably mainly due to random noise in the sensor output, although the possibility of the production of ozone fluctuations by chemical reactions cannot be dismissed entirely. Terms in the budget equation for ozone were estimated from the aircraft measurements and the divergence of the ozone flux was found to be large compared to the flux at the surface divided by the boundary-layer height.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/42507/1/10546_2004_Article_BF00117223.pd

Effect of large-scale coherent structures on turbulent convection

We study an effect of large-scale coherent structures on global properties of turbulent convection in laboratory experiments in air flow in a rectangular chamber with aspect ratios $A \approx 2$ and $A\approx 4$ (with the Rayleigh numbers varying in the range from $5 \times 10^6$ to $10^8$). The large-scale coherent structures comprise the one-cell and two-cell flow patterns. We found that a main contribution to the turbulence kinetic energy production in turbulent convection with large-scale coherent structures is due to the non-uniform large-scale motions. Turbulence in large Rayleigh number convection with coherent structures is produced by shear, rather than by buoyancy. We determined the scalings of global parameters (e.g., the production and dissipation of turbulent kinetic energy, the turbulent velocity and integral turbulent scale, the large-scale shear, etc.) of turbulent convection versus the temperature difference between the bottom and the top walls of the chamber. These scalings are in an agreement with our theoretical predictions. We demonstrated that the degree of inhomogeneity of the turbulent convection with large-scale coherent structures is small.Comment: 10 pages, 12 figures, REVTEX

ToppCluster: a multiple gene list feature analyzer for comparative enrichment clustering and network-based dissection of biological systems

ToppCluster is a web server application that leverages a powerful enrichment analysis and underlying data environment for comparative analyses of multiple gene lists. It generates heatmaps or connectivity networks that reveal functional features shared or specific to multiple gene lists. ToppCluster uses hypergeometric tests to obtain list-specific feature enrichment P-values for currently 17 categories of annotations of human-ortholog genes, and provides user-selectable cutoffs and multiple testing correction methods to control false discovery. Each nameable gene list represents a column input to a resulting matrix whose rows are overrepresented features, and individual cells per-list P-values and corresponding genes per feature. ToppCluster provides users with choices of tabular outputs, hierarchical clustering and heatmap generation, or the ability to interactively select features from the functional enrichment matrix to be transformed into XGMML or GEXF network format documents for use in Cytoscape or Gephi applications, respectively. Here, as example, we demonstrate the ability of ToppCluster to enable identification of list-specific phenotypic and regulatory element features (both cis-elements and 3′UTR microRNA binding sites) among tissue-specific gene lists. ToppCluster’s functionalities enable the identification of specialized biological functions and regulatory networks and systems biology-based dissection of biological states. ToppCluster can be accessed freely at http://toppcluster.cchmc.org