Regulatory activity revealed by dynamic correlations in gene expression noise

Gene regulatory interactions are context dependent, active in some cellular states but not in others. Stochastic fluctuations, or 'noise', in gene expression propagate through active, but not inactive, regulatory links^(1,2). Thus, correlations in gene expression noise could provide a noninvasive means to probe the activity states of regulatory links. However, global, 'extrinsic', noise sources generate correlations even without direct regulatory links. Here we show that single-cell time-lapse microscopy, by revealing time lags due to regulation, can discriminate between active regulatory connections and extrinsic noise. We demonstrate this principle mathematically, using stochastic modeling, and experimentally, using simple synthetic gene circuits. We then use this approach to analyze dynamic noise correlations in the galactose metabolism genes of Escherichia coli. We find that the CRP-GalS-GalE feed-forward loop is inactive in standard conditions but can become active in a GalR mutant. These results show how noise can help analyze the context dependence of regulatory interactions in endogenous gene circuits

An Instrumental Approach to Full Employment: with Policy Implication

Dissertation advisor: Mathew Forstater.Includes bibliographic references (pages 221-235).Title from PDF of title page, viewed on December 13, 2010.Vita.Dissertation (Ph.D.)--College of Arts and Sciences. University of Missouri--Kansas City, 2010.The study proposes that in order to assure full employment, policy measures must address both Keynesian unemployment, and unemployment caused by structural and technological change. It is possible to attain full employment via expansionary fiscal policy advocated by Keynes. However given on-going technological change, it is not possible to maintain full employment with Keynesian policy alone. In order for any full employment policy to be effective it must address both of these issues. The purpose here is an investigation of the theory of unemployment from a Keynesian perspective and a structuralist perspective. I will make an argument that these are two sides of the same coin. Using an input-output framework it will be shown how the ELR program formally fits into the economy and addresses both types of unemployment. Furthermore, it will be shown that the ELR program works in conjunction with the private sector. The initial introduction of the ELR program causes an increase in the final demand for private sector goods and services, thus creating additional employment in the private sector. In order for the investigation of structural/technological unemployment, a structural framework of the ELR program is required. The dissertation will lay out a structural model of the economy with and without an ELR program. This then allows for an investigation of comparative benefits of such a program in addressing unemployment over current government policies. Simulations of model economy with and without the ELR program will be done to show that the ELR program stabilizes final demand. Additionally it will be seen that the ELR sector maintains full employment given structural and technological change.Abstract -- List of Illustrations -- List of Tables -- Post Keynesian Approaches to Economic Theory -- The Problem of Unemployment -- Heterodox Approaches to Production -- Employer of Last Resort: A Structural Approach -- Concluding Notes and Areas for Further Research -- Simulated Input Output Tables -- Reference List -- Vita

Unleash Physical Limitations: Virtual Emergency Preparedness Planning Simulation Training, Methodology and a Case Study

Simulation is perhaps the most widely used method for training emergency management workers. Despite its wide application, traditional simulation suffers from several constraints and limitations, which motivate us to pursue a different way – virtual simulation, as an alternative and supplement for the traditional training method. Utilization of groupware, network, and other information technologies makes virtual simulation more flexible and easier to prepare. Although virtual simulation can overcome some of the constraints related to physical simulation, so far there are little evidences that this new method can achieve similar or even better training effects compared with traditional simulation training method. To test the effects of this new training approach and the methodology to run it, several pilot trials have been conducted in the U.S. and Europe. This article is an exploratory study of a pilot emergency preparedness planning virtual simulation conducted in NJIT in late 2004. This study will help us understand the nature of virtual simulation, and help us improve the theories and designs of virtual simulation for emergency preparedness

Spatial epidemiological patterns suggest mechanisms of land-sea transmission for Sarcocystis neurona in a coastal marine mammal.

Sarcocystis neurona was recognised as an important cause of mortality in southern sea otters (Enhydra lutris nereis) after an outbreak in April 2004 and has since been detected in many marine mammal species in the Northeast Pacific Ocean. Risk of S. neurona exposure in sea otters is associated with consumption of clams and soft-sediment prey and is temporally associated with runoff events. We examined the spatial distribution of S. neurona exposure risk based on serum antibody testing and assessed risk factors for exposure in animals from California, Washington, British Columbia and Alaska. Significant spatial clustering of seropositive animals was observed in California and Washington, compared with British Columbia and Alaska. Adult males were at greatest risk for exposure to S. neurona, and there were strong associations with terrestrial features (wetlands, cropland, high human housing-unit density). In California, habitats containing soft sediment exhibited greater risk than hard substrate or kelp beds. Consuming a diet rich in clams was also associated with increased exposure risk. These findings suggest a transmission pathway analogous to that described for Toxoplasma gondii, with infectious stages traveling in freshwater runoff and being concentrated in particular locations by marine habitat features, ocean physical processes, and invertebrate bioconcentration

XBootes: An X-Ray Survey of the NDWFS Bootes Field - Paper I Overview and Initial Results

We obtained a 5 ksec deep Chandra X-ray Observatory ACIS-I map of the 9.3 square degree Bootes field of the NOAO Deep Wide-Field Survey. Here we describe the data acquisition and analysis strategies leading to a catalog of 4642 (3293) point sources with 2 or more (4 or more) counts, corresponding to a limiting flux of roughly 4(8)x10^{-15} erg cm^{-2}s^{-1} in the 0.5-7 keV band. These Chandra XBootes data are unique in that they consitute the widest contiguous X-ray field yet observed to such a faint flux limit. Because of the extraordinarily low background of the ACIS, we expect only 14% (0.7%) of the sources to be spurious. We also detected 43 extended sources in this survey. The distribution of the point sources among the 126 pointings (ACIS-I has a 16 x 16 arcminute field of view) is consistent with Poisson fluctuations about the mean of 36.8 sources per pointing. While a smoothed image of the point source distribution is clumpy, there is no statistically significant evidence of large scale filamentary structure. We do find however, that for theta>1 arcminute, the angular correlation function of these sources is consistent with previous measurements, following a power law in angle with slope -0.7. In a 1.4 deg^{2} sample of the survey, approximately 87% of the sources with 4 or more counts have an optical counterpart to R ~26 mag. As part of a larger program of optical spectroscopy of the NDWFS Bootes area, spectra have been obtained for \~900 of the X-ray sources, most of which are QSOs or AGN.Comment: 18 Pages, 10 figures (AASTex Preprint format

The Chandra XBootes Survey - III: Optical and Near-IR Counterparts

The XBootes Survey is a 5-ks Chandra survey of the Bootes Field of the NOAO Deep Wide-Field Survey (NDWFS). This survey is unique in that it is the largest (9.3 deg^2), contiguous region imaged in X-ray with complementary deep optical and near-IR observations. We present a catalog of the optical counterparts to the 3,213 X-ray point sources detected in the XBootes survey. Using a Bayesian identification scheme, we successfully identified optical counterparts for 98% of the X-ray point sources. The optical colors suggest that the optically detected galaxies are a combination of z<1 massive early-type galaxies and bluer star-forming galaxies whose optical AGN emission is faint or obscured, whereas the majority of the optically detected point sources are likely quasars over a large redshift range. Our large area, X-ray bright, optically deep survey enables us to select a large sub-sample of sources (773) with high X-ray to optical flux ratios (f_x/f_o>10). These objects are likely high redshift and/or dust obscured AGN. These sources have generally harder X-ray spectra than sources with 0.1<f_x/f_o<10. Of the 73 X-ray sources with no optical counterpart in the NDWFS catalog, 47 are truly optically blank down to R~25.5 (the average 50% completeness limit of the NDWFS R-band catalogs). These sources are also likely to be high redshift and/or dust obscured AGN.Comment: 19 pages, 13 figures, ApJ accepted. Catalog can be found at: http://www.noao.edu/noao/noaodeep or ftp://archive.noao.edu/pub/catalogs/xbootes