Genome-wide co-expression analysis in multiple tissues

Expression quantitative trait loci (eQTLs) represent genetic control points of gene expression, and can be categorized as cis- and trans-acting, reflecting local and distant regulation of gene expression respectively. Although there is evidence of co-regulation within clusters of trans-eQTLs, the extent of co-expression patterns and their relationship with the genotypes at eQTLs are not fully understood. We have mapped thousands of cis- and trans-eQTLs in four tissues (fat, kidney, adrenal and left ventricle) in a large panel of rat recombinant inbred (RI) strains. Here we investigate the genome-wide correlation structure in expression levels of eQTL transcripts and underlying genotypes to elucidate the nature of co-regulation within cis- and trans-eQTL datasets. Across the four tissues, we consistently found statistically significant correlations of cis-regulated gene expression to be rare (<0.9% of all pairs tested). Most (>80%) of the observed significant correlations of cis-regulated gene expression are explained by correlation of the underlying genotypes. In comparison, co-expression of trans-regulated gene expression is more common, with significant correlation ranging from 2.9%-14.9% of all pairs of trans-eQTL transcripts. We observed a total of 81 trans-eQTL clusters (hot-spots), defined as consisting of > or =10 eQTLs linked to a common region, with very high levels of correlation between trans-regulated transcripts (77.2-90.2%). Moreover, functional analysis of large trans-eQTL clusters (> or =30 eQTLs) revealed significant functional enrichment among genes comprising 80% of the large clusters. The results of this genome-wide co-expression study show the effects of the eQTL genotypes on the observed patterns of correlation, and suggest that functional relatedness between genes underlying trans-eQTLs is reflected in the degree of co-expression observed in trans-eQTL clusters. Our results demonstrate the power of an integrative, systematic approach to the analysis of a large gene expression dataset to uncover underlying structure, and inform future eQTL studies

Diamond like carbon coatings for potential application in biological implants – a review

Production of wear debris has been linked to the failure of numerous hip implants. With the current focus on increasing the implant longevity, thus wear and corrosion resistance is important. Hard coatings have the potential to reduce the wear and corrosion. Diamond like Carbon (DLC) coatings exhibit properties that could make them viable for implants. This paper critically reviews previously published research into usage of DLC coatings for implants. Overall DLCs seem to be an effective coating for implants but with the variance in results, further testing is required for clarification of us

A low-voltage retarding-field Mott polarimeter for photocathode characterization

Nuclear physics experiments at Thomas Jefferson National Accelerator Facility's CEBAF rely on high polarization electron beams. We describe a recently commissioned system for prequalifying and studying photocathodes for CEBAF with a load-locked, low-voltage polarized electron source coupled to a compact retarding-field Mott polarimeter. The polarimeter uses simplified electrode structures and operates from 5 to 30 kV. The effective Sherman function for this device has been calibrated by comparison with the CEBAF 5 MeV Mott polarimeter. For elastic scattering from a thick gold target at 20 keV, the effective Sherman function is 0.201(5). Its maximum efficiency at 20 keV, defined as the detected count rate divided by the incident particle current, is 5.4(2) x 10-4, yielding a figure-of-merit, or analyzing power squared times efficiency, of 1.0(1) x 10-5. The operating parameters of this new polarimeter design are compared to previously published data for other compact Mott polarimeters of the retarding-field type.Comment: 9 figure

Remotely Keyed Cryptographics: Secure Remote Display Access Using (Mostly) Untrusted Hardware

Software that covertly monitors user actions, also known as spyware, has become a first-level security threat due to its ubiquity and the difficulty of detecting and removing it. Such software may be inadvertently installed by a user that is casually browsing the web, or may be purposely installed by an attacker or even the owner of a system. This is particularly problematic in the case of utility computing, early manifestations of which are Internet cafes and thin-client computing. Traditional trusted computing approaches offer a partial solution to this by significantly increasing the size of the trusted computing base (TCB) to include the operating system and other software. We examine the problem of protecting a user accessing specific services in such an environment. We focus on secure video broadcasts and remote desktop access when using any convenient, and often untrusted, terminal as two example applications. We posit that, at least for such applications, the TCB can be confined to a suitably modified graphics processing unit (GPU). Specifically, to prevent spyware on untrusted clients from accessing the user's data, we restrict the boundary of trust to the client's GPU by moving image decryption into GPUs. This allows us to leverage existing capabilities as opposed to designing a new component from scratch. We discuss the applicability of GPU-based decryption in the two scenarios. We identify limitations due to current GPU capabilities and propose straightforward modifications to GPUs that will allow the realization of our approach

A Brief History, Status, and Perspective of Modified Oligonucleotides for Chemotherapeutic Applications

The advent of rapid and efficient methods of oligonucleotide synthesis has allowed the design of modified oligonucleotides that are complementary to specific nucleotide sequences in mRNA targets. Such modified oligonucleotides can be used to disrupt the flow of genetic information from transcribed mRNAs to proteins. This antisense strategy has been used to develop therapeutic oligonucleotides against cancer and various infectious diseases in humans. This overview reports recent advances in the application of oligonucleotides as drug candidates, describes the relationship between oligonucleotide modifications and their therapeutic profiles, and provides general guidelines for enhancing oligonucleotide drug properties.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/143788/1/cpnc0401.pd

Review article: MHD wave propagation near coronal null points of magnetic fields

We present a comprehensive review of MHD wave behaviour in the neighbourhood of coronal null points: locations where the magnetic field, and hence the local Alfven speed, is zero. The behaviour of all three MHD wave modes, i.e. the Alfven wave and the fast and slow magnetoacoustic waves, has been investigated in the neighbourhood of 2D, 2.5D and (to a certain extent) 3D magnetic null points, for a variety of assumptions, configurations and geometries. In general, it is found that the fast magnetoacoustic wave behaviour is dictated by the Alfven-speed profile. In a $\beta=0$ plasma, the fast wave is focused towards the null point by a refraction effect and all the wave energy, and thus current density, accumulates close to the null point. Thus, null points will be locations for preferential heating by fast waves. Independently, the Alfven wave is found to propagate along magnetic fieldlines and is confined to the fieldlines it is generated on. As the wave approaches the null point, it spreads out due to the diverging fieldlines. Eventually, the Alfven wave accumulates along the separatrices (in 2D) or along the spine or fan-plane (in 3D). Hence, Alfven wave energy will be preferentially dissipated at these locations. It is clear that the magnetic field plays a fundamental role in the propagation and properties of MHD waves in the neighbourhood of coronal null points. This topic is a fundamental plasma process and results so far have also lead to critical insights into reconnection, mode-coupling, quasi-periodic pulsations and phase-mixing.Comment: 34 pages, 5 figures, invited review in Space Science Reviews => Note this is a 2011 paper, not a 2010 pape

Relativistic Hydrodynamic Evolutions with Black Hole Excision

We present a numerical code designed to study astrophysical phenomena involving dynamical spacetimes containing black holes in the presence of relativistic hydrodynamic matter. We present evolutions of the collapse of a fluid star from the onset of collapse to the settling of the resulting black hole to a final stationary state. In order to evolve stably after the black hole forms, we excise a region inside the hole before a singularity is encountered. This excision region is introduced after the appearance of an apparent horizon, but while a significant amount of matter remains outside the hole. We test our code by evolving accurately a vacuum Schwarzschild black hole, a relativistic Bondi accretion flow onto a black hole, Oppenheimer-Snyder dust collapse, and the collapse of nonrotating and rotating stars. These systems are tracked reliably for hundreds of M following excision, where M is the mass of the black hole. We perform these tests both in axisymmetry and in full 3+1 dimensions. We then apply our code to study the effect of the stellar spin parameter J/M^2 on the final outcome of gravitational collapse of rapidly rotating n = 1 polytropes. We find that a black hole forms only if J/M^2<1, in agreement with previous simulations. When J/M^2>1, the collapsing star forms a torus which fragments into nonaxisymmetric clumps, capable of generating appreciable ``splash'' gravitational radiation.Comment: 17 pages, 14 figures, submitted to PR

Diamond like carbon coatings for potential application in biological implants—a review

Production of wear debris has been linked to the failure of numerous hip implants. With the current focus on increasing the implant longevity, thus wear and corrosion resistance is important. Hard coatings have the potential to reduce the wear and corrosion. Diamond like Carbon (DLC) coatings exhibit properties that could make them viable for implants. This paper critically reviews previously published research into usage of DLC coatings for implants. Overall DLCs seem to be an effective coating for implants but with the variance in results, further testing is required for clarification of us

Connectivity: insights from the U.S. Long Term Ecological Research Network

Ecosystems across the United States are changing in complex and surprising ways. Ongoing demand for critical ecosystem services requires an understanding of the populations and communities in these ecosystems in the future. This paper represents a synthesis effort of the U.S. National Science Foundation-funded Long-Term Ecological Research (LTER) network addressing the core research area of “populations and communities.” The objective of this effort was to show the importance of long-term data collection and experiments for addressing the hardest questions in scientific ecology that have significant implications for environmental policy and management. Each LTER site developed at least one compelling case study about what their site could look like in 50–100 yr as human and environmental drivers influencing specific ecosystems change. As the case studies were prepared, five themes emerged, and the studies were grouped into papers in this LTER Futures Special Feature addressing state change, connectivity, resilience, time lags, and cascading effects. This paper addresses the “connectivity” theme and has examples from the Phoenix (urban), Niwot Ridge (alpine tundra), McMurdo Dry Valleys (polar desert), Plum Island (coastal), Santa Barbara Coastal (coastal), and Jornada (arid grassland and shrubland) sites. Connectivity has multiple dimensions, ranging from multi-scalar interactions in space to complex interactions over time that govern the transport of materials and the distribution and movement of organisms. The case studies presented here range widely, showing how land-use legacies interact with climate to alter the structure and function of arid ecosystems and flows of resources and organisms in Antarctic polar desert, alpine, urban, and coastal marine ecosystems. Long-term ecological research demonstrates that connectivity can, in some circumstances, sustain valuable ecosystem functions, such as the persistence of foundation species and their associated biodiversity or, it can be an agent of state change, as when it increases wind and water erosion. Increased connectivity due to warming can also lead to species range expansions or contractions and the introduction of undesirable species. Continued long-term studies are essential for addressing the complexities of connectivity. The diversity of ecosystems within the LTER network is a strong platform for these studies

Measurement of the Charged Multiplicities in b, c and Light Quark Events from Z0 Decays

Average charged multiplicities have been measured separately in $b$, $c$ and light quark ($u,d,s$) events from $Z^0$ decays measured in the SLD experiment. Impact parameters of charged tracks were used to select enriched samples of $b$ and light quark events, and reconstructed charmed mesons were used to select $c$ quark events. We measured the charged multiplicities: $\bar{n}_{uds} = 20.21 \pm 0.10 (\rm{stat.})\pm 0.22(\rm{syst.})$, $\bar{n}_{c} = 21.28 \pm 0.46(\rm{stat.}) ^{+0.41}_{-0.36}(\rm{syst.})$ $\bar{n}_{b} = 23.14 \pm 0.10(\rm{stat.}) ^{+0.38}_{-0.37}(\rm{syst.})$, from which we derived the differences between the total average charged multiplicities of $c$ or $b$ quark events and light quark events: $\Delta \bar{n}_c = 1.07 \pm 0.47(\rm{stat.})^{+0.36}_{-0.30}(\rm{syst.})$ and $\Delta \bar{n}_b = 2.93 \pm 0.14(\rm{stat.})^{+0.30}_{-0.29}(\rm{syst.})$. We compared these measurements with those at lower center-of-mass energies and with perturbative QCD predictions. These combined results are in agreement with the QCD expectations and disfavor the hypothesis of flavor-independent fragmentation.Comment: 19 pages LaTex, 4 EPS figures, to appear in Physics Letters