Application of Relational Contracting Methods to Federal Construction Projects

Relational contracting is a method designed to improve relationships between contracted parties. The federal construction sector was a leader in the development and implementation of an early form of relational contracting known as partnering. Since then, alliancing has emerged as the new evolution of relational contracts. While it provides many potential benefits to contracting parties, alliancing has not yet been utilized in federal construction procurement, which is subject to stringent regulations. A commercially available standard form alliancing contract was selected for analysis against the Federal Acquisition Regulation. Key practices that characterize the alliancing method were identified. Utilizing a panel of federal contracting experts, qualitative data were gathered to analyze which of these key practices do or do not comply with federal regulations, why certain practices do not comply, and how those practices could achieve compliance. The results show that most alliancing key practices can be utilized in a federal acquisition project. While some practices cannot be used effectively under current regulations, these limitations do not significantly hinder the use of a comprehensive and effective federal alliancing contract

A Context-based Approach to Robot-human Interaction

AbstractCARIL (Context-Augmented Robotic Interaction Layer) is a human-robot interaction system that leverages cognitive representations of shared context as a basis for a fundamentally new approach to human-robotic interaction. CARIL gives a robot a human-like representation of context and an ability to reason about context in order to adapt its behavior to that of the humans around it. This capability is “action compliance.” A prototype CARIL implementation focuses on a fundamental form of action compliance called non-interference -- “not being underfoot or in a human's way”. Non-interference is key for the safety of human-co-workers, and is also foundational to more complex interactive and teamwork skills. CARIL is tested via simulation in a space-exploration use-case. The live CARIL prototype directs a single simulated robot in a simulated space station where four simulated astronauts are engaging in a variety of tightly-scheduled work activities. The robot is scheduled to perform background tasks away from the astronauts, but must quickly adapt and not be underfoot as astronaut activities diverge from plan and encroach on the robot's space. The robot, driven by CARIL, demonstrates non-interference action compliance in three benchmarks situations, demonstrating the viability of the CARIL technology and concept

Network analysis of pseudogene-gene relationships: from pseudogene evolution to their functional potentials

Pseudogenes are fossil relatives of genes. Pseudogenes have long been thought of as "junk DNAs", since they do not code proteins in normal tissues. Although most of the human pseudogenes do not have noticeable functions, ∼20% of them exhibit transcriptional activity. There has been evidence showing that some pseudogenes adopted functions as lncRNAs and work as regulators of gene expression. Furthermore, pseudogenes can even be "reactivated" in some conditions, such as cancer initiation. Some pseudogenes are transcribed in specific cancer types, and some are even translated into proteins as observed in several cancer cell lines. All the above have shown that pseudogenes could have functional roles or potentials in the genome. Evaluating the relationships between pseudogenes and their gene counterparts could help us reveal the evolutionary path of pseudogenes and associate pseudogenes with functional potentials. It also provides an insight into the regulatory networks involving pseudogenes with transcriptional and even translational activities.In this study, we develop a novel approach integrating graph analysis, sequence alignment and functional analysis to evaluate pseudogene-gene relationships, and apply it to human gene homologs and pseudogenes. We generated a comprehensive set of 445 pseudogene-gene (PGG) families from the original 3,281 gene families (13.56%). Of these 438 (98.4% PGG, 13.3% total) were non-trivial (containing more than one pseudogene). Each PGG family contains multiple genes and pseudogenes with high sequence similarity. For each family, we generate a sequence alignment network and phylogenetic trees recapitulating the evolutionary paths. We find evidence supporting the evolution history of olfactory family (both genes and pseudogenes) in human, which also supports the validity of our analysis method. Next, we evaluate these networks in respect to the gene ontology from which we identify functions enriched in these pseudogene-gene families and infer functional impact of pseudogenes involved in the networks. This demonstrates the application of our PGG network database in the study of pseudogene function in disease context

Detection of Water Vapor in the Thermal Spectrum of the Non-Transiting Hot Jupiter upsilon Andromedae b

The upsilon Andromedae system was the first multi-planet system discovered orbiting a main sequence star. We describe the detection of water vapor in the atmosphere of the innermost non-transiting gas giant ups~And~b by treating the star-planet system as a spectroscopic binary with high-resolution, ground-based spectroscopy. We resolve the signal of the planet's motion and break the mass-inclination degeneracy for this non-transiting planet via deep combined flux observations of the star and the planet. In total, seven epochs of Keck NIRSPEC $L$ band observations, three epochs of Keck NIRSPEC short wavelength $K$ band observations, and three epochs of Keck NIRSPEC long wavelength $K$ band observations of the ups~And~system were obtained. We perform a multi-epoch cross correlation of the full data set with an atmospheric model. We measure the radial projection of the Keplerian velocity ($K_P$ = 55 $\pm$ 9 km/s), true mass ($M_b$ = 1.7 $^{+0.33}_{-0.24}$ $M_J$), and orbital inclination \big($i_b$ = 24 $\pm$ 4$^{\circ}$\big), and determine that the planet's opacity structure is dominated by water vapor at the probed wavelengths. Dynamical simulations of the planets in the ups~And~system with these orbital elements for ups~And~b show that stable, long-term (100 Myr) orbital configurations exist. These measurements will inform future studies of the stability and evolution of the ups~And~system, as well as the atmospheric structure and composition of the hot Jupiter.Comment: Accepted to A

Ground- and Space-based Detection of the Thermal Emission Spectrum of the Transiting Hot Jupiter KELT-2Ab

We describe the detection of water vapor in the atmosphere of the transiting hot Jupiter KELT-2Ab by treating the star-planet system as a spectroscopic binary with high-resolution, ground-based spectroscopy. We resolve the signal of the planet's motion with deep combined flux observations of the star and the planet. In total, six epochs of Keck NIRSPEC $L$-band observations were obtained, and the full data set was subjected to a cross correlation analysis with a grid of self-consistent atmospheric models. We measure a radial projection of the Keplerian velocity, $K_P$, of 148 $\pm$ 7 km s$^{-1}$, consistent with transit measurements, and detect water vapor at 3.8$\sigma$. We combine NIRSPEC $L$-band data with $Spitzer$ IRAC secondary eclipse data to further probe the metallicity and carbon-to-oxygen ratio of KELT-2Ab's atmosphere. While the NIRSPEC analysis provides few extra constraints on the $Spitzer$ data, it does provide roughly the same constraints on metallicity and carbon-to-oxygen ratio. This bodes well for future investigations of the atmospheres of non-transiting hot Jupiters.Comment: accepted to A

A protocol to evaluate RNA sequencing normalization methods

Background RNA sequencing technologies have allowed researchers to gain a better understanding of how the transcriptome affects disease. However, sequencing technologies often unintentionally introduce experimental error into RNA sequencing data. To counteract this, normalization methods are standardly applied with the intent of reducing the non-biologically derived variability inherent in transcriptomic measurements. However, the comparative efficacy of the various normalization techniques has not been tested in a standardized manner. Here we propose tests that evaluate numerous normalization techniques and applied them to a large-scale standard data set. These tests comprise a protocol that allows researchers to measure the amount of non-biological variability which is present in any data set after normalization has been performed, a crucial step to assessing the biological validity of data following normalization. Results In this study we present two tests to assess the validity of normalization methods applied to a large-scale data set collected for systematic evaluation purposes. We tested various RNASeq normalization procedures and concluded that transcripts per million (TPM) was the best performing normalization method based on its preservation of biological signal as compared to the other methods tested. Conclusion Normalization is of vital importance to accurately interpret the results of genomic and transcriptomic experiments. More work, however, needs to be performed to optimize normalization methods for RNASeq data. The present effort helps pave the way for more systematic evaluations of normalization methods across different platforms. With our proposed schema researchers can evaluate their own or future normalization methods to further improve the field of RNASeq normalization

Buruli ulcer disease prevalence in Benin, West Africa: associations with land use/cover and the identification of disease clusters

© 2008 Wagner et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution Licens

Spatially Resolved Outflows in a Seyfert Galaxy at z = 2.39

We present the first spatially resolved analysis of rest-frame optical and UV imaging and spectroscopy for a lensed galaxy at z = 2.39 hosting a Seyfert active galactic nucleus (AGN). Proximity to a natural guide star has enabled high signal-to-noise VLT SINFONI + adaptive optics observations of rest-frame optical diagnostic emission lines, which exhibit an underlying broad component with FWHM ~ 700 km/s in both the Balmer and forbidden lines. Measured line ratios place the outflow robustly in the region of the ionization diagnostic diagrams associated with AGN. This unique opportunity - combining gravitational lensing, AO guiding, redshift, and AGN activity - allows for a magnified view of two main tracers of the physical conditions and structure of the interstellar medium in a star-forming galaxy hosting a weak AGN at cosmic noon. By analyzing the spatial extent and morphology of the Ly-alpha and dust-corrected H-alpha emission, disentangling the effects of star formation and AGN ionization on each tracer, and comparing the AGN induced mass outflow rate to the host star formation rate, we find that the AGN does not significantly impact the star formation within its host galaxy.Comment: 16 pages, 5 figures, accepted for publication in Ap

Murine cytomegalovirus protein pM79 is a key regulator for viral late transcription

Herpesvirus genes are temporally expressed during permissive infections, but how their expression is regulated at late times is poorly understood. Previous studies indicate that the human cytomegalovirus (CMV) gene, UL79, is required for late gene expression. However, the mechanism remains to be fully elucidated, and UL79 homologues in other CMVs have not been studied. Here, we characterized the role of the conserved murine CMV (MCMV) gene M79. We showed that M79 encoded a protein (pM79) which was expressed with early-late kinetics and localized to nuclear viral replication compartments. M79 transcription was significantly decreased in the absence of viral DNA synthesis but markedly stimulated by pM79. To investigate its role, we created the recombinant virus SMin79, in which pM79 expression was disrupted. While marker-rescued virus grew efficiently in fibroblasts, SMin79 failed to produce infectious progeny but was rescued by pM79 expression in trans. During SMin79 infection, representative viral immediate-early and early gene products as well as viral DNA accumulated sufficiently. Formation of viral replication compartments also appeared normal. Pulsed-field gel electrophoresis analysis indicated that the overall structure of replicating viral DNA was indistinguishable between wild-type and SMin79 infection. Viral tiled array and quantitative PCR analysis revealed that many late transcripts sensitive to a viral DNA synthesis inhibitor (phosphonoacetic acid) were markedly reduced by pM79 mutation. This study indicates that cytomegaloviruses use a conserved mechanism to promote transcription at late stages of infection and that pM79 is a critical regulator for at least a subset of viral DNA synthesis-dependent transcripts

Evidence for the Direct Detection of the Thermal Spectrum of the Non-Transiting Hot Gas Giant HD 88133 b

We target the thermal emission spectrum of the non-transiting gas giant HD 88133 b with high-resolution near-infrared spectroscopy, by treating the planet and its host star as a spectroscopic binary. For sufficiently deep summed flux observations of the star and planet across multiple epochs, it is possible to resolve the signal of the hot gas giant's atmosphere compared to the brighter stellar spectrum, at a level consistent with the aggregate shot noise of the full data set. To do this, we first perform a principal component analysis to remove the contribution of the Earth's atmosphere to the observed spectra. Then, we use a cross-correlation analysis to tease out the spectra of the host star and HD 88133 b to determine its orbit and identify key sources of atmospheric opacity. In total, six epochs of Keck NIRSPEC L band observations and three epochs of Keck NIRSPEC K band observations of the HD 88133 system were obtained. Based on an analysis of the maximum likelihood curves calculated from the multi-epoch cross correlation of the full data set with two atmospheric models, we report the direct detection of the emission spectrum of the non-transiting exoplanet HD 88133 b and measure a radial projection of the Keplerian orbital velocity of 40 $\pm$ 15 km/s, a true mass of 1.02$^{+0.61}_{-0.28}M_J$, a nearly face-on orbital inclination of 15${^{+6}_{-5}}^{\circ}$, and an atmosphere opacity structure at high dispersion dominated by water vapor. This, combined with eleven years of radial velocity measurements of the system, provides the most up-to-date ephemeris for HD 88133.Comment: 9 pages, 6 figures; accepted for publication in Ap