Mobile Manipulation Platform for Autonomous Indoor Inspections in Low-Clearance Areas

Mobile manipulators have been used for inspection, maintenance and repair tasks over the years, but there are some key limitations. Stability concerns typically require mobile platforms to be large in order to handle far-reaching manipulators, or for the manipulators to have drastically reduced workspaces to fit onto smaller mobile platforms. Therefore we propose a combination of two widely-used robots, the Clearpath Jackal unmanned ground vehicle and the Kinova Gen3 six degree-of-freedom manipulator. The Jackal has a small footprint and works well in low-clearance indoor environments. Extensive testing of localization, navigation and mapping using LiDAR sensors makes the Jackal a well developed mobile platform suitable for mobile manipulation. The Gen3 has a long reach with reasonable power consumption for manipulation tasks. A wrist camera for RGB-D sensing and a customizable end effector interface makes the Gen3 suitable for a myriad of manipulation tasks. Typically these features would result in an unstable platform, however with a few minor hardware and software modifications, we have produced a stable, high-performance mobile manipulation platform with significant mobility, reach, sensing, and maneuverability for indoor inspection tasks, without degradation of the component robots' individual capabilities. These assertions were investigated with hardware via semi-autonomous navigation to waypoints in a busy indoor environment, and high-precision self-alignment alongside planar structures for intervention tasks.Comment: 5 pages, 7 figures, to be published in IDETC-CIE 202

Synthesis of novel polyhydroxylated quinolizidines: Ring expanded analogs of glycosidase inhibitory indolizidines

Two polyhydroxylated quinolizidines, (1R,2R,3R,9S,9aR)-1,2,3,9-tetrahydroxyquinolizidine 9 and (1R,2R,3R,9R,9aS-1,2,3,9-tetrahydroxyquinolizidine 10, have been synthesized by the reductive double cyclization of 15[alpha] and 15[beta]. Quinolizidine 9 can be viewed either as a ring expanded analog of 6-epicastanospermine or of 8-episwainsonine, while 10 is a ring expanded analog of 1,6,8a-triepicastanospermine or of 8a-episwainsonine.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/30391/1/0000009.pd

Laboratory Directed Research and Development Annual Report - Fiscal Year 2000

The projects described in this report represent the Laboratory's investment in its future and are vital to maintaining the ability to develop creative solutions for the scientific and technical challenges faced by DOE and the nation. In accordance with DOE guidelines, the report provides, a) a director's statement, b) an overview of the laboratory's LDRD program, including PNNL's management process and a self-assessment of the program, c) a five-year project funding table, and d) project summaries for each LDRD project

Determination of the Cosmic Distance Scale from Sunyaev-Zel'dovich Effect and Chandra X-ray Measurements of High Redshift Galaxy Clusters

We determine the distance to 38 clusters of galaxies in the redshift range 0.14 < z < 0.89 using X-ray data from Chandra and Sunyaev-Zeldovich Effect data from the Owens Valley Radio Observatory and the Berkeley-Illinois-Maryland Association interferometric arrays. The cluster plasma and dark matter distributions are analyzed using a hydrostatic equilibrium model that accounts for radial variations in density, temperature and abundance, and the statistical and systematic errors of this method are quantified. The analysis is performed via a Markov chain Monte Carlo technique that provides simultaneous estimation of all model parameters. We measure a Hubble constant of 76.9 +3.9-3.4 +10.0-8.0 km/s/Mpc (statistical followed by systematic uncertainty at 68% confidence) for an Omega_M=0.3, Omega_Lambda=0.7 cosmology. We also analyze the data using an isothermal beta model that does not invoke the hydrostatic equilibrium assumption, and find H_0=73.7 +4.6-3.8 +9.5-7.6 km/s/Mpc; to avoid effects from cool cores in clusters, we repeated this analysis excluding the central 100 kpc from the X-ray data, and find H_0=77.6 +4.8-4.3 +10.1-8.2 km/s/Mpc. The consistency between the models illustrates the relative insensitivity of SZE/X-ray determinations of H_0 to the details of the cluster model. Our determination of the Hubble parameter in the distant universe agrees with the recent measurement from the Hubble Space Telescope key project that probes the nearby universe.Comment: ApJ submitted (revised version

Microbiome diversity protects against pathogens by nutrient blocking

The human gut microbiome plays an important role in resisting colonization of the host by pathogens, but we lack the ability to predict which communities will be protective. We studied how human gut bacteria influence colonization of two major bacterial pathogens, both in vitro and in gnotobiotic mice. Whereas single species alone had negligible effects, colonization resistance greatly increased with community diversity. Moreover, this community-level resistance rested critically upon certain species being present. We explained these ecological patterns through the collective ability of resistant communities to consume nutrients that overlap with those used by the pathogen. Furthermore, we applied our findings to successfully predict communities that resist a novel target strain. Our work provides a reason why microbiome diversity is beneficial and suggests a route for the rational design of pathogen-resistant communities

X-ray and Sunyaev-Zel'dovich Effect Measurements of the Gas Mass Fraction in Galaxy Clusters

We present gas mass fractions of 38 massive galaxy clusters spanning redshifts from 0.14 to 0.89, derived from Chandra X-ray data and OVRO/BIMA interferometric Sunyaev-Zel'dovich Effect measurements. We use three models for the gas distribution: (1) an isothermal beta-model fit jointly to the X-ray data at radii beyond 100 kpc and to all of the SZE data,(2) a non-isothermal double beta-model fit jointly to all of the X-ray and SZE data, and (3) an isothermal beta-model fit only to the SZE spatial data. We show that the simple isothermal model well characterizes the intracluster medium (ICM) outside of the cluster core in clusters with a wide range of morphological properties. The X-ray and SZE determinations of mean gas mass fractions for the 100 kpc-cut isothermal beta-model are fgas(X-ray)=0.110 +0.003-0.003 +0.006-0.018 and fgas(SZE)=0.116 +0.005-0.005 +0.009-0.026, where uncertainties are statistical followed by systematic at 68% confidence. For the non-isothermal double beta-model, fgas(X-ray)=0.119 +0.003-0.003 +0.007-0.014 and fgas(SZE)=0.121 +0.005-0.005 +0.009-0.016. For the SZE-only model, fgas(SZE)=0.120 +0.009-0.009 +0.009-0.027. Our results indicate that the ratio of the gas mass fraction within r2500 to the cosmic baryon fraction is 0.68 +0.10-0.16 where the range includes statistical and systematic uncertainties. By assuming that cluster gas mass fractions are independent of redshift, we find that the results are in agreement with standard LambdaCDM cosmology and are inconsistent with a flat matter dominated universe.Comment: ApJ, submitted. 47 pages, 5 figures, 8 table

Elovl4 haploinsufficiency does not induce early onset retinal degeneration in mice

AbstractELOVL4 was first identified as a disease-causing gene in Stargardt macular dystrophy (STGD3, MIM 600110.) To date, three ELOVL4 mutations have been identified, all of which result in truncated proteins which induce autosomal dominant juvenile macular degenerations. Based on sequence homology, ELOVL4 is thought to be another member within a family of proteins functioning in the elongation of long chain fatty acids. However, the normal function of ELOVL4 is unclear. We generated Elovl4 knockout mice to determine if Elovl4 loss affects retinal development or function. Here we show that Elovl4 knockout mice, while perinatal lethal, exhibit normal retinal development prior to death at day of birth. Further, postnatal retinal development in Elovl4 heterozygous mice appears normal. Therefore haploinsufficiency for wildtype ELOVL4 in autosomal dominant macular degeneration likely does not contribute to juvenile macular degeneration in STGD3 patients. We found, however, that Elovl4+/− mice exhibit enhanced ERG scotopic and photopic a and b waves relative to wildtype Elovl4+/+ mice suggesting that reduced Elovl4 levels may impact retinal electrophysiological responses

Identification of disease causing loci using an array-based genotyping approach on pooled DNA

BACKGROUND: Pooling genomic DNA samples within clinical classes of disease followed by genotyping on whole-genome SNP microarrays, allows for rapid and inexpensive genome-wide association studies. Key to the success of these studies is the accuracy of the allelic frequency calculations, the ability to identify false-positives arising from assay variability and the ability to better resolve association signals through analysis of neighbouring SNPs. RESULTS: We report the accuracy of allelic frequency measurements on pooled genomic DNA samples by comparing these measurements to the known allelic frequencies as determined by individual genotyping. We describe modifications to the calculation of k-correction factors from relative allele signal (RAS) values that remove biases and result in more accurate allelic frequency predictions. Our results show that the least accurate SNPs, those most likely to give false-positives in an association study, are identifiable by comparing their frequencies to both those from a known database of individual genotypes and those of the pooled replicates. In a disease with a previously identified genetic mutation, we demonstrate that one can identify the disease locus through the comparison of the predicted allelic frequencies in case and control pools. Furthermore, we demonstrate improved resolution of association signals using the mean of individual test-statistics for consecutive SNPs windowed across the genome. A database of k-correction factors for predicting allelic frequencies for each SNP, derived from several thousand individually genotyped samples, is provided. Lastly, a Perl script for calculating RAS values for the Affymetrix platform is provided. CONCLUSION: Our results illustrate that pooling of DNA samples is an effective initial strategy to identify a genetic locus. However, it is important to eliminate inaccurate SNPs prior to analysis by comparing them to a database of individually genotyped samples as well as by comparing them to replicates of the pool. Lastly, detection of association signals can be improved by incorporating data from neighbouring SNPs

Determining the Cosmic Distance Scale from Interferometric Measurements of the Sunyaev-Zel'dovich Effect

We determine the distances to 18 galaxy clusters with redshifts ranging from z~0.14 to z~0.78 from a maximum likelihood joint analysis of 30 GHz interferometric Sunyaev-Zel'dovich effect (SZE) and X-ray observations. We model the intracluster medium (ICM) using a spherical isothermal beta model. We quantify the statistical and systematic uncertainties inherent to these direct distance measurements, and we determine constraints on the Hubble parameter for three different cosmologies. These distances imply a Hubble constant of 60 (+4, -4) (+13, -18) km s-1 Mpc-1 for an Omega_M = 0.3, Omega_Lambda = 0.7 cosmology, where the uncertainties correspond to statistical followed by systematic at 68% confidence. With a sample of 18 clusters, systematic uncertainties clearly dominate. The systematics are observationally approachable and will be addressed in the coming years through the current generation of X-ray satellites (Chandra & XMM-Newton) and radio observatories (OVRO, BIMA, & VLA). Analysis of high redshift clusters detected in future SZE and X-ray surveys will allow a determination of the geometry of the universe from SZE determined distances.Comment: ApJ Submitted; 40 pages, 9 figures (fig 3 B&W for size constraint), 13 tables, uses emulateapj5 styl

Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features

In the growing field of genomics, multiple alignment programs are confronted with ever increasing amounts of data. To address this growing issue we have dramatically improved the running time and memory requirement of Kalign, while maintaining its high alignment accuracy. Kalign version 2 also supports nucleotide alignment, and a newly introduced extension allows for external sequence annotation to be included into the alignment procedure. We demonstrate that Kalign2 is exceptionally fast and memory-efficient, permitting accurate alignment of very large numbers of sequences. The accuracy of Kalign2 compares well to the best methods in the case of protein alignments while its accuracy on nucleotide alignments is generally superior. In addition, we demonstrate the potential of using known or predicted sequence annotation to improve the alignment accuracy. Kalign2 is freely available for download from the Kalign web site (http://msa.sbc.su.se/)