Intersecting hypersurfaces, topological densities and Lovelock Gravity

Intersecting hypersurfaces in classical Lovelock gravity are studied exploiting the description of the Lovelock Lagrangian as a sum of dimensionally continued Euler densities. We wish to present an interesting geometrical approach to the problem. The analysis allows us to deal most efficiently with the division of space-time into a honeycomb network of cells produced by an arbitrary arrangement of membranes of matter. We write the gravitational action as bulk terms plus integrals over each lower dimensional intersection. The spin connection is discontinuous at the shared boundaries of the cells, which are spaces of various dimensionalities. That means that at each intersection there are more than one spin connections. We introduce a multi-parameter family of connections which interpolate between the different connections at each intersection. The parameters live naturally on a simplex. We can then write the action including all the intersection terms in a simple way. The Lagrangian of Lovelock gravity is generalized so as to live on the simplices as well. Each intersection term of the action is then obtained as an integral over an appropriate simplex. Lovelock gravity and the associated topological (Euler) density are used as an example of a more general formulation. In this example one finds that singular sources up to a certain co-dimensionality naturally carry matter without introducing conical or other singularities in spacetime geometry.Comment: 24 pages, 2 figures, version 4: lengthened introduction, section on explicit junction conditions for intersections added. Accepted in Journal of Geometry and Physic

Externally Fed Accretion onto Protostars

The asymmetric molecular emission lines from dense cores reveal slow, inward motion in the clouds' outer regions. This motion is present both before and after the formation of a central star. Motivated by these observations, we revisit the classic problem of steady, spherical accretion of gas onto a gravitating point mass, but now include self-gravity of the gas and impose a finite, subsonic velocity as the outer boundary condition. We find that the accretion rate onto the protostar is lower than values obtained for isolated, collapsing clouds, by a factor that is the Mach number of the outer flow. Moreover, the region of infall surrounding the protostar spreads out more slowly, at a speed close to the subsonic, incoming velocity. Our calculation, while highly idealized, provides insight into two longstanding problems -- the surprisingly low accretion luminosities of even the most deeply embedded stellar sources, and the failure so far to detect spatially extended, supersonic infall within their parent dense cores. Indeed, the observed subsonic contraction in the outer regions of dense cores following star formation appears to rule out a purely hydrodynamic origin for these clouds.Comment: accepted by MNRA

Allosteric modulation of hormone release from thyroxine and corticosteroid-binding globulins.

The release of hormones from thyroxine-binding globulin (TBG) and corticosteroid-binding globulin (CBG) is regulated by movement of the reactive center loop in and out of the β-sheet A of the molecule. To investigate how these changes are transmitted to the hormone-binding site, we developed a sensitive assay using a synthesized thyroxine fluorophore and solved the crystal structures of reactive loop cleaved TBG together with its complexes with thyroxine, the thyroxine fluorophores, furosemide, and mefenamic acid. Cleavage of the reactive loop results in its complete insertion into the β-sheet A and a substantial but incomplete decrease in binding affinity in both TBG and CBG. We show here that the direct interaction between residue Thr(342) of the reactive loop and Tyr(241) of the hormone binding site contributes to thyroxine binding and release following reactive loop insertion. However, a much larger effect occurs allosterically due to stretching of the connecting loop to the top of the D helix (hD), as confirmed in TBG with shortening of the loop by three residues, making it insensitive to the S-to-R transition. The transmission of the changes in the hD loop to the binding pocket is seen to involve coherent movements in the s2/3B loop linked to the hD loop by Lys(243), which is, in turn, linked to the s4/5B loop, flanking the thyroxine-binding site, by Arg(378). Overall, the coordinated movements of the reactive loop, hD, and the hormone binding site allow the allosteric regulation of hormone release, as with the modulation demonstrated here in response to changes in temperature

Gene-Boosted Assembly of a Novel Bacterial Genome from Very Short Reads

Recent improvements in technology have made DNA sequencing dramatically faster and more efficient than ever before. The new technologies produce highly accurate sequences, but one drawback is that the most efficient technology produces the shortest read lengths. Short-read sequencing has been applied successfully to resequence the human genome and those of other species but not to whole-genome sequencing of novel organisms. Here we describe the sequencing and assembly of a novel clinical isolate of Pseudomonas aeruginosa, strain PAb1, using very short read technology. From 8,627,900 reads, each 33 nucleotides in length, we assembled the genome into one scaffold of 76 ordered contiguous sequences containing 6,290,005 nucleotides, including one contig spanning 512,638 nucleotides, plus an additional 436 unordered contigs containing 416,897 nucleotides. Our method includes a novel gene-boosting algorithm that uses amino acid sequences from predicted proteins to build a better assembly. This study demonstrates the feasibility of very short read sequencing for the sequencing of bacterial genomes, particularly those for which a related species has been sequenced previously, and expands the potential application of this new technology to most known prokaryotic species

Variational quantum Monte Carlo study of two-dimensional Wigner crystals: exchange, correlation, and magnetic field effects

The two-dimensional Wigner crystals are studied with the variational quantum Monte Carlo method. The close relationship between the ground-state wavefunction and the collective excitations in the system is illustrated, and used to guide the construction of the ground-state wavefunction of the strongly correlated solid. Exchange, correlation, and magnetic field effects all give rise to distinct physical phenomena. In the absence of any external magnetic field, interesting spin-orderings are observed in the ground-state of the electron crystal in various two-dimensional lattices. In particular, two-dimensional bipartite lattices are shown not to lead necessarily to an antiferromagnetic ground-state. In the quantum Hall effect regime, a strong magnetic field introduces new energy and length scales. The magnetic field quenches the kinetic energy and poses constraints on how the electrons may correlate with each other. Care is taken to ensure the appropriate translational properties of the wavefunction when the system is in a uniform magnetic field. We have examined the exchange, intra-Landau-level correlation as well as Landau-level-mixing effects with various variational wavefunctions. We also determine their dependences on the experimental parameters such as the carrier effective mass at a modulation-doped semiconductor heterojunction. Our results, when combined with some recent calculations for the energy of the fractional quantum Hall liquid including Landau-level-mixing, show quantitatively that in going from $n$-doping to $p$-doping in $GaAS/AlGaAS$ heterojunction systems, the crossover filling factor from the fractional quantum Hall liquid to the Wigner crystal changes from filling factor $\nu \sim 1/5$ to $\nu \sim 1/3$. This lends strong support to the claim that theComment: LaTex file, 14 figures available from [email protected]

Population stratification may bias analysis of PGC-1α as a modifier of age at Huntington disease motor onset

Huntington’s disease (HD) is an inherited neurodegenerative disorder characterized by motor, cognitive and behavioral disturbances, caused by the expansion of a CAG trinucleotide repeat in the HD gene. The CAG allele size is the major determinant of age at onset (AO) of motor symptoms, although the remaining variance in AO is highly heritable. The rs7665116 SNP in PPARGC1A, encoding the mitochondrial regulator PGC-1α, has been reported to be a significant modifier of AO in three European HD cohorts, perhaps due to affected cases from Italy. We attempted to replicate these findings in a large collection of (1,727) HD patient DNA samples of European origin. In the entire cohort, rs7665116 showed a significant effect in the dominant model (p value = 0.008) and the additive model (p value = 0.009). However, when examined by origin, cases of Southern European origin had an increased rs7665116 minor allele frequency (MAF), consistent with this being an ancestry-tagging SNP. The Southern European cases, despite similar mean CAG allele size, had a significantly older mean AO (p < 0.001), suggesting population-dependent phenotype stratification. When the generalized estimating equations models were adjusted for ancestry, the effect of the rs7665116 genotype on AO decreased dramatically. Our results do not support rs7665116 as a modifier of AO of motor symptoms, as we found evidence for a dramatic effect of phenotypic (AO) and genotypic (MAF) stratification among European cohorts that was not considered in previously reported association studies. A significantly older AO in Southern Europe may reflect population differences in genetic or environmental factors that warrant further investigation

The Eighth Data Release of the Sloan Digital Sky Survey: First Data from SDSS-III

The Sloan Digital Sky Survey (SDSS) started a new phase in August 2008, with new instrumentation and new surveys focused on Galactic structure and chemical evolution, measurements of the baryon oscillation feature in the clustering of galaxies and the quasar Ly alpha forest, and a radial velocity search for planets around ~8000 stars. This paper describes the first data release of SDSS-III (and the eighth counting from the beginning of the SDSS). The release includes five-band imaging of roughly 5200 deg^2 in the Southern Galactic Cap, bringing the total footprint of the SDSS imaging to 14,555 deg^2, or over a third of the Celestial Sphere. All the imaging data have been reprocessed with an improved sky-subtraction algorithm and a final, self-consistent photometric recalibration and flat-field determination. This release also includes all data from the second phase of the Sloan Extension for Galactic Understanding and Evolution (SEGUE-2), consisting of spectroscopy of approximately 118,000 stars at both high and low Galactic latitudes. All the more than half a million stellar spectra obtained with the SDSS spectrograph have been reprocessed through an improved stellar parameters pipeline, which has better determination of metallicity for high metallicity stars.Comment: Astrophysical Journal Supplements, in press (minor updates from submitted version

The Ninth Data Release of the Sloan Digital Sky Survey: First Spectroscopic Data from the SDSS-III Baryon Oscillation Spectroscopic Survey

The Sloan Digital Sky Survey III (SDSS-III) presents the first spectroscopic data from the Baryon Oscillation Spectroscopic Survey (BOSS). This ninth data release (DR9) of the SDSS project includes 535,995 new galaxy spectra (median z=0.52), 102,100 new quasar spectra (median z=2.32), and 90,897 new stellar spectra, along with the data presented in previous data releases. These spectra were obtained with the new BOSS spectrograph and were taken between 2009 December and 2011 July. In addition, the stellar parameters pipeline, which determines radial velocities, surface temperatures, surface gravities, and metallicities of stars, has been updated and refined with improvements in temperature estimates for stars with T_eff<5000 K and in metallicity estimates for stars with [Fe/H]>-0.5. DR9 includes new stellar parameters for all stars presented in DR8, including stars from SDSS-I and II, as well as those observed as part of the SDSS-III Sloan Extension for Galactic Understanding and Exploration-2 (SEGUE-2). The astrometry error introduced in the DR8 imaging catalogs has been corrected in the DR9 data products. The next data release for SDSS-III will be in Summer 2013, which will present the first data from the Apache Point Observatory Galactic Evolution Experiment (APOGEE) along with another year of data from BOSS, followed by the final SDSS-III data release in December 2014.Comment: 9 figures; 2 tables. Submitted to ApJS. DR9 is available at http://www.sdss3.org/dr

Candidate glutamatergic and dopaminergic pathway gene variants do not influence Huntington’s disease motor onset

Huntington’s disease (HD) is a neurodegenerative disorder characterized by motor, cognitive, and behavioral disturbances. It is caused by the expansion of the HTT CAG repeat, which is the major determinant of age at onset (AO) of motor symptoms. Aberrant function of N-methyl-D-aspartate receptors and/or overexposure to dopamine has been suggested to cause significant neurotoxicity, contributing to HD pathogenesis. We used genetic association analysis in 1,628 HD patients to evaluate candidate polymorphisms in N-methyl-D-aspartate receptor subtype genes (GRIN2A rs4998386 and rs2650427, and GRIN2B rs1806201) and functional polymorphisms in genes in the dopamine pathway (DAT1 3′ UTR 40-bp variable number tandem repeat (VNTR), DRD4 exon 3 48-bp VNTR, DRD2 rs1800497, and COMT rs4608) as potential modifiers of the disease process. None of the seven polymorphisms tested was found to be associated with significant modification of motor AO, either in a dominant or additive model, after adjusting for ancestry. The results of this candidate-genetic study therefore do not provide strong evidence to support a modulatory role for these variations within glutamatergic and dopaminergic genes in the AO of HD motor manifestations