Vortices in attractive Bose-Einstein condensates in two dimensions

The form and stability of quantum vortices in Bose-Einstein condensates with attractive atomic interactions is elucidated. They appear as ring bright solitons, and are a generalization of the Townes soliton to nonzero winding number $m$. An infinite sequence of radially excited stationary states appear for each value of $m$, which are characterized by concentric matter-wave rings separated by nodes, in contrast to repulsive condensates, where no such set of states exists. It is shown that robustly stable as well as unstable regimes may be achieved in confined geometries, thereby suggesting that vortices and their radial excited states can be observed in experiments on attractive condensates in two dimensions.Comment: 4 pages, 3 figure

Vortices and Ring Solitons in Bose-Einstein Condensates

The form and stability properties of axisymmetric and spherically symmetric stationary states in two and three dimensions, respectively, are elucidated for Bose-Einstein condensates. These states include the ground state, central vortices, and radial excitations of both. The latter are called ring solitons in two dimensions and spherical shells in three. The nonlinear Schrodinger equation is taken as the fundamental model; both extended and harmonically trapped condensates are considered. It is found that the presence of a vortex stabilizes ring solitons in a harmonic trap, in contrast to the well known instability of such solutions in the optics context. This is the first known example of a dark soliton in the cubic nonlinear Schrodinger equation which is stable in a number of dimensions greater than one.Comment: 15 pages, 9 figures -- final versio

Searching QTL by gene expression: analysis of diabesity

BACKGROUND: Recent developments in sequence databases provide the opportunity to relate the expression pattern of genes to their genomic position, thus creating a transcriptome map. Quantitative trait loci (QTL) are phenotypically-defined chromosomal regions that contribute to allelically variant biological traits, and by overlaying QTL on the transcriptome, the search for candidate genes becomes extremely focused. RESULTS: We used our novel data mining tool, ExQuest, to select genes within known diabesity QTL showing enriched expression in primary diabesity affected tissues. We then quantified transcripts in adipose, pancreas, and liver tissue from Tally Ho mice, a multigenic model for Type II diabetes (T2D), and from diabesity-resistant C57BL/6J controls. Analysis of the resulting quantitative PCR data using the Global Pattern Recognition analytical algorithm identified a number of genes whose expression is altered, and thus are novel candidates for diabesity QTL and/or pathways associated with diabesity. CONCLUSION: Transcription-based data mining of genes in QTL-limited intervals followed by efficient quantitative PCR methods is an effective strategy for identifying genes that may contribute to complex pathophysiological processes

Enamel ribbons, surface nodules, and octacalcium phosphate in C57BL/6 Amelxâ /â mice and Amelx+/â lyonization

BackgroundAmelogenin is required for normal enamel formation and is the most abundant protein in developing enamel.MethodsAmelx+/+, Amelx+/â , and Amelxâ /â molars and incisors from C57BL/6 mice were characterized using RTâ PCR, Western blotting, dissecting and light microscopy, immunohistochemistry (IHC), transmission electron microscopy (TEM), scanning electron microscopy (SEM), backscattered SEM (bSEM), nanohardness testing, and Xâ ray diffraction.ResultsNo amelogenin protein was detected by Western blot analyses of enamel extracts from Amelxâ /â mice. Amelxâ /â incisor enamel averaged 20.3 ± 3.3 μm in thickness, or only 1/6th that of the wild type (122.3 ± 7.9 μm). Amelxâ /â incisor enamel nanohardness was 1.6 Gpa, less than half that of wildâ type enamel (3.6 Gpa). Amelx+/â incisors and molars showed vertical banding patterns unique to each tooth. IHC detected no amelogenin in Amelxâ /â enamel and varied levels of amelogenin in Amelx+/â incisors, which correlated positively with enamel thickness, strongly supporting lyonization as the cause of the variations in enamel thickness. TEM analyses showed characteristic mineral ribbons in Amelx+/+ and Amelxâ /â enamel extending from mineralized dentin collagen to the ameloblast. The Amelxâ /â enamel ribbons were not well separated by matrix and appeared to fuse together, forming plates. Xâ ray diffraction determined that the predominant mineral in Amelxâ /â enamel is octacalcium phosphate (not calcium hydroxyapatite). Amelxâ /â ameloblasts were similar to wildâ type ameloblasts except no Tomesâ processes extended into the thin enamel. Amelxâ /â and Amelx+/â molars both showed calcified nodules on their occlusal surfaces. Histology of D5 and D11 developing molars showed nodules forming during the maturation stage.ConclusionAmelogenin forms a resorbable matrix that separates and supports, but does not shape early secretoryâ stage enamel ribbons. Amelogenin may facilitate the conversion of enamel ribbons into hydroxyapatite by inhibiting the formation of octacalcium phosphate. Amelogenin is necessary for thickening the enamel layer, which helps maintain ribbon organization and development and maintenance of the Tomesâ process.We thoroughly characterized enamel formation in amelogenin null mice and determined that the mineral covering dentin in these animals is octacalcium phosphate. The initial enamel mineral has a ribbon shape, similar to the wild type. Thus, amelogenin is not required to shape the ribbons, as is currently thought, but is required to ensure that the final mineral phase is calcium hydroxyapatite.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/134766/1/mgg3252_am.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/134766/2/mgg3252-sup-0001-AppendixS1-21.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/134766/3/mgg3252.pd

Superfluid to solid crossover in a rotating Bose-Einstein condensed gas

The properties of a rotating Bose-Einstein condensate confined in a prolate cylindrically symmetric trap are explored both analytically and numerically. As the rotation frequency increases, an ever greater number of vortices are energetically favored. Though the cloud anisotropy and moment of inertia approach those of a classical fluid at high frequencies, the observed vortex density is consistently lower than the solid-body estimate. Furthermore, the vortices are found to arrange themselves in highly regular triangular arrays, with little distortion even near the condensate surface. These results are shown to be a direct consequence of the inhomogeneous confining potential.Comment: 4+e pages, 5 embedded figures, revte

Anomalous modes drive vortex dynamics in confined Bose-Einstein condensates

The dynamics of vortices in trapped Bose-Einstein condensates are investigated both analytically and numerically. In axially symmetric traps, the critical rotation frequency for the metastability of an isolated vortex coincides with the largest vortex precession frequency (or anomalous mode) in the Bogoliubov excitation spectrum. As the condensate becomes more elongated, the number of anomalous modes increases. The largest frequency of these modes exceeds both the thermodynamic critical frequency and the nucleation frequency at which vortices are created dynamically. Thus, anomalous modes describe not only the critical rotation frequency for creation of the first vortex in an elongated condensate but also the vortex precession in a single-component spherical condensate.Comment: 4 pages revtex, 3 embedded figure

Particle growth in urban and industrial plumes in Texas

Particle size distributions and gas-phase particle precursors and tracer species were measured aboard an aircraft in the plumes downwind from industrial and urban sources in the vicinity of Houston, TX during the daytime in late August and early September 2000. Plumes originating from the Parish gas-fired and coal-fired power plant, petrochemical industries along the Houston ship channel, the petrochemical facilities near the Gulf coast, and the urban center of Houston were studied. Most of the particle mass flux advected downwind of Houston came from the industries and electrical utilities at the periphery of the city rather than from sources in the urban core. In SO2-rich plumes that did not contain elevated concentrations of volatile organic compounds (VOCs), particle volume increased with increasing plume oxidation (age) at a rate consistent with condensation and neutralization of the gas-phase oxidation products Of SO2. In plumes that were rich in both SO2 and VOCs, observed particle growth greatly exceeded that expected from SO2 oxidation, indicating the formation of organic particulate mass. In plumes that were enhanced in VOCs but not in SO2, and in the plume of the Houston urban center, no particle volume growth with increasing plume oxidation was detected. Since substantial particle volume growth was associated only with SO2-rich plumes, these results suggest that photochemical oxidation of SO2 is the key process regulating particle mass growth in all the studied plumes in this region. However, uptake of organic matter probably contributes substantially to particle mass in petrochemical plumes rich in both SO2 and VOCs. Quantitative studies of particle formation and growth in photochemical systems containing nitrogen oxides (NOx = NO + NO2 ), VOCs, and SO2 are recommended to extend those previously made in NOx-VOC systems

Evaluation of commercially available RNA amplification kits for RNA sequencing using very low input amounts of total RNA

This article includes supplemental data. Please visit http://www.fasebj.org to obtain this information.Multiple recent publications on RNA sequencing (RNA-seq) have demonstrated the power of next-generation sequencing technologies in whole-transcriptome analysis. Vendor-specific protocols used for RNA library construction often require at least 100 ng total RNA. However, under certain conditions, much less RNA is available for library construction. In these cases, effective transcriptome profiling requires amplification of subnanogram amounts of RNA. Several commercial RNA amplification kits are available for amplification prior to library construction for next-generation sequencing, but these kits have not been comprehensively field evaluated for accuracy and performance of RNA-seq for picogram amounts of RNA. To address this, 4 types of amplification kits were tested with 3 different concentrations, from 5 ng to 50 pg, of a commercially available RNA. Kits were tested at multiple sites to assess reproducibility and ease of use. The human total reference RNA used was spiked with a control pool of RNA molecules in order to further evaluate quantitative recovery of input material. Additional control data sets were generated from libraries constructed following polyA selection or ribosomal depletion using established kits and protocols. cDNA was collected from the different sites, and libraries were synthesized at a single site using established protocols. Sequencing runs were carried out on the Illumina platform. Numerous metrics were compared among the kits and dilutions used. Overall, no single kit appeared to meet all the challenges of small input material. However, it is encouraging that excellent data can be recovered with even the 50 pg input total RNA