Guiding-center dynamics of vortex dipoles in Bose-Einstein condensates

A quantized vortex dipole is the simplest vortex molecule, comprising two counter-circulating vortex lines in a superfluid. Although vortex dipoles are endemic in two-dimensional superfluids, the precise details of their dynamics have remained largely unexplored. We present here several striking observations of vortex dipoles in dilute-gas Bose-Einstein condensates, and develop a vortex-particle model that generates vortex line trajectories that are in good agreement with the experimental data. Interestingly, these diverse trajectories exhibit essentially identical quasi-periodic behavior, in which the vortex lines undergo stable epicyclic orbits.Comment: 4 pages, 2 figure

Toward a Surrogate Marker of Malaria Exposure: Modeling Longitudinal Antibody Measurements under Outbreak Conditions

Background: Biomarkers of exposure to Plasmodium falciparum would be a useful tool for the assessment of malaria burden and analysis of intervention and epidemiological studies. Antibodies to pre-erythrocytic antigens represent potential surrogates of exposure. Methods and Findings: In an outbreak cohort of U.S. Marines deployed to Liberia, we modeled pre- and post-deployment IgG against P. falciparum sporozoites by immunofluorescence antibody test, and both IgG and IgM against the P. falciparum circumsporozoite protein by enzyme-linked immunosorbant assay. Modeling seroconversion thresholds by a fixed ratio, linear regression or nonlinear regression produced sensitivity for identification of exposed U.S. Marines between 58-70% and specificities between 87-97%, compared with malaria-naïve U.S. volunteers. Exposure was predicted in 30-45% of the cohort. Conclusion: Each of the three models tested has merits in different studies, but further development and validation in endemic populations is required. Overall, these models provide support for an antibody-based surrogate marker of exposure to malaria

Stratification of co-evolving genomic groups using ranked phylogenetic profiles

<p>Abstract</p> <p>Background</p> <p>Previous methods of detecting the taxonomic origins of arbitrary sequence collections, with a significant impact to genome analysis and in particular metagenomics, have primarily focused on compositional features of genomes. The evolutionary patterns of phylogenetic distribution of genes or proteins, represented by phylogenetic profiles, provide an alternative approach for the detection of taxonomic origins, but typically suffer from low accuracy. Herein, we present <it>rank-BLAST</it>, a novel approach for the assignment of protein sequences into genomic groups of the same taxonomic origin, based on the ranking order of phylogenetic profiles of target genes or proteins across the reference database.</p> <p>Results</p> <p>The rank-BLAST approach is validated by computing the phylogenetic profiles of all sequences for five distinct microbial species of varying degrees of phylogenetic proximity, against a reference database of 243 fully sequenced genomes. The approach - a combination of sequence searches, statistical estimation and clustering - analyses the degree of sequence divergence between sets of protein sequences and allows the classification of protein sequences according to the species of origin with high accuracy, allowing taxonomic classification of 64% of the proteins studied. In most cases, a main cluster is detected, representing the corresponding species. Secondary, functionally distinct and species-specific clusters exhibit different patterns of phylogenetic distribution, thus flagging gene groups of interest. Detailed analyses of such cases are provided as examples.</p> <p>Conclusion</p> <p>Our results indicate that the rank-BLAST approach can capture the taxonomic origins of sequence collections in an accurate and efficient manner. The approach can be useful both for the analysis of genome evolution and the detection of species groups in metagenomics samples.</p

Observations of Coupling between Surface Wind Stress and Sea Surface Temperature in the Eastern Tropical Pacific

Satellite measurements of surface wind stress from the QuikSCAT scatterometer and sea surface temperature (SST) from the Tropical Rainfall Measuring Mission Microwave Imager are analyzed for the three-month period 21 July–20 October 1999 to investigate ocean–atmosphere coupling in the eastern tropical Pacific. Oceanic tropical instability waves (TIWs) with periods of 20–40 days and wavelengths of 1000–2000 km perturb the SST fronts that bracket both sides of the equatorial cold tongue, which is centered near 1°S to the east of 130°W. These perturbations are characterized by cusp-shaped features that propagate systematically westward on both sides of the equator. The space–time structures of these SST perturbations are reproduced with remarkable detail in the surface wind stress field. The wind stress divergence is shown to be linearly related to the downwind component of the SST gradient with a response on the south side of the cold tongue that is about twice that on the north side. The wind stress curl is linearly related to the crosswind component of the SST gradient with a response that is approximately half that of the wind stress divergence response to the downwind SST gradient. The perturbed SST and wind stress fields propagate synchronously westward with the TIWs. This close coupling between SST and wind stress supports the Wallace et al. hypothesis that surface winds vary in response to SST modification of atmospheric boundary layer stability

Mapping interactions with the chaperone network reveals factors that protect against tau aggregation.

A network of molecular chaperones is known to bind proteins ('clients') and balance their folding, function and turnover. However, it is often unclear which chaperones are critical for selective recognition of individual clients. It is also not clear why these key chaperones might fail in protein-aggregation diseases. Here, we utilized human microtubule-associated protein tau (MAPT or tau) as a model client to survey interactions between ~30 purified chaperones and ~20 disease-associated tau variants (~600 combinations). From this large-scale analysis, we identified human DnaJA2 as an unexpected, but potent, inhibitor of tau aggregation. DnaJA2 levels were correlated with tau pathology in human brains, supporting the idea that it is an important regulator of tau homeostasis. Of note, we found that some disease-associated tau variants were relatively immune to interactions with chaperones, suggesting a model in which avoiding physical recognition by chaperone networks may contribute to disease

Imaging of ependymomas: MRI and CT

The imaging features of intracranial and spinal ependymoma are reviewed with an emphasis on conventional magnetic resonance imaging (MRI), perfusion MRI and proton magnetic resonance spectroscopy, and computed tomography. Imaging manifestations of leptomeningeal dissemination of disease are described. Finally, salient imaging features obtained in the postoperative period to evaluate completeness of surgical resection, and thereafter for long-term surveillance for disease recurrence, are reviewed