Literature Mapping with PubAtlas — extending PubMed with a ‘BLASTing interface’ *

PubAtlas (www.pubatlas.org) is a web service and standalone program providing literature maps for the biomedical research literature. It accepts user-defined sets of terms (PubMed queries) as input, and permits ‘BLASTing’ of one set against another: for all terms x and y in these sets, deriving the results of the pairwise intersections x AND y. This all vs. all capability extends PubMed with a literature analysis interface. Correspondingly, the basic form of literature map that PubAtlas provides for exploring associations among sets of terms is an interactive tabular display, in heatmap/microarray format

Molecular and clinical characterization of a claudin-low subtype of gastric cancer

Purpose Claudin-low molecular subtypes have been identified in breast and bladder cancers and are characterized by low expression of claudins, enrichment for epithelial-to-mesenchymal transition (EMT), and tumor-initiating cell (TIC) features. We evaluated whether the claudin-low subtype also exists in gastric cancer. Materials and Methods Four hundred fifteen tumors from The Cancer Genome Atlas (TCGA) gastric cancer mRNA data set were clustered on the claudin, EMT, and TIC gene sets to identify claudin-low tumors. We derived a 24-gene predictor that classifies gastric cancer into claudin-low and non-claudin-low subtypes. This predictor was validated with the Asian Cancer Research Group(ACRG)data set. We characterized molecular and clinical features of claudin-low tumors. Results We identified 46 tumors that had consensus enrichment for claudin-low features in TCGA data set. Claudin-low tumors were most commonly diffuse histologic type (82%) and originally classified as TCGA genomically stable(GS)subtype (78%). Compared with GS subtype, claudin-low subtype had significant activation in Rho family of GTPases signaling, which appears to play a key role in its EMT and TIC properties. In the ACRG data set, 28 of 300 samples were classified as claudin-low tumors by the 24-gene predictor and were phenotypically similar to the initially derived claudin-low tumors. Clinically, claudin-low subtype had the worst overall survival. Of note, the hazard ratios that compared claudin-low versus GS subtype were 2.10 (95% CI, 1.07 to 4.11) in TCGA and 2.32 (95% CI, 1.18 to 4.55) in the ACRG cohorts, with adjustment for age and pathologic stage. Conclusion We identified a gastric claudin-low subtype that carries a poor prognosis likely related to therapeutic resistance as a result of its EMT and TIC phenotypes

Matter wave solitons at finite temperatures

We consider the dynamics of a dark soliton in an elongated harmonically trapped Bose-Einstein condensate. A central question concerns the behavior at finite temperatures, where dissipation arises due to the presence of a thermal cloud. We study this problem using coupled Gross-Pitaevskii and $N$-body simulations, which include the mean field coupling between the condensate and thermal cloud. We find that the soliton decays relatively quickly even at very low temperatures, with the decay rate increasing with rising temperature.Comment: 6 pages, 2 figures, submitted to the Proceedings of QFS '0

THE HIGGS-YUKAWA MODEL IN CURVED SPACETIME

The Higgs-Yukawa model in curved spacetime (renormalizable in the usual sense) is considered near the critical point, employing the $1/N$--expansion and renormalization group techniques. By making use of the equivalence of this model with the standard NJL model, the effective potential in the linear curvature approach is calculated and the dynamically generated fermionic mass is found. A numerical study of chiral symmetry breaking by curvature effects is presented.Comment: LaTeX, 9 pages, 1 uu-figur

Bounded version vectors

Version vectors play a central role in update tracking under optimistic distributed systems, allowing the detection of obsolete or inconsistent versions of replicated data. Version vectors do not have a bounded representation; they are based on integer counters that grow indefinitely as updates occur. Existing approaches to this problem are scarce; the mechanisms proposed are either unbounded or operate only under specific settings. This paper examines version vectors as a mechanism for data causality tracking and clarifies their role with respect to vector clocks. Then, it introduces bounded stamps and proves them to be a correct alternative to integer counters in version vectors. The resulting mechanism, bounded version vectors, represents the first bounded solution to data causality tracking between replicas subject to local updates and pairwise symmetrical synchronization.FCT project POSI/ICHS/44304/2002, FCT under grant BSAB/390/2003

Scalable and accurate causality tracking for eventually consistent stores

Lecture Notes in Computer Science 8460, 2014In cloud computing environments, data storage systems often rely on optimistic replication to provide good performance and availability even in the presence of failures or network partitions. In this scenario, it is important to be able to accurately and efficiently identify updates executed concurrently. Current approaches to causality tracking in optimistic replication have problems with concurrent updates: they either (1) do not scale, as they require replicas to maintain information that grows linearly with the number of writes or unique clients; (2) lose information about causality, either by removing entries from client-id based version vectors or using server-id based version vectors, which cause false conflicts. We propose a new logical clock mechanism and a logical clock framework that together support a traditional key-value store API, while capturing causality in an accurate and scalable way, avoiding false conflicts. It maintains concise information per data replica, only linear on the number of replica servers, and allows data replicas to be compared and merged linear with the number of replica servers and versions.(undefined

Locating current sheets in the solar corona

Current sheets are essential for energy dissipation in the solar corona, in particular by enabling magnetic reconnection. Unfortunately, sufficiently thin current sheets cannot be resolved observationally and the theory of their formation is an unresolved issue as well. We consider two predictors of coronal current concentrations, both based on geometrical or even topological properties of a force free coronal magnetic field. First, there are separatrices related to magnetic nulls. Through separatrices the magnetic connectivity changes discontinuously. Coronal magnetic nulls are, however, very rare. At second, inspired by the concept of generalized magnetic reconnection without nulls, quasi-separatrix layers (QSL) were suggested. Through QSL the magnetic connectivity changes continuously, though strongly. The strength of the connectivity change can be quantified by measuring the squashing of the flux tubes which connect the magnetically conjugated photospheres. We verify the QSL and separatrix concepts by comparing the sites of magnetic nulls and enhanced squashing with the location of current concentrations in the corona. Due to the known difficulties of their direct observation we simulated the coronal current sheets by numerically calculating the response of the corona to energy input from the photosphere heating a simultaneously observed EUV Bright Point. We did not find coronal current sheets not at the separatrices but at several QSL locations. The reason is that although the geometrical properties of force free extrapolated magnetic fields can indeed, hint at possible current concentrations, a necessary condition for current sheet formation is the local energy input into the corona

Real spin glasses relax slowly in the shade of hierarchical trees

The Parisi solution of the mean-field spin glass has been widely accepted and celebrated. Its marginal stability in 3d and its complexity however raised the question of its relevance to real spin glasses. This paper gives a short overview of the important experimental results which could be understood within the mean-field solution. The existence of a true phase transition and the particular behaviour of the susceptibility below the freezing temperature, predicted by the theory, are clearly confirmed by the experimental results. The behaviour of the complex order parameter and of the Fluctuation Dissipation ratio are in good agreement with results of spontaneous noise measurements. The very particular ultrametric symmetry, the key feature of the theory, provided us with a simple description of the rejuvenation and memory effects observed in experiment. Finally, going a step beyond mean-field, the paper shortly discusses new analyses in terms of correlated domains characterized by their length scales, as well as new experiments on superspin glasses which compare well with recent theoretical simulations.Comment: To appear in the proceedings of "Wandering with Curiosity in Complex Landscapes", a scientific conference in honour of Giorgio Parisi for his 60th birthday, Roma, September 8-10 2008 (submitted for the special issue of the Journal of Statistical Physics, 2009

Acoustic Power Absorption and its Relation with Vector Magnetic Field of a Sunspot

The distribution of acoustic power over sunspots shows an enhanced absorption near the umbra--penumbra boundary. Earlier studies revealed that the region of enhanced absorption coincides with the region of strongest transverse potential field. The aim of this paper is to (i) utilize the high-resolution vector magnetograms derived using Hinode SOT/SP observations and study the relationship between the vector magnetic field and power absorption and (ii) study the variation of power absorption in sunspot penumbrae due to the presence of spine-like radial structures. It is found that (i) both potential and observed transverse fields peak at a similar radial distance from the center of the sunspot, and (ii) the magnitude of the transverse field, derived from Hinode observations, is much larger than the potential transverse field derived from SOHO/MDI longitudinal field observations. In the penumbra, the radial structures called spines (intra-spines) have stronger (weaker) field strength and are more vertical (horizontal). The absorption of acoustic power in the spine and intra-spine shows different behaviour with the absorption being larger in the spine as compared to the intra-spine.Comment: 18 pages, 7 figures, In Press Solar Physics, Topical Issue on Helio-and-Astroseismolog