String and Fivebrane Solitons: Singular or Non-singular?

We ask whether the recently discovered superstring and superfivebrane solutions of D=10 supergravity admit the interpretation of non-singular solitons even though, in the absence of Yang-Mills fields, they exhibit curvature singularities at the origin. We answer the question using a test probe/source approach, and find that the nature of the singularity is probe-dependent. If the test probe and source are both superstrings or both superfivebranes, one falls into the other in a finite proper time and the singularity is real, whereas if one is a superstring and the other a superfivebrane it takes an infinite proper time (the force is repulsive!) and the singularity is harmless. Black strings and fivebranes, on the other hand, always display real singularities.Comment: 15 page

Structural elucidation of o-linked glycopeptides by high energy collision-induced dissociation

O-linked glycopeptides that bear a GalNAc core with and without the presence of sialic acid have been analyzed by high energy collision-induced dissociation (CID). We show that the CID spectra from the glycosylated precursor ions contain sufficient information to identify the peptide sequence and to determine the glycosylated site(s). Asialo O-linked glycopeptides, previously prepared from a tryptic digest of bovine fetuin were studied. One of the glycopeptides contained only a single Hex (hexose)-HexNAc (N-acetylhexosamine) substitution at Thr262, whereas the other exhibited Hex-HexNAc moieties at both Thr262 and Ser264. In addition, sialo and asialo fetuin glycopeptides from a pronase digest were derivatized with t-butoxycarbonyl-tyrosine, and characterized by high energy CID analysis. The presence of a Galβ(1,3)GalNAc core structure at Ser264 was confirmed by using the substrate specificity of endo-α-N-acetylgalactosaminidase. These studies revealed the presence of a β-galactosidase specific for β(1,4) linkages in the endo-α-N-acetylgalactosaminidase preparation employed. Finally, the relative stability of N-and O-glycosyl bonds to high energy CID is addressed based upon comparison of the behavior of a synthetic N-linked glycopeptide with analogous O-linked structures

Euclidean wormholes with Phantom field and Phantom field accompanied by perfect fluid

We study the classical Euclidean wormhole solutions for the gravitational systems with minimally coupled pure Phantom field and minimally coupled Phantom field accompanied by perfect fluid. It is shown that such solutions do exist and then the general forms of the Phantom field potential are obtained for which there are classical Euclidean wormhole solutions.Comment: 15 pages, major revision with perfect flui

Intersecting D-Branes in ten and six dimensions

We show how, via $T$-duality, intersecting $D$-Brane configurations in ten (six) dimensions can be obtained from the elementary $D$-Brane configurations by embedding a Type IIB $D$-Brane into a Type IIB Nine-Brane (Five-Brane) and give a classification of such configurations. We show that only a very specific subclass of these configurations can be realized as (supersymmetric) solutions to the equations of motion of IIA/IIB supergravity. Whereas the elementary $D$-brane solutions in $d=10$ are characterized by a single harmonic function, those in $d=6$ contain two independent harmonic functions and may be viewed as the intersection of two $d=10$ elementary $D$-branes. Using string/string/string triality in six dimensions we show that the heterotic version of the elementary $d=6$ $D$-Brane solutions correspond in ten dimensions to intersecting Neveu-Schwarz/Neveu-Schwarz (NS/NS) strings or five-branes and their $T$-duals. We comment on the implications of our results in other than ten and six dimensions.Comment: 18 pages, Latex, (substantial changes in section 2

Supermembranes and Super Matrix Models

We review recent developments in the theory of supermembranes and their relation to matrix models.Comment: Invited lecture presented at the Corfu Workshop, September 20 - 26, 1998, of the TMR Project "Quantum Aspects of Gauge Theories, Supersymmetry and Unification" (ERBFMRXCT96-0045), to appear in the proceedings. Latex 41 p

Gauge Theory and the Excision of Repulson Singularities

We study brane configurations that give rise to large-N gauge theories with eight supersymmetries and no hypermultiplets. These configurations include a variety of wrapped, fractional, and stretched branes or strings. The corresponding spacetime geometries which we study have a distinct kind of singularity known as a repulson. We find that this singularity is removed by a distinctive mechanism, leaving a smooth geometry with a core having an enhanced gauge symmetry. The spacetime geometry can be related to large-N Seiberg-Witten theory.Comment: 31 pages LaTeX, 2 figures (v3: references added

Coupled oscillators as models of phantom and scalar field cosmologies

We study a toy model for phantom cosmology recently introduced in the literature and consisting of two oscillators, one of which carries negative kinetic energy. The results are compared with the exact phase space picture obtained for similar dynamical systems describing, respectively, a massive canonical scalar field conformally coupled to the spacetime curvature, and a conformally coupled massive phantom. Finally, the dynamical system describing exactly a minimally coupled phantom is studied and compared with the toy model.Comment: 18 pages, LaTeX, to appear in Physical Review

Proteome profiling outperforms transcriptome profiling for coexpression based gene function prediction

Coexpression of mRNAs under multiple conditions is commonly used to infer cofunctionality of their gene products despite well-known limitations of this "guilt-by-association" (GBA) approach. Recent advancements in mass spectrometry-based proteomic technologies have enabled global expression profiling at the protein level; however, whether proteome profiling data can outperform transcriptome profiling data for coexpression based gene function prediction has not been systematically investigated. Here, we address this question by constructing and analyzing mRNA and protein coexpression networks for three cancer types with matched mRNA and protein profiling data from The Cancer Genome Atlas (TCGA) and the Clinical Proteomic Tumor Analysis Consortium (CPTAC). Our analyses revealed a marked difference in wiring between the mRNA and protein coexpression networks. Whereas protein coexpression was driven primarily by functional similarity between coexpressed genes, mRNA coexpression was driven by both cofunction and chromosomal colocalization of the genes. Functionally coherent mRNA modules were more likely to have their edges preserved in corresponding protein networks than functionally incoherent mRNA modules. Proteomic data strengthened the link between gene expression and function for at least 75% of Gene Ontology (GO) biological processes and 90% of KEGG pathways. A web application Gene2Net (http://cptac.gene2net.org) developed based on the three protein coexpression networks revealed novel gene-function relationships, such as linking ERBB2 (HER2) to lipid biosynthetic process in breast cancer, identifying PLG as a new gene involved in complement activation, and identifying AEBP1 as a new epithelial-mesenchymal transition (EMT) marker. Our results demonstrate that proteome profiling outperforms transcriptome profiling for coexpression based gene function prediction. Proteomics should be integrated if not preferred in gene function and human disease studies

The Strong Energy Condition and the S-Brane Singularity Problem

Recently it has been argued that, because tachyonic matter satisfies the Strong Energy Condition [SEC], there is little hope of avoiding the singularities which plague S-Brane spacetimes. Meanwhile, however, Townsend and Wohlfarth have suggested an ingenious way of circumventing the SEC in such situations, and other suggestions for actually violating it in the S-Brane context have recently been proposed. Of course, the natural context for discussions of [effective or actual] violations of the SEC is the theory of asymptotically deSitter spacetimes, which tend to be less singular than ordinary FRW spacetimes. However, while violating or circumventing the SEC is necessary if singularities are to be avoided, it is not at all clear that it is sufficient. That is, we can ask: would an asymptotically deSitter S-brane spacetime be non-singular? We show that this is difficult to achieve; this result is in the spirit of the recently proved "S-brane singularity theorem". Essentially our results suggest that circumventing or violating the SEC may not suffice to solve the S-Brane singularity problem, though we do propose two ways of avoiding this conclusion.Comment: 13 pages, minor corrections and improvements, references adde

Star Models with Dark Energy

We have constructed star models consisting of four parts: (i) a homogeneous inner core with anisotropic pressure (ii) an infinitesimal thin shell separating the core and the envelope; (iii) an envelope of inhomogeneous density and isotropic pressure; (iv) an infinitesimal thin shell matching the envelope boundary and the exterior Schwarzschild spacetime. We have analyzed all the energy conditions for the core, envelope and the two thin shells. We have found that, in order to have static solutions, at least one of the regions must be constituted by dark energy. The results show that there is no physical reason to have a superior limit for the mass of these objects but for the ratio of mass and radius.Comment: 20 pages, 1 figure, references and some comments added, typos corrected, in press GR