The N=2 vector-tensor multiplet, central charge superspace, and Chern-Simons couplings

We present a new, alternative interpretation of the vector-tensor multiplet as a 2-form in central charge superspace. This approach provides a geometric description of the (non-trivial) central charge transformations ab initio and is naturally generalized to include couplings of Chern-Simons forms to the antisymmetric tensor gauge field, giving rise to a N=2 supersymmetric version of the Green-Schwarz anomaly cancellation mechanism.Comment: 11 pages, LaTe

General Matter Coupled N=4 Gauged Supergravity in Five Dimensions

We construct the general form of matter coupled N=4 gauged supergravity in five dimensions. Depending on the structure of the gauge group, these theories are found to involve vector and/or tensor multiplets. When self-dual tensor fields are present, they must be charged under a one-dimensional Abelian group and cannot transform non-trivially under any other part of the gauge group. A short analysis of the possible ground states of the different types of theories is given. It is found that AdS ground states are only possible when the gauge group is a direct product of a one-dimensional Abelian group and a semi-simple group. In the purely Abelian, as well as in the purely semi-simple gauging, at most Minkowski ground states are possible. The existence of such Minkowski ground states could be proven in the compact Abelian case.Comment: 30 pages, Latex, some references modified, typos in eq. (4.18) and (5.3) corrected. Version to appear in Nuclear Physics

Clustering proteins from interaction networks for the prediction of cellular functions

BACKGROUND: Developing reliable and efficient strategies allowing to infer a function to yet uncharacterized proteins based on interaction networks is of crucial interest in the current context of high-throughput data generation. In this paper, we develop a new algorithm for clustering vertices of a protein-protein interaction network using a density function, providing disjoint classes. RESULTS: Applied to the yeast interaction network, the classes obtained appear to be biological significant. The partitions are then used to make functional predictions for uncharacterized yeast proteins, using an annotation procedure that takes into account the binary interactions between proteins inside the classes. We show that this procedure is able to enhance the performances with respect to previous approaches. Finally, we propose a new annotation for 37 previously uncharacterized yeast proteins. CONCLUSION: We believe that our results represent a significant improvement for the inference of cellular functions, that can be applied to other organism as well as to other type of interaction graph, such as genetic interactions

Time course of information processing in visual and haptic object classification

Peer reviewedPublisher PD

Domain walls in five dimensional supergravity with non-trivial hypermultiplets

We study BPS domain wall solutions of 5-dimensional N=2 supergravity where isometries of the hypermultiplet geometry have been gauged. We derive the corresponding supersymmetric flow equations and define an appropriate c-function. As an example we discuss a domain wall solution of Freedman, Gubser, Pilch and Warner which is related to a RG-flow in a dual superconformal field theory.Comment: 20 page

N=2 central charge superspace and a minimal supergravity multiplet

We extend the notion of central charge superspace to the case of local supersymmetry. Gauged central charge transformations are identified as diffeomorphisms at the same footing as space-time diffeomorphisms and local supersymmetry transformations. Given the general structure we then proceed to the description of a particular vector-tensor supergravity multiplet of 24+24 components, identified by means of rather radical constraints

Ab initio identification of putative human transcription factor binding sites by comparative genomics

We discuss a simple and powerful approach for the ab initio identification of cis-regulatory motifs involved in transcriptional regulation. The method we present integrates several elements: human-mouse comparison, statistical analysis of genomic sequences and the concept of coregulation. We apply it to a complete scan of the human genome. By using the catalogue of conserved upstream sequences collected in the CORG database we construct sets of genes sharing the same overrepresented motif (short DNA sequence) in their upstream regions both in human and in mouse. We perform this construction for all possible motifs from 5 to 8 nucleotides in length and then filter the resulting sets looking for two types of evidence of coregulation: first, we analyze the Gene Ontology annotation of the genes in the set, searching for statistically significant common annotations; second, we analyze the expression profiles of the genes in the set as measured by microarray experiments, searching for evidence of coexpression. The sets which pass one or both filters are conjectured to contain a significant fraction of coregulated genes, and the upstream motifs characterizing the sets are thus good candidates to be the binding sites of the TF's involved in such regulation. In this way we find various known motifs and also some new candidate binding sites.Comment: 22 pages, 2 figures. Supplementary material available from the author

SimCT: a generic tool to visualize ontology-based relationships for biological objects

Summary: We present a web-based service, SimCT, which allows to graphically display the relationships between biological objects (e.g. genes or proteins) based on their annotations to a biomedical ontology. The result is presented as a tree of these objects, which can be viewed and explored through a specific java applet designed to highlight relevant features. Unlike the numerous tools that search for overrepresented terms, SimCT draws a simplified representation of biological terms present in the set of objects, and can be applied to any ontology for which annotation data is available. Being web-based, it does not require prior installation, and provides an intuitive, easy-to-use service

N=4 Supergravity with Antisymmetric Tensor in Central Charge Superspace

A concise geometrical formulation of N=4 supergravity containing an antisymmetric tensor gauge field is given in central charge superspace: graviphotons are identified in the super-vielbein on the same footing as the vierbein and the Rarita-Schwinger fields. As a consequence of superspace soldering, Chern-Simons terms in the fieldstrength of the antisymmetric tensor arise as an intrinsic property of superspace with central charge coordinates.Comment: Latex, 13 pages, minor clarification about a referenc