Genome-wide profiling of uncapped mRNA

Gene transcripts are under extensive posttranscriptional regulation, including the regulation of their stability. A major route for mRNA degradation produces uncapped mRNAs, which can be generated by decapping enzymes, endonucleases, and small RNAs. Profiling uncapped mRNA molecules is important for the understanding of the transcriptome, whose composition is determined by a balance between mRNA synthesis and degradation. In this chapter, we describe a method to profile these uncapped mRNAs at the genome scale

Use of q-values to Improve a Genetic Algorithm to Identify Robust Gene Signatures

Several approaches have been proposed for the analysis of DNA microarray datasets, focusing on the performance and robustness of the final feature subsets. The novelty of this paper arises in the use of q-values to pre-filter the features of a DNA microarray dataset identifying the most significant ones and including this information into a genetic algorithm for further feature selection. This method is applied to a lung cancer microarray dataset resulting in similar performance rates and greater robustness in terms of selected features (on average a 36.21% of robustness improvement) when compared to results of the standard algorithm

Scattering Amplitudes and Toric Geometry

In this paper we provide a first attempt towards a toric geometric interpretation of scattering amplitudes. In recent investigations it has indeed been proposed that the all-loop integrand of planar N=4 SYM can be represented in terms of well defined finite objects called on-shell diagrams drawn on disks. Furthermore it has been shown that the physical information of on-shell diagrams is encoded in the geometry of auxiliary algebraic varieties called the totally non negative Grassmannians. In this new formulation the infinite dimensional symmetry of the theory is manifest and many results, that are quite tricky to obtain in terms of the standard Lagrangian formulation of the theory, are instead manifest. In this paper, elaborating on previous results, we provide another picture of the scattering amplitudes in terms of toric geometry. In particular we describe in detail the toric varieties associated to an on-shell diagram, how the singularities of the amplitudes are encoded in some subspaces of the toric variety, and how this picture maps onto the Grassmannian description. Eventually we discuss the action of cluster transformations on the toric varieties. The hope is to provide an alternative description of the scattering amplitudes that could contribute in the developing of this very interesting field of research.Comment: 58 pages, 25 figures, typos corrected, a reference added, to be published in JHE

Heavy Squarks at the LHC

The LHC, with its seven-fold increase in energy over the Tevatron, is capable of probing regions of SUSY parameter space exhibiting qualitatively new collider phenomenology. Here we investigate one such region in which first generation squarks are very heavy compared to the other superpartners. We find that the production of these squarks, which is dominantly associative, only becomes rate-limited at mSquark > 4(5) TeV for L~10(100) fb-1. However, discovery of this scenario is complicated because heavy squarks decay primarily into a jet and boosted gluino, yielding a dijet-like topology with missing energy (MET) pointing along the direction of the second hardest jet. The result is that many signal events are removed by standard jet/MET anti-alignment cuts designed to guard against jet mismeasurement errors. We suggest replacing these anti-alignment cuts with a measurement of jet substructure that can significantly extend the reach of this channel while still removing much of the background. We study a selection of benchmark points in detail, demonstrating that mSquark= 4(5) TeV first generation squarks can be discovered at the LHC with L~10(100)fb-1

Quantum biology on the edge of quantum chaos

We give a new explanation for why some biological systems can stay quantum coherent for long times at room temperatures, one of the fundamental puzzles of quantum biology. We show that systems with the right level of complexity between chaos and regularity can increase their coherence time by orders of magnitude. Systems near Critical Quantum Chaos or Metal-Insulator Transition (MIT) can have long coherence times and coherent transport at the same time. The new theory tested in a realistic light harvesting system model can reproduce the scaling of critical fluctuations reported in recent experiments. Scaling of return probability in the FMO light harvesting complex shows the signs of universal return probability decay observed at critical MIT. The results may open up new possibilities to design low loss energy and information transport systems in this Poised Realm hovering reversibly between quantum coherence and classicality

Emerging Non-Anomalous Baryonic Symmetries in the AdS_5/CFT_4 Correspondence

We study the breaking of baryonic symmetries in the AdS_5/CFT_4 correspondence for D3 branes at Calabi-Yau three-fold singularities. This leads, for particular VEVs, to the emergence of non-anomalous baryonic symmetries during the renormalization group flow. We claim that these VEVs correspond to critical values of the B-field moduli in the dual supergravity backgrounds. We study in detail the C^3/Z_3 orbifold, the cone over F_0 and the C^3/Z_5 orbifold. For the first two examples, we study the dual supergravity backgrounds that correspond to the breaking of the emerging baryonic symmetries and identify the expected Goldstone bosons and global strings in the infra-red. In doing so we confirm the claim that the emerging symmetries are indeed non-anomalous baryonic symmetries.Comment: 65 pages, 15 figures;v2: minor changes, published versio

A slice of AdS_5 as the large N limit of Seiberg duality

A slice of AdS_5 is used to provide a 5D gravitational description of 4D strongly-coupled Seiberg dual gauge theories. An (electric) SU(N) gauge theory in the conformal window at large N is described by the 5D bulk, while its weakly coupled (magnetic) dual is confined to the IR brane. This framework can be used to construct an N = 1 MSSM on the IR brane, reminiscent of the original Randall-Sundrum model. In addition, we use our framework to study strongly-coupled scenarios of supersymmetry breaking mediated by gauge forces. This leads to a unified scenario that connects the extra-ordinary gauge mediation limit to the gaugino mediation limit in warped space.Comment: 47 Pages, axodraw4j.st

Towards the F-Theorem: N=2 Field Theories on the Three-Sphere

For 3-dimensional field theories with {\cal N}=2 supersymmetry the Euclidean path integrals on the three-sphere can be calculated using the method of localization; they reduce to certain matrix integrals that depend on the R-charges of the matter fields. We solve a number of such large N matrix models and calculate the free energy F as a function of the trial R-charges consistent with the marginality of the superpotential. In all our {\cal N}=2 superconformal examples, the local maximization of F yields answers that scale as N^{3/2} and agree with the dual M-theory backgrounds AdS_4 x Y, where Y are 7-dimensional Sasaki-Einstein spaces. We also find in toric examples that local F-maximization is equivalent to the minimization of the volume of Y over the space of Sasakian metrics, a procedure also referred to as Z-minimization. Moreover, we find that the functions F and Z are related for any trial R-charges. In the models we study F is positive and decreases along RG flows. We therefore propose the "F-theorem" that we hope applies to all 3-d field theories: the finite part of the free energy on the three-sphere decreases along RG trajectories and is stationary at RG fixed points. We also show that in an infinite class of Chern-Simons-matter gauge theories where the Chern-Simons levels do not sum to zero, the free energy grows as N^{5/3} at large N. This non-trivial scaling matches that of the free energy of the gravity duals in type IIA string theory with Romans mass.Comment: 66 pages, 10 figures; v2: refs. added, minor improvement

Entanglement Entropy and Wilson Loop in St\"{u}ckelberg Holographic Insulator/Superconductor Model

We study the behaviors of entanglement entropy and vacuum expectation value of Wilson loop in the St\"{u}ckelberg holographic insulator/superconductor model. This model has rich phase structures depending on model parameters. Both the entanglement entropy for a strip geometry and the heavy quark potential from the Wilson loop show that there exists a "confinement/deconfinement" phase transition. In addition, we find that the non-monotonic behavior of the entanglement entropy with respect to chemical potential is universal in this model. The pseudo potential from the spatial Wilson loop also has a similar non-monotonic behavior. It turns out that the entanglement entropy and Wilson loop are good probes to study the properties of the holographic superconductor phase transition.Comment: 23 pages,12 figures. v2: typos corrected, accepted in JHE