Failed "nonaccelerating" models of prokaryote gene regulatory networks

Much current network analysis is predicated on the assumption that important biological networks will either possess scale free or exponential statistics which are independent of network size allowing unconstrained network growth over time. In this paper, we demonstrate that such network growth models are unable to explain recent comparative genomics results on the growth of prokaryote regulatory gene networks as a function of gene number. This failure largely results as prokaryote regulatory gene networks are "accelerating" and have total link numbers growing faster than linearly with network size and so can exhibit transitions from stationary to nonstationary statistics and from random to scale-free to regular statistics at particular critical network sizes. In the limit, these networks can undergo transitions so marked as to constrain network sizes to be below some critical value. This is of interest as the regulatory gene networks of single celled prokaryotes are indeed characterized by an accelerating quadratic growth with gene count and are size constrained to be less than about 10,000 genes encoded in DNA sequence of less than about 10 megabases. We develop two "nonaccelerating" network models of prokaryote regulatory gene networks in an endeavor to match observation and demonstrate that these approaches fail to reproduce observed statistics.Comment: Corrected error in biological input parameter: 13 pages, 9 figure

Validating module network learning algorithms using simulated data

In recent years, several authors have used probabilistic graphical models to learn expression modules and their regulatory programs from gene expression data. Here, we demonstrate the use of the synthetic data generator SynTReN for the purpose of testing and comparing module network learning algorithms. We introduce a software package for learning module networks, called LeMoNe, which incorporates a novel strategy for learning regulatory programs. Novelties include the use of a bottom-up Bayesian hierarchical clustering to construct the regulatory programs, and the use of a conditional entropy measure to assign regulators to the regulation program nodes. Using SynTReN data, we test the performance of LeMoNe in a completely controlled situation and assess the effect of the methodological changes we made with respect to an existing software package, namely Genomica. Additionally, we assess the effect of various parameters, such as the size of the data set and the amount of noise, on the inference performance. Overall, application of Genomica and LeMoNe to simulated data sets gave comparable results. However, LeMoNe offers some advantages, one of them being that the learning process is considerably faster for larger data sets. Additionally, we show that the location of the regulators in the LeMoNe regulation programs and their conditional entropy may be used to prioritize regulators for functional validation, and that the combination of the bottom-up clustering strategy with the conditional entropy-based assignment of regulators improves the handling of missing or hidden regulators.Comment: 13 pages, 6 figures + 2 pages, 2 figures supplementary informatio

Gaugino Mass without Singlets

In models with dynamical supersymmetry breaking in the hidden sector, the gaugino masses in the observable sector have been believed to be extremely suppressed (below 1 keV), unless there is a gauge singlet in the hidden sector with specific couplings to the observable sector gauge multiplets. We point out that there is a pure supergravity contribution to gaugino masses at the quantum level arising from the superconformal anomaly. Our results are valid to all orders in perturbation theory and are related to the `exact' beta functions for soft terms. There is also an anomaly contribution to the A terms proportional to the beta function of the corresponding Yukawa coupling. The gaugino masses are proportional to the corresponding gauge beta functions, and so do not satisfy the usual GUT relations.Comment: 25 pages, references added, typos and grammar correcte

Renormalization group flows for gauge theories in axial gauges

Gauge theories in axial gauges are studied using Exact Renormalisation Group flows. We introduce a background field in the infrared regulator, but not in the gauge fixing, in contrast to the usual background field gauge. It is shown how heat-kernel methods can be used to obtain approximate solutions to the flow and the corresponding Ward identities. Expansion schemes are discussed, which are not applicable in covariant gauges. As an application, we derive the one-loop effective action for covariantly constant field strength, and the one-loop beta-function for arbitrary regulator

Renormalization Ambiguities and Conformal Anomaly in Metric-Scalar Backgrounds

We analyze the problem of the existing ambiguities in the conformal anomaly in theories with external scalar field in curved backgrounds. In particular, we consider the anomaly of self-interacting massive scalar field theory and of Yukawa model in the massless conformal limit. In all cases the ambiguities are related to finite renormalizations of a local non-minimal terms in the effective action. We point out the generic nature of this phenomenon and provide a general method to identify the theories where such an ambiguity can arise.Comment: RevTeX, 10 pages, no figures. Small comment and two references added. Accepted for publication in Physical Review

Fermionic Glauber Operators and Quark Reggeization

We derive, in the framework of soft-collinear effective field theory (SCET), a Lagrangian describing the $t$-channel exchange of Glauber quarks in the Regge limit. The Glauber quarks are not dynamical, but are incorporated through non-local fermionic potential operators. These operators are power suppressed in $|t|/s$ relative to those describing Glauber gluon exchange, but give the first non-vanishing contributions in the Regge limit to processes such as $q\bar q \to gg$ and $q\bar q \to \gamma \gamma$. They therefore represent an interesting subset of power corrections to study. The structure of the operators, which describe certain soft and collinear emissions to all orders through Wilson lines, is derived from the symmetries of the effective theory combined with constraints from power and mass dimension counting, as well as through explicit matching calculations. Lightcone singularities in the fermionic potentials are regulated using a rapidity regulator, whose corresponding renormalization group evolution gives rise to the Reggeization of the quark at the amplitude level and the BFKL equation at the cross section level. We verify this at one-loop, deriving the Regge trajectory of the quark in the $3$ color channel, as well as the leading logarithmic BFKL equation. Results in the $\bar 6$ and $15$ color channels are obtained by the simultaneous exchange of a Glauber quark and a Glauber gluon. SCET with quark and gluon Glauber operators therefore provides a framework to systematically study the structure of QCD amplitudes in the Regge limit, and derive constraints on higher order amplitudes.Comment: 31 pages, many figure