Dynamics of genetic code evolution: The emergence of universality.

We study the dynamics of genetic code evolution. The model of Vetsigian et al. [Proc. Natl. Acad. Sci. USA 103, 10696 (2006)PNASA60027-842410.1073/pnas.0603780103] and Vetsigian [Collective evolution of biological and physical systems, Ph.D. thesis, 2005] uses the mechanism of horizontal gene transfer to demonstrate convergence of the genetic code to a near universal solution. We reproduce and analyze the algorithm as a dynamical system. All the parameters used in the model are varied to assess their impact on convergence and optimality score. We show that by allowing specific parameters to vary with time, the solution exhibits attractor dynamics. Finally, we study automorphisms of the genetic code arising due to this model. We use this to examine the scaling of the solutions to re-examine universality and find that there is a direct link to mutation rate.

Machine-learning a virus assembly fitness landscape.

Realistic evolutionary fitness landscapes are notoriously difficult to construct. A recent cutting-edge model of virus assembly consists of a dodecahedral capsid with 12 corresponding packaging signals in three affinity bands. This whole genome/phenotype space consisting of 312 genomes has been explored via computationally expensive stochastic assembly models, giving a fitness landscape in terms of the assembly efficiency. Using latest machine-learning techniques by establishing a neural network, we show that the intensive computation can be short-circuited in a matter of minutes to astounding accuracy.

Traintracks through Calabi-Yau Manifolds: Scattering Amplitudes beyond Elliptic Polylogarithms.

We describe a family of finite, four-dimensional, L-loop Feynman integrals that involve weight-(L+1) hyperlogarithms integrated over (L-1)-dimensional elliptically fibered varieties we conjecture to be Calabi-Yau manifolds. At three loops, we identify the relevant K3 explicitly and we provide strong evidence that the four-loop integral involves a Calabi-Yau threefold. These integrals are necessary for the representation of amplitudes in many theories-from massless φ^{4} theory to integrable theories including maximally supersymmetric Yang-Mills theory in the planar limit-a fact we demonstrate.

Influence of Old Age, Gender, and Internal Mammary Artery Grafting on Operative Mortality and Morbidity in Coronary Artery Bypass Grafting.

Operative risk may change its pattern from time to time. To investigate determinants for operative mortality in patients undergoing CABG since the mid 1980s and the influence of age, gender, and IMAG on mortality, the data of 6,360 patients who underwent CABG from January 1986 through June 1993 were analyzed. Of these patients, 2,153 had SVG alone and 4,207 had IMAG including UIMAG (3,957) and BIMAG (250). Overall mortality was 4.34%. OM (in hospital death) for IMAG (2.69%) was lower than for SVG (7.57%, p is less than 0.0001). There was no difference in mortality between BIMAG (3.2%) and UIMAG patients (2.65%, p equals 0.6) or UIMAG/SVG patients (4.29%, p equals 0.36). Fewer IMAG patients had postoperative complications (LCO, insertion of IABP, prolonged ventilation, reoperation for bleeding, neurological complications, perioperative MI, and infection of legs) than SVG patients. There was no difference in the incidence of sternal infection. To determine risk factors for mortality and the influence of IMAG on the outcome, 82 variables (31 preoperative, 17 intraoperative, and 34 postoperative) were analyzed by univariate analysis. Significant variables or the variables having a trend (p is less than 0.2) to be associated with mortality were included in stepwise multiple logistic regression analyses. Two regression analyses were separately performed. Regression 1 only included pre- and intraoperative variables whereas regression 2 included postoperative variables as well. The logistic regressions demonstrate that preoperative (low EF, age at or above 70, female gender, history of CHF or arrhythmia, and functional Class), intraoperative (emergency operation, reoperation, long perfusion time, and lack of IMAG), and postoperative (complications) variables are independently associated with higher mortality. Female gender is an independent determinant for mortality and not dependent on small body surface area. Neither use of BIMAG or right IMAG, nor number of grafts is associated with the OM. The identification of these risk factors may have important implications in further improvement of the results for CABG.