Constraints on inflation in closed universe

We investigate inflation in closed Friedmann-Robertson-Walker universe filled with the scalar field with power-law potential. For a wide range of powers and parameters of the potential we numerically calculated the slow-roll parameters and scalar spectral index at the epoch when present Hubble scale leaves the horizon and at the end of inflation. Also we compare results of our numerical calculations with recent observation data. This allows us to set a constraint on the power of the potential: alpha < (3.5 - 4.5).Comment: 5 pages, 5 figures; extended versio

Constraining slow-roll inflation with WMAP and 2dF

We constrain slow-roll inflationary models using the recent WMAP data combined with data from the VSA, CBI, ACBAR and 2dF experiments. We find the slow-roll parameters to be $0 < \epsilon_1 < 0.032$ and $\epsilon_2 + 5.0 \epsilon_1 = 0.036 \pm 0.025$. For inflation models $V \propto \phi^{\alpha}$ we find that $\alpha< 3.9, 4.3$ at the 2$\sigma$ and $3\sigma$ levels, indicating that the $\lambda\phi^4$ model is under very strong pressure from observations. We define a convergence criterion to judge the necessity of introducing further power spectrum parameters such as the spectral index and running of the spectral index. This criterion is typically violated by models with large negative running that fit the data, indicating that the running cannot be reliably measured with present data.Comment: 8 pages RevTeX4 file with six figures incorporate

Improved Estimates of Cosmological Perturbations

We recently derived exact solutions for the scalar, vector and tensor mode functions of a single, minimally coupled scalar plus gravity in an arbitrary homogeneous and isotropic background. These solutions are applied to obtain improved estimates for the primordial scalar and tensor power spectra of anisotropies in the cosmic microwave background.Comment: 31 pages, 4 figures, LaTeX 2epsilon, this version corrects an embarrasing mistake (in the published version) for the parameter q_C. Affected eqns are 105, 109-110, 124, 148-153 and 155-15

An Exact Algorithm for Side-Chain Placement in Protein Design

Computational protein design aims at constructing novel or improved functions on the structure of a given protein backbone and has important applications in the pharmaceutical and biotechnical industry. The underlying combinatorial side-chain placement problem consists of choosing a side-chain placement for each residue position such that the resulting overall energy is minimum. The choice of the side-chain then also determines the amino acid for this position. Many algorithms for this NP-hard problem have been proposed in the context of homology modeling, which, however, reach their limits when faced with large protein design instances. In this paper, we propose a new exact method for the side-chain placement problem that works well even for large instance sizes as they appear in protein design. Our main contribution is a dedicated branch-and-bound algorithm that combines tight upper and lower bounds resulting from a novel Lagrangian relaxation approach for side-chain placement. Our experimental results show that our method outperforms alternative state-of-the art exact approaches and makes it possible to optimally solve large protein design instances routinely

Scalar perturbation spectra from warm inflation

We present a numerical integration of the cosmological scalar perturbation equations in warm inflation. The initial conditions are provided by a discussion of the thermal fluctuations of an inflaton field and thermal radiation using a combination of thermal field theory and thermodynamics. The perturbation equations include the effects of a damping coefficient $\Gamma$ and a thermodynamic potential $V$. We give an analytic expression for the spectral index of scalar fluctuations in terms of a new slow-roll parameter constructed from $\Gamma$. A series of toy models, inspired by spontaneous symmetry breaking and a known form of the damping coefficient, lead to a spectrum with $n_s>1$ on large scales and $n_s<1$ on small scales.Comment: 12 pages, 5 figures, RevTeX 4, revised with extra figure

The Evolutionary Rewiring of Ubiquitination Targets Has Reprogrammed the Regulation of Carbon Assimilation in the Pathogenic Yeast \u3ci\u3eCandida albicans\u3c/i\u3e

Microbes must assimilate carbon to grow and colonize their niches. Transcript profiling has suggested that Candida albicans, a major pathogen of humans, regulates its carbon assimilation in an analogous fashion to the model yeast Saccharomyces cerevisiae, repressing metabolic pathways required for the use of alterative nonpreferred carbon sources when sugars are available. However, we show that there is significant dislocation between the proteome and transcriptome in C. albicans. Glucose triggers the degradation of the ICL1 and PCK1 transcripts in C. albicans, yet isocitrate lyase (Icl1) and phosphoenolpyruvate carboxykinase (Pck1) are stable and are retained. Indeed, numerous enzymes required for the assimilation of carboxylic and fatty acids are not degraded in response to glucose. However, when expressed in C. albicans, S. cerevisiae Icl1 (ScIcl1) is subjected to glucose-accelerated degradation, indicating that like S. cerevisiae, this pathogen has the molecular apparatus required to execute ubiquitin-dependent catabolite inactivation. C. albicans Icl1 (CaIcl1) lacks analogous ubiquitination sites and is stable under these conditions, but the addition of a ubiquitination site programs glucose-accelerated degradation of CaIcl1. Also, catabolite inactivation is slowed in C. albicans ubi4 cells. Ubiquitination sites are present in gluconeogenic and glyoxylate cycle enzymes from S. cerevisiae but absent from their C. albicans homologues. We conclude that evolutionary rewiring of ubiquitination targets has meant that following glucose exposure, C. albicans retains key metabolic functions, allowing it to continue to assimilate alternative carbon sources. This metabolic flexibility may be critical during infection, facilitating the rapid colonization of dynamic host niches containing complex arrays of nutrients

Estimating the tensor-to-scalar ratio and the effect of residual foreground contamination

We consider future balloon-borne and ground-based suborbital experiments designed to search for inflationary gravitational waves, and investigate the impact of residual foregrounds that remain in the estimated cosmic microwave background maps. This is achieved by propagating foreground modelling uncertainties from the component separation, under the assumption of a spatially uniform foreground frequency scaling, through to the power spectrum estimates, and up to measurement of the tensor to scalar ratio in the parameter estimation step. We characterize the error covariance due to subtracted foregrounds, and find it to be subdominant compared to instrumental noise and sample variance in our simulated data analysis. We model the unsubtracted residual foreground contribution using a two-parameter power law and show that marginalization over these foreground parameters is effective in accounting for a bias due to excess foreground power at low $\ell$. We conclude that, at least in the suborbital experimental setups we have simulated, foreground errors may be modeled and propagated up to parameter estimation with only a slight degradation of the target sensitivity of these experiments derived neglecting the presence of the foregrounds.Comment: 19 pages, 12 figures, accepted for publication in JCA

Unravelling the temporal association between lameness and body condition score in dairy cattle using a multistate modelling approach

Recent studies have reported associations between lameness and body condition score (BCS) in dairy cattle, however the impact of change in the dynamics of BCS on both lameness occurrence and recovery is currently unknown. The aim of this study was to investigate in a longitudinal study the effect of change in BCS on the transitions from the non-lame to lame, and lame to non-lame states. A total of 731 cows with 6889 observations from 4 UK herds were included in the study. Mobility score (MS) and body condition score (BCS) were recorded every 13-15 days from July 2010 until December 2011. A multilevel multistate discrete time event history model was built to investigate the transition of lameness over time. There were 1042 non-lame episodes and 593 lame episodes of which approximately 50% (519/1042) of the non-lame episodes transitioned to the lame state and 81% (483/593) of the lame episodes ended with a transition to the non-lame state. Cows with a lower BCS at calving (BCS Group 1 (1.00-1.75) and Group 2 (2.00-2.25)) had a higher probability of transition from non-lame to lame and a lower probability of transition from lame to non-lame compared to cows with BCS 2.50-2.75 i.e. they were more likely to become lame and if lame, they were less likely to recover. Similarly, cows who suffered a greater decrease in BCS (compared to their BCS at calving) had a higher probability of becoming lame and a lower probability of recovering in the next 15 days. An increase in BCS from calving was associated with the converse effect i.e. a lower probability of cows moving from the non-lame to the lame state and higher probability of transition from lame to non-lame. Days of lactation, months of calving and parity was associated with both lame and non-lame transitions and there was evidence of heterogeneity among cows in lameness occurrence and recovery. This study suggests loss of BCS and increase of BCS could influence the risk of becoming lame and the chance of recovery from lameness. Regular monitoring and maintenance of BCS on farms could be a key tool for reducing lameness. Further work is urgently needed in this area to allow a better understanding of the underlying mechanisms behind these relationships