Skewness and kurtosis of net baryon-number distributions at small values of the baryon chemical potential

We present results for the ratios of mean (MB), variance (σ2B), skewness (SB) and kurtosis (κB) of net baryon-number fluctuations obtained in lattice QCD calculations with physical values of light and strange quark masses. Using next-to-leading order Taylor expansions in baryon chemical potential we find that qualitative features of these ratios closely resemble the corresponding experimentally measured cumulant ratios of net proton-number fluctuations for beam energies down to √sNN≥19.6  GeV. We show that the difference in cumulant ratios for the mean net baryon-number, MB/σ2B=χB1(T,μB)/χB2(T,μB), and the normalized skewness, SBσB=χB3(T,μB)/χB2(T,μB), naturally arises in QCD thermodynamics. Moreover, we establish a close relation between skewness and kurtosis ratios, SBσ3B/MB=χB3(T,μB)/χB1(T,μB) and κBσ2B=χB4(T,μB)/χB2(T,μB), valid at small values of the baryon chemical potential

Retroviral DNA Integration: ASLV, HIV, and MLV Show Distinct Target Site Preferences

The completion of the human genome sequence has made possible genome-wide studies of retroviral DNA integration. Here we report an analysis of 3,127 integration site sequences from human cells. We compared retroviral vectors derived from human immunodeficiency virus (HIV), avian sarcoma-leukosis virus (ASLV), and murine leukemia virus (MLV). Effects of gene activity on integration targeting were assessed by transcriptional profiling of infected cells. Integration by HIV vectors, analyzed in two primary cell types and several cell lines, strongly favored active genes. An analysis of the effects of tissue-specific transcription showed that it resulted in tissue-specific integration targeting by HIV, though the effect was quantitatively modest. Chromosomal regions rich in expressed genes were favored for HIV integration, but these regions were found to be interleaved with unfavorable regions at CpG islands. MLV vectors showed a strong bias in favor of integration near transcription start sites, as reported previously. ASLV vectors showed only a weak preference for active genes and no preference for transcription start regions. Thus, each of the three retroviruses studied showed unique integration site preferences, suggesting that virus-specific binding of integration complexes to chromatin features likely guides site selection

QCD equation of state to O(μB6) from lattice QCD

We calculated the QCD equation of state using Taylor expansions that include contributions from up to sixth order in the baryon, strangeness and electric charge chemical potentials. Calculations have been performed with the Highly Improved Staggered Quark action in the temperature range T∈[135  MeV,330  MeV] using up to four different sets of lattice cutoffs corresponding to lattices of size N3σ×Nτ with aspect ratio Nσ/Nτ=4 and Nτ=6−16. The strange quark mass is tuned to its physical value, and we use two strange to light quark mass ratios ms/ml=20 and 27, which in the continuum limit correspond to a pion mass of about 160 and 140 MeV, respectively. Sixth-order results for Taylor expansion coefficients are used to estimate truncation errors of the fourth-order expansion. We show that truncation errors are small for baryon chemical potentials less then twice the temperature (μB≤2T). The fourth-order equation of state thus is suitable for the modeling of dense matter created in heavy ion collisions with center-of-mass energies down to √sNN∼12  GeV. We provide a parametrization of basic thermodynamic quantities that can be readily used in hydrodynamic simulation codes. The results on up to sixth-order expansion coefficients of bulk thermodynamics are used for the calculation of lines of constant pressure, energy and entropy densities in the T−μB plane and are compared with the crossover line for the QCD chiral transition as well as with experimental results on freeze-out parameters in heavy ion collisions. These coefficients also provide estimates for the location of a possible critical point. We argue that results on sixth-order expansion coefficients disfavor the existence of a critical point in the QCD phase diagram for μB/T≤2 and T/Tc(μB=0)>0.9

Skewness and kurtosis of net baryon-number distributions at small values of the baryon chemical potential

We present results for the ratios of mean (MB), variance (sigma(2)(B)), skewness (SB) and kurtosis(kappa B) of net baryon-number fluctuations obtained in lattice QCD calculations with physical values of light and strange quark masses. Using next-to-leading order Taylor expansions in baryon chemical potential we find that qualitative features of these ratios closely resemble the corresponding experimentally measured cumulant ratios of net proton-number fluctuations for beam energies down to root s(NN) >= 19.6 GeV. We show that the difference in cumulant ratios for the mean net baryon-number, M-B/sigma(2)(B) = chi(1)(B) (T, mu(B)) / chi(2)(B) (T, mu(B)), and the normalized skewness, S-B sigma(B) = chi(B)(3) (T, mu(B)) / chi(B)(2) (T, mu B), naturally arises in QCD thermodynamics. Moreover, we establish a close relation between skewness and kurtosis ratios, S-B sigma(3)(B) / M-B = chi(B)(3) (T, mu(B)) / chi(B)(1) (T, mu(B)) and kappa(B)sigma(2)(B) = chi(B)(4) (T, mu(B)) /chi(B)(2) (T, mu(B)), valid at small values of the baryon chemical potential

The population biology and evolutionary significance of Ty elements in Saccharomyces cerevisiae

The basic structure and properties of Ty elements are considered with special reference to their role as agents of evolutionary change. Ty elements may generate genetic variation for fitness by their action as mutagens, as well as by providing regions of portable homology for recombination. The mutational spectra generated by Ty 1 transposition events may, due to their target specificity and gene regulatory capabilities, possess a higher frequency of adaptively favorable mutations than spectra resulting from other types of mutational processes. Laboratory strains contain between 25–35 elements, and in both these and industrial strains the insertions appear quite stable. In contrast, a wide variation in Ty number is seen in wild isolates, with a lower average number/genome. Factors which may determine Ty copy number in populations include transposition rates (dependent on Ty copy number and mating type), and stabilization of Ty elements in the genome as well as selection for and against Ty insertions in the genome. Although the average effect of Ty transpositions are deleterious, populations initiated with a single clone containing a single Ty element steadily accumulated Ty elements over 1,000 generations. Direct evidence that Ty transposition events can be selectively favored is provided by experiments in which populations containing large amounts of variability for Ty1 copy number were maintained for ∼100 generations in a homogeneous environment. At their termination, the frequency of clones containing 0 Ty elements had decreased to ∼0.0, and the populations had became dominated by a small number of clones containing >0 Ty elements. No such reduction in variability was observed in populations maintained in a structured environment, though changes in Ty number were observed. The implications of genetic (mating type and ploidy) changes and environmental fluctuations for the long-term persistence of Ty elements within the S. cerevisiae species group are discussed.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/42799/1/10709_2004_Article_BF00133718.pd

The Pseudocritical Line in the QCD Phase Diagram

We report about ongoing work to determine the chiral transition line in 2+1 flavour QCD for small values of the light quark chemical potential. The curvature of this line can be derived from a scaling analysis of the chiral condensate and its derivative with respect to the chemical potential. We outline the method and show results as available

Positive and Negative Regulatory Elements Control Expression of the Yeast Retrotransposon Ty3

We report the results of an analysis of Ty3 transcription and identification of Ty3 regions that mediate pheromone and mating-type regulation to coordinate its expression with the yeast life cycle. A set of strains was constructed which was isogenic except for the number of Ty3 elements, which varied from zero to three. Analysis of Ty3 expression in these strains showed that each of the three elements was transcribed and that each element was regulated. Dissection of the long terminal repeat regulatory region by Northern blot analysis of deletion mutants and reporter gene analysis showed that the upstream junction of Ty3 with flanking chromosomal sequences contained a negative control region. A 19-bp fragment (positions 56-74) containing one consensus copy and one 7 of 8-bp match to the pheromone response element (PRE) consensus was sufficient to mediate pheromone induction in either haploid cell type. Deletion of this region, however, did not abolish expression, indicating that other sequences also activate transcription. A 24-bp block immediately downstream of the PRE region contained a sequence similar to the a1-α2 consensus that conferred mating-type control. A single base pair mutation in the region separating the PRE and a1-α2 sequences blocked pheromone induction, but not mating-type control. Thus, the long terminal repeat of Ty3 is a compact, highly regulated, mobile promoter which is responsive to cell type and mating