Chiral crossover in QCD at zero and non-zero chemical potentials

We present results for pseudo-critical temperatures of QCD chiral crossovers at zero and non-zero values of baryon ($B$), strangeness ($S$), electric charge ($Q$), and isospin ($I$) chemical potentials $\mu_{X=B,Q,S,I}$. The results were obtained using lattice QCD calculations carried out with two degenerate up and down dynamical quarks and a dynamical strange quark, with quark masses corresponding to physical values of pion and kaon masses in the continuum limit. By parameterizing pseudo-critical temperatures as $T_c(\mu_X) = T_c(0) \left[ 1 -\kappa_2^{X}(\mu_{X}/T_c(0))^2 -\kappa_4^{X}(\mu_{X}/T_c(0))^4 \right]$, we determined $\kappa_2^X$ and $\kappa_4^X$ from Taylor expansions of chiral observables in $\mu_X$. We obtained a precise result for $T_c(0)=(156.5\pm1.5)\;\mathrm{MeV}$. For analogous thermal conditions at the chemical freeze-out of relativistic heavy-ion collisions, i.e., $\mu_{S}(T,\mu_{B})$ and $\mu_{Q}(T,\mu_{B})$ fixed from strangeness-neutrality and isospin-imbalance, we found $\kappa_2^B=0.012(4)$ and $\kappa_4^B=0.000(4)$. For $\mu_{B}\lesssim300\;\mathrm{MeV}$, the chemical freeze-out takes place in the vicinity of the QCD phase boundary, which coincides with the lines of constant energy density of $0.42(6)\;\mathrm{GeV/fm}^3$ and constant entropy density of $3.7(5)\;\mathrm{fm}^{-3}$

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

A genome-wide investigation of insidious uveitis in Appaloosa horses.

BackgroundEquine recurrent uveitis (ERU), an inflammatory eye disease, is the leading cause of blindness among horses. Insidious uveitis, a form of ERU, is especially pervasive within the Appaloosa breed and is highly heritable (h2 = 0.68-1.0). To date only one risk locus, leopard complex (LP), has been identified, and it explained 0.16-0.33 of the heritability estimate, suggesting that insidious uveitis is a complex genetic disease within the Appaloosa horse breed with multiple unknown predisposing loci.ResultsA genome-wide association study (GWAS) using relatedness, LP genotype, sex, and age as covariates was performed on a sample of 96 Appaloosas (36 cases and 60 controls) and identified a 9.7 Kb region of association on ECA X (chrX:14528106-14537812) as significantly associated (P = 2.11 × 10-8). Sex stratification followed by meta-analysis provided additional support for the association on ECA X (P = 1.35 × 10-8). A logistic regression model was performed to test for epistasis between LP and the locus on ECA X, and the results did not support an interaction between the two loci. In the second phase of the study, single-nucleotide variants (SNVs) were identified in the region on ECA X by whole genome sequencing (WGS) of 18 horses from the GWAS (9 cases and 9 controls). Five reference markers from the GWAS, two previously associated coat color loci (LP and PATN1), and 102 SNVs were further evaluated in a combined dataset of 157 horses (70 cases and 87 controls, including the original 96 horses from the GWAS). Using logistic regression, none of the SNVs identified from the WGS analysis were significantly associated with phenotype; however, LP and the top three SNP markers from ECA X (ECA X: 14.5 Mb) were significantly associated in the larger dataset (PLP = 2.34 × 10-6 and PX = 4.06 × 10-5).ConclusionIn addition to the LP locus, our investigation identified a locus on chromosome X with a significant association to insidious uveitis in Appaloosas. Replication testing in an independent cohort is necessary to determine if this locus is indeed a causal risk locus

Meson screening masses in (2+1)-flavor QCD

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Chiral crossover in QCD at zero and non-zero chemical potentials

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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

A single zinc finger optimizes the DNA interactions of the nucleocapsid protein of the yeast retrotransposon Ty3

Reverse transcription in retroviruses and retrotransposons requires nucleic acid chaperones, which drive the rearrangement of nucleic acid conformation. The nucleic acid chaperone properties of the human immunodeficiency virus type-1 (HIV-1) nucleocapsid (NC) protein have been extensively studied, and nucleic acid aggregation, duplex destabilization and rapid binding kinetics have been identified as major components of its activity. However, the properties of other nucleic acid chaperone proteins, such as retrotransposon Ty3 NC, a likely ancestor of HIV-1 NC, are not well understood. In addition, it is unclear whether a single zinc finger is sufficient to optimize the properties characteristic of HIV-1 NC. We used single-molecule DNA stretching as a method for detailed characterization of Ty3 NC chaperone activity. We found that wild type Ty3 NC aggregates single- and double-stranded DNA, weakly stabilizes dsDNA, and exhibits rapid binding kinetics. Single-molecule studies in the presence of Ty3 NC mutants show that the N-terminal basic residues and the unique zinc finger at the C-terminus are required for optimum chaperone activity in this system. While the single zinc finger is capable of optimizing Ty3 NC's DNA interaction kinetics, two zinc fingers may be necessary in order to facilitate the DNA destabilization exhibited by HIV-1 NC

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

Evidence for a retroviral insertion in TRPM1 as the cause of congenital stationary night blindness and leopard complex spotting in the horse

Leopard complex spotting is a group of white spotting patterns in horses caused by an incompletely dominant gene (LP) where homozygotes (LP/LP) are also affected with congenital stationary night blindness. Previous studies implicated Transient Receptor Potential Cation Channel, Subfamily M, Member 1 (TRPM1) as the best candidate gene for both CSNB and LP. RNA-Seq data pinpointed a 1378 bp insertion in intron 1 of TRPM1 as the potential cause. This insertion, a long terminal repeat (LTR) of an endogenous retrovirus, was completely associated with LP, testing 511 horses (χ²=1022.00, p<<0.0005), and CSNB, testing 43 horses (χ2=43, p<<0.0005). The LTR was shown to disrupt TRPM1 transcription by premature poly-adenylation. Furthermore, while deleterious transposable element insertions should be quickly selected against the identification of this insertion in three ancient DNA samples suggests it has been maintained in the horse gene pool for at least 17,000 years. This study represents the first description of an LTR insertion being associated with both a pigmentation phenotype and an eye disorder.Rebecca R. Bellone … David L. Adelson, Sim Lin Lim … et al