Can we detect Hot or Cold spots in the CMB with Minkowski Functionals?

In this paper, we investigate the utility of Minkowski Functionals as a probe of cold/hot disk-like structures in the CMB. In order to construct an accurate estimator, we resolve a long-standing issue with the use of Minkowski Functionals as probes of the CMB sky -- namely that of systematic differences ("residuals") when numerical and analytical MF are compared. We show that such residuals are in fact by-products of binning, and not caused by pixelation or masking as originally thought. We then derive a map-independent estimator that encodes the effects of binning, applicable to beyond our present work. Using this residual-free estimator, we show that small disk-like effects (as claimed by Vielva et al.) can be detected only when a large sample of such maps are averaged over. In other words, our estimator is noise-dominated for small disk sizes at WMAP resolution. To confirm our suspicion, we apply our estimator to the WMAP7 data to obtain a null result.Comment: 15 pages, 13 figure

Coronary disease is not associated with robust alterations in inflammatory gene expression in human epicardial fat

Epicardial adipose tissue (EAT) is the visceral fat depot of the heart. Inflammation of EAT is thought to contribute to coronary artery disease (CAD). Therefore, we hypothesized that the EAT of patients with CAD would have increased inflammatory gene expression compared with controls without CAD. Cardiac surgery patients with (n = 13) or without CAD (n = 13) were consented, and samples of EAT and subcutaneous adipose tissue (SAT) were obtained. Transcriptomic analysis was performed using Affymetrix Human Gene 1.0 ST arrays. Differential expression was defined as a 1.5-fold change (ANOVA P \u3c 0.05). Six hundred ninety-three genes were differentially expressed between SAT and EAT in controls and 805 in cases. Expression of 326 genes was different between EAT of cases and controls; expression of 14 genes was increased in cases, while 312 were increased in controls. Quantitative reverse transcription PCR confirmed that there was no difference in expression of CCL2, CCR2, TNF-alpha, IL-6, IL-8, and PAI1 between groups. Immunohistochemistry showed more macrophages in EAT than SAT, but there was no difference in their number or activation state between groups. In contrast to prior studies, we did not find increased inflammatory gene expression in the EAT of patients with CAD. We conclude that the specific adipose tissue depot, rather than CAD status, is responsible for the majority of differential gene expression

Entanglement Entropy for Singular Surfaces

We study entanglement entropy for regions with a singular boundary in higher dimensions using the AdS/CFT correspondence and find that various singularities make new universal contributions. When the boundary CFT has an even spacetime dimension, we find that the entanglement entropy of a conical surface contains a term quadratic in the logarithm of the UV cut-off. In four dimensions, the coefficient of this contribution is proportional to the central charge 'c'. A conical singularity in an odd number of spacetime dimensions contributes a term proportional to the logarithm of the UV cut-off. We also study the entanglement entropy for various boundary surfaces with extended singularities. In these cases, similar universal terms may appear depending on the dimension and curvature of the singular locus.Comment: 66 pages,4 figures. Some typos are removed and a reference is adde

MAP4K4 impairs energy metabolism in endothelial cells and promotes insulin resistance in obesity

The blood vasculature responds to insulin, influencing hemodynamic changes in the periphery, which promotes tissue nutrient and oxygen delivery and thus metabolic function. The lymphatic vasculature regulates fluid and lipid homeostasis, and impaired lymphatic function can contribute to atherosclerosis and obesity. Recent studies have suggested a role for endothelial cell (EC) Mitogen activated protein kinase kinase kinase kinase 4 (Map4k4) in developmental angiogenesis and lymphangiogenesis as well as atherosclerosis. Here, we show that inducible EC Map4k4 deletion in adult mice ameliorates metabolic dysfunction in obesity despite the development of chylous ascites and a concomitant striking increase in adipose tissue lymphocyte content. Despite these defects, animals lacking endothelial Map4k4 were protected from skeletal muscle microvascular rarefaction in obesity, and primary ECs lacking Map4k4 displayed reduced senescence and increased metabolic capacity. Thus, endothelial Map4k4 has complex and opposing functions in the blood and lymphatic endothelium post-development. Whereas blood endothelial Map4k4 promotes vascular dysfunction and impairs glucose homeostasis in adult animals, lymphatic endothelial Map4k4 is required to maintain lymphatic vascular integrity and regulate immune cell trafficking in obesity

EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences

Next generation sequencing (NGS) technologies have led to a ubiquity of molecular sequence data. This data avalanche is particularly challenging in metagenetics, which focuses on taxonomic identification of sequences obtained from diverse microbial environments. Phylogenetic placement methods determine how these sequences fit into an evolutionary context. Previous implementations of phylogenetic placement algorithms, such as the evolutionary placement algorithm (EPA) included in RAxML, or PPLACER, are being increasingly used for this purpose. However, due to the steady progress in NGS technologies, the current implementations face substantial scalability limitations. Herein, we present EPA-NG, a complete reimplementation of the EPA that is substantially faster, offers a distributed memory parallelization, and integrates concepts from both, RAxML-EPA and PPLACER. EPA-NG can be executed on standard shared memory, as well as on distributed memory systems (e.g., computing clusters). To demonstrate the scalability of EPA-NG, we placed 1 billion metagenetic reads from the Tara Oceans Project onto a reference tree with 3748 taxa in just under 7 h, using 2048 cores. Our performance assessment shows that EPA-NG outperforms RAxML-EPA and PPLACER by up to a factor of 30 in sequential execution mode, while attaining comparable parallel efficiency on shared memory systems. We further show that the distributed memory parallelization of EPA-NG scales well up to 2048 cores. EPA-NG is available under the AGPLv3 license

Tracing a phase transition with fluctuations of the largest fragment size: Statistical multifragmentation models and the ALADIN S254 data

A phase transition signature associated with cumulants of the largest fragment size distribution has been identified in statistical multifragmentation models and examined in analysis of the ALADIN S254 data on fragmentation of neutron-poor and neutron-rich projectiles. Characteristics of the transition point indicated by this signature are weakly dependent on the A/Z ratio of the fragmenting spectator source. In particular, chemical freeze-out temperatures are estimated within the range 5.9 to 6.5 MeV. The experimental results are well reproduced by the SMM model.Comment: 7 pages, 3 figures, Proceedings of the International Workshop on Multifragmentation and Related Topics (IWM2009), Catania, Italy, November 2009

The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs

We developed a pair of databases that support two important tasks: annotation of anonymous RNA transcripts and discovery of novel non-coding RNAs. The database combo is called the Functional RNA Database and consists of two databases: a rewrite of the original version of the Functional RNA Database (fRNAdb) and the latest version of the UCSC GenomeBrowser for Functional RNA. The former is a sequence database equipped with a powerful search function and hosts a large collection of known/predicted non-coding RNA sequences acquired from existing databases as well as novel/predicted sequences reported by researchers of the Functional RNA Project. The latter is a UCSC Genome Browser mirror with large additional custom tracks specifically associated with non-coding elements. It also includes several functional enhancements such as a presentation of a common secondary structure prediction at any given genomic window ⩽500 bp. Our GenomeBrowser supports user authentication and user-specific tracks. The current version of the fRNAdb is a complete rewrite of the former version, hosting a larger number of sequences and with a much friendlier interface. The current version of UCSC GenomeBrowser for Functional RNA features a larger number of tracks and richer features than the former version. The databases are available at http://www.ncrna.org/