R2R - software to speed the depiction of aesthetic consensus RNA secondary structures

<p>Abstract</p> <p>Background</p> <p>With continuing identification of novel structured noncoding RNAs, there is an increasing need to create schematic diagrams showing the consensus features of these molecules. RNA structural diagrams are typically made either with general-purpose drawing programs like Adobe Illustrator, or with automated or interactive programs specific to RNA. Unfortunately, the use of applications like Illustrator is extremely time consuming, while existing RNA-specific programs produce figures that are useful, but usually not of the same aesthetic quality as those produced at great cost in Illustrator. Additionally, most existing RNA-specific applications are designed for drawing single RNA molecules, not consensus diagrams.</p> <p>Results</p> <p>We created R2R, a computer program that facilitates the generation of aesthetic and readable drawings of RNA consensus diagrams in a fraction of the time required with general-purpose drawing programs. Since the inference of a consensus RNA structure typically requires a multiple-sequence alignment, the R2R user annotates the alignment with commands directing the layout and annotation of the RNA. R2R creates SVG or PDF output that can be imported into Adobe Illustrator, Inkscape or CorelDRAW. R2R can be used to create consensus sequence and secondary structure models for novel RNA structures or to revise models when new representatives for known RNA classes become available. Although R2R does not currently have a graphical user interface, it has proven useful in our efforts to create 100 schematic models of distinct noncoding RNA classes.</p> <p>Conclusions</p> <p>R2R makes it possible to obtain high-quality drawings of the consensus sequence and structural models of many diverse RNA structures with a more practical amount of effort. R2R software is available at <url>http://breaker.research.yale.edu/R2R</url> and as an Additional file.</p

Dirac Equation at Finite Temperature

In this paper, we propose finite temperature Dirac equation, which can describe the quantum systems in an arbitrary temperature for a relativistic particle of spin-1/2. When the temperature T=0, it become Dirac equation. With the equation, we can study the relativistic quantum systems in an arbitrary temperature.Comment: arXiv admin note: text overlap with arXiv:1005.2751, arXiv:hep-ph/0004125, arXiv:hep-ph/0005272 by other author

Quantum Gravity in Everyday Life: General Relativity as an Effective Field Theory

This article is meant as a summary and introduction to the ideas of effective field theory as applied to gravitational systems. Contents: 1. Introduction 2. Effective Field Theories 3. Low-Energy Quantum Gravity 4. Explicit Quantum Calculations 5. ConclusionsComment: 56 pages, 2 figures, JHEP style, Invited review to appear in Living Reviews of Relativit

Axion Protection from Flavor

The QCD axion fails to solve the strong CP problem unless all explicit PQ violating, Planck-suppressed, dimension n<10 operators are forbidden or have exponentially small coefficients. We show that all theories with a QCD axion contain an irreducible source of explicit PQ violation which is proportional to the determinant of the Yukawa interaction matrix of colored fermions. Generically, this contribution is of low operator dimension and will drastically destabilize the axion potential, so its suppression is a necessary condition for solving the strong CP problem. We propose a mechanism whereby the PQ symmetry is kept exact up to n=12 with the help of the very same flavor symmetries which generate the hierarchical quark masses and mixings of the SM. This "axion flavor protection" is straightforwardly realized in theories which employ radiative fermion mass generation and grand unification. A universal feature of this construction is that the heavy quark Yukawa couplings are generated at the PQ breaking scale.Comment: 16 pages, 2 figure

Hemodynamic Environments from Opposing Sides of Human Aortic Valve Leaflets Evoke Distinct Endothelial Phenotypes In Vitro

The regulation of valvular endothelial phenotypes by the hemodynamic environments of the human aortic valve is poorly understood. The nodular lesions of calcific aortic stenosis (CAS) develop predominantly beneath the aortic surface of the valve leaflets in the valvular fibrosa layer. However, the mechanisms of this regional localization remain poorly characterized. In this study, we combine numerical simulation with in vitro experimentation to investigate the hypothesis that the previously documented differences between valve endothelial phenotypes are linked to distinct hemodynamic environments characteristic of these individual anatomical locations. A finite-element model of the aortic valve was created, describing the dynamic motion of the valve cusps and blood in the valve throughout the cardiac cycle. A fluid mesh with high resolution on the fluid boundary was used to allow accurate computation of the wall shear stresses. This model was used to compute two distinct shear stress waveforms, one for the ventricular surface and one for the aortic surface. These waveforms were then applied experimentally to cultured human endothelial cells and the expression of several pathophysiological relevant genes was assessed. Compared to endothelial cells subjected to shear stress waveforms representative of the aortic face, the endothelial cells subjected to the ventricular waveform showed significantly increased expression of the “atheroprotective” transcription factor Kruppel-like factor 2 (KLF2) and the matricellular protein Nephroblastoma overexpressed (NOV), and suppressed expression of chemokine Monocyte-chemotactic protein-1 (MCP-1). Our observations suggest that the difference in shear stress waveforms between the two sides of the aortic valve leaflet may contribute to the documented differential side-specific gene expression, and may be relevant for the development and progression of CAS and the potential role of endothelial mechanotransduction in this disease.National Institutes of Health (U.S.) (Molecular, Cellular, and Tissue Biomechanics training grant (T32 EB006348))National Institutes of Health (U.S.) (NHLBI RO1-HL7066686)Charles Stark Draper Laboratory (Fellowship

Theoretical Constraints on the Higgs Effective Couplings

We derive constraints on the sign of couplings in an effective Higgs Lagrangian using prime principles such as the naturalness principle, global symmetries, and unitarity. Specifically, we study four dimension-six operators, O_H, O_y, O_g, and O_gamma, which contribute to the production and decay of the Higgs boson at the Large Hadron Collider (LHC), among other things. Assuming the Higgs is a fundamental scalar, we find: 1) the coefficient of O_H is positive except when there are triplet scalars, resulting in a reduction in the Higgs on-shell coupling from their standard model (SM) expectations if no other operators contribute, 2) the linear combination of O_H and O_y controlling the overall Higgs coupling to fermion is always reduced, 3) the sign of O_g induced by a new colored fermion is such that it interferes destructively with the SM top contribution in the gluon fusion production of the Higgs, if the new fermion cancels the top quadratic divergence in the Higgs mass, and 4) the correlation between naturalness and the sign of O_gamma is similar to that of O_g, when there is a new set of heavy electroweak gauge bosons. Next considering a composite scalar for the Higgs, we find the reduction in the on-shell Higgs couplings persists. If further assuming a collective breaking mechanism as in little Higgs theories, the coefficient of O_H remains positive even in the presence of triplet scalars. In the end, we conclude that the gluon fusion production of the Higgs boson is reduced from the SM rate in all composite Higgs models. Our study suggests a wealth of information could be revealed by precise measurements of the Higgs couplings, providing strong motivations for both improving on measurements at the LHC and building a precision machine such as the linear collider.Comment: 37 pages, one figure; v2: improved discussion on dispersion relation and other minor modifications; version accepted for publication

Bidirectional Transcription Directs Both Transcriptional Gene Activation and Suppression in Human Cells

Small RNAs targeted to gene promoters in human cells have been shown to modulate both transcriptional gene suppression and activation. However, the mechanism involved in transcriptional activation has remained poorly defined, and an endogenous RNA trigger for transcriptional gene silencing has yet to be identified. Described here is an explanation for siRNA-directed transcriptional gene activation, as well as a role for non-coding antisense RNAs as effector molecules driving transcriptional gene silencing. Transcriptional activation of p21 gene expression was determined to be the result of Argonaute 2–dependent, post-transcriptional silencing of a p21-specific antisense transcript, which functions in Argonaute 1–mediated transcriptional control of p21 mRNA expression. The data presented here suggest that in human cells, bidirectional transcription is an endogenous gene regulatory mechanism whereby an antisense RNA directs epigenetic regulatory complexes to a sense promoter, resulting in RNA-directed epigenetic gene regulation. The observations presented here support the notion that epigenetic silencing of tumor suppressor genes, such as p21, may be the result of an imbalance in bidirectional transcription levels. This imbalance allows the unchecked antisense RNA to direct silent state epigenetic marks to the sense promoter, resulting in stable transcriptional gene silencing

On theories of enhanced CP violation in B_s,d meson mixing

The DO collaboration has measured a deviation from the standard model (SM) prediction in the like sign dimuon asymmetry in semileptonic b decay with a significance of 3.2 sigma. We discuss how minimal flavour violating (MFV) models with multiple scalar representations can lead to this deviation through tree level exchanges of new MFV scalars. We review how the two scalar doublet model can accommodate this result and discuss some of its phenomenology. Limits on electric dipole moments suggest that in this model the coupling of the charged scalar to the right handed u-type quarks is suppressed while its coupling to the d-type right handed quarks must be enhanced. We construct an extension of the MFV two scalar doublet model where this occurs naturally.Comment: 10 pages, 7 figures, v3 final JHEP versio

Fluids in cosmology

We review the role of fluids in cosmology by first introducing them in General Relativity and then by applying them to a FRW Universe's model. We describe how relativistic and non-relativistic components evolve in the background dynamics. We also introduce scalar fields to show that they are able to yield an inflationary dynamics at very early times (inflation) and late times (quintessence). Then, we proceed to study the thermodynamical properties of the fluids and, lastly, its perturbed kinematics. We make emphasis in the constrictions of parameters by recent cosmological probes.Comment: 34 pages, 4 figures, version accepted as invited review to the book "Computational and Experimental Fluid Mechanics with Applications to Physics, Engineering and the Environment". Version 2: typos corrected and references expande

Massive benign pericardial cyst presenting with simultaneous superior vena cava and middle lobe syndromes

A 66 year old woman presented in extremis with symptoms and clinical and radiological signs of simultaneous obstruction of superior vena cava and middle lobe of right lung secondary to compression by a massive benign anterior mediastinal cyst. Excision of the cyst at median sternotomy resulted in complete resolution of all symptoms. This report is unusual on account of a) the concomitant presence of superior vena cava and middle lobe syndromes caused by a benign cyst because of its sheer size producing obstruction of these structures and b) the complete resolution of all symptoms and signs after removal of the cyst. Benign anterior mediastinal cysts are unknown to cause either of the two syndromes. To our knowledge, it is the first report of a benign anterior mediastinal cyst causing either superior vena cava syndrome or middle lobe syndrome or both simultaneously. Etiologies of both superior vena cava and middle lobe syndromes are discussed in detail