Correlation between nucleotide composition and folding energy of coding sequences with special attention to wobble bases

Background: The secondary structure and complexity of mRNA influences its accessibility to regulatory molecules (proteins, micro-RNAs), its stability and its level of expression. The mobile elements of the RNA sequence, the wobble bases, are expected to regulate the formation of structures encompassing coding sequences. Results: The sequence/folding energy (FE) relationship was studied by statistical, bioinformatic methods in 90 CDS containing 26,370 codons. I found that the FE (dG) associated with coding sequences is significant and negative (407 kcal/1000 bases, mean +/- S.E.M.) indicating that these sequences are able to form structures. However, the FE has only a small free component, less than 10% of the total. The contribution of the 1st and 3rd codon bases to the FE is larger than the contribution of the 2nd (central) bases. It is possible to achieve a ~ 4-fold change in FE by altering the wobble bases in synonymous codons. The sequence/FE relationship can be described with a simple algorithm, and the total FE can be predicted solely from the sequence composition of the nucleic acid. The contributions of different synonymous codons to the FE are additive and one codon cannot replace another. The accumulated contributions of synonymous codons of an amino acid to the total folding energy of an mRNA is strongly correlated to the relative amount of that amino acid in the translated protein. Conclusion: Synonymous codons are not interchangable with regard to their role in determining the mRNA FE and the relative amounts of amino acids in the translated protein, even if they are indistinguishable in respect of amino acid coding.Comment: 14 pages including 6 figures and 1 tabl

Chemical equilibration and thermal dilepton production from the quark gluon plasma at finite baryon density

The chemical equilibration of a highly unsaturated quark-gluon plasma has been studied at finite baryon density. It is found that in the presence of small amount of baryon density, the chemical equilibration for gluon becomes slower and the temperature decreases less steeply as compared to the baryon free plasma. As a result, the space time integrated yield of dilepton is enhanced if the initial temperature of the plasma is held fixed. Even at a fixed initial energy density, the suppression of the dilepton yields at higher baryo-chemical potential is compensated, to a large extent, by the slow cooling of the plasma.Comment: Latex, 19 pages, 8 postscript figures. To appear in Phys. Rev.

A 3-mode, Variable Velocity Jet Model for HH 34

Variable ejection velocity jet models can qualitatively explain the appearance of successive working surfaces in Herbig-Haro (HH) jets. This paper presents an attempt to explore which features of the HH-34 jet can indeed be reproduced by such a model. From previously published data on this object, we find evidence for the existence of a 3-mode ejection velocity variability, and then explore the implications of such a variability. From simple, analytic considerations it is possible to show that the longer period modes produce a modulation on the shorter period modes, resulting in the formation of ``trains'' of multiple knots. The knots observed close to the source of HH-34 could correspond to such a structure. Finally, a numerical simulation with the ejection velocity variability deduced from the HH-34 data is computed. This numerical simulation shows a quite remarkable resemblance with the observed properties of the HH-34 jet.Comment: 28 pages LaTex, 10 postscript figure

Forming Disoriented Chiral Condensates through Fluctuations

Using the influence functional formalism, classical equations of motion for the O(N) model are derived in the presence of a heat bath, in both the symmetric phase as well as the phase of spontaneously broken symmetry. The heat bath leads to dissipation and fluctuation terms in the classical equations of motion, which are explicitly computed to lowest order in perturbation theory. In the broken phase these terms are found to be large for the sigma field, even at zero temperature, due to the decay process sigma -> pi pi, while they are small for the pi fields at temperatures below T_c = 160 MeV. It is shown that in large volumes the presence of dissipation and fluctuations suppresses the formation of disoriented chiral condensates (DCC's). In small volumes, however, fluctuations become sufficiently large to induce the formation of DCC's even if chiral symmetry has not been restored in the initial stage of the system's evolution.Comment: 34 pages, 11 figures, ReVTeX, eps-, aps-, psfig-style files require

Value-based genomic screening. Exploring genomic screening for chronic diseases using triple value principles

Background: Genomic screening has unique challenges which makes it difficult to easily implement on a wide scale. If the costs, benefits and tradeoffs of investing in genomic screening are not evaluated properly, there is a risk of wasting finite healthcare resources and also causing avoidable harm. Main text: If healthcare professionals - including policy makers, payers and providers - wish to incorporate genomic screening into healthcare while minimizing waste, maximizing benefits, and considering results that matter to patients, using the principles of triple value (allocative, technical, and personal value) could help them to evaluate tough decisions and tradeoffs. Allocative value focuses on the optimal distribution of limited healthcare resources to maximize the health benefits to the entire population while also accounting for all the costs of care delivery. Technical value ensures that for any given condition, the right intervention is chosen and delivered in the right way. Various methods (e.g. ACCE, HTA, and Wilson and Jungner screening criteria) exist that can help identify appropriate genomic applications. Personal value incorporates preference based informed decision making to ensure that patients are informed about the benefits and harms of the choices available to them and to ensure they make choices based on their values and preferences. Conclusions: Using triple value principles can help healthcare professionals make reasoned and tough judgements about benefits and tradeoffs when they are exploring the role genomic screening for chronic diseases could play in improving the health of their patients and populations

Transverse momentum distributions and their forward- backward correlations in the percolating colour string approach

The forward-backward correlations in the $p_T$ distributions, which present a clear signature of non-linear effects in particle production, are studied in the model of percolating colour strings. Quantitative predictions are given for these correlations at SPS, RHIC and LHC energies. Interaction of strings also naturally explains the flattening of $p_T$ distributions and increase of $$ with energy and atomic number for nuclear collisionsComment: 6 pages in LaTex, 3 figures in Postscrip

Jets and the shaping of the giant bipolar envelope of the planetary nebula KjPn 8

A hydrodynamic model involving cooling gas in the stagnation region of a collimated outflow is proposed for the formation of the giant parsec-scale bipolar envelope that surrounds the planetary nebula KjPn 8. Analytical calculations and numerical simulations are presented to evaluate the model. The envelope is considered to consist mainly of environmental gas swept-up by shocks driven by an episodic, collimated, bipolar outflow. In this model, which we call the ``free stagnation knot'' mechanism, the swept-up ambient gas located in the stagnation region of the bow-shock cools to produce a high density knot. This knot moves along with the bow-shock. When the central outflow ceases, pressurization of the interior of the envelope stops and its expansion slows down. The stagnation knot, however, has sufficient momentum to propagate freely further along the axis, producing a distinct nose at the end of the lobe. The model is found to successfully reproduce the peculiar shape and global kinematics of the giant bipolar envelope of KjPn 8.Comment: 20 pages + 8 figures (in 1 tar-file 0.67 Mb

MHD Models of Axisymmetric Protostellar Jets

We present the results of a series of axisymmetric time-dependent magnetohydrodynamic (MHD) simulations of the propagation of cooling, overdense jets, motivated by the properties of outflows associated with young stellar objects. A variety of initial field strengths and configurations are explored for both steady and time-variable (pulsed) jets. Even apparently weak magnetic fields with strengths B < 60 micro-G in the pre-shocked jet beam can have a significant effect on the dynamics, for example by altering the density, width, and fragmentation of thin shells formed by cooling gas. A linear analysis predicts that axisymmetric pinch modes of the MHD Kelvin-Helmholtz instability should grow only slowly for the highly supermagnetosonic jets studied here; we find no evidence for them in our simulations. Some of our models appear unstable to current-driven pinch modes, however the resulting pressure and density variations induced in the jet beam are not large, making this mechanism an unlikely source of emission knots in the jet beam. In the case of pulsed jets, radial hoop stresses confine shocked jet material in the pulses to the axis, resulting in a higher density in the pulses in comparison to purely hydrodynamic models.Comment: 28 pages, 16 figures, accepted by Ap.

Nonlinear evolution of the momentum dependent condensates in strong interaction: the ``pseudoscalar laser''

We discuss the relaxation of the scalar and pseudoscalar condensates after a rapid quench from an initial state with fluctuations. If we include not only the zero-mode but also higher modes of the condensates in the classical evolution, we observe parametric amplification of those ``hard'' modes. Thus, they couple nonlinearly to the ``soft'' modes. As a consequence, domains of coherent pi-field emerge long after the initial spinodal decomposition. The momentum-space distribution of pions emerging from the decay of that momentum-dependent condensate is discussed.Comment: 6 Pages, REVTEX, 8 Figures; one reference and one figure adde