Simple sequence repeats in zebra finch (Taeniopygia guttata) expressed sequence tags: a new resource for evolutionary genetic studies of passerines

Background Passerines (perching birds) are widely studied across many biological disciplines including ecology, population biology, neurobiology, behavioural ecology and evolutionary biology. However, understanding the molecular basis of relevant traits is hampered by the paucity of passerine genomics tools. Efforts to address this problem are underway, and the zebra finch (Taeniopygia guttata) will be the first passerine to have its genome sequenced. Here we describe a bioinformatic analysis of zebra finch expressed sequence tag (EST) Genbank entries. Results A total of 48,862 ESTs were downloaded from GenBank and assembled into contigs, representing an estimated 17,404 unique sequences. The unique sequence set contained 638 simple sequence repeats (SSRs) or microsatellites of length ≥20 bp and purity ≥90% and 144 simple sequence repeats of length ≥30 bp. A chromosomal location for the majority of SSRs was predicted by BLASTing against assembly 2.1 of the chicken genome sequence. The relative exonic location (5' untranslated region, coding region or 3' untranslated region) was predicted for 218 of the SSRs, by BLAST search against the ENSEMBL chicken peptide database. Ten loci were examined for polymorphism in two zebra finch populations and two populations of a distantly related passerine, the house sparrow Passer domesticus. Linkage was confirmed for four loci that were predicted to reside on the passerine homologue of chicken chromosome 7. Conclusion We show that SSRs are abundant within zebra finch ESTs, and that their genomic location can be predicted from sequence similarity with the assembled chicken genome sequence. We demonstrate that a useful proportion of zebra finch EST-SSRs are likely to be polymorphic, and that they can be used to build a linkage map. Finally, we show that many zebra finch EST-SSRs are likely to be useful in evolutionary genetic studies of other passerines

Phase Space Derivation of a Variational Principle for One Dimensional Hamiltonian Systems

We consider the bifurcation problem u'' + \lambda u = N(u) with two point boundary conditions where N(u) is a general nonlinear term which may also depend on the eigenvalue \lambda. A new derivation of a variational principle for the lowest eigenvalue \lambda is given. This derivation makes use only of simple algebraic inequalities and leads directly to a more explicit expression for the eigenvalue than what had been given previously.Comment: 2 pages, Revtex, no figure

Coupled-channel effective field theory and proton-7^7Li scattering

We apply the renormalisation group (RG) to analyse scattering by short-range forces in systems with coupled channels. For two S-wave channels, we find three fixed points, corresponding to systems with zero, one or two bound or virtual states at threshold. We use the RG to determine the power countings for the resulting effective field theories. In the case of a single low-energy state, the resulting theory takes the form of an effective-range expansion in the strongly interacting channel. We also extend the analysis to include the effects of the Coulomb interaction between charged particles. The approach is then applied to the coupled $p+{^7}$Li and $n+{^7}$Be channels which couple to a $J^P=2^-$ state of $^8$Be very close to the $n+{^7}$Be threshold. At next-to-leading order, we are able to get a good description of the $p+{^7}$Li phase shift and the ${^7}$Be(n,p)${^7}$Li cross section using four parameters. Fits at one order higher are similarly good but the available data are not sufficient to determine all five parameters uniquely.Comment: 22 pages, 2 figures, RevTeX4, typos corrected, accepted for publication in European Physical Journal

Control of Rayleigh-Taylor instability by vertical vibration in large aspect ratio containers

We consider a horizontal heavy fluid layer supported by a light, immiscible one in a wide (as compared to depth) container, which is vertically vibrated intending to counterbalance the Rayleigh-Taylor instability of the flat, rigid-body vibrating state. In the simplest case when the density and viscosity of the lighter fluid are small compared to their counterparts in the heavier fluid, we apply a long wave, weakly nonlinear analysis that yields a generalized Cahn-Hilliard equation for the evolution of the fluid interface. This equation shows that the stabilizing effect of vibration is like that of surface tension, and is used to analyze the linear stability of the flat state, the local bifurcation at the instability threshold and some global existence and stability properties concerning the steady states without dry spots. The analysis is extended to two cases of practical interest. Namely, (a) the viscosity of one of the fluids is much smaller than that of the other one, and (b) the densities and viscosities of both fluids are quite close to each other

A Re-examination of the Portevin-Le Chatelier Effect in Alloy 718 in Connection with Oxidation-Assisted Intergranular Cracking

In Alloy 718, a sharp transition exists in the fracture path changing from an intergranular brittle mode to a transgranular ductile mode which is associated with a transition of flow behavior from smooth in the dynamic strain aging regime to a serrated one in the Portevin-Le Chatelier (PLC) regime. In order to better understand both deformation and rupture behavior, PLC phenomenon in a precipitation-hardened nickel-base superalloy was carefully investigated in a wide range of temperatures [573 K to 973 K (300°C to 700°C)] and strain rates (109^-5 to 3.2910^-2 s^-1 ). Distinction was made between two PLC domains characterized by different evolutions of the critical strain to the onset of the first serration namely normal and inverse behavior. The apparent activation energies associated with both domains were determined using different methods. Results showed that normal and inverse behavior domains are related to dynamic interaction of dislocations with, respectively, interstitial and substitutional solutes atoms. This analysis confirms that normal PLC regime may be associated to the diffusion of carbon atoms, whereas the substitutional species involves in the inverse regime is discussed with an emphasis on the role of Nb and Mo

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Uncertainty and Surprise Jointly Predict Musical Pleasure and Amygdala, Hippocampus, and Auditory Cortex Activity

Listening to music often evokes intense emotions [1, 2]. Recent research suggests that musical pleasure comes from positive reward prediction errors, which arise when what is heard proves to be better than expected [3]. Central to this view is the engagement of the nucleus accumbens—a brain region that processes reward expectations—to pleasurable music and surprising musical events [4, 5, 6, 7, 8]. However, expectancy violations along multiple musical dimensions (e.g., harmony and melody) have failed to implicate the nucleus accumbens [9, 10, 11], and it is unknown how music reward value is assigned [12]. Whether changes in musical expectancy elicit pleasure has thus remained elusive [11]. Here, we demonstrate that pleasure varies nonlinearly as a function of the listener’s uncertainty when anticipating a musical event, and the surprise it evokes when it deviates from expectations. Taking Western tonal harmony as a model of musical syntax, we used a machine-learning model [13] to mathematically quantify the uncertainty and surprise of 80,000 chords in US Billboard pop songs. Behaviorally, we found that chords elicited high pleasure ratings when they deviated substantially from what the listener had expected (low uncertainty, high surprise) or, conversely, when they conformed to expectations in an uninformative context (high uncertainty, low surprise). Neurally, we found using fMRI that activity in the amygdala, hippocampus, and auditory cortex reflected this interaction, while the nucleus accumbens only reflected uncertainty. These findings challenge current neurocognitive models of music-evoked pleasure and highlight the synergistic interplay between prospective and retrospective states of expectation in the musical experience

Assessing the impact of closely-spaced intersections on traffic operations and pollutant emissions on a corridor level

Traffic lights or roundabouts along corridors are usually installed to address location-specific operational needs. An understanding of the impacts on traffic regarding to highly-congested closely-spaced intersections has not been fully addressed. Accordingly, consideration should be given to how these specific segments affect corridor performance as a whole. One mixed roundabout/traffic light/stop-controlled junctions corridor was evaluated with the microscopic traffic model (VISSIM) and emissions methodology (Vehicle Specific Power – VSP). The analysis was focused on two major intersections of the corridor, a roundabout and a traffic light spaced lower than 170 m apart under different traffic demand levels. The traffic data and corridor geometry were coded into VISSIM and compared with an alternative scenario where the traffic light was replaced by a single-lane roundabout. This research also tested a method to improve corridor performance and emissions by examining the integrated effect of the spacing between these intersections on traffic delay and vehicular emissions (carbon dioxide, monoxide carbon, nitrogen oxides, and hydrocarbons). The Fast Non-Dominated Sorting Genetic Algorithm (NSGA-II) was used to find the optimal spacing for these intersections. The analysis showed that the roundabout could achieve lower queue length (∼64%) and emissions (16–27%, depending on the pollutant) than the traffic light. The results also suggested that 200 m of spacing using the best traffic control would provide a moderate advantage in traffic operations and emissions as compared with the existing spacing