Enhancing genome assemblies by integrating non-sequence based data

INTRODUCTION Many genome projects were underway before the advent of high-throughput sequencing and have thus been supported by a wealth of genome information from other technologies. Such information frequently takes the form of linkage and physical maps, both of which can provide a substantial amount of data useful in de novo sequencing projects. Furthermore, the recent abundance of genome resources enables the use of conserved synteny maps identified in related species to further enhance genome assemblies. METHODS The tammar wallaby (Macropus eugenii) is a model marsupial mammal with a low coverage genome. However, we have access to extensive comparative maps containing over 14,000 markers constructed through the physical mapping of conserved loci, chromosome painting and comprehensive linkage maps. Using a custom Bioperl pipeline, information from the maps was aligned to assembled tammar wallaby contigs using BLAT. This data was used to construct pseudo paired-end libraries with intervals ranging from 5-10 MB. We then used Bambus (a program designed to scaffold eukaryotic genomes by ordering and orienting contigs through the use of paired-end data) to scaffold our libraries. To determine how map data compares to sequence based approaches to enhance assemblies, we repeated the experiment using a 0.5× coverage of unique reads from 4 KB and 8 KB Illumina paired-end libraries. Finally, we combined both the sequence and non-sequence-based data to determine how a combined approach could further enhance the quality of the low coverage de novo reconstruction of the tammar wallaby genome. RESULTS Using the map data alone, we were able order 2.2% of the initial contigs into scaffolds, and increase the N50 scaffold size to 39 KB (36 KB in the original assembly). Using only the 0.5× paired-end sequence based data, 53% of the initial contigs were assigned to scaffolds. Combining both data sets resulted in a further 2% increase in the number of initial contigs integrated into a scaffold (55% total) but a 35% increase in N50 scaffold size over the use of sequence-based data alone. CONCLUSIONS We provide a relatively simple pipeline utilizing existing bioinformatics tools to integrate map data into a genome assembly which is available at http://www.mcb.uconn.edu/fac.php?name=paska. While the map data only contributed minimally to assigning the initial contigs to scaffolds in the new assembly, it greatly increased the N50 size. This process added structure to our low coverage assembly, greatly increasing its utility in further analyses

The Emergence of Group Potency and Its Implications for Team Effectiveness

Much of the previous research on the emergence of team-level constructs has overlooked their inherently dynamic nature by relying on static, cross-sectional approaches. Although theoretical arguments regarding emergent states have underscored the importance of considering time, minimal work has examined the dynamics of emergent states. In the present research, we address this limitation by investigating the dynamic nature of group potency, a crucial emergent state, over time. Theory around the “better-than-average” effect (i.e., an individual’s tendency to think he/she is better than the average person) suggests that individuals may have elevated expectations of their group’s early potency, but may decrease over time as team members interact gain a more realistic perspective of their group’s potential. In addition, as members gain experience with each other, they will develop a shared understanding of their team’s attributes. The current study used latent growth and consensus emergence modeling to examine how potency changes over time, and its relation with team effectiveness. Further, in accordance with the input-process-output framework, we investigated how group potency mediated the relations between team-level compositions of conscientiousness and extraversion and team effectiveness. We collected data at three time points throughout an engineering design course from 337 first-year engineering students that comprised 77 project teams. Results indicated that group potency decreased over time in a linear trend, and that group consensus increased over time. We also found that teams’ initial potency was a significant predictor of team effectiveness, but that change in potency was not related to team effectiveness. Finally, we found that the indirect effect linking conscientiousness to effectiveness, through initial potency, was supported. Overall, the current study offers a unique understanding of the emergence of group potency, and facilitate a number theoretical and practical implications, which are discussed

A Bayesian nonparametric analysis of the 2003 outbreak of highly pathogenic avian influenza in the Netherlands

Infectious diseases on farms pose both public and animal health risks, so understanding how they spread between farms is crucial for developing disease control strategies to prevent future outbreaks. We develop novel Bayesian nonparametric methodology to fit spatial stochastic transmission models in which the infection rate between any two farms is a function that depends on the distance between them, but without assuming a specified parametric form. Making nonparametric inference in this context is challenging since the likelihood function of the observed data is intractable because the underlying transmission process is unobserved. We adopt a fully Bayesian approach by assigning a transformed Gaussian process prior distribution to the infection rate function, and then develop an efficient data augmentation Markov Chain Monte Carlo algorithm to perform Bayesian inference. We use the posterior predictive distribution to simulate the effect of different disease control methods and their economic impact. We analyse a large outbreak of avian influenza in the Netherlands and infer the between-farm infection rate, as well as the unknown infection status of farms which were pre-emptively culled. We use our results to analyse ring-culling strategies, and conclude that although effective, ring-culling has limited impact in high-density areas

Mapping evaporative water loss in desert passerines reveals an expanding threat of lethal dehydration

Extreme high environmental temperatures produce a variety of consequences for wildlife, including mass die-offs. Heat waves are increasing in frequency, intensity, and extent, and are projected to increase further under climate change. However, the spatial and temporal dynamics of die-off risk are poorly understood. Here, we examine the effects of heat waves on evaporative water loss (EWL) and survival in five desert passerine birds across the southwestern United States using a combination of physiological data, mechanistically informed models, and hourly geospatial temperature data. We ask how rates of EWL vary with temperature across species; how frequently, over what areas, and how rapidly lethal dehydration occurs; how EWL and die-off risk vary with body mass; and how die-off risk is affected by climate warming. We find that smaller-bodied passerines are subject to higher rates of mass-specific EWL than larger-bodied counterparts and thus encounter potentially lethal conditions much more frequently, over shorter daily intervals, and over larger geographic areas. Warming by 4 °C greatly expands the extent, frequency, and intensity of dehydration risk, and introduces new threats for larger passerine birds, particularly those with limited geographic ranges. Our models reveal that increasing air temperatures and heat wave occurrence will potentially have important impacts on the water balance, daily activity, and geographic distribution of arid-zone birds. Impacts may be exacerbated by chronic effects and interactions with other environmental changes. This work underscores the importance of acute risks of high temperatures, particularly for small-bodied species, and suggests conservation of thermal refugia and water sources

Projective dynamics and first integrals

We present the theory of tensors with Young tableau symmetry as an efficient computational tool in dealing with the polynomial first integrals of a natural system in classical mechanics. We relate a special kind of such first integrals, already studied by Lundmark, to Beltrami's theorem about projectively flat Riemannian manifolds. We set the ground for a new and simple theory of the integrable systems having only quadratic first integrals. This theory begins with two centered quadrics related by central projection, each quadric being a model of a space of constant curvature. Finally, we present an extension of these models to the case of degenerate quadratic forms.Comment: 39 pages, 2 figure

Search for Point Sources of Ultra-High Energy Cosmic Rays Above 40 EeV Using a Maximum Likelihood Ratio Test

We present the results of a search for cosmic ray point sources at energies above 40 EeV in the combined data sets recorded by the AGASA and HiRes stereo experiments. The analysis is based on a maximum likelihood ratio test using the probability density function for each event rather than requiring an a priori choice of a fixed angular bin size. No statistically significant clustering of events consistent with a point source is found.Comment: 7 pages, 7 figures. Accepted for publication in The Astrophysical Journa

Chiral Transparency

Color transparency is the vanishing of initial and final state interactions, predicted by QCD to occur in high momentum transfer quasielastic nuclear reactions. For specific reactions involving nucleons, the initial and final state interactions are expected to be dominated by exchanges of pions. We argue that these interactions are also suppressed in high momentum transfer nuclear quasielastic reactions; this is ``chiral transparency". We show that studies of the $e ^3He \to e'\Delta^{++} nn$ reaction could reveal the influence of chiral transparency.Comment: 20 pages, three figures available by fax from [email protected]; submitted to Phys. Rev.

Deformations of quantum field theories on spacetimes with Killing vector fields

The recent construction and analysis of deformations of quantum field theories by warped convolutions is extended to a class of curved spacetimes. These spacetimes carry a family of wedge-like regions which share the essential causal properties of the Poincare transforms of the Rindler wedge in Minkowski space. In the setting of deformed quantum field theories, they play the role of typical localization regions of quantum fields and observables. As a concrete example of such a procedure, the deformation of the free Dirac field is studied.Comment: 35 pages, 3 figure

Flux-lattice melting in two-dimensional disordered superconductors

The flux line lattice melting transition in two-dimensional pure and disordered superconductors is studied by a Monte Carlo simulation using the lowest Landau level approximation and quasi-periodic boundary condition on a plane. The position of the melting line was determined from the diffraction pattern of the superconducting order parameter. In the clean case we confirmed the results from earlier studies which show the existence of a quasi-long range ordered vortex lattice at low temperatures. Adding frozen disorder to the system the melting transition line is shifted to slightly lower fields. The correlations of the order parameter for translational long range order of the vortex positions seem to decay slightly faster than a power law (in agreement with the theory of Carpentier and Le Doussal) although a simple power law decay cannot be excluded. The corresponding positional glass correlation function decays as a power law establishing the existence of a quasi-long range ordered positional glass formed by the vortices. The correlation function characterizing a phase coherent vortex glass decays however exponentially ruling out the possible existence of a phase coherent vortex glass phase.Comment: 12 pages, 21 figures, final version to appear in Phys. Rev.