Improved characterisation of among-lineage rate variation in cetacean mitogenomes using codon-partitioned relaxed clocks

Background and aims. There is extensive variation in substitution rates among metazoan mitochondrial genomes, including differences among lineages and among sites. Differences in substitution rates among lineages are routinely taken into account in molecular phylogenetic and dating analyses. However, this is rarely the case for differences in the lineage-specific patterns of rate variation among sites.Materials and methods. We analysed an alignment of 32 cetacean mitogenomes using a partitioned relaxed-clock approach, in which a separate relaxed-clock model was applied to each of the three codon positions of the protein-coding genes.Results. By comparing Bayes factors, we found overwhelming support for this model compared with a strict-clock model and less-complex models comprising fewer relaxed clocks. Our analyses reveal the presence of substantial rate heterogeneity among cetacean lineages, and that these patterns of variation differ between codon positions. However, we find no evidence of mitochondrial rate autocorrelation throughout the cetacean phylogeny.Conclusions. Our study confirms the feasibility of applying a partitioned relaxed-clock model to mitogenomic data, and suggests that molecular phylogenetic and dating analyses may be improved by the application of these models

Trees of Unusual Size: Biased Inference of Early Bursts from Large Molecular Phylogenies

An early burst of speciation followed by a subsequent slowdown in the rate of diversification is commonly inferred from molecular phylogenies. This pattern is consistent with some verbal theory of ecological opportunity and adaptive radiations. One often-overlooked source of bias in these studies is that of sampling at the level of whole clades, as researchers tend to choose large, speciose clades to study. In this paper, we investigate the performance of common methods across the distribution of clade sizes that can be generated by a constant-rate birth-death process. Clades which are larger than expected for a given constant-rate branching process tend to show a pattern of an early burst even when both speciation and extinction rates are constant through time. All methods evaluated were susceptible to detecting this false signature when extinction was low. Under moderate extinction, both the gamma-statistic and diversity-dependent models did not detect such a slowdown but only because the signature of a slowdown was masked by subsequent extinction. Some models which estimate time-varying speciation rates are able to detect early bursts under higher extinction rates, but are extremely prone to sampling bias. We suggest that examining clades in isolation may result in spurious inferences that rates of diversification have changed through time.Comment: 17 pages, 5 figure

A Rotating Disk in the HH 111 Protostellar System

The HH 111 protostellar system is a young Class I system with two sources, VLA 1 and VLA 2, at a distance of 400 pc. Previously, a flattened envelope has been seen in C18O to be in transition to a rotationally supported disk near the VLA 1 source. The follow-up study here is to confirm the rotationally supported disk at 2-3 times higher angular resolutions, at ~ 0.3" (or 120 AU) in 1.33 mm continuum, and ~ 0.6" (or 240 AU) in 13CO (J=2-1) and 12CO (J=2-1) emission obtained with the Submillimeter Array. The 1.33 mm continuum emission shows a resolved dusty disk associated with the VLA 1 source perpendicular to the jet axis, with a Gaussian deconvolved size of ~ 240 AU. The 13CO and 12CO emissions toward the dusty disk show a Keplerian rotation, indicating that the dusty disk is rotationally supported. The density and temperature distributions in the disk derived from a simple disk model are found to be similar to those found in bright T-Tauri disks, suggesting that the disk can evolve into a T-Tauri disk in the late stage of star formation. In addition, a hint of a low-velocity molecular outflow is also seen in 13CO and 12CO coming out from the disk.Comment: 16 pages including 5 figure

Revitalizing the moment distribution method: A fast and exact analysis of multibay, multi-story frames.

The conventional moment distribution method is revitalized with a new approach which requires only one-cycle of balance and carry-over and no iteration. For a continuous beam, the method begins by assuming the value of the balancing moment, say x, at the first joint. By invoking the moment equilibrium condition successively from the first towards the last joints, balancing and carry-over moments at other joints can be determined in terms of the unknown x without iteration. By means of moment equilibrium of the last joint, the unknown x can be solved exactly, regardless of the number of spans, and the final moment distribution of the whole structure can be easily obtained. Further, for multi-bay, single story frames, the analysis is carried out without the need to separate the analysis into two stages as in conventional MDM, and the final exact moments are found by solving two unknowns only, regardless of the number of bays. As such, the revitalized MDM is particularly advantageous for solving continuous beams and single-story frames with large number of spans or bays. Five examples are given herein to demonstrate the procedures and efficiency of the proposed method

The role of atrial natriuretic peptide to attenuate inflammation in a mouse skin wound and individually perfused rat mesenteric microvessels.

We tested the hypothesis that the anti-inflammatory actions of atrial natriuretic peptide (ANP) result from the modulation of leukocyte adhesion to inflamed endothelium and not solely ANP ligation of endothelial receptors to stabilize endothelial barrier function. We measured vascular permeability to albumin and accumulation of fluorescent neutrophils in a full-thickness skin wound on the flank of LysM-EGFP mice 24 h after formation. Vascular permeability in individually perfused rat mesenteric microvessels was also measured after leukocytes were washed out of the vessel lumen. Thrombin increased albumin permeability and increased the accumulation of neutrophils. The thrombin-induced inflammatory responses were attenuated by pretreating the wound with ANP (30 min). During pretreatment ANP did not lower permeability, but transiently increased baseline albumin permeability concomitant with the reduction in neutrophil accumulation. ANP did not attenuate acute increases in permeability to histamine and bradykinin in individually perfused rat microvessels. The hypothesis that anti-inflammatory actions of ANP depend solely on endothelial responses that stabilize the endothelial barrier is not supported by our results in either individually perfused microvessels in the absence of circulating leukocytes or the more chronic skin wound model. Our results conform to the alternate hypothesis that ANP modulates the interaction of leukocytes with the inflamed microvascular wall of the 24 h wound. Taken together with our previous observations that ANP reduces deformability of neutrophils and their strength of attachment, rolling, and transvascular migration, these observations provide the basis for additional investigations of ANP as an anti-inflammatory agent to modulate leukocyte-endothelial cell interactions

Spectral data for doubly excited states of helium with non-zero total angular momentum

A spectral approach is used to evaluate energies and widths for a wide range of singlet and triplet resonance states of helium. Data for total angular momentum $L=1,...,4$ is presented for resonances up to below the 5th single ionization threshold. In addition the expectation value of $\cos(\theta_{12})$ is given for the calculated resonances.Comment: 35 pages, 16 tables, to be published in Atomic Data and Nuclear Data Table

Perturbative Approach to Higher Derivative and Nonlocal Theories

We review a perturbative approach to deal with Lagrangians with higher or infinite order time derivatives. It enables us to construct a consistent Poisson structure and Hamiltonian with only first time derivatives order by order in coupling. To the lowest order, the Hamiltonian is bounded from below whenever the potential is. We consider spacetime noncommutative field theory as an example.Comment: 19 pages, Latex, reference adde

Theory of Electron-Phonon Dynamics in Insulating Nanoparticles

We discuss the rich vibrational dynamics of nanometer-scale semiconducting and insulating crystals as probed by localized electronic impurity states, with an emphasis on nanoparticles that are only weakly coupled to their environment. Two principal regimes of electron-phonon dynamics are distinguished, and a brief survey of vibrational-mode broadening mechanisms is presented. Recent work on the effects of mechanical interaction with the environment is discussed.Comment: Revte