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

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

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

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

Catecholamine stress alters neutrophil trafficking and impairs wound healing by β2-adrenergic receptor-mediated upregulation of IL-6.

Stress-induced hormones can alter the inflammatory response to tissue injury; however, the precise mechanism by which epinephrine influences inflammatory response and wound healing is not well defined. Here we demonstrate that epinephrine alters the neutrophil (polymorphonuclear leukocyte (PMN))-dependent inflammatory response to a cutaneous wound. Using noninvasive real-time imaging of genetically tagged PMNs in a murine skin wound, chronic, epinephrine-mediated stress was modeled by sustained delivery of epinephrine. Prolonged systemic exposure of epinephrine resulted in persistent PMN trafficking to the wound site via an IL-6-mediated mechanism, and this in turn impaired wound repair. Further, we demonstrate that β2-adrenergic receptor-dependent activation of proinflammatory macrophages is critical for epinephrine-mediated IL-6 production. This study expands our current understanding of stress hormone-mediated impairment of wound healing and provides an important mechanistic link to explain how epinephrine stress exacerbates inflammation via increased number and lifetime of PMNs

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

A contracting circumbinary molecular ring with an inner cavity of about 140 AU around Ori 139-409

Sensitive and subarcsecond resolution ($\sim$ 0.7\arcsec) CH$_3$OH(7$_{-2,6}$ $\to$ 6$_{-2,5}$) line and 890 $\mu$m continuum observations made with the Submillimeter Array (SMA) towards the hot molecular circumbinary ring associated with the young multiple star Ori 139-409 are presented. The CH$_3$OH(7$_{-2,6}$ - 6$_{-2,5}$) emission from the ring is well resolved at this angular resolution revealing an inner cavity with a size of about 140 AU. A LTE model of a Keplerian disk with an inner cavity of the same size confirms the presence of this cavity. Additionally, this model suggests that the circumbinary ring is contracting with a velocity of V$_{inf}$ $\sim$ 1.5 km s$^{-1}$ toward the binary central compact circumstellar disks reported at a wavelength of 7 mm. {\bf The inner central cavity seems to be formed by the tidal effects of the young stars in the middle of the ring.} The ring appears to be not a stationary object. Furthermore, the infall velocity we determine is about a factor of 3 slower than the free-fall velocity corresponding to the dynamical mass. This would correspond to a mass accretion rate of about 10$^{-5}$ M$_\odot$/yr. We found that the dust emission associated with Ori 139-409 appears to be arising from the circumstellar disks with no strong contribution from the molecular gas ring. A simple comparison with other classical molecular dusty rings (e.g. GG Tau, UZ Tau, and UY Aur) suggests that Ori 139-409 could be one of the youngest circumbinary rings reported up to date. Finally, our results confirm that the circumbinary rings are actively funneling fresh gas material to the central compact binary circumstellar disks, i.e. to the protostars in the very early phases of their evolution.Comment: Accepted by MNRA

Haemogenic endocardium contributes to transient definitive haematopoiesis.

Haematopoietic cells arise from spatiotemporally restricted domains in the developing embryo. Although studies of non-mammalian animal and in vitro embryonic stem cell models suggest a close relationship among cardiac, endocardial and haematopoietic lineages, it remains unknown whether the mammalian heart tube serves as a haemogenic organ akin to the dorsal aorta. Here we examine the haemogenic activity of the developing endocardium. Mouse heart explants generate myeloid and erythroid colonies in the absence of circulation. Haemogenic activity arises from a subset of endocardial cells in the outflow cushion and atria earlier than in the aorta-gonad-mesonephros region, and is transient and definitive in nature. Interestingly, key cardiac transcription factors, Nkx2-5 and Isl1, are expressed in and required for the haemogenic population of the endocardium. Together, these data suggest that a subset of endocardial/endothelial cells serve as a de novo source for transient definitive haematopoietic progenitors