When can we reconstruct the ancestral state? Beyond Brownian motion

Reconstructing the ancestral state of a group of species helps answer many important questions in evolutionary biology. Therefore, it is crucial to understand when we can estimate the ancestral state accurately. Previous works provide a necessary and sufficient condition, called the big bang condition, for the existence of an accurate reconstruction method under discrete trait evolution models and the Brownian motion model. In this paper, we extend this result to a wide range of continuous trait evolution models. In particular, we consider a general setting where continuous traits evolve along the tree according to stochastic processes that satisfy some regularity conditions. We verify these conditions for popular continuous trait evolution models including Ornstein-Uhlenbeck, reflected Brownian Motion, and Cox-Ingersoll-Ross

High expression FUT1 and B3GALT5 is an independent predictor of postoperative recurrence and survival in hepatocellular carcinoma.

Cancer may arise from dedifferentiation of mature cells or maturation-arrested stem cells. Previously we reported that definitive endoderm from which liver was derived, expressed Globo H, SSEA-3 and SSEA-4. In this study, we examined the expression of their biosynthetic enzymes, FUT1, FUT2, B3GALT5 and ST3GAL2, in 135 hepatocellular carcinoma (HCC) tissues by qRT-PCR. High expression of either FUT1 or B3GALT5 was significantly associated with advanced stages and poor outcome. Kaplan Meier survival analysis showed significantly shorter relapse-free survival (RFS) for those with high expression of either FUT1 or B3GALT5 (P = 0.024 and 0.001, respectively) and shorter overall survival (OS) for those with high expression of B3GALT5 (P = 0.017). Combination of FUT1 and B3GALT5 revealed that high expression of both genes had poorer RFS and OS than the others (P < 0.001). Moreover, multivariable Cox regression analysis identified the combination of B3GALT5 and FUT1 as an independent predictor for RFS (HR: 2.370, 95% CI: 1.505-3.731, P < 0.001) and OS (HR: 2.153, 95% CI: 1.188-3.902, P = 0.012) in HCC. In addition, the presence of Globo H, SSEA-3 and SSEA-4 in some HCC tissues and their absence in normal liver was established by immunohistochemistry staining and mass spectrometric analysis

Exploring quantum criticality based on ultracold atoms in optical lattices

Critical behavior developed near a quantum phase transition, interesting in its own right, offers exciting opportunities to explore the universality of strongly-correlated systems near the ground state. Cold atoms in optical lattices, in particular, represent a paradigmatic system, for which the quantum phase transition between the superfluid and Mott insulator states can be externally induced by tuning the microscopic parameters. In this paper, we describe our approach to study quantum criticality of cesium atoms in a two-dimensional lattice based on in situ density measurements. Our research agenda involves testing critical scaling of thermodynamic observables and extracting transport properties in the quantum critical regime. We present and discuss experimental progress on both fronts. In particular, the thermodynamic measurement suggests that the equation of state near the critical point follows the predicted scaling law at low temperatures.Comment: 15 pages, 6 figure

Magnetorotational collapse of very massive stars to black holes in full general relativity

We perform axisymmetric simulations of the magnetorotational collapse of very massive stars in full general relativity. Our simulations are applicable to the collapse of supermassive stars (M > 10^3M_sun) and to very massive Pop III stars. We model our initial configurations by n=3 polytropes. The ratio of magnetic to rotational kinetic energy in these configurations is chosen to be small (1% and 10%). We find that such magnetic fields do not affect the initial collapse significantly. The core collapses to a black hole, after which black hole excision is employed to continue the evolution long enough for the hole to reach a quasi-stationary state. We find that the black hole mass is M_h = 0.95M and its spin parameter is J_h/M_h^2 = 0.7, with the remaining matter forming a torus around the black hole. We freeze the spacetime metric ("Cowling approximation") and continue to follow the evolution of the torus after the black hole has relaxed to quasi-stationary equilibrium. In the absence of magnetic fields, the torus settles down following ejection of a small amount of matter due to shock heating. When magnetic fields are present, the field lines gradually collimate along the hole's rotation axis. MHD shocks and the MRI generate MHD turbulence in the torus and stochastic accretion onto the central black hole. When the magnetic field is strong, a wind is generated in the torus, and the torus undergoes radial oscillations that drive episodic accretion onto the hole. These oscillations produce long-wavelength gravitational waves potentially detectable by LISA. The final state of the magnetorotational collapse always consists of a central black hole surrounded by a collimated magnetic field and a hot, thick accretion torus. This system is a viable candidate for the central engine of a long-soft gamma-ray burst.Comment: 17 pages, 13 figures, replaced with the published versio

Relativistic Radiation Magnetohydrodynamics in Dynamical Spacetimes: Numerical Methods and Tests

Many systems of current interest in relativistic astrophysics require a knowledge of radiative transfer in a magnetized gas flowing in a strongly-curved, dynamical spacetime. Such systems include coalescing compact binaries containing neutron stars or white dwarfs, disks around merging black holes, core collapse supernovae, collapsars, and gamma-ray burst sources. To model these phenomena, all of which involve general relativity, radiation (photon and/or neutrino), and magnetohydrodynamics, we have developed a general relativistic code capable of evolving MHD fluids and radiation in dynamical spacetimes. Our code solves the coupled Einstein-Maxwell-MHD-Radiation system of equations both in axisymmetry and in full 3+1 dimensions. We evolve the metric by integrating the BSSN equations, and use a conservative, high-resolution shock-capturing scheme to evolve both the MHD and radiation moment equations. In this paper, we implement our scheme for optically thick gases and grey-body opacities. Our code gives accurate results in a suite of tests involving radiating shocks and nonlinear waves propagating in Minkowski spacetime. In addition, to test our code's ability to evolve the relativistic radiation-MHD equations in strong-field dynamical spacetimes, we study "thermal Oppenheimer-Snyder collapse" to a black hole, and find good agreement between analytic and numerical solutions.Comment: 20 pages, 8 figures, submitted to PR

Direct and indirect control of the initiation of meiotic recombination by DNA damage checkpoint mechanisms in budding yeast

Meiotic recombination plays an essential role in the proper segregation of chromosomes at meiosis I in many sexually reproducing organisms. Meiotic recombination is initiated by the scheduled formation of genome-wide DNA double-strand breaks (DSBs). The timing of DSB formation is strictly controlled because unscheduled DSB formation is detrimental to genome integrity. Here, we investigated the role of DNA damage checkpoint mechanisms in the control of meiotic DSB formation using budding yeast. By using recombination defective mutants in which meiotic DSBs are not repaired, the effect of DNA damage checkpoint mutations on DSB formation was evaluated. The Tel1 (ATM) pathway mainly responds to unresected DSB ends, thus the sae2 mutant background in which DSB ends remain intact was employed. On the other hand, the Mec1 (ATR) pathway is primarily used when DSB ends are resected, thus the rad51 dmc1 double mutant background was employed in which highly resected DSBs accumulate. In order to separate the effect caused by unscheduled cell cycle progression, which is often associated with DNA damage checkpoint defects, we also employed the ndt80 mutation which permanently arrests the meiotic cell cycle at prophase I. In the absence of Tel1, DSB formation was reduced in larger chromosomes (IV, VII, II and XI) whereas no significant reduction was found in smaller chromosomes (III and VI). On the other hand, the absence of Rad17 (a critical component of the ATR pathway) lead to an increase in DSB formation (chromosomes VII and II were tested). We propose that, within prophase I, the Tel1 pathway facilitates DSB formation, especially in bigger chromosomes, while the Mec1 pathway negatively regulates DSB formation. We also identified prophase I exit, which is under the control of the DNA damage checkpoint machinery, to be a critical event associated with down-regulating meiotic DSB formation

Investigation of Low-Cost Surface Processing Techniques for Large-Size Multicrystalline Silicon Solar Cells

The subject of the present work is to develop a simple and effective method of enhancing conversion efficiency in large-size solar cells using multicrystalline silicon (mc-Si) wafer. In this work, industrial-type mc-Si solar cells with area of 125×125 mm2 were acid etched to produce simultaneously POCl3 emitters and silicon nitride deposition by plasma-enhanced chemical vapor deposited (PECVD). The study of surface morphology and reflectivity of different mc-Si etched surfaces has also been discussed in this research. Using our optimal acid etching solution ratio, we are able to fabricate mc-Si solar cells of 16.34% conversion efficiency with double layers silicon nitride (Si3N4) coating. From our experiment, we find that depositing double layers silicon nitride coating on mc-Si solar cells can get the optimal performance parameters. Open circuit (Voc) is 616 mV, short circuit current (Jsc) is 34.1 mA/cm2, and minority carrier diffusion length is 474.16 μm. The isotropic texturing and silicon nitride layers coating approach contribute to lowering cost and achieving high efficiency in mass production

Efficiency Improved by H

The photovoltaic (PV) effects have been investigated and improved using efficient treatments both on single-crystalline (sc) and on multicrystalline (mc) silicon (Si) solar cells. The major effect of forming gas (FG) treatment on solar cell performance is the fill-factor values, which increase 3.75% and 8.28%, respectively, on sc-Si and mc-Si solar cells. As for the optimal 15%-H2 ratio and 40-minute FG treatment, the conversion efficiency (η) values drastically increase to 14.89% and 14.31%, respectively, for sc- and mc-Si solar cells. Moreover, we can measure the internal quantum efficiency (IQE) values increase with H2-FG treatment under visible wavelength (400~900 nm) radiation. Thus based on the work in this research, we confirm that H2 passivation has become crucial both in PV as well as in microelectronics fields. Moreover, the developed mc-Si solar cell by proper H2 FG treatment is quite suitable for commercial applications