The mean, variance and limiting distribution of two statistics sensitive to phylogenetic tree balance

For two decades, the Colless index has been the most frequently used statistic for assessing the balance of phylogenetic trees. In this article, this statistic is studied under the Yule and uniform model of phylogenetic trees. The main tool of analysis is a coupling argument with another well-known index called the Sackin statistic. Asymptotics for the mean, variance and covariance of these two statistics are obtained, as well as their limiting joint distribution for large phylogenies. Under the Yule model, the limiting distribution arises as a solution of a functional fixed point equation. Under the uniform model, the limiting distribution is the Airy distribution. The cornerstone of this study is the fact that the probabilistic models for phylogenetic trees are strongly related to the random permutation and the Catalan models for binary search trees.Comment: Published at http://dx.doi.org/10.1214/105051606000000547 in the Annals of Applied Probability (http://www.imstat.org/aap/) by the Institute of Mathematical Statistics (http://www.imstat.org

Intrinsic peculiarities of real material realizations of a spin-1/2 kagome lattice

Spin-1/2 magnets with kagome geometry, being for years a generic object of theoretical investigations, have few real material realizations. Recently, a DFT-based microscopic model for two such materials, kapellasite Cu3Zn(OH)6Cl2 and haydeeite Cu3Mg(OH)6Cl2, was presented [O. Janson, J. Richter and H. Rosner, arXiv:0806.1592]. Here, we focus on the intrinsic properties of real spin-1/2 kagome materials having influence on the magnetic ground state and the low-temperature excitations. We find that the values of exchange integrals are strongly dependent on O--H distance inside the hydroxyl groups, present in most spin-1/2 kagome compounds up to date. Besides the original kagome model, considering only the nearest neighbour exchange, we emphasize the crucial role of the exchange along the diagonals of the kagome lattice.Comment: 4 pages, 4 figures. A paper for the proceedings of the HFM 2008 conferenc

A novel bacterial l-arginine sensor controlling c-di-GMP levels in Pseudomonas aeruginosa

Nutrients such as amino acids play key roles in shaping the metabolism of microorganisms in natural environments and in host–pathogen interactions. Beyond taking part to cellular metabolism and to protein synthesis, amino acids are also signaling molecules able to influence group behavior in microorganisms, such as biofilm formation. This lifestyle switch involves complex metabolic reprogramming controlled by local variation of the second messenger 3′, 5′-cyclic diguanylic acid (c-di-GMP). The intracellular levels of this dinucleotide are finely tuned by the opposite activity of dedicated diguanylate cyclases (GGDEF signature) and phosphodiesterases (EAL and HD-GYP signatures), which are usually allosterically controlled by a plethora of environmental and metabolic clues. Among the genes putatively involved in controlling c-di-GMP levels in P. aeruginosa, we found that the multidomain transmembrane protein PA0575, bearing the tandem signature GGDEF-EAL, is an l-arginine sensor able to hydrolyse c-di-GMP. Here, we investigate the basis of arginine recognition by integrating bioinformatics, molecular biophysics and microbiology. Although the role of nutrients such as l-arginine in controlling the cellular fate in P. aeruginosa (including biofilm, pathogenicity and virulence) is already well established, we identified the first l-arginine sensor able to link environment sensing, c-di-GMP signaling and biofilm formation in this bacterium

Delayed feedback as a means of control of noise-induced motion

Time--delayed feedback is exploited for controlling noise--induced motion in coherence resonance oscillators. Namely, under the proper choice of time delay, one can either increase or decrease the regularity of motion. It is shown that in an excitable system, delayed feedback can stabilize the frequency of oscillations against variation of noise strength. Also, for fixed noise intensity, the phenomenon of entrainment of the basic oscillation period by the delayed feedback occurs. This allows one to steer the timescales of noise-induced motion by changing the time delay.Comment: 4 pages, 4 figures. In the replacement file Fig. 2 and Fig. 4(b),(d) were amended. The reason is numerical error found, that affected the quantitative estimates of correlation time, but did not affect the main messag

Magnetic pyroxenes LiCrGe2O6 and LiCrSi2O6: dimensionality crossover in a non-frustrated S=3/2 Heisenberg model

The magnetism of magnetoelectric $S$ = 3/2 pyroxenes LiCrSi$_2$O$_6$ and LiCrGe$_2$O$_6$ is studied by density functional theory (DFT) calculations, quantum Monte Carlo (QMC) simulations, neutron diffraction, as well as low-field and high-field magnetization measurements. In contrast with earlier reports, we find that the two compounds feature remarkably different, albeit non-frustrated magnetic models. In LiCrSi$_2$O$_6$, two relevant exchange integrals, $J_1 \simeq$ 9 K along the structural chains and $J_{\text{ic1}}$ $\simeq$ 2 K between the chains, form a 2D anisotropic honeycomb lattice. In contrast, the spin model of LiCrGe$_2$O$_6$ is constituted of three different exchange couplings. Surprisingly, the leading exchange $J_{\text{ic1}}$ $\simeq$ 2.3 K operates between the chains, while $J_1$ $\simeq$ 1.2 K is about two times smaller. The additional interlayer coupling $J_{\text{ic2}}$ $\simeq$ $J_1$ renders this model 3D. QMC simulations reveal excellent agreement between our magnetic models and the available experimental data. Underlying mechanisms of the exchange couplings, magnetostructural correlations, as well as implications for other pyroxene systems are discussed.Comment: 11 pages, 8 figures, 3 tables + Supplementary informatio

Functional characterization and structure-guided mutational analysis of the transsulfuration enzyme cystathionine γ-lyase from toxoplasma gondii

Sulfur-containing amino acids play essential roles in many organisms. The protozoan parasite Toxoplasma gondii includes the genes for cystathionine β-synthase and cystathionine γ-lyase (TgCGL), as well as for cysteine synthase, which are crucial enzymes of the transsulfuration and de novo pathways for cysteine biosynthesis, respectively. These enzymes are specifically expressed in the oocyst stage of T. gondii. However, their functionality has not been investigated. Herein, we expressed and characterized the putative CGL from T. gondii. Recombinant TgCGL almost exclusively catalyses the α,γ-hydrolysis of L-cystathionine to form L-cysteine and displays marginal reactivity toward L-cysteine. Structure-guided homology modelling revealed two striking amino acid differences between the human and parasite CGL active-sites (Glu59 and Ser340 in human to Ser77 and Asn360 in toxoplasma). Mutation of Asn360 to Ser demonstrated the importance of this residue in modulating the specificity for the catalysis of α,β-versus α,γ-elimination of L-cystathionine. Replacement of Ser77 by Glu completely abolished activity towards L-cystathionine. Our results suggest that CGL is an important functional enzyme in T. gondii, likely implying that the reverse transsulfuration pathway is operative in the parasite; we also probed the roles of active-site architecture and substrate binding conformations as determinants of reaction specificity in transsulfuration enzymes

Modeling the Searching Behavior of Social Monkeys

We discuss various features of the trajectories of spider monkeys looking for food in a tropical forest, as observed recently in an extensive {\it in situ} study. Some of the features observed can be interpreted as the result of social interactions. In addition, a simple model of deterministic walk in a random environment reproduces the observed angular correlations between successive steps, and in some cases, the emergence of L\'evy distributions for the length of the steps.Comment: 7 pages, 3 figure

Discovery of a stellar companion to the nearby solar-analogue HD 104304

Sun-like stars are promising candidates to host exoplanets and are often included in exoplanet surveys by radial velocity (RV) and direct imaging. In this paper we report on the detection of a stellar companion to the nearby solar-analogue star HD 104304, which previously was considered to host a planetary mass or brown dwarf companion. We searched for close stellar and substellar companions around extrasolar planet host stars with high angular resolution imaging to characterize planet formation environments. The detection of the stellar companion was achieved by high angular resolution measurements, using the "Lucky Imaging" technique at the ESO NTT 3.5m with the AstraLux Sur instrument. We combined the results with VLT/NACO archive data, where the companion could also be detected. The results were compared to precise RV measurements of HD 104304, obtained at the Lick and Keck observatories from 2001-2010. We confirmed common proper motion of the binary system. A spectral type of M4V of the companion and a mass of 0.21 M_Sun was derived. Due to comparison of the data with RV measurements of the unconfirmed planet candidate listed in the Extrasolar Planets Encyclopaedia, we suggest that the discovered companion is the origin of the RV trend and that the inclination of the orbit of approximately 35 degrees explains the relatively small RV signal.Comment: 4 pages, 4 PNG figures, use aa.cls, accepted for publication in Astronomy & Astrophysic

The first order convergence law fails for random perfect graphs

We consider first order expressible properties of random perfect graphs. That is, we pick a graph $G_n$ uniformly at random from all (labelled) perfect graphs on $n$ vertices and consider the probability that it satisfies some graph property that can be expressed in the first order language of graphs. We show that there exists such a first order expressible property for which the probability that $G_n$ satisfies it does not converge as $n\to\infty$.Comment: 11 pages. Minor corrections since last versio

Off-pump coronary artery bypass (OPCAB) in complex coronary artery bypass procedures – a report of four cases and review of the literature

Off-pump coronary artery bypass (OPCAB) surgery is a procedure that is still not widely used by all cardiac surgeons. In the USA about 20-25% of coronary artery bypass graft (CABG) surgery is done offpump. Current literature suggests that both OPCAB and CABG with cardiopulmonary bypass have similar mortality rates, but OPCAB surgery does offer less morbidity, and advantages in terms of mortality and stroke rates in certain high risk patients. We discuss the role of OPCAB surgery in high risk patients, especially redo operations through a left thoracotomy to protect an intact internal mammary artery (LIMA) graft to the left anterior descending artery (LAD) and in patients with a calcified ascending aorta. Four case reports are used as examples and the literature is reviewed, which shows a superior outcome with OPCAB surgery in these complicated cases