Phylogeny of Prokaryotes and Chloroplasts Revealed by a Simple Composition Approach on All Protein Sequences from Complete Genomes Without Sequence Alignment

The complete genomes of living organisms have provided much information on their phylogenetic relationships. Similarly, the complete genomes of chloroplasts have helped to resolve the evolution of this organelle in photosynthetic eukaryotes. In this paper we propose an alternative method of phylogenetic analysis using compositional statistics for all protein sequences from complete genomes. This new method is conceptually simpler than and computationally as fast as the one proposed by Qi et al. (2004b) and Chu et al. (2004). The same data sets used in Qi et al. (2004b) and Chu et al. (2004) are analyzed using the new method. Our distance-based phylogenic tree of the 109 prokaryotes and eukaryotes agrees with the biologists tree of life based on 16S rRNA comparison in a predominant majority of basic branching and most lower taxa. Our phylogenetic analysis also shows that the chloroplast genomes are separated to two major clades corresponding to chlorophytes s.l. and rhodophytes s.l. The interrelationships among the chloroplasts are largely in agreement with the current understanding on chloroplast evolution

Possible scale invariant linear magnetoresistance in pyrochlore iridates Bi2Ir2O7

We report the observation of a linear magnetoresistance in single crystals and epitaxial thin films of the pyrochlore iridate Bi2Ir2O7. The linear magnetoresistance is positive and isotropic at low temperatures, without any sign of saturation up to 35 T. As temperature increases, the linear field dependence gradually evolves to a quadratic field dependence. The temperature and field dependence of magnetoresistance of Bi2Ir2O7 bears strikingly resemblance to the scale invariant magnetoresistance observed in the strange metal phase in high Tc cuprates. However, the residual resistivity of Bi2Ir2O7 is more than two orders of magnitude higher than the curpates. Our results suggest that the correlation between linear magnetoresistance and quantum fluctuations may exist beyond high temperature superconductors

Tolerance of high-intensity focused ultrasound ablation in patients with hepatocellular carcinoma

BACKGROUND: High-intensity focused ultrasound (HIFU) ablation is a relatively new, noninvasive way of ablation for treating hepatocellular carcinoma (HCC). Emerging evidence has shown that it is effective for the treatment of HCC, even in patients with poor liver function. There is currently no data on the safety limit of HIFU ablation in patients with cirrhosis. However, this information is vital for the selection of appropriate patients for the procedure. We analyzed HCC patients who had undergone HIFU ablation and determined the lower limit of liver function and other patient factors with which HCC patients can tolerate this treatment modality. METHODS: Preoperative variables of 100 patients who underwent HIFU ablation for HCC were analyzed to identify the risk factors in HIFU intolerance in terms of stress-induced complications. Factors that may contribute to postablation complications were compared. RESULTS: Thirteen (13 %) patients developed a total of 18 complications. Morbidity was mainly due to skin and subcutaneous tissue injuries (n = 9). Five patients had first-degree skin burn, one had second-degree skin burn, and three had third-degree skin burn. Four complications were grade 3a in the Clavien classification and 14 were below this grade. Univariate analysis showed that age (p = 0.022) was the only independent factor in HIFU intolerance. CONCLUSIONS: HIFU ablation is generally well tolerated in HCC patients with cirrhosis. It is safe for Child-Pugh A and B patients and selected Child-Pugh C patients. With this new modality, HCC patients who were deemed unsalvageable by other surgical means in the past because of simultaneous Child-Pugh B or C disease now have a new hope.published_or_final_versio

D-branes with Lorentzian signature in the Nappi-Witten model

Lorentzian signature D-branes of all dimensions for the Nappi-Witten string are constructed. This is done by rewriting the gluing condition $J_+=FJ_-$ for the model chiral currents on the brane as a well posed first order differential problem and by solving it for Lie algebra isometries $F$ other than Lie algebra automorphisms. By construction, these D-branes are not twined conjugacy classes. Metrically degenerate D-branes are also obtained.Comment: 22 page

Geometric construction of D-branes in WZW models

The geometric description of D-branes in WZW models is pushed forward. Our starting point is a gluing condition\, $J_{+}=FJ_-$ that matches the model's chiral currents at the worldsheet boundary through a linear map $F$ acting on the WZW Lie algebra. The equivalence of boundary and gluing conditions of this type is studied in detail. The analysis involves a thorough discussion of Frobenius integrability, shows that $F$ must be an isometry, and applies to both metrically degenerate and nondegenerate D-branes. The isometry $F$ need not be a Lie algebra automorphism nor constantly defined over the brane. This approach, when applied to isometries of the form $F=R$ with $R$ a constant Lie algebra automorphism, validates metrically degenerate $R$-twined conjugacy classes as D-branes. It also shows that no D-branes exist in semisimple WZW models for constant\, $F=-R$.Comment: 23 pages, discussion of limitations of the gluing condition approach adde

Quantized Nambu-Poisson Manifolds in a 3-Lie Algebra Reduced Model

We consider dimensional reduction of the Bagger-Lambert-Gustavsson theory to a zero-dimensional 3-Lie algebra model and construct various stable solutions corresponding to quantized Nambu-Poisson manifolds. A recently proposed Higgs mechanism reduces this model to the IKKT matrix model. We find that in the strong coupling limit, our solutions correspond to ordinary noncommutative spaces arising as stable solutions in the IKKT model with D-brane backgrounds. In particular, this happens for S^3, R^3 and five-dimensional Neveu-Schwarz Hpp-waves. We expand our model around these backgrounds and find effective noncommutative field theories with complicated interactions involving higher-derivative terms. We also describe the relation of our reduced model to a cubic supermatrix model based on an osp(1|32) supersymmetry algebra.Comment: 22 page

Universal time-dependent deformations of Schrodinger geometry

We investigate universal time-dependent exact deformations of Schrodinger geometry. We present 1) scale invariant but non-conformal deformation, 2) non-conformal but scale invariant deformation, and 3) both scale and conformal invariant deformation. All these solutions are universal in the sense that we could embed them in any supergravity constructions of the Schrodinger invariant geometry. We give a field theory interpretation of our time-dependent solutions. In particular, we argue that any time-dependent chemical potential can be treated exactly in our gravity dual approach.Comment: 24 pages, v2: references adde

De novo large rare copy-number variations contribute to conotruncal heart disease in Chinese patients

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ADC Nonlinearity Correction for the Majorana Demonstrator

Imperfections in analog-to-digital conversion (ADC) cannot be ignored when signal digitization requirements demand both wide dynamic range and high resolution, as is the case for the Majorana Demonstrator 76Ge neutrinoless double-beta decay search. Enabling the experiment's high-resolution spectral analysis and efficient pulse shape discrimination required careful measurement and correction of ADC nonlinearities. A simple measurement protocol was developed that did not require sophisticated equipment or lengthy data-taking campaigns. A slope-dependent hysteresis was observed and characterized. A correction applied to digitized waveforms prior to signal processing reduced the differential and integral nonlinearities by an order of magnitude, eliminating these as dominant contributions to the systematic energy uncertainty at the double-beta decay Q value

Use of clinical chromosomal microarray in Chinese patients with autism spectrum disorder—implications of a copy number variation involving DPP10

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