Phylo-mLogo: an interactive and hierarchical multiple-logo visualization tool for alignment of many sequences

BACKGROUND: When aligning several hundreds or thousands of sequences, such as epidemic virus sequences or homologous/orthologous sequences of some big gene families, to reconstruct the epidemiological history or their phylogenies, how to analyze and visualize the alignment results of many sequences has become a new challenge for computational biologists. Although there are several tools available for visualization of very long sequence alignments, few of them are applicable to the alignments of many sequences. RESULTS: A multiple-logo alignment visualization tool, called Phylo-mLogo, is presented in this paper. Phylo-mLogo calculates the variabilities and homogeneities of alignment sequences by base frequencies or entropies. Different from the traditional representations of sequence logos, Phylo-mLogo not only displays the global logo patterns of the whole alignment of multiple sequences, but also demonstrates their local homologous logos for each clade hierarchically. In addition, Phylo-mLogo also allows the user to focus only on the analysis of some important, structurally or functionally constrained sites in the alignment selected by the user or by built-in automatic calculation. CONCLUSION: With Phylo-mLogo, the user can symbolically and hierarchically visualize hundreds of aligned sequences simultaneously and easily check the changes of their amino acid sites when analyzing many homologous/orthologous or influenza virus sequences. More information of Phylo-mLogo can be found at URL

The peaked response of transpiration rate to vapour pressure deficit in field conditions can be explained by the temperature optimum of photosynthesis

Leaf transpiration rate (E) frequently shows a peaked response to increasing vapour pressure deficit (D). The mechanisms for the decrease in E at high D, known as the 'apparent feed-forward response', are strongly debated but explanations to date have exclusively focused on hydraulic processes. However, stomata also respond to signals related to photosynthesis. We investigated whether the apparent feed-forward response of E to D in the field can be explained by the response of photosynthesis to temperature (T), which normally co-varies with D in field conditions. As photosynthesis decreases with increasing T past its optimum, it may drive a decrease in stomatal conductance (gs) that is additional to the response of gs to increasing D alone. If this additional decrease is sufficiently steep and coupling between A and gs occurs, it could cause an overall decrease in E with increasing D. We tested this mechanism using a gas exchange model applied to leaf-scale and whole-tree CO2 and H2O fluxes measured on Eucalyptus saligna growing in whole-tree chambers. A peaked response of E to D was observed at both leaf and whole-tree scales. We found that this peaked response was matched by a gas exchange model only when T effects on photosynthesis were incorporated. We conclude that field-based studies of the relationship between E and D need to consider signals related to changing photosynthetic rates in addition to purely hydraulic mechanisms. © 2014 Elsevier B.V

SinicView: A visualization environment for comparisons of multiple nucleotide sequence alignment tools

BACKGROUND: Deluged by the rate and complexity of completed genomic sequences, the need to align longer sequences becomes more urgent, and many more tools have thus been developed. In the initial stage of genomic sequence analysis, a biologist is usually faced with the questions of how to choose the best tool to align sequences of interest and how to analyze and visualize the alignment results, and then with the question of whether poorly aligned regions produced by the tool are indeed not homologous or are just results due to inappropriate alignment tools or scoring systems used. Although several systematic evaluations of multiple sequence alignment (MSA) programs have been proposed, they may not provide a standard-bearer for most biologists because those poorly aligned regions in these evaluations are never discussed. Thus, a tool that allows cross comparison of the alignment results obtained by different tools simultaneously could help a biologist evaluate their correctness and accuracy. RESULTS: In this paper, we present a versatile alignment visualization system, called SinicView, (for Sequence-aligning INnovative and Interactive Comparison VIEWer), which allows the user to efficiently compare and evaluate assorted nucleotide alignment results obtained by different tools. SinicView calculates similarity of the alignment outputs under a fixed window using the sum-of-pairs method and provides scoring profiles of each set of aligned sequences. The user can visually compare alignment results either in graphic scoring profiles or in plain text format of the aligned nucleotides along with the annotations information. We illustrate the capabilities of our visualization system by comparing alignment results obtained by MLAGAN, MAVID, and MULTIZ, respectively. CONCLUSION: With SinicView, users can use their own data sequences to compare various alignment tools or scoring systems and select the most suitable one to perform alignment in the initial stage of sequence analysis

Constraints on Fluid Dynamics from Equilibrium Partition Functions

We study the thermal partition function of quantum field theories on arbitrary stationary background spacetime, and with arbitrary stationary background gauge fields, in the long wavelength expansion. We demonstrate that the equations of relativistic hydrodynamics are significantly constrained by the requirement of consistency with any partition function. In examples at low orders in the derivative expansion we demonstrate that these constraints coincide precisely with the equalities between hydrodynamical transport coefficients that follow from the local form of the second law of thermodynamics. In particular we recover the results of Son and Surowka on the chiral magnetic and chiral vorticity flows, starting from a local partition function that manifestly reproduces the field theory anomaly, without making any reference to an entropy current. We conjecture that the relations between transport coefficients that follow from the second law of thermodynamics agree to all orders in the derivative expansion with the constraints described in this paper.Comment: Typos corrected, References adde

Holographic dilepton production in a thermalizing plasma

We determine the out-of-equilibrium production rate of dileptons at rest in strongly coupled N=4 Super Yang-Mills plasma using the AdS/CFT correspondence. Thermalization is achieved via the gravitational collapse of a thin shell of matter in AdS_5 space and the subsequent formation of a black hole, which we describe in a quasistatic approximation. Prior to thermalization, the dilepton spectral function is observed to oscillate as a function of frequency, but the amplitude of the oscillations decreases when thermal equilibrium is approached. At the same time, we follow the flow of the quasinormal spectrum of the corresponding U(1) vector field towards its equilibrium limit.Comment: 21 pages, 7 figures. v2: Version accepted for publication in JHEP; minor modifications, added reference

Constraints on Superfluid Hydrodynamics from Equilibrium Partition Functions

Following up on recent work in the context of ordinary fluids, we study the equilibrium partition function of a 3+1 dimensional superfluid on an arbitrary stationary background spacetime, and with arbitrary stationary background gauge fields, in the long wavelength expansion. We argue that this partition function is generated by a 3 dimensional Euclidean effective action for the massless Goldstone field. We parameterize the general form of this action at first order in the derivative expansion. We demonstrate that the constitutive relations of relativistic superfluid hydrodynamics are significantly constrained by the requirement of consistency with such an effective action. At first order in the derivative expansion we demonstrate that the resultant constraints on constitutive relations coincide precisely with the equalities between hydrodynamical transport coefficients recently derived from the second law of thermodynamics.Comment: 46 page

Electrified plasma in AdS/CFT correspondence

We construct new gravity backgrounds holographic dual to neutral plasma with U(1) global symmetry in the presence of constant electric field, considering its full back-reactions to the metric. As the electric field and the induced current cause a net energy in-flow to the system, the plasma is continually heated up and the corresponding gravity solution has an expanding horizon. After proposing a consistent late-time expansion scheme, we present analytic solutions in the scheme up to next-leading order, and our solutions are new time-dependent solutions of 5D asymptotic AdS Einstein-Maxwell(-Chern-Simons) theory. To extract dual CFT stress tensor and U(1) current from the solutions, we perform a rigorous holographic renormalization of Einstein-Maxwell-Chern-Simons theory including full back-reactions, which can in itself be an interesting addition to literatures. As by-products, we obtain interesting modifications of energy-momentum/current Ward identities due to the U(1) symmetry and its triangle anomaly.Comment: 27 pages, no figure, v3, minor typos fixed, matches with published versio

Charged, conformal non-relativistic hydrodynamics

We embed a holographic model of an U(1) charged fluid with Galilean invariance in string theory and calculate its specific heat capacity and Prandtl number. Such theories are generated by a R-symmetry twist along a null direction of a N=1 superconformal theory. We study the hydrodynamic properties of such systems employing ideas from the fluid-gravity correspondence.Comment: 31 pages, 1 figure, JHEP3 style, refs added, typos corrected, missing terms in spatial charge current and field corrections added, to be published in JHE

Facile Synthesis of High Quality Graphene Nanoribbons

Graphene nanoribbons have attracted attention for their novel electronic and spin transport properties1-6, and because nanoribbons less than 10 nm wide have a band gap that can be used to make field effect transistors. However, producing nanoribbons of very high quality, or in high volumes, remains a challenge. Here, we show that pristine few-layer nanoribbons can be produced by unzipping mildly gas-phase oxidized multiwalled carbon nanotube using mechanical sonication in an organic solvent. The nanoribbons exhibit very high quality, with smooth edges (as seen by high-resolution transmission electron microscopy), low ratios of disorder to graphitic Raman bands, and the highest electrical conductance and mobility reported to date (up to 5e2/h and 1500 cm2/Vs for ribbons 10-20 nm in width). Further, at low temperature, the nanoribbons exhibit phase coherent transport and Fabry-Perot interference, suggesting minimal defects and edge roughness. The yield of nanoribbons was ~2% of the starting raw nanotube soot material, which was significantly higher than previous methods capable of producing high quality narrow nanoribbons1. The relatively high yield synthesis of pristine graphene nanoribbons will make these materials easily accessible for a wide range of fundamental and practical applications.Comment: Nature Nanotechnology in pres