Sequence-Based Analysis of Thermal Adaptation and Protein Energy Landscapes in an Invasive Blue Mussel (Mytilus galloprovincialis).

Adaptive responses to thermal stress in poikilotherms plays an important role in determining competitive ability and species distributions. Amino acid substitutions that affect protein stability and modify the thermal optima of orthologous proteins may be particularly important in this context. Here, we examine a set of 2,770 protein-coding genes to determine if proteins in a highly invasive heat tolerant blue mussel (Mytilus galloprovincialis) contain signals of adaptive increases in protein stability relative to orthologs in a more cold tolerant M. trossulus. Such thermal adaptations might help to explain, mechanistically, the success with which the invasive marine mussel M. galloprovincialis has displaced native species in contact zones in the eastern (California) and western (Japan) Pacific. We tested for stabilizing amino acid substitutions in warm tolerant M. galloprovincialis relative to cold tolerant M. trossulus with a generalized linear model that compares in silico estimates of recent changes in protein stability among closely related congeners. Fixed substitutions in M. galloprovincialis were 3,180.0 calories per mol per substitution more stabilizing at genes with both elevated dN/dS ratios and transcriptional responses to heat stress, and 705.8 calories per mol per substitution more stabilizing across all 2,770 loci investigated. Amino acid substitutions concentrated in a small number of genes were more stabilizing in M. galloprovincialis compared with cold tolerant M. trossulus. We also tested for, but did not find, enrichment of a priori GO terms in genes with elevated dN/dS ratios in M. galloprovincialis. This might indicate that selection for thermodynamic stability is generic across all lineages, and suggests that the high change in estimated protein stability that we observed in M. galloprovincialis is driven by selection for extra stabilizing substitutions, rather than by higher incidence of selection in a greater number of genes in this lineage. Nonetheless, our finding of more stabilizing amino acid changes in the warm adapted lineage is important because it suggests that adaption for thermal stability has contributed to M. galloprovincialis' superior tolerance to heat stress, and that pairing tests for positive selection and tests for transcriptional response to heat stress can identify candidates of protein stability adaptation

Impulsive noise removal from color images with morphological filtering

This paper deals with impulse noise removal from color images. The proposed noise removal algorithm employs a novel approach with morphological filtering for color image denoising; that is, detection of corrupted pixels and removal of the detected noise by means of morphological filtering. With the help of computer simulation we show that the proposed algorithm can effectively remove impulse noise. The performance of the proposed algorithm is compared in terms of image restoration metrics and processing speed with that of common successful algorithms.Comment: The 6th international conference on analysis of images, social networks, and texts (AIST 2017), 27-29 July, 2017, Moscow, Russi

Texture and shape of two-dimensional domains of nematic liquid crystal

We present a generalized approach to compute the shape and internal structure of two-dimensional nematic domains. By using conformal mappings, we are able to compute the director field for a given domain shape that we choose from a rich class, which includes drops with large and small aspect ratios, and sharp domain tips as well as smooth ones. Results are assembled in a phase diagram that for given domain size, surface tension, anchoring strength, and elastic constant shows the transitions from a homogeneous to a bipolar director field, from circular to elongated droplets, and from sharp to smooth domain tips. We find a previously unaccounted regime, where the drop is nearly circular, the director field bipolar and the tip rounded. We also find that bicircular director fields, with foci that lie outside the domain, provide a remarkably accurate description of the optimal director field for a large range of values of the various shape parameters.Comment: 12 pages, 10 figure

DAC-Less amplifier-less generation and transmission of QAM signals using sub-volt silicon-organic hybrid modulators

We demonstrate generation and transmission of optical signals by directly interfacing highly efficient silicon-organic hybrid (SOH) modulators to binary output ports of a field-programmable gate array. Using an SOH Mach-Zehnder modulator (MZM) and an SOH IQ modulator we generate ON-OFF- keying and binary phase-shift keying signals as well as quadrature phase-shift keying and 16-state quadrature amplitude modulation (16QAM) formats. Peak-to-peak voltages amount to only 0.27 V-pp for driving the MZM and 0.41 V-pp for the IQ modulator. Neither digital-to-analog converters nor drive amplifiers are required, and the RF energy consumption in the modulator amounts to record-low 18 fJ/bit for 16QAM signaling

Perturbations in neuroinflammatory pathways are associated with paclitaxel-induced peripheral neuropathy in breast cancer survivors.

Paclitaxel is a common chemotherapy drug associated with the development of chronic paclitaxel-induced peripheral neuropathy (PIPN). PIPN is associated with neuroinflammatory mechanisms in pre-clinical studies. Here, we evaluated for differential gene expression (DGE) in peripheral blood between breast cancer survivors with and without PIPN and for neuroinflammatory (NI) related signaling pathways and whole-transcriptome profiles from other experiments. Pathway impact analysis identified 8 perturbed NI related pathways. Expression profile analysis found 15 experiments having similar whole-transcriptome profiles of DGE related to neuroinflammation and PIPN. These findings suggest that perturbations in pathways associated with neuroinflammation are found in cancer survivors with PIPN

Discovery of CH and OH in the -513 km s-1 Ejecta of Eta Carinae

The very massive star, Eta Carinae, is enshrouded in an unusual complex of stellar ejecta, which is highly depleted in C and O, and enriched in He and N. This circumstellar gas gives rise to distinct absorption components corresponding to at least 20 different velocities along the line-of-sight. The velocity component at -513 kms-1 exhibits very low ionization with predominantly neutral species of iron-peak elements. Our statistical equilibrium/photoionization modeling indicates that the low temperature (T = 760 K) and high density (n_H=10^7 cm^-3) of the -513 kms-1 component is conducive to molecule formation including those with the elements C and O. Examination of echelle spectra obtained with the Space Telescope Imaging Spectrograph (STIS) aboard the confirms the model's predictions. The molecules, H_2, CH, and most likely OH, have been identified in the -513 kms-1 absorption spectrum. This paper presents the analysis of the HST/STIS spectra with the deduced column densities for CH, OH and C I, and upper limit for CO. It is quite extraordinary to see molecular species in a cool environment at such a high velocity. The sharp molecular and ionic absorptions in this extensively CNO- processed material offers us a unique environment for studying the chemistry, dust formation processes, and nucleosynthesis in the ejected layers of a highly evolved massive star.Comment: tentatively scheduled for the ApJ 1 September 2005, v630, 1 issu

Robust T1-Weighted Structural Brain Imaging and Morphometry at 7T Using MP2RAGE.

PURPOSE: To suppress the noise, by sacrificing some of the signal homogeneity for numerical stability, in uniform T1 weighted (T1w) images obtained with the magnetization prepared 2 rapid gradient echoes sequence (MP2RAGE) and to compare the clinical utility of these robust T1w images against the uniform T1w images. MATERIALS AND METHODS: 8 healthy subjects (29.0±4.1 years; 6 Male), who provided written consent, underwent two scan sessions within a 24 hour period on a 7T head-only scanner. The uniform and robust T1w image volumes were calculated inline on the scanner. Two experienced radiologists qualitatively rated the images for: general image quality; 7T specific artefacts; and, local structure definition. Voxel-based and volume-based morphometry packages were used to compare the segmentation quality between the uniform and robust images. Statistical differences were evaluated by using a positive sided Wilcoxon rank test. RESULTS: The robust image suppresses background noise inside and outside the skull. The inhomogeneity introduced was ranked as mild. The robust image was significantly ranked higher than the uniform image for both observers (observer 1/2, p-value = 0.0006/0.0004). In particular, an improved delineation of the pituitary gland, cerebellar lobes was observed in the robust versus uniform T1w image. The reproducibility of the segmentation results between repeat scans improved (p-value = 0.0004) from an average volumetric difference across structures of ≈6.6% to ≈2.4% for the uniform image and robust T1w image respectively. CONCLUSIONS: The robust T1w image enables MP2RAGE to produce, clinically familiar T1w images, in addition to T1 maps, which can be readily used in uniform morphometry packages

A reduced model for shock and detonation waves. II. The reactive case

We present a mesoscopic model for reactive shock waves, which extends a previous model proposed in [G. Stoltz, Europhys. Lett. 76 (2006), 849]. A complex molecule (or a group of molecules) is replaced by a single mesoparticle, evolving according to some Dissipative Particle Dynamics. Chemical reactions can be handled in a mean way by considering an additional variable per particle describing a rate of reaction. The evolution of this rate is governed by the kinetics of a reversible exothermic reaction. Numerical results give profiles in qualitative agreement with all-atom studies

The gravitational analogue to the hydrogen atom (A summer study at the borders of quantum mechanics and general relativity)

This article reports on a student summer project performed in 2006 at the University of Frankfurt. It is addressed to undergraduate students familiar with the basic principles of relativistic quantum mechanics and general relativity. The aim of the project was to study the Dirac equation in curved space time. To obtain the general relativistic Dirac equation we use the formulation of gravity as a gauge theory in the first part. After these general considerations we restrict the further discussion to the special case of the Schwarzschild metric. This setting corresponds to the hydrogen atom, with the electromagnetic field replaced by gravity. Although there is a singularity at the event horizon it turns out that a regular solution of the time independent Dirac equation exists. Finally the Dirac equation is solved numerically using suitable boundary conditions.Comment: 19 pages, 3 figure