FTIR spectroscopic and theoretical study of matrix-isolated (E)-1-(cyclopropyldiazenyl)naphthalen-2-ol

Photochromic systems are important due to their industrial applications in variable optical transmission materials and optobioelectronic devices. For such applications, the organic photochromic compounds involved are usually incorporated in polymers, liquid crystalline materials, or other convenient host matrices [1, 2]. Herein, a photochromic compound, (E)-1-(cyclopropyldiazenyl)naphthalen-2-ol (show in Figure 1), which was synthesized by a published method [3] and characterized, was isolated in a cryogenic argon matrix and its structure as well as UV-induced phototransformations were characterized by IR spectroscopy. The structures of the starting compound and of the generated photoproducts were identified by comparison of their experimental IR spectra with the spectra theoretically calculated at the DFT (B3LYP)/6-311++G(d,p) level for several possible tautomeric and rotameric forms.Fundação para a Ciência e a Tecnologia (FCT

Kombucha microbiome as a probiotic: a view from the perspective of post-genomics and synthetic ecology

Probiotics are essential for establishing and maintaining optimal immune health. The probiotic therapy is known from alternative medicine for ages; however, the recent demonstration of the normal microflora to induce innate immunity has introduced the science-based concept of therapeutic application of potentially beneficial probiotic microorganisms for a treatment of functional disorders. Traditionally, probiotics are associated with dairy products, however, novel formulations are needed, first of all, originated from naturally occurring symbiotic microbial communities as the most robust assemblages. Especially, safe and robust probiotics are needed for long-term expeditions, outposts, extraterrestrial permanently-manned bases, where humans are exposed to adverse environmental factors. Kombucha beverage is Symbiotic Culture of Bacteria and Yeast (SCOBY) and associated with health-promoting effects. Kombucha tea/mat is being in use in human livings within millennia as a probiotic drink for healing and health prophylaxis effects, however, new research opportunities promise its «renaissance», going to be used pharmacologically

Low-temperature infrared spectra and hydrogen bonding in polycrystalline dl-serine and deuterated derivatives

The FT-IR spectra of polycrystalline dl-serine [[alpha]-amino-[beta]-hydroxypropionic acid; HO-CH2-CH(NH3)+-COO-] and isotopically substituted [ND/ODAlcohol (90% D); CD2 (>98% D)] dl-serine were recorded in the range 4000-500 cm-1 in the temperature range 300-10 K, and fully assigned. The isotopic-doping/low-temperature methodology, which allows for decoupling of individual proton vibrational modes from the crystal bulk vibrations, was used to estimate the energies of the different H-bonds present in dl-serine crystal. To this end, the frequency shifts observed in both the NH/OH stretching and out-of-plane bending spectral regions (relatively to reference values for these vibrations in non-hydrogen-bonded dl-serine molecules) were used, together with previously developed empirical correlations. The results are compared with available structural data on this amino acid.http://www.sciencedirect.com/science/article/B6THW-4J91R39-2/1/f8f35f435466c8a5204879d330cbade

Nonlinear evolution of short-wavelength torsional Alfvén waves

We analyze nonlinear evolution of torsional Alfvén waves in a straight magnetic flux tube filled in with a low-β plasma, and surrounded with a plasma of lower density. Such magnetic tubes model, in particular, a segment of a coronal loop or a polar plume. The wavelength is taken comparable to the tube radius. We perform a numerical simulation of the wave propagation using ideal magnetohydrodynamics. We find that a torsional wave nonlinearly induces three kinds of compressive flows: the parallel flow at the Alfvén speed, which constitutes a bulk plasma motion along the magnetic field, the tube wave, and also transverse flows in the radial direction, associated with sausage fast magnetoacoustic modes. In addition, the nonlinear torsional wave steepens and its propagation speed increases. The latter effect leads to the progressive distortion of the torsional wave front, i.e., nonlinear phase mixing. Because of the intrinsic non-uniformity of the torsional wave amplitude across the tube radius, the nonlinear effects are more pronounced in regions with higher wave amplitudes. They are always absent at the axes of the flux tube. In the case of a linear radial profile of the wave amplitude, the nonlinear effects are localized in an annulus region near the tube boundary. Thus, the parallel compressive flows driven by torsional Alfvén waves in the solar and stellar coronae, are essentially non-uniform in the perpendicular direction. The presence of additional sinks for the wave energy reduces the efficiency of the nonlinear parallel cascade in torsional Alfvén waves

The cBio cancer Genomics portal: An open platform for exploring multidimensional cancer genomics data

Cataloged from PDF version of article.The cBio Cancer Genomics Portal (http://cbioportal.org) is an open-access resource for interactive exploration of multidimensional cancer genomics data sets, currently providing access to data from more than 5,000 tumor samples from 20 cancer studies. The cBio Cancer Genomics Portal significantly lowers the barriers between complex genomic data and cancer researchers who want rapid, intuitive, and high-quality access to molecular profiles and clinical attributes from large-scale cancer genomics projects and empowers researchers to translate these rich data sets into biologic insights and clinical applications. © 2012 American Association for Cancer Research

Improving the in silico assessment of pathogenicity for compensated variants

Understanding the functional sequelae of amino-acid replacements is of fundamental importance in medical genetics. Perhaps, the most intuitive way to assess the potential pathogenicity of a given human missense variant is by measuring the degree of evolutionary conservation of the substituted amino-acid residue, a feature that generally serves as a good proxy metric for the functional/structural importance of that residue. However, the presence of putatively compensated variants as the wild-type alleles in orthologous proteins of other mammalian species not only challenges this classical view of amino-acid essentiality but also precludes the accurate evaluation of the functional impact of this type of missense variant using currently available bioinformatic prediction tools. Compensated variants constitute at least 4% of all known missense variants causing human-inherited disease and hence represent an important potential source of error in that they are likely to be disproportionately misclassified as benign variants. The consequent under-reporting of compensated variants is exacerbated in the context of next-generation sequencing where their inappropriate exclusion constitutes an unfortunate natural consequence of the filtering and prioritization of the very large number of variants generated. Here we demonstrate the reduced performance of currently available pathogenicity prediction tools when applied to compensated variants and propose an alternative machine-learning approach to assess likely pathogenicity for this particular type of variant

Identification of a pan-cancer oncogenic microRNA superfamily anchored by a central core seed motif

MicroRNAs modulate tumorigenesis through suppression of specific genes. As many tumour types rely on overlapping oncogenic pathways, a core set of microRNAs may exist, which consistently drives or suppresses tumorigenesis in many cancer types. Here we integrate The Cancer Genome Atlas (TCGA) pan-cancer data set with a microRNA target atlas composed of publicly available Argonaute Crosslinking Immunoprecipitation (AGO-CLIP) data to identify pan-tumour microRNA drivers of cancer. Through this analysis, we show a pan-cancer, coregulated oncogenic microRNA ‘superfamily’ consisting of the miR-17, miR-19, miR-130, miR-93, miR-18, miR-455 and miR-210 seed families, which cotargets critical tumour suppressors via a central GUGC core motif. We subsequently define mutations in microRNA target sites using the AGO-CLIP microRNA target atlas and TCGA exome-sequencing data. These combined analyses identify pan-cancer oncogenic cotargeting of the phosphoinositide 3-kinase, TGFβ and p53 pathways by the miR-17-19-130 superfamily members

On factorization hierarchy of equations for banana Feynman amplitudes

We present a review of the relations between various equations for maximal cut banana Feynman diagrams, i.e. amplitudes with propagators substituted with $\delta$-functions. We consider both equal and generic masses. There are three types of equation to consider: those in coordinate space, their Fourier transform and Picard-Fuchs equations originating from the parametric representation. First, we review the properties of the corresponding differential operators themselves, mainly their factorization properties at the equal mass locus and their form at special values of the dimension. Then we study the relation between the Fourier transform of the coordinate space equations and the Picard-Fuchs equations and show that they are related by factorization as well. The equations in question are the counterparts of the Virasoro constraints in the much-better studied theory of eigenvalue matrix models and are the first step towards building a full-fledged theory of Feynman integrals, which will reveal their hidden integrable structure.Comment: 13 page