First-principles GW calculations for DNA and RNA nucleobases

On the basis of first-principles GW calculations, we study the quasiparticle properties of the guanine, adenine, cytosine, thymine, and uracil DNA and RNA nucleobases. Beyond standard G0W0 calculations, starting from Kohn-Sham eigenstates obtained with (semi)local functionals, a simple self-consistency on the eigenvalues allows to obtain vertical ionization energies and electron affinities within an average 0.11 eV and 0.18 eV error respectively as compared to state-of-the-art coupled-cluster and multi-configurational perturbative quantum chemistry approaches. Further, GW calculations predict the correct \pi -character of the highest occupied state, thanks to several level crossings between density functional and GW calculations. Our study is based on a recent gaussian-basis implementation of GW with explicit treatment of dynamical screening through contour deformation techniques.Comment: 5 pages, 3 figure

Platelet-Activating Factor-Induced Reduction in Contact Hypersensitivity Responses Is Mediated by Mast Cells via Cyclooxygenase-2-Dependent Mechanisms

Platelet-activating factor (PAF) stimulates numerous cell types via activation of the G protein-coupled PAF receptor (PAFR). PAFR activation not only induces acute proinflammatory responses, but it also induces delayed systemic immunosuppressive effects by modulating host immunity. Although enzymatic synthesis and degradation of PAF are tightly regulated, oxidative stressors, such as UVB, chemotherapy, and cigarette smoke, can generate PAF and PAF-like molecules in an unregulated fashion via the oxidation of membrane phospholipids. Recent studies have demonstrated the relevance of the mast cell (MC) PAFR in PAFR-induced systemic immunosuppression. The current study was designed to determine the exact mechanisms and mediators involved in MC PAFR-mediated systemic immunosuppression. By using a contact hypersensitivity model, the MC PAFR was not only found to be necessary, but also sufficient to mediate the immunosuppressive effects of systemic PAF. Furthermore, activation of the MC PAFR induces MC-derived histamine and PGE2 release. Importantly, PAFR-mediated systemic immunosuppression was defective in mice that lacked MCs, or in MC-deficient mice transplanted with histidine decarboxylase- or cyclooxygenase-2-deficient MCs. Lastly, it was found that PGs could modulate MC migration to draining lymph nodes. These results support the hypothesis that MC PAFR activation promotes the immunosuppressive effects of PAF in part through histamine- and PGE2-dependent mechanisms

Disordered, stretched, and semiflexible biopolymers in two dimensions

We study the effects of intrinsic sequence-dependent curvature for a two dimensional semiflexible biopolymer with short-range correlation in intrinsic curvatures. We show exactly that when not subjected to any external force, such a system is equivalent to a system with a well-defined intrinsic curvature and a proper renormalized persistence length. We find the exact expression for the distribution function of the equivalent system. However, we show that such an equivalent system does not always exist for the polymer subjected to an external force. We find that under an external force, the effect of sequence-disorder depends upon the averaging order, the degree of disorder, and the experimental conditions, such as the boundary conditions. Furthermore, a short to moderate length biopolymer may be much softer or has a smaller apparent persistent length than what would be expected from the "equivalent system". Moreover, under a strong stretching force and for a long biopolymer, the sequence-disorder is immaterial for elasticity. Finally, the effect of sequence-disorder may depend upon the quantity considered

Checklist and new records of Christmas Island fishes: the influence of isolation, biogeography and habitat availability on species abundance and community composition

Christmas Island (Indian Ocean) is an oceanic high island that is situated 300 km southwest of Java, Indonesia. From 2010 to 2014, the fish community of Christmas Island was surveyed using underwater visual surveys for shallow water (0–60 m) fishes, and line fishing (bottom fishing and trolling) for deepwater (60–300 m) and pelagic fishes. Forty-seven new records (from 22 families) were identified, thereby increasing the total number of fishes described from Christmas Island to 681 (from 91 families). Notable new records include the first records for the families Alopiidae, Anomalopidae, Muraenesocidae, Tetrarogidae and Trichonotidae, and the first reports of Pacific Ocean species Plectranthias yamakawai, and Polylepion russelli in the Indian Ocean. The ten most species-rich families accounted for 58% of the community and included: Labridae (13%), Pomacentridae (8%), Epinephelidae (6%), Acanthuridae (5%), Chaetodontidae (5%), Muraenidae (5%), Gobiidae (5%), Blenniidae (4%), Apogonidae (4%) and Scorpaenidae (3%). The majority (89%) of species inhabit shallow coral reefs, with deep reefs (60–300 m) and pelagic waters only accounting for 7% and 2% of fish community. Approximately 76% of thefishes are widespread Indo-Pacific species, 12% are Pacific Ocean species, 5% are circumtropical, 4% are Indian Ocean species and approximately 1% are endemic. Abundance surveys revealed that endemic species, and species at the edge of their geographic range, do not conform to terrestrial-based predictions of low abundance. The structure and composition of the Christmas Island fish community is influenced by three main factors. Firstly, the isolation of the island means that fishes with poor dispersal abilities (e.g., syngnathids) are underrepresented. Secondly, thebiogeographic position of the island results in a unique mixing of Indian and Pacific Ocean species. Thirdly, the lack of lagoonal habitats means that fishes that use these habitats (e.g., ophichthids, lethrinids, epinephelids) are underrepresented or have low abundance

Mast Cells Regulate Epidermal Barrier Function and the Development of Allergic Skin Inflammation

Atopic dermatitis is a chronic inflammatory skin disease characterized by infiltration of eosinophils, T helper cells, and mast cells. The role of mast cells in atopic dermatitis is not completely understood. To define the effects of mast cells on skin biology, we observed that mast cells regulate the homeostatic expression of epidermal differentiation complex and other skin genes. Decreased epidermal differentiation complex gene expression in mice that genetically lack mast cells (Kit(W-sh/W-sh) mice) is associated with increased uptake of protein antigens painted on the skin by dendritic cells (DCs) compared with similarly treated wild-type mice, suggesting a protective role for mast cells in exposure to nominal environmental allergens. To test this further, we crossed Kit(W-sh/W-sh) mice with signal transducer and activator of transcription 6 (i.e., Stat6) VT transgenic mice that develop spontaneous atopic dermatitis-like disease that is dependent on T helper cell 2 cytokines and is associated with high serum concentrations of IgE. We observed that Stat6VT × Kit(W-sh/W-sh) mice developed more frequent and more severe allergic skin inflammation than Stat6VT transgenic mice that had mast cells. Together, these studies suggest that mast cells regulate epidermal barrier function and have a potential protective role in the development of atopic dermatitis-like diseas

A Model for Force Fluctuations in Bead Packs

We study theoretically the complex network of forces that is responsible for the static structure and properties of granular materials. We present detailed calculations for a model in which the fluctuations in the force distribution arise because of variations in the contact angles and the constraints imposed by the force balance on each bead of the pile. We compare our results for force distribution function for this model, including exact results for certain contact angle probability distributions, with numerical simulations of force distributions in random sphere packings. This model reproduces many aspects of the force distribution observed both in experiment and in numerical simulations of sphere packings

Force Distribution in a Granular Medium

We report on systematic measurements of the distribution of normal forces exerted by granular material under uniaxial compression onto the interior surfaces of a confining vessel. Our experiments on three-dimensional, random packings of monodisperse glass beads show that this distribution is nearly uniform for forces below the mean force and decays exponentially for forces greater than the mean. The shape of the distribution and the value of the exponential decay constant are unaffected by changes in the system preparation history or in the boundary conditions. An empirical functional form for the distribution is proposed that provides an excellent fit over the whole force range measured and is also consistent with recent computer simulation data.Comment: 6 pages. For more information, see http://mrsec.uchicago.edu/granula

Stress transmission in granular matter

The transmission of forces through a disordered granular system is studied by means of a geometrical-topological approach that reduces the granular packing into a set of layers. This layered structure constitutes the skeleton through which the force chains set up. Given the granular packing, and the region where the force is applied, such a skeleton is uniquely defined. Within this framework, we write an equation for the transmission of the vertical forces that can be solved recursively layer by layer. We find that a special class of analytical solutions for this equation are L\'evi-stable distributions. We discuss the link between criticality and fragility and we show how the disordered packing naturally induces the formation of force-chains and arches. We point out that critical regimes, with power law distributions, are associated with the roughness of the topological layers. Whereas, fragility is associated with local changes in the force network induced by local granular rearrangements or by changes in the applied force. The results are compared with recent experimental observations in particulate matter and with computer simulations.Comment: 14 pages, Latex, 5 EPS figure

On equations over sets of integers

Systems of equations with sets of integers as unknowns are considered. It is shown that the class of sets representable by unique solutions of equations using the operations of union and addition S+T=\makeset{m+n}{m \in S, \: n \in T} and with ultimately periodic constants is exactly the class of hyper-arithmetical sets. Equations using addition only can represent every hyper-arithmetical set under a simple encoding. All hyper-arithmetical sets can also be represented by equations over sets of natural numbers equipped with union, addition and subtraction S \dotminus T=\makeset{m-n}{m \in S, \: n \in T, \: m \geqslant n}. Testing whether a given system has a solution is $\Sigma^1_1$-complete for each model. These results, in particular, settle the expressive power of the most general types of language equations, as well as equations over subsets of free groups.Comment: 12 apges, 0 figure

Force correlations and arches formation in granular assemblies

In the context of a simple microscopic schematic scalar model we study the effects of spatial correlations in force transmission in granular assemblies. We show that the parameters of the normalized weights distribution function, $P(v)\sim v^{\alpha}\exp(-v/\phi)$, strongly depend on the spatial extensions, $\xi_V$, of such correlations. We show, then, the connections between measurable macroscopic quantities and microscopic mechanisms enhancing correlations. In particular we evaluate how the exponential cut-off, $\phi(\xi_V)$, and the small forces power law exponent, $\alpha(\xi_V)$, depend on the correlation length, $\xi_V$. If correlations go to infinity, weights are power law distributed.Comment: 6 page