Large-Scale Pathway-Based Analysis of Bladder Cancer Genome-Wide Association Data from Five Studies of European Background

Pathway analysis of genome-wide association studies (GWAS) offer a unique opportunity to collectively evaluate genetic variants with effects that are too small to be detected individually. We applied a pathway analysis to a bladder cancer GWAS containing data from 3,532 cases and 5,120 controls of European background (n = 5 studies). Thirteen hundred and ninety-nine pathways were drawn from five publicly available resources (Biocarta, Kegg, NCI-PID, HumanCyc, and Reactome), and we constructed 22 additional candidate pathways previously hypothesized to be related to bladder cancer. In total, 1421 pathways, 5647 genes and ∼90,000 SNPs were included in our study. Logistic regression model adjusting for age, sex, study, DNA source, and smoking status was used to assess the marginal trend effect of SNPs on bladder cancer risk. Two complementary pathway-based methods (gene-set enrichment analysis [GSEA], and adapted rank-truncated product [ARTP]) were used to assess the enrichment of association signals within each pathway. Eighteen pathways were detected by either GSEA or ARTP at P≤0.01. To minimize false positives, we used the I2 statistic to identify SNPs displaying heterogeneous effects across the five studies. After removing these SNPs, seven pathways (‘Aromatic amine metabolism’ [PGSEA = 0.0100, PARTP = 0.0020], ‘NAD biosynthesis’ [PGSEA = 0.0018, PARTP = 0.0086], ‘NAD salvage’ [PARTP = 0.0068], ‘Clathrin derived vesicle budding’ [PARTP = 0.0018], ‘Lysosome vesicle biogenesis’ [PGSEA = 0.0023, PARTP<0.00012], ’Retrograde neurotrophin signaling’ [PGSEA = 0.00840], and ‘Mitotic metaphase/anaphase transition’ [PGSEA = 0.0040]) remained. These pathways seem to belong to three fundamental cellular processes (metabolic detoxification, mitosis, and clathrin-mediated vesicles). Identification of the aromatic amine metabolism pathway provides support for the ability of this approach to identify pathways with established relevance to bladder carcinogenesis

Solvation of Na? in the Sodide Solution, LiNa?10MeNH2.

Alkalides, the alkali metals in their ?1 oxidation state, represent some of the largest and most polarizable atomic species in condensed phases. This study determines the solvation environment around the sodide anion, Na?, in a system of co-solvated Li+. We present isotopically varied total neutron scattering experiments alongside empirical potential structure refinement and ab initio molecular dynamics simulations for the alkali?alkalide system, LiNa?10MeNH2. Both local coordination modes and the intermediate range liquid structure are determined, which demonstrate that distinct structural correlations between cation and anion in the liquid phase extend beyond 8.6 ?. Indeed, the local solvation around Na? is surprisingly well defined with strong solvent orientational order, in contrast to the classical description of alkalide anions not interacting with their environment. The ion-paired Li(MeNH2)4+?Na? species appears to be the dominant alkali?alkalide environment in these liquids, whereby Li+ and Na? share a MeNH2 molecule through the amine group in their primary solvation spheres

Trajectory of the selective dissolution of charged single-walled carbon nanotubes

© 2017 American Chemical Society. Single-walled carbon nanotubes (SWCNTs) are typically produced as a mixture of different lengths and electronic types. Methods for sorting these as-produced mixtures typically require damaging and unscalable techniques to first overcome the strong bundling forces between the nanotubes. Previously, it has been shown that negatively charging SWCNTs can lead to their thermodynamically driven, gentle dissolution in polar solvents, and moreover that this process can selectively dissolve different SWCNT species. However, there are several conflicting claims of selectivity that must be resolved before the full potential of this method for scalably postprocessing SWCNTs can be realized. Here we carefully investigate dissolution as a function of charge added to the as-produced SWCNT sample, using a range of complementary techniques. We uncover a far richer dependence on charge of SWCNT dissolution than previously imagined. At low values of charge added, amorphous carbons preferentially dissolve, followed sequentially by metallic, larger diameter (>9 Å) semiconducting SWCNTs, and finally smaller diameter semiconducting SWCNTs as more charge is added. At an optimal stoichiometry of NaC10, the dissolution yield is maximized across all species. However, at higher charge the larger diameter and metallic SWCNTs are so highly charged that they are no longer soluble, leaving smaller diameter SWCNTs in solution. Our results clearly demonstrate two interconnected mechanisms for dissolution: the sequential charging of the SWCNTs and their solution thermodynamics. This work reconciles conflicting reports in the literature, demonstrates that upon charge added the different SWCNTs behave like discrete molecular species, and points toward selective dissolution as a scalable method for SWCNT separation

Production of phosphorene nanoribbons.

Phosphorene is a mono-elemental, two-dimensional (2D) substance with outstanding, highly directional properties and a bandgap that depends on the number of layers of the material1-8. Nanoribbons, meanwhile, combine the flexibility and unidirectional properties of one-dimensional nanomaterials, the high surface area of 2D nanomaterials and the electron-confinement and edge effects of both. The structures of nanoribbons can thus lead to exceptional control over electronic band structure, the emergence of novel phenomena and unique architectures for applications5,6,9-24. Phosphorene's intrinsically anisotropic structure has motivated numerous theoretical calculations of phosphorene nanoribbons (PNRs), predicting extraordinary properties5,6,12-24. So far, however, discrete PNRs have not been produced. Here we present a method for creating quantities of high-quality, individual PNRs by ionic scissoring of macroscopic black phosphorus crystals. This top-down process results in stable liquid dispersions of PNRs with typical widths of 4-50 nm, predominantly single-layer thickness, measured lengths of up to 75 μm and aspect ratios of up to 1,000. The nanoribbons are atomically flat single crystals, aligned exclusively in the zigzag crystallographic orientation. The ribbons have remarkably uniform widths along their entire lengths, and are extremely flexible. These properties-together with the ease of downstream manipulation via liquid-phase methods-should enable the search for predicted exotic states6,12-14,17-19,21, and an array of applications in which PNRs have been predicted to offer transformative advantages. These applications range from thermoelectric devices to high-capacity fast-charging batteries and integrated high-speed electronic circuits6,14-16,20,23,24