Towards a Tetravalent Chemistry of Colloids

We propose coating spherical particles or droplets with anisotropic nano-sized objects to allow micron-scale colloids to link or functionalize with a four-fold valence, similar to the sp3 hybridized chemical bonds associated with, e.g., carbon, silicon and germanium. Candidates for such coatings include triblock copolymers, gemini lipids, metallic or semiconducting nanorods and conventional liquid crystal compounds. We estimate the size of the relevant nematic Frank constants, discuss how to obtain other valences and analyze the thermal distortions of ground state configurations of defects on the sphere.Comment: Replaced to improve figures. 4 figures Nano Letter

Differences in behavior and distribution of permafrost-related lakes in Central Yakutia and their response to climatic drivers

The Central Yakutian permafrost landscape is rapidly being modified by land use and global warming, but small-scale thermokarst process variability and hydrological conditions are poorly understood. We analyze lake-area changes and thaw subsidence of young thermokarst lakes on ice-complex deposits (yedoma lakes) in comparison to residual lakes in alas basins during the last 70 years for a local study site and we record regional lake size and distribution on different ice-rich permafrost terraces using satellite and historical airborne imagery. Statistical analysis of climatic and ground-temperature data identified driving factors of yedoma- and alas-lake changes. Overall, lake area is larger today than in 1944 but alas-lake levels have oscillated greatly over 70 years, with a mean alas-lake-radius change rate of 1.663.0 m/yr. Anthropogenic disturbance and forest degradation initiated, and climate forced rapid, continuous yedoma-lake growth. The mean yedoma lake-radius change rate equals 1.261.0 m/yr over the whole observation period. Mean thaw subsidence below yedoma lakes is 6.261.4 cm/yr. Multiple regression analysis suggests that winter precipitation, winter temperature, and active-layer properties are primary controllers of area changes in both lake types; summer weather and permafrost conditions additionally influence yedoma-lake growth rates. The main controlling factors of alas-lake changes are unclear due to larger catchment areas and subsurface hydrological conditions. Increasing thermokarst activity is currently linked to older terraces with higher ground-ice contents, but thermokarst activity will likely stay high and wet conditions will persist within the near future in Central Yakutian alas basins

A probabilistic model for gene content evolution with duplication, loss, and horizontal transfer

We introduce a Markov model for the evolution of a gene family along a phylogeny. The model includes parameters for the rates of horizontal gene transfer, gene duplication, and gene loss, in addition to branch lengths in the phylogeny. The likelihood for the changes in the size of a gene family across different organisms can be calculated in O(N+hM^2) time and O(N+M^2) space, where N is the number of organisms, $h$ is the height of the phylogeny, and M is the sum of family sizes. We apply the model to the evolution of gene content in Preoteobacteria using the gene families in the COG (Clusters of Orthologous Groups) database

Structural correlations in heterogeneous electron transfer at monolayer and multilayer graphene electrodes

As a new form of carbon, graphene is attracting intense interest as an electrode material with widespread applications. In the present study, the heterogeneous electron transfer (ET) activity of graphene is investigated using scanning electrochemical cell microscopy (SECCM), which allows electrochemical currents to be mapped at high spatial resolution across a surface for correlation with the corresponding structure and properties of the graphene surface. We establish that the rate of heterogeneous ET at graphene increases systematically with the number of graphene layers, and show that the stacking in multilayers also has a subtle influence on ET kinetics. © 2012 American Chemical Society

Pseudo-single crystal electrochemistry on polycrystalline electrodes : visualizing activity at grains and grain boundaries on platinum for the Fe2+/Fe3+ redox reaction

The influence of electrode surface structure on electrochemical reaction rates and mechanisms is a major theme in electrochemical research, especially as electrodes with inherent structural heterogeneities are used ubiquitously. Yet, probing local electrochemistry and surface structure at complex surfaces is challenging. In this paper, high spatial resolution scanning electrochemical cell microscopy (SECCM) complemented with electron backscatter diffraction (EBSD) is demonstrated as a means of performing ‘pseudo-single-crystal’ electrochemical measurements at individual grains of a polycrystalline platinum electrode, while also allowing grain boundaries to be probed. Using the Fe2+/3+ couple as an illustrative case, a strong correlation is found between local surface structure and electrochemical activity. Variations in electrochemical activity for individual high index grains, visualized in a weakly adsorbing perchlorate medium, show that there is higher activity on grains with a significant (101) orientation contribution, compared to those with (001) and (111) contribution, consistent with findings on single-crystal electrodes. Interestingly, for Fe2+ oxidation in a sulfate medium a different pattern of activity emerges. Here, SECCM reveals only minor variations in activity between individual grains, again consistent with single-crystal studies, with a greatly enhanced activity at grain boundaries. This suggests that these sites may contribute significantly to the overall electrochemical behavior measured on the macroscale

Field-effect transistors assembled from functionalized carbon nanotubes

We have fabricated field effect transistors from carbon nanotubes using a novel selective placement scheme. We use carbon nanotubes that are covalently bound to molecules containing hydroxamic acid functionality. The functionalized nanotubes bind strongly to basic metal oxide surfaces, but not to silicon dioxide. Upon annealing, the functionalization is removed, restoring the electronic properties of the nanotubes. The devices we have fabricated show excellent electrical characteristics.Comment: 5 pages, 6 figure

Tunable anisotropy in inverse opals and emerging optical properties

Using self-assembly, nanoscale materials can be fabricated from the bottom up. Opals and inverse opals are examples of self-assembled nanomaterials made from crystallizing colloidal particles. As self-assembly requires a high level of control, it is challenging to use building blocks with anisotropic geometry to form complex opals, which limits the realizable structures. Typically, spherical colloids are employed as building blocks, leading to symmetric, isotropic superstructures. However, a significantly richer palette of directionally dependent properties are expected if less symmetric, anisotropic structures can be created, especially originating from the assembly of regular, spherical particles. Here we show a simple method to introduce anisotropy into inverse opals by subjecting them to a post-assembly thermal treatment that results in directional shrinkage of the silica matrix caused by condensation of partially hydrated sol-gel silica structures. In this way, we can tailor the shape of the pores, and the anisotropy of the final inverse opal preserves the order and uniformity of the self-assembled structure, while completely avoiding the need to synthesize complex oval-shaped particles and crystallize them into such target geometries. Detailed X-ray photoelectron spectroscopy (XPS) and infrared (IR) spectroscopy studies clearly identify increasing degrees of sol-gel condensation in confinement as a mechanism for the structure change. A computer simulation of structure changes resulting from the condensation-induced shrinkage further confirmed this mechanism. As an example of property changes induced by the introduction of anisotropy, we characterized the optical spectra of the anisotropic inverse opals and found that the optical properties can be controlled in a precise way using calcination temperature

Algorithms: simultaneous error-correction and rooting for gene tree reconciliation and the gene duplication problem

<p>Abstract</p> <p>Background</p> <p>Evolutionary methods are increasingly challenged by the wealth of fast growing resources of genomic sequence information. Evolutionary events, like gene duplication, loss, and deep coalescence, account more then ever for incongruence between gene trees and the actual species tree. Gene tree reconciliation is addressing this fundamental problem by invoking the minimum number of gene duplication and losses that reconcile a rooted gene tree with a rooted species tree. However, the reconciliation process is highly sensitive to topological error or wrong rooting of the gene tree, a condition that is not met by most gene trees in practice. Thus, despite the promises of gene tree reconciliation, its applicability in practice is severely limited.</p> <p>Results</p> <p>We introduce the problem of reconciling unrooted and erroneous gene trees by simultaneously rooting and error-correcting them, and describe an efficient algorithm for this problem. Moreover, we introduce an error-corrected version of the gene duplication problem, a standard application of gene tree reconciliation. We introduce an effective heuristic for our error-corrected version of the gene duplication problem, given that the original version of this problem is NP-hard. Our experimental results suggest that our error-correcting approaches for unrooted input trees can significantly improve on the accuracy of gene tree reconciliation, and the species tree inference under the gene duplication problem. Furthermore, the efficiency of our algorithm for error-correcting reconciliation is capable of handling truly large-scale phylogenetic studies.</p> <p>Conclusions</p> <p>Our presented error-correction approach is a crucial step towards making gene tree reconciliation more robust, and thus to improve on the accuracy of applications that fundamentally rely on gene tree reconciliation, like the inference of gene-duplication supertrees.</p

Histone Acetylation-Mediated Regulation of the Hippo Pathway

The Hippo pathway is a signaling cascade recently found to play a key role in tumorigenesis therefore understanding the mechanisms that regulate it should open new opportunities for cancer treatment. Available data indicate that this pathway is controlled by signals from cell-cell junctions however the potential role of nuclear regulation has not yet been described. Here we set out to verify this possibility and define putative mechanism(s) by which it might occur. By using a luciferase reporter of the Hippo pathway, we measured the effects of different nuclear targeting drugs and found that chromatin-modifying agents, and to a lesser extent certain DNA damaging drugs, strongly induced activity of the reporter. This effect was not mediated by upstream core components (i.e. Mst, Lats) of the Hippo pathway, but through enhanced levels of the Hippo transducer TAZ. Investigation of the underlying mechanism led to the finding that cancer cell exposure to histone deacetylase inhibitors induced secretion of growth factors and cytokines, which in turn activate Akt and inhibit the GSK3 beta associated protein degradation complex in drug-affected as well as in their neighboring cells. Consequently, expression of EMT genes, cell migration and resistance to therapy were induced. These processes were suppressed by using pyrvinium, a recently described small molecule activator of the GSK 3 beta associated degradation complex. Overall, these findings shed light on a previously unrecognized phenomenon by which certain anti-cancer agents may paradoxically promote tumor progression by facilitating stabilization of the Hippo transducer TAZ and inducing cancer cell migration and resistance to therapy. Pharmacological targeting of the GSK3 beta associated degradation complex may thus represent a unique approach to treat cancer. © 2013 Basu et al

Building professional discourse in emerging markets: Language, context and the challenge of sensemaking

Using ethnographic evidence from the former Soviet republics, this article examines a relatively new and mainly unobserved in the International Business (IB) literature phenomenon of communication disengagement that manifests itself in many emerging markets. We link it to the deficiencies of the local professional business discourse rooted in language limitations reflecting lack of experience with the market economy. This hampers cognitive coherence between foreign and local business entities, adding to the liability of foreignness as certain instances of professional experience fail to find adequate linguistic expression, and complicates cross-cultural adjustments causing multi-national companies (MNCs) financial losses. We contribute to the IB literature by examining cross-border semantic sensemaking through a retrospectively constructed observational study. We argue that a relative inadequacy of the national professional idiom is likely to remain a feature of business environment in post-communist economies for some time and therefore should be factored into business strategies of MNCs. Consequently, we recommend including discursive hazards in the risk evaluation of international projects