Rice University

Hybrid density functionals are very successful in describing a wide range of molecular properties accurately. In large molecules and solids, however, calculating the exact (Hartree–Fock) exchange is computationally expensive, especially for systems with metallic characteristics. In the present work, we develop a new hybrid density functional based on a screened Coulomb potential for the exchange interaction which circumvents this bottleneck. The results obtained for structural and thermodynamic properties of molecules are comparable in quality to the most widely used hybrid functionals. In addition, we present results of periodic boundary condition calculations for both semiconducting and metallic single wall carbon nanotubes. Using a screened Coulomb potential for Hartree–Fock exchange enables fast and accurate hybrid calculations, even of usually difficult metallic systems. The high accuracy of the new screened Coulomb potential hybrid, combined with its computational advantages, makes it widely applicable to large molecules and periodic systems.

An improved method for the preparation of graphene oxide (GO) is described. Currently, Hummers' method (KMnO(4), NaNO(3), H(2)SO(4)) is the most common method used for preparing graphene oxide. We have found that excluding the NaNO(3), increasing the amount of KMnO(4), and performing the reaction in a 9:1 mixture of H(2)SO(4)/H(3)PO(4) improves the efficiency of the oxidation process. This improved method provides a greater amount of hydrophilic oxidized graphene material as compared to Hummers' method or Hummers' method with additional KMnO(4). Moreover, even though the GO produced by our method is more oxidized than that prepared by Hummers' method, when both are reduced in the same chamber with hydrazine, chemically converted graphene (CCG) produced from this new method is equivalent in its electrical conductivity. In contrast to Hummers' method, the new method does not generate toxic gas and the temperature is easily controlled. This improved synthesis of GO may be important for large-scale production of GO as well as the construction of devices composed of the subsequent CCG.

Popular modern generalized gradient approximations are biased toward the description of free-atom energies. Restoration of the first-principles gradient expansion for exchange over a wide range of density gradients eliminates this bias. We introduce a revised Perdew-Burke-Ernzerhof generalized gradient approximation that improves equilibrium properties of densely packed solids and their surfaces.

The study of extracellular vesicles (EVs) has the potential to identify unknown cellular and molecular mechanisms in intercellular communication and in organ homeostasis and disease. Exosomes, with an average diameter of ~100 nanometers, are a subset of EVs. The biogenesis of exosomes involves their origin in endosomes, and subsequent interactions with other intracellular vesicles and organelles generate the final content of the exosomes. Their diverse constituents include nucleic acids, proteins, lipids, amino acids, and metabolites, which can reflect their cell of origin. In various diseases, exosomes offer a window into altered cellular or tissue states, and their detection in biological fluids potentially offers a multicomponent diagnostic readout. The efficient exchange of cellular components through exosomes can inform their applied use in designing exosome-based therapeutics.

The 1000 Genomes Project aims to provide a deep characterization of human genome sequence variation as a foundation for investigating the relationship between genotype and phenotype. Here we present results of the pilot phase of the project, designed to develop and compare different strategies for genome-wide sequencing with high-throughput platforms. We undertook three projects: low-coverage whole-genome sequencing of 179 individuals from four populations; high-coverage sequencing of two mother–father–child trios; and exon-targeted sequencing of 697 individuals from seven populations. We describe the location, allele frequency and local haplotype structure of approximately 15 million single nucleotide polymorphisms, 1 million short insertions and deletions, and 20,000 structural variants, most of which were previously undescribed. We show that, because we have catalogued the vast majority of common variation, over 95% of the currently accessible variants found in any individual are present in this data set. On average, each person is found to carry approximately 250 to 300 loss-of-function variants in annotated genes and 50 to 100 variants previously implicated in inherited disorders. We demonstrate how these results can be used to inform association and functional studies. From the two trios, we directly estimate the rate of de novo germline base substitution mutations to be approximately 10−8 per base pair per generation. We explore the data with regard to signatures of natural selection, and identify a marked reduction of genetic variation in the neighbourhood of genes, due to selection at linked sites. These methods and public data will support the next phase of human genetic research. This issue of Nature contains the first publication from The 1000 Genomes Project, an international collaboration that will produce an extensive public catalogue of human genetic variation. The plan, in fact, is to sequence about 2,000 unidentified individuals from 20 populations around the world. This first paper presents the results from the project's pilot phase, testing three different strategies for genome-wide sequencing with high-throughput platforms: low-coverage whole-genome sequencing of 179 individuals in three population groups, high-coverage sequencing of two mother–father–child trios, and exon-targeted sequencing of 697 individuals from seven populations. The goal of the 1000 Genomes Project is to provide in-depth information on variation in human genome sequences. In the pilot phase reported here, different strategies for genome-wide sequencing, using high-throughput sequencing platforms, were developed and compared. The resulting data set includes more than 95% of the currently accessible variants found in any individual, and can be used to inform association and functional studies.

This review surveys an emergent methodological trend in anthropological research that concerns the adaptation of long-standing modes of ethnographic practices to more complex objects of study. Ethnography moves from its conventional single-site location, contextualized by macro-constructions of a larger social order, such as the capitalist world system, to multiple sites of observation and participation that cross-cut dichotomies such as the “local” and the “global,” the “lifeworld” and the “system.” Resulting ethnographies are therefore both in and out of the world system. The anxieties to which this methodological shift gives rise are considered in terms of testing the limits of ethnography, attenuating the power of fieldwork, and losing the perspective of the subaltern. The emergence of multi-sited ethnography is located within new spheres of interdisciplinary work, including media studies, science and technology studies, and cultural studies broadly. Several “tracking” strategies that shape multi-sited ethnographic research are considered. The review concludes with observations about the reflexive persona of the ethnographer as “circumstantial activist” in which methodological discussions about multi-sited research in anthropology are now being developed.

The electron density, its gradient, and the Kohn-Sham orbital kinetic energy density are the local ingredients of a meta-generalized gradient approximation (meta-GGA). We construct a meta-GGA density functional for the exchange-correlation energy that satisfies exact constraints without empirical parameters. The exchange and correlation terms respect two paradigms: one- or two-electron densities and slowly varying densities, and so describe both molecules and solids with high accuracy, as shown by extensive numerical tests. This functional completes the third rung of "Jacob's ladder" of approximations, above the local spin density and GGA rungs.

This work reexamines the effect of the exchange screening parameter omega on the performance of the Heyd-Scuseria-Ernzerhof (HSE) screened hybrid functional. We show that variation of the screening parameter influences solid band gaps the most. Other properties such as molecular thermochemistry or lattice constants of solids change little with omega. We recommend a new version of HSE with the screening parameter omega=0.11 bohr(-1) for further use. Compared to the original implementation, the new parametrization yields better thermochemical results and preserves the good accuracy for band gaps and lattice constants in solids.

Mobile users' data rate and quality of service are limited by the fact that, within the duration of any given call, they experience severe variations in signal attenuation, thereby necessitating the use of some type of diversity. In this two-part paper, we propose a new form of spatial diversity, in which diversity gains are achieved via the cooperation of mobile users. Part I describes the user cooperation strategy, while Part II (see ibid., p.1939-48) focuses on implementation issues and performance analysis. Results show that, even though the interuser channel is noisy, cooperation leads not only to an increase in capacity for both users but also to a more robust system, where users' achievable rates are less susceptible to channel variations.

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is thatthere is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure flux through the autophagy pathway (i.e., the completeprocess including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defined as increasedautophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in manycases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as forreviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multipleassays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation, it is imperative to target by gene knockout or RNA interference more than one autophagyrelated protein. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways implying that not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular assays, we hope to encourage technical innovation in the field.

Fullerene single-wall nanotubes (SWNTs) were produced in yields of more than 70 percent by condensation of a laser-vaporized carbon-nickel-cobalt mixture at 1200degreesC. X-ray diffraction and electron microscopy showed that these SWNTs are nearly uniform in diameter and that they self-organize into "ropes," which consist of 100 to 500 SWNTs in a two-dimensional triangular lattice with a lattice constant of 17 angstroms. The x-ray form factor is consistent with that of uniformly charged cylinders 13.8 +/- 0.2 angstroms in diameter. The ropes were metallic, with a single-rope resistivity of <10(-4) ohm-centimeters at 300 kelvin. The uniformity of SWNT diameter is attributed to the efficient annealing of an initial fullerene tubelet kept open by a few metal atoms; the optimum diameter is determined by competition between the strain energy of curvature of the graphene sheet and the dangling-bond energy of the open edge, where growth occurs. These factors strongly favor the metallic (10,10) tube with C5v symmetry and an open edge stabilized by triple bonds.

In order to discriminate between approximations to the exchange-correlation energy EXC[ρ↑,ρ↓], we employ the criterion of whether the functional is fitted to a certain experimental data set or if it is constructed to satisfy physical constraints. We present extensive test calculations for atoms and molecules, with the nonempirical local spin-density (LSD) and the Perdew–Burke–Ernzerhof (PBE) functional and compare our results with results obtained with more empirical functionals. For the atomization energies of the G2 set, we find that the PBE functional shows systematic errors larger than those of commonly used empirical functionals. The PBE ionization potentials, electron affinities, and bond lengths are of accuracy similar to those obtained from empirical functionals. Furthermore, a recently proposed hybrid scheme using exact exchange together with PBE exchange and correlation is investigated. For all properties studied here, the PBE hybrid gives an accuracy comparable to the frequently used empirical B3LYP hybrid scheme. Physical principles underlying the PBE and PBE hybrid scheme are examined and the range of their validity is discussed.

Abstract This article presents nearly 10 year's worth of System Usability Scale (SUS) data collected on numerous products in all phases of the development lifecycle. The SUS, developed by CitationBrooke (1996), reflected a strong need in the usability community for a tool that could quickly and easily collect a user's subjective rating of a product's usability. The data in this study indicate that the SUS fulfills that need. Results from the analysis of this large number of SUS scores show that the SUS is a highly robust and versatile tool for usability professionals. The article presents these results and discusses their implications, describes nontraditional uses of the SUS, explains a proposed modification to the SUS to provide an adjective rating that correlates with a given score, and provides details of what constitutes an acceptable SUS score.

Time-dependent density-functional (TDDFT) methods are applied within the adiabatic approximation to a series of molecules including C70. Our implementation provides an efficient approach for treating frequency-dependent response properties and electronic excitation spectra of large molecules. We also present a new algorithm for the diagonalization of large non-Hermitian matrices which is needed for hybrid functionals and is also faster than the widely used Davidson algorithm when employed for the Hermitian case appearing in excited energy calculations. Results for a few selected molecules using local, gradient-corrected, and hybrid functionals are discussed. We find that for molecules with low lying excited states TDDFT constitutes a considerable improvement over Hartree–Fock based methods (like the random phase approximation) which require comparable computational effort.

Organic aerosol (OA) particles affect climate forcing and human health, but their sources and evolution remain poorly characterized. We present a unifying model framework describing the atmospheric evolution of OA that is constrained by high-time-resolution measurements of its composition, volatility, and oxidation state. OA and OA precursor gases evolve by becoming increasingly oxidized, less volatile, and more hygroscopic, leading to the formation of oxygenated organic aerosol (OOA), with concentrations comparable to those of sulfate aerosol throughout the Northern Hemisphere. Our model framework captures the dynamic aging behavior observed in both the atmosphere and laboratory: It can serve as a basis for improving parameterizations in regional and global models.

ABSTRACT We examine the pricing of aggregate volatility risk in the cross‐section of stock returns. Consistent with theory, we find that stocks with high sensitivities to innovations in aggregate volatility have low average returns. Stocks with high idiosyncratic volatility relative to the Fama and French (1993, Journal of Financial Economics 25, 2349) model have abysmally low average returns. This phenomenon cannot be explained by exposure to aggregate volatility risk. Size, book‐to‐market, momentum, and liquidity effects cannot account for either the low average returns earned by stocks with high exposure to systematic volatility risk or for the low average returns of stocks with high idiosyncratic volatility.

Elaboration of Bayesian phylogenetic inference methods has continued at pace in recent years with major new advances in nearly all aspects of the joint modelling of evolutionary data. It is increasingly appreciated that some evolutionary questions can only be adequately answered by combining evidence from multiple independent sources of data, including genome sequences, sampling dates, phenotypic data, radiocarbon dates, fossil occurrences, and biogeographic range information among others. Including all relevant data into a single joint model is very challenging both conceptually and computationally. Advanced computational software packages that allow robust development of compatible (sub-)models which can be composed into a full model hierarchy have played a key role in these developments. Developing such software frameworks is increasingly a major scientific activity in its own right, and comes with specific challenges, from practical software design, development and engineering challenges to statistical and conceptual modelling challenges. BEAST 2 is one such computational software platform, and was first announced over 4 years ago. Here we describe a series of major new developments in the BEAST 2 core platform and model hierarchy that have occurred since the first release of the software, culminating in the recent 2.5 release.

The hippocampus shrinks in late adulthood, leading to impaired memory and increased risk for dementia. Hippocampal and medial temporal lobe volumes are larger in higher-fit adults, and physical activity training increases hippocampal perfusion, but the extent to which aerobic exercise training can modify hippocampal volume in late adulthood remains unknown. Here we show, in a randomized controlled trial with 120 older adults, that aerobic exercise training increases the size of the anterior hippocampus, leading to improvements in spatial memory. Exercise training increased hippocampal volume by 2%, effectively reversing age-related loss in volume by 1 to 2 y. We also demonstrate that increased hippocampal volume is associated with greater serum levels of BDNF, a mediator of neurogenesis in the dentate gyrus. Hippocampal volume declined in the control group, but higher preintervention fitness partially attenuated the decline, suggesting that fitness protects against volume loss. Caudate nucleus and thalamus volumes were unaffected by the intervention. These theoretically important findings indicate that aerobic exercise training is effective at reversing hippocampal volume loss in late adulthood, which is accompanied by improved memory function.

Abstract This article discusses ggplot2, an open source R package, based on a grammatical theory of graphics. The underlying theory has been discussed in depth elsewhere so this article illustrates some of the consequences of the theory for creating new graphics, the importance of programmable graphics, and the rich ecosystem that has grown up around ggplot2. WIREs Comp Stat 2011 3 180–185 DOI: 10.1002/wics.147 This article is categorized under: Software for Computational Statistics &gt; Software/Statistical Software Statistical and Graphical Methods of Data Analysis &gt; Statistical Graphics and Visualization

Hi-C experiments explore the 3D structure of the genome, generating terabases of data to create high-resolution contact maps. Here, we introduce Juicer, an open-source tool for analyzing terabase-scale Hi-C datasets. Juicer allows users without a computational background to transform raw sequence data into normalized contact maps with one click. Juicer produces a hic file containing compressed contact matrices at many resolutions, facilitating visualization and analysis at multiple scales. Structural features, such as loops and domains, are automatically annotated. Juicer is available as open source software at http://aidenlab.org/juicer/.