Showing papers by "Pennsylvania State University published in 2014"

TaintDroid: An Information-Flow Tracking System for Realtime Privacy Monitoring on Smartphones

Abstract: Today’s smartphone operating systems frequently fail to provide users with visibility into how third-party applications collect and share their private data. We address these shortcomings with TaintDroid, an efficient, system-wide dynamic taint tracking and analysis system capable of simultaneously tracking multiple sources of sensitive data. TaintDroid enables realtime analysis by leveraging Android’s virtualized execution environment. TaintDroid incurs only 32p performance overhead on a CPU-bound microbenchmark and imposes negligible overhead on interactive third-party applications. Using TaintDroid to monitor the behavior of 30 popular third-party Android applications, in our 2010 study we found 20 applications potentially misused users’ private information; so did a similar fraction of the tested applications in our 2012 study. Monitoring the flow of privacy-sensitive data with TaintDroid provides valuable input for smartphone users and security service firms seeking to identify misbehaving applications.

mediation: R Package for Causal Mediation Analysis

Abstract: In this paper, we describe the R package mediation for conducting causal mediation analysis in applied empirical research. In many scientific disciplines, the goal of researchers is not only estimating causal effects of a treatment but also understanding the process in which the treatment causally affects the outcome. Causal mediation analysis is frequently used to assess potential causal mechanisms. The mediation package implements a comprehensive suite of statistical tools for conducting such an analysis. The package is organized into two distinct approaches. Using the model-based approach, researchers can estimate causal mediation effects and conduct sensitivity analysis under the standard research design. Furthermore, the design-based approach provides several analysis tools that are applicable under different experimental designs. This approach requires weaker assumptions than the model-based approach. We also implement a statistical method for dealing with multiple (causally dependent) mediators, which are often encountered in practice. Finally, the package also offers a methodology for assessing causal mediation in the presence of treatment noncompliance, a common problem in randomized trials.

Improved cosmological constraints from a joint analysis of the SDSS-II and SNLS supernova samples

Abstract: Aims. We present cosmological constraints from a joint analysis of type Ia supernova (SN Ia) observations obtained by the SDSS-II and SNLS collaborations. The dataset includes several low-redshift samples (z< 0.1), all three seasons from the SDSS-II (0.05

Vertical and in-plane heterostructures from WS2/MoS2 monolayers.

Abstract: Layer-by-layer stacking or lateral interfacing of atomic monolayers has opened up unprecedented opportunities to engineer two-dimensional heteromaterials. Fabrication of such artificial heterostructures with atomically clean and sharp interfaces, however, is challenging. Here, we report a one-step growth strategy for the creation of high-quality vertically stacked as well as in-plane interconnected heterostructures of WS2/MoS2 via control of the growth temperature. Vertically stacked bilayers with WS2 epitaxially grown on top of the MoS2 monolayer are formed with preferred stacking order at high temperature. A strong interlayer excitonic transition is observed due to the type II band alignment and to the clean interface of these bilayers. Vapour growth at low temperature, on the other hand, leads to lateral epitaxy of WS2 on MoS2 edges, creating seamless and atomically sharp in-plane heterostructures that generate strong localized photoluminescence enhancement and intrinsic p-n junctions. The fabrication of heterostructures from monolayers, using simple and scalable growth, paves the way for the creation of unprecedented two-dimensional materials with exciting properties.

Defining the role of common variation in the genomic and biological architecture of adult human height

Abstract: Using genome-wide data from 253,288 individuals, we identified 697 variants at genome-wide significance that together explained one-fifth of the heritability for adult height. By testing different numbers of variants in independent studies, we show that the most strongly associated ∼2,000, ∼3,700 and ∼9,500 SNPs explained ∼21%, ∼24% and ∼29% of phenotypic variance. Furthermore, all common variants together captured 60% of heritability. The 697 variants clustered in 423 loci were enriched for genes, pathways and tissue types known to be involved in growth and together implicated genes and pathways not highlighted in earlier efforts, such as signaling by fibroblast growth factors, WNT/β-catenin and chondroitin sulfate-related genes. We identified several genes and pathways not previously connected with human skeletal growth, including mTOR, osteoglycin and binding of hyaluronic acid. Our results indicate a genetic architecture for human height that is characterized by a very large but finite number (thousands) of causal variants.

FlowDroid: precise context, flow, field, object-sensitive and lifecycle-aware taint analysis for Android apps

Abstract: Today's smartphones are a ubiquitous source of private and confidential data. At the same time, smartphone users are plagued by carelessly programmed apps that leak important data by accident, and by malicious apps that exploit their given privileges to copy such data intentionally. While existing static taint-analysis approaches have the potential of detecting such data leaks ahead of time, all approaches for Android use a number of coarse-grain approximations that can yield high numbers of missed leaks and false alarms. In this work we thus present FlowDroid, a novel and highly precise static taint analysis for Android applications. A precise model of Android's lifecycle allows the analysis to properly handle callbacks invoked by the Android framework, while context, flow, field and object-sensitivity allows the analysis to reduce the number of false alarms. Novel on-demand algorithms help FlowDroid maintain high efficiency and precision at the same time. We also propose DroidBench, an open test suite for evaluating the effectiveness and accuracy of taint-analysis tools specifically for Android apps. As we show through a set of experiments using SecuriBench Micro, DroidBench, and a set of well-known Android test applications, FlowDroid finds a very high fraction of data leaks while keeping the rate of false positives low. On DroidBench, FlowDroid achieves 93% recall and 86% precision, greatly outperforming the commercial tools IBM AppScan Source and Fortify SCA. FlowDroid successfully finds leaks in a subset of 500 apps from Google Play and about 1,000 malware apps from the VirusShare project.

Anion-exchange membranes in electrochemical energy systems

Abstract: This article provides an up-to-date perspective on the use of anion-exchange membranes in fuel cells, electrolysers, redox flow batteries, reverse electrodialysis cells, and bioelectrochemical systems (e.g. microbial fuel cells). The aim is to highlight key concepts, misconceptions, the current state-of-the-art, technological and scientific limitations, and the future challenges (research priorities) related to the use of anion-exchange membranes in these energy technologies. All the references that the authors deemed relevant, and were available on the web by the manuscript submission date (30th April 2014), are included.

The man behind the curtain: x-rays drive the uv through nir variability in the 2013 active galactic nucleus outburst in ngc 2617

Abstract: After the All-Sky Automated Survey for SuperNovae discovered a significant brightening of the inner region of NGC 2617, we began a ∼70 day photometric and spectroscopic monitoring campaign from the X-ray through near-infrared (NIR) wavelengths. We report that NGC 2617 went through a dramatic outburst, during which its X-ray flux increased by over an order of magnitude followed by an increase of its optical/ultraviolet (UV) continuum flux by almost an order of magnitude. NGC 2617, classified as a Seyfert 1.8 galaxy in 2003, is now a Seyfert 1 due to the appearance of broad optical emission lines and a continuum blue bump. Such 'changing look active galactic nuclei (AGNs)' are rare and provide us with important insights about AGN physics. Based on the Hβ line width and the radius-luminosity relation, we estimate the mass of central black hole (BH) to be (4 ± 1) × 10{sup 7} M {sub ☉}. When we cross-correlate the light curves, we find that the disk emission lags the X-rays, with the lag becoming longer as we move from the UV (2-3 days) to the NIR (6-9 days). Also, the NIR is more heavily temporally smoothed than the UV. This can largely be explained bymore » a simple model of a thermally emitting thin disk around a BH of the estimated mass that is illuminated by the observed, variable X-ray fluxes.« less

A comparative encyclopedia of DNA elements in the mouse genome

Abstract: The laboratory mouse shares the majority of its protein-coding genes with humans, making it the premier model organism in biomedical research, yet the two mammals differ in significant ways To gain greater insights into both shared and species-specific transcriptional and cellular regulatory programs in the mouse, the Mouse ENCODE Consortium has mapped transcription, DNase I hypersensitivity, transcription factor binding, chromatin modifications and replication domains throughout the mouse genome in diverse cell and tissue types By comparing with the human genome, we not only confirm substantial conservation in the newly annotated potential functional sequences, but also find a large degree of divergence of sequences involved in transcriptional regulation, chromatin state and higher order chromatin organization Our results illuminate the wide range of evolutionary forces acting on genes and their regulatory regions, and provide a general resource for research into mammalian biology and mechanisms of human diseases

Nanoscale thermal transport. II. 2003–2012

Abstract: A diverse spectrum of technology drivers such as improved thermal barriers, higher efficiency thermoelectric energy conversion, phase-change memory, heat-assisted magnetic recording, thermal management of nanoscale electronics, and nanoparticles for thermal medical therapies are motivating studies of the applied physics of thermal transport at the nanoscale. This review emphasizes developments in experiment, theory, and computation in the past ten years and summarizes the present status of the field. Interfaces become increasingly important on small length scales. Research during the past decade has extended studies of interfaces between simple metals and inorganic crystals to interfaces with molecular materials and liquids with systematic control of interface chemistry and physics. At separations on the order of ∼1 nm, the science of radiative transport through nanoscale gaps overlaps with thermal conduction by the coupling of electronic and vibrational excitations across weakly bonded or rough interface...

Dextran Sulfate Sodium (DSS)-Induced Colitis in Mice

Abstract: Inflammatory bowel diseases (IBD), mainly comprising ulcerative colitis and Crohn's Disease, are complex and multifactorial diseases with unknown etiology. For the past 20 years, to study human IBD mechanistically, a number of murine models of colitis have been developed. These models are indispensable tools to decipher underlying mechanisms of IBD pathogenesis as well as to evaluate a number of potential therapeutics. Among various chemically induced colitis models, the dextran sulfate sodium (DSS)-induced colitis model is widely used because of its simplicity and many similarities with human ulcerative colitis. This model has both advantages and disadvantages that must be considered when employed. This protocol describes the DSS-induced colitis model, focusing on details and factors that could affect DSS-induced pathology.

The tenth data release of the Sloan digital sky survey: First spectroscopic data from the SDSS-iii apache point observatory galactic evolution experiment

Abstract: The Sloan Digital Sky Survey (SDSS) has been in operation since 2000 April. This paper presents the Tenth Public Data Release (DR10) from its current incarnation, SDSS-III. This data release includes the first spectroscopic data from the Apache Point Observatory Galaxy Evolution Experiment (APOGEE), along with spectroscopic data from the Baryon Oscillation Spectroscopic Survey (BOSS) taken through 2012 July. The APOGEE instrument is a near-infrared R ~ 22,500 300 fiber spectrograph covering 1.514-1.696 μm. The APOGEE survey is studying the chemical abundances and radial velocities of roughly 100,000 red giant star candidates in the bulge, bar, disk, and halo of the Milky Way. DR10 includes 178,397 spectra of 57,454 stars, each typically observed three or more times, from APOGEE. Derived quantities from these spectra (radial velocities, effective temperatures, surface gravities, and metallicities) are also included. DR10 also roughly doubles the number of BOSS spectra over those included in the Ninth Data Release. DR10 includes a total of 1,507,954 BOSS spectra comprising 927,844 galaxy spectra, 182,009 quasar spectra, and 159,327 stellar spectra selected over 6373.2 deg2.

Observation of high-energy astrophysical neutrinos in three years of icecube data

Abstract: A search for high-energy neutrinos interacting within the IceCube detector between 2010 and 2012 provided the first evidence for a high-energy neutrino flux of extraterrestrial origin. Results from an analysis using the same methods with a third year (2012-2013) of data from the complete IceCube detector are consistent with the previously reported astrophysical flux in the 100 TeV-PeV range at the level of 10(-8) GeV cm(-2) s(-1) sr(-1) per flavor and reject a purely atmospheric explanation for the combined three-year data at 5.7 sigma. The data are consistent with expectations for equal fluxes of all three neutrino flavors and with isotropic arrival directions, suggesting either numerous or spatially extended sources. The three-year data set, with a live time of 988 days, contains a total of 37 neutrino candidate events with deposited energies ranging from 30 to 2000 TeV. The 2000-TeV event is the highest-energy neutrino interaction ever observed.

Highly active electrocatalysis of the hydrogen evolution reaction by cobalt phosphide nanoparticles.

Abstract: Nanoparticles of cobalt phosphide, CoP, have been prepared and evaluated as electrocatalysts for the hydrogen evolution reaction (HER) under strongly acidic conditions (0.50 M H_2SO_4, pH 0.3). Uniform, multi-faceted CoP nanoparticles were synthesized by reacting Co nanoparticles with trioctylphosphine. Electrodes comprised of CoP nanoparticles on a Ti support (2 mg cm^(−2) mass loading) produced a cathodic current density of 20 mA cm^(−2) at an overpotential of −85 mV. The CoP/Ti electrodes were stable over 24 h of sustained hydrogen production in 0.50 M H_2SO_4. The activity was essentially unchanged after 400 cyclic voltammetric sweeps, suggesting long-term viability under operating conditions. CoP is therefore amongst the most active, acid-stable, earth-abundant HER electrocatalysts reported to date.

Spin-transfer torque generated by a topological insulator

Abstract: Magnetic devices are a leading contender for the implementation of memory and logic technologies that are non-volatile, that can scale to high density and high speed, and that do not wear out. However, widespread application of magnetic memory and logic devices will require the development of efficient mechanisms for reorienting their magnetization using the least possible current and power. There has been considerable recent progress in this effort; in particular, it has been discovered that spin-orbit interactions in heavy-metal/ferromagnet bilayers can produce strong current-driven torques on the magnetic layer, via the spin Hall effect in the heavy metal or the Rashba-Edelstein effect in the ferromagnet. In the search for materials to provide even more efficient spin-orbit-induced torques, some proposals have suggested topological insulators, which possess a surface state in which the effects of spin-orbit coupling are maximal in the sense that an electron's spin orientation is fixed relative to its propagation direction. Here we report experiments showing that charge current flowing in-plane in a thin film of the topological insulator bismuth selenide (Bi2Se3) at room temperature can indeed exert a strong spin-transfer torque on an adjacent ferromagnetic permalloy (Ni81Fe19) thin film, with a direction consistent with that expected from the topological surface state. We find that the strength of the torque per unit charge current density in Bi2Se3 is greater than for any source of spin-transfer torque measured so far, even for non-ideal topological insulator films in which the surface states coexist with bulk conduction. Our data suggest that topological insulators could enable very efficient electrical manipulation of magnetic materials at room temperature, for memory and logic applications.

Phylotranscriptomic analysis of the origin and early diversification of land plants

Abstract: Reconstructing the origin and evolution of land plants and their algal relatives is a fundamental problem in plant phylogenetics, and is essential for understanding how critical adaptations arose, including the embryo, vascular tissue, seeds, and flowers. Despite advances in molecular systematics, some hypotheses of relationships remain weakly resolved. Inferring deep phylogenies with bouts of rapid diversification can be problematic; however, genome-scale data should significantly increase the number of informative characters for analyses. Recent phylogenomic reconstructions focused on the major divergences of plants have resulted in promising but inconsistent results. One limitation is sparse taxon sampling, likely resulting from the difficulty and cost of data generation. To address this limitation, transcriptome data for 92 streptophyte taxa were generated and analyzed along with 11 published plant genome sequences. Phylogenetic reconstructions were conducted using up to 852 nuclear genes and 1,701,170 aligned sites. Sixty-nine analyses were performed to test the robustness of phylogenetic inferences to permutations of the data matrix or to phylogenetic method, including supermatrix, supertree, and coalescent-based approaches, maximum-likelihood and Bayesian methods, partitioned and unpartitioned analyses, and amino acid versus DNA alignments. Among other results, we find robust support for a sister-group relationship between land plants and one group of streptophyte green algae, the Zygnematophyceae. Strong and robust support for a clade comprising liverworts and mosses is inconsistent with a widely accepted view of early land plant evolution, and suggests that phylogenetic hypotheses used to understand the evolution of fundamental plant traits should be reevaluated.

Branched-chain amino acids in metabolic signalling and insulin resistance

Abstract: Branched-chain amino acids (BCAAs) are important nutrient signals that have direct and indirect effects. Frequently, BCAAs have been reported to mediate antiobesity effects, especially in rodent models. However, circulating levels of BCAAs tend to be increased in individuals with obesity and are associated with worse metabolic health and future insulin resistance or type 2 diabetes mellitus (T2DM). A hypothesized mechanism linking increased levels of BCAAs and T2DM involves leucine-mediated activation of the mammalian target of rapamycin complex 1 (mTORC1), which results in uncoupling of insulin signalling at an early stage. A BCAA dysmetabolism model proposes that the accumulation of mitotoxic metabolites (and not BCAAs per se) promotes β-cell mitochondrial dysfunction, stress signalling and apoptosis associated with T2DM. Alternatively, insulin resistance might promote aminoacidaemia by increasing the protein degradation that insulin normally suppresses, and/or by eliciting an impairment of efficient BCAA oxidative metabolism in some tissues. Whether and how impaired BCAA metabolism might occur in obesity is discussed in this Review. Research on the role of individual and model-dependent differences in BCAA metabolism is needed, as several genes (BCKDHA, PPM1K, IVD and KLF15) have been designated as candidate genes for obesity and/or T2DM in humans, and distinct phenotypes of tissue-specific branched chain ketoacid dehydrogenase complex activity have been detected in animal models of obesity and T2DM.

Nitrogen-Doped Mesoporous Carbon Promoted Chemical Adsorption of Sulfur and Fabrication of High-Areal-Capacity Sulfur Cathode with Exceptional Cycling Stability for Lithium-Sulfur Batteries

Abstract: As one important component of sulfur cathodes, the carbon host plays a key role in the electrochemical performance of lithium-sulfur (Li-S) batteries. In this paper, a mesoporous nitrogen-doped carbon (MPNC)-sulfur nanocomposite is reported as a novel cathode for advanced Li-S batteries. The nitrogen doping in the MPNC material can effectively promote chemical adsorption between sulfur atoms and oxygen functional groups on the carbon, as verifi ed by X-ray absorption near edge structure spectroscopy, and the mechanism by which nitrogen enables the behavior is further revealed by density functional theory calculations. Based on the advantages of the porous structure and nitrogen doping, the MPNC-sulfur cathodes show excellent cycling stability (95% retention within 100 cycles) at a high current density of 0.7 mAh cm −2 with a high sulfur loading (4.2 mg S cm −2 ) and a sulfur content (70 wt%). A high areal capacity (≈3.3 mAh cm −2 ) is demonstrated by using the novel cathode, which is crucial for the practical application of Li-S batteries. It is believed that the important role of nitrogen doping promoted chemical adsorption can be extended for development of other high performance carbon-sulfur composite cathodes for Li-S batteries.

Decoding the Fingerprint of Ferroelectric Loops: Comprehension of the Material Properties and Structures

Abstract: Due to the nature of domains, ferroics, including ferromagnetic, ferroelectric, and ferroelastic materials, exhibit hysteresis phenomena with respect to external driving fields (magnetic field, electric field, or stress). In principle, every ferroic material has its own hysteresis loop, like a fingerprint, which contains information related to its properties and structures. For ferroelectrics, many characteristic parameters, such as coercive field, spontaneous, and remnant polarizations can be directly extracted from the hysteresis loops. Furthermore, many impact factors, including the effect of materials (grain size and grain boundary, phase and phase boundary, doping, anisotropy, thickness), aging (with and without poling), and measurement conditions (applied field amplitude, fatigue, frequency, temperature, stress), can affect the hysteretic behaviors of the ferroelectrics. In this feature article, we will first give the background of the ferroic materials and multiferroics, with an emphasis on ferroelectrics. Then it is followed by an introduction of the characterizing techniques for the loops, including the polarization–electric field loops and strain–electric field curves. A caution is made to avoid misinterpretation of the loops due to the existence of conductivity. Based on their morphologic features, the hysteresis loops are categorized to four groups and the corresponding material usages are introduced. The impact factors on the hysteresis loops are discussed based on recent developments in ferroelectric and related materials. It is suggested that decoding the fingerprint of loops in ferroelectrics is feasible and the comprehension of the material properties and structures through the hysteresis loops is established.

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

Abstract: We present primary results from the Sequencing Quality Control (SEQC) project, coordinated by the US Food and Drug Administration. Examining Illumina HiSeq, Life Technologies SOLiD and Roche 454 platforms at multiple laboratory sites using reference RNA samples with built-in controls, we assess RNA sequencing (RNA-seq) performance for junction discovery and differential expression profiling and compare it to microarray and quantitative PCR (qPCR) data using complementary metrics. At all sequencing depths, we discover unannotated exon-exon junctions, with >80% validated by qPCR. We find that measurements of relative expression are accurate and reproducible across sites and platforms if specific filters are used. In contrast, RNA-seq and microarrays do not provide accurate absolute measurements, and gene-specific biases are observed for all examined platforms, including qPCR. Measurement performance depends on the platform and data analysis pipeline, and variation is large for transcript-level profiling. The complete SEQC data sets, comprising >100 billion reads (10Tb), provide unique resources for evaluating RNA-seq analyses for clinical and regulatory settings.

Nitrogen-Doped Mesoporous Carbon Promoted Chemical Adsorption of Sulfur and Fabrication of High-Areal-Capacity Sulfur Cathode with Exceptional Cycling Stability for Lithium-Sulfur Batteries

Abstract: As one important component of sulfur cathodes, the carbon host plays a key role in the electrochemical performance of lithium-sulfur (Li-S) batteries. In this paper, a mesoporous nitrogen-doped carbon (MPNC)-sulfur nanocomposite is reported as a novel cathode for advanced Li-S batteries. The nitrogen doping in the MPNC material can effectively promote chemical adsorption between sulfur atoms and oxygen functional groups on the carbon, as verifi ed by X-ray absorption near edge structure spectroscopy, and the mechanism by which nitrogen enables the behavior is further revealed by density functional theory calculations. Based on the advantages of the porous structure and nitrogen doping, the MPNC-sulfur cathodes show excellent cycling stability (95% retention within 100 cycles) at a high current density of 0.7 mAh cm −2 with a high sulfur loading (4.2 mg S cm −2 ) and a sulfur content (70 wt%). A high areal capacity (≈3.3 mAh cm −2 ) is demonstrated by using the novel cathode, which is crucial for the practical application of Li-S batteries. It is believed that the important role of nitrogen doping promoted chemical adsorption can be extended for development of other high performance carbon-sulfur composite cathodes for Li-S batteries.

Topologically associating domains are stable units of replication-timing regulation

Abstract: Eukaryotic chromosomes replicate in a temporal order known as the replication-timing program. In mammals, replication timing is cell-type-specific with at least half the genome switching replication timing during development, primarily in units of 400-800 kilobases ('replication domains'), whose positions are preserved in different cell types, conserved between species, and appear to confine long-range effects of chromosome rearrangements. Early and late replication correlate, respectively, with open and closed three-dimensional chromatin compartments identified by high-resolution chromosome conformation capture (Hi-C), and, to a lesser extent, late replication correlates with lamina-associated domains (LADs). Recent Hi-C mapping has unveiled substructure within chromatin compartments called topologically associating domains (TADs) that are largely conserved in their positions between cell types and are similar in size to replication domains. However, TADs can be further sub-stratified into smaller domains, challenging the significance of structures at any particular scale. Moreover, attempts to reconcile TADs and LADs to replication-timing data have not revealed a common, underlying domain structure. Here we localize boundaries of replication domains to the early-replicating border of replication-timing transitions and map their positions in 18 human and 13 mouse cell types. We demonstrate that, collectively, replication domain boundaries share a near one-to-one correlation with TAD boundaries, whereas within a cell type, adjacent TADs that replicate at similar times obscure replication domain boundaries, largely accounting for the previously reported lack of alignment. Moreover, cell-type-specific replication timing of TADs partitions the genome into two large-scale sub-nuclear compartments revealing that replication-timing transitions are indistinguishable from late-replicating regions in chromatin composition and lamina association and accounting for the reduced correlation of replication timing to LADs and heterochromatin. Our results reconcile cell-type-specific sub-nuclear compartmentalization and replication timing with developmentally stable structural domains and offer a unified model for large-scale chromosome structure and function.

Autocratic breakdown and regime transitions: A new data set

Abstract: When the leader of an autocratic regime loses power, one of three things happens. The incumbent leadership group is replaced by democratically elected leaders. Someone from the incumbent leadership group replaces him, and the regime persists. Or the incumbent leadership group loses control to a different group that replaces it with a new autocracy. Much scholarship exists on the first kind of transition, but little on transitions from one autocracy to another, though they make up about half of all regime changes. We introduce a new data set that facilitates the investigation of all three kinds of transition. It provides transition information for the 280 autocratic regimes in existence from 1946 to 2010. The data identify how regimes exit power, how much violence occurs during transitions, and whether the regimes that precede and succeed them are autocratic. We explain the data set and show how it differs from currently available data. The new data identify autocratic regime breakdowns regardless of whether the country democratizes, which makes possible the investigation of why the ouster of dictators sometimes leads to democracy but often does not, and many other questions. We present a number of examples to highlight how the new data can be used to explore questions about why dictators start wars and why autocratic breakdown sometimes results in the establishment of a new autocratic regime rather than democratization. We discuss the implications of these findings for the Arab Spring.

Investigating variation in replicability: A “Many Labs” replication project

Abstract: Although replication is a central tenet of science, direct replications are rare in psychology. This research tested variation in the replicability of 13 classic and contemporary effects across 36 independent samples totaling 6,344 participants. In the aggregate, 10 effects replicated consistently. One effect – imagined contact reducing prejudice – showed weak support for replicability. And two effects – flag priming influencing conservatism and currency priming influencing system justification – did not replicate. We compared whether the conditions such as lab versus online or US versus international sample predicted effect magnitudes. By and large they did not. The results of this small sample of effects suggest that replicability is more dependent on the effect itself than on the sample and setting used to investigate the effect.

Architecture of Kepler's multi-transiting systems. II. New investigations with twice as many candidates

Abstract: We report on the orbital architectures of Kepler systems having multiple-planet candidates identified in the analysis of data from the first six quarters of Kepler data and reported by Batalha et al. (2013). These data show 899 transiting planet candidates in 365 multiple-planet systems and provide a powerful means to study the statistical properties of planetary systems. Using a generic mass–radius relationship, we find that only two pairs of planets in these candidate systems (out of 761 pairs total) appear to be on Hill-unstable orbits, indicating ~96% of the candidate planetary systems are correctly interpreted as true systems. We find that planet pairs show little statistical preference to be near mean-motion resonances. We identify an asymmetry in the distribution of period ratios near first-order resonances (e.g., 2:1, 3:2), with an excess of planet pairs lying wide of resonance and relatively few lying narrow of resonance. Finally, based upon the transit duration ratios of adjacent planets in each system, we find that the interior planet tends to have a smaller transit impact parameter than the exterior planet does. This finding suggests that the mode of the mutual inclinations of planetary orbital planes is in the range 1°.0–2°.2, for the packed systems of small planets probed by these observations.

In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features

Abstract: RNA structure has critical roles in processes ranging from ligand sensing to the regulation of translation, polyadenylation and splicing. However, a lack of genome-wide in vivo RNA structural data has limited our understanding of how RNA structure regulates gene expression in living cells. Here we present a high-throughput, genome-wide in vivo RNA structure probing method, structure-seq, in which dimethyl sulphate methylation of unprotected adenines and cytosines is identified by next-generation sequencing. Application of this method to Arabidopsis thaliana seedlings yielded the first in vivo genome-wide RNA structure map at nucleotide resolution for any organism, with quantitative structural information across more than 10,000 transcripts. Our analysis reveals a three-nucleotide periodic repeat pattern in the structure of coding regions, as well as a less-structured region immediately upstream of the start codon, and shows that these features are strongly correlated with translation efficiency. We also find patterns of strong and weak secondary structure at sites of alternative polyadenylation, as well as strong secondary structure at 5' splice sites that correlates with unspliced events. Notably, in vivo structures of messenger RNAs annotated for stress responses are poorly predicted in silico, whereas mRNA structures of genes related to cell function maintenance are well predicted. Global comparison of several structural features between these two categories shows that the mRNAs associated with stress responses tend to have more single-strandedness, longer maximal loop length and higher free energy per nucleotide, features that may allow these RNAs to undergo conformational changes in response to environmental conditions. Structure-seq allows the RNA structurome and its biological roles to be interrogated on a genome-wide scale and should be applicable to any organism.

The essence of innocence: Consequences of dehumanizing Black children.

Abstract: The social category "children" defines a group of individuals who are perceived to be distinct, with essential characteristics including innocence and the need for protection (Haslam, Rothschild, & Ernst, 2000). The present research examined whether Black boys are given the protections of childhood equally to their peers. We tested 3 hypotheses: (a) that Black boys are seen as less "childlike" than their White peers, (b) that the characteristics associated with childhood will be applied less when thinking specifically about Black boys relative to White boys, and (c) that these trends would be exacerbated in contexts where Black males are dehumanized by associating them (implicitly) with apes (Goff, Eberhardt, Williams, & Jackson, 2008). We expected, derivative of these 3 principal hypotheses, that individuals would perceive Black boys as being more responsible for their actions and as being more appropriate targets for police violence. We find support for these hypotheses across 4 studies using laboratory, field, and translational (mixed laboratory/field) methods. We find converging evidence that Black boys are seen as older and less innocent and that they prompt a less essential conception of childhood than do their White same-age peers. Further, our findings demonstrate that the Black/ape association predicted actual racial disparities in police violence toward children. These data represent the first attitude/behavior matching of its kind in a policing context. Taken together, this research suggests that dehumanization is a uniquely dangerous intergroup attitude, that intergroup perception of children is underexplored, and that both topics should be research priorities.

Defining functional DNA elements in the human genome

Abstract: With the completion of the human genome sequence, attention turned to identifying and annotating its functional DNA elements. As a complement to genetic and comparative genomics approaches, the Encyclopedia of DNA Elements Project was launched to contribute maps of RNA transcripts, transcriptional regulator binding sites, and chromatin states in many cell types. The resulting genome-wide data reveal sites of biochemical activity with high positional resolution and cell type specificity that facilitate studies of gene regulation and interpretation of noncoding variants associated with human disease. However, the biochemically active regions cover a much larger fraction of the genome than do evolutionarily conserved regions, raising the question of whether nonconserved but biochemically active regions are truly functional. Here, we review the strengths and limitations of biochemical, evolutionary, and genetic approaches for defining functional DNA segments, potential sources for the observed differences in estimated genomic coverage, and the biological implications of these discrepancies. We also analyze the relationship between signal intensity, genomic coverage, and evolutionary conservation. Our results reinforce the principle that each approach provides complementary information and that we need to use combinations of all three to elucidate genome function in human biology and disease.

Aryl hydrocarbon receptor ligands in cancer: friend and foe

Abstract: The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor that is best known for mediating the toxicity and tumour-promoting properties of the carcinogen 2,3,7,8-tetrachlorodibenzo-p-dioxin, commonly referred to as ‘dioxin’. AHR influences the major stages of tumorigenesis — initiation, promotion, progression and metastasis — and physiologically relevant AHR ligands are often formed during disease states or during heightened innate and adaptive immune responses. Interestingly, ligand specificity and affinity vary between rodents and humans. Studies of aggressive tumours and tumour cell lines show increased levels of AHR and constitutive localization of this receptor in the nucleus. This suggests that the AHR is chronically activated in tumours, thus facilitating tumour progression. This Review discusses the role of AHR in tumorigenesis and the potential for therapeutic modulation of its activity in tumours.