Showing papers by "University of Notre Dame published in 2010"

Selective inhibition of BET bromodomains.

Abstract: Epigenetic proteins are intently pursued targets in ligand discovery. So far, successful efforts have been limited to chromatin modifying enzymes, or so-called epigenetic 'writers' and 'erasers'. Potent inhibitors of histone binding modules have not yet been described. Here we report a cell-permeable small molecule (JQ1) that binds competitively to acetyl-lysine recognition motifs, or bromodomains. High potency and specificity towards a subset of human bromodomains is explained by co-crystal structures with bromodomain and extra-terminal (BET) family member BRD4, revealing excellent shape complementarity with the acetyl-lysine binding cavity. Recurrent translocation of BRD4 is observed in a genetically-defined, incurable subtype of human squamous carcinoma. Competitive binding by JQ1 displaces the BRD4 fusion oncoprotein from chromatin, prompting squamous differentiation and specific antiproliferative effects in BRD4-dependent cell lines and patient-derived xenograft models. These data establish proof-of-concept for targeting protein-protein interactions of epigenetic 'readers', and provide a versatile chemical scaffold for the development of chemical probes more broadly throughout the bromodomain family.

Review of Particle Physics

Abstract: This biennial Review summarizes much of particle physics. Using data from previous editions, plus 2158 new measurements from 551 papers, we list, evaluate, and average measured properties of gauge bosons, leptons, quarks, mesons, and baryons. We also summarize searches for hypothetical particles such as Higgs bosons, heavy neutrinos, and supersymmetric particles. All the particle properties and search limits are listed in Summary Tables. We also give numerous tables, figures, formulae, and reviews of topics such as the Standard Model, particle detectors, probability, and statistics. Among the 108 reviews are many that are new or heavily revised including those on neutrino mass, mixing, and oscillations, QCD, top quark, CKM quark-mixing matrix, V-ud & V-us, V-cb & V-ub, fragmentation functions, particle detectors for accelerator and non-accelerator physics, magnetic monopoles, cosmological parameters, and big bang cosmology.

When is a Liability not a Liability? Textual Analysis, Dictionaries, and 10-Ks

Abstract: Previous research uses negative word counts to measure the tone of a text. We show that word lists developed for other disciplines misclassify common words in financial text. In a large sample of 10 Ks during 1994 to 2008, almost three-fourths of the words identified as negative by the widely used Harvard Dictionary are words typically not considered negative in financial contexts. We develop an alternative negative word list, along with five other word lists, that better reflect tone in financial text. We link the word lists to 10 K filing returns, trading volume, return volatility, fraud, material weakness, and unexpected earnings.

Low-Voltage Tunnel Transistors for Beyond CMOS Logic

Abstract: Steep subthreshold swing transistors based on interband tunneling are examined toward extending the performance of electronics systems. In particular, this review introduces and summarizes progress in the development of the tunnel field-effect transistors (TFETs) including its origin, current experimental and theoretical performance relative to the metal-oxide-semiconductor field-effect transistor (MOSFET), basic current-transport theory, design tradeoffs, and fundamental challenges. The promise of the TFET is in its ability to provide higher drive current than the MOSFET as supply voltages approach 0.1 V.

The Chicxulub Asteroid Impact and Mass Extinction at the Cretaceous-Paleogene Boundary

Abstract: The Cretaceous-Paleogene boundary similar to 65.5 million years ago marks one of the three largest mass extinctions in the past 500 million years. The extinction event coincided with a large asteroid impact at Chicxulub, Mexico, and occurred within the time of Deccan flood basalt volcanism in India. Here, we synthesize records of the global stratigraphy across this boundary to assess the proposed causes of the mass extinction. Notably, a single ejecta-rich deposit compositionally linked to the Chicxulub impact is globally distributed at the Cretaceous-Paleogene boundary. The temporal match between the ejecta layer and the onset of the extinctions and the agreement of ecological patterns in the fossil record with modeled environmental perturbations (for example, darkness and cooling) lead us to conclude that the Chicxulub impact triggered the mass extinction.

Dielectric Barrier Discharge Plasma Actuators for Flow Control

Abstract: The term plasma actuator has now been a part of the fluid dynamics flow-control vernacular for more than a decade. A particular type of plasma actuator that has gained wide use is based on a single–dielectric barrier discharge (SDBD) mechanism that has desirable features for use in air at atmospheric pressures. For these actuators, the mechanism of flow control is through a generated body-force vector field that couples with the momentum in the external flow. The body force can be derived from first principles, and the effect of plasma actuators can be easily incorporated into flow solvers so that their placement and operation can be optimized. They have been used in a wide range of internal and external flow applications. Although initially considered useful only at low speeds, plasma actuators are effective in a number of applications at high subsonic, transonic, and supersonic Mach numbers, owing largely to more optimized actuator designs that were developed through better understanding and modeling of...

Anchoring semiconductor and metal nanoparticles on a two-dimensional catalyst mat. Storing and shuttling electrons with reduced graphene oxide.

Abstract: Using reduced graphene oxide (RGO) as a two-dimensional support, we have succeeded in selective anchoring of semiconductor and metal nanoparticles at separate sites. Photogenerated electrons from UV-irradiated TiO2 are transported across RGO to reduce silver ions into silver nanoparticles at a location distinct from the TiO2 anchored site. The ability of RGO to store and shuttle electrons, as visualized via a stepwise electron transfer process, demonstrates its capability to serve as a catalyst nanomat and transfer electrons on demand to adsorbed species. These findings pave the way for the development of next generation catalyst systems and can spur advancements in graphene-based composites for chemical and biological sensors.

Graphene-Based Nanoarchitectures. Anchoring Semiconductor and Metal Nanoparticles on a Two-Dimensional Carbon Support

Abstract: Graphene based two-dimensional carbon nanostructures serve as a support to disperse catalyst nanoparticles. Reduced graphene oxide is used as a support to anchor semiconductor and metal nanoparticles. Such a design strategy would enable the development of a multifunctional catalyst mat. This Perspective focuses on the interaction between graphene oxide−semiconductor (TiO2, ZnO) and graphene oxide−metal (Au, Pt) nanoparticles and discusses potential applications in catalysis, light energy conversion, and fuel cells.

Microvesicles: mediators of extracellular communication during cancer progression

Abstract: Microvesicles are generated by the outward budding and fission of membrane vesicles from the cell surface. Recent studies suggest that microvesicle shedding is a highly regulated process that occurs in a spectrum of cell types and, more frequently, in tumor cells. Microvesicles have been widely detected in various biological fluids including peripheral blood, urine and ascitic fluids, and their function and composition depend on the cells from which they originate. By facilitating the horizontal transfer of bioactive molecules such as proteins, RNAs and microRNAs, they are now thought to have vital roles in tumor invasion and metastases, inflammation, coagulation, and stem-cell renewal and expansion. This Commentary summarizes recent literature on the properties and biogenesis of microvesicles and their potential role in cancer progression.

The jina reaclib database: its recent updates and impact on type-i x-ray bursts

Abstract: We present results from the JINA REACLIB project, an ongoing effort to maintain a current and accurate library of thermonuclear reaction rates for astrophysical applications. Ongoing updates are transparently documented and version tracked, and any set of rates is publicly available and can be downloaded via a Web interface at http://groups.nscl.msu.edu/jina/reaclib/db/. We discuss here our library V1.0, a snapshot of recommended rates for stable and explosive hydrogen and helium burning. We show that the updated reaction rates lead to modest but significant changes in full network, one-dimensional X-ray burst model calculations, compared with calculations with previously used reaction rate sets. The late time behavior of X-ray burst light curves shows significant changes, suggesting that the previously found small discrepancies between model calculations and observations may be solved with a better understanding of the nuclear input. Our X-ray burst model calculations are intended to serve as a benchmark for future model comparisons and sensitivity studies, as the complete underlying nuclear physics is fully documented and publicly available.

Functional and evolutionary insights from the genomes of three parasitoid Nasonia species.

Abstract: We report here genome sequences and comparative analyses of three closely related parasitoid wasps: Nasonia vitripennis, N. giraulti, and N. longicornis. Parasitoids are important regulators of arthropod populations, including major agricultural pests and disease vectors, and Nasonia is an emerging genetic model, particularly for evolutionary and developmental genetics. Key findings include the identification of a functional DNA methylation tool kit; hymenopteran-specific genes including diverse venoms; lateral gene transfers among Pox viruses, Wolbachia, and Nasonia; and the rapid evolution of genes involved in nuclear-mitochondrial interactions that are implicated in speciation. Newly developed genome resources advance Nasonia for genetic research, accelerate mapping and cloning of quantitative trait loci, and will ultimately provide tools and knowledge for further increasing the utility of parasitoids as pest insect-control agents.

Uncertainty and Economic Activity: Evidence from Business Survey Data

Abstract: What is the impact of time-varying business uncertainty on economic activity? Using partly confidential business survey data from the U.S. and Germany in structural VARs, we find that positive innovations to business uncertainty lead to prolonged declines in economic activity. In contrast, their high-frequency impact is small. We find no evidence of the "wait-and-see"-effect - large declines of economic activity on impact and subsequent fast rebounds - that the recent literature associates with positive uncertainty shocks. Rather, positive innovations to business uncertainty have effects similar to negative business confidence innovations. Once we control for their low-frequency effect, we find little statistically or economically significant impact of uncertainty innovations on activity. We argue that high uncertainty events are a mere epiphenomenon of bad economic times: recessions breed uncertainty.

Equimolar CO2 Absorption by Anion-Functionalized Ionic Liquids

Abstract: Amino acid ionic liquid trihexyl(tetradecyl)phosphonium methioninate [P66614][Met] and prolinate [P66614][Pro] absorb CO2 in nearly 1:1 stoichiometry, surpassing by up to a factor of 2 the CO2 capture efficiency of previously reported ionic liquid and aqueous amine absorbants for CO2. Room temperature isotherms are obtained by barometric measurements in an accurately calibrated stirred cell, and the product identity is confirmed using in situ IR. Density functional theory (DFT) calculations support the 1:1 reaction stoichiometry and predict reaction enthalpies in good agreement with calorimetric measurements and isotherms.

Observation of long-range, near-side angular correlations in proton-proton collisions at the LHC

Abstract: This is the pre-print version of the Published Article, which can be accessed from the link below - Copyright @ 2010 Springer Verlag

Beyond Photovoltaics: Semiconductor Nanoarchitectures for Liquid-Junction Solar Cells

Abstract: 3.1. Fundamental Characterization 6672 3.2. Photocurrent Action Spectroscopy 6673 3.3. Optical Characterization 6673 3.4. Characterization of Electron Transfer 6673 4. Electron Transport in Metal Oxide Films 6674 4.1. Mechanism of Photoinduced Carrier Transport 6674 4.2. Characterization of Diffusion Length 6675 4.3. One-Dimensional (1-D) Transport Architectures 6675 4.4. Electrolyte Interactions 6676 5. Recent Trends in Liquid-Junction Solar Cells 6676 5.1. Dye Sensitized Solar Cells 6677 5.2. Quantum Dot Sensitized Solar Cells 6678 5.3. Carbon Nanostructure Based Photochemical Solar Cells 6679

New perspectives and methods in link prediction

Abstract: This paper examines important factors for link prediction in networks and provides a general, high-performance framework for the prediction task. Link prediction in sparse networks presents a significant challenge due to the inherent disproportion of links that can form to links that do form. Previous research has typically approached this as an unsupervised problem. While this is not the first work to explore supervised learning, many factors significant in influencing and guiding classification remain unexplored. In this paper, we consider these factors by first motivating the use of a supervised framework through a careful investigation of issues such as network observational period, generality of existing methods, variance reduction, topological causes and degrees of imbalance, and sampling approaches. We also present an effective flow-based predicting algorithm, offer formal bounds on imbalance in sparse network link prediction, and employ an evaluation method appropriate for the observed imbalance. Our careful consideration of the above issues ultimately leads to a completely general framework that outperforms unsupervised link prediction methods by more than 30% AUC.

A review of allochthonous organic matter dynamics and metabolism in streams

Abstract: The role of allochthonous organic matter in lotic ecosystems has been an important research topic among aquatic ecologists since the seminal work by Lindeman was published in 1942. Since 1986, studies on organic matter budgets, ecosystem metabolism, and decomposition published in J-NABS have made significant contributions to the overall understanding of organic matter dynamics in streams. In this review, we summarize the utility of organic matter budgets, cover the major advances in research on ecosystem metabolism, and describe the intrinsic and extrinsic factors influencing organic matter decomposition. We also discuss future directions and current applications of research and highlight the need for additional studies on the role of land use and climate change, as well as continued use of organic matter processing as a functional metric in biomonitoring studies. We emphasize the need for continued data synthesis into comprehensive organic matter budgets. Such comparative studies can elucidate important drivers of organic matter dynamics and can assist in the understanding of large continental/ global changes that might be occurring now and in the near future. In general, continued emphasis on synthesizing information into a larger framework for streams and rivers will improve our overall understanding of the importance of organic matter in lotic ecosystems.

Polarization-Induced Hole Doping in Wide–Band-Gap Uniaxial Semiconductor Heterostructures

Abstract: Impurity-based p-type doping in wide-band-gap semiconductors is inefficient at room temperature for applications such as lasers because the positive-charge carriers (holes) have a large thermal activation energy. We demonstrate high-efficiency p-type doping by ionizing acceptor dopants using the built-in electronic polarization in bulk uniaxial semiconductor crystals. Because the mobile hole gases are field-ionized, they are robust to thermal freezeout effects and lead to major improvements in p-type electrical conductivity. The new doping technique results in improved optical emission efficiency in prototype ultraviolet light-emitting-diode structures. Polarization-induced doping provides an attractive solution to both p- and n-type doping problems in wide-band-gap semiconductors and offers an unconventional path for the development of solid-state deep-ultraviolet optoelectronic devices and wide-band-gap bipolar electronic devices of the future.

Searches for Lepton Flavor Violation in the Decays tau(+/-) -> e(+/-)gamma and tau(+/-) -> mu(+/-)gamma

Abstract: Searches for lepton-flavor-violating decays of a tau lepton to a lighter mass lepton and a photon have been performed with the entire data set of (963 +/- 7) x 10(6) tau decays collected by the BABAR detector near the Y(4S), Y(3S) and Y(2S) resonances. The searches yield no evidence of signals and we set upper limits on the branching fractions of B(tau(+/-) -> e(+/-)gamma) mu(+/-)gamma) < 4.4 X 10(-8) at 90% confidence level.

Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle

Abstract: As an obligatory parasite of humans, the body louse (Pediculus humanus humanus) is an important vector for human diseases, including epidemic typhus, relapsing fever, and trench fever. Here, we present genome sequences of the body louse and its primary bacterial endosymbiont Candidatus Riesia pediculicola. The body louse has the smallest known insect genome, spanning 108 Mb. Despite its status as an obligate parasite, it retains a remarkably complete basal insect repertoire of 10,773 protein-coding genes and 57 microRNAs. Representing hemimetabolous insects, the genome of the body louse thus provides a reference for studies of holometabolous insects. Compared with other insect genomes, the body louse genome contains significantly fewer genes associated with environmental sensing and response, including odorant and gustatory receptors and detoxifying enzymes. The unique architecture of the 18 minicircular mitochondrial chromosomes of the body louse may be linked to the loss of the gene encoding the mitochondrial single-stranded DNA binding protein. The genome of the obligatory louse endosymbiont Candidatus Riesia pediculicola encodes less than 600 genes on a short, linear chromosome and a circular plasmid. The plasmid harbors a unique arrangement of genes required for the synthesis of pantothenate, an essential vitamin deficient in the louse diet. The human body louse, its primary endosymbiont, and the bacterial pathogens that it vectors all possess genomes reduced in size compared with their free-living close relatives. Thus, the body louse genome project offers unique information and tools to use in advancing understanding of coevolution among vectors, symbionts, and pathogens.

Ionic Liquids for CO2 Capture and Emission Reduction

Abstract: Ionic liquids, especially those functionalized with amine groups, show significant potential for a wide variety of CO2 separations, including postcombustion CO2 capture. By tethering the amine to the anion, the stoichiometry of the reaction can be doubled from one CO2 for every two amines (as is the case with aqueous monoethanolamine) to one CO2 for each amine. Moreover, the reaction enthalpy can be actively tuned by the design of the anion, adjusting capacity and regeneration energy. In addition, ILs can be used without added water, further reducing the parasitic energy required for CO2 removal from flue gas.

Iterative Decoding Threshold Analysis for LDPC Convolutional Codes

Abstract: An iterative decoding threshold analysis for terminated regular LDPC convolutional (LDPCC) codes is presented. Using density evolution techniques, the convergence behavior of an iterative belief propagation decoder is analyzed for the binary erasure channel and the AWGN channel with binary inputs. It is shown that for a terminated LDPCC code ensemble, the thresholds are better than for corresponding regular and irregular LDPC block codes.

Transverse-Momentum and Pseudorapidity Distributions of Charged Hadrons in pp Collisions at root s=7 TeV

Abstract: Charged-hadron transverse-momentum and pseudorapidity distributions in proton-proton collisions at root s = 7 TeV are measured with the inner tracking system of the CMS detector at the LHC. The charged-hadron yield is obtained by counting the number of reconstructed hits, hit pairs, and fully reconstructed charged-particle tracks. The combination of the three methods gives a charged-particle multiplicity per unit of pseudorapidity dN(ch)/d eta vertical bar(vertical bar eta vertical bar<0.5) = 5.78 +/- 0.01(stat) +/- 0.23(stat) for non-single-diffractive events, higher than predicted by commonly used models. The relative increase in charged-particle multiplicity from root s = 0.9 to 7 TeV is [66.1 +/- 1.0(stat) +/- 4.2(syst)]%. The mean transverse momentum is measured to be 0.545 +/- 0.005(stat) +/- 0.015(syst) GeV/c. The results are compared with similar measurements at lower energies.

Sequencing of Culex quinquefasciatus Establishes a Platform for Mosquito Comparative Genomics

Abstract: Culex quinquefasciatus (the southern house mosquito) is an important mosquito vector of viruses such as West Nile virus and St. Louis encephalitis virus, as well as of nematodes that cause lymphatic filariasis. C. quinquefasciatus is one species within the Culex pipiens species complex and can be found throughout tropical and temperate climates of the world. The ability of C. quinquefasciatus to take blood meals from birds, livestock, and humans contributes to its ability to vector pathogens between species. Here, we describe the genomic sequence of C. quinquefasciatus: Its repertoire of 18,883 protein-coding genes is 22% larger than that of Aedes aegypti and 52% larger than that of Anopheles gambiae with multiple gene-family expansions, including olfactory and gustatory receptors, salivary gland genes, and genes associated with xenobiotic detoxification.

A primer on spatial modeling and analysis in wireless networks

Abstract: The performance of wireless networks depends critically on their spatial configuration, because received signal power and interference depend critically on the distances between numerous transmitters and receivers. This is particularly true in emerging network paradigms that may include femtocells, hotspots, relays, white space harvesters, and meshing approaches, which are often overlaid with traditional cellular networks. These heterogeneous approaches to providing high-capacity network access are characterized by randomly located nodes, irregularly deployed infrastructure, and uncertain spatial configurations due to factors like mobility and unplanned user-installed access points. This major shift is just beginning, and it requires new design approaches that are robust to spatial randomness, just as wireless links have long been designed to be robust to fading. The objective of this article is to illustrate the power of spatial models and analytical techniques in the design of wireless networks, and to provide an entry-level tutorial.

The Role of Proactive Personality in Job Satisfaction and Organizational Citizenship Behavior: A Relational Perspective

Abstract: Drawing from a relational approach, the authors conceptualize the quality of leader-member exchange as a mediator and procedural justice climate as a contextual moderator for understanding the role of proactive personality in job satisfaction and organizational citizenship behavior. Data from a sample of 200 Chinese employees within 54 work groups were used to examine the hypothesized models. Results show that having a proactive personality was associated with employees establishing a high-quality exchange relationship with their supervisors; in turn, the quality of leader-member exchange was associated with greater job satisfaction and more organizational citizenship behaviors. Additionally, the relationship between proactive personality and organizational citizenship behavior was positively moderated by procedural justice climate within the group. Implications for management theory and practice are discussed.

Cluster Algebras and Poisson Geometry

Abstract: Cluster algebras, introduced by Fomin and Zelevinsky in 2001, are commutative rings with unit and no zero divisors equipped with a distinguished family of generators (cluster variables) grouped in overlapping subsets (clusters) of the same cardinality (the rank of the cluster algebra) connected by exchange relations Examples of cluster algebras include coordinate rings of many algebraic varieties that play a prominent role in representation theory, invariant theory, the study of total positivity, etc The theory of cluster algebras has witnessed a spectacular growth, first and foremost due to the many links to a wide range of subjects including representation theory, discrete dynamical systems, Teichmuller theory, and commutative and non-commutative algebraic geometry This book is the first devoted to cluster algebras After presenting the necessary introductory material about Poisson geometry and Schubert varieties in the first two chapters, the authors introduce cluster algebras and prove their main properties in Chapter 3 This chapter can be viewed as a primer on the theory of cluster algebras In the remaining chapters, the emphasis is made on geometric aspects of the cluster algebra theory, in particular on its relations to Poisson geometry and to the theory of integrable systems|Cluster algebras, introduced by Fomin and Zelevinsky in 2001, are commutative rings with unit and no zero divisors equipped with a distinguished family of generators (cluster variables) grouped in overlapping subsets (clusters) of the same cardinality (the rank of the cluster algebra) connected by exchange relations Examples of cluster algebras include coordinate rings of many algebraic varieties that play a prominent role in representation theory, invariant theory, the study of total positivity, etc The theory of cluster algebras has witnessed a spectacular growth, first and foremost due to the many links to a wide range of subjects including representation theory, discrete dynamical systems, Teichmuller theory, and commutative and non-commutative algebraic geometry This book is the first devoted to cluster algebras After presenting the necessary introductory material about Poisson geometry and Schubert varieties in the first two chapters, the authors introduce cluster algebras and prove their main properties in Chapter 3 This chapter can be viewed as a primer on the theory of cluster algebras In the remaining chapters, the emphasis is made on geometric aspects of the cluster algebra theory, in particular on its relations to Poisson geometry and to the theory of integrable systems

FRVT 2006 and ICE 2006 Large-Scale Experimental Results

Abstract: This paper describes the large-scale experimental results from the Face Recognition Vendor Test (FRVT) 2006 and the Iris Challenge Evaluation (ICE) 2006. The FRVT 2006 looked at recognition from high-resolution still frontal face images and 3D face images, and measured performance for still frontal face images taken under controlled and uncontrolled illumination. The ICE 2006 evaluation reported verification performance for both left and right irises. The images in the ICE 2006 intentionally represent a broader range of quality than the ICE 2006 sensor would normally acquire. This includes images that did not pass the quality control software embedded in the sensor. The FRVT 2006 results from controlled still and 3D images document at least an order-of-magnitude improvement in recognition performance over the FRVT 2002. The FRVT 2006 and the ICE 2006 compared recognition performance from high-resolution still frontal face images, 3D face images, and the single-iris images. On the FRVT 2006 and the ICE 2006 data sets, recognition performance was comparable for high-resolution frontal face, 3D face, and the iris images. In an experiment comparing human and algorithms on matching face identity across changes in illumination on frontal face images, the best performing algorithms were more accurate than humans on unfamiliar faces.

Tailored TiO2-SrTiO3 heterostructure nanotube arrays for improved photoelectrochemical performance.

Abstract: TiO2 nanotube arrays formed on Ti substrate by electrochemical anodization have been converted into TiO2−SrTiO3 heterostructures by controlled substitution of Sr under hydrothermal conditions. The growth of SrTiO3 crystallites on the nanotube array electrode was probed by electron microscopy and X-ray diffraction. As the degree of Sr substitution increases with the duration of hydrothermal treatment, an increase in the size of SrTiO3 crystallites was observed. Consequently, with increasing SrTiO3 fraction in the TiO2−SrTiO3 nanotube arrays, we observed a shift in the flat band potential to more negative potentials, thus confirming the influence of SrTiO3 in the modification of the photoelectrochemical properties. The TiO2−SrTiO3 composite heterostructures obtained with 1 h or less hydrothermal treatment exhibit the best photoelectrochemical performance with nearly 100% increase in external quantum efficiency at 360 nm. The results presented here provide a convenient way to tailor the photoelectrochemical ...