bluuebunny/crossref_metadata_2025 huggingface dataset:
Roughness of fault surfaces over nine decades of length scales
Authors: Candela Thibault , Renard François , Klinger Yann , Mair Karen , Schmittbuhl Jean , Brodsky Emily E.
Published: June 2012

We report on the topographic roughness measurements of five exhumed faults and thirteen surface earthquake ruptures over a large range of scales: from 50 μm to 50 km. We used three scanner devices (LiDAR, laser profilometer, white light interferometer), spanning complementary scale ranges from 50 μm to 10 m, to measure the 3‐D topography of the same objects, i.e., five exhumed slip surfaces (Vuache‐Sillingy, Bolu, Corona Heights, Dixie Valley, Magnola). A consistent geometrical property, i.e., self‐affinity, emerges as the morphology of the slip surfaces shows at first order, a linear behavior on a log‐log plot where axes are fault roughness and spatial length scale, covering five decades of length‐scales. The observed fault roughness is scale dependent, with an anisotropic self‐affine behavior described by four parameters: two power law exponents H, constant among all the faults studied but slightly anisotropic (H∥ = 0.58 ± 0.07 in the slip direction and H⊥ = 0.81 ± 0.04 perpendicular to it), and two pre‐factors showing variability over the faults studied. For larger scales between 200 m and 50 km, we have analyzed the 2‐D roughness of the surface rupture of thirteen major continental earthquakes. These ruptures show geometrical properties consistent with the slip‐perpendicular behavior of the smaller‐scale measurements. Our analysis suggests that the inherent non‐alignment between the exposed traces and the along or normal slip direction results in sampling the slip‐perpendicular geometry. Although a data gap exists between the scanned fault scarps and rupture traces, the measurements are consistent within the error bars with a single geometrical description, i.e., consistent dimensionality, over nine decades of length scales.
A framework for using ant colony optimization to schedule environmental flow management alternatives for rivers, wetlands, and floodplains
Authors: Szemis J. M. , Maier H. R. , Dandy G. C.
Published: June 2012

Rivers, wetlands, and floodplains are in need of management as they have been altered from natural conditions and are at risk of vanishing because of river development. One method to mitigate these impacts involves the scheduling of environmental flow management alternatives (EFMA); however, this is a complex task as there are generally a large number of ecological assets (e.g., wetlands) that need to be considered, each with species with competing flow requirements. Hence, this problem evolves into an optimization problem to maximize an ecological benefit within constraints imposed by human needs and the physical layout of the system. This paper presents a novel optimization framework which uses ant colony optimization to enable optimal scheduling of EFMAs, given constraints on the environmental water that is available. This optimization algorithm is selected because, unlike other currently popular algorithms, it is able to account for all aspects of the problem. The approach is validated by comparing it to a heuristic approach, and its utility is demonstrated using a case study based on the Murray River in South Australia to investigate (1) the trade‐off between plant recruitment (i.e., promoting germination) and maintenance (i.e., maintaining habitat) flow requirements, (2) the trade‐off between flora and fauna flow requirements, and (3) a hydrograph inversion case. The results demonstrate the usefulness and flexibility of the proposed framework as it is able to determine EFMA schedules that provide optimal or near‐optimal trade‐offs between the competing needs of species under a range of operating conditions and valuable insight for managers.
An apparent “vital effect” of calcification rate on the Sr/Ca temperature proxy in the reef coral Montipora capitata
Authors: Kuffner Ilsa B. , Jokiel Paul L. , Rodgers Ku'ulei S. , Andersson Andreas J. , Mackenzie Fred T.
Published: June 2012

Measuring the strontium to calcium ratio in coral skeletons reveals information on seawater temperatures during skeletal deposition, but studies have shown additional variables may affect the ratio. Here we measured Sr/Ca in the reef coral Montipora capitata grown in six mesocosms continuously supplied with seawater from the adjacent reef flat. Three mesocosms were ambient controls, and three had seawater chemistry simulating “ocean acidification” (OA). We found that Sr/Ca was not affected by the OA treatment and neither was coral calcification for these small colonies (larger colonies did show an OA effect). The lack of OA effects allowed us to test the hypothesis that coral growth rate can affect Sr/Ca using the natural range in calcification rates of the corals grown at the same temperature. We found that Sr/Ca was inversely related to calcification rate (Sr/Ca = 9.385 − 0.0040 (calcification rate)). Using a previously published calibration curve for this species, a 22 mg d−1 colony−1increase in calcification rate introduced a 1°C warmer temperature estimate, with the 27 corals reporting “temperatures” ranging from 24.9 to 28.9°C, with mean 26.6 ± 0.9°C standard deviation. Our results lend support to hypotheses invoking kinetic processes and growth rate to explain vital effects on Sr/Ca. However, uncertainty in the slope of the regression of Sr/Ca on calcification and a low R‐squared value lead us to conclude that Sr/Ca could still be a useful proxy in this species given sufficient replication or by including growth rate in the calibration.
A method for disentangling El Niño–mean state interaction
Authors: Watanabe Masahiro , Wittenberg Andrew T.
Published: June 2012

The amplitude of the El Niño‐Southern Oscillation (ENSO) is known to fluctuate in long records derived from observations and general circulation models (GCMs), even when driven by constant external forcings. This involves an interaction between the ENSO cycle and the background mean state, which affects the climatological precipitation over the eastern equatorial Pacific. The changes in climatological rainfall may be ascribed to several factors: changes in mean sea surface temperature (SST), changes in SST variability, and changes in the sensitivity of precipitation to SST. We propose a method to separate these effects in model ensembles. A case study with a single GCM demonstrates that the method works well, and suggests that each factor plays a role in changing mean precipitation. Applying the method to 16 pre‐industrial control simulations archived in the Coupled Model Intercomparison Project phase 5 (CMIP5) reveals that the inter‐model diversity in mean precipitation arises mostly from differences in the mean SST and atmospheric sensitivity to SST, rather than from differences in ENSO amplitude.
Punctuated global tropical cyclone activity over the past 5,000 years
Authors: Nott Jonathan , Forsyth Anthony
Published: June 2012

There are now a substantial number of millennial scale records of tropical cyclones from a variety of locations globally. Some of these, such as those in the Atlantic and Gulf of Mexico, show patterns of long‐term, generally intense, tropical cyclone (TC) behaviour that have been suggested to be due to either variations in ENSO or shifts in the position of the Atlantic High pressure system and the jet stream. Comparisons are made here of the sedimentary overwash records from the Gulf of Mexico and Atlantic Ocean Basin with the overwash records from the north‐west Pacific and beach ridge records from the south‐west Pacific and south east Indian Ocean basins. There is a substantial degree of synchroneity in global intense TC behaviour over the past 3,000 to 5,000 years. One of the most striking aspects of these records is they all display extended alternating periods (centuries to millennia) of relative quiescence and heightened intense TC activity irrespective of both the resolution and type of long‐term TC record. The cause(s) of this punctuated activity are at present difficult to identify but are likely exogenic in origin rather than due to an intrinsic aspect of the records or the methods used to derive them. The identification of punctuated global long‐term TC behaviour is important for understanding future TC activity and for assessing risk to coastal communities.
Modulation of plasmaspheric hiss intensity by thermal plasma density structure
Authors: Chen Lunjin , Thorne Richard M. , Li Wen , Bortnik Jacob , Turner Drew , Angelopoulos Vassilis
Published: June 2012

Plasmaspheric hiss is an electromagnetic whistler‐mode emission confined to high density regions such as the plasmasphere and plasmaspheric plumes. We present a dayside THEMIS event showing that the hiss emission intensity is strongly modulated by thermal plasma density variations. The calculated local growth rate is small (less than 5 dB/RE) and increases as the plasma density increases, which partly accounts for the modulation. Ray tracing shows that chorus rays, which eventually evolve into plasmaspheric hiss, are focused towards field lines of higher density and defocused away from field lines of lower density. We suggest that the observed modulation is caused by a combined effect of local cyclotron resonant amplification together with ray focusing during propagation.
Crystals stirred up: 1. Direct numerical simulations of crystal settling in nondilute magmatic suspensions
Authors: Suckale Jenny , Sethian James A. , Yu Jiun‐der , Elkins‐Tanton Linda T.
Published: June 2012

This is the first paper in a two‐part series examining the fluid dynamics of crystal settling and flotation in the lunar magma ocean. A key challenge in constraining solidification processes is determining the ability of individual crystals to decouple from vigorous thermal convection and settle out or float. The goal of this paper is to develop a computational methodology capable of capturing the complex solid‐fluid interactions that determine settling and flotation. In the second paper, we use this computational approach to explore the conditions under which plagioclase feldspar would be able to buoyantly float and form the earliest crust on the Moon. The direct numerical method described in this paper relies on a fictitious domain approach and captures solid‐body motion in 2D and 3D with little overhead beyond single fluid calculations. The two main innovations of our numerical implementation of a fictitious domain approach are an analytical quadrature scheme, which increases accuracy and reduces computational expense, and the derivation of a multibody collision scheme. Advantages of this approach over previous simulations of crystal‐bearing magmatic suspensions include the following: (1) we fully resolve the two‐way interaction between fluid and solid phases, implying that crystals are not only passively advected in an ambient flow field but are also actively driving flow, and (2) we resolve the flow around each individual crystal without assuming specific settling speeds or drag coefficients. We present several benchmark problems and convergence tests to validate our approach.
Extreme rainfall in West Africa: A regional modeling
Authors: Panthou G. , Vischel T. , Lebel T. , Blanchet J. , Quantin G. , Ali A.
Published: June 2012

In a world of increasing exposure of populations to natural hazards, the mapping of extreme rainfall remains a key subject of study. Such maps are required for both flood risk management and civil engineering structure design, the challenge being to take into account the local information provided by point rainfall series as well as the necessity of some regional coherency. Two approaches based on the extreme value theory are compared here, with an application to extreme rainfall mapping in West Africa. The first approach is a local fit and interpolation (LFI) consisting of a spatial interpolation of the generalized extreme value (GEV) distribution parameters estimated independently at each station. The second approach is a spatial maximum likelihood estimation (SMLE); it directly estimates the GEV distribution over the entire region by a single maximum likelihood fit using jointly all measurements combined with spatial covariates. Five LFI and three SMLE methods are considered, using the information provided by 126 daily rainfall series covering the period 1950–1990. The methods are first evaluated in calibration. Then the predictive skills and the robustness are assessed through a cross validation and an independent network validation process. The SMLE approach, especially when using the mean annual rainfall as covariate, appears to perform better for most of the scores computed. Using the Niamey 104 year time series, it is also shown that the SMLE approach has the capacity to deal more efficiently with the effect of local outliers by using the spatial information provided by nearby stations.
Axially coordinated chiral salen Mn(iii) anchored onto azole onium modified ZnPS-PVPA as effective catalysts for asymmetric epoxidation of unfunctionalized olefins
Authors: Huang Jing , Fu Xiangkai , Wang Gang , Miao Qiang , Wang Guomin
Published: June 2012

The asymmetric epoxidation of α-methylstyrene catalyzed by chiral salen Mn(iii) catalyst immobilized in nanopores.
Calcium sensing receptor regulates cardiomyocyte function through nuclear calcium
Authors: Zhong Xin , Liu Jun , Lu Fanghao , Wang Yuwen , Zhao Yajun , Dong Shiyun , Leng Xiaoning , Jia Jing , Ren Huan , Xu Changqing , Zhang Weihua
Published: June 2012

Nuclear Ca2+ plays a pivotal role in the regulation of gene expression. IP3 (inositol‐1,4,5‐trisphosphate) is an important regulator of nuclear Ca2+. We hypothesized that the CaR (calcium sensing receptor) stimulates nuclear Ca2+ release through IICR (IP3‐induced calcium release) from perinuclear stores. Spontaneous Ca2+ oscillations and the spark frequency of nuclear Ca2+ were measured simultaneously in NRVMs (neonatal rat ventricular myocytes) using confocal imaging. CaR‐induced nuclear Ca2+ release through IICR was abolished by inhibition of CaR and IP3Rs (IP3 receptors). However, no effect on the inhibition of RyRs (ryanodine receptors) was detected. The results suggest that CaR specifically modulates nuclear Ca2+ signalling through the IP3R pathway. Interestingly, nuclear Ca2+ was released from perinuclear stores by CaR activator‐induced cardiomyocyte hypertrophy through the Ca2+‐dependent phosphatase CaN (calcineurin)/NFAT (nuclear factor of activated T‐cells) pathway. We have also demonstrated that the activation of the CaR increased the NRVM protein content, enlarged cell size and stimulated CaN expression and NFAT nuclear translocation in NRVMs. Thus, CaR enhances the nuclear Ca2+ transient in NRVMs by increasing fractional Ca2+ release from perinuclear stores, which is involved in cardiac hypertrophy through the CaN/NFAT pathway.
Isotropic–nematic phase transition in the Lebwohl–Lasher model from density of states simulations
Authors: Shekhar Raj , Whitmer Jonathan K. , Malshe Rohit , Moreno-Razo J. A. , Roberts Tyler F. , de Pablo Juan J.
Published: June 2012

Density of states Monte Carlo simulations have been performed to study the isotropic–nematic (IN) transition of the Lebwohl–Lasher model for liquid crystals. The IN transition temperature was calculated as a function of system size using expanded ensemble density of states simulations with histogram reweighting. The IN temperature for infinite system size was obtained by extrapolation of three independent measures. A subsequent analysis of the kinetics in the model showed that the transition occurs via spinodal decomposition through aggregation of clusters of liquid crystal molecules.
Electron attachment to antipyretics: Possible implications of their metabolic pathways
Authors: Pshenichnyuk Stanislav A. , Modelli Alberto
Published: June 2012

The empty-level structures and formation of negative ion states via resonance attachment of low-energy (0–15 eV) electrons into vacant molecular orbitals in a series of non-steroidal anti-inflammatory drugs (NSAIDs), namely aspirin, paracetamol, phenacetin, and ibuprofen, were investigated in vacuo by electron transmission and dissociative electron attachment (DEA) spectroscopies, with the aim to model the behavior of these antipyretic agents under reductive conditions in vivo. The experimental findings are interpreted with the support of density functional theory calculations. The negative and neutral fragments formed by DEA in the gas phase display similarities with the main metabolites of these commonly used NSAIDs generated in vivo by the action of cytochrome P450 enzymes, as well as with several known active agents. It is concluded that xenobiotic molecules which possess pronounced electron-accepting properties could in principle follow metabolic pathways which parallel the gas-phase dissociative decay channels observed in the DEA spectra at incident electron energies below 1 eV. Unwanted side effects as, e.g., hepatoxicity or carcinogenicity produced by the NSAIDs under study in human organism are discussed within the “free radical model” framework, reported earlier to describe the toxic action of the well-known model toxicant carbon tetrachloride.
Interactive multiobjective daily volt/var control of distribution networks considering wind power and fuel-cell power plants
Authors: Niknam Taher , Zare Mohsen , Aghaei Jamshid , Azizipanah-Abarghooee Rasoul
Published: June 2012

This paper deals with a multiobjective daily volt/var control (MDVVC) for radial distribution feeders integrated renewable energy sources (RES) by means of the tap position of the under load tap changer (ULTC) transformers, shunt capacitors, and active and reactive power of RES. The multiple objective functions to be minimized are the electrical energy losses, the voltage deviations, and the total emissions of RES and substations. Discrete behavior of equipments in the distribution systems and nonlinear power flow equations change the VVC problem into a mixed integer non-linear programming (MINLP). Hence, a new optimization method based upon the shuffled frog leaping algorithm (SFLA) is presented to solve the optimization problem. The SFLA is modified for resolving the disadvantages of the original algorithm. Besides of accurately passing local optima, the MSFLA takes less time to achieve the optimal response. Furthermore, the tribe-MSFLA is proposed through using the concept of the tribe. Dealing with the multiobjective optimization problem, an interactive fuzzy satisfying method is used while the objective functions are formulated by a fuzzy set theory. An 85-bus radial distribution system is used to test and assess the performance of the proposed algorithm.
First principles calculation of the electronic properties and lattice dynamics of Cu2ZnSn(S1−xSex)4
Authors: Khare Ankur , Himmetoglu Burak , Cococcioni Matteo , Aydil Eray S.
Published: June 2012

Using density functional theory, we calculated the electronic structure, the lattice dynamics, and the Raman spectra of Cu2ZnSn(S1−xSex)4, (CZTSSe) an emerging photovoltaic material for thin-film solar cells. In particular, we investigated the effects of the local arrangement of S and Se within the unit cell on the electronic properties of these materials. We find that the S-to-Se ratio (e.g., x) and the spatial distribution of the anions in the unit cell can significantly alter the band structure. In particular, the S-to-Se ratio and anion distribution determine the energy splitting between the electronic states at the top of the valence band and the hole mobility in CZTSSe alloys and solar cells. Moreover, we find that x-ray diffraction patterns and phonon dispersion curves are sensitive to the local anion ordering. The predicted Raman scattering frequencies and their variation with x agree with experimentally determined values and trends.
Molecular dynamics simulation of Si nanoclusters in high rate and low temperature epitaxy
Authors: Chen L. W. , Shibuta Y. , Kambara M. , Yoshida T.
Published: June 2012

Si nanocluster formation during rapid cooling from high temperature Si vapors and its subsequent interaction with substrate was simulated by molecular dynamics. It was confirmed that several nm sized clusters with a loosely bound structure form during rapid cooling and their metastable structures are retained even at temperatures below the Si melting point. Such globular clusters tend to rearrange themselves upon impingement to be a similar structure to that of the substrate, at least near the cluster/substrate interface. This is suggestive of the role of clusters formed under the mesoplasma condition as growth precursors for fast rate epitaxy.
Real-time digital compensation to reduce acceleration's sensitivity in quartz resonator
Authors: Qingxiao Shan , Jun Yang , Jianyun Chen , Longzhe Ji , Feijiang Huang
Published: June 2012

The paper presents a digital compensator imposing real-time voltage to compensate the frequency offset of quartz resonator under acceleration. To begin with, a triple-axis MEMS acceleration sensor, whose package is less than 3 mm × 3 mm × 0.9 mm, is mounted at the bottom of quartz resonator. Then acceleration sensitivity vector, based on sensor's coordinator, can be calculated by imposing sinusoidal vibration on singular axis and measuring the amplitude of sideband. So, the frequency offset can be calculated and the compensate value can also be inferred. A digital circuit is designed to generate compensate voltage real time to counteract the frequency offset. A FPGA is employed, which can realize computation in one clock period. Experiments show that the digital compensator presented here has a good effect at low frequency vibration just at which mechanical cushion is ineffective. At steady state, it can almost eliminate the frequency offset. Because of the integration and miniaturization of digital elements, the whole compensator is flexible, low cost, and easy to be applied.
Spin resolved conductance in semiconductor mesoscopic rings: not spin gate response
Authors: Heidari Semiromi Ebrahim
Published: June 2012

Based on the equilibrium Green’s function formalism, we study the spin resolved conductance in a semiconductor mesoscopic ring when it bridges two source and drain electrodes. Effects of Rashba spin-orbit interaction (RSOI) and Dresselhaus spin-orbit interaction (DSOI) on the spin transport is taken into account. It is shown that complete spin inversion can occur in the presence of RSOI and/or DSOI and in the absence of applied magnetic field threading the ring. Results of this study can be used to designing a perfect not spin gate or spin inverter. We have also investigated the effects of a tunnel barrier and of asymmetric relative positions of incoming and outgoing electrodes on the spin resolved conductance and spin inversion effect.
Spin-torque microwave detector with out-of-plane precessing magnetic moment
Authors: Prokopenko O. V. , Krivorotov I. N. , Bankowski E. , Meitzler T. , Jaroch S. , Tiberkevich V. S. , Slavin A. N.
Published: June 2012

Operation of a spin-torque microwave detector (STMD) in a weak perpendicular bias magnetic field has been studied theoretically. It is shown that in this geometry a novel dynamical regime of STMD operation, characterized by large-angle out-of-plane magnetization precession, can be realized. The excitation of the large-angle precession has threshold character and is possible only for input microwave currents exceeding a certain frequency-dependent critical value. The output voltage of an STMD increases with the frequency of the input signal but is virtually independent of its power. An STMD working in the regime of large-amplitude out-of-plane precession functions as a non-resonant threshold detector of low frequency microwave signals, due to the large nonlinear shift of its operating frequency. Therefore, it is particularly suitable for applications in microwave energy harvesting.
Implementation of an in-vessel calibration light source for JET
Authors: Biewer T. M. , Belcher C. , Hassall I. , Hillis D. L. , Kaveney G. , Scharpf D. , Stamp M. F. , Stunell C. , Zastrow K.-D. ,   JET-EFDA Contributors
Published: June 2012

An in-vessel calibration light source (ICLS) has been implemented for remote use during extended shutdown periods of the Joint European Torus (JET). The ICLS facilitated the in situ calibration of optical diagnostics, which previously were performed when the diagnostics were removed from JET. Since the ICLS is used to calibrate diagnostics over the entire, exact optical path as used when plasma discharge data are measured, the ICLS calibration implicitly accounts for any vignetting losses in the JET vessel viewports in addition to the vacuum window transmission. At least ten diagnostic systems have benefited from the ICLS during the extended ITER-like wall shutdown of 2009–2011. Examples of the use of the ICLS in JET are given.
Development of an in situ magnetoelastic magneto-optical Kerr effect magnetometer
Authors: Will I. G. , Ding A. , Xu Y. B.
Published: June 2012

Reported here is the development and implementation of an integrated in situ magnetoelastic measurement setup with a MOKE magnetometer, repositionable electromagnet, and sample transfer/straining device. The former were used within a molecular beam epitaxial vacuum growth chamber. Consequently the magnetostriction constants for both Cr capped and uncapped Fe/GaAs(100) films were acquired without film oxidization occurring. Samples were bent in a four point bending geometry to produce a quantifiable tensile mechanical strain on the films during magnetoelastic measurements. In addition, a laser measurement system was developed to confirm the induced strain in the samples.
High sensitivity, low noise Mirnov coil array on Prairie View rotamak
Authors: Yang X. , Houshmandyar S. , Dada O. , Reddic E. , Huang T. S.
Published: June 2012

An array of 32 Mirnov coils with novel features of high sensitivity and low noise has been installed on the outside chamber surface of Prairie View rotamak. This BR-oriented coil array has proven to be very reliable in the plasma driven by rotating magnetic field; it can resolve magnetic perturbation signals of 0.1 G. With this new diagnostic, the n = 1 tilt, radial shift, and kink modes are observed for the first time in rotamak plasmas.
Magnetic anisotropy in ordered textured Co nanowires
Authors: Vivas L. G. , Escrig J. , Trabada D. G. , Badini-Confalonieri G. A. , Vázquez M.
Published: June 2012

The magnetization reversal in ordered arrays of Co nanowires with tailored hcp-phase texture, controlled by pH synthesis and nanowires length, has been investigated. The angular dependence of coercivity has been experimentally determined for different crystal textures, and the corresponding magnetization reversal mode is interpreted by analytical modelling. The results show that reversal takes place by propagation of a transverse-like domain wall mode. The fitting of experimental and calculated data allows us the quantitative evaluation of the magnetocrystalline anisotropy constant strength whose magnetization easy direction evolves from parallel to the wires toward in-plane orientation with the change of hcp-phase texture.
High-temperature gold metallization for ZnO nanowire device on a SiC substrate
Authors: Gurwitz Ron , Tuboul Guy , Shikler Boaz , Shalish Ilan
Published: June 2012

Gold is commonly used nowadays in metal contacts to nanowire devices. Due to their small size, nanowire devices often get heat up enough to cause a reaction of the contact and substrate, whether during operation or as a result of a spontaneous pulse of an electrostatic discharge. In most cases, the point of failure is the metallization, as is the case studied here. Gold is useful not only for its good electrical conductance but also because it is a good heat conductor and inert to the ambient. To improve the survivability of a gold metallization for nanowire devices incorporating ZnO nanowire atop a SiC substrate, we used a sputter-deposited Ti-Si-N ternary diffusion barrier layer and a Ti adhesion layer between the top gold layer and a 4H-SiC substrate that survives 30 min of vacuum annealing at 850 °C and 5 days of annealing at 500 °C in Ar. Rutherford backscattering spectrometry and x-ray photoelectron spectroscopy were used to test the integrity of the layers before and after annealing both with and without the diffusion barrier. Current-voltage characteristics were measured up to 75 V in air to test the metallization.
First-principles insights on the magnetism of cubic SrTi1−xCoxO3−δ
Authors: Florez J. M. , Ong S. P. , Onbaşli M. C. , Dionne G. F. , Vargas P. , Ceder G. , Ross C. A.
Published: June 2012

We present hybrid density functional calculations suggesting that magnetism in cubic SrTi1−xCoxO3−δ (STCO) with x = 0.25 is sensitive to the nearest neighbor arrangement of the Co and the presence of oxygen vacancies. Spin polarized calculations for x = 0.25 in which the nearest neighbor (nn) Co spacing is a, 2a or 3a with a the lattice parameter predict lowest energies for the 2a nn separation and favor the ferromagnetic state. Oxygen deficiency (δ=0.125) lowers the average Co valence state and favors mixed valence and spin states (high spin for the Co adjacent to the vacancy and low for the non-adjacent Co), an increase of the band gap and an expansion of the lattice parameter compared to stoichiometric STCO in which both Co ions are low spin. Predicted configurations of the two neighboring Co ions are (t2g5eg0, t2g5eg0) and (t2g4eg2, t2g6eg0) with average 1.0 and 1.6 μB/Co for stoichiometric and 1-O-vacancy systems, respectively.
Minimizing interfacial losses in inverted organic solar cells comprising Al-doped ZnO
Authors: Gadisa Abay , Liu Yingchi , Samulski Edward T. , Lopez Rene
Published: June 2012

We demonstrated a 35% enhancement in the efficiency of inverted solar cells as a result of increased open-circuit voltage and fill factor by adsorbing an ultrathin layer of a ruthenium dye N719 on an aluminum-doped zinc oxide (ZnO-Al) electron collecting interfacial layer. The interface modification with N719 changes the charge injection levels as indicated by ultraviolet photoemission spectroscopy. The efficiency of inverted solar cells comprising a bulk heterojunction photo-active film of poly(3-hexylthiophene) and phenyl-C61-butyric acid methyl ester has increased from ∼2.80% to 3.80% upon employing the dye modification of the electrode interface.
Single GaInP nanowire p-i-n junctions near the direct to indirect bandgap crossover point
Authors: Wallentin Jesper , Barrutia Poncela Laura , Jansson Anna M. , Mergenthaler Kilian , Ek Martin , Jacobsson Daniel , Reine Wallenberg L. , Deppert Knut , Samuelson Lars , Hessman Dan , Borgström Magnus T.
Published: June 2012

Axially defined GaInP single nanowire (NW) p-i-n junctions are demonstrated, with photocurrent response and yellow-green electroluminescence near the indirect bandgap crossover point at 2.18 eV (569 nm). We use DEZn and H2S as p- and n-type dopants, and find that they both affect the material composition and the crystal structure. The photovoltaic efficiency is comparable to single NW devices from binary III-V materials. These results demonstrate the potential of GaInP nanowires as a high-bandgap material for multijunction solar cells and light-emitting devices in the visible regime.
The occludin and ZO-1 complex, defined by small angle X-ray scattering and NMR, has implications for modulating tight junction permeability
Authors: Tash Brian R. , Bewley Maria C. , Russo Mariano , Keil Jason M. , Griffin Kathleen A. , Sundstrom Jeffrey M. , Antonetti David A. , Tian Fang , Flanagan John M.
Published: June 2012

Tight junctions (TJs) are dynamic cellular structures that are critical for compartmentalizing environments within tissues and regulating transport of small molecules, ions, and fluids. Phosphorylation-dependent binding of the transmembrane protein occludin to the structural organizing protein ZO-1 contributes to the regulation of barrier properties; however, the details of their interaction are controversial. Using small angle X-ray scattering (SAXS), NMR chemical shift perturbation, cross-saturation, in vitro binding, and site-directed mutagenesis experiments. we define the interface between the ZO-1 PDZ3-SH3-U5-GuK (PSG) and occludin coiled-coil (CC) domains. The interface is comprised of basic residues in PSG and an acidic region in CC. Complex formation is blocked by a peptide (REESEEYM) that corresponds to CC residues 468–475 and includes a previously uncharacterized phosphosite, with the phosphorylated version having a larger effect. Furthermore, mutation of E470 and E472 reduces cell border localization of occludin. Together, these results localize the interaction to an acidic region in CC and a predominantly basic helix V within the ZO-1 GuK domain. This model has important implications for the phosphorylation-dependent regulation of the occludin∶ZO-1 complex.
Mouse model of endemic Burkitt translocations reveals the long-range boundaries of
Ig
-mediated oncogene deregulation
Authors: Kovalchuk Alexander L. , Ansarah-Sobrinho Camilo , Hakim Ofir , Resch Wolfgang , Tolarová Helena , Dubois Wendy , Yamane Arito , Takizawa Makiko , Klein Isaac , Hager Gordon L. , Morse Herbert C. , Potter Michael , Nussenzweig Michel C. , Casellas Rafael
Published: June 2012

Human Burkitt lymphomas are divided into two main clinical variants: the
endemic
form, affecting African children infected with malaria and the Epstein-Barr virus, and the
sporadic
form, distributed across the rest of the world. However, whereas
sporadic
translocations decapitate
Myc
from 5′ proximal regulatory elements, most endemic events occur hundreds of kilobases away from
Myc
. The origin of these rearrangements and how they deregulate oncogenes at such distances remain unclear. We here recapitulate endemic Burkitt lymphoma-like translocations in plasmacytomas from uracil
N
-glycosylase and activation-induced cytidine deaminase-deficient mice. Mapping of translocation breakpoints using an acetylated histone H3 lysine 9 chromatin immunoprecipitation sequencing approach reveals
Igh
fusions up to ∼350 kb upstream of
Myc
or the related oncogene
Mycn
. A comprehensive analysis of epigenetic marks, PolII recruitment, and transcription in tumor cells demonstrates that the 3′
Igh
enhancer (Eα) vastly remodels ∼450 kb of chromatin into translocated sequences, leading to significant polymerase occupancy and constitutive oncogene expression. We show that this long-range epigenetic reprogramming is directly proportional to the physical interaction of Eα with translocated sites. Our studies thus uncover the extent of epigenetic remodeling by
Ig
3′ enhancers and provide a rationale for the long-range deregulation of translocated oncogenes in endemic Burkitt lymphomas. The data also shed light on the origin of endemic-like chromosomal rearrangements.
Small molecule perimeter defense in entomopathogenic bacteria
Authors: Crawford Jason M. , Portmann Cyril , Zhang Xu , Roeffaers Maarten B. J. , Clardy Jon
Published: June 2012

Two Gram-negative insect pathogens,
Xenorhabdus nematophila
and
Photorhabdus luminescens
, produce rhabduscin, an amidoglycosyl- and vinyl-isonitrile-functionalized tyrosine derivative. Heterologous expression of the rhabduscin pathway in
Escherichia coli
, precursor-directed biosynthesis of rhabduscin analogs, biochemical assays, and visualization using both stimulated Raman scattering and confocal fluorescence microscopy established rhabduscin’s role as a potent nanomolar-level inhibitor of phenoloxidase, a key component of the insect’s innate immune system, as well as rhabduscin’s localization at the bacterial cell surface. Stimulated Raman scattering microscopy visualized rhabduscin at the periphery of wild-type
X. nematophila
cells and
E. coli
cells heterologously expressing the rhabduscin pathway. Precursor-directed biosynthesis created rhabduscin mimics in
X. nematophila
pathway mutants that could be accessed at the bacterial cell surface by an extracellular bioorthogonal probe, as judged by confocal fluorescence microscopy. Biochemical assays using both wild-type and mutant
X. nematophila
cells showed that rhabduscin was necessary and sufficient for potent inhibition (low nM) of phenoloxidases, the enzymes responsible for producing melanin (the hard black polymer insects generate to seal off microbial pathogens). These observations suggest a model in which rhabduscin’s physical association at the bacterial cell surface provides a highly effective inhibitor concentration directly at the site of phenoloxidase contact. This class of molecules is not limited to insect pathogens, as the human pathogen
Vibrio cholerae
also encodes rhabduscin’s aglycone, and bacterial cell-coated immunosuppressants could be a general strategy to combat host defenses.
Aquaglyceroporin 2 controls susceptibility to melarsoprol and pentamidine in African trypanosomes
Authors: Baker Nicola , Glover Lucy , Munday Jane C. , Aguinaga Andrés David , Barrett Michael P. , de Koning Harry P. , Horn David
Published: June 2012

African trypanosomes cause sleeping sickness in humans, a disease that is typically fatal without chemotherapy. Unfortunately, drug resistance is common and melarsoprol-resistant trypanosomes often display cross-resistance to pentamidine. Although melarsoprol/pentamidine cross-resistance (MPXR) has been an area of intense interest for several decades, our understanding of the underlying mechanisms remains incomplete. Recently, a locus encoding two closely related aquaglyceroporins, AQP2 and AQP3, was linked to MPXR in a high-throughput loss-of-function screen. Here, we show that AQP2 has an unconventional “selectivity filter.”
AQP2
-specific gene knockout generated MPXR trypanosomes but did not affect resistance to a lipophilic arsenical, whereas recombinant
AQP2
reversed MPXR in cells lacking native
AQP2
and
AQP3
.
AQP2
was also shown to be disrupted in a laboratory-selected MPXR strain. Both AQP2 and AQP3 gained access to the surface plasma membrane in insect life-cycle–stage trypanosomes but, remarkably, AQP2 was specifically restricted to the flagellar pocket in the bloodstream stage. We conclude that the unconventional aquaglyceroporin, AQP2, renders cells sensitive to both melarsoprol and pentamidine and that loss of AQP2 function could explain cases of innate and acquired MPXR.
ZmCCT
and the genetic basis of day-length adaptation underlying the postdomestication spread of maize
Authors: Hung Hsiao-Yi , Shannon Laura M. , Tian Feng , Bradbury Peter J. , Chen Charles , Flint-Garcia Sherry A. , McMullen Michael D. , Ware Doreen , Buckler Edward S. , Doebley John F. , Holland James B.
Published: June 2012

Teosinte, the progenitor of maize, is restricted to tropical environments in Mexico and Central America. The pre-Columbian spread of maize from its center of origin in tropical Southern Mexico to the higher latitudes of the Americas required postdomestication selection for adaptation to longer day lengths. Flowering time of teosinte and tropical maize is delayed under long day lengths, whereas temperate maize evolved a reduced sensitivity to photoperiod. We measured flowering time of the maize nested association and diverse association mapping panels in the field under both short and long day lengths, and of a maize-teosinte mapping population under long day lengths. Flowering time in maize is a complex trait affected by many genes and the environment. Photoperiod response is one component of flowering time involving a subset of flowering time genes whose effects are strongly influenced by day length. Genome-wide association and targeted high-resolution linkage mapping identified
ZmCCT
, a homologue of the rice photoperiod response regulator
Ghd7,
as the most important gene affecting photoperiod response in maize. Under long day lengths
ZmCCT
alleles from diverse teosintes are consistently expressed at higher levels and confer later flowering than temperate maize alleles. Many maize inbred lines, including some adapted to tropical regions, carry
ZmCCT
alleles with no sensitivity to day length. Indigenous farmers of the Americas were remarkably successful at selecting on genetic variation at key genes affecting the photoperiod response to create maize varieties adapted to vastly diverse environments despite the hindrance of the geographic axis of the Americas and the complex genetic control of flowering time.
Very high-temperature impact melt products as evidence for cosmic airbursts and impacts 12,900 years ago
Authors: Bunch Ted E. , Hermes Robert E. , Moore Andrew M.T. , Kennett Douglas J. , Weaver James C. , Wittke James H. , DeCarli Paul S. , Bischoff James L. , Hillman Gordon C. , Howard George A. , Kimbel David R. , Kletetschka Gunther , Lipo Carl P. , Sakai Sachiko , Revay Zsolt , West Allen , Firestone Richard B. , Kennett James P.
Published: June 2012

It has been proposed that fragments of an asteroid or comet impacted Earth, deposited silica-and iron-rich microspherules and other proxies across several continents, and triggered the Younger Dryas cooling episode 12,900 years ago. Although many independent groups have confirmed the impact evidence, the hypothesis remains controversial because some groups have failed to do so. We examined sediment sequences from 18 dated Younger Dryas boundary (YDB) sites across three continents (North America, Europe, and Asia), spanning 12,000 km around nearly one-third of the planet. All sites display abundant microspherules in the YDB with none or few above and below. In addition, three sites (Abu Hureyra, Syria; Melrose, Pennsylvania; and Blackville, South Carolina) display vesicular, high-temperature, siliceous scoria-like objects, or SLOs, that match the spherules geochemically. We compared YDB objects with melt products from a known cosmic impact (Meteor Crater, Arizona) and from the 1945 Trinity nuclear airburst in Socorro, New Mexico, and found that all of these high-energy events produced material that is geochemically and morphologically comparable, including: (i) high-temperature, rapidly quenched microspherules and SLOs; (ii) corundum, mullite, and suessite (Fe3Si), a rare meteoritic mineral that forms under high temperatures; (iii) melted SiO2glass, or lechatelierite, with flow textures (or schlieren) that form at > 2,200 °C; and (iv) particles with features indicative of high-energy interparticle collisions. These results are inconsistent with anthropogenic, volcanic, authigenic, and cosmic materials, yet consistent with cosmic ejecta, supporting the hypothesis of extraterrestrial airbursts/impacts 12,900 years ago. The wide geographic distribution of SLOs is consistent with multiple impactors.
Amyloid precursor protein (APP) traffics from the cell surface via endosomes for amyloid β (Aβ) production in the
trans
-Golgi network
Authors: Choy Regina Wai-Yan , Cheng Zhiliang , Schekman Randy
Published: June 2012

Amyloid precursor protein (APP) is processed sequentially by the β-site APP cleaving enzyme and γ-secretase to generate amyloid β (Aβ) peptides, one of the hallmarks of Alzheimer’s disease. The intracellular location of Aβ production—endosomes or the
trans
-Golgi network (TGN)—remains uncertain. We investigated the role of different postendocytic trafficking events in Aβ
40
production using an RNAi approach. Depletion of Hrs and Tsg101, acting early in the multivesicular body pathway, retained APP in early endosomes and reduced Aβ
40
production. Conversely, depletion of CHMP6 and VPS4, acting late in the pathway, rerouted endosomal APP to the TGN for enhanced APP processing. We found that VPS35 (retromer)-mediated APP recycling to the TGN was required for efficient Aβ
40
production. An interruption of the bidirectional trafficking of APP between the TGN and endosomes, particularly retromer-mediated retrieval of APP from early endosomes to the TGN, resulted in the accumulation of endocytosed APP in early endosomes with reduced APP processing. These data suggest that Aβ
40
is generated predominantly in the TGN, relying on an endocytosed pool of APP recycled from early endosomes to the TGN.
Asters push embryonic nuclei to the brink
Authors: Leslie Mitch
Published: June 2012

Researchers discover how nuclei in insect embryos travel to the cortex.
Nuclear envelope morphology constrains diffusion and promotes asymmetric protein segregation in closed mitosis
Authors: Boettcher Barbara , Marquez-Lago Tatiana T. , Bayer Mathias , Weiss Eric L. , Barral Yves
Published: June 2012

During vegetative growth, Saccharomyces cerevisiae cells divide asymmetrically: the mother cell buds to produce a smaller daughter cell. This daughter asymmetrically inherits the transcription factor Ace2, which activates daughter-specific transcriptional programs. In this paper, we investigate when and how this asymmetry is established and maintained. We show that Ace2 asymmetry is initiated in the elongated, but undivided, anaphase nucleus. At this stage, the nucleoplasm was highly compartmentalized; little exchange was observed for nucleoplasmic proteins between mother and bud. Using photobleaching and in silico modeling, we show that diffusion barriers compartmentalize the nuclear membranes. In contrast, the behavior of proteins in the nucleoplasm is well explained by the dumbbell shape of the anaphase nucleus. This compartmentalization of the nucleoplasm promoted Ace2 asymmetry in anaphase nuclei. Thus, our data indicate that yeast cells use the process of closed mitosis and the morphological constraints associated with it to asymmetrically segregate nucleoplasmic components.
Aster migration determines the length scale of nuclear separation in the Drosophila syncytial embryo
Authors: Telley Ivo A. , Gáspár Imre , Ephrussi Anne , Surrey Thomas
Published: June 2012

In the early embryo of many species, comparatively small spindles are positioned near the cell center for subsequent cytokinesis. In most insects, however, rapid nuclear divisions occur in the absence of cytokinesis, and nuclei distribute rapidly throughout the large syncytial embryo. Even distribution and anchoring of nuclei at the embryo cortex are crucial for cellularization of the blastoderm embryo. The principles underlying nuclear dispersal in a syncytium are unclear. We established a cell-free system from individual Drosophila melanogaster embryos that supports successive nuclear division cycles with native characteristics. This allowed us to investigate nuclear separation in predefined volumes. Encapsulating nuclei in microchambers revealed that the early cytoplasm is programmed to separate nuclei a distinct distance. Laser microsurgery revealed an important role of microtubule aster migration through cytoplasmic space, which depended on F-actin and cooperated with anaphase spindle elongation. These activities define a characteristic separation length scale that appears to be a conserved property of developing insect embryos.
Increasingly Radical Claims about Heredity and Fitness
Authors: Earnshaw-Whyte Eugene
Published: June 2012

On the classical account of evolution by natural selection (ENS) found in Lewontin and many subsequent authors, ENS is conceived as involving three key ingredients: phenotypic variation, fitness differences, and heredity. Through the analysis of three problem cases involving heredity, I argue that the classical conception is substantially flawed, showing that heredity is not required for selection. I consider further problems with the classical account of ENS arising from conflations between three distinct senses of the central concept of ‘fitness’ and offer an alternative to the classical conception of ENS involving the interaction of distinct evolutionary mechanisms.
Leitgeb and Pettigrew on Accuracy and Updating
Authors: Levinstein Benjamin Anders
Published: June 2012

Leitgeb and Pettigrew argue that (1) agents should minimize the expected inaccuracy of their beliefs and (2) inaccuracy should be measured via the Brier score. They show that in certain diachronic cases, these claims require an alternative to Jeffrey Conditionalization. I claim that this alternative is an irrational updating procedure and that the Brier score, and quadratic scoring rules generally, should be rejected as legitimate measures of inaccuracy.