bluuebunny/crossref_metadata_2025 huggingface dataset:
Native point defects and dangling bonds in α-Al2O3
Authors: Choi Minseok , Janotti Anderson , Van de Walle Chris G.
Published: January 2013

We performed hybrid functional calculations of native point defects and dangling bonds (DBs) in α-Al2O3 to aid in the identification of charge-trap and fixed-charge centers in Al2O3/III-V metal-oxide-semiconductor structures. We find that Al vacancies (VAl) are deep acceptors with transition levels less than 2.6 eV above the valence band, whereas Al interstitials (Ali) are deep donors with transition levels within ∼2 eV of the conduction band. Oxygen vacancies (VO) introduce donor levels near midgap and an acceptor level at ∼1 eV below the conduction band, while oxygen interstitials (Oi) are deep acceptors, with a transition level near the mid gap. Taking into account the band offset between α-Al2O3 and III-V semiconductors, our results indicate that VO and Al DBs act as charge traps (possibly causing carrier leakage), while VAl, Ali, Oi, and O DBs act as fixed-charge centers in α-Al2O3/III-V metal-oxide-semiconductor structures.
Influence of phonons on the temperature dependence of the band gap of AlN and AlxGa1−xN alloys with high AlN mole fraction
Authors: Sohal S. , Feng W. , Pandikunta M. , Kuryatkov V. V. , Nikishin S. A. , Holtz M.
Published: January 2013

The temperature dependence of the optical band gap of AlN and AlxGa1−xN alloys, with x ∼ 0.6, has been studied using optical absorption spectroscopy. The band gap shrinkage is interpreted based on electron-phonon interactions using a two-phonon oscillator model. The two-oscillator model includes average acoustic and optic phonon energies and thermal occupation factor described by the Bose function. The temperature dependence of the transition width, from transparent to opaque, is also described based on electron-phonon interactions.
Improved passivation of the ZnO/Si interface by pulsed laser deposition
Authors: Gluba M. A. , Nickel N. H. , Hinrichs K. , Rappich J.
Published: January 2013

Zinc oxide thin-films were grown on crystalline silicon employing magnetron sputtering and pulsed laser deposition. Bulk and interface properties were investigated using scanning electron microscopy, Raman backscattering, photoluminescence, and infrared spectroscopic ellipsometry. Sputter deposited ZnO samples reveal a large degree of disorder and an interface defect density of ≈1012 cm−2. A significant improvement of the structural quality is observed in samples grown by pulsed laser deposition. The bulk defect density is further reduced, when introducing monatomic oxygen during deposition. Simultaneously, the defect density at the ZnO/Si interface decreases by about a factor of five. Implications for devices containing ZnO/Si interfaces are discussed.
Concentrated ion beam emitted from an enlarged cylindrical-anode-layer Hall plasma accelerator and mechanism
Authors: Geng S. F. , Tang D. L. , Wang C. X. , Qiu X. M. , Chu Paul K.
Published: January 2013

An enlarged cylindrical-anode-layer Hall plasma accelerator with an outlet diameter of 150 mm is experimentally demonstrated to produce a concentrated ion beam, especially at a high discharge voltage, with a high current utilization efficiency of up to ∼0.9. Numerical investigation based on the three-dimensional particle-in-cell method is performed to study the ion dynamics and elucidate the origin of the ion beam characteristics. The simulation results reveal that the equipotential lines play an important role in the surface near the anode emitting the ions. The ion emitting surface is determined by the magnetic field lines near the anode and the magnetic mirror contributes to the concentrated beam significantly. The high current utilization efficiency results from the appropriate obliquity of the magnetic mirror.
Physical properties of Al doped Ba hexagonal ferrite thin films
Authors: Harward Ian , Nie Yan , Chen Daming , Baptist Josh , Shaw Justin M. , Jakubisová Lišková Eva , Višňovský Štefan , Široký Petr , Lesňák Michal , Pištora Jaromir , Celinski Zbigniew
Published: January 2013

We developed the thin film microwave magnetic material, M-type barium hexagonal ferrite (BaM) doped with Al, for signal processing devices operating above 40 GHz with little to no applied magnetic field. Al was chosen as the dopant material because it significantly increases the already strong anisotropy field of BaM. A series of thin film BaAlxFe12-xO19 samples, x ranging from 0 to 2 in 0.25 steps, were deposited on Pt templates using a metal-organic decomposition growth technique. The resulting films are polycrystalline and highly textured, with the hexagonal c-axis directed out of plane. These films are also self-biasing; easy axis hysteresis loops have a high squareness ratio, s, in the 0.83-0.92 range. As expected, the anisotropy field increases with x, ranging from 1.34 to 2.19 × 106 A/m (16.9-27.5 kOe) for x = 0-2, while the saturation magnetization Ms decreases with x, ranging from 0.334 to 0.175 × 106 A/m (4πMs = 4.2-2.2 kG) for x = 0-2. These values were measured at room temperature, but the temperature dependence of these quantities was also measured below room temperature, down to 30 K. The measured ferromagnetic resonance linewidths, on the order of 12-30 × 103 A/m (140–370 Oe) for compositions below x = 1, indicate device-quality films. Above a certain threshold, the linewidth increases linearly with frequency at a rate of 0.2-0.64 × 103 (A/m)/GHz (2.5-8 Oe/GHz) for x = 0–1, respectively. The behavior of the linewidth is correlated with the structural properties of the films measured using x-ray diffraction and atomic force microscopy. The results of magnetic force microscopy, Curie point measurements, spectral ellipsometry (index of refraction), and magneto-optical measurements are also included and discussed.
A double-plasma source of continuous bipolar ion-ion beam
Authors: Dudin S. V. , Rafalskyi D. V.
Published: January 2013

A double-plasma source capable of the generation of a continuous bipolar ion-ion beam is described. The quasi-neutral ion-ion flow to an extraction electrode is formed in the system containing primary inductively coupled plasma separated from a secondary plasma by an electrostatic grid-type filter. The total current of each ion species to the 250 mm diameter extraction electrode is about 80 mA; the electron current does not exceed 30% of the ion current. Method of positive/negative ion current ratio control is proposed, allowing the ion currents ratio variation in wide range.
Piezo-strain induced non-volatile resistance states in (011)-La2/3Sr1/3MnO3/0.7Pb(Mg2/3Nb1/3)O3-0.3PbTiO3 epitaxial heterostructures
Authors: Yang Yuanjun , Luo Z. L. , Meng Yang Meng , Huang Haoliang , Wang Haibo , Bao J. , Pan Guoqiang , Gao C. , Hao Qiang , Wang Shutong , Jokubaitis Michael , Zhang Wenzhe , Xiao Gang , Yao Yiping , Liu Yukuai , Li X. G.
Published: January 2013

The non-volatile resistance states induced by converse piezoelectric effect are observed in ferromagnetic/ferroelectric epitaxial heterostructures of (011)-La2/3Sr1/3MnO3/0.7Pb(Mg2/3Nb1/3)O3-0.3PbTiO3 (LSMO/PMN0.7PT0.3). Three stable remnant strain states and the corresponding resistance states are achieved by properly reversing the electric field from the depolarized direction in ferroelectric PMN0.7PT0.3 substrate. The non-volatile resistance states of the LSMO film can be manipulated by applied electric-field pulse sequence as a result of the large coupling between the electronic states of LSMO film and the strain transferred from the ferroelectric substrate. The electrically tunable, non-volatile resistance states observed exhibit potential for applications in low-power-consumption electronic devices.
Stochastic nonlinear electrical characteristics of graphene
Authors: Jun Shin Young , Gopinadhan Kalon , Narayanapillai Kulothungasagaran , Kalitsov Alan , Bhatia Charanjit S. , Yang Hyunsoo
Published: January 2013

A stochastic nonlinear electrical characteristic of graphene is reported. Abrupt current changes are observed from voltage sweeps between the source and drain with an on/off ratio up to 103. It is found that graphene channel experiences the topological change. Active radicals in an uneven graphene channel cause local changes of electrostatic potential. Simulation results based on the self-trapped electron and hole mechanism account well for the experimental data. Our findings illustrate an important issue of reliable electron transports and help for the understanding of transport properties in graphene devices.
Growth and stability of zinc blende MgS on GaAs, GaP, and InP substrates
Authors: Rajan Akhil , Moug Richard T. , Prior Kevin A.
Published: January 2013

The molecular beam epitaxial growth of zinc blende (ZB) MgS on GaAs, GaP, and InP substrates has been investigated by X-ray diffraction and RHEED, with MgS layer strain varying between 3.1% compressive strain (GaP) and 4.4% tensile strain (InP). ZB MgS could be grown on all three substrates. X-ray diffraction showed substantial MgS relaxation during growth before conversion to the rock salt phase. Results are compared with predictions that stable growth on GaP is unlikely and relaxed ZB MgS does not grow in layers over a few Å thick. Our results imply growth of ZB MgS is truly metastable.
Vibration energy harvesting using a phononic crystal with point defect states
Authors: Lv Hangyuan , Tian Xiaoyong , Wang Michael Yu , Li Dichen
Published: January 2013

A vibration energy harvesting generator was studied in the present research using point-defect phononic crystal with piezoelectric material. By removing a rod from a perfect phononic crystal, a resonant cavity was formed. The elastic waves in the range of gap frequencies were all forbidden in any direction, while the waves with resonant frequency were localized and enhanced in the resonant cavity. The collected vibration energy was converted into electric energy by putting a polyvinylidene fluoride film in the middle of the defect. This structure can be used to simultaneously realize both vibration damping and broad-distributed vibration energy harvesting.
Pneumatically switchable graded index metamaterial lens
Authors: Khodasevych I. E. , Shadrivov I. V. , Powell D. A. , Rowe W. S. T. , Mitchell A.
Published: January 2013

A low-profile pneumatically switchable graded index metamaterial lens operating at 9 GHz is proposed and practically demonstrated. An effective graded refractive index is engineered using an array of electric resonators of differing resonant frequency. Normal orientation of the resonators allows ultrathin single metamaterial layer lens design. Switching between focusing and non-focusing states is practically demonstrated by shorting the gaps in split ring resonators and eliminating the resonant response and the phase difference between the elements across the lens with pneumatically actuated metal patches that are pressed against the gaps of the resonators as the pressure in the chamber is reduced.
Generation of high-power tunable terahertz-radiation by nonrelativistic beam-echo harmonic effect
Authors: Gong Huarong , Travish Gil , Xu Jin , Wei Yanyu , Feng Jinjun , Gong Yubin
Published: January 2013

A new type of terahertz radiation source based on the nonrelativistic electron beam-wave interaction is proposed. Here, the beam echo harmonic effect is applied to a traveling wave tube like device. The scheme is configured as a combination of a frequency multiplier and amplifier with, for instance, W-band (millimeter wave) input signals and terahertz output power. A one-dimensional model of this device shows that a 10th order harmonic-wave can be generated while other harmonic waves are suppressed. The device only requires a readily available input source (W-band), and the output frequency can be tuned continuously over a wide band.
Evolving the Ideal Visual-to-Auditory Sensory Substitution Device Using Interactive Genetic Algorithms
Authors: Wright Thomas D , McAllister Graham , Ward Jamie
Published: January 2013

Visual-to-auditory sensory substitution devices have various benefits over tactile counterparts (eg, less hardware limitations), but they also suffer from several drawbacks (eg, learning time, potentially unpleasant sounds). An ‘ideal’ device would be intuitive to learn, pleasant to listen to, and capture relevant visual information in sufficient detail. In this presentation, we outline the general problem of how to convert an image into sound, and we give an overview of some possible approaches to the problem. We then go on to describe our own recent explorations using Interactive Genetic Algorithms (IGAs). IGAs enable a highly dimensional problem space to be explored rapidly. Initially, a set of orthogonally varying settings need to be identified (eg, different levels of maximum and minimum pitch, different ways of mapping lightness-loudness, musical vs non-musical intervals), and a set of random permutations of these settings are chosen. Participants then evaluate the ‘fitness’ of these different algorithms (eg, by selecting what the correct image is for a given sound). The fittest algorithms are then ‘bred’ together over successive generations. Using this approach, we compare the performance of evolved devices against one of the main existing devices (the vOICe) in three tasks: audio-visual matching, aesthetic preference, and auditory discrimination.
Wind and insect pollination (ambophily) of Mallotus spp. (Euphorbiaceae) in tropical and temperate forests
Authors: Yamasaki Eri , Sakai Shoko
Published: January 2013

Relatively few flowering plants show ambophily (pollination by both wind and insects), and whether and when ambophily is advantageous has not been studied well. In the present study, we report ambophily in two dioecious pioneer tree species, Mallotus japonicus Müll.Arg. in a temperate forest of Japan, and Mallotus wrayi King ex Hook.f. in a tropical forest of Borneo, and discuss the conditions that contribute to the maintenance of ambophily. Both species are pollinated by wind because they set fruits even when flower visitors were excluded and because substantial amounts of airborne pollen reached female trees. Insects may also contribute to fruit set, because insects with body pollen visited female inflorescences. Because M. japonicus and M. wrayi exhibit floral characteristics that are adapted to both wind and insect pollination, ambophily may be actively maintained in the two species at the study sites and perhaps elsewhere. Whereas previous studies have indicated that ambophily is advantageous for pioneer plants because of changing wind conditions during forest succession, our preliminary data suggest that changes in population density also contribute to the maintenance of ambophily in M. japonicus.
Facile Fabrication of Au–F127 Nanocolloids with Different Morphologies and their Potential Bioapplications
Authors: Zhu Qinshu , Sun Chong , Yan Jie , Yang Kai , Fu Rongjin , Mao Chun , Shen Jian
Published: January 2013

Three kinds of novel facile fabrication routes to prepare Au–F127 nanocolloids with different morphologies including rambutan-like Au–F127 hybrid nanospheres, Au@F127 core–shell nanostructure, and multiple shapes of Au nanosheets are reported. The different Au–F127 nanocolloids are characterised by transmission electron microscopy, electron diffraction patterns, and UV-vis spectroscopy. The different formation mechanisms of the Au–F127 nanocolloids with different morphologies are discussed. The intrinsic properties and application potential of Au–F127 nanocolloids are determined by their size, shape, composition, and structure. A biosensor made of rambutan-like Au–F127 hybrid nanospheres exhibited a good electrocatalytic activity for the reduction of hydrogen peroxide. The Au@F127 core–shell nanoparticles exhibited good blood compatibility attributable to the surface hydrophilicity of the F127 layer. These strategies open up the exciting possibility of using F127 in synthesis of gold nanomaterials of variable morphology, and provide a promising platform for biomedical applications in future.
Variation and constraint inHoxgene evolution
Authors: Heffer Alison , Xiang Jie , Pick Leslie
Published: January 2013

Despite enormous body plan variation, genes regulating embryonic development are highly conserved. Here, we probe the mechanisms that predispose ancient regulatory genes to reutilization and diversification rather than evolutionary loss. TheHoxgenefushi tarazu(ftz) arose as a homeotic gene but functions as a pair-rule segmentation gene inDrosophila.ftzshows extensive variation in expression and protein coding regions but has managed to elude loss from arthropod genomes. We asked what properties prevent this loss by testing the importance of different protein motifs and partners in the developing CNS, whereftzexpression is conserved.DrosophilaFtz proteins with mutated protein motifs were expressed under the control of a neurogenic-specificftz cis-regulatory element (CRE) in aftzmutant background rescued for segmentation defects. Ftz CNS function did not require the variable motifs that mediate differential cofactor interactions involved in homeosis or segmentation, which vary in arthropods. Rather, CNS function did require the shared DNA-binding homeodomain, which plays less of a role in Ftz segmentation activity. The Antennapedia homeodomain substituted for Ftz homeodomain function in theDrosophilaCNS, but full-length Antennapedia did not rescue CNS defects. These results suggest that a core CNS function retainsftzin arthropod genomes. Acquisition of a neurogenic CRE led toftzexpression in unique CNS cells, differentiating its role from neighboringHoxgenes, rendering it nonredundant. The inherent flexibility of modular CREs and protein domains allows for stepwise acquisition of new functions, explaining broad retention of regulatory genes during animal evolution.
Evolution of fairness in the one-shot anonymous Ultimatum Game
Authors: Rand David G. , Tarnita Corina E. , Ohtsuki Hisashi , Nowak Martin A.
Published: January 2013

Classical economic models assume that people are fully rational and selfish, while experiments often point to different conclusions. A canonical example is the Ultimatum Game: one player proposes a division of a sum of money between herself and a second player, who either accepts or rejects. Based on rational self-interest, responders should accept any nonzero offer and proposers should offer the smallest possible amount. Traditional, deterministic models of evolutionary game theory agree: in the one-shot anonymous Ultimatum Game, natural selection favors low offers and demands. Experiments instead show a preference for fairness: often responders reject low offers and proposers make higher offers than needed to avoid rejection. Here we show that using stochastic evolutionary game theory, where agents make mistakes when judging the payoffs and strategies of others, natural selection favors fairness. Across a range of parameters, the average strategy matches the observed behavior: proposers offer between 30% and 50%, and responders demand between 25% and 40%. Rejecting low offers increases relative payoff in pairwise competition between two strategies and is favored when selection is sufficiently weak. Offering more than you demand increases payoff when many strategies are present simultaneously and is favored when mutation is sufficiently high. We also perform a behavioral experiment and find empirical support for these theoretical findings: uncertainty about the success of others is associated with higher demands and offers; and inconsistency in the behavior of others is associated with higher offers but not predictive of demands. In an uncertain world, fairness finishes first.
Oxygen tolerance of an
in silico
-designed bioinspired hydrogen-evolving catalyst in water
Authors: Sit Patrick H.-L. , Car Roberto , Cohen Morrel H. , Selloni Annabella
Published: January 2013

Certain bacterial enzymes, the diiron hydrogenases, have turnover numbers for hydrogen production from water as large as 10
4
/s. Their much smaller common active site, composed of earth-abundant materials, has a structure that is an attractive starting point for the design of a practical catalyst for electrocatalytic or solar photocatalytic hydrogen production from water. In earlier work, our group has reported the computational design of [FeFe]
P
/FeS
2
, a hydrogenase-inspired catalyst/electrode complex, which is efficient and stable throughout the production cycle. However, the diiron hydrogenases are highly sensitive to ambient oxygen by a mechanism not yet understood in detail. An issue critical for practical use of [FeFe]
P
/FeS
2
is whether this catalyst/electrode complex is tolerant to the ambient oxygen. We report demonstration by ab initio simulations that the complex is indeed tolerant to dissolved oxygen over timescales long enough for practical application, reducing it efficiently. This promising hydrogen-producing catalyst, composed of earth-abundant materials and with a diffusion-limited rate in acidified water, is efficient as well as oxygen tolerant.
Inward-facing conformation of the zinc transporter YiiP revealed by cryoelectron microscopy
Authors: Coudray Nicolas , Valvo Salvatore , Hu Minghui , Lasala Ralph , Kim Changki , Vink Martin , Zhou Ming , Provasi Davide , Filizola Marta , Tao Juoehi , Fang Jia , Penczek Pawel A. , Ubarretxena-Belandia Iban , Stokes David L.
Published: January 2013

YiiP is a dimeric Zn
2+
/H
+
antiporter from
Escherichia coli
belonging to the cation diffusion facilitator family. We used cryoelectron microscopy to determine a 13-Å resolution structure of a YiiP homolog from
Shewanella oneidensis
within a lipid bilayer in the absence of Zn
2+
. Starting from the X-ray structure in the presence of Zn
2+
, we used molecular dynamics flexible fitting to build a model consistent with our map. Comparison of the structures suggests a conformational change that involves pivoting of a transmembrane, four-helix bundle (M1, M2, M4, and M5) relative to the M3-M6 helix pair. Although accessibility of transport sites in the X-ray model indicates that it represents an outward-facing state, our model is consistent with an inward-facing state, suggesting that the conformational change is relevant to the alternating access mechanism for transport. Molecular dynamics simulation of YiiP in a lipid environment was used to address the feasibility of this conformational change. Association of the C-terminal domains is the same in both states, and we speculate that this association is responsible for stabilizing the dimer that, in turn, may coordinate the rearrangement of the transmembrane helices.
Domain-swapped chain connectivity and gated membrane access in a Fab-mediated crystal of the human TRAAK K
+
channel
Authors: Brohawn Stephen G. , Campbell Ernest B. , MacKinnon Roderick
Published: January 2013

TRAAK (TWIK-related arachidonic acid-stimulated K
+
channel, K2P4.1) K
+
ion channels are expressed predominantly in the nervous system to control cellular resting membrane potential and are regulated by mechanical and chemical properties of the lipid membrane. TRAAK channels are twofold symmetric, which precludes a direct extension of gating mechanisms that close canonical fourfold symmetric K
+
channels. We present the crystal structure of human TRAAK in complex with antibody antigen-binding fragments (Fabs) at 2.75-Å resolution. In contrast to a previous structure, this structure reveals a domain-swapped chain connectivity enabled by the helical cap that exchanges two opposing outer helices 180° around the channel. An unrelated conformational change of an inner helix seals a side opening to the membrane bilayer and is associated with structural changes around the K
+
-selectivity filter that may have implications for mechanosensitivity and gating of TRAAK channels.
Lesions of cortical area LIP affect reach onset only when the reach is accompanied by a saccade, revealing an active eye–hand coordination circuit
Authors: Yttri Eric A. , Liu Yuqing , Snyder Lawrence H.
Published: January 2013

The circuits that drive visually guided eye and arm movements transform generic visual inputs into effector-specific motor commands. As part of the effort to elucidate these circuits, the primate lateral intraparietal area (LIP) has been interpreted as a priority map for saccades (oculomotor-specific) or a salience map of space (not effector-specific). It has also been proposed as a locus for eye–hand coordination. We reversibly inactivated LIP while monkeys performed memory-guided saccades and reaches. Coordinated saccade and reach reaction times were similarly impaired, consistent with a nonspecific role. However, reaches made without an accompanying saccade remained intact, and the relative temporal coupling of saccades and reaches was unchanged. These results suggest that LIP contributes to saccade planning but not to reach planning. Coordinated reaches are delayed as a result of an eye–hand coordination mechanism, located outside of LIP, that actively delays reaches until shortly after the onset of an associated saccade. We conclude with a discussion of how to reconcile specificity for saccades with a possible role in directing attention.
Centennial-scale analysis of the creation and fate of reactive nitrogen in China (1910–2010)
Authors: Cui Shenghui , Shi Yalan , Groffman Peter M. , Schlesinger William H. , Zhu Yong-Guan
Published: January 2013

Human mobilization and use of reactive nitrogen (Nr) has been one of the major aspects of global change over the past century. Nowhere has that change been more dramatic than in China, where annual net Nr creation increased from 9.2 to 56 Tg from 1910 to 2010. Since 1956, anthropogenic Nr creation exceeded natural Nr creation, contributing over 80% of total Nr until 2010. There is great interest and uncertainty in the fate and effects of this Nr in China. Here, a comprehensive inventory of Nr in China shows that Nr (including recycled Nr) has continuously and increasingly accumulated on land (from 17 to 45 Tg), accompanied by increasing transfers to the atmosphere (before deposition; from 7.6 to 20 Tg), inland waters (from 2.7 to 9.6 Tg), and coastal waters (from 4.5 to 7.7 Tg) over the past 30 y. If current trends continue, Nr creation from human activities will increase to 63 Tg by 2050, raising concerns about deleterious environmental consequences for land, air, and water at regional and global scales. Tremendous amounts of Nr have accumulated in plants, soils, and waters in China over the past 30 y, but the retention capacity of the terrestrial landscape seems to be declining. There is a possibility that the negative environmental effects of excessive Nr may accelerate in coming decades, increasing the urgency to alter the trajectory of increasing Nr imbalance. Here, a conceptual framework of the relationships between human drivers and Nr cycling in China is oriented and well-targeted to Chinese abatement strategies for Nr environmental impact.
Control of cell-fate plasticity and maintenance of multipotency by DAF-16/FoxO in quiescent
Caenorhabditis elegans
Authors: Karp Xantha , Greenwald Iva
Published: January 2013

The
Caenorhabditis elegans
vulval precursor cells (VPCs) offer a paradigm for investigating how multipotency of progenitor cells is maintained during periods of quiescence. The VPCs are born in the first larval stage. When hermaphrodites are grown under favorable conditions, the EGF-mediated “inductive” signal and the LIN-12/Notch-mediated “lateral” signal confer a precise spatial pattern of distinct vulval cell fates in the third larval stage, a day after hatching. Under adverse conditions, hermaphrodites undergo a prolonged quiescent period as dauer larvae, which can endure for several months with progenitor cells such as VPCs in developmental arrest. If favorable conditions ensue, larvae recover and resume development as postdauer third stage larvae, with the same VPC spatial-patterning events as in continuously developing third stage larvae. Here, we identify several consequences of dauer life history for VPC specification. In wild-type dauers, VPCs undergo a phenomenon reminiscent of natural direct reprogramming to maintain or reestablish multipotency; they acquire an active block to signal transduction by EGF receptor and LIN-12/Notch and have a different mechanism for regulating transcription of the lateral signal. Furthermore, DAF-16/FoxO, a target of insulin/insulin-like growth factor signaling, is required to promote VPC fate plasticity during dauer and for normal vulval patterning after passage through dauer, suggesting that DAF-16/FoxO coordinates environment and life history with plasticity of cell fate.
Validation of a Predictive Model for Fish Tissue Mercury Concentrations
Authors: Sackett Dana K. , Aday D. Derek , Rice James A. , Cope W. Gregory
Published: January 2013

In an effort to reconcile the extensive variability in fish tissue mercury (Hg) in North Carolina, we previously created a predictive model using data collected from 1990 to 2006. Our model identified four factors—fish trophic status, fish species, ecoregion, and water pH—that explained 81% of the variation in fish tissue Hg. Herein, we evaluate the performance of this model by using two independently collected data sets describing fish tissue Hg in North Carolina and Virginia. Our model explained 75% of the variation in independently collected tissue Hg data from North Carolina and 68% of the variation in data collected from the same ecoregion types in Virginia. Although the relationships were relatively strong, the model generally underestimated observed tissue Hg. Residual analysis indicated that at least some of the model bias was due to error in predictions for sites near (within 10 km of) coal‐fired power plants. The model was not significantly biased when sites near power plants were removed from the independent data set, suggesting that the model was best at predicting mean tissue Hg in adult fish collected from water bodies greater than 10 km from power plants; such sites constitute the majority of the landscape. Fortuitously, fish at sites near power plants have significantly less tissue Hg than fish at sites far from power plants and are therefore of less concern to public health officials. The validated model can serve as a fish tissue Hg screening tool for use by state and federal agencies because it was created to predict Hg levels in numerous species and systems, and it only requires data that are readily available or relatively simple and inexpensive to measure. Identification of specific systems that may have highly contaminated fish and would not otherwise be sampled due to limited resources will help to focus sampling and enhance efforts to protect fish consumers.
COX19 mediates the transduction of a mitochondrial redox signal from SCO1 that regulates ATP7A-mediated cellular copper efflux
Authors: Leary Scot C. , Cobine Paul A. , Nishimura Tamiko , Verdijk Robert M. , de Krijger Ronald , de Coo René , Tarnopolsky Mark A. , Winge Dennis R. , Shoubridge Eric A.
Published: January 2013

SCO1 and SCO2 are metallochaperones whose principal function is to add two copper ions to the catalytic core of cytochrome c oxidase (COX). However, affected tissues of SCO1 and SCO2 patients exhibit a combined deficiency in COX activity and total copper content, suggesting additional roles for these proteins in the regulation of cellular copper homeostasis. Here we show that both the redox state of the copper-binding cysteines of SCO1 and the abundance of SCO2 correlate with cellular copper content and that these relationships are perturbed by mutations in SCO1 or SCO2, producing a state of apparent copper overload. The copper deficiency in SCO patient fibroblasts is rescued by knockdown of ATP7A, a trans-Golgi, copper-transporting ATPase that traffics to the plasma membrane during copper overload to promote efflux. To investigate how a signal from SCO1 could be relayed to ATP7A, we examined the abundance and subcellular distribution of several soluble COX assembly factors. We found that COX19 partitions between mitochondria and the cytosol in a copper-dependent manner and that its knockdown partially rescues the copper deficiency in patient cells. These results demonstrate that COX19 is necessary for the transduction of a SCO1-dependent mitochondrial redox signal that regulates ATP7A-mediated cellular copper efflux.
Computational phosphorylation site prediction in plants using random forests and organism-specific instance weights
Authors: Trost Brett , Kusalik Anthony
Published: January 2013

Motivation: Phosphorylation is the most important post-translational modification in eukaryotes. Although many computational phosphorylation site prediction tools exist for mammals, and a few were created specifically for Arabidopsis thaliana, none are currently available for other plants.

Results: In this article, we propose a novel random forest-based method called PHOSFER (PHOsphorylation Site FindER) for applying phosphorylation data from other organisms to enhance the accuracy of predictions in a target organism. As a test case, PHOSFER is applied to phosphorylation sites in soybean, and we show that it more accurately predicts soybean sites than both the existing Arabidopsis-specific predictors, and a simpler machine-learning scheme that uses only known phosphorylation sites and non-phosphorylation sites from soybean. In addition to soybean, PHOSFER will be extended to other organisms in the near future.

Availability: PHOSFER is available via a web interface at http://saphire.usask.ca.

Contact:  brett.trost@usask.ca

Supplementary information:  Supplementary data are available at Bioinformatics online.
TACTICS, an interactive platform for customized high-content bioimaging analysis
Authors: Shimoni Raz , Pham Kim , Yassin Mohammed , Gu Min , Russell Sarah M.
Published: January 2013

Summary: We describe a modular MATLAB® Toolbox named TACTICS for time-lapse image analysis that meets several requirements not generally offered by currently available software packages: (i) the ability to assess quality of extracted imaging information by directly linking data end points to the original position, (ii) massively parallel analysis of each parameter, for flow cytometry-like assessment of possible relationships between parameters within sub-populations of the images, (iii) options for user control of the tracking such as an interface to restrict the analysis region, (iv) manual correction of automated processes and (v) user interfaces for post-tracking analysis that is linked to the original images, including options to view cell pedigrees and normalized polarization ratios based on fluorescence ratiometric measurements.

Availability and implementation: We provide TACTICS source code as well as video tutorials, data sample and comprehensive user guide on the TACTICS toolbox website (http://www.tactics-toolbox.com). Installation of TACTICS requires MATLAB 7.6 (R2008a) with the presence of Image Processing Toolbox™ and Statistics Toolbox™.

Contact: sarah.russell@petermac.org.
Fishery management advice with ecosystem considerations
Authors: Lassen Hans , Pedersen Søren Anker , Frost Hans , Hoff Ayoe
Published: January 2013

Lassen, H., Pedersen, S. A., Frost, H., and Hoff. A. 2013. Fishery management advice with ecosystem considerations. – ICES Journal of Marine Science, 70: 471–479. The European Union Marine Strategy Framework Directive (MSFD) includes four descriptors of Good Environmental Status (GES) which are affected by fishing activity. These descriptors are: biodiversity, fish stocks, foodweb, and seabed integrity. This paper shows how these descriptors can be related to variables within an ecological model and how an ecological model can be used to analyse whether the fishing pressure that is estimated based on bioeconomic criteria is within general sustainable limits. The paper presents an example of such an analysis of the Eastern Baltic cod fishery using two models: a bioeconomic model and an ecological model. The models are calibrated based on historic data. The mapping between the descriptors specified by MSFD and variables available for analysis in the models is incomplete, e.g. genetics and spatial structures are not included in the models. The models can be used strategically, providing a qualitative understanding of the anticipated relative changes.
Rapid evolution of troglomorphic characters suggests selection rather than neutral mutation as a driver of eye reduction in cave crabs
Authors: Klaus Sebastian , Mendoza José C. E. , Liew Jia Huan , Plath Martin , Meier Rudolf , Yeo Darren C. J.
Published: January 2013

This study asked whether reductive traits in cave organisms evolve at a slower pace (suggesting neutral evolution under relaxed selection) than constructive changes, which are likely to evolve under directional selection. We investigated 11 subterranean and seven surface populations ofSundathelphusafreshwater crabs on Bohol Island, Philippines, and examined constructive traits associated with improved food finding in darkness (increased leg and setae length) and reductive traits (reduced cornea size and eyestalk length). All changes occurred rapidly, given that the age of the most recent common ancestor was estimated to be 722–271 ka based on three mitochondrial markers. In order to quantify the speed of character change, we correlated the degree of morphological change with genetic distances between surface and subterranean individuals. The temporal pattern of character change following the transition to subterranean life was indistinguishable for constructive and reductive traits, characterized by an immediate onset and rapid evolutionary change. We propose that the evolution of these reductive traits—just like constructive traits—is most likely driven by strong directional selection.
Dark survival in a warming world
Authors: McMinn A. , Martin A.
Published: January 2013

Most algae regularly experience periods of darkness ranging from a few hours to a few days. During this time, they are unable to photosynthesize, and so must consume stored energy products. However, some organisms such as polar algae and some microalgal cysts and spores are exposed to darkness for months to years, and these must use alternative strategies to survive. Some taxa, such as dinoflagellates, form cysts and become dormant. Others use physiological methods or adopt mixotrophy. The longest documented survival of more than a century was for dinoflagellates buried in sediments in a Norwegian fjord. Seasonal changes in daylight hours are naturally unaffected by climate change. This means that polar microalgae will in the future need to survive the same period of seasonal darkness but at higher temperatures, and this will require a greater drawdown of stored energy. Recent experimental work has shown that both Arctic and Antarctic phytoplankton are able to survive increases of up to 6°C in the dark.
Role and Interrelationship of Gα Protein, Hydrogen Peroxide, and Nitric Oxide in Ultraviolet B-Induced Stomatal Closure in Arabidopsis Leaves
Authors: He Jun-Min , Ma Xian-Ge , Zhang Ying , Sun Tie-Feng , Xu Fei-Fei , Chen Yi-Ping , Liu Xiao , Yue Ming
Published: January 2013

Heterotrimeric G proteins have been shown to transmit ultraviolet B (UV-B) signals in mammalian cells, but whether they also transmit UV-B signals in plant cells is not clear. In this paper, we report that 0.5 W m−2 UV-B induces stomatal closure in Arabidopsis (Arabidopsis thaliana) by eliciting a cascade of intracellular signaling events including Gα protein, hydrogen peroxide (H2O2), and nitric oxide (NO). UV-B triggered a significant increase in H2O2 or NO levels associated with stomatal closure in the wild type, but these effects were abolished in the single and double mutants of AtrbohD and AtrbohF or in the Nia1 mutants, respectively. Furthermore, we found that UV-B-mediated H2O2 and NO generation are regulated by GPA1, the Gα-subunit of heterotrimeric G proteins. UV-B-dependent H2O2 and NO accumulation were nullified in gpa1 knockout mutants but enhanced by overexpression of a constitutively active form of GPA1 (cGα). In addition, exogenously applied H2O2 or NO rescued the defect in UV-B-mediated stomatal closure in gpa1 mutants, whereas cGα AtrbohD/AtrbohF and cGα nia1 constructs exhibited a similar response to AtrbohD/AtrbohF and Nia1, respectively. Finally, we demonstrated that Gα activation of NO production depends on H2O2. The mutants of AtrbohD and AtrbohF had impaired NO generation in response to UV-B, but UV-B-induced H2O2 accumulation was not impaired in Nia1. Moreover, exogenously applied NO rescued the defect in UV-B-mediated stomatal closure in the mutants of AtrbohD and AtrbohF. These findings establish a signaling pathway leading to UV-B-induced stomatal closure that involves GPA1-dependent activation of H2O2 production and subsequent Nia1-dependent NO accumulation.
Orchestration of Thiamin Biosynthesis and Central Metabolism by Combined Action of the Thiamin Pyrophosphate Riboswitch and the Circadian Clock in Arabidopsis
Authors: Bocobza Samuel E. , Malitsky Sergey , Araújo Wagner L. , Nunes-Nesi Adriano , Meir Sagit , Shapira Michal , Fernie Alisdair R. , Aharoni Asaph
Published: January 2013

Riboswitches are natural RNA elements that posttranscriptionally regulate gene expression by binding small molecules and thereby autonomously control intracellular levels of these metabolites. Although riboswitch-based mechanisms have been examined extensively, the integration of their activity with global physiology and metabolism has been largely overlooked. Here, we explored the regulation of thiamin biosynthesis and the consequences of thiamin pyrophosphate riboswitch deficiency on metabolism in Arabidopsis thaliana. Our results show that thiamin biosynthesis is largely regulated by the circadian clock via the activity of the THIAMIN C SYNTHASE (THIC  ) promoter, while the riboswitch located at the 3′ untranslated region of this gene controls overall thiamin biosynthesis. Surprisingly, the results also indicate that the rate of thiamin biosynthesis directs the activity of thiamin-requiring enzymes and consecutively determines the rate of carbohydrate oxidation via the tricarboxylic acid cycle and pentose-phosphate pathway. Our model suggests that in Arabidopsis, the THIC promoter and the thiamin-pyrophosphate riboswitch act simultaneously to tightly regulate thiamin biosynthesis in a circadian manner and consequently sense and control vital points of core cellular metabolism.
Organ Evolution in Angiosperms Driven by Correlated Divergences of Gene Sequences and Expression Patterns
Authors: Yang Ruolin , Wang Xiangfeng
Published: January 2013

The evolution of a species involves changes in its genome and its transcriptome. Divergence in expression patterns may be more important than divergence in sequences for determining phenotypic changes, particularly among closely related species. We examined the relationships between organ evolution, sequence evolution, and expression evolution in Arabidopsis thaliana, rice (Oryza sativa), and maize (Zea mays). We found correlated divergence of gene sequences and expression patterns, with distinct divergence rates that depend on the organ types in which a gene is expressed. For instance, genes specifically expressed in reproductive organs (i.e., stamen) evolve more quickly than those specifically expressed in vegetative organs (e.g., root). The different rates in organ evolution may be due to different degrees of functional constraint associated with the different physiological functions of plant organs. Additionally, the evolutionary rate of a gene sequence is correlated with the breadth of its expression in terms of the number of tissues, the number of coregulation modules, and the number of species in which the gene is expressed, as well as the number of genes with which it may interact. This linkage supports the hypothesis that constitutively expressed genes may experience higher levels of functional constraint accumulated from multiple tissues than do tissue-specific genes.
ACCOUNTING FOR THE TIMING OF FIRST MARRIAGE*
Authors: Díaz‐Giménez Javier , Giolito Eugenio
Published: January 2013

Among first marriages in the United States, grooms are on average 1.7 years older than their brides. Traditionally, this fact is explained by sex differences in income. We use a general equilibrium, overlapping generations search model economy to show instead that sex differences in fecundity are essential to account for the age gap at first marriage, whereas sex differences in income play a secondary role. Our model economy also accounts for other facts on the timing of first marriages that the literature has overlooked.
COMPETITION AND CROWDING OUT IN THE MARKET FOR OUTPATIENT SUBSTANCE ABUSE TREATMENT*
Authors: Cohen Andrew , Freeborn Beth , McManus Brian
Published: January 2013

U.S. markets for outpatient substance abuse treatment (OSAT) include for‐profit, nonprofit, and public clinics. We study OSAT provision using new methods on equilibrium market structure in differentiated product markets. This allows us to describe clinics as heterogeneous in their objectives, their responses to exogenous market characteristics, and their responses to one another. Consistent with crowding out of private treatment, we find that markets with public clinics are less likely to have private clinics. In markets with low insurance coverage, low incomes, or high shares of nonwhite addicts, however, public clinics are relatively likely to be the sole willing providers of OSAT.
In and Out of Place: Tibetan Artists' Travels in the Contemporary Art World
Authors: Harris Clare
Published: January 2013

The contemporary art world is often imagined as a placeless utopia where artists are free to circulate and their nationhood or ethnicity is of little relevance. However, this essay argues that the art world is actually a rather difficult domain to enter and inhabit. For a group of contemporary Tibetan artists, it initially seemed to offer an escape from the strictures of their home locations and an arena in which to unite when geopolitics otherwise divided them. But as their experiences of participating in a number of exhibitions reveals, the art world is a very real place, with its own boundary markers and criteria for inclusion and exclusion. It may not always be a paradise.
Nestling sex predicts susceptibility to parasitism and influences parasite population size within avian broods
Authors: O’Brien Erin L. , Dawson Russell D.
Published: January 2013

Vertebrate hosts differ in their level of parasite susceptibility and infestation. In avian broods, variation in susceptibility of nestlings to ectoparasites may be associated with non‐uniform distributions of parasites among brood mates, with parasites concentrating feeding on the most vulnerable hosts. The presence of a highly susceptible nestling in a brood can benefit the remaining young by reducing the parasite pressure they experience; however, from a parasite’s perspective, broods with fewer susceptible hosts may provide effectively fewer resources than broods of the same size containing a greater abundance of susceptible hosts, and this could limit the number of parasites that a host brood can sustain. To test whether variation in number of susceptible hosts affects the number of parasites in bird nests, we first examined the role of host sex and induced immunity (via methionine supplementation) on susceptibility of mountain bluebirds Sialia currucoides to parasitism by blow flies Protocalliphora spp. We then assessed the effect of variation in number of susceptible hosts on the number of parasites inhabiting the nest. Only females showed a benefit of methionine supplementation, gaining mass more rapidly following supplementation compared to males. This suggests that females are more susceptible to parasites in this system; this was further supported by parasite feeding trials, in which parasites extracted larger blood meals from female than male hosts. Finally, the abundance of parasites in nests was predicted by brood sex ratio: broods containing more female young harboured more parasites. Hence, within‐brood variation in host susceptibility to parasites can not only influence the costs of parasitism for individual nestlings, but may also have consequences for the size of parasite populations within nests. If patterns of maternal investment affect the abundance of nest‐dwelling parasites, these interactions may be important for understanding fitness consequences of maternal resource allocation in many vertebrate hosts.