bluuebunny/crossref_metadata_2025 huggingface dataset:
Multi-reference approach to the calculation of photoelectron spectra including spin-orbit coupling
Authors: Grell Gilbert , Bokarev Sergey I. , Winter Bernd , Seidel Robert , Aziz Emad F. , Aziz Saadullah G. , Kühn Oliver
Published: August 2015

X-ray photoelectron spectra provide a wealth of information on the electronic structure. The extraction of molecular details requires adequate theoretical methods, which in case of transition metal complexes has to account for effects due to the multi-configurational and spin-mixed nature of the many-electron wave function. Here, the restricted active space self-consistent field method including spin-orbit coupling is used to cope with this challenge and to calculate valence- and core-level photoelectron spectra. The intensities are estimated within the frameworks of the Dyson orbital formalism and the sudden approximation. Thereby, we utilize an efficient computational algorithm that is based on a biorthonormal basis transformation. The approach is applied to the valence photoionization of the gas phase water molecule and to the core ionization spectrum of the [Fe(H2O)6]2+ complex. The results show good agreement with the experimental data obtained in this work, whereas the sudden approximation demonstrates distinct deviations from experiments.
Stress-directed compositional patterning of SiGe substrates for lateral quantum barrier manipulation
Authors: Ghosh Swapnadip , Kaiser Daniel , Bonilla Jose , Sinno Talid , Han Sang M.
Published: August 2015

While vertical stacking of quantum well and dot structures is well established in heteroepitaxial semiconductor materials, manipulation of quantum barriers in the lateral directions poses a significant engineering challenge. Here, we demonstrate lateral quantum barrier manipulation in a crystalline SiGe alloy using structured mechanical fields to drive compositional redistribution. To apply stress, we make use of a nano-indenter array that is pressed against a Si0.8Ge0.2 wafer in a custom-made mechanical press. The entire assembly is then annealed at high temperatures, during which the larger Ge atoms are selectively driven away from areas of compressive stress. Compositional analysis of the SiGe substrates reveals that this approach leads to a transfer of the indenter array pattern to the near-surface elemental composition, resulting in near 100% Si regions underneath each indenter that are separated from each other by the surrounding Si0.8Ge0.2 bulk. The “stress transfer” process is studied in detail using multiscale computer simulations that demonstrate its robustness across a wide range of applied stresses and annealing temperatures. While the “Si nanodot” structures formed here are not intrinsically useful as quantum structures, it is anticipated that the stress transfer process may be modified by judicious control of the SiGe film thickness and indenter array pattern to form more technologically useful structures.
Dark-to-arc transition in field emission dominated atmospheric microdischarges
Authors: Tholeti Siva Sashank , Semnani Abbas , Peroulis Dimitrios , Alexeenko Alina A.
Published: August 2015

We study the voltage-current characteristics of gas discharges driven by field emission of electrons at the microscale. Particle-in-cell with Monte Carlo collision calculations are first verified by comparison with breakdown voltage measurements and then used to investigate atmospheric discharges in nitrogen at gaps from 1 to 10 μm. The results indicate the absence of the classical glow discharge regime because field electron emission replaces secondary electron emission as the discharge sustaining mechanism. Additionally, the onset of arcing is significantly delayed due to rarefied effects in electron transport. While field emission reduces the breakdown voltage, the power required to sustain an arc of the same density in microgaps is as much as 30% higher than at macroscale.
The effects of intrinsic noise on the behaviour of bistable cell regulatory systems under quasi-steady state conditions
Authors: de la Cruz Roberto , Guerrero Pilar , Spill Fabian , Alarcón Tomás
Published: August 2015

We analyse the effect of intrinsic fluctuations on the properties of bistable stochastic systems with time scale separation operating under quasi-steady state conditions. We first formulate a stochastic generalisation of the quasi-steady state approximation based on the semi-classical approximation of the partial differential equation for the generating function associated with the chemical master equation. Such approximation proceeds by optimising an action functional whose associated set of Euler-Lagrange (Hamilton) equations provides the most likely fluctuation path. We show that, under appropriate conditions granting time scale separation, the Hamiltonian can be re-scaled so that the set of Hamilton equations splits up into slow and fast variables, whereby the quasi-steady state approximation can be applied. We analyse two particular examples of systems whose mean-field limit has been shown to exhibit bi-stability: an enzyme-catalysed system of two mutually inhibitory proteins and a gene regulatory circuit with self-activation. Our theory establishes that the number of molecules of the conserved species is order parameters whose variation regulates bistable behaviour in the associated systems beyond the predictions of the mean-field theory. This prediction is fully confirmed by direct numerical simulations using the stochastic simulation algorithm. This result allows us to propose strategies whereby, by varying the number of molecules of the three conserved chemical species, cell properties associated to bistable behaviour (phenotype, cell-cycle status, etc.) can be controlled.
Nuclear velocity perturbation theory for vibrational circular dichroism: An approach based on the exact factorization of the electron-nuclear wave function
Authors: Scherrer Arne , Agostini Federica , Sebastiani Daniel , Gross E. K. U. , Vuilleumier Rodolphe
Published: August 2015

The nuclear velocity perturbation theory (NVPT) for vibrational circular dichroism (VCD) is derived from the exact factorization of the electron-nuclear wave function. This new formalism offers an exact starting point to include correction terms to the Born-Oppenheimer (BO) form of the molecular wave function, similar to the complete-adiabatic approximation. The corrections depend on a small parameter that, in a classical treatment of the nuclei, is identified as the nuclear velocity. Apart from proposing a rigorous basis for the NVPT, we show that the rotational strengths, related to the intensity of the VCD signal, contain a new contribution beyond-BO that can be evaluated with the NVPT and that only arises when the exact factorization approach is employed. Numerical results are presented for chiral and non-chiral systems to test the validity of the approach.
On the mesoscopic origins of high viscosities in some polyelectrolyte-surfactant mixtures
Authors: Hoffmann Ingo , Farago Bela , Schweins Ralf , Falus Peter , Sharp Melissa , Prévost Sylvain , Gradzielski Michael
Published: August 2015

Oppositely charged polyelectrolyte (PE) surfactant mixtures allow the control of rheological parameters of a solution even at fairly low concentrations. For example, addition of 0.3 wt. % of anionic surfactant to a 1 wt. % solution of the polycation JR 400 increases the viscosity by 4 orders of magnitude. Recently, we could show that this increase is related to the formation of mixed, rod-like PE/surfactant aggregates which interconnect several polyelectrolyte chains [Hoffmann et al., Europhys. Lett. 104, 28001 (2013)]. In this paper, we refine our structural model of the aggregates to obtain a more consistent picture of their internal structure for different anionic surfactants. Combining small angle neutron scattering (SANS) and neutron spin-echo (NSE) allows us to determine the size of the aggregates. By comparing different contrasts, the internal structure of the aggregates can be elucidated and it is seen that the PE in the aggregates retains a relatively high freedom of movement. We proceeded to investigate the influence of the surfactant concentration and the surfactant type on structure and dynamics of the mixed aggregates. It is seen that the structural parameters of the aggregates depend very little on the surfactant concentration and headgroup. However, it is crucial to incorporate a sufficient amount of PE in the aggregates to increase the viscosity of the aggregates. By comparing viscous samples at 1 wt. % PE concentration with samples at a PE concentration of 0.3 wt. %, where no significant increase in viscosity is observed, we find that similar aggregates are formed already at this lower PE concentrations. However, the amount of PE incorporated in them is insufficient to interconnect several PE chains and therefore, they do not increase viscosity. So, our detailed investigation combining contrast variation SANS and NSE does not only allow to explain the viscosity behavior but also to deduced detailed information regarding the structures and the dynamics especially of the polyelectrolyte within the complexes.
Theoretical study of the electronic spectra of neutral and cationic NpO and NpO2
Authors: Kovács Attila , Infante Ivan
Published: August 2015

The electronic of neutral NpO and NpO2 as well as of their mono- (NpO+, NpO2+) and dications (NpO2+, NpO22+) were studied using multiconfigurational relativistic quantum chemical calculations at the complete active space self-consistent field/CASPT2 level of taking into account The active space included 16 orbitals: all the 7s, 6d, and 5f orbitals of together with selected orbitals of oxygen. The vertical on the geometries have been computed up to ca. 35 000 cm−1. The gas-phase electronic were evaluated on the basis of the computed Einstein coefficients at 298 K and 3000 K. The computed vertical transition show good agreement with previous condensed-phase results on NpO2+ and NpO22+.
Spatial mapping and statistical reproducibility of an array of 256 one-dimensional quantum wires
Authors: Al-Taie H. , Smith L. W. , Lesage A. A. J. , See P. , Griffiths J. P. , Beere H. E. , Jones G. A. C. , Ritchie D. A. , Kelly M. J. , Smith C. G.
Published: August 2015

We utilize a multiplexing architecture to measure the conductance properties of an array of 256 split gates. We investigate the reproducibility of the pinch off and one-dimensional definition voltage as a function of spatial location on two different cooldowns, and after illuminating the device. The reproducibility of both these properties on the two cooldowns is high, the result of the density of the two-dimensional electron gas returning to a similar state after thermal cycling. The spatial variation of the pinch-off voltage reduces after illumination; however, the variation of the one-dimensional definition voltage increases due to an anomalous feature in the center of the array. A technique which quantifies the homogeneity of split-gate properties across the array is developed which captures the experimentally observed trends. In addition, the one-dimensional definition voltage is used to probe the density of the wafer at each split gate in the array on a micron scale using a capacitive model.
Indication of non-thermal contribution to visible femtosecond laser-induced CO oxidation on Ru(0001)
Authors: Öberg H. , Gladh J. , Marks K. , Ogasawara H. , Nilsson A. , Pettersson L. G. M. , Öström H.
Published: August 2015

We studied CO oxidation on Ru(0001) induced by 400 nm and 800 nm femtosecond laser pulses where we find a branching ratio between CO oxidation and desorption of 1:9 and 1:31, respectively, showing higher selectivity towards CO oxidation for the shorter wavelength excitation. Activation energies computed with density functional theory show discrepancies with values extracted from the experiments, indicating both a mixture between different adsorbed phases and importance of non-adiabatic effects on the effective barrier for oxidation. We simulated the reactions using kinetic modeling based on the two-temperature model of laser-induced energy transfer in the substrate combined with a friction model for the coupling to adsorbate vibrations. This model gives an overall good agreement with experiment except for the substantial difference in yield ratio between CO oxidation and desorption at 400 nm and 800 nm. However, including also the initial, non-thermal effect of electrons transiently excited into antibonding states of the O-Ru bond yielded good agreement with all experimental results.
Fragmentation of mercury compounds under ultraviolet light irradiation
Authors: Kokkonen E. , Löytynoja T. , Hautala L. , Jänkälä K. , Huttula M.
Published: August 2015

Ultraviolet light induced photofragmentation of mercury compounds is studied experimentally with electron energy resolved photoelectron-photoion coincidence techniques and theoretically with computational quantum chemical methods. A high resolution photoelectron spectrum using synchrotron radiation is presented. Fragmentation of the molecule is studied subsequent to ionization to the atomic-mercury-like d orbitals. State dependent fragmentation behaviour is presented and specific reactions for dissociation pathways are given. The fragmentation is found to differ distinctly in similar orbitals of different mercury compounds.
Properties of the extreme ultraviolet emission from germanium and gallium plasmas
Authors: Li Bowen , Hara Hiroyuki , Suzuki Yuhei , Arai Goki , Higashiguchi Takeshi , Ohashi Hayato , Jiang Weihua , Makimura Tetsuya , Sakaue Hiroyuki A. , Suzuki Chihiro , Kato Daiji , Murakami Izumi , Dunne Padraig , Long Elaine , Sheridan Paul , Chen Ximeng , O'Sullivan Gerry
Published: August 2015

We report on the usefulness of germanium (Ge) and gallium (Ga) plasmas as potential extreme ultraviolet (EUV) sources at both 6.x and 13.5 nm, wavelengths of interest for lithography and metrology applications. Spectra from plasmas produced using neodymium-doped yttrium-aluminum-garnet (Nd:YAG) lasers with pulse durations of 170 ps and 7 ns [full width at half-maximum] and a compact electron beam ion trap have been used to determine the charge states responsible while theoretical calculations using atomic structure Cowan and HULLAC codes enabled the identification of structure in the Ge spectrum arising from strong transitions of the type 3d – 4p and 3d – 4f. Transitions of the type 3d – 4f in Ge10+ and Ga11+ were found to lie in the 6.x nm region, while 3p−3d transitions from a range of stages in both elements contribute in the 13.5 nm region. We also studied the emission spectra of galinstan plasmas, and the results imply that galinstan might provide a promising candidate for EUV applications that exploit the progress in the development of multilayer mirrors for operation at 6.x nm.
A multi criterion analysis for renewable energy integration process of a standalone hybrid energy system with internal combustion generator
Authors: Perera A. T. D. , Nadeesh Madusanka A. , Attalage R. A. , Perera K. K. C. K.
Published: August 2015

Integrating renewable energy into standalone Internal Combustion Generator (ICG) systems is an economical and eco-friendly option. However, previous studies demonstrate the difficulties in replacing the ICGs completely by using Solar PV (SPV) and wind energy with a dispatchable energy storage. This makes it interesting to analyze the limitations in integrating the SPV and wind energy into Hybrid Energy System. A multi criterion analysis is presented in this study, considering Levelized Energy Cost, Loss of Load Probability, and Fuel Consumption varying the scale of the ICG capacity to attain aforementioned objective. Changes in the system design with the integration of the SPV and wind energy were analyzed using Pareto multi-objective optimization considering Renewable Energy Capacity as an objective function. Sensitivity of the ICG capacity on optimum Renewable Energy Technology, role of the ICG in improving system reliability, etc., were subsequently analyzed. The results depict that the ICG capacity notably influence to the balance between wind and SPV capacity. An increase in the ICG capacity does increase the contribution from dispatchable energy source in most of the scenarios. Furthermore, it facilitates to amalgamate highly fluctuating renewable energy sources at a relatively low cost. This makes it inevitable to replace ICG with non-dispatchable renewable energy sources and energy storage.
Explicitly correlated similarity transformed equation-of-motion coupled-cluster method
Authors: Bokhan Denis , Trubnikov Dmitrii N. , Bartlett Rodney J.
Published: August 2015

Similarity transformed equation-of-motion method, based on linearly approximated explicitly correlated coupled-cluster singles and doubles [CCSD(F12)] model, has been formulated and implemented. An extension of similarity transformation operator is introduced in order to treat short-range correlation effects for excited states. Additionally, effective reduction of the number of active virtuals can be obtained by such modification. Numerical tests for sets of valence and Rydberg excited states of several molecules are conducted. Statistical measures of errors in excitation energies show that explicitly correlated results are accurate up to 0.1 e.V already at a double-ζ level compared to those in the complete basis set limit, if the excitation energy is not too close to an ionization threshold. An example of long-range charge transfer excitation is also considered and highly accurate results are obtained.
A new procedure for wind energy systems maintenance design
Authors: Costa A. M. , Fraguela F. , Orosa J. A. , Pérez J. A.
Published: August 2015

The present study introduces a new procedure to analyze and design wind farms maintenance plans, based on analysis of variance, that can be directly implemented by the own operator. This methodology, based on a one-way analysis of variance study of weather variables and wind turbine working conditions, allows to define the exact operating range at which each of the most frequent errors in wind farms used to happen. Typically, most frequent errors, like freezing of anemometers, excessive orientation time errors, brake shoe excessive temperature, emergency stop, and asymmetric currents, appear under certain weather, temperature, and wind velocity conditions, in such a way that they can be modeled as a function of wind velocity and wind direction. In a similar way, other analyzed errors, such as starting problems and errors in current phase sequence, showed a tendency to appear under specific wind orientations.
A combined dynamic economic emission dispatch and time of use demand response mathematical modelling framework
Authors: Nwulu N. I. , Xia X.
Published: August 2015

In this paper, we integrate a Demand Response (DR) program into the multi-objective dynamic economic emission dispatch (DEED) optimization problem. The resulting optimization problem is termed DR-DEED. The DR program is a time based program known as the Time of Use DR program. The DR program has been developed using the customers' Price Elasticity Matrices, which models the customer behavior under different conditions. An interactive control strategy between utility and consumers is proposed for the combined DR-DEED model, which determines the optimal power to be generated by minimizing fuel, emissions, and DR costs and also the optimal price. The customer in light of the utility's optimal price minimizes its electricity cost and optimally schedules power consumption. Obtained results indicate that DR programs are mutually beneficial to utility and consumers alike and can bring about desired demand reduction in the power system.
Experimental estimation of oxidation-induced Si atoms emission on Si(001) surfaces
Authors: Ogawa Shuichi , Tang Jiayi , Takakuwa Yuji
Published: August 2015

Kinetics of Si atoms emission during the oxidation of Si(001) surfaces have been investigated using reflection high energy electron diffraction combined with Auger electron spectroscopy. The area ratio of the 1 × 2 and the 2 × 1 domains on a clean Si(001) surface changed with the oxidation of the surface by Langmuir-type adsorption. This change in the domain ratio is attributed to the emission of Si atoms. We can describe the changes in the domain ratio using the Si emission kinetics model, which states that (1) the emission rate is proportional to the oxide coverage, and (2) the emitted Si atoms migrate on the surface and are trapped at SB steps. Based on our model, we find experimentally that up to 0.4 ML of Si atoms are emitted during the oxidation of a Si(001) surface at 576 °C.
PlantBottle™ Packaging program is continuing its journey to pursue bio-mono-ethylene glycol using agricultural waste
Authors: Ren Haiyu , Qiao Fangqing , Shi Yu , Knutzen Michael W. , Wang Zhou , Du Huanzheng , Zhang Huaying
Published: August 2015

Since launching the PlantBottle™ Packaging program in 2009, The Coca-Cola Company has distributed more than 30 × 109 bottles in nearly 40 countries using its current PlantBottle packaging, which is made from up to 30% plant-based materials. It is estimated the use of PlantBottle packaging since launch has helped save the equivalent annual emissions of more than 315 000 metric tons of carbon dioxide. To expand the application of this innovative packaging material, a sustainable feedstock needs to be identified, and a new technology needs to be developed to allow its integration into PlantBottle technology, for using agriculture waste to produce bio-polyethylene terephthalate (bio-PET), and develop an economically viable supply chain of bio-PET in China. These breakthroughs can also be applied beyond packaging and have the potential to help companies around the world reach their own sustainability goals. Using renewable feedstock to produce bio-PET reduces dependence on petro-based resources, mitigates carbon emissions, and promotes sustainable development. Under the China-US EcoPartnership program, The Coca-Cola Company partners with the Yangtze River Delta Circular Economy Institute of Technologyto identify and advance commercial technologies for converting local agricultural residues or wastes (e.g., corn cob and stover) into the base ingredient, mono-ethylene glycol (MEG), for manufacturing polyester resin/fiber. The Coca-Cola Company is developing bio-MEG conversion technology with a technology and implementation partner, and finalizing the technical conversion process for commercial production. Yangtze River Delta Circular Economy Institute of Technology is exploring the related supply chain and feedstock logistics. Any advancement using agricultural wastes today are likely to have continued relevance to this second part of the journey toward realizing sustainably sourced and fully recyclable PET plastic product solutions.
Electrical properties of GaAs metal–oxide–semiconductor structure comprising Al2O3 gate oxide and AlN passivation layer fabricated in situ using a metal–organic vapor deposition/atomic layer deposition hybrid system
Authors: Aoki Takeshi , Fukuhara Noboru , Osada Takenori , Sazawa Hiroyuki , Hata Masahiko , Inoue Takayuki
Published: August 2015

This paper presents a compressive study on the fabrication and optimization of GaAs metal–oxide–semiconductor (MOS) structures comprising a Al2O3 gate oxide, deposited via atomic layer deposition (ALD), with an AlN interfacial passivation layer prepared in situ via metal–organic chemical vapor deposition (MOCVD). The established protocol afforded self-limiting growth of Al2O3 in the atmospheric MOCVD reactor. Consequently, this enabled successive growth of MOCVD-formed AlN and ALD-formed Al2O3 layers on the GaAs substrate. The effects of AlN thickness, post-deposition anneal (PDA) conditions, and crystal orientation of the GaAs substrate on the electrical properties of the resulting MOS capacitors were investigated. Thin AlN passivation layers afforded incorporation of optimum amounts of nitrogen, leading to good capacitance–voltage (C–V) characteristics with reduced frequency dispersion. In contrast, excessively thick AlN passivation layers degraded the interface, thereby increasing the interfacial density of states (Dit) near the midgap and reducing the conduction band offset. To further improve the interface with the thin AlN passivation layers, the PDA conditions were optimized. Using wet nitrogen at 600 °C was effective to reduce Dit to below 2 × 1012 cm−2 eV−1. Using a (111)A substrate was also effective in reducing the frequency dispersion of accumulation capacitance, thus suggesting the suppression of traps in GaAs located near the dielectric/GaAs interface. The current findings suggest that using an atmosphere ALD process with in situ AlN passivation using the current MOCVD system could be an efficient solution to improving GaAs MOS interfaces.
Effective landfill gas management strategies for methane control and reuse technology
Authors: Mahajan Devinder , Tonjes David J. , Mamalis Sotirios , Boudreaux Rebecca , Hasty Julia K. , Danhui Xin , Youcai Zhao , Jianglin Cao , Wentao Zhao , Xiaoli Chai
Published: August 2015

In keeping with the Energy and Environment theme of the EcoPartnership program, the Stony Brook-Tongji collaboration is addressing greenhouse gas emissions from landfills, one of the most critical issues of our time. Tongji is developing a model that can significantly improve the accuracy of emissions estimates, while Stony Brook is perfecting an innovative technology to economically removal impurities and produce a clean fuel for transportation, heating, or electricity generation. The environmental impact of the process being developed under this collaboration versus releasing fugitive gases is noted. By the culmination of this partnership, both sides have developed economical pathways to effectively utilize fugitive gases and commercialized technologies for transportation use and power generation for offering in both countries.
Compliance current dependence of conversion between bipolar, unipolar, and threshold resistance switching in Mn3O4 films
Authors: Wu Shuxiang , Li Shuwei
Published: August 2015

We report deterministic conversion between bipolar, unipolar and threshold resistance switching in Pt/Mn3O4/Pt memory devices via tuning compliance current. The conversion between bipolar and unipolar switching is reversible, while that between memory switching and threshold switching is irreversible. The nonvolatile bipolar resistance switching behaviors could be attributed to modification of Schottky barrier at Pt/Mn3O4 interface due to the migration of positively charged oxygen vacancies. With the increase of current, the incomplete filament formed in the set operation of bipolar switching could continue to grow and until completely form. The subsequent rupture and formation of filament consisting of oxygen vacancies under electric field are responsible for the unipolar resistance switching. Further increase of compliance current causes the volatile threshold switching behavior in the Pt/Mn3O4/Pt devices, which could be originated from formation and rupture of filament consisting of Mn ions due to the high Joule heat generated by large current.
Effects of glycerin and essential oils (Anacardium occidentale and Ricinus communis) on the meat quality of crossbred bulls finished in a feedlot
Authors: Prado I. N. , Cruz O. T. B. , Valero M. V. , Zawadzki F. , Eiras C. E. , Rivaroli D. C. , Prado R. M. , Visentainer J. V.
Published: August 2015

The aim of this study was to investigate the effects on meat quality of crossbred bulls finished in a feedlot when some corn is replaced by glycerin and essential oils (EO) are added to the diet. Thirty bulls weighing 311 kg ± 28.8 kg (22 ± 2 months old) were randomly assigned to one of three diets: CON – Control (diet without glycerin and EO); GLY – 16.1% glycerin in dry matter (DM); and GEO – 16.1% glycerin in DM and EO (cashew: Anacardium occidentale; castor: Ricinus communis) at 442 mg/kg DM consumed. The bulls were kept in a feedlot for 115 days and slaughtered at an average weight of 467 ± 27.9 kg (25 ± 2 months old). The bulls were fed on sorghum silage, cracked corn, glycerin, soybean meal, urea, limestone, and mineral salt. Replacing corn with glycerin plus EO adding to the diet had no effect on the fat thickness, Longissimus muscle (LM) area, marbling, texture, colour, Warner–Bratzler shear force, or chemical composition of the LM. The fatty acid composition in the LM was similar among the diets, except for percentages of myristic and margaric acids. The diets had no effect on the percentage of saturated and polyunsaturated fatty acids. Animals fed on glycerin had a lower ratio of n-6 to n-3 in the LM when compared with the CON diet. Partial replacing of corn with glycerin and EO improved meat flavour, tenderness, and the preference of consumers. Corn may be replaced by glycerin to a 15% level of DM without any detrimental effect on the carcass characteristics or the chemical composition of the LM.
Re-analysis of plant CO2 responses during the exponential growth phase: interactions with light, temperature, nutrients and water availability
Authors: Kirschbaum Miko U. F. , Lambie Suzanne M.
Published: August 2015

Many short-term experiments have been conducted under increasing CO2 but results have been varied and have not yet led to a conclusive quantitative understanding of the CO2 response of plant growth. This may have been partly due to a lack of explicit consideration of the positive feedback inherent in plant growth during periods of exponential growth. This feedback can increase an initial physiological enhancement of relative growth rate (RGR) into a much larger biomass enhancement. To overcome this problem, we re-analysed existing experimental data from 78 publications. We calculated the RGRs of C3 plants and their relative enhancement under elevated CO2 and derived response indices that were independent of the duration of experiments and the RGR at normal atmospheric CO2. The RGR of unstressed plants increased by 14 ± 2% under doubled CO2, with observed RGR enhancement linearly correlated with calculated photosynthetic enhancements (based on the Farquhar-von Caemmerer-Berry photosynthesis model), but at only half their numeric values. Calculated RGR enhancements did not change significantly for temperatures from 12 to 40°C, but were reduced under nutrient limitation, and were increased under water stress or low irradiance. We concluded that short-term experiments can offer simple and cost-effective insights into plant CO2 responses, provided they are analysed by calculating relative changes in RGR during the strictly exponential initial growth phase.
The influence of urban encroachment on squirrel gliders (Petaurus norfolcensis): effects of road density, light and noise pollution
Authors: Francis Mitchell J. , Spooner Peter G. , Matthews Alison
Published: August 2015

Context Loss and degradation of habitat from urban development is a key threat to the squirrel glider (Petaurus norfolcensis), because its distribution coincides where most people live in Australia. Squirrel gliders are known to occur in or around urban fringes where native vegetation is retained; however, little is known about specific anthropogenic factors that may affect their persistence. Aims We investigated the relative influence of biophysical and urban factors on the use of large hollow-bearing Eucalyptus trees, which are a key resource for squirrel gliders. The study was located in a typical urban growth area located in southern New South Wales. Methods A stratified random sampling approach was used to survey squirrel gliders in urban and rural areas. Infrared, motion-sensor cameras were placed in 34 selected trees for 17 nights to record squirrel glider occupancy and activity. Data on urban (e.g. light and noise pollution levels, road and housing density) and biophysical (e.g. tree height, hollow-bearing tree density, vegetation cover) variables were recorded at each survey tree. Data were statistically analysed using general linear modelling approaches. Key results Squirrel gliders were detected more frequently in the rural matrix (23.4% of camera trap-nights) than in urban areas (9.5%). Model results showed that tree height, and the distance to neighbouring trees, had a significant influence on the occurrence and activity of squirrel gliders. Road density and light pollution were included in ‘best’ models to explain glider activity (a negative influence), and noise pollution negatively influenced glider occurrence. Although gliders used large trees in both urban and rural areas, activity generally decreased as levels of urbanisation increased. Conclusions and implications Access to and availability of key resources such as tall, hollow-bearing trees is critical for gliders to persist in urban environments. Squirrel gliders will tolerate human stressors such as roads, noise and light pollution to a certain extent, but impacts on population viability remain largely unknown. Novel solutions need to be developed to lessen the effects of anthropogenic factors (such as light and noise) on patches of native vegetation retained in urban areas for conservation purposes.
Cyclin-dependent kinase 5 activates guanine nucleotide exchange factor GIV/Girdin to orchestrate migration–proliferation dichotomy
Authors: Bhandari Deepali , Lopez-Sanchez Inmaculada , To Andrew , Lo I-Chung , Aznar Nicolas , Leyme Anthony , Gupta Vijay , Niesman Ingrid , Maddox Adam L. , Garcia-Marcos Mikel , Farquhar Marilyn G. , Ghosh Pradipta
Published: August 2015

Significance

The guanine nucleotide exchange factor (GEF) GIV/Girdin has previously been shown to trigger noncanonical activation of trimeric G proteins in response to multiple chemical stimuli at the plasma membrane and at various locations within cells. In this work we identified a single phosphoevent and pinpointed cyclin-dependent kinase 5 (CDK5) as the responsible kinase that activates GIV's GEF function and initiates noncanonical G protein signaling via GIV. These studies provide evidence that CDK5 is essential for maximal activation of GIV-GEF in cells and insights into a hitherto unrecognized crosstalk between CDK5 and G proteins via GIV. Such crosstalk may shape migration–proliferation dichotomy during several physiological and pathological scenarios such as wound healing and cancer metastasis.
Perspective taking in referring to objects behind versus in front of an observer: Frames of reference, intraindividual consistency, and response latencies
Authors: Beller Sieghard , Bohlen Judith , Hüther Lisa , Bender Andrea
Published: August 2015

Speakers of English and German typically adopt the reflection variant of the relative frame of reference (FoR) in order to describe how nonoriented objects that are located in front of them are related to one another. Little is known, however, about how they proceed in dorsal settings, with objects located in their back. In this article, we explore the turn hypothesis, which assumes a (mental) 180° turn of the observer to face the objects, converting the dorsal into a frontal situation, so that the preferred FoR variant for frontal settings can be applied. To elicit spatial references, we used photographs that showed an observer and two objects either in the observer's visual field ( frontal condition) or in the observer's back ( dorsal condition). The observer was looking either in the same direction as the referencing individual ( aligned perspectives) or in the opposite direction ( vis-à-vis perspective). Data from two experiments show that while participants do adopt the observer's perspective, their references in dorsal settings are incompatible with the turn hypothesis. Analyses of response latencies indicate additional cognitive costs for establishing a FoR for the very first item in the dorsal condition as compared to the frontal condition, but fast adaption for subsequent items, and high intraindividual consistency in FoR choice in both conditions. Maintaining the assumption that references in dorsal settings should be compatible with the variant of the relative FoR adopted in frontal settings, participants’ references can be explained by assuming a backward projection that gets by without a (mental) turn of the observer.
GenomeLaser: fast and accurate haplotyping from pedigree genotypes
Authors: Li Wenzhi , Fu Guoxing , Rao Weinian , Xu Wei , Ma Li , Guo Shiwen , Song Qing
Published: August 2015

Summary: We present a software tool called GenomeLaser that determines the haplotypes of each person from unphased high-throughput genotypes in family pedigrees. This method features high accuracy, chromosome-range phasing distance, linear computing, flexible pedigree types and flexible genetic marker types.

Availability and implementation:  http://www.4dgenome.com/software/genomelaser.html.

Contact:  qsong@msm.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
An integrated structure- and system-based framework to identify new targets of metabolites and known drugs
Authors: Naveed Hammad , Hameed Umar S. , Harrus Deborah , Bourguet William , Arold Stefan T. , Gao Xin
Published: August 2015

Motivation: The inherent promiscuity of small molecules towards protein targets impedes our understanding of healthy versus diseased metabolism. This promiscuity also poses a challenge for the pharmaceutical industry as identifying all protein targets is important to assess (side) effects and repositioning opportunities for a drug.

Results: Here, we present a novel integrated structure- and system-based approach of drug-target prediction (iDTP) to enable the large-scale discovery of new targets for small molecules, such as pharmaceutical drugs, co-factors and metabolites (collectively called ‘drugs’). For a given drug, our method uses sequence order–independent structure alignment, hierarchical clustering and probabilistic sequence similarity to construct a probabilistic pocket ensemble (PPE) that captures promiscuous structural features of different binding sites on known targets. A drug’s PPE is combined with an approximation of its delivery profile to reduce false positives. In our cross-validation study, we use iDTP to predict the known targets of 11 drugs, with 63% sensitivity and 81% specificity. We then predicted novel targets for these drugs—two that are of high pharmacological interest, the peroxisome proliferator-activated receptor gamma and the oncogene B-cell lymphoma 2, were successfully validated through in vitro binding experiments. Our method is broadly applicable for the prediction of protein-small molecule interactions with several novel applications to biological research and drug development.

Availability and implementation: The program, datasets and results are freely available to academic users at http://sfb.kaust.edu.sa/Pages/Software.aspx.

Contact:  xin.gao@kaust.edu.sa and stefan.arold@kaust.edu.sa

Supplementary information:  Supplementary data are available at Bioinformatics online.
Experimental analysis of the use of fishery closures and cooperatives to reduce economic rent dissipation caused by assignment problems
Authors: Emery Timothy J. , Tisdell John , Green Bridget S. , Hartmann Klaas , Gardner Caleb , León Rafael
Published: August 2015

Assignment problems in quota-managed fisheries are caused by spatial and temporal heterogeneity in the productivity of the stock. If the quota management system is not fully delineated (e.g. harvest rights assigned to particular areas) then fishers will compete with each other and overexploit parts of the fishery where or when the quota unit value is highest (i.e. fishing costs low and/or market price high), leading to economic rent dissipation. This study used experimental economics to assess the effectiveness of fishery temporal closures and income-sharing fishery cooperatives in resolving assignment problems across three different fisheries with varying levels of fisher heterogeneity (i.e. numbers of quota owners and lease quota fishers). While most fisheries were successful in reducing economic rent dissipation under the fishery closure management structure relative to their baseline(s), fisheries characterized by a greater number of lease quota fishers were less effective. This was due to the differential values that lease quota fishers place on the resource relative to quota owners, due to having insecurity of tenure and diminished wealth in having to bid for a quota package and pay for it using their revenue from fishing. Conversely, income-sharing fishery cooperatives were equally successful across all three fisheries in reducing assignment problems relative to their baseline(s). This was because income-sharing created an incentive to coordinate fishing effort, particularly among heterogeneous groups. While requiring further exposition in the field, these experimental results represent a first step in identifying management institutions that may assist fishers under quota management to resolve assignment problems in a dynamic environment.
Chemopreventive effects of pequi oil (Caryocar brasiliense Camb.) on preneoplastic lesions in a mouse model of hepatocarcinogenesis
Authors: Palmeira Simone M. , Silva Paula R.P. , Ferrão Juliana S.P. , Ladd Aliny A.B.L. , Dagli Maria L.Z. , Grisolia Cesar K. , Hernandez-Blazquez Francisco J.
Published: August 2015

Pequi (Caryocar brasiliense Camb.), a fruit from Brazil’s central region, was evaluated for its chemopreventive effects on preneoplastic liver lesions induced by the carcinogen diethylnitrosamine (DEN) in mice. BALB/c mice, 14 days of age, received an intraperitoneal injection at 10 µg/g of DEN. The mice received either of two doses of pequi oil (100 or 400 mg/kg) daily from the age of 30 days and were killed at the age of 189 days. Stereological parameters, including the volume density (V
v) and the total volume (V
tot) of the lesions (preneoplastic and adenomas), were measured and the expression of cytokeratins CK8/18 was evaluated. The total volume of lesions and adenomas was reduced by 51% in the group treated with the carcinogen and 400 mg/kg of pequi oil administered daily by an oral gavage for 25 consecutive weeks. In addition, some mice in this group did not develop lesions. Among the remaining preneoplastic lesions in this group, the number of remodelled profiles increased by 2.4-fold in the 400-mg pequi oil-treated mice relative to the 100-mg-treated mice. Our results show that pequi oil exerts a hepatoprotective effect against DEN-induced development of preneoplastic lesions and adenoma in mice and the potential for its use in the prevention of liver cancer.
Blockade of GPR55 in the dorsolateral striatum impairs performance of rats in a T-maze paradigm
Authors: Marichal-Cancino Bruno A. , Sánchez-Fuentes Asai , Méndez-Díaz Mónica , Ruiz-Contreras Alejandra E. , Prospéro-García Oscar
Published: August 2015

To investigate the role of GPR55 receptors, which are expressed in human and rat striatum (a structure that regulates procedural memory), Wistar rats received five training sessions (10 trials/session, 1 session/day) to solve a T-maze paradigm. From these data, we constructed learning curves following pharmacological manipulation of GPR55. Five minutes before each session, animals received bilateral intradorsolateral striatum injections of noladin-ether (3.1 nmol/l; endogenous agonist of GPR55 and CB1 receptors), CID16020036 (5.6 nmol/l; GPR55 antagonist), AM251 (5.6 nmol/l; CB1 antagonist), or a combination of noladin-ether with each antagonist. Noladin-ether by itself induced no significant changes in the learning curve. Nevertheless, while simultaneously blocking CB1 receptors (with AM251), noladin-ether improved acquisition. In contrast, while simultaneously blocking GPR55 (with CID16020036), noladin-ether weakened acquisition. CID16020036 by itself impaired learning, whereas AM251 by itself reduced the efficiency in the task. There were no differences between groups in the latency to reach the arms from the starting point; thus, no motor coordination impairments interfered with this task. These results strongly suggest a role of GPR55 in procedural memory and constitute the first evidence indicating that this receptor regulates cognitive processes.
Prospective evaluation of the Eppendorf–Cologne Scale
Authors: Hoffmann Michael , Lehmann Wolfgang , Schroeder Malte , Cramer Christopher , Grossterlinden Lars G. , Rueger Johannes M. , Lefering Rolf
Published: August 2015

Objectives

Early diagnosis of traumatic brain injury and reliable prediction of outcome are essential for determining treatment strategies and allocating resources. This study re-evaluates the Eppendorf–Cologne Scale (ECS) and its predictive accuracy for outcome compared with the Glasgow Coma Scale (GCS).

Methods

A prospective cohort analysis of severely injured trauma patients registered in the Trauma Registry of the German Society for Trauma Surgery from 2012–2013 was carried out. Only directly admitted patients alive on admission with complete data on GCS, ECS and outcome in terms of survival to hospital discharge or death were included. The predictive accuracy in terms of the outcome of the ECS and the GCS was modelled using area under the receiver operating characteristic (AUROC) curve analysis.

Results

A total of 17 616 patients fulfilled the study inclusion criteria. The ECS outmatched the predictive accuracy of the GCS for outcome (AUROC, 0.853, 95% confidence interval, 0.831–0.854; and AUROC 0.836; 95% confidence interval, 0.825–0.848, respectively; P=0.062). An ECS score of 8 was associated with a 25-fold higher mortality compared with an ECS score of 0. Patients who had an ECS score of 8 had a 1.5-fold higher mortality compared with patients allocated a GCS score of 3.

Conclusion

The ECS shows a higher accuracy for prediction of outcome compared with the GCS and enables further differentiation within the critical GCS 3 collective.
Which adverse events should be reported in an emergency department? A Delphi study
Authors: Robinson Susan M. , Walker Ben F. , Brown Ruth M.
Published: August 2015

Objective

The aim of this study was to determine if emergency medicine specific triggers for completing an incident form could be agreed and if a common definition for contributory factors could be achieved. Such definitions could be used to improve safety within the emergency department (ED) and share learning across the specialty.

Participants and methods

One hundred and fifteen ED safety leads in the UK and Ireland were invited to participate in a Delphi study. This process took 1 year to complete. In the first round, participants listed 20 events that should be reported as an adverse event and 20 contributory factors that could contribute to risk or harm. An 80% concordance level was sought for both aspects.

Results

Eighty-four per cent of safety leads participated in the first round, although this decreased over subsequent rounds to 43%. Four hundred and eighty-five triggers were initially suggested; eventually, 27 triggers that should always or usually be reported achieved 80% concordance. Sixty-eight contributory factors were initially identified with eventual agreement being reached on 27 remediable contributory factors.

Conclusion

The process demonstrated agreement amongst emergency physicians in the UK and Ireland on the type of events that should be formally reported. The lists emerging from this process should not be viewed as exhaustive; rather they should be used to encourage the reporting of incidents and designing safer systems and processes within the ED.