bluuebunny/crossref_metadata_2025 huggingface dataset:
Six-dimensional quantum dynamics study for the dissociative adsorption of DCl on Au(111) surface
Authors: Liu Tianhui , Fu Bina , Zhang Dong H.
Published: April 2014

We carried out six-dimensional quantum dynamics calculations for the dissociative adsorption of deuterium chloride (DCl) on Au(111) surface using the initial state-selected time-dependent wave packet approach. The four-dimensional dissociation probabilities are also obtained with the center of mass of DCl fixed at various sites. These calculations were all performed based on an accurate potential energy surface recently constructed by neural network fitting to density function theory energy points. The origin of the extremely small dissociation probability for DCl/HCl (v = 0, j = 0) fixed at the top site compared to other fixed sites is elucidated in this study. The influence of vibrational excitation and rotational orientation of DCl on the reactivity was investigated by calculating six-dimensional dissociation probabilities. The vibrational excitation of DCl enhances the reactivity substantially and the helicopter orientation yields higher dissociation probability than the cartwheel orientation. The site-averaged dissociation probability over 25 fixed sites obtained from four-dimensional quantum dynamics calculations can accurately reproduce the six-dimensional dissociation probability.
A hybrid magnetic/complementary metal oxide semiconductor three-context memory bit cell for non-volatile circuit design
Authors: Jovanović B. , Brum R. M. , Torres L.
Published: April 2014

After decades of continued scaling to the beat of Moore's law, it now appears that conventional silicon based devices are approaching their physical limits. In today's deep-submicron nodes, a number of short-channel and quantum effects are emerging that affect the manufacturing process, as well as, the functionality of the microelectronic systems-on-chip. Spintronics devices that exploit both the intrinsic spin of the electron and its associated magnetic moment, in addition to its fundamental electronic charge, are promising solutions to circumvent these scaling threats. Being compatible with the CMOS technology, such devices offer a promising synergy of radiation immunity, infinite endurance, non-volatility, increased density, etc. In this paper, we present a hybrid (magnetic/CMOS) cell that is able to store and process data both electrically and magnetically. The cell is based on perpendicular spin-transfer torque magnetic tunnel junctions (STT-MTJs) and is suitable for use in magnetic random access memories and reprogrammable computing (non-volatile registers, processor cache memories, magnetic field-programmable gate arrays, etc). To demonstrate the potential our hybrid cell, we physically implemented a small hybrid memory block using 45 nm × 45 nm round MTJs for the magnetic part and 28 nm fully depleted silicon on insulator (FD-SOI) technology for the CMOS part. We also report the cells measured performances in terms of area, robustness, read/write speed and energy consumption.
Ultrafast all-optical switching via coherent modulation of metamaterial absorption
Authors: Fang Xu , Lun Tseng Ming , Ou Jun-Yu , MacDonald Kevin F. , Ping Tsai Din , Zheludev Nikolay I.
Published: April 2014

We report on the demonstration of a femtosecond all-optical modulator providing, without nonlinearity and therefore at arbitrarily low intensity, ultrafast light-by-light control. The device engages the coherent interaction of optical waves on a metamaterial nanostructure only 30 nm thick to efficiently control absorption of near-infrared (750–1040 nm) femtosecond pulses, providing switching contrast ratios approaching 3:1 with a modulation bandwidth in excess of 2 THz. The functional paradigm illustrated here opens the path to a broad family of meta-devices for ultrafast optical data processing in coherent networks.
First-principles study of carrier-induced ferromagnetism in bilayer and multilayer zigzag graphene nanoribbons
Authors: Sawada Keisuke , Ishii Fumiyuki , Saito Mineo
Published: April 2014

We studied magnetism in bilayer and multilayer zigzag graphene nanoribbons (ZGNRs) through first-principles density functional theory calculations. We found that the magnetic ground state of bilayer ZGNRs is the C-type antiferromagnetic (AFM) state, which is the AFM order between intraplane-edge carbon atoms and ferromagnetic (FM) order between interplane edge carbon atoms. In the cases of infinitely stacked multilayer ZGNRs, i.e., zigzag graphite nanoribbons, the C-type AFM state is also the most stable. By carrier doping, we found that the magnetic ground state changed from the C-AFM state to the FM state and, thus, realized two-dimensional FM surface (edge) states of graphite with a metallic conductivity.
Behavior of rotating magnetic microrobots above the step-out frequency with application to control of multi-microrobot systems
Authors: Mahoney Arthur W. , Nelson Nathan D. , Peyer Kathrin E. , Nelson Bradley J. , Abbott Jake J.
Published: April 2014

This paper studies the behavior of rotating magnetic microrobots, constructed with a permanent magnet or a soft ferromagnet, when the applied magnetic field rotates faster than a microrobot's step-out frequency (the frequency requiring the entire available magnetic torque to maintain synchronous rotation). A microrobot's velocity dramatically declines when operated above the step-out frequency. As a result, it has generally been assumed that microrobots should be operated beneath their step-out frequency. In this paper, we report and demonstrate properties of a microrobot's behavior above the step-out frequency that will be useful for the design and control of multi-microrobot systems.
High thermal stability and low Gilbert damping constant of CoFeB/MgO bilayer with perpendicular magnetic anisotropy by Al capping and rapid thermal annealing
Authors: Wang Ding-Shuo , Lai Shu-Yu , Lin Tzu-Ying , Chien Cheng-Wei , Ellsworth David , Wang Liang-Wei , Liao Jung-Wei , Lu Lei , Wang Yung-Hung , Wu Mingzhong , Lai Chih-Huang
Published: April 2014

We demonstrate that the magnetic anisotropy of the CoFeB/MgO bilayer can be manipulated by adding an aluminum capping layer. After rapid thermal annealing, we can achieve large perpendicular magnetic anisotropy of CoFeB with a high thermal stability factor (Δ = 72) while the Gilbert damping constant can be reduced down to only 0.011 simultaneously. The boron and residual oxygen in the bulk CoFeB layer are properly absorbed by the Al capping layer during annealing, leading to the enhanced exchange stiffness and reduced damping. The interfacial Fe-O bonding can be optimized by tuning annealing temperature and thickness of Al, resulting in enhanced perpendicular anisotropy.
Anisotropic strain, magnetic properties, and lattice dynamics in self-assembled multiferroic CoFe2O4-PbTiO3 nanostructures
Authors: Tsai C. Y. , Chen H. R. , Chang F. C. , Kuo H. H. , Cheng H. M. , Tsai W. C. , Chu Y. H. , Lai C. H. , Hsieh W. F.
Published: April 2014

We investigate the anisotropic stress dependent magnetic and phonon behaviors in self-assembled CoFe2O4-PbTiO3 (CFO-PTO) nanostructures deposited on SrRuO3 buffered SrTiO3 substrates of various thickness. The increased vertical compressed stress with increasing thickness enhances the vertical magnetic anisotropy of CFO while gradually reducing the vertical polarization of PTO. By applying the magnetic-field dependent Raman scattering, the CFO-A1g and T2g(1) phonon frequencies shift oppositely because of the magnetostriction. Moreover, the PTO-A1 mode intensities anomalously enhance and the A1 and E mode frequencies, respectively, increase and decrease, which prove the existence of the stress-mediated magnetoelectric (ME) effect. This study shows that the ME transmission process is dominated by interfacial stress, which is critical for enhancing the ME efficiency.
Pulsed laser induced ohmic back contact in CdTe solar cells
Authors: Simonds Brian J. , Palekis Vasilios , Van Devener Brian , Ferekides Christos , Scarpulla Michael A.
Published: April 2014

Creating an ohmic back contact has long been a problem for making efficient CdTe solar cells. Current devices utilize some combination of preferential chemical etching, buffer layer, and Cu doping with additional cost, time, and complexity added for each step. In this Letter, these processes are eschewed and replaced with a nanosecond pulsed ultraviolet laser treatment. It is shown that this treatment can eliminate the rollover effect seen in photovoltaic current-voltage (J-V) curves that is indicative of a non-ohmic back contact. Transfer length measurements show that a single UV laser pulse can reduce the specific contact resistivity by a factor of 24 versus untreated samples. X-Ray photoemission spectroscopy shows evidence of increased conductivity and of elemental Te created at the surface by laser pulses. Finally, finite element modeling is used to model the laser-sample interaction, which predicts both the temperature and the amounts of Cd and Te lost during a laser pulse.
Polarization conversion in U-shaped chiral metamaterial with four-fold symmetry breaking
Authors: Zhu Weiren , Rukhlenko Ivan D. , Xiao Fajun , Premaratne Malin
Published: April 2014

Despite chiral metamaterials being widely appreciated for their giant optical activity and negative refractive index with respect to the transmitted electromagnetic waves, little research efforts are devoted to effects occurring upon optical reflection from such metamaterials. Here, we theoretically demonstrate highly energy-efficient cross-polarization conversion for a normally incident wave reflecting from metamaterial with a broken four-fold symmetry of chiral structure. We do this by designing metamaterial that makes the polarization plane of a linearly polarized electromagnetic wave reflected from its surface almost perpendicular to the polarization plane of the incident wave. Using reflection from this metamaterial, one can also freely convert between left-handed and right-handed circular polarizations without significant energy loss. The proposed chiral metamaterial may prove useful in electromagnetic communication systems, polarization controllable antennas, and on-chip biomedical sensors.
Cryogenic motion performances of a piezoelectric single crystal micromotor
Authors: Li Xiaotian , Wu Yuting , Chen Zhijiang , Wei Xiaoyong , Luo Haosu , Dong Shuxiang
Published: April 2014

This study investigates the cryogenic performances of a millimeter-size piezoelectric ultrasonic linear micromotor. The piezoelectric vibrator of the micromotor is made of Pb(In1/2Nb1/2)O3 -Pb(Mg1/3Nb2/3)-PbTiO3 single crystal and operated in first-bending wobbling mode. Experiments show that the piezoelectric single crystal micromotor works effectively even at extremely low temperature of −175 °C, although its resonance peaks vary with temperature significantly. This work confirms the feasibility of cryogenic operation of the piezo-micromotor, which is meaningful for aerospace or superconducting microwave application.
Coupled wind-wave time domain analysis of floating offshore wind turbine based on Computational Fluid Dynamics method
Authors: Ren Nianxin , Li Yugang , Ou Jinping
Published: April 2014

As offshore wind farms are extending into the deep sea around the world, the coupled aerodynamic and hydrodynamic time domain analysis of floating offshore wind turbine is of both profound academic interests and important practical interests. In this work, one typical tension leg platform of 5 MW wind turbine system has been chosen to the objective. The aerodynamic loads of the NREL 5 MW offshore wind turbine have been simulated based on Navier-Stokes equations and renormalization group (RNG) k-ε turbulence mode, which is suitable for the analysis of rotational flow field near wind turbine blades. The hydrodynamic loads of the floating wind turbine platform have been simulated by viscous numerical flume based on volume-of-fluid method. The dynamic responses of the floating wind turbine system could be obtained by solving the dynamic equations of the floating system under typical coupled wind-wave sea cases, and the motion of the floating platform under different time steps would be simulated by advanced sliding mesh technique. As a result, the fluid-structure interactions between the floating wind turbine structure and the coupled wind-wave flow field have been successfully simulated. Furthermore, the availability of the coupled numerical method has been verified by comparing the numerical results with corresponding scale model test data.
Efficiency improvement of CdS and CdSe quantum dot-sensitized solar cells by TiO2 surface treatment
Authors: Jun H. K. , Careem M. A. , Arof A. K.
Published: April 2014

CdS and CdSe quantum dots (QDs) have been synthesized via successive ionic layer adsorption and reaction for the fabrication of quantum dot-sensitized solar cells (QDSSCs). In this work, several approaches such as incorporation of ZnS passivation layer, scattering layer, treatment with TiCl4, and increasing the TiO2 layer thickness have been applied on TiO2 layer in order to improve the solar cell performance. By passivating the QD-sensitized TiO2 layer with ZnS, the performance of the cells increased due to reduction of charge recombination at the photoanode/electrolyte interface. With a thicker TiO2 layer thickness of 26 μm, further enhancement was observed. The efficiency of the CdS and CdSe QDSSCs improved from 1.06% to 1.48% and from 1.41% to 3.05%, respectively. On the other hand, scattering layer and treatment with TiCl4 did not bring much improvement to the cells.
The role of group index engineering in series-connected photonic crystal microcavities for high density sensor microarrays
Authors: Zou Yi , Chakravarty Swapnajit , Zhu Liang , Chen Ray T.
Published: April 2014

We experimentally demonstrate an efficient and robust method for series connection of photonic crystal microcavities that are coupled to photonic crystal waveguides in the slow light transmission regime. We demonstrate that group index taper engineering provides excellent optical impedance matching between the input and output strip waveguides and the photonic crystal waveguide, a nearly flat transmission over the entire guided mode spectrum and clear multi-resonance peaks corresponding to individual microcavities that are connected in series. Series connected photonic crystal microcavities are further multiplexed in parallel using cascaded multimode interference power splitters to generate a high density silicon nanophotonic microarray comprising 64 photonic crystal microcavity sensors, all of which are interrogated simultaneously at the same instant of time.
Diving with Donna Haraway and the Promise of a Blue Planet
Authors: Picken Felicity , Ferguson Tristan
Published: April 2014

It has been two decades since Haraway spoke about the ‘promise of monsters’, and seventy years since a novel kind of sea monster was created through the Aqua-Lung, giving ‘underwater worlds’ better access to humans. By revisiting and examining the combinatory effects of these historical moments, this paper illustrates the ‘promise of scuba divers’ who are somewhat monstrous in their potential to disturb common ideas about being human and life on land. In exchanging ‘sacred ground’ for submersion beneath the sea, scuba diving redefines the limits of human experience and emphasises the historical and largely forgotten primacy of land-based coordinates in theorising human life. Under the sea, these coordinates are vastly altered so that even preconscious markers, like breathing, are transformed through a circuitry that includes humans, science, technology, and nature in a ‘body-incorporate’. ‘Immersion’ becomes a threshold beyond which humans and nature, society and space are discovered anew in the reversal of the significance of territory to planetary life.
Synthesis of New-structured PbTiO3 Nanowires With Reversible Bending Properties
Authors: Wang Jiang , Li Jian , Wang Youwen
Published: April 2014

One-dimensional PbTiO3 nanowires 40–500 nm in diameter and ~400 μm in length were synthesized via a hydrothermal strategy and characterized by X-ray diffraction, electron backscatter diffraction, scanning electron microscopy, and transmission electron microscopy. The results show that the PbTiO3 nanowires exhibit a new acicular crystal structure, which is a tetragonal superstructure composed of a large unit cell of 40 atoms (Pb : Ti : O = 1 : 1 : 3) with a = 12.35 Å, c = 3.83 Å. The PbTiO3 has a feature of unidirectional bending when observed through transmission electron microscopy several times. The bending can be controlled by the electron beam intensity in transmission electron microscopy and the bending process is reversible. Moreover, a possible mechanism for the bending behaviour was also studied, which indicates that macroscopic polarization is in the {110} plane and the direction is not consistent with the electric field, giving the possible driving force for the bending.
Retrotransposon-based molecular markers for assessment of genomic diversity
Authors: Alzohairy Ahmed M. , Gyulai Gábor , Ramadan Mohamed F. , Edris Sherif , Sabir Jamal S. M. , Jansen Robert K. , Eissa Hala F. , Bahieldin Ahmed
Published: April 2014

Retrotransposons (RTs) are major components of most eukaryotic genomes. They are ubiquitous, dispersed throughout the genome, and their abundance correlates with genome size. Their copy-and-paste lifestyle in the genome consists of three molecular steps involving transcription of an RNA copy from the genomic RT, followed by reverse transcription to generate cDNA, and finally, reintegration into a new location in the genome. This process leads to new genomic insertions without excision of the original element. The target sites of insertions are relatively random and independent for different taxa; however, some elements cluster together in ‘repeat seas’ or have a tendency to cluster around the centromeres and telomeres. The structure and copy number of retrotransposon families are strongly influenced by the evolutionary history of the host genome. Molecular markers play an essential role in all aspects of genetics and genomics, and RTs represent a powerful tool compared with other molecular and morphological markers. All features of integration activity, persistence, dispersion, conserved structure and sequence motifs, and high copy number suggest that RTs are appropriate genomic features for building molecular marker systems. To detect polymorphisms for RTs, marker systems generally rely on the amplification of sequences between the ends of the RT, such as (long-terminal repeat)-retrotransposons and the flanking genomic DNA. Here, we review the utility of some commonly used PCR retrotransposon-based molecular markers, including inter-primer binding sequence (IPBS), sequence-specific amplified polymorphism (SSAP), retrotransposon-based insertion polymorphism (RBIP), inter retrotransposon amplified polymorphism (IRAP), and retrotransposon-microsatellite amplified polymorphism (REMAP).
Experimental modelling of crown fire initiation in open and closed shrubland systems
Authors: Tachajapong Watcharapong , Lozano Jesse , Mahalingam Shankar , Weise David R.
Published: April 2014

The transition of surface fire to live shrub crown fuels was studied through a simplified laboratory experiment using an open-topped wind tunnel. Respective surface and crown fuels used were excelsior (shredded Populus tremuloides wood) and live chamise (Adenostoma fasciculatum, including branches and foliage). A high crown fuel bulk density of 6.8kgm–3 with a low crown fuel base height of 0.20m was selected to ensure successful crown fire initiation. Diagnostics included flame height and surface fire evolution. Experimental results were compared with similar experiments performed in an open environment, in which the side walls of the wind tunnel were removed. The effect of varying wind speed in the range 0–1.8ms–1, representing a Froude number range of 0–1.1, on crown fire initiation was investigated. The suppression of lateral entrainment due to wind tunnel walls influenced surface fire behaviour. When wind speed increased from 1.5 to 1.8ms–1, the rate of spread of surface fire and surface fire depth increased from 5.5 to 12.0cms–1 and 0.61 to 1.02m. As a result, the residence time of convective heating significantly increased from 16.0 to 24.0s and the hot gas temperature at the crown base increased from 994 to 1141K. The change in surface fire characteristics significantly affected the convective energy transfer process. Thus, the net energy transfer to the crown fuel increased so the propensity for crown fire initiation increased. In contrast, increasing wind speed decreased the tendency for crown fuel initiation in an open environment because of the cooling effect from fresh air entrainment via the lateral sides of surface fire.
A fire weather index as a basis for an early warning system in Spain
Authors: Mestre A. , Manta M. I.
Published: April 2014

This research focuses on the evaluation of the economic value that can be achieved by the use of decision threshold values for the Canadian Fire Weather Index for the projection of different specific wildfire events, as a basis for wildfire prevention activities. The study was done in two testing areas in Spain, corresponding to La Coruña and Alicante provinces. The applied methodology makes use of a simple binary decision model, which has been widely applied for the verification of quantitative meteorological forecasts. Meteorological and wildfire data from a 10-year period (1997–2006) were used. The results show that use of the Fire Weather Index results in potential economic savings, especially in the case of La Coruña. Therefore, the use of the Canadian Fire Weather Index as a basis to develop an early warning system for wildfire is recommended in the two provinces under study.
Wildfire evacuation and its alternatives: perspectives from four United States’ communities
Authors: McCaffrey Sarah , Rhodes Alan , Stidham Melanie
Published: April 2014

Recent years have seen growing interest within the United States fire management community in exploring alternatives to the standard approach of evacuating entire populations that are threatened by a wildfire. There has been particular interest in what can be learned from the Australian approach, whereby residents choose whether or not to evacuate under the ‘prepare, stay and defend or leave early’ approach, also called Stay or Go. Given these developments, it is useful to understand what elements are taken into consideration by those who would be most affected by a new approach when they think through the pros and cons of mass evacuation v. an alternative strategy should a wildfire occur. This paper reports on findings from interviews in four communities in the United States where some alternative to mass evacuation during a wildfire was being considered. In each community, emergency responders and community members were asked for their perspective on the pros and cons of evacuation and the alternative being considered. The results show that opinions were mixed on whether evacuation or an alternative approach was more appropriate. Individuals who were primarily thinking of improving safety and reducing uncertainty for emergency responders tended to think mass evacuation was the best approach, whereas those who were primarily thinking of increasing safety and reducing uncertainty for homeowners were more likely to think that alternative responses were a valid option. These findings demonstrate the complicated nature of developing evacuation strategies that are beneficial to all parties involved.
Guanylate binding proteins promote caspase-11–dependent pyroptosis in response to cytoplasmic LPS
Authors: Pilla Danielle M. , Hagar Jon A. , Haldar Arun K. , Mason Ashley K. , Degrandi Daniel , Pfeffer Klaus , Ernst Robert K. , Yamamoto Masahiro , Miao Edward A. , Coers Jörn
Published: April 2014

Significance

A major component of the cell envelope of Gram-negative bacteria is LPS, also known as endotoxin. LPS produced during bacterial infections triggers inflammation, which can lead to septic shock and death. Our immune system can recognize LPS both outside and inside of cells. The recognition of extracellular and vacuolar LPS by LPS binding proteins is well described, but little is known about the recognition of cytoplasmic LPS. Here, we show that cytoplasmic LPS derived from the intracellular bacterial pathogen
Legionella
activated a proinflammatory immune response. We further identified host guanylate binding proteins as critical mediators of immunity triggered by cytoplasmic LPS. These findings are likely to advance our understanding of how cells can sense intracellular LPS.
How oxygen reacts with oxygen-tolerant respiratory [NiFe]-hydrogenases
Authors: Wulff Philip , Day Christopher C. , Sargent Frank , Armstrong Fraser A.
Published: April 2014

Significance

Mass spectrometry experiments with a nickel-containing respiratory hydrogenase from
Escherichia coli
provide conclusive proof that it catalyzes the four-electron reduction of oxygen by hydrogen, a reaction analogous to combustion. Hydrogenase-1 is a membrane-bound enzyme that oxidizes hydrogen in the periplasm to reduce respiratory-chain quinones. If oxygen is present and enters the buried active site, a package of electrons, derived from hydrogen oxidation and held in the iron–sulfur cluster relay system, transfers back to convert it cleanly to water. The enzyme thus avoids production of reactive oxygen intermediates that would otherwise cause inactivation. This study establishes the basis of the oxygen tolerance in respiratory nickel–iron hydrogenases and demonstrates biology’s unexpected use of nickel in the active site of a four-electron oxidase.
Outer membrane β-barrel protein folding is physically controlled by periplasmic lipid head groups and BamA
Authors: Gessmann Dennis , Chung Yong Hee , Danoff Emily J. , Plummer Ashlee M. , Sandlin Clifford W. , Zaccai Nathan R. , Fleming Karen G.
Published: April 2014

Significance

The folding of outer membrane proteins (OMPs) in biological membranes in vivo requires an evolutionarily conserved and essential protein, β-barrel assembly machinery subunit A (BamA). By investigating the folding kinetics of OMPs into membranes composed of
Escherichia coli
lipids, we discovered that periplasmic lipid head groups impose a kinetic barrier to OMP folding. This barrier serves as a negative selection to prevent OMPs from folding into inner bacterial membranes where they would dissipate the proton motive force and kill the cell. We showed that BamA enables OMPs to overcome this barrier at bacterial outer membranes by enhancing their observed folding rates. We propose BamA does so by creating bilayer defects, which are known to accelerate the intrinsic folding reaction.
Importance of positioning for microbial evolution
Authors: Kim Wook , Racimo Fernando , Schluter Jonas , Levy Stuart B. , Foster Kevin R.
Published: April 2014

Significance

Microbes commonly form dense communities that are central to many diseases and bioremediation. Here we demonstrate a simple and general principle of living in dense communities: microbes will commonly compete to reach nutrients at the community edge, akin to plants competing for light. We follow the evolution of a highly competitive genotype in colonies of a soil bacterium. We show that the genotype gains its advantage not from its intrinsic growth rate but by positioning itself at the surface of the community, where it gains preferential access to oxygen. A large-scale genetic analysis reveals striking parallel evolution and evidence of strong natural selection. Our work suggests that positioning is a major basis for evolutionary competition in dense microbial communities.
The Myth of ‘Three Italies’: Differences and Similarities in Environmental Values Between Macro-Regions
Authors: Veltri Giuseppe A.
Published: April 2014

One of the most frequently perceived divisions in Italy is that of a substantial cultural discrepancy in the environmental values of the North, the Centre and the South. The recent and prolonged waste crisis in Southern Italy reinforced this common public discourse. There are, however, no recent studies that have explored these alleged differences. This study aims to fill this hiatus by analysing differences across macro-regions in terms of the endorsement of basic environmental values. Differences in environmental values are examined using the New Ecological Paradigm (NEP) scale with a multi-level variance components analysis. The findings suggest that whilst dissimilarities between macro-regions do exist, they are not in fact as significant as might be expected, thus indicating the existence of a national cultural homogeneity in terms of ‘primitive’ beliefs towards nature and humanity's relationship with it. The findings also highlight the problems of ‘Ecological Fallacy’ and underscore the complexity of the relationship between values and behaviour.
ProQM-resample: improved model quality assessment for membrane proteins by limited conformational sampling
Authors: Wallner Björn
Published: April 2014

Summary: Model Quality Assessment Programs (MQAPs) are used to predict the quality of modeled protein structures. These usually use two approaches: methods using consensus of many alternative models and methods requiring only a single model to do its prediction. The consensus methods are useful to improve overall accuracy; however, they frequently fail to pick out the best possible model and cannot be used to generate and score new structures. Single-model methods, on the other hand, do not have these inherent shortcomings and can be used to both sample new structures and improve existing consensus methods. Here, we present ProQM-resample , a membrane protein-specific single-model MQAP, that couples side-chain resampling with MQAP rescoring by ProQM to improve model selection. The side-chain resampling is able to improve side-chain packing for 96% of all models, and improve model selection by 24% as measured by the sum of the Z-score for the first-ranked model (from 25.0 to 31.1), even better than the state-of-the-art consensus method Pcons. The improved model selection can be attributed to the improved side-chain quality, which enables the MQAP to rescue good backbone models with poor side-chain packing.

Availability and implementation:  http://proqm.wallnerlab.org/download/ .

Contact:  bjornw@ifm.liu.se

Supplementary information:  Supplementary data are available at Bioinformatics online.
Measuring Adverse Events in Hospitalized Patients: An Administrative Method for Measuring Harm
Authors: Martin John , Benjamin Evan M. , Craver Christopher , Kroch Eugene A. , Nelson Eugene C. , Bankowitz Richard
Published: April 2014

Context

Current methods for tracking harm either require costly full manual chart review (FMCR) or rely on proxy methods that have questionable accuracy. We propose an administrative measure of harm detection that uses electronically captured data.

Objective

Determine the level of agreement on harm event occurrence when harm is detected based on an administrative harm measurement tool (AHMT) compared with FMCR.

Design

A retrospective chart review was used to measure the level of agreement in harm detection between an AHMT that uses electronically captured data and a FMCR.

Setting

The inpatient hospital setting was used.

Patients

Approximately 771 medical records from 5 hospitals were reviewed.

Main Outcome Measures

Measures of positive predictive value, negative predictive value, weighted sensitivity, weighted specificity, and concordance were used to evaluate agreement between the 2 methods.

Results

Although there was agreement at the harm-event level, the results were not all as high as desired: adjusted sensitivity 65%, adjusted specificity 85%, positive predictive value (PPV) 59%, negative predictive value (NPV) 88%, and concordance 75%. The patient-level results show greater agreement: adjusted sensitivity 95%, adjusted specificity 86%, PPV 61%, NPV 99%, and concordance 81%.

Conclusion

The AHMT is sufficiently accurate for use as a within hospital tool to reliably detect and track harm. Nevertheless, it is not recommended as a tool to make comparisons across institutions, which has policy and payment implications. Further research using administrative harm detection, including the use of a broader set of measures and electronic health records, is needed.
Learning multiple routes in homing pigeons
Authors: Flack Andrea , Guilford Tim , Biro Dora
Published: April 2014

The aerial lifestyle of central-place foraging birds allows wide-ranging movements, raising fundamental questions about their remarkable navigation and memory systems. For example, we know that pigeons (
Columba livia
), long-standing models for avian navigation, rely on individually distinct routes when homing from familiar sites. But it remains unknown how they cope with the task of learning several routes in parallel. Here, we examined how learning multiple routes influences homing in pigeons. We subjected groups of pigeons to different training protocols, defined by the sequence in which they were repeatedly released from three different sites, either sequentially, in rotation or randomly. We observed that pigeons from all groups successfully developed and applied memories of the different release sites (RSs), irrespective of the training protocol, and that learning several routes in parallel did not impair their capacity to quickly improve their homing efficiency over multiple releases. Our data also indicated that they coped with increasing RS uncertainty by adjusting both their initial behaviour upon release and subsequent homing efficiency. The results of our study broaden our understanding of avian route following and open new possibilities for studying learning and memory in free-flying animals.
Three-dimensional computer simulations of feeding behaviour in red and giant pandas relate skull biomechanics with dietary niche partitioning
Authors: Figueirido Borja , Tseng Zhijie Jack , Serrano-Alarcón Francisco J. , Martín-Serra Alberto , Pastor Juan F.
Published: April 2014

The red (
Ailurus fulgens
) and giant (
Ailuropoda melanoleuca
) pandas are mammalian carnivores convergently adapted to a bamboo feeding diet. However, whereas
Ailurus
forages almost entirely on younger leaves, fruits and tender trunks,
Ailuropoda
relies more on trunks and stems. Such difference in foraging mode is considered a strategy for resource partitioning where they are sympatric. Here, we use finite-element analysis to test for mechanical differences and similarities in skull performance between
Ailurus
and
Ailuropoda
related to diet. Feeding simulations suggest that the two panda species have similar ranges of mechanical efficiency and strain energy profiles across the dentition, reflecting their durophagous diet. However, the stress distributions and peaks in the skulls of
Ailurus
and
Ailuropoda
are remarkably different for biting at all tooth locations. Although the skull of
Ailuropoda
is capable of resisting higher stresses than the skull of
Ailurus
, the latter is able to distribute stresses more evenly throughout the skull. These differences in skull biomechanics reflect their distinct bamboo feeding preferences.
Ailurus
uses repetitive chewing in an extended mastication to feed on soft leaves, and
Ailuropoda
exhibits shorter and more discrete periods of chomp-and-swallow feeding to break down hard bamboo trunks.
In situ
X-ray scattering evaluation of heat-induced ultrastructural changes in dental tissues and synthetic hydroxyapatite
Authors: Sui Tan , Sandholzer Michael A. , Lunt Alexander J. G. , Baimpas Nikolaos , Smith Andrew , Landini Gabriel , Korsunsky Alexander M.
Published: April 2014

Human dental tissues consist of inorganic constituents (mainly crystallites of hydroxyapatite, HAp) and organic matrix. In addition, synthetic HAp powders are frequently used in medical and chemical applications. Insights into the ultrastructural alterations of skeletal hard tissues exposed to thermal treatment are crucial for the estimation of temperature of exposure in forensic and archaeological studies. However, at present, only limited data exist on the heat-induced structural alterations of human dental tissues. In this paper, advanced non-destructive small- and wide angle X-ray scattering (SAXS/WAXS) synchrotron techniques were used to investigate the
in situ
ultrastructural alterations in thermally treated human dental tissues and synthetic HAp powders. The crystallographic properties were probed by WAXS, whereas HAp grain size distribution changes were evaluated by SAXS. The results demonstrate the important role of the organic matrix that binds together the HAp crystallites in responding to heat exposure. This is highlighted by the difference in the thermal behaviour between human dental tissues and synthetic HAp powders. The X-ray analysis results are supported by thermogravimetric analysis. The results concerning the HAp crystalline architecture in natural and synthetic HAp powders provide a reliable basis for deducing the heating history for dental tissues in the forensic and archaeological context, and the foundation for further development and optimization of biomimetic material design.
Tiger beetles pursue prey using a proportional control law with a delay of one half-stride
Authors: Haselsteiner Andreas F. , Gilbert Cole , Wang Z. Jane
Published: April 2014

Tiger beetles are fast diurnal predators capable of chasing prey under closed-loop visual guidance. We investigated this control system using statistical analyses of high-speed digital recordings of beetles chasing a moving prey dummy in a laboratory arena. Correlation analyses reveal that the beetle uses a proportional control law in which the angular position of the prey relative to the beetle's body axis drives the beetle's angular velocity with a delay of about 28 ms. The proportionality coefficient or system gain, 12 s−1, is just below critical damping. Pursuit simulations using the derived control law predict angular orientation during pursuits with a residual error of about 7°. This is of the same order of magnitude as the oscillation imposed by the beetle's alternating tripod gait, which was not factored into the control law. The system delay of 28 ms equals a half-stride period, i.e. the time between the touch down of alternating tripods. Based on these results, we propose a physical interpretation of the observed control law: to turn towards its prey, the beetle on average exerts a sideways force proportional to the angular position of the prey measured a half-stride earlier.
Propagation in waveguides with varying cross section and curvature: a new light on the role of supplementary modes in multi-modal methods
Authors: Maurel Agnès , Mercier Jean-François , Félix Simon
Published: April 2014

We present an efficient multi-modal method to describe the acoustic propagation in waveguides with varying curvature and cross section. A key feature is the use of a flexible geometrical transformation to a virtual space in which the waveguide is straight and has unitary cross section. In this new space, the pressure field has to satisfy a modified wave equation and associated modified boundary conditions. These boundary conditions are in general not satisfied by the Neumann modes, used for the series representation of the field. Following previous work, an improved modal method (MM) is presented, by means of the use of two supplementary modes. Resulting increased convergences are exemplified by comparison with the classical MM. Next, the following question is addressed: when the boundary conditions are verified by the Neumann modes, does the use of supplementary modes improve or degrade the convergence of the computed solution? Surprisingly, although the supplementary modes degrade the behaviour of the solution at the walls, they improve the convergence of the wavefield and of the scattering coefficients. This sheds a new light on the role of the supplementary modes and opens the way for their use in a wide range of scattering problems.
Cumulative distribution function solutions of advection–reaction equations with uncertain parameters
Authors: Boso F. , Broyda S. V. , Tartakovsky D. M.
Published: April 2014

We derive deterministic cumulative distribution function (CDF) equations that govern the evolution of CDFs of state variables whose dynamics are described by the first-order hyperbolic conservation laws with uncertain coefficients that parametrize the advective flux and reactive terms. The CDF equations are subjected to uniquely specified boundary conditions in the phase space, thus obviating one of the major challenges encountered by more commonly used probability density function equations. The computational burden of solving CDF equations is insensitive to the magnitude of the correlation lengths of random input parameters. This is in contrast to both Monte Carlo simulations (MCSs) and direct numerical algorithms, whose computational cost increases as correlation lengths of the input parameters decrease. The CDF equations are, however, not exact because they require a closure approximation. To verify the accuracy and robustness of the large-eddy-diffusivity closure, we conduct a set of numerical experiments which compare the CDFs computed with the CDF equations with those obtained via MCSs. This comparison demonstrates that the CDF equations remain accurate over a wide range of statistical properties of the two input parameters, such as their correlation lengths and variance of the coefficient that parametrizes the advective flux.
Marine biological shifts and climate
Authors: Beaugrand Grégory , Goberville Eric , Luczak Christophe , Kirby Richard R
Published: April 2014

Phenological, biogeographic and community shifts are among the reported responses of marine ecosystems and their species to climate change. However, despite both the profound consequences for ecosystem functioning and services, our understanding of the root causes underlying these biological changes remains rudimentary. Here, we show that a significant proportion of the responses of species and communities to climate change are deterministic at some emergent spatio-temporal scales, enabling testable predictions and more accurate projections of future changes. We propose a theory based on the concept of the ecological niche to connect phenological, biogeographic and long-term community shifts. The theory explains approximately 70% of the phenological and biogeographic shifts of a key zooplankton
Calanus finmarchicus
in the North Atlantic and approximately 56% of the long-term shifts in copepods observed in the North Sea during the period 1958–2009.
Climate change and frog calls: long-term correlations along a tropical altitudinal gradient
Authors: Narins Peter M. , Meenderink Sebastiaan W. F.
Published: April 2014

Temperature affects nearly all biological processes, including acoustic signal production and reception. Here, we report on advertisement calls of the Puerto Rican coqui frog (
Eleutherodactylus coqui
) that were recorded along an altitudinal gradient and compared these with similar recordings along the same altitudinal gradient obtained 23 years earlier. We found that over this period, at any given elevation, calls exhibited both significant increases in pitch and shortening of their duration. All of the observed differences are consistent with a shift to higher elevations for the population, a well-known strategy for adapting to a rise in ambient temperature. Using independent temperature data over the same time period, we confirm a significant increase in temperature, the magnitude of which closely predicts the observed changes in the frogs’ calls. Physiological responses to long-term temperature rises include reduction in individual body size and concomitantly, population biomass. These can have potentially dire consequences, as coqui frogs form an integral component of the food web in the Puerto Rican rainforest.
Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines
Authors: Huang Wen , Massouras Andreas , Inoue Yutaka , Peiffer Jason , Ràmia Miquel , Tarone Aaron M. , Turlapati Lavanya , Zichner Thomas , Zhu Dianhui , Lyman Richard F. , Magwire Michael M. , Blankenburg Kerstin , Carbone Mary Anna , Chang Kyle , Ellis Lisa L. , Fernandez Sonia , Han Yi , Highnam Gareth , Hjelmen Carl E. , Jack John R. , Javaid Mehwish , Jayaseelan Joy , Kalra Divya , Lee Sandy , Lewis Lora , Munidasa Mala , Ongeri Fiona , Patel Shohba , Perales Lora , Perez Agapito , Pu LingLing , Rollmann Stephanie M. , Ruth Robert , Saada Nehad , Warner Crystal , Williams Aneisa , Wu Yuan-Qing , Yamamoto Akihiko , Zhang Yiqing , Zhu Yiming , Anholt Robert R.H. , Korbel Jan O. , Mittelman David , Muzny Donna M. , Gibbs Richard A. , Barbadilla Antonio , Johnston J. Spencer , Stone Eric A. , Richards Stephen , Deplancke Bart , Mackay Trudy F.C.
Published: April 2014

The Drosophila melanogaster Genetic Reference Panel (DGRP) is a community resource of 205 sequenced inbred lines, derived to improve our understanding of the effects of naturally occurring genetic variation on molecular and organismal phenotypes. We used an integrated genotyping strategy to identify 4,853,802 single nucleotide polymorphisms (SNPs) and 1,296,080 non-SNP variants. Our molecular population genomic analyses show higher deletion than insertion mutation rates and stronger purifying selection on deletions. Weaker selection on insertions than deletions is consistent with our observed distribution of genome size determined by flow cytometry, which is skewed toward larger genomes. Insertion/deletion and single nucleotide polymorphisms are positively correlated with each other and with local recombination, suggesting that their nonrandom distributions are due to hitchhiking and background selection. Our cytogenetic analysis identified 16 polymorphic inversions in the DGRP. Common inverted and standard karyotypes are genetically divergent and account for most of the variation in relatedness among the DGRP lines. Intriguingly, variation in genome size and many quantitative traits are significantly associated with inversions. Approximately 50% of the DGRP lines are infected with Wolbachia, and four lines have germline insertions of Wolbachia sequences, but effects of Wolbachia infection on quantitative traits are rarely significant. The DGRP complements ongoing efforts to functionally annotate the Drosophila genome. Indeed, 15% of all D. melanogaster genes segregate for potentially damaged proteins in the DGRP, and genome-wide analyses of quantitative traits identify novel candidate genes. The DGRP lines, sequence data, genotypes, quality scores, phenotypes, and analysis and visualization tools are publicly available.
Plasma Membranes Are Subcompartmentalized into a Plethora of Coexisting and Diverse Microdomains inArabidopsisandNicotiana benthamiana
Authors: Jarsch Iris K. , Konrad Sebastian S.A. , Stratil Thomas F. , Urbanus Susan L. , Szymanski Witold , Braun Pascal , Braun Karl-Heinz , Ott Thomas
Published: April 2014

Eukaryotic plasma membranes are highly compartmentalized structures. So far, only a few individual proteins that function in a wide range of cellular processes have been shown to segregate into microdomains. However, the biological roles of most microdomain-associated proteins are unknown. Here, we investigated the heterogeneity of distinct microdomains and the complexity of their coexistence. This diversity was determined in living cells of intact multicellular tissues using 20 different marker proteins from Arabidopsis thaliana, mostly belonging to the Remorin protein family. These proteins associate with microdomains at the cytosolic leaflet of the plasma membrane. We characterized these membrane domains and determined their lateral dynamics by extensive quantitative image analysis. Systematic colocalization experiments with an extended subset of marker proteins tested in 45 different combinations revealed the coexistence of highly distinct membrane domains on individual cell surfaces. These data provide valuable tools to study the lateral segregation of membrane proteins and their biological functions in living plant cells. They also demonstrate that widely used biochemical approaches such as detergent-resistant membranes cannot resolve this biological complexity of membrane compartmentalization in vivo.