bluuebunny/crossref_metadata_2025 huggingface dataset:
Large Reynolds number self-similar states of unstably stratified homogeneous turbulence
Authors: Burlot A. , Gréa B.-J. , Godeferd F. S. , Cambon C. , Soulard O.
Published: June 2015

We study the influence of the large scale energy distribution on the long term dynamics of unstably stratified homogeneous turbulence at high Reynolds number Re = 106, using a statistical two-point spectral model based on the eddy-damped quasi-normal closure. We consider several initial spectral scalings ks in the infrared range with s ∈ [1; 5] and we establish that the resulting kinetic energy growth rates are controlled by s, with the appearance of backscatter effects for s ≳ 3.5. We then assess that only for s ≤ 4 do we observe self-similarity in the infrared and in the inertial ranges, but not in the dissipative range. Compensated energy and buoyancy spectra exhibit the expected Kolmogorov-Obukhov k−5/3 scaling at long time, and a trend to the theoretically predicted k−7/3 scaling for velocity-buoyancy cross-correlation spectrum thanks to the very large Reynolds number. We also show a direct link between the late-time anisotropy of the flows and the infrared spectrum, thus demonstrating long-lasting effect of initial conditions on unstably stratified turbulence. We show that, in addition to the Kolmogorov k−5/3 scaling, the kinetic energy spectrum inertial range includes a k−3 zone due to polarization anisotropy, and we confirm the clear sin2θ dependence of the velocity-buoyancy spectrum in the inertial range, where θ is the orientation of the wave vector to the axis of gravity. However, an unexpected quick return to isotropy of the scalar spectra has been identified, which cannot be explained by a standard dimensional analysis.
On the fractional Eulerian numbers and equivalence of maps with long term power-law memory (integral Volterra equations of the second kind) to Grünvald-Letnikov fractional difference (differential) equations
Authors: Edelman Mark
Published: June 2015

In this paper, we consider a simple general form of a deterministic system with power-law memory whose state can be described by one variable and evolution by a generating function. A new value of the system's variable is a total (a convolution) of the generating functions of all previous values of the variable with weights, which are powers of the time passed. In discrete cases, these systems can be described by difference equations in which a fractional difference on the left hand side is equal to a total (also a convolution) of the generating functions of all previous values of the system's variable with the fractional Eulerian number weights on the right hand side. In the continuous limit, the considered systems can be described by the Grünvald-Letnikov fractional differential equations, which are equivalent to the Volterra integral equations of the second kind. New properties of the fractional Eulerian numbers and possible applications of the results are discussed.
Three-dimensional non-linear magnetohydrodynamic modeling of massive gas injection triggered disruptions in JET
Authors: Fil A. , Nardon E. , Hoelzl M. , Huijsmans G. T. A , Orain F. , Becoulet M. , Beyer P. , Dif-Pradalier G. , Guirlet R. , Koslowski H. R. , Lehnen M. , Morales J. , Pamela S. , Passeron C. , Reux C. , Saint-Laurent F. ,   JET Contributors
Published: June 2015

JOREK 3D non-linear MHD simulations of a D2 Massive Gas Injection (MGI) triggered disruption in JET are presented and compared in detail to experimental data. The MGI creates an overdensity that rapidly expands in the direction parallel to the magnetic field. It also causes the growth of magnetic islands (m/n=2/1 and 3/2 mainly) and seeds the 1/1 internal kink mode. O-points of all island chains (including 1/1) are located in front of the MGI, consistently with experimental observations. A burst of MHD activity and a peak in plasma current take place at the same time as in the experiment. However, the magnitude of these two effects is much smaller than in the experiment. The simulated radiation is also much below the experimental level. As a consequence, the thermal quench is not fully reproduced. Directions for progress are identified. Radiation from impurities is a good candidate.
Measurement of carbon condensates using small-angle x-ray scattering during detonation of the high explosive hexanitrostilbene
Authors: Bagge-Hansen M. , Lauderbach L. , Hodgin R. , Bastea S. , Fried L. , Jones A. , van Buuren T. , Hansen D. , Benterou J. , May C. , Graber T. , Jensen B. J. , Ilavsky J. , Willey T. M.
Published: June 2015

The dynamics of carbon condensation in detonating high explosives remains controversial. Detonation model validation requires data for processes occurring at nanometer length scales on time scales ranging from nanoseconds to microseconds. A new detonation endstation has been commissioned to acquire and provide time-resolved small-angle x-ray scattering (SAXS) from detonating explosives. Hexanitrostilbene (HNS) was selected as the first to investigate due to its ease of initiation using exploding foils and flyers, vacuum compatibility, high thermal stability, and stoichiometric carbon abundance that produces high carbon condensate yields. The SAXS data during detonation, collected with 300 ns time resolution, provide unprecedented signal fidelity over a broad q-range. This fidelity permits the first analysis of both the Guinier and Porod/power-law regions of the scattering profile during detonation, which contains information about the size and morphology of the resultant carbon condensate nanoparticles. To bolster confidence in these data, the scattering angle and intensity were additionally cross-referenced with a separate, highly calibrated SAXS beamline. The data show that HNS produces carbon particles with a radius of gyration of 2.7 nm in less than 400 ns after the detonation front has passed, and this size and morphology are constant over the next several microseconds. These data directly contradict previous pioneering work on RDX/TNT mixtures and TATB, where observations indicate significant particle growth (50% or more) continues over several microseconds. The power-law slope is about −3, which is consistent with a complex disordered, irregular, or folded sp2 sub-arrangement within a relatively monodisperse structure possessing radius of gyration of 2.7 nm after the detonation of HNS.
Site occupancy and magnetic properties of Al-substituted M-type strontium hexaferrite
Authors: Dixit Vivek , Nandadasa Chandani N. , Kim Seong-Gon , Kim Sungho , Park Jihoon , Hong Yang-Ki , Liyanage Laalitha S. I. , Moitra Amitava
Published: June 2015

We use first-principles total-energy calculations based on density functional theory to study the site occupancy and magnetic properties of Al-substituted M-type strontium hexaferrite SrFe12−xAlxO19 with x = 0.5 and x = 1.0. We find that the non-magnetic Al3+ ions preferentially replace Fe3+ ions at two of the majority spin sites, 2a and 12k, eliminating their positive contribution to the total magnetization causing the saturation magnetization Ms to be reduced as Al concentration x is increased. Our formation probability analysis further provides the explanation for increased magnetic anisotropy field when the fraction of Al is increased. Although Al3+ ions preferentially occupy the 2a sites at a low temperature, the occupation probability of the 12k site increases with the rise of the temperature. At a typical annealing temperature (>700 °C) Al3+ ions are much more likely to occupy the 12k site than the 2a site. Although this causes the magnetocrystalline anisotropy K1 to be reduced slightly, the reduction in Ms is much more significant. Their combined effect causes the anisotropy field Ha to increase as the fraction of Al is increased, consistent with recent experimental measurements.
Photoluminescence-based detection of particle contamination on extreme ultraviolet reticles
Authors: Gao A. , Rizo P. J. , Scaccabarozzi L. , Lee C. J. , Banine V. , Bijkerk F.
Published: June 2015

Here, we propose a comparison-free inspection technique to detect particle contamination on the reticle of extreme ultraviolet (EUV) lithography systems, based on the photoluminescence spectral characteristics of the contaminant particles and their elemental composition. We have analyzed the spectra from different particles found on reticles in EUV lithographic systems and have determined the minimum detectable particle size: 25 nm for organic particles and 100 nm for Al particles. Stainless steel coatings (50 nm thick and 50 × 50 μm2 in area) exhibit detectable photoluminescence, and the estimated minimum detectable particle is 2 μm.
Accurate ab initio vibrational energies of methyl chloride
Authors: Owens Alec , Yurchenko Sergei N. , Yachmenev Andrey , Tennyson Jonathan , Thiel Walter
Published: June 2015

Two new nine-dimensional potential energy surfaces (PESs) have been generated using high-level ab initio theory for the two main isotopologues of methyl chloride, CH335Cl and CH337Cl. The respective PESs, CBS-35 HL, and CBS-37 HL, are based on explicitly correlated coupled cluster calculations with extrapolation to the complete basis set (CBS) limit, and incorporate a range of higher-level (HL) additive energy corrections to account for core-valence electron correlation, higher-order coupled cluster terms, scalar relativistic effects, and diagonal Born-Oppenheimer corrections. Variational calculations of the vibrational energy levels were performed using the computer program TROVE, whose functionality has been extended to handle molecules of the form XY 3Z. Fully converged energies were obtained by means of a complete vibrational basis set extrapolation. The CBS-35 HL and CBS-37 HL PESs reproduce the fundamental term values with root-mean-square errors of 0.75 and 1.00 cm−1, respectively. An analysis of the combined effect of the HL corrections and CBS extrapolation on the vibrational wavenumbers indicates that both are needed to compute accurate theoretical results for methyl chloride. We believe that it would be extremely challenging to go beyond the accuracy currently achieved for CH3Cl without empirical refinement of the respective PESs.
ChiMS: Open-source instrument control software platform on LabVIEW for imaging/depth profiling mass spectrometers
Authors: Cui Yang , Hanley Luke
Published: June 2015

ChiMS is an open-source data acquisition and control software program written within LabVIEW for high speed imaging and depth profiling mass spectrometers. ChiMS can also transfer large datasets from a digitizer to computer memory at high repetition rate, save data to hard disk at high throughput, and perform high speed data processing. The data acquisition mode generally simulates a digital oscilloscope, but with peripheral devices integrated for control as well as advanced data sorting and processing capabilities. Customized user-designed experiments can be easily written based on several included templates. ChiMS is additionally well suited to non-laser based mass spectrometers imaging and various other experiments in laser physics, physical chemistry, and surface science.
Design of a low cost spinneret assembly for coaxial electrospinning
Authors: Raheja Anant , Chandra T. S. , Natarajan T. S.
Published: June 2015

Coaxial electrospinning makes use of a concentric arrangement of spinneret orifices for synthesis of core-shell polymer nanofibers. Most laboratories purchase the spinneret from commercial manufacturers at a significant expense, or design it indigenously to save costs but compromise on manufacturing precision. Therefore, the present work suggests the use of a relatively lower priced McIntyre cannula needle, conventionally used for ophthalmic surgeries, as a coaxial spinneret for electrospinning. The McIntyre cannula needle was modified to synthesize hollow fibers of nylon 6, which acted as sheath with hydrogen peroxide as core during electrospinning. In addition, encapsulation of bioactives, viz., red blood cells, bacterial cells, and lysozyme (enzyme protein) was attempted, using their aqueous suspensions as core, with polycaprolactone solution as sheath. Resulting fibers had an integral core-shell structure with the bioactives encapsulated in the core. This indicated that the modified McIntyre cannula functions suitably as a spinneret for coaxial electrospinning. Thus, apart from being a clinical device, the modified McIntyre cannula needle provides an economic alternative to conventional coaxial spinneret assemblies.
On the use of a charged tunnel layer as a hole collector to improve the efficiency of amorphous silicon thin-film solar cells
Authors: Ke Cangming , Peters Ian Marius , Sahraei Nasim , Aberle Armin G. , Stangl Rolf
Published: June 2015

A new concept, using a negatively charged tunnel layer as a hole collector, is proposed and theoretically investigated for application in amorphous silicon thin-film solar cells. The concept features a glass/transparent conductive oxide/ultra-thin negatively charged tunnel layer/intrinsic a-Si:H/n-doped a-Si:H/metal structure. The key feature of this so called t+-i-n structure is the introduction of a negatively charged tunnel layer (attracting holes from the intrinsic absorber layer), which substitutes the highly recombination active p-doped a-Si:H layer in a conventional p-i-n configuration. Atomic layer deposited aluminum oxide (ALD AlOx) is suggested as a potential candidate for such a tunnel layer. Using typical ALD AlOx parameters, a 27% relative efficiency increase (i.e., from 9.7% to 12.3%) is predicted theoretically for a single-junction a-Si:H solar cell on a textured superstrate. This prediction is based on parameters that reproduce the experimentally obtained external quantum efficiency and current-voltage characteristics of a conventional processed p-i-n a-Si:H solar cell, reaching 9.7% efficiency and serving as a reference. Subsequently, the p-doped a-Si:H layer is replaced by the tunnel layer (studied by means of numerical device simulation). Using a t+-i-n configuration instead of a conventional p-i-n configuration will not only increase the short-circuit current density (from 14.4 to 14.9 mA/cm2, according to our simulations), it also enhances the open-circuit voltage and the fill factor (from 917 mV to 1.0 V and from 74% to 83%, respectively). For this concept to work efficiently, a high work function front electrode material or a high interface charge is needed.
Low-threshold InAs-based interband cascade lasers operating at high temperatures
Authors: Li Lu , Jiang Yuchao , Ye Hao , Yang Rui Q. , Mishima Tetsuya D. , Santos Michael B. , Johnson Matthew B.
Published: June 2015

InAs-based interband cascade (IC) lasers with improved optical confinement have achieved high-temperature operation with a threshold current density as low as 247 A/cm2 at 300 K for emission near 4.6 μm. The threshold current density is the lowest ever reported among semiconductor mid-infrared lasers at similar wavelengths. These InAs-based IC devices lased in pulsed mode at temperatures up to 377 K near 5.1 μm. Narrow-ridge devices were able to operate in continuous-wave mode at temperatures up to 308 K near 4.8 μm. The implications and prospects of these results are discussed.
Impact of punctual flat magnetic shear on the field line transport
Authors: Abud C. V. , Caldas I. L.
Published: June 2015

We investigate the magnetic field line transport for tokamak equilibria with monotonic magnetic shear perturbed by resonant fields. We show that when the local profile is flat at the plasma edge a transport barrier can be created leading to a field line transport reduction. This transport reduction is due to the field lines topological modifications, caused by a local flattened profile that reduces the global field lines escape pattern. The results are obtained by applying a symplectic map that describes perturbed magnetic field lines in large aspect ratio tokamaks.
Processing and crystallographic structure of non-equilibrium Si-doped HfO2
Authors: Hou Dong , Fancher Chris M. , Zhao Lili , Esteves Giovanni , Jones Jacob L.
Published: June 2015

Si-doped HfO2 was confirmed to exist as a non-equilibrium state. The crystallographic structures of Si-doped HfO2 were studied using high-resolution synchrotron X-ray diffraction and the Rietveld refinement method. Incorporation of Si into HfO2 and diffusion of Si out of (Hf,Si)O2 were determined as a function of calcination temperature. Higher thermal energy input at elevated calcination temperatures resulted in the formation of HfSiO4, which is the expected major secondary phase in Si-doped HfO2. The effect of SiO2 particle size (nano- and micron-sized) on the formation of Si-doped HfO2 was also determined. Nano-crystalline SiO2 was found to incorporate into HfO2 more readily.
Galvanic corrosion of structural non-stoichiometric silicon nitride thin films and its implications on reliability of microelectromechanical devices
Authors: Broas M. , Liu X. , Ge Y. , Mattila T. T. , Paulasto-Kröckel M.
Published: June 2015

This paper describes a reliability assessment and failure analysis of a poly-Si/non-stoichiometric silicon nitride thin film composite structure. A set of poly-Si/SiNx thin film structures were exposed to a mixed flowing gas (MFG) environment, which simulates outdoor environments, for 90 days, and an elevated temperature and humidity (85 °C/95% R.H.) test for 140 days. The mechanical integrity of the thin films was observed to degrade during exposure to the chemically reactive atmospheres. The degree of degradation was analyzed with nanoindentation tests. Statistical analysis of the forces required to initiate a fracture in the thin films indicated degradation due to the exposure to the MFG environment in the SiNx part of the films. Scanning electron microscopy revealed a porous-like reaction layer on top of SiNx. The morphology of the reaction layer resembled that of galvanically corroded poly-Si. Transmission electron microscopy further clarified the microstructure of the reaction layer which had a complex multi-phase structure extending to depths of ∼100 nm. Furthermore, the layer was oxidized two times deeper in a 90 days MFG-tested sample compared to an untested reference. The formation of the layer is proposed to be caused by galvanic corrosion of elemental silicon in non-stoichiometric silicon nitride during hydrofluoric acid etching. The degradation is proposed to be due uncontrolled oxidation of the films during the stress tests.
Pressure, temperature, and electric field dependence of phase transformations in niobium modified 95/5 lead zirconate titanate
Authors: Dong Wen D. , Carlos Valadez J. , Gallagher John A. , Jo Hwan R. , Sahul Raffi , Hackenberger Wes , Lynch Christopher S.
Published: June 2015

Ceramic niobium modified 95/5 lead zirconate-lead titanate (PZT) undergoes a pressure induced ferroelectric to antiferroelectric phase transformation accompanied by an elimination of polarization and a volume reduction. Electric field and temperature drive the reverse transformation from the antiferroelectric to ferroelectric phase. The phase transformation was monitored under pressure, temperature, and electric field loading. Pressures and temperatures were varied in discrete steps from 0 MPa to 500 MPa and 25 °C to 125 °C, respectively. Cyclic bipolar electric fields were applied with peak amplitudes of up to 6 MV m−1 at each pressure and temperature combination. The resulting electric displacement–electric field hysteresis loops were open “D” shaped at low pressure, characteristic of soft ferroelectric PZT. Just below the phase transformation pressure, the hysteresis loops took on an “S” shape, which split into a double hysteresis loop just above the phase transformation pressure. Far above the phase transformation pressure, when the applied electric field is insufficient to drive an antiferroelectric to ferroelectric phase transformation, the hysteresis loops collapse to linear dielectric behavior. Phase stability maps were generated from the experimental data at each of the temperature steps and used to form a three dimensional pressure–temperature–electric field phase diagram.
In-season expression of nitrate and ammonium transporter genes in roots of winter wheat (Triticum aestivum L.) genotypes with different nitrogen-uptake efficiencies
Authors: Liu Jinshan , Fu Jie , Tian Hui , Gao Yajun
Published: June 2015

Although nitrate and ammonium transporter genes of wheat have been cloned, little is known about their expression characteristics. A greenhouse experiment was established to study temporal expression patterns over a growing season for four nitrate-transporter genes (TaNRT2.1, TaNRT2.2, TaNRT2.3 and TaNRT1.2) and two ammonium-transporter genes (TaAMT1.1 and TaAMT1.2) in wheat genotypes with different nitrogen (N)-uptake efficiencies. Genotypes that were N-efficient (XY107) and N-inefficient (XY6) were planted in soils that were N-limited (no N added) and N-adequate (added 0.3 g N kg–1 soil). Roots were sampled at tillering, jointing, heading and grain-filling stages, and the expression of the six genes was quantified using real-time, reverse transcription PCR (polymerase chain reaction). Results indicated that maintaining active N uptake during reproduction was the main strategy used by genotype XY107 to sustain its high N-uptake efficiencies in both N treatments. The expression of all NRT and AMT genes showed significant temporal dynamics, and generally matched the pattern of in-season N uptake of wheat plants. Several NRT or AMT genes (especially TaNRT2.1) showed greater expression at reproduction in the N-efficient genotype, XY107, than in the N-inefficient genotype, XY6, suggesting that nitrate and ammonium transporters play important roles in determining the genotypic variation of N uptake in wheat.
Weighting the differential water capacity to account for declining hydraulic conductivity in a drying coarse-textured soil
Authors: Grant C. D. , Groenevelt P. H.
Published: June 2015

Water availability to plants growing in coarse-textured soils during a drying cycle relies on the declining abilities of the soil to release water (differential water capacity) and to deliver it to the plant (unsaturated hydraulic conductivity) under varying evaporative demand. In this context, the availability of water can be quantified using the concept of the integral water capacity, IWC, in which the differential water capacity is weighted by means of a restrictive hydraulic function before integrating. We argue here that the diffusivity is an appropriate component of the restrictive hydraulic function, which leads to the employment of the so-called ‘matric flux potential’ (which we propose to re-name as the ‘matric flux transform’). As the starting point to apply the diffusivity function, we choose the inflection point of the water-retention curve drawn on semi-log paper, which, for the Groenevelt–Grant equation, occurs at a matric head, h, of precisely k0 metres. An illustrative example of the procedures is provided for a coarse-textured soil, which reveals that the restrictive function may not be sufficiently restrictive for all cases. We therefore apply an additional weighting coefficient to account for varying sensitivity of different plants to hydraulic restrictions.
Backbones of evolutionary history test biodiversity theory for microbes
Authors: O’Dwyer James P. , Kembel Steven W. , Sharpton Thomas J.
Published: June 2015

Significance

Linking mechanism and data to explain patterns of biodiversity is a central goal in ecology. Microbial communities provide new challenges in addressing this goal, among them the potential for novel ecological mechanisms at work and also the difficulty in applying an unambiguous species concept. Patterns of evolutionary history, or phylogenetic diversity, provide an alternative framework, circumventing the need to define microbial species. We document multiple patterns of phylogenetic diversity, finding striking and unexpected similarities in these patterns across habitats, and we find that these patterns are inconsistent with neutral biodiversity theory, which has been successful in describing patterns of species diversity for macroscopic organisms. Our results suggest that a new, alternative family of models provides a better description for microbes.
CD14 dependence of TLR4 endocytosis and TRIF signaling displays ligand specificity and is dissociable in endotoxin tolerance
Authors: Rajaiah Rajesh , Perkins Darren J. , Ireland Derek D. C. , Vogel Stefanie N.
Published: June 2015

Significance

MyD88-dependent signaling is cluster of differentiation 14 (CD14)-dependent only at low LPS concentrations, whereas activation of the TIR-domain–containing adapter-inducing IFN-β (TRIF) pathway requires CD14 at all LPS concentrations, leading to internalization of the Toll-like receptor 4 (TLR4) complex into endosomes whereupon TRIF is recruited. Using alternative TLR4 agonists, or macrophages rendered tolerant to LPS, we dissociate TLR4 complex internalization from CD14 and TRIF-dependent signaling. In response to LPS, CD14 contributes to the formation of a TLR4/MD2 complex dimer that, in turn, promotes endocytosis and IRF3 activation.
Engineered cellular gene-replacement platform for selective and inducible proteolytic profiling
Authors: Morgan Charles W. , Diaz Juan E. , Zeitlin Samantha G. , Gray Daniel C. , Wells James A.
Published: June 2015

Significance

Apoptosis, a type of programmed cell death, is critical for the removal of diseased or superfluous cells and is essential in maintaining tissue homeostasis. At the molecular level, apoptosis leads to the highly coordinated selective proteolysis of more than a thousand cellular proteins. Until now, determining the individual molecular consequence of proteolysis has been largely out of reach. Our article reports biotechnological advances that enable rapid and reliable posttranscriptional gene replacement for robust inducible and selective proteolysis of the replacement allele. We go on to further show the utility of our technology in deciphering synthetic lethality resulting from coordinated proteolysis of caspase substrates that control the apoptotic hallmark of chromatin fragmentation.
Tissue stiffness regulates serine/arginine-rich protein-mediated splicing of the extra domain B-fibronectin isoform in tumors
Authors: Bordeleau Francois , Califano Joseph P. , Negrón Abril Yashira L. , Mason Brooke N. , LaValley Danielle J. , Shin Sandra J. , Weiss Robert S. , Reinhart-King Cynthia A.
Published: June 2015

Significance

Alternative splicing is the main mechanism that drives protein diversity; however, little is known about the physiological cues that control splicing. Here, we show that the stiffness of the extracellular matrix mediates protein splicing in cells both in vitro and in vivo. Alternative splicing mediated by matrix stiffness occurs through the phosphorylation of splicing regulatory factors, serine/arginine rich (SR) proteins, and depends on the PI3K signaling pathway. Because the SR family of proteins are conserved among both vertebrates and invertebrates and are known to also be involved in genome stabilization, translation, and mRNA export, these results suggest a previously unidentified mechanism by which cells can respond and adapt to their mechanical microenvironment in both healthy and diseased states.
A retro-biosynthetic approach to the prediction of biosynthetic pathways from position-specific isotope analysis as shown for tramadol
Authors: Romek Katarzyna M. , Nun Pierrick , Remaud Gérald S. , Silvestre Virginie , Taïwe Germain Sotoing , Lecerf-Schmidt Florine , Boumendjel Ahcène , De Waard Michel , Robins Richard J.
Published: June 2015

Significance

The extraction of tramadol from the roots of
Nauclea latifolia
excited great interest worldwide. This was the first time that a widely marketed synthetic drug was found as an apparently natural product at high abundance. In this article, we describe the position-specific distribution of
13
C in this tramadol. As a conventional approach to study its probable biosynthetic precursors, enzymatic steps, and intermediate metabolites is not currently feasible, we herein propose the concept of a retro-biosynthesis by examining the position-specific isotope distribution within the molecule and rationally interpreting the data in terms of known plant biochemical processes that may be involved in a biosynthesis of tramadol. Thus, clear guidance is given for future labeling studies.
Implications of fisheries impacts to seabed biodiversity and ecosystem-based management
Authors: Thrush Simon F. , Ellingsen Kari E. , Davis Kathryn
Published: June 2015

Biodiversity has many key roles in ecosystems, and many elements of biodiversity support fish species and therefore also fisheries. At the same time, cooperation fisheries also often affect seabed biodiversity. Furthermore, fisheries may also change the composition of fish communities, and we illustrate why changes in fish communities can matter to seabed biodiversity. These issues should matter to fisheries management. Biodiversity research by definition addresses heterogeneity and this should influence the nature of questions the science seeks to address and how empirical studies are designed. However, to date biodiversity research has not been fully incorporated into mainstream fisheries science. We aim to facilitate the transition to a more transdisciplinary framework, and move beyond the fisheries-focused management. Human pressure is increasing, and many ecosystems are affected by cumulative impacts from different sources of disturbance. We discuss insights from biodiversity and ecosystem function research, and we advocate for a focus on cumulative impacts from disturbance and resilience. We consider these to be critical elements of the transition into ecosystem-based management. The ecological systems and the services that they generate can be either degraded and support less biodiversity and a smaller range of human values, or they can be resorted. The choice is ours. We advocate for a development of participatory multi-sector management that integrates different institutions to contribute to cultural, social, economic, and biodiversity values for ocean governance.
Weather During Critical Epidemiological Periods and Subsequent Severity of Powdery Mildew on Grape Berries
Authors: Moyer Michelle M. , Gadoury David M. , Wilcox Wayne F. , Seem Robert C.
Published: June 2015

Recorded severity of grape powdery mildew on berries of untreated, susceptible hybrid cultivars varied from 0.2 to 50.5% across a 30-year period in Geneva, NY; within 7 of those years, cluster disease severity ranged from 3.42 to 99.5% on Vitis vinifera ‘Chardonnay’. Although existing temperature-driven risk models could not account for this annual variation, pan evaporation (Epan), an environmental variable influenced by the collective effects of temperature, vapor pressure deficit, solar radiation, and wind speed, did. Logistic regression analysis (LRA) was used to classify epidemics as either mild or severe. Recursive partition analysis (RPA) provided a simplified decision tree for calculation of powdery mildew risk and incorporated (i) an estimate of the relative primary inoculum levels based on temperatures in the previous late summer and (ii) the current season favorability for pathogen development during the grapevine phenological period critical for berry infection by Erysiphe necator. Although the LRA had fewer instances of misclassification, RPA provided a rapid means for seasonal risk classification. Both the RPA and LRA models are able to describe disease severity risk in real time or can be used to forecast risk, thereby allowing growers to adjust management programs in a responsive manner.
Computer-Aided Design and Computer-Aided Manufacturing Hydroxyapatite/Epoxide Acrylate Maleic Compound Construction for Craniomaxillofacial Bone Defects
Authors: Zhang Lei , Shen Shunyao , Yu Hongbo , Shen Steve Guofang , Wang Xudong
Published: June 2015

The aim of this study was to investigate the use of computer-aided design and computer-aided manufacturing hydroxyapatite (HA)/epoxide acrylate maleic (EAM) compound construction artificial implants for craniomaxillofacial bone defects. Computed tomography, computer-aided design/computer-aided manufacturing and three-dimensional reconstruction, as well as rapid prototyping were performed in 12 patients between 2008 and 2013. The customized HA/EAM compound artificial implants were manufactured through selective laser sintering using a rapid prototyping machine into the exact geometric shapes of the defect. The HA/EAM compound artificial implants were then implanted during surgical reconstruction. Color-coded superimpositions demonstrated the discrepancy between the virtual plan and achieved results using Geomagic Studio. As a result, the HA/EAM compound artificial bone implants were perfectly matched with the facial areas that needed reconstruction. The postoperative aesthetic and functional results were satisfactory. The color-coded superimpositions demonstrated good consistency between the virtual plan and achieved results. The three-dimensional maximum deviation is 2.12 ± 0.65 mm and the three-dimensional mean deviation is 0.27 ± 0.07 mm.

No facial nerve weakness or pain was observed at the follow-up examinations. Only 1 implant had to be removed 2 months after the surgery owing to severe local infection. No other complication was noted during the follow-up period. In conclusion, computer-aided, individually fabricated HA/EAM compound construction artificial implant was a good craniomaxillofacial surgical technique that yielded improved aesthetic results and functional recovery after reconstruction.
Circular Excision and Purse-String Closure for Pediatric Facial Skin Lesions
Authors: Hassanein Aladdin H. , Couto Javier A. , Greene Arin K.
Published: June 2015

Standard resection of pediatric facial skin lesions consists of lenticular excision and linear closure. This one-stage procedure for circular lesions results in a linear scar 3 times longer than the diameter of the removed specimen. Circular excision and purse-string closure has been described for infantile hemangiomas to reduce the length of scar. The purpose of this study was to analyze the application of this technique for any type of circular facial skin lesion in the pediatric population.

Records of consecutive pediatric patients with facial skin lesions treated with circular excision and purse-string closure from 2007–2014 were reviewed. Patient age, sex, type of lesion, location, and size were recorded. Number of stages necessary to remove the area and complications were analyzed.

Seventy-seven children (74% female) underwent circular excision and purse-string closure for an infantile hemangioma (46%), pigmented nevus (27%), Spitz nevus (7%), pilomatrixoma (5%), pyogenic granuloma (5%), vascular malformation (4%), or another type of skin lesion (6%). Age at the time of resection was 6.0 years (range 4 months–17 years) and mean lesion area was 3.9 cm2 (range 0.2–19.6); 30% of patients underwent a second procedure and no infection or wound dehiscence occurred.

Circular excision and purse-string closure is an effective technique to manage any type of circular skin lesion in the pediatric population. It is particularly useful for lesions on the face because it limits the length of a scar. A subset of patients may benefit from second procedure to convert the circular scar from a circle into a line.
The Effect of Nasal Septal Deviation on Frontal and Maxillary Sinus Volumes and Development of Sinusitis
Authors: Karataş Duran , Koç Ali , Yüksel Fatih , Doğan Murat , Bayram Ali , Cihan Mehmet C.
Published: June 2015

The purpose of this study was to determine the possible role of nasal septal deviation on volume of maxillary and frontal sinuses. Between February 2011 and October 2013, paranasal sinus computed tomography (CT) findings of 732 patients (410 males, 322 females) who were admitted to Ear Nose and Throat Department of Kayseri Research and Training Hospital were retrospectively analyzed. By excluding the other coexistent sinonasal pathologies, 83 consecutive patients with nasal septal deviations were included in the study. The volume of each maxillary and frontal sinus (ipsi- and contralateral to the deviation side) was also calculated using the computer program. There was no statistically significant difference between ipsilateral and contralateral maxillary sinus volumes in group 1 and group 3 (P > 0.05). There was a statistically significant difference between ipsilateral and contralateral maxillary sinus volumes in group 2 (P < 0.05). There was no statistically significant difference between ipsilateral and contralateral frontal sinus volumes in group 1, group 2, and group 3 (P > 0.05). Moderate septal deviation significantly affects the volume of maxillary sinus. Mild and severe septal deviation does not significantly affect the volume of maxillary sinus. Effect of septal deviation on frontal sinus volume was not detected. The probability to encounter maxillary and frontal sinusitis ipsilateral to the all septum deviation groups was significantly increased in both right- and left-sided subjects.
Racehorses are getting faster
Authors: Sharman Patrick , Wilson Alastair J.
Published: June 2015

Previous studies have concluded that thoroughbred racehorse speed is improving very slowly, if at all, despite heritable variation for performance and putatively intensive selective breeding. This has led to the suggestion that racehorses have reached a selection limit. However, previous studies have been limited, focusing only on the winning times of a few elite races run over middle and long distances, and failing to account for potentially confounding factors. Using a much larger dataset covering the full range of race distances and accounting for variation in factors such as ground softness, we show that improvement is, in fact, ongoing for the population as a whole, but driven largely by increasing speed in sprint races. In contrast, speed over middle and long distances, at least at the elite level, appears to be reaching an asymptote. Whether this reflects a selection limit to speed over middle and long distances or a shift in breeding practices to target sprint performances remains to be determined.
Romundina
and the evolutionary origin of teeth
Authors: Rücklin Martin , Donoghue Philip C. J.
Published: June 2015

Theories on the origin of vertebrate teeth have long focused on chondrichthyans as reflecting a primitive condition—but this is better informed by the extinct placoderms, which constitute a sister clade or grade to the living gnathostomes. Here, we show that ‘supragnathal’ toothplates from the acanthothoracid placoderm
Romundina stellina
comprise multi-cuspid teeth, each composed of an enameloid cap and core of dentine. These were added sequentially, approximately circumferentially, about a pioneer tooth. Teeth are bound to a bony plate that grew with the addition of marginal teeth. Homologous toothplates in arthrodire placoderms exhibit a more ordered arrangement of teeth that lack enameloid, but their organization into a gnathal, bound by layers of cellular bone associated with the addition of each successional tooth, is the same. The presence of enameloid in the teeth of
Romundina
suggests that it has been lost in other placoderms. Its covariation in the teeth and dermal skeleton of placoderms suggests a lack of independence early in the evolution of jawed vertebrates. It also appears that the dentition—manifest as discrete gnathal ossifications—was developmentally discrete from the jaws during this formative episode of vertebrate evolution.
Adhesive interactions of geckos with wet and dry fluoropolymer substrates
Authors: Stark Alyssa Y. , Dryden Daniel M. , Olderman Jeffrey , Peterson Kelly A. , Niewiarowski Peter H. , French Roger H. , Dhinojwala Ali
Published: June 2015

Fluorinated substrates like Teflon
®
(poly(tetrafluoroethylene); PTFE) are well known for their role in creating non-stick surfaces. We showed previously that even geckos, which can stick to most surfaces under a wide variety of conditions, slip on PTFE. Surprisingly, however, geckos can stick reasonably well to PTFE if it is wet. In an effort to explain this effect, we have turned our attention to the role of substrate surface energy and roughness when shear adhesion occurs in media other than air. In this study, we removed the roughness component inherent to commercially available PTFE and tested geckos on relatively smooth wet and dry fluoropolymer substrates. We found that roughness had very little effect on shear adhesion in air or in water and that the level of fluorination was most important for shear adhesion, particularly in air. Surface energy calculations of the two fluorinated substrates and one control substrate using the Tabor–Winterton approximation and the Young–Dupré equation were used to determine the interfacial energy of the substrates. Using these interfacial energies we estimated the ratio of wet and dry normal adhesion for geckos clinging to the three substrates. Consistent with the results for rough PTFE, our predictions show a qualitative trend in shear adhesion based on fluorination, and the quantitative experimental differences highlight the unusually low shear adhesion of geckos on dry smooth fluorinated substrates, which is not captured by surface energy calculations. Our work has implications for bioinspired design of synthetics that can preferentially stick in water but not in air.
An efficient interpolation technique for jump proposals in reversible-jump Markov chain Monte Carlo calculations
Authors: Farr W. M. , Mandel I. , Stevens D.
Published: June 2015

Selection among alternative theoretical models given an observed dataset is an important challenge in many areas of physics and astronomy. Reversible-jump Markov chain Monte Carlo (RJMCMC) is an extremely powerful technique for performing Bayesian model selection, but it suffers from a fundamental difficulty and it requires jumps between model parameter spaces, but cannot efficiently explore both parameter spaces at once. Thus, a naive jump between parameter spaces is unlikely to be accepted in the Markov chain Monte Carlo (MCMC) algorithm and convergence is correspondingly slow. Here, we demonstrate an interpolation technique that uses samples from single-model MCMCs to propose intermodel jumps from an approximation to the single-model posterior of the target parameter space. The interpolation technique, based on a kD-tree data structure, is adaptive and efficient in modest dimensionality. We show that our technique leads to improved convergence over naive jumps in an RJMCMC, and compare it to other proposals in the literature to improve the convergence of RJMCMCs. We also demonstrate the use of the same interpolation technique as a way to construct efficient ‘global’ proposal distributions for single-model MCMCs without prior knowledge of the structure of the posterior distribution, and discuss improvements that permit the method to be used in higher dimensional spaces efficiently.
Perturbation theory for propagating magnetic droplet solitons
Authors: Bookman L. D. , Hoefer M. A.
Published: June 2015

Droplet solitons are strongly nonlinear, inherently dynamic structures in the magnetization of ferromagnets, balancing dispersion (exchange energy) with focusing nonlinearity (strong perpendicular anisotropy). Large droplet solitons have the approximate form of a circular domain wall sustained by precession and, in contrast to single magnetic vortices, are predicted to propagate in an extended, homogeneous magnetic medium. In this work, multiscale perturbation theory is used to develop an analytical framework for investigating the impact of additional physical effects on the behaviour of a propagating droplet. After first developing soliton perturbation theory in the general context of Hamiltonian systems, a number of physical phenomena of current interest are investigated. These include droplet–droplet and droplet–boundary interactions, spatial magnetic field inhomogeneities, spin transfer torque induced forcing in a nanocontact device and damping. Their combined effects demonstrate the fundamental mechanisms for a previously observed droplet drift instability and under what conditions a slowly propagating droplet can be supported by the nanocontact, important considerations for applications. This framework emphasizes the particle-like dynamics of the droplet, providing analytically tractable and practical predictions for modern experimental configurations.
An elastocapillary model of wood-fibre collapse
Authors: Akbari Amir , Hill Reghan J. , van de Ven Theo G. M.
Published: June 2015

An elastocapillary model for drying-induced collapse is proposed. We consider a circular elastic membrane with a hole at the centre that is deformed by the capillary pressure of simply and doubly connected menisci. The membrane overlays a cylindrical cavity with rigid walls, trapping a prescribed volume of water. This geometry may be suitable for studying structural failures and stiction in micro-electromechanical systems during wet etching, where capillary surfaces experience catastrophic transitions. The dry state is determined using the dihedral-angle and volume-turning-point stability criteria. Open and collapsed conformations are predicted from the scaled hole radius, cavity aspect ratio, meniscus contact angle with the membrane and cavity walls, and an elastocapillary number measuring the membrane stretching rigidity relative to the water surface tension. For a given scaled hole radius and cavity aspect ratio, there is a critical elastocapillary number above which the system does not collapse upon drying. The critical elastocapillary number is weakly influenced by the contact angle over a wide range of the scaled hole radius, thus indicating a limitation of surface hydrophobization for controlling the dry-state conformation. The model is applied to the drying of wood fibres above the fibre saturation point, determining the conditions leading to collapse.
Why the high-frequency inverse scattering by topological sensitivity may work
Authors: Guzina Bojan B. , Pourahmadian Fatemeh
Published: June 2015

This study deciphers the topological sensitivity (TS) as a tool for the reconstruction and characterization of impenetrable anomalies in the high-frequency regime. It is assumed that the anomaly is simply connected and convex, and that the measurements of the scattered field are of the far-field type. In this setting, the formula for TS—which quantifies the perturbation of a cost functional due to a point-like impenetrable scatterer—is expressed as a pair of nested surface integrals: one taken over the boundary of a hidden obstacle, and the other over the measurement surface. Using multipole expansion, the latter integral is reduced to a set of antilinear forms featuring Green's function and its gradient. The remaining expression is distilled by evaluating the scattered field on the surface of an obstacle via Kirchhoff approximation, and pursuing an asymptotic expansion of the resulting Fourier integral. In this way, the TS is found to survive upon three asymptotic lynchpins, namely (i) the near-boundary approximation for sampling points close to the ‘exposed’ surface of an obstacle; (ii) uniform expansions synthesizing the diffraction catastrophes for sampling points near caustic surfaces, lines and points; and (iii) stationary phase approximation. Within the framework of catastrophe theory, it is shown that, in the case of the full source aperture, the TS is asymptotically dominated by the (explicit) near-boundary term—which explains the previously reported reconstruction capabilities of this class of indicator functionals. The analysis further shows that, when the (Dirichlet or Neumann) character of an anomaly is unknown beforehand, the latter can be effectively exposed by assuming point-like Dirichlet perturbation and considering the sign of the leading term inside the reconstruction.