bluuebunny/crossref_metadata_2025 huggingface dataset:
Modularized architecture of address generation units suitable for real-time processing MR data on an FPGA
Authors: Li Limin , Wyrwicz Alice M.
Published: June 2016

In this paper, we describe a modular approach to the design of an Address Generation Unit (AGU). The approach consists of development of a generic Address Generation Core (AGC) as a basic building block and the construction of an AGU from the AGCs. We illustrate this concept with AGUs capable of handling 2D- and 3D-structured data, and as well as their setup for executing 2D and 3D FFT algorithms on a Field Programmable Gate Array (FPGA). The AGUs developed using our proposed method are simple and easily expandable. Furthermore, they can potentially support irregularly structured data which are often generated from the wide variety of pulse sequences in magnetic resonance imaging. Our experimental results show that these AGUs are capable of generating addresses with a user-predefined pattern automatically at the speed of one address per clock cycle and operate at clock rates up to 80 MHz. They can operate concurrently with other processes and thus do not introduce additional operation latencies. Although we focus on applying the developed AGUs to executing 2D and 3D FFT, we expect that the modular design method should have much wider applications.
Multiplexed immunosensing and kinetics monitoring in nanofluidic devices with highly enhanced target capture efficiency
Authors: Lin Yii-Lih , Huang Yen-Jun , Teerapanich Pattamon , Leïchlé Thierry , Chou Chia-Fu
Published: June 2016

Nanofluidic devices promise high reaction efficiency and fast kinetic responses due to the spatial constriction of transported biomolecules with confined molecular diffusion. However, parallel detection of multiple biomolecules, particularly proteins, in highly confined space remains challenging. This study integrates extended nanofluidics with embedded protein microarray to achieve multiplexed real-time biosensing and kinetics monitoring. Implementation of embedded standard-sized antibody microarray is attained by epoxy-silane surface modification and a room-temperature low-aspect-ratio bonding technique. An effective sample transport is achieved by electrokinetic pumping via electroosmotic flow. Through the nanoslit-based spatial confinement, the antigen-antibody binding reaction is enhanced with ∼100% efficiency and may be directly observed with fluorescence microscopy without the requirement of intermediate washing steps. The image-based data provide numerous spatially distributed reaction kinetic curves and are collectively modeled using a simple one-dimensional convection-reaction model. This study represents an integrated nanofluidic solution for real-time multiplexed immunosensing and kinetics monitoring, starting from device fabrication, protein immobilization, device bonding, sample transport, to data analysis at Péclet number less than 1.
Thermal rectification in silicon by a graded distribution of defects
Authors: Dettori Riccardo , Melis Claudio , Rurali Riccardo , Colombo Luciano
Published: June 2016

We discuss about computer experiments based on nonequilibrium molecular dynamics simulations providing evidence that thermal rectification can be obtained in bulk Si by a non-uniform distribution of defects. We consider a graded population of both Ge substitutional defects and nanovoids, distributed along the direction of an applied thermal bias, and predict a rectification factor comparable to what is observed in other low–dimensional Si–based nanostructures. By considering several defect distribution profiles, thermal bias conditions, and sample sizes, the present results suggest that a possible way for tuning the thermal rectification is by defect engineering.
Effect of annealing on the laser induced damage of polished and CO2 laser-processed fused silica surfaces
Authors: Doualle T. , Gallais L. , Cormont P. , Donval T. , Lamaignère L. , Rullier J. L.
Published: June 2016

We investigate the effect of different heat treatments on the laser-induced damage probabilities of fused silica samples. Isothermal annealing in a furnace is applied, with different temperatures in the range 700–1100 °C and 12 h annealing time, to super-polished fused silica samples. The surface flatness and laser damage probabilities at 3 ns, 351 nm are measured before and after the different annealing procedures. We have found a significant improvement of the initial laser damage probabilities of the silica surface after annealing at 1050 °C for 12 h. A similar study has been conducted on CO2 laser-processed sites on the surface of the samples. Before and after annealing, we have studied the morphology of the sites, the evolution of residual stress, and the laser-induced damage threshold measured at 351 nm, 3 ns. In this case, we observe that the laser damage resistance of the laser created craters can reach the damage level of the bare fused silica surface after the annealing process, with a complete stress relieve. The obtained results are then compared to the case of local annealing process by CO2 laser irradiation during 1 s, and we found similar improvements in both cases. The different results obtained in the study are compared to numerical simulations made with a thermo-mechanical model based on finite-element method that allows the simulation of the isothermal or the local annealing process, the evolution of stress and fictive temperature. The simulation results were found to be very consistent with experimental observations for the stresses evolution after annealing and estimation of the heat affected area during laser-processing based on the density dependence with fictive temperature. Following this work, the temperature for local annealing should reach 1330–1470 °C for an optimized reduction of damage probability and be below the threshold for material removal, whereas furnace annealing should be kept below the annealing point to avoid sample deformation.
Inter-ribbon tunneling in graphene: An atomistic Bardeen approach
Authors: Van de Put Maarten L. , Vandenberghe William G. , Sorée Bart , Magnus Wim , Fischetti Massimo V.
Published: June 2016

A weakly coupled system of two crossed graphene nanoribbons exhibits direct tunneling due to the overlap of the wavefunctions of both ribbons. We apply the Bardeen transfer Hamiltonian formalism, using atomistic band structure calculations to account for the effect of the atomic structure on the tunneling process. The strong quantum-size confinement of the nanoribbons is mirrored by the one-dimensional character of the electronic structure, resulting in properties that differ significantly from the case of inter-layer tunneling, where tunneling occurs between bulk two-dimensional graphene sheets. The current-voltage characteristics of the inter-ribbon tunneling structures exhibit resonance, as well as stepwise increases in current. Both features are caused by the energetic alignment of one-dimensional peaks in the density-of-states of the ribbons. Resonant tunneling occurs if the sign of the curvature of the coupled energy bands is equal, whereas a step-like increase in the current occurs if the signs are opposite. Changing the doping modulates the onset-voltage of the effects as well as their magnitude. Doping through electrostatic gating makes these structures promising for application towards steep slope switching devices. Using the atomistic empirical pseudopotentials based Bardeen transfer Hamiltonian method, inter-ribbon tunneling can be studied for the whole range of two-dimensional materials, such as transition metal dichalcogenides. The effects of resonance and of step-like increases in the current we observe in graphene ribbons are also expected in ribbons made from these alternative two-dimensional materials, because these effects are manifestations of the one-dimensional character of the density-of-states.
Band engineering in transition metal dichalcogenides: Stacked versus lateral heterostructures
Authors: Guo Yuzheng , Robertson John
Published: June 2016

We calculate a large difference in the band alignments for transition metal dichalcogenide (TMD) heterojunctions when arranged in the stacked layer or lateral (in-plane) geometries, using direct supercell calculations. The stacked case follows the unpinned limit of the electron affinity rule, whereas the lateral geometry follows the strongly pinned limit of alignment of charge neutrality levels. TMDs therefore provide one of the few clear tests of band alignment models, whereas three-dimensional semiconductors give less stringent tests because of accidental chemical trends in their properties.
Numerical and experimental study of Lamb wave propagation in a two-dimensional acoustic black hole
Authors: Yan Shiling , Lomonosov Alexey M. , Shen Zhonghua
Published: June 2016

The propagation of laser-generated Lamb waves in a two-dimensional acoustic black-hole structure was studied numerically and experimentally. The geometrical acoustic theory has been applied to calculate the beam trajectories in the region of the acoustic black hole. The finite element method was also used to study the time evolution of propagating waves. An optical system based on the laser-Doppler vibration method was assembled. The effect of the focusing wave and the reduction in wave speed of the acoustic black hole has been validated.
CdSe/ZnS quantum dot fluorescence spectra shape-based thermometry via neural network reconstruction
Authors: Munro Troy , Liu Liwang , Glorieux Christ , Ban Heng
Published: June 2016

As a system of interest gets small, due to the influence of the sensor mass and heat leaks through the sensor contacts, thermal characterization by means of contact temperature measurements becomes cumbersome. Non-contact temperature measurement offers a suitable alternative, provided a reliable relationship between the temperature and the detected signal is available. In this work, exploiting the temperature dependence of their fluorescence spectrum, the use of quantum dots as thermomarkers on the surface of a fiber of interest is demonstrated. The performance is assessed of a series of neural networks that use different spectral shape characteristics as inputs (peak-based—peak intensity, peak wavelength; shape-based—integrated intensity, their ratio, full-width half maximum, peak normalized intensity at certain wavelengths, and summation of intensity over several spectral bands) and that yield at their output the fiber temperature in the optically probed area on a spider silk fiber. Starting from neural networks trained on fluorescence spectra acquired in steady state temperature conditions, numerical simulations are performed to assess the quality of the reconstruction of dynamical temperature changes that are photothermally induced by illuminating the fiber with periodically intensity-modulated light. Comparison of the five neural networks investigated to multiple types of curve fits showed that using neural networks trained on a combination of the spectral characteristics improves the accuracy over use of a single independent input, with the greatest accuracy observed for inputs that included both intensity-based measurements (peak intensity) and shape-based measurements (normalized intensity at multiple wavelengths), with an ultimate accuracy of 0.29 K via numerical simulation based on experimental observations. The implications are that quantum dots can be used as a more stable and accurate fluorescence thermometer for solid materials and that use of neural networks for temperature reconstruction improves the accuracy of the measurement.
Optimization of carbon nanotube ultracapacitor for cell design
Authors: Orphanou Antonis , Yamada Toshishige , Yang Cary Y.
Published: June 2016

We report a methodology to optimize vertically grown carbon nanotube (CNT) ultracapacitor (CNU) geometrical features such as CNT length, electrode-to-electrode separation, and CNT packing density. The electric field and electrolyte ionic motion within the CNU are critical in determining the device performance. Using a particle-based model (PBM) based on the molecular dynamics techniques we developed and reported previously, we compute the electric field in the device, keep track of the electrolyte ionic motion in the device volume, and evaluate the CNU electrical performance as a function of the aforementioned geometrical features. We show that the PBM predicts an optimal CNT density. Electrolyte ionic trapping occurs in the high CNT density regime, which limits the electrolyte ions from forming a double layer capacitance. In this regime, the CNU capacitance does not increase with the CNT packing density as expected, but dramatically decreases. Our results compare well with existing experimental data and the PBM methodology can be applied to an ultracapacitor built from any metallic electrode materials, as well as the vertical CNTs studied here.
Structural transition in sputter-deposited amorphous germanium films by aging at ambient temperature
Authors: Okugawa M. , Nakamura R. , Ishimaru M. , Watanabe K. , Yasuda H. , Numakura H.
Published: June 2016

The structure of amorphous Ge (a-Ge) films prepared by sputter-deposition and the effects of aging at ambient temperature and pressure were studied by pair-distribution-function (PDF) analysis from electron scattering and molecular dynamics simulations. The PDFs of the as-deposited and aged samples for 3–13 months showed that the major peaks for Ge-Ge bonds decrease in intensity and broaden with aging for up to 7 months. In the PDFs of a-Ge of molecular dynamics simulation obtained by quenching liquid at different rates, the major peak intensities of a slowly cooled model are higher than those of a rapidly cooled model. Analyses on short- and medium-range configurations show that the slowly cooled model includes a certain amount of medium-range ordered (MRO) clusters, while the rapidly cooled model includes liquid-like configurations rather than MRO clusters. The similarity between experimental and computational PDFs implies that as-deposited films are similar in structure to the slowly cooled model, whereas the fully aged films are similar to the rapidly cooled model. It is assumed that as they undergo room-temperature aging, the MRO clusters disintegrate and transform into liquid-like regions in the same matrix. This transition in local configurations is discussed in terms of instability and the non-equilibrium of nanoclusters produced by a vapor-deposition process.
Bifurcation of transition paths induced by coupled bistable systems
Authors: Tian Chengzhe , Mitarai Namiko
Published: June 2016

We discuss the transition paths in a coupled bistable system consisting of interacting multiple identical bistable motifs. We propose a simple model of coupled bistable gene circuits as an example and show that its transition paths are bifurcating. We then derive a criterion to predict the bifurcation of transition paths in a generalized coupled bistable system. We confirm the validity of the theory for the example system by numerical simulation. We also demonstrate in the example system that, if the steady states of individual gene circuits are not changed by the coupling, the bifurcation pattern is not dependent on the number of gene circuits. We further show that the transition rate exponentially decreases with the number of gene circuits when the transition path does not bifurcate, while a bifurcation facilitates the transition by lowering the quasi-potential energy barrier.
Near-field thermal radiation between homogeneous dual uniaxial electromagnetic metamaterials
Authors: Chang Jui-Yung , Basu Soumyadipta , Yang Yue , Wang Liping
Published: June 2016

Recently, near-field thermal radiation has attracted much attention in several fields since it can exceed the Planck blackbody limit through the coupling of evanescent waves. In this work, near-field radiative heat transfer between two semi-infinite dual uniaxial electromagnetic metamaterials with two different material property sets is theoretically analyzed. The near-field radiative heat transfer is calculated using fluctuational electrodynamics incorporated with anisotropic wave optics. The underlying mechanisms, namely, magnetic hyperbolic mode, magnetic surface polariton, electrical hyperbolic mode, and electrical surface polariton, between two homogeneous dual uniaxial electromagnetic metamaterials are investigated by examining the transmission coefficient and the spectral heat flux. The effect of vacuum gap distance is also studied, which shows that the enhancement at smaller vacuum gap is mainly due to hyperbolic mode and surface plasmon polariton modes. In addition, the results show that the contribution of s-polarized waves is significant and should not be excluded due to the strong magnetic response regardless of vacuum gap distances. The fundamental understanding and insights obtained here will facilitate the finding and application of novel materials for near-field thermal radiation.
Real-time dual-comb spectroscopy with a free-running bidirectionally mode-locked fiber laser
Authors: Mehravar S. , Norwood R. A. , Peyghambarian N. , Kieu K.
Published: June 2016

Dual-comb technique has enabled exciting applications in high resolution spectroscopy, precision distance measurements, and 3D imaging. Major advantages over traditional methods can be achieved with dual-comb technique. For example, dual-comb spectroscopy provides orders of magnitude improvement in acquisition speed over standard Fourier-transform spectroscopy while still preserving the high resolution capability. Wider adoption of the technique has, however, been hindered by the need for complex and expensive ultrafast laser systems. Here, we present a simple and robust dual-comb system that employs a free-running bidirectionally mode-locked fiber laser operating at telecommunication wavelength. Two femtosecond frequency combs (with a small difference in repetition rates) are generated from a single laser cavity to ensure mutual coherent properties and common noise cancellation. As the result, we have achieved real-time absorption spectroscopy measurements without the need for complex servo locking with accurate frequency referencing, and relatively high signal-to-noise ratio.
Enhanced current-perpendicular-to-plane giant magnetoresistance effect in half-metallic NiMnSb based nanojunctions with multiple Ag spacers
Authors: Wen Zhenchao , Kubota Takahide , Yamamoto Tatsuya , Takanashi Koki
Published: June 2016

Current-perpendicular-to-plane giant magnetoresistance (CPP-GMR) heterostructure devices using half-metallic NiMnSb Heusler alloy electrodes with single, dual, and triple Ag spacers were fabricated. The NiMnSb alloy films and Ag spacers show (001) epitaxial growth in all CPP-GMR multilayer structures. The dual-spacer CPP-GMR nanojunction exhibited an enhanced CPP-GMR ratio of 11% (a change in the resistance-area product, ΔRA, of 3.9 mΩ μm2) at room temperature, which is approximately twice (thrice) of 6% (1.3 mΩ μm2) in the single-spacer device. The enhancement of the CPP-GMR effects in the dual-spacer devices could be attributed to improved interfacial spin asymmetry. Moreover, it was observed that the CPP-GMR ratios increased monotonically as the temperatures decreased. At 4.2 K, a CPP-GMR ratio of 41% (ΔRA = 10.5 mΩ μm2) was achieved in the dual-spacer CPP-GMR device. This work indicates that multispacer structures provide an efficient enhancement of CPP-GMR effects in half-metallic material-based CPP-GMR systems.
Stability and efficacy of synthetic cationic antimicrobial peptides nebulized using high frequency acoustic waves
Authors: Wang Ying , Rezk Amgad R. , Khara Jasmeet Singh , Yeo Leslie Y. , Ee Pui Lai Rachel
Published: June 2016

Surface acoustic wave (SAW), a nanometer amplitude electroelastic wave generated and propagated on low-loss piezoelectric substrates (such as LiNbO3), is an extremely efficient solid–fluid energy transfer mechanism. The present study explores the use of SAW nebulization as a solution for effective pulmonary peptide delivery. In vitro deposition characteristics of the nebulized peptides were determined using a Next Generation Cascade Impactor. 70% of the peptide-laden aerosols generated were within a size distribution favorable for deep lung distribution. The integrity of the nebulized peptides was found to be retained, as shown via mass spectrometry. The anti-mycobacterial activity of the nebulized peptides was found to be uncompromised compared with their non-nebulized counterparts, as demonstrated by the minimum inhibition concentration and the colony forming inhibition activity. The peptide concentration and volume recoveries for the SAW nebulizer were significantly higher than 90% and found to be insensitive to variation in the peptide sequences. These results demonstrate the potential of the SAW nebulization platform as an effective delivery system of therapeutic peptides through the respiratory tract to the deep lung.
On the exhaust of electromagnetic drive
Authors: Grahn Patrick , Annila Arto , Kolehmainen Erkki
Published: June 2016

Recent reports about propulsion without reaction mass have been met on one hand with enthusiasm and on the other hand with some doubts. Namely, closed metal cavities, when fueled with microwaves, have delivered thrust that could eventually maintain satellites on orbits using solar power. However, the measured thrust appears to be without any apparent exhaust. Thus the Law of Action-Reaction seems to have been violated. We consider the possibility that the exhaust is in a form that has so far escaped both experimental detection and theoretical attention. In the thruster’s cavity microwaves interfere with each other and invariably some photons will also end up co-propagating with opposite phases. At the destructive interference electromagnetic fields cancel. However, the photons themselves do not vanish for nothing but continue in propagation. These photon pairs without net electromagnetic field do not reflect back from the metal walls but escape from the resonator. By this action momentum is lost from the cavity which, according to the conservation of momentum, gives rise to an equal and opposite reaction. We examine theoretical corollaries and practical concerns that follow from the paired-photon conclusion.
Improvement of electron mobility in La:BaSnO3 thin films by insertion of an atomically flat insulating (Sr,Ba)SnO3 buffer layer
Authors: Shiogai Junichi , Nishihara Kazuki , Sato Kazuhisa , Tsukazaki Atsushi
Published: June 2016

One perovskite oxide, ASnO3 (A = Sr, Ba), is a candidate for use as a transparent conductive oxide with high electron mobility in single crystalline form. However, the electron mobility of films grown on SrTiO3 substrates does not reach the bulk value, probably because of dislocation scattering that originates from the large lattice mismatch. This study investigates the effect of insertion of bilayer BaSnO3 / (Sr,Ba)SnO3 for buffering this large lattice mismatch between La:BaSnO3 and SrTiO3 substrate. The insertion of 200-nm-thick BaSnO3 on (Sr,Ba)SnO3 bilayer buffer structures reduces the number of dislocations and improves surface smoothness of the films after annealing as proved respectively by scanning transmission electron microscopy and atomic force microscopy. A systematic investigation of BaSnO3 buffer layer thickness dependence on Hall mobility of the electron transport in La:BaSnO3 shows that the highest obtained value of mobility is 78 cm2V−1s−1 because of its fewer dislocations. High electron mobility films based on perovskite BaSnO3 can provide a good platform for transparent-conducting-oxide electronic devices and for creation of fascinating perovskite heterostructures.
Thickness-dependent electron mobility of single and few-layer MoS2 thin-film transistors
Authors: Kim Ji Heon , Kim Tae Ho , Lee Hyunjea , Park Young Ran , Choi Woong , Lee Cheol Jin
Published: June 2016

We investigated the dependence of electron mobility on the thickness of MoS2 nanosheets by fabricating bottom-gate single and few-layer MoS2 thin-film transistors with SiO2 gate dielectrics and Au electrodes. All the fabricated MoS2 transistors showed on/off-current ratio of ∼107 and saturated output characteristics without high-k capping layers. As the MoS2 thickness increased from 1 to 6 layers, the field-effect mobility of the fabricated MoS2 transistors increased from ∼10 to ∼18 cm2V−1s−1. The increased subthreshold swing of the fabricated transistors with MoS2 thickness suggests that the increase of MoS2 mobility with thickness may be related to the dependence of the contact resistance and the dielectric constant of MoS2 layer on its thickness.
Research culture in allied health: a systematic review
Authors: Borkowski Donna , McKinstry Carol , Cotchett Matthew , Williams Cylie , Haines Terry
Published: June 2016

Research evidence is required to guide optimal allied health practice and inform policymakers in primary health care. Factors that influence a positive research culture are not fully understood, and nor is the impact of a positive research culture on allied health professionals. The aim of this systematic review was to identify factors that affect allied health research culture and capacity. An extensive search of 11 databases was conducted in June 2015. Studies were included if they were published in English, had full-text availability and reported research findings relating to allied health professions. Study quality was evaluated using the McMaster Critical Review Forms. Fifteen studies were eligible for inclusion. A meta-analysis was not performed because of heterogeneity between studies. Allied health professionals perceive that their individual research skills are lower in comparison to their teams and organisation. Motivators for conducting research for allied health professionals include developing skills, increasing job satisfaction and career advancement. Barriers include a lack of time, limited research skills and other work roles taking priority. Multilayered strategies, such as collaborations with external partners and developing research leadership positions, aimed at addressing barriers and enablers, are important to enhance allied health research culture and capacity.
Unraveling the evolution of uniquely human cognition
Authors: MacLean Evan L.
Published: June 2016

A satisfactory account of human cognitive evolution will explain not only the psychological mechanisms that make our species unique, but also how, when, and why these traits evolved. To date, researchers have made substantial progress toward defining uniquely human aspects of cognition, but considerably less effort has been devoted to questions about the evolutionary processes through which these traits have arisen. In this article, I aim to link these complementary aims by synthesizing recent advances in our understanding of what makes human cognition unique, with theory and data regarding the processes of cognitive evolution. I review evidence that uniquely human cognition depends on synergism between both representational and motivational factors and is unlikely to be accounted for by changes to any singular cognitive system. I argue that, whereas no nonhuman animal possesses the full constellation of traits that define the human mind, homologies and analogies of critical aspects of human psychology can be found in diverse nonhuman taxa. I suggest that phylogenetic approaches to the study of animal cognition—which can address questions about the selective pressures and proximate mechanisms driving cognitive change—have the potential to yield important insights regarding the processes through which the human cognitive phenotype evolved.
Photodegradation of retinal bisretinoids in mouse models and implications for macular degeneration
Authors: Ueda Keiko , Zhao Jin , Kim Hye Jin , Sparrow Janet R.
Published: June 2016

Significance

Visual cycle adducts having bisretinoid structures accumulate in retinal pigment epithelial cells as lipofuscin. These light-sensitive compounds are implicated in disease mechanisms leading to visual impairment in some inherited and age-related forms of macular degeneration. The means by which these diretinal adducts impart chronic damage is not fully understood. By studying mice raised under varying levels of intraocular light and by analyzing mice treated with vitamin E, we provide evidence of chronic bisretinoid photooxidation and degradation in the eye. These processes could shed light on oxidative and light-related mechanisms involved in disease pathogenesis and provide support for therapeutic approaches that target bisretinoids.
Ecological consequences of human niche construction: Examining long-term anthropogenic shaping of global species distributions
Authors: Boivin Nicole L. , Zeder Melinda A. , Fuller Dorian Q. , Crowther Alison , Larson Greger , Erlandson Jon M. , Denham Tim , Petraglia Michael D.
Published: June 2016

The exhibition of increasingly intensive and complex niche construction behaviors through time is a key feature of human evolution, culminating in the advanced capacity for ecosystem engineering exhibited by
Homo sapiens
. A crucial outcome of such behaviors has been the dramatic reshaping of the global biosphere, a transformation whose early origins are increasingly apparent from cumulative archaeological and paleoecological datasets. Such data suggest that, by the Late Pleistocene, humans had begun to engage in activities that have led to alterations in the distributions of a vast array of species across most, if not all, taxonomic groups. Changes to biodiversity have included extinctions, extirpations, and shifts in species composition, diversity, and community structure. We outline key examples of these changes, highlighting findings from the study of new datasets, like ancient DNA (aDNA), stable isotopes, and microfossils, as well as the application of new statistical and computational methods to datasets that have accumulated significantly in recent decades. We focus on four major phases that witnessed broad anthropogenic alterations to biodiversity—the Late Pleistocene global human expansion, the Neolithic spread of agriculture, the era of island colonization, and the emergence of early urbanized societies and commercial networks. Archaeological evidence documents millennia of anthropogenic transformations that have created novel ecosystems around the world. This record has implications for ecological and evolutionary research, conservation strategies, and the maintenance of ecosystem services, pointing to a significant need for broader cross-disciplinary engagement between archaeology and the biological and environmental sciences.
Southern Ocean phytoplankton turnover in response to stepwise Antarctic cooling over the past 15 million years
Authors: Crampton James S. , Cody Rosie D. , Levy Richard , Harwood David , McKay Robert , Naish Tim R.
Published: June 2016

Significance

Based on data of unprecedented resolution, we show that phytoplankton (diatoms) in the Southern Ocean have experienced five major pulses of species extinction and origination over the past 15 My that were linked to large cooling transitions in southern high latitudes. Our findings suggest that phytoplankton communities around Antarctica have been robust to “baseline” glacial–interglacial climate variability but were sensitive to large-scale changes in mean climate state driven by a combination of long-period variations in orbital forcing and atmospheric carbon dioxide perturbations.
The
Pseudomonas aeruginosa
efflux pump MexGHI-OpmD transports a natural phenazine that controls gene expression and biofilm development
Authors: Sakhtah Hassan , Koyama Leslie , Zhang Yihan , Morales Diana K. , Fields Blanche L. , Price-Whelan Alexa , Hogan Deborah A. , Shepard Kenneth , Dietrich Lars E. P.
Published: June 2016

Significance

Efflux-based drug resistance complicates the treatment of infectious diseases and cancers. Cellular exposure to ecological toxins or reactive metabolites may influence the conservation and activity of efflux pumps. Yet, for most such systems, we know very little about their natural substrates and the signals controlling pump expression. Using diverse approaches, including a chip-based method of electrochemical detection, we show that the endogenous and reactive antibiotic 5-methylphenazine-1-carboxylate (5-Me-PCA) is transported by the efflux pump MexGHI-OpmD in
Pseudomonas aeruginosa
. Furthermore, we demonstrate that 5-Me-PCA activates expression of its cognate transporter and that it is required for normal
P. aeruginosa
biofilm morphogenesis. Our results provide insight into mechanisms of self-resistance and determinants of multicellular behavior in this major cause of biofilm-based infections.
Tau protein is essential for stress-induced brain pathology
Authors: Lopes Sofia , Vaz-Silva João , Pinto Vitor , Dalla Christina , Kokras Nikolaos , Bedenk Benedikt , Mack Natalie , Czisch Michael , Almeida Osborne F. X. , Sousa Nuno , Sotiropoulos Ioannis
Published: June 2016

Significance

Exposure to stressful events is a well-known inducer of neuronal atrophy implicated in the development of neuropsychiatric and neurological pathologies (e.g., depression and Alzheimer’s disease), although the underlying molecular mechanisms remain elusive. The current study demonstrates that absence of the cytoskeletal protein Tau blocks stress-evoked hippocampal synaptic signaling and morphofunctional damages related to both neuronal structure and connectivity as well as subsequent behavioral deficits. These findings suggest, for the first time to our knowledge, that Tau protein is a key regulator of neuronal malfunction found in stress-driven hippocampal pathology.
Bison phylogeography constrains dispersal and viability of the Ice Free Corridor in western Canada
Authors: Heintzman Peter D. , Froese Duane , Ives John W. , Soares André E. R. , Zazula Grant D. , Letts Brandon , Andrews Thomas D. , Driver Jonathan C. , Hall Elizabeth , Hare P. Gregory , Jass Christopher N. , MacKay Glen , Southon John R. , Stiller Mathias , Woywitka Robin , Suchard Marc A. , Shapiro Beth
Published: June 2016

The Ice Free Corridor has been invoked as a route for Pleistocene human and animal dispersals between eastern Beringia and more southerly areas of North America. Despite the significance of the corridor, there are limited data for when and how this corridor was used. Hypothetical uses of the corridor include: the first expansion of humans from Beringia into the Americas, northward postglacial expansions of fluted point technologies into Beringia, and continued use of the corridor as a contact route between the north and south. Here, we use radiocarbon dates and ancient mitochondrial DNA from late Pleistocene bison fossils to determine the chronology for when the corridor was open and viable for biotic dispersals. The corridor was closed after ∼23,000 until 13,400 calendar years ago (cal y BP), after which we find the first evidence, to our knowledge, that bison used this route to disperse from the south, and by 13,000 y from the north. Our chronology supports a habitable and traversable corridor by at least 13,000 cal y BP, just before the first appearance of Clovis technology in interior North America, and indicates that the corridor would not have been available for significantly earlier southward human dispersal. Following the opening of the corridor, multiple dispersals of human groups between Beringia and interior North America may have continued throughout the latest Pleistocene and early Holocene. Our results highlight the utility of phylogeographic analyses to test hypotheses about paleoecological history and the viability of dispersal routes over time.
Encounter with mesoscale eddies enhances survival to settlement in larval coral reef fishes
Authors: Shulzitski Kathryn , Sponaugle Su , Hauff Martha , Walter Kristen D. , Cowen Robert K.
Published: June 2016

Significance

Quantifying connectivity among geographically separated subpopulations is necessary for successful management and conservation of marine resources, and a mechanistic understanding of growth and mortality during the pelagic larval stage is essential for obtaining accurate predictions of dispersal and population replenishment. Our finding that the pelagic environment encountered by larvae of coral reef fishes significantly influences larval growth, selective mortality, and the composition of survivors has important implications for understanding population connectivity. High productivity oceanographic features enhance larval survival and potentially increase the contribution of locally spawned larvae to reef populations. Incorporation of spatially explicit larval growth and survivorship into dispersal models will improve quantification of population connectivity for marine organisms both now and in the future.
DEG9, a serine protease, modulates cytokinin and light signaling by regulating the level of
ARABIDOPSIS
RESPONSE REGULATOR 4
Authors: Chi Wei , Li Jing , He Baoye , Chai Xin , Xu Xiumei , Sun Xuwu , Jiang Jingjing , Feng Peiqiang , Zuo Jianru , Lin Rongcheng , Rochaix Jean-David , Zhang Lixin
Published: June 2016

Significance

Selective protein proteolysis is essential for many plant signal transduction pathways and regulates developmental stages of a plant. In addition to the well-characterized ubiquitin-proteasome system, other factors appear to be involved in the degradation of plant signaling components. Here we describe the function of the serine protease degradation of periplasmic protein 9 (DEG9) in plant signaling. We found that DEG9 mediates the degradation of
ARABIDOPSIS
RESPONSE REGULATOR 4, which is critical for regulating the cross-talk between cytokinin and light-signaling pathways. This study adds to our knowledge about the function of DEG proteases, which are common in the plant kingdom, and emphasizes their importance in plant development.
Digital design of multimaterial photonic particles
Authors: Tao Guangming , Kaufman Joshua J. , Shabahang Soroush , Rezvani Naraghi Roxana , Sukhov Sergey V. , Joannopoulos John D. , Fink Yoel , Dogariu Aristide , Abouraddy Ayman F.
Published: June 2016

Significance

We present an approach for the facile fabrication of dielectric particles having the size of an optical wavelength yet endowed with a complex multimaterial internal nanoscale architecture. This methodology amounts to “digitally designing” the particle by precisely allocating the desired material at prescribed coordinates within the 3D volume of the particle. The digital design of such a photonic particle enables sophisticated strategies for controlling light scattering. As an example, without changing the size of a core–shell particle, its optical scattering strength can be tuned above or below that afforded by its constitutive materials by changing the core–shell diameter ratio. This work may lead to the development of new optical coatings and paints with exotic functionality.
Chiral modes and directional lasing at exceptional points
Authors: Peng Bo , Özdemir Şahin Kaya , Liertzer Matthias , Chen Weijian , Kramer Johannes , Yılmaz Huzeyfe , Wiersig Jan , Rotter Stefan , Yang Lan
Published: June 2016

Significance

Exceptional points (EPs) emerge when a system with loss or gain is tuned such that its eigenvalues and the corresponding eigenstates coalesce. By operating close to two EPs, we achieved a dynamic control of the rotation direction of light in a whispering-gallery-mode (WGM) resonator. This enabled us to tune the emission direction of a WGM microlaser from bidirectional, when the system is away from the EPs, to unidirectional emission at EPs and to reverse the emission direction by moving from one EP to the other. This feature provides WGM resonators new functionalities useful for lasing, sensing, optomechanics, and cavity quantum electrodynamics. Our findings will help to develop novel technologies for controlling the light flow on-chip and could affect scientific fields beyond optics.
Elucidation of cladofulvin biosynthesis reveals a cytochrome P450 monooxygenase required for anthraquinone dimerization
Authors: Griffiths Scott , Mesarich Carl H. , Saccomanno Benedetta , Vaisberg Abraham , De Wit Pierre J. G. M. , Cox Russell , Collemare Jérôme
Published: June 2016

Significance

Anthraquinones are potent secondary metabolites produced by many fungi and plants used in traditional Chinese and Indian medicine. Many display useful biological properties, including antineoplastic, antiinflammatory, antiinfective, or antiparasitic activities. The chemical structure of anthraquinones is very diverse, with many occurring as homo- and heterodimers. Anthraquinone biosynthetic pathways must be elucidated before novel structurally complex chemicals with new or enhanced biological activity can be engineered. In this study, we identified an enzyme involved in asymmetrical dimerization of nataloe-emodin, which results in increased cytotoxicity toward a range of cancer cell lines. Mastering the substrate specificity of this enzyme (and other similar enzymes) could lead to the dimerization of anthraquinone-related compounds with medicinal activities.
Transplantation of iPSC-derived TM cells rescues glaucoma phenotypes in vivo
Authors: Zhu Wei , Gramlich Oliver W. , Laboissonniere Lauren , Jain Ankur , Sheffield Val C. , Trimarchi Jeffrey M. , Tucker Budd A. , Kuehn Markus H.
Published: June 2016

Significance

The regulation of intraocular pressure (IOP) is vital for the health of the eye. Failure to maintain IOP frequently leads to vision loss in glaucoma. The IOP is maintained by the trabecular meshwork (TM), which exhibits decreased cellular density with age and disease. Here we demonstrate that induced pluripotent stem cells differentiated into TM cells (designated iPSC-TM) restore TM function for over 9 wk, regulate IOP, and prevent neuronal loss in a glaucoma mouse model. Transplanted iPSC-TM survive in the TM, but the most pronounced effect of transplantation is a robust proliferative response of endogenous TM cells. These findings suggest that lasting restoration of IOP control through iPSC-TM transplantation is possible and may represent a novel treatment approach for glaucoma.
APE1/Ref-1 facilitates recovery of gray and white matter and neurological function after mild stroke injury
Authors: Stetler R. Anne , Gao Yanqin , Leak Rehana K. , Weng Zhongfang , Shi Yejie , Zhang Lili , Pu Hongjian , Zhang Feng , Hu Xiaoming , Hassan Sulaiman , Ferguson Carolyn , Homanics Gregg E. , Cao Guodong , Bennett Michael V. L. , Chen Jun
Published: June 2016

Significance

AP endonuclease-1 (APE1)/redox effector factor-1 (Ref-1) is an essential DNA repair enzyme that has been difficult to study mechanistically because of embryonic lethality in conventional knockout animals. Thus, we generated a conditional APE1 knockout model to examine the protective role of endogenous APE1 in experimental stroke. Induced APE1 knockout in adulthood greatly exacerbated neuron and oligodendrocyte loss after mild ischemic stroke and prevented the intrinsic, long-term recovery of sensorimotor function and spatial learning and memory. APE1 knockout also aggravated ischemia-induced destruction of myelin and impairment of axon conduction in white matter. We conclude that APE1 dictates fundamental life and death decisions in both gray and white matter and plays an indispensable role in intrinsic recovery after mild ischemic injury.
Pattern substitution in Wuxi tone sandhi and its implication for phonological learning
Authors: Yan Hanbo , Zhang Jie
Published: June 2016

Tone sandhi in Wuxi Chinese involves “pattern substitution,” whereby the base tone on the first syllable is first substituted by another tone, then spread to the sandhi domain. We conducted a wug test to investigate native Wuxi speakers’ tacit knowledge of tone sandhi and found that the substituion aspect of the sandhi is not fully productive, but the extension aspect is, and sandhi productivity is influenced by the phonetic similarity between base and sandhi tones. These results are discussed in the context of how phonological opacity, phonetic naturalness, and lexical frequency influence phonological learning, and a grammatical learning model that can predict Wuxi speakers’ experimental behavior is proposed.
Intersubjectivity and the diachronic development of counterfactualalmost
Authors: Ziegeler Debra
Published: June 2016

Former studies have attributed little attention to the historical factors surrounding the development of counterfactual meanings inalmost, though some refer to evidence of expletive negation found in proximatives crosslinguistically. In this study, the historical development of the adverb will be considered in investigating more recent data from Late Modern English, in which an overwhelming number of counterfactual uses appear with a complement referring to undesirable events, some even hyperbolic in nature. It is hypothesised that the presence of intersubjectivity contributed significantly to the development of counterfactual meanings, in focusing attention on the aversion of, rather than the proximity to, the event described in the complement. Intersubjectivity also explains the evidence of expletive negation in proximatives in other languages though this is not attested in the history of Englishalmost.
On the rise of types of clause-final pragmatic markers in English
Authors: Traugott Elizabeth Closs
Published: June 2016

Much work on pragmatic markers in the history of English has been devoted to expressions used clause-initially at “left periphery”. By contrast, this study provides an account in broad outlines of the incremental development of pragmatic markers in clause-final “right periphery” position. Particular attention is paid to the rise of comment clauses, question tags, general extenders, and retrospective contrastive markers. Traditional characterizations of pragmatic markers, such as occurrence primarily at left periphery and with prosodic breaks are critiqued.
The three silences of Sir Thomas More
Authors: Kurzon Dennis
Published: June 2016

The paper discusses three instances of silence in the life and writings of Sir Thomas More in terms of conversational and thematic silence. The first is the silence of the London citizenry in More’sHistory of Richard the Third(1513). The second is the House of Commons’ response of silence, in 1523, to Cardinal Wolsey’s request to provide him, the Chancellor, with a substantial grant for state affairs; at that time, More was Speaker of the House. The third is More’s fatal silence when he was required to take an oath supporting Henry VIII’s divorce from Catherine and subsequent marriage to Anne Boleyn, and his refusal to discuss Henry’s break from the Pope and the Roman Church.
The dual role of homophone dominance. Why homophone intrusions on regular verb forms so often go unnoticed
Authors: Verhaert Nina , Danckaert Ellen , Sandra Dominiek
Published: June 2016

We investigated whether the effect of Homophone Dominance that has been reported for spelling errors on Dutch verb homophones (Sandra, Frisson, & Daems, 1999) also occurs in perception. This effect was indeed observed: participants in a proofreading experiment overlooked more homophone intrusions when the intruder was more dominant than the target form, irrespective of the inflectional ending. Participant groups whose grammatical awareness was better developed made fewer errors but also showed the effect of Homophone Dominance. The findings are explained in terms of a Computational and Similarity-Based Race model, in which a conscious and slow computational process in working memory, implementing the spelling rule, competes with an automatic and fast, frequency-sensitive process of lexical access. The presence of the effect in both spelling and reading explains why these errors on descriptively simple verb forms in Dutch are so persistent.