bluuebunny/crossref_metadata_2025 huggingface dataset:
Sequence analysis, expression profiles and function of thioredoxin 2 and thioredoxin reductase 1 in resistance to nucleopolyhedrovirus in Helicoverpa armigera
Authors: Zhang Songdou , Li Zhen , Nian Xiaoge , Wu Fengming , Shen Zhongjian , Zhang Boyu , Zhang Qingwen , Liu Xiaoxia
Published: October 2015

The thioredoxin system, including NADPH, thioredoxin (Trx) and thioredoxin reductase (TrxR), plays significant roles in maintaining intracellular redox homeostasis and protecting organisms against oxidative damage. In this study, the characteristics and functions of H. armigera HaTrx2 and HaTrxR1 were identified. Sequence analysis showed that HaTrx2 and HaTrxR1 were both highly conserved and shared high sequence identity with other insect counterparts. The mRNA of HaTrx2 was expressed the highest in 5th instar 96 h and was mainly detected in heads and epidermis. The expression of HaTrxR1 was highly concentrated in 5th instar 72 h and 96 h and higher in malpighian tube, midgut and hemocyte than other examined tissues. HaTrx2 and HaTrxR1 were markedly induced by various types of stress. HaTrx2- or HaTrxR1-knockdown increased ROS production in hemocytes and also increased the lipid damage in NPV infected H. armigera larvae. Furthermore, interference with expression of HaTrx2 or HaTrxR1 transcripts in H. armigera larvae resulted in increased sensitivity to NPV infection and shortened LT50 values. Our findings indicated that HaTrx2 and HaTrxR1 contribute to the susceptibility of H. armigera to NPV and also provided the theoretical basis for the in-depth study of insect thioredoxin system.
Novel Monte Carlo approach quantifies data assemblage utility and reveals power of integrating molecular and clinical information for cancer prognosis
Authors: Verleyen Wim , Langdon Simon P. , Faratian Dana , Harrison David J. , Smith V. Anne
Published: October 2015

Current clinical practice in cancer stratifies patients based on tumour histology to determine prognosis. Molecular profiling has been hailed as the path towards personalised care, but molecular data are still typically analysed independently of known clinical information. Conventional clinical and histopathological data, if used, are added only to improve a molecular prediction, placing a high burden upon molecular data to be informative in isolation. Here, we develop a novel Monte Carlo analysis to evaluate the usefulness of data assemblages. We applied our analysis to varying assemblages of clinical data and molecular data in an ovarian cancer dataset, evaluating their ability to discriminate one-year progression-free survival (PFS) and three-year overall survival (OS). We found that Cox proportional hazard regression models based on both data types together provided greater discriminative ability than either alone. In particular, we show that proteomics data assemblages that alone were uninformative (p = 0.245 for PFS, p = 0.526 for OS) became informative when combined with clinical information (p = 0.022 for PFS, p = 0.048 for OS). Thus, concurrent analysis of clinical and molecular data enables exploitation of prognosis-relevant information that may not be accessible from independent analysis of these data types.
Suppression of Shear Banding and Transition to Necking and Homogeneous Flow in Nanoglass Nanopillars
Authors: Adibi Sara , Branicio Paulo S. , Joshi Shailendra P.
Published: October 2015

In order to improve the properties of metallic glasses (MG) a new type of MG structure, composed of nanoscale grains, referred to as nanoglass (NG), has been recently proposed. Here, we use large-scale molecular dynamics (MD) simulations of tensile loading to investigate the deformation and failure mechanisms of Cu64Zr36NG nanopillars with large, experimentally accessible, 50 nm diameter. Our results reveal NG ductility and failure by necking below the average glassy grain size of 20 nm, in contrast to brittle failure by shear band propagation in MG nanopillars. Moreover, the results predict substantially larger ductility in NG nanopillars compared with previous predictions of MD simulations of bulk NG models with columnar grains. The results, in excellent agreement with experimental data, highlight the substantial enhancement of plasticity induced in experimentally relevant MG samples by the use of nanoglass architectures and point out to exciting novel applications of these materials.
Concurrence of oral and genital human papillomavirus infection in healthy men: a population-based cross-sectional study in rural China
Authors: Liu Fangfang , Hang Dong , Deng Qiuju , Liu Mengfei , Xi Longfu , He Zhonghu , Zhang Chaoting , Sun Min , Liu Ying , Li Jingjing , Pan Yaqi , Ning Tao , Guo Chuanhai , Liang Yongmei , Xu Ruiping , Zhang Lixin , Cai Hong , Ke Yang
Published: October 2015

Human papillomavirus (HPV) infection, a primary cause of genital cancer, is also related to the increasing incidence of oropharyngeal cancer among young men. Relatively little is known about the concurrence of oral and genital infection among healthy individuals. Oral and genital swab exfoliated cells were collected simultaneously from 2566 men in rural China. Using general primer-mediated (SPF1/GP6+) PCR and sequencing, HPV testing results were obtained from 2228 men with both valid oral and genital specimens (β-globin-positive). The prevalence of HPV infection was 6.7% in the oral cavity and 16.9% for the external genitalia. Among 43 men (1.9%, 43/2228) with oral-genital coinfection, 60.5% (26/43) harbored an identical HPV type at both sites. The risk of oral HPV infection was higher among men with genital infection than among uninfected men (11.4% vs. 5.7%, Adjusted OR = 2.3, 95% CI: 1.6–3.4). In addition, having multiple lifetime sexual partners was a significant risk for oral-genital HPV coinfection (Adjusted OR = 2.6, 95% CI: 1.0–7.0; 2 partners vs. 1 partner). These findings provide a basis for further understanding the natural history and transmission dynamics of oral HPV infection.
The native ant, Tapinoma melanocephalum, improves the survival of an invasive mealybug, Phenacoccus solenopsis, by defending it from parasitoids
Authors: Feng Dong-Dong , Michaud J.P. , Li Pan , Zhou Zhong-Shi , Xu Zai-Fu
Published: October 2015

Mutualistic ants can protect their partners from natural enemies in nature. Aenasius bambawalei is an important parasitoid of the the invasive mealybug Phenacoccus solenopsis. We hypothesized that mutualism between native ants and mealybugs would favor survival of mealybugs. To test this, we examined effects of tending by the native mutualistic ant Tapinoma melanocephalum on growth of P. solenopsis colonies on Chinese hibiscus, Hibiscus rosa-sinensis, in a field setting. Ant workers with access to honeydew of mealybugs lived much longer than those provisioned only with water in the laboratory and number of ant workers foraging increased significantly with growth of mealybug colonies in the field. In later observations, there were significant differences in densities of mealybugs between ant-tended and -excluded treatments. Survival rate of mealybugs experiencing parasitoid attack was significantly higher on ant-tended plants than on ant-excluded plants. When the parasitoid was excluded, there was no difference in survival rate of mealybugs between ant-tended and -excluded plants. In most cases, ants directly attacked the parasitoid, causing the parasitoid to take evasive action. We conclude that native ants such as T. melanocephalum have the potential to facilitate invasion and spread of P. solenopsis in China by providing them with protection from parasitoids.
Fourier-transform spectroscopy using an Er-doped fiber femtosecond laser by sweeping the pulse repetition rate
Authors: Lee Keunwoo , Lee Joohyung , Jang Yoon-Soo , Han Seongheum , Jang Heesuk , Kim Young-Jin , Kim Seung-Woo
Published: October 2015

Femtosecond lasers allow for simultaneous detection of multiple absorption lines of a specimen over a broad spectral range of infrared or visible light with a single spectroscopic measurement. Here, we present an 8-THz bandwidth, 0.5-GHz resolution scheme of Fourier-transform spectroscopy using an Er-doped fiber femtosecond laser. A resolving power of 1.6 × 104 about a 1560-nm center wavelength is achieved by sweeping the pulse repetition rate of the light source on a fiber Mach-Zehnder interferometer configured to capture interferograms with a 0.02-fs temporal sampling accuracy through a well-stabilized 60-m unbalance arm length. A dual-servo mechanism is realized by combining a mechanical linear stage with an electro-optic modulator (EOM) within the fiber laser cavity, enabling stable sweeping control of the pulse repetition rate over a 1.0-MHz scan range with 0.4-Hz steps with reference to the Rb clock. Experimental results demonstrate that the P-branch lines of the H13CN reference cell can be observed with a signal-to-noise ratio reaching 350 for the most intense line.
Acid-induced off-response of PKD2L1 channel in Xenopus oocytes and its regulation by Ca2+
Authors: Hussein Shaimaa , Zheng Wang , Dyte Chris , Wang Qian , Yang JungWoo , Zhang Fan , Tang Jingfeng , Cao Ying , Chen Xing-Zhen
Published: October 2015

Polycystic kidney disease (PKD) protein 2 Like 1 (PKD2L1), also called transient receptor potential polycystin-3 (TRPP3), regulates Ca2+-dependent hedgehog signalling in primary cilia, intestinal development and sour tasting but with an unclear mechanism. PKD2L1 is a Ca2+-permeable cation channel that is activated by extracellular Ca2+ (on-response) in Xenopus oocytes. PKD2L1 co-expressed with PKD protein 1 Like 3 (PKD1L3) exhibits extracellular acid-induced activation (off-response, i.e., activation following acid removal) but whether PKD1L3 participates in acid sensing remains unclear. Here we used the two-microelectrode voltage-clamp, site directed mutagenesis, Western blotting, reverse transcriptase-polymerase chain reaction (RT-PCR) and immunofluorescence and showed that PKD2L1 expressed in oocytes exhibits sustained off-response currents in the absence of PKD1L3. PKD1L3 co-expression augmented the PKD2L1 plasma membrane localization but did not alter the observed properties of the off-response. PKD2L1 off-response was inhibited by an increase in intracellular Ca2+. We also identified two intra-membrane residues aspartic acid 349 (D349) and glutamic acid 356 (E356) in the third transmembrane domain that are critical for PKD2L1 channel function. Our study suggests that PKD2L1 may itself sense acids and defines off-response properties in the absence of PKD1L3.
Retinal oxygen extraction in humans
Authors: Werkmeister René M. , Schmidl Doreen , Aschinger Gerold , Doblhoff-Dier Veronika , Palkovits Stefan , Wirth Magdalena , Garhöfer Gerhard , Linsenmeier Robert A. , Leitgeb Rainer A. , Schmetterer Leopold
Published: October 2015

Adequate function of the retina is dependent on proper oxygen supply. In humans, the inner retina is oxygenated via the retinal circulation. We present a method to calculate total retinal oxygen extraction based on measurement of total retinal blood flow using dual-beam bidirectional Doppler optical coherence tomography and measurement of oxygen saturation by spectrophotometry. These measurements were done on 8 healthy subjects while breathing ambient room air and 100% oxygen. Total retinal blood flow was 44.3 ± 9.0 μl/min during baseline and decreased to 18.7 ± 4.2 μl/min during 100% oxygen breathing (P < 0.001) resulting in a pronounced decrease in retinal oxygen extraction from 2.33 ± 0.51 μl(O2)/min to 0.88 ± 0.14 μl(O2)/min during breathing of 100% oxygen. The method presented in this paper may have significant potential to study oxygen metabolism in hypoxic retinal diseases such as diabetic retinopathy.
Gold(i)-catalyzed highly stereoselective synthesis of polycyclic indolines: the construction of four contiguous stereocenters
Authors: Yang Jin-Ming , Li Peng-Hua , Wei Yin , Tang Xiang-Ying , Shi Min
Published: October 2015

A convenient and efficient synthetic method has been developed to construct highly functionalized polycyclic indoline skeletons with four contiguous stereocenters.
In silico characterization of protein partial molecular volumes and hydration shells
Authors: Del Galdo Sara , Marracino Paolo , D'Abramo Marco , Amadei Andrea
Published: October 2015

In this paper we present a computational approach, based on NVT molecular dynamics trajectories, that allows the direct evaluation of the protein partial molecular volume.
SDS-assisted solvothermal synthesis of rose-like BiOBr partially enclosed by {111} facets and enhanced visible-light photocatalytic activity
Authors: Zhao Yang , Yu Tao , Tan Xin , Xie Chuang , Wang Shucong
Published: October 2015

Rose-like BiOBr nanostructures with exposed {111} facets were firstly synthesized with the assistance of an anionic surfactant, sodium dodecyl sulfate (SDS), via a facile solvothermal route.
A 2-(2′-hydroxyphenyl)benzothiazole (HBT)–quinoline conjugate: a highly specific fluorescent probe for Hg2+ based on ESIPT and its application in bioimaging
Authors: Sahana Sunanda , Mishra Gargi , Sivakumar Sri , Bharadwaj Parimal K.
Published: October 2015

A new benzothiazole-based 8-aminoquinoline functionalized compound as a selective and sensitive fluorogenic chemosensor for Hg2+ and also being used in cell imaging.
High depth-resolution laser ablation chemical analysis of additive-assisted Cu electroplating for microchip architectures
Authors: Riedo A. , Grimaudo V. , Moreno-García P. , Neuland M. B. , Tulej M. , Wurz P. , Broekmann P.
Published: October 2015

Highly sensitive LIMS measurements allow for the first time quantitative grain boundary analysis at the nanometre regime.
Electroanalytical devices with pins and thread
Authors: Glavan Ana C. , Ainla Alar , Hamedi Mahiar M. , Fernández-Abedul M. Teresa , Whitesides George M.
Published: October 2015

This work describes the adaptive use of conventional stainless steel pins—used in unmodified form or coated with carbon paste—as working, counter and quasi-reference electrodes in electrochemical devices fabricated using cotton thread or embossed omniphobic RF paper to contain the electrolyte and sample.
Feasible energy level tuning in polymer solar cells based on broad band-gap polytriphenylamine derivatives
Authors: Zhang Bin , Chen Guiting , Xu Jin , Hu Liwen , Yang Wei
Published: October 2015

Four triphenylamine based broad band-gap polymers with different substituted groups [–OC8H17, –C8H17, –CF3, –(CF3)2] were designed and synthesized, and the HOMO energy levels and Vocs of these polymer based PSCs could be tuned feasibly.
A study on the AMACR catalysed elimination reaction and its application to inhibitor testing
Authors: Yevglevskis Maksims , Lee Guat L. , Sun Jenny , Zhou Shiyi , Sun Xiaolong , Kociok-Köhn Gabriele , James Tony D. , Woodman Timothy J. , Lloyd Matthew D.
Published: October 2015

The elimination of fluoride from 3-fluoro-2-methylacyl-CoA substrates by α-methylacyl-CoA racemase (AMACR 1A; P504S) was investigated as a method for determining enzyme activity and inhibitor potency.
Metal catalyzed defunctionalization reactions
Authors: Modak Atanu , Maiti Debabrata
Published: October 2015

The chronological development of metal assisted defunctionalization reactions is discussed from the stoichiometric to the catalytic stage with their application in synthetic organic chemistry.
Iteratively variable subset optimization for multivariate calibration
Authors: Wang Weiting , Yun Yonghuan , Deng Baichuan , Fan Wei , Liang Yizeng
Published: October 2015

IVSO is a variable selection method, which shows good prediction and stability and can eliminate uninformative variables gradually and gently.
Application of the central composite design to optimize the calcium carbonate-HPMC co-processed excipient prepared by co-spray drying
Authors: Li JinZhi , Lin Xiao , Wu Fei , Shen Lan , Wang YouJie , Feng Yi
Published: October 2015

The central composite design-response surface methodology provided theoretical guidance for development of co-processed excipients based on calcium carbonate and HPMC.
One-pot oxidative Ugi-type three-component reaction of aromatic hydrocarbons of petroleum naphtha: comparing catalytic effect of cellulose- and wool–SO3H supported with manganese dioxide nanostructures
Authors: Shaabani Ahmad , Hezarkhani Zeinab , Badali Elham
Published: October 2015

A novel domino oxidative Ugi-type three-component reaction (OU-3CR) of aromatic hydrocarbons of petroleum naphtha has been investigated using two biopolymer supported MnO2nanostructured catalysts, MnO2@cellulose–SO3H and MnO2@wool–SO3H.
An elegant synthesis of chitosan grafted hydrotalcite nano-bio composite material and its effective catalysis for solvent-free synthesis of jasminaldehyde
Authors: Adwani Jacky H. , Khan Noor-ul H. , Shukla Ram S.
Published: October 2015

A novel nano-bio composite of chitosan and a layered double hydroxide elegantly synthesized by a co-precipitation method had effectively and selectively catalysed the jasminaldehyde synthesis.
A dual soft-template synthesis of hollow mesoporous silica spheres decorated with Pt nanoparticles as a CO oxidation catalyst
Authors: Li Yunqi , Bastakoti Bishnu Prasad , Abe Hideki , Liu Zongwen , Minett Andrew , ALOthman Zeid A. , Yamauchi Yusuke
Published: October 2015

Hollow mesoporous silica spheres decorated with fine Pt nanoparticles are prepared through a dual soft-template system and used as a catalyst for high-temperature CO oxidation.
Fluorescent magnesium nanocomplex in a protein scaffold for cell nuclei imaging applications
Authors: Pandya Alok , Tripathi Apritam , Purohit Rahul , Singh Sanjay , Nandasiri Manjula I. , Karakoti Ajay , Singh Surinder P. , Shanker Rishi
Published: October 2015

For the first time, we report a facile strategy for the synthesis of ultra-fine blue-green emitting fluorescent magnesium nanoparticles–protein complex (MgNC) which shows excellent photo stability and also stain cell nuclei with high specificity.
Carbazole-based gold(i) complexes with alkyl chains of different lengths: tunable solid-state fluorescence, aggregation-induced emission (AIE), and reversible mechanochromism characteristics
Authors: Chen Zhao , Yang Lan , Hu Yuxuan , Wu Di , Yin Jun , Yu Guang-Ao , Liu Sheng Hua
Published: October 2015

Seven gold(i) complexes with alkyl chains of different lengths were synthesized, these luminogens exhibited AIE and mechanochromism characteristics.
Bi2S3/poly(vinylidene fluoride) composite with high dielectric constant and unusual low dielectric loss based on preferentially oriented fillers
Authors: Liu Jie , Luo Yu , Wang Yao , Deng Yuan , Xie Xitong
Published: October 2015

In this work, a novel two-phase ferroelectric polymer composite, consisting of semiconducting bismuth sulfide nanorods and a poly(vinylidene fluoride) matrix, was fabricated by a sequence of casting, hot-stretching and hot-pressing techniques.
Effects of Ga doping and hollow structure on the band-structures and photovoltaic properties of SnO2 photoanode dye-sensitized solar cells
Authors: Duan Yandong , Zheng Jiaxin , Fu Nianqing , Hu Jiangtao , Liu Tongchao , Fang Yanyan , Zhang Qian , Zhou Xiaowen , Lin Yuan , Pan Feng
Published: October 2015

By introducing the rough hollow microspheres structure and Ga-doping technique, a high power conversion efficiency (η) up to 7.11% is obtained for SnO2 based DSSCs.
Mechanistic investigations of a bifunctional squaramide organocatalyst in asymmetric Michael reaction and observation of stereoselective retro-Michael reaction
Authors: Varga Eszter , Mika László Tamás , Csámpai Antal , Holczbauer Tamás , Kardos György , Soós Tibor
Published: October 2015

The mechanism of cinchona–squaramide organocatalytic Michael addition was studied usingin situIR and NMR experiments. As a result, not only kinetic parameters were determined but a stereoselective retro-Michael reaction was also observed.
New hybrid materials based on halogenated metalloporphyrins for enhanced visible light photocatalysis
Authors: Dąbrowski Janusz M. , Pucelik Barbara , Pereira Mariette M. , Arnaut Luis G. , Macyk Wojciech , Stochel Grażyna
Published: October 2015

The impregnation of TiO2 with functionalized halogenated (metallo)porphyrins leads to novel materials with a superior photocatalytic activity.
1,2,3-Triazoles derived from olanzapine: their synthesis via an ultrasound assisted CuAAC method and evaluation as inhibitors of PDE4B
Authors: Nallapati Suresh Babu , Sreenivas B. Yogi , Bankala Ramudu , Parsa Kishore V. L. , Sripelly Shivashankar , Mukkanti K. , Pal Manojit
Published: October 2015

An ultrasound assisted CuAAC method afforded novel 1,2,3-triazoles derived from olanzapine as inhibitors of PDE4B.
Synthesis and fast-response of a photodetector of hydrothermally grown ZnO nanorods through the use of a graphene oxide/ZnO seed layer
Authors: Nam Giwoong , Leem Jae-Young
Published: October 2015

We used a hydrothermal method combined with a graphene oxide (GO)/ZnO seed layer to fabricate a ZnO nanorod based fast-response UV detector.
K2xSn4−xS8−x(x = 0.65–1): a new metal sulfide for rapid and selective removal of Cs+, Sr2+and UO22+ions
Authors: Sarma Debajit , Malliakas Christos D. , Subrahmanyam K. S. , Islam Saiful M. , Kanatzidis Mercouri G.
Published: October 2015

The synthesis and crystal structure of K2xSn4−xS8−x(x= 0.65–1, KTS-3) a material which exhibits excellent Cs+, Sr2+and UO22+ion exchange properties in varying conditions are reported.
A new concept for molecular engineering of artificial enzymes: a multiscale simulation
Authors: Komarov Pavel V. , Khalatur Pavel G. , Khokhlov Alexei R.
Published: October 2015

We have designed, for the first time, a functional analog of chymotrypsin from synthetic monomers imitating protein amino acid residues.
Hierarchical core–shell heterostructure of porous carbon nanofiber@ZnCo2O4nanoneedle arrays: advanced binder-free electrodes for all-solid-state supercapacitors
Authors: Niu Hao , Yang Xue , Jiang He , Zhou Dan , Li Xin , Zhang Ting , Liu Jiuyu , Wang Qian , Qu Fengyu
Published: October 2015

Hierarchical ZnCo2O4nanoneedle arrays are vertically grown on porous carbon nanofibers (PCFs) to form a core–shell heterostructure through a facile hydrothermal method followed by thermal treatment.
Corner detection using Chebyshev fitting‐based continuous curvature estimation
Authors: Zhang Shizheng , Yang Dan , Huang Sheng , Tu Liyun , Zhang Xiaohong
Published: October 2015

Extensive contour‐based corner detection methods have been proposed to estimate the curvature of a planar curve and most of them estimated it in digital spaces. However, the curvature should be intuitively continuous. Presented is a novel approach which addresses the corner detection issue by employing the Chebyshev polynomial fitting to estimate the curvature in a continuous way. Experimental results demonstrate that the approach achiever a promising performance in comparison with three representative corner detectors based on discrete curvature estimation and two other state‐of‐the‐art methods.
Cardiac image segmentation by random walks with dynamic shape constraint
Authors: Yang Xulei , Su Yi , Duan Rubing , Fan Haijin , Yeo Si Yong , Lim Calvin , Zhong Liang , Tan Ru San
Published: October 2015

The quantitative analysis of the left ventricle (LV) contractile function is one of the key steps in the assessment of cardiovascular disease. Such analysis greatly depends on the accurate delineation of LV boundary from cardiac sequences. However, segmentation of the LV still remains a challenging problem due to its subtle boundary, occlusion, and image inhomogeneity. To overcome such difficulties, the authors propose a novel segmentation method by incorporating a dynamic shape constraint into the weighting function of the random walks segmentation algorithm. This approach involves iterative updates on the intermediate result to achieve the desired solution. The inclusion of a shape constraint restricts the solution space of the segmentation result to handle misleading information that may come from noise, weak boundaries and clutter, leading to increased robustness of the algorithm. The authors describe the details of the proposed method and demonstrate its effectiveness in segmenting the LV from real cardiac magnetic resonance (CMR) image sets. The experimental results demonstrate that the proposed method obtains better segmentation performance than the standard method.
A high intensity H2+ multicusp ion source for the isotope decay-at-rest experiment, IsoDAR
Authors: Axani S. , Winklehner D. , Alonso J. , Conrad J. M.
Published: October 2015

The Isotope Decay-At-Rest (IsoDAR) experimental program aims to decisively test the sterile neutrino hypothesis. In essence, it is a novel cyclotron based neutrino factory that will improve the frontiers in both high-intensity cyclotrons and electron flavor anti-neutrino sources. By using a source in which the usual H− ions are replaced with the more tightly bound H2+ ions, we can negate the effects of Lorentz stripping in a cyclotron, reduce the overall perveance due to the space-charge effect, and deliver twice the number of protons per nuclei on target. To produce the H2+, we are currently developing a dedicated multicusp ion source, MIST-1 (generation-1 Multicusp Ion Source Technologies at MIT), and a low-energy beam transport system for the IsoDAR cyclotron. This will increase the overall H2+ current leading up to the cyclotron and improve the emittance of the beam injected into the cyclotron.
Acoustic scattering cancellation of irregular objects surrounded by spherical layers in the resonant regime
Authors: Guild Matthew D. , Hicks Ashley J. , Haberman Michael R. , Alù Andrea , Wilson Preston S.
Published: October 2015

In this work, acoustic scattering cancellation is expanded to cases of acoustic waves interacting with non-spherical elastic objects and collections of closely packed objects. The proposed method for achieving this is by using spherical fluid layers to represent the objects as effective spherical targets, with multiple fluid layers and an elastic core, for which scattering cancellation is used to determine the necessary layer properties. Three representative objects are considered here to illustrate this approach: a sphere with dimples, a sphere with bumps, and a bicone. Theoretical results are presented for each of the non-spherical objects in water, which indicate a reduction of 30–40 dB in scattering strength when coated with a two-layer fluid cancellation shell. This cancellation is achieved for objects in the resonant scattering regime, which is characterized by constructive and destructive interference patterns that arise from higher scattering modes. The analytical results are verified using three-dimensional finite element simulations.
Smoothing tautologies, hidden dynamics, and sigmoid asymptotics for piecewise smooth systems
Authors: Jeffrey Mike R.
Published: October 2015

Switches in real systems take many forms, such as impacts, electronic relays, mitosis, and the implementation of decisions or control strategies. To understand what is lost, and what can be retained, when we model a switch as an instantaneous event, requires a consideration of so-called hidden terms. These are asymptotically vanishing outside the switch, but can be encoded in the form of nonlinear switching terms. A general expression for the switch can be developed in the form of a series of sigmoid functions. We review the key steps in extending Filippov's method of sliding modes to such systems. We show how even slight nonlinear effects can hugely alter the behaviour of an electronic control circuit, and lead to “hidden” attractors inside the switching surface.
Effect of Coulomb collision on the negative ion extraction mechanism in negative ion sources
Authors: Goto I. , Miyamoto K. , Nishioka S. , Mattei S. , Lettry J. , Abe S. , Hatayama A.
Published: October 2015

To improve the H− ion beam optics, it is necessary to understand the energy relaxation process of surface produced H− ions in the extraction region of Cs seeded H− ion sources. Coulomb collisions of charged particles have been introduced to the 2D3V-PIC (two dimension in real space and three dimension in velocity space particle-in-cell) model for the H− extraction by using the binary collision model. Due to Coulomb collision, the lower energy part of the ion energy distribution function of H− ions has been greatly increased. The mean kinetic energy of the surface produced H− ions has been reduced to 0.65 eV from 1.5 eV. It has been suggested that the beam optics of the extracted H− ion beam is strongly affected by the energy relaxation process due to Coulomb collision.
Thermally driven smoothening of molecular thin films: Structural transitions in n-alkane layers studied in real-time
Authors: Pithan Linus , Meister Eduard , Jin Chenyu , Weber Christopher , Zykov Anton , Sauer Katrein , Brütting Wolfgang , Riegler Hans , Opitz Andreas , Kowarik Stefan
Published: October 2015

We use thermal annealing to improve smoothness and to increase the lateral size of crystalline islands of n-tetratetracontane (TTC, C44H90) films. With in situ x-ray diffraction, we find an optimum temperature range leading to improved texture and crystallinity while avoiding an irreversible phase transition that reduces crystallinity again. We employ real-time optical phase contrast microscopy with sub-nm height resolution to track the diffusion of TTC across monomolecular step edges which causes the unusual smoothing of a molecular thin film during annealing. We show that the lateral island sizes increase by more than one order of magnitude from 0.5 μm to 10 μm. This desirable behavior of 2d-Ostwald ripening and smoothing is in contrast to many other organic molecular films where annealing leads to dewetting, roughening, and a pronounced 3d morphology. We rationalize the smoothing behavior with the highly anisotropic attachment energies and low surface energies for TTC. The results are technically relevant for the use of TTC as passivation layer and as gate dielectric in organic field effect transistors.
Mechanisms for pressure-induced crystal-crystal transition, amorphization, and devitrification of SnI4
Authors: Liu H. , Tse J. S. , Hu M. Y. , Bi W. , Zhao J. , Alp E. E. , Pasternak M. , Taylor R. D. , Lashley J. C.
Published: October 2015

The pressure-induced amorphization and subsequent recrystallization of SnI4 have been investigated using first principles molecular dynamics calculations together with high-pressure 119Sn nuclear resonant inelastic x-ray scattering measurements. Above ∼8 GPa, we observe a transformation from an ambient crystalline phase to an intermediate crystal structure and a subsequent recrystallization into a cubic phase at ∼64 GPa. The crystalline-to-amorphous transition was identified on the basis of elastic compatibility criteria. The measured tin vibrational density of states shows large amplitude librations of SnI4 under ambient conditions. Although high pressure structures of SnI4 were thought to be determined by random packing of equal-sized spheres, we detected electron charge transfer in each phase. This charge transfer results in a crystal structure packing determined by larger than expected iodine atoms.
Breaking axi-symmetry in stenotic flow lowers the critical transition Reynolds number
Authors: Samuelsson J. , Tammisola O. , Juniper M. P.
Published: October 2015

Flow through a sinuous stenosis with varying degrees of non-axisymmetric shape variations and at Reynolds number ranging from 250 to 750 is investigated using direct numerical simulation (DNS) and global linear stability analysis. At low Reynolds numbers (Re < 390), the flow is always steady and symmetric for an axisymmetric geometry. Two steady state solutions are obtained when the Reynolds number is increased: a symmetric steady state and an eccentric, non-axisymmetric steady state. Either one can be obtained in the DNS depending on the initial condition. A linear global stability analysis around the symmetric and non-axisymmetric steady state reveals that both flows are linearly stable for the same Reynolds number, showing that the first bifurcation from symmetry to antisymmetry is subcritical. When the Reynolds number is increased further, the symmetric state becomes linearly unstable to an eigenmode, which drives the flow towards the non-axisymmetric state. The symmetric state remains steady up to Re = 713, while the non-axisymmetric state displays regimes of periodic oscillations for Re ≥ 417 and intermittency for Re ≳ 525. Further, an offset of the stenosis throat is introduced through the eccentricity parameter E. When eccentricity is increased from zero to only 0.3% of the pipe diameter, the bifurcation Reynolds number decreases by more than 50%, showing that it is highly sensitive to non-axisymmetric shape variations. Based on the resulting bifurcation map and its dependency on E, we resolve the discrepancies between previous experimental and computational studies. We also present excellent agreement between our numerical results and previous experimental results.
Effect of dust charge fluctuation on multidimensional instability of dust-acoustic solitary waves in a magnetized dusty plasma with nonthermal ions
Authors: Shahmohammadi Nafise , Dorranian Davoud
Published: October 2015

Simultaneous effects of dust charge fluctuation and nonthermal ions on the threshold point and growth rate of three-dimensional instability of dust-acoustic solitary waves (DASW) in magnetized dusty plasma have been investigated. In this model, dusty plasma consists of Maxwellian electrons, nonthermal ions, and micron size negatively charged dust particles. Modified Zakharov-Kuznetsov equation for DASW was derived employing a reductive perturbation method and its solitary answer under the influence of dust charge fluctuation and nonthermal ions has been studied. The dispersion relation of DASW has been derived using a small-k perturbation method. Results show that the direction and the magnitude of external magnetic field at which the instability takes place are strongly affected by the rate of dust charge fluctuation and nonthermality of ions. With increasing the number of nonthermal ions, the growth rate of instability decreases, while increasing the dust charge fluctuation increases the growth rate of instability.
Verification of nonlinear particle simulation of radio frequency waves in tokamak
Authors: Kuley A. , Lin Z. , Bao J. , Wei X. S. , Xiao Y. , Zhang W. , Sun G. Y. , Fisch N. J.
Published: October 2015

Nonlinear simulation model for radio frequency waves in fusion plasmas has been developed and verified using fully kinetic ion and drift kinetic electron. Ion cyclotron motion in the toroidal geometry is implemented using Boris push in the Boozer coordinates. Linear dispersion relation and nonlinear particle trapping are verified for the lower hybrid wave and ion Bernstein wave (IBW). Parametric decay instability is observed where a large amplitude pump wave decays into an IBW sideband and an ion cyclotron quasimode (ICQM). The ICQM induces an ion perpendicular heating, with a heating rate proportional to the pump wave intensity.
Tensile behavior of laser treated Fe-Si-B metallic glass
Authors: Joshi Sameehan S. , Samimi Peyman , Ghamarian Iman , Katakam Shravana , Collins Peter C. , Dahotre Narendra B.
Published: October 2015

Fe-Si-B metallic glass foils were treated with a linear laser track using a continuous wave Nd-YAG laser and its effect on the overall tensile behavior was investigated. Microstructure and phase evolutions were evaluated using X-ray diffraction, resistivity measurements, and transmission electron microscopy. Crystallization fraction was estimated via the differential scanning calorimetry technique. Metallic glass foils treated with the lower laser fluences (<0.49 J/mm2) experienced structural relaxation, whereas higher laser fluences led to crystallization within the laser treated region. The overall tensile behavior was least impacted by structural relaxation, whereas crystallization severely reduced the ultimate tensile strength of the laser treated metallic glass foils.
Periodicity, chaos, and multiple attractors in a memristor-based Shinriki's circuit
Authors: Kengne J. , Njitacke Tabekoueng Z. , Kamdoum Tamba V. , Nguomkam Negou A.
Published: October 2015

In this contribution, a novel memristor-based oscillator, obtained from Shinriki's circuit by substituting the nonlinear positive conductance with a first order memristive diode bridge, is introduced. The model is described by a continuous time four-dimensional autonomous system with smooth nonlinearities. The basic dynamical properties of the system are investigated including equilibria and stability, phase portraits, frequency spectra, bifurcation diagrams, and Lyapunov exponents' spectrum. It is found that in addition to the classical period-doubling and symmetry restoring crisis scenarios reported in the original circuit, the memristor-based oscillator experiences the unusual and striking feature of multiple attractors (i.e., coexistence of a pair of asymmetric periodic attractors with a pair of asymmetric chaotic ones) over a broad range of circuit parameters. Results of theoretical analyses are verified by laboratory experimental measurements.
All-optical evaluation of spin-orbit interaction based on diffusive spin motion in a two-dimensional electron gas
Authors: Kohda M. , Altmann P. , Schuh D. , Ganichev S. D. , Wegscheider W. , Salis G.
Published: October 2015

A method is presented that enables the measurement of spin-orbit coefficients in a diffusive two-dimensional electron gas without the need for processing the sample structure, applying electrical currents or resolving the spatial pattern of the spin mode. It is based on the dependence of the average electron velocity on the spatial distance between local excitation and detection of spin polarization, resulting in a variation of spin precession frequency that in an external magnetic field is linear in the spatial separation. By scanning the relative positions of the exciting and probing spots in a time-resolved Kerr rotation microscope, frequency gradients along the [100] and [010] crystal axes of GaAs/AlGaAs QWs are measured to obtain the Rashba and Dresselhaus spin-orbit coefficients, α and β. This simple method can be applied in a variety of materials with electron diffusion for evaluating spin-orbit coefficients.
Effect of ferroelectric substrate on carrier mobility in graphene field-effect transistors
Authors: Bidmeshkipour S. , Vorobiev A. , Andersson M. A. , Kompany A. , Stake J.
Published: October 2015

Effect of LiNbO3 ferroelectric substrate on the carrier mobility in top gated graphene field-effect transistors (G-FETs) is demonstrated. It is shown that, at the same residual concentration of the charge carriers, the mobility in the G-FETs on the LiNbO3 substrate is higher than that on the SiO2/Si substrate. The effect is associated with reduction of Coulomb scattering via screening the charged impurity field by the field induced in the ferroelectric substrate, but significant only for mobilities below 1000 cm2/V s. Raman spectra analysis and correlations established between mobility and microwave loss tangent of the Al2O3 gate dielectric indicate that the charged impurities are located predominantly at the gate dielectric and/or at the gate dielectric/graphene interface and are likely associated with oxygen vacancies.
Note: Cold spectra of the electronic transition A2Σ+-X2Π of N2O+ radical: High resolution analysis of the bands 000-100, 100-100, and 001-101
Authors: Lessa L. L. , Martins A. S. , Fellows C. E.
Published: October 2015

In this note, three vibrational bands of the electronic transition A2Σ+-X2Π of the N2O+ radical (000-100, 100-100, and 001-101) were theoretically analysed. Starting from Hamiltonian models proposed for this kind of molecule, their parameters were calculated using a Levenberg-Marquardt fit procedure in order to reduce the root mean square deviation from the experimental transitions below to 0.01 cm−1. The main objective of this work is to obtain new and reliable values for rotational constant B″ and the spin-orbit interaction parameter A of the analysed vibrational levels of the X2Π electronic state of this molecule.
Out of sight but not out of mind: corvids prey extensively on eggs of burrow-nesting penguins
Authors: Ekanayake Kasun B. , Sutherland Duncan R. , Dann Peter , Weston Michael A.
Published: October 2015

Context
Egg depredation is a major cause of reproductive failure among birds and can drive population declines. In this study we investigate predatory behaviour of a corvid (little raven; Corvus mellori) that has only recently emerged, leading to widespread and intense depredation of eggs of a burrow-nesting seabird (little penguin; Eudyptula minor).

Aims
The main objective of this study was to measure the rate of penguin egg depredation by ravens to determine potential threat severity. We also examined whether penguin burrow characteristics were associated with the risk of egg depredation. Ravens generally employ two modes of predatory behaviour when attacking penguin nests; thus we examined whether burrow characteristics were associated with these modes of attack.

Methods
Remote-sensing cameras were deployed on penguin burrows to determine egg predation rates. Burrow measurements, including burrow entrance and tunnel characteristics, were measured at the time of camera deployment.

Key results
Overall, clutches in 61% of monitored burrows (n = 203) were depredated by ravens, the only predator detected by camera traps. Analysis of burrow characteristics revealed two distinct types of burrows, only one of which was associated with egg depredation by ravens. Clutches depredated by ravens had burrows with wider and higher entrances, thinner soil or vegetation layer above the egg chamber, shorter and curved tunnels and greater areas of bare ground and whitewash near entrances. In addition, 86% were covered by bower spinach (Tetragonia implexicoma), through which ravens could excavate. Ravens used two modes to access the eggs: they attacked through the entrance (25% of burrow attacks, n = 124); or dug a hole through the burrow roof (75% of attacks, n = 124). Burrows that were subject to attack through the entrance had significantly shorter tunnels than burrows accessed through the roof.

Conclusions
The high rates of clutch loss recorded here highlight the need for population viability analysis of penguins to assess the effect of egg predation on population growth rates.

Implications
The subterranean foraging niche of a corvid described here may have implications for burrow-nesting species worldwide because many corvid populations are increasing, and they exhibit great capacity to adopt new foraging strategies to exploit novel prey.
Discovery and functional characterization of a neomorphic PTEN mutation
Authors: Costa Helio A. , Leitner Michael G. , Sos Martin L. , Mavrantoni Angeliki , Rychkova Anna , Johnson Jeffrey R. , Newton Billy W. , Yee Muh-Ching , De La Vega Francisco M. , Ford James M. , Krogan Nevan J. , Shokat Kevan M. , Oliver Dominik , Halaszovich Christian R. , Bustamante Carlos D.
Published: October 2015

Significance

Identification of putative functional genetic mutations involved in cancer has been dramatically accelerated by developments in next generation sequencing technologies. However, analyzing an individual patient genome and interpreting mutation spectra to inform cancer origin and targeted treatment have been challenging. This study presents a framework interpreting a single patient’s genome and identifies a novel causal mutation in the phosphatase and tensin homolog (PTEN) tumor suppressor. Through computational and experimental approaches, we demonstrate that this mutation causes PTEN to retain known tumor suppressor function while gaining protumor activity. This finding suggests a new role for PTEN and other tumor suppressor involvement in cancer formation and reveals the potential wealth of biological information currently underexploited by the lack of systematic approaches for cancer genome interpretation services.
Exploring the influence of ancient and historic megaherbivore extirpations on the global methane budget
Authors: Smith Felisa A. , Hammond John I. , Balk Meghan A. , Elliott Scott M. , Lyons S. Kathleen , Pardi Melissa I. , Tomé Catalina P. , Wagner Peter J. , Westover Marie L.
Published: October 2015

Significance

Most large mammals are endangered or vulnerable across the globe. Although the loss of charismatic fauna is of great concern, their role in ecosystem function remains poorly characterized. Here, we quantify one potential effect of the decline of large herbivores: the reduction of the greenhouse gas methane released as a byproduct of plant digestion. We examine three time periods where large-scale losses of megaherbivores occurred—the African rinderpest epizootic of the 1890s, the massive Great Plains bison kill-off in the 1860s, and the terminal Pleistocene extinction of megafauna. We find detectable decreases in the global methane budget related to the extirpation of megaherbivores. Our findings underscore the importance of large mammals in regulating ecosystems and feedbacks on climate.
Science for a wilder Anthropocene: Synthesis and future directions for trophic rewilding research
Authors: Svenning Jens-Christian , Pedersen Pil B. M. , Donlan C. Josh , Ejrnæs Rasmus , Faurby Søren , Galetti Mauro , Hansen Dennis M. , Sandel Brody , Sandom Christopher J. , Terborgh John W. , Vera Frans W. M.
Published: October 2015

Trophic rewilding is an ecological restoration strategy that uses species introductions to restore top-down trophic interactions and associated trophic cascades to promote self-regulating biodiverse ecosystems. Given the importance of large animals in trophic cascades and their widespread losses and resulting trophic downgrading, it often focuses on restoring functional megafaunas. Trophic rewilding is increasingly being implemented for conservation, but remains controversial. Here, we provide a synthesis of its current scientific basis, highlighting trophic cascades as the key conceptual framework, discussing the main lessons learned from ongoing rewilding projects, systematically reviewing the current literature, and highlighting unintentional rewilding and spontaneous wildlife comebacks as underused sources of information. Together, these lines of evidence show that trophic cascades may be restored via species reintroductions and ecological replacements. It is clear, however, that megafauna effects may be affected by poorly understood trophic complexity effects and interactions with landscape settings, human activities, and other factors. Unfortunately, empirical research on trophic rewilding is still rare, fragmented, and geographically biased, with the literature dominated by essays and opinion pieces. We highlight the need for applied programs to include hypothesis testing and science-based monitoring, and outline priorities for future research, notably assessing the role of trophic complexity, interplay with landscape settings, land use, and climate change, as well as developing the global scope for rewilding and tools to optimize benefits and reduce human–wildlife conflicts. Finally, we recommend developing a decision framework for species selection, building on functional and phylogenetic information and with attention to the potential contribution from synthetic biology.