bluuebunny/crossref_metadata_2025 huggingface dataset:
Dynamic and static control of the optical phase of guided p-polarized light for near-field focusing at large angles of incidence
Authors: Huang Danhong , Michelle Easter M. , David Wellems L. , Mozer Henry , Gumbs Godfrey , Cardimona D. A. , Maradudin A. A.
Published: July 2013

Both dynamic and static approaches are proposed and investigated for controlling the optical phase of a p-polarized light wave guided through a surface-patterned metallic structure with subwavelength features. For dynamic control, the important role of photo-excited electrons in a slit-embedded atomic system with field-induced transparency (FIT) is discovered within a narrow frequency window for modulating the intensity of focused transmitted light in the near-field region. This is facilitated by electromagnetic coupling to surface plasmons between the two FIT-atom embedded slits. The near-field distribution can be adjusted by employing a symmetric (or asymmetric) slit configuration and by a small (or large) slit separation. In addition, the cross-transmission of a light beam is also predicted as a result of this strong coupling between optical transitions in embedded FIT atoms and surface plasmons. For static control, the role of surface curvature is found for focused transmitted light passing through a Gaussian-shaped metallic microlens embedded with a linear array of slits. A negative light-refraction pattern, which is associated with higher-order diffraction modes, was also found for large angles of incidence in the near-field region. This anomalous negative refraction can be suppressed when higher-order waveguide modes of light leak through a very thin film. In addition, this negative refraction can also be suppressed with a reinforced reflection at the left foothill of a Gaussian-shaped slit array of the forward-propagating surface-plasmon wave at large angles of incidence. A prediction is given of near-field focusing of light with its sharpness dynamically controlled by the frequency of the light in a very narrow window. Moreover, a different scheme based on Green's second integral identity is proposed for overcoming a difficulty in calculating the near-field distribution very close to a metallic surface by means of a finite-difference-time-domain method.
Investigation anisotropic mode splitting induced by electro-optic birefringence in an InGaAs/GaAs/AlGaAs vertical-cavity surface-emitting laser
Authors: Yu J. L. , Cheng S. Y. , Lai Y. F. , Chen Y. H.
Published: July 2013

The mode splitting induced by electro-optic birefringence in an P-I-N InGaAs/GaAs/AlGaAs vertical-cavity surface-emitting laser (VCSEL) has been studied by photocurrent difference spectroscopy (PCDS) at room temperature. The mode splitting, anisotropic broadening width, and the anisotropic integrated area of the two orthogonal polarized modes for a VCSEL device are determined. The mode splitting changes linearly with the injected current, which agree very well with theoretical calculations using a Jones matrix approach. It is demonstrated that the PCDS is a powerful tool to study the cavity anisotropy of a VCSEL device.
Change of Mott variable range to small polaronic hole hopping conduction mechanism and formation of Schottky barriers in Nd0.9Sr0.1FeO3
Authors: Ahmad I. , Akhtar M. J. , Khan R. T. A. , Hasan M. M.
Published: July 2013

In this work, single phase Nd0.9Sr0.1FeO3 electroceramic material has been synthesized by solid state reaction method. Phase purity and microstructure were analyzed by X-ray diffraction and SEM. By employing impedance spectroscopy, ac electrical properties have been measured in wide temperature (77–358 K) and frequency (1–1.5 × 107 Hz) range. To correlate the electrical properties an equivalent circuit (RgQg)(RgbQgb)(RcQc) has been used at lower temperatures which gradually changed to (Rgb)(RcQc) at higher temperatures. Around 218 K, the conduction mechanism changed from variable range hole hopping to small polaronic hole hopping mechanism which was also confirmed by ac conductivity and magnetization measurements. The localization length calculated for grains and grain boundaries are 1.17 Å and 1.06 Å, respectively. Hall measurements pointed out that majority of the charge carriers are p-type. The dc bias measurements confirmed the presence of non-ohmic electrode contacts and obeyed the Mott-Schottky law. The observed permittivity of grains is from 8 to 10, whereas the high permittivity at elevated temperatures may be due to the formation of different Schottky barriers, as a result of ceramic interfaces, ceramic surfaces, and electrode effects.
Local bond length variations in boron-doped nanocrystalline diamond measured by spatially resolved electron energy-loss spectroscopy
Authors: Lu Ying-Gang , Turner Stuart , Verbeeck Johan , Janssens Stoffel D. , Haenen Ken , Van Tendeloo Gustaaf
Published: July 2013

Variations in local bond length and coordination in boron-doped nanocrystalline diamond (NCD) films have been studied through changes in the fine structure of boron and carbon K-edges in electron energy-loss spectra, acquired in a scanning transmission electron microscope. The presence of high concentrations of B in pristine diamond regions and enrichment of B at defects in single NCD grains is demonstrated. Local bond length variations are evidenced through an energy shift of the carbon 1s → σ* edge at B-rich defective regions within single diamond grains, indicating an expansion of the diamond bond length at sites with local high B content.
Kinetic evolution of blistering in hydrogen-implanted silicon
Authors: Coupeau C. , Parry G. , Colin J. , David M.-L. , Labanowski J. , Grilhé J.
Published: July 2013

Silicon wafers have been implanted with hydrogen at high fluence. The kinetic evolution of the buckling structures has been observed in situ by atomic force microscopy during a thermal annealing at 200 °C. It is shown that the blistering of the silicon wafers occurs at the first stage of the annealing without any noticeable threshold. The deflection of the blisters continuously increases with time, and some blisters are observed to coalesce. The time evolution of the internal pressure inside the cavities is finally determined from the blister dimensions with the help of an elastic analytical model.
Shear and transverse stress in a thin superconducting layer in simplified coated conductor architecture with a pre-existing detachment
Authors: Jing Ze , Yong Huadong , Zhou Youhe
Published: July 2013

The thermal-electro-mechanical behavior of second generation YBa2Cu3O7−δ coated conductors subjected to thermal cooling and electric charging is investigated in this paper. Shear stress at the interface and transverse normal stress in the film are analyzed through the elasticity theory. The plane strain approach is assumed, and a singular integral equation governing the problem is derived in terms of the interfacial shear stress, thermal strain, and the electromagnetic force. After that, we evaluate the shear and transverse stress distribution in the conductor during cool down and electric charging, respectively. The results show that large residual compressive stress (about 150 MPa) and interfacial shear stress (about 400 MPa) remain in the conductor during cool down. In the electric charging process while small compared to the thermal one destructive tensile stress present near the edges of the conductor. Effects of the stiffness of substrate on the stress distribution in the conductor are investigated also.
Perylenediimide-based distributed feedback lasers with holographic relief gratings on dichromated gelatine
Authors: Ramírez Manuel G. , Quintana José A. , Villalvilla José M. , Boj Pedro G. , Retolaza Aritz , Merino Santos , Díaz-García María A.
Published: July 2013

One dimensional second-order distributed feedback (DFB) lasers consisting of polystyrene (PS) films doped with a perylenediimide laser dye, deposited over dichromated gelatine (DCG) photoresist layers with solvent resistant relief gratings recorded by holographic lithography, are reported. The advantage of using the grating on DCG in the final device is that the fabrication process is simplified and the grating pattern better preserved, since no etching methods to transfer the grating to another substrate are needed. A very simple model, proposed to explain the experimental waveguide properties, has allowed identifying the waveguide mode at which DFB emission appears, which was the key to optimize the device performance. In the frame of this model, the thickness of the PS and DCG films could be adjusted in order to minimize the laser threshold and to control its wavelength tuneability. The performance of these lasers is comparable to that of recently reported devices based on the same active material, but deposited over high-quality DFB gratings engraved on SiO2 by nanoimprint lithography.
Thermochromic VO2 nanorods made by sputter deposition: Growth conditions and optical modeling
Authors: Li Shu-Yi , Namura Kyoko , Suzuki Motofumi , Niklasson Gunnar A. , Granqvist Claes G.
Published: July 2013

Reactive dc magnetron sputtering onto glass-based substrates yielded deposits of thermochromic VO2 with well-developed nanorods and nanowires. Their formation was promoted by high substrate temperature (above ∼500 °C), sufficient film thickness, proper inlet of the reactive gas, dispersed gold “seeds,” and pronounced substrate roughness. Rutherford back scattering ascertained mass thicknesses, scanning electron microscopy depicted the nanostructures, and glancing incidence X-ray diffraction proved that single-phase VO2 was normally formed. Spectrophotometric measurements of total and diffuse transmittance and reflectance on VO2 thin films, at room temperature and ∼100 °C, allowed us to determine complex dielectric functions below and above the “critical” temperature for thermochromic switching (∼68 °C). These data were then used in computations based on the Bruggeman effective medium theory applied to randomly oriented prolate spheroidal structural units to derive the optical properties of the deposits. Experimental and computed data on spectral absorptance were found to be in good qualitative agreement.
Optofluidic manipulation of Escherichia coli in a microfluidic channel using an abruptly tapered optical fiber
Authors: Xin Hongbao , Li Yayi , Li Lingshan , Xu Rui , Li Baojun
Published: July 2013

We report stable optical trapping and controlled manipulation of Escherichia coli cells in a microfluidic channel using an abruptly tapered optical fiber with 980-nm wavelength laser light launched. Stability of the trapping at different optical powers (10–70 mW) was demonstrated in fluids under different flow directions and velocities. The experimental results were supported by finite-element simulations and analytic calculations.
Raman studies of cation distribution and thermal stability of epitaxial spinel NiCo2O4 films
Authors: Iliev M. N. , Silwal P. , Loukya B. , Datta R. , Kim D. H. , Todorov N. D. , Pachauri N. , Gupta A.
Published: July 2013

Epitaxial thin films of spinel NiCo2O4 (NCO) grown on MgAl2O4 (001) substrates are reported to exhibit dramatic changes in the magnetic and transport properties with deposition temperature. While films grown at lower temperatures (<450°C) are ferrimagnetic with metallic characteristics, those grown at higher temperatures are non-magnetic and insulating. Detailed polarized Raman spectroscopy studies indicate that the higher temperature films have close to the ideal inverse spinel cation distribution, Co3+[Ni2+Co3+]O42−, whereas those deposited at lower temperature are characterized by mixed cation/charge distribution at both the tetragonal (A) and octahedral (B) sites. Additionally, temperature-dependent Raman studies demonstrate that, unlike bulk polycrystalline samples, all the NCO films are robust against thermal treatment with full reversibility after annealing at 600°C in oxygen and air. However, partial decomposition is observed after annealing in vacuum.
Current-induced distortion of the band structure and formation of pseudogaps in magnonic crystals
Authors: Polushkin N. I.
Published: July 2013

Using numerical simulations, we have studied how electric current, passing along the periodicity direction in a lateral magnetic superlattice with modulated saturation magnetization, affects the propagation of magnetostatic surface spin waves (MSSWs) across it. It is shown that when the current flows against the normal lattice modes excited by a built-in antenna, it mediates excitation of new MSSW modes. These current-assisted modes are found to be co-propagating with the normal lattice ones but travel with negative group velocities and their wave-packet dispersions opposite to those in the normal lattice modes. Surprisingly, their intensity is high enough to effectively interact with the normal lattice modes under realistic parameters of the lattice and current. This intermode interaction gives rise to new frequency bands where the MSSW intensity is lowered but essentially nonzero (pseudogaps). The pseudogap positions can be shifted by several gigahertz either upwards or downwards with respect to the bandgaps occurring at Brillouin zone edges in the absence of current. The pseudogap shifting depends on the strength of the current and on the lattice magnetization and period.
Anisotropic magnetism and spin-dependent transport in Co nanoparticle embedded ZnO thin films
Authors: Li D. Y. , Zeng Y. J. , Pereira L. M. C. , Batuk D. , Hadermann J. , Zhang Y. Z. , Ye Z. Z. , Temst K. , Vantomme A. , Van Bael M. J. , Van Haesendonck C.
Published: July 2013

Oriented Co nanoparticles were obtained by Co ion implantation in crystalline ZnO thin films grown by pulsed laser deposition. Transmission electron microscopy revealed the presence of elliptically shaped Co precipitates with nanometer size, which are embedded in the ZnO thin films, resulting in anisotropic magnetic behavior. The low-temperature resistance of the Co-implanted ZnO thin films follows the Efros-Shklovskii type variable-range-hopping. Large negative magnetoresistance (MR) exceeding 10% is observed in a magnetic field of 1 T at 2.5 K and the negative MR survives up to 250 K (0.3%). The negative MR reveals hysteresis as well as anisotropy that correlate well with the magnetic properties, clearly demonstrating the presence of spin-dependent transport.
Structural effects on mechanical response of MoS2 nanostructures during compression
Authors: Bucholz Eric W. , Sinnott Susan B.
Published: July 2013

In recent years, inorganic nanostructures, such as fullerene-like MoS2 and WS2 nanoparticles, have been shown to be promising candidates for friction and wear reduction in tribological applications. However, it has been demonstrated experimentally that the mechanical response of any given inorganic nanostructure varies depending on its individual structural characteristics such as size, shape, and crystallinity. Here, classical molecular dynamics simulations are performed that investigate the mechanical responses of different types of MoS2 nanostructures during uniaxial compression. The results illustrate the dependence of mechanical behavior on nanoparticle structure and, in particular, indicate that the mechanical properties of MoS2 nanostructures vary significantly with changes in the orientation of the MoS2 walls at the interface.
Probing structure and strain transfer in dry-spun carbon nanotube fibers by depth-profiled Raman spectroscopy
Authors: Zhou Jinyuan , Sun Gengzhi , Zhan Zhaoyao , An Jianing , Zheng Lianxi , Xie Erqing
Published: July 2013

The structural properties of dry-spun carbon nanotube (CNT) fibers were characterized by depth-profiled polarized Raman spectroscopy. Results showed that the twisting cannot be fully transferred through the whole fiber and the CNTs within fibers possess non-uniform alignments in radial direction. Effective twisting depth was determined from the residue strain distribution within fibers. Larger surface twisting angles can result in higher residue strain, better alignment degree, and deeper twisting depth. This research suggests a balance should be built between the enhancement of CNT interactions and the increase of defect density to obtain high-performance fibers.
Control of stacking direction and optical anisotropy in InAs/GaAs quantum dots by In flux
Authors: Bessho Yusuke , Harada Yukihiro , Kita Takashi , Taguchi Eiji , Yasuda Hidehiro
Published: July 2013

We have developed a technique to control the stacking direction of InAs/GaAs quantum dots (QDs) grown on GaAs(001) by varying the direction of the In flux. Transmission-electron microscope images of the stacked QDs reveal that the stacking direction tilts along the [110] direction according to the projection of the In flux direction on the (−110) and does not tilt in the [−110] direction. This anisotropic tilting behavior of the stacked QDs is considered to be caused by an anisotropic migration of In atoms on the (001) growth front. The linear polarization feature of the edge-emitted photoluminescence (PL) demonstrates a strong anisotropy of the strain distribution attributable to the tilted direction of the stacked QDs. According to multidirectional observations of the polarized PL, anisotropic valence band mixing was caused by strain symmetry lowering owing to the tilted stacking direction.
Structural anisotropy in amorphous SnO2 film probed by X-ray absorption spectroscopy
Authors: Zhu Q. , Ma Q. , Buchholz D. B. , Chang R. P. H. , Bedzyk M. J. , Mason T. O.
Published: July 2013

Polarization-dependent X-ray absorption measurements reveal the existence of structural anisotropy in amorphous (a-) SnO2 film. The anisotropy is readily seen for the second neighbor interaction whose magnitude differs along three measured directions. The differences can be well accounted for by 10%–20% variation in the Debye-Waller factor. Instead of a single Gaussian distribution found in crystalline SnO2, the Sn-O bond distribution is bimodal in a-SnO2 whose separation shows a weak angular dependence. The oxygen vacancies, existing in the a-SnO2 film in the order of 1021 cm−3, distribute preferentially along the film surface direction.
Magnetoelectric sensor with miniature universal tunable bias magnetic circuit
Authors: Shi Zhan , Tong Yongshuai , Deng Shuwen , Xue Hao , Yang Shuiyuan , Lu Yong , Wang Cuiping , Liu Xingjun
Published: July 2013

This paper presents a miniature alternating magnetic field sensor made from magnetoelectric (ME) laminated materials with a universal tunable bias magnetic circuit. By adjusting the width of the bypass passage in the bias magnetic circuit, the magnetic flux in the ME materials could be tuned and make the ME sensor work under the optimal bias magnetic field. In our design, the sensor's dimension is as small as 8 mm along the detecting direction. Due to the excellent linearity when measuring low frequency alternating magnetic fields of 50 Hz, this miniature sensor is ideally suited for power line current measurement.
The effect of oxygen flow rate and radio frequency plasma power on cubic ZnMgO ultraviolet sensors grown by plasma-enhanced molecular beam epitaxy
Authors: Casey Boutwell R. , Wei Ming , Schoenfeld Winston V.
Published: July 2013

Cubic Zn1−xMgxO thin films were produced by Plasma-Enhanced Molecular Beam Epitaxy. Oxygen flow rate and applied Radio-Frequency (RF) plasma power were varied to investigate the impact on film growth and optoelectronic device performance. Solar-blind and visible-blind detectors were fabricated with metal-semiconductor-metal interdigitated Ni/Mg/Au contacts and responsivity is compared under different growth conditions. Increasing oxygen flow rate and RF plasma power increased Zn incorporation in the film, which leads to phase segregation at relatively high Zn/Mg ratio. Responsivity as high as 61 A/W was measured in phase-segregated ZnMgO visible-blind detectors.
Room temperature positive magnetoresistance via charge trapping in polyaniline-iron oxide nanoparticle composites
Authors: Lin Aigu L. , Wu Tom , Chen Wei , Wee Andrew T. S.
Published: July 2013

We demonstrate a polyaniline-iron oxide nanoparticle (PANI-NP) organic hybrid composite device with room temperature positive magnetoresistance of 85.7%. Temperature dependent resistivity measurements attribute this observation to the decrease in localization length of the charge carriers in the presence of an external magnetic field which result in them being trapped within the device between the insulating PANI layer, hence allowing the device to maintain its resistive state even when the power is switched off, thus exhibiting a memory effect.
Current density enhancement nano-contact phase-change memory for low writing current
Authors: Yin You , Hosaka Sumio , Ik Park Woon , Sik Jung Yeon , Jae Lee Keon , Kuk You Byoung , Liu Yang , Yu Qi
Published: July 2013

In this work, a phase-change memory (PCM) with self-assembled nanostructures and an oxidized thin phase-change layer is proposed and intensively investigated for low writing reset current by finite element analysis. Current density is significantly enhanced in our nano-contact memory because of the existence of nanostructures and oxidized phase-change layer. The writing current of our proposed memory is about 1/10-3/10 that of conventional cell, which is in good agreement with our experimental results. The heat efficiency in the nano-contact PCM cell is greatly improved and its power consumption can be as low as about 1/10 that of the conventional cell.
Correlation between defects and conductivity of Sb-doped tin oxide thin films
Authors: Mao Wenfeng , Xiong Bangyun , Liu Yong , He Chunqing
Published: July 2013

Defects in undoped and antimony (Sb)-doped tin oxide thin films fabricated via a sol-gel method have been investigated using a slow positron beam by which an annihilation lineshape parameter is used to evaluate defects in the films. With increasing calcination temperature, the resistivity for undoped films increased because of removal of oxygen vacancies in them; however, the resistivity gradually declined for Sb-doped films upon annealing at higher temperatures, mainly due to weakened carrier scattering with fewer residual defects. The results show that defects as well as dopants play an important role in determining the resistivity of tin oxide films.
Accelerator-based neutron source using a cold deuterium target with degenerate electrons
Authors: Phillips R. E. , Ordonez C. A.
Published: July 2013

A neutron generator is considered in which a beam of tritons is incident on a hypothetical cold deuterium target with degenerate electrons. The energy efficiency of neutron generation is found to increase substantially with electron density. Recent reports of potential targets are discussed.
The novel chamber hardware design to improve the thin film deposition quality in both 12″ (300 mm) and 18″ (450 mm) wafers with the development of 3D full chamber modeling and experimental visual technique
Authors: Liao M.-H. , Chen C.-H.
Published: July 2013

The thin film deposition property and the process difference during the wafer size migration from 12″ (300 mm) to 18″ (450 mm) in the Chemical Vapor Deposition (CVD) equipment is improved and reduced, respectively, when the chamber hardware is designed with the help of 3D full chamber modeling and 3D experimental visual technique developed in this work. The accuracy of 3D chamber simulation model is demonstrated with the experimental visual technique measurement. With the CVD chamber hardware design of placing the inlet position and optimizing the distance between the susceptor edge and the reactor wall, the better thin film deposition property and the larger process compatibility during the wafer size migration from 12″ (300 mm) to 18″ (450 mm) for the industry cost reduction can be achieved. Non-dimensional Nusselt parameter is also found to be the effective indicator to monitor the thin film deposition property.
Effects of dietary probiotics on growth performance, faecal microbiota and serum profiles in weaned piglets
Authors: Dong Xiaoli , Zhang Naifeng , Zhou Meng , Tu Yan , Deng Kaidong , Diao Qiyu
Published: July 2013

This study was conducted to evaluate the effects of dietary supplementation with probiotics on growth performance, faecal microbiota, and serum profiles in weaned piglets. Large White × Landrace piglets (n = 144) weaned at 35–37 days of age were selected and divided into four groups, and the piglets from each group were assigned randomly to six pens (replicates) with six animals each. Each group was fed one of four diets for 5 weeks: a basal diet without antibiotics and probiotics (control), or the basal diet supplemented with Lactobacillus plantarum GF103, Bacillus subtilis B27, or a mixture of L. plantarum GF103 and B. subtilis B27. During the first 2 weeks of the supplementation, the piglets supplemented with probiotics had lower (P < 0.05) average daily feed intake than control piglets. The feed conversion ratio was improved (P < 0.05) in probiotic-supplemented groups compared with that of control. The population of E. coli in faeces of the piglets supplemented with L. plantarum GF103 was lower (P < 0.05) than that of control piglets. On day 14, dietary supplementation of the combination of L. plantarum GF103 and B. subtilis B27 increased (P < 0.05) the serum concentrations of total protein, globulin, and creatinine, but decreased (P < 0.05) the ratio of serum albumin to serum globulin, compared with the basal diet. On day 14, dietary supplementation with probiotics increased (P < 0.05) the serum IgM concentration compared with the basal diet. Supplementation of B. subtilis B27 or the combination of L. plantarum GF103 and B. subtilis B27 increased (P < 0.05) the serum IgA concentration at the end of the trial. These results suggest that dietary probiotics improved growth performance and enhanced immune responses at the early stage of the post-weaning period in piglets.
Pentose phosphate pathway activity: effect on in vitro maturation and oxidative status of bovine oocytes
Authors: Gutnisky Cynthia , Dalvit Gabriel C. , Thompson Jeremy G. , Cetica Pablo D.
Published: July 2013

The relationship between pentose phosphate pathway (PPP) activity in cumulus–oocyte complexes (COCs) and oxidative and mitochondrial activity in bovine oocytes was evaluated with the aim of analysing the impact of two inhibitors (NADPH and 6-aminonicotinamide (6-AN)) and a stimulator (NADP) of the key enzymes of the PPP on the maturation rate, oxidative and mitochondrial activity and the mitochondrial distribution in oocytes. The proportion of COCs with measurable PPP activity (assessed using brilliant cresyl blue staining), glucose uptake, lactate production and meiotic maturation rate diminished when 6-AN (0.1, 1, 5 and 10 mM for 22 h) was added to the maturation medium (P < 0.05). The addition of NADPH did not modify glucose uptake or lactate production, but reduced PPP activity in COCs and meiotic maturation rates (P < 0.05). The presence of NADP (0.0125, 0.125, 1.25 and 12.5 mM for 22 h of culture) in the maturation medium had no effect on PPP activity in COCs, glucose uptake, lactate production and meiotic maturation rate. However, in the absence of gonadotropin supplementation, NADP stimulated both glucose uptake and lactate production at 12.5 mM (the highest concentration tested; P < 0.05). NADP did not modify cleavage rate, but decreased blastocyst production (P < 0.05). During IVM, oocyte oxidative and mitochondrial activity was observed to increase at 15 and 22 h maturation, which was also related to progressive mitochondrial migration. Inhibiting the PPP with 6-AN or NADPH led to reduced oxidative and mitochondrial activity compared with the respective control groups and inhibition of mitochondrial migration (P < 0.05). Stimulation of the PPP with NADP increased oxidative and mitochondrial activity at 9 h maturation (P < 0.05) and delayed mitochondrial migration. The present study shows the significance of altering PPP activity during bovine oocyte IVM, revealing that there is a link between the activity of the PPP and the oxidative status of the oocyte.
Lariat sequencing in a unicellular yeast identifies regulated alternative splicing of exons that are evolutionarily conserved with humans
Authors: Awan Ali R. , Manfredo Amanda , Pleiss Jeffrey A.
Published: July 2013

Alternative splicing is a potent regulator of gene expression that vastly increases proteomic diversity in multicellular eukaryotes and is associated with organismal complexity. Although alternative splicing is widespread in vertebrates, little is known about the evolutionary origins of this process, in part because of the absence of phylogenetically conserved events that cross major eukaryotic clades. Here we describe a lariat-sequencing approach, which offers high sensitivity for detecting splicing events, and its application to the unicellular fungus,
Schizosaccharomyces pombe
, an organism that shares many of the hallmarks of alternative splicing in mammalian systems but for which no previous examples of exon-skipping had been demonstrated. Over 200 previously unannotated splicing events were identified, including examples of regulated alternative splicing. Remarkably, an evolutionary analysis of four of the exons identified here as subject to skipping in
S. pombe
reveals high sequence conservation and perfect length conservation with their homologs in scores of plants, animals, and fungi. Moreover, alternative splicing of two of these exons have been documented in multiple vertebrate organisms, making these the first demonstrations of identical alternative-splicing patterns in species that are separated by over 1 billion y of evolution.
Nuclear dynamics in a fungal chimera
Authors: Roper Marcus , Simonin Anna , Hickey Patrick C. , Leeder Abby , Glass N. Louise
Published: July 2013

A fungal colony is a syncytium composed of a branched and interconnected network of cells. Chimerism endows colonies with increased virulence and ability to exploit nutritionally complex substrates. Moreover, chimera formation may be a driver for diversification at the species level by allowing lateral gene transfer between strains that are too distantly related to hybridize sexually. However, the processes by which genomic diversity develops and is maintained within a single colony are little understood. In particular, both theory and experiments show that genetically diverse colonies may be unstable and spontaneously segregate into genetically homogenous sectors. By directly measuring patterns of nuclear movement in the model ascomycete fungus
Neurospora crassa
, we show that genetic diversity is maintained by complex mixing flows of nuclei at all length scales within the hyphal network. Mathematical modeling and experiments in a morphological mutant reveal some of the exquisite hydraulic engineering necessary to create the mixing flows. In addition to illuminating multinucleate and multigenomic lifestyles, the adaptation of a hyphal network for mixing nuclear material provides a previously unexamined organizing principle for understanding morphological diversity in the more-than-a-million species of filamentous fungi.
Generation of functionally competent and durable engineered blood vessels from human induced pluripotent stem cells
Authors: Samuel Rekha , Daheron Laurence , Liao Shan , Vardam Trupti , Kamoun Walid S. , Batista Ana , Buecker Christa , Schäfer Richard , Han Xiaoxing , Au Patrick , Scadden David T. , Duda Dan G. , Fukumura Dai , Jain Rakesh K.
Published: July 2013

Efficient generation of competent vasculogenic cells is a critical challenge of human induced pluripotent stem (hiPS) cell-based regenerative medicine. Biologically relevant systems to assess functionality of the engineered vessels in vivo are equally important for such development. Here, we report a unique approach for the derivation of endothelial precursor cells from hiPS cells using a triple combination of selection markers—CD34, neuropilin 1, and human kinase insert domain-containing receptor—and an efficient 2D culture system for hiPS cell-derived endothelial precursor cell expansion. With these methods, we successfully generated endothelial cells (ECs) from hiPS cells obtained from healthy donors and formed stable functional blood vessels in vivo, lasting for 280 d in mice. In addition, we developed an approach to generate mesenchymal precursor cells (MPCs) from hiPS cells in parallel. Moreover, we successfully generated functional blood vessels in vivo using these ECs and MPCs derived from the same hiPS cell line. These data provide proof of the principle that autologous hiPS cell-derived vascular precursors can be used for in vivo applications, once safety and immunological issues of hiPS-based cellular therapy have been resolved. Additionally, the durability of hiPS-derived blood vessels in vivo demonstrates a potential translation of this approach in long-term vascularization for tissue engineering and treatment of vascular diseases. Of note, we have also successfully generated ECs and MPCs from type 1 diabetic patient-derived hiPS cell lines and use them to generate blood vessels in vivo, which is an important milestone toward clinical translation of this approach.
Crystal structure of a GroEL-ADP complex in the relaxed allosteric state at 2.7 Å resolution
Authors: Fei Xue , Yang Dong , LaRonde-LeBlanc Nicole , Lorimer George H.
Published: July 2013

Significance

Chaperonins GroEL and GroES facilitate the folding of diverse substrate proteins driven by ATP hydrolysis. GroEL subunits cycle through a series of allosteric states in a concerted manner, enabling work to be performed on substrate proteins. Removing two salt bridges that ordinarily break during the allosteric transitions of the WT permitted the structure of GroEL in the relaxed R state to be solved. Whereas the equatorial and intermediate domains display almost perfect sevenfold symmetry, the apical domains display remarkable asymmetry. Freed of intersubunit contacts, each subunit adopts a different conformation, suggesting a flexibility that permits interaction with diverse substrate proteins.
Dagger closure and solid closure in graded dimension two
Authors: Brenner Holger , Stäbler Axel
Published: July 2013

We introduce a graded version of dagger closure and prove that it coincides with solid closure for homogeneous ideals in two-dimensional

N

\mathbb {N}

-graded domains of finite type over a field.
Multifunctional roles of urokinase plasminogen activator (uPA) in cancer stemness and chemoresistance of pancreatic cancer
Authors: Asuthkar Swapna , Stepanova Victoria , Lebedeva Tatiana , Holterman AiXuan L. , Estes Norman , Cines Douglas B. , Rao Jasti S. , Gondi Christopher S.
Published: July 2013

Pancreatic ductal adenocarcinoma (PDAC) is almost always lethal. One of the underlying reasons for this lethality is believed to be the presence of cancer stem cells (CSC), which impart chemoresistance and promote recurrence, but the mechanisms responsible are unclear. Recently the poor prognosis of PDAC has been correlated with increased expression of urokinase plasminogen activator (uPA). In the present study we examine the role of uPA in the generation of PDAC CSC. We observe a subset of cells identifiable as a side population (SP) when sorted by flow cytometry of MIA PaCa-2 and PANC-1 pancreatic cancer cells that possess the properties of CSC. A large fraction of these SP cells are CD44 and CD24 positive, are gemcitabine resistant, possess sphere-forming ability, and exhibit increased tumorigenicity, known characteristics of cancer stemness. Increased tumorigenicity and gemcitabine resistance decrease after suppression of uPA. We observe that uPA interacts directly with transcription factors LIM homeobox-2 (Lhx2), homeobox transcription factor A5 (HOXA5), and Hey to possibly promote cancer stemness. uPA regulates Lhx2 expression by suppressing expression of miR-124 and p53 expression by repressing its promoter by inactivating HOXA5. These results demonstrate that regulation of gene transcription by uPA contributes to cancer stemness and clinical lethality.
Epidemiology of Coeliac Disease and Comorbidity in Norwegian Children
Authors: Størdal Ketil , Bakken Inger Johanne , Surén Pål , Stene Lars C.
Published: July 2013

Objectives:

The aim of this study was to describe the occurrence of clinically diagnosed coeliac disease in children ages 0 to 12 years in Norway, including regional variation and coexisting type 1 diabetes mellitus, thyroid disease, and Down syndrome.

Methods:

The Norwegian Patient Register (NPR) contains individual‐level hospital data from 2008 onward. Small‐bowel biopsies for establishing the coeliac disease diagnosis are only performed at public hospitals reporting to the NPR. Data on all hospital contacts during 2008–2011 when a diagnosis of coeliac disease was registered were retrieved from the NPR for patients born between 1999 and 2011, allowing estimation of the proportion registered with coeliac disease at ages 0 to 12 years in a cohort study.

Results:

A total of 3006 individuals (58.2% girls) were recorded as having coeliac disease among 797,360 children, corresponding to a proportion of 3.8/1000 (95% confidence interval [CI] 3.7–3.9/1000) children, 4.5 (CI 4.3–4.7) among girls and 3.1 (CI 2.9–3.3/1000) among boys (P < 0.001). The proportion increased with age up to approximately 6 years and was 5.0/1000 (CI 4.5–5.6) at the age of 12 years, and was slightly higher in the south/west (3.9/1000) as compared to the middle/north (3.5/1000) regions of Norway (P = 0.013). A total of 214 of 3006 (7.1%) patients with coeliac disease were registered with coexisting conditions: type 1 diabetes mellitus (n = 142, 4.7%), Down syndrome (n = 47, 1.6%), or thyroid disease (n = 41, 1.4%).

Conclusions:

In this first nationwide study of clinically diagnosed coeliac disease in Norwegian children, we found a high occurrence, comparable with that in Sweden. Comorbidity was common, but routine screening of high‐risk groups contributed to a limited number of cases.
Do
Heliconius
butterfly species exchange mimicry alleles?
Authors: Smith Joel , Kronforst Marcus R.
Published: July 2013

Hybridization has the potential to transfer beneficial alleles across species boundaries, and there are a growing number of examples in which this has apparently occurred. Recent studies suggest that
Heliconius
butterflies have transferred wing pattern mimicry alleles between species via hybridization, but ancestral polymorphism could also produce a signature of shared ancestry around mimicry genes. To distinguish between these alternative hypotheses, we measured DNA sequence divergence around putatively introgressed mimicry loci and compared this with the rest of the genome. Our results reveal that putatively introgressed regions show strongly reduced sequence divergence between co-mimetic species, suggesting that their divergence times are younger than the rest of the genome. This is consistent with introgression and not ancestral variation. We further show that this signature of introgression occurs at sites throughout the genome, not just around mimicry genes.
The Stokesian flow field of an oscillatory submerged viscous jet impinging on a planar wall
Authors: Davis A. M. J. , Kim J. H. , Gunter G. M. , Ratnanather J. T.
Published: July 2013

This model of experiments on auditory sensory hair cells extends previous work via distributions on a cylindrical pipe of tangentially and normally directed oscillatory point forces, which are modified to achieve no-slip at the wall in two stages. Starting with the pressure and vorticity jumps associated with the oscillatory pressure-driven flow upstream in the pipe, the adjustment of the interior pipe flow from its upstream complex-valued profile to its exit profile is fully included. This is essentially achieved by modifying the steps of the steady case analysis. The flow field oscillates with phase dependent on position, and the level curves of the streamfunction indicate instantaneous particle motion but not streamlines. Thus, an eddy is not indicated by the closed curve that occurs midway through the two half cycles and is due to competing forces between the inflow and outflow, particularly in the second half cycle as the fluid enters the pipe. The wall pressure and wall shear stress also oscillate with the non-uniformities concentrated near the origin, but are relatively damped midway through the two half cycles. Independent of the orifice location, there is a small effect of frequency on the wall pressure and the wall shear stress.
Reproductive competence: a recurrent logic module in eukaryotic development
Authors: Noble Luke M. , Andrianopoulos Alex
Published: July 2013

Developmental competence is the ability to differentiate in response to an appropriate stimulus, as first elaborated by Waddington in relation to organs and tissues. Competence thresholds operate at all levels of biological systems from the molecular (e.g. the cell cycle) to the ontological (e.g. metamorphosis and reproduction). Reproductive competence, an organismal process, is well studied in mammals (sexual maturity) and plants (vegetative phase change), though far less than later stages of terminal differentiation. The phenomenon has also been documented in multiple species of multicellular fungi, mostly in early, disparate literature, providing a clear example of physiological differentiation in the absence of morphological change. This review brings together data on reproductive competence in Ascomycete fungi, particularly the model filamentous fungusAspergillus nidulans, contrasting mechanisms within Unikonts and plants. We posit reproductive competence is an elementary logic module necessary for coordinated development of multicellular organisms or functional units. This includes unitary multicellular life as well as colonial species both unicellular and multicellular (e.g. social insects such as ants). We discuss adaptive hypotheses for developmental and reproductive competence systems and suggest experimental work to address the evolutionary origins, generality and genetic basis of competence in the fungal kingdom.
A remarkable short-snouted horned dinosaur from the Late Cretaceous (late Campanian) of southern Laramidia
Authors: Sampson Scott D. , Lund Eric K. , Loewen Mark A. , Farke Andrew A. , Clayton Katherine E.
Published: July 2013

The fossil record of centrosaurine ceratopsids is largely restricted to the northern region of western North America (Alberta, Montana and Alaska). Exceptions consist of single taxa from Utah (
Diabloceratops
) and China (
Sinoceratops
), plus otherwise fragmentary remains from the southern Western Interior of North America. Here, we describe a remarkable new taxon,
Nasutoceratops titusi
n. gen. et sp., from the late Campanian Kaiparowits Formation of Utah, represented by multiple specimens, including a nearly complete skull and partial postcranial skeleton. Autapomorphies include an enlarged narial region, pneumatic nasal ornamentation, abbreviated snout and elongate, rostrolaterally directed supraorbital horncores. The subrectangular parietosquamosal frill is relatively unadorned and broadest in the mid-region. A phylogenetic analysis indicates that
Nasutoceratops
is the sister taxon to
Avaceratops
, and that a previously unknown subclade of centrosaurines branched off early in the group's history and persisted for several million years during the late Campanian. As the first well-represented southern centrosaurine comparable in age to the bulk of northern forms,
Nasutoceratops
provides strong support for the provincialism hypothesis, which posits that Laramidia—the western landmass formed by inundation of the central region of North America by the Western Interior Seaway—hosted at least two coeval dinosaur communities for over a million years of late Campanian time.
Trophic omnivory across a productivity gradient: intraguild predation theory and the structure and strength of species interactions
Authors: Novak Mark
Published: July 2013

Intraguild predation theory centres on two predictions: (i) for an omnivore and an intermediate predator (IG-prey) to coexist on shared resources, the IG-prey must be the superior resource competitor, and (ii) increasing resource productivity causes the IG-prey's equilibrium abundance to decline. I tested these predictions with a series of species-rich food webs along New Zealand's rocky shores, focusing on two predatory whelks,
Haustrum haustorium
, a trophic omnivore, and
Haustrum scobina
, the IG-prey. In contrast to theory, the IG-prey's abundance increased with productivity. Furthermore, feeding rates and allometric considerations indicate a competitive advantage for the omnivore when non-shared prey are considered, despite the IG-prey's superiority for shared prey. Nevertheless, clear and regular cross-gradient changes in network structure and interaction strengths were observed that challenge the assumptions of current theory. These insights suggest that the consideration of consumer-dependent functional responses, non-equilibrium dynamics, the dynamic nature of prey choice and non-trophic interactions among basal prey will be fruitful avenues for theoretical development.
Eyespots divert attacks by fish
Authors: Kjernsmo Karin , Merilaita Sami
Published: July 2013

Eyespots (colour patterns consisting of concentric rings) are found in a wide range of animal taxa and are often assumed to have an anti-predator function. Previous experiments have found strong evidence for an intimidating effect of eyespots against passerine birds. Some eyespots have been suggested to increase prey survival by diverting attacks towards less vital body parts or a direction that would facilitate escape. While eyespots in aquatic environments are widespread, their function is extremely understudied. Therefore, we investigated the protective function of eyespots against attacking fish. We used artificial prey and predator-naive three-spined sticklebacks (Gasterosteus aculeatus) as predators to test both the diversion (deflection) and the intimidation hypothesis. Interestingly, our results showed that eyespots smaller than the fish’ own eye very effectively draw the attacks of the fish towards them. Furthermore, our experiment also showed that this was not due to the conspicuousness of the eyespot, because attack latency did not differ between prey items with and without eyespots. We found little support for an intimidating effect by larger eyespots. Even though also other markings might misdirect attacks, we can conclude that the misdirecting function may have played an important role in the evolution of eyespots in aquatic environments.
The excuse principle can maintain cooperation through forgivable defection in the Prisoner's Dilemma game
Authors: Krams Indrikis , Kokko Hanna , Vrublevska Jolanta , Āboliņš-Ābols Mikus , Krama Tatjana , Rantala Markus J.
Published: July 2013

Reciprocal altruism describes a situation in which an organism acts in a manner that temporarily reduces its fitness while increasing another organism's fitness, but there is an ultimate fitness benefit based on an expectation that the other organism will act in a similar manner at a later time. It creates the obvious dilemma in which there is always a short-term benefit to cheating, therefore cooperating individuals must avoid being exploited by non-cooperating cheaters. This is achieved by following various decision rules, usually variants of the tit-for-tat (TFT) strategy. The strength of TFT, however, is also its weakness—mistakes in implementation or interpretation of moves, or the inability to cooperate, lead to a permanent breakdown in cooperation. We show that pied flycatchers (
Ficedula hypoleuca
) use a TFT with an embedded ‘excuse principle’ to forgive the neighbours that were perceived as unable to cooperate during mobbing of predators. The excuse principle dramatically increases the stability of TFT-like behavioural strategies within the Prisoner's Dilemma game.