bluuebunny/crossref_metadata_2025 huggingface dataset:
Localized optical resonances in low refractive index rolled-up microtube cavity for liquid-core optofluidic detection
Authors: Bolaños Quiñones Vladimir A. , Ma Libo , Li Shilong , Jorgensen Matthew , Kiravittaya Suwit , Schmidt Oliver G.
Published: October 2012

Spatially localized high order axial resonant modes are observed in a SiO/SiO2-based microtube cavity rolled-up from a prestrained nanomembrane. A diameter variation of the tube structure is revealed which provides localized axial confinement. Optofluidic detection is demonstrated by filling the tube core with salt solution and subsequently detecting the shifts of spectral mode positions and axial mode spacings. A sensing methodology is proposed by monitoring axial mode spacing changes.
Poole Frenkel current and Schottky emission in SiN gate dielectric in AlGaN/GaN metal insulator semiconductor heterostructure field effect transistors
Authors: Hanna Mina J. , Zhao Han , Lee Jack C.
Published: October 2012

We analyze the anomalous I-V behavior in SiN prepared by plasma enhanced chemical vapor deposition for use as a gate insulator in AlGaN/GaN metal insulator semiconductor heterostructure filed effect transistors (HFETs). We observe leakage current across the dielectric with opposite polarity with respect to the applied electric field once the voltage sweep reaches a level below a determined threshold. This is observed as the absolute minimum of the leakage current does not occur at minimum voltage level (0 V) but occurs earlier in the sweep interval. Curve-fitting analysis suggests that the charge-transport mechanism in this region is Poole-Frenkel current, followed by Schottky emission due to band bending. Despite the current anomaly, the sample devices have shown a notable reduction of leakage current of over 2 to 6 order of magnitudes compared to the standard Schottky HFET. We show that higher pressures and higher silane concentrations produce better films manifesting less trapping. This conforms to our results that we reported in earlier publications. We found that higher chamber pressure achieves higher sheet carrier concentration that was found to be strongly dependent on the trapped space charge at the SiN/GaN interface. This would suggest that a lower chamber pressure induces more trap states into the SiN/GaN interface.
Using the fringing electric field in microfluidic volume sensors to enhance sensitivity and accuracy
Authors: Riordon Jason , M.-Catafard Nicolas , Godin Michel
Published: October 2012

The particle trajectory above impedance-monitoring coplanar electrodes in a microfluidic channel dramatically influences the measured electric current change. We use finite element modeling to predict changes in ionic current for microspheres flowing in highly fringing fields, and validate these results by introducing a buoyancy-based particle focusing technique. Using 6 μm polystyrene particles in solutions of varying density, we control the height of the particle trajectories near the sensing electrodes and show that sensitivity can be increased by up to 3.5× when particles flow close to the electrodes compared to particles flowing further away, while simultaneously improving accuracy.
Influence of V/III growth flux ratio on trap states in m-plane GaN grown by ammonia-based molecular beam epitaxy
Authors: Zhang Z. , Hurni C. A. , Arehart A. R. , Speck J. S. , Ringel S. A.
Published: October 2012

Deep level transient spectroscopy (DLTS) and deep level optical spectroscopy (DLOS) were utilized to investigate the behavior of deep states in m-plane, n-type GaN grown by ammonia-based molecular beam epitaxy (NH3-MBE) as a function of systematically varied V/III growth flux ratios. Levels were detected at EC − 0.14 eV, EC − 0.21 eV, EC − 0.26 eV, EC − 0.62 eV, EC − 0.67 eV, EC − 2.65 eV, and EC − 3.31 eV, with the concentrations of several traps exhibiting systematic dependencies on V/III ratio. The DLTS spectra are dominated by traps at EC − 0.14 eV and EC − 0.67 eV, whose concentrations decreased monotonically with increasing V/III ratio and decreasing oxygen impurity concentration, and by a trap at EC − 0.21 eV that revealed no dependence of its concentration on growth conditions, suggestive of different physical origins. Higher concentrations of deeper trap states detected by DLOS with activation energies of EC − 2.65 eV and EC − 3.31 eV in each sample did not display measureable sensitivity to the intentionally varied V/III ratio, necessitating further study on reducing these deep traps through growth optimization for maximizing material quality of NH3-MBE grown m-plane GaN.
Ground state terahertz quantum cascade lasers
Authors: Chan Chun Wang I. , Hu Qing , Reno John L.
Published: October 2012

A terahertz quantum cascade laser (THz QCL) architecture is presented in which only the ground state subbands of each quantum well are involved in the transport and lasing transition. Compared to state-of-the art THz QCLs based on the resonant-phonon scheme, ground state QCLs employ narrower wells so that all high-energy subbands are pushed up far above the occupied subband levels, significantly reducing parasitic interactions. Data on the experimental realization of two types of ground state QCLs are presented, in which the result of lasing above 5 THz is demonstrated.
Observation of polyamorphism in the phase change alloy Ge1Sb2Te4
Authors: Kalkan B. , Sen S. , Cho J.-Y. , Joo Y.-C. , Clark S. M.
Published: October 2012

A high-pressure synchrotron x-ray diffraction study of the phase change alloy Ge1Sb2Te4 demonstrates the existence of a polyamorphic phase transition between the “as deposited” low density amorphous (LDA) phase and a high density amorphous (HDA) phase at ∼10 GPa. The entropy of the HDA phase is expected to be higher than that of the LDA phase resulting in a negative Clapeyron slope for this transition. These phase relations may enable the polyamorphic transition to play a role in the memory and data storage applications.
Strain effects and band parameters in MgO, ZnO, and CdO
Authors: Yan Qimin , Rinke Patrick , Winkelnkemper Momme , Qteish Abdallah , Bimberg Dieter , Scheffler Matthias , Van de Walle Chris G.
Published: October 2012

We have derived consistent sets of band parameters (bandgaps, crystal-field splittings, effective masses, Luttinger, and EP parameters) and strain deformation potentials for MgO, ZnO, and CdO in the wurtzite phase. To overcome the limitations of density-functional theory in the local-density and generalized gradient approximations, we employ a hybrid functional as well as exact-exchange-based quasiparticle energy calculations in the G0W0 approach. We demonstrate that the band and strain parameters derived in this fashion are in very good agreement with the available experimental data and provide predictions for all parameters that have not been determined experimentally so far.
Development of pulsed laser deposition for CdS/CdTe thin film solar cells
Authors: Li Bing , Liu Jianwei , Xu Guowei , Lu Rongtao , Feng Lianghuan , Wu Judy
Published: October 2012

This work explores in situ fabrication of thin film CdS (100 nm)/CdTe (1.5 μm) solar cells using pulsed laser deposition (PLD). Optimization of the PLD processing conditions, including laser energy density, substrate temperature, and the PLD chamber pressure, was achieved with respect to pinhole-free CdS and CdTe layers and solar power conversion efficiency. High efficiency up to 6.68% has been demonstrated and better performance is anticipated with optimization of the PLD process.
Hall effect measurements on InAs nanowires
Authors: Blömers Ch. , Grap T. , Lepsa M. I. , Moers J. , Trellenkamp St. , Grützmacher D. , Lüth H. , Schäpers Th.
Published: October 2012

We have processed Hall contacts on InAs nanowires grown by molecular beam epitaxy using an electron beam lithography process with an extremely high alignment accuracy. The carrier concentrations determined from the Hall effect measurements on these nanowires are lower by a factor of about 4 in comparison with those measured by the common field-effect technique. The results are used to evaluate quantitatively the charging effect of the interface and surface states.
A graphene field-effect capacitor sensor in electrolyte
Authors: Chen Si , Zhang Zhi-Bin , Ma Laipeng , Ahlberg Patrik , Gao Xindong , Qiu Zhijun , Wu Dongping , Ren Wencai , Cheng Hui-Ming , Zhang Shi-Li
Published: October 2012

The unique electronic properties of graphene are exploited for field-effect sensing in both capacitor and transistor modes when operating the sensor device in electrolyte. The device is fabricated using large-area graphene thin films prepared by means of layer-by-layer stacking. Although essentially the same device, its operation in the capacitor mode is found to yield more information than in the transistor mode. The capacitor sensor can simultaneously detect the variations of surface potential and electrical-double-layer capacitance at the graphene/electrolyte interface when altering the ion concentration. The capacitor-mode operation further facilitates studies of the molecular binding-adsorption kinetics by monitoring the capacitance transient.
Plasma transport induced by kinetic Alfvén wave turbulence
Authors: Izutsu T. , Hasegawa H. , Nakamura T. K. M. , Fujimoto M.
Published: October 2012

At the Earth's magnetopause that separates the hot-tenuous magnetospheric plasma from the cold dense solar wind plasma, often seen is a boundary layer where plasmas of both origins coexist. Plasma diffusions of various forms have been considered as the cause of this plasma mixing. Here, we investigate the plasma transport induced by wave-particle interaction in kinetic Alfvén wave (KAW) turbulence, which is one of the candidate processes. We clarify that the physical origin of the KAW-induced cross-field diffusion is the drift motions of those particles that are in Cerenkov resonance with the wave: E×B-like drift that emerges in the presence of non-zero parallel electric field component and grad-B drift due to compressional magnetic fluctuations. We find that KAW turbulence, which has a spectral breakpoint at which an MHD inertial range transits to a dissipation range, causes selective transport for particles whose parallel velocities are specified by the local Alfvén velocity and the parallel phase velocity at the spectral breakpoint. This finding leads us to propose a new data analysis method for identifying whether or not a mixed plasma in the boundary layer is a consequence of KAW-induced transport across the magnetopause. The method refers to the velocity space distribution function data obtained by a spacecraft that performs in situ observations and, in principle, is applicable to currently available dataset such as that provided by the NASA's THEMIS mission.
A semiconductor under insulator technology in indium phosphide
Authors: Mnaymneh K. , Dalacu D. , Frédérick S. , Lapointe J. , Poole P. J. , Williams R. L.
Published: October 2012

This letter introduces a semiconductor-under-insulator (SUI) technology in InP for designing strip waveguides that interface InP photonic crystal membrane structures. Strip waveguides in InP-SUI are supported under an atomic layer deposited insulator layer in contrast to strip waveguides in silicon supported on insulator. We show a substantial improvement in optical transmission when using InP-SUI strip waveguides interfaced with localized photonic crystal membrane structures when compared with extended photonic crystal waveguide membranes. Furthermore, SUI makes available various fiber-coupling techniques used in SOI, such as sub-micron coupling, for planar membrane III-V systems.
Expression and inheritance of perenniality and other qualitative traits in hybrids between mungbean cultivars and Australian wild accessions
Authors: Nguyen Thuan D. , Lawn R. J. , Bielig L. M.
Published: October 2012

The expression and inheritance of several qualitative traits was examined in four cultivated × wild hybrid populations involving each of two mungbean (Vigna radiata ssp. radiata) cultivars, cvv. Berken and Kiloga, and each of two Australian accessions of the wild subspecies (V. radiata ssp. sublobata). One of the wild accessions, ACC 1, was representative of a prostrate, fine-stemmed, gracile type and the other, ACC 87, was representative of a more robust perennial form endemic in north-eastern Australia. For each of the four cultivated × wild populations, trait expression was observed in plants from the parent, F1, F2, and the two F1–parental backcross generations, when grown under favourable conditions in large pots on benches in the field at CSIRO Davies Laboratory, Townsville, Australia. Models of inheritance were inferred based on the segregation patterns in the different generations of the cultivated v. wild phenotypes. For most traits, the model of inheritance depended more on the wild than the cultivated parent, with more traits in the crosses involving ACC 1 being digenic than in those involving ACC 87. For all the observed morphological and seed traits, the wild phenotype was dominant, consistent with the cultivated phenotype having arisen through mutations that inhibited expression of the wild type. In contrast, the apparent resistance of the wild parents to field strains of powdery mildew disease was recessive to the strong susceptibility of the two cultivars. The segregation patterns for presence or absence of tuberous roots were remarkably similar in the two crosses involving the perennial accession ACC 87, and were consistent with the formation of tuberous roots being conditioned by two complementary, dominant genes. The fact that an apparently complex trait like perenniality might be conditioned by so few genes suggested that perenniality may also be an ancestral wild trait, disruption of which has led to the now more common, annual form. Linkage analyses suggested that perenniality was associated with the wild-type seed traits, black speckled testa and pigmented hilum, which previous molecular studies have indicated are both located on mungbean linkage group 2.
Effects of treatment with human chorionic gonadotrophin or intravaginal progesterone-releasing device after AI on circulating progesterone concentrations in lactating dairy cows
Authors: Nascimento A. B. , Souza A. H. , Guenther J. N. , Costa F. P. Dalla , Sartori R. , Wiltbank M. C.
Published: October 2012

Adequate circulating progesterone (P4) is important for pregnancy. Lactating dairy cattle have lower circulating P4, particularly when smaller follicles are ovulated during timed AI protocols. The aim of the present study was to determine the supplementation strategy that resulted in P4 concentrations in lactating dairy cattle similar to those in heifers. Lactating Holstein cows (n = 61) were synchronised using the Double-Ovsynch method and, on Day 5, were randomly assigned to receive no treatment (control), controlled internal drug release (CIDR), human chorionic gonadotrophin (hCG; 3300 IU) or CIDR+hCG. Heifers after normal oestrus were followed as controls (n = 10). Profiles of circulating P4 concentrations were compared using repeated-measures ANOVA. Heifers had greater P4 concentrations than control cows at all times after Day 5 (P < 0.0001). Cows receiving CIDR had lower P4 concentrations than heifers (P = 0.0037) on Days 8–16. Treatment with hCG generally caused ovulation and resulted in circulating P4 concentrations greater than those in control lactating cows by 3 days after treatment (Day 8 after AI), but the treatment × time interaction (P = 0.01) showed that cows treated with hCG generally had lower P4 concentrations than heifers. Supplementation with CIDR+hCG resulted in P4 concentration profiles similar to those in heifers. Thus, the use of CIDR and the production of an accessory corpus luteum with hCG elevates P4 concentrations in lactating cows to those seen in heifers. This information may be useful for designing future trials into P4 supplementation and fertility.
A direct benefit of native saltbush revegetation for an endemic lizard (Tiliqua rugosa) in southern Australia
Authors: Lancaster Melanie L. , Gardner Michael G. , Fitch Alison J. , Ansari Talat H. , Smyth Anita K.
Published: October 2012

Land alteration for intensive agriculture has been a major cause of species decline and extinction globally. In marginal grazing regions of southern Australia, native perennial shrubs are increasingly being planted to supplement pasture feeding of stock. Such revegetation has the benefits of reducing erosion and salinity, and importantly, the potential provision of habitat for native fauna. We explored the use of revegetated native saltbush by the sleepy lizard (Tiliqua rugosa) an endemic Australian species common in the region. We repeatedly sampled revegetated saltbush throughout 2010 and 2011 for adults (n = 55) and juveniles (n = 26). Using genotypes from eight microsatellite loci, parents were assigned to half of all juveniles with high statistical confidence. Parents were sampled in the same patch of revegetated saltbush as their offspring, thus supporting the observation that juvenile sleepy lizards remain within the home range of their parents before dispersal. Most importantly, our findings indicate that revegetated saltbush provides important habitat for T. rugosa at significant life stages – before and during breeding for adults, and before dispersal for juveniles. We conclude that revegetation using simple, monoculture plantations provides beneficial habitat for T. rugosa and may also be beneficial habitat for other native species in human-altered agricultural landscapes.
Interpersonal coordination tendencies supporting the creation/prevention of goal scoring opportunities in futsal
Authors: Vilar LuÍs , Araújo Duarte , Davids Keith , Travassos Bruno , Duarte Ricardo , Parreira João
Published: October 2012

Research on 1vs1 sub‐phases in team sports has shown how one player coordinates his/her actions with his/her opponent and the location of a target/goal to attain performance objectives. In this study, we extended this approach to analysis of 5vs5 competitive performance in the team sport of futsal to provide a performance analysis framework that explains how players coordinate their actions to create/prevent opportunities to score goals. For this purpose, we recorded all 10 futsal matches of the 2009 Lusophony Games held in Lisbon. We analysed the displacement trajectories of a shooting attacker and marking defender in plays ending in a goal, a goalkeeper's save, and a defender's interception, at four specific moments during performance: (1) assisting attacker's ball reception and (2) moment of passing, (3) shooter's ball reception, and (4), shot on goal. Statistical analysis showed that when a goal was scored, the defender's angle to the goal and to the attacker tended to decrease, the attacker was able to move to the same distance to the goal alongside the defender, and the attacker was closer to the defender and moving at the same velocity (at least) as the defender. This study identified emergent patterns of coordination between attackers and defenders under key competitive task constraints, such as the location of the goal, which supported successful performance in futsal.
FAST HOLOGRAPHIC DECONVOLUTION: A NEW TECHNIQUE FOR PRECISION RADIO INTERFEROMETRY
Authors: Sullivan I. S. , Morales M. F. , Hazelton B. J. , Arcus W. , Barnes D. , Bernardi G. , Briggs F. H. , Bowman J. D. , Bunton J. D. , Cappallo R. J. , Corey B. E. , Deshpande A. , deSouza L. , Emrich D. , Gaensler B. M. , Goeke R. , Greenhill L. J. , Herne D. , Hewitt J. N. , Johnston-Hollitt M. , Kaplan D. L. , Kasper J. C. , Kincaid B. B. , Koenig R. , Kratzenberg E. , Lonsdale C. J. , Lynch M. J. , McWhirter S. R. , Mitchell D. A. , Morgan E. , Oberoi D. , Ord S. M. , Pathikulangara J. , Prabu T. , Remillard R. A. , Rogers A. E. E. , Roshi A. , Salah J. E. , Sault R. J. , Shankar N. Udaya , Srivani K. S. , Stevens J. , Subrahmanyan R. , Tingay S. J. , Wayth R. B. , Waterson M. , Webster R. L. , Whitney A. R. , Williams A. , Williams C. L. , Wyithe J. S. B.
Published: October 2012

We introduce the Fast Holographic Deconvolution method for analyzing interferometric radio data. Our new method is an extension of A-projection/software-holography/forward modeling analysis techniques and shares their precision deconvolution and wide-field polarimetry, while being significantly faster than current implementations that use full direction-dependent antenna gains. Using data from the MWA 32 antenna prototype, we demonstrate the effectiveness and precision of our new algorithm. Fast Holographic Deconvolution may be particularly important for upcoming 21 cm cosmology observations of the Epoch of Reionization and Dark Energy where foreground subtraction is intimately related to the precision of the data reduction.
Evidence for the electrolysis of water by atmospheric-pressure plasmas formed at the surface of aqueous solutions
Authors: Witzke Megan , Rumbach Paul , Go David B , Sankaran R Mohan
Published: October 2012

The formation of atmospheric-pressure plasmas with liquid electrodes holds great importance for a number of emerging technologies and applications, yet fundamental questions remain about the nature of the interactions at the plasma/liquid interface. In particular, when the liquid serves as the anode, the plasma supplies gas-phase electrons to the liquid surface, and how these electrons interact with the liquid has not been fully explained. In this work, we present experimental evidence that in the case of water, plasma electrons are involved in electrolytic reactions leading to the conversion of protons (H+) to hydrogen gas. Reactions associated with water electrolysis are indirectly characterized by pH measurements that show qualitatively and quantitatively that the liquid at the plasma interface increases in basicity, consistent with the reduction of protons by plasma electrons. Mass spectrometry measurements confirm the evolution of hydrogen gas, directly providing evidence of water electrolysis. This work highlights the critical role that plasma electrons can play in plasma/liquid interactions with broad implications for any plasma system involving an aqueous electrode, including emerging applications in plasma medicine and plasma–liquid materials synthesis.
Reactivity of inorganic nanoparticles in biological environments: insights into nanotoxicity mechanisms
Authors: Casals E , Gonzalez E , Puntes V F
Published: October 2012

A deeper understanding of the behaviour of inorganic nanoparticles in biological media is needed not only to fully control and develop the potential of these materials but also to increase knowledge of the physical chemistry of inorganic materials when their morphology approaches that of molecular entities. Although this knowledge and control is not yet entirely acquired, industry and society are already using nanomaterials in greater quantities and in consumer products. As normally happens when something new arrives in society, the interest in the broader implications of this emerging technology has grown together with unfounded ‘nanoeuphoria’ and ‘nanoscares’. In this context, only by understanding the mechanisms of the nano–bio interaction will it be possible to safely develop nanotechnology. In this review, we discuss on how nanoparticles behave once they are naturally or intentionally produced and are exposed to humans and the environment. The response of nanoparticles inside organisms or released to the environment is complex and diverse, and depends on a variety of parameters involved. Mainly, they may (i) be aggregated into microscopic particles or embedded in exposed materials; (ii) the surfaces of the nanoparticles, which determine their bioactivity, experience constant modifications; and (iii) nanoparticles may corrode and dissolve or they can suffer morphological modifications.
Stress-induced state transitions in flexible liquid-crystal devices
Authors: Ho I-Lin , Chang Yia-Chung
Published: October 2012

This work studies the stress–strain dynamics for the transient optoelectronic characteristics of flexible liquid-crystal (LC) devices. Due to the fast response of LC directors, the configuration of the LC is assumed to be in quasi-equilibrium during the process of elastic deformations of the flexible structures. The LC medium hence can be treated effectively as a thin-film layer and can approximately follow the strain–stress mechanism in the solids. Relevant theoretical algorithms are studied in this work, and numerical results present the stress-induced state transitions in the π cell.
Structural, optical and electrical properties of spray-deposited CZTS thin films under a non-equilibrium growth condition
Authors: Patel M , Mukhopadhyay I , Ray A
Published: October 2012

Spray pyrolysed thin films of quaternary Cu2ZnSnS4 (CZTS) were successfully deposited on soda lime glass substrates at 320 °C under a non-equilibrium condition (by varying Zn, Sn and S precursor concentrations) and without additional sulfurization. The effect of deficiency and enrichment of these three elements (normalized with respect to Cu) on the film's microstrain, optical band-gap and Hall mobility was investigated. A large non-uniform microstrain of (5–6) × 10−3 and compressive nature were observed for both Zn- and Sn-enriched films from Williamson–Hall analysis of x-ray diffraction (XRD) data. However, a tensile strain of (2–3) × 10−3 was revealed in Sn-poor and S-rich samples. The optical band-gap (E
g) in stoichiometric CZTS was found to be 1.45 eV and Hall mobility (μ
H) in the range 87–92 cm2 V−1 s−1 was observed for S- and Zn-enriched films. The tensile nature of microstrain and inhomogeneities in E
g and μ
H were observed with greater magnitude due to the existence of other secondary phases, which were confirmed complementarily by FTIR spectroscopy and XRD.
An electromagnetically induced transparency metamaterial with polarization insensitivity based on multi-quasi-dark modes
Authors: Zhu Lei , Meng Fan-Yi , Fu Jia-Hui , Wu Qun
Published: October 2012

To investigate the polarization and angle insensitive mechanism of an electromagnetically induced transparency (EIT) metamaterial, we designed, fabricated and measured a planar symmetry metamaterial structure. The planar symmetry metamaterial's cell consists of eight identical inner rings surrounded by a bigger outer ring, which serve as multi-quasi-dark elements and a bright element, respectively. A polarization and angle insensitive transparency window is clearly observed in the spectrum owing to the coupling between the multi-quasi-dark modes and the bright mode, which is verified by numerical simulations and experiments. A wider angle consistency is achieved because the multi-quasi-dark modes commonly participate in the destructive interference of scattering field. In addition, the excited principle and the resonance nature of EIT-like effects are investigated numerically. Simulation results show that the EIT-like effect is associated with the anti-symmetry current, which is induced by coupling fields introducing the phase delay. Finally, the slow wave property of the metamaterial is verified by numerical simulation.
Wound healing modeling: investigating ambient gas plasma treatment efficacy
Authors: Orazov Marat , Sakiyama Yukinori , Graves David B
Published: October 2012

Chronic wounds are thought to be caused, in part, by the presence and persistence of aerobic microbes that deplete the local oxygen concentration and prevent or slow the rate of oxygen-dependent healing. Atmospheric-pressure gas plasmas have been shown to be strong bactericidal agents and there is evidence that plasma treatment can safely kill bacteria in wounds and speed wound healing. In this study, we adapted a six-species reaction–diffusion model of epithelial wound healing and used it to predict the efficacy of various plasma treatment protocols. We assume that the only effect of plasma application to the wound is to reduce the bacterial load and that this in turn reduces the bacterial oxygen consumption in the wound. The model follows the spatial and temporal concentration or density profiles within the wound of oxygen, chemoattractants, capillary sprouts, blood vessels, fibroblasts and extracellular matrix material. We highlight the importance of the effects of plasma application on the rate of bacterial regrowth in the wound. Even a relatively large initial reduction in the bacterial wound population may not be sufficient for improved healing if bacterial regrowth is not limited. Although it is clear that current efforts to model wound healing in general and the effects of plasma in particular are in their early stage, the present results suggest several important directions for coupling plasma models with models of tissue biochemical responses.
Carbon dioxide enhances fragility of ice crystals
Authors: Qin Zhao , Buehler Markus J
Published: October 2012

Ice caps and glaciers cover 7% of the Earth, greater than the land area of Europe and North America combined, and play an important role in global climate. The small-scale failure mechanisms of ice fracture, however, remain largely elusive. In particular, little understanding exists about how the presence and concentration of carbon dioxide molecules, a significant component in the atmosphere, affects the propensity of ice to fracture. Here we use atomic simulations with the first-principles based ReaxFF force field capable of describing the details of chemical reactions at the tip of a crack, applied to investigate the effects of the presence of carbon dioxide molecules on ice fracture. Our result shows that increasing concentrations of carbon dioxide molecules significantly decrease the fracture toughness of the ice crystal, making it more fragile. Using enhanced molecular sampling with metadynamics we reconstruct the free energy landscape in varied chemical microenvironments and find that carbon dioxide molecules affect the bonds between water molecules at the crack tip and decrease their strength by altering the dissociation energy of hydrogen bonds. In the context of glacier dynamics our findings may provide a novel viewpoint that could aid in understanding the breakdown and melting of glaciers, suggesting that the chemical composition of the atmosphere can be critical to mediate the large-scale motion of large volumes of ice.
Positron annihilation studies on the behaviour of vacancies in LaAlO3/SrTiO3 heterostructures
Authors: Yuan Guoliang , Li Chen , Yin Jiang , Liu Zhiguo , Wu Di , Uedono Akira
Published: October 2012

The formation and diffusion of vacancies are studied in LaAlO3/SrTiO3 heterostructures. Oxygen vacancies (V
OS) appear easily in the SrTiO3 substrate during LaAlO3 film growth at 700 °C and 10−4 Pa oxygen pressure rather than at 10−3–10−1 Pa, thus the latter two-dimensional electron gas should come from the polarity discontinuity at the (LaO)+/(TiO2)0 interface. For SrTiO3−δ
/LaAlO3/SrTiO3, high-density V
OS of the SrTiO3−δ
film can pass through the LaAlO3 film and then diffuse to 1.7 µm depth in the SrTiO3 substrate, suggesting that LaAlO3 has V
OS at its middle-deep energy levels within the band gap. Moreover, high-density V
OS may combine with a strontium/titanium vacancy (V
Sr/Ti) to form V
Sr/Ti–O complexes in the SrTiO3 substrate at 700 °C.
Representations of metaplectic groups II: Hecke algebra correspondences
Authors: Gan Wee , Savin Gordan
Published: October 2012

The metaplectic group is defined by its oscillator or Weil representation. Using the types of the Weil representations we define two Hecke algebras that govern two Bernstein’s components containing the even and the odd Weil representation, respectively.
Human Cdc14A regulates Wee1 stability by counteracting CDK-mediated phosphorylation
Authors: Ovejero Sara , Ayala Patricia , Bueno Avelino , Sacristán María P.
Published: October 2012

The activity of Cdk1–cyclin B1 mitotic complexes is regulated by the balance between the counteracting activities of Wee1/Myt1 kinases and Cdc25 phosphatases. These kinases and phosphatases must be strictly regulated to ensure proper mitotic timing. One masterpiece of this regulatory network is Cdk1, which promotes Cdc25 activity and suppresses inhibitory Wee1/Myt1 kinases through direct phosphorylation. The Cdk1-dependent phosphorylation of Wee1 primes phosphorylation by additional kinases such as Plk1, triggering Wee1 degradation at the onset of mitosis. Here we report that Cdc14A plays an important role in the regulation of Wee1 stability. Depletion of Cdc14A results in a significant reduction in Wee1 protein levels. Cdc14A binds to Wee1 at its amino-terminal domain and reverses CDK-mediated Wee1 phosphorylation. In particular, we found that Cdc14A inhibits Wee1 degradation through the dephosphorylation of Ser-123 and Ser-139 residues. Thus the lack of phosphorylation of these two residues prevents the interaction with Plk1 and the consequent efficient Wee1 degradation at the onset of mitosis. These data support the hypothesis that Cdc14A counteracts Cdk1–cyclin B1 activity through Wee1 dephosphorylation.
Evidence for Functional Diversification Within a Fungal NEP1-Like Protein Family
Authors: Santhanam Parthasarathy , van Esse H. Peter , Albert Isabell , Faino Luigi , Nürnberger Thorsten , Thomma Bart P. H. J.
Published: October 2012

In this study, we functionally analyzed the gene family encoding necrosis- and ethylene-inducing-like proteins (NLP) of the vascular wilt pathogen Verticillium dahliae. We show that the composition of the NLP gene family varies little among V. dahliae isolates. The cytotoxic activity of NLP family members of a tomato-pathogenic V. dahliae strain was determined, demonstrating that only two of the seven NLP induced plant cell death. The genes encoding these cytotoxic NLP were found to be induced in V. dahliae upon colonization of tomato. Interestingly, targeted deletion of either of the two genes in V. dahliae significantly compromised virulence on tomato as well as on Arabidopsis plants, whereas deletion of only one of the two genes affected virulence on Nicotiana benthamiana. This could be attributed to differential induction of the two NLP genes in V. dahliae upon N. benthamiana colonization, revealing that the in planta induction of NLP genes varies between plant hosts. Intriguingly, one of the NLP genes appears to also affect vegetative growth and conidiospore production, because the corresponding deletion strain produced significantly fewer conidiospores and developed extensive aerial mycelium. In conclusion, we demonstrate that the expanded V. dahliae NLP family shows functional diversification, revealing not only differential cytotoxicity between family members but also that the cytotoxic NLP play a role in vegetative growth and asexual reproduction in addition to their contribution to virulence.
The buckling of capillaries in solid tumours
Authors: MacLaurin James , Chapman Jon , Jones Gareth Wyn , Roose Tiina
Published: October 2012

We develop a model of the buckling (both planar and axial) of capillaries in cancer tumours, using nonlinear solid mechanics. The compressive stress in the tumour interstitium is modelled as a consequence of the rapid proliferation of the tumour cells, using a multiplicative decomposition of the deformation gradient. In turn, the tumour cell proliferation is determined by the oxygen concentration (which is governed by the diffusion equation) and the solid stress. We apply a linear stability analysis to determine the onset of mechanical instability, and the Liapunov–Schmidt reduction to determine the postbuckling behaviour. We find that planar modes usually go unstable before axial modes, so that our model can explain the buckling of capillaries, but not as easily their tortuosity. We also find that the inclusion of anisotropic growth in our model can substantially affect the onset of buckling. Anisotropic growth also results in a feedback effect that substantially affects the magnitude of the buckle.
Noni Juice Improves Serum Lipid Profiles and Other Risk Markers in Cigarette Smokers
Authors: Wang Mian-Ying , Peng Lin , Weidenbacher-Hoper Vicki , Deng Shixin , Anderson Gary , West Brett J.
Published: October 2012

Cigarette smoke-induced oxidative stress leads to dyslipidemia and systemic inflammation.Morinda citrifolia(noni) fruit juice has been found previously to have a significant antioxidant activity. One hundred thirty-two adult heavy smokers completed a randomized, double blind, placebo-controlled clinical trial designed to investigate the effect of noni juice on serum cholesterol, triglyceride, low density lipoprotein cholesterol (LDL), high density lipoprotein cholesterol (HDL), high-sensitivity C-reactive protein (hs-CRP), and homocysteine. Volunteers drank noni juice or a fruit juice placebo daily for one month. Drinking 29.5 mL to 188 mL of noni juice per day significantly reduced cholesterol levels, triglycerides, and hs-CRP. Decreases in LDL and homocysteine, as well increases in HDL, were also observed among noni juice drinkers. The placebo, which was devoid of iridoid glycosides, did not significantly influence blood lipid profiles or hs-CRP. Noni juice was able to mitigate cigarette smoke-induced dyslipidemia, an activity associated with the presence of iridoids.
SmartGrain: High-Throughput Phenotyping Software for Measuring Seed Shape through Image Analysis
Authors: Tanabata Takanari , Shibaya Taeko , Hori Kiyosumi , Ebana Kaworu , Yano Masahiro
Published: October 2012

Seed shape and size are among the most important agronomic traits because they affect yield and market price. To obtain accurate seed size data, a large number of measurements are needed because there is little difference in size among seeds from one plant. To promote genetic analysis and selection for seed shape in plant breeding, efficient, reliable, high-throughput seed phenotyping methods are required. We developed SmartGrain software for high-throughput measurement of seed shape. This software uses a new image analysis method to reduce the time taken in the preparation of seeds and in image capture. Outlines of seeds are automatically recognized from digital images, and several shape parameters, such as seed length, width, area, and perimeter length, are calculated. To validate the software, we performed a quantitative trait locus (QTL) analysis for rice (Oryza sativa) seed shape using backcrossed inbred lines derived from a cross between japonica cultivars Koshihikari and Nipponbare, which showed small differences in seed shape. SmartGrain removed areas of awns and pedicels automatically, and several QTLs were detected for six shape parameters. The allelic effect of a QTL for seed length detected on chromosome 11 was confirmed in advanced backcross progeny; the cv Nipponbare allele increased seed length and, thus, seed weight. High-throughput measurement with SmartGrain reduced sampling error and made it possible to distinguish between lines with small differences in seed shape. SmartGrain could accurately recognize seed not only of rice but also of several other species, including Arabidopsis (Arabidopsis thaliana). The software is free to researchers.
Fungal palaeodiversity revealed using high‐throughput metabarcoding of ancient DNA from arctic permafrost
Authors: Bellemain Eva , Davey Marie L. , Kauserud Håvard , Epp Laura S. , Boessenkool Sanne , Coissac Eric , Geml Jozsef , Edwards Mary , Willerslev Eske , Gussarova Galina , Taberlet Pierre , Brochmann Christian
Published: October 2012

The taxonomic and ecological diversity of ancient fungal communities was assessed by combining next generation sequencing and metabarcoding of DNA preserved in permafrost. Twenty‐six sediment samples dated 16 000–32 000 radiocarbon years old from two localities in Siberia were analysed for fungal ITS. We detected 75 fungal OTUs from 21 orders representing three phyla, although rarefaction analyses suggested that the full diversity was not recovered despite generating an average of 6677 ± 3811 (mean ± SD) sequences per sample and that preservation bias likely has considerable effect on the recovered DNA. Most OTUs (75.4%) represented ascomycetes. Due to insufficient sequencing depth, DNA degradation and putative preservation biases in our samples, the recovered taxa probably do not represent the complete historic fungal community, and it is difficult to determine whether the fungal communities varied geographically or experienced a composition shift within the period of 16 000–32 000 bp. However, annotation of OTUs to functional ecological groups provided a wealth of information on the historic communities. About one‐third of the OTUs are presumed plant‐associates (pathogens, saprotrophs and endophytes) typical of graminoid‐ and forb‐rich habitats. We also detected putative insect pathogens, coprophiles and keratinophiles likely associated with ancient insect and herbivore faunas. The detection of putative insect pathogens, mycoparasites, aquatic fungi and endophytes broadens our previous knowledge of the diversity of fungi present in Beringian palaeoecosystems. A large group of putatively psychrophilic/psychrotolerant fungi was also detected, most likely representing a modern, metabolically active fungal community.
Farm‐by‐farm analysis of microsatellite, mtDNA and SNP genotype data reveals inbreeding and crossbreeding as threats to the survival of a native Spanish pig breed
Authors: Herrero‐Medrano J. M. , Megens H. J. , Crooijmans R. P. , Abellaneda J. M. , Ramis G.
Published: October 2012

The Chato Murciano (CM), a pig breed from the Murcia region in the southeastern region of Spain, is a good model for endangered livestock populations. The remaining populations are bred on approximately 15 small farms, and no herdbook exists. To assess the genetic threats to the integrity and survival of the CM breed, and to aid in designing a conservation program, three genetic marker systems – microsatellites, SNPs and mtDNA – were applied across the majority of the total breeding stock. In addition, mtDNA and SNPs were genotyped in breeds that likely contributed genetically to the current CM gene pool. The analyses revealed the levels of genetic diversity within the range of other European local breeds (He = 0.53). However, when the eight farms that rear at least 10 CM pigs were independently analyzed, high levels of inbreeding were found in some. Despite the evidence for recent crossbreeding with commercial breeds on a few farms, the entire breeding stock remains readily identifiable as CM, facilitating the design of traceability assays. The genetic management of the breed is consistent with farm size, farm owner and presence of other pig breeds on the farm, demonstrating the highly ad hoc nature of current CM breeding. The results of genetic diversity and substructure of the entire breed, as well as admixture and crossbreeding obtained in the present study, provide a benchmark to develop future conservation strategies. Furthermore, this study demonstrates that identifying farm‐based practices and farm‐based breeding stocks can aid in the design of a sustainable breeding program for minority breeds.
Assessing the Relationship Between Cervical Ectopy and HIV Susceptibility: Implications for HIV Prevention in Women
Authors: Venkatesh Kartik K. , Cu‐Uvin Susan
Published: October 2012

Cervical ectopy, which occurs when the columnar epithelium of the endocervical canal extends outwards into the ectocervix, has been suggested to increase the susceptibility to HIV infection in at‐risk women. This study summarizes observational studies, primarily conducted in sub‐Saharan Africa, that have assessed a possible causative association between cervical ectopy and HIV acquisition and also examines the biological plausibility as well as other cofactors that may mediate this association. Only about half of the studies reviewed found cervical ectopy to be a significant risk factor for HIV acquisition. The reasons for these divergent results still remain to be fully elucidated. Understanding biological factors that affect HIV susceptibility provide opportunities to identify prevention strategies to reduce the risk of HIV acquisition.
Protein tyrosine phosphatase SHP2 regulates TGF‐β1 production in airway epithelia and asthmatic airway remodeling in mice
Authors: Qin X.‐J. , Zhang G.‐S. , Zhang X. , Qiu Z.‐W. , Wang P.‐L. , Li Y.‐W. , Li W. , Xie Q.‐M. , Ke Y.‐H. , Lee J. J , Shen H.‐H.
Published: October 2012

Background

Transforming growth factor (TGF)‐β1 produced in airway epithelia has been suggested as a contributor to the airway remodeling observed in asthma patients. The protein tyrosine phosphatase SHP2 is a demonstrable modulator of TGF‐β1 production and thus a potential regulator of airway remodeling.

Objectives

To define the signal event by which SHP2 regulates asthmatic responses in airway epithelial cells by using a mouse model of experimental OVA‐induced airway remodeling.

Methods

The airways of Shp2flox/flox mice were infected with recombinant adenovirus vectors expressing a Cre recombinase–green fluorescence protein (GFP) fusion protein as part of allergen provocation studies using mice sensitized with ovalbumin (OVA) and repeatedly challenged with OVA. Several endpoint pathologies were assessed, including airway hyper‐responsiveness (AHR), lung inflammatory score, peribronchial collagen deposition, and α‐smooth muscle actin (SMA) hyperplasia. In vitro studies using airway epithelial cells (BEAS‐2B) were used to investigate the role of SHP2 in the regulation of pulmonary remodeling events, including the expression of collagen, α‐SMA, and TGF‐β1.

Results

Chronic OVA challenges in wild‐type mice resulted in airway remodeling and lung dysfunction (e.g., increased inflammatory scores, collagen deposition (fibrosis), smooth muscle hyperplasia, and a significant increase in AHR). These endpoint pathology metrics were each significantly attenuated by conditional shp2 gene knockdown in airway epithelia. In vitro studies using BEAS‐2B cells also demonstrated that the level of TGF‐β1 production by these cells correlated with the extent of shp2 gene expression.

Conclusions

SHP2 activities in airway epithelial cells appear to modulate TGF‐β1 production and, in turn, regulate allergic airway remodeling following allergen provocation.

Clinical Implications

Our findings identify SHP2 as a previously underappreciated contributor to the airway remodeling and lung dysfunction associated with allergen challenge. As such, SHP2 represents a potentially novel therapeutic target for the treatment of asthmatics.

Capsule summary

Airway epithelial protein tyrosine phosphatase SHP2 appears to modulate TGF‐β1 activities as part of one or more cellular pathways leading to regulating the airway remodeling and lung dysfunction occurring in mouse models of allergic respiratory inflammation.
Ovarian failure in HAX1‐deficient patients: is there a gender‐specific difference in pubertal development in severe congenital neutropenia or Kostmann disease?
Authors: Carlsson Göran , Kriström Berit , Nordenskj˶ld Magnus , Henter Jan‐Inge , Fadeel Bengt
Published: October 2012

Aim

Severe congenital neutropenia (SCN) is a rare disorder of myelopoiesis characterized by neutropenia, recurrent bacterial infections and a maturation arrest of the myelopoiesis in the bone marrow. Homozygous mutations in the HAX1 gene were described in patients with autosomal recessive SCN or Kostmann disease. Some of these patients display neurological disease. We noted, during the course of clinical management of patients with Kostmann disease, insufficient pubertal development in female patients, but not in our male patients. The study objective was to provide a detailed account of this phenotype and its possible relation to HAX1 mutations.

Methods

Detailed clinical histories and laboratory investigations of three patients with Kostmann disease belonging to the original kindred in northern Sweden described by Rolf Kostmann are reported.

Results

We report one male patient with normal puberty and two female patients with insufficient pubertal development. Elevated levels of LH and FSH were recorded in both patients. All three patients harbour the same p.Glu190X mutation in the HAX1 gene.

Conclusions

We show for the first time that female patients with Kostmann disease display primary gonadal insufficiency. This suggests a possible role for HAX1 in the development and/or function of the human ovary.