bluuebunny/crossref_metadata_2025 huggingface dataset:
Identifying finite-time coherent sets from limited quantities of Lagrangian data
Authors: Williams Matthew O. , Rypina Irina I. , Rowley Clarence W.
Published: July 2015

A data-driven procedure for identifying the dominant transport barriers in a time-varying flow from limited quantities of Lagrangian data is presented. Our approach partitions state space into coherent pairs, which are sets of initial conditions chosen to minimize the number of trajectories that “leak” from one set to the other under the influence of a stochastic flow field during a pre-specified interval in time. In practice, this partition is computed by solving an optimization problem to obtain a pair of functions whose signs determine set membership. From prior experience with synthetic, “data rich” test problems, and conceptually related methods based on approximations of the Perron-Frobenius operator, we observe that the functions of interest typically appear to be smooth. We exploit this property by using the basis sets associated with spectral or “mesh-free” methods, and as a result, our approach has the potential to more accurately approximate these functions given a fixed amount of data. In practice, this could enable better approximations of the coherent pairs in problems with relatively limited quantities of Lagrangian data, which is usually the case with experimental geophysical data. We apply this method to three examples of increasing complexity: The first is the double gyre, the second is the Bickley Jet, and the third is data from numerically simulated drifters in the Sulu Sea.
Intermediate-range chemical ordering of cations in molten RbCl-AgCl
Authors: Tahara S. , Kawakita Y. , Shimakura H. , Ohara K. , Fukami T. , Takeda S.
Published: July 2015

A first sharp diffraction peak (FSDP) is observed in the X-ray total structure factor of a molten mixture of RbCl-AgCl, while both pure melts of RbCl and AgCl do not exhibit FSDP individually. Molecular dynamics simulations were performed to investigate the origin of the FSDP with the polarizable ion model (PIM). Coexistence of covalent Ag–Cl and ionic Rb–Cl bonds leads the system to evolve intermediate range ordering, which is simulated by introducing the induced polarization in different ways between Ag–Cl with fully polarizable treatment based on Vashishta-Raman potential and Rb–Cl with suppression over-polarization in the nearest neighbor contribution based on Born-Meyer potential. The partial structure factors for both the Ag–Ag and Rb–Rb correlations, SAgAg(Q) and SRbRb(Q), show a positive contribution to the FSDP, while SAgRb(Q) for the Ag–Rb correlation exhibits a negative contribution, indicating that Ag and Rb ions are distributed in an alternating manner within the intermediate-range length scale. The origin of the intermediate-range chemical ordering of cations can be ascribed to the preferred direction of the dipole moments of anions in the PIM.
Current-perpendicular-to-the-plane giant magnetoresistance in spin-valves with AgSn alloy spacers
Authors: Read J. C. , Nakatani T. M. , Smith Neil , Choi Y.-S. , York B. R. , Brinkman E. , Childress J. R.
Published: July 2015

We investigate the use of AgSn alloys as the spacer layer in current-perpendicular-to-the-plane magnetoresistance devices. Alloying with Sn increases resistivity but results in a reasonably long (>10 nm) spin-diffusion length, so large magnetoresistance can be achieved with thin AgSn spacers. Compared to Ag thin films, AgSn forms smaller grain sizes, reduced roughness, and exhibits less interdiffusion upon annealing, resulting in decreased interlayer magnetic coupling in exchange biased spin-valves. AgSn also shows improved corrosion resistance compared to Ag, which is advantageous for nanofabrication, including magnetic recording head sensors. Combining a AgSn spacer with Co-based Heusler alloy ferromagnet in an exchange biased, polycrystalline trilayer thinner than 12 nm results in magnetoresistance values up to 15% at room temperature.
Comparison of gate dielectric plasma damage from plasma-enhanced atomic layer deposited and magnetron sputtered TiN metal gates
Authors: Brennan Christopher J. , Neumann Christopher M. , Vitale Steven A.
Published: July 2015

Fully depleted silicon-on-insulator transistors were fabricated using two different metal gate deposition mechanisms to compare plasma damage effects on gate oxide quality. Devices fabricated with both plasma-enhanced atomic-layer-deposited (PE-ALD) TiN gates and magnetron plasma sputtered TiN gates showed very good electrostatics and short-channel characteristics. However, the gate oxide quality was markedly better for PE-ALD TiN. A significant reduction in interface state density was inferred from capacitance-voltage measurements as well as a 1200× reduction in gate leakage current. A high-power magnetron plasma source produces a much higher energetic ion and vacuum ultra-violet (VUV) photon flux to the wafer compared to a low-power inductively coupled PE-ALD source. The ion and VUV photons produce defect states in the bulk of the gate oxide as well as at the oxide-silicon interface, causing higher leakage and potential reliability degradation.
Magnetic flux studies in horizontally cooled elliptical superconducting cavities
Authors: Martinello M. , Checchin M. , Grassellino A. , Crawford A. C. , Melnychuk O. , Romanenko A. , Sergatskov D. A.
Published: July 2015

Previous studies on magnetic flux expulsion as a function of cooldown procedures for elliptical superconducting radio frequency (SRF) niobium cavities showed that when the cavity beam axis is placed parallel to the helium cooling flow and sufficiently large thermal gradients are achieved, all magnetic flux could be expelled and very low residual resistance could be achieved. In this paper, we investigate flux trapping for the case of resonators positioned perpendicularly to the helium cooling flow, which is more representative of how SRF cavities are cooled in accelerators and for different directions of the applied magnetic field surrounding the resonator. We show that different field components have a different impact on the surface resistance, and several parameters have to be considered to fully understand the flux dynamics. A newly discovered phenomenon of concentration of flux lines at the cavity top leading to temperature rise at the cavity equator is presented.
Direct numerical simulation of moderate-Reynolds-number flow past arrays of rotating spheres
Authors: Zhou Qiang , Fan Liang-Shih
Published: July 2015

Direct numerical simulations with an immersed boundary-lattice Boltzmann method are used to investigate the effects of particle rotation on flows past random arrays of mono-disperse spheres at moderate particle Reynolds numbers. This study is an extension of a previous study of the authors [Q. Zhou and L.-S. Fan, “Direct numerical simulation of low-Reynolds-number flow past arrays of rotating spheres,” J. Fluid Mech. 765, 396–423 (2015)] that explored the effects of particle rotation at low particle Reynolds numbers. The results of this study indicate that as the particle Reynolds number increases, the normalized Magnus lift force decreases rapidly when the particle Reynolds number is in the range lower than 50. For the particle Reynolds number greater than 50, the normalized Magnus lift force approaches a constant value that is invariant with solid volume fractions. The proportional dependence of the Magnus lift force on the rotational Reynolds number (based on the angular velocity and the diameter of the spheres) observed at low particle Reynolds numbers does not change in the present study, making the Magnus lift force another possible factor that can significantly affect the overall dynamics of fluid-particle flows other than the drag force. Moreover, it is found that both the normalized drag force and the normalized torque increase with the increase of the particle Reynolds number and the solid volume fraction. Finally, correlations for the drag force, the Magnus lift force, and the torque in random arrays of rotating spheres at arbitrary solids volume fractions, rotational Reynolds numbers, and particle Reynolds numbers are formulated.
Experimental study of the behavior of two laser produced plasmas in air
Authors: Yang Zefeng , Wei Wenfu , Han Jiaxun , Wu Jian , Li Xingwen , Jia Shenli
Published: July 2015

The interactions among two laser ablated Al plasmas and their shock wave fronts (SWFs) induced by double laser pulses in air were studied experimentally. The evolution processes, including the expansion and interaction of the two plasmas and their shocks, were investigated by laser shadowgraphs, schlieren images, and interferograms. Remarkably, the distribution of the compressed air and the laser plasmas during the colliding process was clearly obtained using the Mach-Zehnder interferometer. From the refractive index profiles, typical plasmas density and gas density behind the shock front were estimated as ∼5.2 × 1018 cm−3 and ∼2.4 × 1020 cm−3. A stagnation layer formed by the collision of gas behind the shock front is observed. The SWFs propagated, collided, and reflected with a higher velocity than plasmas. The results indicated that the slower plasma collided at middle, leading to the formation of the soft stagnation.
Fiber composite slices for multiplexed immunoassays
Authors: Kim Jiyun , Bae Sangwook , Song Seowoo , Chung Keumsim , Kwon Sunghoon
Published: July 2015

Fabrication methods for the development of multiplexed immunoassay platforms primarily depend on the individual functionalization of reaction chambers to achieve a heterogeneous reacting substrate composition, which increases the overall manufacturing time and cost. Here, we describe a new type of low-cost fabrication method for a scalable immunoassay platform based on cotton threads. The manufacturing process involves the fabrication of functionalized fibers and the arrangement of these fibers into a bundle; this bundle is then sectioned to make microarray-like particles with a predefined surface architecture. With these sections, composed of heterogeneous thread fragments with different types of antibodies, we demonstrated quantitative and 7-plex immunoassays. We expect that this methodology will prove to be a versatile, low-cost, and highly scalable method for the fabrication of multiplexed bioassay platforms.
Exploring hardness enhancement in superhard tungsten tetraboride-based solid solutions using radial X-ray diffraction
Authors: Xie Miao , Mohammadi Reza , Turner Christopher L. , Kaner Richard B. , Kavner Abby , Tolbert Sarah H.
Published: July 2015

In this work, we explore the hardening mechanisms in WB4-based solid solutions upon addition of Ta, Mn, and Cr using in situ radial X-ray diffraction techniques under non-hydrostatic pressure. By examining the lattice-supported differential strain, we provide insights into the mechanism for hardness increase in binary solid solutions at low dopant concentrations. Speculations on the combined effects of electronic structure and atomic size in ternary WB4 solid solutions containing Ta with Mn or Cr are also included to understand the extremely high hardness of these materials.
Negative bias-and-temperature stress-assisted activation of oxygen-vacancy hole traps in 4H-silicon carbide metal-oxide-semiconductor field-effect transistors
Authors: Ettisserry D. P. , Goldsman N. , Akturk A. , Lelis A. J.
Published: July 2015

We use hybrid-functional density functional theory-based Charge Transition Levels (CTLs) to study the electrical activity of near-interfacial oxygen vacancies located in the oxide side of 4H-Silicon Carbide (4H-SiC) power Metal-Oxide-Semiconductor Field-Effect Transistors (MOSFETs). Based on the “amorphousness” of their local atomic environment, oxygen vacancies are shown to introduce their CTLs either within (permanently electrically active) or outside of (electrically inactive) the 4H-SiC bandgap. The “permanently electrically active” centers are likely to cause threshold voltage (Vth) instability at room temperature. On the other hand, we show that the “electrically inactive” defects could be transformed into various “electrically active” configurations under simultaneous application of negative bias and high temperature stresses. Based on this observation, we present a model for plausible oxygen vacancy defects that could be responsible for the recently observed excessive worsening of Vth instability in 4H-SiC power MOSFETs under high temperature-and-gate bias stress. This model could also explain the recent electrically detected magnetic resonance observations in 4H-SiC MOSFETs.
Generation of a 2.2 nJ picosecond optical pulse with blue-violet wavelength using a GaInN master oscillator power amplifier
Authors: Koda Rintaro , Takiguchi Yoshiro , Kono Shunsuke , Watanabe Hideki , Hanzawa Yasunari , Nakajima Hiroshi , Shiozaki Masaki , Sugawara Nobuhiro , Kuramoto Masaru , Narui Hironobu
Published: July 2015

We report the generation of a picosecond optical pulse with 2.2 nJ pulse energy at blue-violet wavelengths using a GaN-based mode-locked laser diode (MLLD) and a semiconductor optical amplifier (SOA). The picosecond optical pulse generated by MLLD at a frequency of 812 MHz was amplified effectively by SOA. We optimized SOA with a widely flared waveguide structure to generate a high optical pulse energy.
Equivalent ambipolar carrier injection of electrons and holes with Au electrodes in air-stable field effect transistors
Authors: Kanagasekaran Thangavel , Shimotani Hidekazu , Ikeda Susumu , Shang Hui , Kumashiro Ryotaro , Tanigaki Katsumi
Published: July 2015

Carrier injection from Au electrodes to organic thin-film active layers can be greatly improved for both electrons and holes by nano-structural surface control of organic semiconducting thin films using long-chain aliphatic molecules on a SiO2 gate insulator. In this paper, we demonstrate a stark contrast for a 2,5-bis(4-biphenylyl)bithiophene (BP2T) active semiconducting layer grown on a modified SiO2 dielectric gate insulator between two different modifications of tetratetracontane and poly(methyl methacrylate) thin films. Important evidence that the field effect transistor (FET) characteristics are independent of electrode metals with different work functions is given by the observation of a conversion of the metal-semiconductor contact from the Schottky limit to the Bardeen limit. An air-stable light emitting FET with an Au electrode is demonstrated.
The effects of temperature on the lattice barrier for twin wall motion
Authors: Zreihan Noam , Faran Eilon , Shilo Doron
Published: July 2015

The sideways motion of twin walls in ferroic materials requires overcoming an intrinsic energy barrier that originates from the periodicity of the crystal structure. Here, we measure the temperature dependence of the lattice barrier in a ferromagnetic Ni-Mn-Ga crystal using the pulsed magnetic field method. Our results reveal a monotonic decrease in the lattice barrier with increasing temperature. Yet, the barrier does not vanish as the temperature approaches the temperature of the martensite to austenite transformation. These findings enable the formulation of an analytical expression that correlates the lattice barrier to the physical properties of the twin wall, such as its thickness and the associated transformation strain. The derived relation provides a good quantitative description of the data measured in Ni-Mn-Ga.
Enhanced lithium ion storage in nanoimprinted carbon
Authors: Wang Peiqi , Chen Qian Nataly , Xie Shuhong , Liu Xiaoyan , Li Jiangyu
Published: July 2015

Disordered carbons processed from polymers have much higher theoretical capacity as lithium ion battery anode than graphite, but they suffer from large irreversible capacity loss and have poor cyclic performance. Here, a simple process to obtain patterned carbon structure from polyvinylpyrrolidone was demonstrated, combining nanoimprint lithography for patterning and three-step heat treatment process for carbonization. The patterned carbon, without any additional binders or conductive fillers, shows remarkably improved cycling performance as Li-ion battery anode, twice as high as the theoretical value of graphite at 98 cycles. Localized electrochemical strain microscopy reveals the enhanced lithium ion activity at the nanoscale, and the control experiments suggest that the enhancement largely originates from the patterned structure, which improves surface reaction while it helps relieving the internal stress during lithium insertion and extraction. This study provides insight on fabricating patterned carbon architecture by rational design for enhanced electrochemical performance.
Tuning carrier mobility without spin transport degrading in copper-phthalocyanine
Authors: Jiang S. W. , Wang P. , Chen B. B. , Zhou Y. , Ding H. F. , Wu D.
Published: July 2015

We demonstrate more than one order of magnitude of carrier mobility tuning for the copper-phthalocyanine (CuPc) without spin transport degrading in organic spin valve devices. Depending on the preparation conditions, organic spin valves with the CuPc film mobility of 5.78 × 10−3 and 1.11 × 10−4 cm2/V s are obtained for polycrystalline and amorphous CuPc, respectively. Strikingly, the spin diffusion lengths are almost the same regardless of their mobilities that are ∼50 times different, which is in sharp contrast with previous prediction. These findings directly support that the spin relaxation in CuPc is dominated by the spin-orbit coupling.
Splitting of neutral mechanical plane of conformal, multilayer piezoelectric mechanical energy harvester
Authors: Su Yewang , Li Shuang , Li Rui , Dagdeviren Canan
Published: July 2015

Flexible piezoelectric mechanical energy harvesters (MEHs) are of recent interest as an important emerging variant of traditional piezoelectric devices. The design of stacking multilayer MEHs with adhesive in between is an effective way to enhance the magnitude of power generation. Here, we present an analytic model to study the mechanical behavior of the multilayer MEHs based on lead zirconate titanate (PZT) subjected to Euler buckling. Being different from the hypothesis of the plane section for the entire stack, it is found that each polyimide (PI) layer holds plane section of its own, while soft adhesives serve as shear lags. Accordingly, the neutral mechanical plane is split into multiple ones. The deformation is almost the same for each PI layer, as well as PZT arrays, which is very beneficial to avoid the premature failure of devices. The extreme cases and the transition of these cases are all captured quantitatively with a unified analytic model which is verified by the finite element method. A dimensionless parameter is obtained to characterize the degree of the splitting of neutral mechanical plane, which is significant for the design of the multilayer PZT MEHs.
Cesium telluride cathodes for the next generation of high-average current high-brightness photoinjectors
Authors: Filippetto D. , Qian H. , Sannibale F.
Published: July 2015

We report on the performances of a Cs2Te photocathode under extreme conditions of high peak time-dependent accelerating fields, continuous wave operations, and MHz pulse extraction with up to 0.3 mA average current. The measurements, performed in a normal conducting cavity, show extended lifetime and robustness, elucidate the main mechanisms for cathode degradation, and set the required system vacuum performance for compatibility with the operations of a high average power X-ray free electron laser user facility, opening the doors to the next generation of MHz-scale ultrafast scientific instruments.
Change in equilibrium position of misfit dislocations at the GaN/sapphire interface by Si-ion implantation into sapphire—I. Microstructural characterization
Authors: Lee Sung Bo , Ju Jin-Woo , Kim Young-Min , Yoo Seung Jo , Kim Jin-Gyu , Han Heung Nam , Lee Dong Nyung
Published: July 2015

Much research has been done to reduce dislocation densities for the growth of GaN on sapphire, but has paid little attention to the elastic behavior at the GaN/sapphire interface. In this study, we have examined effects of the addition of Si to a sapphire substrate on its elastic property and on the growth of GaN deposit. Si atoms are added to a c-plane sapphire substrate by ion implantation. The ion implantation results in scratches on the surface, and concomitantly, inhomogeneous distribution of Si. The scratch regions contain a higher concentration of Si than other regions of the sapphire substrate surface, high-temperature GaN being poorly grown there. However, high-temperature GaN is normally grown in the other regions. The GaN overlayer in the normally-grown regions is observed to have a lower TD density than the deposit on the bare sapphire substrate (with no Si accommodated). As compared with the film on an untreated, bare sapphire, the cathodoluminescence defect density decreases by 60 % for the GaN layer normally deposited on the Si-ion implanted sapphire. As confirmed by a strain mapping technique by transmission electron microscopy (geometric phase analysis), the addition of Si in the normally deposited regions forms a surface layer in the sapphire elastically more compliant than the GaN overlayer. The results suggest that the layer can largely absorb the misfit strain at the interface, which produces the overlayer with a lower defect density. Our results highlight a direct correlation between threading-dislocation density in GaN deposits and the elastic behavior at the GaN/sapphire interface, opening up a new pathway to reduce threading-dislocation density in GaN deposits.
Photonic crystal cavities with metallic Schottky contacts
Authors: Quiring W. , Al-Hmoud M. , Rai A. , Reuter D. , Wieck A. D. , Zrenner A.
Published: July 2015

We report about the fabrication and analysis of high Q photonic crystal cavities with metallic Schottky-contacts. The structures are based on GaAs n-i membranes with an InGaAs quantum well in the i-region and nanostructured low ohmic metal top-gates. They are designed for photocurrent readout within the cavity and fast electric manipulations. The cavity structures are characterized by photoluminescence and photocurrent spectroscopy under resonant excitation. We find strong cavity resonances in the photocurrent spectra and surprisingly high Q-factors up to 6500. Temperature dependent photocurrent measurements in the region between 4.5 K and 310 K show an exponential enhancement of the photocurrent signal and an external quantum efficiency up to 0.26.
Printable ink holograms
Authors: Zhao Qiancheng , Yetisen Ali K. , Anthony Carl J. , Fowler William R. , Yun Seok Hyun , Butt Haider
Published: July 2015

The development of single-step printable holographic recording techniques can enable applications in rapid data storage, imaging, and bio-sensing. The personalized use of holography is limited due to specialist level of knowledge, time consuming recording techniques, and high-cost equipment. Here, we report a rapid and feasible in-line reflection recording strategy for printing surface holograms consisting of ink using a single pulse of a laser light within seconds. The laser interference pattern and periodicity of surface grating as a function of tilt angle are predicted by computationally and demonstrated experimentally to create 2D linear gratings and three-dimensional (3D) images. We further demonstrate the utility of our approach in creating personalized handwritten signatures and 3D images.
Buckling, bending and penetration response of the Taraxacum officinalae (Dandelions) to macadam loading
Authors: Greene Peter R. , Greene Virginia A.
Published: July 2015

A multi-stemmed, multi-leaved dandelion plant (Taraxacum officinale) can lift an overhead weight of 2–3 N, sustaining this force for 3–4 weeks, which can cause yielding and cracking of a macadam surface. In the present report, Euler buckling theory was applied to experiments on flower stems and leaf stalks of the dandelion plant, allowing an estimate of the internal stresses, strains and Young’s modulus of the plant-tube wall, under unusual loading conditions imposed by overhead weight. Stalk buckling-strength scaled with length L as 1/L2, stalk bending scaled as L3. Young’s modulus for the leaf stalks and flower stems was measured at 3–14 MPa, compressive wall stress at buckling was 0.1–0.2 MPa, being comparable to the cell turgor pressure. Because the dandelion plant is a natural source of latex and grows in a wide variety of climates, one practical application of this work may be using stress to enhance growth rates. Theory and experiments agree with correlation | r | > 0.94 for bending and buckling.
Phytoplankton–bacterial interactions mediate micronutrient colimitation at the coastal Antarctic sea ice edge
Authors: Bertrand Erin M. , McCrow John P. , Moustafa Ahmed , Zheng Hong , McQuaid Jeffrey B. , Delmont Tom O. , Post Anton F. , Sipler Rachel E. , Spackeen Jenna L. , Xu Kai , Bronk Deborah A. , Hutchins David A. , Allen Andrew E.
Published: July 2015

Significance

The coastal Southern Ocean is a critical climate system component and home to high rates of photosynthesis. Here we show that cobalamin (vitamin B12) and iron availability can simultaneously limit phytoplankton growth in late Austral summer coastal Antarctic sea ice edge communities. Unlike other growth-limiting nutrients, the sole cobalamin source is production by bacteria and archaea. By identifying microbial gene expression changes in response to altered micronutrient availability, we describe the molecular underpinnings of limitation by both cobalamin and iron and offer evidence that this limitation is driven by multiple delicately balanced phytoplankton–bacterial interactions. These results support a growing body of research suggesting that relationships between bacteria and phytoplankton are key to understanding controls on marine primary productivity.
SOD1 aggregation in ALS mice shows simplistic test tube behavior
Authors: Lang Lisa , Zetterström Per , Brännström Thomas , Marklund Stefan L. , Danielsson Jens , Oliveberg Mikael
Published: July 2015

Significance

Here, we address the longstanding question to what extent protein fibrillation behavior as measured under simplified conditions in the test tube is transferrable to protein aggregation disease? Somewhat unexpectedly, we find that superoxide dismutase 1 (SOD1) fibrillation in vitro and growth of pathological SOD1 aggregates in transgenic ALS mice are mechanistically indistinguishable: Both processes reveal exponential kinetics and the typical characteristics of fragment-assisted growth. Although this precise agreement between in vitro and in vivo data opens new possibilities for quantitative examination of the molecular mechanism of neural damage at tissue level, it also moves the question about the medical relevance of our existing experimental tools one step farther: to what extent is protein aggregation in overexpressing mice transferable to late-onset human disease?
Between the state and the artist: Representations of femininity and masculinity in the formation of ideas of the nation in Central Asia
Authors: Kudaibergenova Diana T.
Published: July 2015

After the Soviet collapse, the newly independent states of Central Asia found themselves in the process of forming their own national “imagined communities.” This was done to legitimize their existing territorial integrity, their rights to their titular ethnicities, and the position of political elites. This process expressed itself through the creation of particular symbols, myths, and rituals which distinguished the nation but were also used to legitimize the nation's right to exist. The symbolic and ideological construction was influenced by the former Soviet era. For example, symbolically the country was still called Rodina (motherland), but most of the symbols of power were represented by male images, for example, Amir Timur in Uzbekistan or Ablay Khan in Kazakhstan. The tradition of representing power through a male connotation had a long history in Soviet Central Asia. Interestingly, however, some contemporary artists took an alternative view and used feminine images as strong, central symbols of their interpretation of national identity, contesting the official view of nation-building. This paper seeks to trace the development of the feminine and masculine dichotomy of representation by comparing official iconography with works of famous female artists such as Umida Akhmedova from Uzbekistan and Saule Suleimenova and Almagul Menlibayeva from Kazakhstan.
Securitization, history, and identity: some conceptual clarifications and examples from politics of Finnish war history
Authors: Jutila Matti
Published: July 2015

This article shows how we can use the securitization framework to study extreme history politics.Securitizationrefers to a speech act or discursive process in which an actor makes a claim that some referent object, deemed worthy of survival, is existentially threatened. If successful, securitization justifies the use of extraordinary measures to counter the threat. After introducing the concept of securitization in detail, the article presents three ways in which history and securitization can be connected: history can serve as a facilitating condition of securitization; history can be explicitly used to strengthen a securitizing move; or history, or a particular interpretation of it, can be the referent object of securitization. The second half of the article is devoted to a discussion on the role of history in the securitization of national identities. Historical myths are the standard building blocks of national identities; challenging these myths can be presented as threats to the survival of the nation. The article also discusses potential forms of resistance against securitization of history/national identities. Illustrative examples from the political use of WWII history in Finland will be used to show the practical consequences of various conceptual choices.
Rapid and Sensitive Detection of Vibrio alginolyticus by Loop-Mediated Isothermal Amplification Combined with a Lateral Flow Dipstick Targeted to the rpoX Gene
Authors: Plaon Saranya , Longyant Siwaporn , Sithigorngul Paisarn , Chaivisuthangkura Parin
Published: July 2015

Vibrio alginolyticus is a major bacterial pathogen causing disease in marine animals. The present study aimed to develop a loop-mediated isothermal amplification (LAMP) coupled with a lateral flow dipstick (LFD) for rapid and simple visual detection of V. alginolyticus–specific amplicons. The biotin-labeled LAMP amplicons from the targeted portion of a gene encoding rpoS-like sigma factor (rpoX) were generated at 60°C for 1 h and then hybridized with a fluorescein isothiocyanate–labeled probe for 5 min for visual detection with LFD. In pure cultures, the detection limit of the LAMP–LFD technique for V. alginolyticus was 1.8 × 102 CFU/mL while that of PCR was 1.8 × 103 CFU/mL. In spiked whiteleg shrimp samples Penaeus vannamei, the sensitivity for V. alginolyticus detection was 2 × 103 CFU/g (equivalent to 4 CFU per reaction) while PCR was 10 times less sensitive. The LAMP–LFD method for V. alginolyticus correctly identified 21 isolates of V. alginolyticus but did not recognize 23 non-V. alginolyticus Vibrio isolates and 15 non-Vibrio isolates. In summary, this LAMP–LFD method targeted to the rpoX gene is a convenient assay for specific identification of V. alginolyticus with high sensitivity.

Received November 11, 2014; accepted March 29, 2015
Kinetic study of the quenching reaction of singlet oxygen by seven rice bran extracts in ethanol solution. Development of a singlet oxygen absorption capacity (SOAC) assay method
Authors: Mukai Kazuo , Ishikawa Eri , Abe Takumi , Ouchi Aya , Nagaoka Shin-ichi , Murata Kazumasa , Miyazawa Teruo , Nakagawa Kiyotaka
Published: July 2015

Measurements of singlet oxygen (1O2) quenching rates (kQ (S)) and the relative singlet oxygen absorption capacity (SOAC) values were performed for seven rice bran extracts 1–7, which contained different concentrations of antioxidants (AOs) (such as α-, β-, γ-, and δ-tocopherols and -tocotrienols, three carotenoids (lutein, β-carotene, and zeaxanthin), and γ-oryzanol), in ethanol at 35 °C using UV–vis spectrophotometry. The concentrations of four tocopherols and four tocotrienols, three carotenoids, and γ-oryzanol contained in the extracts were determined using HPLC-MS/MS, UV-HPLC, and UV–vis absorption spectroscopy, respectively. Furthermore, comparisons of kQ (S) (Obsd.) values observed for the above extracts 1–7 with the sum of the product { [AO-i]} of the values obtained for each AO-i and the concentration ([AO-i]) of AO-i contained in extracts 1–7 were performed. From the results, it has been ascertained that the SOAC method is applicable to general food extracts to evaluate their 1O2-quenching activity.
On Poincaré extensions of rational maps
Authors: Cabrera Carlos , Makienko Peter , Sienra Guillermo
Published: July 2015

There is a classical extension of Möbius automorphisms of the Riemann sphere into isometries of the hyperbolic space

H

3

\mathbb {H}^3

which is called the Poincaré extension. In this paper, we construct extensions of rational maps on the Riemann sphere over endomorphisms of

H

3

\mathbb {H}^3

exploiting the fact that any holomorphic covering between Riemann surfaces is Möbius for a suitable choice of coordinates. We show that these extensions define conformally natural homomorphisms on suitable subsemigroups of the semigroup of Blaschke maps. We extend the complex multiplication to a product in

H

3

\mathbb {H}^3

that allows us to construct an extension of any given rational map which is right equivariant with respect to the action of

P
S
L
(
2
,

C

)

PSL(2,\mathbb {C})

.
Involvement of the Tyro3 receptor and its intracellular partner Fyn signaling in Schwann cell myelination
Authors: Miyamoto Yuki , Torii Tomohiro , Takada Shuji , Ohno Nobuhiko , Saitoh Yurika , Nakamura Kazuaki , Ito Akihito , Ogata Toru , Terada Nobuo , Tanoue Akito , Yamauchi Junji
Published: July 2015

During early development of the peripheral nervous system, Schwann cell precursors proliferate, migrate, and differentiate into premyelinating Schwann cells. After birth, Schwann cells envelop neuronal axons with myelin sheaths. Although some molecular mechanisms underlying myelination by Schwann cells have been identified, the whole picture remains unclear. Here we show that signaling through Tyro3 receptor tyrosine kinase and its binding partner, Fyn nonreceptor cytoplasmic tyrosine kinase, is involved in myelination by Schwann cells. Impaired formation of myelin segments is observed in Schwann cell neuronal cultures established from Tyro3-knockout mouse dorsal root ganglia (DRG). Indeed, Tyro3-knockout mice exhibit reduced myelin thickness. By affinity chromatography, Fyn was identified as the binding partner of the Tyro3 intracellular domain, and activity of Fyn is down-regulated in Tyro3-knockout mice, suggesting that Tyro3, acting through Fyn, regulates myelination. Ablating Fyn in mice results in reduced myelin thickness. Decreased myelin formation is observed in cultures established from Fyn-knockout mouse DRG. Furthermore, decreased kinase activity levels and altered expression of myelination-associated transcription factors are observed in these knockout mice. These results suggest the involvement of Tyro3 receptor and its binding partner Fyn in Schwann cell myelination. This constitutes a newly recognized receptor-linked signaling mechanism that can control Schwann cell myelination.
MetTailor: dynamic block summary and intensity normalization for robust analysis of mass spectrometry data in metabolomics
Authors: Chen Gengbo , Cui Liang , Teo Guo Shou , Ong Choon Nam , Tan Chuen Seng , Choi Hyungwon
Published: July 2015

Motivation: Accurate cross-sample peak alignment and reliable intensity normalization is a critical step for robust quantitative analysis in untargetted metabolomics since tandem mass spectrometry (MS/MS) is rarely used for compound identification. Therefore shortcomings in the data processing steps can easily introduce false positives due to misalignments and erroneous normalization adjustments in large sample studies.

Results: In this work, we developed a software package MetTailor featuring two novel data preprocessing steps to remedy drawbacks in the existing processing tools. First, we propose a novel dynamic block summarization (DBS) method for correcting misalignments from peak alignment algorithms, which alleviates missing data problem due to misalignments. For the purpose of verifying correct re-alignments, we propose to use the cross-sample consistency in isotopic intensity ratios as a quality metric. Second, we developed a flexible intensity normalization procedure that adjusts normalizing factors against the temporal variations in total ion chromatogram (TIC) along the chromatographic retention time (RT). We first evaluated the DBS algorithm using a curated metabolomics dataset, illustrating that the algorithm identifies misaligned peaks and correctly realigns them with good sensitivity. We next demonstrated the DBS algorithm and the RT-based normalization procedure in a large-scale dataset featuring >100 sera samples in primary Dengue infection study. Although the initial alignment was successful for the majority of peaks, the DBS algorithm still corrected ∼7000 misaligned peaks in this data and many recovered peaks showed consistent isotopic patterns with the peaks they were realigned to. In addition, the RT-based normalization algorithm efficiently removed visible local variations in TIC along the RT, without sacrificing the sensitivity of detecting differentially expressed metabolites.

Availability and implementation: The R package MetTailor is freely available at the SourceForge website http://mettailor.sourceforge.net/.

Contact:  hyung_won_choi@nuhs.edu.sg

Supplementary information:  Supplementary data are available at Bioinformatics online.
FermiKit: assembly-based variant calling for Illumina resequencing data
Authors: Li Heng
Published: July 2015

Summary: FermiKit is a variant calling pipeline for Illumina whole-genome germline data. It de novo assembles short reads and then maps the assembly against a reference genome to call SNPs, short insertions/deletions and structural variations. FermiKit takes about one day to assemble 30-fold human whole-genome data on a modern 16-core server with 85 GB RAM at the peak, and calls variants in half an hour to an accuracy comparable to the current practice. FermiKit assembly is a reduced representation of raw data while retaining most of the original information.

Availability and implementation:  https://github.com/lh3/fermikit

Contact:  hengli@broadinstitute.org
Association of Immune Response to Endothelial Cell Growth Factor With Early Disseminated and Late Manifestations of Lyme Disease but Not Posttreatment Lyme Disease Syndrome
Authors: Tang Kevin S. , Klempner Mark S. , Wormser Gary P. , Marques Adriana R. , Alaedini Armin
Published: July 2015

Endothelial cell growth factor has been recently proposed as a potential autoantigen in manifestations of Lyme disease that are thought to involve immune-mediated mechanisms. Our findings indicate that a humoral immune response to this protein is not associated with posttreatment Lyme disease syndrome.
The Urochloa Foliar Blight and Collar Rot Pathogen Rhizoctonia solani AG-1 IA Emerged in South America Via a Host Shift from Rice
Authors: Chavarro Mesa Edisson , Ceresini Paulo C. , Ramos Molina Lina M. , Pereira Danilo A. S. , Schurt Daniel A. , Vieira José R. , Poloni Nadia M. , McDonald Bruce A.
Published: July 2015

The fungus Rhizoctonia solani anastomosis group (AG)-1 IA emerged in the early 1990s as an important pathogen causing foliar blight and collar rot on pastures of the genus Urochloa (signalgrass) in South America. We tested the hypothesis that this pathogen emerged following a host shift or jump as a result of geographical overlapping of host species. The genetic structure of host and regional populations of R. solani AG-1 IA infecting signalgrass, rice, and soybean in Colombia and Brazil was analyzed using nine microsatellite loci in 350 isolates to measure population differentiation and infer the pathogen reproductive system. Phylogeographical analyses based on the microsatellite loci and on three DNA sequence loci were used to infer historical migration patterns and test hypotheses about the origin of the current pathogen populations. Cross pathogenicity assays were conducted to measure the degree of host specialization in populations sampled from different hosts. The combined analyses indicate that the pathogen populations currently infecting Urochloa in Colombia and Brazil most likely originated from a population that originally infected rice. R. solani AG-1 IA populations infecting Urochloa exhibit a mixed reproductive system including both sexual reproduction and long-distance dispersal of adapted clones, most likely on infected seed. The pathogen population on Urochloa has a genetic structure consistent with a high evolutionary potential and showed evidence for host specialization.
Out of the blue: adaptive visual pigment evolution accompanies Amazon invasion
Authors: Van Nynatten Alexander , Bloom Devin , Chang Belinda S. W. , Lovejoy Nathan R.
Published: July 2015

Incursions of marine water into South America during the Miocene prompted colonization of freshwater habitats by ancestrally marine species and present a unique opportunity to study the molecular evolution of adaptations to varying environments. Freshwater and marine environments are distinct in both spectra and average intensities of available light. Here, we investigate the molecular evolution of rhodopsin, the photosensitive pigment in the eye that activates in response to light, in a clade of South American freshwater anchovies derived from a marine ancestral lineage. Using likelihood-based comparative sequence analyses, we found evidence for positive selection in the rhodopsin of freshwater anchovy lineages at sites known to be important for aspects of rhodopsin function such as spectral tuning. No evidence was found for positive selection in marine lineages, nor in three other genes not involved in vision. Our results suggest that an increased rate of rhodopsin evolution was driven by diversification into freshwater habitats, thereby constituting a rare example of molecular evolution mirroring large-scale palaeogeographic events.
Biomechanics of oral mucosa
Authors: Chen Junning , Ahmad Rohana , Li Wei , Swain Michael , Li Qing
Published: July 2015

The prevalence of prosthodontic treatment has been well recognized, and the need is continuously increasing with the ageing population. While the oral mucosa plays a critical role in the treatment outcome, the associated biomechanics is not yet fully understood. Using the literature available, this paper provides a critical review on four aspects of mucosal biomechanics, including static, dynamic, volumetric and interactive responses, which are interpreted by its elasticity, viscosity/permeability, apparent Poisson's ratio and friction coefficient, respectively. Both empirical studies and numerical models are analysed and compared to gain anatomical and physiological insights. Furthermore, the clinical applications of such biomechanical knowledge on the mucosa are explored to address some critical concerns, including stimuli for tissue remodelling (interstitial hydrostatic pressure), pressure–pain thresholds, tissue displaceability and residual bone resorption. Through this review, the state of the art in mucosal biomechanics and their clinical implications are discussed for future research interests, including clinical applications, computational modelling, design optimization and prosthetic fabrication.
Cell shape regulation through mechanosensory feedback control
Authors: Mohan Krithika , Luo Tianzhi , Robinson Douglas N. , Iglesias Pablo A.
Published: July 2015

Cells undergo controlled changes in morphology in response to intracellular and extracellular signals. These changes require a means for sensing and interpreting the signalling cues, for generating the forces that act on the cell's physical material, and a control system to regulate this process. Experiments on
Dictyostelium
amoebae have shown that force-generating proteins can localize in response to external mechanical perturbations. This mechanosensing, and the ensuing mechanical feedback, plays an important role in minimizing the effect of mechanical disturbances in the course of changes in cell shape, especially during cell division, and likely in other contexts, such as during three-dimensional migration. Owing to the complexity of the feedback system, which couples mechanical and biochemical signals involved in shape regulation, theoretical approaches can guide further investigation by providing insights that are difficult to decipher experimentally. Here, we present a computational model that explains the different mechanosensory and mechanoresponsive behaviours observed in
Dictyostelium
cells. The model features a multiscale description of myosin II bipolar thick filament assembly that includes cooperative and force-dependent myosin–actin binding, and identifies the feedback mechanisms hidden in the observed mechanoresponsive behaviours of
Dictyostelium
cells during micropipette aspiration experiments. These feedbacks provide a mechanistic explanation of cellular retraction and hence cell shape regulation.
On bounded continuous solutions of the archetypal equation with rescaling
Authors: Bogachev Leonid V. , Derfel Gregory , Molchanov Stanislav A.
Published: July 2015

The ‘archetypal’ equation with rescaling is given by

y
(
x
)
=

∬

R

2

y
(
a
(
x
−
b
)
)
μ
(

d

a

,

d

b

)

(

x
∈

R

), where
μ
is a probability measure; equivalently,

y
(
x
)
=

E

{
y
(
α
(
x
−
β
)
)
}

, with random
α
,
β
and

E

denoting expectation. Examples include (i) functional equation

y
(
x
)
=

∑

i

p

i

y
(

a
i

(
x
−

b
i

)
)

; (ii) functional–differential (‘pantograph’) equation

y
′

(
x
)
+
y
(
x
)
=

∑

i

p

i

y
(

a
i

(
x
−

c
i

)
)

(
p

i

>0,

∑

i

p

i

=
1

). Interpreting solutions
y
(
x
) as harmonic functions of the associated Markov chain (
X

n

), we obtain Liouville-type results asserting that any bounded continuous solution is constant. In particular, in the ‘critical’ case

E

{
ln
⁡

|

α

|

}
=
0

such a theorem holds subject to uniform continuity of
y
(
x
); the latter is guaranteed under mild regularity assumptions on
β
, satisfied e.g. for the pantograph equation (ii). For equation (i) with
a

i

=
q

m

i

(

m
i

∈

Z

,

∑
i

p
i

m
i

=
0

), the result can be proved without the uniform continuity assumption. The proofs exploit the iterated equation

y
(
x
)
=

E

{
y
(

X
τ

)
 

|

 

X
0

=
x
}

(with a suitable stopping time
τ
) due to Doob's optional stopping theorem applied to the martingale
y
(
X

n

).
Environmental variability uncovers disruptive effects of species' interactions on population dynamics
Authors: Gudmundson Sara , Eklöf Anna , Wennergren Uno
Published: July 2015

How species respond to changes in environmental variability has been shown for single species, but the question remains whether these results are transferable to species when incorporated in ecological communities. Here, we address this issue by analysing the same species exposed to a range of environmental variabilities when (i) isolated or (ii) embedded in a food web. We find that all species in food webs exposed to temporally uncorrelated environments (white noise) show the same type of dynamics as isolated species, whereas species in food webs exposed to positively autocorrelated environments (red noise) can respond completely differently compared with isolated species. This is owing to species following their equilibrium densities in a positively autocorrelated environment that in turn enables species–species interactions to come into play. Our results give new insights into species' response to environmental variation. They especially highlight the importance of considering both species' interactions and environmental autocorrelation when studying population dynamics in a fluctuating environment.