bluuebunny/crossref_metadata_2025 huggingface dataset:
The effects of turbulence on nanoparticle growth in turbulent reacting jets
Authors: Das Shankhadeep , Garrick Sean C.
Published: October 2010

The effects of turbulence on nanoparticle growth in turbulent reacting flows are studied via a priori analysis of direct numerical simulation data. The formation and growth of titanium dioxide nanoparticles in incompressible planar jets are simulated via gas-phase hydrolysis of titanium tetrachloride. The particle field is captured by utilizing a nodal approach which accounts for nucleation, condensation, and Brownian coagulation. Simulations are performed at a single Reynolds number and two different precursor concentration levels. Instantaneous, filtered, and averaged data are presented to convey the nature of turbulent or unresolved contributions to the growth of nanoparticles. The effects of turbulence on particle dynamics, in the context of both Reynolds-averaged Navier–Stokes simulation and large-eddy simulation, are assessed by comparing the exact, turbulent, and subgrid-scale growth rates. The results show that large particles are produced in the regions away from the jet core, and an increase in the precursor concentration level increases the particle mean diameter. Particles grow faster when the precursor concentration is increased. It is further observed that the growth rate of the particles is higher inside the eddies and it increases as the jet grows. Additionally, the results show that the unresolved small-scale fluctuations can both augment and inhibit particle growth. However the predominant effect is to reduce particle growth. This tendency is increased (in magnitude) as the precursor concentration level is increased.
Different growth rates for catalyst-induced and self-induced GaN nanowires
Authors: Chèze C. , Geelhaar L. , Jenichen B. , Riechert H.
Published: October 2010

The catalyst- and self-induced pathways of GaN nanowire growth by molecular beam epitaxy are compared. The catalyst-induced nanowires elongate faster than the self-induced ones and their growth rate is fully determined by the impinging N rate. The self-induced nanowire growth rate is identical on both Si(111) and Si(001) and approaches the impinging N rate only for the few longest nanowires. This difference is attributed to the presence of the Ni-catalyst which enhances the incorporation of Ga at the nanowire tip while for the self-induced nanowires, growth is limited by the different incorporation rates on the nanowire tip and sidewall facets.
Nonlinear development of two-layer Couette–Poiseuille flow in the presence of surfactant
Authors: Bassom Andrew P. , Blyth M. G. , Papageorgiou D. T.
Published: October 2010

The two-dimensional nonlinear evolution of the interface between two superposed layers of viscous fluid moving in a channel in the presence of an insoluble surfactant is examined. A pair of coupled weakly nonlinear equations is derived describing the interfacial and surfactant dynamics when one of the two fluid layers is very thin in comparison to the other. In contrast to previous work, the dynamics in the thin film are coupled to the dynamics in the thicker layer through a nonlocal integral term. For asymptotically small Reynolds number, the flow in the thicker layer is governed by the Stokes equations. A linearized analysis confirms the linear instability identified by previous workers and it is proven that the film flow is linearly unstable if the undisturbed surfactant concentration exceeds a threshold value. Numerical simulations of the weakly nonlinear equations reveal the existence of finite amplitude traveling-wave solutions. For order one Reynolds number, the flow in the thicker layer is governed by the linearized Navier–Stokes equations. In this case the weakly nonlinear film dynamics are more complex and include the possibility of periodic traveling-waves and chaotic flow.
Study of transparent and nontransparent regimes of implosion in star wire arrays
Authors: Ivanov V. V. , Astanovitskiy A. L. , Papp D. , Chittenden J. P. , Bland S. N. , Jones B. , Altemara S. D.
Published: October 2010

Star wire arrays were used to control the imploding plasma flows and study plasma interpenetration. These arrays consisted of linear “rays” aligned azimuthally and extending from the vertical axis. Star arrays with two close located wires (“gates”) instead of a single wire on the inner cylinder were studied for transparent and nontransparent regimes of propagation of imploding plasma through the gates. Nontransparent mode of collision is typical for regular star wire arrays and it was also observed in Al stars with gate wires of regular length and with the gate width of 0.3–2 mm. The cascade process of implosion in stars and trapping of imploding plasma in 1–2 mm gates were modeled with the three-dimensional resistive magnetohydrodynamics code. The intermediate semitransparent mode of collision was observed in Al stars with long Al “gate” wires. A transparent mode was observed in Al stars with long stainless steel or W gate wires. Applications of wire arrays with controlled plasma flows are discussed.
Reaction mechanism of CO oxidation on Cu2O(111): A density functional study
Authors: Sun Bao-Zhen , Chen Wen-Kai , Xu Yi-Jun
Published: October 2010

The possible reaction mechanisms for CO oxidation on the perfect Cu2O(111) surface have been investigated by performing periodic density functional theoretical calculations. We find that Cu2O(111) is able to facilitate the CO oxidation with different mechanisms. Four possible mechanisms are explored (denoted as MER1, MER2, MLH1, and MLH2, respectively): MER1 is CO(gas)+O2(ads)→CO2(gas); MER2 is CO(gas)+O2(ads)→CO3(ads)→O(ads)+CO2(gas); MLH1 refers to CO(ads)+O2(ads)→O(ads)+CO2(ads); and MLH2 refers to CO(ads)+O2(ads)→OOCO(ads)→O(ads)+CO2(ads). Our transition state calculations clearly reveal that MER1 and MLH2 are both viable; but MER1 mechanism preferentially operates, in which only a moderate energy barrier (60.22 kJ/mol) needs to be overcome. When CO oxidation takes place along MER2 path, it is facile for CO3 formation, but is difficult for its decomposition, thereby CO3 species can stably exist on Cu2O(111). Of course, the reaction of CO with lattice O of Cu2O(111) is also considered. However, the calculated barrier is 600.00 kJ/mol, which is too large to make the path feasible. So, we believe that on Cu2O(111), CO reacts with adsorbed O, rather than lattice O, to form CO2. This is different from the usual Mars–van Krevene mechanism. The present results enrich our understanding of the catalytic oxidation of CO by copper-based and metal-oxide catalysts.
Influence of Mn on the magnetocaloric effect of nanoperm-type alloys
Authors: Caballero-Flores R. , Franco V. , Conde A. , Kiss L. F.
Published: October 2010

In this paper, the influence of the Mn content on the magnetocaloric response of ribbon-shaped amorphous samples of Fe80−xMnxB20 (x=10, 15, 18, 20, and 24), has been studied. For this purpose, the temperature and field dependence of the magnetic entropy change (ΔSM) have been obtained from magnetization curves. The partial substitution of Fe by Mn leads to a monotonous change in the Curie temperature (TC) of the alloys from 438 K for x=10 to 162 K for x=24, in agreement with the coherent-potential approximation. These Curie temperatures could make them good candidates to be used for magnetic refrigeration at room temperature. For an applied field of 1.5 T, the maximum entropy change (ΔSMpk) passes from 1 J K−1 kg−1 (x=10) to 0.5 J K−1 kg−1 (x=24), and the refrigerant capacity varies between 117 J kg−1 (x=10) and 68 J kg−1 (x=24). A linear relationship between ΔSMpk and the average magnetic moment per transition metal atom (⟨μ⟩Fe,Mn) has been presented.
Communication: Conditions for one-photon coherent phase control in isolated and open quantum systems
Authors: Spanner Michael , Arango Carlos A. , Brumer Paul
Published: October 2010

Coherent control of observables using the phase properties of weak light that induces one-photon transitions is considered. Measurable properties are shown to be categorizable as either class A, where control is not possible, or class B, where control is possible. Using formal arguments, we show that phase control in open systems can be environmentally assisted.
Cerenkov radiation in metallic metamaterials
Authors: So Jin-Kyu , Won Jong-Hyo , Sattorov M. A. , Bak Seung-Ho , Jang Kyu-Ha , Park Gun-Sik , Kim D. S. , Garcia-Vidal F. J.
Published: October 2010

The electromagnetic response of a metallic metamaterial to fast-moving electrons is studied by numerical simulations. The considered metamaterial is a one-dimensional array of slits perforated on a metallic film and is found to generate Cerenkov wakes when the electron beam travels near its surface. There is no energy threshold for the generation of such wakes, which would be promising to lower the operation energy of the electron beam in compact Cerenkov free-electron-lasers. Moreover, by analyzing the spectral dependence of the Cerenkov light, it is possible to map the dispersion relation of the guided modes supported by the metamaterial.
Thermoelectric properties of bipolar diffusion effect on In4Se3−xTex compounds
Authors: Rhyee Jong-Soo , Cho Eunseog , Ahn Kyunghan , Lee Kyu Hyoung , Lee Sang Mock
Published: October 2010

We present thermoelectric properties and electronic structure of the series compounds of In4Se3−xTex (0.0≤x≤3.0). Even if the Te-doping is an isoelectronic substitution, we found that the electron dominated carrier transport in Se-rich region (x≤0.2) evolves into the electron-hole bipolar transport properties in Te-rich region (x≥2.5) from the temperature-dependent thermal conductivity κ(T), Seebeck coefficient S(T), and Hall coefficient RH(T) measurements. The electronic band structures of In4Se3−xTex (x=0.0, 2.75, and 3.0) are not changed significantly with respect to Te-substitution concentrations. From the Boltzmann transport calculation, the electron-hole bipolar effect on thermoelectric transport properties in Te-rich region can be understood by lowering the chemical potential to the valence band maximum in the Te-rich compounds.
The possible equilibrium shapes of static pendant drops
Authors: Sumesh P. T. , Govindarajan Rama
Published: October 2010

Analytical and numerical studies are carried out on the shapes of two-dimensional and axisymmetric pendant drops hanging under gravity from a solid surface. Drop shapes with both pinned and equilibrium contact angles are obtained naturally from a single boundary condition in the analytical energy optimization procedure. The numerical procedure also yields optimum energy shapes, satisfying Young’s equation without the explicit imposition of a boundary condition at the plate. It is shown analytically that a static pendant two-dimensional drop can never be longer than 3.42 times the capillary length. A related finding is that a range of existing solutions for long two-dimensional drops correspond to unphysical drop shapes. Therefore, two-dimensional drops of small volume display only one static solution. In contrast, it is known that axisymmetric drops can display multiple solutions for a given volume. We demonstrate numerically that there is no limit to the height of multiple-lobed Kelvin drops, but the total volume is finite, with the volume of successive lobes forming a convergent series. The stability of such drops is in question, though. Drops of small volume can attain large heights. A bifurcation is found within the one-parameter space of Laplacian shapes, with a range of longer drops displaying a minimum in energy in the investigated space. Axisymmetric Kelvin drops exhibit an infinite number of bifurcations.
Effects of back interface trap states on the fully depleted strained-silicon-on-insulator capacitorless single transistor dynamic random access memory cells
Authors: Kim Min-Soo , Cho Won-Ju
Published: October 2010

A series of systematic experiments were carried out to investigate the effects of silicon back interface state density between silicon channel layer and buried oxide layer on the memory characteristics. The back interface states of fully depleted strained-silicon-on-insulator (FD sSOI) substrate were intentionally generated by controlling the temperature of rapid thermal annealing (RTA) process and the amount of back interface trap was evaluated by using the backgated metal-oxide-semiconductor field-effect transistor method. As a result, the trap density of back interface increased with RTA temperature, which causes the degradation of FD sSOI single transistor dynamic random access memory.
Functional calculus via Laplace transform and equations with infinitely many derivatives
Authors: Górka P. , Prado H. , Reyes E. G.
Published: October 2010

We study nonlocal linear equations of the form f(∂t)ϕ=J(t), t≥0, in which f is an entire function. We develop an appropriate functional calculus via Laplace transform, we solve the aforementioned equation completely in the space of exponentially bounded functions, and we analyze the delicate issue of the formulation of initial value problems for nonlocal equations.
Nanowire superconducting single-photon detectors on GaAs for integrated quantum photonic applications
Authors: Gaggero A. , Nejad S. Jahanmiri , Marsili F. , Mattioli F. , Leoni R. , Bitauld D. , Sahin D. , Hamhuis G. J. , Nötzel R. , Sanjines R. , Fiore A.
Published: October 2010

We demonstrate efficient nanowire superconducting single photon detectors (SSPDs) based on NbN thin films grown on GaAs. NbN films ranging from 3 to 5 nm in thickness have been deposited by dc magnetron sputtering on GaAs substrates at 350 °C. These films show superconducting properties comparable to similar films grown on sapphire and MgO. In order to demonstrate the potential for monolithic integration, SSPDs were fabricated and measured on GaAs/AlAs Bragg mirrors, showing a clear cavity enhancement, with a peak quantum efficiency of 18.3% at λ=1300 nm and T=4.2 K.
Mapping emissive channels of quantum dots: Influence of size and environment on energy transfer in the time domain
Authors: Faulques E. , Massuyeau F. , Wang Q. , Seo D.-K. , Jobic S.
Published: October 2010

In the quantum confinement regime, the time-resolved photoluminescence mapping of CdSe nanocrystals reveals unusual size-dependent characteristics in solute or solid-state environments. The former case typifies long-lived intradot exciton recombinations, while in the latter energy-dependent Kohlrausch relaxations quench luminescence via interdot energy transfer. The observed energy transfer rate increases for larger size (1.5×108 s−1 for d=2.5 nm and 6.4×108 s−1 for d=10 nm).
Growth kinetics and compositional analysis of silicon rich a-SiNx:H film: A soft x-ray reflectivity study
Authors: Singh Sarab Preet , Modi Mohammed H. , Srivastava P.
Published: October 2010

We report soft x-ray reflectivity measurements near the Si L2,3 absorption edge for Si-rich silicon nitride thin film obtained by Hg-sensitized photochemical vapor deposition. We demonstrate that the precise analysis of optical index profile derived over extended energy region gives compositional details of the film. This nondestructive approach is used in Si-rich silicon nitride film to reveal buried Si-rich interfacial layer. Further, the combined study of soft x-ray reflectivity and optical density obtained from the reflectivity fitting at various photon energies provide a qualitative estimation of the film composition and its growth.
Indium tin oxide-free and metal-free semitransparent organic solar cells
Authors: Zhou Yinhua , Cheun Hyeunseok , Choi Seungkeun , Potscavage William J. , Fuentes-Hernandez Canek , Kippelen Bernard
Published: October 2010

We report on indium tin oxide (ITO)-free and metal-free semitransparent organic solar cells with a high-conductivity poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) (PH1000) as both the bottom and the top electrodes. The PH1000 film showed a conductivity of 680±50 S/cm. A ZnO layer was used as an interlayer to produce an electron-selective electrode. The semitransparent devices with a structure of glass/PH1000/ZnO/poly(3-hexylthiophene):phenyl-C61-butyric acid methyl ester/PEDOT:PSS (CPP 105 D)/PH1000 exhibited an average power conversion efficiency of 1.8% estimated for 100 mW/cm2 air mass 1.5 global illumination. This geometry alleviates the need of vacuum deposition of a top electrode.
Base metal alloys with self-healing native conductive oxides for electrical contact materials
Authors: Aindow M. , Alpay S. P. , Liu Y. , Mantese J. V. , Senturk B. S.
Published: October 2010

Base metals for electrical contacts exhibit high bulk conductivities but form low-conductivity native oxide scales in air, leading to unacceptably high contact resistances. Here we show that alloying base metals can lead to higher conductivity native scales by: doping to enhance carrier concentration; inducing mixed oxidation states to give electron/polaron hopping; and/or phase separation for conducting pathways. Data from Cu–La, Fe–V, and Ni–Ru alloys demonstrate the viability of these approaches, yielding contact resistances up to 106 times lower than that for oxidized Cu.
Toward an objective evaluation of cell transfection performance
Authors: Orlando Viviana , Pozzi Daniela , Caracciolo Giulio , Augusti-Tocco Gabriella , Biagioni Stefano
Published: October 2010

In this study, we considered the interplay between the efficiency and cytotoxicity of multicomponent cationic liposome/DNA complexes, in cell lines of different origin, as NIH 3T3, HEK 293T, N18TG2, and SK-N-SH. We show that both efficiency and cytotoxicity vary considerably depending on used transfection agents and cells lines. Such variations are largely overcome when transfection is evaluated by a parameter, R, that combines the percentages of transfected, nonviable, and nonadherent cells. These findings provide a strong validation of R as an unbiased indicator for transfection performance across cell lines and transfection agents.
Classification of (n+3)-dimensional metric n-Lie algebras
Authors: Geng Qiaozhi , Ren Mingming , Chen Zhiqi
Published: October 2010

In this paper, we focus on (n+3)-dimensional metric n-Lie algebras. To begin with, we give some properties on (n+3)-dimensional n-Lie algebras. Then based on the properties, we obtain the classification of (n+3)-dimensional metric n-Lie algebras.
First and second-order Raman scattering in Si nanostructures within silicon nitride
Authors: Mercaldo Lucia V. , Esposito Emilia M. , Veneri Paola Delli , Fameli Giuseppe , Mirabella Salvo , Nicotra Giuseppe
Published: October 2010

First and second-order Raman analysis on annealed silicon nitride films is reported. Possible formation of amorphous Si nanoparticles after an intermediate treatment is deduced from the occurrence of a resonant spectrum. After nucleation of Si nanocrystals, with a model description of the first-order spectra it is possible to access information regarding mean radius, size dispersion, and crystalline phase fraction consistent with the fundamental data derived from microscopy. Substantial increase in second to first order intensity ratio is also observed: Enhanced electron–phonon coupling in both amorphous and crystalline Si nanoparticles is suggested.
Sub-Doppler spectroscopy of mixed state levels in CH2
Authors: Chang Chih-Hsuan , Hall Gregory E. , Sears Trevor J.
Published: October 2010

Perturbations in the 716 and 818 mixed singlet/triplet levels of ã A11(0,0,0) methylene, CH2, have been reinvestigated by frequency-modulated laser sub-Doppler saturation spectroscopy. The hyperfine structure was completely resolved for both the predominantly singlet and the predominantly triplet components of these mixed rotational levels using b̃ B11−ã A11 optical transitions near 12 200 cm−1 with megahertz resolution. The mixing coefficients were obtained from the observed hyperfine splittings and a two-level deperturbation model. The analysis also determines the energy separation of the unperturbed zero-order levels and the unperturbed hyperfine splittings for the triplet perturbing levels 615 X̃ B31(0,3,0) and 937 X̃ B31(0,2,0).
Geometrical phase transition on WO3 surface
Authors: Saberi Abbas Ali
Published: October 2010

A topographical study on an ensemble of height profiles obtained from atomic force microscopy techniques on various independently grown samples of tungsten oxide WO3 is presented by using ideas from percolation theory. We find that a continuous “geometrical” phase transition occurs at a certain critical level-height δc below which an infinite island appears. By using the finite-size scaling analysis of three independent percolation observables, i.e., percolation probability, percolation strength, and the mean island-size, we compute some critical exponents which characterize the transition. Our results are compatible with those of long-range correlated percolation. This method can be generalized to a topographical classification of rough surface models.
Binding Energies in Atomic Negative Ions: II
Authors: Hotop H. , Lineberger W. C.
Published: October 2010

This article updates a ten-year-old review of this subject [J. Chem. Phys. Ref. Data 4, 539 (1975)]. A survey of the electron affinity determinations for the elements up to Z=85 is presented, and based upon these data, a set of recommended electron affinities is established. Recent calculations of atomic electron affinities and the major semiempirical methods are discussed and compared with experiment. The experimental methods which yield electron binding energy data are described and intercompared. Fine structure splittings of these ions and excited state term energies are given.
Standard Chemical Thermodynamic Properties of Alkylnaphthalene Isomer Groups
Authors: Alberty Robert A. , Bloomstein Theodore M.
Published: October 2010

The chemical thermodynamic properties of alkylnaphthalene isomer groups for C10H8 and C11H10 in the ideal gas phase have been calculated from 298.15 to 1000 K from tables of Stull, Westrum, and Sinke. In the absence of literature data on all isomers of higher isomer groups, the properties of isomers of C12H12 to C14H16 have been calculated using Benson group values. A new Benson group value for the 1,8-dimethyl steric hindrance has been calculated from recent experimental data. The increments in isomer group properties per carbon atom have been calculated to show the extent to which thermodynamic properties of higher isomer groups may be obtained by linear extrapolation. Equilibrium mole fractions within isomer groups have been calculated for the ideal gas state from 298.15 to 1000 K. Values of C○p, S°, ΔfH°, and ΔfG° are given for all species from C10H8 to C14H16 with energy units of joules for a standard state pressure of 1 bar.
Spontaneous emergence of social influence in online systems
Authors: Onnela Jukka-Pekka , Reed-Tsochas Felix
Published: October 2010

Social influence drives both offline and online human behavior. It pervades cultural markets, and manifests itself in the adoption of scientific and technical innovations as well as the spread of social practices. Prior empirical work on the diffusion of innovations in spatial regions or social networks has largely focused on the spread of one particular technology among a subset of all potential adopters. Here we choose an online context that allows us to study social influence processes by tracking the popularity of a complete set of applications installed by the user population of a social networking site, thus capturing the behavior of all individuals who can influence each other in this context. By extending standard fluctuation scaling methods, we analyze the collective behavior induced by 100 million application installations, and show that two distinct regimes of behavior emerge in the system. Once applications cross a particular threshold of popularity, social influence processes induce highly correlated adoption behavior among the users, which propels some of the applications to extraordinary levels of popularity. Below this threshold, the collective effect of social influence appears to vanish almost entirely, in a manner that has not been observed in the offline world. Our results demonstrate that even when external signals are absent, social influence can spontaneously assume an on–off nature in a digital environment. It remains to be seen whether a similar outcome could be observed in the offline world if equivalent experimental conditions could be replicated.
Cell-permeable Foxp3 protein alleviates autoimmune disease associated with inflammatory bowel disease and allergic airway inflammation
Authors: Choi Je-Min , Shin Jae-Hun , Sohn Myung-Hyun , Harding Martha J. , Park Jong-Hyun , Tobiasova Zuzana , Kim Da-Young , Maher Stephen E. , Chae Wook-Jin , Park Sung-Ho , Lee Chun-Geun , Lee Sang-Kyou , Bothwell Alfred L. M.
Published: October 2010

Foxp3 is a key transcription factor for differentiation and function of regulatory T (Treg) cells that is critical for maintaining immunological self-tolerance. Therefore, increasing Treg function by Foxp3 transduction to regulate an inflammatory immune response is an important goal for the treatment of autoimmune and allergic diseases. Here we have generated a cell-permeable Foxp3 protein by fusion with the unique human HHph-1-PTD (protein transduction domain), examined its regulatory function in T cells, and characterized its therapeutic effect in autoimmune and allergic disease models. HHph-1-Foxp3 was rapidly and effectively transduced into cells within 30 min and conferred suppressor function to CD4+CD25−T cells as well as directly inhibiting T-cell activation and proliferation. Systemic delivery of HHph-1 Foxp3 remarkably inhibited the autoimmune symptoms of scurfy mice and the development of colitis induced by scurfy or wild-type CD4 T cells. Moreover, intranasal delivery of HHph-1-Foxp3 strongly suppressed ovalbumin-induced allergic airway inflammation. These results demonstrate the clinical potential of the cell-permeable recombinant HHph-1-Foxp3 protein in autoimmune and hypersensitive allergic diseases.
Probability landscape of heritable and robust epigenetic state of lysogeny in phage lambda
Authors: Cao Youfang , Lu Hsiao-Mei , Liang Jie
Published: October 2010

Computational studies of biological networks can help to identify components and wirings responsible for observed phenotypes. However, studying stochastic networks controlling many biological processes is challenging. Similar to Schrödinger’s equation in quantum mechanics, the chemical master equation (CME) provides a basic framework for understanding stochastic networks. However, except for simple problems, the CME cannot be solved analytically. Here we use a method called discrete chemical master equation (dCME) to compute directly the full steady-state probability landscape of the lysogeny maintenance network in phage lambda from its CME. Results show that wild-type phage lambda can maintain a constant level of repressor over a wide range of repressor degradation rate and is stable against UV irradiation, ensuring heritability of the lysogenic state. Furthermore, it can switch efficiently to the lytic state once repressor degradation increases past a high threshold by a small amount. We find that beyond bistability and nonlinear dimerization, cooperativity between repressors bound to
O

R

1 and
O

R

2 is required for stable and heritable epigenetic state of lysogeny that can switch efficiently. Mutants of phage lambda lack stability and do not possess a high threshold. Instead, they are leaky and respond to gradual changes in degradation rate. Our computation faithfully reproduces the hair triggers for UV-induced lysis observed in mutants and the limitation in robustness against mutations. The landscape approach computed from dCME is general and can be applied to study broad issues in systems biology.
Monitoring ion-channel function in real time through quantum decoherence
Authors: Hall Liam T. , Hill Charles D. , Cole Jared H. , Städler Brigitte , Caruso Frank , Mulvaney Paul , Wrachtrup Jörg , Hollenberg Lloyd C. L.
Published: October 2010

In drug discovery, there is a clear and urgent need for detection of cell-membrane ion-channel operation with wide-field capability. Existing techniques are generally invasive or require specialized nanostructures. We show that quantum nanotechnology could provide a solution. The nitrogen-vacancy (NV) center in nanodiamond is of great interest as a single-atom quantum probe for nanoscale processes. However, until now nothing was known about the quantum behavior of a NV probe in a complex biological environment. We explore the quantum dynamics of a NV probe in proximity to the ion channel, lipid bilayer, and surrounding aqueous environment. Our theoretical results indicate that real-time detection of ion-channel operation at millisecond resolution is possible by directly monitoring the quantum decoherence of the NV probe. With the potential to scan and scale up to an array-based system, this conclusion may have wide-ranging implications for nanoscale biology and drug discovery.
IL-33 is a crucial amplifier of innate rather than acquired immunity
Authors: Oboki Keisuke , Ohno Tatsukuni , Kajiwara Naoki , Arae Ken , Morita Hideaki , Ishii Akina , Nambu Aya , Abe Takaya , Kiyonari Hiroshi , Matsumoto Kenji , Sudo Katsuko , Okumura Ko , Saito Hirohisa , Nakae Susumu
Published: October 2010

IL-33, a member of the IL-1-related cytokines, is considered to be a proallergic cytokine that is especially involved in Th2-type immune responses. Moreover, like IL-1α, IL-33 has been suggested to act as an “alarmin” that amplifies immune responses during tissue injury. In contrast to IL-1, however, the precise roles of IL-33 in those settings are poorly understood. Using IL-1- and IL-33-deficient mice, we found that IL-1, but not IL-33, played a substantial role in induction of T cell-mediated type IV hypersensitivity such as contact and delayed-type hypersensitivity and autoimmune diseases such as experimental autoimmune encephalomyelitis. Most notably, however, IL-33 was important for innate-type mucosal immunity in the lungs and gut. That is, IL-33 was essential for manifestation of T cell-independent protease allergen-induced airway inflammation as well as OVA-induced allergic topical airway inflammation, without affecting acquisition of antigen-specific memory T cells. IL-33 was significantly involved in the development of dextran-induced colitis accompanied by T cell-independent epithelial cell damage, but not in streptozocin-induced diabetes or Con A-induced hepatitis characterized by T cell-mediated apoptotic tissue destruction. In addition, IL-33-deficient mice showed a substantially diminished LPS-induced systemic inflammatory response. These observations indicate that IL-33 is a crucial amplifier of mucosal and systemic innate, rather than acquired, immune responses.
Nematogalectin, a nematocyst protein with GlyXY and galectin domains, demonstrates nematocyte-specific alternative splicing in
Hydra
Authors: Hwang Jung Shan , Takaku Yasuharu , Momose Tsuyoshi , Adamczyk Patrizia , Özbek Suat , Ikeo Kazuho , Khalturin Konstantin , Hemmrich Georg , Bosch Thomas C. G. , Holstein Thomas W. , David Charles N. , Gojobori Takashi
Published: October 2010

Taxonomically restricted genes or lineage-specific genes contribute to morphological diversification in metazoans and provide unique functions for particular taxa in adapting to specific environments. To understand how such genes arise and participate in morphological evolution, we have investigated a gene called nematogalectin in
Hydra
, which has a structural role in the formation of nematocysts, stinging organelles that are unique to the phylum Cnidaria. Nematogalectin is a 28-kDa protein with an N-terminal GlyXY domain (glycine followed by two hydrophobic amino acids), which can form a collagen triple helix, followed by a galactose-binding lectin domain. Alternative splicing of the nematogalectin transcript allows the gene to encode two proteins, nematogalectin A and nematogalectin B. We demonstrate that expression of nematogalectin A and B is mutually exclusive in different nematocyst types: Desmonemes express nematogalectin B, whereas stenoteles and isorhizas express nematogalectin B early in differentiation, followed by nematogalectin A. Like
Hydra
, the marine hydrozoan
Clytia
also has two nematogalectin transcripts, which are expressed in different nematocyte types. By comparison, anthozoans have only one nematogalectin gene. Gene phylogeny indicates that tandem duplication of nematogalectin B exons gave rise to nematogalectin A before the divergence of Anthozoa and Medusozoa and that nematogalectin A was subsequently lost in Anthozoa. The emergence of nematogalectin A may have played a role in the morphological diversification of nematocysts in the medusozoan lineage.
Pheochromocytoma in rats with multiple endocrine neoplasia (MENX) shares gene expression patterns with human pheochromocytoma
Authors: Molatore Sara , Liyanarachchi Sandya , Irmler Martin , Perren Aurel , Mannelli Massimo , Ercolino Tonino , Beuschlein Felix , Jarzab Barbara , Wloch Jan , Ziaja Jacek , Zoubaa Saida , Neff Frauke , Beckers Johannes , Höfler Heinz , Atkinson Michael J. , Pellegata Natalia S.
Published: October 2010

Pheochromocytomas are rare neoplasias of neural crest origin arising from chromaffin cells of the adrenal medulla and sympathetic ganglia (extra-adrenal pheochromocytoma). Pheochromocytoma that develop in rats homozygous for a loss-of-function mutation in p27Kip1 (MENX syndrome) show a clear progression from hyperplasia to tumor, offering the possibility to gain insight into tumor pathobiology. We compared the gene-expression signatures of both adrenomedullary hyperplasia and pheochromocytoma with normal rat adrenal medulla. Hyperplasia and tumor show very similar transcriptome profiles, indicating early determination of the tumorigenic signature. Overrepresentation of developmentally regulated neural genes was a feature of the rat lesions. Quantitative RT-PCR validated the up-regulation of 11 genes, including some involved in neural development:Cdkn2a,Cdkn2c,Neurod1,Gal,Bmp7, andPhox2a. Overexpression of these genes precedes histological changes in affected adrenal glands. Their presence at early stages of tumorigenesis indicates they are not acquired during progression and may be a result of the lack of functional p27Kip1. Adrenal and extra-adrenal pheochromocytoma development clearly follows diverged molecular pathways in MENX rats. To correlate these findings to human pheochromocytoma, we studied nine genes overexpressed in the rat lesions in 46 sporadic and familial human pheochromocytomas. The expression ofGAL,DGKH,BMP7,PHOX2A,L1CAM,TCTE1,EBF3,SOX4, andHASH1was up-regulated, although with different frequencies. Immunohistochemical staining detected high L1CAM expression selectively in 27 human pheochromocytomas but not in 140 nonchromaffin neuroendocrine tumors. These studies reveal clues to the molecular pathways involved in rat and human pheochromocytoma and identify previously unexplored biomarkers for clinical use.
Global demographic trends and future carbon emissions
Authors: O'Neill Brian C. , Dalton Michael , Fuchs Regina , Jiang Leiwen , Pachauri Shonali , Zigova Katarina
Published: October 2010

Substantial changes in population size, age structure, and urbanization are expected in many parts of the world this century. Although such changes can affect energy use and greenhouse gas emissions, emissions scenario analyses have either left them out or treated them in a fragmentary or overly simplified manner. We carry out a comprehensive assessment of the implications of demographic change for global emissions of carbon dioxide. Using an energy–economic growth model that accounts for a range of demographic dynamics, we show that slowing population growth could provide 16–29% of the emissions reductions suggested to be necessary by 2050 to avoid dangerous climate change. We also find that aging and urbanization can substantially influence emissions in particular world regions.
Unfolding free energy of a two-domain transmembrane sugar transport protein
Authors: Findlay Heather E. , Rutherford Nicholas G. , Henderson Peter J. F. , Booth Paula J.
Published: October 2010

Understanding how an amino acid sequence folds into a functional, three-dimensional structure has proved to be a formidable challenge in biological research, especially for transmembrane proteins with multiple alpha helical domains. Mechanistic folding studies on helical membrane proteins have been limited to unusually stable, single domain proteins such as bacteriorhodopsin. Here, we extend such work to flexible, multidomain proteins and one of the most widespread membrane transporter families, the major facilitator superfamily, thus showing that more complex membrane proteins can be successfully refolded to recover native substrate binding. We determine the unfolding free energy of the two-domain,
Escherichia coli
galactose transporter, GalP; a bacterial homologue of human glucose transporters. GalP is reversibly unfolded by urea. Urea causes loss of substrate binding and a significant reduction in alpha helical content. Full recovery of helical structure and substrate binding occurs in dodecylmaltoside micelles, and the unfolding free energy can be determined. A linear dependence of this free energy on urea concentration allows the free energy of unfolding in the absence of urea to be determined as +2.5 kcal·mol
-1
. Urea has often been found to be a poor denaturant for transmembrane helical structures. We attribute the denaturation of GalP helices by urea to the dynamic nature of the transporter structure allowing denaturant access via the substrate binding pocket, as well as to helical structure that extends beyond the membrane. This study gives insight into the final, critical folding step involving recovery of ligand binding for a multidomain membrane transporter.
Bayesian model of dynamic image stabilization in the visual system
Authors: Burak Yoram , Rokni Uri , Meister Markus , Sompolinsky Haim
Published: October 2010

Humans can resolve the fine details of visual stimuli although the image projected on the retina is constantly drifting relative to the photoreceptor array. Here we demonstrate that the brain must take this drift into account when performing high acuity visual tasks. Further, we propose a decoding strategy for interpreting the spikes emitted by the retina, which takes into account the ambiguity caused by retinal noise and the unknown trajectory of the projected image on the retina. A main difficulty, addressed in our proposal, is the exponentially large number of possible stimuli, which renders the ideal Bayesian solution to the problem computationally intractable. In contrast, the strategy that we propose suggests a realistic implementation in the visual cortex. The implementation involves two populations of cells, one that tracks the position of the image and another that represents a stabilized estimate of the image itself. Spikes from the retina are dynamically routed to the two populations and are interpreted in a probabilistic manner. We consider the architecture of neural circuitry that could implement this strategy and its performance under measured statistics of human fixational eye motion. A salient prediction is that in high acuity tasks, fixed features within the visual scene are beneficial because they provide information about the drifting position of the image. Therefore, complete elimination of peripheral features in the visual scene should degrade performance on high acuity tasks involving very small stimuli.
Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors
Authors: Benson Andrew K. , Kelly Scott A. , Legge Ryan , Ma Fangrui , Low Soo Jen , Kim Jaehyoung , Zhang Min , Oh Phaik Lyn , Nehrenberg Derrick , Hua Kunjie , Kachman Stephen D. , Moriyama Etsuko N. , Walter Jens , Peterson Daniel A. , Pomp Daniel
Published: October 2010

In vertebrates, including humans, individuals harbor gut microbial communities whose species composition and relative proportions of dominant microbial groups are tremendously varied. Although external and stochastic factors clearly contribute to the individuality of the microbiota, the fundamental principles dictating how environmental factors and host genetic factors combine to shape this complex ecosystem are largely unknown and require systematic study. Here we examined factors that affect microbiota composition in a large (
n
= 645) mouse advanced intercross line originating from a cross between C57BL/6J and an ICR-derived outbred line (HR). Quantitative pyrosequencing of the microbiota defined a core measurable microbiota (CMM) of 64 conserved taxonomic groups that varied quantitatively across most animals in the population. Although some of this variation can be explained by litter and cohort effects, individual host genotype had a measurable contribution. Testing of the CMM abundances for cosegregation with 530 fully informative SNP markers identified 18 host quantitative trait loci (QTL) that show significant or suggestive genome-wide linkage with relative abundances of specific microbial taxa. These QTL affect microbiota composition in three ways; some loci control individual microbial species, some control groups of related taxa, and some have putative pleiotropic effects on groups of distantly related organisms. These data provide clear evidence for the importance of host genetic control in shaping individual microbiome diversity in mammals, a key step toward understanding the factors that govern the assemblages of gut microbiota associated with complex diseases.
Invasive honeysuckle eradication reduces tick-borne disease risk by altering host dynamics
Authors: Allan Brian F. , Dutra Humberto P. , Goessling Lisa S. , Barnett Kirk , Chase Jonathan M. , Marquis Robert J. , Pang Genevieve , Storch Gregory A. , Thach Robert E. , Orrock John L.
Published: October 2010

Despite the ubiquity of invasive organisms and their often deleterious effects on native flora and fauna, the consequences of biological invasions for human health and the ecological mechanisms through which they occur are rarely considered. Here we demonstrate that a widespread invasive shrub in North America, Amur honeysuckle (
Lonicera maackii
), increases human risk of exposure to ehrlichiosis, an emerging infectious disease caused by bacterial pathogens transmitted by the lone star tick (
Amblyomma americanum
). Using large-scale observational surveys in natural areas across the St. Louis, Missouri region, we found that white-tailed deer (
Odocoileus virginianus)
, a preeminent tick host and pathogen reservoir, more frequently used areas invaded by honeysuckle. This habitat preference translated into considerably greater numbers of ticks infected with pathogens in honeysuckle-invaded areas relative to adjacent honeysuckle-uninvaded areas. We confirmed this biotic mechanism using an experimental removal of honeysuckle, which caused a decrease in deer activity and infected tick numbers, as well as a proportional shift in the blood meals of ticks away from deer. We conclude that disease risk is likely to be reduced when honeysuckle is eradicated, and suggest that management of biological invasions may help ameliorate the burden of vector-borne diseases on human health.
Ecosystem-specific selection pressures revealed through comparative population genomics
Authors: Coleman Maureen L. , Chisholm Sallie W.
Published: October 2010

Bacterial populations harbor vast genetic diversity that is continually shaped by abiotic and biotic selective pressures, as well as by neutral processes. Individuals coexisting in the same geographically defined population often have significantly different gene content, but whether this variation is largely adaptive or neutral remains poorly understood. Here we quantify heterogeneity in gene content for two model marine microbes,ProchlorococcusandPelagibacter, within and between populations in the Atlantic and Pacific Oceans, to begin to understand the selective pressures that are shaping these “population genomes.” We discovered a large fraction of genes that are rare in each population, reflecting continual gene transfer and loss. Despite this high variation within each population, only a few genes significantly differ in abundance between the two biogeochemically distinct environments; nearly all of these are related to phosphorus acquisition and are enriched in the Atlantic relative to the Pacific. Moreover, P-related genes from the two sites form phylogenetically distinct clusters, whereas housekeeping genes do not, consistent with a recent spread of adaptive P-related genes in the Atlantic populations. These findings implicate phosphorus availability as the dominant selective force driving divergence between these populations, and demonstrate the promise of this approach for revealing selective agents in more complex microbial systems.
Initiation of the proton pump of cytochrome
c
oxidase
Authors: Belevich Ilya , Gorbikova Elena , Belevich Nikolai P. , Rauhamäki Virve , Wikström Mårten , Verkhovsky Michael I.
Published: October 2010

Cytochrome
c
oxidase is the terminal enzyme of the respiratory chain that is responsible for biological energy conversion in mitochondria and aerobic bacteria. The membrane-bound enzyme converts free energy from oxygen reduction to an electrochemical proton gradient by functioning as a redox-coupled proton pump. Although the 3D structure and functional studies have revealed proton conducting pathways in the enzyme interior, the location of proton donor and acceptor groups are not fully identified. We show here by time-resolved optical and FTIR spectroscopy combined with time-resolved electrometry that some mutant enzymes incapable of proton pumping nevertheless initiate catalysis by proton transfer to a proton-loading site. A conserved tyrosine in the so-called D-channel is identified as a potential proton donor that determines the efficiency of this reaction.
β-Adrenergic–regulated phosphorylation of the skeletal muscle CaV1.1 channel in the fight-or-flight response
Authors: Emrick Michelle A. , Sadilek Martin , Konoki Keiichi , Catterall William A.
Published: October 2010

CaV1 channels initiate excitation–contraction coupling in skeletal and cardiac muscle. During the fight-or-flight response, epinephrine released by the adrenal medulla and norepinephrine released from sympathetic nerves increase muscle contractility by activation of the β-adrenergic receptor/cAMP-dependent protein kinase pathway and up-regulation of CaV1 channels in skeletal and cardiac muscle. Although the physiological mechanism of this pathway is well defined, the molecular mechanism and the sites of protein phosphorylation required for CaV1 channel regulation are unknown. To identify the regulatory sites of phosphorylation under physiologically relevant conditions, CaV1.1 channels were purified from skeletal muscle and sites of phosphorylation on the α1 subunit were identified by mass spectrometry. Two phosphorylation sites were identified in the proximal C-terminal domain, serine 1575 (S1575) and threonine 1579 (T1579), which are conserved in cardiac CaV1.2 channels (S1700 and T1704, respectively). In vitro phosphorylation revealed that CaV1.1-S1575 is a substrate for both cAMP-dependent protein kinase and calcium/calmodulin-dependent protein kinase II, whereas CaV1.1-T1579 is a substrate for casein kinase 2. Treatment of rabbits with isoproterenol to activate β-adrenergic receptors increased phosphorylation of S1575 in skeletal muscle CaV1.1 channels in vivo, and treatment with propranolol to inhibit β-adrenergic receptors reduced phosphorylation. As S1575 and T1579 in CaV1.1 channels and their homologs in CaV1.2 channels are located at a key regulatory interface between the distal and proximal C-terminal domains, it is likely that phosphorylation of these sites in skeletal and cardiac muscle is directly involved in calcium channel regulation in response to the sympathetic nervous system in the fight-or-flight response.