bluuebunny/crossref_metadata_2025 huggingface dataset:
Propagation management methods have altered the genetic variability of two traditional mango varieties in Myanmar, as revealed by SSR
Authors: Hirano R. , Ishii H. , Htun Oo Than , Gilani S. A. , Kikuchi A. , Watanabe K. N.
Published: February 2011

Mango (Mangifera indica L.) is an important fruit crop with a long cultivation history in Myanmar. This study evaluated the genetic variation within two economically important traditional varieties, ‘Yin Kwe’ and ‘Sein Ta Lone’, and the relationship between genetic variation and propagation practices. Genetic variation was estimated by genotyping 94 individuals with 12 single sequence repeat markers. ‘Yin Kwe’ (n = 53) showed higher levels of observed heterozygosity (Ho = 0.59) and average genetic distance among individuals (Da = 0.29) than did ‘Sein Ta Lone’ (n = 41; Ho = 0.45; Da = 0.09). The differences between the two varieties at the DNA level were significant (Fst = 0.44). The broader genetic background in ‘Yin Kwe’ compared with ‘Sein Ta Lone’ was also demonstrated by neighbour-joining and principal coordinates analyses. Differences in variety uses and propagation practices were determined by interviewing local specialists in Lower Myanmar (southern Myanmar). ‘Yin Kwe’ was often used as a rootstock for ‘Sein Ta Lone’. Clonal propagation by grafting was observed frequently for ‘Sein Ta Lone’ but never for ‘Yin Kwe’. The differences in genetic variation between these two varieties might have been caused by the propagation practices for each variety, which result from their respective uses.
What should be the standards for scholarly criticism?
Authors: SHIRLEY MARY M.
Published: February 2011

Should scholars, like columnists, exaggerate and aggregate opposing views into men of straw? I analyse an example of scholarly criticism that characterizes the treatment of development in institutional economics as a simplistic and extremist paradigm. I argue that scholarly standards demand a complete and honest portrayal of contrary opinions and that straw men should be banished from scholarly discourse.
Institutions really don't matter for development? A response to Chang
Authors: KEEFER PHILIP
Published: February 2011

Ha-Joon Chang, in his article ‘Institutions and Economic Development: Theory, Policy and History’, argues that the institutions and development literature is theoretically and empirically flawed, trapped by a failure to account for the contextual factors that influence the institutions that drive development. These judgments emerge from a lack of appreciation of the methodological standards of that literature and, especially, from a description of the institutions and development literature that few contributors to it would recognize. At the same time, despite the emphasis he gives to contextual factors, his critique ignores the role of politicians and the progress made in the institutions literature in understanding their incentives to pursue development.
An integrated observational and model‐based analysis of the hydrologic response of prairie pothole systems to variability in climate
Authors: Liu Ganming , Schwartz Franklin W.
Published: February 2011

We developed a hydrologic model capable of simulating pothole complexes composed of tens of thousands or more individual closed‐basin water bodies. It was applied to simulate the hydrologic response of a prairie pothole complex to climatic variability over a 105 year period (1901–2005) in an area of the Prairie Pothole Region in North Dakota. The model was calibrated and validated with a genetic algorithm by comparing the simulated results with observed power law relationships on water area–frequency derived from Landsat images and a 27 year record of water depths from six wetlands in the Cottonwood Lake area. The simulated behavior in water area and water body frequency showed good agreement with the observations under average, dry, and wet conditions. Analysis of simulation results over the last century showed that the power laws changed intra‐annually and interannually as a function of climate. Major droughts and deluges can produce marked variability in the power law function (e.g., up to 1.5 orders of magnitude variability in intercept from the extreme Dust Bowl drought to the extreme 1993–2001 deluge). Analyses also revealed the frequency of occurrence of small potholes and puddles did not follow pure power law behavior and that details of the departure from linear behavior were closely related to the climatic conditions. A general equation, which encompasses both the linear power law segment for large potholes and nonlinear unimodal body for small potholes and puddles, was used to build conceptual models to describe how the numbers of water bodies as a function of water area respond to fluctuations in climate.
What about ‘information’?
Authors: Pigliucci Massimo
Published: February 2011

Various groups misinterpret ‘information’ as evidence of design or consciousness. But information is just a form of matter or energy; it does not require consciousness to receive and process it.
CD27‐deficient mice show normal NK‐cell differentiation but impaired function upon stimulation
Authors: De Colvenaer Veerle , Taveirne Sylvie , Delforche Maarten , De Smedt Magda , Vandekerckhove Bart , Taghon Tom , Boon Louis , Plum Jean , Leclercq Georges
Published: February 2011

Natural killer (NK) cells are part of the first line defense against tumors, parasites and virus‐infected cells. Therefore, factors that control NK‐cell numbers and their function are important. CD27 is constitutively expressed on NK cells and its expression correlates with sequential phases in NK‐cell development, discriminating phenotypically and functionally different subsets within the NK‐cell population. Although CD27 has been described to have an important regulatory role in effector and memory T and B lymphocytes, its role in NK‐cell biology remains to be addressed. In this study, we used CD27−/− mice to investigate the role of CD27 in NK‐cell development and function, both during the resting state and upon stimulation. The results show that NK‐cell numbers are not impaired in CD27−/− mice. Moreover, CD27−/− NK cells reach full phenotypic maturity, evidenced by normal expression of CD49b, CD43 and CD11b. Expression of activating receptors is unaltered, whereas expression of several inhibitory receptors is increased. Cytotoxicity and interferon‐γ production by NK cells from CD27−/− mice in the resting state are normal. However, upon in vivo anti‐CD40‐ or poly‐I:C‐mediated activation, or in vitro interleukin‐15 priming plus anti‐NKp46 stimulation, the absence of CD27 results in decreased cytolytic activity and cytokine production by spleen and liver NK cells. In conclusion, this study demonstrates that CD27 is dispensable for the development of functional NK cells. However, upon stimulation of NK cells, CD27 displays an important role in their activation and functionality.
Intensive Stuttering Therapy With Telepractice Follow-up: A Case Study
Authors: Irani Farzan , Gabel Rodney
Published: February 2011

This case report describes the positive outcome of a therapeutic intervention that integrated an intensive, residential component with follow-up telepractice for a 21 year old male who stutters. This therapy utilized an eclectic approach to intensive therapy in conjunction with a 12-month follow-up via video telepractice. The results indicated that the client benefited from the program as demonstrated by a reduction in percent stuttered syllables, a reduction in stuttering severity, and a change in attitudes and feelings related to stuttering and speaking.
Response to Intervention: How Do Fluency Disorders Fit In?
Authors: Gottwald Sheryl R. , Reeves Nina A.
Published: February 2011

In this article, we provide a description of response to intervention (RTI) and review research from within and outside of the speech and language field examining RTI and its efficacy. Next we discuss the strengths and weaknesses of RTI when considering the needs of students who stutter. Finally, we make recommendations about how RTI should and should not be used for students who stutter.
Mutual diffusion coefficients of heptane isomers in nitrogen: A molecular dynamics study
Authors: Chae Kyungchan , Violi Angela
Published: February 2011

The accurate knowledge of transport properties of pure and mixture fluids is essential for the design of various chemical and mechanical systems that include fluxes of mass, momentum, and energy. In this study we determine the mutual diffusion coefficients of mixtures composed of heptane isomers and nitrogen using molecular dynamics (MD) simulations with fully atomistic intermolecular potential parameters, in conjunction with the Green–Kubo formula. The computed results were compared with the values obtained using the Chapman–Enskog (C–E) equation with Lennard-Jones (LJ) potential parameters derived from the correlations of state values: MD simulations predict a maximum difference of 6% among isomers while the C–E equation presents that of 3% in the mutual diffusion coefficients in the temperature range 500–1000 K. The comparison of two approaches implies that the corresponding state principle can be applied to the models, which are only weakly affected by the anisotropy of the interaction potentials and the large uncertainty will be included in its application for complex polyatomic molecules. The MD simulations successfully address the pure effects of molecular structure among isomers on mutual diffusion coefficients by revealing that the differences of the total mutual diffusion coefficients for the six mixtures are caused mainly by heptane isomers. The cross interaction potential parameters, collision diameter $\sigma _{12} $σ12, and potential energy well depth $\varepsilon _{12}$ɛ12 of heptane isomers and nitrogen mixtures were also computed from the mutual diffusion coefficients.
Geometry and quadratic nonlinearity of charge transfer complexes in solution using depolarized hyper-Rayleigh scattering
Authors: Pandey Ravindra , Ghosh Sampa , Mukhopadhyay S. , Ramasesha S. , Das Puspendu K.
Published: February 2011

We report large quadratic nonlinearity in a series of 1:1 molecular complexes between methyl substituted benzene donors and quinone acceptors in solution. The first hyperpolarizability, βHRS, which is very small for the individual components, becomes large by intermolecular charge transfer (CT) interaction between the donor and the acceptor in the complex. In addition, we have investigated the geometry of these CT complexes in solution using polarization resolved hyper-Rayleigh scattering (HRS). Using linearly (electric field vector along X direction) and circularly polarized incident light, respectively, we have measured two macroscopic depolarization ratios $D = I_{2\omega,X,X}/I_{2\omega,Z,X}$D=I2ω,X,X/I2ω,Z,X and $D^\prime = I_{2\omega,X,C}/I_{2\omega,Z,C}$D′=I2ω,X,C/I2ω,Z,C in the laboratory fixed XYZ frame by detecting the second harmonic scattered light in a polarization resolved fashion. The experimentally obtained first hyperpolarizability, βHRS, and the value of macroscopic depolarization ratios, D and D′, are then matched with the theoretically deduced values from single and double configuration interaction calculations performed using the Zerner's intermediate neglect of differential overlap self-consistent reaction field technique. In solution, since several geometries are possible, we have carried out calculations by rotating the acceptor moiety around three different axes keeping the donor molecule fixed at an optimized geometry. These rotations give us the theoretical βHRS, D and D′ values as a function of the geometry of the complex. The calculated βHRS, D, and D′ values that closely match with the experimental values, give the dominant equilibrium geometry in solution. All the CT complexes between methyl benzenes and chloranil or 1,2-dichloro-4,5-dicyano-p-benzoquinone investigated here are found to have a slipped parallel stacking of the donors and the acceptors. Furthermore, the geometries are staggered and in some pairs, a twist angle as high as 30° is observed. Thus, we have demonstrated in this paper that the polarization resolved HRS technique along with theoretical calculations can unravel the geometry of CT complexes in solution.
Investigation of low-angle laser light scattering patterns using the modified Twomey iterative method for particle sizing
Authors: Igushi Tatsuo , Yoshida Hideto
Published: February 2011

We first applied the Twomey iteration method to the low-angle laser light scattering (LALLS) method. The Twomey method is known by the simple iteration algorithm for Fredholm integral equation. However, the algorithm is not applied to the LALLS result itself because the kernel function pattern is not stable. We solved the unstable kernel issue by modifying the Twomey algorithm to fit the LALLS data in this study. The performance of inversion was studied by computer simulation and experimental results from detectors containing 24 elements from angle 0.0005 to 2.5 rad. The computer simulation was carried out for particles of mean sizes from 0.1 to 1000 μm with mono-dispersion and log-normal distributions. A conventional algorithm is also carried out to compare the performance of the Twomey method. The noise effect of the inverse problem was tested by computer simulation. Experimental results were measured with standard polystyrene latex from 0.081 to 1007 μm. All the tests were performed under conditions in which the light from a linearly polarized laser at 633 nm was scattered by a diluted aqueous suspension. The modified Twomey (MT) method and conventional method show good reproduction results for particles with log-normal distributions. However, narrow distribution particles indicate that the MT method shows excellent reproduction results when compared with the conventional method.
Development of a high resolution and high dispersion Thomson parabola
Authors: Jung D. , Hörlein R. , Kiefer D. , Letzring S. , Gautier D. C. , Schramm U. , Hübsch C. , Öhm R. , Albright B. J. , Fernandez J. C. , Habs D. , Hegelich B. M.
Published: February 2011

Here, we report on the development of a novel high resolution and high dispersion Thomson parabola for simultaneously resolving protons and low-Z ions of more than 100 MeV/nucleon necessary to explore novel laser ion acceleration schemes. High electric and magnetic fields enable energy resolutions of ΔE/E < 5% at 100 MeV/nucleon and impede premature merging of different ion species at low energies on the detector plane. First results from laser driven ion acceleration experiments performed at the Trident Laser Facility demonstrate high resolution and superior species and charge state separation of this novel Thomson parabola for ion energies of more than 30 MeV/nucleon.
A comparison of the Liptay theory of electroabsorption spectroscopy with the sum-over-state model and its modification for the degenerate case
Authors: Saito Keisuke , Yanagi Kazuhiro , Cogdell Richard. J. , Hashimoto Hideki
Published: February 2011

This study has theoretically clarified the relationship between two descriptions of electroabsorption (EA) spectrum: the Liptay equation and the sum-over-state (SOS) model. The former describes the EA spectrum by the linear combination of derivatives of the linear absorption and the latter describes it by a third-order nonlinear optical susceptibility. The EA spectrum described by the SOS model is equivalent to that by the Liptay equation except the coefficient of the zeroth-order derivative, when the optically forbidden (dark) state is not degenerate with the optically allowed (bright) state. Also when the dark state is degenerate with the bright state, the EA spectrum can be described by a formal Liptay equation with some modifications of the coefficients, as well as by the SOS model. Such a modified Liptay equation can bring us new information on the transition dipole moment concerned with the dark state, as demonstrated in an experiment for β−carotene homologs. Differences between the two descriptions are discussed, and our results are compared with the previous two-state model.
Role of adsorption effects on absolute electron-molecule cross-section calibration using the relative flow technique
Authors: Homem M. G. P. , Iga I. , Sugohara R. T. , Sanches I. P. , Lee M. T.
Published: February 2011

In this work, we report an experimental investigation on relative flow-rate determination for vapors. The mechanism of adsorption-desorption of vapors on surfaces is considered. In contrast to previous investigations, our study shows that the adsorption of vapors on surfaces may significantly affect the flow-rate determination and consequently the measured cross sections. Particularly, for water, it can result in an overestimation of 35% in the cross sections.
Laser-guided cell micropatterning system
Authors: Pirlo Russell K. , Ma Zhen , Sweeney Andrew , Liu Honghai , Yun Julie X. , Peng Xiang , Yuan Xiaocong , Guo George X. , Gao Bruce Z.
Published: February 2011

Employing optical force, our laser-guided cell micropatterning system, is capable of patterning different cell types onto and within standard cell research devices, including commercially available multielectrode arrays (MEAs) with glass culture rings, 35 mm Petri dishes, and microdevices microfabricated with polydimethylsiloxane on 22 mm × 22 mm cover glasses. We discuss the theory of optical forces for generating laser guidance and the calculation of optimal beam characteristics for cell guidance. We describe the hardware design and software program for the cell patterning system. Finally, we demonstrate the capabilities of the system by (1) patterning neurons to form an arbitrary pattern, (2) patterning neurons onto the electrodes of a standard MEA, and (3) patterning and aligning adult cardiomyocytes in a polystyrene Petri dish.
Effect of the field-like spin torque on the switching current and switching speed of magnetic tunnel junction with perpendicularly magnetized free layers
Authors: Zhou Yan
Published: February 2011

We have studied the effect of the fieldlike spin torque term bJ, present in magnetic tunneling junctions (MTJs) with perpendicular magnetic anisotropy in the free layer, on switching characteristics of the devices. We find that bJ has a strong impact on the switching current density and switching speed. The theoretical limit of the switching current density can be significantly reduced and the theoretical limit of the switching time will be lowered compare to the spin-valve (SV) devices. These results strongly suggest that the spin transfer torque random access memory based on the MTJs with perpendicularly magnetized free layer will likely have the multiple benefits of much larger intrinsic signal, smaller switching current, and faster switching speed than the SV devices.
Unraveling the properties of octamethylcyclotetrasiloxane under nanoscale confinement: Atomistic view of the liquidlike state from molecular dynamics simulation
Authors: Matsubara Hiroki , Pichierri Fabio , Kurihara Kazue
Published: February 2011

We developed an atomistic model of octamethylcyclotetrasiloxane (OMCTS) liquid confined within the nanospace between two flat mica surfaces. Molecular dynamics simulation was carried out for the liquidlike state where OMCTS liquid is not frozen, while forming molecular layers parallel to the surface. With the aid of a layer by layer analysis of the intra- and interlayer microscopic structures and the dynamics, it is found that the difference in the properties of the inner layers and the bulk liquid are relatively small in spite of the clear differences in the structure. This leads to the conclusion that the layered structure itself is an appearance of the microscopic structure that already exists in the bulk liquid. The most striking difference from the bulk liquid is mainly seen in the contact layer, where characteristic molecular orientations that are not seen in the crystalline phase appeared, and the dynamics of the liquid becomes 2–3 orders of magnitude slower than that of the bulk.
Lithium cluster anions: Photoelectron spectroscopy and ab initio calculations
Authors: Alexandrova Anastassia N. , Boldyrev Alexander I. , Li Xiang , Sarkas Harry W. , Hendricks Jay H. , Arnold Susan T. , Bowen Kit H.
Published: February 2011

Structural and energetic properties of small, deceptively simple anionic clusters of lithium, Lin−, n = 3–7, were determined using a combination of anion photoelectron spectroscopy and ab initio calculations. The most stable isomers of each of these anions, the ones most likely to contribute to the photoelectron spectra, were found using the gradient embedded genetic algorithm program. Subsequently, state-of-the-art ab initio techniques, including time-dependent density functional theory, coupled cluster, and multireference configurational interactions methods, were employed to interpret the experimental spectra.
Multiple emissions of benzil at room temperature and 77 K and their assignments from ab initio quantum chemical calculations
Authors: Bhattacharya Bhaswati , Jana Barnali , Bose Debosreeta , Chattopadhyay Nitin
Published: February 2011

Multiple emissions have been observed from benzil under different conditions in solutions at room temperature as well as in low temperature glass matrices at 77 K. Low temperature emission has been monitored in rigid matrices frozen under different conditions of illumination. Steady state and time-resolved results together with the ab initio quantum chemical calculations provide, for the first time, the assignments of the different fluorescence bands to the different geometries and/or electronic states of the fluorophore molecule. It is revealed that the skew form of benzil emits from the first (S1) as well as the second excited singlet (S2) states depending on the excitation wavelength, while the relaxed transplanar conformer fluoresces only from the S1 state. The yet unexplored emission band peaking at around 360 nm has been assigned to originate from the S2 state. Ab initio calculations using the density functional theory at B3LYP/6-31G** level corroborate well with the experimental observations.
Critical assessment of the issues in the modeling of ablation and plasma expansion processes in the pulsed laser deposition of metals
Authors: Marla Deepak , Bhandarkar Upendra V. , Joshi Suhas S.
Published: February 2011

This paper presents a review on the modeling of ablation and plasma expansion processes in the pulsed laser deposition of metals. The ablation of a target is the key process that determines the amount of material to be deposited; while, the plasma expansion governs the characteristics of the deposited material. The modeling of ablation process involves a study of two complex phenomena: (i) laser-target interaction and (ii) plasma formation and subsequent shielding of the incoming radiation. The laser-target interaction is a function of pulse duration, which is captured by various models that are described in this paper. The plasma produced as a result of laser–target interaction, further interacts with the incoming radiation, causing the shielding of the target. The shielding process has been modeled by considering the various photon absorption mechanisms operative inside the plasma, namely: inverse Bremsstrahlung, photoionization, and Mie absorption. Concurrently, the plasma expands freely until the ablated material gets deposited on the substrate. Various models describing the plasma expansion process have been presented. The ability of the theoretical models in predicting various ablation and plasma characteristics has also been compared with the relevant experimental data from the literature. The paper concludes with identification of critical issues and recommendations for future modeling endeavors.
Rovibrational spectra of ammonia. II. Detailed analysis, comparison, and prediction of spectroscopic assignments for 14NH3,15NH3, and 14ND3
Authors: Huang Xinchuan , Schwenke David W. , Lee Timothy J.
Published: February 2011

Several aspects of ammonia rovibrational spectra have been investigated using the new HSL-2 potential energy surface that includes an approximate correction for nonadiabatic effects. The unprecedented accuracy of rovibrational energy levels and transition energies computed using HSL-2 was demonstrated in Part I of this study. For 14NH3, new assignments for a few ν3 + ν4 band transitions and energy levels are suggested, and discrepancies between computed and HITRAN energy levels in the 2ν4 band are analyzed (2ν4 is the most difficult band below 5000 cm−1). New assignments are suggested for existing or missing 2ν4 levels. Several new vibrational bands are identified from existing, unassigned HITRAN data, including 2ν2 + ν4, (ν3 + ν4) -A′/A″, ν1 + 2ν2, and 2ν2 + 2ν4. The strong mixing between the 2ν4 and 2ν2 + ν4 bands is carefully examined and found to be the source of the difficulties in the experimental modeling of 2ν4. Discussion is presented for preliminary J = 10 results, where the overall root-mean-square error is estimated to be less than 0.039 cm−1. The analysis of the 4ν2 band demonstrates both the reliability and the accuracy of predictions from HSL-2. The full list of computed J = 0 band origins (with assignments) and the inversion splittings up to 7000–8000 cm−1 above the zero-point energy are presented. J = 0–2 levels are reported for those bands below 5100 cm−1 that are missing from the HITRAN database. For 15NH3, excellent agreement is found for the available ν2 and ν3 + ν4(E) transition energies, but significant deficiencies are shown for HITRAN levels and several corrections are suggested. The 15N isotopic effects are presented for the J = 0–6 levels of 13 HITRAN bands. For 14ND3, we reproduce the pure rotational inversion spectra line frequencies with an accuracy similar to that for 14NH3. However, it is not possible to reproduce simultaneously all four pairs of inversion–split vibrational fundamentals to better than 0.05 cm−1 uncertainty. It is suggested that a reanalysis of some suspicious 14ND3 fundamental bands is required. The analyses presented here and in Part I show that rovibrational energy levels and transition frequencies computed with HSL-2 (with nonadiabatic corrections) remain highly accurate well beyond the experimental data used in the refinement procedure. Calculations using HSL-2 are capable of revealing many deficiencies in experimental analyses of ammonia spectra and provide reliable predictions with similar accuracy. It is expected that the results of this study will be useful in the future interpretation of high-resolution spectra from laboratory experiments or from astronomical observations. The present work represents a very significant advance in the state of our knowledge of the spectroscopy of ammonia and its isotopologues.
Kinetics of ejected particles during breakdown in fused silica by nanosecond laser pulses
Authors: Raman Rajesh N. , Negres Raluca A. , Demos Stavros G.
Published: February 2011

The temporal evolution and kinetic properties of material particles ejected from the surface of fused silica under nanosecond laser irradiation are investigated using a time-resolved microscope system. The experiments provide information on the particle size, shape, and speed as a function of delay time, as well as on the duration of the material ejection process. The results suggest that the processes involved are much more complex than those predicted by current models.
Partial strain relaxation by stacking fault generation in InGaN multiple quantum wells grown on (11¯01) semipolar GaN
Authors: Wu Z. H. , Tanikawa T. , Murase T. , Fang Y.-Y. , Chen C. Q. , Honda Y. , Yamaguchi M. , Amano H. , Sawaki N.
Published: February 2011

We have investigated the structural properties and relaxation phenomenon of InGaN multiple quantum wells (QWs) on (11¯01) semipolar GaN templates grown on patterned (001) silicon substrates by selective area growth technique. Our studies by transmission electron microscopy and x-ray diffraction reciprocal space mapping reveal that QWs emitting light at 540 nm experience significant strain relaxation along the in-plane [11¯02¯] direction by the generation of an array of basal stacking faults (BSF). The generation of BSFs in 540 nm QWs could be an important factor limiting its luminescence efficiency.
Nonlinear dynamics of relativistic charged particle beams
Authors: Nunes R. P. , Rizzato F. B.
Published: February 2011

The idea behind this work is to analyze the transversal dynamics of a relativistic charged particle beam. The beam is azimuthally symmetric, focused by a constant magnetic field and supposed to be initially cold. While mismatched, nonrelativistic, and homogeneous beams oscillate with an invariant cold density profile, it is shown that relativistic homogeneous beams progressively heat and lose an important amount of constituents during its magnetic confinement. This heating process starts with phase-space wave-breaking, a mechanism observed before in initially inhomogeneous beams. The results have been obtained with full self-consistent N-particle beam numerical simulations.
Generation of correlated photon pairs in a chalcogenide As2S3 waveguide
Authors: Xiong C. , Marshall G. D. , Peruzzo A. , Lobino M. , Clark A. S. , Choi D.-Y. , Madden S. J. , Natarajan C. M. , Tanner M. G. , Hadfield R. H. , Dorenbos S. N. , Zijlstra T. , Zwiller V. , Thompson M. G. , Rarity J. G. , Steel M. J. , Luther-Davies B. , Eggleton B. J. , O’Brien J. L.
Published: February 2011

We demonstrate a 1550 nm correlated photon-pair source in an integrated glass platform—a chalcogenide As2S3 waveguide. A measured pair coincidence rate of 80s−1 was achieved using 57 mW of continuous-wave pump. The coincidence to accidental ratio was shown to be limited by spontaneous Raman scattering effects that are expected to be mitigated by using a pulsed pump source.
Transmission electron microscopy observations of dislocation annihilation and storage in nanograins
Authors: Wang Lihua , Zhang Ze , Ma En , Han X. D.
Published: February 2011

A detailed in situ investigation of dislocation processes has been rare for nanograined materials with grain sized near or less than 10 nm. Here, we report a time-resolved and atomic-scale in situ transmission electron microscopy observation of the nucleation, motion, annihilation, and storage of full dislocations in nanograins with diameters less than ∼10 nm. Annihilation of dislocation dipoles appears to be a major contributor to the reduction in dislocation density, in addition to annihilation at grain boundary sinks. The accumulation of a high density of dislocations inside nanograins is found to be possible when they are surrounded by neighboring grains.
Child–Langmuir law in the Coulomb blockade regime
Authors: Zhu Yingbin , Ang L. K.
Published: February 2011

The one-dimensional (1D) classical Child–Langmuir (CL) law has been extended to the Coulomb blockade (single to few electrons) regime, including the effect of single-electron charging. It is found that there is a threshold of voltage (Vth) equals to one-half of the single-electron charging energy for electron injection assuming zero barrier at the interface. For voltage in the range of 1<V/Vth<2, there is only one electron inside the gap, and the time-averaged single-electron injected current is equal or higher than the 1D CL current.
Color center formation in vacuum sintered Nd3xY3−3xAl5O12 transparent ceramics
Authors: Stevenson Adam J. , Bittel Brad C. , Leh Christopher G. , Li Xin , Dickey Elizabeth C. , Lenahan Patrick M. , Messing Gary L.
Published: February 2011

Color center formation was studied in vacuum sintered Nd3xY3−3xAl5O12 transparent ceramics. The primary color centers were F- and F+-centers as evidenced by optical absorption in the 250–400 nm wavelength range and the presence of an electron spin resonance (ESR) line at g=1.9977. Annealing in air at 1600 °C for 10 h reduced the number of color centers to below the detection limit of ESR. Color center formation is controlled by oxidation and reduction of Fe2+/3+ impurities.
Transmission electron microscopy of transparent conductive oxide films made by atmospheric pressure chemical vapor deposition
Authors: Mannie G. J. A. , van Deelen J. , Niemantsverdriet J. W. , Thüne P. C.
Published: February 2011

The properties of crystalline films are strongly dependent on the morphology development during the first stages of growth, that is, the nucleation and growth of the first crystallites. The ideal method to investigate such films at atomic resolution is transmission electron microscopy (TEM). However, this technique usually requires extensive sample preparation. In this study we present a simple method to investigate thin film morphology with TEM. The key to this approach is the use of TEM membranes as growth substrates. As an illustration we describe fine grains of SnO2 deposited on these TEM membranes by atmospheric pressure chemical vapor deposition.
Intrinsic metastability of orthorhombic HfTiO4 in thin film hafnia-titania
Authors: Cisneros-Morales Massiel Cristina , Aita Carolyn Rubin
Published: February 2011

Orthorhombic (o) HfTiO4 is crystallized when sputter deposited hafnia-titania nanolaminates with ultrathin layers and bilayer (HfO2)0.5(TiO2)0.5 composition are annealed between 573 and 1173 K. However, o-HfTiO4 demixes after annealing at 1273 K, a result not predicted from bulk thermodynamics. X-ray diffraction and Raman microscopy are used here to study structural changes as o-HfTiO4 demixes upon long-term annealing at 1273 K into Ti-doped monoclinic HfO2 and Hf-doped rutile TiO2. We conclude that o-HfTiO4 crystallized at low temperature is intrinsically metastable. A space group symmetry analysis shows that demixing can be accomplished by a continuous phase transition chain.
Probing residual strain in epitaxial graphene layers on 4H-SiC(0001¯) with Raman spectroscopy
Authors: Strudwick A. J. , Creeth G. L. , Johansson N. A. B. , Marrows C. H.
Published: February 2011

Raman microspectroscopy was used to measure compressive strain within epitaxial graphene (EG) grown on the carbon-terminated SiC(0001¯) face as a function of annealing time for a growth temperature of 1400 °C. A maximum strain of −0.5% was seen at the longest time of 55 min. This differs from the −0.9% expected for strain caused by cooling from the growth temperature due to the differential thermal contraction between the SiC and EG layer, despite good agreement between this model and data on EG on SiC(0001). We suggest that this is due to the different EG bonding mechanisms on the two SiC faces.
Stress control during thermal annealing of copper interconnects
Authors: Yang C.-C. , Witt C. , Wang P.-C. , Edelstein D. , Rosenberg R.
Published: February 2011

Grain growth of Cu interconnects in an ultralow k dielectric was achieved at an elevated anneal temperature of 300 °C without stress voiding related problems. For this, a TaN metal passivation layer was deposited on the Cu interconnect surface prior to the thermal annealing process, which suppressed void formation within the Cu features during the anneal process and reduced inelastic deformation within the interconnects after cooling down to room temperature. As compared to the conventional anneal process at 100 °C, the passivation layer enabled further Cu grain growth at elevated temperatures, which then resulted in lower electrical resistance in the Cu interconnects.
Experiments reveal a Bose–Einstein condensate of photons
Authors: Wilson R. Mark
Published: February 2011

Key to the achievement is the confinement of photons and molecules in an optical cavity long enough for them to reach thermal equilibrium.
Cell-free protein synthesis sheds light on intracellular dynamics
Authors: Miller Johanna L.
Published: February 2011

Primarily a tool to produce large amounts of protein quickly, the cell-free system is being adapted to the study of complex biological processes.
Room-temperature source delivers record-power terahertz beam
Authors: Smart Ashley G.
Published: February 2011

The nonlinear optics device could help to resolve one of astronomy’s lingering blind spots.
Drive to end civilian use of HEU collides with medical isotope production
Authors: Kramer David
Published: February 2011

Completing the global conversion to low-enriched uranium remains many years away for molybdenum-99 production, despite a recent milestone and financial aid from the US. Now the Department of Energy is acting to create a domestic supply source for the isotope.
Quantum criticality
Authors: Sachdev Subir , Keimer Bernhard
Published: February 2011

A phase transition brought on by quantum fluctuations at absolute zero may seem like an abstract theoretical idea of little practical consequence. But it is the key to explaining a wide variety of experiments.
Overexpression of the MYB-related transcription factor GCC7 in Arabidopsis thaliana leads to increased levels of Pi and changed P-dependent gene regulation
Authors: Lundmark Maria , Nilsson Lena , Kørner Camilla J. , Nielsen Tom H.
Published: February 2011

A proper concentration and turnover of inorganic phosphate (Pi) is essential to maintain cellular processes. Consequently, plants have mechanisms to control Pi homeostasis and to alleviate Pi limitation. The MYB-related transcription factor, PHR1, is important for gene induction during Pi starvation. PHR1 belongs to a family, characterised by the presence of a GARP- and a coiled coil domain. We propose that this family, with 15 members in Arabidopsis thaliana (L.) Heynh., be termed the GCC-family. In this study, transgenic plants overexpressing one member, GCC7, and a T-DNA knockout mutant, gcc7, are characterised. We find overexpressor plants to accumulate more Pi in shoots, irrespective of the Pi supply. Therefore, GCC7 was characterised in relation to Pi starvation. We conclude that GCC7 is not strictly required for a P-starvation response since the gcc7 mutant responds to Pi limitation. However, overexpression of GCC7 strongly interferes with the P-starvation response, abolishing induction of several P-responsive genes including AT4, IPS1 and several P-transporter genes, whereas GCC7 does not directly interfere with the PHR1 (GCC1) dependent regulation of miR399d. Thus GCC7 influences P-accumulation and P-dependent gene regulation, but GCC7 has a function entirely different from PHR1.
Plant nutrient acquisition and utilisation in a high carbon dioxide world
Authors: Cavagnaro T. R. , Gleadow R. M. , Miller R. E.
Published: February 2011

Producing enough food to meet the needs of an increasing global population is one of the greatest challenges we currently face. The issue of food security is further complicated by impacts of elevated CO2 and climate change. In this viewpoint article, we begin to explore the impacts of elevated CO2 on two specific aspects of plant nutrition and resource allocation that have traditionally been considered separately. First, we focus on arbuscular mycorrhizas, which play a major role in plant nutrient acquisition. We then turn our attention to the allocation of resources (specifically N and C) in planta, with an emphasis on the secondary metabolites involved in plant defence against herbivores. In doing so, we seek to encourage a more integrated approach to investigation of all aspects of plant responses to eCO2.
Regulation of induced colonic inflammation byLactobacillus acidophilusdeficient in lipoteichoic acid
Authors: Mohamadzadeh Mansour , Pfeiler Erika A. , Brown Jeffrey B. , Zadeh Mojgan , Gramarossa Matthew , Managlia Elizabeth , Bere Praveen , Sarraj Bara , Khan Mohammad W. , Pakanati Krishna Chaitanya , Ansari M. Javeed , O'Flaherty Sarah , Barrett Terrence , Klaenhammer Todd R.
Published: February 2011

Imbalance in the regulatory immune mechanisms that control intestinal cellular and bacterial homeostasis may lead to induction of the detrimental inflammatory signals characterized in humans as inflammatory bowel disease. Induction of proinflammatory cytokines (i.e., IL-12) induced by dendritic cells (DCs) expressing pattern recognition receptors may skew naive T cells to T helper 1 polarization, which is strongly implicated in mucosal autoimmunity. Recent studies show the ability of probiotic microbes to treat and prevent numerous intestinal disorders, includingClostridium difficile-induced colitis. To study the molecular mechanisms involved in the induction and repression of intestinal inflammation, the phosphoglycerol transferase gene that plays a key role in lipoteichoic acid (LTA) biosynthesis inLactobacillus acidophilusNCFM (NCK56) was deleted. The data show that theL. acidophilusLTA-negative in LTA (NCK2025) not only down-regulated IL-12 and TNFα but also significantly enhanced IL-10 in DCs and controlled the regulation of costimulatory DC functions, resulting in their inability to induce CD4+T-cell activation. Moreover, treatment of mice with NCK2025 compared with NCK56 significantly mitigated dextran sulfate sodium and CD4+CD45RBhighT cell-induced colitis and effectively ameliorated dextran sulfate sodium-established colitis through a mechanism that involves IL-10 and CD4+FoxP3+T regulatory cells to dampen exaggerated mucosal inflammation. Directed alteration of cell surface components ofL. acidophilusNCFM establishes a potential strategy for the treatment of inflammatory intestinal disorders.
Enhanced T-cell signaling in cells bearing linker for activation of T-cell (LAT) molecules resistant to ubiquitylation
Authors: Balagopalan Lakshmi , Ashwell Benjamin A. , Bernot Kelsie M. , Akpan Itoro O. , Quasba Naeha , Barr Valarie A. , Samelson Lawrence E.
Published: February 2011

Linker for activation of T cells (LAT) plays a central role in T-cell activation by nucleating signaling complexes that are critical for the propagation of T-cell signals from the plasma membrane to the cellular interior. The role of phosphorylation and palmitoylation in LAT function has been well studied, but not much is known about other strategies by which the cell modulates LAT activity. We have focused on LAT ubiquitylation and have mapped the sites on which LAT is ubiquitylated. To elucidate the biological role of this process, we substituted LAT lysines with arginines. This resulted in a dramatic decrease in overall LAT ubiquitylation. Ubiquitylation-resistant mutants of LAT were internalized at rates comparable to wild-type LAT in a mechanism that required Cbl family proteins. However, these mutants displayed a defect in protein turnover rates. T-cell signaling was elevated in cells reconstituted with LAT mutants resistant to ubiquitylation, indicating that inhibition of LAT ubiquitylation enhances T-cell potency. These results support LAT ubiquitylation as a molecular checkpoint for attenuation of T-cell signaling.
Draft genome of the red harvester ant
Pogonomyrmex barbatus
Authors: Smith Chris R. , Smith Christopher D. , Robertson Hugh M. , Helmkampf Martin , Zimin Aleksey , Yandell Mark , Holt Carson , Hu Hao , Abouheif Ehab , Benton Richard , Cash Elizabeth , Croset Vincent , Currie Cameron R. , Elhaik Eran , Elsik Christine G. , Favé Marie-Julie , Fernandes Vilaiwan , Gibson Joshua D. , Graur Dan , Gronenberg Wulfila , Grubbs Kirk J. , Hagen Darren E. , Viniegra Ana Sofia Ibarraran , Johnson Brian R. , Johnson Reed M. , Khila Abderrahman , Kim Jay W. , Mathis Kaitlyn A. , Munoz-Torres Monica C. , Murphy Marguerite C. , Mustard Julie A. , Nakamura Rin , Niehuis Oliver , Nigam Surabhi , Overson Rick P. , Placek Jennifer E. , Rajakumar Rajendhran , Reese Justin T. , Suen Garret , Tao Shu , Torres Candice W. , Tsutsui Neil D. , Viljakainen Lumi , Wolschin Florian , Gadau Jürgen
Published: February 2011

We report the draft genome sequence of the red harvester ant,
Pogonomyrmex barbatus
. The genome was sequenced using 454 pyrosequencing, and the current assembly and annotation were completed in less than 1 y. Analyses of conserved gene groups (more than 1,200 manually annotated genes to date) suggest a high-quality assembly and annotation comparable to recently sequenced insect genomes using Sanger sequencing. The red harvester ant is a model for studying reproductive division of labor, phenotypic plasticity, and sociogenomics. Although the genome of
P. barbatus
is similar to other sequenced hymenopterans (
Apis mellifera
and
Nasonia vitripennis
) in GC content and compositional organization, and possesses a complete CpG methylation toolkit, its predicted genomic CpG content differs markedly from the other hymenopterans. Gene networks involved in generating key differences between the queen and worker castes (e.g., wings and ovaries) show signatures of increased methylation and suggest that ants and bees may have independently co-opted the same gene regulatory mechanisms for reproductive division of labor. Gene family expansions (e.g., 344 functional odorant receptors) and pseudogene accumulation in chemoreception and P450 genes compared with
A. mellifera
and
N. vitripennis
are consistent with major life-history changes during the adaptive radiation of
Pogonomyrmex
spp., perhaps in parallel with the development of the North American deserts.
Antigen-independent signalosome of CARMA1, PKCθ, and TNF receptor-associated factor 2 (TRAF2) determines NF-κB signaling in T cells
Authors: So Takanori , Soroosh Pejman , Eun So-Young , Altman Amnon , Croft Michael
Published: February 2011

NF-κB activation is essential for T-cell responses, and costimulatory molecules in the TNF receptor (TNFR) superfamily are viewed as a major source of this signal. Although the TNFR family recruits TNFR-associated factor (TRAF) molecules leading to IKKα/β/γ activation, it is not clear whether simple binding of TRAFs explains why they are such strong activators of NF-κB and so important for T-cell immunity. We now show that one TNFR family member, OX40 (CD134), after ligation by OX40L, assembles a unique complex that not only contains TRAF2, RIP, and IKKα/β/γ but also CARMA1, MALT1, BCL10, and PKCθ, molecules previously shown to regulate NF-κB activation through the T-cell receptor (TCR). The OX40 signalosome is formed in membrane microdomains irrespective of TCR engagement, and strongly promotes NF-κB activation only if CARMA1 and PKCθ are recruited. This NF-κB signal allows effector/memory T cells to survive when antigen is no longer available. Thus, by recruiting TCR-related intracellular molecules into the TRAF2 complex, OX40 provides the T cell with a high level of NF-κB activity needed for longevity.
Role of social networks in shaping disease transmission during a community outbreak of 2009 H1N1 pandemic influenza
Authors: Cauchemez Simon , Bhattarai Achuyt , Marchbanks Tiffany L. , Fagan Ryan P. , Ostroff Stephen , Ferguson Neil M. , Swerdlow David ,   the Pennsylvania H1N1 working group, Sodha Samir V. , Moll Mària E. , Angulo Frederick J. , Palekar Rakhee , Archer W. Roodly , Finelli Lyn
Published: February 2011

Evaluating the impact of different social networks on the spread of respiratory diseases has been limited by a lack of detailed data on transmission outside the household setting as well as appropriate statistical methods. Here, from data collected during a H1N1 pandemic (pdm) influenza outbreak that started in an elementary school and spread in a semirural community in Pennsylvania, we quantify how transmission of influenza is affected by social networks. We set up a transmission model for which parameters are estimated from the data via Markov chain Monte Carlo sampling. Sitting next to a case or being the playmate of a case did not significantly increase the risk of infection; but the structuring of the school into classes and grades strongly affected spread. There was evidence that boys were more likely to transmit influenza to other boys than to girls (and vice versa), which mimicked the observed assortative mixing among playmates. We also investigated the presence of abnormally high transmission occurring on specific days of the outbreak. Late closure of the school (i.e., when 27% of students already had symptoms) had no significant impact on spread. School-aged individuals (6–18 y) facilitated the introduction and spread of influenza in households, but only about one in five cases aged >18 y was infected by a school-aged household member. This analysis shows the extent to which clearly defined social networks affect influenza transmission, revealing strong between-place interactions with back-and-forth waves of transmission between the school, the community, and the household.