bluuebunny/crossref_metadata_2025 huggingface dataset:
First results of the refurbished SOUSY radar: Tropopause altitude climatology at 78°N, 16°E, 2008
Authors: Hall C. M. , Röttger J. , Kuyeng K. , Sigernes F. , Claes S. , Chau J.
Published: September 2009

The second generation SOUSY MST radar at 78°N, 16°E on Svalbard has recently completed its inaugural year of combined troposphere and mesosphere observations. Here, troposphere observations have been processed using a robust detection algorithm designed for obtaining tropopause climatology by automatic data processing, and the resulting monthly statistics have been compared with corresponding surface air temperatures. As our main objective, we describe the new radar system, present the tropopause detection method, and validate the results using radiosonde and surface temperature data. The tropopause height depends on the temperature of the underlying atmosphere but is also influenced by downward control from the stratosphere. We find that the climatological tropopause height is correlated with the surface temperature but with the former lagging the latter by approximately 1 month.
No‐search algorithm for direction of arrival estimation
Authors: Tuncer T. Engin , Özgen M. Tankut
Published: September 2009

Direction of arrival estimation (DOA) is an important problem in ionospheric research and electromagnetics as well as many other fields. When superresolution techniques are used, a computationally expensive search should be performed in general. In this paper, a no‐search algorithm is presented. The idea is to separate the source signals in the time‐frequency plane by using the Short‐Time Fourier Transform. The direction vector for each source is found by coherent summation over the instantaneous frequency (IF) tracks of the individual sources which are found automatically by employing morphological image processing. Both overlapping and nonoverlapping source IF tracks can be processed and identified by the proposed approach. The CLEAN algorithm is adopted in order to isolate the IF tracks of the overlapping sources with different powers. The proposed method is very effective in finding the IF tracks and can be applied for signals with arbitrary IF characteristics. While the proposed method can be applied to any sensor geometry, planar uniform circular arrays (UCA) bring additional advantages. Different properties of the UCA are presented, and it is shown that the DOA angles can be found as the mean‐square error optimum solution of a linear matrix equation. Several simulations are done, and it is shown that the proposed approach performs significantly better than the conventional methods.
Thymocyte expansion and maturation: crosstalk of CD44v6 on thymocytes and panCD44 on stroma cells
Authors: Rajasagi Mohini , Marhaba Rachid , Vitacolonna Mario , Zöller Margot
Published: September 2009

Re‐acquisition of immunocompetence after allogeneic bone marrow cell (BMC) transplantation depends on intrathymic maturation of the allogeneic T progenitor cells. We recently reported that CD44 promotes progenitor homing into the thymus and T‐cell maturation and now elucidate the molecular mechanisms of CD44‐supported thymocyte maturation. Lethally irradiated, tumor‐bearing mice, allogeneically reconstituted with T‐cell‐depleted BMC and a small number of common lymphoid progenitor 2 cells (CLP2) from transgenic (TG) mice, that express ratCD44v4‐v7 under the Thy1 promoter, showed accelerated immunocompetent T‐cell recovery compared with mice reconstituted with non‐transgenic (NTG) CLP2. In addition, graft‐versus‐host disease was strongly reduced after tumor vaccination. TG, but not NTG double‐negative (DN) thymocytes showed high proliferative potential, accompanied by constitutive association of lck with CD44. Importantly, when thymocyte adhesion was strengthened by anti‐CD44, co‐cultures of DN thymocytes with thymic stroma supported DN thymocyte maturation. The close contact between DN thymocytes and thymic stroma promoted persisting activation of lck and ERK1/2, particularly in CD44v6+ DN thymocytes. Thus, intrathymic T‐cell maturation in allogeneically reconstituted, leukemia‐bearing hosts can be considerably accelerated by high CD44v6 expression in early thymocytes, in which proliferation‐supporting signals are initiated by a crosstalk between CD44v6 on thymocytes and panCD44 on the thymic stroma.
Simple SVM based whole-genome segmentation
Authors: Bedo Justin , Macintyre Geoff , Haviv Izhak , Kowalczyk Adam
Published: September 2009

We present a support vector machine (SVM) based framework for DNA segmentation into binary classes. Two applications are explored: transcription start site prediction and transcription factor binding prediction. Experiments demonstrate our approach has significantly better performance than other methods on both tasks.
Ferroelectric characterization of nondensified particle-based structures
Authors: Lehnert T. , Adam J. , Veith M.
Published: September 2009

Increasing requirements concerning the powder quality for fine-grained ferroelectric ceramics or for low temperature coating technologies provoke further improvements in particle characterization methods. So far, a correct quantitative measurement of the ferroelectric properties for as synthesized particles is lacking and only already sintered ceramics can be measured precisely. We report on a measurement setup to characterize films made of as synthesized ferroelectric particles. The chosen measurement setup enables the definite determination of ferroelectricity in such nondensified particle-based structures. A centrifugally casted BaTiO3 particulate film with 50% porosity is used for characterization. The correct value of the remanent polarization for this porous film obtained by the new method is almost half the value estimated by conventional measurement setups. Compared to a sintered BaTiO3 ceramic the achieved remanent polarization is much lower (10%). At the same time a higher maximum field has to be applied to the sample as lower fields act on the individual particles because of the porosity of this film.
Effect of Co, Ni, and Cu substitution on the electronic structure of hexagonal YMnO3 studied by x-ray absorption spectroscopy
Authors: Asokan K. , Chen Y. S. , Pao C. W. , Tsai H. M. , Lee C. W. O. , Lin C. H. , Hsueh H. C. , Ling D. C. , Pong W. F. , Chiou J. W. , Tsai M.-H. , Peña O. , Moure C.
Published: September 2009

X-ray absorption spectroscopy measurements have been performed to elucidate local electronic and atomic structures of orthorhombic 3d-transition metal-doped yttrium manganites (YMnO3) with chemical formulae YMn2/3Me1/3O3 (Me=Co, Ni, and Cu). The Mn L3- and K-edges x-ray absorption near-edge structure (XANES) demonstrate the direct substitution of Me2+ for Mn3+, so that the positive effective charge of Mn ions are increased. Me-doping is also found to induce substantial broadening of the Mn L3-edge feature, which suggests enhancement of the delocalization of Mn 3d eg subbands and conductivity. Local spin density approximation (LSDA)+U (Hubbard U parameter) calculations were used to understand their electronic structures.
Refinement of microstructure and highly improved electrical properties of Bi1.6Pb0.5Sr1.925Ho0.075Ca1.1Cu2.1O8+δ superconductor
Authors: Vinu S. , Sarun P. M. , Shabna R. , Syamaprasad U.
Published: September 2009

The importance of rare-earth (RE) doping and precise tuning of sintering temperature on the microstructural features, electrical properties, and magnetic performance of a (Bi,Pb)-2212 superconductor sintered between 846 and 860 °C has been investigated. The results show that the RE (holmium) atoms enter into the crystal structure and induce significant changes in the hole concentration, lattice parameter values, microstructure, normal state conductivity, self- and in-field critical current densities, and flux pinning properties of the system. The microstructural analysis shows that the samples sintered at a comparatively lower sintering temperature (846 °C) have more grain boundaries with smaller grains, while those sintered at a higher sintering temperature (856 °C) contain larger grains with good texturing. Also, the irreversibility lines are shifted to higher temperatures and magnetic fields to different extents depending on the sintering temperature. The flux pinning force density (FP) curves are theoretically fitted using the Dew-Hughes model, which shows that the main pinning mechanism is the point defect arising due to the substitution of holmium atoms at the strontium site of the (Bi,Pb)-2212 system. Also, for samples sintered at 846 °C, FPmax appeared at a reduced field value of h=0.39, which shows that in addition to point pinning, grain boundary pinning is also effective in these samples. The changes in microstructure followed by a very high enhancement of superconductivity and flux pinning properties due to RE doping within a small sintering temperature range are of great scientific and technological significance.
18.9% efficient full area laser doped silicon solar cell
Authors: Eisele S. J. , Röder T. C. , Köhler J. R. , Werner J. H.
Published: September 2009

A record in full area laser doped emitter solar cells with an efficiency η=18.9% is reported. Our patented, scanned laser doping process allows for the fabrication of defect free pn junctions via liquid state diffusion of predeposited dopant layers in ambient atmosphere without the need of clean room conditions. Our cells display an open circuit voltage Voc=677 mV, demonstrating laser doping to be comparable to furnace diffusion. Combining laser diffused pn junctions with a textured front side has the potential to boost the short circuit current density Jsc and thus the solar cell efficiency η to η>21%.
Modeling CO2 laser ablation impulse of polymers in vapor and plasma regimes
Authors: Sinko John E. , Phipps Claude R.
Published: September 2009

An improved model for CO2 laser ablation impulse in polyoxymethylene and similar polymers is presented that describes the transition effects from the onset of vaporization to the plasma regime in a continuous fashion. Several predictions are made for ablation behavior.
Influence of reservoir size on the adsorption path in an ideal pore
Authors: Puibasset Joël , Kierlik Edouard , Tarjus Gilles
Published: September 2009

We consider the influence of the relative size of the gas reservoir on the states visited by a simple fluid adsorbed in a nanopore of ideal geometry (a slit). We focus on the intermediate states that appear in between the main hysteresis branches comprising gaslike and liquidlike states and we study the adsorption and desorption paths actually followed by the system as one changes the reservoir size. We find that these paths may display discontinuous sections associated with transitions between different nonuniform states. We also discuss the stability of the states in such situations.
From nanoparticle to nanocable: Impact of size and geometrical constraints on the optical modes of Si/SiO2 core/shell nanostructures
Authors: Wang Juan , Wang Xiao-Jing , Jiao Yang , Li Quan , Chu Ming-Wen , Malac Marek
Published: September 2009

In the extinction spectra of Si/SiO2 core/shell nanostructures, peak features in the near UV region (3–5 eV) appear when the nanostructure geometrical configuration changes from spherical nanoparticles to cylindrical nanocables, with the peak features become more intense in the nanocables of smaller core diameter. Similar feature at ∼4.2 eV is also observed in the spatially resolved electron energy loss spectra (SREELS) of individual nanocable, but not in the nanoparticle. The EELS simulations unravel the origin of such excitation as the monopolar interface plasmon in cylindrical nano-objects, being responsible for the observed near UV extinction modes in nanocables.
Electrical stress-induced instability of amorphous indium-gallium-zinc oxide thin-film transistors under bipolar ac stress
Authors: Lee Sangwon , Jeon Kichan , Park Jun-Hyun , Kim Sungchul , Kong Dongsik , Kim Dong Myong , Kim Dae Hwan , Kim Sangwook , Kim Sunil , Hur Jihyun , Park Jae Chul , Song Ihun , Kim Chang Jung , Park Youngsoo , Jung U-In
Published: September 2009

Bipolar ac stress-induced instability of amorphous indium-gallium-zinc oxide (a-IGZO) thin-film transistors is comparatively investigated with that under a positive dc gate bias stress. While the positive dc gate bias stress-induced threshold voltage shift (ΔVT) is caused by the charge trapping into the interface/gate dielectric as reported in previous works, the dominant mechanism of the ac stress-induced ΔVT is observed to be due to the increase in the acceptorlike deep states of the density of states (DOS) in the a-IGZO active layer. Furthermore, it is found that the variation of deep states in the DOS makes a parallel shift in the IDS-VGS curve with an insignificant change in the subthreshold slope, as well as the deformation of the CG-VG curves.
The importance of electron temperature in silicon-based terahertz quantum cascade lasers
Authors: Lever L. , Valavanis A. , Evans C. A. , Ikonić Z. , Kelsall R. W.
Published: September 2009

Quantum cascade lasers (QCLs) are compact sources of coherent terahertz radiation. Although all existing QCLs use III-V compound semiconductors, silicon-based devices are highly desirable due to the high thermal conductivity and mature processing technology. We use a semiclassical rate-equation model to show that Ge/SiGe THz QCL active region gain is strongly enhanced by reducing the electron temperature. We present a bound-to-continuum QCL design employing L-valley intersubband transitions, using high Ge fraction barriers to reduce interface roughness scattering, and a low electric field to reduce the electron temperature. We predict a gain of ∼50 cm−1, which exceeds the calculated waveguide losses.
Surface structure and chemical states of a-plane and c-plane InN films
Authors: Nagata Takahiro , Koblmüller Gregor , Bierwagen Oliver , Gallinat Chad S. , Speck James S.
Published: September 2009

The surface electron accumulation layer, surface structure, and surface chemical states of a-plane (nonpolar) and c-plane (polar) InN epitaxial films were investigated. Electrical measurements indicated electron accumulation layers on the surface of both the InN films. Angle-resolved x-ray photoelectron spectroscopy (XPS) measurements indicated a strong band bending at both surfaces, thus confirming the surface electron accumulation. Further XPS analysis of the near-surface chemical states indicated an In adlayer at the surface of c-plane InN and an oxygen adsorbed layer on the a-plane InN. These results suggest different ad-layers to cause the surface electron accumulation on c-plane and a-plane InN.
Ultrasmall penetration depth in nanoscale thermal radiation
Authors: Basu S. , Zhang Z. M.
Published: September 2009

Near-field thermal radiation can significantly exceed that predicted by the Stefan–Boltzmann law, especially when surface polaritons are excited such that the energy transfer is through photon tunneling. The penetration depth, or skin depth, of evanescent waves is usually a few tenths of a wavelength. This letter demonstrates that an extremely small skin depth (on the order of a nanometer) can exist for nanoscale thermal radiation between two plates separated by a vacuum gap, even though the dominant wavelengths are in the infrared. Furthermore, the skin depth is proportional to the separation distance.
Wideband vibration energy harvester with high permeability magnetic material
Authors: Xing X. , Lou J. , Yang G. M. , Obi O. , Driscoll C. , Sun N. X.
Published: September 2009

A vibration energy harvester based on a high permeability cantilever beam was demonstrated, which overcomes the limitation of the existing approaches in output power and working bandwidth. Magnetostatic coupling between the vibrating highly permeable beam and bias magnetic field leads to maximized flux change and large induced voltage. The coexistence of magnetostatic and elastic potential energy results in the nonlinear oscillation with wide bandwidth. The harvester showed a maximum power of 74 mW and power density of 1.07 mW/cm3 at 54 Hz under acceleration of 0.57 g (with g=9.8 m/s2), and bandwidth of 10 Hz (or 18.5% of the operating frequency).
Silicon electronics on silk as a path to bioresorbable, implantable devices
Authors: Kim Dae-Hyeong , Kim Yun-Soung , Amsden Jason , Panilaitis Bruce , Kaplan David L. , Omenetto Fiorenzo G. , Zakin Mitchell R. , Rogers John A.
Published: September 2009

Many existing and envisioned classes of implantable biomedical devices require high performance electronics/sensors. An approach that avoids some of the longer term challenges in biocompatibility involves a construction in which some parts or all of the system resorbs in the body over time. This paper describes strategies for integrating single crystalline silicon electronics, where the silicon is in the form of nanomembranes, onto water soluble and biocompatible silk substrates. Electrical, bending, water dissolution, and animal toxicity studies suggest that this approach might provide many opportunities for future biomedical devices and clinical applications.
Angular resolved effective optical properties of a Swiss cross metamaterial
Authors: Menzel C. , Helgert C. , Üpping J. , Rockstuhl C. , Kley E.-B. , Wehrspohn R. B. , Pertsch T. , Lederer F.
Published: September 2009

We both experimentally and theoretically study the effective optical properties of a Swiss cross metamaterial at oblique incidence and reveal their angular dependence. Almost perfect agreement between measured and calculated data is achieved. We show that the spectral and angular domains of negative refraction as well as its strength depend strongly on the light’s propagation direction and polarization state. Our results clearly indicate that a description of a Swiss cross metamaterial in terms of effective material parameters is impossible.
In situ studies of Al2O3 and HfO2 dielectrics on graphite
Authors: Pirkle Adam , Wallace Robert M. , Colombo Luigi
Published: September 2009

Deposition of Al2O3 and HfO2 dielectrics on graphite is studied as a route to the formation of a high-κ dielectric on graphene. Electron beam evaporation of metal Al and Hf is followed by a separate oxidation step. Reactive e-beam deposition of HfO2 by introduction of O2 to the deposition chamber is also demonstrated as an alternative to the two-step metal deposition and oxidation approach. We employ in situ x-ray photoelectron spectroscopy to study reactions between the substrate and deposited film and ex situ atomic force microscopy to examine the dielectric film morphology.
Ab initio study of the spectroscopy of AgBr: A CASSCF+Averaged Coupled Pair Functional approach to the lowest excited states including spin-orbit couplings
Authors: Amaro-Estrada J. I. , Ramírez-Solís A.
Published: September 2009

The nine lowest-lying singlet and triplet (X Σ1+, 2 Σ1+, 3 Σ1+, Σ3+, 1 Π3,1, 2 Π3, and Δ3,1) electronic states of AgBr were studied through state-specific Complete Active Space Self-Consistent Field with 16 active electrons in 12 orbitals followed by extensive Averaged Coupled Pair Functional and CIPT2 calculations with large optimized valence basis sets. The spin-orbit effects were included to obtain the Ω fine-structure states arising from the |ΛSΣ⟩ parents. Even before the inclusion of the spin-orbit effects, the 2 Σ1+ and 3 Σ1+ states present shallow minima near the equilibrium geometry of the ground state. The 2 Σ1+ state has another minimum around 8.0 a.u. and is attractive up to 20 a.u. The lowest Π3,1 states were found to be totally repulsive while the Δ3,1 states present deep minima around 4.8 a.u. Most of the calculated spectroscopic constants for the ground and B states are slightly improved with respect to the previous theoretical study using the much smaller CASSCF(16,10) reference wave functions [M. Guichemerre et al., Chem. Phys. 280, 71 (2002)]. The observed B←X transition is confirmed as arising from the singlet-to-singlet 0+(2 Σ1+)←0+(X Σ1+) excitation around 31 900 cm−1. However, at variance with the previous theoretical prediction, the C(Ω=0+) state is dominated around the equilibrium geometry of the ground state by the third Σ1+ state with a small contribution from the 2 Π3 state around 43 500 cm−1; thus the X-C excitation is now explained as arising also from a singlet-to-singlet spin-allowed transition.
Adiabatic connection for strictly correlated electrons
Authors: Liu Zhen-Fei , Burke Kieron
Published: September 2009

Modern density functional theory (DFT) calculations employ the Kohn–Sham system of noninteracting electrons as a reference, with all complications buried in the exchange-correlation energy (EXC). The adiabatic connection formula gives an exact expression for EXC. We consider DFT calculations that instead employ a reference of strictly correlated electrons. We define a “decorrelation energy” that relates this reference to the real system, and derive the corresponding adiabatic connection formula. We illustrate this theory in three situations, namely, the uniform electron gas, Hooke’s atom, and the stretched hydrogen molecule. The adiabatic connection for strictly correlated electrons provides an alternative perspective for understanding DFT and constructing approximate functionals.
Phase-space geometry of the generalized Langevin equation
Authors: Bartsch Thomas
Published: September 2009

The generalized Langevin equation is widely used to model the influence of a heat bath upon a reactive system. This equation will here be studied from a geometric point of view. A dynamical phase space that represents all possible states of the system will be constructed, the generalized Langevin equation will be formally rewritten as a pair of coupled ordinary differential equations, and the fundamental geometric structures in phase space will be described. It will be shown that the phase space itself and its geometric structure depend critically on the preparation of the system: A system that is assumed to have been in existence forever has a larger phase space with a simpler structure than a system that is prepared at a finite time. These differences persist even in the long-time limit, where one might expect the details of preparation to become irrelevant.
Gauge origin independent calculations of nuclear magnetic shieldings in relativistic four-component theory
Authors: Iliaš Miroslav , Saue Trond , Enevoldsen Thomas , Jensen Hans Jørgen Aa.
Published: September 2009

The use of perturbation-dependent London atomic orbitals, also called gauge including atomic orbitals, has proven efficient for calculations of NMR shielding constants and other magnetic properties in the nonrelativistic framework. In this paper, the theory of London atomic orbitals for NMR shieldings is extended to the four-component relativistic framework and our implementation is described. The relevance of London atomic orbitals in four-component calculations as well as computational aspects are illustrated with test calculations on hydrogen iodide. We find that the use of London atomic orbitals is an efficient method for reliable calculations of NMR shielding constants with standard basis sets, also for four-component calculations with spin-orbit coupling effects included in the wave function optimization. Furthermore, we find that it is important that the small component basis functions fulfill the magnetic balance for accurate description of the diamagnetic shielding and that the role of London atomic orbitals in the relativistic domain is to provide atomic magnetic balance even in the molecular case, thus greatly improving basis set convergence. The Sternheim approximation, which calculates the diamagnetic contribution as an expectation value, leads to significant errors and is not recommended.
Electron temperature difference between the o-point and x-point of a magnetic island
Authors: Yang Jinhong , Yu Qingquan , Zhu Sizheng , Zhuang G.
Published: September 2009

The electron temperature difference between the o-point and the x-point of a magnetic island is studied numerically by solving the two-dimensional energy transport equation. It is found that, even without a localized radio-frequency heating at the island's o-point, there is usually a temperature difference between these two points. This difference depends on the radial profile of the heating power deposition, the ratio between the parallel and the perpendicular heat conductivity and the island width, and it takes a minimum when the island width is about twice the local heat diffusion layer width. The effect of the temperature difference on the island growth is further studied, and the peaked heating power density profile at magnetic axis is found be destabilizing.
Evolution of weakly dissipative hybrid dust ion-acoustic solitons in complex plasmas
Authors: Losseva T. V. , Popel S. I. , Golub’ A. P. , Shukla P. K.
Published: September 2009

Possibility for hybrid ion-acoustic solitons to exist in complex (dusty) plasmas is investigated. Rarefactive solitonlike perturbations are damped and slowed down, mainly due to the plasma absorption and ion scattering on microparticles. Nevertheless, the amplitude of the evolving perturbation at any moment is given by the amplitude of the “conservative” soliton for the corresponding Mach number (so far as the conservative soliton exists). That property allows us to interpret the evolving rarefactive perturbation as a “weakly dissipative” hybrid dust ion-acoustic soliton. The weakly dissipative hybrid dust ion-acoustic solitons can be studied experimentally in laboratory complex plasmas.
GaN and InGaN(112̱2) surfaces: Group-III adlayers and indium incorporation
Authors: Northrup John E.
Published: September 2009

First-principles calculations for clean and In-rich GaN(112̱2) surfaces indicate that indium will, for the same indium chemical potential, incorporate in higher concentrations on the (112̱2) surface than on the (101̱0) surface. Because In atoms are larger than Ga atoms, there is a strain-induced repulsive interaction between incorporated In atoms on the surface. This interaction is weaker on the (112̱2) surface in comparison to the (101̱0) surface.
Translating oscillatory nonlinear structure in a plasma boundary
Authors: Haas F. , Shukla P. K.
Published: September 2009

By means of a Madelung decomposition, exact periodic traveling solutions are constructed for a modified nonlinear Schrödinger equation derived by Stenflo and Gradov, describing electrostatic surface waves in semi-infinite plasma. The condition for the existence of bistable equilibria is discussed. A conservation law as well as the modulational instability admitted by the model are analyzed.
Factors affecting nest-site selection and nest success of translocated greater sage grouse
Authors: Baxter Rick J. , Flinders Jerran T. , Whiting David G. , Mitchell Dean L.
Published: September 2009

Translocations have been used for decades to restore or augment wildlife populations, yet more often than not, little to no data and/or arbitrary means are used for determining translocation success. The objectives of our study were to describe nesting habitat utilised by the greater sage grouse translocated into an extant population and to identify factors related to nest success, thereby demonstrating the adaptability of the birds to their new environment and producing one measure of long-term translocation success. We trapped female grouse individuals during the spring on and near leks of source populations, fitted them with radio-transmitters, and released them in the morning onto an active lek in an extant population in Strawberry Valley, Utah. We monitored translocated females for nesting activity and documented nesting attempts, nest success, clutch size and embryo viability. Data were recorded on habitat variables associated with nest sites and paired-random sites, including factors known to be important for resident females that nested successfully. We used logistic regression and an a priori information-theoretic approach for modelling nest v. paired-random sites and successful v. unsuccessful nest sites. Our analyses suggested that crown area of the nest shrub and percentage grass cover were the two variables that discriminated between nest and paired-random sites. Females that nested successfully selected sites with more total shrub canopy cover, intermediate size-shrub crown area, aspects other than NW and SE, and steeper slopes than for unsuccessful nests. After being translocated from distant sites with differing habitat characteristics, these birds were able to initiate a nest, nest successfully, and select micro-habitat features similar to those selected by resident sage grouse across the species range. Our results demonstrate the adaptability of the translocated female sage grouse individuals and produce one tangible measure of long-term translocation success.
Impacts on a threatened bird population of removals for translocation
Authors: Bain David , French Kristine
Published: September 2009

The removal of individuals from a population may occur for several reasons and responses of populations will vary depending on the magnitude and nature of the removal and the life history of the species. An understanding of the effects of loss of individuals on these populations, and the mechanism of replacement, will be important to conservation. This may be particularly important where wild individuals are used for the increasingly popular conservation strategy of translocation. During the recent translocation of the endangered eastern bristlebird (Dasyornis brachypterus), two monitoring sites were established in the wild source population, one where removals were to take place and another as a control to assess the impact of the removals on the population. The removal of 44 eastern bristlebirds across 3 years from a single area in the source population had no significant detectable impact in the numbers of individuals surveyed. Individuals that were removed appeared to have been replaced within 6 months of their removal, although to a lesser extent in the later part of the study. The origin of the replacement eastern bristlebirds was unknown and the quick recovery was suggested to be a result of juvenile dispersal, perhaps combined with territory uptake by previously non-territorial and non-calling (thus undetectable) individuals within the population. Such a surplus may be a result of insufficient suitable habitat for population expansion, and will also have implications for monitoring populations of rare and cryptic species. It is also suggested that some territorial species may have several mechanisms that can replace losses of individuals from a population.
Shedding new light on old species identifications: morphological and genetic evidence suggest a need for conservation status review of the critically endangered bat, Saccolaimus saccolaimus
Authors: Milne Damian J. , Jackling Felicity C. , Sidhu Manpreet , Appleton Belinda R.
Published: September 2009

Information based on the accurate identification of species is a vital component for achieving successful outcomes of biodiversity conservation and management. It is difficult to manage species that are poorly known or that are misidentified with other similar species. This is particularly problematic for rare and threatened species. Species that are listed under endangered species classification schemes need to be identified accurately and categorised correctly so that conservation efforts are appropriately allocated. In Australia, the emballonurid Saccolaimus saccolaimus is currently listed as ‘Critically Endangered’. On the basis of new observations and existing museum specimens, we used a combination of genetic (mitochondrial DNA sequence) and morphological (pelage characteristics, dig III : phalanx I length ratio, inter-upper canine distance) analyses to identify six new geographic records for S. saccolaimus, comprising ~100 individuals. Our analyses also suggested that there are likely to be more records in museum collections misidentified as S. flaviventris specimens. The external morphological similarities to S. flaviventris were addressed and genetic, morphological and echolocation analyses were used in an attempt to provide diagnostic characters that can be used to readily identify the two species in the field. We recommend genetic testing of all museum specimens of Australian Saccolaimus to clarify species’ distributions and provide data for reassessing the conservation status for both S. saccolaimus and S. flaviventris. Museum curators, taxonomists and wildlife managers need to be aware of potential species misidentifications, both in the field and laboratory. Misidentifications that result in misclassification of both threatened and non-threatened species can have significant implications.
Does habitat structure influence capture probabilities? A study of reptiles in a eucalypt forest
Authors: Craig Michael D. , Grigg Andrew H. , Garkaklis Mark J. , Hobbs Richard J. , Grant Carl D. , Fleming Patricia A. , Hardy Giles E. St J.
Published: September 2009

Pitfall traps are commonly used to examine differences in reptile communities among habitat types and disturbance regimes that differ in structure. However, capture rates and probabilities may be influenced by habitat structure, which invalidates comparisons of relative abundance among habitat types. To assess whether pitfall traps provide accurate reflections of density and whether habitat structure affects capture probabilities, we trapped at six sites in various jarrah-forest habitat types in south-western Australia, then intensively searched 150-m2 total-removal plots around each pitfall grid to obtain absolute densities of reptiles. Pitfall captures were significantly correlated with numbers on total-removal plots for Hemiergis initialis and Lerista distinguenda, indicating that pitfall traps provided accurate reflections of density for these species. Capture probabilities of H. initialis and L. distinguenda and all reptiles combined showed no significant correlations with any structural variables, indicating that capture probabilities were consistent across sites. We conclude that trapping provided accurate estimates of relative abundance for some species and that capture probabilities were not influenced by vegetation structure. Because many studies use trapping to estimate abundances among habitat types, we encourage researchers to investigate how vegetation structure influences capture probabilities, so that general patterns can be determined; we also suggest improvements for any future studies.
Practicality and humaneness of euthanasia of pest birds with compressed carbon dioxide (CO2) and carbon monoxide (CO) from petrol engine exhaust
Authors: Tidemann Christopher R. , King Daryl H.
Published: September 2009

Feral birds degrade the environment and have an adverse impact on human health, welfare and economy in many parts of the world. In eastern Australia, common myna (Acridotheres tristis), common starling (Sturnus vulgaris) and house sparrow (Passer domesticus) have recently become targets of community groups seeking to control impacts by selective live-trapping. We sought a safe and practical euthanasia method that could be recommended to such groups for humanely destroying trapped birds. We compared the practicality and humaneness of the following two commonly available inhalant euthanasia agents: (1) carbon dioxide (CO2) from cylinders and (2) carbon monoxide (CO) from cooled exhaust from idling petrol engines. Test birds were euthanased in conditions that promoted calm (small groups of birds; small covered chambers with perches). Video recordings were analysed in real time and at 1/10 speed for signs of distress, and times to recumbency and last movement. In all, 25 mynas and 24 starlings were euthanased with CO2, and 32 mynas, 30 starlings and 8 sparrows with CO. Times to recumbency for birds euthanased with CO2 varied from 20 to 85 s and time to last movement from 65 to 153 s. For birds euthanased with CO, these times were 7–180 s and 43–240 s respectively. Mynas and starlings euthanased with CO2 showed substantially more signs of distress (gaping and head-shaking) before recumbency than did birds euthanased with CO, although this was less pronounced if the concentration was increased slowly. No signs of distress were observed in any birds euthanased with CO, irrespective of the rate at which the concentration was increased. CO produced a comparably rapid, and more humane death than did CO2 in birds of all three study species. The study indicated that, with simple precautions to avoid accidental exposure, CO in cooled exhaust from petrol engines provides a safe, rapid and humane agent for euthanasing mynas, starlings and sparrows, that is readily available at a very low cost. We tested only three species, and the results suggested that it would be useful to re-examine the embargo against animal euthanasia via engine exhaust, that exists in many jurisdictions.
Functionally diverse reef-fish communities ameliorate coral disease
Authors: Raymundo Laurie J. , Halford Andrew R. , Maypa Aileen P. , Kerr Alexander M.
Published: September 2009

Coral reefs, the most diverse of marine ecosystems, currently experience unprecedented levels of degradation. Diseases are now recognized as a major cause of mortality in reef-forming corals and are complicit in phase shifts of reef ecosystems to algal-dominated states worldwide. Even so, factors contributing to disease occurrence, spread, and impact remain poorly understood. Ecosystem resilience has been linked to the conservation of functional diversity, whereas overfishing reduces functional diversity through cascading, top-down effects. Hence, we tested the hypothesis that reefs with trophically diverse reef fish communities have less coral disease than overfished reefs. We surveyed reefs across the central Philippines, including well-managed marine protected areas (MPAs), and found that disease prevalence was significantly negatively correlated with fish taxonomic diversity. Further, MPAs had significantly higher fish diversity and less disease than unprotected areas. We subsequently investigated potential links between coral disease and the trophic components of fish diversity, finding that only the density of coral-feeding chaetodontid butterflyfishes, seldom targeted by fishers, was positively associated with disease prevalence. These previously uncharacterized results are supported by a second large-scale dataset from the Great Barrier Reef. We hypothesize that members of the charismatic reef-fish family Chaetodontidae are major vectors of coral disease by virtue of their trophic specialization on hard corals and their ecological release in overfished areas, particularly outside MPAs.
CD39 deletion exacerbates experimental murine colitis and human polymorphisms increase susceptibility to inflammatory bowel disease
Authors: Friedman David J. , Künzli Beat M. , A-Rahim Yousif I. , Sevigny Jean , Berberat Pascal O. , Enjyoji Keiichi , Csizmadia Eva , Friess Helmut , Robson Simon C.
Published: September 2009

CD39/ENTPD1 hydrolyzes proinflammatory nucleotides to generate adenosine. As purinergic mediators have been implicated in intestinal inflammation, we hypothesized that CD39 might protect against inflammatory bowel disease. We studied these possibilities in a mouse model of colitis using mice with global CD39 deletion. We then tested whether human genetic polymorphisms in the CD39 gene might influence susceptibility to Crohn's disease. We induced colitis in mice using Dextran Sodium Sulfate (DSS). Readouts included disease activity scores, histological evidence of injury, and markers of inflammatory activity. We used HapMap cell lines to find SNPs that tag for CD39 expression, and then compared the frequency of subjects with high vs. low CD39-expression genotypes in a case-control cohort for Crohn's disease. Mice null for CD39 were highly susceptible to DSS injury, with heterozygote mice showing an intermediate phenotype compared to wild type (WT). We identified a common SNP that tags CD39 mRNA expression levels in man. The SNP tagging low levels of CD39 expression was associated with increased susceptibility to Crohn's disease in a case-control cohort comprised of 1,748 Crohn's patients and 2,936 controls (P= 0.005–0.0006). Our data indicate that CD39 deficiency exacerbates murine colitis and suggest that CD39 polymorphisms are associated with inflammatory bowel disease in humans.
Evolutionary replacement of UV vision by violet vision in fish
Authors: Tada Takashi , Altun Ahmet , Yokoyama Shozo
Published: September 2009

The vertebrate ancestor possessed ultraviolet (UV) vision and many species have retained it during evolution. Many other species switched to violet vision and, then again, some avian species switched back to UV vision. These UV and violet vision are mediated by short wavelength-sensitive (SWS1) pigments that absorb light maximally (λmax) at approximately 360 and 390–440 nm, respectively. It is not well understood why and how these functional changes have occurred. Here, we cloned the pigment of scabbardfish (Lepidopus fitchi) with a λmaxof 423 nm, an example of violet-sensitive SWS1 pigment in fish. Mutagenesis experiments and quantum mechanical/molecular mechanical (QM/MM) computations show that the violet-sensitivity was achieved by the deletion of Phe-86 that converted the unprotonated Schiff base-linked 11-cis-retinal to a protonated form. The finding of a violet-sensitive SWS1 pigment in scabbardfish suggests that many other fish also have orthologous violet pigments. The isolation and comparison of such violet and UV pigments in fish living in different ecological habitats will open an unprecedented opportunity to elucidate not only the molecular basis of phenotypic adaptations, but also the genetics of UV and violet vision.
Identification of functional marker proteins in the mammalian growth cone
Authors: Nozumi Motohiro , Togano Tetsuya , Takahashi-Niki Kazuko , Lu Jia , Honda Atsuko , Taoka Masato , Shinkawa Takashi , Koga Hisashi , Takeuchi Kosei , Isobe Toshiaki , Igarashi Michihiro
Published: September 2009

Identification of proteins in the mammalian growth cone has the potential to advance our understanding of this critical regulator of neuronal growth and formation of neural circuit; however, to date, only one growth cone marker protein, GAP-43, has been reported. Here, we successfully used a proteomic approach to identify 945 proteins present in developing rat forebrain growth cones, including highly abundant, membrane-associated and actin-associated proteins. Almost 100 of the proteins appear to be highly enriched in the growth cone, as determined by quantitative immunostaining, and for 17 proteins, the results of RNAi suggest a role in axon growth. Most of the proteins we identified have not previously been implicated in axon growth and thus their identification presents a significant step forward, providing marker proteins and candidate neuronal growth-associated proteins.
Groucho corepressor functions as a cofactor for the Knirps short-range transcriptional repressor
Authors: Payankaulam Sandhya , Arnosti David N.
Published: September 2009

Despite the pervasive roles for repressors in transcriptional control, the range of action of these proteins on
cis
regulatory elements remains poorly understood. Knirps has essential roles in patterning the
Drosophila
embryo by means of short-range repression, an activity that is essential for proper regulation of complex transcriptional control elements. Short-range repressors function in a local fashion to interfere with the activity of activators or basal promoters within ≈100 bp. In contrast, long-range repressors such as Hairy act over distances >1 kb. The functional distinction between these two classes of repressors has been suggested to stem from the differential recruitment of the CtBP corepressor to short-range repressors and Groucho to long-range repressors. Contrary to this differential recruitment model, we report that Groucho is a functional part of the Knirps short-range repression complex. The corepressor interaction is mediated via an eh-1 like motif present in the N terminus and a conserved region present in the central portion of Knirps. We also show that this interaction is important for the CtBP-independent repression activity of Knirps and is required for regulation of
even-skipped
. Our study uncovers a previously uncharacterized interaction between proteins previously thought to function in distinct repression pathways, and indicates that the Groucho corepressor can be differentially harnessed to execute short- and long-range repression.
Cell surface-bound IL-1α is an upstream regulator of the senescence-associated IL-6/IL-8 cytokine network
Authors: Orjalo Arturo V. , Bhaumik Dipa , Gengler Bridget K. , Scott Gary K. , Campisi Judith
Published: September 2009

Inflammation underlies most age-related diseases, including cancer, but the etiology is poorly understood. One proposed factor is the presence of senescent cells, which increase with age. The senescence response arrests the proliferation of potentially oncogenic cells, and most senescent cells secrete high levels of proinflammatory cytokines and other proteins. The complex senescence-associated secretory phenotype is likely regulated at multiple levels, most of which are unknown. We show that cell surface-bound IL-1α is essential for signaling the senescence-associated secretion of IL-6 and IL-8, 2 proinflammatory cytokines that also reinforce the senescence growth arrest. Senescent human fibroblasts expressed high levels of IL-1α mRNA, intracellular protein, and cell surface-associated protein, but secreted very little protein. An IL-1 receptor (IL1R) antagonist, neutralizing IL-1α antibodies, and IL-1α depletion by RNA interference all markedly reduced senescence-associated IL-6/IL-8 secretion. Depletion of the key IL-1R signaling component IRAK1 also suppressed this secretion, and IL-1α neutralizing antibodies prevented IRAK1 degradation, indicating engagement of the IL-1R signaling pathway. Furthermore, IL-1α depletion reduced the DNA binding activity of NF-κB and C/EBPβ, which stimulate IL-6/IL-8 transcription. IL-1α was a general regulator of senescence-associated IL-6/IL-8 secretion because IL-1α blockade reduced IL-6/IL-8 secretion whether cells senesced owing to DNA damage, replicative exhaustion, oncogenic RAS, or chromatin relaxation. Furthermore, conditioned medium from IL-1α-depleted senescent cells markedly reduced the IL-6/IL-8-dependent invasiveness of metastatic cancer cells, indicating that IL-1α regulates the biological effects of these cytokines. Thus, cell surface IL-1α is an essential cell-autonomous regulator of the senescence-associated IL-6/IL-8 cytokine network.
Spectroelectrochemical determination of the redox potential of pheophytina, the primary electron acceptor in photosystem II
Authors: Kato Yuki , Sugiura Miwa , Oda Akinori , Watanabe Tadashi
Published: September 2009

Thin-layer cell spectroelectrochemistry, featuring rigorous potential control and rapid redox equilibration within the cell, was used to measure the redox potentialEm(Phea/Phea−) of pheophytin (Phe)a, the primary electron acceptor in an oxygen-evolving photosystem (PS) II core complex from a thermophilic cyanobacteriumThermosynechococcus elongatus. Interferences from dissolved O2and water reductions were minimized by airtight sealing of the sample cell added with dithionite and mercury plating on the gold minigrid working electrode surface, respectively. The result obtained at a physiological pH of 6.5 wasEm(Phea/Phea−) = −505 ± 6 mV vs. SHE, which is by ≈100 mV more positive than the values measured ≈30 years ago at nonphysiological pH and widely accepted thereafter in the field of photosynthesis research. Using the P680* − Pheafree energy difference, as estimated from kinetic analyses by previous authors, the present result would locate theEm(P680/P680+) value, which is one of the key parameters but still resists direct measurements, at approximately +1,210 mV. In view of these pieces of information, a renewed diagram is proposed for the energetics in PS II.