bluuebunny/crossref_metadata_2025 huggingface dataset:
Influence of nonstoichiometry on ferroelectric phase transition in BaTiO3
Authors: Lee Soonil , Liu Zi-Kui , Kim Myong-Ho , Randall Clive A.
Published: March 2007

The ferroelectric phase transition behavior in equilibrated nonstoichiometric BaTiO3 powder samples was characterized by a differential scanning calorimeter. The transition temperature (TC) and enthalpy of transition (ΔHTC) between the paraelectric and ferroelectric phases were varied systematically with defect concentrations through the Ba∕Ti ratio, temperature, and oxygen partial pressure [p(O2)]. It was observed that the different defects such as titanium, barium, and oxygen vacancies all contribute to the changes of TC and ΔHTC. The TC decreased with increasing concentration of TiO2 partial Schottky defects and BaO partial Schottky defects. The annealing temperature increased the TC due to a complex mechanism with the increase of full Schottky defect reactions. In terms of p(O2), TC is constant in the ionic compensation region, and increases with the nonstoichiometry in the electronically compensated p(O2) region.
Synthesis of monocrystal aluminum nitride nanowires at low temperature
Authors: Lv Huimin , Chen Guangde , Ye Honggang , Yan Guojun
Published: March 2007

Hexagonal monocrystal aluminum nitride (h-AlN) nanowires are synthesized through the direct reaction of AlCl3 with NaN3 in a nonsolvent system at low temperatures. The h-AlN nanowires are characterized by the high-resolution transmission electron microscope, electron diffraction, x-ray diffraction, and photoluminescence spectra. The analysis shows that the nanowire has a long straight-wire morphology with a diameter ranging from 40to60nm, the longest one up to several micrometers, and they are of pure monocrystal hexagonal or face center structure which has a relatively narrow emission peak, centered at 413nm (3.00eV). In addition, a possible growth mechanism for h-AlN nanowire is discussed.
Polarized light emission from semipolar GaInN quantum wells on {11¯01} GaN facets
Authors: Feneberg M. , Lipski F. , Sauer R. , Thonke K. , Brückner P. , Neubert B. , Wunderer T. , Scholz F.
Published: March 2007

GaInN quantum wells with reduced piezoelectric field deposited epitaxially on the {11¯01} facets of selectively grown GaN stripes show distinct polarization properties of the emitted light. Systematic electro- and photoluminescence studies demonstrate that the light is linearly polarized parallel to the stripes, representing the ⟨112¯0⟩ direction of the GaN crystal. Our model calculations show that this is a consequence of the strain-induced valence-band splitting depending on the crystal orientation. The polarization ratio is calculated and compared to measured values.
Intrinsic photoluminescence of M-plane GaN films on LiAlO2 substrates
Authors: Rivera Carlos , Misra Pranob , Pau José Luis , Muñoz Elías , Brandt Oliver , Grahn Holger T. , Ploog Klaus H.
Published: March 2007

Polarized photoluminescence spectra of M-plane GaN films grown on LiAlO2 substrates demonstrate the existence of a large polarization anisotropy in the near-band-gap excitonic transitions, which is consistent with the reduction of the in-plane crystal symmetry and the anisotropic strain generated by the lattice mismatch between GaN and LiAlO2. Band structure calculations based on the k∙p formalism support the observed experimental results and allow us to explain the temperature dependence of the photoluminescence energy. From the results of these calculations and the measured excitonic transition energies, we accurately determined the in-plane strain. The strain relaxation as a function of temperature and the role of the film thickness in the in-plane strain anisotropy are also discussed.
Magnetization process in a ferromagnetic disk measured by a semiconductor two-dimensional electron gas
Authors: Hara Masahiro , Otani Yoshichika
Published: March 2007

We have monitored a magnetization process in a ferromagnetic disk by measuring a bend resistance of semiconductor two-dimensional electron gas (2DEG) lying beneath the disk. Annihilation and nucleation of a vortex in the ferromagnetic disk are clearly seen in the trace of the bend resistance as a function of in-plane magnetic field. The large change in the signal is well reproduced by a simulation based on a semiclassical billiard model.
Abnormal I-V characteristics and metal-insulator transition of Fe-doped amorphous carbon∕silicon p-n junction
Authors: Hao Lanzhong , Xue Qingzhong , Gao Xili , Li Qun , Zheng Qingbin , Yan Keyou
Published: March 2007

Simple p-C∕n-Si junctions have been fabricated by magnetron sputtering at room temperature and their current-voltage (I-V) characteristics have been investigated. The p-n junctions show good rectifying properties in a large voltage scope and interesting I-V characteristics. The most interesting phenomenon observed in these p-n junctions is that the temperature dependence of some junction resistance shows a metal-insulator transition whose transition temperature is hugely modulated from 162to236K by a bias voltage increasing from 20to40V. This work shows that amorphous carbon films combined with other semiconductor materials can result in some interesting properties that may have potential applications.
Inverse magnetocaloric effect in ferromagnetic Ni50Mn37+xSb13−x Heusler alloys
Authors: Khan Mahmud , Ali Naushad , Stadler Shane
Published: March 2007

A study of the magnetocaloric effect (MCE) in the ferromagnetic Heusler alloys Ni50Mn37+xSb13−x (x=0,0.5,1) has been carried out through magnetization measurements. An inverse magnetocaloric effect was observed in the vicinity of the first order martensitic transition. A maximum positive magnetic entropy change of ΔSm≈19J∕kgK at approximately 297K for a magnetic field change of 5T was observed. It is demonstrated that the martensitic transformation temperature, and the corresponding ΔSm, can be tuned through a slight variation in composition.
Magnetic, electrical, and microstructural characterization of ZnO thin films codoped with Co and Cu
Authors: Chakraborti D. , Ramachandran S. , Trichy G. , Narayan J. , Prater J. T.
Published: March 2007

Here we report on systematic studies of the epitaxial growth and properties of Co and Cu codoped ZnO thin films deposited onto sapphire c-plane single crystals using pulsed-laser deposition. The films display ferromagnetic behavior at room temperature. Detailed atomic scale characterization rules out the presence of clusters and secondary phases as the source of ferromagnetism. Optical measurements and x-ray photoelectron spectroscopy confirm the direct substitution of dopant atoms into Zn lattice sites. At low concentrations of Cu (∼5%) the magnetic moment of Zn1−(0.05+x)Co0.05CuxO materials appears to be additive. At higher concentrations of Cu the net magnetic moment per atom drops off sharply and seems to be relatively insensitive to the Co content. There is a dramatic increase in resistivity of the Co-doped films that accompanies Cu doping. Yet, this change of resistivity does not affect the magnetic moment, suggesting that free carrier mediated mechanism is not a feasible explanation for ferromagnetism in these films. The known presence of high oxygen vacancies in these films does allow for possible defect mediated mechanisms (e.g., bound magnetic polarons) for mediating exchange coupling of the dopant (Co,Cu) ions resulting in room temperature ferromagnetism.
High-mobility and air-stable organic thin-film transistors with highly ordered semiconducting polymer films
Authors: Umeda Tokiyoshi , Tokito Shizuo , Kumaki Daisuke
Published: March 2007

We report on high crystalline thin films of liquid-crystalline polythiophene derivative, poly(2,5-bis(3-hexadecylthiophene-2-yl)thieno[3,2-b]thiophene) (PB16TTT) that exhibit terrace structures and molecular steps of its polymer chains by annealing in its liquid-crystalline phase. The crystallinity of the PB16TTT polymer films formed on SiO2 gate insulating layers with smooth self-assembled monolayer was improved by changing the octyltrichlorosilane treatment time for the SiO2, which led to reproducible high field-effect mobilities of the polymer thin-film transistors up to 0.44cm2∕Vs. High stability of the transistor for repeated stressing in ambient air was also demonstrated.
Wafer-level filling of microfabricated atomic vapor cells based on thin-film deposition and photolysis of cesium azide
Authors: Liew Li-Anne , Moreland John , Gerginov Vladislav
Published: March 2007

The thin-film deposition and photodecomposition of cesium azide are demonstrated and used to fill arrays of miniaturized atomic resonance cells with cesium and nitrogen buffer gas for chip-scale atomic-based instruments. Arrays of silicon cells are batch fabricated on wafers into which cesium azide is deposited by vacuum thermal evaporation. After vacuum sealing, the cells are irradiated with ultraviolet radiation, causing the azide to photodissociate into pure cesium and nitrogen in situ. This technology integrates the vapor-cell fabrication and filling procedures into one continuous and wafer-level parallel process, and results in cells that are optically transparent and chemically pure.
Design of a crystalline undulator based on patterning by tensile Si3N4 strips on a Si crystal
Authors: Guidi V. , Lanzoni L. , Mazzolari A. , Martinelli G. , Tralli A.
Published: March 2007

A crystalline undulator consists of a crystal with a periodic deformation in which channeled particles undergo oscillations and emit coherent undulator radiation. Patterning by an alternate series of tensile Si3N4 strips on a Si crystal is shown to be a tractable method to construct a crystalline undulator. The method allows periodic deformation of the crystal with the parameters suitable for implementation of a crystalline undulator. The resulting periodic deformation is present in the bulk of the Si crystal with an essentially uniform amplitude, making the entire volume of the crystal available for channeling and in turn for emission of undulator radiation.
Global action-angle coordinates for completely integrable systems with noncompact invariant submanifolds
Authors: Fiorani E. , Sardanashvily G.
Published: March 2007

The obstruction to the existence of global action-angle coordinates of Abelian and noncommutative (non-Abelian) completely integrable systems with compact invariant submanifolds has been studied. We extend this analysis to the case of noncompact invariant submanifolds.
Relaxor-like behavior of lead-free Sr2LaTi2Nb3O15 ceramics with tetragonal tungsten bronze structure
Authors: Bovtun V. , Kamba S. , Veljko S. , Nuzhnyy D. , Knížek K. , Savinov M. , Petzelt J.
Published: March 2007

Lead-free tetragonal tungsten bronze Sr2LaTi2Nb3O15 ceramics were prepared and its crystal structure determined. Dielectric response of Sr2LaTi2Nb3O15 was investigated in a broad frequency (100 Hz–90 THz) and temperature range. The observed relaxor-like behavior can be generally described in the framework of polar nanocluster dynamics concept. However, some peculiarities in the dielectric response, relaxational, and crystal lattice dynamics (e.g., hardly resolved Vogel–Fulcher part of the relaxation, reduced dielectric strength of the cluster flipping mechanism, absence of ferroelectric phase under electric field, absence of the polar soft phonon, etc.) were revealed. Therefore, we claim that Sr2LaTi2Nb3O15 is more alike to dipolar glasses than lead-based perovskite relaxor ferroelectrics.
Effect of fluorination on the electronic structure and optical excitations of π-conjugated molecules
Authors: Milián Medina Begoña , Beljonne David , Egelhaaf Hans-Joachim , Gierschner Johannes
Published: March 2007

Fluorination of π-conjugated organic molecules is a strategy to obtain possible n-type conducting and air-stable materials due to the lowering of the frontier molecular orbitals (MOs) by the high electronegativity of fluorine. Nevertheless, the resulting optical gaps may be widened or narrowed, depending on the molecular backbone and/or the number and position of the fluorine atoms. The authors have performed time-dependent density functional theory calculations to address the subtle influence of fluorine substitution on the absolute MO energies and the subsequent impact on the optical transitions in homologous conjugated oligomers based on thiophene and acene units.
Ab initio studies of crystalline nitromethane under high pressure
Authors: Zerilli Frank J. , Hooper Joseph P. , Kuklja Maija M.
Published: March 2007

We have studied the mechanical compressibility and band structure of solid nitromethane both in equilibrium and compressed states using Hartree-Fock and density functional theory (DFT) with atom-centered all-electron linear combination of atomic orbitals basis sets. Hartree-Fock calculations with a 6-21G basis set, uncorrected for basis set superposition error, gave the best agreement with experimental compression studies. These results may be due to the cancellation of basis set superposition error with dispersion force errors. The equilibrium DFT band gap is comparable to the lowest-energy feature in electron-impact spectroscopy of nitromethane but underpredicts the optical absorption gap; we interpret these features in terms of the presence of tightly bound excitons. Only minor changes in the gap are observed under hydrostatic compression.
Synthesis and band gap of ZnO particles with hexagonal bilayer structure
Authors: Zhang Jianhui , Liu Huaiyong , Wang Zhenlin , Ming Naiben
Published: March 2007

The unique water/PVP (polyvinylpyrrolidone)/n-pentanol interface has been developed to prepare the ZnO particles with hexagonal bilayer structure. By modifying the interface through varying the amount of PVP and water, one can readily tune the particle size and change the particle shape from hexagonal bilayer to capped potlike to hemispherical features. The study of the growth dynamics and extinction spectra suggests that the bilayer structure arises from the selective adsorption of PVP on the ZnO crystallographic planes. Both the photoluminescence and extinction spectra show that the band gap of the hexagonal bilayer ZnO particles shrinks with increasing particle size.
Magneto-optical and magnetotransport properties of heavily Mn-doped GaMnAs
Authors: Ohya Shinobu , Ohno Kenichi , Tanaka Masaaki
Published: March 2007

The authors have studied the magneto-optical and magnetotrasnport properties of Ga1−xMnxAs thin films with high Mn concentrations (x=12.2%–21.3%) grown by molecular-beam epitaxy. These heavily Mn-doped GaMnAs films were formed by decreasing the growth temperature to as low as 150–190°C and by reducing the film thickness to 10nm in order to prevent precipitation of hexagonal MnAs clusters. Magnetic circular dichroism and anomalous Hall effect measurements indicate that these GaMnAs films have the nature of intrinsic ferromagnetic semiconductors with high ferromagnetic transition temperature up to 170K.
Organic light-emitting diodes with photonic crystals on glass substrate fabricated by nanoimprint lithography
Authors: Ishihara Kuniaki , Fujita Masayuki , Matsubara Ippei , Asano Takashi , Noda Susumu , Ohata Hiroshi , Hirasawa Akira , Nakada Hiroshi , Shimoji Noriyuki
Published: March 2007

The authors have fabricated organic light-emitting diodes (OLEDs) having two-dimensional photonic crystals (PC) as light extraction elements by employing nanoimprint lithography technique. PCs were imprinted on the glass substrate and OLED layers were formed on the imprinted side of the glass substrate. The device having PC showed the improvement of luminance by a factor of 1.5 compared to normal devices. The authors conclude that the nanoimprint lithography is very useful for the fabrication of the OLEDs with PC.
Rapid rise time pulsed magnetic field circuit for pump-probe field effect studies
Authors: Salaoru T. A. , Woodward Jonathan R.
Published: March 2007

Here we describe an electronic circuit capable of producing rapidly switched dc magnetic fields of up to 20mT with a rise time of 10ns and a pulse length variable from 50ns to more than 10μs, suitable for use in the study of magnetic field effects on radical pair (RP) reactions. This corresponds to switching the field on a time scale short relative to the lifetime of typical RPs and maintaining it well beyond their lifetimes. Previous experiments have involved discharging a capacitor through a low inductance coil for a limited time using a switching circuit. These suffer from decaying field strength over the duration of the pulse given primarily by the ratio of the pulse width to the RC constant of the circuit. We describe here a simple yet elegant solution that completely eliminates this difficulty by employing a feedback loop. This allows a constant field to be maintained over the entire length of the pulse.
Scaling of interface displacement in a microfluidic comparator
Authors: Vanapalli S. A. , van den Ende D. , Duits M. H. G. , Mugele F.
Published: March 2007

The authors quantify both experimentally and theoretically the scaling behavior between interface displacement and excess pressure drop in a microfluidic comparator. Unlike previous studies, the authors measure the interface displacement in the outlet channel of the comparator that yields a unique power-law scaling. For an outlet channel width to depth ratio r=3, the authors experimentally determine the scaling exponent to be 0.60±0.01, which is in excellent agreement with theory. In general, the authors find the scaling exponent to increase from 0.51 for square channels (r=1) to 0.93 for very wide channels (r>100). This geometry dependent scaling exponent offers greater sensitivity and flexibility in measurement of hydrodynamic resistance of soft objects.
Design and performance of a sub-nanoradian resolution autocollimating optical lever
Authors: Cowsik R. , Srinivasan R. , Kasturirengan S. , Kumar A. Senthil , Wagoner K.
Published: March 2007

Precision goniometry using optics has the advantage that it does not impose much stress on the object of investigation and, as such, is adopted extensively in gravitational wave detection, in torsion balances investigating fundamental forces, in specialized studies of biological samples, and it has potential applications in condensed matter physics. In this article we present the considerations that go into designing optical levers and discuss the performance of the instrument we have constructed. We motivate the design by considering an idealized setup and the limitations to the angular resolution induced by statistical fluctuations of the photon count rate and diffraction at the apertures. The effects of digitization of the count rate and of the spatial location of the photons on the image plane motivating the actual design are discussed next. Based on these considerations, we have developed an autocollimating optical lever which has a very high resolution and dynamic range. An array of 110 slits, of 90 μm width and a pitch of 182 μm, is located in the focal plane of a field lens, of focal length 1000 mm, and is illuminated by a CCFL tube. This array is imaged back onto the focal plane after retroreflection from a mirror placed just beyond the lens. The image is recorded on a linear charge-coupled device array at the rate of 1000 images/s and is processed through a special algorithm to obtain the centroid. The instrument has a centroid stability of ∼3×10−10 rad Hz−1∕2 and a dynamic range of ∼107.
Portable chamber for the study of UHV prepared electrochemical interfaces by hard x-ray diffraction
Authors: Renner Frank Uwe , Gründer Yvonne , Zegenhagen Jörg
Published: March 2007

We report on a new electrochemical cell setup, combined with a portable UHV chamber, for in situ x-ray diffraction using synchrotron radiation. In contrast to more traditional electrochemical sample preparation schemes, atomically clean and well-ordered surfaces are routinely prepared by UHV methods, even in the case of reactive elements or alloys. Samples can be transferred from larger UHV systems into the portable chamber without exposure to ambient air. They can then be studied successively in UHV, in controlled gas atmospheres, and in contact with electrolyte solutions under applied electrochemical potential. The electrochemical setup employs a droplet geometry, which guarantees good electrochemical conditions during in situ x-ray measurements combined with voltammetry. We present first experimental results of Cu deposition on GaAs(001) and on freshly produced nanometric Pd(001) islands on Cu0.83Pd0.17(001), respectively.
Impact of sheep grazing on the soil seed bank of a managed ephemeral wetland: implications for management
Authors: Nicol Jason , Muston Sally , D'Santos Paula , McCarthy Bernard , Zukowski Sylvia
Published: March 2007

The seed bank is an important mechanism for the persistence of species in ephemeral wetlands, but grazing by domestic stock may change the seed bank and in turn the capacity of the system to recover from disturbance. The sediments of two areas in Thegoa Lagoon (Murray–Darling Basin), one area grazed by sheep when dry and the other ungrazed, were examined. The objective of the study was to determine whether and how the (1) germinable seed bank and (2) final plant communities differ between the grazed and ungrazed areas. The seed banks were subjected to one of the following three water depths: 5 cm above the surface of the water, 5 cm below the surface and 50 cm below the surface. The composition of the seed bank was determined by using the seedling-emergence technique for 12 weeks, with seedlings removed every 2 weeks. The final plant communities were determined at 12 weeks without removing seedlings. The seed bank from the grazed area had a significantly lower seed density (5600 ± 593 seeds m–2) and species richness (7 species) than the ungrazed area (37 683 ± 4492 seeds m–2, 16 species) (ANOVA: F1, 10 = 50.16, P < 0.0001). The floristic composition of the seed bank was also significantly different between the areas (NPMANOVA: F1, 10 = 15.44, P = 0.0032). Glinus lotoides was in higher abundance in the grazed area and Alternanthera denticulata, Persicaria lapathifolium, Polygonum plebium, Typha domingensis and Centipeda cunninghamii in the ungrazed area. Similarly, the final communities derived from the grazed and ungrazed areas were significantly different from each other (NPMANOVA: F1, 10 = 15.53, P = 0.0032). Greater numbers of Centipeda cunninghamii were present in the community from the grazed area and Alternanthera denticulata and Cuscuta campestris were present in larger numbers in the community from the ungrazed area. Water depth also had an impact on germination; no germination occurred in seed banks flooded to 50 cm and one Typha domingensis seedling was observed in a sample flooded to 5 cm. These results showed that grazing reduces the density and species richness of the seed bank and in turn changes the plant communities derived from the seed bank; however, if grazing is removed pest plants such as Cuscuta campestris may require control. In addition, managed drawdown or water-level fluctuations are important in exposing wetland sediments and allowing for species to recruit from the seed bank.
The role of cells refractory to productive infection in acute hepatitis B viral dynamics
Authors: Ciupe Stanca M. , Ribeiro Ruy M. , Nelson Patrick W. , Dusheiko Geoffrey , Perelson Alan S.
Published: March 2007

During acute hepatitis B virus (HBV) infection viral loads reach high levels (≈1010HBV DNA per ml), and nearly every hepatocyte becomes infected. Nonetheless, ≈85–95% of infected adults clear the infection. Although the immune response has been implicated in mediating clearance, the precise mechanisms remain to be elucidated. As infection clears, infected cells are replaced by uninfected ones. During much of this process the virus remains plentiful but nonetheless does not rekindle infection. Here, we analyze data from a set of individuals identified during acute HBV infection and develop mathematical models to test the role of immune responses in various stages of early HBV infection. Fitting the models to data we are able to separate the kinetics of the noncytolytic and the cytolytic immune responses, thus explaining the relative contribution of these two processes. We further show that we need to hypothesize that newly generated uninfected cells are refractory to productive infection. Without this assumption, viral resurgence is observed as uninfected cells are regenerated. Such protection, possibly mediated by cytokines, may also be important in resolving other acute viral infections.
Predicting coupling limits from an experimentally determined energy landscape
Authors: Street Timothy O. , Bradley Christina M. , Barrick Doug
Published: March 2007

Repeat proteins are composed of tandem structural modules in which close contacts do not extend beyond adjacent repeats. Despite the local nature of these close contacts, repeat proteins often unfold as a single, highly coupled unit. Previous studies on the Notch ankyrin domain suggest that this lack of equilibrium unfolding intermediates results both from stabilizing interfaces between each repeat and from a roughly uniform distribution of stability across the folding energy landscape. To investigate this idea, we have generated 15 variants of the Notch ankyrin domain with single and multiple destabilizing substitutions that make the energy landscape uneven. By applying a free energy additivity analysis to these variants, we quantified the destabilization threshold over which repeats 6 and 7 decouple from repeats 1–5. The free energy coupling limit suggested by this additivity analysis (≈4 kcal/mol) is also reflected in
m
-value analysis and in differences among equilibrium unfolding transitions as monitored by CD versus fluorescence for all 15 variants. All of these observations are quantitatively predicted by analyzing the response of the experimentally determined energy landscape to increasing unevenness. These results highlight the importance of a uniform distribution of local stability in achieving cooperative unfolding.
Legionella pneumophila
inhibits macrophage apoptosis by targeting pro-death members of the Bcl2 protein family
Authors: Banga Simran , Gao Ping , Shen Xihui , Fiscus Valena , Zong Wei-Xing , Chen Lingling , Luo Zhao-Qing
Published: March 2007

To establish a vacuole that supports bacterial replication,
Legionella pneumophila
translocates a large number of bacterial proteins into host cells via the Dot/Icm type IV secretion system. Functions of most of these translocated proteins are unknown, but recent investigations suggest their roles in modulating diverse host processes such as vesicle trafficking, autophagy, ubiquitination, and apoptosis. Cells infected by
L. pneumophila
exhibited resistance to apoptotic stimuli, but the bacterial protein directly involved in this process remained elusive. We show here that SidF, one substrate of the Dot/Icm transporter, is involved in the inhibition of infected cells from undergoing apoptosis to allow maximal bacterial multiplication. Permissive macrophages harboring a replicating
sidF
mutant are more apoptotic and more sensitive to staurosporine-induced cell death. Furthermore, cells expressing SidF are resistant to apoptosis stimuli. SidF contributes to apoptosis resistance in
L. pneumophila
-infected cells by specifically interacting with and neutralizing the effects of BNIP3 and Bcl-rambo, two proapoptotic members of Bcl2 protein family. Thus, inhibiting the functions of host pro-death proteins by translocated effectors constitutes a mechanism for
L. pneumophila
to protect host cells from apoptosis.
DNA barcodes affirm that 16 species of apparently generalist tropical parasitoid flies (Diptera, Tachinidae) are not all generalists
Authors: Smith M. Alex , Wood D. Monty , Janzen Daniel H. , Hallwachs Winnie , Hebert Paul D. N.
Published: March 2007

Many species of tachinid flies are viewed as generalist parasitoids because what is apparently a single species of fly has been reared from many species of caterpillars. However, an ongoing inventory of the tachinid flies parasitizing thousands of species of caterpillars in Area de Conservación Guanacaste, northwestern Costa Rica, has encountered >400 species of specialist tachinids with only a few generalists. We DNA-barcoded 2,134 flies belonging to what appeared to be the 16 most generalist of the reared tachinid morphospecies and encountered 73 mitochondrial lineages separated by an average of 4% sequence divergence. These lineages are supported by collateral ecological information and, where tested, by independent nuclear markers (28S and ITS1), and we therefore view these lineages as provisional species. Each of the 16 apparently generalist species dissolved into one of four patterns: (
i
) a single generalist species, (
ii
) a pair of morphologically cryptic generalist species, (
iii
) a complex of specialist species plus a generalist, or (
iv
) a complex of specialists with no remaining generalist. In sum, there remained 9 generalist species among the 73 mitochondrial lineages we analyzed, demonstrating that a generalist lifestyle is possible for a tropical caterpillar parasitoid fly. These results reinforce the emerging suspicion that estimates of global species richness are likely underestimates for parasitoids (which may constitute as much as 20% of all animal life) and that the strategy of being a tropical generalist parasitic fly may be yet more unusual than has been envisioned for tachinids.
Accurate, conformation-dependent predictions of solvent effects on protein ionization constants
Authors: Barth P. , Alber T. , Harbury P. B.
Published: March 2007

Predicting how aqueous solvent modulates the conformational transitions and influences the pKa values that regulate the biological functions of biomolecules remains an unsolved challenge. To address this problem, we developed FDPB_MF, a rotamer repacking method that exhaustively samples side chain conformational space and rigorously calculates multibody protein–solvent interactions. FDPB_MF predicts the effects on pKa values of various solvent exposures, large ionic strength variations, strong energetic couplings, structural reorganizations and sequence mutations. The method achieves high accuracy, with root mean square deviations within 0.3 pH unit of the experimental values measured for turkey ovomucoid third domain, hen lysozyme,
Bacillus circulans
xylanase, and human and
Escherichia coli
thioredoxins. FDPB_MF provides a faithful, quantitative assessment of electrostatic interactions in biological macromolecules.
Single-molecule measurements of the opening and closing of the DNA gate by eukaryotic topoisomerase II
Authors: Smiley R. Derike , Collins Tammy R. L. , Hammes Gordon G. , Hsieh Tao-Shih
Published: March 2007

Type II DNA topoisomerases are essential and ubiquitous enzymes that perform important functions in chromosome condensation and segregation and in regulating intracellular DNA supercoiling. Topoisomerases carry out these DNA transactions by passing one segment of DNA through the other by using a reversible, enzyme-bridged double strand break. The transient enzyme/DNA adduct is mediated by a phosphodiester bond between the active-site tyrosine and a backbone phosphate of DNA. The opening and closing of the DNA gate, a critical step for strand passage during the catalytic cycle, is coupled to this cleavage/religation. We designed a unique oligonucleotide substrate with a pair of fluorophores straddling the topoisomerase II cleavage site, allowing the use of FRET to monitor the opening of the DNA gate. The DNA substrate undergoes an enzyme-mediated transition between a closed and open state in the presence of ATP, similar to the overall topoisomerase II catalyzed reaction. Single-molecule fluorescence microscopy measurements demonstrate that the transition has comparable rate constants for both the opening and closing reaction during steady-state ATP hydrolysis, with an apparent equilibrium constant near unity. In the presence of AMPPNP, a reduction in FRET occurs, suggesting an opening or partial opening of the DNA gate. However, the single-molecule experiments indicate that the open and closed states do not interconvert at a measurable rate.
Coxsackie B4 virus infection of β cells and natural killer cell insulitis in recent-onset type 1 diabetic patients
Authors: Dotta Francesco , Censini Stefano , van Halteren Astrid G. S. , Marselli Lorella , Masini Matilde , Dionisi Sabrina , Mosca Franco , Boggi Ugo , Muda Andrea Onetti , Prato Stefano Del , Elliott John F. , Covacci Antonello , Rappuoli Rino , Roep Bart O. , Marchetti Piero
Published: March 2007

Type 1 diabetes is characterized by T cell-mediated autoimmune destruction of pancreatic β cells. Several studies have suggested an association between Coxsackie enterovirus seroconversion and onset of disease. However, a direct link between β cell viral infection and islet inflammation has not been established. We analyzed pancreatic tissue from six type 1 diabetic and 26 control organ donors. Immunohistochemical, electron microscopy, whole-genome
ex vivo
nucleotide sequencing, cell culture, and immunological studies demonstrated Coxsackie B4 enterovirus in specimens from three of the six diabetic patients. Infection was specific of β cells, which showed nondestructive islet inflammation mediated mainly by natural killer cells. Islets from enterovirus-positive samples displayed reduced insulin secretion in response to glucose and other secretagogues. In addition, virus extracted from positive islets was able to infect β cells from human islets of nondiabetic donors, causing viral inclusions and signs of pyknosis. None of the control organ donors showed signs of viral infection. These studies provide direct evidence that enterovirus can infect β cells in patients with type 1 diabetes and that infection is associated with inflammation and functional impairment.
Reduction of 1-Cys peroxiredoxins by ascorbate changes the thiol-specific antioxidant paradigm, revealing another function of vitamin C
Authors: Monteiro Gisele , Horta Bruno B. , Pimenta Daniel Carvalho , Augusto Ohara , Netto Luis E. S.
Published: March 2007

Peroxiredoxins (Prx) are widely distributed peroxidases that can be divided into 1-Cys and 2-Cys Prx groups based on the number of conserved cysteine residues that participate in their catalytical cycle. Prx have been described to be strictly dependent on thiols, but here, we show that ascorbate (vitamin C) also reduces 1-Cys Prx, but not 2-Cys Prx, from several taxonomic groups. Reduction by ascorbate is partly related to the fact that the oxidized form of 1-Cys Prx is a stable sulfenic acid (Cys-SOH) instead of a disulfide. In addition, a histidine residue in the active site is required. In fact, we engineered a 2-Cys Prx with these two features, and it displayed ascorbate peroxidase activity. These data represent a breakthrough in the thiol-specific antioxidant paradigm. Ascorbate may be the long-sought-after biological reductant of 1-Cys Prx. Because ascorbate is present in high amounts in cells, the ascorbate/protein sulfenic acid pair represents an aspect of redox biochemistry that has yet to be explored
in vivo
.
Stage-dependent reactivity of thymocytes to self-peptide–MHC complexes
Authors: Leng Qibin , Ge Qing , Nguyen Tam , Eisen Herman N. , Chen Jianzhu
Published: March 2007

In mice that express a transgene for the 2C T cell antigen-receptor (TCR) and lack a recombinase-activating gene (2C+RAG−/−mice) most of the peripheral T cells are CD8+, a few are CD4+, and a significant fraction are CD4−CD8−[double negative (DN)]. The DN 2C cells, like DN T cells that are abundant in various other αβ TCR-transgenic mice, appear to be derived directly from DN thymocytes that prematurely express the TCR transgene. The DN 2C cells are virtually absent in mice deficient in major histocompatibility complex class II (MHC-II) but more abundant in mice deficient in MHC-I, suggesting that the DN 2C thymocytes are positively selected by self-peptide–MHC-II (pMHC-II) complexes and negatively selected by self-pMHC-I complexes. The pMHC-I complexes, however, positively select CD8+2C T cells in the same mice. The different effects of thymic pMHC-I on DN and CD8+thymocytes are consistent with the finding that DN 2C thymocytes are more sensitive than more mature CD4+CD8+[double positive (DP)] thymocytes to a weak pMHC-I agonist for the 2C TCR. Together with previous evidence that DP thymocytes respond more sensitively than T cells in the periphery to weak pMHC agonists, the findings suggest progressive decreases in responsiveness to self-pMHC-I complexes as thymocytes develop from DN to DP thymocytes and then to mature naïve T cells in the periphery.
A bile acid-like steroid modulates
Caenorhabditis elegans
lifespan through nuclear receptor signaling
Authors: Gerisch Birgit , Rottiers Veerle , Li Dongling , Motola Daniel L. , Cummins Carolyn L. , Lehrach Hans , Mangelsdorf David J. , Antebi Adam
Published: March 2007

Broad aspects of
Caenorhabditis elegans
life history, including larval developmental timing, arrest at the dauer diapause, and longevity, are regulated by the nuclear receptor DAF-12. Endogenous DAF-12 ligands are 3-keto bile acid-like steroids, called dafachronic acids, which rescue larval defects of hormone-deficient mutants, such as
daf-9
/cytochrome P450 and
daf-36
/Rieske oxygenase, and activate DAF-12. Here we examined the effect of dafachronic acid on pathways controlling lifespan. Dafachronic acid supplementation shortened the lifespan of long-lived
daf-9
mutants and abolished their stress resistance, indicating that the ligand is “proaging” in response to signals from the dauer pathways. However, the ligand extended the lifespan of germ-line ablated
daf-9
and
daf-36
mutants, showing that it is “antiaging” in the germ-line longevity pathway. Thus, dafachronic acid regulates
C. elegans
lifespan according to signaling state. These studies provide key evidence that bile acid-like steroids modulate aging in animals.
Kif5B and Kifc1 Interact and Are Required for Motility and Fission of Early Endocytic Vesicles in Mouse Liver
Authors: Nath Sangeeta , Bananis Eustratios , Sarkar Souvik , Stockert Richard J. , Sperry Ann O. , Murray John W. , Wolkoff Allan W.
Published: March 2007

Early endocytic vesicles loaded with Texas Red asialoorosomucoid were prepared from mouse liver. These vesicles bound to microtubules in vitro, and upon ATP addition, they moved bidirectionally, frequently undergoing fission into two daughter vesicles. There was no effect of vanadate (inhibitor of dynein) on motility, whereas 5′-adenylylimido-diphosphate (kinesin inhibitor) was highly inhibitory. Studies with specific antibodies confirmed that dynein was not associated with these vesicles and that Kif5B and the minus-end kinesin Kifc1 mediated their plus- and minus-end motility, respectively. More than 90% of vesicles associated with Kifc1 also contained Kif5B, and inhibition of Kifc1 with antibody resulted in enhancement of plus-end–directed motility. There was reduced vesicle fission when either Kifc1 or Kif5B activity was inhibited by antibody, indicating that the opposing forces resulting from activity of both motors are required for fission to occur. Immunoprecipitation of native Kif5B by FLAG antibody after expression of FLAG-Kifc1 in 293T cells indicates that these two motors can interact with each other. Whether they interact directly or through a complex of potential regulatory proteins will need to be clarified in future studies. However, the present study shows that coordinated activity of these kinesins is essential for motility and processing of early endocytic vesicles.
The γ/σ1 and α/σ2 Hemicomplexes of Clathrin Adaptors AP-1 and AP-2 Harbor the Dileucine Recognition Site
Authors: Doray Balraj , Lee Intaek , Knisely Jane , Bu Guojun , Kornfeld Stuart
Published: March 2007

The clathrin adaptors AP-1 and AP-2 bind cargo proteins via two types of motifs: tyrosine-based Yxxφ and dileucine-based [DE]XXXL[LI]. Although it is well established that Yxxφ motifs bind to the μ subunits of AP-1 or AP-2, dileucine motifs have been reported to bind to either the μ or β subunits of these adaptors as well as the γ/σ1 hemicomplex of AP-1. To clarify this controversy, the various subunits of AP-1 and AP-2 were expressed individually and in hemicomplex form in insect cells, and they were used in glutathione S-transferase pull-down assays to determine their binding properties. We report that the γ/σ1 or α/σ2 hemicomplexes bound the dileucine-based motifs of several proteins quite strongly, whereas binding by the β1/μ1 and β2/μ2 hemicomplexes, and the individual β or μ subunits, was extremely weak or undetectable. The γ/σ1 and α/σ2 hemicomplexes displayed substantial differences in their preference for particular dileucine-based motifs. Most strikingly, an aspartate at position −4 compromised binding to the γ/σ1 hemicomplex, whereas minimally affecting binding to α/σ2. There was an excellent correlation between binding to the α/σ2 hemicomplex and in vivo internalization mediated by the dileucine-based sorting signals. These findings provide new insights into the trafficking mechanisms of D/EXXXL[LI]-mediated sorting signals.
Determinants of Synaptobrevin Regulation in Membranes
Authors: Siddiqui Tabrez J. , Vites Olga , Stein Alexander , Heintzmann Rainer , Jahn Reinhard , Fasshauer Dirk
Published: March 2007

Neuronal exocytosis is driven by the formation of SNARE complexes between synaptobrevin 2 on synaptic vesicles and SNAP-25/syntaxin 1 on the plasma membrane. It has remained controversial, however, whether SNAREs are constitutively active or whether they are down-regulated until fusion is triggered. We now show that synaptobrevin in proteoliposomes as well as in purified synaptic vesicles is constitutively active. Potential regulators such as calmodulin or synaptophysin do not affect SNARE activity. Substitution or deletion of residues in the linker connecting the SNARE motif and transmembrane region did not alter the kinetics of SNARE complex assembly or of SNARE-mediated fusion of liposomes. Remarkably, deletion of C-terminal residues of the SNARE motif strongly reduced fusion activity, although the overall stability of the complexes was not affected. We conclude that although complete zippering of the SNARE complex is essential for membrane fusion, the structure of the adjacent linker domain is less critical, suggesting that complete SNARE complex assembly not only connects membranes but also drives fusion.
Oral Bromelain Attenuates Inflammation in an Ovalbumin‐Induced Murine Model of Asthma
Authors: Secor Eric R. , Carson William F. , Singh Anurag , Pensa Mellisa , Guernsey Linda A. , Schramm Craig M. , Thrall Roger S.
Published: March 2007

Bromelain, a widely used pineapple extract with cysteine protease activity, has been shown to have immunomodulatory effects in a variety of immune system models. The purpose of the present study was to determine the effects of orally administered bromelain in an ovalbumin (OVA)‐induced murine model of acute allergic airway disease (AAD). To establish AAD, female C57BL/6J mice were sensitized with intraperitoneal (i.p.) OVA/alum and then challenged with OVA aerosols for 3 days. Mice were gavaged with either (phosphate buffered saline)PBS or 200 mg/kg bromelain in PBS, twice daily for four consecutive days, beginning 1 day prior to OVA aerosol challenge. Airway reactivity and methacholine sensitivity, bronchoalveolar lavage (BAL) cellular differential, Th2 cytokines IL‐5 and IL‐13, and lung histology were compared between treatment groups. Oral bromelain‐treatment of AAD mice demonstrated therapeutic efficacy as evidenced by decreased methacholine sensitivity (P ≤ 0.01), reduction in BAL eosinophils (P ≤ 0.02) and IL‐13 concentrations (P ≤ 0.04) as compared with PBS controls. In addition, oral bromelain significantly reduced BAL CD19+ B cells (P ≤ 0.0001) and CD8+ T cells (P ≤ 0.0001) in AAD mice when compared with controls. These results suggest that oral treatment with bromelain had a beneficial therapeutic effect in this murine model of asthma and bromelain may also be effective in human conditions.
Interaction of Aqueous Extract of Pleurotus pulmonarius (Fr.) Quel‐Champ. with Glyburide in Alloxan Induced Diabetic Mice
Authors: Badole Sachin L. , Patel Naimesh M. , Thakurdesai Prasad A. , Bodhankar Subhash L.
Published: March 2007

Mushrooms are low calorie food with very little fat and are highly suitable for obese persons. With no starch and very low sugars, they are the ‘delight of the diabetics’. Combination of herbal drugs (or isolated phytochemicals) is found to be beneficial in certain diseases when given along with conventional drugs. The aim of the present study was to evaluate the effects of aqueous extract of Pleurotus pulmonarius (Lentinaceae) (called as PP‐aqu) and its interaction with glyburide in alloxan induced diabetic mice. The diabetic mice treated were with PP‐aqu (500 mg/kg, p.o.) alone or combination with glyburide (10 mg/kg, p.o.) for 28 days. Blood samples were collected by orbital sinus puncture using heparinized capillary glass tubes and were analyzed for serum glucose on 0, 7th, 14th, 21st and 28th days. Body weights and mortality were noted during the study period. In oral glucose tolerance test (OGTT), glucose (2.5 g/kg, p.o.) was administered with either vehicle, PP‐aqu alone or in combination with glyburide and serum glucose level analyzed at 0, 30, 60 and 120 min after drug administration. Administration of PP‐aqu (500 mg/kg) and its combination with glyburide (10 mg/kg) significantly (P < 0.001) decreased serum glucose level in diabetic mice. In OGTT, glyburide or PP‐aqu treatment alone or their combination produced significant (P < 0.001) increase in glucose threshold. Thus we suggest that P. pulmonarius showed potent and synergistic antihyperglycemic effect in combination with glyburide.
Property Rights, Family, and Business Partnership in Nineteenth- and Twentieth-Century Brazil: The Case of the St. John d'el Rey Mining Company, 1834–1960
Authors: Triner Gail D.
Published: March 2007

This article uses a case study to illustrate the dynamics of firm structure and property rights in Brazil during the nineteenth and twentieth centuries. The St. John d´el Rey Mining Company was a British mining company in Brazil. Its experiences demonstrate that, property rights were not under-specified; they were over-specified and varying provisions for rights were mutually inconsistent. Precise laws protected capital investment to such an extent that dissolving partnerships became problematic. At the same time, inheritance laws mandated partible division of personal estates among heirs. The mining company's history demonstrates the opportunities for posthumously emerged heirs, essentially, to claim partnership rights.
Red, White, and “Big Blue”: IBM and the Business-Government Interface in the United States, 1956–2000
Authors: Hart David
Published: March 2007

This article describes the evolution of IBM's effort to manage its relationships with the U.S. government from the time that Thomas Watson, Jr. became CEO. While the Watson family controlled the firm, the family members served as the main bridges between IBM and the government. This personalized approach began to give way in the 1960s, as the intensity and scope of pressure from the firm's political environment grew beyond the capability of any individual to handle. During the 1970s and 1980s, IBM constructed a managerial hierarchy, with a newly opened Washington office at its center, which could gather more detailed intelligence and execute more sophisticated political strategies. The firm's crisis in the early 1990s provoked a second major restructuring of the interface, as IBM became more of a Washington “special interest.” Yet, some traces of the Watson imprint remained, even in the Gerstner era. Tracing IBM's evolution helps us to understand better the broader interactions between U.S. firms and their environments in this period. These interactions entailed adaptation by firms to environmental change but also efforts by firms to exert control over external forces, including public policy.