bluuebunny/crossref_metadata_2025 huggingface dataset:
Formulation of the relativistic moment implicit particle-in-cell method
Authors: Noguchi Koichi , Tronci Cesare , Zuccaro Gianluca , Lapenta Giovanni
Published: April 2007

A new formulation is presented for the implicit moment method applied to the time-dependent relativistic Vlasov-Maxwell system. The new approach is based on a specific formulation of the implicit moment method that allows us to retain the same formalism that is valid in the classical case despite the formidable complication introduced by the nonlinear nature of the relativistic equations of motion. To demonstrate the validity of the new formulation, an implicit finite difference algorithm is developed to solve the Maxwell’s equations and equations of motion. A number of benchmark problems are run: two stream instability, ion acoustic wave damping, Weibel instability, and Poynting flux acceleration. The numerical results are all in agreement with analytical solutions.
Coupling quantum dot spins to a photonic crystal nanocavity
Authors: Imamoğlu A. , Fält S. , Dreiser J. , Fernandez G. , Atatüre M. , Hennessy K. , Badolato A. , Gerace D.
Published: April 2007

We present a method that allows for deterministic coupling of charge-tunable quantum dots to high-Q photonic crystal nanocavity modes. The realization of cavity-mediated coherent coupling of two distant spins is hindered by large fluctuations in quantum dot optical (trion) transition energy and interdot separation. We show that flexible cavity design and gate-voltage-tunable trion transitions in quantum dot molecules can be used to overcome these limitations and to achieve conditional quantum dynamics of two confined spins.
Is inelastic cotunneling phase coherent?
Authors: Sigrist M. , Ihn T. , Ensslin K. , Reinwald M. , Wegscheider W.
Published: April 2007

For low biases the linear conductance of quantum dots is based on elastic transport processes. At finite bias in the Coulomb blockade regime, inelastic cotunneling sets in once the applied bias exceeds the energy between ground and excited state in the dot. Here we report on transport experiments through an Aharonov-Bohm ring containing a quantum dot in each arm of the ring. The tunnel coupling between the two dots can be tuned by electrostatic gates. For strong tunnel coupling and low bias we observe pronounced Aharonov-Bohm oscillations in the ring with visibilities exceeding 80%. For quantum dots which are purely capacitively coupled, the Aharonov-Bohm amplitude is reduced to a more standard 10%. For finite bias, where transport through excited states becomes possible and a conductance onset is observed, the visibility of the Aharonov-Bohm oscillations remains basically unchanged, while the phase typically undergoes a change of π. We discuss these observations in view of the possible elastic and inelastic transport processes and their contributions to coherent transport.
Microscopic origins of surface states on nitride surfaces
Authors: Van de Walle Chris G. , Segev David
Published: April 2007

We report a systematic and comprehensive computational study of the electronic structure of GaN and InN surfaces in various orientations, including the polar c plane, as well as the nonpolar a and m planes. Surface band structures and density-of-states plots show the energetic position of surface states, and by correlating the electronic structure with atomistic information we are able to identify the microscopic origins of each of these states. Fermi-level pinning positions are identified, depending on surface stoichiometry and surface polarity. For polar InN we find that all the surface states are located above the conduction-band minimum, and explain the source of the intrinsic electron accumulation that has been universally observed on InN surfaces.
Observation of subband standing waves in superlattices by low-temperature scanning tunneling spectroscopy
Authors: Suzuki K. , Kanisawa K. , Perraud S. , Ueki M. , Takashina K. , Hirayama Y.
Published: April 2007

The local density of states (LDOS) of InAs/GaSb long period superlattices was investigated on the cleaved (110) surface at atomic resolution by low-temperature scanning tunneling microscopy and low-temperature scanning tunneling spectroscopy (LT-STS). We present definitive features showing the broken-gap energy band profiles (the overlap of the conduction band of the InAs and the valence band of the GaSb in energy) in the LT-STS spectra complemented by distinct, atomically resolved topographic images. Furthermore, vivid standing waves in LDOS corresponding to the single quantum well-like subband confined in the InAs layer were observed.
Cornered drops and rivulets
Authors: Snoeijer J. H. , Le Grand-Piteira N. , Limat L. , Stone H. A. , Eggers J.
Published: April 2007

We present theoretical and experimental results for a drop of viscous liquid running down an inclined plane at speed U. For U>Ucr the rear of the drop forms a corner whose opening half-angle ϕ decreases with U. By matching the interior of the drop to the contact line, we calculate ϕ analytically. We find that above a second critical speed Uriv this solution no longer exists and instead a slender rivulet comes out of the tip of the corner. To compute the width of the rivulet, we match it to the front of the drop, where it is rounded. Our theoretical results on the opening angle, the rivulet width and the drop velocity are in good agreement with experiment.
Imaging correlated wave functions of few-electron quantum dots: Theory and scanning tunneling spectroscopy experiments
Authors: Rontani Massimo , Molinari Elisa , Maruccio Giuseppe , Janson Martin , Schramm Andreas , Meyer Christian , Matsui Tomohiro , Heyn Christian , Hansen Wolfgang , Wiesendanger Roland
Published: April 2007

We show both theoretically and experimentally that scanning tunneling spectroscopy (STS) images of semiconductor quantum dots may display clear signatures of electron-electron correlation. We apply many-body tunneling theory to a realistic model, which fully takes into account correlation effects and dot anisotropy. Comparing measured STS images of freestanding InAs quantum dots with those calculated by the full configuration interaction method, we explain the wave-function sequence in terms of images of one- and two-electron states. The STS map corresponding to double charging is significantly distorted by electron correlation with respect to the noninteracting case.
Optical and electrical spin injection and spin transport in hybrid Fe/GaAs devices
Authors: Crooker S. A. , Furis M. , Lou X. , Crowell P. A. , Smith D. L. , Adelmann C. , Palmstrøm C. J.
Published: April 2007

We discuss methods for imaging the nonequilibrium spin polarization of electrons in Fe/GaAs spin transport devices. Both optically and electrically injected spin distributions are studied by scanning magneto-optical Kerr rotation microscopy. Related methods are used to demonstrate electrical spin detection of optically injected spin-polarized currents. Dynamical properties of spin transport are inferred from studies based on the Hanle effect, and the influence of strain on spin transport data in these devices is discussed.
Photoluminescence dynamics in GaAs along an optically induced Mott transition
Authors: Amo A. , Martín M. D. , Viña L. , Toropov A. I. , Zhuravlev K. S.
Published: April 2007

We present a detailed experimental study of the effects of the optically induced transition from the excitonic, insulating regime, to the plasma, metallic regime, on the spectra and on the photoluminescence dynamics of GaAs. The transition is rather abrupt and presents a Mott-like behavior. The critical temperature, of 49 K, corresponds to the exciton binding energy. Through the study of the characteristics of the photoluminescence dynamics, the critical density for the transition has been obtained with unprecedented resolution.
High resolution laser excitation spectroscopy of the B̃E2-X̃A12 transitions of calcium and strontium monoborohydride
Authors: Dick M. J. , Sheridan P. M. , Wang J.-G. , Bernath P. F.
Published: April 2007

High resolution spectra of the B̃E2-X̃A12 transitions of CaBH4 and SrBH4 have been recorded using laser excitation spectroscopy in a laser ablation/molecular jet source. Because of rotational cooling in the molecular jet and nuclear spin statistics, transitions arising from only the K′=1←K″=0, K′=2←K″=1, and K′=0←K″=1 subbands have been observed. For each molecule, an analysis of the data using E2 and A12 symmetric top Hamiltonians yielded rotational, spin-orbit, and spin-rotation parameters for the observed states. For both molecules the rotational constants compare well with those calculated for a tridentate borohydride structure. A large reduction in the spin-orbit splitting and in the metal-ligand separation for each molecule indicates an increase in the amount of d atomic orbital character in the first excited E2 states of the monoborohydrides as compared to the monomethyl derivatives. For each molecule no evidence of internal rotation of the BH4− ligand was found. A change in the magnitude and sign of the spin-rotation constant ε1 confirms an energy reordering of the first excited E2 and A12 states in both CaBH4 and SrBH4 as compared to CaCH3 and SrCH3. The data also suggest that the B̃E1∕22 rotational energy levels of CaBH4 may be perturbed by a vibronic component of the ÃA12 state.
An optical horn structure for single-photon source using quantum dots at telecommunication wavelength
Authors: Takemoto Kazuya , Takatsu Motomu , Hirose Shinichi , Yokoyama Naoki , Sakuma Yoshiki , Usuki Tatsuya , Miyazawa Toshiyuki , Arakawa Yasuhiko
Published: April 2007

We succeeded in efficiently generating single-photon pulses from an InAs/InP quantum dot at a wavelength of 1.5 μm. Our optical structure, named a single photon horn, can propagate over 95% photon pulses in InP substrate. We extracted the photon pulses through an anti-reflection coating on a substrate, and then we injected them into an objective lens. Total extraction efficiency from the quantum dot to the lens reached ∼11%, which was estimated using a photon correlation measurement. Furthermore we directly observed the single-photon pulse width ∼1.6 ns as an exciton lifetime in the quantum dot, which opens up the possibility of operating the single photon horn over 100 MHz.
Direct observation of the donor nuclear spin in a near-gap bound exciton transition: P31 in highly enriched S28i
Authors: Thewalt M. L. W. , Yang A. , Steger M. , Karaiskaj D. , Cardona M. , Riemann H. , Abrosimov N. V. , Gusev A. V. , Bulanov A. D. , Kovalev I. D. , Kaliteevskii A. K. , Godisov O. N. , Becker P. , Pohl H. J. , Haller E. E. , Ager J. W. , Itoh K. M.
Published: April 2007

We report on ultrahigh resolution studies of the bound exciton states associated with the shallow acceptor B and the shallow donor P in highly enriched S28i using a tuneable single frequency laser to perform photoluminescence excitation spectroscopy. The linewidths and fine structure of the transitions, which were too narrow to be resolved previously using an available photoluminescence apparatus, are now fully revealed. The P bound exciton transition shows a complicated additional structure, which the Zeeman spectroscopy demonstrates to be a result of the splitting of the donor ground state by the hyperfine interaction between the spin of the donor electron and that of the P31 nucleus. The P31 nuclear spin populations can thus be determined, and hopefully modified, by optical means. The predominant Auger recombination channel of these bound excitons is used to observe the same resolved hyperfine transitions in the photocurrent spectrum. This demonstrates that donors in specific electronic and nuclear spin configurations can be selectively photoionized. Possible applications of these results to quantum computing and quantum information systems are discussed.
Single semiconductor nanocrystals: Physics and applications
Authors: Woggon U.
Published: April 2007

Semiconductor nanocrystals are nanoscale light sources that received much attention in recent years. We will give an overview about semiconductor colloidal nanocrystals as active optical materials in photonic structures and hybrid colloidal-epitaxial devices, for realizations of cavity quantum electrodynamics (cavity QED) concepts, or for probing field intensities in coupled resonator optical waveguides.
Large bulk polarization and regular domain structure in ceramic BiFeO3
Authors: Shvartsman V. V. , Kleemann W. , Haumont R. , Kreisel J.
Published: April 2007

Regularly twinned domain structures are observed by scanning piezoforce microscopy on single crystalline grains of BiFeO3 ceramics being grown by a special low temperature sintering process. The domains are considerably larger than those observed in thin films. Their spontaneous polarization comes close to that predicted theoretically and overcomes restrictions hitherto being set to bulk single crystals. The observed ferroelastic twin domain structure resembles that of classic T domains in rhombohedrally distorted NiO, but is additionally superimposed by ferroelectric twin domain patterns.
Low-noise optical injection locking of a resonant tunneling diode to a stable optical frequency comb
Authors: Ramond T. M. , Hollberg L. , Juodawlkis P. W. , Calawa S. D.
Published: April 2007

Optical injection locking of a resonant tunneling diode (RTD) oscillator has been demonstrated using ultrashort pulses from a mode-locked Ti:sapphire laser operating at a 1GHz pulse rate. The source of the optical signal is a mode-locked femtosecond laser whose optical frequency comb is phase locked to a H-maser stabilized frequency synthesizer. An exceptionally large capture range of more than 5MHz is observed. The system produces stable microwave signals with low phase noise, which at 1GHz is less than −74dBc∕Hz for a 10Hz offset. The noise of the microwave injection-locked RTD signal matches that of the input optical pulses.
Coherent phonon control
Authors: Synnergren O. , Hansen T. N. , Canton S. , Enquist H. , Sondhauss P. , Srivastava A. , Larsson J.
Published: April 2007

Trains of ultrashort laser pulses have been used to generate and to coherently control acoustic phonons in bulk InSb. The coherent acoustic phonons have been probed via time-resolved x-ray diffraction. The authors show that phonons of a particular frequency can either be enhanced or canceled. They have carried out simulations to understand the size of the effects and the levels of cancellation.
Ambipolar light-emitting organic field-effect transistors using a wide-band-gap blue-emitting small molecule
Authors: Sakanoue Tomo , Yahiro Masayuki , Adachi Chihaya , Uchiuzou Hiroyuki , Takahashi Takayoshi , Toshimitsu Akio
Published: April 2007

The authors applied a wide-band-gap (2.9eV) molecule of 4,-4′-bis(styryl)biphenyl (BSBP) as an active layer in light-emitting organic field-effect transistors. They found that BSBP provided both relatively high field-effect hole mobility of 0.01cm2∕Vs and photoluminescence efficiency of 20% in thin film. They achieved ambipolar operation by without breaking vacuum through devices’ preparation and measurements, applying aluminum contacts, and inserting a hydroxyl-free poly(methylmethacrylate) layer, and light emission was observed when the device was operated in the ambipolar mode. The results presented here will open the way to fabricating efficient light-emitting transistors with high mobility.
Direct observation of trapped carriers in polydiacetylene films by optical second harmonic generation
Authors: Manaka Takaaki , Kohn Hideki , Ohshima Yuki , Lim Eunju , Iwamoto Mitsumasa
Published: April 2007

Trapped carriers in polydiacetylene (PDA) films were directly observed by the electric field induced second harmonic generation (EFISHG) using field effect transistor (FET) structure. Response of EFISHG signal from PDA-FET with applying voltage depended strongly on the polarity of gate voltage. For negative bias, which promotes hole injection from source electrode, EFISHG signal was not observed during bias application, whereas it was enhanced after turning off the bias. Electric field formed by trapped holes in PDA activated the EFISHG signal for the negative bias condition.
Electron spin resonance observations of oxygen deficient silicon atoms in the interfacial layer of hafnium oxide based metal-oxide-silicon structures
Authors: Ryan J. T. , Lenahan P. M. , Bersuker G. , Lysaght P.
Published: April 2007

Conventional electron spin resonance measurements indicate gross processing dependent differences in the densities of paramagnetic oxygen deficient silicon sites, E′ centers, in the interfacial layer of unstressed hafnium oxide based metal-oxide-silicon structures. (E′ centers are not usually observed in unstressed oxides.) The volume densities of these centers can be quite high (∼1×1019cm−3). Electrically detected magnetic resonance measurements suggest that related oxygen deficient sites may significantly degrade device performance and reliability.
Characterization of structure and morphology of an advanced p-channel field effect transistor under uniaxial stress by synchrotron x-ray diffraction
Authors: Parikh A. , Yarbrough W. , Mason M. , Sridhar S. , Chidambaram P. R. , Cai Z.
Published: April 2007

Direct measurement of strain in an individual leading-edge p-channel field effect transistor embedded with SiGe was carried out using a synchrotron x-ray source. Diffraction space maps of these scans from two nonparallel reflecting planes, (004) and (115), detected the presence of strain in the channel. Detailed analysis showed that a maximum strain occurred at the top with gradual decay towards the substrate. Strain in the channel is relieved by formation of tilt boundary at the Si–SiGe interface. The lattice parameters in two directions are derived from measured data and the strain is calculated under the plane strain condition.
Time- and locally resolved photoluminescence of semipolar GaInN∕GaN facet light emitting diodes
Authors: Wunderer Thomas , Brückner Peter , Hertkorn Joachim , Scholz Ferdinand , Beirne Gareth J. , Jetter Michael , Michler Peter , Feneberg Martin , Thonke Klaus
Published: April 2007

The authors investigate the carrier lifetime and photoluminescence (PL) intensity of a semipolar GaInN∕GaN sample which was realized by growing five GaInN∕GaN quantum wells on the {11¯01} side facets of selectively grown n-GaN stripes that have a triangular shape running along the ⟨112¯0⟩ direction. Time- and locally resolved PL measurements show drastically reduced lifetimes for the semipolar sample of only 650ps at 4K whereas lifetimes exceeding 50ns were found for a polar reference sample. Furthermore, more than a doubling of the luminescence intensity and a significantly reduced blueshift of the PL peak wavelength with increasing excitation power density provide further evidence for the presence of reduced piezoelectric fields in the semipolar sample.
Observations of the influence of threading dislocations on the recombination enhanced partial dislocation glide in 4H-silicon carbide epitaxial layers
Authors: Chen Y. , Dudley M. , Liu K. X. , Stahlbush R. E.
Published: April 2007

Electron-hole recombination enhanced glide of Shockley partial dislocations bounding expanding stacking faults and their interactions with threading dislocations have been studied in 4H- silicon carbide epitaxial layers. The mobile silicon-core Shockley partial dislocations bounding the stacking faults are observed to cut through threading edge dislocations, leaving no trailing dislocation segments in their wake. When the Shockley partial dislocations interact with threading screw dislocations, 30° partial dislocation dipoles are initially deposited in their wake. These partial dislocation dipoles quickly and spontaneously snap into screw orientation whereupon they cross slip and annihilate, leaving a prismatic stacking fault on the (21¯1¯0) plane.
Hall magnetoresistivity response under microwave excitation revisited
Authors: Iñarrea Jesús
Published: April 2007

The authors theoretically analyzed the microwave-induced modification of the Hall magnetoresistivity in high mobility two-dimensional electron systems. These systems present diagonal magnetoresistivity oscillations and zero-resistance states when subjected to microwave radiation. The most surprising modification of the Hall magnetoresistivity is a periodic reduction which correlates with a periodic increase in the diagonal resistivity. The authors present a model that explains the experimental results considering that radiation affects directly only the diagonal resistivity and that the observed Hall resistivity changes come from the tensor relationship between them.
Air-stable p-n junction diodes based on single-walled carbon nanotubes encapsulating Fe nanoparticles
Authors: Li Y. F. , Hatakeyama R. , Shishido J. , Kato T. , Kaneko T.
Published: April 2007

The authors report electrical transport properties of p-n junction based on semiconducting single-walled carbon nanotubes (SWCNTs). The formation of p-n junction is realized in SWCNTs, which are encapsulated with Fe nanoparticles at low filling fractions. The devices exhibit an excellent rectifying behavior, and no current down to 10−14A level flows when the device is biased in reverse. During measurements performed in the temperature range from 10to300K, the devices maintain high reproducibility. More importantly, even after exposure to air, the rectifying characteristic keeps stable, which strongly suggests that ideal p-n junction diodes can be fabricated by SWCNTs.
Can a Space-Perception Conflict Be Solved with Three Sense Modalities?
Authors: Bedford Felice L
Published: April 2007

A cross-modal conflict over location was resolved in an unexpected way. When vision and proprioception provide conflicting information, which modality should dominate is ambiguous. A visual – proprioceptive conflict was created with a prism and, to logically disambiguate the problem, auditory information was added that either agreed with vision (group 1), agreed with proprioception (group 2), or was absent (group 3). While a scarcity of research addresses the interaction of three modalities, I predicted error should be attributed to the modality in the minority. Instead, the opposite was found: adaptation consisted of a large change in arm proprioception and a small change affecting vision in group 2, and the reverse in group 1. Group 1 was not different than group 3. Findings suggested adaptation to separate two-way conflicts, possibly influenced by direction of attention, rather than a direct solution to a three-way modality problem.
Mental Rotation of Letters and Shapes in Developmental Dyslexia
Authors: Rusiak Patrycja , Lachmann Thomas , Jaskowski Piotr , van Leeuwen Cees
Published: April 2007

Extending the work of Corballis et al (1985, Cortex 21 225–236), we investigated mental rotation of letters (experiment 1), and of letters and shapes (experiment 2) in normal readers and developmental dyslexics. Whereas the overall response times were equal for shapes in both groups, for letters they were slower in dyslexics. For letters as well as for shapes, however, the same mental-rotation effects were obtained between the groups. The results are interpreted as support for the notion of developmental dyslexia as a deficit in functional coordination between graphemic and phonological letter representations.
Enzymatic analysis of a rhomboid intramembrane protease implicates transmembrane helix 5 as the lateral substrate gate
Authors: Baker Rosanna P. , Young Keith , Feng Liang , Shi Yigong , Urban Sinisa
Published: April 2007

Intramembrane proteolysis is a core regulatory mechanism of cells that raises a biochemical paradox of how hydrolysis of peptide bonds is accomplished within the normally hydrophobic environment of the membrane. Recent high-resolution crystal structures have revealed that rhomboid proteases contain a catalytic serine recessed into the plane of the membrane, within a hydrophilic cavity that opens to the extracellular face, but protected laterally from membrane lipids by a ring of transmembrane segments. This architecture poses questions about how substrates enter the internal active site laterally from membrane lipid. Because structures are static glimpses of a dynamic enzyme, we have taken a structure–function approach analyzing >40 engineered variants to identify the gating mechanism used by rhomboid proteases. Importantly, our analyses were conducted with a substrate that we show is cleaved at two intramembrane sites within the previously defined Spitz substrate motif. Engineered mutants in the L1 loop and active-site region of the GlpG rhomboid protease suggest an important structural, rather than dynamic, gating function for the L1 loop that was first proposed to be the substrate gate. Conversely, three classes of mutations that promote transmembrane helix 5 displacement away from the protease core dramatically enhanced enzyme activity 4- to 10-fold. Our functional analyses have identified transmembrane helix 5 movement to gate lateral substrate entry as a rate-limiting step in intramembrane proteolysis. Moreover, our mutagenesis also underscores the importance of other residue interactions within the enzyme that warrant further scrutiny.
Targeted delivery of proteins across the blood–brain barrier
Authors: Spencer Brian J. , Verma Inder M.
Published: April 2007

Treatment of many neuronal degenerative disorders will require delivery of a therapeutic protein to neurons or glial cells across the whole CNS. The presence of the blood–brain barrier hampers the delivery of these proteins from the blood, thus necessitating a new method for delivery. Receptors on the blood–brain barrier bind ligands to facilitate their transport to the CNS; therefore, we hypothesized that by targeting these receptors, we may be able to deliver proteins to the CNS for therapy. Here, we report the use of the lentivirus vector system to deliver the lysosomal enzyme glucocerebrosidase and a secreted form of GFP to the neurons and astrocytes in the CNS. We fused the low-density lipoprotein receptor-binding domain of the apolipoprotein B to the targeted protein. This approach proved to be feasible for delivery of the protein and could possibly be used as a general method for delivery of therapeutic proteins to the CNS.
Toxicity from different SOD1 mutants dysregulates the complement system and the neuronal regenerative response in ALS motor neurons
Authors: Lobsiger Christian S. , Boillée Séverine , Cleveland Don W.
Published: April 2007

Global, age-dependent changes in gene expression from rodent models of inherited ALS caused by dominant mutations in superoxide-dismutase 1 (SOD1) were identified by using gene arrays and RNAs isolated from purified embryonic and adult motor neurons. Comparison of embryonic motor neurons expressing a dismutase active ALS-linked mutant SOD1 with those expressing comparable levels of wild-type SOD1 revealed the absence of mutant-induced mRNA changes. An age-dependent mRNA change that developed presymptomatically in adult motor neurons collected by laser microdissection from mice expressing dismutase active ALS-linked mutants was dysregulation of the
d
/
l
-serine biosynthetic pathway, previously linked to both excitotoxic and neurotrophic effects. An unexpected dysregulation common to motor neurons expressing either dismutase active or inactive mutants was induction of neuronally derived components of the classic complement system and the regenerative/injury response. Alteration of these mutant SOD1-induced pathways identified a set of targets for therapies for inherited ALS.
Mapping allosteric connections from the receptor to the nucleotide-binding pocket of heterotrimeric G proteins
Authors: Oldham William M. , Van Eps Ned , Preininger Anita M. , Hubbell Wayne L. , Hamm Heidi E.
Published: April 2007

Heterotrimeric G proteins function as molecular relays that mediate signal transduction from heptahelical receptors in the cell membrane to intracellular effector proteins. Crystallographic studies have demonstrated that guanine nucleotide exchange on the Gα subunit causes specific conformational changes in three key “switch” regions of the protein, which regulate binding to Gβγ subunits, receptors, and effector proteins. In the present study, nitroxide side chains were introduced at sites within the switch I region of Gαi to explore the structure and dynamics of this region throughout the G protein cycle. EPR spectra obtained for each of the Gα(GDP), Gα(GDP)βγ heterotrimer and Gα(GTPγS) conformations are consistent with the local environment observed in the corresponding crystal structures. Binding of the heterotrimer to activated rhodopsin to form the nucleotide-free (empty) complex, for which there is no crystal structure, causes prominent changes relative to the heterotrimer in the structure of switch I and contiguous sequences. The data identify a putative pathway of allosteric changes triggered by receptor binding and, together with previously published data, suggest elements of a mechanism for receptor-catalyzed nucleotide exchange.
The emerging structure of global agricultural trade in the aftermath of the Doha Round.
Authors: Bigman D.
Published: April 2007

The main goal of the Doha Round was to reduce and gradually eliminate trade barriers on agricultural trade that are damaging for developing countries. The Doha Round was therefore referred to as the 'Development Round', but it eventually encountered a stalemate that was primarily due to difficulties in reaching the agreement on agricultural trade. There are considerable disagreements on the reasons for the stalemate of the negotiations and on the resulting impact on the least developed countries (LDCs). This article provides an overview of the negotiations in this round and discusses the reasons for the difficulties that the negotiations encountered as well as the different opinions on the resulting impact on the LDCs; the conclusion offers an evaluation of the emerging structure of agricultural production and trade in the developing countries in the aftermath of the Doha Round.
Grassland science in Europe facing new challenges: biodiversity and global environmental change.
Authors: Soussana J. F. , Duru M.
Published: April 2007

In Europe, grassland is one of the dominant forms of land use. Within 20 years, the area of permanent grasslands and pastures in Western Europe has declined by 12%. Semi-natural grasslands are often hot spots of biodiversity and are threatened both by intensive farming and by the abandonment of farmland in marginal areas. In this review, we show that biodiversity, climate change, C sequestration and farming systems issues are highly interconnected in grassland ecosystems. In this context, there are new risks (induced by climate change), new opportunities (linked to carbon sequestration and biodiversity conservation for example) and new challenges (concerning farm management and agricultural practices) for managed grasslands. An assessment of the current research perspectives underlines some key questions: (i) How to reduce the sensitivity and increase the resilience of grassland biodiversity to heat waves and droughts in an altered climate? (ii) How to protect soil organic carbon stocks under global warming? (iii) How to preserve the habitat for rare or endangered species, while managing the functional diversity of the vegetation for agricultural purposes? (iv) How to maintain the heterogeneity and diversity of grassland vegetation at the farm and landscape levels? (v) How to design innovative farming systems that integrate the impacts of farm activity on biodiversity, water and air quality, fossil energy use and greenhouse gas effect? (vi) How to produce integrated knowledge taking account of the consistency of the different management practices and their feasibility at farm level according to four criteria (profitability, labour, agricultural and environmental performance)?
Lupins as a protein source in pig diets.
Authors: Kim J. C. , Pluske J. R. , Mullan B. P.
Published: April 2007

Lupins are a valuable source of protein that can partially replace traditional proteins of animal origin such as meat and bone meal and fish meal. Lupins also have been used as alternatives for soyabean meal (SBM) and other oilseed meals in some countries such as Australia and northeastern Europe where use of locally-grown lupins in pig diets is cost-effective. However, the presence of high levels of antinutritional factors (ANF), such as non-starch polysaccharides (NSP), oligosaccharides, protease inhibitors, tannins, saponins and alkaloids, have hampered progressive use of lupins in pig diets. Advances in lupin breeding programmes have contributed to the release of varieties with improved digestibility and lower ANF contents. The scope of this review is to evaluate the nutritional value of current varieties of lupins and to summarize recent nutritional concepts covering the strengths and weaknesses of lupins as ingredients in pig diets. The topics discussed will include: (1) chemical characteristics of currently available lupin species; (2) energy and amino acid availability; (3) performance and carcass composition response to lupin-based diets; (4) ANF in lupins; and (5) processing of lupins to improve nutrient digestibility.
Irrigated rice production systems and greenhouse gas emissions: crop and residue management trends, climate change impacts and mitigation strategies.
Authors: Wassmann R. , Butterbach-Bahl K. , Dobermann A.
Published: April 2007

The overall purpose of this review is to assess current and future greenhouse gas (GHG) emissions from irrigated rice fields with emphasis on the ongoing trends in both, (i) crop and residue management practices and (ii) global climate change. While irrigated rice fields were traditionally flooded for the entire vegetation period or at least a substantial portion thereof, current trends in crop management encompass lower consumption of irrigation water through intensification (using water more efficiently under high yield levels) and diversification (replacing the second or third rice crop per year by an upland crop like wheat or maize). These trends have numerous impacts on the GHG budget. Methane emissions will be lower, but these emission savings are at least in part offset by increased nitrous oxide emissions. Moreover, the shift to prevailing upland conditions entails (in most cases) losses in soil organic carbon that translate into carbon dioxide emissions and may threaten the sustainability of the cropping system as a whole. Increasing temperatures exert another risk for rice production systems mainly through spikelet sterility as the principal mechanism of heat damage in rice plants. However, the temperature effect has to be seen in context with the simultaneous increase in carbon dioxide (CO
2
). Based on the available results for temperature and CO
2
effects, we assume that GHG emissions will increase unless the production base of the irrigated rice systems is severely damaged. The ongoing pressure on rice production systems from societal and environmental drivers limits the scope for designing mitigation options. We have outlined several mitigation approaches of crop and residue management as promising candidates that reconcile low emissions and high production levels and that can also be seen as adaptive response to changing socio-economic and environmental conditions.
DITOP: drug-induced toxicity related protein database
Authors: Zhang Jing-Xian , Huang Wei-Juan , Zeng Jing-Hua , Huang Wen-Hui , Wang Yi , Zhao Rui , Han Bu-Cong , Liu Qing-Feng , Chen Yu-Zong , Ji Zhi-Liang
Published: April 2007

Motivation: Drug-induced toxicity related proteins (DITRPs) are proteins that mediate adverse drug reactions (ADRs) or toxicities through their binding to drugs or reactive metabolites. Collection of these proteins facilitates better understanding of the molecular mechanisms of drug-induced toxicity and the rational drug discovery. Drug-induced toxicity related protein database (DITOP) is such a database that is intending to provide comprehensive information of DITRPs. Currently, DITOP contains 1501 records, covering 618 distinct literature-reported DITRPs, 529 drugs/ligands and 418 distinct toxicity terms. These proteins were confirmed experimentally to interact with drugs or their reactive metabolites, thus directly or indirectly cause adverse effects or toxicities. Five major types of drug-induced toxicities or ADRs are included in DITOP, which are the idiosyncratic adverse drug reactions, the dose-dependent toxicities, the drug–drug interactions, the immune-mediated adverse drug effects (IMADEs) and the toxicities caused by genetic susceptibility. Molecular mechanisms underlying the toxicity and cross-links to related resources are also provided while available. Moreover, a series of user-friendly interfaces were designed for flexible retrieval of DITRPs-related information. The DITOP can be accessed freely at http://bioinf.xmu.edu.cn/databases/ADR/index.html

Contact: zhiliang.ji@gmail.com or appo@bioinf.xmu.edu.cn

Supplementary information: Supplementary data are available at Bioinformatics online.
Identifying the biologically relevant gene categories based on gene expression and biological data: an example on prostate cancer
Authors: Huang D. , Chow Tommy W. S.
Published: April 2007

Motivation: Most gene-expression based studies aim to identify genes with the capability of distinguishing different phenotypes. Although analysis at the genomic level is important, results of the molecular/cellular level are essential for understanding biological mechanisms. To deliver molecular/cellular-level results, a two-stage scheme is widely employed. This scheme just evaluates biological processes/molecular activities individually, totally overlooking the relationship between processes/activities. This treatment conflicts with the fact that most biological processes/molecular activities do not work alone. In order to deliver improved results, this shortcoming should be addressed.

Results: We design a selection model from a novel perspective to directly detect important gene functional categories (each category represents a cellular process or a molecular activity). More importantly, the correlations between gene categories are considered. Contributed by this capability, the proposed method shows its advantages over others.

Availability: the source code in Matlab is accessible via http://www.ee.cityu.edu.hk/~twschow/category_selection/category_selection.htm

Contact:  ifkorf@ucdavis.edu

Supplementary information:  http://www.ee.cityu.edu.hk/~twschow/category_selection/category_selection.htm
A quantitative model for linking two disparate sets of articles in MEDLINE
Authors: Torvik Vetle I. , Smalheiser Neil R.
Published: April 2007

Background: Identifying information that implicitly links two disparate sets of articles is a fundamental and intuitive data mining strategy that can help investigators address real scientific questions. The Arrowsmith two-node search finds title words and phrases (so-called B-terms) that are shared across two sets of articles within MEDLINE and displays them in a manner that facilitates human assessment. A serious stumbling-block has been the lack of a quantitative model for predicting which of the hundreds if not thousands of B-terms computed for a given search are most likely to be relevant to the investigator.

Methodology/Principal Findings: Using a public two-node search interface, field testers devised a set of two-node searches under real life conditions and a certain number of B-terms were marked relevant. These were employed as ‘gold standards;’ each B-term was characterized according to eight complementary features that were strongly correlated with relevance. A logistic regression model was developed that permits one to estimate the probability of relevance for each B-term, to rank B-terms according to their likely relevance, and to estimate the overall number of relevant B-terms inherent in a given two-node search.

Conclusions/Significance: The model greatly simplifies and streamlines the process of carrying out a two-node search, and may be applicable to a number of other literature-based discovery applications, including the so-called one-node search and related gene-centric strategies that incorporate implicit links to predict how genes may be related to each other and to human diseases. This should encourage much wider exploration of text mining for implicit information among the general scientific community.

Availability: Two-node searches can be carried out freely at http://arrowsmith.psych.uic.edu

Contact: neils@uic.edu, vtorvik@uic.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
Vaccine-induced pathogen strain replacement: what are the mechanisms?
Authors: Martcheva Maia , Bolker Benjamin M , Holt Robert D
Published: April 2007

Host immune systems impose natural selection on pathogen populations, which respond by evolving different antigenic signatures. Like many evolutionary processes, pathogen evolution reflects an interaction between different levels of selection; pathogens can win in between-strain competition by taking over individual hosts (within-host level) or by infecting more hosts (population level). Vaccination, which intensifies and modifies selection by protecting hosts against one or more pathogen strains, can drive the emergence of new dominant pathogen strains—a phenomenon called
vaccine-induced pathogen strain replacement
. Here, we review reports of increased incidence of subdominant variants after vaccination campaigns and extend the current model for pathogen strain replacement, which assumes that pathogen strain replacement occurs only through the differential effectiveness of vaccines against different pathogen strains. Based on a recent theoretical study, we suggest a broader range of possible mechanisms, some of which allow pathogen strain replacement even when vaccines are
perfect
—that is, they protect all vaccinated individuals completely against all pathogen strains. We draw an analogy with ecological and evolutionary explanations for competitive dominance and coexistence that allow for tradeoffs between different competitive and life-history traits.
The S‐curve Dynamics of US Bilateral Trade*
Authors: Bahmani‐Oskooee Mohsen , Ratha Artatrana
Published: April 2007

A few studies in dynamic general‐equilibrium setting have argued that the trade balance is negatively correlated with current and future movements in the terms of trade but positively correlated with past movements, hence the S‐curve phenomenon. Using aggregate trade data and the terms of trade has not provided strong empirical counterpart. However, in this paper, when we disaggregate the trade data between the US and her trading partners we find stronger results in support of the S‐curve.
International Technology Transfer: Who Gains and Who Loses?*
Authors: Ruffin Roy J. , Jones Ronald W.
Published: April 2007

When one country has a superior technology in all commodities, a Ricardian model with two goods and two countries is used to examine uncompensated transfers of superior technology in one or both goods. A transfer of the superior but second‐best technology always benefits the advanced country because it was improting that good initially and now gets it cheaper. But the free gift of the first‐best technology can also benefit the advanced country if a certain productivity condition is satisfied because that country may now export its former import good at an even better terms of trade.
International Productivity Differences, Infrastructure, and Comparative Advantage*
Authors: Yeaple Stephen R. , Golub Stephen S.
Published: April 2007

This paper provides an empirical analysis of the effect of infrastructure provision on industry‐level productivity and international specialization, as suggested by Clarida and Findlay’s (1992) model. We calculate total factor productivity (TFP) for 18 developed and developing countries and 10 manufacturing industries, and study the effects of supplies of roads, telecommunications and electric power on international variations in sectoral TFP, i.e. comparative advantage. We also examine the effects of infrastructure on the sectoral composition of output across countries. Using a three‐stage least‐squares estimation strategy to control for endogeneity of infrastructure provision, we find that infrastructure, especially roads, helps to explain patterns of comparative advantage and international specialization.
Government Bonds in Domestic and Foreign Currency: the Role of Institutional and Macroeconomic Factors*
Authors: Claessens Stijn , Klingebiel Daniela , Schmukler Sergio L.
Published: April 2007

In contrast to some recent research, this paper finds that institutional and macroeconomic factors are related to the depth and currency composition of government bond markets. Using panel data for developed and emerging economies, we find several factors to be systematically associated with bond markets. Aside from economic size (already shown to affect the currency composition), this paper shows that investor bases matter. Economies with deeper domestic financial systems (measured by bank deposits and stock market capitalization) have larger domestic currency bond markets and issue less foreign currency debt, whereas foreign investor demand is positively related to the size and share of foreign currency bonds. Moreover, less flexible exchange rate regimes are associated with more foreign currency issuance. Other relevant variables include inflation, fiscal burden, legal origin, and capital account openness.
Effects of the nitrification inhibitor dicyandiamide on soil mineral N, pasture yield, nutrient uptake and pasture quality in a grazed pasture system
Authors: Moir J. L. , Cameron K. C. , Di H. J.
Published: April 2007

Recent lysimeter studies have demonstrated that the nitrification inhibitor, dicyandiamide (DCD), can reduce nitrate (NO) leaching losses from cow urine patches in grazed pasture systems. The objective of this study was to quantify the effects of fine particle suspension (FPS) DCD on soil mineral N components, pasture yield, nutrient uptake and pasture quality under grazed pasture conditions. A field study was conducted on the Lincoln University dairy farm, Canterbury, New Zealand, from 2002 to 2006. FPS DCD was applied to grazed pasture plots at 10 kg ha−1 in early May in addition to applied cow urine patches at a nitrogen (N) loading rate of 1000 kg N ha−1, with DCD reapplied in early August. Soil mineral N levels in the urine patches were monitored. Pasture yield, N and cation concentrations and uptake were measured in treatment urine patches and inter‐urine areas of the pasture. Comparisons were made with control plots which did not receive DCD. NO levels under the DCD‐treated urine patches (0–7.5 cm) were in the order of 10 kg N ha−1 compared with 40–80 kg N ha−1 under untreated patches, and soil ammonium (NH) levels were consistently higher under the DCD‐treated patches. The DCD significantly and consistently increased pasture yield in both the urine patches, and inter‐urine areas of the pasture in all 4 years of the trial. Mean annual dry matter (DM) yields over 4 years were inter‐urine areas, 10.3; inter‐urine + DCD, 12.4; urine, 12.4 and urine +DCD 16.0 t DM ha−1, representing an average DM yield increase of 20 and 29% in inter‐urine and urine patch areas, respectively. On a whole paddock basis, the increase in annual DM yield resulting from DCD application was estimated to be 21%. N, calcium (Ca), magnesium (Mg) and potassium (K) concentrations in pasture were unaffected by treatment with DCD; however, total annual uptake of these nutrients by pasture was significantly higher in all years where DCD had been applied. Pasture DM, protein, carbohydrate, metabolizable energy and fibre levels and sward clover content were not affected by treatment with DCD. The results demonstrate the agronomic value of the DCD treatment in addition to the environmental benefits in a grazed pasture system.