bluuebunny/crossref_metadata_2025 huggingface dataset:
Monte Carlo studies of magnetism and superconductivity on the triangular lattice
Authors: Su Shi-Quan , Huang Zhong-Bing , Lin Hai-Qing
Published: March 2008

To study the magnetic and superconducting properties of the NaxCoO2⋅yH2O materials, we perform quantum Monte Carlo calculation on the single-band Hubbard model on a triangular lattice. Through the observation of magnetic susceptibility as a function of electron filling and temperature, it is interesting to see that the ferromagnetic fluctuation dominates in the high-filling region ⟨n⟩=1.5–1.85 and competes with the antiferromagnetic fluctuation in the filling region ⟨n⟩∼1.33. We also observe that triplet pairing is favorable around the ferromagnetic region, and the f-wave pairing correlation tends to increase faster with decreasing temperature than other pairing channels.
Hydrophobic interactions between methane and a nanoscopic pocket: Three dimensional distribution of potential of mean force revealed by computer simulations
Authors: Setny Piotr
Published: March 2008

We consider a model system of methane molecule and a hemispherical, hydrophobic pocket of an 8Å radius, remaining together in aqueous environment. A spatial map of potential of mean force acting on methane molecule due to presence of pocket is constructed, based on a series of explicit solvent molecular dynamics simulations. A relation between free energy variations associated with methane translocations and accompanying changes in solvent density distribution is analyzed. A funnel-like area where free energy is diminished with respect to bulk is present over the pocket entrance and extends up to 9Å toward the bulk solvent. In order to get into the pocket, however, methane has to cross a free energy barrier, which is more prominent around the circumferential part of pocket entrance, while achieving bulklike free energy values at the very center. As a methane molecule crosses this barrier, the pocket gets completely dehydrated, which leads to “hydrophobic collapse,” manifested by a sharp decrease in free energy. We find that the observed free energy changes are closely related to interactions between the methane hydration shell and the surrounding solvent. Results presented here are a continuation of our previous studies of methane-pocket systems.
Free-electron laser triggered photocathodes
Authors: Sabia E. , Dattoli G. , Dipace A. , Messina G.
Published: March 2008

The possibility of using free-electron laser (FEL) triggered photocathodes to produce high-quality e-beams for self-amplified spontaneous emission or oscillator FEL devices is explored. The use of the same e-beam, driving the photocathode and the FEL, makes the system naturally free of any synchronization problem, arising when an external laser is used. Examples of the interplay between the generation of electron and optical bursts are also investigated.
Spatially autoresonant stimulated Raman scattering in nonuniform plasmas
Authors: Yaakobi O. , Friedland L. , Lindberg R. R. , Charman A. E. , Penn G. , Wurtele J. S.
Published: March 2008

New solutions to the coupled three-wave equations in a nonuniform plasma medium are presented that include both space and time dependence of the waves. By including the dominant nonlinear frequency shift of the material wave, it is shown that if the driving waves are sufficiently strong (in relation to the medium gradient), a nonlinearly phase-locked solution develops that is characteristic of autoresonance. In this case, the material (electrostatic) wave develops into a front starting at the linear resonance point and moving with the wave group velocity in a manner such that the intensity increases linearly with the propagation distance. The forms of the other two (electromagnetic) waves follow naturally from the Manley–Rowe relations.
Fragmentation branching ratios of highly excited hydrocarbon molecules CnH and their cations CnH+ (n⩽4)
Authors: Tuna T. , Chabot M. , Pino T. , Désesquelles P. , LePadellec A. , Martinet G. , Barat M. , Lucas B. , Mezdari F. , Montagnon L. , Van-Oanh N. T. , Lavergne L. , Lachaize A. , Carpentier Y. , Béroff K.
Published: March 2008

We have measured fragmentation branching ratios of neutral CnH and CnH+ cations produced in high velocity (4.5a.u) collisions between incident CnH+ cations and helium atoms. Electron capture gives rise to excited neutral species CnH and electronic excitation to excited cations CnH+. Thanks to a dedicated setup, based on coincident detection of all fragments, the dissociations of the neutral and cationic parents were recorded separately and in a complete way. For the fragmentation of CnH, the H-loss channel is found to be dominant, as already observed by other authors. By contrast, the H-loss and C-loss channels equally dominate the two-fragment break up of CnH+ species. For these cations, we provide the first fragmentation data (n>2). Results are also discussed in the context of astrochemistry.
Shape dynamics in anisotropically strained two-dimensional self-assembling systems
Authors: Medhekar N. V. , Shenoy V. B.
Published: March 2008

We analyze the evolution of equilibrium and growth shapes of anisotropically strained two-dimensional self-assembled structures using a dynamic growth model. As examples of such structures, we study the shapes of nanowires grown heteroepitaxially on cubic (001) surfaces and monolayer islands or stress domains grown homoepitaxially on Si(001) surface. In the former case, the anisotropy in the mismatch strain in the two principal directions is large, while in the latter case, the principal components of the strain are equal in magnitude and opposite in sign. In the case of nanowires, we find that the slow kinetics of growth limits the formation of wirelike shapes with constant widths as predicted by equilibrium models. In particular, the aspect ratios of nanowires during growth are considerably smaller than the equilibrium aspect ratios. For monolayer islands on Si(001), we show that the anisotropy in strain gives rise to a novel fourfold symmetry in their equilibrium shapes. This strain-induced symmetry, coupled with the kinetics of growth, is shown to result in rich shape dynamics of monolayer islands on Si(001) as seen in recent experiments.
III-V junctions on silicon substrates using BeTe buffer layers for solar cell applications
Authors: Clark K. , Maldonado E. , Kirk W. P.
Published: March 2008

Epitaxial growth of AlGaAs–GaAs quantum well junctions on beryllium telluride layers on silicon was investigated as an approach toward multijunction solar cells. BeTe maintained a well-ordered, planar growth mode on silicon, while it relaxed the lattice constant for subsequent AlGaAs growth. AlGaAs on BeTe growth initiation using solid-phase epitaxy beginning from near room temperature was required to maintain planar growth, attributed to surface energy effects. AlGaAs on BeTe films required several hundred angstrom thickness low temperature growth to be stable against roughening with further growth at normal growth conditions. I-V measurements showed that the n+-Si∕As∕p+-BeTe junction formed a low resistance tunnel junction. The photocurrent of the AlGaAs–GaAs quantum well p-i-n junction under one sun condition was as high as JSC=7.9mA∕cm2 with VOC=600mV. Junctions grown on BeTe∕Si substrates were compared to similar junctions grown on GaAs substrates.
Strength of polycrystalline coarse-grained platinum to 330GPa and of nanocrystalline platinum to 70GPa from high-pressure x-ray diffraction data
Authors: Singh Anil K. , Liermann Hanns-Peter , Akahama Yuichi , Saxena Surendra K. , Menéndez-Proupin Eduardo
Published: March 2008

X-ray diffraction patterns from platinum foil (∼300nm grain size) have been recorded up to 330GPa using a beveled-anvil diamond cell. The compressive strength has been determined from the analysis of the diffraction linewidths. In a separate set of experiments, coarse-grained platinum powder (∼300nm grain size) is compressed up to 64GPa in a diamond anvil cell with 300μm flat-face anvils and diffraction patterns are recorded. The strengths as functions of pressure derived in the two sets of experiments agree well. The strength increases linearly from 0.21(2)GPa at zero pressure to 9.8(4)GPa at a pressure of 330GPa. The nanocrystalline platinum sample (∼20nm average grain size) exhibits much higher strength and increases linearly from 3.0(1)to8.0(3)GPa as the pressure is increased from zero pressure to 70GPa. The grain size of nanocrystalline sample decreases with increasing pressure. The effect of nonhydrostatic compression on the pressures determined with platinum as a pressure marker in high-pressure x-ray diffraction studies is discussed.
Microscale laser peen forming of single crystal
Authors: Wang Youneng , Fan Yajun , Kysar Jeffrey W. , Vukelic Sinisa , Yao Y. Lawrence
Published: March 2008

As the result of quickly increased requirement in many industrial products resulting from microtechnology, laser thermal microforming and microsurface treatment [microscale laser shock peening (μLSP)] have been well studied. By combining the beneficial effects of these two processes with a controlled bending deformation, microscale laser peen forming (μLPF) attracts more attention recently since it not only improves the fatigue life of the material but also shapes microscale metallic parts at the same time. In the present study, μLSP of single crystal aluminum was presented to study anisotropic material response. Local plastic deformation was characterized by lattice rotation measured through electron backscatter diffraction. Residual stress distributions of both sides of a peened sample, characterized by x-ray microdiffraction, were compared with the results obtained from finite element method simulation. μLPF anisotropic behavior was investigated in three effective slip systems via both the anisotropic slip line theory and numerical method. Also, the work hardening effect resulted from self-hardening, and latent hardening was analyzed through comparing the results with and without considering hardening.
Simulation studies of internal mechanisms in the static deflection of a cellulose electroactive paper actuator
Authors: Joshi R. P. , Mbaye F. , Basappa P. , Jang S. D. , Kim J. , Hall J. C.
Published: March 2008

Studies of voltage-induced deflections in electroactive paper (EAPap) have been carried out. On the experimental side, measurements of bias-dependent deflections and strain, water absorption as a function of time, and relative humidity were obtained for the cellulose EAPap actuator. In addition, model simulations have also been carried out to probe and quantify the role of the various internal mechanisms responsible for the deflection. Our simulation predictions yield good agreement with the measured deflection data for the EAPap. The modeling suggests that internal ion content and its migration, water absorption leading to a nonuniform permittivity, random variations in the transverse piezoelectric-coupling coefficient d31,i, and the modulus of elasticity all collectively contribute to the EAPap deflection electrophysics. It also appears that higher sensitivity, with a minimal bias dependence, could be achieved by deliberately adding ions during EAPap processing.
The remarkable similarity between the scaling of kurtosis with squared skewness for TORPEX density fluctuations and sea-surface temperature fluctuations
Authors: Krommes John A.
Published: March 2008

The striking similarity between the statistics of plasma density fluctuations in the TORPEX device [Labit et al., Phys. Rev. Lett. 98, 255002 (2007)] and sea-surface temperature fluctuations [Sura and Sardeshmukh, J. Phys. Oceanogr. 38, 638 (2007)] (SS) is discussed. A nonlinear Langevin theory due to SS is generalized to include linear wave propagation. An interpretation of the nonlinear Langevin equation based on statistical closure theory is proposed.
Anomalous p-channel amorphous oxide transistors based on tin oxide and their complementary circuits
Authors: Ou Chun-Wei , Dhananjay  , Ho Zhong Yo , Chuang You-Che , Cheng Shiau-Shin , Wu Meng-Chyi , Ho Kuo-Chuan , Chu Chih-Wei
Published: March 2008

In this article, we report the fabrication of SnO2 thin film transistors (TFTs) fabricated by reactive evaporation. Different from the previous reports, the fabricated TFTs exhibit p-type conductivity in its undoped form. The postdeposition annealing temperature was tuned to achieve p-channel SnO2 TFTs. The on/off ratio and the field-effect mobility were ∼103 and 0.011cm2∕Vs, respectively. To demonstrate inverter circuit, two devices with different threshold voltages were combined and an output gain of 2.8 was achieved. The realization of p-channel oxide TFTs would open up new challenges in the area of transparent electronics.
Effect of the radial boundary condition on Alfvén wave dynamics in reduced magnetohydrodynamics
Authors: Denton R. E. , Rogers B. , Lotko W. , Streltsov A. V.
Published: March 2008

The effects of different boundary conditions on Alfvén wave dynamics in reduced magnetohydrodynamics are described. If one assumes that the derivative or the second derivative of the electrostatic potential Φ is zero at one of the radial (across the magnetic field) boundaries, radially localized (guided) Alfvén wave solutions are possible, but if Φ is set to zero (grounded) at both boundaries, the solutions consistent with the boundary condition exhibit radial propagation of energy. To confirm the ideas discussed, numerical tests were done in slab geometry with a density gradient across the magnetic field.
A model for the efficient coupling between intense lasers and subwavelength grating targets
Authors: Wang W.-M. , Sheng Z.-M. , Zhang J.
Published: March 2008

The interaction of an ultrashort intense laser pulse with a subwavelength rectangular grating target is studied by an analytical model and particle-in-cell simulations. Such interaction excites strong periodic charge separation at the grating surface. With the presence of formed electrostatic fields, the laser field can intensively heat electrons, causing near 100% light absorption. Its dependence on grating parameters is given. At low or moderate laser intensity, there are optimized sizes of grating gibbous cells and grooves as well as groove depths at which absorption maximums are found. At high intensity, the absorption is weakly affected by groove sizes and depths.
Femtosecond dynamics of resonant tunneling and superlattice relaxation in quantum cascade lasers
Authors: Choi Hyunyong , Norris Theodore B. , Gresch Tobias , Giovannini Marcella , Faist Jérôme , Diehl Laurent , Capasso Federico
Published: March 2008

Time-resolved mid-infrared pump-probe measurements are performed on a quantum cascade laser below and above the threshold. The gain recovery is determined by the electron transport through the cascade heterostructure. Subpicosecond resonant tunneling injection from the injector ground state into the upper lasing state is found to be incoherent due to the strong dephasing in the active subband. The gain recovery due to transport through superlattice is interpreted in terms of dielectric relaxation within the superlattice miniband.
Nonlinear reflection effects on Fresnel phase matching
Authors: Raybaut Myriam , Godard Antoine , Toulouse Alexis , Lubin Clément , Rosencher Emmanuel
Published: March 2008

An experimental study of the second harmonic generation conversion efficiency of Fresnel phase matching as a function of a gallium arsenide sample length is presented. It shows a strong deviation from the classical quadratic law, explaining the low conversion yields related in the literature. In order to explain these experimental results, a highly multimodal nonlinear waveguide model is developed which shows a good agreement with the experimental results. It highlights the detrimental role of nonlinear reflection.
Magnetic field induced concentration gradients in magnetic nanoparticle suspensions: Theory and experiment
Authors: Erb Randall M. , Sebba David S. , Lazarides Anne A. , Yellen Benjamin B.
Published: March 2008

An approach for studying steady-state nanoparticle concentration gradients arising in magnetic nanoparticle suspensions in response to strong magnetic field gradient is presented. The experimental approach makes use of microscopic optical absorption measurements of ferrofluid interacting with arrays of patterned magnets. Experimental results are found to be consistent with a simple theoretical description that predicts the local nanoparticle concentration over a wide range of magnetic field conditions and ferrofluid volume fractions.
Hydrocarbon lithography on graphene membranes
Authors: Meyer Jannik C. , Girit C. O. , Crommie M. F. , Zettl A.
Published: March 2008

We present a simple and efficient way to obtain freestanding graphene membranes. On these membranes, we demonstrate that electron-beam induced deposition of carbon can be used to obtain arbitrary patterns with a nanometer-scale resolution. In the case of a periodic grating, we obtain a half-pitch of 2.5nm. Electron-beam induced deposition on graphene might be used to create nanometer-scale doping patterns, diffraction gratings, or etch masks in this novel electronic material.
Direct observation and kinetic analysis of grain rotation in anisotropic tin under electromigration
Authors: Wu Albert T. , Hsieh Y. C.
Published: March 2008

The resistance of β-tin decreases by 10% under electromigration because of the anisotropic properties of the material during electromigration and the consequent rotation of grains. The diameter of the grains was measured ex situ and the angle of the rotating grains was directly calculated. The angle of rotating grains increased in proportion to the time for which the current was applied. At higher temperature, at which electromigration effect was stronger, an unexpected rotation behavior was observed. The kinetics of atomic movement along the a and c axes under various test conditions is discussed.
Localized surface plasmon assisted microfluidic mixing
Authors: Miao Xiaoyu , Wilson Benjamin K. , Lin Lih Y.
Published: March 2008

We present an optical microfluidic mixing approach via thermally induced convective flow sustained by localized surface plasmon (LSP) energy. The phonon energy associated with the nonradiative damping of LSP from a Au nanoparticle (NP) array under optical excitation creates a thermal gradient which initiates a convective fluidic flow. Experimental evidence and modeling results both show that LSP from the Au NPs is crucial in establishing a temperature gradient with sufficient magnitude to induce the convective flow with low input optical intensity.
Sorption-induced static bending of microcantilevers coated with viscoelastic material
Authors: Wenzel M. J. , Josse F. , Heinrich S. M. , Yaz E. , Datskos P. G.
Published: March 2008

Absorption of a chemical analyte into a polymer coating results in an expansion governed by the concentration and type of analyte that has diffused into the bulk of the coating. When the coating is attached to a microcantilever, this expansion results in bending of the device. Assuming that absorption (i.e., diffusion across the surface barrier into the bulk of the coating) is Fickian, with a rate of absorption that is proportional to the difference between the absorbed concentration and the equilibrium concentration, and the coating is elastic, the bending response of the coated device should exhibit a first-order behavior. However, for polymer coatings, complex behaviors exhibiting an overshoot that slowly decays to the steady-state value have been observed. A theoretical model of absorption-induced static bending of a microcantilever coated with a viscoelastic material is presented, starting from the general stress/strain relationship for a viscoelastic material. The model accounts for viscoelastic stress relaxation and possible coating plasticization. Calculated responses show that the model is capable of reproducing the same transient behavior exhibited in the experimental data. The theory presented can also be used for extracting viscoelastic properties of the coating from the measured bending data.
Effect of strain compensation on quantum dot enhanced GaAs solar cells
Authors: Hubbard S. M. , Cress C. D. , Bailey C. G. , Raffaelle R. P. , Bailey S. G. , Wilt D. M.
Published: March 2008

GaP tensile strain compensation (SC) layers were introduced into GaAs solar cells enhanced with a five layer stack of InAs quantum dots (QDs). One sun air mass zero illuminated current-voltage curves show that SC results in improved conversion efficiency and reduced dark current. The strain compensated QD solar cell shows a slight increase in short circuit current compared to a baseline GaAs cell due to sub-GaAs bandgap absorption by the InAs QD. Quantum efficiency and electroluminescence were also measured and provide further insight to the improvements due to SC.
Fabrication of gate stack with high gate work function for implantless enhancement-mode GaAs n-channel metal-oxide-semiconductor field effect transistor applications
Authors: Zhu Ming , Chin Hock-Chun , Samudra Ganesh S. , Yeo Yee-Chia
Published: March 2008

The guidelines for the selection of gate stacks in using an implantless enhancement-mode GaAs n-channel metal-oxide-semiconductor field effect transistor, which is based on a gate material with high work function, are studied using two dimensional device simulation. By employing the silane surface passivation, a high quality gate stack on GaAs substrate comprising of a complementary metal-oxide semiconductor compatible tungsten nitride (WNx) metal gate, which can be easily etched, and a high-permittivity HfAlO gate dielectric is demonstrated. The high work function of 4.97eV and the equivalent oxide thickness of 2.3nm were achieved for this gate stack, which meets the above mentioned normally off operation requirements.
Identification of a vesicular nucleotide transporter
Authors: Sawada Keisuke , Echigo Noriko , Juge Narinobu , Miyaji Takaaki , Otsuka Masato , Omote Hiroshi , Yamamoto Akitsugu , Moriyama Yoshinori
Published: March 2008

ATP is a major chemical transmitter in purinergic signal transmission. Before secretion, ATP is stored in secretory vesicles found in purinergic cells. Although the presence of active transport mechanisms for ATP has been postulated for a long time, the proteins responsible for its vesicular accumulation remains unknown. The transporter encoded by the human and mouse SLC17A9 gene, a novel member of an anion transporter family, was predominantly expressed in the brain and adrenal gland. The mouse and bovine counterparts were associated with adrenal chromaffin granules. Proteoliposomes containing purified transporter actively took up ATP, ADP, and GTP by using membrane potential as the driving force. The uptake properties of the reconstituted transporter were similar to that of the ATP uptake by synaptic vesicles and chromaffin granules. Suppression of endogenous SLC17A9 expression in PC12 cells decreased exocytosis of ATP. These findings strongly suggest that SLC17A9 protein is a vesicular nucleotide transporter and should lead to the elucidation of the molecular mechanism of ATP secretion in purinergic signal transmission.
Perception of emotional expressions is independent of face selectivity in monkey inferior temporal cortex
Authors: Hadj-Bouziane Fadila , Bell Andrew H. , Knusten Tamara A. , Ungerleider Leslie G. , Tootell Roger B. H.
Published: March 2008

The ability to perceive and differentiate facial expressions is vital for social communication. Numerous functional MRI (fMRI) studies in humans have shown enhanced responses to faces with different emotional valence, in both the amygdala and the visual cortex. However, relatively few studies have examined how valence influences neural responses in monkeys, thereby limiting the ability to draw comparisons across species and thus understand the underlying neural mechanisms. Here we tested the effects of macaque facial expressions on neural activation within these two regions using fMRI in three awake, behaving monkeys. Monkeys maintained central fixation while blocks of different monkey facial expressions were presented. Four different facial expressions were tested: (
i
) neutral, (
ii
) aggressive (open-mouthed threat), (
iii
) fearful (fear grin), and (
iv
) submissive (lip smack). Our results confirmed that both the amygdala and the inferior temporal cortex in monkeys are modulated by facial expressions. As in human fMRI, fearful expressions evoked the greatest response in monkeys—even though fearful expressions are physically dissimilar in humans and macaques. Furthermore, we found that valence effects were not uniformly distributed over the inferior temporal cortex. Surprisingly, these valence maps were independent of two related functional maps: (
i
) the map of “face-selective” regions (faces versus non-face objects) and (
ii
) the map of “face-responsive” regions (faces versus scrambled images). Thus, the neural mechanisms underlying face perception and valence perception appear to be distinct.
The
Drosophila
homolog of human tumor suppressor TSC-22 promotes cellular growth, proliferation, and survival
Authors: Wu Xiaodong , Yamada-Mabuchi Megumu , Morris Erick J. , Tanwar Pradeep Singh , Dobens Leonard , Gluderer Silvia , Khan Sabina , Cao Jing , Stocker Hugo , Hafen Ernst , Dyson Nick J. , Raftery Laurel A.
Published: March 2008

TSC22D1
, which encodes transforming growth factor β-stimulated clone 22 (TSC-22), is thought to be a tumor suppressor because its expression is lost in many glioblastoma, salivary gland, and prostate cancers. TSC-22 is the founding member of the TSC-22/DIP/Bun family of leucine zipper transcription factors; its functions have not been investigated in a multicellular environment. Genetic studies in the model organism
Drosophila melanogaster
often provide fundamental insights into mechanisms disrupted in carcinogenesis, because of the strong evolutionary conservation of molecular mechanisms between flies and humans. Whereas humans and mice have four TSC-22 domain genes with numerous isoforms,
Drosophila
has only one TSC-22 domain gene,
bunched
(
bun
), which encodes both large and small protein isoforms. Surprisingly,
Drosophila
Bun proteins promote cellular growth and proliferation in ovarian follicle cells. Loss of both large isoforms has the strongest phenotypes, including increased apoptosis. Cultured S2 cells depleted for large Bun isoforms show increased apoptosis and less frequent cell division, with decreased cell size. Altogether, these data indicate that
Drosophila
TSC-22/DIP/Bun proteins are necessary for cellular growth, proliferation, and survival both in culture and in an epithelial context. Previous work demonstrated that
bun
prevents recruitment of epithelial cells to a migratory fate and, thus, maintains epithelial organization. We speculate that reduced
TSC22D1
expression generally reduces cellular fitness and only contributes to carcinogenesis in specific tissue environments.
NMDA receptors inhibit synapse unsilencing during brain development
Authors: Adesnik Hillel , Li Guangnan , During Matthew J. , Pleasure Samuel J. , Nicoll Roger A.
Published: March 2008

How the billions of synapses in the adult mammalian brain are precisely specified remains one of the fundamental questions of neuroscience. Although a genetic program is likely to encode the basic neural blueprint, much evidence suggests that experience-driven activity through NMDA receptors wires up neuronal circuits by inducing a process similar to long-term potentiation. To test this notion directly, we eliminated NMDA receptors before and during synaptogenesis in single cells
in vitro
and
in vivo
. Although the prevailing model would predict that NMDA receptor deletion should strongly inhibit the maturation of excitatory circuits, we find that genetic ablation of NMDA receptor function profoundly increases the number of functional synapses between neurons. Conversely, reintroduction of NMDA receptors into NR1-deficient neurons reduces the number of functional inputs, a process requiring network activity and NMDA receptor function. Although NMDA receptor deletion increases the strength of unitary connections, it does not alter neuronal morphology, suggesting that basal NMDA receptor activation blocks the recruitment of AMPA receptors to silent synapses. Based on these results we suggest a new model for the maturation of excitatory synapses in which ongoing activation of NMDA receptors prevents premature synaptic maturation by ensuring that only punctuated bursts of activity lead to the induction of a functional synapse for the activity-dependent wiring of neural circuitry.
Molecular recognition of parathyroid hormone by its G protein-coupled receptor
Authors: Pioszak Augen A. , Xu H. Eric
Published: March 2008

Parathyroid hormone (PTH) is central to calcium homeostasis and bone maintenance in vertebrates, and as such it has been used for treating osteoporosis. It acts primarily by binding to its receptor, PTH1R, a member of the class B G protein-coupled receptor (GPCR) family that also includes receptors for glucagon, calcitonin, and other therapeutically important peptide hormones. Despite considerable interest and much research, determining the structure of the receptor–hormone complex has been hindered by difficulties in purifying the receptor and obtaining diffraction-quality crystals. Here, we present a method for expression and purification of the extracellular domain (ECD) of human PTH1R engineered as a maltose-binding protein (MBP) fusion that readily crystallizes. The 1.95-Å structure of PTH bound to the MBP-PTH1R-ECD fusion reveals that PTH docks as an amphipathic helix into a central hydrophobic groove formed by a three-layer α–β–βα fold of the PTH1R ECD, resembling a hot dog in a bun. Conservation in the ECD scaffold and the helical structure of peptide hormones emphasizes this hot dog model as a general mechanism of hormone recognition common to class B GPCRs. Our findings reveal critical insights into PTH actions and provide a rational template for drug design that targets this hormone signaling pathway.
Dynamic interactions between the promoter and terminator regions of the mammalian
BRCA1
gene
Authors: Tan-Wong Sue Mei , French Juliet D. , Proudfoot Nicholas J. , Brown Melissa A.
Published: March 2008

The 85-kb breast cancer-associated gene
BRCA1
is an established tumor suppressor gene, but its regulation is poorly understood. We demonstrate by gene conformation analysis in both human cell lines and mouse mammary tissue that gene loops are imposed on
BRCA1
between the promoter, introns, and terminator region. Significantly, association between the
BRCA1
promoter and terminator regions change upon estrogen stimulation and during lactational development. Loop formation is transcription-dependent, suggesting that transcriptional elongation plays an active role in
BRCA1
loop formation. We show that the
BRCA1
terminator region can suppress estrogen-induced transcription and so may regulate
BRCA1
expression. Significantly,
BRCA1
promoter and terminator interactions vary in different breast cancer cell lines, indicating that defects in
BRCA1
chromatin structure may contribute to dysregulated expression of
BRCA1
seen in breast tumors.
Identification of two inner-membrane proteins required for the transport of lipopolysaccharide to the outer membrane of
Escherichia coli
Authors: Ruiz Natividad , Gronenberg Luisa S. , Kahne Daniel , Silhavy Thomas J.
Published: March 2008

The outer membrane (OM) of most Gram-negative bacteria contains lipopolysaccharide (LPS) in the outer leaflet. LPS, or endotoxin, is a molecule of important biological activities. In the host, LPS elicits a potent immune response, while in the bacterium, it plays a crucial role by establishing a barrier to limit entry of hydrophobic molecules. Before LPS is assembled at the OM, it must be synthesized at the inner membrane (IM) and transported across the aqueous periplasmic compartment. Much is known about the biosynthesis of LPS but, until recently, little was known about its transport and assembly. We applied a reductionist bioinformatic approach that takes advantage of the small size of the proteome of the Gram-negative endosymbiont
Blochmannia floridanus
to search for novel factors involved in OM biogenesis. This led to the discovery of two essential
Escherichia coli
IM proteins of unknown function, YjgP and YjgQ, which are required for the transport of LPS to the cell surface. We propose that these two proteins, which we have renamed LptF and LptG, respectively, are the missing transmembrane components of the ABC transporter that, together with LptB, functions to extract LPS from the IM en route to the OM.
Dynamic development of the calyx of Held synapse
Authors: Rodríguez-Contreras Adrián , van Hoeve John Silvio Soria , Habets Ron L. P. , Locher Heiko , Borst J. Gerard G.
Published: March 2008

The calyx of Held is probably the largest synaptic terminal in the brain, forming a unique one-to-one connection in the auditory ventral brainstem. During early development, calyces have many collaterals, whose function is unknown. Using electrophysiological recordings and fast-calcium imaging in brain slices, we demonstrate that these collaterals are involved in synaptic transmission. We show evidence that the collaterals are pruned and that the pruning already begins 1 week before the onset of hearing. Using two-photon microscopy to image the calyx of Held in neonate rats, we report evidence that both axons and nascent calyces are structurally dynamic, showing the formation, elimination, extension, or retraction of up to 65% of their collaterals within 1 hour. The observed dynamic behavior of axons may add flexibility in the choice of postsynaptic partners and thereby contribute to ensuring that each principal cell eventually is contacted by a single calyx of Held.
Cross-Transmission of Multidrug-ResistantAcinetobacter baumanniiClonal Strains Causing Episodes of Sepsis in a Trauma Intensive Care Unit
Authors: Markogiannakis Antonios , Fildisis George , Tsiplakou Sofia , Ikonomidis Alexandras , Koutsoukou Alexandra , Pournaras Spyros , Manolis Evangelos N. , Baltopoulos George , Tsakris Athanassios
Published: March 2008

Objective.

To investigate the mode of transmission of imipenem-resistantAcinetobacter baumanniistrains causing episodes of sepsis.

Setting.

A 7-bed trauma intensive care unit (ICU) in an orthopedic hospital in Greece.

Design.

During a 14-week period (from January 10 to April 16, 2006), clinical specimens, along with samples taken on a weekly basis from the ICU environment and from the hands of health care workers (HCWs), were prospectively tested for imipenem-resistantA. baumannii.Pulsed-field gel electrophoresis was used to study the genetic relatedness of the isolates recovered from these specimens and samples.

Results.

During the survey, imipenem-resistantA. baumanniiwas identified in 14 hospitalized patients, from whom 40 multidrug-resistant and imipenem-resistantA. baumaniiisolates were recovered. These pathogens caused episodes of bacteremia and sepsis in all but one of the patients and contributed to the death of 3 patients. Samples for culture were obtained from the environment and from the hands of HCWs; 29 imipenem-resistantA. baumanniiisolates were recovered from the environment, and 12 from HCWs. One predominant genotype and 2 less predominant genotypes were detected among the 81 imipenem-resistantA. baumanniiisolates. All 3 of these genotypes were found among patients and HCWs and were recovered from environmental samples.

Interventions.

Control measures consisted of the closure of the ICU and the transfer of the patients to other units. The ICU was disinfected, and adherence to proper hand hygiene protocol was reinforced. These same clonal isolates were not recovered from clinical or environmental samples during the month after the reopening of the ICU.

Conclusions.

The extensive dissemination of imipenem-resistantA. baumanniiclonal strains causing episodes of bacteremia and/or sepsis resulted from modes of transmission via multiple contaminated surfaces and objects and transiently colonized HCWs' hands. Closure of the ICU and its meticulous environmental decontamination led to the successful control of the outbreak.
Brain regeneration from pluripotent stem cells in planarian
Authors: Agata Kiyokazu , Umesono Yoshihiko
Published: March 2008

How can planarians regenerate their brain? Recently we have identified many genes critical for this process. Brain regeneration can be divided into five steps: (1) anterior blastema formation, (2) brain rudiment formation, (3) pattern formation, (4) neural network formation, and (5) functional recovery. Here we will describe the structure and process of regeneration of the planarian brain in the first part, and then introduce genes involved in brain regeneration in the second part. Especially, we will speculate about molecular events during the early steps of brain regeneration in this review. The finding providing the greatest insight thus far is the discovery of thenou-darake(ndk; ‘brains everywhere’ in Japanese) gene, since brain neurons are formed throughout the entire body as a result of loss of function of thendkgene. This finding provides a clue for elucidating the molecular and cellular mechanisms underlying brain regeneration. Here we describe the molecular action of thenou-darakegene and propose a new model to explain brain regeneration and restriction in the head region of the planarians.
Bloodlines of haematopoietic stem cell research in Japan
Authors: Ema Hideo , Nakauchi Hiromitsu
Published: March 2008

Haematopoietic stem cells (HSCs) can supply all blood cells throughout the adult life of individuals. Based on this property, HSCs have been used for bone marrow and cord blood transplantation. Among various stem cells, HSCs were recognized earliest and were studied most extensively, providing a model for other stem cells. Knowledge of HSC regulation has rapidly accumulated of late. Contributions of scientists in Japan to progress HSC biology are here briefly overviewed. Focusing on the original work accomplished in Japan in the last two decades, people who have led such activities are introduced and their relationships with one another are sketched.
The Highly SimilarArabidopsisHomologs of Trithorax ATX1 and ATX2 Encode Proteins with Divergent Biochemical Functions
Authors: Saleh Abdelaty , Alvarez-Venegas Raul , Yilmaz Mehtap , Le Oahn , Hou Guichuan , Sadder Monther , Al-Abdallat Ayed , Xia Yuannan , Lu Guoqinq , Ladunga Istvan , Avramova Zoya
Published: March 2008

Gene duplication followed by functional specialization is a potent force in the evolution of biological diversity. A comparative study of two highly conserved duplicated genes, ARABIDOPSIS TRITHORAX-LIKE PROTEIN1 (ATX1) and ATX2, revealed features of both partial redundancy and of functional divergence. Although structurally similar, their regulatory sequences have diverged, resulting in distinct temporal and spatial patterns of expression of the ATX1 and ATX2 genes. We found that ATX2 methylates only a limited fraction of nucleosomes and that ATX1 and ATX2 influence the expression of largely nonoverlapping gene sets. Even when coregulating shared targets, ATX1 and ATX2 may employ different mechanisms. Most remarkable is the divergence of their biochemical activities: both proteins methylate K4 of histone H3, but while ATX1 trimethylates it, ATX2 dimethylates it. ATX2 and ATX1 provide an example of separated K4 di from K4 trimethyltransferase activity.
The F-Box Protein ACRE189/ACIF1 Regulates Cell Death and Defense Responses Activated during Pathogen Recognition in Tobacco and Tomato
Authors: van den Burg Harrold A. , Tsitsigiannis Dimitrios I. , Rowland Owen , Lo Jane , Rallapalli Ghanasyam , MacLean Daniel , Takken Frank L.W. , Jones Jonathan D.G.
Published: March 2008

Virus-induced gene silencing identified the Avr9/Cf-9 RAPIDLY ELICITED gene ACRE189 as essential for the Cf-9– and Cf-4–mediated hypersensitive response (HR) in Nicotiana benthamiana. We report a role for ACRE189 in disease resistance in tomato (Solanum lycopersicum) and tobacco (Nicotiana tabacum). ACRE189 (herein renamed Avr9/Cf-9–INDUCED F-BOX1 [ACIF1]) encodes an F-box protein with a Leu-rich-repeat domain. ACIF1 is widely conserved and is closely related to F-box proteins regulating plant hormone signaling. Silencing of tobacco ACIF1 suppressed the HR triggered by various elicitors (Avr9, Avr4, AvrPto, Inf1, and the P50 helicase of Tobacco mosaic virus [TMV]). ACIF1 is recruited to SCF complexes (a class of ubiquitin E3 ligases), and the expression of ACIF1 F-box mutants in tobacco compromises the HR similarly to ACIF1 silencing. ACIF1 affects N gene–mediated responses to TMV infection, including lesion formation and salicylic acid accumulation. Loss of ACIF1 function also reduced confluent cell death induced by Pseudomonas syringae pv tabaci. ACIF1 silencing in Cf9 tomato attenuated the Cf-9–dependent HR but not Cf-9 resistance to Cladosporium fulvum. Resistance conferred by the Cf-9 homolog Cf-9B, however, was compromised in ACIF1-silenced tomato. Analysis of public expression profiling data suggests that Arabidopsis thaliana homologs of ACIF1 (VFBs) regulate defense responses via methyl jasmonate– and abscisic acid–responsive genes. Together, these findings support a role of ACIF1/VFBs in plant defense responses.
Assessment of species diversity from species abundance distributions at different localities
Authors: Engen Steinar , Sæther Bernt‐Erik , Sverdrup‐Thygeson Anne , Grøtan Vidar , Ødegaard Frode
Published: March 2008

We show how the spatial structure of species diversity can be analyzed using the correlation between the log abundances of the species in the communities, assuming that two communities at different localities can be described by a bivariate lognormal species abundance distribution. A useful property of this approach is that the log abundances of the species at two localities can be considered as samples from a bivariate normal distribution defined by only five parameters. The variances and the correlation can be estimated by maximum likelihood methods even if there is no information about the sampling intensity and the number of unobserved species. This method also enables estimation of over‐dispersion in the sampling relative to a Poisson distribution that allows sampling adjustment of the estimate of β‐diversity. Furthermore, we also obtain a partitioning of species diversity into additive components of α‐, β‐ and γ‐diversity. For instance, if the correlation between the log abundances of the species is close to one, the same species will be common and rare in the two communities and the β‐diversity will be low. We illustrate this approach by analysing similarities of communities of rare and endangered species of oak‐living beetles in south‐eastern Norway. The number of recorded species was estimated to be only 48.1% of the total number of species actually present in these communities. The correlations among communities dropped rather quickly with distance with a scaling of order 200 km. This illustrates large spatial heterogeneity in species composition, which should be accounted for in the design of schemes of such devices for assessing species diversity in these habitat‐types.
Invasion dynamics of an introduced squirrel in Argentina
Authors: Guichón M. Laura , Doncaster C. Patrick
Published: March 2008

Biological invasions are one of the major threats to both ecosystem and economic functioning. Their management typically involves culling of the pest or removal of its habitat. The Asiatic red‐bellied beautiful squirrelCallosciurus erythraeusis the first known introduction of a squirrel into South America. It established from five releases in 1973, using exotic trees to spread through Argentinean Pampas. It now causes substantial economic damage in agricultural and urban areas across >680 km2, and its continued spread threatens indigenous species. We developed a spatially explicit model of the invasion for the likely range of life‐history parameters, matched against empirical data on patch occupancy in 2004. The two best‐fitting models suggest the current population to be on the cusp of an explosive expansion. These models were used to predict future trends under alternative scenarios of strategic culling or habitat removal aimed at slowing the spread. The predictions for 18 yr into the future were that 1) the present lack of systematic management will lead to a 5‐fold increase in area of occupancy, 2) removal of habitat down to half carrying capacity will thin the population but accelerate its spread, 3) 10 yr of culling above the maximum sustainable yield (MSY) will precipitate declines in abundance and patch occupancy towards extinction, but with immediate recovery upon cessation of the cull. We recommend continuous culling above the MSY in priority patches, aimed at slowing arrival to valuable conservation areas. This study demonstrates the need for prompt action to terminate invasions before they establish. The squirrel invasion is now irreversible after 30 yr of slow spread across fragmented habitat. Although culling requires public awareness campaigns and sustained governmental commitment, it is now the best feasible strategy for managing this invasion.
Enhancer of zeste homolog 2 downregulates E‐cadherin by mediating histone H3 methylation in gastric cancer cells
Authors: Fujii Satoshi , Ochiai Atsushi
Published: March 2008

Overexpression of enhancer of zeste homolog 2 (EZH2), an epigenetic repressor, occurs in various malignancies and is associated with poor prognosis; however, the functional role of EZH2 overexpression in cancer versus non‐cancerous tissue remains unclear. In this study, we found an inverse correlation between EZH2 and E‐cadherin gene expression in gastric cancer cells. Knockdown of EZH2 by short interfering RNA in gastric cancer cells resulted in a restoration of the E‐cadherin gene. We showed that the EZH2 complex existed with histone H3 and Lys27, which were methylated on E‐cadherin promoter regions in gastric cancer cells. The restoration of E‐cadherin was not involved in the change of the DNA methylation status in the E‐cadherin promoter region. Immunofluorescence staining confirmed the expression of E‐cadherin protein present in the cell membrane was restored after knockdown of EZH2, resulting in changing the cancer phenotype, such as its invasive capacity. In vivo, the relationship of inverse expression between EZH2 protein and E‐cadherin protein was observed at the individual cellular level in gastric cancer tissue. This study provides into the mechanisms underlying the functional role of EZH2 overexpression in gastric cancer cells and a new modality of regulation of E‐cadherin expression in silencing mechanisms of tumor suppressor genes. Our present study paves the way for exploring the blockade of EZH2 overexpression as a novel approach to treating cancer. (Cancer Sci 2008; 99: 738–746)