bluuebunny/crossref_metadata_2025 huggingface dataset:
Electrical resistivity of Gd4(Co1−xCux)3 compounds
Authors: Seixas T. M. , Machado da Silva J. M. , Braun H. F. , Eska G.
Published: January 2008

In order to study the effects caused by substituting Co for Cu on the electronic and transport properties of Gd4(Co1−xCux)3 compounds with x=0.05, 0.1, 0.2, and 0.3, electrical resistivity [ρ(T)] measurements were performed in the temperature range 12–300K. The paramagnetic-ferrimagnetic and spin-reorientation transitions are marked by clear anomalies in dρ∕dT. For x=0.2, however, the onset of ferrimagnetic order at TC produces just a comparatively small peak in dρ∕dT. This fact is compatible with a hypothetical mixed ferrimagnetic phase exhibiting partial disorder of the magnetic moments, as suggested by magnetic measurements [T. M. Seixas, J. M. Machado da Silva, H. F. Braun, and G. Eska (unpublished)]. The spin disorder resistivity shows a pronounced decrease with increasing x that can be attributed to the observed reduction of the magnetic moment of Co atoms. This stresses the important role played by 3d-band electrons in both magnetic state and in the strong s-d electron scattering. Magnon-induced electron scattering is also apparent in all compounds through well-defined maxima in dρ∕dT, at temperatures ranging from 37to48K, where the magnetic contribution to dρ∕dT largely exceeds the phonon contribution.
Influence of Ge addition on the magnetocaloric effect of a Co-containing Nanoperm-type alloy
Authors: Franco V. , Blázquez J. S. , Conde A.
Published: January 2008

The influence of the partial substitution of B by Ge on the magnetocaloric response of Fe78Co5Zr6B10Cu1 is studied. Ge addition produces a reduction in the temperature at which the peak entropy change takes place, as well as a slight decrease in the magnitude of the peak, ∣ΔSMpk∣. The refrigerant capacity, RC, and its field dependence is also analyzed: although Ge addition increases RC of the Co-containing alloy, the largest RC value corresponds to the Co- and Ge-free alloy. This will be discussed on the basis of the recently proposed universal curve for the magnetic entropy change, which is also followed by the FeZrBCu(Co,Ge) alloy series.
Precision polarimetry with real-time mitigation of optical-window birefringence
Authors: Park B. K. , Sushkov A. O. , Budker D.
Published: January 2008

Optical-window birefringence is frequently a major obstacle in experiments measuring changes in the polarization state of light traversing a sample under investigation. It can contribute a signal indistinguishable from that due to the sample and complicate the analysis. Here, we explore a method to measure and compensate for the birefringence of an optical window using the reflection from the last optical surface before the sample. We demonstrate that this arrangement can cancel out false signals due to the optical-window birefringence-induced ellipticity drift to about 1%, for the values of total ellipticity less than 0.25rad.
Structural modulations in Bi2Te3
Authors: Peranio N. , Eibl O.
Published: January 2008

Bi 2 Te 3 is known for its large thermopower, a low thermal conductivity, and thereby a large thermoelectric figure of merit ZT at room temperature. Particularly, the low thermal conductivity is attributed to a high structural disorder. Electron probe microanalysis, transmission electron microscopy (TEM), and energy dispersive x-ray spectrometry in the TEM were applied on n-type Bi2(Te,Se)3 and p-type (Bi,Sb)2Te3 bulk materials for structural and chemical analysis. Significant variations in stoichiometry were found on the micrometer scale. Bulk materials showed a texture, grain sizes of 1−10 μm, and dislocations in the basal plane with a density of 109 cm−2 having a high mobility at room temperature. A structural modulation [natural nanostructure (nns)] was found on the nanometer scale. This nns was also observed in Bi2Te3 thin films and Bi2Te3/Bi2(Te,Se)3 superlattices and turned out to be of general character for Bi2Te3 materials. The nns was analyzed in detail by stereomicroscopy in the TEM and by image simulation. The nns was found to be a pure sinusoidal displacement field with (i) a displacement vector parallel to ⟨5,−5,1⟩ and an amplitude of about 10 pm and (ii) a wave vector parallel to {1,0,10} and a wavelength of 10 nm. Bi2Te3 samples from different batches produced under similar conditions showed different characteristics with respect to the nns: none, one, or two superimposed nns were observed. The nns is present in all parts of the sample with the same orientation. The formation of the nns is either bound to a certain stoichiometry range or to the thermal history of a sample and is related to the tendency of Te compounds to form amorphous phases. An ordered network of dislocations a few nanometers apart and chemical fluctuations on the nanometer scale as origins of the nns were ruled out. The displacement field of the nns is superimposed to the average structure and should significantly affect the thermoelectric properties. Particularly, the lattice thermal conductivity should be decreased due to phonon scattering on the sinusoidal strain field of the nns. Also, the nns should yield a one-dimensional or zero-dimensional behavior of the phonons and anisotropic transport coefficients in the basal plane.
Measurement of ultrafast carrier dynamics in epitaxial graphene
Authors: Dawlaty Jahan M. , Shivaraman Shriram , Chandrashekhar Mvs , Rana Farhan , Spencer Michael G.
Published: January 2008

Using ultrafast optical pump-probe spectroscopy, we have measured carrier relaxation times in epitaxial graphene layers grown on SiC wafers. We find two distinct time scales associated with the relaxation of nonequilibrium photogenerated carriers. An initial fast relaxation transient in the 70–120fs range is followed by a slower relaxation process in the 0.4–1.7ps range. The slower relaxation time is found to be inversely proportional to the degree of crystalline disorder in the graphene layers as measured by Raman spectroscopy. We relate the measured fast and slow time constants to carrier-carrier and carrier-phonon intraband and interband scattering processes in graphene.
First-principles study of structural, elastic, and electronic properties of chromium carbides
Authors: Jiang Chao
Published: January 2008

Using first-principles calculations, we systematically studied the structural, elastic, and electronic properties of the technologically important chromium carbides: Cr3C2, Cr7C3, Cr23C6, Cr3C, and CrC. Our calculations show that the ground state structure for Cr7C3 is hexagonal, not orthorhombic. We further predict WC to be the energetically most stable structure for CrC. Our results indicate that all chromium carbides considered in this study are metallic and mechanically stable under the ambient condition. Among all chromium carbides, WC-type CrC exhibits the highest bulk and shear moduli and the lowest Poisson’s ratio, and is a potential low-compressibility and hard material.
Optically isotropic-nanostructured liquid crystal composite with high Kerr constant
Authors: Choi Suk-Won , Yamamoto Shin-Ichi , Haseba Yasuhiro , Higuchi Hiroki , Kikuchi Hirotsugu
Published: January 2008

The relationship between material parameters of host nematic liquid crystals (LCs) and Kerr constant of their nanostructured chiral LC composites was investigated. We made certain that the Kerr constant of nanostrutured chiral LC composites was closely related to the parameters of their host LCs, such as value of the difference of refractive index (Δn), the dielectric anisotropy (Δε), and bend to splay elastic constant ratio (K33∕K11).
Experimental analysis for the effect of dynamic capillarity on stress transformation in porous silicon
Authors: Qiu Wei , Kang Yi-Lan , Li Qiu , Lei Zhen-Kun , Qin Qing-Hua
Published: January 2008

The evolution of real-time stress in porous silicon (PS) during drying is investigated using micro-Raman spectroscopy. The results show that the PS sample underwent non-negligible stress when immersed in liquid and suffered a stress impulsion during drying. Such nonlinear transformation and nonhomogeneneous distribution of stress are regarded as the coupling effects of several physical phenomena attributable to the intricate topological structure of PS. The effect of dynamic capillarity can induce microcracks and even collapse in PS structures during manufacture and storage.
In situ arsenic-doped Si1−yCy selective epitaxial growth under atmospheric pressure
Authors: Ikuta Tetsuya , Fujita Shigeru , Iwamoto Hayato , Kadomura Shingo , Shimura Takayoshi , Watanabe Heiji , Yasutake Kiyoshi
Published: January 2008

We investigated the characteristics of in situ As-doped Si1−yCy selective epitaxial growth (SEG) under atmospheric pressure. We succeeded in obtaining an in situ doped Si1−yCy SEG film with a high As concentration of 2.6×1019atoms∕cm3. The film exhibited a high crystalline quality, high strain, constant As and C concentration profiles, and an abrupt change in the dopant profile at the interface. It was found that the increase in As concentration under atmospheric pressure increases the C concentration and the growth rate by competitive surface segregation between As and C atoms, leading to a highly strained Si1−yCy SEG film with a low resistivity.
Electrical characterization of CeO2∕Si interface properties of metal-oxide-semiconductor field-effect transistors with CeO2 gate dielectric
Authors: Chen Chun-Heng , Chang Ingram Yin-Ku , Lee Joseph Ya-Min , Chiu Fu-Chien
Published: January 2008

Metal-oxide-semiconductor field-effect transistors with CeO2 gate dielectrics were fabricated. The lowest interface trap density (Dit) of CeO2∕Si interface in comparison with other high-κ gated diodes is 1.47×1012cm−2eV−1 due to the very low lattice mismatch of CeO2∕Si. The interfacial properties were characterized by gated-diode measurements. The surface recombination velocity (s0) and the minority carrier lifetime in the field-induced depletion region (τ0,FIJ) measured from the gated diodes are about 1.03×104cm∕s and 2.73×10−8s, respectively. The effective capture cross section of surface state (σs) extracted using the gated diode technique and the subthreshold swing measurement is about 8.68×10−15cm2.
Alignment of particles in microfluidic systems using standing surface acoustic waves
Authors: Wood C. D. , Evans S. D. , Cunningham J. E. , O’Rorke R. , Wälti C. , Davies A. G.
Published: January 2008

We report on the use of standing surface acoustic waves, formed on a single-crystal piezoelectric substrate, to organize micron-scale latex particles into an array comprising a series of lines in an adjacent microfluidic system. The lines of particles are formed parallel to the substrate surface and perpendicular to the surface acoustic wave vector. They extend across the width of the acoustic beam aperture, with a periodicity of one-half the surface acoustic wavelength. The position and spacing of the particle arrays can be altered by adjusting the acoustic wave frequency within the device passband. We discuss the mechanism responsible for the formation of the lines, which could be widely applicable to the alignment of microscopic objects held in suspension.
Vibrational dephasing time imaging by time-resolved broadband coherent anti-Stokes Raman scattering microscopy
Authors: Lee Young Jong , Cicerone Marcus T.
Published: January 2008

Time delay control in broadband coherent anti-Stokes Raman scattering (CARS) allows acquisition of time-resolved CARS images free of nonresonant background (NRB). We demonstrate that, in some cases, CARS image contrast is not chemical contrast but simply due to differences in NRB. Time-resolved CARS is used to rectify this by eliminating the NRB. We also construct a vibrational dephasing time image from a sequence of time-resolved CARS images of polystyrene beads in toluene. In doing so, we demonstrate the potential of imaging local molecular interactions between molecules and their surrounding in a structured medium.
Direct write of microlens array using digital projection photopolymerization
Authors: Lu Yi , Chen Shaochen
Published: January 2008

Microlens array is a key element in the field of information processing, optoelectronics, and integrated optics. Many existing fabrication processes remain expensive and complicated even though relatively low-cost replication processes have been developed. Here, we demonstrate the fabrication of microlens arrays through projection photopolymerization using a digital micromirror device (DMD) as a dynamic photomask. The DMD projects grayscale images, which are designed in a computer, onto a photocurable resin. The resin is then solidified with its thickness determined by a grayscale ultraviolet light and exposure time. Therefore, various geometries can be formed in a single-step, massively parallel fashion. We present microlens arrays made of acrylate-based polymer precursor. The physical and optical characteristics of the resulting lenses suggest that this fabrication technique is potentially suitable for applications in integrated optics.
Thermoelectric properties of InxGa1−xN alloys
Authors: Pantha B. N. , Dahal R. , Li J. , Lin J. Y. , Jiang H. X. , Pomrenke G.
Published: January 2008

Thermoelectric (TE) properties of InxGa1−xN alloys grown by metal organic chemical vapor deposition have been investigated. It was found that as indium concentration increases, the thermal conductivity decreases and power factor increases, which leads to an increase in the TE figure of merit (ZT). The value of ZT was found to be 0.08 at 300K and reached 0.23 at 450K for In0.36Ga0.64N alloy, which is comparable to those of SiGe based alloys. The results indicate that InGaN alloys could be potentially important TE materials for many applications, especially for prolonged TE device operation at high temperatures, such as for recovery of waste heat from automobile, aircrafts, and power plants due to their superior physical properties, including the ability of operating at high temperature/high power conditions, high mechanical strength and stability, and radiation hardness.
Energy-band alignment of HfO2∕SiO2∕SiC gate dielectric stack
Authors: Mahapatra R. , Chakraborty Amit K. , Horsfall A. B. , Wright N. G. , Beamson G. , Coleman Karl S.
Published: January 2008

The band alignment of HfO2∕SiO2∕SiC gate dielectric stack has been investigated by x-ray photoelectron spectroscopy and electrical characterization. Two types of valence band offsets are observed in the stack layer; the smaller value of 1.5eV corresponds to the HfO2∕SiC band offset while the larger one of 2.2eV is due to the interfacial SiO2∕SiC. The barrier height is extracted to be 1.5eV from the Schottky emission characteristics and is higher than the reported value for HfO2 on SiC without interfacial SiO2. Thus, presence of an interfacial SiO2 layer increases band offsets to reduce the leakage current characteristics.
Effect of edge roughness on electronic transport in graphene nanoribbon channel metal-oxide-semiconductor field-effect transistors
Authors: Basu D. , Gilbert M. J. , Register L. F. , Banerjee S. K. , MacDonald A. H.
Published: January 2008

Results of quantum mechanical simulations of the influence of edge disorder on transport in graphene nanoribbon metal-oxide-semiconductor field-effect transistors (MOSFETs) are reported. The addition of edge disorder significantly reduces ON-state currents and increases OFF-state currents, and introduces wide variability across devices. These effects decrease as ribbon widths increase and as edges become smoother. However, the band gap decreases with increasing width, thereby increasing the band-to-band tunneling mediated subthreshold leakage current even with perfect nanoribbons. These results suggest that without atomically precise edge control during fabrication, MOSFET performance gains through use of graphene will be difficult to achieve in complementary MOS applications.
Evidence of different metabolic phenotypes in humans
Authors: Assfalg Michael , Bertini Ivano , Colangiuli Donato , Luchinat Claudio , Schäfer Hartmut , Schütz Birk , Spraul Manfred
Published: January 2008

The study of metabolic responses to drugs, environmental changes, and diseases is a new promising area of metabonomic research. Metabolic fingerprints can be obtained by analytical techniques such as nuclear magnetic resonance (NMR). In principle, alterations of these fingerprints due to appearance/disappearance or concentration changes of metabolites can provide early evidences of, for example, onset of diseases. A major drawback in this approach is the strong day-to-day variability of the individual metabolic fingerprint, which should be rather called a metabolic “snapshot.” We show here that a thorough statistical analysis performed on NMR spectra of human urine samples reveals an invariant part characteristic of each person, which can be extracted from the analysis of multiple samples of each single subject. This finding (
i
) provides evidence that individual metabolic phenotypes may exist and (
ii
) opens new perspectives to metabonomic studies, based on the possibility of eliminating the daily “noise” by multiple sample collection.
Circulation and long-term fate of functionalized, biocompatible single-walled carbon nanotubes in mice probed by Raman spectroscopy
Authors: Liu Zhuang , Davis Corrine , Cai Weibo , He Lina , Chen Xiaoyuan , Dai Hongjie
Published: January 2008

Carbon nanotubes are promising new materials for molecular delivery in biological systems. The long-term fate of nanotubes intravenously injected into animalsin vivois currently unknown, an issue critical to potential clinical applications of these materials. Here, using the intrinsic Raman spectroscopic signatures of single-walled carbon nanotubes (SWNTs), we measured the blood circulation of intravenously injected SWNTs and detect SWNTs in various organs and tissues of miceex vivoover a period of three months. Functionalization of SWNTs by branched polyethylene-glycol (PEG) chains was developed, enabling thus far the longest SWNT blood circulation up to 1 day, relatively low uptake in the reticuloendothelial system (RES), and near-complete clearance from the main organs in ≈2 months. Raman spectroscopy detected SWNT in the intestine, feces, kidney, and bladder of mice, suggesting excretion and clearance of SWNTs from mice via the biliary and renal pathways. No toxic side effect of SWNTs to mice was observed in necropsy, histology, and blood chemistry measurements. These findings pave the way to future biomedical applications of carbon nanotubes.
Postsettlement survival linked to larval life in a marine fish
Authors: Hamilton Scott L. , Regetz James , Warner Robert R.
Published: January 2008

There is a growing realization that the scale and degree of population connectivity are crucial to the dynamics and persistence of spatially structured populations. For marine organisms with complex life cycles, experiences during larval life may influence phenotypic traits, performance, and the probability of postsettlement survival. For a Caribbean reef fish (Thalassoma bifasciatum) on an oceanic island, we used otolith (ear stone) elemental profiles of lead (Pb) to assign recent settlers to a group that developed in waters elevated in Pb concentrations throughout larval life (i.e., nearshore signature) and a group that developed in waters depleted in Pb (i.e., offshore signature), potentially dispersing from upstream sources across oceanic waters. Larval history influenced early life history traits: offshore developers initially grew slowly but compensated with fast growth upon entering nearshore waters and metamorphosed in better condition with higher energy reserves. As shown in previous studies, local production contributed heavily to settlement: at least 45% of settlers developed nearshore. However, only 23% of survivors after the first month displayed a nearshore otolith profile. Therefore, settlers with different larval histories suffered differential mortality. Importantly, selective mortality was mediated by larval history, in that the postsettlement intensity of selection was much greater for fish that developed nearshore, potentially because they had developed in a less selectively intense larval environment. Given the potential for asymmetrical postsettlement source-based survival, successful spatial management of marine populations may require knowledge of “realized connectivity” on ecological scales, which takes into account the postsettlement fitness of individuals from different sources.
Down-regulation of NKG2D and NKp80 ligands by Kaposi's sarcoma-associated herpesvirus K5 protects against NK cell cytotoxicity
Authors: Thomas Mair , Boname Jessica M. , Field Sarah , Nejentsev Sergey , Salio Mariolina , Cerundolo Vincenzo , Wills Mark , Lehner Paul J.
Published: January 2008

Natural killer (NK) cells are important early mediators of host immunity to viral infections. The NK activatory receptors NKG2D and NKp80, both C-type lectin-like homodimeric receptors, stimulate NK cell cytotoxicity toward target cells. Like other herpesviruses, Kaposi's sarcoma-associated herpesvirus (KSHV) down-regulates MHC class I molecules to avoid detection by cytotoxic T lymphocytes but renders cells susceptible to NK cell cytotoxicity. We now show that the KSHV immune evasion gene, K5, reduces cell surface expression of the NKG2D ligands MHC class I-related chain A (MICA), MICB, and the newly defined ligand for NKp80, activation-induced C-type lectin (AICL). Down-regulation of both MICA and AICL requires the ubiquitin E3 ligase activity of K5 to target substrate cytoplasmic tail lysine residues. The common MICA *008 allele has a frameshift mutation leading to a premature stop codon and is resistant to down-regulation because of the loss of lysine residues. K5-mediated ubiquitylation signals internalization but not degradation of MICA and causes a potent reduction in NK cell-mediated cytotoxicity. The down-regulation of ligands for both the NKG2D and NKp80 activation pathways provides KSHV with a powerful mechanism for evasion of NK cell antiviral functions.
Identification and analysis of recombineering functions from Gram-negative and Gram-positive bacteria and their phages
Authors: Datta Simanti , Costantino Nina , Zhou Xiaomei , Court Donald L.
Published: January 2008

We report the identification and functional analysis of nine genes from Gram-positive and Gram-negative bacteria and their phages that are similar to lambda (λ)
bet
or
Escherichia coli recT
. Beta and RecT are single-strand DNA annealing proteins, referred to here as recombinases. Each of the nine other genes when expressed in
E. coli
carries out oligonucleotide-mediated recombination. To our knowledge, this is the first study showing single-strand recombinase activity from diverse bacteria. Similar to
bet
and
recT
, most of these other recombinases were found to be associated with putative exonuclease genes. Beta and RecT in conjunction with their cognate exonucleases carry out recombination of linear double-strand DNA. Among four of these foreign recombinase/exonuclease pairs tested for recombination with double-strand DNA, three had activity, albeit barely detectable. Thus, although these recombinases can function in
E. coli
to catalyze oligonucleotide recombination, the double-strand DNA recombination activities with their exonuclease partners were inefficient. This study also demonstrated that Gam, by inhibiting host RecBCD nuclease activity, helps to improve the efficiency of λ Red-mediated recombination with linear double-strand DNA, but Gam is not absolutely essential. Thus, in other bacterial species where Gam analogs have not been identified, double-strand DNA recombination may still work in the absence of a Gam-like function. We anticipate that at least some of the recombineering systems studied here will potentiate oligonucleotide and double-strand DNA-mediated recombineering in their native or related bacteria.
Structure of the ROC domain from the Parkinson's disease-associated leucine-rich repeat kinase 2 reveals a dimeric GTPase
Authors: Deng Junpeng , Lewis Patrick A. , Greggio Elisa , Sluch Eli , Beilina Alexandra , Cookson Mark R.
Published: January 2008

Mutations in leucine-rich repeat kinase 2 (
LRRK2
) are the most common cause of Parkinson's disease (PD). LRRK2 contains a Ras of complex proteins (ROC) domain that may act as a GTPase to regulate its protein kinase activity. The structure of ROC and the mechanism(s) by which it regulates kinase activity are not known. Here, we report the crystal structure of the LRRK2 ROC domain in complex with GDP-Mg
2+
at 2.0-Å resolution. The structure displays a dimeric fold generated by extensive domain-swapping, resulting in a pair of active sites constructed with essential functional groups contributed from both monomers. Two PD-associated pathogenic residues, R1441 and I1371, are located at the interface of two monomers and provide exquisite interactions to stabilize the ROC dimer. The structure demonstrates that loss of stabilizing forces in the ROC dimer is likely related to decreased GTPase activity resulting from mutations at these sites. Our data suggest that the ROC domain may regulate LRRK2 kinase activity as a dimer, possibly via the C-terminal of ROC (COR) domain as a molecular hinge. The structure of the LRRK2 ROC domain also represents a signature from a previously undescribed class of GTPases from complex proteins and results may provide a unique molecular target for therapeutics in PD.
The PINK1/Parkin pathway regulates mitochondrial morphology
Authors: Poole Angela C. , Thomas Ruth E. , Andrews Laurie A. , McBride Heidi M. , Whitworth Alexander J. , Pallanck Leo J.
Published: January 2008

Loss-of-function mutations in the
PTEN-induced kinase 1
(
PINK1
) or
parkin
genes, which encode a mitochondrially localized serine/threonine kinase and a ubiquitin-protein ligase, respectively, result in recessive familial forms of Parkinsonism. Genetic studies in
Drosophila
indicate that PINK1 acts upstream of Parkin in a common pathway that influences mitochondrial integrity in a subset of tissues, including flight muscle and dopaminergic neurons. The mechanism by which PINK1 and Parkin influence mitochondrial integrity is currently unknown, although mutations in the
PINK1
and
parkin
genes result in enlarged or swollen mitochondria, suggesting a possible regulatory role for the PINK1/Parkin pathway in mitochondrial morphology. To address this hypothesis, we examined the influence of genetic alterations affecting the machinery that governs mitochondrial morphology on the
PINK1
and
parkin
mutant phenotypes. We report that heterozygous loss-of-function mutations of
drp1
, which encodes a key mitochondrial fission-promoting component, are largely lethal in a
PINK1
or
parkin
mutant background. Conversely, the flight muscle degeneration and mitochondrial morphological alterations that result from mutations in
PINK1
and
parkin
are strongly suppressed by increased
drp1
gene dosage and by heterozygous loss-of-function mutations affecting the mitochondrial fusion-promoting factors OPA1 and Mfn2. Finally, we find that an eye phenotype associated with increased PINK1/Parkin pathway activity is suppressed by perturbations that reduce mitochondrial fission and enhanced by perturbations that reduce mitochondrial fusion. Our studies suggest that the PINK1/Parkin pathway promotes mitochondrial fission and that the loss of mitochondrial and tissue integrity in
PINK1
and
parkin
mutants derives from reduced mitochondrial fission.
Amantadine-induced conformational and dynamical changes of the influenza M2 transmembrane proton channel
Authors: Cady Sarah D. , Hong Mei
Published: January 2008

The M2 protein of influenza A virus forms a transmembrane proton channel important for viral infection and replication. Amantadine blocks this channel, thus inhibiting viral replication. Elucidating the high-resolution structure of the M2 protein and its change upon amantadine binding is crucial for designing antiviral drugs to combat the growing resistance of influenza A viruses against amantadine. We used magic-angle-spinning solid-state NMR to determine the conformation and dynamics of the transmembrane domain of the protein M2TMP in the apo- and amantadine-bound states in lipid bilayers.
13
C chemical shifts and torsion angles of the protein in 1,2-dilauroyl-
sn
-glycero-3-phosphatidylcholine (DLPC) bilayers indicate that M2TMP is α-helical in both states, but the average conformation differs subtly, especially at the G34–I35 linkage and V27 side chain. In the liquid-crystalline membrane, the complexed M2TMP shows dramatically narrower lines than the apo peptide. Analysis of the homogeneous and inhomogeneous line widths indicates that the apo-M2TMP undergoes significant microsecond-time scale motion, and amantadine binding alters the motional rates, causing line-narrowing. Amantadine also reduces the conformational heterogeneity of specific residues, including the G34/I35 pair and several side chains. Finally, amantadine causes the helical segment N-terminal to G34 to increase its tilt angle by 3°, and the G34–I35 torsion angles cause a kink of 5° in the amantadine-bound helix. These data indicate that amantadine affects the M2 proton channel mainly by changing the distribution and exchange rates among multiple low-energy conformations and only subtly alters the average conformation and orientation. Amantadine-resistant mutations thus may arise from binding-incompetent changes in the conformational equilibrium.
Atypical nicotinic agonist bound conformations conferring subtype selectivity
Authors: Tomizawa Motohiro , Maltby David , Talley Todd T. , Durkin Kathleen A. , Medzihradszky Katalin F. , Burlingame Alma L. , Taylor Palmer , Casida John E.
Published: January 2008

The nicotinic acetylcholine (ACh) receptor (nAChR) plays a crucial role in excitatory neurotransmission and is an important target for drugs and insecticides. Diverse nAChR subtypes with various subunit combinations confer differential selectivity for nicotinic drugs. We investigated the subtype selectivity of nAChR agonists by comparing two ACh-binding proteins (AChBPs) as structural surrogates with distinct pharmacological profiles [i.e.,
Lymnaea stagnalis
(
Ls
) AChBP of low neonicotinoid and high nicotinoid sensitivities and
Aplysia californica
(
Ac
) AChBP of high neonicotinoid sensitivity] mimicking vertebrate and insect nAChR subtypes, respectively. The structural basis of subtype selectivity was examined here by photoaffinity labeling. Two azidoneonicotinoid probes in the
Ls
-AChBP surprisingly modified two distinct and distant subunit interface sites: loop F Y164 of the complementary or (−)-face subunit and loop C Y192 of the principal or (+)-face subunit, whereas three azidonicotinoid probes derivatized only Y192. Both the neonicotinoid and nicotinoid probes labeled
Ac
-AChBP at only one position at the interface between loop C Y195 and loop E M116. These findings were used to establish structural models of the two AChBP subtypes. In the
Ac
-AChBP, the neonicotinoids and nicotinoids are nestled in similar bound conformations. Intriguingly, for the
Ls
-AChBP, the neonicotinoids have two bound conformations that are inverted relative to each other, whereas nicotinoids appear buried in only one conserved conformation as seen for the
Ac
-AChBP subtype. Accordingly, the subtype selectivity is based on two disparate bound conformations of nicotinic agonists, thereby establishing an atypical concept for neonicotinoid versus nicotinoid selectivity between insect and vertebrate nAChRs.
Modelling of pedestal transport during ELM suppression by external magnetic field perturbations
Authors: Tokar M.Z. , Evans T.E. , Gupta A. , Kalupin D. , Nicolai A. , Singh R. , Unterberg B.
Published: January 2008

Particle and energy transport in the edge transport barrier is analysed in the presence of magnetic field perturbations from external resonant coils successfully used recently for the mitigation of type I edge localized modes (ELMs). The modification of transport due to charged particle and heat flows along perturbed field lines in a small region near the separatrix, spanning from 2% to 4% of the total poloidal flux, where complete stochastization is provided by the overlap of the main magnetic islands, is taken into account. The observed reduction of the density in plasmas of low collisionality is explained by the generation of charged particle flows along perturbed field lines, the increase in the electron and ion temperatures in the barrier—by the reduction of the perpendicular neoclassical transport with decreasing density and non-locality of parallel heat transport. On the basis of the heat flux limit concept in a deeply collisionless regime, the parallel thermal conductivities are taken to be 17 times smaller for electrons and 7 times smaller for ions than from a standard free-streaming estimate. The model elaborated before is developed further by taking into account the radial variation of the inclination angle of stochastic field lines and convective energy losses including the acceleration of ions by the pressure gradient and ambipolar electric field. It is demonstrated that convection of parallel kinetic energy of ions gives greater losses than parallel thermal conduction in the outer 50% of the stochastic layer and its inclusion improves the agreement with experimental results. This modelling is performed by assuming in agreement with observations that the influx of recycling neutrals through the separatrix is not reduced with I-coils compared with its level between ELMs before the mitigation stage. By trying to match experimental profiles with this influx decrease, some enhanced thermal losses of another nature than that considered here are needed in order to mitigate the drop in the perpendicular thermal conductivities for the assumed density scaling. The impact of the neutral particle influx increase by gas puffing applied in order to restore the plasma density is investigated.
Effects of an externally produced static magnetic island on edge MHD modes in the Large Helical Device
Authors: Watanabe F. , Toi K. , Ohdachi S. , Sakakibara S. , Morita S. , Narihara K. , Narushima Y. , Morisaki T. , Suzuki C. , Tanaka K. , Tokuzawa T. , Watanabe K.Y.
Published: January 2008

In high beta plasmas and plasmas with an edge transport barrier on the Large Helical Device (LHD), pressure-driven edge MHD modes such asm/n= 1/1, 3/4, 2/3, 3/5 and 1/2 (m,n: poloidal and toroidal mode numbers) are excited in the magnetic hill region of the plasma edge. When a sizable static magnetic island with the mode number ofm/n= 1/1 was externally generated at the ι/2π = 1 surface near the plasma edge using the perturbation field coils called the local island divertor coil, the edge pressure gradient was modified in the toroidal and poloidal directions by the formation of an X-point and an O-point of the island and the achieved volume-averaged beta was appreciably reduced. This modification changed the excited mode numbers of these edge MHD modes and their radial mode structures at the inboard and outboard sides of LHD. In particular, these edge MHD fluctuations observed by soft x-ray detectors exhibited obvious enhancement on the outboard side (larger major radius) and reduction on the inboard side, regardless of the O-point/X-point position.
Inactivation of Cleavage Factor I Components Rna14p and Rna15p Induces Sequestration of Small Nucleolar Ribonucleoproteins at Discrete Sites in the Nucleus
Authors: Carneiro Tiago , Carvalho Célia , Braga José , Rino José , Milligan Laura , Tollervey David , Carmo-Fonseca Maria
Published: January 2008

Small nucleolar RNAs (snoRNAs) associate with specific proteins forming small nucleolar ribonucleoprotein (snoRNP) particles, which are essential for ribosome biogenesis. The snoRNAs are transcribed, processed, and assembled in snoRNPs in the nucleoplasm. Mature particles are then transported to the nucleolus. In yeast, 3′-end maturation of snoRNAs involves the activity of Rnt1p endonuclease and cleavage factor IA (CFIA). We report that after inhibition of CFIA components Rna14p and Rna15p, the snoRNP proteins Nop1p, Nop58p, and Gar1p delocalize from the nucleolus and accumulate in discrete nucleoplasmic foci. The U14 snoRNA, but not U3 snoRNA, similarly redistributes from the nucleolus to the nucleoplasmic foci. Simultaneous depletion of either Rna14p or Rna15p and the nuclear exosome component Rrp6p induces accumulation of poly(A)+ RNA at the snoRNP-containing foci. We propose that the foci detected after CFIA inactivation correspond to quality control centers in the nucleoplasm.
Aggressive biases towards similarly coloured males in Lake Malawi cichlid fishes
Authors: Pauers Michael J , Kapfer Joshua M , Fendos Christopher E , Berg Craig S
Published: January 2008

In haplochromine cichlids, female mate choice based on male nuptial coloration has played an important role in speciation. Recent studies suggest that male coloration strongly influences the distribution of these fishes based on male–male aggression; males direct more aggression towards similarly coloured opponents while tolerating differently coloured individuals. We explored the role of male nuptial colour in aggression among the mbuna of Lake Malawi, examining aggression by male
Metriaclima mbenjii
, the red top cobalt zebra, towards conspecific opponents, similarly coloured heterospecific opponents and differently coloured heterospecifics. In trials in which focal males were offered a single opponent, while the total number of aggressive behaviours did not vary among opponent species, the types of behaviours did; focal males directed more lateral displays towards conspecifics than towards the other opponent species. When focal males were offered two opponents simultaneously,
M. mbenjii
directed more aggressive behaviours and more lateral displays towards similarly coloured opponents, regardless of species. Furthermore, when offered a conspecific and a similarly coloured opponent simultaneously, there were no differences in behaviour towards either opponent. Thus, nuptial coloration is used by males to identify competitors, and it suggests that male–male aggression may have also been an important diversifying force in speciation in rock-dwelling Lake Malawi cichlids.
A continuous model for mode mixing in graded-index multimode fibres with random imperfections
Authors: Perrey-Debain Emmanuel , Abrahams I. David , Love John D
Published: January 2008

This article investigates the evolution of the distribution of propagating modes in a graded-index multimode fibre with random imperfections. These perturbations may be microscopic random bends and ellipticity, or an index of refraction fluctuations, introduced during manufacture. For large-diameter fibres (with respect to a typical electromagnetic wavelength), the number of guided modes becomes large, and so we can regard the discrete set as a continuum in which the mode number is treated as a continuous variable. The theory is applied to the propagation of guided optical modes in round fibres with a parabolic refractive index profile. This continuous model offers the great advantage of elucidating the relevant physical parameters that participate in the mode mixing dynamics, and leads to a numerically tractable problem. Numerical results are presented for the specific problem of random micro-bends, demonstrating that the theoretically predicted behaviour is achieved.
Synchrotron X-ray studies of austenite and bainitic ferrite
Authors: Stone H.J , Peet M.J , Bhadeshia H.K.D.H , Withers P.J , Babu S.S , Specht E.D
Published: January 2008

High-resolution synchrotron X-ray diffraction has been used to conduct
in situ
studies of the temporal evolution of phases during the isothermal growth of bainite. Two populations of austenitic material were identified: one corresponding to the initial austenite and the other to the carbon-enriched austenite associated with the bainitic ferrite. The observed lattice parameters and the asymmetry of the peaks from the residual austenite have been interpreted in terms of the carbon partitioning due to the transformation. The results are contrasted with an earlier study in which the austenite unit cell appeared to split into two distinct densities prior to the onset of transformation.
On the absence of the Eshelby property for slender non-ellipsoidal inhomogeneities
Authors: Andrianov Igor V , Argatov Ivan I , Weichert Dieter
Published: January 2008

The method of matched asymptotic expansions is applied to construct an asymptotic model for the Eshelby inhomogeneity problem in the case of a slender sufficiently rigid inhomogeneity. On the basis of the obtained asymptotic model, it is shown that the only infinitesimal perturbations of the elongated ellipsoid that preserve constancy of stresses inside the inhomogeneity are those into another elongated ellipsoid.
Age-specific reproduction in a long-lived species: the combined effects of senescence and individual quality
Authors: McCleery R.H , Perrins C.M , Sheldon B.C , Charmantier A
Published: January 2008

Apparent changes in breeding performance with age measured at the population level can be due to changes in individual capacity at different ages, or to the differential survival of individuals with different capabilities. Estimating the relative importance of the two is important for understanding ageing patterns in natural populations, but there are few studies of such populations in which these effects have been disentangled. We analysed laying date and clutch size as measures of individual performance in a population of mute swans (Cygnus olor) studied over 25 years at Abbotsbury, UK. On both measures of breeding performance, individuals tended to improve up to the age of 6 or 7, and to decline after about the age of 12. Individuals with longer lifespans performed better at all ages (earlier laying, larger clutches) than animals that ceased breeding earlier. We conclude that the apparent mean increase in performance with age in mute swans is due to both individual improvement and differential survival of individuals who perform well, while the decline in older age groups is due to individual loss of function. Our results underline the need to take individual differences into account when testing hypotheses about life histories in wild populations.
Proximity to forest edge does not affect crop production despite pollen limitation
Authors: Chacoff Natacha P , Aizen Marcelo A , Aschero Valeria
Published: January 2008

A decline in pollination function has been linked to agriculture expansion and intensification. In northwest Argentina, pollinator visits to grapefruit, a self-compatible but pollinator-dependent crop, decline by approximately 50% at 1 km from forest edges. We evaluated whether this decrease in visitation also reduces the pollination service in this crop. We analysed the quantity and quality of pollen deposited on stigmas, and associated limitation of fruit production at increasing distances (edge: 10, 100, 500 and 1000 m) from the remnants of Yungas forest. We also examined the quantitative and qualitative efficiency of honeybees as pollen vectors. Pollen receipt and pollen tubes in styles decreased with increasing distance from forest edge; however, this decline did not affect fruit production. Supplementation of natural pollen with self- and cross-pollen revealed that both pollen quantity and quality limited fruit production. Despite pollen limitation, honeybees cannot raise fruit production because they often do not deposit sufficient high-quality pollen per visit to elicit fruit development. However, declines in visitation frequency well below seven visits during a flower's lifespan could decrease production beyond current yields. In this context, the preservation of forest remnants, which act as pollinator sources, could contribute to resilience in crop production. Like wild plants, pollen limitation of the yield among animal-pollinated crops may be common and indicative not only of pollinator scarcity, but also of poor pollination quality, whereby pollinator efficiency, rather than just abundance, can play a broader role than previously appreciated.
Place memory in crickets
Authors: Wessnitzer Jan , Mangan Michael , Webb Barbara
Published: January 2008

Certain insect species are known to relocate nest or food sites using landmarks, but the generality of this capability among insects, and whether insect place memory can be used in novel task settings, is not known. We tested the ability of crickets to use surrounding visual cues to relocate an invisible target in an analogue of the Morris water maze, a standard paradigm for spatial memory tests on rodents. Adult femaleGryllus bimaculatuswere released into an arena with a floor heated to an aversive temperature, with one hidden cool spot. Over 10 trials, the time taken to find the cool spot decreased significantly. The best performance was obtained when a natural scene was provided on the arena walls. Animals can relocate the position from novel starting points. When the scene is rotated, they preferentially approach the fictive target position corresponding to the rotation. We note that this navigational capability does not necessarily imply the animal has an internal spatial representation.
Novel reptilian uncoupling proteins: molecular evolution and gene expression during cold acclimation
Authors: Schwartz Tonia S , Murray Shauna , Seebacher Frank
Published: January 2008

Many animals upregulate metabolism in response to cold. Uncoupling proteins (UCPs) increase proton conductance across the mitochondrial membrane and can thereby alleviate damage from reactive oxygen species that may form as a result of metabolic upregulation. Our aim in this study was to determine whether reptiles (Crocodylus porosus) possess UCP genes. If so, we aimed to place reptilian UCP genes within a phylogenetic context and to determine whether the expression of UCP genes is increased during cold acclimation. We provide the first evidence that UCP2 and UCP3 genes are present in reptiles. Unlike in other vertebrates, UCP2 and UPC3 are expressed in liver and skeletal muscle of the crocodile, and both are upregulated in liver during cold acclimation but not in muscle. We identified two transcripts of UCP3, one of which produces a truncated protein similar to the UCP3S transcript in humans, and the resulting protein lacks the predicted nucleotide-binding regulatory domain. Our molecular phylogeny suggests that uncoupling protein 1 (UCP1) is ancestral and has been lost in archosaurs. In birds, UCP3 may have assumed a similar function as UCP1 in mammals, which has important ramifications for understanding endothermic heat production.
The application of the research work of James Clerk Maxwell in electromagnetics to industrial frequency problems
Authors: Lowther D.A , Freeman E.M
Published: January 2008

Faraday's work inspired the development of electrical motors and generators. Until Maxwell pointed out the significance of Ampere's Law, there was no rigorous design method for magnetic devices. His interpretation strongly influenced the creation, by others, of the ‘magnetic circuit’ approach, which became the seminal design technique. This, utilizing the concept of reluctance, led to the design method for magnetic machines that is still widely in use today. The direct solution of the Maxwell equations (less the displacement current term) had to await the development of modern continuum methods to yield the field everywhere in, and around, the devices of interest, and this then permitted the application of the Maxwell stress tensor. This final refinement yielded forces and torques, and this resulted in the accurate prediction of electrical machine performance.