bluuebunny/crossref_metadata_2025 huggingface dataset:
Coevolutionary dynamics of adaptive radiation for food‐web development
Authors: Ito Hiroshi C. , Shimada Masakazu , Ikegami Takashi
Published: October 2008

To investigate how complex food‐webs can develop through repeated evolutionary diversification, a predator–prey model was analyzed. In the model, each individual has two traits: trait x as a predator and trait y as a prey. These traits constitute a two‐dimensional phenotype space, in which the whole group of individuals are represented as a phenotype distribution. Predator–prey interactions among the phenotypes are determined by their relative positions in the phenotype space. Each phenotypic cluster was treated as a species. Each species evolves in y to escape from predation, while it evolves in x to chase their prey. Analytical investigation provided two predictions. First, coupled evolutionary diversifications of y and x may occur when the x of predators have caught up with their prey's y, which may be repeated. Second, complex food‐webs may develop when species’ competitive strengths are kept similar within the communities. If the functional response is close to the ratio‐dependent response, the competitive strengths of all species are similar when the relationship between predators and prey corresponds to the ideal free distribution (IFD). These predictions were confirmed by numerical simulations.
Pulsed-wave Doppler tissue imaging velocities in normal geriatric cats and geriatric cats with primary or systemic diseases linked to specific cardiomyopathies in humans, and the influence of age and heart rate upon these velocities
Authors: Simpson Kerry E. , Gunn-Moore Danièlle A. , Shaw Darren J. , French Anne T. , Dukes-McEwan Joanna , Moran Carmel M. , Corcoran Brendan M.
Published: October 2008

Pulsed-wave Doppler tissue imaging (pw-DTI) techniques allow the non-invasive assessment of myocardial dynamics. pw-DTI has demonstrated regional and global diastolic impairment in various forms of human and feline cardiomyopathy. We hypothesise that in geriatric cats with systemic diseases that have been linked to specific cardiomyopathies in human beings, the myocardial velocity profile will be altered when compared to either normal or hypertrophic cardiomyopathy (HCM) cats; and that both age and heart rate have a significant affect upon pw-DTI velocities. The aims of this study were to determine whether the feline M-mode or myocardial velocity profile is altered in geriatric cats with disease states that have been linked to specific cardiomyopathies in humans when compared to normal geriatric cats or geriatric cats with HCM and to determine whether age or heart rate has a significant effect upon pw-DTI velocities within these groups of cats. Sixty-six cats aged 8 years or above were included in the study, and were divided as follows: Unaffected ( n=8), basilar septal bulge (BSB) (17), HCM (14), hyperthyroid (HiT4) (12) and chronic renal failure (CRF) (15). Systolic blood pressure was normal in all the cats. pw-DTI systolic ( S′), early ( E′) and late diastolic ( A′) velocities were assessed from standardised sites within the myocardium, and the relationships between these and disease group, age and heart rate were then assessed. In cats with HCM, the E′ velocity was decreased at various sites. Conversely, the HiT4 cats demonstrated increased S′ velocities. The only site at which the age of the cat was significantly related to myocardial velocities was the S′ velocity from the apical mid-septum. There were also significant positive relationships between heart rate and the magnitude of myocardial S′, E′ and A′ velocities of radial motion and S′ and A′ velocities of longitudinal motion. pw-DTI detected diastolic dysfunction in untreated cats with HCM and increased systolic function in HiT4 cats. The age of the cat was of little significance, whereas heart rate significantly influenced myocardial velocity profiles.
When Apologies for Injustice Matter
Authors: De Cremer David , Schouten Barbara C.
Published: October 2008

The present research examined the idea that the effectiveness of apologies on promoting fairness perceptions depends on how meaningful and sincere the apology is experienced. More precisely, it was predicted that apologies are more effective when they are communicated by an authority being respectful to others. A study using a cross-sectional organizational survey showed that an apology (relative to giving no apology) revealed higher fairness perceptions, but only so when the authority was respectful rather than disrespectful. In a subsequent experimental laboratory study the same interaction effect (as in Study 1) on fairness perceptions was found. In addition, a similar interaction effect also emerged on participants’ self-evaluations in terms of relational appreciation (i.e., feeling valued and likeable). Finally, these self-evaluations accounted (at least partly) for the interactive effect on fairness perceptions.
Seismic velocity structure and depth‐dependence of anisotropy in the Red Sea and Arabian shield from surface wave analysis
Authors: Hansen Samantha E. , Gaherty James B. , Schwartz Susan Y. , Rodgers Arthur J. , Al‐Amri Abdullah M. S.
Published: October 2008

We investigate the lithospheric and upper mantle shear wave velocity structure and the depth‐dependence of anisotropy along the Red Sea and beneath the Arabian Peninsula using receiver function constraints and phase velocities of surface waves traversing two transects of stations from the Saudi Arabian National Digital Seismic Network. Frequency‐dependent phase delays of fundamental‐mode Love and Rayleigh waves, measured using a cross‐correlation procedure, require very slow shear velocities and the presence of anisotropy to depths of at least 180 km in the upper mantle. Linearized inversion of these data produce path‐averaged 1D radially anisotropic models with ∼4% anisotropy in the lithosphere and across the lithosphere‐asthenosphere boundary (LAB). Models with reasonable crustal velocities in which the mantle lithosphere is isotropic cannot satisfy the data. The lithosphere, which ranges in thickness from about 70 km near the Red Sea coast to about 90 km beneath the Arabian Shield, is underlain by a pronounced low‐velocity zone with shear velocities as low as 4.1 km/s. Forward models of azimuthal anisotropy, which are constructed from previously determined shear wave splitting estimates, can reconcile surface and body wave observations of anisotropy. The low shear velocities extend to greater depth than those observed in other continental rift and oceanic ridge environments. The depth extent of these low velocities combined with the sharp velocity contrast across the LAB may indicate the influence of the Afar hot spot and the presence of partial melt beneath Arabia. The anisotropic signature primarily reflects a combination of plate‐ and density‐driven flow associated with rifting processes in the Red Sea.
Discharge predictions of a rainfall‐driven theoretical hydrograph compared to common models and observed data
Authors: Criss Robert E. , Winston William E.
Published: October 2008

A theoretical hydrograph based on Darcy's law and the diffusion equation has been extended into a predictive model for the discharge of diffuse springs and small rivers from a detailed rainfall record, using only a single free parameter, the basin time constant b. The model accurately predicts the flow variations of natural hydrographs, including the magnitude and timing of peak flow, total flow volume, inflection points, and recession rate, all as a function of effective rainfall amounts, basin area, and the time constant b. Predicted hydrographs for a sharp storm event in an unimpounded basin are compared to results for two common transfer functions, and our more parsimonious model is statistically superior. Modeling of a long‐term record in proximal basins illustrates the effect of variations in b. Potential applications of the model include flood prediction, comparative studies of basin response in a regional context, and estimation of actual evapotranspiration.
Plumes anchored by a high viscosity lower mantle in a 3D mantle convection model featuring dynamically evolving plates
Authors: Lowman J. P. , Gait A. D. , Gable C. W. , Kukreja H.
Published: October 2008

Previous studies have shown that 3D vigorously convecting systems featuring plate‐like surface motion and lower mantle viscosities much greater than the upper mantle viscosity can yield long lived intraplate plumes if plate boundaries remain fixed. We investigate whether plumes originating in a lower mantle 90 times more viscous than the upper mantle will maintain relatively fixed positions when dynamic plate evolution is present. We compare the findings from a pair of calculations featuring four plates in a 3 × 3 × 1 periodic Cartesian geometry model. In both calculations, plate velocities are determined dynamically in response to the stresses acting on the viscously defined lithosphere. In one case plate boundaries are held fixed, in the second dynamically determined plate evolution is enabled. In both cases, long lived mantle plumes are observed. Moreover, the locations of the plumes remain relatively fixed even as plates systematically evolve to a completely different arrangement from their initial configuration.
Maximum entropy production and earthquake dynamics
Authors: Main Ian G. , Naylor Mark
Published: October 2008

We examine the consistency of natural and model seismicity with the maximum entropy production hypothesis for open, slowly‐driven, steady‐state, dissipative systems. Assuming the commonly‐observed power‐law feedback between remote boundary stress and strain rate at steady state, several natural observations are explained by the system organizing to maximize entropy production in a near but strictly sub‐critical state. These include the low but finite seismic efficiency and stress drop, an upper magnitude cut‐off that is large but finite, and the universally‐ observed Gutenberg‐Richter b‐value of 1 in frequency‐magnitude data. In this state the model stress field organizes into coherent domains, providing a physical mechanism for retaining a finite memory of past events. This implies a finite degree of predictability, strongly limited theoretically by the proximity to criticality and practically by the difficulty of directly observing Earth's stress field at an equivalent resolution.
Mechanism and control of sidewall growth and catalyst diffusion on oxide nanowire vapor-liquid-solid growth
Authors: Nagashima Kazuki , Yanagida Takeshi , Oka Keisuke , Tanaka Hidekazu , Kawai Tomoji
Published: October 2008

Oxide nanowires formed via the vapor-liquid-solid (VLS) mechanism are attractive building blocks toward nanowire-based electronic devices due to their fascinating physical properties. Although well-defined oxide nanowires are strongly required for the applications, tapering during oxide nanowire VLS growth has been detrimental and uncontrollable. Here we demonstrate the mechanism to control the tapering during oxide VLS growth. Suppressing simultaneously both the oxidization of adatoms at the sidewall and the catalyst diffusion from the tip was found to be essential to avoid the tapering. This mechanism would be universal in various oxide nanowire VLS growths.
The role of dimensionality on the quenching of spin-orbit effects in the optics of gold nanostructures
Authors: Castro Alberto , Marques Miguel A. L. , Romero Aldo H. , Oliveira Micael J. T. , Rubio Angel
Published: October 2008

By first-principles time-dependent density-functional calculations, we show the relevance of relativistic effects to shape the photoabsorption cross section of small gold clusters (Aun, n⩽8, and n=20) and small nanowires (n⩽7). The relativistic effects not only dictate the stabilization of planar geometries (as it has already been shown by treating the core electrons relativistically): The spin-orbit coupling also has a strong impact in the absorption spectra (resonances and oscillator strengths). This is especially true for nanowires, where the effect of spin orbit is large and not substantially reduced with the chain length, in contrast to more compact gold clusters where this spin-orbit effect tends to be quenched. These results have far reaching consequences in fields such as electronic transport, where gold nanowires are often used, but where spin-orbit effects are generally disregarded.
Mechanism of the linear electro-optic effect in potassium dihydrogen phosphate crystals
Authors: Huang He , Lin Z. S. , Chen C. T.
Published: October 2008

The linear electro-optic effect in KH2PO4 (KDP) is studied using first-principles calculations combined with semiempirical methods previously proposed [Chem. Phys. Lett. 397, 222 (2004)]. The protons in the hydrogen bonds are much more flexible and better able to respond an external field than the other atoms in KDP, implying that displacement of hydrogen atoms makes the main contribution to the linear electro-optic effect in KDP. Optical property calculations show that the changes in the refractive indices induced by the displacement of hydrogen atoms are pertinent to the flexible degree of the lattice in our semiempirical model.
Approximation of center manifolds on the renormalization group method
Authors: Chiba Hayato
Published: October 2008

The renormalization group (RG) method for differential equations is one of the perturbation methods for obtaining approximate solutions. This article shows that the RG method is effectual for obtaining an approximate center manifold and an approximate flow on it when applied to equations having a center manifold.
Tomographic nanofabrication of ultrasharp three-dimensional nanostructures
Authors: Saghi Zineb , Gnanavel Thirunavukkarasu , Peng Yong , Inkson Beverley J. , Cullis Anthony G. , Gibbs Mike R. , Möbus Günter
Published: October 2008

We present the extension of electron tomography from a pure characterization technique into a three-dimensional nanofabrication technique using focused electron beams in the scanning transmission electron microscope. Two-dimensional surface patterning techniques are insufficient to achieve full three-dimensional nanosculpting, instead, multiple sample rotations under the beam are required. We demonstrate fabrication of ultrafine tips and hollow structures with applications in scanning probe microscopy, atom probe tomography, or in magnetoconductance of nanobridges. A sharpened tip radius of <3 nm is achieved, an order of magnitude finer than with standard methods.
Intrinsic generation of OH groups in dry silicon dioxide upon thermal treatments
Authors: Nuccio Laura , Agnello Simonpietro , Boscaino Roberto
Published: October 2008

We show the existence of an intrinsic generation mechanism of OH groups in synthetic dry silica upon thermal treatments. Samples are treated for ∼160 h at 390 °C in He at 2.7 or 180 bar, and the growth of the OH IR absorption band at 3670 cm−1 is observed. An OH concentration of ∼1018 cm−3 is estimated. Possible contributions of reactions with molecules absorbed from the atmosphere are excluded. Reactions with H2O already contained in the samples are rejected by IR measurements. The observed OH generation is attributed to the reaction of network sites with H2 already present in the material. Possible reaction paths are examined.
MgO thickness dependence of spin injection efficiency in spin-light emitting diodes
Authors: Lu Y. , Truong V. G. , Renucci P. , Tran M. , Jaffrès H. , Deranlot C. , George J.-M. , Lemaître A. , Zheng Y. , Demaille D. , Binh P.-H. , Amand T. , Marie X.
Published: October 2008

We have studied the electron spin injection efficiency from a CoFeB/MgO spin injector into AlGaAs/GaAs semiconductor light emitting diodes. The circular polarization of the electroluminescence signal reaches a value as large as 32% at 100K under a 0.8T magnetic field. We show that the spin injection efficiency increases with the increase in the MgO barrier thickness from 1.4to4.3nm. Moreover, a higher spin injection efficiency is obtained for MgO barriers grown at 300°C compared to the ones grown at room temperature. This effect is attributed to the MgO texturing occurring at high temperatures.
Time-resolved cathodoluminescence of Mg-doped GaN
Authors: Fischer A. M. , Srinivasan S. , Ponce F. A. , Monemar B. , Bertram F. , Christen J.
Published: October 2008

The optical properties of GaN films doped with magnesium concentrations of the order of 1018 and 1019cm−3 have been analyzed by picosecond time-resolved cathodoluminescence spectroscopy. Two luminescence bands in the vicinity of ∼3.45 and ∼3.27eV are observed to increase in intensity with Mg concentration. They have been identified as related to acceptor-bound exciton and donor-acceptor pair (DAP) transitions, respectively. Time-resolved cathodoluminescence spectra, taken at low temperatures (∼4K), show that the lifetime of the DAP peak (3.27eV) and of what appears to be its first longitudinal-optical phonon replica at ∼3.19eV decrease with increasing Mg concentration. These peaks differ in their recombination kinetics, strongly suggesting the existence of an underlying broad emission band which may be related to Mg.
Comparing the phosphorus requirements of wheat, lupin, and canola
Authors: Bolland M. D. A. , Brennan R. F.
Published: October 2008

Spring wheat (Triticum aestivum L.), lupin (Lupinus angustifolius L.), and canola (Brassica napus L.) are the major crop species grown in rotation on the predominantly sandy soils of south-western Australia. Comparisons among the species for yield responses to applied phosphorus (P), effects of applied P on growth rates of shoots, P response efficiency for shoot and grain production, and the pattern for accumulation of P into shoots during growth and into grain at maturity are rare, or are not known, and were quantified in the glasshouse study reported here. Size and P content (P concentration multiplied by yield) of sown seed were in the order canola < wheat < lupin. Therefore, yield responses to applied P were first observed at ~10 days after sowing (DAS) for canola, ~17 DAS for wheat, and ~60 DAS for lupin. Lupin shoots showed no yield response to applied P at the first harvest at 51 DAS. Otherwise all species showed large yield, P concentration, and P content responses to applied P for all harvests at 51, 78, 87, 101, 121, and 172 DAS. To produce 90% of the maximum grain yield, the relevant data for cropping, lupin required ~67% less P than wheat, canola required ~40% less P than wheat, and canola required ~75% more P than lupin. Growth rates, and P response efficiency, were generally largest for canola, followed by wheat, then lupin. For shoots, P accumulation was in the order lupin > wheat > canola at 51 DAS, canola > wheat > lupin at 78 and 87 DAS, canola > wheat = lupin at 101 DAS, and all 3 species were about similar at 121 DAS. For accumulation of P into shoots plus grain at maturity (172 DAS) the order was canola > lupin > wheat, and for grain only was canola > wheat = lupin.
Molecular genetic distance and hybrid performance between Chinese and American maize (Zea mays L.) inbreds
Authors: Zheng Da-Hao , Van Kyujung , Wang Li , Lee Suk-Ha
Published: October 2008

Development of superior hybrids depends on the identification and exploitation of heterotic groups based on divergent germplasms. The polymorphisms among 13 Chinese and 13 American parental maize inbreds were evaluated at 107 simple sequence repeat (SSR) loci. Grain yield of 169 F1 hybrids and corresponding molecular genetic distance (GD) for parents were partitioned into general and specific combining ability (GCA and SCA) and general and specific genetic distance (GGD and SGD), respectively. SSR data revealed that different geographic sources of inbreds were substantially divergent with several germplasm-specific alleles. GDs between Chinese and American inbreds showed greater mean values and narrower ranges than those within each set of inbreds. The parental inbreds were clustered into four groups. F1 performance was highly correlated with SCA for grain yield regardless of the type of cross. F1 performance and SCA were correlated with GD and SGD in hybrids created only with temperate inbreds. Maize superior hybrids were produced only by crosses of different germplasm with greater GDs. BSSS enhances the heterotic pattern with any other inbreds from China. Iowa Corn Borer Synthetic No. 1 (BSCB1) and CIMMYT Pool41 were new promising germplasms for establishment of potential heterotic patterns in the Chinese maize breeding program.
Morphological variation in the biological control agent Neoseiulus californicus (McGregor) (Acari:Phytoseiidae): consequences for diagnostic reliability and synonymies
Authors: Tixier Marie-Stéphane , Guichou Sabine , Kreiter Serge
Published: October 2008

The extent intraspecific variation among 42 morphological characters within Neoseiulus californicus (McGregor) (Acari : Phytoseiidae) is examined. Neoseiulus californicus is an important biological control agent used commercially worldwide to control pest mites in many crops. The correct diagnosis of this species is thus of prime importance for successful biological control and agricultural development. Incorrect interpretation of intraspecific variation could lead to misidentification and potentially to the description of new species that may be invalid. Three hundred female N. californicus representing ten populations collected from all over the world were measured and compared with the types of two morphologically close species: Neoseiulus marinus (Willmann) and Neoseiulus ornatus (Athias-Henriot). Significant differences between the populations were observed for almost all of the characters considered. However, these differences were small and low within-population standard errors in measurement data were observed. The mites collected in Chile were very different from the specimens of the other populations of N. californicus considered. The level of intraspecific morphological variation found within N. californicus indicates that caution must be applied to correctly determine species boundaries within this genus and morphological variation needs to be considered more in species’ descriptions. Based on our morphological analysis we conclude that N. ornatus, N. marinus and N. californicus are valid species. Redescriptions of these three species are given in this paper.
Morphological phylogeny of the family Actinostolidae (Anthozoa:Actiniaria) with description of a new genus and species of hydrothermal vent sea anemone redefining the family Actinoscyphiidae
Authors: Rodríguez Estefanía , Castorani Christopher N. , Daly Marymegan
Published: October 2008

We describe a new genus and species of hydrothermal vent sea anemone from the eastern north Pacific Ocean. The combination of characters in Alvinactis reu, gen. et sp. nov. is unique among currently known genera of the actiniarian superfamily Mesomyaria; most notable among its external features is a belt of verrucae and cinclides in the distal column. We assess the placement of Alvinactis, gen. nov. and evaluate taxonomic features used to distinguish groups within Actinostolidae Carlgren, 1893 and Actinoscyphiidae Stephenson, 1920 with a cladistic analysis of morphological characters. Phylogenetic analysis reveals that Alvinactis, gen. nov. and several genera previously ascribed to Actinostolidae belong in Actinoscyphiidae. Morphological evidence fails to support monophyly of Actinostolidae, but does support monophyly of the previously proposed subfamily Actinostolinae.
The oldest representative of the Trichomyiinae (Diptera:Psychodidae) from the Lower Cenomanian French amber studied with phase-contrast synchrotron X-ray imaging
Authors: Lak Malvina , Azar Dany , Nel André , Néraudeau Didier , Tafforeau Paul
Published: October 2008

Trichomyia lengleti, sp. nov., is described from the Lower Cenomanian amber of La Buzinie, Charente (south-west France) from a piece of fully opaque amber. The Upper Albian Trichomyia swinhoei Cockerell, 1917 is transferred from the Trichomyiinae to the Sycoracinae incertae sedis, stat. nov. Trichomyia lengleti, sp. nov. is the oldest representative of the subfamily Trichomyiinae, supporting at least a Cretaceous diversification for the Psychodidae. The discovery of this fossil fly and its study (thanks to propagation-phase-contrast synchrotron X-ray imaging) improves our knowledge of the biodiversity and the historical evolution of psychodoid flies. A checklist of fossil trichomyiine species is given.
Phylogeny of the Serpula - Crucigera - Hydroides clade (Serpulidae:Annelida) using molecular and morphological data: implications for operculum evolution
Authors: Kupriyanova E. K. , Bastida-Zavala R. , Halt M. N. , Lee M. S. Y. , Rouse G. W.
Published: October 2008

The type genus of Serpulidae, Serpula Linnaeus, 1758, along with closely related genera Crucigera Benedict, 1887 and Hydroides Gunnerus, 1768, accounts for approximately one-third of all described species in the family. Although previous morphological and molecular studies unequivocally indicate that these three genera constitute a monophyletic group, the status of each genus remains unknown. In this study, the relationships among and within the genera Serpula, Crucigera, and Hydroides were investigated using maximum parsimony and Bayesian analyses of nuclear (18S and 28S rDNA) and mitochondrial (cytochrome b) genomic molecular markers plus morphology. The phylogeny supports the monophyly of Hydroides, but Serpula forms a paraphyletic basal grade and Crucigera is polyphyletic. The lack of close relationship between Hydroides and Crucigera indicates that their similar opercular features are not homologous.
High frequency new particle formation in the Himalayas
Authors: Venzac Hervé , Sellegri Karine , Laj Paolo , Villani Paolo , Bonasoni Paolo , Marinoni Angela , Cristofanelli Paolo , Calzolari Francescopiero , Fuzzi Sandro , Decesari Stefano , Facchini Maria-Cristina , Vuillermoz Elisa , Verza Gian Pietro
Published: October 2008

Rising air pollution levels in South Asia will have worldwide environmental consequences. Transport of pollutants from the densely populated regions of India, Pakistan, China, and Nepal to the Himalayas may lead to substantial radiative forcing in South Asia with potential effects on the monsoon circulation and, hence, on regional climate and hydrological cycles, as well as to dramatic impacts on glacier retreat. An improved description of particulate sources is needed to constrain the simulation of future regional climate changes. Here, the first evidence of very frequent new particle formation events occurring up to high altitudes is presented. A 16-month record of aerosol size distribution from the Nepal Climate Observatory at Pyramid (Nepal, 5,079 m above sea level), the highest atmospheric research station, is shown. Aerosol concentrations are driven by intense ultrafine particle events occurring on >35% of the days at the interface between clean tropospheric air and the more polluted air rising from the valleys. During a pilot study, we observed a significant increase of ion cluster concentrations with the onset of new particle formation events. The ion clusters rapidly grew to a 10-nm size within a few hours, confirming, thus, that
in situ
nucleation takes place up to high altitudes. The initiation of the new particle events coincides with the shift from free tropospheric downslope winds to thermal upslope winds from the valley in the morning hours. The new particle formation events represent a very significant additional source of particles possibly injected into the free troposphere by thermal winds.
Brain potentials to native phoneme discrimination reveal the origin of individual differences in learning the sounds of a second language
Authors: Díaz Begoña , Baus Cristina , Escera Carles , Costa Albert , Sebastián-Gallés Núria
Published: October 2008

Human beings differ in their ability to master the sounds of their second language (L2). Phonetic training studies have proposed that differences in phonetic learning stem from differences in psychoacoustic abilities rather than speech-specific capabilities. We aimed at finding the origin of individual differences in L2 phonetic acquisition in natural learning contexts. We consider two alternative explanations: a general psychoacoustic origin vs. a speech-specific one. For this purpose, event-related potentials (ERPs) were recorded from two groups of early, proficient Spanish-Catalan bilinguals who differed in their mastery of the Catalan (L2) phonetic contrast /e-ε/. Brain activity in response to acoustic change detection was recorded in three different conditions involving tones of different length (duration condition), frequency (frequency condition), and presentation order (pattern condition). In addition, neural correlates of speech change detection were also assessed for both native (/o/-/e/) and nonnative (/o/-/ö/) phonetic contrasts (speech condition). Participants' discrimination accuracy, reflected electrically as a mismatch negativity (MMN), was similar between the two groups of participants in the three acoustic conditions. Conversely, the MMN was reduced in poor perceivers (PP) when they were presented with speech sounds. Therefore, our results support a speech-specific origin of individual variability in L2 phonetic mastery.
Network model of survival signaling in large granular lymphocyte leukemia
Authors: Zhang Ranran , Shah Mithun Vinod , Yang Jun , Nyland Susan B. , Liu Xin , Yun Jong K. , Albert Réka , Loughran Thomas P.
Published: October 2008

T cell large granular lymphocyte (T-LGL) leukemia features a clonal expansion of antigen-primed, competent, cytotoxic T lymphocytes (CTL). To systematically understand signaling components that determine the survival of CTL in T-LGL leukemia, we constructed a T-LGL survival signaling network by integrating the signaling pathways involved in normal CTL activation and the known deregulations of survival signaling in leukemic T-LGL. This network was subsequently translated into a predictive, discrete, dynamic model. Our model suggests that the persistence of IL-15 and PDGF is sufficient to reproduce all known deregulations in leukemic T-LGL. This finding leads to the following predictions: (
i
) Inhibiting PDGF signaling induces apoptosis in leukemic T-LGL. (
ii
) Sphingosine kinase 1 and NFκB are essential for the long-term survival of CTL in T-LGL leukemia. (
iii
) NFκB functions downstream of PI3K and prevents apoptosis through maintaining the expression of myeloid cell leukemia sequence 1. (
iv
) T box expressed in T cells (T-bet) should be constitutively activated concurrently with NFκB activation to reproduce the leukemic T-LGL phenotype. We validated these predictions experimentally. Our study provides a model describing the signaling network involved in maintaining the long-term survival of competent CTL in humans. The model will be useful in identifying potential therapeutic targets for T-LGL leukemia and generating long-term competent CTL necessary for tumor and cancer vaccine development.
Structural basis for glycyl radical formation by pyruvate formate-lyase activating enzyme
Authors: Vey Jessica L. , Yang Jian , Li Meng , Broderick William E. , Broderick Joan B. , Drennan Catherine L.
Published: October 2008

Pyruvate formate-lyase activating enzyme generates a stable and catalytically essential glycyl radical on G
734
of pyruvate formate-lyase via the direct, stereospecific abstraction of a hydrogen atom from pyruvate formate-lyase. The activase performs this remarkable feat by using an iron-sulfur cluster and
S
-adenosylmethionine (AdoMet), thus placing it among the AdoMet radical superfamily of enzymes. We report here structures of the substrate-free and substrate-bound forms of pyruvate formate-lyase-activating enzyme, the first structures of an AdoMet radical activase. To obtain the substrate-bound structure, we have used a peptide substrate, the 7-mer RVS
G
YAV, which contains the sequence surrounding G
734
. Our structures provide fundamental insights into the interactions between the activase and the G
734
loop of pyruvate formate-lyase and provide a structural basis for direct and stereospecific H atom abstraction from the buried G
734
of pyruvate formate-lyase.
Potent HIV fusion inhibitors against Enfuvirtide-resistant HIV-1 strains
Authors: He Yuxian , Cheng Jianwei , Lu Hong , Li Jingjing , Hu Jie , Qi Zhi , Liu Zhonghua , Jiang Shibo , Dai Qiuyun
Published: October 2008

T20 (generic name: Enfuvirtide, brand name: Fuzeon) is the only FDA-approved HIV fusion inhibitor that is being used for treatment of HIV/AIDS patients who have failed to respond to current antiretroviral drugs. However, it rapidly induces drug resistance
in vitro
and
in vivo
. On the basis of the structural and functional information of anti-HIV peptides from a previous study, we designed an HIV fusion inhibitor named CP32M, a 32-mer synthetic peptide that is highly effective in inhibiting infection by a wide range of primary HIV-1 isolates from multiple genotypes with R5- or dual-tropic (R5X4) phenotype, including a group O virus (BCF02) that is resistant to T20 and C34 (another anti-HIV peptide). Strikingly, CP32M is exceptionally potent (at low picomolar level) against infection by a panel of HIV-1 mutants highly resistant to T20 and C34. These findings suggest that CP32M can be further developed as an antiviral therapeutic against multidrug resistant HIV-1.
Dynamic stabilization of actin filaments
Authors: Kueh Hao Yuan , Brieher William M. , Mitchison Timothy J.
Published: October 2008

We report here that actin filaments in vitro exist in two populations with significantly different shrinkage rates. Newly polymerized filaments shrink rapidly, primarily from barbed ends, at 1.8/s, but as they age they switch to a stable state that shrinks slowly, primarily from pointed ends, at ≈0.1/s. This dynamic filament stabilization runs opposite to the classical prediction that actin filaments become more unstable with age as they hydrolyze their bound ATP and release phosphate. Upon cofilin treatment, aged filaments revert to a dynamic state that shows accelerated shrinkage from both ends at a combined rate of 5.9/s. In light of recent electron microscopy studies [Orlova A,
et al.
(2004) Actin-destabilizing factors disrupt filaments by means of a time reversal of polymerization.
Proc Natl Acad Sci USA
101:17664–17668], we propose that dynamic stabilization arises from rearrangement of the filament structure from a relatively disordered state immediately after polymerization to the canonical Holmes helix, a change that is reversed by cofilin binding. Our results suggest that plasticity in the internal structure of the actin filament may play a fundamental role in regulating actin dynamics and may help cells build actin assemblies with vastly different turnover rates.
α1-Antitrypsin monotherapy induces immune tolerance during islet allograft transplantation in mice
Authors: Lewis Eli C. , Mizrahi Mark , Toledano Michel , DeFelice Nathaniel , Wright Joanne L. , Churg Andrew , Shapiro Leland , Dinarello Charles A.
Published: October 2008

Human pancreatic islet transplantation offers diabetic patients tight glucose control but has low graft survival rates. The immunosuppressive drugs that are administered to graft recipients lack the antiinflammatory benefits of corticosteroids because of their diabetogenic effects. The serum protease inhibitor α1-antitrypsin (AAT) possesses antiinflammatory properties and reduces cytokine-mediated islet damage. In the present study, diabetic mice were grafted with allogeneic islets and treated with AAT monotherapy (
n
= 24). After 14 days of treatment, mice remained normoglycemic and islet allografts were functional for up to 120 treatment-free days. After graft removal and retransplantation, mice accepted same-strain islets but rejected third-strain islets, thus confirming that specific immune tolerance had been induced. Explanted grafts exhibited a population of T regulatory cells in transplant sites. According to RT-PCR, grafts contained high levels of mRNA for foxp3, cytotoxic T lymphocyte antigen-4, TGF-β, IL-10, and IL-1 receptor antagonist; expression of proinflammatory mediators was low or absent. After implantation of skin allografts, AAT-treated mice had greater numbers of foxp3-positive cells in draining lymph nodes (DLNs) compared with control treatment mice. Moreover, dendritic cells in DLNs exhibited an immature phenotype with decreased CD86 activation marker. Although the number of CD3 transcripts decreased in the DLNs, AAT did not affect IL-2 activity
in vitro
. Thus, AAT monotherapy provides allografts with antiinflammatory conditions that favor development of antigen-specific T regulatory cells. Because AAT treatment in humans is safe, its use during human islet transplantation may be considered.
Curative and β cell regenerative effects of α1-antitrypsin treatment in autoimmune diabetic NOD mice
Authors: Koulmanda Maria , Bhasin Manoj , Hoffman Lauren , Fan Zhigang , Qipo Andi , Shi Hang , Bonner-Weir Susan , Putheti Prabhakar , Degauque Nicolas , Libermann Towia A. , Auchincloss Hugh , Flier Jeffrey S. , Strom Terry B.
Published: October 2008

Invasive insulitis is a destructive T cell-dependent autoimmune process directed against insulin-producing β cells that is central to the pathogenesis of type 1 diabetes mellitus (T1DM) in humans and the clinically relevant nonobese diabetic (NOD) mouse model. Few therapies have succeeded in restoring long-term, drug-free euglycemia and immune tolerance to β cells in overtly diabetic NOD mice, and none have demonstrably enabled enlargement of the functional β cell mass. Recent studies have emphasized the impact of inflammatory cytokines on the commitment of antigen-activated T cells to various effector or regulatory T cell phenotypes and insulin resistance and defective insulin signaling. Hence, we tested the hypothesis that inflammatory mechanisms trigger insulitis, insulin resistance, faulty insulin signaling, and the loss of immune tolerance to islets. We demonstrate that treatment with α1-antitrypsin (AAT), an agent that dampens inflammation, does not directly inhibit T cell activation, ablates invasive insulitis, and restores euglycemia, immune tolerance to β cells, normal insulin signaling, and insulin responsiveness in NOD mice with recent-onset T1DM through favorable changes in the inflammation milieu. Indeed, the functional mass of β cells expands in AAT-treated diabetic NOD mice.
Integrated analysis of homozygous deletions, focal amplifications, and sequence alterations in breast and colorectal cancers
Authors: Leary Rebecca J. , Lin Jimmy C. , Cummins Jordan , Boca Simina , Wood Laura D. , Parsons D. Williams , Jones Siân , Sjöblom Tobias , Park Ben-Ho , Parsons Ramon , Willis Joseph , Dawson Dawn , Willson James K. V. , Nikolskaya Tatiana , Nikolsky Yuri , Kopelovich Levy , Papadopoulos Nick , Pennacchio Len A. , Wang Tian-Li , Markowitz Sanford D. , Parmigiani Giovanni , Kinzler Kenneth W. , Vogelstein Bert , Velculescu Victor E.
Published: October 2008

We have performed a genome-wide analysis of copy number changes in breast and colorectal tumors using approaches that can reliably detect homozygous deletions and amplifications. We found that the number of genes altered by major copy number changes, deletion of all copies or amplification to at least 12 copies per cell, averaged 17 per tumor. We have integrated these data with previous mutation analyses of the Reference Sequence genes in these same tumor types and have identified genes and cellular pathways affected by both copy number changes and point alterations. Pathways enriched for genetic alterations included those controlling cell adhesion, intracellular signaling, DNA topological change, and cell cycle control. These analyses provide an integrated view of copy number and sequencing alterations on a genome-wide scale and identify genes and pathways that could prove useful for cancer diagnosis and therapy.
Nicotine decreases DNA methyltransferase 1 expression and glutamic acid decarboxylase 67 promoter methylation in GABAergic interneurons
Authors: Satta R. , Maloku E. , Zhubi A. , Pibiri F. , Hajos M. , Costa E. , Guidotti A.
Published: October 2008

Tobacco smoking is frequently abused by schizophrenia patients (SZP). The major synaptically active component inhaled from cigarettes is nicotine, hence the smoking habit of SZP may represent an attempt to use nicotine self-medication to correct (
i
) a central nervous system nicotinic acetylcholine receptor (nAChR) dysfunction, (
ii
) DNA-methyltransferase 1 (DMT1) overexpression in GABAergic neurons, and (
iii
) the down-regulation of reelin and GAD
67
expression caused by the increase of DNMT1-mediated hypermethylation of promoters in GABAergic interneurons of the telencephalon. Nicotine (4.5–22 μmol/kg s.c., 4 injections during the 12-h light cycle for 4 days) decreases DNMT1 mRNA and protein and increases GAD
67
expression in the mouse frontal cortex (FC). This nicotine-induced decrease of DNMT1 mRNA expression is greater (80%) in laser microdissected FC layer I GABAergic neurons than in the whole FC (40%), suggesting selectivity differences for the specific nicotinic receptor populations expressed in GABAergic neurons of different cortical layers. The down-regulation of DNMT1 expression induced by nicotine in the FC is also observed in the hippocampus but not in striatal GABAergic neurons. Furthermore, these data show that in the FC, the same doses of nicotine that decrease DNMT1 expression also (
i
) diminished the level of cytosine-5-methylation in the GAD
67
promoter and (
ii
) prevented the methionine-induced hypermethylation of the same promoter. Pretreatment with mecamylamine (6 μmol/kg s.c.), an nAChR blocker that penetrates the blood–brain barrier, prevents the nicotine-induced decrease of FC DNMT1 expression. Taken together, these results suggest that nicotine, by activating nAChRs located on cortical or hippocampal GABAergic interneurons, can up-regulate GAD
67
expression via an epigenetic mechanism. Nicotine is not effective in striatal medium spiny GABAergic neurons that primarily express muscarinic receptors.
Function of the
Bacillus subtilis
transcription elongation factor NusG in hairpin-dependent RNA polymerase pausing in the
trp
leader
Authors: Yakhnin Alexander V. , Yakhnin Helen , Babitzke Paul
Published: October 2008

NusA and NusG are transcription elongation factors that bind to RNA polymerase (RNAP) after σ subunit release.
Escherichia coli
NusA (NusA
Ec
) stimulates intrinsic termination and RNAP
Ec
pausing, whereas NusG
Ec
promotes Rho-dependent termination and pause escape. Both Nus factors also participate in the formation of RNAP
Ec
antitermination complexes. We showed that
Bacillus subtilis
NusA (NusA
Bs
) stimulates intrinsic termination and RNAP
Bs
pausing at U107 and U144 in the
trpEDCFBA
operon leader. Pausing at U107 and U144 participates in the transcription attenuation and translational control mechanisms, respectively, presumably by providing additional time for
trp
RNA-binding attenuation protein (TRAP) to bind to the nascent
trp
leader transcript. Here, we show that NusG
Bs
causes modest pause stimulation at U107 and dramatic pause stimulation at U144. NusA
Bs
and NusG
Bs
act synergistically to increase the U107 and U144 pause half-lives. NusG
Bs
-stimulated pausing at U144 requires RNAP
Bs
, whereas NusA
Bs
stimulates pausing of RNAP
Bs
and RNAP
Ec
at the U144 and
E. coli his
pause sites. Although NusG
Ec
does not stimulate pausing at U144, it competes with NusG
Bs
-stimulated pausing, suggesting that both proteins bind to the same surface of RNAP
Bs
. Inactivation of
nusG
results in the loss of RNAP pausing at U144
in vivo
and elevated
trp
operon expression, whereas plasmid-encoded NusG complements the mutant defects. Overexpression of
nusG
reduces
trp
operon expression to a larger extent than overexpression of
nusA
.
Palpable breast masses with probably benign morphology at sonography: can biopsy be deferred?
Authors: Park Y.-M. , Kim E.-K. , Lee J.-H. , Ryu J.-H. , Han S.-S. , Choi S.-J. , Lee S.-J. , Yoon H.-K.
Published: October 2008

Background: When a palpable breast mass is detected, a biopsy is usually performed even if the mass reveals probably benign morphologic features on imaging, as there is relatively little data reporting the outcome of such breast masses.

Purpose: To determine the negative predictive value for sonographic evaluation of palpable breast masses with probably benign morphology, and to assess whether follow-up may be an acceptable alternative to immediate biopsy.

Material and Methods: Of the 1399 sonograms of palpable masses from January 2004 to September 2005, there were 397 patients with masses of probably benign morphology. This study included 274 of these patients (age range 12–64 years, mean age 34 years) with 312 palpable masses that were pathologically confirmed by fine-needle aspiration ( n=7), ultrasound (US)-guided core needle biopsy ( n=180), or surgical biopsy ( n=125). The false-negative rate, negative predictive value (NPV), and 95% confidence interval (CI) were calculated using the SPSS statistical software package for Windows, version 12.0. A P value <0.05 was considered statistically significant.

Results: Of the 312 masses, there were 310 benign lesions and two malignancies, resulting in a false-negative rate of 0.6% (NPV 99.4%, P value=0.0432, 95% CI 0.0–1.5%).

Conclusion: The negative predictive value of sonography for palpable breast masses with probably benign morphology is high (99.4%). Therefore, short-term imaging follow-up can be an acceptable alternative to immediate biopsy, similar to the management of nonpalpable probably benign lesions (BI-RADS category 3).
Voxel-based correlation between coregistered single-photon emission computed tomography and dynamic susceptibility contrast magnetic resonance imaging in subjects with suspected alzheimer disease
Authors: Cavallin L. , Axelsson R. , Wahlund L. O. , Öksengard A. R. , Svensson L. , Juhlin P. , Wiberg M. Kristoffersen , Frank A.
Published: October 2008

Background: Current diagnosis of Alzheimer disease is made by clinical, neuropsychologic, and neuroimaging assessments. Neuroimaging techniques such as magnetic resonance imaging (MRI) and single-photon emission computed tomography (SPECT) could be valuable in the differential diagnosis of Alzheimer disease, as well as in assessing prognosis.

Purpose: To compare SPECT and MRI in a cohort of patients examined for suspected dementia, including patients with no objective cognitive impairment (control group), mild cognitive impairment (MCI), and Alzheimer disease (AD).

Material and Methods: 24 patients, eight with AD, 10 with MCI, and six controls, were investigated with SPECT using 99mTc-hexamethylpropyleneamine oxime (HMPAO, Ceretec; GE Healthcare Ltd., Little Chalsont UK) and dynamic susceptibility contrast magnetic resonance imaging (DSC-MRI) with a contrast-enhancing gadobutrol formula (Gadovist; Bayer Schering Pharma, Berlin, Germany). Voxel-based correlation between coregistered SPECT and DSC-MR images was calculated. Region-of-interest (ROI) analyses were then performed in 24 different brain areas using brain registration and analysis of SPECT studies (BRASS; Nuclear Diagnostics AB, Stockholm, Sweden) on both SPECT and DSC-MRI.

Results: Voxel-based correlation between coregistered SPECT and DSC-MR showed a high correlation, with a mean correlation coefficient of 0.94. ROI analyses of 24 regions showed significant differences between the control group and AD patients in 10 regions using SPECT and five regions in DSC-MR.

Conclusion: SPECT remains superior to DSC-MRI in differentiating normal from pathological perfusion, and DSC-MRI could not replace SPECT in the diagnosis of patients with Alzheimer disease.