bluuebunny/crossref_metadata_2025 huggingface dataset:
Optical observations of the growth and day‐to‐day variability of equatorial plasma bubbles
Authors: Makela J. J. , Miller E. S.
Published: March 2008

A new narrow‐field ionospheric imaging system, the Portable Ionospheric Camera and Small‐Scale Observatory, has been installed at the Cerro Tololo Inter‐American Observatory near La Serena, Chile (geographic 30.17°S, 289.19°E; geomagnetic 16.72°S, 0.42°E). We present observations of the naturally occurring nightglow emission at 630.0 nm on three consecutive nights demonstrating the day‐to‐day variability in the occurrence of equatorial plasma bubbles or depletions. On two nights, large‐scale undulations with a wavelength on the order of 300–600 km are observed in the emission regions magnetically connected to the bottomside of the equatorial F layer. We demonstrate that at each crest of these large‐scale waves, zero, one, or multiple depletions may grow. Thus, the presence of a large‐scale wave on the bottomside alone is not sufficient for irregularity growth. This variability is presumably due to the presence, or lack, of small‐scale seed waves or some other mechanism needed to increase the instability growth rate past the critical threshold.
Introduction to special section on Annual Cycles on the Arctic Ocean Shelf
Authors: Fortier Louis , Cochran J. Kirk
Published: March 2008

The perennial sea‐ice cover of the Arctic Ocean is shrinking rapidly in response to the anthropogenic warming of Earth's lower atmosphere. From September 2002 to September 2004 the Canadian Arctic Shelf Exchange Study (CASES) logged over 14,500 scientist‐days at sea to document the potential impacts of a shift in sea‐ice regime on the ecosystem of the Mackenzie Shelf in the southeastern Beaufort Sea. In particular, teams from Canada, Denmark, Japan, Norway, Spain, the United Kingdom, and the United States totaling over 200 scientists took rotations on the CCS Amundsen to study all aspects of the ecosystem during a 385‐day over‐wintering expedition in the region from September 2003 to September 2004. The resulting wealth of information has revealed an unexpectedly active food web under the winter sea ice of the coastal Beaufort Sea. From the thermodynamics of snow to the reconstruction of local paleo‐climate, this special section focuses on how sea‐ice cover dynamics dictate biological processes and biogeochemical fluxes on and at the margin of the shallow Arctic continental shelf. The highly successful CASES program has initiated ongoing time series of key measurements of the response of the marine ecosystem to change that have been expanded to other Arctic regions through the ArcticNet project and the International Polar Year.
Effects of paleoclimate and time‐varying canopy structures on paleowater fluxes
Authors: Yin Jun , Young Michael H. , Yu Zhongbo
Published: March 2008

We combined a long‐term (18,000 years) climatological record and time‐varying vegetation conditions to evaluate the role that climate change and vegetation might play in paleowater fluxes in arid settings. The HYDRUS‐1D model, which solves Richards Equation for variably saturated flow, the convection‐dispersion equation for chloride transport and the heat flow equation, was used to simulate water flux and chloride (Cl) transport. Six distinct case studies were compared for different boundary conditions and root distributions. A Mojave Desert–type canopy including evergreens, drought deciduous shrubs, annuals, grasses, and succulents was used as representative vegetation to transpire soil water and was modeled using ground cover percentage and leaf area index (LAI) as the bases for partitioning evapotranspiration (ET). The results showed that under water limited conditions, realistic root zone distributions and climate sequences (including extreme events) were both needed to simulate the accumulation of Cl in Mojave Desert soils. Results also showed that increasing precipitation intensity affected paleowater fluxes. However, contrary to the results of other researchers, we found that simulated chloride bulges were located at depths of around 20–30 cm, rather than at the base of the root zone, if current and normal climate conditions were applied. Moreover, the climatic shift beginning in the late Pleistocene was not the major reason for the chloride accumulation.
Relationships between horizontal transport flux and vertical deposition flux during dry deposition of atmospheric dust particles
Authors: Goossens Dirk
Published: March 2008

Wind tunnel experiments were conducted to investigate the relationships between vertically settling dust and the horizontal dust flow from which the particles originate. The study primarily focused on the grain size characteristics and on the horizontal and vertical sediment fluxes. Simultaneous samplings of vertical deposition flux and horizontal transport flux were carried out at an almost identical altimetric level (a very narrow layer immediately above a water surface generating no resuspension). This made it possible to relate deposition flux to the horizontal transport flux and to study how deposition alters the sedimentological characteristics of horizontally moving dust. The use of water as a deposition surface implied that the dust was subjected to some degree of dispersion after the settling. This restricted the analysis to grains >10 μm, but the trends for grains <10 μm were easy to reconstruct. The experiments show that deposited dust is generally coarser than the parent dust from which it originates but only for friction velocities below 0.34 m s−1. For higher wind speeds the median grain diameter of settling dust does not differ from that of the parent dust. Similar observations were made for the horizontal and vertical dust fluxes. At a constant horizontal transport flux (Fh) vertical deposition flux (Fs) drops with wind speed; however, from the same critical friction velocity of 0.34 m s−1 the ratio Fs/Fh remains constant. It was also found that the relationships between Fh and Fs depend on the grain size of the particles but only for sufficiently fine particles. Particles >50 μm no longer affect these relationships. Vertical mixing created by the turbulent nature of the flow strongly affects deposition of atmospheric dust. Mixing significantly hampers deposition of the grains, especially the small ones. The wind tunnel experiments allowed the magnitude of the effect mixing exerts on deposition to be calculated. For coarse grains the effect is small, but for fine grains mixing may hamper deposition by several dozen per cent. Theoretical dust deposition models should thus consider vertical mixing or otherwise include it in the numerical value of the velocity of deposition vd.
Orbital scale variations and timescales from the Arctic Ocean
Authors: Pälike Heiko , Spofforth David J. A. , O'Regan Matthew , Gattacceca Jérôme
Published: March 2008

We investigate geochemical measurements from the Arctic Coring Expedition to derive sedimentation rates for selected intervals in the early and middle Eocene. This analysis is performed by quantifying cyclical variations in physical property data and elemental concentrations derived with an X‐ray fluorescence (XRF) core scanner. Our results show that physical properties and XRF‐derived elemental concentrations are coherent and correlated to each other. Changes in elemental concentrations occur on depth scales from decimeters to meters and correspond to varying contributions of detrital minerals and biogenic silica. We confirm and refine sedimentation rates of the order of 10 to 25 m Ma−1. These rates were obtained independently through biostratigraphic and magnetostratigraphic methods. We observe a strong imprint of astronomically sourced cycles, particularly through climatic precession. This observation allows us to test recently proposed theoretical calculations of insolation.
Accuracy of models of hmF2 used for long‐term trend analyses
Authors: McNamara Leo F.
Published: March 2008

One of the largest expected ionospheric effects of the increasing concentrations of greenhouse gases is a decrease in the height of the F2 region peak density, hmF2, by ∼20 km. Analyses of long‐term trends of hmF2 in historical data to confirm this change must rely on models of hmF2 based on a limited number of ionogram characteristics, because a full analysis of historical analog (pre–digital age) ionograms to derive the plasma frequency profiles and hmF2 was a tedious and usually rare procedure. This paper discusses the accuracy of three models/formulas of hmF2 that have been used for long‐term trend studies, namely (1) the simple parabolic model, which sets hmF2 equal to the ionogram virtual height at 0.834 foF2, (2) the Dudeney (1974, 1983) model, and (3) the Bilitza et al. (1979) model. The models have been validated using ionograms calculated from plasma frequency profiles given by the International Reference Ionosphere (IRI). The best model would be the one with the smallest seasonal and solar cycle variations in the errors, even if it has a systematic error. Analysis of the errors (relative to the IRI) in the three models shows that all three are useful, but at different times of day.
Distributed and localized faulting in extensional settings: Insight from the North Ethiopian Rift–Afar transition area
Authors: Soliva Roger , Schultz Richard A.
Published: March 2008

Extensional fault systems in the Earth's crust can exhibit two end‐member geometries that we identify as distributed and localized faulting regimes. A satellite image analysis of fault populations from the Main Ethiopian Rift‐Afar area reveals that the rift architecture contains these two faulting regimes. The occurrence of these regimes reveals a jump in the scale of fault segmentation and linkage. Strain localization at rift border zones exhibits particularly large‐scale fault linkage and a power law size distribution. This regime replaces prior distributed fault systems, showing small‐scale fault linkage and an exponential size distribution. The distributed faulting is interpreted as confined to the thick trap basalt carapace. We show that continental fault systems can develop by a combination of these two geometries, and we demonstrate how to quantitatively decipher the jump between them.
Associations Between Obesity and Changes in Adult BMI Over Time and Colon Cancer Risk
Authors: Nock Nora L. , Thompson Cheryl L. , Tucker Thomas C. , Berger Nathan A. , Li Li
Published: March 2008

Obesity has been associated with increased colon cancer risk in epidemiological studies; however, the specific time periods during which obesity may be most relevant as well as how changes in adult body size over time affect colon cancer risk have not been well explored. We evaluated potential associations between BMI in each age decade(20s, 30s, 40s, 50s, and 2 years before study recruitment (“recruitment period”)) and in BMI changes over timeand colon cancer risk in a population‐based case–control study comprising 438 cases and 491 controls. We found that obese (BMI ≥ 30.0 kg/m2) compared to normal (BMI ≥ 18.5 to <25.0 kg/m2) body size at the recruitment period was associated with increased colon cancer risk (odds ratio (OR) = 1.54; 95% confidence interval (CI) = 1.03−2.31; P = 0.03). No associations were observed for obese body size in the other age decades. An increased risk was found for changes in BMI between the 30s decade and the recruitment period of 5–10 kg/m2 (OR = 1.54; 95%CI = 1.02−2.34; P = 0.04) and >10 kg/m2 (OR = 2.40; 95% CI = 1.23−4.66;P = 0.01) (P trend = 0.01). Stratification by gender revealed that BMI changes >10 kg/m2 increased risk in women but not men. Similar results were found for BMI changes between the 20s decade and the recruitment period but effect sizes were smaller. Our results provide additional support to obesity's role in colon cancer and suggest large body size increases exceeding 10 kg/m2 may potentially be more important after age 30, particularly among women; however, prospective studies with sex hormone, growth factor, and pro‐inflammatory biomarkers are needed to provide insights to the underlying biological mechanism(s).
Temperature dependent high-bias electrical properties of C60 microrods
Authors: Goyal Anubha , Kumar Ashavani , Kar Swastik , Ajayan Pulickel M. , Soldano Caterina
Published: March 2008

We present the fabrication, characterization, and temperature dependent electrical properties of individual submicron-sized hexagonal rods of C60. These rods were synthesized by liquid-liquid interfacial precipitation methods and characterized by scanning electron and transmission electron microscopies and Raman spectroscopy. The microscopic analysis reveals highly developed crystalline order. Two-probe platinum-contacted devices were fabricated using long (∼30–50μm) individual C60 rods by focused ion beam assisted deposition on insulating (Si∕SiO2) substrates. Current-voltage (IV) measurements were performed on these devices in the temperature range of 18–300K under an applied voltage of −20to20V. Our measurements reveal an overall decrease in conductivity with decreasing temperature, with structures appearing commensurately with the known positions of the phase transitions. Cyclic high-bias measurements show substantial hysteretic behavior below T∼260K, expected from a sudden and large increase in the dielectric constant of the system. The IV “loops” show significant nonlinearity and asymmetry and the shapes of the loops evolve with change in temperature, with sharp changes across the phase transition regions.
Twisted Dirac operators over quantum spheres
Authors: Sitarz Andrzej
Published: March 2008

We construct new families of spectral triples over quantum spheres, with a particular attention focused on the standard Podleś quantum sphere and twisted Dirac operators.
Magnetization reversal process in elongated Co rings with engineered defects
Authors: Gao X. S. , Adeyeye A. O. , Ross C. A.
Published: March 2008

We report a significant modification of the magnetization reversal process in thin film rings with engineered defects created by a focused ion beam. Using magnetic force microscopy, with in situ in-plane field, we observe that the traditional onion-vortex transition that occurs in defect-free rings can be suppressed, and the reversal instead takes place through domain wall motion. We have also investigated the effects of defect size, location, and distribution on the overall magnetization state. The results are explained in terms of pinning of domain walls by the engineered defects.
A time-dependent quantum dynamics investigation of the guanine-cytosine system: A six-dimensional model
Authors: Villani Giovanni
Published: March 2008

The dynamics of the guanine-cytosine base pair has been studied in the time-dependent quantum approach. A six-dimensional model involving the nonlinear three hydrogen bridges has been utilized. The modifications induced in the hydrogen transfer from a base to the other by the explicit inclusion of the out-of-plane hydrogen atom position in the three bridges have been evidenced and the consequences on stacking interaction and base pair opening are considered. The relevance of these aspects in biological properties has been suggested.
Concurrent triple-scale simulation of molecular liquids
Authors: Delgado-Buscalioni Rafael , Kremer Kurt , Praprotnik Matej
Published: March 2008

We present a triple-scale simulation of a molecular liquid, in which the atomistic, coarse-grained, and continuum descriptions of the liquid are concurrently coupled. The presented multiscale approach, which covers the length scales ranging from the micro- to macroscale, is a combination of two dual-scale models: a particle-based adaptive resolution scheme (AdResS), which couples the atomic and mesoscopic scales, and a hybrid continuum-molecular dynamics scheme (HybridMD). The combined AdResS-HybridMD scheme successfully sorts out the problem of large molecule insertion in the hybrid particle-continuum simulations of molecular liquids. The combined model is shown to correctly describe the hydrodynamics within a hybrid particle-continuum framework. The presented approach opens up the possibility to perform efficient grand-canonical molecular dynamics simulations of truly open molecular liquid systems.
Dyadic Green’s functions and guided surface waves for a surface conductivity model of graphene
Authors: Hanson George W.
Published: March 2008

An exact solution is obtained for the electromagnetic field due to an electric current in the presence of a surface conductivity model of graphene. The graphene is represented by an infinitesimally thin, local, and isotropic two-sided conductivity surface. The field is obtained in terms of dyadic Green’s functions represented as Sommerfeld integrals. The solution of plane wave reflection and transmission is presented, and surface wave propagation along graphene is studied via the poles of the Sommerfeld integrals. For isolated graphene characterized by complex surface conductivity σ=σ′+jσ″, a proper transverse-electric surface wave exists if and only if σ″>0 (associated with interband conductivity), and a proper transverse-magnetic surface wave exists for σ″<0 (associated with intraband conductivity). By tuning the chemical potential at infrared frequencies, the sign of σ″ can be varied, allowing for some control over surface wave properties.
Electron transport of L-shaped graphene nanoribbons
Authors: Chen Yuan Ping , Xie Yue E. , Yan Xiao Hong
Published: March 2008

L-shaped graphene nanoribbons (LGNRs) are important components of nanoelectronics and nanocircuits. By using the Green’s function method, we study the transport properties of LGNRs, which consist of a semi-infinite armchair edged nanoribbon (AGNR) and a semi-infinite zigzag edged nanoribbon (ZGNR). The width of AGNR determines whether the LGNR is metallic or not. The LGNR with a small included angle has high reflectance to the electrons, while the LGNR with a large included angle is nearly reflectionless. These are opposite to the transport characteristics of the LGNRs, which consist of two semi-infinite ZGNRs. As to the right-angle LGNR, its transport properties are associated with the width of ZGNR. The increase of width will decrease the conductance around the Fermi energy and simultaneously induce sharp conductance dips. In addition, an interesting spatially resolved local density of state is found in the right-angle LGNR.
Superior characteristics of organic chalcone single crystals as efficient nonlinear optical material
Authors: Kiran A. John , Kim H. C. , Kim K. , Rotermund F. , Ravindra H. J. , Dharmaprakash S. M. , Lim H.
Published: March 2008

High-quality biaxial single crystals of chalcone derivatives were grown by solution growth technique. Their molecular structures were designed to possess large second-order nonlinearities by choosing proper donor/acceptor groups while retaining a high transparency in the visible and infrared spectral regions. The second-order nonlinear optical coefficients, determined by applying the Maker fringe technique, were found to be much larger than those of LiB3O5, KTiOPO4, KH2PO4, and urea. The advantages, such as easy synthesis and crystal growth, low cutoff wavelength (<450nm), large optical nonlinearity, and high damage threshold (>7.2GW∕cm2), make these organic crystals promising for efficient frequency doubling.
A supertrace identity and its applications to superintegrable systems
Authors: Ma Wen-Xiu , He Jing-Song , Qin Zhen-Yun
Published: March 2008

A supertrace identity on Lie superalgebras is established. It provides a tool for constructing super-Hamiltonian structures of zero curvature equations associated with Lie superalgebras. Applications in the case of the Lie superalgebra B(0,1) present super-Hamiltonian structures of a super-AKNS soliton hierarchy and a super-Dirac soliton hierarchy.
Equivariant symplectic geometry of gauge fixing in Yang–Mills theory
Authors: Akant Levent
Published: March 2008

The Faddeev–Popov gauge fixing in Yang–Mills theory is interpreted as equivariant localization. It is shown that the Faddeev–Popov procedure amounts to a construction of a symplectic manifold with a Hamiltonian group action. The BRST cohomology is shown to be equivalent to the equivariant cohomology based on this symplectic manifold with Hamiltonian group action. The ghost operator is interpreted as a (pre)symplectic form and the gauge condition as the moment map corresponding to the Hamiltonian group action. This results in the identification of the gauge fixing action as a closed equivariant form, the sum of an equivariant symplectic form, and a certain closed equivariant 4-form, which ensures convergence. An almost complex structure compatible with the symplectic form is constructed. The equivariant localization principle is used to localize the path integrals onto the gauge slice. The Gribov problem is also discussed in the context of equivariant localization principle. As a simple illustration of the methods developed in the paper, the partition function of N=2 supersymmetric quantum mechanics is calculated by equivariant localization.
Defect and electronic structures of acceptor substituted lead titanate
Authors: Zhang Zhen , Wu Ping , Lu Li , Shu Chang
Published: March 2008

The defects and electronic structures of the group IIIB (Al, Ga, In, and Tl) and group VB (Sb and Bi) element substituted lead titanates were studied using density functional theory calculations. All substitutes are found to favor immobile acceptor-oxygen-vacancy-acceptor defect clusters, which weaken the space charge effects by limiting the motions of oxygen vacancies. Furthermore, we found that the group IIIB and group VB substitutes take two distinct defect-cluster structures, respectively, along the z direction and in the xy plane, mainly due to the difference in the ionic size and the electronegativity. While the domain pinning enforced by the tail-to-tail polarization patterns along the z direction are relieved by the group IIIB substitutes, the group VB substitutes induce head-to-head polarization patterns in the xy plane, which make the domain pinning effects even weaker.
High-phase-purity zinc-blende InN on r-plane sapphire substrate with controlled nitridation pretreatment
Authors: Hsiao Ching-Lien , Liu Ting-Wei , Wu Chien-Ting , Hsu Hsu-Cheng , Hsu Geng-Ming , Chen Li-Chyong , Shiao Wen-Yu , Yang C. C. , Gällström Andreas , Holtz Per-Olof , Chen Chia-Chun , Chen Kuei-Hsien
Published: March 2008

High-phase-purity zinc-blende (zb) InN thin film has been grown by plasma-assisted molecular-beam epitaxy on r-plane sapphire substrate pretreated with nitridation. X-ray diffraction analysis shows that the phase of the InN films changes from wurtzite (w) InN to a mixture of w-InN and zb-InN, to zb-InN with increasing nitridation time. High-resolution transmission electron microscopy reveals an ultrathin crystallized interlayer produced by substrate nitridation, which plays an important role in controlling the InN phase. Photoluminescence emission of zb-InN measured at 20K shows a peak at a very low energy, 0.636eV, and an absorption edge at ∼0.62eV is observed at 2K, which is the lowest bandgap reported to date among the III-nitride semiconductors.
Magnetotransport in Gd-implanted wurtzite GaN∕AlxGa1−xN high electron mobility transistor structures
Authors: Lo F.-Y. , Melnikov A. , Reuter D. , Cordier Y. , Wieck A. D.
Published: March 2008

Ga N ∕ Al x Ga 1 − x N heterostructures containing a two-dimensional electron gas (2DEG) 27nm underneath the surface were focused-ion-beam implanted with 300keV Gd ions at room temperature. At 4.2K, current-voltage characteristics across implanted rectangles showed that the structures remained conducting up to a Gd dose of 1×1012cm−2. Extraordinary Hall effect and anisotropic magnetoresistance were observed at T=4.2K for structures implanted with 3×1011cm−2 Gd. This dose corresponds to a 23% reduction in electron concentration and a decrease in the mobility by a factor of 14 at 4.2K. However, the still-conducting 2DEG is now embedded in a ferromagnetic semiconductor which opens the possibility to polarize its spins.
Organic bulk heterojunction solar cells using poly(2,5-bis(3-tetradecyllthiophen-2-yl)thieno[3,2,-b]thiophene)
Authors: Parmer Jack E. , Mayer Alex C. , Hardin Brian E. , Scully Shawn R. , McGehee Michael D. , Heeney Martin , McCulloch Iain
Published: March 2008

By transitioning to semicrystalline polymers, the performance of polymer-based solar cells has recently increased to over 5% [W. Ma et al., Adv. Fund. Mater. 15, 1665 (2005); G. Li et al., Nat. Mater. 4, 864 (2005); M. Reyes-Reyes et al., Org. Lett. 7, 5749 (2005); J. Y. Kim et al., Adv. Mater. (Weinheim, Ger.) 18, 572 (2005); J. Peet et al., Nat. Mater. 6, 497 (2007)]. Poly(2,5-bis(3-tetradecyllthiophen-2-yl)thieno[3,2-b]thiophene) (pBTTT) has caused recent excitement in the organic electronics community because of its high reported hole mobility (0.6cm2V−1s−1) that was measured in field effect transistors and its ability to form large crystals. In this letter, we investigate the potential of pBTTT as light absorber and hole transporter in a bulk heterojunction solar cell. We find that the highest efficiency of 2.3% is achieved by using a 1:4 blend of pBTTT and[6,6]-phenyl C61-butyric acid methyl ester. The hole mobility as measured by space charge limited current modeling was found to be 3.8×10−4cm2V−1s−1 in this blend.
Light deprivation damages monoamine neurons and produces a depressive behavioral phenotype in rats
Authors: Gonzalez M. M. C. , Aston-Jones G.
Published: March 2008

Light is an important environmental factor for regulation of mood. There is a high frequency of seasonal affective disorder in high latitudes where light exposure is limited, and bright light therapy is a successful antidepressant treatment. We recently showed that rats kept for 6 weeks in constant darkness (DD) have anatomical and behavioral features similar to depressed patients, including dysregulation of circadian sleep–waking rhythms and impairment of the noradrenergic (NA)-locus coeruleus (LC) system. Here, we analyzed the cell viability of neural systems related to the pathophysiology of depression after DD, including NA-LC, serotoninergic-raphe nuclei and dopaminergic-ventral tegmental area neurons, and evaluated the depressive behavioral profile of light-deprived rats. We found increased apoptosis in the three aminergic systems analyzed when compared with animals maintained for 6 weeks in 12:12 light-dark conditions. The most apoptosis was observed in NA-LC neurons, associated with a significant decrease in the number of cortical NA boutons. Behaviorally, DD induced a depression-like condition as measured by increased immobility in a forced swim test (FST). DD did not appear to be stressful (no effect on adrenal or body weights) but may have sensitized responses to subsequent stressors (increased fecal number during the FST). We also found that the antidepressant desipramine decreases these neural and behavioral effects of light deprivation. These findings indicate that DD induces neural damage in monoamine brain systems and this damage is associated with a depressive behavioral phenotype. Our results suggest a mechanism whereby prolonged limited light intensity could negatively impact mood.
Activation of Trk neurotrophin receptors by glucocorticoids provides a neuroprotective effect
Authors: Jeanneteau Freddy , Garabedian Michael J. , Chao Moses V.
Published: March 2008

Glucocorticoids (GCs) display both protective and destructive effects in the nervous system. In excess, GCs produce neuronal damage after stress or brain injury; however, the neuroprotective effects of adrenal steroids also have been reported. The mechanisms that account for the positive actions are not well understood. Here we report that GCs can selectively activate Trk receptor tyrosine kinases afterin vivoadministration in the brain and in cultures of hippocampal and cortical neurons. Trk receptors are normally activated by neurotrophins, such as NGF and brain-derived neurotrophic factor, but the activation of Trk receptors by GCs does not depend on increased production of neurotrophins. Other tyrosine kinase receptors, such as EGF and FGF receptors, were not activated by GCs. The ability of GCs to increase Trk receptor activity resulted in the neuroprotection of neurons deprived of trophic support and could be modulated by steroid-converting enzymes. Pharmacological and shRNA experiments indicate that Trk receptor activation by GCs depends on a genomic action of the GC receptor. The ability of GCs to promote Trk receptor activity represents a molecular mechanism that integrates the actions of GCs and neurotrophins.
Chemokine receptor CXCR3 and its ligands CXCL9 and CXCL10 are required for the development of murine cerebral malaria
Authors: Campanella Gabriele S. V. , Tager Andrew M. , El Khoury Joseph K. , Thomas Seddon Y. , Abrazinski Tabitha A. , Manice Lindsay A. , Colvin Richard A. , Luster Andrew D.
Published: March 2008

Cerebral malaria is a significant cause of global mortality, causing an estimated two million deaths per year, mainly in children. The pathogenesis of this disease remains incompletely understood. Chemokines have been implicated in the development of cerebral malaria, and the IFN-inducible CXCR3 chemokine ligand IP-10 (CXCL10) was recently found to be the only serum biomarker that predicted cerebral malaria mortality in Ghanaian children. We show that the CXCR3 chemokine ligands IP-10 and Mig (CXCL9) were highly induced in the brains of mice with murine cerebral malaria caused by
Plasmodium berghei
ANKA. Mice deficient in CXCR3 were markedly protected against cerebral malaria and had far fewer T cells in the brain compared with wild-type mice. In competitive transfer experiments, CXCR3-deficient CD8
+
T cells were 7-fold less efficient at migrating into the infected brains than wild-type CD8
+
T cells. Adoptive transfer of wild-type CD8
+
effector T cells restored susceptibility of CXCR3-deficient mice to cerebral malaria and also restored brain proinflammatory cytokine and chemokine production and recruitment of T cells, independent of CXCR3. Mice deficient in IP-10 or Mig were both partially protected against cerebral malaria mortality when infected with
P. berghei
ANKA. Brain immunohistochemistry revealed Mig staining of endothelial cells, whereas IP-10 staining was mainly found in neurons. These data demonstrate that CXCR3 on CD8
+
T cells is required for T cell recruitment into the brain and the development of murine cerebral malaria and suggest that the CXCR3 ligands Mig and IP-10 play distinct, nonredundant roles in the pathogenesis of this disease.
The insulator factor CTCF controls MHC class II gene expression and is required for the formation of long-distance chromatin interactions
Authors: Majumder Parimal , Gomez Jorge A. , Chadwick Brian P. , Boss Jeremy M.
Published: March 2008

Knockdown of the insulator factor CCCTC binding factor (CTCF), which binds XL9, an intergenic element located between HLA-DRB1 and HLA-DQA1, was found to diminish expression of these genes. The mechanism involved interactions between CTCF and class II transactivator (CIITA), the master regulator of major histocompatibility complex class II (MHC-II) gene expression, and the formation of long-distance chromatin loops between XL9 and the proximal promoter regions of these MHC-II genes. The interactions were inducible and dependent on the activity of CIITA, regulatory factor X, and CTCF. RNA fluorescence in situ hybridizations show that both genes can be expressed simultaneously from the same chromosome. Collectively, the results suggest a model whereby both HLA-DRB1 and HLA-DQA1 loci can interact simultaneously with XL9, and describe a new regulatory mechanism for these MHC-II genes involving the alteration of the general chromatin conformation of the region and their regulation by CTCF.
A natural smooth compactification of the space of elliptic curves in projective space
Authors: Vakil Ravi , Zinger Aleksey
Published: March 2008

The space of smooth genus-

0
0

curves in projective space has a natural smooth compactification: the moduli space of stable maps, which may be seen as the generalization of the classical space of complete conics. In arbitrary genus, no such natural smooth model is expected, as the space satisfies “Murphy’s Law”. In genus

1
1

, however, the situation remains beautiful. We give a natural smooth compactification of the space of elliptic curves in projective space, and describe some of its properties. This space is a blowup of the space of stable maps. It can be interpreted as a result of blowing up the most singular locus first, then the next most singular, and so on, but with a twist—these loci are often entire components of the moduli space. We give a number of applications in enumerative geometry and Gromov-Witten theory. For example, this space is used by the second author to prove physicists’ predictions for genus-1 Gromov-Witten invariants of a quintic threefold. The proof that this construction indeed gives a desingularization will appear in a subsequent paper.
𝑝-rational characters and self-normalizing Sylow 𝑝-subgroups
Authors: Navarro Gabriel , Tiep Pham , Turull Alexandre
Published: March 2008

Let

G
G

be a finite group,

p
p

a prime, and

P
P

a Sylow

p
p

-subgroup of

G
G

. Several recent refinements of the McKay conjecture suggest that there should exist a bijection between the irreducible characters of

p
′

p’

-degree of

G
G

and the irreducible characters of

p
′

p’

-degree of

N

G

(
P
)

\mathbf {N}_G(P)

, which preserves field of values of correspondent characters (over the

p
p

-adics). This strengthening of the McKay conjecture has several consequences. In this paper we prove one of these consequences: If

p
>
2

p>2

, then

G
G

has no non-trivial

p
′

p’

-degree

p
p

-rational irreducible characters if and only if

N

G

(
P
)
=
P

\mathbf {N}_G(P)=P

.
Id1 Overexpression Induces Tetraploidization and Multiple Abnormal Mitotic Phenotypes by Modulating Aurora A
Authors: Man Cornelia , Rosa Jack , Yip Y. L. , Cheung Annie Lai-Man , Kwong Y. L. , Doxsey Stephen J. , Tsao S. W.
Published: March 2008

The basic helix-loop-helix transcription factor, Id1, was shown to induce tetraploidy in telomerase-immortalized nasopharyngeal epithelial cells in this study. Using both transient and stable Id1-expressing cell models, multiple mitotic aberrations were detected, including centrosome amplification, binucleation, spindle defects, and microtubule perturbation. Many of these abnormal phenotypes have previously been reported in cells overexpressing Aurora A. Further experiments showed that Id1 could stabilize Aurora A, whereas knocking down Aurora A expression in Id1-expressing cells could rescue some of the mitotic defects. The mechanisms by which Aurora A could be modulated by Id1 were explored. DNA amplification of the Aurora A locus was not involved. Id1 could only weakly activate the transcriptional activity of the Aurora A promoter. We found that Id1 overexpression could affect Aurora A degradation, leading to its stabilization. Aurora A is normally degraded from mitosis exit by the APC/CCdh1-mediated proteasomal proteolysis pathway. Our results revealed that Id1 and Cdh1 are binding partners. The association of Id1 and Cdh1 was found to be dependent on the canonical destruction box motif of Id1, the increased binding of which may compete with the interaction between Cdh1 and Aurora A, leading to stabilization of Aurora A in Id1-overexpressing cells.
A noise model for mass spectrometry based proteomics
Authors: Du Peicheng , Stolovitzky Gustavo , Horvatovich Peter , Bischoff Rainer , Lim Jihyeon , Suits Frank
Published: March 2008

Motivation: Mass spectrometry data are subjected to considerable noise. Good noise models are required for proper detection and quantification of peptides. We have characterized noise in both quadrupole time-of-flight (Q-TOF) and ion trap data, and have constructed models for the noise.

Results: We find that the noise in Q-TOF data from Applied Biosystems QSTAR fits well to a combination of multinomial and Poisson model with detector dead-time correction. In comparison, ion trap noise from Agilent MSD-Trap-SL is larger than the Q-TOF noise and is proportional to Poisson noise. We then demonstrate that the noise model can be used to improve deisotoping for peptide detection, by estimating appropriate cutoffs of the goodness of fit parameter at prescribed error rates. The noise models also have implications in noise reduction, retention time alignment and significance testing for biomarker discovery.

Contact:  pdu@us.ibm.com

Supplementary information: Supplementary data are available at Bioinfomatics Online.
GlycoBase and autoGU: tools for HPLC-based glycan analysis
Authors: Campbell Matthew P. , Royle Louise , Radcliffe Catherine M. , Dwek Raymond A. , Rudd Pauline M.
Published: March 2008

Summary: The development of robust high-performance liquid chromatography (HPLC) technologies continues to improve the detailed analysis and sequencing of glycan structures released from glycoproteins. Here, we present a database (GlycoBase) and analytical tool (autoGU) to assist the interpretation and assignment of HPLC-glycan profiles. GlycoBase is a relational database which contains the HPLC elution positions for over 350 2-AB labelled N-glycan structures together with predicted products of exoglycosidase digestions. AutoGU assigns provisional structures to each integrated HPLC peak and, when used in combination with exoglycosidase digestions, progressively assigns each structure automatically based on the footprint data. These tools are potentially very promising and facilitate basic research as well as the quantitative high-throughput analysis of low concentrations of glycans released from glycoproteins.

Availability:  http://glycobase.ucd.ie

Contact:  matthew.campbell@nibrt.ie
Unequal group variances in microarray data analyses
Authors: Demissie Meaza , Mascialino Barbara , Calza Stefano , Pawitan Yudi
Published: March 2008

Motivation: In searching for differentially expressed (DE) genes in microarray data, we often observe a fraction of the genes to have unequal variability between groups. This is not an issue in large samples, where a valid test exists that uses individual variances separately. The problem arises in the small-sample setting, where the approximately valid Welch test lacks sensitivity, while the more sensitive moderated t-test assumes equal variance.

Methods: We introduce a moderated Welch test (MWT) that allows unequal variance between groups. It is based on (i) weighting of pooled and unpooled standard errors and (ii) improved estimation of the gene-level variance that exploits the information from across the genes.

Results: When a non-trivial proportion of genes has unequal variability, false discovery rate (FDR) estimates based on the standard t and moderated t-tests are often too optimistic, while the standard Welch test has low sensitivity. The MWT is shown to (i) perform better than the standard t, the standard Welch and the moderated t-tests when the variances are unequal between groups and (ii) perform similarly to the moderated t, and better than the standard t and Welch tests when the group variances are equal. These results mean that MWT is more reliable than other existing tests over wider range of data conditions.

Availability: R package to perform MWT is available at http://www.meb.ki.se/~yudpaw

Contact:  yudi.pawitan@ki.se

Supplementary information: Supplementary data are available at Bioinformatics online.
Variations in the biomass of Antarctic krill (Euphausia superba) around the South Shetland Islands, 1996–2006
Authors: Reiss Christian S. , Cossio Anthony M. , Loeb Valerie , Demer David A.
Published: March 2008

Reiss, C. S., Cossio, A. M., Loeb, V., and Demer, D. A. 2008. Variations in the biomass of Antarctic krill (Euphausia superba) around the South Shetland Islands, 1996–2006. – ICES Journal of Marine Science, 65: 497–508. The time-series of acoustically surveyed Antarctic krill (Euphausia superba) biomass near the South Shetland Islands (SSI) between 1996 and 2006 is re-estimated using a validated physics-based model of target strength (TS), and a species-discrimination algorithm based on the length-range of krill in plankton samples to identify krill acoustically, derived from TS-model predictions. The SSI area is surveyed each austral summer by the US Antarctic Marine Living Resources Program, and the acoustic data are used to examine trends in krill biomass and to assess the potential impact of fishing to the reproductive success of land-based predators (seals and penguins). The time-series of recomputed biomass densities varies greatly from that computed using an empirical log-linear TS-model and fixed-ranges of differences in volume–backscattering strengths (ΔSv), conventionally used to identify krill acoustically. The new acoustic estimates of biomass are significantly correlated with both proportional recruitment and krill abundance estimated from zooplankton samples. Two distinct peaks in biomass (1996 and 2003) are in accord with recruitment events shown by net-based krill time-series. The foundation for the new TS-model and the associated krill-discrimination algorithm, coupled with the agreement between acoustic- and net-survey results, provides strong support for the use of the new analytical technique. Variable biases in the re-estimated krill biomass have been greatly reduced. However, survey variability increased as a result of the increased rejection of acoustic backscatter previously attributed to krill. Management of Southern Ocean krill stocks based on a precautionary approach may therefore result in decreased allocations of krill, given its dependence on the variability of survey estimates.
Visualization of growth signal transduction cascades in living cells with genetically encoded probes based on Förster resonance energy transfer
Authors: Aoki Kazuhiro , Kiyokawa Etsuko , Nakamura Takeshi , Matsuda Michiyuki
Published: March 2008

Fluorescence probes based on the principle of Förster resonance energy transfer (FRET) have shed new light on our understanding of signal transduction cascades. Among them, unimolecular FRET probes containing fluorescence proteins are rapidly increasing in number because these genetically encoded probes can be easily loaded into living cells and allow simple acquisition of FRET images. We have developed probes for small GTPases, tyrosine kinases, serine–threonine kinases and phosphoinositides. Images obtained with these probes have revealed that membrane protrusions such as nascent lamellipodia or neurites provide an active signalling platform in the growth factor-stimulated cells.
Prevalence of genes encoding extracellular virulence factors among meticillin-resistant Staphylococcus aureus isolates from the University Hospital, Olomouc, Czech Republic
Authors: Sauer P. , Síla J. , Štosová T. , Večeřová R. , Hejnar P. , Vágnerová I. , Kolář M. , Raclavský V. , Petrželová J. , Lovečková Y. , Koukalová D.
Published: March 2008

A rather fast and complicated progression of an infection caused by some strains ofStaphylococcus aureuscould be associated with the expression and co-action of virulence factor complexes in these strains. This study screened the antibiotic susceptibility and prevalence of virulence markers in isolates of meticillin-resistantS. aureus(MRSA) obtained from patients hospitalized at the University Hospital in Olomouc, Czech Republic. A total of 100 isolates was screened for 13 genes encoding extracellular virulence determinants (tst,pvl,eta,etb,sea,seb,sec,sed,see,seg,seh,seiandsej) and for their distribution in sample types. Eighty-nine isolates were positive for at least one of the genes. Genes foretb,pvl,seeandsehwere not detected in any of the MRSA isolates. No statistically significant differences in the occurrence of the determinants studied among sample types were found.
Virulence characteristics of community-associated Staphylococcus aureus and in vitro activities of moxifloxacin alone and in combination against community-associated and healthcare-associated meticillin-resistant and -susceptible S. aureus
Authors: Goldstein Ellie J. C. , Citron Diane M. , Warren Yumi A. , Tyrrell Kerin L. , Rybak Michael J.
Published: March 2008

The increasing prevalence of community-associated meticillin-resistant Staphylococcus aureus (CA-MRSA) poses a challenge for antimicrobial therapy of skin and soft tissue infections (SSTIs). To determine whether another antimicrobial agent might enhance the activity of moxifloxacin against CA-MRSA, this study analysed its activity alone and in chequerboard combination with doxycycline, rifampicin, clindamycin, trimethoprim, sulfamethoxazole/trimethoprim (SXT) and vancomycin against recent SSTI clinical isolates, and also characterized the isolates for Panton–Valentine leukocidin (PVL), agr groups, staphylococcal cassette chromosome mec (SSCmec) types and δ-haemolysin production. For comparison, 25 strains of outpatient meticillin-susceptible S. aureus (MSSA), 24 strains of healthcare-associated (HA)-MRSA and six historical strains of vancomycin-intermediate S. aureus (VISA) were included. It was found that 21/25 CA-MRSA strains tested were PVL-positive, SSCmec type 4 and agr type 1, whilst 4/25 were PVL-negative, SSCmec type 2 and agr type 2. Two of the agr type 2 strains were negative for δ-haemolysin but all other strains were positive. Moxifloxacin MIC50/90 values (μg ml−1) were 1/8 for CA-MRSA, 4/32 for HA-MRSA and ≤0.03/1 for MSSA and MIC50 of 2 for VISA. The D-test for inducible clindamycin resistance was positive for 3/27 CA-MRSA, 5/14 HA-MRSA and none of the MSSA isolates. In chequerboard studies, fractional inhibitory concentration indices (FICIs) showed that most interactions were additive or indifferent (FICI value >0.5 to ≤2) as follows: rifampicin 43/52 strains, clindamycin 44/44, SXT 44/47, trimethoprim 41/42 and vancomycin 37/43. The FICI values for doxycycline were 3–6 for 32/34 strains, indicating antagonism, suggesting that it should not be used in combination with moxifloxacin.
Genotyping analysis of Mycoplasma pneumoniae clinical strains in Japan between 1995 and 2005: type shift phenomenon of M. pneumoniae clinical strains
Authors: Kenri Tsuyoshi , Okazaki Norio , Yamazaki Tsutomu , Narita Mitsuo , Izumikawa Kinich , Matsuoka Mayumi , Suzuki Satowa , Horino Atsuko , Sasaki Tsuguo
Published: March 2008

Mycoplasma pneumoniae clinical isolates obtained between 1995 and 2005 were examined to determine the prevalent genotype. One hundred and twenty-seven strains isolated from bronchitis and pneumonia patients were genotyped by a PCR-RFLP method based on nucleotide sequence polymorphisms of the p1 gene, which encodes the major adhesin protein. The typing results established that 66 of the isolates were group I strains, 45 were group II strains and 16 were group II variants. Analysis of the annual occurrence of these isolates showed a predominance of group II strains between 1995 and 2001 (n=37). No group I strain was found during this period. However, group I strains appeared in the isolates from 2002 (2/5 isolates, 40 %) and increased in specimens taken after 2003, thereby constituting a large proportion of the isolates. In 2004 and 2005, no group II strains were found among the isolates (n=49), although there were nine group II variants. Throat swabs and sputum samples obtained from patients with respiratory infections between 1997 and 2005 were also analysed by PCR-RFLP or a new nested PCR to detect the p1 gene DNA. Typing analysis of these p1 gene DNAs also showed that the group I p1 gene was not present in specimens taken before 2000, but was present and dominant in specimens taken after 2001. These results indicate that, in Japan, the prevalent type of M. pneumoniae changed from a group II strain to a group I strain around 2002.