bluuebunny/crossref_metadata_2025 huggingface dataset:
Vacuum ultraviolet excitation spectroscopy of the autoionizing Rydberg states of atomic sulfur in the 73350–84950cm−1 frequency range
Authors: Yang Xueliang , Zhou Jingang , Jones Brant , Ng C. Y. , Jackson William M.
Published: February 2008

The photoionization efficiency (PIE) spectra of metastable sulfur (S) atoms in the D1 and S1 states have been recorded in the 73350–84950cm−1 frequency range by using a velocity-mapped ion imaging apparatus that uses a tunable vacuum ultraviolet laser as the ionization source. The S(D1) and S(S1) atoms are produced by the 193nm photodissociation of CS2. The observed PIE spectra of S(D1) and S(S1) shows 35 autoionizing resonances with little or no contribution from direct photoionization into the S+(S3∕24)+e− ionization continuum. Velocity-mapped ion images of the S+ at the individual autoionizing Rydberg resonances are used to distinguish whether the lower state of the resonance originates from the D1, S1, or P3 states. The analysis and assignment of the Rydberg peaks revealed 22 new Rydberg states that were not previously known. The autoionization lifetimes τ of the Rydberg states are derived from the linewidths by fitting the lines with the Fano formula. Deviations from the scaling law of τ(n*)∝n*3, where n* is the effective quantum number of the Rydberg state, are observed. This observation is ascribed to perturbations by nearby triplet Rydberg states, which shorten the autoionization lifetimes of the singlet Rydberg levels.
Systematically convergent basis sets for explicitly correlated wavefunctions: The atoms H, He, B–Ne, and Al–Ar
Authors: Peterson Kirk A. , Adler Thomas B. , Werner Hans-Joachim
Published: February 2008

Correlation consistent basis sets have been optimized for use with explicitly correlated F12 methods. The new sets, denoted cc-pVnZ-F12 (n=D,T,Q), are similar in size and construction to the standard aug-cc-pVnZ and aug-cc-pV(n+d)Z basis sets, but the new sets are shown in the present work to yield much improved convergence toward the complete basis set limit in MP2-F12/3C calculations on several small molecules involving elements of both the first and second row. For molecules containing only first row atoms, the smallest cc-pVDZ-F12 basis set consistently recovers nearly 99% of the MP2 valence correlation energy when combined with the MP2-F12/3C method. The convergence with basis set for molecules containing second row atoms is slower, but the new DZ basis set still recovers 97%–99% of the frozen core MP2 correlation energy. The accuracy of the new basis sets for relative energetics is demonstrated in benchmark calculations on a set of 15 chemical reactions.
Integrated experimental and theoretical approach for the structural characterization of Hg2+ aqueous solutions
Authors: D’Angelo Paola , Migliorati Valentina , Mancini Giordano , Barone Vincenzo , Chillemi Giovanni
Published: February 2008

The structural and dynamic properties of the solvated Hg2+ ion in aqueous solution have been investigated by a combined experimental-theoretical approach employing x-ray absorption spectroscopy and molecular dynamics (MD) simulations. This method allows one to perform a quantitative analysis of the x-ray absorption near-edge structure (XANES) spectra of ionic solutions using a proper description of the thermal and structural fluctuations. XANES spectra have been computed starting from the MD trajectory, without carrying out any minimization in the structural parameter space. The XANES experimental data are accurately reproduced by a first-shell heptacoordinated cluster only if the second hydration shell is included in the calculations. These results confirm at the same time the existence of a sevenfold first hydration shell for the Hg2+ ion in aqueous solution and the reliability of the potentials used in the MD simulations. The combination of MD and XANES is found to be very helpful to get important new insights into the quantitative estimation of structural properties of disordered systems.
Ab initio calculation of carbon clusters. II. Relative stabilities of fullerene and nonfullerene C24
Authors: An Wei , Shao Nan , Bulusu Satya , Zeng X. C.
Published: February 2008

Chemical stabilities of six low-energy isomers of C24 derived from global-minimum search are investigated. The six isomers include one classical fullerene (isomer 1) whose cage is composed of only five- and six-membered rings (5∕6-MRs), three nonclassical fullerene structures whose cages contain at least one four-membered ring (4-MR), one plate, and one monocyclic ring. Chemical and electronic properties of the six C24 isomers are calculated based on a density-functional theory method (hybrid PBE1PBE functional and cc-pVTZ basis set). The properties include the nucleus-independent chemical shifts (NICS), singlet-triplet splitting, electron affinity, ionization potential, and gap between the highest occupied molecular orbital and the lowest unoccupied molecular orbital (HOMO-LUMO) gap. The calculation suggests that the neutral isomer 2, a nonclassical fullerene with two 4-MRs, may be more chemically stable than the classical fullerene (isomer 1). Analyses of molecular orbital NICS show that the incorporations of 4-MRs into the cage considerably reduce paratropic contributions from HOMO, HOMO-1, and HOMO-2, which are mainly responsible for the sign change in NICS from positive for isomer 1 (42) to negative (−19) for isomer 2, although C24 clusters satisfy neither 4N+2 nor 2(N+1)2 aromaticity rule. Anion photoelectron spectra of four cage isomers, one plate, one monocyclic ring, and one tadpole isomer, as well as three bicyclic ring isomers are calculated. The simulated photoelectron spectra of mono- and bicyclic rings (with C1 symmetry) appear to match the measured HOMO-LUMO gap (between the first and second band in the experimental spectra) [S. Yang et al., Chem. Phys. Lett. 144, 431 (1988)]. Nevertheless, the nonclassical fullerene isomers 3 and 4 apparently also match the measured vertical detachment energy (2.90eV) reasonably well. These results suggest possible coexistence of nonclassical fullerene isomers with the mono- and bicyclic ring isomers of C24− under the experimental conditions.
Thermopower and thermal conductance through parallel coupled quantum dots
Authors: Franco R. , Silva–Valencia J. , Figueira M. S.
Published: February 2008

We study the thermoelectric transport properties through two parallel coupled, gate-defined quantum dots (QDs), in the framework of the X-boson treatment for the impurity Anderson model. We compute the thermopower S, the thermal conductance κ, the electrical conductance G, and the product of the thermoelectric figure of merit and the temperature ZT, as function of the dot energy. We concentrate the calculations on ZT, that is, a measure of the usefulness of materials or devices as thermopower generators or cooling systems. If the coupling between the QDs is weak, ZT is greater than 1 when T≃Δ (Δ is the mixing width between the QD and the leads) but when the system is coupled, the second dot can tune the temperature region where ZT>1. This result increases the possibilities of practical application of the system in mesoscopic cooling process.
Ion flow convergence in spherical inertial electrostatic confinement devices
Authors: Meyer R. M. , Smith Z. M. , Prelas M. A. , Loyalka S. K.
Published: February 2008

Data collected with automated double and single probes is used to evaluate the convergence of ion flow in a spherical inertial electrostatic confinement device operated in glow discharge mode. A novel method based on the invasive nature of electrostatic probes is used to evaluate the width of the ion density peak. Over much of the star mode discharge regime, it is found that Rc∕Rg∼0.125 to 0.167 where Rc is the ion core radius, and Rg is the radius of the cathode grid, which remains fixed for all discharge conditions considered here. Near the star-to-jet mode transition, the technique shows that Rc∕Rg∼0.250, in agreement with direct measurements of the ion density profile with the double probe. The influences of space charge accumulation and cathode grid deflection are evaluated with floating potential measurements and tangential electric field measurements, respectively. It is concluded that the observed core growth is a result of ion microchannel degradation caused by an increased frequency in inelastic and elastic molecular encounters, while the effects of space charge are negligible.
Precession axis modification to a semianalytical Landau–Lifshitz solution technique
Authors: Porter D. G. , Donahue M. J.
Published: February 2008

A recent article [Van de Wiele et al., IEEE Trans. Magn. 43, 2917 (2007)] presents a semianalytical method to solve the Landau–Lifshitz (LL) equation. Spin motion is computed analytically as precession about the effective field H, where H is assumed fixed over the time step. However, the exchange field dominates at short range and varies at the time scale of neighbor spin precessions, undermining the fixed field assumption. We present an axis corrected version of this algorithm. We add a scalar multiple of m to H (preserving torque and hence the LL solution) to produce a more stable precession axis parallel to the cross product of the torques m×H at two closely spaced time steps. We build a predictor-corrector solver on this foundation. The second order convergence of the solver enables calculation of adjustable time steps to meet a desired error magnitude.
Electro-optic nature of ultrafast pump-probe reflectivity response from multilayer semiconductor heterostructures
Authors: Glinka Y. D. , Tolk N. H. , Liu X. , Sasaki Y. , Furdyna J. K.
Published: February 2008

We provide the evidence for the electro-optic nature of the transient reflectivity change (TRC) response from GaAs∕GaSb∕InAs heterostructures measured in ultrafast pump-probe experiments. The evidence is based on the correlation between TRC and the transient electric-field-induced second harmonic generation change signals, which have been measured simultaneously. The TRC signal is induced through the second- and third-order nonlinearities by the interfacial dc electric fields originating from the charge separation of pump-excited carriers among the layers. The effect of the interface type between GaSb and InAs layers on the interfacial field strength was analyzed.
Calorimetric versus kinetic glass transitions in viscous monohydroxy alcohols
Authors: Wang Li-Min , Tian Yongjun , Liu Riping , Richert Ranko
Published: February 2008

An extensive comparison of calorimetric and dielectric measurements is carried out for generic molecular liquids and monohydroxy alcohols with focus on the identification of the dielectric modes which are associated with the glass transition. For generic liquids, the calorimetric glass transition temperatures (Tg-cal) are always greater than their kinetic counterparts (Tg-kin), but the difference remains below 3K. Also, the nonexponentiality parameters of the Tool-Narayanaswamy-Moynihan-Hodge model applied to the calorimetric data and the stretching exponents of the dielectric measurements show remarkable agreement. The same behavior is found for glass-forming monohydroxy alcohols, provided that the faster and smaller non-Debye relaxation rather than the large dielectric Debye process is assigned to the structural relaxation. The study emphasizes that the dielectric signature of the glass transition in monohydroxy alcohols is a dispersive loss peak that is faster and significantly smaller than the prominent Debye feature.
Origin of uniaxial magnetic anisotropy in epitaxial MnAs film on GaAs(001) substrate
Authors: Ryu Kwang-Su , Kim JinBae , Lee YoungPak , Akinaga Hiro , Manago Takashi , Viswan Ravindranath , Shin Sung-Chul
Published: February 2008

We investigate the origin of in-plane uniaxial magnetic anisotropy of epitaxial ferromagnetic MnAs film on GaAs(001). Interestingly, as temperature increases, the in-plane uniaxial magnetic anisotropy along the MnAs[112¯0] direction changes and then disappears. Direct microscopic domain observations show that the type of domain structure changes from a simple domain to a closure one with increasing temperature. From these results, the temperature-dependent change of the in-plane magnetic anisotropy is ascribed to a decrease in the shape anisotropy induced by the decrease in the width of the ferromagnetic α-stripe.
The sticking of H and D atoms on a graphite (0001) surface: The effects of coverage and energy dissipation
Authors: Kerwin Jay , Jackson Bret
Published: February 2008

Classical trajectory methods are used to examine the trapping and sticking of H and D atoms on the graphite (0001) surface. Total energy calculations based on density functional theory are used to construct the model potential energy surface, and graphite clusters of up to 121 atoms are considered. For hydrogen to chemisorb, the bonding carbon must pucker out of the surface plane by roughly 0.4Å. For incident energies above the 0.2eV barrier, any trapped H atoms must rapidly dissipate their excess energy into the surrounding lattice within a few vibrations of the C–H stretch in order to remain bound. For sufficiently large clusters, the C–H bond stabilizes within about 0.1ps. The sticking probability for D at 150K is in the range of 5%–10%, more-or-less consistent with the most recent measurements in the limit of zero coverge. Variation with isotope and substrate temperature is weak. We estimate that the sticking cross section for adsorption at the para site, directly across the sixfold carbon ring from an already adsorbed H atom, can be four or more times larger that the zero coverage sticking cross section.
Composition dependence of dielectric function in ferroelectric BaCoxTi1−xO3 films grown on quartz substrates by transmittance spectra
Authors: Hu Z. G. , Li Y. W. , Zhu M. , Zhu Z. Q. , Chu J. H.
Published: February 2008

Near-infrared-ultraviolet optical properties of BaCoxTi1−xO3 (BCT) (x from 1.0% to 10%) films have been investigated by the transmittance spectra. The dispersion functions in the photon energy range of 1.24–6.2eV have been extracted by fitting the experimental data with Adachi’s model. It was found that the oscillator and dispersion energies linearly increase with the Co composition and the maximum optical transition occurs near the energy range of 4.3–5.0eV for the BCT materials. The absorption coefficient at the visible region linearly increases with the composition due to grain boundaries and disorder induced band tail into the forbidden gap.
A mechanism for dynamic lateral polarization in CdZnTe under high flux x-ray irradiation
Authors: Bale Derek S. , Soldner Stephen A. , Szeles Csaba
Published: February 2008

It has been observed that pixillated CdZnTe detectors fabricated from crystals with low hole transport properties (μhτh<10−5cm2V−1) experience a dynamic lateral polarization when exposed to a high flux of x-rays. In this effect, counts are transferred from pixels near the edge of the irradiated region to pixels in the interior. In this letter, we propose a mechanism capable of explaining the observed dynamical effect. The mechanism is based on a transverse electric field that is generated due to space charge that builds within the material. This transverse field, in turn, is responsible for the altered carrier trajectories toward the center of the irradiated region.
High-efficiency and color-stable white organic light-emitting devices based on sky blue electrofluorescence and orange electrophosphorescence
Authors: Ho Cheuk-Lam , Lin Mei-Fang , Wong Wai-Yeung , Wong Wai-Kwok , Chen Chin H.
Published: February 2008

Highly efficient and color-stable two-wavelength white organic light-emitting devices (WOLEDs) combining an orange phosphor [Ir(Cz–CF3)] and a sky blue fluorescent dye BUBD-1 are fabricated where the host singlet is resonant with the fluorophore singlet state and the host triplet is resonant with the phosphor triplet level. A thin layer of 1,3,5-tris[N-(phenyl)benzimidazole]benzene between the phosphorescent and the fluorescent regions confines both singlet and triplet excitons efficiently and suppress Dexter transfer of the phosphor excitons to the nonradiative triplet state of BUBD-1. The best device reaches peak efficiencies of 19.3cd∕A and 11.1lm∕W which are superior to common two-color all-fluorescent or all-phosphor WOLEDs.
Dispersion control and slow light in slotted photonic crystal waveguides
Authors: Di Falco A. , O’Faolain L. , Krauss T. F.
Published: February 2008

Slotted photonic crystal waveguides combine the ability to confine light in air with the dispersion control available from photonic crystals. Here, we study the dependence of their dispersion properties on geometry, especially the slot width, and demonstrate slow light operation with group indices in excess of 100.
Near-infrared waveguide-based nickel silicide Schottky-barrier photodetector for optical communications
Authors: Zhu Shiyang , Yu M. B. , Lo G. Q. , Kwong D. L.
Published: February 2008

Integrated silicon-on-insulator waveguide-based silicide Schottky-barrier photodetectors were fabricated using low-cost standard Si complementary metal-oxide-semiconductor processing technology. The thin epitaxial NiSi2 layer formed by solid-state Ti-interlayer mediated epitaxy on the top of Si-waveguide absorbs light propagating through the waveguide effectively and exhibits excellent rectifying property on both p-Si and n-Si. NiSi2∕p-Si detectors with tapered geometry demonstrate dark current of ∼3.0nA at room temperature, responsivity of ∼4.6mA∕W at wavelengths ranging from 1520to1620nm, and 3dB bandwidth of ∼2.0GHz. The approaches for further improvement in responsivity are addressed.
Effects of freshwater flow on the year-class strength of a non-diadromous estuarine finfish, king threadfin (Polydactylus macrochir), in a dry-tropical estuary
Authors: Halliday Ian A. , Robins Julie B. , Mayer David G. , Staunton-Smith Jonathan , Sellin Michelle J.
Published: February 2008

The year-class strength of the commercial catch of king threadfin (Polydactylus macrochir (Gunther, 1876)) was correlated with freshwater flows into a dry-tropical estuary over five consecutive years. The year-class strength of king threadfin, a non-diadromous estuarine species, fluctuated and correlated significantly with freshwater flow and coastal rainfall in spring and summer; a result similar to that found for the catadromous barramundi (Lates calcarifer) within the same estuarine system. All sub-sets general linear models were used to screen relationships between year-class strength and freshwater variables. King threadfin spawn from spring to summer in north-eastern Australia, when hydrological conditions adjacent to estuaries have high salinities and are optimal for egg and post-larval survival. Young-of-the-year enter estuaries during the wet season, enabling them to take advantage of salinity gradients and the seasonal blooms in prey species such as Acetes spp. and juvenile penaeids that are accentuated in wet years. Freshwater flows in spring and summer are important drivers of the year-class strength of estuarine finfish, and reduction in these flows, through the development of water infrastructure and abstraction or long-term climate change, will potentially reduce the size of the population of estuarine fish available for human harvest.
Food resource variability in an Australian dryland river: evidence from the diet of two generalist native fish species
Authors: Sternberg David , Balcombe Stephen , Marshall Jonathan , Lobegeiger Jaye
Published: February 2008

To examine how food resource availability links with natural variation in primary productivity in the Moonie River, south-west Queensland, the diets of two native Australian fish species (Nematalosa erebi and Macquaria ambigua) were examined from fifteen waterholes in February, May and September 2006. N. erebi diets reflected strong ‘boom and bust’ patterns of food consumption, with high concentrations of benthic (non-filamentous) algae during boom (flow) times, moving to higher concentrations of filamentous algae and detritus during bust (no flow) periods. M. ambigua diets were primarily dominated by aquatic insects in all sampling periods. Although there was no clear ‘boom to bust’ pattern in relation to flow, M. ambigua secondary prey consumption revealed a compensatory switch between high energy prey (crustaceans) during more productive periods with terrestrial insects during less productive periods. The ability of both species of fish to switch from high to low concentrations of food quality under a variable environmental background allows them to persist through both high productive and low productive periods. This interaction between native biota and variable ‘boom’ and ‘bust’ conditions, and how changes to the natural hydrology will affect it is an important consideration of any future water resource development plans.
Rapid depletion of genotypes with fast growth and bold personality traits from harvested fish populations
Authors: Biro Peter A. , Post John R.
Published: February 2008

The possibility for fishery-induced evolution of life history traits is an important but unresolved issue for exploited fish populations. Because fisheries tend to select and remove the largest individuals, there is the evolutionary potential for lasting effects on fish production and productivity. Size selection represents an indirect mechanism of selection against rapid growth rate, because individual fish may be large because of rapid growth or because of slow growth but old age. The possibility for direct selection on growth rate, whereby fast-growing genotypes are more vulnerable to fishing irrespective of their size, is unexplored. In this scenario, faster-growing genotypes may be more vulnerable to fishing because of greater appetite and correspondingly greater feeding-related activity rates and boldness that could increase encounter with fishing gear and vulnerability to it. In a realistic whole-lake experiment, we show that fast-growing fish genotypes are harvested at three times the rate of the slow-growing genotypes within two replicate lake populations. Overall, 50% of fast-growing individuals were harvested compared with 30% of slow-growing individuals, independent of body size. Greater harvest of fast-growing genotypes was attributable to their greater behavioral vulnerability, being more active and bold. Given that growth is heritable in fishes, we speculate that evolution of slower growth rates attributable to behavioral vulnerability may be widespread in harvested fish populations. Our results indicate that commonly used minimum size-limits will not prevent overexploitation of fast-growing genotypes and individuals because of size-independent growth-rate selection by fishing.
Pharmacological disruption of calcium channel trafficking by the α
2
δ ligand gabapentin
Authors: Hendrich Jan , Van Minh Alexandra Tran , Heblich Fay , Nieto-Rostro Manuela , Watschinger Katrin , Striessnig Jörg , Wratten Jack , Davies Anthony , Dolphin Annette C.
Published: February 2008

The mechanism of action of the antiepileptic and antinociceptive drugs of the gabapentinoid family has remained poorly understood. Gabapentin (GBP) binds to an exofacial epitope of the α
2
δ-1 and α
2
δ-2 auxiliary subunits of voltage-gated calcium channels, but acute inhibition of calcium currents by GBP is either very minor or absent. We formulated the hypothesis that GBP impairs the ability of α
2
δ subunits to enhance voltage-gated Ca
2+
channel plasma membrane density by means of an effect on trafficking. Our results conclusively demonstrate that GBP inhibits calcium currents, mimicking a lack of α
2
δ only when applied chronically, but not acutely, both in heterologous expression systems and in dorsal root-ganglion neurons. GBP acts primarily at an intracellular location, requiring uptake, because the effect of chronically applied GBP is blocked by an inhibitor of the system-L neutral amino acid transporters and enhanced by coexpression of a transporter. However, it is mediated by α
2
δ subunits, being prevented by mutations in either α
2
δ-1 or α
2
δ-2 that abolish GBP binding, and is not observed for α
2
δ-3, which does not bind GBP. Furthermore, the trafficking of α
2
δ-2 and Ca
V
2 channels is disrupted both by GBP and by the mutation in α
2
δ-2, which prevents GBP binding, and we find that GBP reduces cell-surface expression of α
2
δ-2 and Ca
V
2.1 subunits. Our evidence indicates that GBP may act chronically by displacing an endogenous ligand that is normally a positive modulator of α
2
δ subunit function, thereby impairing the trafficking function of the α
2
δ subunits to which it binds.
Origin and progeny of reactive gliosis: A source of multipotent cells in the injured brain
Authors: Buffo Annalisa , Rite Inmaculada , Tripathi Pratibha , Lepier Alexandra , Colak Dilek , Horn Ana-Paula , Mori Tetsuji , Götz Magdalena
Published: February 2008

Reactive gliosis is the universal reaction to brain injury, but the precise origin and subsequent fate of the glial cells reacting to injury are unknown. Astrocytes react to injury by hypertrophy and up-regulation of the glial-fibrillary acidic protein (GFAP). Whereas mature astrocytes do not normally divide, a subpopulation of the reactive GFAP
+
cells does so, prompting the question of whether the proliferating GFAP
+
cells arise from endogenous glial progenitors or from mature astrocytes that start to proliferate in response to brain injury. Here we show by genetic fate mapping and cell type-specific viral targeting that quiescent astrocytes start to proliferate after stab wound injury and contribute to the reactive gliosis and proliferating GFAP
+
cells. These proliferating astrocytes remain within their lineage
in vivo
, while a more favorable environment
in vitro
revealed their multipotency and capacity for self-renewal. Conversely, progenitors present in the adult mouse cerebral cortex labeled by NG2 or the receptor for the platelet-derived growth factor (PDGFRα) did not form neurospheres after (or before) brain injury. Taken together, the first fate-mapping analysis of astrocytes in the adult mouse cerebral cortex shows that some astrocytes acquire stem cell properties after injury and hence may provide a promising cell type to initiate repair after brain injury.
PD-1 deficiency reveals various tissue-specific autoimmunity by H-2band dose-dependent requirement of H-2g7for diabetes in NOD mice
Authors: Yoshida Taku , Jiang Fang , Honjo Tasuku , Okazaki Taku
Published: February 2008

Although many autoimmune diseases are associated with particular HLA/H-2 haplotypes, the mechanisms through which specific HLA/H-2 haplotypes afford autoimmune susceptibility remain enigmatic. Here, we analyzed the effects of the diabetes-associated (H-2g7) and an antidiabetogenic (H-2b) H-2 haplotypes in NOD mice deficient for programmed cell death-1 (PD-1,Pdcd1), a unique model of type 1 diabetes that confers complete penetrance and rapid onset of the disease. NOD-H2b/bPdcd1−/−mice were completely protected from diabetes, confirming that H-2g7is indispensable for diabetes even in the absence of PD-1. However, NOD-H2b/bPdcd1−/−mice developed autoimmune inflammation in multiple tissues including peripheral nerves, stomachs, and exocrine tissues, demonstrating that autoreactive T cells are generated in the context of H-2b. These autoreactive T cells damaged target tissues only in the absence of PD-1, confirming that PD-1 deficiency unravels the hidden autoimmune susceptibility of the strain by reducing the threshold of T cell activation. Transfer experiments revealed that CD4 T cells are the effector cells of neuritis, and nerve-infiltrating CD4 T cells are strongly deviated toward Th1. Interestingly, neuritogenic T cells were also generated in the context of H-2g7, in sharp contrast to the strict requirement of H-2g7for diabetes. In addition, 60% of the NOD-H2b/g7Pdcd1−/−mice developed diabetes, suggesting that H-2bdoes not dominantly suppress diabetes and that H-2g7induces diabetes in a dose-dependent fashion.
Two-step site selection for serine-integrase-mediated excision: DNA-directed integrase conformation and central dinucleotide proofreading
Authors: Ghosh Pallavi , Bibb Lori A. , Hatfull Graham F.
Published: February 2008

Bacteriophage-encoded serine-integrases are members of the large family of serine-recombinases and catalyze site-specific integrative recombination between a phage
attP
site and a bacterial
attB
site to form an integrated prophage. Prophage excision involves a second site-specific recombination event, in which the sites generated by integration,
attL
and
attR
, are used as substrates to regenerate
attP
and
attB
. Excision is catalyzed by integrase but also requires a phage-encoded recombination directionality factor (RDF). The Bxb1 recombination sites,
attP
and
attB
, are small (<50 bp), different in sequence, and quasisymmetrical, and they give rise to
attL
- and
attR
-recombinant products that are asymmetric but similar to each other, each being composed of B- and P-type half-sites. We show here that the determination of correct excision products is a two-step process, with a presynaptic RDF-dependent step that aligns
attL
and
attR
in the correct orientation and a postsynaptic step in which the nonpalindromic central dinucleotide confers identity to
attL
and
attR
and prevents each from recombining with itself.
Hydrogen and oxygen isotope ratios in human hair are related to geography
Authors: Ehleringer James R. , Bowen Gabriel J. , Chesson Lesley A. , West Adam G. , Podlesak David W. , Cerling Thure E.
Published: February 2008

We develop and test a model to predict the geographic region-of-origin of humans based on the stable isotope composition of their scalp hair. This model incorporates exchangeable and nonexchangeable hydrogen and oxygen atoms in amino acids to predict the δ
2
H and δ
18
O values of scalp hair (primarily keratin). We evaluated model predictions with stable isotope analyses of human hair from 65 cities across the United States. The model, which predicts hair isotopic composition as a function of drinking water, bulk diet, and dietary protein isotope ratios, explains >85% of the observed variation and reproduces the observed slopes relating the isotopic composition of hair samples to that of local drinking water. Based on the geographical distributions of the isotope ratios of tap waters and the assumption of a “continental supermarket” dietary input, we constructed maps of the expected average H and O isotope ratios in human hair across the contiguous 48 states. Applications of this model and these observations are extensive and include detection of dietary information, reconstruction of historic movements of individuals, and provision of region-of-origin information for unidentified human remains.
Loss of Bardet–Biedl syndrome proteins alters the morphology and function of motile cilia in airway epithelia
Authors: Shah Alok S. , Farmen Sara L. , Moninger Thomas O. , Businga Thomas R. , Andrews Michael P. , Bugge Kevin , Searby Charles C. , Nishimura Darryl , Brogden Kim A. , Kline Joel N. , Sheffield Val C. , Welsh Michael J.
Published: February 2008

Mutations in a group of genes that contribute to ciliary function cause Bardet–Biedl syndrome (BBS). Most studies of BBS have focused on primary, sensory cilia. Here, we asked whether loss of BBS proteins would also affect motile cilia lining the respiratory tract. We found that BBS genes were expressed in human airway epithelia, and BBS2 and BBS4 localized to cellular structures associated with motile cilia. Although BBS proteins were not required for ciliogenesis, their loss caused structural defects in a fraction of cilia covering mouse airway epithelia. The most common abnormality was bulges filled with vesicles near the tips of cilia. We discovered this same misshapen appearance in airway cilia fromBbs1,Bbs2,Bbs4, andBbs6mutant mice. The structural abnormalities were accompanied by functional defects; ciliary beat frequency was reduced inBbsmutant mice. Previous reports suggested BBS might increase the incidence of asthma. However, compared with wild-type controls, neither airway hyperresponsiveness nor inflammation increased inBbs2−/−orBbs4−/−mice immunized with ovalbumin. Instead, these animals were partially protected from airway hyperresponsiveness. These results emphasize the role of BBS proteins in both the structure and function of motile cilia. They also invite additional scrutiny of motile cilia dysfunction in patients with this disease.
Broad dispersion and lung localization of virus-specific memory B cells induced by influenza pneumonia
Authors: Joo Hye Mee , He Yuxia , Sangster Mark Y.
Published: February 2008

Although memory B cells (BMem) contribute significantly to resistance to infection, BMempopulation characteristics that may relate to protective efficacy have received little attention. Here, we report a comprehensive quantitative analysis of virus-specific IgG and IgA BMemdispersion after transient influenza pneumonia in mice. From early in the response, BMemcirculated continuously and dispersed widely to secondary lymphoid tissues. However, a complicated picture emerged with BMemfrequency differences between secondary lymphoid tissues indicating an influence of local tissue factors on trafficking. BMemnumbers increased and stabilized at tissue-specific frequencies without contraction of the BMempool during the period of analysis. The lung was notable as a nonsecondary lymphoid tissue where a rapid influx of IgG and IgA BMemestablished relatively high frequencies that were maintained long term. Our findings provide insights into the pattern of BMemdispersion, and emphasize the lung as a complex repository of immune memory after local infection.
A genome-wide signature of positive selection in ancient and recent invasive expansions of the honey bee
Apis mellifera
Authors: Zayed Amro , Whitfield Charles W.
Published: February 2008

Apis mellifera
originated in Africa and extended its range into Eurasia in two or more ancient expansions. In 1956, honey bees of African origin were introduced into South America, their descendents admixing with previously introduced European bees, giving rise to the highly invasive and economically devastating “Africanized” honey bee. Here we ask whether the honey bee's out-of-Africa expansions, both ancient and recent (invasive), were associated with a genome-wide signature of positive selection, detected by contrasting genetic differentiation estimates (
F
ST
) between coding and noncoding SNPs. In native populations, SNPs in protein-coding regions had significantly higher
F
ST
estimates than those in noncoding regions, indicating adaptive evolution in the genome driven by positive selection. This signal of selection was associated with the expansion of honey bees from Africa into Western and Northern Europe, perhaps reflecting adaptation to temperate environments. We estimate that positive selection acted on a minimum of 852–1,371 genes or ≈10% of the bee's coding genome. We also detected positive selection associated with the invasion of African-derived honey bees in the New World. We found that introgression of European-derived alleles into Africanized bees was significantly greater for coding than noncoding regions. Our findings demonstrate that Africanized bees exploited the genetic diversity present from preexisting introductions in an adaptive way. Finally, we found a significant negative correlation between
F
ST
estimates and the local GC content surrounding coding SNPs, suggesting that AT-rich genes play an important role in adaptive evolution in the honey bee.
Induction of antigen-specific regulatory T cells in wild-type mice: Visualization and targets of suppression
Authors: Verginis Panayotis , McLaughlin Katherine A. , Wucherpfennig Kai W. , von Boehmer Harald , Apostolou Irina
Published: February 2008

Antigen-specific transplantation tolerance in the absence of immunosuppressive drugs is a rarely achieved goal. Immune responses to Y chromosome-encoded transplantation antigens (HY) can have life-threatening consequences in the clinic. Here, we have adopted a procedure developed in T cell antigen receptor (TCR)-transgenic mice to convert naïve T cells into male-specific Foxp3+regulatory T cells (Tregs) in WT female mice. For this purpose, female mice were infused by osmotic minipumps with a single class II MHC-presented HY peptide and Tregs visualized by tetramer staining. As a result, animals developed Treg-mediated long-term tolerance to all HY transplantation antigens, irrespective of whether they were recognized by CD4 or CD8 T cells, on skin or hematopoietic grafts from male donors.
Spontaneous rupture of pheochromocytoma: computed tomography–pathologic features and correlation
Authors: Park B. K. , Kim C. K. , Kwon G. Y.
Published: February 2008

Spontaneous rupture is a rare complication of pheochromocytoma. Its preoperative diagnosis is of great importance in determining treatment and prognosis. We describe computed tomography pathologic findings and correlate their features in a case with ruptured pheochromocytoma.
Book Reviews
Authors: Skaane Per
Published: February 2008

Clinical Breast Imaging: A Patient Focused Teaching File. By G. Cardenosa. Philadelphia, PA: Lippincott Williams & Wilkins, 2007. ISBN: 978-0-7817-6267-0. 528 pages. Price hardcover: USD 129.00
Esophageal bronchus: case report and review of the literature
Authors: Verma A. , Mohan S. , Kathuria M. , Baijal S. S.
Published: February 2008

Communicating bronchopulmonary foregut malformation (CBPFM) is a rare abnormality that is characterized by persistent communication between the bronchial tree and the gastrointestinal tract. We report a case of CBPFM in a young girl, with a description of the imaging and surgical details and a short review of the relevant literature.
Self-implanted artificial nodules: a computed tomography mimic of penile pathology
Authors: Levy G. , Mercer D. , Amosi D. , Arad E.
Published: February 2008

Self-introduction of foreign bodies along the penile shaft has been reported in several ethnic and social groups, mainly in Asia, and recently has been described in Europe. We present the case of a 34-year-old homeless Russian immigrant who had an abdominal CT performed during an emergency department visit. On the CT scan, several hyperdense, well-demarcated subcutaneous nodules along the penile shaft were noted. Following a focused history and physical examination, the nodules were found to represent artificial foreign bodies made of glass, which were self-introduced by the patient in order to allegedly increase the pleasure of sexual partners. Penile nodules may be a manifestation of diverse pathological entities including infectious, inflammatory, and neoplastic processes. It is important for the radiologist to be familiar with this social phenomenon and its radiological appearance in order to avoid erroneous diagnosis.
Primary treatment of ruptured blood blister-like aneurysms with stent-assisted coil embolization: report of two cases
Authors: Korja M. , Rautio R. , Valtonen S. , Haapanen A.
Published: February 2008

Blood blister-like aneurysms (BBAs) are among the most hazardous cerebrovascular aneurysms to treat; microsurgical treatment of these small, wide-necked, and exceptionally fragile aneurysms place patients at significant risk of morbidity or mortality. We report two cases of ruptured BBAs attempted to be treated for the first time with stent-assisted coil embolization solely and review the current literature on treatment options. Our patients underwent stent-assisted coil embolization of the aneurysms in the acute stage of subarachnoid hemorrhage (SAH). One patient was successfully treated without procedure-related complications. The other patient died after surgical internal carotid artery (ICA) occlusion, carried out after intraoperative rerupture of the aneurysm during the endovascular treatment. In the successful case, 8-month and 19-month follow-up angiograms demonstrated incomplete (>90%) occlusion with residual filling of the aneurysm neck, which did not need additional coil embolization. Even though stent-assisted coil embolization of ruptured BBAs in the acute stage appears to be a technically feasible treatment option, the present stent-related endovascular technology has potentially hazardous drawbacks.
White matter brain lesions in midlife familial hypercholesterolemic patients at 3-tesla magnetic resonance imaging
Authors: Schmitz S. A. , O'Regan D. P. , Fitzpatrick J. , Neuwirth C. , Potter E. , Tosi I. , Hajnal J. V. , Naoumova R. P.
Published: February 2008

Background: Patients with hypercholesterolemia of 60 years and older have an increased risk for white matter brain lesions and dementia.

Purpose: To investigate whether patients with familial hypercholesterolemia (FH) develop white matter lesions at 3-Tesla (T) MRI as early as in midlife.

Material and Methods: Non-diabetic, nonsmoking, and non-hypertensive heterozygous FH patients on treatment with maximally tolerated dose of a statin for more than 5 years ( n = 14) and matched controls ( n = 22) aged 25 to 60 years of age were studied. Imaging was performed at 3T with a fluid-attenuated T2-weighted MR pulse sequence and a T1-weighted spin-echo pulse sequence following 10 ml of i.v. gadopentetate dimeglumine. Images were evaluated by two independent readers. Fasting blood samples were taken. Student's t test was employed at P<0.05.

Results: Three volunteers and one FH patient had white matter lesions ( P<0.53). No other evidence of past ischemic stroke was observed. Mean total serum cholesterol and low-density lipoprotein (LDL) cholesterol were significantly higher in the FH group (6.0±1.1 vs. 5.1±0.9 mmol/l, P<0.02 and 4.1±0.9 vs. 3.1±0.8 mmol/l, P<0.004, respectively).

Conclusion: Heterozygous FH patients on statin treatment in the age range of 25 to 60 years are not at increased risk of white matter lesions at 3T MRI.
Detection of cerebrospinal fluid leakage: initial experience with three-dimensional fast spin-echo magnetic resonance myelography
Authors: Tomoda Y. , Korogi Y. , Aoki T. , Morioka T. , Takahashi H. , Ohno M. , Takeshita I.
Published: February 2008

Background: The pathogenesis of cerebrospinal fluid (CSF) hypovolemia is supposed to be caused by CSF leakage through small dural defects.

Purpose: To compare source three-dimensional (3D) fast spin-echo (FSE) images of magnetic resonance (MR) myelography with radionuclide cisternography findings, and to evaluate the feasibility of MR myelography in the detection of CSF leakage.

Material and Methods: A total of 67 patients who were clinically suspected of CSF hypovolemia underwent indium-111 radionuclide cisternography, and 27 of those who had direct findings of CSF leakage were selected for evaluation. MR myelography with 3D FSE sequences (TR/TE 6000/203 ms) was performed at the lumbar spine for all patients. We evaluated source images and maximum intensity projection (MIP) images of MR myelography, and the findings were correlated with radionuclide cisternography findings. MR myelography of five healthy volunteers was used as a reference. The MR visibility of the CSF leakage was graded as definite (leakage clearly visible), possible (leakage poorly seen), or absent (not shown).

Results: CSF leakage was identified with source 3D FSE images in 22 (81.5%) of 27 patients. Of the 22 patients, 16 were graded as definite and six were graded as possible. For the definite cases, 3D FSE images clearly showed the extent of the leaked CSF in the paraspinal structures. In the remaining five patients with absent findings, radionuclide cisternography showed only slight radionuclide activity out of the arachnoid space.

Conclusion: Source 3D FSE images of MR myelography seem useful in the detection of CSF leakage. Invasive radionuclide cisternography may be reserved for equivocal cases only.
Temporal Generalization under Time Pressure in Humans
Authors: Klapproth Florian , Müller Martin
Published: February 2008

In two experiments, participants performed a temporal generalization task in which they were asked to decide whether or not the durations of comparison stimuli were different from those of standard stimuli (750 ms, 1,000 ms, or 1,250 ms). One half of the participants was instructed to respond as quickly as possible, while the other half received no instruction concerning the speed of response. The relationship between stimulus duration and the time of response and the effect of time pressure on duration discrimination were examined. Response time increased as a linear function of the duration of the to-be-judged stimuli until a certain instant, which was defined as T2 = s/(1 – b), where s refers to the internal representation of the standard duration and b to the decision threshold. Moreover, the participants systematically overestimated the presented intervals if they were asked to respond as fast as possible when the standard duration was either 1,000 ms or 1,250 ms, but not when the standard duration was 750 ms.
Short Article: Scene Structure Enhances Change Detection
Authors: Alexander Varakin D. , Levin Daniel T.
Published: February 2008

Theories of objects recognition, scene perception, and neural representation of scenes imply that jumbling a coherent scene should reduce change detection. However, evidence from the change detection literature questions whether jumbling affects change detection. The experiments reported here demonstrate that jumbling does, in fact, reduce change detection. In Experiments 1 and 2, change detection was better for normal scenes than for jumbled scenes. In Experiment 3, inversion failed to interfere with change detection, demonstrating that the disruption of surface and object continuity inherent to jumbling is responsible for reduced change detection. These findings provide a crucial commonality between change detection research and theories of scene perception and neural representation. We also discuss why previous research may have failed to find effects of jumbling.
Endosomal entry regulates Notch receptor activation in Drosophila melanogaster
Authors: Vaccari Thomas , Lu Han , Kanwar Ritu , Fortini Mark E. , Bilder David
Published: February 2008

Signaling through the transmembrane receptor Notch is widely used throughout animal development and is a major regulator of cell proliferation and differentiation. During canonical Notch signaling, internalization and recycling of Notch ligands controls signaling activity, but the involvement of endocytosis in activation of Notch itself is not well understood. To address this question, we systematically assessed Notch localization, processing, and signaling in a comprehensive set of Drosophila melanogaster mutants that block access of cargo to different endocytic compartments. We find that γ-secretase cleavage and signaling of endogenous Notch is reduced in mutants that impair entry into the early endosome but is enhanced in mutants that increase endosomal retention. In mutants that block endosomal entry, we also uncover an alternative, low-efficiency Notch trafficking route that can contribute to signaling. Our data show that endosomal access of the Notch receptor is critical to achieve physiological levels of signaling and further suggest that altered residence in distinct endocytic compartments could underlie pathologies involving aberrant Notch pathway activation.