bluuebunny/crossref_metadata_2025 huggingface dataset:
The Humbling of ‘High Presumption’: Tobias Crisp Dismantles the Puritan Ordo Salutis
Authors: PARNHAM DAVID
Published: March 2005

Tobias Crisp presented a sophisticated, if highly tendentious, critique of the Puritan way to salvation. Having taken the view that the Puritan ordo salutis required of its practitioners a works-based devotion that sprang from a principal commitment to ‘law’ rather than ‘grace’, Crisp attacked both the theological and pastoral shortcomings of Puritanism. He then proceeded to develop a counter-theology of his own that promised a pastoral direction very different from that presided over by Puritan divines. This article addresses these dimensions of Crisp's discourse, and also assesses the self-defence mounted by Puritan respondents to Crisp.
Modeling the speciation and biogeochemistry of iron at the Bermuda Atlantic Time‐series Study site
Authors: Weber L. , Völker C. , Schartau M. , Wolf‐Gladrow D. A.
Published: March 2005

By means of numerical modeling, we analyze the cycling of iron between its various physical (dissolved, colloidal, particulate) and chemical (redox state and organic complexation) forms in the upper mixed layer. With our proposed model it is possible to obtain a first quantitative assessment of how this cycling influences iron uptake by phytoplankton and its loss via particle export. The model is forced with observed dust deposition rates, mixed layer depths, and solar radiation at the site of the Bermuda Atlantic Time‐series Study (BATS). It contains an objectively optimized ecosystem model which yields results close to the observational data from BATS that has been used for the data‐assimilation procedure. It is shown that the mixed layer cycle strongly influences the cycling of iron between its various forms. This is mainly due to the light dependency of photoreductive processes, and to the seasonality of primary production. The daily photochemical cycle is driven mainly by the production of superoxide, and its amplitude depends on the concentration and speciation of dissolved copper. Model results are almost insensitive to the dominant form of dissolved iron within dust deposition, and also to the form of iron that is taken up directly during algal growth. In our model solutions, the role of the colloidal pumping mechanism depends strongly on assumptions on the colloid aggregation and photoreduction rate.
Interactions of the iron and phosphorus cycles: A three‐dimensional model study
Authors: Dutkiewicz S. , Follows M. J. , Parekh P.
Published: March 2005

We use an ocean circulation, biogeochemistry, and ecosystem model to explore the interactions between ocean circulation, macro‐ and micro‐nutrient supply to the euphotic layer, and biological productivity. The model suggests a tight coupling between the degree of iron limitation in the upwelling subpolar and tropical oceans and the productivity of the adjacent subtropical gyres. This coupling is facilitated by lateral Ekman transfer of macro‐nutrients in the surface ocean. We describe a coarse resolution configuration of the MIT ocean circulation and biogeochemistry model in which there are fully prognostic representations of the oceanic cycles of phosphorus, iron, and silicon. The pelagic ecosystem is represented using two functional groups of phytoplankton and a single grazer. Using present‐day forcing, the model qualitatively captures the observed basin and gyre scale patterns of nutrient distributions and productivity. In a suite of sensitivity studies we find significant regional variations in response to changes in the aeolian iron supply. In a dustier (model) world, the Southern Ocean and Indo‐Pacific upwelling regions are more productive, but there is a decrease in productivity in the subtropical gyres and throughout the Atlantic basin. These results can be described most easily by a simple conceptual classification of the Southern and Indo‐Pacific oceans into two regimes: (1) upwelling, iron limited regions and (2) macro‐nutrient limited, oligotrophic subtropical gyres. Enhancing the aeolian iron supply to the upwelling regions relieves iron limitation and increases local primary and export production, but reduces the Ekman transfer of phosphate to the neighboring subtropical gyres. Consequently, over time, the gyres become further depleted in macro‐nutrients and productivity decreases in response to global scale iron fertilization. In a large‐scale analogy, the macro‐nutrient budget of the Atlantic is maintained by lateral transfer of nutrients in the upper ocean. Enhanced aeolian supply of iron leads to increased productivity in the Southern Ocean and Indo‐Pacific upwelling regions, reducing the lateral transfer of macro‐nutrients to the Atlantic basin, which becomes increasingly macro‐nutrient limited throughout.
Bending of the subducting oceanic plate and its implication for rupture propagation of large interplate earthquakes off Miyagi, Japan, in the Japan Trench subduction zone
Authors: Ito Aki , Fujie Gou , Miura Seiichi , Kodaira Shuichi , Kaneda Yoshiyuki , Hino Ryota
Published: March 2005

We present the results of an onshore–offshore wide‐angle refraction and reflection experiment off Miyagi, in the central Japan Trench forearc region. There are two rupture zones of large interplate earthquakes here: the landward rupture zone and the trenchward rupture zone. To examine the influence of plate boundary geometry on the distributions of the rupture zones, we determined reflector geometries from reflections. The subducting oceanic plate increases its dip from about 5° to 13° around 143.2°E. This bending point in the oceanic plate corresponds to the eastern edge of the trenchward rupture zone. Moreover, another bending point may be present at approximately 142.3°E, which corresponds to the eastern edge of the landward rupture zone. The coincidence between bending points in the oceanic plate and the edges of rupture zones suggests that changes in the plate boundary geometry may affect rupture propagation of interplate earthquakes in the direction of plate convergence.
Long‐range transport of ozone, carbon monoxide, and aerosols to the NE Pacific troposphere during the summer of 2003: Observations of smoke plumes from Asian boreal fires
Authors: Bertschi Isaac T. , Jaffe Daniel A.
Published: March 2005

Using a small aircraft, we conducted nine flights from 27 May through 5 August 2003 to collect vertical profiles of ozone, carbon monoxide, and total aerosol scattering in the 0–6 km column off the coast of Washington State. During 27 May, 2 June, and 5 August 2003 we observed air masses containing highly correlated and well‐defined layers of O3, CO, and aerosol enhancements within the 0–6 km column. The largest of these pollution episodes, or “events,” occurred on 2 June 2003 when O3 and CO mixing ratios exceeded 100 and 220 ppbv, respectively. A suite of meteorological data indicated that these polluted layers were not due to local sources. NOAA Hysplit backward trajectories indicate that the polluted air masses originated from a vast region in Asia bounded by 35°–70°N and 70°–170°E and transited the Pacific Ocean at middle and upper latitudes to North America in 7–10 days. Satellite data and global aerosol transport models suggest that Siberian boreal fire emissions were the primary source of the three events. Our observations indicate that ozone and aerosol scattering enhancement ratios, O3/CO and σsp (550 nm)/CO ERs, during these episodes were relatively large and varied from 0.15 to 0.84 ppbv ppbv−1 and 0.24 to 1.24 Mm−1 ppbv−1, respectively. These observations coupled with ground‐based measurements suggest that under certain circumstances, Siberian smoke was transported to the surface and had a significant influence on regional air quality in western Washington State. Notably, the 2 June event coincides with a period when O3 concentrations exceeded the U.S. Environmental Protection Agency 8‐hour standard (>84 ppbv) in Enumclaw, Washington, and the 5 August event corresponded with air quality degradation in Seattle, Washington, when 24‐hour average fine particle (PM2.5) concentrations exceeded 18 μg m−3 during the first week of August.
Electron wave interferometry through an asymmetric Aharonov–Bohm ring
Authors: Hedin E. R. , Cosby R. M. , Joe Y. S. , Satanin A. M.
Published: March 2005

A nanoscale Aharonov–Bohm (AB) ring functioning as an electron wave interferometer is investigated. The total transmission through the ring is calculated as a function of electron energy and threaded magnetic flux for a fixed upper to lower arm length asymmetry ratio. In addition, we model the effects of an asymmetry in the arm transverse widths by inserting an attractive potential well (dot) in one arm. The combined transmission resonance effects as a function of these variables will be presented. It is shown that an attractive potential in one of the arms in the AB ring generates an asymmetric Fano resonance in the transmission. Our theoretical AB-ring model is compared qualitatively to experimental results from measurements of an asymmetric ring fabricated onto a GaAs∕AlGaAs heterostructure, where Fano resonance has been observed.
Vibronic fine structure in the absorption spectrum of oligothiophene thin films
Authors: Zhao Zhen , Spano Frank C.
Published: March 2005

A multimode Holstein Hamiltonian is used to describe optical excitations in quaterthiophene pinwheel aggregates. The Hamiltonian includes the coupling of excitons originating from the 1Ag→1Bu electronic transition to phonons originating from the five intramolecular vibrational modes known from oligothiophene solution absorption/emission spectroscopy. The resulting eigenstates with lowest energy are best described as hybrid polaron phonons. The polarons are formed by coupling excitons with the higher frequency (688, 1235, and 1551cm−1) vibrational modes, while the (optical) phonons arise from the lower frequency (161 and 333cm−1) modes. The polaron phonons are responsible for the fine structure defining the A1 band in the low-energy region of the absorption spectrum, ranging from the band origin to ≈1500cm−1 beyond. The calculated A1 band of quaterthiophene aggregates agrees favorably with that observed from thin films.
Adsorption of multiblock copolymers onto a chemically heterogeneous surface: A model of pattern recognition
Authors: Kriksin Yury A. , Khalatur Pavel G. , Khokhlov Alexei R.
Published: March 2005

We present a statistical mechanical model, which is used to investigate the adsorption behavior of two-letter (AB) copolymers on chemically heterogeneous surfaces. The surfaces with regularly distributed stripes of two types (A and B) and periodic multiblock copolymers (AℓBℓ)x are studied. It is assumed that A(B)-type segments selectively adsorb onto A(B)-type stripes. It is shown that the adsorption strongly depends on the copolymer sequence distribution and the arrangement of selectively adsorbing regions on the surface. The polymer-surface binding proceeds as a two-step process. At the first step, the copolymer having short blocks adsorbs onto the surface as an effective homopolymer, which does not feel chemical pattern. At the second step, when the polymer-surface attraction is sufficiently strong, the adsorbed chain adjusts its equilibrium conformation to reach the perfect bound state, thereby demonstrating ability for pattern recognition. The key element of this mechanism is the redistribution of strongly adsorbed copolymer diblocks AℓBℓ, which behave as surfactants, between multiple AB interfaces separating A and B stripes on the adsorbing surface. Such redistribution is accompanied by a well-pronounced decrease in the system entropy. We have found that marked pattern recognition is possible for copolymers with relatively short blocks at high polymer/surface affinities, beyond the adsorption threshold.
Rotationally inelastic scattering of HD from Cu(100) and Pd(111)
Authors: Shackman Leah C. , Sitz Greg O.
Published: March 2005

Rotational excitation of HD scattered from Cu(100), Pd(111), and Pd(111):H(D) was measured using molecular beam and quantum-state-specific laser spectroscopy techniques. Greater than 91% of the incident HD population was in the v=0, J=0 state. The final rotational distributions from Cu(100), Pd(111), and Pd(111):H(D) were compared for a HD beam at an incident energy of 74meV. For all the three surfaces studied, rotationally inelastic scattering probabilities were large. We find that the final HD rotational distributions are remarkably similar for the three surfaces even though Pd(111) is very reactive to dissociative adsorption of HD whereas Cu(100) and Pd(111):H(D) are chemically inert.
Computing the Soret coefficient in aqueous mixtures using boundary driven nonequilibrium molecular dynamics
Authors: Nieto-Draghi Carlos , Ávalos Josep Bonet , Rousseau Bernard
Published: March 2005

We have computed the Soret coefficient in aqueous mixtures using a boundary driven nonequilibrium molecular dynamics algorithm and standard molecular force fields. The choice of this specific approach is justified by the nature of the mixtures studied here. Four aqueous solutions, including methanol, ethanol, acetone, and dimethyl-sulfoxide (DMSO) have been studied at ambient conditions for different compositions. The experimental behavior of water-alcohol mixtures was reproduced, including the change of sign of the Soret coefficient with composition, in excellent agreement with existing experimental data. The methodology has been applied to obtain pure predictions for water-acetone and water-DMSO where no experimental data are accessible. A change of sign is also observed in the same range of composition as in water-alcohol mixtures. It is suggested that the nature and strength of the molecular interactions, rather than the mass or shape ratio of the components, dominates the behavior of the Soret coefficient versus composition for the aqueous associating mixtures studied here.
First principles study of the carbon-(silicon-) doped La13 clusters
Authors: Zhang Dong-Bo , Shen Jiang , Chen Nan-Xian
Published: March 2005

The structural stability and physical properties have been studied for carbon-(silicon-) doped La13 clusters using DMOL method based on density-functional theory. Doped La13 clusters prefer to be icosahedron. Substitutional doping with a carbon or silicon impurity makes some clusters closed electronic shell, especially in icosahedral isomers. Substitutional doping of icosahedral La13 clusters is found to be favorable at surface sites of clusters, especially for Si-doped La13 cluster, which is very likely to be formed during the doping process. In addition, the structural distortions due to the doping are discussed.
Relationship between density peaking, particle thermodiffusion, Ohmic confinement, and microinstabilities in ASDEX Upgrade L-mode plasmas
Authors: Angioni C. , Peeters A. G. , Ryter F. , Jenko F. , Conway G. D. , Dannert T. , Fahrbach H. U. , Reich M. , Suttrop W. , Team ASDEX Upgrade , Fattorini L.
Published: March 2005

New experimental results obtained in ASDEX Upgrade [O. Gruber, H.-S. Bosch, S. Günter et al., Nucl. Fusion 39, 1321 (1999)] plasmas in low confinement mode with central electron cyclotron heating are presented in which transitions in both the particle and electron heat transport properties have been observed. A comprehensive albeit qualitative explanation for both the transport channels is provided in the framework of the theory of ion temperature gradient and trapped electron mode microinstabilities. The different transport behaviors are related to the dominant instability at play and to the collisionality regime. In particular, central electron heating induces a flattening of the density profile when the dominant instability is a trapped electron mode, and density peaking is observed to increase with decreasing collisionality.
Luminescence properties of defects in GaN
Authors: Reshchikov Michael A. , Morkoç Hadis
Published: March 2005

Gallium nitride (GaN) and its allied binaries InN and AIN as well as their ternary compounds have gained an unprecedented attention due to their wide-ranging applications encompassing green, blue, violet, and ultraviolet (UV) emitters and detectors (in photon ranges inaccessible by other semiconductors) and high-power amplifiers. However, even the best of the three binaries, GaN, contains many structural and point defects caused to a large extent by lattice and stacking mismatch with substrates. These defects notably affect the electrical and optical properties of the host material and can seriously degrade the performance and reliability of devices made based on these nitride semiconductors. Even though GaN broke the long-standing paradigm that high density of dislocations precludes acceptable device performance, point defects have taken the center stage as they exacerbate efforts to increase the efficiency of emitters, increase laser operation lifetime, and lead to anomalies in electronic devices. The point defects include native isolated defects (vacancies, interstitial, and antisites), intentional or unintentional impurities, as well as complexes involving different combinations of the isolated defects. Further improvements in device performance and longevity hinge on an in-depth understanding of point defects and their reduction. In this review a comprehensive and critical analysis of point defects in GaN, particularly their manifestation in luminescence, is presented. In addition to a comprehensive analysis of native point defects, the signatures of intentionally and unintentionally introduced impurities are addressed. The review discusses in detail the characteristics and the origin of the major luminescence bands including the ultraviolet, blue, green, yellow, and red bands in undoped GaN. The effects of important group-II impurities, such as Zn and Mg on the photoluminescence of GaN, are treated in detail. Similarly, but to a lesser extent, the effects of other impurities, such as C, Si, H, O, Be, Mn, Cd, etc., on the luminescence properties of GaN are also reviewed. Further, atypical luminescence lines which are tentatively attributed to the surface and structural defects are discussed. The effect of surfaces and surface preparation, particularly wet and dry etching, exposure to UV light in vacuum or controlled gas ambient, annealing, and ion implantation on the characteristics of the defect-related emissions is described.
Size-selected cluster beam source based on radio frequency magnetron plasma sputtering and gas condensation
Authors: Pratontep S. , Carroll S. J. , Xirouchaki C. , Streun M. , Palmer R. E.
Published: March 2005

We report on a source for producing size-selected nanoclusters based on the combination of radio frequency magnetron plasma sputtering and gas condensation. The use of plasma sputtering to vaporize a target is applicable to a large range of materials; Ag, Au, Cu, and Si have been attempted to date. The source, combined with a time-of-flight mass filter, can produce clusters in the size range from 2 up to at least 70 000 atoms, depending on the target material, with a constant mass (M) resolution (M∕ΔM∼25) at an intensity that produces atomic monolayer coverage in as little as a few minutes. The source is also attached to an ultrahigh vacuum analysis chamber, which allows in situ surface chemical and structural analysis. Examples of cluster deposition experiments with the source are also presented.
Spin current injection by intersubband transitions in quantum wells
Authors: Sherman E. Ya. , Najmaie Ali , Sipe J. E.
Published: March 2005

We show that a pure spin current can be injected in quantum wells by the absorption of linearly polarized infrared radiation, leading to transitions between subbands. The magnitude and the direction of the spin current depend on the Dresselhaus and Rashba spin–orbit coupling constants and light frequency and, therefore, can be manipulated by changing the light frequency and/or applying an external bias across the quantum well. The injected spin current should be observable either as a voltage generated via the anomalous spin-Hall effect, or by spatially resolved pump–probe optical spectroscopy.
Ultrabroadband (>2500cm−1) multiplex coherent anti-Stokes Raman scattering microspectroscopy using a supercontinuum generated from a photonic crystal fiber
Authors: Kano Hideaki , Hamaguchi Hiro-o
Published: March 2005

We have developed ultrabroadband multiplex coherent anti-Stokes Raman scattering (CARS) microspectroscopy using a coherent supercontinuum in the near-infrared region generated from a photonic crystal fiber. Owing to the ultrabroadband Stokes radiation obtained from the supercontinuum, multiple vibrational modes can be excited simultaneously in the wave-number range of more than 2500cm−1. A CARS imaging of a lipid vesicle is demonstrated with a high vibrational contrast.
F-doping effects on electrical and optical properties of ZnO nanocrystalline films
Authors: Xu H. Y. , Liu Y. C. , Mu R. , Shao C. L. , Lu Y. M. , Shen D. Z. , Fan X. W.
Published: March 2005

F-doped and undoped ZnO nanocrystalline films were prepared from thermal oxidation of ZnF2 films deposited on a silica substrate by electron beam evaporation. The F-doped ZnO film has very low electrical resistivity of 7.95×10−4Ωcm and a high optical transmittance. The study also indicated that (1) the substitutional F atoms in the film serve as donors to increase the carrier concentration and the optical band gap with respect to undoped ZnO film, and (2) F passivation reduces the known number of Os2−/Os− surface states and increases carrier mobility.
Midgap levels in both n- and p-type 4H–SiC epilayers investigated by deep level transient spectroscopy
Authors: Danno K. , Kimoto T. , Matsunami H.
Published: March 2005

Midgap levels in n- and p-type 4H–SiC epilayers have been investigated by deep level transient spectroscopy (DLTS). The EH6∕7 center (Ec−1.55eV) is the dominant midgap level as observed in DLTS spectra for n-type epilayers. The activation energy of EH6∕7 center is unchanged regardless of applied electric field, indicating that the charge state of the EH6∕7 center may be neutral after electron emission [acceptor-like (0∕−) trap]. In p-type epilayers, a deep level located at 1.49eV above the valence band edge has been detected. The lack of Poole–Frenkel effect in emission time constant from this deep level suggests that this level is donor-like (+∕0). From the energy level and charge state, this defect center may originate from a single carbon vacancy (VC), which has been extensively studied by electron paramagnetic resonance.
Electric-field-induced charge transfer between gold nanoparticle and capping 2-naphthalenethiol and organic memory cells
Authors: Ouyang Jianyong , Chu Chih-Wei , Sieves Douglas , Yang Yang
Published: March 2005

An electrical transition, induced by a high electric field, was observed in a device consisting of a polystyrene film containing 2-naphthalenethiol-capped Au nanoparticles sandwiched between two Al electrodes. The current through the device changed from a charge-injection-controlled current to a space-charge-limited current. The latter current is higher than the former by more than three orders of magnitude at 2 V. Asymmetrical current-voltage curve was observed along the two polarity directions for the device after the transition. This transition is attributed to an electric-field-induced charge transfer between the Au nanoparticle and the capping 2-naphthalenethiol. The device exhibits good stability in the high conductivity state, so it can be used as a write-once-read-many times electronic memory.
Stable ⩾8% efficient nanocrystalline dye-sensitized solar cell based on an electrolyte of low volatility
Authors: Wang Peng , Klein Cédric , Humphry-Baker Robin , Zakeeruddin Shaik M. , Grätzel Michael
Published: March 2005

We demonstrate a ⩾8% efficient nanocrystalline dye-sensitized solar cell retaining over 98% of its initial performance after 1000 h of accelerated tests subjected to thermal stress at 80 °C in the dark. Device degradation was also negligible following 1000 h of visible light soaking at 60 °C. This high performance and stable device was realized by using a robust electrolyte of low volatility in conjunction with the amphiphilic ruthenium sensitizer [Ru(4,4′-dicarboxylic acid-2,2′-bipyridine)(4,4′-bis(p-hexyloxystyryl)-2,2′-bipyridine)(NCS)2], coded as K-19, which was grafted together with 1-decylphosphonic acid on the mesoporous titania film acting as photoanode.
Waveguide structures in heavy metal oxide glass written with femtosecond laser pulses above the critical self-focusing threshold
Authors: Siegel J. , Fernández-Navarro J. M. , García-Navarro A. , Diez-Blanco V. , Sanz O. , Solis J. , Vega F. , Armengol J
Published: March 2005

We study the feasibility of femtosecond laser writing of optical waveguides in bulk 35PbO∙35Bi2O3∙15Ga2O3∙15GeO2 glass, motivated by the extended transparency interval of heavy metal oxide glasses in the mid-infrared regime. Its large linear and nonlinear refractive indices cause critical self-focusing to occur even at low laser energies, leading to filamentary propagation and material damage. However, the vicinity of the laser-damaged region shows a considerable increase in the refractive index, which we attribute to a collateral, stress-induced densification due to the high pressures generated in the focal region. These regions of increased refractive index are strongly birefringent and sufficiently large to support efficient light propagation in transversally written structures. Optical waveguides with a refractive index increase ⩾10−3 and minimal mode ellipticity have been obtained.
Colonic tumorigenesis in
BubR1
+/–
Apc

Min
/+

compound mutant mice is linked to premature separation of sister chromatids and enhanced genomic instability
Authors: Rao Chinthalapally V. , Yang Yang-Ming , Swamy Malisetty V. , Liu Tongyi , Fang Yuqiang , Mahmood Radma , Jhanwar-Uniyal Meena , Dai Wei
Published: March 2005

Faithful chromosome segregation is essential for the maintenance of genetic stability during cell division and it is at least partly monitored by the spindle checkpoint, a surveillance mechanism preventing the cell from prematurely entering anaphase. The adenomatous polyposis coli (
Apc
) gene also plays an important role in regulating genomic stability, as mutations of
Apc
cause aneuploidy. Here we show that whereas

Apc
Min

/+
mice developed many adenomatous polyps, mostly in the small intestine, by 3 mo of age;
BubR1
+/–

Apc
Min

/+
compound mutant mice developed 10 times more colonic tumors than

Apc
Min

/+
mice. The colonic tumors in
BubR1
+/–

Apc
Min

/+
mice were in higher grades than those observed in

Apc
Min

/+
mice. Consistently,
BubR1
+/–

Apc
Min

/+
murine embryonic fibroblasts (MEFs) contained more β-catenin and proliferated at a faster rate than WT or
BubR1
+/–
MEFs. Moreover,
BubR1
+/–

Apc
Min

/+
MEFs slipped through mitosis in the presence of nocodazole and exhibited a higher rate of genomic instability than that of WT or
BubR1
+/–
or

Apc
Min

/+
MEFs, accompanied by premature separation of sister chromatids. Together, our studies suggest that
BubR1
and
Apc
functionally interact in regulating metaphase–anaphase transition, deregulation of which may play a key role in genomic instability and development and progression of colorectal cancer.
From cyclohydrolase to oxidoreductase: Discovery of nitrile reductase activity in a common fold
Authors: Van Lanen Steven G. , Reader John S. , Swairjo Manal A. , de Crécy-Lagard Valérie , Lee Bobby , Iwata-Reuyl Dirk
Published: March 2005

The enzyme YkvM from
Bacillus subtilis
was identified previously along with three other enzymes (YkvJKL) in a bioinformatics search for enzymes involved in the biosynthesis of queuosine, a 7-deazaguanine modified nucleoside found in tRNA
GUN
of Bacteria and Eukarya. Genetic analysis of
ykvJKLM
mutants in
Acinetobacter
confirmed that each was essential for queuosine biosynthesis, and the genes were renamed
queCDEF
. QueF exhibits significant homology to the type I GTP cyclohydrolases characterized by FolE. Given that GTP is the precursor to queuosine and that a cyclohydrolase-like reaction was postulated as the initial step in queuosine biosynthesis, QueF was proposed to be the putative cyclohydrolase-like enzyme responsible for this reaction. We have cloned the
queF
genes from
B. subtilis
and
Escherichia coli
and characterized the recombinant enzymes. Contrary to the predictions based on sequence analysis, we discovered that the enzymes, in fact, catalyze a mechanistically unrelated reaction, the NADPH-dependent reduction of 7-cyano-7-deazaguanineto7-aminomethyl-7-deazaguanine, a late step in the biosynthesis of queuosine. We report here
in vitro
and
in vivo
studies that demonstrate this catalytic activity, as well as preliminary biochemical and bioinformatics analysis that provide insight into the structure of this family of enzymes.
Vibrational energy relaxation in proteins
Authors: Fujisaki Hiroshi , Straub John E.
Published: March 2005

An overview of theories related to vibrational energy relaxation (VER) in proteins is presented. VER of a selected mode in cytochromecis studied by using two theoretical approaches. One approach is the equilibrium simulation approach with quantum correction factors, and the other is the reduced model approach, which describes the protein as an ensemble of normal modes interacting through nonlinear coupling elements. Both methods result in similar estimates of the VER time (subpicoseconds) for a CD stretching mode in the protein at room temperature. The theoretical predictions are in accord with previous experimental data. A perspective on directions for the detailed study of time scales and mechanisms of VER in proteins is presented.
Evidence that
CRABS CLAW
and
TOUSLED
have conserved their roles in carpel development since the ancestor of the extant angiosperms
Authors: Fourquin Chloé , Vinauger-Douard Marion , Fogliani Bruno , Dumas Christian , Scutt Charles P.
Published: March 2005

The carpel is the female reproductive organ specific to flowering plants. We aim to define the genes that controlled carpel development in the common ancestor of this group as a step toward determining the molecular events that were responsible for the evolution of the carpel.
CRABS CLAW
(
CRC
) and
TOUSLED
(
TSL
) control important aspects of carpel development in the model plant,
Arabidopsis thaliana
. The basal angiosperm species
Amborella trichopoda
and
Cabomba aquatica
very likely represent the two most early diverging groups of flowering plants. We have identified putative orthologues of
CRC
and
TSL
from
A
.
trichopoda and C
.
aquatica
, respectively. We demonstrate the expression patterns of these genes in carpels to be very highly conserved, both spatially and temporally, with those of their
Arabidopsis
orthologues. We argue that
CRC
and
TSL
in
Arabidopsis
are likely to have conserved their respective roles in carpel development since the common ancestor of the living flowering plants. We conclude that a divergent role shown for the
CRC
orthologue in rice,
DROOPING LEAF
, most probably arose specifically in the monocot lineage. We show that, in addition to its expression in carpels, the
TSL
orthologue of
C
.
aquatica
is expressed in tissues that contribute to buoyancy and argue that its role in these tissues may have arisen later than its role in carpel development.
Juxtaposition of C(2)M and the transverse filament protein C(3)G within the central region of
Drosophila
synaptonemal complex
Authors: Anderson Lorinda K. , Royer Suzanne M. , Page Scott L. , McKim Kim S. , Lai Ann , Lilly Mary A. , Hawley R. Scott
Published: March 2005

The synaptonemal complex (SC) is intimately involved in the process of meiotic recombination in most organisms, but its exact role remains enigmatic. One reason for this uncertainty is that the overall structure of the SC is evolutionarily conserved, but many SC proteins are not. Two putative SC proteins have been identified in
Drosophila
: C(3)G and C(2)M. Mutations in either gene cause defects in SC structure and meiotic recombination. Although neither gene is well conserved at the amino acid level, the predicted secondary structure of C(3)G is similar to that of transversefilament proteins, and C(2)M is a distantly related member of the α-kleisin family that includes Rec8, a meiosis-specific cohesin protein. Here, we use immunogold labeling of SCs in
Drosophila
ovaries to localize C(3)G and C(2)M at the EM level. We show that both C(3)G and C(2)M are components of the SC, that the orientation of C(3)G within the SC is similar to other transverse-filament proteins, and that the N terminus of C(2)M is located in the central region adjacent to the lateral elements (LEs). Based on our data and the known phenotypes of C(2)M and C(3)G mutants, we propose a model of SC structure in which C(2)M links C(3)G to the LEs.
Inhibitors of type II NADH:menaquinone oxidoreductase represent a class of antitubercular drugs
Authors: Weinstein Edward A. , Yano Takahiro , Li Lin-Sheng , Avarbock David , Avarbock Andrew , Helm Douglas , McColm Andrew A. , Duncan Ken , Lonsdale John T. , Rubin Harvey
Published: March 2005

Mycobacterium tuberculosis
(Mtb) is an obligate aerobe that is capable of long-term persistence under conditions of low oxygen tension. Analysis of the Mtb genome predicts the existence of a branched aerobic respiratory chain terminating in a cytochrome
bd
system and a cytochrome

aa
3

system. Both chains can be initiated with type II NADH:menaquinone oxidoreductase. We present a detailed biochemical characterization of the aerobic respiratory chains from Mtb and show that phenothiazine analogs specifically inhibit NADH:menaquinone oxidoreductase activity. The emergence of drug-resistant strains of Mtb has prompted a search for antimycobacterial agents. Several phenothiazines analogs are highly tuberculocidal
in vitro
, suppress Mtb growth in a mouse model of acute infection, and represent lead compounds that may give rise to a class of selective antibiotics.
Lack of heme synthesis in a free-living eukaryote
Authors: Rao Anita U. , Carta Lynn K. , Lesuisse Emmanuel , Hamza Iqbal
Published: March 2005

In most free-living eukaryotes studied thus far, heme is synthesized from a series of intermediates through a well defined evolutionarily conserved pathway. We found that free-living worms, including the model genetic organism
Caenorhabditis elegans
, and parasitic helminths are unable to synthesize heme
de novo
, even though these animals contain hemoproteins that function in key biological processes. Radioisotope, fluorescence labeling, and heme analog studies suggest that
C. elegans
acquires heme from exogenous sources. Iron-deprived worms were unable to grow in the presence of adequate heme unless rescued by increasing heme levels in the growth medium. These data indicate that although worms use dietary heme for incorporation into hemoproteins, ingested heme is also used as an iron source when iron is limiting. Our results provide a biochemical basis for the dependence of worm growth and development on heme, and they suggest that pharmacologic targeting of heme transport pathways in worms could be an important control measure for helminthic infections.
Bargaining Community exemptions: the role of Italian actors in the negotiation of state aid to labour and industry
Authors: Giraudi Giorgio
Published: March 2005

This article analyses the role of Italian (institutional and non-institutional) actors in the area of state aid to labour and industry, two particularly sensitive European policies. The comparison between two decisions—the one concerning state incentives for youth employment and the other concerning the double recapitalization of Alitalia—allows the author to conclude that Italian policy preferences are best promoted when a viable compromise solution is first reached domestically and then pushed through the Union, and when Italian actors manage to argue their case in EU-compatible terms.
Investigation of a new intervention for children with word‐finding problems
Authors: Best Wendy
Published: March 2005

Background: Around one‐quarter of children attending language support services have difficulty in retrieving words. Therapy studies with such children have shown that both semantic and phonological techniques can improve word finding. A new approach to intervention is described using a computerized aid that converts letters into sound cues.

Aims: (1) To assess the word‐finding abilities in a small series of children with word‐finding difficulties. (2) To investigate whether intervention with a computerized aid can improve children's ability to find words. (3) To evaluate the effect of therapy on connected speech (using the Test of Word Finding in Discourse) and in relation to children's, parents' and other practitioners' views (using a questionnaire). (4) To understand the outcome in relation to an interactive model of speech production.

Methods & Procedures: Five children (aged 6:10–10:7) were assessed on a variety of background measures. Following baseline assessment, two sets of items were included in therapy: a research set (with matched control items) and a further set selected for their functional relevance for each child. Intervention using the computerized aid took place once a week for half a term (6 weeks).

Outcomes & Results: The children differed from one another in their language development and non‐verbal abilities, but all had difficulties in word retrieval. All children showed significant improvement in naming intervention items after therapy. This effect was maintained half a term later. Despite very different profiles, the children benefited similarly from the intervention, suggesting a common processing source for change. After the intervention, two children showed a significant reduction in word‐finding behaviours (e.g. use of substitutions, repetitions and empty words) on the Test of Word Finding in Discourse. The views of participants, parents and professionals were varied but generally positive.

Conclusions: The main effect of therapy can be understood, in relation to an interactive model of speech production, as strengthening links from meaning to form. Use of the aid in therapy improved word finding for targeted items and this occurred within a clinically realistic timeframe. The finding that the gains in word retrieval maintained suggests that the intervention can be functionally useful if target items are chosen appropriately. Measurable change for two children in connected speech suggests wider benefits can also occur. Overall, the aid can be a useful additional tool for therapists/teachers working with children with this difficulty.
Inhibition of NGF deprivation–induced death by low oxygen involves suppression of BIMEL and activation of HIF-1
Authors: Xie Liang , Johnson Randall S. , Freeman Robert S.
Published: March 2005

Changes in O2 tension can significantly impact cell survival, yet the mechanisms underlying these effects are not well understood. Here, we report that maintaining sympathetic neurons under low O2 inhibits apoptosis caused by NGF deprivation. Low O2 exposure blocked cytochrome c release after NGF withdrawal, in part by suppressing the up-regulation of BIMEL. Forced BIMEL expression removed the block to cytochrome c release but did not prevent protection by low O2. Exposing neurons to low O2 also activated hypoxia-inducible factor (HIF) and expression of a stabilized form of HIF-1α (HIF-1αPP→AG) inhibited cell death in normoxic, NGF-deprived cells. Targeted deletion of HIF-1α partially suppressed the protective effect of low O2, whereas deletion of HIF-1α combined with forced BIMEL expression completely reversed the ability of low O2 to inhibit cell death. These data suggest a new model for how O2 tension can influence apoptotic events that underlie trophic factor deprivation–induced cell death.
CFTR Gating I
Authors: Bompadre Silvia G. , Ai Tomohiko , Cho Jeong Han , Wang Xiaohui , Sohma Yoshiro , Li Min , Hwang Tzyh-Chang
Published: March 2005

The CFTR chloride channel is activated by phosphorylation of serine residues in the regulatory (R) domain and then gated by ATP binding and hydrolysis at the nucleotide binding domains (NBDs). Studies of the ATP-dependent gating process in excised inside-out patches are very often hampered by channel rundown partly caused by membrane-associated phosphatases. Since the severed ΔR-CFTR, whose R domain is completely removed, can bypass the phosphorylation-dependent regulation, this mutant channel might be a useful tool to explore the gating mechanisms of CFTR. To this end, we investigated the regulation and gating of the ΔR-CFTR expressed in Chinese hamster ovary cells. In the cell-attached mode, basal ΔR-CFTR currents were always obtained in the absence of cAMP agonists. Application of cAMP agonists or PMA, a PKC activator, failed to affect the activity, indicating that the activity of ΔR-CFTR channels is indeed phosphorylation independent. Consistent with this conclusion, in excised inside-out patches, application of the catalytic subunit of PKA did not affect ATP-induced currents. Similarities of ATP-dependent gating between wild type and ΔR-CFTR make this phosphorylation-independent mutant a useful system to explore more extensively the gating mechanisms of CFTR. Using the ΔR-CFTR construct, we studied the inhibitory effect of ADP on CFTR gating. The Ki for ADP increases as the [ATP] is increased, suggesting a competitive mechanism of inhibition. Single channel kinetic analysis reveals a new closed state in the presence of ADP, consistent with a kinetic mechanism by which ADP binds at the same site as ATP for channel opening. Moreover, we found that the open time of the channel is shortened by as much as 54% in the presence of ADP. This unexpected result suggests another ADP binding site that modulates channel closing.
Differential Effects of β1 and β2 Subunits on BK Channel Activity
Authors: Orio Patricio , Latorre Ramon
Published: March 2005

High conductance, calcium- and voltage-activated potassium (BK) channels are widely expressed in mammals. In some tissues, the biophysical properties of BK channels are highly affected by coexpression of regulatory (β) subunits. β1 and β2 subunits increase apparent channel calcium sensitivity. The β1 subunit also decreases the voltage sensitivity of the channel and the β2 subunit produces an N-type inactivation of BK currents. We further characterized the effects of the β1 and β2 subunits on the calcium and voltage sensitivity of the channel, analyzing the data in the context of an allosteric model for BK channel activation by calcium and voltage (Horrigan and Aldrich, 2002). In this study, we used a β2 subunit without its N-type inactivation domain (β2IR). The results indicate that the β2IR subunit, like the β1 subunit, has a small effect on the calcium binding affinity of the channel. Unlike the β1 subunit, the β2IR subunit also has no effect on the voltage sensitivity of the channel. The limiting voltage dependence for steady-state channel activation, unrelated to voltage sensor movements, is unaffected by any of the studied β subunits. The same is observed for the limiting voltage dependence of the deactivation time constant. Thus, the β1 subunit must affect the voltage sensitivity by altering the function of the voltage sensors of the channel. Both β subunits reduce the intrinsic equilibrium constant for channel opening (L0). In the allosteric activation model, the reduction of the voltage dependence for the activation of the voltage sensors accounts for most of the macroscopic steady-state effects of the β1 subunit, including the increase of the apparent calcium sensitivity of the BK channel. All allosteric coupling factors need to be increased in order to explain the observed effects when the α subunit is coexpressed with the β2IR subunit.
Bacteria recovered from dental pulp induce apoptosis of lymph node cells
Authors: Ribeiro-Sobrinho A P , Rabelo F LA , Figueiredo C BO , Alvarez-Leite J I , Nicoli J R , Uzeda M , Vieira L Q
Published: March 2005

Apoptosis is critical in the pathogenesis of several infectious diseases. The induction of apoptosis was assessed in mouse lymph node cells by four bacteria recovered from infected human dental pulp:Gemella morbillorum,Clostridium butyricum,Fusobacterium nucleatumandBifidobacterium adolescentis. Smaller lymph nodes and smaller numbers of cells were observed after experimental dental pulp infection withC. butyricum, suggesting that this bacterium induces cell death. Apoptosis was evaluated by determination of cell ploidy and detection of DNA degradation in cells cultured with killed bacteria. Paraformaldehyde-killedC. butyricumand heat-killedG. morbilloruminduced substantial cell death, whileF. nucleatumandB. adolescentisinduced cell death at lower levels. No bacterial preparations induced apoptosis in cells from mice genetically deficient for tumour necrosis factor receptor p55 (TNFRp55), implicating this receptor directly or indirectly as a mediator in the process. It was concluded that apoptosis may be induced during periapical lesions of pulpal origin.
Role of interleukin-18 in experimental infections with Streptococcus pneumoniae
Authors: Paterson G K , Blue C E , Mitchell T J
Published: March 2005

IL-18, a multifunctional cytokine, has been shown to be involved in the immune response to numerous pathogens including several bacterial species. To study its role in infection by the Gram-positive bacteriumStreptococcus pneumoniae, wild-type and IL-18 knockout BALB/c mice were compared in murine models of pneumococcal pneumonia, bacteraemia and nasopharyngeal colonization. The influence of IL-18 varied with the infection type, whereby it contributed to increased bacterial loads in pneumonia, reduced levels of colonization and had no effect on levels of bacteraemia following intravenous challenge. Likewise, the influence of IL-18 on pneumonia varied between two infecting pneumococcal strains. Comparison of these results with previous data also suggested that the influence of IL-18 in pneumococcal pneumonia differs with the mouse strain genetic background. Overall, these results demonstrate the complex influence of IL-18 in the response to the pneumococcus.
The bHLH factor Olig3 coordinates the specification of dorsal neurons in the spinal cord
Authors: Müller Thomas , Anlag Katrin , Wildner Hendrik , Britsch Stefan , Treier Mathias , Birchmeier Carmen
Published: March 2005

Neurons of the dorsal horn integrate and relay sensory information and arise during development in the dorsal spinal cord, the alar plate. Class A and B neurons emerge in the dorsal and ventral alar plate, differ in their dependence on roof plate signals for specification, and settle in the deep and superficial dorsal horn, respectively. We show here that the basic helix-loop-helix (bHLH) gene Olig3 is expressed in progenitor cells that generate class A (dI1-dI3) neurons and that Olig3 is an important factor in the development of these neuronal cell types. In Olig3 mutant mice, the development of class A neurons is impaired; dI1 neurons are generated in reduced numbers, whereas dI2 and dI3 neurons are misspecified and assume the identity of class B neurons. Conversely, Olig3 represses the emergence of class B neurons in the chick spinal cord. We conclude that Olig3 expression distinguishes the two major classes of progenitors in the dorsal spinal cord and determines the distinct specification program of class A neurons.
SIR2004: an improved tool for crystal structure determination and refinement
Authors: Burla Maria C. , Caliandro Rocco , Camalli Mercedes , Carrozzini Benedetta , Cascarano Giovanni L. , De Caro Liberato , Giacovazzo Carmelo , Polidori Giampiero , Spagna Riccardo
Published: March 2005

SIR2004is the evolution of theSIR2002program [Burla, Camalli, Carrozzini, Cascarano, Giacovazzo, Polidori & Spagna (2003).J. Appl. Cryst.36, 1103]. It is devoted to the solution of crystal structures by direct and Patterson methods. Several new features implemented inSIR2004make this program efficient: it is able to solveab initioboth small/medium-size structures as well as macromolecules (up to 2000 atoms in the asymmetric unit). In favourable circumstances, the program is also able to solve protein structures with data resolution up to 1.4–1.5 Å, and to provide interpretable electron density maps. A powerful user-friendly graphical interface is provided.