bluuebunny/crossref_metadata_2025 huggingface dataset:
Microwave performance of high-density bulk MgB2
Authors: Findikoglu A. T. , Serquis A. , Civale L. , Liao X. Z. , Zhu Y. T. , Hawley M. E. , Mueller F. M. , Nesterenko V. F. , Gu Y.
Published: July 2003

We have performed microwave measurements on superconducting hot-isostatically pressed (HIPed) bulk MgB2 using a parallel-plate resonator technique. The high density and strength of the HIPed material allowed preparation of samples with mirror-like surfaces for microwave measurements. The microwave effective surface resistance Rs decreased by about 40% at 20 K when the root-mean-square surface roughness was reduced from 220 to 110 nm through surface polishing and ion milling. The Rs was independent of surface microwave magnetic field at least up to 4 Oe and below 30 K. We attribute this behavior, and the overall low Rs (∼0.8 mΩ at 10 GHz and 20 K), to the high density of our samples and the absence of weak links between grains.
Magnetoresistance measurement of unpatterned magnetic tunnel junction wafers by current-in-plane tunneling
Authors: Worledge D. C. , Trouilloud P. L.
Published: July 2003

We demonstrate a method for measuring magnetoresistance (MR) and resistance area product (RA) of unpatterned magnetic tunnel junction film stacks. The RA is measured by making a series of four point probe resistance measurements on the surface of an unpatterned wafer at various probe spacings. The key to this technique is in placing the probes at the appropriate spacings, on the order of microns for typical applications. The MR is obtained by repeating the measurement at different magnetic fields. A simple conceptual model and an exact analytical solution in good agreement with experimental data are presented. The current-in-plane tunneling method requires no processing, is fast, and provides reliable data which are reflective of the deposition only.
GaAs metal–oxide–semiconductor field-effect transistor with nanometer-thin dielectric grown by atomic layer deposition
Authors: Ye P. D. , Wilk G. D. , Yang B. , Kwo J. , Chu S. N. G. , Nakahara S. , Gossmann H.-J. L. , Mannaerts J. P. , Hong M. , Ng K. K. , Bude J.
Published: July 2003

A GaAs metal–oxide–semiconductor field-effect transistor (MOSFET) with thin Al2O3 gate dielectric in nanometer (nm) range grown by atomic layer deposition is demonstrated. The nm-thin oxide layer with significant gate leakage current suppression is one of the key factors in downsizing field-effect transistors. A 1 μm gate-length depletion-mode n-channel GaAs MOSFET with an Al2O3 gate oxide thickness of 8 nm, an equivalent SiO2 thickness of ∼3 nm, shows a broad maximum transconductance of 120 mS/mm and a drain current of more than 400 mA/mm. The device shows a good linearity, low gate leakage current, and negligible hysteresis in drain current in a wide range of bias voltage.
Magnetism of Co-doped titania thin films prepared by spray pyrolysis
Authors: Manivannan A. , Seehra M. S. , Majumder S. B. , Katiyar R. S.
Published: July 2003

Co-doped TiO2 (anatase) films prepared by spray pyrolysis at 500 °C are investigated for the possible existence of room temperature ferromagnetism (RTF). These films were characterized by x-ray diffraction, Raman spectroscopy, and x-ray photoelectron spectroscopy at room temperature, followed by studies of the temperature and magnetic field dependence of the magnetization by squid magnetometry. For Co doping of upto 10 at. %, no phase other than anatase could be detected, and there is no RTF in these films. Instead, the magnetic susceptibility χ fits the modified Curie–Weiss law χ=χ0+C/(T+θ), with θ≃5 K and magnitude of C consistent with Co2+ paramagnetism in Ti1−xCoxO2−x. Only for T⩽5 K, a hysteresis loop with coercivity Hc=200 Oe is observed. These observations suggest Co2+ paramagnetism, with exchange interaction becoming important for T⩽5 K in the case of 10% Co/TiO2 films.
Competing step instabilities at surfaces under stress
Authors: Léonard François , Tersoff J.
Published: July 2003

We compare the different instability modes of a vicinal (stepped) surface under stress, for permeable as well as impermeable steps. With increasing step spacing, there is a crossover of the dominant stress-driven instability from step bunching to step undulation. The step spacing for this crossover depends exponentially on the stress. Atom attachment barriers tend to suppress these stress-driven instabilities.
Dependence of soft x-ray conversion on atomic composition in laser produced plasma of gold–copper mix-Z targets
Authors: Chakera J. A. , Arora V. , Sailaja S. , Kumbhare S. R. , Naik P. A. , Gupta P. D. , Gupta N. K. , Godwal B. K.
Published: July 2003

A comparative experimental study of soft x-ray emission from laser-irradiated Au–Cu mix-Z targets of different atomic compositions has been performed. Plasma was produced from planar targets using second-harmonic laser pulses from an Nd:glass laser at a focused intensity of ∼1013 W cm−2. Radiation intensity in the spectral region ∼15–150 Å and integrated x-ray yield for mix-Z target were observed to be higher than those for individual elements. The maximum conversion occurred for an atomic composition of Au 0.43–Cu 0.57. These observations are consistent with the variation of Rosseland mean opacity with atomic composition calculated using a screened hydrogenic average atom model.
Photoluminescence enhancement by inductively coupled argon plasma exposure for quantum-well intermixing
Authors: Djie H. S. , Mei T. , Arokiaraj J.
Published: July 2003

The exposure of InGaAs/InGaAsP quantum-well (QW) structures to argon (Ar) plasma in an inductively coupled system has been studied. An increase in photoluminescence (PL) intensity without PL peak shift was observed for 5-min Ar plasma exposure compared to the as-grown sample. The exposure creates point defects, and upon rapid thermal annealing produces intermixing between barriers and QWs, resulting in the blueshift of QWs. A selective intermixing using a 200-nm-thick of SiO2 layer as an intermixing mask exhibited a differential band-gap blueshift of 86 nm, with a differential linewidth broadening of 0.3 nm between masked and unmasked section. The improvement of PL intensity in combination with selective intermixing process can pave the way for high-quality hybrid photonic and optoelectronic integrated circuits.
Realization of p-type ZnO thin films via phosphorus doping and thermal activation of the dopant
Authors: Kim Kyoung-Kook , Kim Hyun-Sik , Hwang Dae-Kue , Lim Jae-Hong , Park Seong-Ju
Published: July 2003

A p-type ZnO was prepared on a sapphire substrate using P2O5 as a phosphorus dopant. As-grown n-type ZnO films doped with phosphorus showed electron concentrations of 1016–1017/cm3 and these films were converted to p-type ZnO by a thermal annealing process at a temperature above 800 °C under a N2 ambient. The electrical properties of the p-type ZnO showed a hole concentration of 1.0×1017–1.7×1019/cm3, a mobility of 0.53–3.51 cm2/V s, and a low resistivity of 0.59–4.4 Ω cm. The phosphorus-doped ZnO thin films showed a strong photoluminescence peak at 3.35 eV at 10 K, which is closely related to neutral acceptor bound excitons of the p-type ZnO. This thermal activation process was very reproducible and effective in producing phosphorus-doped p-type ZnO thin films, and the produced p-type ZnO was very stable.
Reduced reflectance cathode for organic light-emitting devices using metalorganic mixtures
Authors: Aziz Hany , Liew Yoon-Fei , Michelle Grandin H. , Popovic Zoran D.
Published: July 2003

Conductive light-absorbing layers made of mixtures of metals and organic materials are used as cathodes in organic light-emitting devices (OLEDs). Devices utilizing the reduced reflectance cathode, named Black Cathode™ OLEDs, demonstrate enhanced contrast even in high ambient illumination. OLEDs with a cathode made of a mixture of tris(8-hydroxyquinoline)aluminum (Alq3), Mg and Ag, or a mixture of Alq3 and Ag are addressed. Optical reflectance and absorption measurements as well as OLED electrical characterization tests are performed on various Black Cathode OLEDs and also on reference device with standard Mg:Ag cathode. The studied Black Cathode OLEDs demonstrate ∼9%–12% sun/eye-integrated reflectance (SEIR), ∼8× lower than that of the reference device, while device turn-on voltage and stability are comparable. In modified Black Cathode OLEDs, ∼1.8% SEIR has been recently realized.
Optical recombination of ZnO nanowires grown on sapphire and Si substrates
Authors: Zhao Q. X. , Willander M. , Morjan R. E. , Hu Q-H. , Campbell E. E. B.
Published: July 2003

ZnO nanowires have been grown on sapphire and Si substrates using catalytic growth. A strong near-band-gap ultraviolet emission is observed at room temperature. By carefully studying the temperature dependence of ZnO wire emission, we found that the room-temperature UV emission contains two different transitions; one is related to the ZnO free exciton and the other is related to the free-to-bound transition. The bound state has a binding energy of about 124 meV. The results from optical measurements show that a high quality of ZnO nanowires grown on sapphire and Si substrates has been achieved.
Mesoscale x-ray diffraction measurement of stress relaxation associated with buckling in compressed thin films
Authors: Goudeau Philippe , Villain Pascale , Tamura Nobumichi , Padmore Howard A.
Published: July 2003

Compressed thin films deposited on substrates may buckle depending on the geometrical and mechanical properties of the film/substrate set. Until recently, the small dimensions of the buckling have prevented measurements of their local in plane internal stress distribution. Using a scanning x-ray microdiffraction technique developed at a third generation x-ray synchrotron source, we obtained thin film internal stress maps for circular blisters and telephone chord buckling with micrometric spatial resolution. A fair agreement was found between the film delamination topology observed by optical microscopy and the measured stress maps. We evidenced residual stress relaxation associated with the film buckling: the top is essentially stress free while adherent region exhibits large compressive stresses.
Single-photon routing by time-division phase modulation in a Sagnac interferometer
Authors: Zhou Chunyuan , Wu Guang , Ding Liang’en , Zeng Heping
Published: July 2003

In this letter, we report the experimental demonstration of a single-photon router based on a time-division Sagnac interferometer, wherein differential phase shifts are applied on either the clockwise or counterclockwise quasi-single-photon pulses to determine the single photon interference and consequently output photon routing. High fidelity (>85%) of single-photon routing was demonstrated over a long-distance Sagnac loop. Stable performance was guaranteed by passive compensation of stress and temperature dependent drifts of the fiber-optic path. Experimental data show that time-division single-photon routing can be realized by controlling the applied electric pulses on the integrated phase modulators in the Sagnac loop, which makes this setup suitable for a practical quantum cryptography system.
Terahertz plasmonic high pass filter
Authors: Wu Dongmin , Fang Nicholas , Sun Cheng , Zhang Xiang , Padilla Willie J. , Basov Dimitri N. , Smith David R. , Schultz Sheldon
Published: July 2003

Metamaterials, which contain engineered subwavelength microstructures, can be designed to have positive or negative ε and μ at desired frequencies. In this letter, we demonstrate a metamaterial which has a “plasmonic” response to electromagnetic waves in the terahertz (THz) range. The sharp change of reflection and transmission at this plasma frequency makes the structure a high pass filter. The reflection response is characterized by Fourier transform infrared spectroscopy, and a plasma frequency at 0.7 THz is observed, which agrees with the theoretical calculation. The metamaterial is a two-dimensional cubic lattice consisting of thin metal wires, having wire diameter of 30 μm, lattice constant of 120 μm, and wire length of 1 mm. The microstereolithography technique is employed to fabricate the high-aspect-ratio lattice.
Attachment of DNA probes on gallium arsenide surface
Authors: Mohaddes-Ardabili Ladan , Martı́nez-Miranda Luz J. , Silverman Joseph , Christou Aristos , Salamanca-Riba Lourdes G. , Al-Sheikhly Mohamad , Bentley William E. , Ohuchi F.
Published: July 2003

Chemical attachment of the thiol-derivatized DNA monolayers on arsenic terminated GaAs (001) has been achieved. The sulfur-As-based covalent bonds of the thiolated oligonucleotids on the arsenic terminated GaAs (001) were observed using x-ray photoelectron spectroscopy. The purpose of our work is to investigate the self-assembly of thiol-derivatized single-stranded DNA oligonucleotides (probes) on GaAs substrate. In this letter, we demonstrate that both the S–H group in the thiolated single-strand DNA, and the N–H group in the DNA bases are functional groups that can be utilized to anchor the DNA molecule, or other biological molecules on the As-terminated GaAs surface.
High-performance and high-temperature continuous-wave-operation 1300 nm InGaAsN quantum well lasers by organometallic vapor phase epitaxy
Authors: Tansu Nelson , Quandt Andrew , Kanskar Manoj , Mulhearn William , Mawst Luke J.
Published: July 2003

Comtinuous-wave (cw) operation of organometallic vapor phase epitaxy-grown In0.4Ga0.6As0.995N0.005 quantum well (QW) lasers has been realized, at a room-temperature near-threshold emission wavelength of 1.295 μm, with a threshold-current density of 220 A/cm2 for 2000 μm cavity-length (Lcav) devices. A threshold current density of only 615 A/cm2 was achieved for cw operation at a temperature of 100 °C, with an emission wavelength of 1.331 μm. A maximum cw-output power of 1.8 W was obtained for InGaAsN QW lasers with cavity lengths of 1000 and 2000 μm, at a heat-sink temperature of 20 °C.
Electroacoustic properties of 〈110〉-oriented Pb(Mg1/3Nb2/3)O3–PbTiO3 crystals under uniaxial stress
Authors: Viehland D. , Li J. F. , Gittings K. , Amin A.
Published: July 2003

The electromechanical properties of 〈110〉-oriented 0.7Pb(Mg1/3Nb2/3)O3–0.3PbTiO3 crystals have been investigated under uniaxial stress (σ). 〈110〉-oriented crystals have a longitudinal electromechanical coupling coefficient (k33) of ∼0.9 and an acoustic power density of 12 dB which decreases to 8 dB with increasing σ between 0 and 4×107 N/m2. The results demonstrate that the advantages in terms of power density and coupling coefficient of oriented piezocrystals are not constrained to the 〈001〉-orientation, but rather can also be obtained along the 〈110〉.
In situ synthesis of superconducting MgB2 fibers within a magnesium matrix
Authors: DeFouw John D. , Dunand David C.
Published: July 2003

Composite wires, consisting of several hundred continuous MgB2 fibers embedded within an Mg matrix, are produced by a casting method, whereby liquid Mg is pressure infiltrated into a preform of aligned B fibers which are subsequently reacted in situ to form MgB2 fibers. Despite defects in the form of small, unreacted B islands and radial cracks from volume expansion, the MgB2 fibers exhibit superconducting properties (Tc=39 K and Jc=360 kA/cm2 at 5 K) comparable to the best results published for bulk MgB2. The fibers are cylindrical and straight, allowing high packing densities within a mechanically tough, thermally dissipating, electrically conductive Mg matrix. The process is scalable to continuous lengths of superconducting Mg/MgB2 wires.
Ratchet effect in an ac-current driven Josephson junction array
Authors: Lee K. H.
Published: July 2003

The current–voltage characteristics have been studied in an underdamped Josephson junction ratchet array driven by dc and ac current. A higher coupling strength along the direction of the vortex flow is used to guide vortices. As the ac current increases, the critical currents become dependent on the bias direction and the current–voltage curves become asymmetric. In some higher ac currents, nonzero voltage is shown even at zero-dc current. This off-center behavior is a rectifying effect of an applied ac current and a clear evidence of the directional motion of vortices.
Influences of the surface reactions on the field emission from multiwall carbon nanotubes
Authors: Dong Changkun , Gupta Mool C.
Published: July 2003

Field emission characteristics from multiwall carbon nanotubes were studied under various gas environments. The experiments on field emission revealed several surface reactions under high-vacuum operating conditions. The Fowler–Nordheim (F–N) analysis showed a field emission regime dominated by the surface adsorbents, operational modes, and nanotube types. The emission-assisted surface reaction process, which enhances the gas adsorptions in low current regimes and desorption under high currents, plays a key role for the observed deviation from the F–N results. Different gas exposures suggested that the nanotube-H2O and nanotube-H2 reactions cause the current increase in the low emission range.
Effect of antiferromagnetic interlayer coupling on current-assisted magnetization switching
Authors: Urazhdin S. , Kurt H. , Pratt W. P. , Bass J.
Published: July 2003

We compare magnetization switching in Co/Cu/Co nanopillars with uncoupled and dipole-field coupled Co layers. In uncoupled nanopillars, current-driven switching is hysteretic at low magnetic field H and changes to reversible, characterized by telegraph noise, at high H. We show that dipolar coupling both affects the switching current and causes the switching to become reversible at small H. The coupling thus changes the switching to reversible, hysteretic, and then reversible again as H increases. We describe our results in terms of current-assisted thermal activation.
Variational calculation of many-body wave functions and energies from density functional theory
Authors: Capelle K.
Published: July 2003

A generating coordinate is introduced into the exchange-correlation functional of density functional theory (DFT). The many-body wave function is represented as a superposition of Kohn–Sham (KS) Slater determinants arising from different values of the generating coordinate. This superposition is used to variationally calculate many-body energies and wave functions from solutions of the KS equation of DFT. The method works for ground and excited states, and does not depend on identifying the KS orbitals and energies with physical ones. Numerical application to the Helium isoelectronic series illustrates the method’s viability and potential.
Mixed Markov models
Authors: Fridman Arthur
Published: July 2003

Markov random fields can encode complex probabilistic relationships involving multiple variables and admit efficient procedures for probabilistic inference. However, from a knowledge engineering point of view, these models suffer from a serious limitation. The graph of a Markov field must connect all pairs of variables that are conditionally dependent even for a single choice of values of the other variables. This makes it hard to encode interactions that occur only in a certain context and are absent in all others. Furthermore, the requirement that two variables be connected unlessalwaysconditionally independent may lead to excessively dense graphs, obscuring the independencies present among the variables and leading to computationally prohibitive inference algorithms. Mumford [Mumford, D. (1996) inICIAM 95, eds. Kirchgassner, K., Marenholtz, O. & Mennicken, R. (Akademie Verlag, Berlin), pp. 233–256] proposed an alternative modeling framework where the graph need not be rigid and completely determineda priori. MixedMarkov models contain node-valued random variables that, when instantiated, augment the graph by a set of transient edges. A single joint probability distribution relates the values of regular and node-valued variables. In this article, we study the analytical and computational properties of mixed Markov models. In particular, we show that positive mixed models have a local Markov property that is equivalent to their global factorization. We also describe a computationally efficient procedure for answering probabilistic queries in mixed Markov models.
Nonvolatile read-out molecular memory
Authors: Liang Y. C. , Dvornikov A. S. , Rentzepis P. M.
Published: July 2003

A versatile molecule is described that performs as a nondestructible
read-out optical-storage molecular memory. This molecular memory is composed
of two distinct molecules that are chemically bonded to each other to form a
single molecule with unique properties. One component is a photochromic
fulgimide, and the other is a strongly fluorescing oxazine dye. This composite
molecule was specifically designed and synthesized to display, under specific
conditions, both the photochromic functions of the first component and the
fluorescence properties of the dye. To store information, the polar, closed
form of the photochromic component is illuminated with 530-nm light, which
converts it to the open, nonpolar form. The information is accessed by
excitation at the 650-nm band of the oxazine dye component, causing the dye to
fluoresce. However, the dye emits intense fluorescence under a nonpolar
environment, which is attained only when the fulgimide component is in its
open, nonpolar structure. The ultrafast kinetics, spectroscopy, and mechanism
of the photoreaction of this molecule and its photoinduced intermediates have
been measured, and fluorescence quantum yields and cross sections were
determined.
A Bayesian framework for combining heterogeneous data sources for gene function prediction (inSaccharomyces cerevisiae)
Authors: Troyanskaya Olga G. , Dolinski Kara , Owen Art B. , Altman Russ B. , Botstein David
Published: July 2003

Genomic sequencing is no longer a novelty, but gene function annotation remains a key challenge in modern biology. A variety of functional genomics experimental techniques are available, from classic methods such as affinity precipitation to advanced high-throughput techniques such as gene expression microarrays. In the future, more disparate methods will be developed, further increasing the need for integrated computational analysis of data generated by these studies. We address this problem withmagic(Multisource Association of Genes by Integration of Clusters), a general framework that uses formal Bayesian reasoning to integrate heterogeneous types of high-throughput biological data (such as large-scale two-hybrid screens and multiple microarray analyses) for accurate gene function prediction. The system formally incorporates expert knowledge about relative accuracies of data sources to combine them within a normative framework.magicprovides a belief level with its output that allows the user to vary the stringency of predictions. We appliedmagictoSaccharomyces cerevisiaegenetic and physical interactions, microarray, and transcription factor binding sites data and assessed the biological relevance of gene groupings using Gene Ontology annotations produced by theSaccaromycesGenome Database. We found that by creating functional groupings based on heterogeneous data types,magicimproved accuracy of the groupings compared with microarray analysis alone. We describe several of the biological gene groupings identified.
Ba
2
LnSbO
6
and Sr
2
LnSbO
6
(Ln = Dy, Ho, Gd) double perovskites: Lanthanides in the geometrically frustrating fcc lattice
Authors: Karunadasa H. , Huang Q. , Ueland B. G. , Schiffer P. , Cava R. J.
Published: July 2003

Magnetic ground states in solids often arise as a result of a delicate
balance between competing factors. One currently active area of research in
magnetic materials involves compounds in which long-range magnetic ordering at
low temperatures is frustrated by the geometry of the crystalline lattice, a
situation known as geometrical magnetic frustration. The number of systems
known to display the effects of such frustration is growing, but those that
are sufficiently simple from theoretical, chemical, and physical perspectives
to allow for detailed understanding remain very few. A search for model
compounds in this family has led us to the double perovskites
Ba
2
LnSbO
6
and Sr
2
LnSbO
6
(Ln = Dy,
Ho, and Gd) reported here.
Ba
2
DySbO
6
,Ba
2
HoSbO
6
,Sr
2
DySbO
6
,
and Sr
2
HoSbO
6
are structurally characterized by powder
neutron diffraction at ambient temperature. The trivalent lanthanides and
pentavalent antimony are found to be fully ordered in the double-perovskite
arrangement of alternating octahedra sharing corner oxygens. In such a
structure, the lanthanide sublattice displays a classical fcc arrangement, an
edge-shared network of tetrahedra known to result in geometric magnetic
frustration. No magnetic ordering is observed in any of these compounds down
to temperatures of 2 K, and in the case of the Dy-based compounds in
particular, frustration of the magnetic ordering is clearly present.
Lanthanide-based double perovskites are proposed to be excellent model systems
for the detailed study of geometric magnetic frustration.
Conservation of genome content and virulence determinants among clinical and environmental isolates of
Pseudomonas aeruginosa
Authors: Wolfgang Matthew C. , Kulasekara Bridget R. , Liang Xiaoyou , Boyd Dana , Wu Kai , Yang Qing , Miyada C. Garrett , Lory Stephen
Published: July 2003

Pseudomonas aeruginosa
is a ubiquitous environmental bacterium
capable of causing a variety of life-threatening human infections. The genetic
basis for preferential infection of certain immunocompromised patients or
individuals with cystic fibrosis by
P. aeruginosa
is not understood.
To establish whether variation in the genomic repertoire of
P.
aeruginosa
strains can be associated with a particular type of infection,
we used a whole-genome DNA microarray to determine the genome content of 18
strains isolated from the most common human infections and environmental
sources. A remarkable conservation of genes including those encoding nearly
all known virulence factors was observed. Phylogenetic analysis of
strain-specific genes revealed no correlation between genome content and
infection type. Clusters of strain-specific genes in the
P.
aeruginosa
genome, termed variable segments, appear to be preferential
sites for the integration of novel genetic material. A specialized cloning
vector was developed for capture and analysis of these genomic segments. With
this capture system a site associated with the strain-specific ExoU
cytotoxin-encoding gene was interrogated and an 80-kb genomic island carrying
exoU
was identified. These studies demonstrate that
P.
aeruginosa
strains possess a highly conserved genome that encodes genes
important for survival in numerous environments and allows it to cause a
variety of human infections. The acquisition of novel genetic material, such
as the
exoU
genomic island, through horizontal gene transfer may
enhance colonization and survival in different host environments.
Dynamics of the Neoproterozoic carbon cycle
Authors: Rothman Daniel H. , Hayes John M. , Summons Roger E.
Published: July 2003

The existence of unusually large fluctuations in the Neoproterozoic (1,000–543 million years ago) carbon-isotopic record implies strong perturbations to the Earth's carbon cycle. To analyze these fluctuations, we examine records of both the isotopic content of carbonate carbon and the fractionation between carbonate and marine organic carbon. Together, these are inconsistent with conventional, steady-state models of the carbon cycle. The records can be well understood, however, as deriving from the nonsteady dynamics of two reactive pools of carbon. The lack of a steady state is traced to an unusually large oceanic reservoir of organic carbon. We suggest that the most significant of the Neoproterozoic negative carbon-isotopic excursions resulted from increased remineralization of this reservoir. The terminal event, at the Proterozoic–Cambrian boundary, signals the final diminution of the reservoir, a process that was likely initiated by evolutionary innovations that increased export of organic matter to the deep sea.
The Sahara as a vicariant agent, and the role of Miocene climatic events, in the diversification of the mammalian order Macroscelidea (elephant shrews)
Authors: Douady Christophe J. , Catzeflis François , Raman Jaishree , Springer Mark S. , Stanhope Michael J.
Published: July 2003

Although the Sahara is a major geographical feature of the African
continent, its role in the diversification of animal species is not well
understood. We present here a molecular phylogeny for members of the endemic
African mammalian order Macroscelidea (elephant shrews) with molecular-clock
calculations; this molecular phylogeny provides convincing evidence that the
genus
Elephantulus
is diphyletic.
Elephantulus rozeti
, the
only elephant shrew species that resides north of the Sahara, is the sister
group of a species from a different genus (
Petrodromus
tetradactylus
), which resides just south of the Sahara. The split between
these taxa coincided with major Miocene climatic events, which triggered the
cooling and aridification of midlatitude continental regions, and a shift in
the Sahara from a tropical to an arid environment. Thus, the North African
distribution of
E. rozeti
is not the result of dispersion from an
eastern species of the genus, but instead the result of a vicariant event
involving the formation of the Sahara. The splitting events involved with most
Elephantulus
species in our analysis appear to coincide with these
climatic events. This coincidence suggests that the environmental consequences
associated with this period played an important role in the radiation of this
order of mammals. The strongly supported phylogeny provides compelling
evidence for a complex history of mosaic evolution, including pronounced
bradytelic morphological evolution in some lineages, accelerated morphological
evolution in others, and a remarkably slow rate of evolution of the male
reproductive structure.
Nur77 as a survival factor in tumor necrosis factor signaling
Authors: Suzuki Shinobu , Suzuki Nobutaka , Mirtsos Christine , Horacek Thomas , Lye Elizabeth , Noh Seo-Kyu , Ho Alexandra , Bouchard Denis , Mak Tak W. , Yeh Wen-Chen
Published: July 2003

The immediate-early gene Nur77, which encodes an orphan nuclear receptor, is rapidly induced by various stress stimuli, including tumor necrosis factor (TNF). Nur77 has been implicated in mediating apoptosis, particularly in T cells and tumor cells. We report here that Nur77 can play a role in antagonizing apoptosis in TNF signaling. Nur77 expression is strongly induced by TNF. Interestingly, unlike most antiapoptotic molecules, this induced expression of Nur77 is largely independent of NF-κB. Ectopic expression of Nur77 can protect wild-type,TRAF2-/-, andRelA-/-cells from apoptosis induced by TNF, whereas expression of a dominant-negative form of Nur77 (DN-Nur77) accelerates TNF-mediated cell death in the mutant cells. In mouse embryonic fibroblasts, Nur77 remains in the nucleus in response to TNF and is not translocated to the mitochondria, where it was reported to mediate apoptosis. Our results suggest that Nur77 is a survival effector protein in the context of TNF-mediated signaling.
Transforming growth factor β signaling impairs Neu-induced mammary tumorigenesis while promoting pulmonary metastasis
Authors: Siegel Peter M. , Shu Weiping , Cardiff Robert D. , Muller William J. , Massagué Joan
Published: July 2003

The influence of transforming growth factor β (TGF-β) signaling
on Neu-induced mammary tumorigenesis and metastasis was examined with
transgenic mouse models. We generated mice expressing an activated TGF-β
type I receptor or dominant negative TGF-β type II receptor under control
of the mouse mammary tumor virus promoter. When crossed with mice expressing
activated forms of the Neu receptor tyrosine kinase that selectively couple to
the Grb2 or Shc signaling pathways the activated type I receptor increased the
latency of mammary tumor formation but also enhanced the frequency of
extravascular lung metastasis. Conversely, expression of the dominant negative
type II receptor decreased the latency of Neu-induced mammary tumor formation
while significantly reducing the incidence of extravascular lung metastases.
These observations argue that TGF-β can promote the formation of lung
metastases while impairing Neu-induced tumor growth and suggest that
extravasation of breast cancer cells from pulmonary vessels is a point of
action of TGF-β in the metastatic process.
Repeated observation of breast tumor subtypes in independent gene expression data sets
Authors: Sørlie Therese , Tibshirani Robert , Parker Joel , Hastie Trevor , Marron J. S. , Nobel Andrew , Deng Shibing , Johnsen Hilde , Pesich Robert , Geisler Stephanie , Demeter Janos , Perou Charles M. , Lønning Per E. , Brown Patrick O. , Børresen-Dale Anne-Lise , Botstein David
Published: July 2003

Characteristic patterns of gene expression measured by DNA microarrays have
been used to classify tumors into clinically relevant subgroups. In this
study, we have refined the previously defined subtypes of breast tumors that
could be distinguished by their distinct patterns of gene expression. A total
of 115 malignant breast tumors were analyzed by hierarchical clustering based
on patterns of expression of 534 “intrinsic” genes and shown to
subdivide into one basal-like, one
ERBB2
-overexpressing, two
luminal-like, and one normal breast tissue-like subgroup. The genes used for
classification were selected based on their similar expression levels between
pairs of consecutive samples taken from the same tumor separated by 15 weeks
of neoadjuvant treatment. Similar cluster analyses of two published,
independent data sets representing different patient cohorts from different
laboratories, uncovered some of the same breast cancer subtypes. In the one
data set that included information on time to development of distant
metastasis, subtypes were associated with significant differences in this
clinical feature. By including a group of tumors from
BRCA1
carriers
in the analysis, we found that this genotype predisposes to the basal tumor
subtype. Our results strongly support the idea that many of these breast tumor
subtypes represent biologically distinct disease entities.
Lie superalgebras graded by
P
(
n
) and
Q
(
n
)
Authors: Martínez Consuelo , Zelmanov Efim I.
Published: July 2003

In this article we study Lie superalgebras graded by the root systems
P
(
n)
and
Q
(
n)
.
Identification of the β cell antigen targeted by a prevalent population of pathogenic CD8+T cells in autoimmune diabetes
Authors: Lieberman Scott M. , Evans Anne M. , Han Bingye , Takaki Toshiyuki , Vinnitskaya Yuliya , Caldwell Jennifer A. , Serreze David V. , Shabanowitz Jeffrey , Hunt Donald F. , Nathenson Stanley G. , Santamaria Pere , DiLorenzo Teresa P.
Published: July 2003

Type 1 diabetes is an autoimmune disease in which autoreactive T cells attack and destroy the insulin-producing pancreatic β cells. CD8+T cells are essential for this β cell destruction, yet their specific antigenic targets are largely unknown. Here, we reveal that the autoantigen targeted by a prevalent population of pathogenic CD8+T cells in nonobese diabetic mice is islet-specific glucose-6-phosphatase catalytic subunit-related protein (IGRP). Through tetramer technology, IGRP-reactive T cells are readily detected in islets and peripheral blood directlyex vivo. The human IGRP gene maps to a diabetes susceptibility locus, suggesting that IGRP also may be an antigen for pathogenic T cells in human type 1 diabetes and, thus, a new, potential target for diagnostic and therapeutic approaches.
A mechanism of covalent substrate binding in the x-ray structure of subunit K of the
Escherichia coli
dihydroxyacetone kinase
Authors: Siebold Christian , García-Alles Luis Fernando , Erni Bernhard , Baumann Ulrich
Published: July 2003

Dihydroxyacetone (Dha) kinases are homologous proteins that use different
phosphoryl donors, a multiphosphoryl protein of the
phospho
enol
pyruvate-dependent carbohydrate:phosphotransferase system
in bacteria, ATP in animals, plants, and some bacteria. The Dha kinase of
Escherichia coli
consists of three subunits, DhaK and DhaL, which are
colinear to the ATP-dependent Dha kinases of eukaryotes, and the
multiphosphoryl protein DhaM. Here we show the crystal structure of the DhaK
subunit in complex with Dha at 1.75 Å resolution. DhaK is a homodimer
with a fold consisting of two six-stranded mixed β-sheets surrounded by
nine α-helices and a β-ribbon covering the exposed edge strand of
one sheet. The core of the N-terminal domain has an α/β fold common
to subunits of carbohydrate transporters and transcription regulators of the
phospho
enol
pyruvate-dependent carbohydrate:phosphotransferase system.
The core of the C-terminal domain has a fold similar to the C-terminal domain
of the cell-division protein FtsZ. A molecule of Dha is covalently bound in
hemiaminal linkage to the Nε2 of His-230. The hemiaminal does not
participate in covalent catalysis but is the chemical basis for discrimination
between short-chain carbonyl compounds and polyols. Paralogs of Dha kinases
occur in association with transcription regulators of the TetR/QacR and the
SorC families, pointing to their biological role as sensors in signaling.
Optimization of protease-inhibitor interactions by randomizing adventitious contacts
Authors: Komiyama Tomoko , VanderLugt Bryan , Fugère Martin , Day Robert , Kaufman Randal J. , Fuller Robert S.
Published: July 2003

Polypeptide protease inhibitors are often found to inhibit targets with
which they did not coevolve, as in the case of high-affinity inhibition of
bacterial subtilisin by the leech inhibitor eglin c. Two kinds of contacts
exist in such complexes: (
i
) reactive site loop-active site contacts
and (
ii
) interactions outside of these that form the broader
enzyme-inhibitor interface. We hypothesized that the second class of
“adventitious” contacts could be optimized to generate significant
increases in affinity for a target enzyme or discrimination of an inhibitor
for closely related target proteases. We began with a modified eglin c,
Arg-42–Arg-45–eglin, in which the reactive site loop had been
optimized for subtilisin-related processing proteases of the Kex2/furin
family. We randomized 10 potential adventitious contact residues and screened
for inhibition of soluble human furin. Substitutions at one of these sites,
Y
49
, were also screened against yeast Kex2 and human PC7. These
screens identified not only variants that exhibited increased affinity (up to
20-fold), but also species that exhibited enhanced selectivity, that is,
increased discrimination between the target enzymes (up to 41-fold for furin
versus PC7 and 20-fold for PC7 versus furin). One variant,
Asp-49–Arg-42–Arg-45–eglin, exhibited a
K
i
of 310 pM for furin and blocked furin-dependent
processing of von Willebrand factor in COS-1 cells when added to the culture
medium of the cells. The exploitation of adventitious contact sites may
provide a versatile technique for developing potent, selective inhibitors for
newly discovered proteases and could in principle be applied to optimize
numerous protein–protein interactions.
Coordinated reduction of genes of oxidative metabolism in humans with insulin resistance and diabetes: Potential role ofPGC1andNRF1
Authors: Patti Mary Elizabeth , Butte Atul J. , Crunkhorn Sarah , Cusi Kenneth , Berria Rachele , Kashyap Sangeeta , Miyazaki Yoshinori , Kohane Isaac , Costello Maura , Saccone Robert , Landaker Edwin J. , Goldfine Allison B. , Mun Edward , DeFronzo Ralph , Finlayson Jean , Kahn C. Ronald , Mandarino Lawrence J.
Published: July 2003

Type 2 diabetes mellitus (DM) is characterized by insulin resistance and pancreatic β cell dysfunction. In high-risk subjects, the earliest detectable abnormality is insulin resistance in skeletal muscle. Impaired insulin-mediated signaling, gene expression, glycogen synthesis, and accumulation of intramyocellular triglycerides have all been linked with insulin resistance, but no specific defect responsible for insulin resistance and DM has been identified in humans. To identify genes potentially important in the pathogenesis of DM, we analyzed gene expression in skeletal muscle from healthy metabolically characterized nondiabetic (family history negative and positive for DM) and diabetic Mexican–American subjects. We demonstrate that insulin resistance and DM associate with reduced expression of multiple nuclear respiratory factor-1 (NRF-1)-dependent genes encoding key enzymes in oxidative metabolism and mitochondrial function. AlthoughNRF-1expression is decreased only in diabetic subjects, expression of both PPARγ coactivator 1-α and-β (PGC1-α/PPARGC1andPGC1-β/PERC), coactivators ofNRF-1andPPARγ-dependent transcription, is decreased in both diabetic subjects and family history-positive nondiabetic subjects. DecreasedPGC1expression may be responsible for decreased expression of NRF-dependent genes, leading to the metabolic disturbances characteristic of insulin resistance and DM.
The lethal effects of transplantation ofSocs1-/-bone marrow cells into irradiated adult syngeneic recipients
Authors: Metcalf Donald , Mifsud Sandra , Di Rago Ladina , Alexander Warren S.
Published: July 2003

Injection of neonatal bone marrow cells from mice lacking the gene encoding suppressor of cytokine signaling 1 (SOCS1) into irradiated syngeneic 129/Sv or C57BL/6 mice led to a decreased survival, more rapidly occurring in 129/Sv than in C57BL/6 mice. Moribund mice did not exhibit the acute or chronic diseases developed bySocs1-/-mice but developed a pathology characteristic of graft-versus-host disease with typical chronic inflammatory lesions in the liver, skin, lungs, and gut. The results indicate that cells derived from theSocs1-/-bone marrow are autoaggressive but did not identify the cell types involved. Failure of the engraftedSocs1-/-marrow cells to reproduce the tissue damage typical ofSocs1-/-disease indicates that loss of SOCS1 from target tissues may also be required for the development of theSocs1-/-diseases, such as fatty degeneration of the liver, polymyositis, or corneal inflammation.
On the mechanism of chaperone activity of the small heat-shock protein ofMethanococcus jannaschii
Authors: Kim Rosalind , Lai Luhua , Lee Hi-Hong , Cheong Gang-Won , Kim Kyeong Kyu , Wu Zheng , Yokota Hisao , Marqusee Susan , Kim Sung-Hou
Published: July 2003

The small heat-shock protein (sHSP) fromMethanococcus jannaschii(Mj HSP16.5) forms a homomeric complex of 24 subunits and has an overall structure of a multiwindowed hollow sphere with an external diameter of ≈120 Å and an internal diameter of ≈65 Å with six square “windows” of ≈17 Å across and eight triangular windows of ≈30 Å across. This sHSP has been known to protect other proteins from thermal denaturation. Using purified single-chain monellin as a substrate and a series of methods such as protease digestion, antibody binding, and electron microscopy, we show that the substrates bind to Mj HSP16.5 at a high temperature (80°C) on the outside surface of the sphere and are prevented from forming insoluble substrate aggregatesin vitro. Circular dichroism studies suggest that a very small, if any, conformational change occurs in sHSP even at 80°C, but substantial conformational changes of the substrate are required for complex formation at 80°C. Furthermore, deletion mutation studies of Mj HSP16.5 suggest that the N-terminal region of the protein has no structural role but may play an important kinetic role in the assembly of the sphere by “preassembly condensation” of multiple monomers before final assembly of the sphere.
Directed nucleation assembly of DNA tile complexes for barcode-patterned lattices
Authors: Yan Hao , LaBean Thomas H. , Feng Liping , Reif John H.
Published: July 2003

The programmed self-assembly of patterned aperiodic molecular structures is
a major challenge in nanotechnology and has numerous potential applications
for nanofabrication of complex structures and useful devices. Here we report
the construction of an aperiodic patterned DNA lattice (barcode lattice) by a
self-assembly process of directed nucleation of DNA tiles around a scaffold
DNA strand. The input DNA scaffold strand, constructed by ligation of shorter
synthetic oligonucleotides, provides layers of the DNA lattice with barcode
patterning information represented by the presence or absence of DNA hairpin
loops protruding out of the lattice plane. Self-assembly of multiple DNA tiles
around the scaffold strand was shown to result in a patterned lattice
containing barcode information of 01101. We have also demonstrated the
reprogramming of the system to another patterning. An inverted barcode pattern
of 10010 was achieved by modifying the scaffold strands and one of the strands
composing each tile. A ribbon lattice, consisting of repetitions of the
barcode pattern with expected periodicity, was also constructed by the
addition of sticky ends. The patterning of both classes of lattices was
clearly observable via atomic force microscopy. These results represent a step
toward implementation of a visual readout system capable of converting
information encoded on a 1D DNA strand into a 2D form readable by advanced
microscopic techniques. A functioning visual output method would not only
increase the readout speed of DNA-based computers, but may also find use in
other sequence identification techniques such as mutation or allele
mapping.
A functional genomics approach toward the understanding of secondary metabolism in plant cells
Authors: Goossens Alain , Häkkinen Suvi T. , Laakso Into , Seppänen-Laakso Tuulikki , Biondi Stefania , De Sutter Valerie , Lammertyn Freya , Nuutila Anna Maria , Söderlund Hans , Zabeau Marc , Inzé Dirk , Oksman-Caldentey Kirsi-Marja
Published: July 2003

Despite the tremendous importance of secondary metabolites for humans as
for the plant itself, plant secondary metabolism remains poorly characterized.
Here, we present an experimental approach, based on functional genomics, to
facilitate gene discovery in plant secondary metabolism. Targeted metabolite
analysis was combined with cDNA-amplified fragment length polymorphism-based
transcript profiling of jasmonate-elicited tobacco Bright yellow 2 cells.
Transcriptome analysis suggested an extensive jasmonate-mediated genetic
reprogramming of metabolism, which correlated well with the observed shifts in
the biosynthesis of the metabolites investigated. This method, which in
addition to transcriptome data also generates gene tags, in the future might
lead to the creation of novel tools for metabolic engineering of medicinal
plant systems in general.