bluuebunny/crossref_metadata_2025 huggingface dataset:
The effect of transcranial magnetic stimulation and peripheral nerve stimulation on corticomuscular coherence in humans
Authors: Liv Hansen Naja , Bo Nielsen Jens
Published: September 2004

Cortex and muscle show coupled oscillations in the 15–35 Hz frequency band during voluntary movements. To obtain evidence of the neuronal network responsible for this rhythmicity we investigated the effect of transcranial magnetic stimulation (TMS) and peripheral nerve stimulation on the coupling between eletcroencephalographic (EEG) activity recorded from the scalp over the motor cortex and electromyographic (EMG) activity recorded from the tibialis anterior (TA) muscle in 15 healthy human subjects. TMS over the leg area at intensities between 0.95 and 1.1 × threshold for a motor evoked potential (MEP) in the TA increased corticomuscular coherence in the 15–35 Hz frequency band. This effect lasted on average for 300 ms, but could last up to 600–800 ms in some subjects. Stimulation of motor nerves from the ankle muscles suppressed corticomuscular coherence in the 15–35 Hz frequency range between leg area EEG and TA EMG for a period up to 600–800 ms. In addition, increased coherence around 10 Hz was observed for a period up to 250 ms after the stimulation. Stimulation of motor nerves in the arm and motor nerves from the ankle muscles in the other leg had no effect. The findings indicate that TMS has direct access to the neuronal circuitry in the motor cortex, which generates the corticomuscular coherence. This effect was caused either by direct activation of corticospinal cells or by activation of local neuronal circuitries in the motor cortex. The effects of peripheral nerve stimulation suggest that an alternative rhythm generator may entrain the cortical cells into a lower 10 Hz rhythm and disrupt the 15–35 Hz rhythm.
NG2‐positive cells in the mouse white and grey matter display distinct physiological properties
Authors: Chittajallu R. , Aguirre A. , Gallo V.
Published: September 2004

Cells that express the NG2 proteoglycan are the largest proliferative progenitor population in the postnatal central nervous system (CNS). Although this entire population has long been considered to be oligodendrocyte progenitors, numerous NG2+ cells are present in the cerebral cortex, where relatively little myelination occurs, and also persist long after myelination is complete in the CNS. Several studies have alluded to the presence of distinct NG2+ cell subtypes based on marker expression, but no experimentally derived hypotheses about the physiological role of these subtypes has been proposed. In the current study, whole‐cell patch‐clamp data from acutely isolated slices demonstrate that subcortical white matter and cortical NG2+ cells display distinct membrane properties in addition to possessing differing K+‐ and Na+‐channel expression profiles. A striking observation is that a subpopulation of cortical, but not white matter NG2+ cells, elicit depolarization‐induced spikes that are akin to immature action potentials. Our data demonstrate that a population of cortical NG2+ cells display physiological properties that differ from their white matter counterparts.
Use of Wavelets for Analyzing Transient Radiative Heat Transfer in an
Inhomogeneous Medium
Authors: Guven Oguzhan , Bayazitoglu Yildiz
Published: September 2004

Transient radiative heat transfer in a two-dimensional inhomogeneous rectangular medium is considered. The medium is gray, absorbing, emitting and strongly scattering, and bounded by cold, black walls. Inhomogeneous zones of various sizes are placed at different locations within the medium. The incident radiant energy due to a short laser pulse produces a highly transient and unique transmittance, which is investigated. The discrete wavelets method is used to solve the corresponding equation of transient radiative transfer. The time dependent transmittance for various inhomogeneous areas and the significance of the size and location of the inhomogeneous zones are computed.
Three-Dimensional Conjugate Heat Transfer in a Horizontal Channel
With Discrete Heating
Authors: Wang Qinghua , Jaluria Yogesh
Published: September 2004

Three-dimensional conjugate heat transfer in a rectangular duct with two discrete flush-mounted heat sources has been studied numerically in the context of cooling of electronic equipments. The Grashof number is fixed as 106 and the working fluid is taken as air. The effects of the spatial arrangement of heat sources, the thermal conductivity ratio of the bottom plate material to air, and the Reynolds numbers on the overall and local heat transfer in the duct are evaluated. The magnitudes of the conduction and the convection transport are compared for different parametric combinations. Of particular interest are the transverse variation in the flow, temperature and heat transfer, the interaction between the heat sources, and the effects of conjugate transport.
A Computational Study on Flame-Solid Radiative Interaction in Flame
Spread Over Thin Solid-Fuel
Authors: Kumar Amit , Tolejko Kevin , T'ien James S.
Published: September 2004

A detailed, two-dimensional, laminar, flame spread model over a thin solid is solved in both a normal gravity downward spread configuration and in a microgravity quiescent atmosphere configuration. The radiation transfer equation is solved using discrete ordinates methods. While flame radiation plays only a secondary role in normal gravity spread, it is crucial in microgravity. By using the solid fuel total emittance and total absorptance as parameters, systematic computations have been performed to isolate the roles of flame radiative loss to the ambient, absorption of flame radiation by the solid and solid emission. Computations show that depending on the values of the solid radiation parameters, trend reversals in spread rate and extinction limits between flames in normal gravity and in microgravity can occur.
A Dual-Scale Computational Method for Correcting Surface Temperature
Measurement Errors
Authors: Tszeng T. C. , Zhou G. F.
Published: September 2004

The present paper addresses the measurement errors in temperature due to the effects of surface-mounted temperature sensors like thermocouples. Heat conduction into or from the installed thermocouple wires can alter the temperature at the thermocouple junction as well as in its immediate vicinity. As a result, the emf appearing at the thermocouple terminals does not correspond to the actual surface temperature. In this paper, we present a dual-scale computational method that can be used to calculate the transient temperatures at the multiple thermocouple junctions during heating or cooling of an object. The basis of the method is a thermocouple submodel embedded in a FEM model for the parent object. The numerical results of the dual-scale computational model are compared with that of the conventional FEM models as well as the analytical solutions available. This paper also discusses the characteristics of surface-mounted thermocouples in a range of configurations.
Reverse Monte Carlo Method for Transient Radiative Transfer in
Participating Media
Authors: Lu Xiaodong , Hsu Pei-feng
Published: September 2004

The Monte Carlo (MC) method has been widely used to solve radiative transfer problems due to its flexibility and simplicity in simulating the energy transport process in arbitrary geometries with complex boundary conditions. However, the major drawback of the conventional (or forward) Monte Carlo method is the long computational time for converged solution. Reverse or backward Monte Carlo (RMC) is considered as an alternative approach when solutions are only needed at certain locations and time. The reverse algorithm is similar to the conventional method, except that the energy bundle (photon ensemble) is tracked in a time-reversal manner. Its migration is recorded from the detector into the participating medium, rather than from the source to the detector as in the conventional MC. There is no need to keep track of the bundles that do not reach a particular detector. Thus, RMC method takes up much less computation time than the conventional MC method. On the other hand, RMC will generate less information about the transport process as only the information at the specified locations, e.g., detectors, is obtained. In the situation where detailed information of radiative transport across the media is needed the RMC may not be appropriate. RMC algorithm is most suitable for diagnostic applications where inverse analysis is required, e.g., optical imaging and remote sensing. In this study, the development of a reverse Monte Carlo method for transient radiative transfer is presented. The results of non-emitting, absorbing, and anisotropically scattering media subjected to an ultra short light pulse irradiation are compared with the forward Monte Carlo and discrete ordinates methods results.
Three-Dimensional Instabilities of Natural Convection Flow in a
Vertical Cylinder With Partially Heated Sidewall
Authors: Rubinov A. , Erenburg V. , Gelfgat A. Yu. , Kit E. , Bar-Yoseph P. Z. , Solan A.
Published: September 2004

The three-dimensional axisymmetry-breaking instability of an axisymmetric convective flow in a vertical cylinder with a partially heated sidewall is studied numerically. The central part of the sidewall is maintained at constant temperature, while its upper and lower parts are thermally insulated. The dependence of the critical Grashof number on the cylinder aspect ratio (A=height/radius) is obtained for a fixed value of the Prandtl number, Pr=0.021, and fixed length of the heated central region, equal to the cylinder radius. Three different modes of the most dangerous three-dimensional perturbations, which replace each other with the variation of the aspect ratio, are found. Comparison with experiment shows a good agreement at the aspect ratio A=8 and 12, while at A=4 a significant disagreement is observed. Possible reasons for this disagreement are discussed. At A=4, the dependence of the critical Grashof number on the Prandtl number is studied in the range 0<Pr<0.05, to rule out the possibility that the disagreement is due to uncertainty in values of fluid properties. The similarities and differences of instabilities in the cylindrical and rectangular geometries are examined. The computations are carried out using two independent numerical approaches, which cross-validate each other.
Numerical Analysis of Natural Convection and Mixing in Two-Fluid
Stratified Pools With Internal Heat Sources
Authors: Gubaidullin A. A. , Sehgal B. R.
Published: September 2004

The heat transport in two-layer fluid systems has been investigated numerically for slice-type semicircular pools with internal heat sources. The fixed interface model has been applied to study natural convection in the system of the immiscible fluids. The double-diffusion model has been employed to describe the heat transfer and mixing for the miscible fluids. The numerical results are compared to data measured in the SIMECO experiments. Based on the numerical simulations, the effect of the ratio of the fluid properties has been quantified. The results are of interest for the corium melt coolability in a postulated severe accident scenario in a light water reactor.
A New Model for the Effect of Calcium Sulfate Scale Formation on Pool
Boiling Heat Transfer
Authors: Jamialahmadi M. , Müller-Steinhagen H.
Published: September 2004

Scale deposition on the heat transfer surfaces from water containing dissolved salts considerably reduces fuel economy and performance of heat transfer equipment. This problem is more serious during nucleate boiling due to the mechanisms of bubble formation and detachment. Using a precision pool boiling test apparatus, the effects of heat flux and calcium sulfate concentration on heat transfer coefficient and formation and growth of deposits are investigated. The transient change in heat transfer is closely related to wick boiling, and the associated changes in bubble departure diameter and bubble site density. A physically sound prediction model was developed for the prediction of heat transfer coefficients as a function of time during deposition processes. Based on comparison with experimental data over a wide range of foulant concentrations and heat fluxes, the model is considered to be sufficiently accurate for practical application.
Nano-Scale Machining Via Electron Beam and Laser Processing
Authors: Wong Basil T. , Mengüç M. Pinar , Vallance R. Ryan
Published: September 2004

It is recently conceptualized that nano-scale machining might be achieved by coupling electron emission with radiation transfer. A laser may be used to heat a workpiece to a threshold temperature, and a nano-probe might then transfer additional energy via electron emission to remove a minute amount of material. To investigate this hypothesis, a detailed numerical study is presented. The electron-beam transport is modeled using a Monte Carlo approach, and a radiation transfer model that includes Fresnel reflections is adapted to simulate laser heating. The numerical study suggests that approximately 0.5 W from a single electron-beam is sufficient to initialize local evaporation from a gold film. With the use of a laser, the required power can be halved if the film is sufficiently thin. This paper describes the details of the numerical study and establishes guidelines for such nano-scale machining processes.
Finite Size Effects in Determination of Thermal Conductivities: Comparing Molecular Dynamics Results With Simple Models
Authors: Chantrenne Patrice , Barrat Jean-Louis
Published: September 2004

The thermal conductivity of nanometric objects or nanostructured materials can be determined using nonequilibrium molecular dynamics (NEMD) simulations. The technique is simple in its principle, and resembles a numerical guarded hot plate experiment. The “sample” is placed between a hot source and a cold source consisting of thermostatted sets of atoms. The thermal conductivity is obtained from the heat flux crossing the sample and the temperature profile in the system. Simulation results, however, exhibit a strong dependence of the thermal conductivity on the sample size. In this paper, we discuss the physical origin of this size dependence, by comparing MD results with those obtained from simple models of thermal conductivity based on harmonic theory of solids. A model is proposed to explain the variation of the thermal conductivity with system size.
The Effects of Nozzle Diameter on Impinging Jet Heat Transfer and
Fluid Flow
Authors: Lee Dae Hee , Song Jeonghoon , Jo Myeong Chan
Published: September 2004

The effects of nozzle diameter on heat transfer and fluid flow are investigated for a round turbulent jet impinging on a flat plate surface. The flow at the nozzle exit has a fully developed velocity profile. A uniform heat flux boundary is created at the plate surface by using gold film Intrex, and liquid crystals are used to measure the plate surface temperature. The experiments are performed for the jet Reynolds number (Re) of 23,000, with a dimensionless distance between the nozzle and plate surface L/d ranging from 2 to 14 and a nozzle diameter (d) ranging from 1.36 to 3.40 cm. The results show that the local Nusselt numbers increase with the increasing nozzle diameter in the stagnation point region corresponding to 0⩽r/d⩽0.5. This may be attributed to an increase in the jet momentum and turbulence intensity level with the larger nozzle diameter, which results in the heat transfer augmentation. In the mean time, the effect of the nozzle diameter on the local Nusselt numbers is negligibly small at the wall jet region corresponding to r/d>0.5.
Entropy Generation Minimization of Fully Developed Internal Flow With
Constant Heat Flux
Authors: Ratts Eric B. , Raut Atul G.
Published: September 2004

This paper uses the entropy generation minimization (EGM) method to optimize a single-phase, convective, fully developed flow with uniform and constant heat flux. For fixed mass flow rate and fixed total heat transfer rate, and the assumption of uniform and constant heat flux, an optimal Reynolds number for laminar and turbulent flow is obtained. The study also compares optimal Reynolds number and minimum entropy generation for cross sections: square, equilateral triangle, and rectangle with aspect ratios of two and eight. The rectangle with aspect ratio of eight had the smallest optimal Reynolds number, the smallest entropy generation number, and the smallest flow length.
The Condensation of Ammonia-Water Mixtures in a Horizontal Shell and
Tube Condenser
Authors: Philpott Chris , Deans Joe
Published: September 2004

The heat transfer rates that develop when ammonia water mixtures condense within a small, un-vented, horizontal, shell and tube condenser are examined. The vapor flow within the condenser was constrained by baffles and the condensate created formed a pool that flowed along the base of the condenser. During the test program the inlet ammonia vapor concentration to the condenser varied from 0 to 10 wt % and the maximum local vapor concentration measured was 26 wt %. The experimental results demonstrate that the condensation heat transfer rates generally decrease with increasing ammonia concentration, however at low ammonia concentrations (<2 wt %) the local and overall heat transfer rates for the condenser were enhanced. When the ammonia concentration was 0.9 wt %, the vapor heat transfer rate was 34 percent greater than that predicted by the Nusselt analysis for steam at the same conditions. This enhancement is attributed to the disturbed morphology of the condensate film, created by Marangoni instabilities.
The Thermal Constriction Resistance for an Eccentric Spot on a
Circular Heat Flux Tube
Authors: Baïri A. , Laraqi N.
Published: September 2004

An analytical solution is proposed to calculate the thermal constriction resistance for an eccentric circular spot with uniform flux on a semi-infinite circular heat flux tube. This solution is developed using the finite cosine Fourier transform and the finite Hankel transform. It allows to calculate the stationary three-dimensional temperature distribution and the thermal constriction resistance. The results of proposed solution are in agreement with available theoretical and experimental studies. We show that the thermal constriction resistance for an eccentric contact is greater than the one of a centered contact (few tens percent), which is consistent with recent studies on random contacts. A simple correlation is also proposed to calculate the thermal constriction resistance as a function of the eccentricity and the relative contact size.
Local Pool Boiling Coefficients on the Inside Surface of a Horizontal
Tube
Authors: Kang Myeong-Gie
Published: September 2004

Nucleate pool boiling heat transfer of water on the inside surface of a horizontal tube of 51 mm internal diameter has been studied experimentally at atmospheric pressure. Experiments were performed at four different azimuthal angles (0 deg, 45 deg, 120 deg, and 180 deg from the tube bottom) to investigate variations in local heat transfer coefficients along the tube periphery. The local coefficient changes much along the tube periphery and the minimum was observed at the tube bottom. It is found that heat transfer on the inside surface is strongly dependent on the intensity of the liquid agitation and the evaporative mechanism.
How Best to Face the Coming Storm
Authors: Dasgupta Partha
Published: September 2004

Red Sky at Morning
America and the Crisis of the Global Environment. James Gustave Speth. Yale University Press, New Haven, CT, 2004. 317 pp. $24, £15.99, €25.60. ISBN 0-300-10232-1.

Writing for a broad popular audience, Speth offers a summary of the current global environmental crisis and a consideration of potential political solutions to it.
Defining a Link with Asthma in Mice Congenitally Deficient in Eosinophils
Authors: Lee James J. , Dimina Dawn , Macias MiMi P. , Ochkur Sergei I. , McGarry Michael P. , O'Neill Katie R. , Protheroe Cheryl , Pero Ralph , Nguyen Thanh , Cormier Stephania A. , Lenkiewicz Elizabeth , Colbert Dana , Rinaldi Lisa , Ackerman Steven J. , Irvin Charles G. , Lee Nancy A.
Published: September 2004

Eosinophils are often dominant inflammatory cells present in the lungs of asthma patients. Nonetheless, the role of these leukocytes remains poorly understood. We have created a transgenic line of mice (PHIL) that are specifically devoid of eosinophils, but otherwise have a full complement of hematopoietically derived cells. Allergen challenge of PHIL mice demonstrated that eosinophils were required for pulmonary mucus accumulation and the airway hyperresponsiveness associated with asthma. The development of an eosinophil-less mouse now permits an unambiguous assessment of a number of human diseases that have been linked to this granulocyte, including allergic diseases, parasite infections, and tumorigenesis.
Middle Miocene Southern Ocean Cooling and Antarctic Cryosphere Expansion
Authors: Shevenell Amelia E. , Kennett James P. , Lea David W.
Published: September 2004

Magnesium/calcium data from Southern Ocean planktonic foraminifera demonstrate that high-latitude (∼55°S) southwest Pacific sea surface temperatures (SSTs) cooled 6° to 7°C during the middle Miocene climate transition (14.2 to 13.8 million years ago). Stepwise surface cooling is paced by eccentricity forcing and precedes Antarctic cryosphere expansion by ∼60 thousand years, suggesting the involvement of additional feedbacks during this interval of inferred low-atmospheric partial pressure of CO
2
(
p
CO
2
). Comparing SSTs and global carbon cycling proxies challenges the notion that episodic
p
CO
2
drawdown drove this major Cenozoic climate transition. SST, salinity, and ice-volume trends suggest instead that orbitally paced ocean circulation changes altered meridional heat/vapor transport, triggering ice growth and global cooling.
Children Creating Core Properties of Language: Evidence from an Emerging Sign Language in Nicaragua
Authors: Senghas Ann , Kita Sotaro , Özyürek Asli
Published: September 2004

A new sign language has been created by deaf Nicaraguans over the past 25 years, providing an opportunity to observe the inception of universal hallmarks of language. We found that in their initial creation of the language, children analyzed complex events into basic elements and sequenced these elements into hierarchically structured expressions according to principles not observed in gestures accompanying speech in the surrounding language. Successive cohorts of learners extended this procedure, transforming Nicaraguan signing from its early gestural form into a linguistic system. We propose that this early segmentation and recombination reflect mechanisms with which children learn, and thereby perpetuate, language. Thus, children naturally possess learning abilities capable of giving language its fundamental structure.
A Critical Role for Eosinophils in Allergic Airways Remodeling
Authors: Humbles Alison A. , Lloyd Clare M. , McMillan Sarah J. , Friend Daniel S. , Xanthou Georgina , McKenna Erin. E. , Ghiran Sorina , Gerard Norma P. , Yu Channing , Orkin Stuart H. , Gerard Craig
Published: September 2004

Features of chronic asthma include airway hyperresponsiveness, inflammatory infiltrates, and structural changes in the airways, termed remodeling. The contribution of eosinophils, cells associated with asthma and allergy, remains to be established. We show that in mice with a total ablation of the eosinophil lineage, increases in airway hyperresponsiveness and mucus secretion were similar to those observed in wild-type mice, but eosinophil-deficient mice were significantly protected from peribronchiolar collagen deposition and increases in airway smooth muscle. These data suggest that eosinophils contribute substantially to airway remodeling but are not obligatory for allergen-induced lung dysfunction, and support an important role for eosinophil-targeted therapies in chronic asthma.
Two Distinct Actin Networks Drive the Protrusion of Migrating Cells
Authors: Ponti A. , Machacek M. , Gupton S. L. , Waterman-Storer C. M. , Danuser G.
Published: September 2004

Cell migration initiates by extension of the actin cytoskeleton at the leading edge. Computational analysis of fluorescent speckle microscopy movies of migrating epithelial cells revealed this process is mediated by two spatially colocalized but kinematically, kinetically, molecularly, and functionally distinct actin networks. A lamellipodium network assembled at the leading edge but completely disassembled within 1 to 3 micrometers. It was weakly coupled to the rest of the cytoskeleton and promoted the random protrusion and retraction of the leading edge. Productive cell advance was a function of the second colocalized network, the lamella, where actomyosin contraction was integrated with substrate adhesion.
Molecular Cloud Origin for the Oxygen Isotope Heterogeneity in the Solar System
Authors: Yurimoto Hisayoshi , Kuramoto Kiyoshi
Published: September 2004

Meteorites and their components have anomalous oxygen isotopic compositions characterized by large variations in
18
O/
16
O and
17
O/
16
O ratios. On the basis of recent observations of star-forming regions and models of accreting protoplanetary disks, we suggest that these variations may originate in a parent molecular cloud by ultraviolet photodissociation processes. Materials with anomalous isotopic compositions were then transported into the solar nebula by icy dust grains during the collapse of the cloud. The icy dust grains drifted toward the Sun in the disk, and their subsequent evaporation resulted in the
17
O- and
18
O-enrichment of the inner disk gas.
Age and Timing of the Permian Mass Extinctions: U/Pb Dating of Closed-System Zircons
Authors: Mundil Roland , Ludwig Kenneth R. , Metcalfe Ian , Renne Paul R.
Published: September 2004

The age and timing of the Permian-Triassic mass extinction have been difficult to determine because zircon populations from the type sections are typically affected by pervasive lead loss and contamination by indistinguishable older xenocrysts. Zircons from nine ash beds within the Shangsi and Meishan sections (China), pretreated by annealing followed by partial attack with hydrofluoric acid, result in suites of consistent and concordant uranium/lead (U/Pb) ages, eliminating the effects of lead loss. The U/Pb age of the main pulse of the extinction is 252.6 ± 0.2 million years, synchronous with the Siberian flood volcanism, and it occurred within the quoted uncertainty.
Zooming In on a Quantitative Trait for Tomato Yield Using Interspecific Introgressions
Authors: Fridman Eyal , Carrari Fernando , Liu Yong-Sheng , Fernie Alisdair R. , Zamir Dani
Published: September 2004

To explore natural biodiversity we developed and examined introgression lines (ILs) containing chromosome segments of wild species (
Solanum pennellii
) in the background of the cultivated tomato (
S. lycopersicum
). We identified
Brix9-2-5
, which is a
S. pennellii
quantitative trait locus (QTL) that increases sugar yield of tomatoes and was mapped within a flower- and fruit-specific invertase (
LIN5
). QTL analysis representing five different tomato species delimited the functional polymorphism of
Brix9-2-5
to an amino acid near the catalytic site of the invertase crystal, affecting enzyme kinetics and fruit sink strength. These results underline the power of diverse ILs for high-resolution perspectives on complex phenotypes.
A Stable Compound Containing a Silicon-Silicon Triple Bond
Authors: Sekiguchi Akira , Kinjo Rei , Ichinohe Masaaki
Published: September 2004

The reaction of 2,2,3,3-tetrabromo-1,1,4,4-tetrakis[bis(trimethylsilyl)methyl]-1,4-diisopropyltetrasilane with four equivalents of potassium graphite (KC
8
) in tetrahydrofuran produces 1,1,4,4-tetrakis[bis(trimethylsilyl)methyl]-1,4-diisopropyl-2-tetrasilyne, a stable compound with a silicon-silicon triple bond, which can be isolated as emerald green crystals stable up to 100°C in the absence of air. The Si

Si triple-bond length (and its estimated standard deviation) is 2.0622(9) angstroms, which shows half the magnitude of the bond shortening of alkynes compared with that of alkenes. Unlike alkynes, the substituents at the Si

Si group are not arranged in a linear fashion, but are trans-bent with a bond angle of 137.44(4)°.
Environmentally Induced Foregut Remodeling by PHA-4/FoxA and DAF-12/NHR
Authors: Ao Wanyuan , Gaudet Jeb , Kent W. James , Muttumu Srikanth , Mango Susan E.
Published: September 2004

Growth and development of the
Caenorhabditis elegans
foregut (pharynx) depends on coordinated gene expression, mediated by pharynx defective (PHA)-4/FoxA in combination with additional, largely unidentified transcription factors. Here, we used whole genome analysis to establish clusters of genes expressed in different pharyngeal cell types. We created an expectation maximization algorithm to identify cis-regulatory elements that activate expression within the pharyngeal gene clusters. One of these elements mediates the response to environmental conditions within pharyngeal muscles and is recognized by the nuclear hormone receptor (NHR) DAF-12. Our data suggest that PHA-4 and DAF-12 endow the pharynx with transcriptional plasticity to respond to diverse developmental and physiological cues. Our combination of bioinformatics and in vivo analysis has provided a powerful means for genome-wide investigation of transcriptional control.
A Linear, O-Coordinated η
1
-CO
2
Bound to Uranium
Authors: Castro-Rodriguez Ingrid , Nakai Hidetaka , Zakharov Lev N. , Rheingold Arnold L. , Meyer Karsten
Published: September 2004

The electron-rich, six-coordinate tris-aryloxide uranium(III) complex [((
Ad
ArO)
3
tacn)U
III
] [where (
Ad
ArOH)
3
tacn = 1,4,7-tris(3-adamantyl-5-
tert
-butyl-2-hydroxybenzyl)1,4,7-triazacyclononane] reacts rapidly with CO
2
to yield [((
Ad
ArO)
3
tacn)U
IV
(CO
2
)], a complex in which the CO
2
ligand is linearly coordinated to the metal through its oxygen atom (η
1
-OCO). The latter complex has been crystallographically and spectroscopically characterized. The inequivalent O–C–O bond lengths [1.122 angstroms (Å) for the O–C bond adjacent to uranium and 1.277 Å for the other], considered together with magnetization data and electronic and vibrational spectra, support the following bonding model: U
IV
=O=C⚫–O
–
↔ U
IV
–O

C–O
–
. In these charge-separated resonance structures, the uranium center is oxidized to uranium(IV) and the CO
2
ligand reduced by one electron.
Culture and Commerce in a Seafood Bazaar
Authors: Gudeman Stephen
Published: September 2004

Tsukiji:
The Fish Market at the Center of the World. Theodore C. Bestor. University of California Press, Berkeley, 2004. 440 pp. $60, £39.95. ISBN 0-520-22023-4. Paper, $24.95, £16.95. ISBN 0-520-22024-2. California Studies in Food and Culture.

The author provides a detailed ethnographic account of Tokyo's seafood market, which he places in the context of the Japanese economy, changes in fish distribution and consumption, and the globalization of the seafood trade.
Hydrophilic Domains of Scaffolding Protein CbpA Promote Glycosyl Hydrolase Activity and Localization of Cellulosomes to the Cell Surface of
Clostridium cellulovorans
Authors: Kosugi Akihiko , Amano Yoshihiko , Murashima Koichiro , Doi Roy H.
Published: September 2004

CbpA, the scaffolding protein of
Clostridium cellulovorans
cellulosomes, possesses one family 3 cellulose binding domain, nine cohesin domains, and four hydrophilic domains (HLDs). Among the three types of domains, the function of the HLDs is still unknown. We proposed previously that the HLDs of CbpA play a role in attaching the cellulosome to the cell surface, since they showed some homology to the surface layer homology domains of EngE. Several recombinant proteins with HLDs (rHLDs) and recombinant EngE (rEngE) were examined to determine their binding to the
C. cellulovorans
cell wall fraction. Tandemly linked rHLDs showed higher affinity for the cell wall than individual rHLDs showed. EngE was shown to have a higher affinity for cell walls than rHLDs have.
C. cellulovorans
native cellulosomes were found to have higher affinity for cell walls than rHLDs have. When immunoblot analysis was carried out with the native cellulosome fraction bound to cell wall fragments, the presence of EngE was also confirmed, suggesting that the mechanism anchoring CbpA to the
C. cellulovorans
cell surface was mediated through EngE and that the HLDs play a secondary role in the attachment of the cellulosome to the cell surface. During a study of the role of HLDs on cellulose degradation, the mini-cellulosome complexes with HLDs degraded cellulose more efficiently than complexes without HLDs degraded cellulose. The rHLDs also showed binding affinity for crystalline cellulose and carboxymethyl cellulose. These results suggest that the CbpA HLDs play a major role and a minor role in
C. cellulovorans
cellulosomes. The primary role increases cellulose degradation activity by binding the cellulosome complex to the cellulose substrate; secondarily, HLDs aid the binding of the CbpA/cellulosome to the
C. cellulovorans
cell surface.
Transcriptional Regulation of
Vibrio cholerae
Hemagglutinin/Protease by the Cyclic AMP Receptor Protein and RpoS
Authors: Silva Anisia J. , Benitez Jorge A.
Published: September 2004

Vibrio cholerae
secretes a Zn-dependent metalloprotease, hemagglutinin/protease (HA/protease), which is encoded by
hapA
and displays a broad range of potentially pathogenic activities. Production of HA/protease requires transcriptional activation by the quorum-sensing regulator HapR. In this study we demonstrate that transcription of
hapA
is growth phase dependent and specifically activated in the deceleration and stationary growth phases. Addition of glucose in these phases repressed
hapA
transcription by inducing
V. cholerae
to resume exponential growth, which in turn diminished the expression of a
rpoS-lacZ
transcriptional fusion. Contrary to a previous observation, we demonstrate that transcription of
hapA
requires the
rpoS
-encoded σ
s
factor. The cyclic AMP (cAMP) receptor protein (CRP) strongly enhanced
hapA
transcription in the deceleration phase. Analysis of
rpoS
and
hapR
mRNA in isogenic CRP
+
and CRP
−
strains suggested that CRP enhances the transcription of
rpoS
and
hapR
. Analysis of strains containing
hapR-lacZ
and
hapA-lacZ
fusions confirmed that
hapA
is transcribed in response to concurrent quorum-sensing and nutrient limitation stimuli. Mutations inactivating the stringent response regulator RelA and the HapR-controlled AphA regulator did not affect HA/protease expression. Electrophoretic mobility shift experiments showed that pure cAMP-CRP and HapR alone do not bind the
hapA
promoter. This result suggests that HapR activation of
hapA
differs from its interaction with the
aphA
promoter and could involve additional factors.
Adaptive Acid Tolerance Response of
Streptococcus sobrinus
Authors: Nascimento Marcelle M. , Lemos José A. C. , Abranches Jacqueline , Gonçalves Reginaldo B. , Burne Robert A.
Published: September 2004

Streptococcus mutans
and
Streptococcus sobrinus
are the bacteria most commonly associated with human dental caries. A major virulence attribute of these and other cariogenic bacteria is acid tolerance. The acid tolerance mechanisms of
S. mutans
have begun to be investigated in detail, including the adaptive acid tolerance response (ATR), but this is not the case for
S. sobrinus
. An analysis of the ATR of two
S. sobrinus
strains was conducted with cells grown to steady state in continuous chemostat cultures. Compared with cells grown at neutral pH,
S. sobrinus
cells grown at pH 5.0 showed an increased resistance to acid killing and were able to drive down the pH through glycolysis to lower values. Unlike what is found for
S. mutans
, the enhanced acid tolerance and glycolytic capacities of acid-adapted
S. sobrinus
were not due to increased F-ATPase activities. Interestingly though,
S. sobrinus
cells grown at pH 5.0 had twofold more glucose phosphoenolpyruvate:sugar phosphotransferase system (PTS) activity than cells grown at pH 7.0. In contrast, glucose PTS activity was actually higher in
S. mutans
grown at pH 7.0 than in cells grown at pH 5.0. Silver staining of two-dimensional gels of whole-cell lysates of
S. sobrinus
6715 revealed that at least 9 proteins were up-regulated and 22 proteins were down-regulated in pH 5.0-grown cells compared with cells grown at pH 7.0. Our results demonstrate that
S. sobrinus
is capable of mounting an ATR but that there are critical differences between the mechanisms of acid adaptation used by
S. sobrinus
and
S. mutans
.
Osmosensitivity Associated with Insertions in
argP
(
iciA
) or
glnE
in Glutamate Synthase-Deficient Mutants of
Escherichia coli
Authors: Nandineni Madhusudan R. , Laishram Rakesh S. , Gowrishankar J.
Published: September 2004

An ampicillin enrichment strategy following transposon insertion mutagenesis was employed to obtain NaCl-sensitive mutants of a
gltBD
(glutamate synthase [GOGAT]-deficient) strain of
Escherichia coli
. It was reasoned that the
gltBD
mutation would sensitize the parental strain even to small perturbations affecting osmotolerance. Insertions conferring an osmosensitive phenotype were identified in the
proU
,
argP
(formerly
iciA
), and
glnE
genes encoding a glycine betaine/proline transporter, a LysR-type transcriptional regulator, and the adenylyltransferase for glutamine synthetase, respectively. The

gltBD
+

derivatives of the strains were not osmosensitive. The
argP
mutation, but not the
glnE
mutation, was associated with reduced glutamate dehydrogenase activity and a concomitant NH
4
+
assimilation defect in the
gltBD
strain. Supplementation of the medium with lysine or a lysine-containing dipeptide phenocopied the
argP
null mutation for both osmosensitivity and NH
4
+
assimilation deficiency in a
gltBD
background, and a dominant gain-of-function mutation in
argP
was associated with suppression of these lysine inhibitory effects. Osmosensitivity in the
gltBD
strains, elicited either by lysine supplementation or by introduction of the
argP
or
glnE
mutations (but not
proU
mutations), was also correlated with a reduction in cytoplasmic glutamate pools in cultures grown at elevated osmolarity. We propose that an inability to accumulate intracellular glutamate at high osmolarity underlies the osmosensitive phenotype of both the
argP gltBD
and
glnE gltBD
mutants, the former because of a reduction in the capacity for NH
4
+
assimilation into glutamate and the latter because of increased channeling of glutamate into glutamine.
Antisense RNA Regulation by Stable Complex Formation in theEnterococcus faecalisPlasmid pAD1parAddiction System
Authors: Weaver Keith E. , Ehli Erik A. , Nelson Jessica S. , Patel Smita
Published: September 2004

Theparstability determinant, encoded by theEnterococcus faecalisplasmid pAD1, is the only antisense RNA regulated postsegregational killing system identified in gram-positive bacteria. Because of the unique organization of theparlocus, theparantisense RNA, RNA II, binds to its target, RNA I, at relatively small, interspersed regions of complementarity. The results of this study suggest that, rather than targeting the antisense bound message for rapid degradation, as occurs in most other antisense RNA regulated systems, RNA I and RNA II form a relatively stable, presumably translationally inactive complex. The stability of the RNA I-RNA II complex would allow RNA I to persist in an untranslated state unless or until the encoding plasmid was lost. After plasmid loss, RNA II would be removed from the complex, allowing translational activation of RNA I. The mechanism of RNA I activation in vivo is unknown, but in vitro dissociation experiments suggest that active removal of RNA II, for example by a cellular RNase, may be required.
Characterization of Three New Competence-Regulated Operons in
Haemophilus influenzae
Authors: VanWagoner Timothy M. , Whitby Paul W. , Morton Daniel J. , Seale Thomas W. , Stull Terrence L.
Published: September 2004

Haemophilus influenzae
is one of a growing number of bacteria in which the natural ability to uptake exogenous DNA for potential genomic transformation has been recognized. To date, several operons involved in transformation in this organism have been described. These operons are characterized by a conserved 22-bp regulatory element upstream of the first gene and are induced coincident with transfer from rich to nutrient-depleted media. The previously identified operons comprised genes encoding proteins that include members of the type II secretion system and type IV pili, shown to be essential for transformation in other bacteria, and other proteins previously identified as required for transformation in
H. influenzae
. In the present study, three novel competence operons were identified by comparative genomics and transcriptional analysis. These operons have been further characterized by construction of null mutants and examination of the resulting transformation phenotypes. The putative protein encoded by the HI0366 gene was shown to be essential for DNA uptake, but not binding, and is homologous to a protein shown to be required for pilus biogenesis and twitching motility in
Pseudomonas aeruginosa
. An insertion in HI0939 abolished both DNA binding and uptake. The predicted product of this gene shares characteristics with PulJ, a pseudopilin involved in pullulanase export in
Klebsiella oxytoca
.
A
Francisella tularensis
Pathogenicity Island Required for Intramacrophage Growth
Authors: Nano Francis E. , Zhang Na , Cowley Siobhán C. , Klose Karl E. , Cheung Karen K. M. , Roberts Michael J. , Ludu Jagjit S. , Letendre Gregg W. , Meierovics Anda I. , Stephens Gwen , Elkins Karen L.
Published: September 2004

Francisella tularensis
is a gram-negative, facultative intracellular pathogen that causes the highly infectious zoonotic disease tularemia. We have discovered a ca. 30-kb pathogenicity island of
F. tularensis
(FPI) that includes four large open reading frames (ORFs) of 2.5 to 3.9 kb and 13 ORFs of 1.5 kb or smaller. Previously, two small genes located near the center of the FPI were shown to be needed for intramacrophage growth. In this work we show that two of the large ORFs, located toward the ends of the FPI, are needed for virulence. Although most genes in the FPI encode proteins with amino acid sequences that are highly conserved between high- and low-virulence strains, one of the FPI genes is present in highly virulent type A
F. tularensis
, absent in moderately virulent type B
F. tularensis
, and altered in
F. tularensis
subsp.
novicida
, which is highly virulent for mice but avirulent for humans. The G+C content of a 17.7-kb stretch of the FPI is 26.6%, which is 6.6% below the average G+C content of the
F. tularensis
genome. This extremely low G+C content suggests that the DNA was imported from a microbe with a very low G+C-containing chromosome.
Genomic Changes Arising in Long-Term Stab Cultures ofEscherichia coli
Authors: Faure D. , Frederick R. , Włoch D. , Portier P. , Blot M. , Adams J.
Published: September 2004

Genomic scans of clones isolated from long-term stab cultures ofEscherichia coliK-12 showed the loss of two large segments of the genome, with each lost segment being approximately 20 kb long. A detailed analysis of one of the deletions, located between 5.4 and 5.9 min, revealed that similar deletions had arisen in several other stab cultures. All deletions of this type exhibited a right terminus ending precisely at an IS5Aelement and a left terminus that varied over an ∼5-kb range but was bordered in all but two cases by sequences belonging to the preferred consensus target sequence for IS5, YTAR. The ubiquity of such deletions in independent stab cultures and the increase in their frequency over time argue that they have a selective advantage. It is speculated that the loss of thecrllocus is responsible for the selective advantage of the deletions.
The Fur Homologue inBorrelia burgdorferi
Authors: Katona Laura I. , Tokarz Rafal , Kuhlow Christopher J. , Benach Jordi , Benach Jorge L.
Published: September 2004

Borrelia burgdorfericontains a gene that codes for a Fur homologue. The function of this Fur protein is unknown; however, spirochetes grown at 23 or 35°C expressedfuras determined by reverse transcriptase PCR. Thefurgene (BB0647) was cloned and overexpressed as a His-Fur fusion protein inEscherichia coli. The fusion protein was purified by zinc-chelate chromatography, and the N-terminal His tag was removed to generate recombinant Fur for use in mobility shift studies. Fur bound DNA containing theE. coliFur box sequence (GATAATGATAATCATTATC) orBacillus subtilisPer box sequence (TTATAAT-ATTATAA) with an apparentKdof ∼20 nM. Fur also bound the upstream sequences of threeBorreliagenes: BB0646 (gene encoding a hydrolase of the α/β-fold family), BB0647 (fur), and BB0690 (napA). Addition of metal ions was not required. Binding activity was greatly decreased by either exposure to oxidizing agents (H2O2,t-butyl hydroperoxide, cumene hydroperoxide, or diamide) or by addition of Zn2+.B. burgdorferiNapA is a homologue of Dps. Dps functions inE. colito protect DNA against damage during periods of redox stress. Fur may function inB. burgdorferias a repressor and regulate oxidative stress genes. Additional genes (10 chromosomal and 15 plasmid) that may be Fur regulated were identified by in silico analysis.
Hetero- and Autoprocessing of the Extracellular Metalloprotease (Mpr) in
Bacillus subtilis
Authors: Park Chi Hye , Lee Sang Jun , Lee Sung Gu , Lee Weon Sup , Byun Si Myung
Published: September 2004

Most proteases are synthesized as inactive precursors which are processed by proteolytic cleavage into a mature active form, allowing regulation of their proteolytic activity. The activation of the glutamic-acid-specific extracellular metalloprotease (Mpr) of
Bacillus subtilis
has been examined. Analysis of Mpr processing in defined protease-deficient mutants by activity assay and Western blotting revealed that the extracellular protease Bpr is required for Mpr processing. pro-Mpr remained a precursor form in
bpr
-deficient strains, and glutamic-acid-specific proteolytic activity conferred by Mpr was not activated in
bpr
-deficient strains. Further, purified pro-Mpr was processed to an active form by purified Bpr protease in vitro. We conclude that Mpr is activated by Bpr in vivo, and that heteroprocessing, rather than autoprocessing, is the major mechanism of Mpr processing in vivo. Exchange of glutamic acid for serine in the cleavage site of Mpr (S93E) allowed processing of Mpr into its mature form, regardless of the presence of other extracellular proteases, including Bpr. Thus, a single amino acid change is sufficient to convert the Mpr processing mechanism from heteroprocessing to autoprocessing.
Bacillus subtilis
ResD Induces Expression of the Potential Regulatory Genes
yclJK
upon Oxygen Limitation
Authors: Härtig Elisabeth , Geng Hao , Hartmann Anja , Hubacek Angela , Münch Richard , Ye Rick W. , Jahn Dieter , Nakano Michiko M.
Published: September 2004

Transcription of the
yclJK
operon, which encodes a potential two-component regulatory system, is activated in response to oxygen limitation in
Bacillus subtilis
. Northern blot analysis and assays of
yclJ-lacZ
reporter gene fusion activity revealed that the anaerobic induction is dependent on another two-component signal transduction system encoded by
resDE
. ResDE was previously shown to be required for the induction of anaerobic energy metabolism. Electrophoretic mobility shift assays and DNase I footprinting experiments showed that the response regulator ResD binds specifically to the
yclJK
regulatory region upstream of the transcriptional start site. In vitro transcription experiments demonstrated that ResD is sufficient to activate
yclJ
transcription. The phosphorylation of ResD by its sensor kinase, ResE, highly stimulates its activity as a transcriptional activator. Multiple nucleotide substitutions in the ResD binding regions of the
yclJ
promoter abolished ResD binding in vitro and prevented the anaerobic induction of
yclJK
in vivo. A weight matrix for the ResD binding site was defined by a bioinformatic approach. The results obtained suggest the existence of a new branch of the complex regulatory system employed for the adaptation of
B. subtilis
to anaerobic growth conditions.