bluuebunny/crossref_metadata_2025 huggingface dataset:
Presence of Acylated Homoserine Lactones (AHLs) and AHL-Producing Bacteria in Meat and Potential Role of AHL in Spoilage of Meat
Authors: Bruhn Jesper Bartholin , Christensen Allan Beck , Flodgaard Lars Ravn , Nielsen Kristian Fog , Larsen Thomas Ostenfeld , Givskov Michael , Gram Lone
Published: July 2004

Quorum-sensing (QS) signals (N-acyl homoserine lactones [AHLs]) were extracted and detected from five commercially produced vacuum-packed meat samples. Ninety-six AHL-producing bacteria were isolated, and 92 were identified asEnterobacteriaceae. Hafnia alveiwas the most commonly identified AHL-producing bacterium. Thin-layer chromatographic profiles of supernatants from sixH. alveiisolates and of extracts from spoiling meat revealed that the major AHL species had anRfvalue and shape similar toN-3-oxo-hexanoyl homoserine lactone (OHHL). Liquid chromatography-mass spectrometry (MS) (high-resolution MS) analysis confirmed the presence of OHHL in pure cultures ofH. alvei. Vacuum-packed meat spoiled at the same rate when inoculated with theH. alveiwild type compared to a corresponding AHL-lacking mutant. Addition of specific QS inhibitors to the AHL-producingH. alveiinoculated in meat or to naturally contaminated meat did not influence the spoilage of vacuum-packed meat. An extracellular protein of approximately 20 kDa produced by theH. alveiwild-type was not produced by the AHL-negative mutant but was restored in the mutant when complemented by OHHL, thus indicating that AHLs do have a regulatory role inH. alvei. Coinoculation ofH. alveiwild-type with an AHL-deficientSerratia proteamaculansB5a, in which protease secretion is QS regulated, caused spoilage of liquid milk. By contrast, coinoculation of AHL-negative strains ofH. alveiandS. proteamaculansB5a did not cause spoilage. In conclusion, AHL and AHL-producing bacteria are present in vacuum-packed meat during storage and spoilage, but AHL does not appear to influence the spoilage of this particular type of conserved meat. Our data indicate that AHL-producingH. alveimay induce food quality-relevant phenotypes in other bacterial species in the same environment.H. alveimay thus influence spoilage of food products in whichEnterobacteriaceaeparticipate in the spoilage process.
Restoration of a Defective
Lactococcus lactis
Xylose Isomerase
Authors: Park Joo-Heon , Batt Carl A.
Published: July 2004

The genes (
xylA
) encoding xylose isomerase (XI) from two
Lactococcus lactis
subsp.
lactis
strains, 210 (Xyl
−
) and IO-1 (Xyl
+
), were cloned, and the activities of their expressed proteins in recombinant strains of
Escherichia coli
were investigated. The nucleotide and amino acid sequence homologies between the
xylA
genes were 98.4 and 98.6%, respectively, and only six amino acid residues differed between the two XIs. The purified IO-1 XI was soluble with
K

m

and
k
cat
being 2.25 mM and 184/s, respectively, while the 210 XI was insoluble and inactive. Site-directed mutagenesis on 210
xylA
showed that a triple mutant possessing R202M/Y218D/V275A mutations regained XI activity and was soluble. The
K

m

and
k
cat
of this mutant were 4.15 mM and 141/s, respectively. One of the IO-1 XI mutants, S388T, was insoluble and showed negligible activity similar to that of 210 XI. The introduction of a K407E mutation to the IO-1 S388T XI mutant restored its activity and solubility. The dissolution of XI activity in
L. lactis
subsp.
lactis
involves a series of mutations that collectively eliminate enzyme activity by reducing the solubility of the enzyme.
Microscale and Molecular Assessment of Impacts of Nickel, Nutrients, and Oxygen Level on Structure and Function of River Biofilm Communities
Authors: Lawrence J. R. , Chenier M. R. , Roy R. , Beaumier D. , Fortin N. , Swerhone G. D. W. , Neu T. R. , Greer C. W.
Published: July 2004

Studies were carried out to assess the influence of nutrients, dissolved oxygen (DO) concentration, and nickel (Ni) on river biofilm development, structure, function, and community composition. Biofilms were cultivated in rotating annular reactors with river water at a DO concentration of 0.5 or 7.5 mg liter
−1
, with or without a combination of carbon, nitrogen, and phosphorus (CNP) and with or without Ni at 0.5 mg liter
−1
. The effects of Ni were apparent in the elimination of cyanobacterial populations and reduced photosynthetic biomass in the biofilm. Application of lectin-binding analyses indicated changes in exopolymer abundance and a shift in the glycoconjugate makeup of the biofilms, as well as in the response to all treatments. Application of the fluorescent live-dead staining (BacLight Live-Dead staining kit; Molecular Probes, Eugene, Oreg.) indicated an increase in the ratio of live to dead cells under low-oxygen conditions. Nickel treatments had 50 to 75% fewer ‘live’ cells than their corresponding controls. Nickel at 0.5 mg liter
−1
corresponding to the industrial release rate concentration for nickel resulted in reductions in carbon utilization spectra relative to control and CNP treatments without nickel. In these cases, the presence of nickel eliminated the positive influence of nutrients on the biofilm. Other culture-dependent analyses (plate counts and most probable number) revealed no significant treatment effect on the biofilm communities. In the presence of CNP and at both DO levels, Ni negatively affected denitrification but had no effect on hexadecane mineralization or sulfate reduction. Analysis of total community DNA indicated abundant eubacterial 16S ribosomal DNA (rDNA), whereas
Archaea
were not detected. Amplification of the
alkB
gene indicated a positive effect of CNP and a negative effect of Ni. The
nirS
gene was not detected in samples treated with Ni at 0.5 mg liter
−1
, indicating a negative effect on specific populations of bacteria, such as denitrifiers, resulting in a reduction in diversity. Denaturing gradient gel electrophoresis revealed that CNP had a beneficial impact on biofilm bacterial diversity at high DO concentrations, but none at low DO concentrations, and that the negative effect of Ni on diversity was similar at both DO concentrations. Notably, Ni resulted in the appearance of unique bands in 16S rDNA from Ni, DO, and CNP treatments. Sequencing results confirmed that the bands belonged to bacteria originating from freshwater and marine environments or from agricultural soils and industrial effluents. The observations indicate that significant interactions occur between Ni, oxygen, and nutrients and that Ni at 0.5 mg liter
−1
may have significant impacts on river microbial community diversity and function.
Development of a Multispecies Oral Bacterial Community in a Saliva-Conditioned Flow Cell
Authors: Foster Jamie S. , Kolenbrander Paul E.
Published: July 2004

Microbial communities within the human oral cavity are dynamic associations of more than 500 bacterial species that form biofilms on the soft and hard tissues of the mouth. Understanding the development and spatial organization of oral biofilms has been facilitated by the use of in vitro models. We used a saliva-conditioned flow cell, with saliva as the sole nutritional source, as a model to examine the development of multispecies biofilm communities from an inoculum containing the coaggregation partners
Streptococcus gordonii
,
Actinomyces naeslundii
,
Veillonella atypica
, and
Fusobacterium nucleatum
. Biofilms inoculated with individual species in a sequential order were compared with biofilms inoculated with coaggregates of the four species. Our results indicated that flow cells inoculated sequentially produced biofilms with larger biovolumes compared to those biofilms inoculated with coaggregates. Individual-species biovolumes within the four-species communities also differed between the two modes of inoculation. Fluorescence in situ hybridization with genus- and species-specific probes revealed that the majority of cells in both sequentially and coaggregate-inoculated biofilms were
S. gordonii
, regardless of the inoculation order. However, the representation of
A. naeslundii
and
V. atypica
was significantly higher in biofilms inoculated with coaggregates compared to sequentially inoculated biofilms. Thus, these results indicate that the development of multispecies biofilm communities is influenced by coaggregations preformed in planktonic phase. Coaggregating bacteria such as certain streptococci are especially adapted to primary colonization of saliva-conditioned surfaces independent of the mode of inoculation and order of addition in the multispecies inoculum. Preformed coaggregations favor other bacterial strains and may facilitate symbiotic relationships.
Fur Is Involved in Manganese-Dependent Regulation of
mntA
(
sitA
) Expression in
Sinorhizobium meliloti
Authors: Platero Raúl , Peixoto Lucía , O'Brian Mark R. , Fabiano Elena
Published: July 2004

Fur is a transcriptional regulator involved in iron-dependent control of gene expression in many bacteria. In this work we analyzed the phenotype of a
fur
mutant in
Sinorhizobium meliloti
, an α-proteobacterium that fixes N
2
in association with host plants. We demonstrated that some functions involved in high-affinity iron transport, siderophore production, and iron-regulated outer membrane protein expression respond to iron in a Fur-independent manner. However, manganese-dependent expression of the MntABCD manganese transport system was lost in a
fur
strain as discerned by constitutive expression of a
mntA::gfp
fusion reporter gene in the mutant. Thus, Fur directly or indirectly regulates a manganese-dependent function. The data indicate a novel function for a bacterial Fur protein in mediating manganese-dependent regulation of gene expression.
Liquid Serial Dilution Is Inferior to Solid Media for Isolation of Cultures Representative of the Phylum-Level Diversity of Soil Bacteria
Authors: Schoenborn Liesbeth , Yates Penelope S. , Grinton Bronwyn E. , Hugenholtz Philip , Janssen Peter H.
Published: July 2004

Representatives of only four well-characterized bacterial phyla were isolated from a pasture soil by using liquid serial dilution culture. In contrast, members of
Acidobacteria
,
Verrucomicrobia
, and
Gemmatimonadetes
and of other poorly represented bacterial lineages were isolated in earlier experiments with solidified versions of the same media. We conclude that, contrary to expectation, liquid serial dilution culture is inferior to culturing on solid media for isolating representatives of many bacterial phyla from soil.
Comparison of Shiga-Toxigenic
Escherichia coli
Prevalences among Dairy, Feedlot, and Cow-Calf Herds in Washington State
Authors: Cobbold Rowland N. , Rice Daniel H. , Szymanski Maryanne , Call Douglas R. , Hancock Dale D.
Published: July 2004

Shiga-toxigenic
Escherichia coli
(STEC) strains were isolated from 7.4% of 1,440 fecal and farm environmental samples. Shiga toxin gene and STEC prevalences were significantly associated with animal production type and season. A range of serogroups were identified. Nine percent of isolates possessed all three principal virulence markers:
stx
2
,
eae
, and
ehx
.
Validation of a PCR-Based Method for Detection of Food-Borne Thermotolerant Campylobacters in a Multicenter Collaborative Trial
Authors: Josefsen M. H. , Cook N. , D'Agostino M. , Hansen F. , Wagner M. , Demnerova K. , Heuvelink A. E. , Tassios P. T. , Lindmark H. , Kmet V. , Barbanera M. , Fach P. , Loncarevic S. , Hoorfar J.
Published: July 2004

A PCR-based method for rapid detection of food-borne thermotolerant campylobacters was evaluated through a collaborative trial with 12 laboratories testing spiked carcass rinse samples. The method showed an interlaboratory diagnostic sensitivity of 96.7% and a diagnostic specificity of 100% for chicken samples, while these values were 94.2 and 83.3%, respectively, for pig samples.
Degradation and Turnover of Extracellular DNA in Marine Sediments: Ecological and Methodological Considerations
Authors: Dell'Anno Antonio , Corinaldesi Cinzia
Published: July 2004

Degradation rates of extracellular DNA determined in marine sediments were much higher than those in the water column. However, due to the high sediment DNA content, turnover times were much shorter in seawater. Results reported here provide new insights into the role of extracellular DNA in P cycling in marine ecosystems.
Isolates of
Piscirickettsia salmonis
from Scotland and Ireland Show Evidence of Clonal Diversity
Authors: Reid H. I. , Griffen A. A. , Birkbeck T. H.
Published: July 2004

Salmonid rickettsial septicemia, caused by
Piscirickettsia salmonis
, causes major mortalities in Chilean salmonid aquaculture and is an increasing problem in Atlantic salmon in Ireland and Scotland. Analysis of 16S-to-23S internal transcribed sequences and 16S ribosomal DNA (rDNA) shows that Irish isolates of
P. salmonis
form two new groups of the organism while Scottish isolates cluster together with Norwegian and Canadian isolates from Atlantic salmon.
Influence of Biosurfactants from Probiotic Bacteria on Formation of Biofilms on Voice Prostheses
Authors: Rodrigues Lígia , van der Mei Henny C. , Teixeira José , Oliveira Rosário
Published: July 2004

Biofilms were grown on preconditioned voice prostheses with biosurfactants obtained from probiotic bacteria
Lactococcus lactis
53 and
Streptococcus thermophilus
A in an artificial throat model. Both biosurfactants greatly reduced microbial numbers on prostheses and also induced a decrease in the airflow resistance that occurs on voice prostheses after biofilm formation. This study presents a promising strategy for prolonging the lifespan of voice prostheses.
Use of Oligonucleotide Microarrays for Rapid Detection and Serotyping of Acute Respiratory Disease-Associated Adenoviruses
Authors: Lin Baochuan , Vora Gary J. , Thach Dzung , Walter Elizabeth , Metzgar David , Tibbetts Clark , Stenger David A.
Published: July 2004

The cessation of the adenovirus vaccination program for military trainees has resulted in several recent acute respiratory disease (ARD) outbreaks. In the absence of vaccination, rapid detection methods are necessary for the timely implementation of measures to prevent adenovirus transmission within military training facilities. To this end, we have combined a fluorogenic real-time multiplex PCR assay with four sets of degenerate PCR primers that target theE1A,fiber, andhexongenes with a long oligonucleotide microarray capable of identifying the most common adenovirus serotypes associated with adult respiratory tract infections (serotypes 3, 4, 7, 16, and 21) and a representative member of adenovirus subgroup C (serotype 6) that is a common cause of childhood ARD and that often persists into adulthood. Analyses with prototype strains demonstrated unique hybridization patterns for representative members of adenovirus subgroups B1, B2, C, and E, thus allowing serotype determination. Microarray-based sensitivity assessments revealed lower detection limits (between 1 and 100 genomic copies) for adenovirus serotype 4 (Ad4) and Ad7 cell culture lysates, clinical nasal washes, and throat swabs and purified DNA from clinical samples. When adenovirus was detected from coded clinical samples, the results obtained by this approach demonstrated an excellent concordance with those obtained by the more established method of adenovirus identification as well as by cell culture with fluorescent-antibody staining. Finally, the utility of this method was further supported by its ability to detect adenoviral coinfections, contamination, and, potentially, recombination events. Taken together, the results demonstrate the usefulness of the simple and rapid diagnostic method developed for the unequivocal identification of ARD-associated adenoviral serotypes from laboratory or clinical samples that can be completed in 1.5 to 4.0 h.
Septic Arthritis of the Knee Due to
Fusobacterium necrophorum
Authors: Sonsale Paresh D , Philipson Mark R. , Bowskill Jilean
Published: July 2004

Gram-negative, anaerobic bacilli are unusual organisms to be isolated in cases of acute septic arthritis. We report the isolation of
Fusobacterium necrophorum
from joint aspirate in a case of acute septic arthritis, which presented 3 weeks after the drainage of a dental abscess.
THE EQUATIONS OF ELASTICITY WITH DISSIPATION AS A NONTRIVIAL EXAMPLE OF THERMODYNAMICALLY CONSISTENT HYPERBOLIC EQUATIONS
Authors: GODUNOV SERGEI K.
Published: July 2004

A thermodynamically consistent Galilean-invariant formalization of the elasticity equations is proposed. The equations under consideration form a symmetric hyperbolic system but they are non-conservative. The conservation laws are valid only on a solution with special initial values. Difficulties arising while introducing the dissipative terms are briefly discussed.
QUANTUM ELECTRODYNAMICS OF RELATIVISTIC BOUND STATES WITH CUTOFFS
Authors: BARBAROUX JEAN-MARIE , DIMASSI MOUEZ , GUILLOT JEAN-CLAUDE
Published: July 2004

We consider a Hamiltonian with ultraviolet and infrared cutoffs, describing the interaction of relativistic electrons and positrons in the Coulomb potential with photons in Coulomb gauge. The interaction includes both interaction of the current density with transversal photons and the Coulomb interaction of charge density with itself.

We prove that the Hamiltonian is self-adjoint and has a ground state for sufficiently small coupling constants.
STRONGLY HYPERBOLIC SYSTEMS IN GENERAL RELATIVITY
Authors: REULA OSCAR A.
Published: July 2004

We discuss several topics related to the notion of strong hyperbolicity which are of interest in general relativity. After introducing the concept and showing its relevance we provide some covariant definitions of strong hyperbolicity. We then prove that if a system is strongly hyperbolic with respect to a given hypersurface, then it is also strongly hyperbolic with respect to any nearby surface.

We then study for how much these hypersurfaces can be deformed and discuss then causality, namely what the maximal propagation speed in any given direction is. In contrast with the symmetric hyperbolic case, for which the proof of causality is geometrical and direct, relaying in energy estimates, the proof for general strongly hyperbolic systems is indirect for it is based in Holmgren's theorem.

To show that the concept is needed in the area of general relativity we discuss two results for which the theory of symmetric hyperbolic systems shows to be insufficient. The first deals with the hyperbolicity analysis of systems which are second order in space derivatives; they include certain versions of the ADM and the BSSN families of equations. This analysis is considerably simplified by introducing pseudo-differential first-order evolution equations. Well-posedness for some members of the latter family systems is established by showing they satisfy the strong hyperbolicity property. Furthermore it is shown that many other systems of such families are only weakly hyperbolic, implying they should not be used for numerical modeling.

The second result deals with systems having constraints. The question posed is which hyperbolicity properties, if any, are inherited from the original evolution system by the subsidiary system satisfied by the constraint quantities. The answer is that, subject to some condition on the constraints, if the evolution system is strongly hyperbolic then the subsidiary system is also strongly hyperbolic and the causality properties of both are identical.
CONFORMAL SCATTERING AND THE GOURSAT PROBLEM
Authors: MASON LIONEL J. , NICOLAS JEAN-PHILIPPE
Published: July 2004

We work on a class of non-stationary vacuum space-times admitting a conformal compactification that is smooth at null and timelike infinity. Via a conformal transformation, the existence of a scattering operator for field equations is interpreted as the well-posedness of a Goursat problem on null infinity. We solve the Goursat problem in the case of Dirac and Maxwell fields. The case of the wave equation is also discussed and it is shown why the method cannot be applied at present. Then the conformal scattering operator is proved to be equivalent to an analytical scattering operator defined in terms of classical wave operators.
THE DYNAMICS OF PRESSURELESS DUST CLOUDS AND DELTA WAVES
Authors: LEVEQUE RANDALL J.
Published: July 2004

The equations of isothermal gas dynamics are studied in the limit when the sound speed vanishes, giving the so-called pressureless gas equations. The collision of two clouds of dust is modeled with these equations in the case where the clouds have finite extent and are surrounded by vacuum. The delta shock that arises in the initial stage of the collision evolves into a delta rarefaction-shock and then into a delta double-rarefaction as first one cloud and then the other is fully accreted into the singularity. A high-resolution finite volume method that captures this behavior is also presented and numerical results shown.
CHEMICAL SENSING AND CATALYSIS BY ONE-DIMENSIONAL METAL-OXIDE NANOSTRUCTURES
Authors: Kolmakov Andrei , Moskovits Martin
Published: July 2004

▪ Abstract  Metal-oxide nanowires can function as sensitive and selective chemical or biological sensors, which could potentially be massively multiplexed in devices of small size. The active nanowire sensor element in such devices can be configured either as resistors whose conductance is altered by charge-transfer processes occurring at their surfaces or as field-effect transistors whose properties can be controlled by applying an appropriate potential onto its gate. Functionalizing the surface of these entities offers yet another avenue for expanding their sensing capability. In turn, because charge exchange between an adsorbate and the nanowire can change the electron density in the nanowire, modifying the nanowire's carrier density by external means, such as applying a potential to the gate, could modify its surface chemical properties and perhaps change the rate and selectivity of catalytic processes occurring at its surface. Although research on the use of metal-oxide nanowires as sensors is still in early stages, several encouraging experiments have been reported that are interesting in their own right and indicative of a promising future.
SEMICONDUCTOR NANOWIRES AND NANOTUBES
Authors: Law Matt , Goldberger Joshua , Yang Peidong
Published: July 2004

▪ Abstract  Semiconductor nanowires and nanotubes exhibit novel electronic and optical properties owing to their unique structural one-dimensionality and possible quantum confinement effects in two dimensions. With a broad selection of compositions and band structures, these one-dimensional semiconductor nanostructures are considered to be the critical components in a wide range of potential nanoscale device applications. To fully exploit these one-dimensional nanostructures, current research has focused on rational synthetic control of one-dimensional nanoscale building blocks, novel properties characterization and device fabrication based on nanowire building blocks, and integration of nanowire elements into complex functional architectures. Significant progress has been made in a few short years. This review highlights the recent advances in the field, using work from this laboratory for illustration. The understanding of general nanocrystal growth mechanisms serves as the foundation for the rational synthesis of semiconductor heterostructures in one dimension. Availability of these high-quality semiconductor nanostructures allows systematic structural-property correlation investigations, particularly of a size- and dimensionality-controlled nature. Novel properties including nanowire microcavity lasing, phonon transport, interfacial stability and chemical sensing are surveyed.
UNUSUAL PROPERTIES AND STRUCTURE OF CARBON NANOTUBES
Authors: Dresselhaus M.S. , Dresselhaus G. , Jorio A.
Published: July 2004

▪ Abstract  The unusual structure and properties of carbon nanotubes are presented, with particular reference to single-wall nanotubes (SWNTs) and nanotube properties that differ from those of their bulk counterparts. The atomic structure; electronic structure; and vibrational, optical, mechanical, and thermal properties are discussed, with reference made to nanotube junctions, nanotube filling, and double-wall nanotubes (DWNTs). Special attention is given to resonance Raman spectroscopy at the single nanotube level. The status of current research in this field is assessed and opportunities for future research are identified.
SIMULATION OF DNA-NANOTUBE INTERACTIONS
Authors: Gao Huajian , Kong Yong
Published: July 2004

▪ Abstract  Carbon nanotubes functionalized with biological molecules (such as protein peptides and nucleic acids) show great potential for application in bioengineering and nanotechnology. Fundamental understanding, description, and regulation of such bio-nano-systems will ultimately lead to a new generation of integrated systems that combine unique properties of the carbon nanotube (CNT) with biological recognition capabilities. In this review, we describe recent advances in understanding the interactions between deoxyribonucleic acids (DNA) and CNT, as well as relevant simulation techniques. We also review progress in simulating DNA noncovalent interactions with CNTs in an aqueous environment. Molecular dynamics simulations indicate that DNA molecules may be encapsulated inside or wrap around CNT owing to van der Waals attraction between DNA and CNT. We focus on the dynamics and energetics of DNA encapsulation inside nanotubes and discuss the mechanism of encapsulation and the effects of nanotube size, nanotube end-group, DNA base sequence, solvent temperature and pressure on the encapsulation process. Finally, we discuss the likely impact of DNA encapsulation on bioengineering and nanotechnology, as well as other potential applications.
MATERIALS ASSEMBLY AND FORMATION USING ENGINEERED POLYPEPTIDES
Authors: Sarikaya Mehmet , Tamerler Candan , Schwartz Daniel T. , Baneyx François
Published: July 2004

▪ Abstract  Molecular biomimetics can be defined as mimicking function, synthesis, or structure of materials and systems at the molecular scale using biological pathways. Here, inorganic-binding polypeptides are used as molecular building blocks to control assembly and formation of functional inorganic and hybrid materials and systems for nano- and nanobiotechnology applications. These polypeptides are selected via phage or cell surface display technologies and modified by molecular biology to tailor their binding and multifunctionality properties. The potential of this approach in creating new materials systems with useful physical and biological properties is enormous. This mostly stems from molecular recognition and self-assembly characteristics of the polypeptides plus the added advantage of genetic manipulation of their composition and structure. In this review, we highlight the basic premises of molecular biomimetics, describe the approaches in selecting and engineering inorganic-binding polypeptides, and present examples of their utility as molecular linkers in current and future applications.
UNCONVENTIONAL NANOFABRICATION
Authors: Gates Byron D. , Xu Qiaobing , Love J. Christopher , Wolfe Daniel B. , Whitesides George M.
Published: July 2004

▪ Abstract  Nanostructures are fabricated using either conventional or unconventional tools—that is, by techniques that are highly developed and widely used or by techniques that are relatively new and still being developed. This chapter reviews techniques of unconventional nanofabrication, and focuses on experimentally simple and inexpensive approaches to pattern features with dimensions <100 nm. The techniques discussed include soft lithography, scanning probe lithography, and edge lithography. The chapter includes recent advances in fabricating nanostructures using each set of techniques, together with demonstrated advantages, limitations, and applications for each.
MODELING AND SIMULATION OF BIOMATERIALS
Authors: Redondo Antonio , LeSar Richard
Published: July 2004

▪ Abstract  Modeling and simulation are becoming increasingly accepted components of materials research. In this review we discuss application of modeling and simulation in the developing field of biomaterials. To restrict the discussion somewhat, we focus primarily on the structure and properties of biomaterials and do not discuss biochemical or biomedical applications. We start with a discussion of how atomistic-level simulation can be used to study molecules and collections of molecules. We then focus on mesoscale simulations of structure and properties, followed by a brief review of continuum-scale approaches. We end with some thoughts on the future of modeling and simulation in biomaterials applications.
Glucocorticoid exposure in late gestation in the rat permanently programs gender-specific differences in adult cardiovascular and metabolic physiology
Authors: O'Regan D. , Kenyon C. J. , Seckl J. R. , Holmes M. C.
Published: July 2004

Glucocorticoid overexposure in utero may underlie the association between low birth weight and subsequent development of common cardiovascular and metabolic pathologies. Previously, we have shown that prenatal dexamethasone (DEX) exposure in rat reduces birth weight and programs the hypothalamic-pituitary axis and fasting and postprandial hyperglycemia in adult males and hypertension in adult males and females. This study aimed to determine 1) whether there were gender differences in prenatal DEX-programmed offspring, and 2) whether the renin-angiotensin system (RAS) plays a role in the programming of hypertension. Rats exposed to DEX in utero (100 μg·kg−1·day−1 from embryonic days 14–21) were of lower birth weight (by 12%, P < 0.01) and displayed full catch-up growth within the first month of postnatal life. DEX-treated male offspring in adulthood selectively displayed elevated plasma adrenocorticotropic hormone (by 221%) and corticosterone (by 188%, P < 0.05), postprandial insulin-glucose ratios (by 100%, P < 0.05), and hepatic expression of the gluconeogenic enzyme phospho enolpyruvate carboxykinase (by 38%, P < 0.05). Conversely, DEX-programmed females were hypertensive (by 11%, P < 0.05), with elevated hepatic angiotensinogen mRNA expression (by 9%, P < 0.05), plasma angiotensinogen (by 61%, P < 0.05), and renin activity (by 88%, P < 0.05). These findings demonstrate that prenatal glucocorticoids program adulthood cardiovascular and metabolic physiology in a gender-specific pattern, and that an activated RAS may in part underlie the hypertension associated with prenatal DEX programming.
Dual-energy X-ray absorptiometry lean soft tissue hydration: independent contributions of intra- and extracellular water
Authors: St-Onge Marie-Pierre , Wang ZiMian , Horlick Mary , Wang Jack , Heymsfield Steven B.
Published: July 2004

Dual-energy X-ray absorptiometry (DEXA) provides a measure of lean soft tissue (LST). LST hydration, often assumed to be constant, is relevant to several aspects of DEXA body composition estimates. The aims of this study were to develop a theoretical model of LST total body water (TBW) content and to examine hydration effects with empirically derived model coefficients and then to experimentally test the model's prediction that, in healthy adults, LST hydration is not constant but varies as a function of extra- and intracellular water distribution (E/I). The initial phase involved TBW/LST model development and application with empirically derived model coefficients. Model predictions were then tested in a cross-sectional study of 215 healthy adults. LST was measured by DEXA, extracellular water (ECW) by NaBr dilution, intracellular water (ICW) by whole body40K counting, and TBW by2H2O dilution. TBW estimates, calculated as ECW + ICW, were highly correlated with ( r = 0.97, SEE = 2.1 kg, P < 0.001) and showed no significant bias compared with TBW measured by2H2O. Model-predicted TBW/LST was almost identical to experimentally derived values (means ± SD) in the total group (0.767 vs. 0.764 ± 0.028). LST hydration was significantly correlated with E/I (total group, r = 0.30, SEE = 0.027, P < 0.001). Although E/I increased with age (men, r = 0.48; women, r = 0.37; both P < 0.001), the association between TBW/LST and age was nonsignificant. Hydration of the DEXA-derived LST compartment is thus not constant but varies predictably with ECW and ICW distribution. This observation has implications for the accuracy of body fat measurements by DEXA and the use of TBW as a means of checking DEXA system calibration.
High-Threshold, Kv3-Like Potassium Currents in Magnocellular Neurosecretory Neurons and Their Role in Spike Repolarization
Authors: Shevchenko Talent , Teruyama Ryoichi , Armstrong William E.
Published: July 2004

We identified Kv3-like high-threshold K+ currents in hypothalamic supraoptic neurons using whole cell recordings in hypothalamic slices and in acutely dissociated neurons. Tetraethylammonium (TEA)-sensitive currents (<1 mM TEA) evoked from −50 mV were characterized by a large component that inactivated in 10–30 ms, and a smaller, persistent component that inactivated in 1–2 s. I/ V relations in dissociated neurons revealed TEA-subtracted currents with a slope and voltage dependency consistent with the presence of Kv3-like channels. In slices, tests with 0.01–0.7 mM TEA produced an IC50 of 200–300 nM for both fast and persistent currents. The fast transient current was similar to currents associated with the expression of Kv3.4 subunits, given that it was sensitive to BDS-I (100 nM). The persistent TEA-sensitive current appeared similar to those attributed to Kv3.1/3.2 subunits. Although qualitatively similar, oxytocin (OT) and vasopressin (VP) neurons in slices differed in the stronger presence of persistent current in VP neurons. In both cell types, the IC50 for TEA-induced spike broadening was similar to that observed for current suppression in voltage clamp. However, TEA had a greater effect on the spike width of VP neurons than of OT neurons. Immunochemical studies revealed a stronger expression of the Kv3.1b α-subunit in VP neurons, which may be related to the greater importance of this current type in VP spike repolarization. Because OT and VP neurons are not considered fast firing, but do exhibit frequency- and calcium-dependent spike broadening, Kv3-like currents may be important for maintaining spike width and calcium influx within acceptable limits during repetitive firing.
Common Input to Motor Units of Digit Flexors During Multi-Digit Grasping
Authors: Winges Sara A. , Santello Marco
Published: July 2004

The control of whole hand grasping relies on complex coordination of multiple forces. While many studies have characterized the coordination of finger forces and torques, the control of hand muscle activity underlying multi-digit grasping has not been studied to the same extent. Motor-unit synchrony across finger muscles or muscle compartments might be one of the factors underlying the limited individuation of finger forces. Such “unwanted” coupling among finger forces, however, might be desirable when a high level of force coupling is required to prevent object slip during grasping. The goal of this study was to quantify the strength of synchrony between single motor units from extrinsic hand muscles as subjects held a device with a five-digit grasp. During the hold phase, we recorded the normal force exerted by each digit and the electrical activity of single motor units from each of the four divisions of the muscle flexor digitorum profundus (FDP) and one thumb flexor muscle, m. flexor pollicis longus (FPL). The strength of motor-unit synchrony was quantified by the common input strength index (CIS). We found moderate to strong motor-unit synchrony between FPL and the index FDP compartment [CIS: 0.49 ± 0.03 (SE)] and across most FDP compartments (0.34 ± 0.02). Weak synchrony, however, was found between FPL and the middle, ring, and little finger FDP compartments (0.25 ± 0.01). This difference might reflect the larger force contribution of the thumb-index finger pair relative to other thumb-finger combinations in five-digit grasping.
Taste Receptor Cells Express pH-Sensitive Leak K+ Channels
Authors: Lin W. , Burks C. A. , Hansen D. R. , Kinnamon S. C. , Gilbertson T. A.
Published: July 2004

Two-pore domain K+ channels encoded by genes KCNK1-17 ( K2p1-17) play important roles in regulating cell excitability. We report here that rat taste receptor cells (TRCs) highly express TASK-2 (KCNK5; K2p5.1), and to a much lesser extent TALK-1 (KCNK16; K2p16.1) and TASK-1 (KCNK3; K2p3.1), and suggest potentially important roles for these channels in setting resting membrane potentials and in sour taste transduction. Whole cell recordings of isolated TRCs show that a leak K+ (Kleak) current in a subset of TRCs exhibited high sensitivity to acidic extracellular pH similar to reported properties of TASK-2 and TALK-1 channels. A drop in bath pH from 7.4 to 6 suppressed 90% of the current, resulting in membrane depolarization. K+ channel blockers, BaCl2, but not tetraethylammonium (TEA), inhibited the current. Interestingly, resting potentials of these TRCs averaged –70 mV, which closely correlated with the amplitude of the pH-sensitive Kleak, suggesting a dominant role of this conductance in setting resting potentials. RT-PCR assays followed by sequencing of PCR products showed that TASK-1, TASK-2, and a functionally similar channel, TALK-1, were expressed in all three types of lingual taste buds. To verify expression of TASK channels, we labeled taste tissue with antibodies against TASK-1, TASK-2, and TASK-3. Strong labeling was seen in some TRCs with antibody against TASK-2 but not TASK-1 and TASK-3. Consistent with the immunocytochemical staining, quantitative real-time PCR assays showed that the message for TASK-2 was expressed at significantly higher levels (10–100 times greater) than was TASK-1, TALK-1, or TASK-3. Thus several K2P channels, and in particular TASK-2, are expressed in rat TRCs, where they may contribute to the establishment of resting potentials and sour reception.
Plasticity of mouse renal collecting duct in response to potassium depletion
Authors: Cheval Lydie , Duong Van Huyen Jean Paul , Bruneval Patrick , Verbavatz Jean-Marc , Elalouf Jean-Marc , Doucet Alain
Published: July 2004

Plasticity of mouse renal collecting duct in response to potassium depletion. —Renal collecting ducts are the main sites for regulation of whole body potassium balance. Changes in dietary intake of potassium induce pleiotropic adaptations of collecting duct cells, which include alterations of ion and water transport properties along with an hypertrophic response. To study the pleiotropic adaptation of the outer medullary collecting duct (OMCD) to dietary potassium depletion, we combined functional studies of renal function (ion, water, and acid/base handling), analysis of OMCD hypertrophy (electron microscopy) and hyperplasia (PCNA labeling), and large scale analysis of gene expression (transcriptome analysis). The transcriptome of OMCD was compared in mice fed either a normal or a potassium-depleted diet for 3 days using serial analysis of gene expression (SAGE) adapted for downsized extracts. SAGE is based on the generation of transcript-specific tag libraries. Approximately 20,000 tags corresponding to 10,000 different molecular species were sequenced in each library. Among the 186 tags differentially expressed ( P < 0.05) between the two libraries, 120 were overexpressed and 66 were downregulated. The SAGE expression profile obtained in the control library was representative of different functional classes of proteins and of the two cell types (principal and α-intercalated cells) constituting the OMCD. Combined with gene expression analysis, results of functional and morphological studies allowed us to identify candidate genes for distinct physiological processes modified by potassium depletion: sodium, potassium, and water handling, hyperplasia and hypertrophy. Finally, comparison of mouse and human OMCD transcriptomes allowed us to address the question of the relevance of the mouse as a model for human physiology and pathophysiology.
Liver gene expression associated with diet and lesion development in atherosclerosis-prone mice: induction of components of alternative complement pathway
Authors: Recinos Adrian , Carr Boyd K. , Bartos David B. , Boldogh Istvan , Carmical J. Russ , Belalcazar L. Maria , Brasier Allan R.
Published: July 2004

Diet-induced changes in serum lipoproteins are a major risk factor for the development of atherosclerosis, the leading cause of mortality in Westernized countries. Atherosclerosis is now appreciated to be a systemic inflammatory disease where increased synthesis of inducible proteins by the liver, such as C-reactive protein (CRP) and others, may play roles in accelerating the disease process. To systematically investigate the genetic response of the liver to diet-induced atherosclerosis, we applied high-density microarray technology in a mouse model of atherosclerosis (LDLR−/−mouse). LDLR−/−mice and congenic (LDLR+/+) controls were placed on low-fat (LF) or high-fat (HF) Western-style diets. The Western diet produced sustained elevations in total cholesterol (2.5-fold for LDLR+/+, 5.0-fold LDLR−/−) relative to the respective LF groups. Tissues were harvested after 12 wk when significant atherosclerotic lesion development was first detectable by en face histomorphometry of oil red O-stained aortas. Diet, rather than genotype, was most highly associated with development of atherosclerotic lesions. Liver mRNA expression profiles of triplicate animals from each group were determined by high-density oligonucleotide microarrays; and genes with transcript levels influenced by genotype and diet were identified by two-way ANOVA. Approximately one-third of the 102 genes identified to be altered by diet [Pr(F) < 0.0005] were involved in lipid metabolism. In addition, we identified components of the alternative complement pathway, including C3, properdin, and factor D, for which mRNA levels were independently confirmed by quantitative real-time RT-PCR analysis, and C3 protein was demonstrated in aortic lesions by immunostaining. These findings suggest that induction of the alternative complement pathway may be an additional mechanism by which a high-fat/Western diet accelerates atherosclerosis.
Reliability of communication networks with delay constraints: computational complexity and complete topologies
Authors: Cancela H. , Petingi L.
Published: July 2004

Let G = (V, E) be a graph with a distinguished set of terminal
vertices K⫅V. We define the K‐diameter of G as
the maximum distance between any pair of vertices of K. If the
edges fail randomly and independently with known probabilities
(vertices are always operational), the
diameter-constrained K-terminal reliability of G,
RK(G, D), is defined as the probability that surviving edges
span a subgraph whose K‐diameter does not exceed D. In general, the computational complexity
of evaluating RK(G, D) is NP‐hard, as this measure subsumes the
classical K‐terminal reliability RK(G), known to belong to
this complexity class. In this note, we show that even though for
two terminal vertices s and t
and D = 2, R{s,t}(G, D)

can be determined in polynomial time, the problem of calculating
R{s,t}(G, D) for fixed values of D, D ≥ 3, is
NP‐hard. We also generalize this result for any fixed number of
terminal vertices. Although it is very unlikely that general
efficient algorithms exist, we present a recursive formulation
for the calculation of R{s,t}(G, D) that yields a
polynomial time evaluation algorithm in the case of complete
topologies where the edge set can be partitioned into at most
four equi‐reliable classes.
Combinatorial polarization, code loops, and codes of high level
Authors: Vojtěchovský Petr
Published: July 2004

We first find the combinatorial degree of any map f : V → F, where F is a finite field and V
is a finite‐dimensional
vector space over F. We then simplify and generalize a certain
construction, due to Chein and Goodaire, that was used in
characterizing code loops as finite Moufang loops that possess at
most two squares. The construction yields binary codes of high
divisibility level with prescribed Hamming weights of
intersections of codewords.
Partially relaxed cocoercive variational inequalities and auxiliary problem principle
Authors: Verma Ram U.
Published: July 2004

Let T : K → H be a mapping from a nonempty closed convex subset K of a finite‐dimensional Hilbert space H into H. Let f : K → ℝ be proper, convex, and lower semicontinuous on K and let h : K → ℝ be continuously Frećhet‐differentiable on K with h′ (gradient of h), α‐strongly monotone, and β‐Lipschitz continuous on K. Then the sequence {xk} generated by the general auxiliary problem principle converges to a solution x* of the variational inequality problem (VIP) described as follows: find an element x* ∈ K such that 〈T(x*), x − x*〉 + f(x) − f(x*) ≥ 0 for all x ∈ K.
On the order of growth of convergent series of independent random variables
Authors: Nam Eunwoo
Published: July 2004

For independent random variables, the order of growth of the convergent series Sn is studied in this paper. More specifically, if the series Sn converges almost surely to a random variable, the tail series is a well‐defined sequence of random variables and converges to 0 almost surely. For the almost surely convergent series Sn, a tail series strong law of large numbers (SLLN) is constructed by investigating the duality between the limiting behavior of partial sums and that of tail series.
Prevalence of backward stochastic differential equations with unique solution
Authors: Bahlali K. , Mezerdi B. , Ouknine Y.
Published: July 2004

We prove that in the sense of Baire category, almost all backward stochastic differential equations (BSDEs) with bounded and continuous coefficient have the properties of existence and uniqueness of solutions as well as the continuous dependence of solutions on the coefficient and the L2‐convergence of their associated successive approximations.
On fuzzy Volterra integral equations with deviating arguments
Authors: Balachandran K. , Prakash P.
Published: July 2004

We investigate the problem of existence of solutions of fuzzy Volterra integral equations with deviating arguments. The results are obtained by using the Darbo fixed point theorem.
A description of stochastic systems using chaotic maps
Authors: Boyarsky Abraham , Góra Paweł
Published: July 2004

Let ρ(x, t) denote a family of probability density functions parameterized by time t. We show the existence of a family {τ1 : t > 0} of deterministic nonlinear (chaotic) point transformations whose invariant probability density functions are precisely ρ(x, t). In particular, we are interested in the densities that arise from the diffusions. We derive a partial differential equation whose solution yields the family of chaotic maps whose density functions are precisely those of the diffusion.
Second‐order neutral stochastic evolution equations with heredity
Authors: McKibben Mark A.
Published: July 2004

Existence, continuous dependence, and approximation results are established for a class of abstract second‐order neutral stochastic evolution equations with heredity in a real separable Hilbert space. A related integro‐differential equation is also mentioned, as well as an example illustrating the theory.
A‐monotonicity and applications to nonlinear variational inclusion problems
Authors: Verma Ram U.
Published: July 2004

A new notion of the A‐monotonicity is introduced, which generalizes the H‐monotonicity. Since the A‐monotonicity originates from hemivariational inequalities, and hemivariational inequalities are connected with nonconvex energy functions, it turns out to be a useful tool proving the existence of solutions of nonconvex constrained problems as well.