bluuebunny/crossref_metadata_2025_split huggingface dataset:
Initial Phases of Biofilm Formation in
Shewanella oneidensis
MR-1
Authors: Thormann Kai M. , Saville Renée M. , Shukla Soni , Pelletier Dale A. , Spormann Alfred M. 
Published: November 2004

ABSTRACT

Shewanella oneidensis
MR-1 is a facultative Fe(III)- and Mn(IV)-reducing microorganism and serves as a model for studying microbially induced dissolution of Fe or Mn oxide minerals as well as biogeochemical cycles. In soil and sediment environments,
S. oneidensis
biofilms form on mineral surfaces and are critical for mediating the metabolic interaction between this microbe and insoluble metal oxide phases. In order to develop an understanding of the molecular basis of biofilm formation, we investigated
S. oneidensis
biofilms developing on glass surfaces in a hydrodynamic flow chamber system. After initial attachment, growth of microcolonies and lateral spreading of biofilm cells on the surface occurred simultaneously within the first 24 h. Once surface coverage was almost complete, biofilm development proceeded with extensive vertical growth, resulting in formation of towering structures giving rise to pronounced three-dimensional architecture. Biofilm development was found to be dependent on the nutrient conditions, suggesting a metabolic control. In global transposon mutagenesis, 173 insertion mutants out of 15,000 mutants screened were identified carrying defects in initial attachment and/or early stages in biofilm formation. Seventy-one of those mutants exhibited a nonswimming phenotype, suggesting a role of swimming motility or motility elements in biofilm formation. Disruption mutations in motility genes (
flhB
,
fliK
, and
pomA
), however, did not affect initial attachment but affected progression of biofilm development into pronounced three-dimensional architecture. In contrast, mutants defective in mannose-sensitive hemagglutinin type IV pilus biosynthesis and in pilus retraction (
pilT
) showed severe defects in adhesion to abiotic surfaces and biofilm formation, respectively. The results provide a basis for understanding microbe-mineral interactions in natural environments.
Crystal Structure of the 65-Kilodalton Heat Shock Protein, Chaperonin 60.2, ofMycobacterium tuberculosis
Authors: Qamra Rohini , Mande Shekhar C. 
Published: November 2004

ABSTRACTChaperonin 60s are a ubiquitous class of proteins that promote folding and assembly of other cellular polypeptides in an ATP-dependent manner. The oligomeric state of chaperonin 60s has been shown to be crucial to their role as molecular chaperones. Chaperonin 60s are also known to be important stimulators of the immune system.Mycobacterium tuberculosispossesses a duplicate set of chaperonin 60s, both of which have been shown to be potent cytokine stimulators. TheM. tuberculosischaperonin 60s are present in the extracellular milieu at concentrations that are extremely low for the formation of an oligomer. Here we present the crystal structure of one of the chaperonin 60s ofM. tuberculosis, also called Hsp65 or chaperonin 60.2, at 3.2-Å resolution. We were able to crystallize the protein in its dimeric state. The unusual dimerization of the protein leads to exposure of certain hydrophobic patches on the surface of the protein, and we hypothesize that this might have relevance in binding to immunogenic peptides, as it does in the eukaryotic homologs.
A Self-Splicing Group I Intron in DNA Polymerase Genes of T7-Like Bacteriophages
Authors: Bonocora Richard P. , Shub David A. 
Published: November 2004

ABSTRACT
Group I introns are inserted into genes of a wide variety of bacteriophages of gram-positive bacteria. However, among the phages of enteric and other gram-negative proteobacteria, introns have been encountered only in phage T4 and several of its close relatives. Here we report the insertion of a self-splicing group I intron in the coding sequence of the DNA polymerase genes of ΦI and W31, phages that are closely related to T7. The introns belong to subgroup IA2 and both contain an open reading frame, inserted into structural element P6a, encoding a protein belonging to the HNH family of homing endonucleases. The introns splice efficiently in vivo and self-splice in vitro under mild conditions of ionic strength and temperature. We conclude that there is no barrier for maintenance of group I introns in phages of proteobacteria.
Type II Isopentenyl Diphosphate Isomerase fromSynechocystissp. Strain PCC 6803
Authors: Barkley Sam J. , Desai Shrivallabh B. , Poulter C. Dale 
Published: November 2004

ABSTRACTOpen reading framesll1556in the cyanobacteriumSynechocystissp. strain 6803 encodes a putative type II isopentenyl diphosphate (IPP) isomerase. The His6-tagged protein was produced inEscherichia coliand purified by Ni2+chromatography. The homotetrameric enzyme required NADPH, flavin mononucleotide, and Mg2+for activity;KmIPPwas 52 μM, andkcatIPPwas 0.23 s−1.
ELECTRON-POSITRON PRODUCTION IN STRONG FIELD PULSES
Authors: MENDES R. VILELA 
Published: November 2004

A short critical review is presented concerning the physical interpretation of electron and positron production data at the GSI accelerator in Darmstadt. The only reliable conclusions seem to be that the creation mechanism is a strong field effect and that the phenomenon is largely independent of the characteristic time of the collision. Before looking for new (exotic) physics it seems reasonable to inquire whether non-perturbative QED is fully understood. Following this motivation a rigorous but, at the same time, sufficiently explicit nonperturbative calculation scheme is developed, for QED in strong fields of short duration. The possible occurrence of correlated e+e− narrow structures is discussed in this framework.
ELECTROWEAK BARYOGENESIS AND THE PHASE TRANSITION DYNAMICS
Authors: YAMAGUCHI AZUSA , SUGAMOTO AKIO 
Published: November 2004

The baryogenesis is reanalyzed based on the model by Cohen et al., in which the lepton number, generated by the neutrinos scattering from the bubble walls appearing in the development of the electroweak phase transition, is converted to the baryon number excess through the sphaleron transition. A formula obtained in this paper on the lepton number production rate is correct for both the thin and thick walls within the linear approximation. Investigation on the time development of the first order phase transition is simulated, including the temporal change of the wall velocity as well as the fusion effect of the bubbles. The details of such phase transition dynamics are found to affect considerably the final value of the baryon number excess.
VARIATIONAL PERTURBATION THEORY
Authors: SISSAKIAN ALEXEY , SOLOVTSOV IGOR , SHEVCHENKO OLEG 
Published: November 2004

A nonperturbative method — variational perturbation theory (VPT) — is discussed. A quantity we are interested in is represented by a series, a finite number of terms of which not only describe the region of small coupling constant but reproduce well the strong coupling limit. The method is formulated only in terms of the Gaussian quadratures, and diagrams of the conventional perturbation theory are used. Its efficiency is demonstrated for the quantum-mechanical anharmonic oscillator. The properties of convergence are studied for series in VPT for the [Formula: see text] model. It is shown that it is possible to choose variational additions such that they lead to convergent series for any values of the coupling constant. Upper and lower estimates for the quantities under investigation are considered. The nonperturbative Gaussian effective potential is derived from a more general approach, VPT. Various versions of the variational procedure are explored and the preference for the anharmonic variational procedure in view of convergence of the obtained series is argued. We investigate the renormalization procedure in the φ4 model in VPT. The nonperturbative β function is derived in the framework of the proposed approach. The obtained result is in agreement with four-loop approximation and has the asymptotic behavior as g3/2 for a large coupling constant. We construct the VPT series for Yang-Mills theory and study its convergence properties. We introduce coupling to spinor fields and demonstrate that they do not influence the VPT series convergence properties.
MAXWELL-CHERN-SIMONS ELECTRODYNAMICS ON A DISK
Authors: BALACHANDRAN A.P. , CHANDAR L. , ERCOLESSI E. , GOVINDARAJAN T.R. , SHANKAR R. 
Published: November 2004

The Maxwell-Chern-Simons (MCS) Lagrangian is the Maxwell Lagrangian augmented by the Chern-Simons term. In this paper, we study the MCS and Maxwell Lagrangians on a disk D. They are of interest for the quantum Hall effect, and also when the disk and its exterior are composed of different media. We show that quantization is not unique, but depends on a nonnegative parameter λ. 1/λ is the penetration depth of the fields described by these Lagrangians into the medium in the exterior of D. For λ=0, there are edge observables and edge states localized at the boundary ∂D for the MCS system. They describe the affine Lie group [Formula: see text]. Their excitations carry zero energy, signifying an infinite degeneracy of all states of the theory. There is also an additional infinity of single particle excitations of exactly the same energy proportional to |k|, k being the strength of the Chern-Simons term. The MCS theory for λ=0 has the huge symmetry group [Formula: see text]. In the Maxwell theory, the last-mentioned excitations are absent while the edge observables, which exist for λ=0, commute. Also, these excitations are described by states which are not localized at ∂D and are characterized by a continuous and infinitely degenerate spectrum. All these degeneracies are lifted and edge observables and their states cease to exist for λ>0. The novel excitations discovered in this paper should be accessible to observations. We will discuss issues related to observations, as also the generalization of the present considerations to vortices, domain walls and monopoles, in a paper under preparation.
HUNTING FOR SUPERSYMMETRY IN INTENSE ELECTROMAGNETIC FIELDS
Authors: KURILIN ALEXANDER V. 
Published: November 2004

We calculate the probabilities of slepton and photino production via a charged lepton decay induced by an arbitrary electromagnetic wave or by a constant homogeneous external field, Fμν. This allows us to estimate the domains where this reaction could be significant. Comparing the process [Formula: see text] with the synchrotron radiation we conclude that for all values of the background field parameter [Formula: see text], with pν being the lepton’s momentum, the following estimate holds: [Formula: see text]. We also study the impact of the intense field on radiative corrections to the lepton’s anomalous magnetic moment. It is found that, when χ exceeds the cube of the masses’ ratios, [Formula: see text], [Formula: see text], the sparticle’s contribution to the anomalous magnetic moment is of the same order as the QED correction. In this region the magnitude of the anomalous magnetic moment of the lepton is very sensitive to the masses of the slepton and the photino.
LINEAR ELECTRIC-DIPOLE POLARIZABILITIES
Authors: BONIN KEITH D. , KADAR-KALLEN MICHAEL A. 
Published: November 2004

This article reviews the main theoretical methods and experimental techniques for determining electric-dipole polarizabilities. This review only considers the lowest-order polarizability which describes the linear response of a particle to an electric field, i.e. the induced electric-dipole moment depends linearly on the applied electric field. The scope of the review is broad: it encompasses atomic, molecular and cluster polarizabilities. Both static and dynamic polarizabilities are covered. Calculational techniques discussed in detail include variational perturbational theory, the local density approximation, and semi-empirical additivity methods. Special attention is paid to basis sets used in polarizability calculations—especially the increasingly popular Gaussian basis sets. Extensive tabulations of polarizability calculations are provided for helium and sodium atoms, the diatomic nitrogen molecule, the fullerene C60, and sodium and potassium clusters. For each of these cases, the most reliable experimental results are also provided for comparison to theory. Many traditional experimental techniques are reviewed including dielectric constant, refractive index, Rayleigh scattering, electro-optic Kerr effect, beam deflection, E—H gradient balance, and the beam resonance technique. New experimental methods for determining polarizabilities such as the light-force method and atom interferometry are also extensively discussed. In addition, a novel detection scheme that is elegant and universal—the position-sensitive time-of-flight spectrometer—is thoroughly described.
SUBSIDIARY HOMOCLINIC ORBITS TO A SADDLE-FOCUS FOR REVERSIBLE SYSTEMS
Authors: CHAMPNEYS A.R. 
Published: November 2004

A dynamical system is said to be reversible if there is an involution of phase space that reverses the direction of the flow. Examples are classical Hamiltonian systems with quadratic kinetic energy. For reversible systems, homoclinic orbits that are invariant under the reversible transformation typically persist as parameters are varied. This paper concerns reversible systems for which a primary homoclinic orbit to a saddle-focus is assumed to exist. The problem under investigation is a characterisation of the subsidiary homoclinic orbits which then exist in a neighbourhood of the primary one. Such orbits have applications as solitary water waves and as buckling solutions of nonlinear struts. A Shil’nikov-type analysis is performed for four-dimensional linearly reversible systems. It is shown that each subsidiary homoclinic orbit can be labelled by a symmetric string of positive integers. All possible strings of length one, two or three correspond to the existence of a homoclinic orbit, whereas only certain of those of length four or greater do. This situation contrasts with known results if the reversible system is also Hamiltonian. The analysis is supported by performing careful numerical experiments on the equation [Formula: see text] where P and α are parameters; a good agreement with the theory is found.
ARNOL’D TONGUES, DEVIL’S STAIRCASE, AND SELF-SIMILARITY IN THE DRIVEN CHUA’S CIRCUIT
Authors: PIVKA LADISLAV , ZHELEZNYAK ALEXANDER L. , CHUA LEON O. 
Published: November 2004

Empirical recurrent relations, governing the structure of the devil’s staircase in the driven Chua’s circuit are given, which reflect the self-similar structure in an algebraic form. In particular, it turns out that the same formulas hold for both winding and period numbers, but with different “initial conditions”. Some of the finer details such as period-doubling along with numerous coexistence phenomena within staircases of mode-locked states have been revealed by computing high-resolution bifurcation diagrams.
LOW AND HIGH ORDER FINITE ELEMENT METHOD: EXPERIENCE IN SEISMIC MODELING
Authors: PADOVANI E. , PRIOLO E. , SERIANI G. 
Published: November 2004

The finite element method (FEM) is a numerical technique well suited to solving problems of elastic wave propagation in complex geometries and heterogeneous media. The main advantages are that very irregular grids can be used, free surface boundary conditions can be easily taken into account, a good reconstruction is possible of irregular surface topography, and complex geometries, such as curved, dipping and rough interfaces, intrusions, cusps, and holes can be defined. The main drawbacks of the classical approach are the need for a large amount of memory, low computational efficiency, and the possible appearance of spurious effects. In this paper we describe some experience in improving the computational efficiency of a finite element code based on a global approach, and used for seismic modeling in geophysical oil exploration. Results from the use of different methods and models run on a mini-superworkstation APOLLO DN10000 are reported and compared. With Chebyshev spectral elements, great accuracy can be reached with almost no numerical artifacts. Static condensation of the spectral element's internal nodes dramatically reduces memory requirements and CPU time. Time integration performed with the classical implicit Newmark scheme is very accurate but not very efficient. Due to the high sparsity of the matrices, the use of compressed storage is shown to greatly reduce not only memory requirements but also computing time. The operation which most affects the performance is the matrix-by-vector product; an effective programming of this subroutine for the storage technique used is decisive. The conjugate gradient method preconditioned by incomplete Cholesky factorization provides, in general, a good compromise between efficiency and memory requirements. Spectral elements greatly increase its efficiency, since the number of iterations is reduced. The most efficient and accurate method is a hybrid iterative-direct solution of the linear system arising from the static condensation of high order elements. The size of 2D models that can be handled in a reasonable time on this kind of computer is nowadays hardly sufficient, and significant 3D modeling is completely unfeasible. However the introduction of new FEM algorithms coupled with the use of new computer architectures is encouraging for the future.
A NONPLANAR SOURCE TO PLANAR APERTURE ALGORITHM
Authors: CHRISTOPHER TED 
Published: November 2004

A new algorithm for modeling the propagation within a nonplanar source is presented. The algorithm represents the effects of diffraction and attenuation in the propagation of acoustic waves from a nonplanar source to the associated source aperture. The algorithm is a generalization of the linear propagation methods of Christopher and Parker [J. Acous. Soc. Am.90, 507–521 (1991)]. When used to propagate the normal velocity source description to obtain a pressure description of the field, the algorithm is equivalent to the Rayleigh integral model of Williams [J. Acous. Soc, Am.17, 219–227 (1946)] and O'Neil [J. Acous. Soc. Am.21, 516–526 (1949)]. Additionally, in propagating the field beyond the aperture plane the new algorithm allows for specified aperture plane conditions and facilitates the use of very efficient linear and nonlinear beam propagation methods. The algorithm can also be extended to approximate the effects of reflections occurring within the nonplanar source. An efficient implementation of the algorithm is presented for axially symmetric sources. The correctness of the algorithm and implementation are demonstrated using a hemispherical reflective source. The results of the algorithm are then compared against the predictions of Coulouvrat [J. Acous. Soc. Am.94, 1663–1675 (1993)] and predictions obtained with the analytical axial solution for an ellipsoidal reflector of Hamilton [J. Acous. Soc. Am.93, 1256–1266 (1993)].
Functional interdependence between septin and actin cytoskeleton
Authors: Schmidt Katja , Nichols Benjamin J 
Published: November 2004

Abstract
Background
Septin2 is a member of a highly conserved GTPase family found in fungi and animals. Septins have been implicated in a diversity of cellular processes including cytokinesis, formation of diffusion barriers and vesicle trafficking. Septin2 partially co-localises with actin bundles in mammalian interphase cells and Septin2-filamentmorphology depends upon an intact actin cytoskeleton. How this interaction is regulated is not known. Moreover, evidence that Septin2 is remodelled or redistributed in response to other changes in actin organisation is lacking.

Results
Septin2 filaments are associated with actin fibres, but Septin2 is not associated with actin at the leading edge of moving cells or in ruffles where actin is highly dynamic. Rather, Septin2 is spatially segregated from these active areas and forms O- and C-shaped structures, similar to those previously observed after latrunculin treatment. FRAP experiments showed that all assemblies formed by Septin2 are highly dynamic with a constant exchange of Septin2 in and out of these structures, and that this property is independent of actin. A combination of RNAi experiments and expression of truncated forms of Septin2 showed that Septin2 plays a significant role in stabilising or maintaining actin bundles.

Conclusion
We show that Septin2 can form dynamic structures with differing morphologies in living cells, and that these morphologies are dependent on the functional state of the actin cytoskeleton. Our data provide a link between the different morphological states of Septin2 and functions of Septin2 in actin-dynamics, and are consistent with the model proposed by Kinoshita and colleagues, that Septin2 filaments play a role in stabilisation of actin stress fibres thus preventing actin turnover.
Missing paternal demographics: A novel indicator for identifying high risk population of adverse pregnancy outcomes
Authors: Tan Hongzhuan , Wen Shi Wu , Walker Mark , Demissie Kitaw 
Published: November 2004

Abstract
Background
One of every 6 United Status birth certificates contains no information on fathers. There might be important differences in the pregnancy outcomes between mothers with versus those without partner information. The object of this study was to assess whether and to what extent outcomes in pregnant women who did not have partner information differ from those who had.

Methods
We carried out a population-based retrospective cohort study based on the registry data in the United States for the period of 1995–1997, which was a matched multiple birth file (only twins were included in the current analysis). We divided the study subjects into three groups according to the availability of partner information: available, partly missing, and totally missing. We compared the distribution of maternal characteristics, maternal morbidity, labor and delivery complications, obstetric interventions, preterm birth, fetal growth restriction, low birth weight, congenital anomalies, fetal death, neonatal death, post-neonatal death, and neonatal morbidity among three study groups.

Results
There were 304466 twins included in our study. Mothers whose partner's information was partly missing and (especially) totally missing tended to be younger, of black race, unmarried, with less education, smoking cigarette during pregnancy, and with inadequate prenatal care. The rates of preterm birth, fetal growth restriction, low birth weight, Apgar score <7, fetal mortality, neonatal mortality, and post-neonatal mortality were significantly increased in mothers whose partner's information was partly or (especially) totally missing.

Conclusions
Mothers whose partner's information was partly and (especially) totally missing are at higher risk of adverse pregnant outcomes, and clinicians and public health workers should be alerted to this important social factor.