bluuebunny/crossref_metadata_2025_split huggingface dataset:
Population Structure and Evolution of the
Bacillus cereus
Group
Authors: Priest Fergus G. , Barker Margaret , Baillie Les W. J. , Holmes Edward C. , Maiden Martin C. J. 
Published: November 2004

ABSTRACT

Representative strains of the
Bacillus cereus
group of bacteria, including
Bacillus anthracis
(11 isolates),
B. cereus
(38 isolates),
Bacillus mycoides
(1 isolate),
Bacillus thuringiensis
(53 isolates from 17 serovars), and
Bacillus weihenstephanensis
(2 isolates) were assigned to 59 sequence types (STs) derived from the nucleotide sequences of seven alleles,
glpF
,
gmk
,
ilvD
,
pta
,
pur
,
pycA
, and
tpi
. Comparisons of the maximum likelihood (ML) tree of the concatenated sequences with individual gene trees showed more congruence than expected by chance, indicating a generally clonal structure to the population. The STs followed two major lines of descent. Clade 1 comprised
B. anthracis
strains, numerous
B. cereus
strains, and rare
B. thuringiensis
strains, while clade 2 included the majority of the
B. thuringiensis
strains together with some
B. cereus
strains. Other species were allocated to a third, heterogeneous clade. The ML trees and split decomposition analysis were used to assign STs to eight lineages within clades 1 and 2. These lineages were defined by bootstrap analysis and by a preponderance of fixed differences over shared polymorphisms among the STs. Lineages were named with reference to existing designations: Anthracis, Cereus I, Cereus II, Cereus III, Kurstaki, Sotto, Thuringiensis, and Tolworthi. Strains from some
B. thuringiensis
serovars were wholly or largely assigned to a single ST, for example, serovar aizawai isolates were assigned to ST-15, serovar kenyae isolates were assigned to ST-13, and serovar tolworthi isolates were assigned to ST-23, while other serovars, such as serovar canadensis, were genetically heterogeneous. We suggest a revision of the nomenclature in which the lineage and clone are recognized through name and ST designations in accordance with the clonal structure of the population.
Essentiality of the Early Transcript in the Replication Origin of the Lactococcal Prolate Phage c2
Authors: Schiemann Anja H. , Rakonjac Jasna , Callanan Michael , Gordon James , Polzin Kayla , Lubbers Mark W. , O'Toole Paul W. 
Published: November 2004

ABSTRACT

The genome of the prolate-headed lytic lactococcal bacteriophage c2 is organized into two divergently oriented blocks consisting of the early genes and the late genes. These blocks are separated by the noncoding origin of DNA replication. We examined the functional role of transcription of the origin in a plasmid model system. Deletion of the early promoter P
E
1 abolished origin function. Introduction of mutations into P
E
1 which did not eliminate promoter activity or replacement of P
E
1 with an unrelated but functional promoter did not abolish replication. The A-T-rich region upstream of P
E
1, which is conserved in prolate phages, was not required for plasmid replication. Replacement of the P
E
1 transcript template sequence with an unrelated sequence with a similar G+C content abolished replication, showing that the sequence encoding the transcript is essential for origin function. Truncated transcript and internal deletion constructs did not support replication except when the deletion was at the very 3′ end of the DNA sequence coding for the transcript. The P
E
1 transcript could be detected for all replication-proficient constructs. Recloning in a plasmid vector allowed detection of P
E
1 transcripts from some fragments that did not support replication, indicating that stability of the transcript alone was not sufficient for replication. The data suggest that production of a transcript of a specific length and with a specific sequence or structure is essential for the function of the phage c2 origin in this model system.
The Chromosomally Encoded Cation Diffusion Facilitator Proteins DmeF and FieF from
Wautersia metallidurans
CH34 Are Transporters of Broad Metal Specificity
Authors: Munkelt Doreen , Grass Gregor , Nies Dietrich H. 
Published: November 2004

ABSTRACT

Genomic sequencing of the β-proteobacterium
Wautersia
(previously
Ralstonia) metallidurans
CH34 revealed the presence of three genes encoding proteins of the cation diffusion facilitator (CDF) family. One, CzcD, was previously found to be part of the high-level metal resistance system Czc that mediates the efflux of Co(II), Zn(II), and Cd(II) ions catalyzed by the CzcCBA cation-proton antiporter. The second CDF protein, FieF, is probably mainly a ferrous iron detoxifying protein but also mediated some resistance against other divalent metal cations such as Zn(II), Co(II), Cd(II), and Ni(II) in
W. metallidurans
or
Escherichia coli
. The third CDF protein, DmeF, showed the same substrate spectrum as FieF, but with different preferences. DmeF plays the central role in cobalt homeostasis in
W. metallidurans
, and a disruption of
dmeF
rendered the high-level metal cation resistance systems Czc and Cnr ineffective against Co(II). This is evidence for the periplasmic detoxification of substrates by RND transporters of the heavy metal efflux family subgroup.
Regulation of Iron Transport inStreptococcus pneumoniaeby RitR, an Orphan Response Regulator
Authors: Ulijasz Andrew T. , Andes David R. , Glasner Jeremy D. , Weisblum Bernard 
Published: November 2004

ABSTRACTRitR (formerly RR489) is an orphan two-component signal transduction response regulator inStreptococcus pneumoniaethat has been shown to be required for lung pathogenicity. In the present study, by using the rough strain R800, inactivation of the orphan response regulator generitRby allele replacement reduced pathogenicity in a cyclophosphamide-treated mouse lung model but not in a thigh model, suggesting a role for RitR in regulation of tissue-specific virulence factors. Analysis of changes in genome-wide transcript mRNA levels associated with the inactivation ofritRcompared to wild-type cells was performed by the use of high-density DNA microarrays. Genes with a change in transcript abundance associated with inactivation ofritRincludedpiuB, encoding an Fe permease subunit, andpiuA, encoding an Fe carrier-binding protein. In addition, adprortholog, encoding an H2O2resistance protein that has been shown to reduce synthesis of reactive oxygen intermediates, was activated in the wild-type (ritR+) strain. Microarray experiments suggested that RitR represses Fe uptake in vitro by negatively regulating the Piu hemin-iron transport system. Footprinting experiments confirmed site-specific DNA-binding activity for RitR and identified three binding sites that partly overlap the +1 site for transcription initiation upstream ofpiuB. Transcripts belonging to other gene categories found to be differentially expressed in our array studies include those associated with (i) H2O2resistance, (ii) repair of DNA damage, (iii) sugar transport and capsule biosynthesis, and (iv) two-component signal transduction elements. These observations suggest that RitR is an important response regulator whose primary role is to maintain iron homeostasis inS. pneumoniae. The nameritR(repressor of iron transport) for the orphan response regulator gene,rr489, is proposed.
The Malic Enzyme Is Required for Optimal Photoautotrophic Growth of
Synechocystis
sp. Strain PCC 6803 under Continuous Light but Not under a Diurnal Light Regimen
Authors: Bricker Terry M. , Zhang Shulu , Laborde Susan M. , Mayer Paul R. , Frankel Laurie K. , Moroney James V. 
Published: November 2004

ABSTRACT

A mutation was recovered in the
slr0721
gene, which encodes the decarboxylating NADP
+
-dependent malic enzyme in the cyanobacterium
Synechocystis
sp. strain PCC 6803, yielding the mutant 3WEZ. Under continuous light, 3WEZ exhibits poor photoautotrophic growth while growing photoheterotrophically on glucose at rates nearly indistinguishable from wild-type rates. Interestingly, under diurnal light conditions (12 h of light and 12 h of dark), normal photoautotrophic growth of the mutant is completely restored.
The Gatehouse Project: can a multilevel school intervention affect emotional wellbeing and health risk behaviours?
Authors: Bond Lyndal , Patton George , Glover Sara , Carlin John B , Butler Helen , Thomas Lyndal , Bowes Glenn 
Published: November 2004

Study objective:The aim of this study was to determine the effect of a multilevel school based intervention on adolescents’ emotional wellbeing and health risk behaviours.Design:School based cluster randomised controlled trial. Students were surveyed using laptop computers, twice in the first year of intervention and annually thereafter for a further two years.Setting:Secondary schools.Participants:2678 year 8 students (74%) participated in the first wave of data collection. Attrition across the waves was less than 3%, 8%, and 10% respectively with no differential response rate between intervention and control groups at the subsequent waves (98%v96%; 92%v92%, and 90%v89% respectively).Main results:A comparatively consistent 3% to 5% risk difference was found between intervention and control students for any drinking, any and regular smoking, and friends’ alcohol and tobacco use across the three waves of follow up. The largest effect was a reduction in the reporting of regular smoking by those in the intervention group (OR 0.57, 0.62, and 0.72 at waves 2, 3, and 4 respectively). There was no significant effect of the intervention on depressive symptoms, and social and school relationships.Conclusions:While further research is required to determine fully the processes of change, this study shows that a focus on general cognitive skills and positive changes to the social environment of the school can have a substantial impact on important health risk behaviours.
ON BOGOLIUBOV TRANSFORMATION OF SCALAR WAVE FUNCTIONS IN DE SITTER SPACE
Authors: SATO HARU-TADA , SUZUKI HISAO 
Published: November 2004

We discuss the Bogoliubov transformation of the scalar wave functions caused by the change of coordinates in four-dimensional de Sitter space. It is shown that the exact Bogoliubov coefficients can be obtained from the global coordinates to the static coordinates where there exists manifest horizon. We consider two types of global coordinates. In one global coordinates, it is shown that the Bogoliubov transformation to the static coordinates can be expressed by the discontinuous integral of Weber and Schafheitlin. The positive and negative energy states in the global coordinates degenerate in the static coordinates. In the other global coordinates, we obtain the Bogoliubov coefficients by using the analytic continuation of the hypergeometric functions in two variables. We also discuss the relation between two types of global coordinates and find an integral relation between the mode functions.
WHERE IS TOP?
Authors: DALITZ R.H. , GOLDSTEIN GARY R. 
Published: November 2004

Possibilities are discussed for determining the top-quark mass mt from observations on the decay processes for top-antitop pairs produced in antiproton-proton collisions at Tevatron energies, assuming that the t→bW+ decay channel is dominant and much faster than hadronization. The final states [Formula: see text] provide the most striking signal, with little background, but they are rare (≈2/81). If all three candidate events prove to be from [Formula: see text], an estimate follows for P(mt| rate ), the probability distribution for mt. The one reported configuration allows an independent estimate for P (mt|μ± e∓ 2 jets ). These two distributions are compatible and can be combined to give an mt estimate of about 122 GeV. Decay events “1 energetic lepton(ℓ)+4 jets” should appear 12 times as often as “ μ± e∓ 2 jets ” events and can be analyzed to give estimates for P(mt|ℓ 4 jets ); this is illustrated for a fictitious event. There may be background from nontop events but suitable cuts on the data and our analysis procedure together reduce this to a low level. The rate observed for these events does not appear to be as large as the factor 12. Identification of either or both of the [Formula: see text] jets would be a great step forward, separating out the “[Formula: see text]” and “[Formula: see text]” events of importance with little background. We advocate an energetic approach to the analysis of individual events [whether 2, 1 or no (b or [Formula: see text]) jets identified] on an event-by-event basis, with the hope of finding a subgroup of events with a common mass estimate.
SPINODAL NUCLEATION
Authors: MONETTE L. 
Published: November 2004

The aim of this paper is to present the theoretical foundations of spinodal nucleation, by reviewing key theoretical and numerical work. The basic ideas of classical nucleation theory are first presented: the classical droplet model, and the Becker-Döring theory, as these concepts are important to the development of the field theoretical formulation of nucleation. The field theoretical framework for classical nucleation is exposed in some detail, followed by the presentation of a similar framework, extended to nucleation in the proximity of a spinodal (non-classical nucleation), in the presence of long-range Ising interactions. The non-classical nucleating droplet is found to be diffuse, hence to strongly depart from the classical prediction of a compact object with a well-defined surface. The fact that the non-classical nucleating droplet is identified with a ramified object prompts the development of an appropriate cluster description. The basic principles of percolation theory are outlined, and some lattice percolation models introduced. The Kastaleyn-Fortuin mapping, which establishes a connection between a particular percolation model and a limit of the Potts model, is briefly described. This mapping is crucial to the development of a second mapping (Coniglio-Klein) of the Ising spinodal point into a percolation model, where the long-range Ising interactions are translated into a long-range connectivity in the appropriate percolation model. The final result consists of the most powerful tool available to identify precisely the non-classical nucleating droplet in numerical simulations of nucleation in proximity of a spinodal. Numerical simulation results are presented, which support the field theoretical formulation of non-classical nucleation. As the numerical results seem to support the fact that the non-classical nucleating droplet is also a percolation cluster, its fractal structure is investigated by considering the mean-field regime of the percolation model, i.e. a percolation model with long-range connectivity. This leads to an apparent contradiction between the field theory and the mean-field percolation model predictions concerning the mass (or density) scaling of the nucleating droplet. This inconsistency is resolved by postulating that the mean-field percolation clusters cannot be non-classical nucleating droplets, and proposing that the non-classical nucleating droplet is in fact the result of a coalescence of many such clusters. Finally, the calculation of the static prefactor in the nucleation rate by assuming a Becker-Döring dynamics for the coalescence mechanism is outlined. The result is found to be consistent with the predictions of the field theory for the static prefactor. Numerical results are also presented in support of the hypothesized coalescence mechanism.
HEAT TRANSFER MODELLING OF A CYLINDRICAL ER CATCH
Authors: SMYTH R. , TAN K. H. , BULLOUGH W. A. 
Published: November 2004

In electro-rheological (ER) devices the control of temperature is often of paramount importance. For a device through which the ER fluid is not able to flow continuously to and from a reservoir, where it may be cooled, this can be a problem. Such a situation occurs in the ER catch. The heat generated there will predominantly be dissipated from the outer surface of the drive/input. The rate of heat transfer is thus principally a function of the speed and area of that surface and the temperatures of the ER fluid and atmosphere. Since these factors reflect on the levels of electro-stress, current requirement and viscosity of the ER fluid, an opportunity exists for optimisation of catch performance. The paper shows the results of an investigation into the effects on the cooling/heating problem of varying the radii of the clutch rotors, their relative rotational speed and inter-electrode spacing. Equilibrium fluid temperatures are confirmed by experimental evidence. The effects of heat generation in run up to speed and clutch locked periods, (through electro viscous drag and dielectric loading respectively) are quantified and compared with the case of a contemporary ER fluid in a cylindrical catch on zero volts idling. At any given operating condition, uniform temperature, viscosity and constant electro stress are assumed throughout the fluid.
BIFURCATIONS IN APPROXIMATE SOLUTIONS OF STOCHASTIC DELAY DIFFERENTIAL EQUATIONS
Authors: BAKER CHRISTOPHER T. H. , FORD JUDITH M. , FORD NEVILLE J. 
Published: November 2004

We consider stochastic delay differential equations of the form [Formula: see text] interpreted in the Itô sense, with Y(t)=Φ(t) for t∈[t0-τ,t0] (here, W(t) is a standard Wiener process and τ>0 is the constant "lag", or "time-lag"). We are interested in bifurcations (that is, changes in the qualitative behavior of solutions of these equations) and we draw on insights from the related deterministic delay differential equation, for which there is a substantial body of known theory, and numerical results that enable us to discuss where changes occur in the behavior of the (exact and approximate) solutions of the equation. Rather diverse components of mathematical background are necessary to understand the questions of interest. In this paper we first review some deterministic results and some basic elements of the stochastic analysis that (i) suggests lines of investigation for the stochastic case and (ii) are expected to facilitate the theoretical investigation of the stochastic problem. We then present the results of numerical experiments that illustrate some of the complexities that arise when considering bifurcations in stochastic delay differential equations. They give prima facie evidence for certain convergence properties of the bifurcation points estimated using the Euler–Maruyama method for the equations considered. We conclude by drawing attention to a number of open questions in the field.
RANDOMNESS AND COMPLEXITY IN PURE MATHEMATICS
Authors: CHAITIN G.J. 
Published: November 2004

One normally thinks that everything that is true is true for a reason. I’ve found mathematical truths that are true for no reason at all. These mathematical truths are beyond the power of mathematical reasoning because they are accidental and random. Using software written in Mathematica that runs on an IBM RS/6000 workstation, I constructed a perverse 200-page algebraic equation with a parameter N and 17,000 unknowns: [Formula: see text] For each whole-number value of the parameter N, we ask whether this equation has a finite or an infinite number of whole number solutions. The answers escape the power of mathematical reason because they are completely random and accidental. This work is an extension of the famous results of Gödel and Turing using ideas from a new field called algorithmic information theory.
IDEAL TURBULENCE IN AN IDEALIZED TIME-DELAYED CHUA’S CIRCUIT
Authors: SHARKOVSKY A.N. 
Published: November 2004

By replacing the parallel LC “resonator” in Chua’s circuit by a lossless transmission line, terminated by a short circuit, we obtain a “time-delayed Chua’s circuit” whose time evolution is described by a pair of linear partial differential equations with a nonlinear boundary condition. If we neglect the capacitance across the Chua’s diode, described by a nonsymmetric piecewiselinear vR–iR characteristic, the resulting idealized time-delayed Chua’s circuit is described exactly by a scalar nonlinear difference equation with continuous time, which makes it possible to characterize its associated nonlinear dynamics and spatial chaotic phenomena. From a mathematical viewpoint, circuits described by ordinary differential equations can generate only temporal chaos, while the time-delayed Chua’s circuit can generate spatiotem poral chaos. Except for stepwise periodic oscillations, the typical solutions of the idealized time-delayed Chua’s circuit consist of either weak turbulence, or strong turbulence, which are examples of “ideal” (or “dry”) turbulence. In both cases, we can observe infinite processes of spatiotemporal coherent structure formations. Under weak turbulence, the graphs of the solution tend to limit sets which are fractals with a Hausdorff dimension between 1 and 3, and is therefore larger than the topological dimension (of sets). Under strong turbulence, the “limit” oscillations are oscillations whose amplitudes are random functions. This means that the attractor of the idealized time-delayed Chua’s circuit already contains random functions, and spatial self-stochasticity phenomenon can be observed.
CHARACTERIZATION OF STOCHASTIC PROPAGATION AND SCATTERING VIA GABOR AND WAVELET TRANSFORMS
Authors: SIBUL L. H. , WEISS L. G. , DIXON T. L. 
Published: November 2004

An application to remote acoustic sensing that remains unexploited is measuring acoustic scattering and spreading effects with wideband, coherent signal processing techniques. Such techniques allow distributed objects, such as a layer of scatterers due to bubbles or biological particles, and first order time variations in an ocean channel to be estimated. This paper presents narrowband and wideband methods for characterizing stochastic propagation and acoustic scattering in a time-varying ocean in terms of spreading functions. It is shown that the Gabor transform is the natural transform for estimating the narrowband spreading function, and the wavelet transform is the natural transform for estimating the wideband spreading function. Both techniques of characterization use a correlator processing structure in a monostatic transmitter/receiver configuration to estimate the spreading function. The narrowband and wideband spreading functions characterize the distribution of scatterers in range and velocity (time and frequency) in a propagation channel. It is shown that the wideband formulation follows directly from a physical derivation. Moreover, wideband processing removes many of the narrowband restrictions and allows first order time variations, caused by inhomogeneities and relative motion in the ocean channel, to be processed. In addition, wideband techniques allow for increased time intervals and, therefore, increased energy transmission when the transmitter is peak-power-limited. Thus, weak scatterers that may have been unidentified with narrowband techniques may be identified with the wideband methods. Numerical examples for wideband characterization of a distributed scatterer are presented.