bluuebunny/crossref_metadata_2025_split huggingface dataset:
The state of play of farmland birds: population trends and conservation status of lowland farmland birds in the United Kingdom
Authors: GREGORY RICHARD D. , G. NOBLE DAVID , CUSTANCE JOHN 
Published: November 2004

Many bird species of lowland farmland have declined substantially in the United Kingdom over the past 30 years. Declines among farmland specialists are steeper than for generalists and were most rapid for these specialists in the 1970s and 1980s. These changes have been linked to increased agricultural intensification and are reflected in Red or Amber conservation concern status for many common farmland species, as well as for rarer ones. We review long‐ and short‐term population trends and the conservation status of lowland farmland birds in the UK using the latest available information from bird surveys, and examine patterns among species. Analyses of demographic parameters suggest broadly that the key factor driving population changes of seed‐eating and migrant birds is overwinter survival, whereas for many non‐passerine species population growth appears to be limited by productivity. Population trends for a suite of lowland farmland species were first combined in the UK Government's headline wild bird indicator published in 1998. This ‘Skylark index’ as it is sometimes known was intended to reflect the health of the wider countryside and struck a chord with the public and decision‐makers. We look at the behaviour of the composite indicator and explore the population dynamics of the increasing and declining species separately. Simple models of population growth in these groups are then used to explore plausible scenarios for delivering the Government's Public Service Agreement target to reverse the long‐term decline in the number of farmland birds by 2020.
Genetic Dissection of the Light-InduciblecarQRSPromoter Region ofMyxococcus xanthus
Authors: Whitworth David E. , Bryan Samantha J. , Berry Andrew E. , McGowan Simon J. , Hodgson David A. 
Published: November 2004

ABSTRACTInMyxococcus xanthusphotoprotective carotenoids are produced in response to illumination due to regulated expression of carotenoid biosynthesis genes at two loci. Induction of the carotenogenesis regulon is dependent on expression of thecarQRSoperon. The first gene product of the operon, CarQ, is a sigma factor belonging to the ECF family and is responsible for light-dependent initiation of transcription at thecarQRSpromoter. We defined the minimalcarQRSpromoter as a 145-bp fragment of DNA upstream of thecarQRStranscriptional start site, which includes the promoter for a divergent gene,gufA. In order to elucidate regions with the promoter required for activity, point mutations were introduced into thecarQRSpromoter between positions −151 and 6. While most sequence changes abolishedcarQRSpromoter activity, two changes enhanced promoter activity and two changes caused the mutant promoter to become constitutive and independent of CarQ. The promoter-null point mutations and 6-bp deletion mutations implied that thecarQRSpromoter requires a functionalgufApromoter for transcriptional activity and vice versa. By mapping the extent of the promoter region, identifying sequences important for promoter activity, and highlighting potential topological effects, we provide a foundation for further analysis of thecarQRSpromoter.
Binding of the C-Terminal Domain of the α Subunit of RNA Polymerase to the Phage Mu Middle Promoter
Authors: Ma Ji , Howe Martha M. 
Published: November 2004

ABSTRACT

The C-terminal domain of the α subunit (αCTD) of
Escherichia coli
RNA polymerase is often involved in transcriptional regulation. The αCTD typically stimulates transcription via interactions with promoter UP element DNA and transcriptional activators. DNase I footprinting and gel mobility shift assays were used to look for potential interaction of the αCTD with the phage Mu middle promoter P
m
and its activator protein Mor. Binding of RNA polymerase to P
m
in the presence of Mor resulted in production of a DNase I footprint downstream of Mor due to open complex formation and generation of a second footprint just upstream of the Mor binding site. Generation of the upstream footprint did not require open complex formation and also occurred in reactions in which the αCTD or His-α proteins were substituted for RNA polymerase. In gel mobility shift assays, the formation of a supershifted ternary complex demonstrated that Mor and His-α bind synergistically to P
m
DNA. Gel shift assays with short DNA fragments demonstrated that only the Mor binding site and a single upstream αCTD binding site were required for ternary complex formation. These results suggest that the αCTD plays a role in P
m
transcription by binding to P
m
DNA just upstream from Mor and making protein-protein interactions with Mor that stabilize the binding of both proteins.
The Recombination Genes
addAB
Are Not Restricted to Gram-Positive Bacteria: Genetic Analysis of the Recombination Initiation Enzymes RecF and AddAB in
Rhizobium etli
Authors: Zuñiga-Castillo Jacobo , Romero David , Martínez-Salazar Jaime M. 
Published: November 2004

ABSTRACT

Single-strand gaps (SSGs) and double-strand breaks (DSBs) are the major initiation sites for recombination. In bacteria, the SSGs are repaired by RecFOR, while the DSBs are processed by RecBCD in gram-negative bacteria and AddAB in gram-positive bacteria. Unexpectedly, instead of
recBCD
genes, the
addAB
genes were found in members of the α-proteobacteria group (gram negative). Taking
Rhizobium etli
as a model, the role of
recF
and
addAB
genes in homologous recombination and repair of damaged DNA was evaluated. Inactivation of either
recF
or
addA
provoked strong sensitivity to UV radiation and mitomycin C, while an additive effect was observed in the
recF-addA
mutant. The DSBs generated by nalidixic acid caused low viability only in the
addA
mutant. The recombination frequency of large and small plasmids was reduced in the
recF
mutant (24- and 36-fold, respectively), whereas a slight decrease (threefold) in the
addA
mutant was observed. Moreover, an additive effect (47- and 90-fold, respectively) was observed in the double mutant, but it was not as dramatic as that in a
recA
mutant. Interestingly, the frequency of deletion and Campbell-type recombination was slightly affected in either single or double mutants. These results suggest that another pathway exists that allows plasmid and Campbell-type recombination in the absence of
recF
and
addA
genes.
A DNA Region Recognized by the Nitric Oxide-Responsive Transcriptional Activator NorR Is Conserved in β- and γ-Proteobacteria
Authors: Büsch Andrea , Pohlmann Anne , Friedrich Bärbel , Cramm Rainer 
Published: November 2004

ABSTRACT

The σ
54
-dependent regulator NorR activates transcription of target genes in response to nitric oxide (NO) or NO-generating agents. In
Ralstonia eutropha
H16, NorR activates transcription of the dicistronic
norAB
operon that encodes NorA, a protein of unknown function, and NorB, a nitric oxide reductase. A constitutively activating NorR derivative (NorR′), in which the N-terminal signaling domain was replaced by MalE, specifically bound to the
norAB
upstream region as revealed by gel retardation analysis. Within a 73-bp DNA segment protected by MalE-NorR′ in a DNase I footprint assay, three conserved inverted repeats, GGT-(N
7
)-ACC (where N is any base), that we consider to be NorR-binding boxes were identified. Mutations altering the spacing or the base sequence of these repeats resulted in an 80 to 90% decrease of transcriptional activation by wild-type NorR. Genome database analyses demonstrate that the GT-(N
7
)-AC core of the inverted repeat is found in several proteobacteria upstream of gene loci encoding proteins of nitric oxide metabolism, including nitric oxide reductase (NorB), flavorubredoxin (NorV), NO dioxygenase (Hmp), and hybrid cluster protein (Hcp).
Transferable Antibiotic Resistance Elements in
Haemophilus influenzae
Share a Common Evolutionary Origin with a Diverse Family of Syntenic Genomic Islands
Authors: Mohd-Zain Zaini , Turner Sarah L. , Cerdeño-Tárraga Ana M. , Lilley Andrew K. , Inzana Thomas J. , Duncan A. Jane , Harding Rosalind M. , Hood Derek W. , Peto Timothy E. , Crook Derrick W. 
Published: November 2004

ABSTRACT

Transferable antibiotic resistance in
Haemophilus influenzae
was first detected in the early 1970s. After this, resistance spread rapidly worldwide and was shown to be transferred by a large 40- to 60-kb conjugative element. Bioinformatics analysis of the complete sequence of a typical
H. influenzae
conjugative resistance element, ICE
Hin1056
, revealed the shared evolutionary origin of this element. ICE
Hin1056
has homology to 20 contiguous sequences in the National Center for Biotechnology Information database. Systematic comparison of these homologous sequences resulted in identification of a conserved syntenic genomic island consisting of up to 33 core genes in 16 β- and γ-
Proteobacteria
. These diverse genomic islands shared a common evolutionary origin, insert into tRNA genes, and have diverged widely, with G+C contents ranging from 40 to 70% and amino acid homologies as low as 20 to 25% for shared core genes. These core genes are likely to account for the conjugative transfer of the genomic islands and may even encode autonomous replication. Accessory gene clusters were nestled among the core genes and encode the following diverse major attributes: antibiotic, metal, and antiseptic resistance; degradation of chemicals; type IV secretion systems; two-component signaling systems; Vi antigen capsule synthesis; toxin production; and a wide range of metabolic functions. These related genomic islands include the following well-characterized structures: SPI-7, found in
Salmonella enterica
serovar Typhi; PAP1 or pKLC102, found in
Pseudomonas aeruginosa
; and the
clc
element, found in
Pseudomonas
sp. strain B13. This is the first report of a diverse family of related syntenic genomic islands with a deep evolutionary origin, and our findings challenge the view that genomic islands consist only of independently evolving modules.
Cost effectiveness of a community based exercise programme in over 65 year olds: cluster randomised trial
Authors: Munro James F , Nicholl Jon P , Brazier John E , Davey Rachel , Cochrane Tom 
Published: November 2004

Objective:To assess the cost effectiveness of a community based exercise programme as a population wide public health intervention for older adults.Design:Pragmatic, cluster randomised community intervention trial.Setting:12 general practices in Sheffield; four randomly selected as intervention populations, and eight as control populations.Participants:All those aged 65 and over in the least active four fifths of the population responding to a baseline survey. There were 2283 eligible participants from intervention practices and 4137 from control practices.Intervention:Eligible subjects were invited to free locally held exercise classes, made available for two years.Main outcome measures:All cause and exercise related cause specific mortality and hospital service use at two years, and health status assessed at baseline, one, and two years using the SF-36. A cost utility analysis was also undertaken.Results:Twenty six per cent of the eligible intervention practice population attended one or more exercise sessions. There were no significant differences in mortality rates, survival times, or admissions. After adjusting for baseline characteristics, patients in intervention practices had a lower decline in health status, although this reached significance only for the energy dimension and two composite scores (p<0.05). The incremental average QALY gain of 0.011 per person in the intervention population resulted in an incremental cost per QALY ratio of €17 174 (95% CI = €8300 to €87 120).Conclusions:Despite a low level of adherence to the exercise programme, there were significant gains in health related quality of life. The programme was more cost effective than many existing medical interventions, and would be practical for primary care commissioning agencies to implement.
Post-disaster health effects: strategies for investigation and data collection. Experiences from the Enschede firework disaster: Figure 1
Authors: Roorda J , van Stiphout W A H J , Huijsman-Rubingh R R R 
Published: November 2004

Background:Public health policy is increasingly concerned with the care for victims of a disaster. This article describes the design and implementation of an epidemiological study, which seeks to match care services to the specific problems of persons affected by a large scale incident. The study was prompted by the explosion of a firework depot in Enschede, the Netherlands.Study population:All those directly affected by this incident (residents, emergency services personnel, and people who happened to be in the area at the time), some of whom suffered personal loss or injury. The project investigates both the physical and psychological effects of the disaster, as well as the target group’s subsequent call on healthcare services.Study design:A questionnaire based follow up survey of those directly affected and an ongoing monitoring of health problems relying on reports from healthcare professionals. The follow up survey started three weeks after the incident and was repeated 18 months and almost four years after the incident. The monitoring is conducted over a four year period by general practitioners, the local mental health services department, occupational health services, and the youth healthcare services department. It provides ongoing information.Results and Conclusions:The results of the study are regularly discussed with healthcare professionals and policy makers, and are made known to the research participants. The paper also explains the considerations that were made in designing the study to help others making up their research plans when confronted with possible health effects of a disaster.
BOSONIZATION OF A TOPOLOGICAL COSET MODEL AND NON-CRITICAL STRING THEORY
Authors: OHTA NOBUYOSHI , SUZUKI HISAO 
Published: November 2004

We analyze the relation between a topological coset model based on super SL(2, R)/U(1) coset and non-critical string theory by using free field realization. We show that the twisted N=2 algebra of the coset model can be naturally transformed into that of non-critical string. The screening operators of the coset models can be identified either with those of the minimal matters or with the cosmological constant operator. We also find that another screening operator, which is intrinsic in our approach, becomes the BRST non-trivial state of ghost number 0 (generator of the ground ring for c=1 gravity). The relation between non-critical strings and topological field theories is the subject of current interest. It has long been suggested that the latter theories describe the unbroken phase of gravity,1 but their precise relation has not been clear. It has been known that the twisting of N=2 superconformal field theory gives rise to topological theory.1,2 This suggests that any non-critical string theories may have hidden N=2 superconformal symmetry. Indeed, several authors have observed that the BRST current and the antighost field b(z) generate an algebra that is quite similar but apparently not identical to the N=2 superconformal algebra.3 It turns out that the BRST current can be modified by total derivative terms so that the antighost and the physical BRST current exactly generate a topologically twisted N=2 superconformal algebra.4,5 This does not identify, however, the structure of the models with N=2 symmetry. Recently, rather non-trivial correspondence between super SL(2, R)k/U(1) coset model6 and c=1 string has been analyzed through twisted N=2 structure. Mukhi and Vafa7 have revealed an amazing correspondence between these two models for k=3. In this letter, we discuss the relation of these models and the generalization of the correspondence to the minimal models coupled to gravity by means of the free field realization. We find that there is another interesting correspondence for k=1. Super SL(2, R)k/U(1) model is described by the bosonic coset model of SL(2, R)k×U(1)/U(1).8 For a representation of SL(2, R)k, we use the following
GAUGE INVARIANCE AND QUANTIZATION OF THE SPINOR STRONG INTERACTION MODEL
Authors: HOH F.C. 
Published: November 2004

The spinor strong interaction model recently proposed to account for the meson spectra is extended to include interaction with external gauge fields. An action integral is constructed and a restricted variational principle is employed to reproduce the earlier basic meson equations. In establishing U(1) gauge invariance, the so-called U(1) problem, the absence of pseudoscalar singlet mesons that do not decay strongly, is naturally resolved. SU(2)× U(1) or SO(3) gauge invariance leads to that pseudoscalar isodoublet or isotriplet mesons can generate masses of the gauge bosons without recourse to the unobserved Higgs bosons of the standard electroweak model. The gauge boson masses relate to the linear confinement potential constant of pseudoscalar mesons. The spinor strong interaction model is quantized in a macroscopic approximation due to the finite size of mesons. Commutation relations and the rest frame Hamiltonian are obtained. In this frame, the relative energy of the quark and antiquark is shown to vanish.
STRONG–WEAK COUPLING DUALITY IN FOUR-DIMENSIONAL STRING THEORY
Authors: SEN ASHOKE 
Published: November 2004

We present several pieces of evidence for strong–weak coupling duality symmetry in the heterotic string theory, compactified on a six-dimensional torus. They include symmetry of the (1) low energy effective action, (2) allowed spectrum of electric and magnetic charges in the theory, (3) allowed mass spectrum of particles saturating the Bogomol'nyi bound, and (4) Yukawa couplings between massless neutral particles and massive charged particles saturating the Bogomol'nyi bound. This duality transformation exchanges the electrically charged elementary string excitations with the magnetically charged soliton states in the theory. It is shown that the existence of a strong–weak coupling duality symmetry in four-dimensional string theory makes definite predictions about the existence of new stable monopole and dyon states in the theory with specific degeneracies, including certain supersymmetric bound states of monopoles and dyons. The relationship between strong–weak coupling duality transformation in string theory and target space duality transformation in the five-brane theory is also discussed.
FUSION IN CONFORMAL FIELD THEORY AS THE TENSOR PRODUCT OF THE SYMMETRY ALGEBRA
Authors: GABERDIEL MATTHIAS 
Published: November 2004

Following a recent proposal of Richard Borcherds to regard fusion as the ringlike tensor product of modules of a quantum ring, a generalization of rings and vertex algebras, we define fusion as a certain quotient of the (vector space) tensor product of representations of the symmetry algebra [Formula: see text]. We prove that this tensor product is associative and symmetric up to equivalence. We also determine explicitly the action of [Formula: see text] on it, under which the central extension is preserved. Having defined fusion in this way, determining the fusion rules is then the algebraic problem of decomposing the tensor product into irreducible representations. We demonstrate how to solve this for the case of the WZW and the minimal models and recover thereby the well-known fusion rules. The action of the symmetry algebra on the tensor product is given in terms of a comultiplication. We calculate the R matrix of this comultiplication and find that it is triangular. This seems to shed some new light on the possible rôle of the quantum group in conformal field theory.
EFFECTIVE LAGRANGIAN, CASIMIR ENERGY AND CONFORMAL FIELD THEORY DESCRIPTION OF THE QUANTUM HALL EFFECT
Authors: CRISTOFANO G. , GIULIANO D. , MAIELLA G. 
Published: November 2004

By using the Girvin–MacDonald effective Lagrangian for the Hall fluid system at filling ν = 1 we are able to evaluate the ground-state energy for a cylinder of infinite length. That is done by using the topological properties of the edge vacuum in the thermodynamic limit, Ne → ∞, ν = 1 fixed, From the vacuum energy we extract the value of the Casimir energy for both filling ν = 1 and ν = 1/m. The results obtained fix the central charge c of the underlying 2D Conformal Field Theory at c = 1. This correspondence is further analyzed by using the bosonic realization of the Kac–Moody algebra on the edge vacuum. Then the off-diagonal long-range order of the effective theory can be seen as an equivalent description of the topological order typical of the 2D CFT.
COMPOSITION DEPENDENCE OF THE TRANSITION TEMPERATURE AND ENERGY GAP OF SUPERCONDUCTING ALLOYS WITH NONMAGNETIC IMPURITIES
Authors: BANERJEE S. , ROY S. K. 
Published: November 2004

Analytic expressions of superconducting transition temperature (T c ) and maximum energy gap (Δ0) of alloys with nonmagnetic impurities are obtained in terms of the alloy composition and the modified normal state electron density of states (DOS), assuming a Lorentzian DOS in the unalloyed state. The calculations were performed within the framework of the BCS theory. As expected, both T c and Δ0 are modified significantly from the BCS expressions. However, the nature of change depends on whether the width of the electron DOS is greater or less than the Debye energy of the alloy.
STATISTICAL PROPERTIES OF EIGENFUNCTIONS OF RANDOM QUASI 1D ONE-PARTICLE HAMILTONIANS
Authors: FYODOROV YAN V. , MIRLIN ALEXANDER D. 
Published: November 2004

The article reviews recent analytical results concerning statistical properties of eigenfunctions of random Hamiltonians with broken time reversal symmetry describing a motion of a quantum particle in a thick wire of finite length L. It is demonstrated that the problem is equivalent to the study of properties of large Random Banded Matrices in the limit of large width of the band. Matrices of this class are relevant for a number of problems in Solid State physics and in the domain of Quantum Chaos. We find the analytical expressions for the distribution of the following quantities: i) the eigenfunction amplitude |ψ(r)|2 at given point of the sample; ii) spatial extent of the eigenfunction measured by the “inverse participation ratio” P=∫V dr|ψ(r)|4; iii) the quantity R=|ψ(r)ψ(r′)|2, points r and r′ belonging to the opposite ends of the sample. For a long sample the quantity –(ln R)/L characterizes the decay rate of a localized eigenfunction (Lyapunov exponent). Relation with available numerical results is discussed.
A TWO-DIMENSIONAL BLAST WAVE IN RELATIVISTIC MAGNETOHYDRODYNAMICS
Authors: VAN PUTTEN MAURICE H.P.M. 
Published: November 2004

The blast wave produced by a star-like object in a magnetic field is studied numerically in the approximation of ideal, fully relativistic magnetohydrodynamics (MHD). Waves of this type are observed to evolve along three episodes. At early time an outgoing shock front and an ingoing rarefaction wave is established. The ingoing rarefaction wave steepens, and gives rise to dust formation in the core. The steep rarefaction wave front becomes an ingoing shock. An annular region of high magnetic pressure about the equatorial plane deforms this shock front radially, whereby it becomes prolate along the axis of symmetry. The core is subsequently refilled as this shock front converges. Subsequent collapse in the center gives rise to high pressures, familiar from the well-known converging shock problem in nonrelativistic hydrodynamics, and high densities unique to the relativistic description. The results are compared with spherical blast waves in relativistic hydrodynamics, where a similar three episodes can be found and where collapse of the interior shock at the center constitutes a fluid singularity. It remains an open question whether such fluid singularity persists in the full MHD problem. The computations employ the covariant equations of constraint-free MHD in divergence form introduced in earlier work. The magnetic field is kept divergence free to within machine round-off error.