bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of Gene Islands Involved in Methanopterin-Linked C
1
Transfer Reactions Reveals New Functions and Provides Evolutionary Insights
Authors: Kalyuzhnaya Marina G. , Korotkova Natalia , Crowther Gregory , Marx Christopher J. , Lidstrom Mary E. , Chistoserdova Ludmila 
Published: June 2005

ABSTRACT

In this study, the occurrence and chromosomal clustering of genes encoding C
1
transfer reactions linked to tetrahydromethanopterin (H
4
MPT) were analyzed in a variety of proteobacteria and in representatives of the
Planctomycetes
via genomic analysis or via partial sequencing by cosmid walking. Although a tendency for clustering was found common for the genes of interest, significant variations in gene order and the degree of clustering were uncovered both between and within different groups of
Proteobacteria
and between
Proteobacteria
and
Planctomycetes
. Phylogenetic analyses suggested that the evolution of genes encoding H
4
MPT-linked reactions in
Proteobacteria
involved lateral transfers within
Proteobacteria
and possibly between
Proteobacteria
and other phyla. Gene cluster comparisons revealed a number of novel genes potentially involved in the C
1
transfer reactions, and these were analyzed by mutation and expression analyses. Four genes, a homolog of
pabB
, and three genes conserved between methanogenic
Archaea
and
Bacteria
possessing H
4
MPT-linked functions,
orfY
,
orf1
, and
afpA
were shown to be involved in formaldehyde oxidation/detoxification, as judged by specific mutant phenotypes. In particular,
pabB
contributes to the biosynthesis of
para
-aminobenzoic acid, a precursor of both tetrahydrofolate and H
4
MPT, and
afpA
apparently encodes a novel dihydromethanopterin reductase, based on mutant complementation experiments.
Complete Genome Sequence and Analysis of the Multiresistant Nosocomial PathogenCorynebacterium jeikeiumK411, a Lipid-Requiring Bacterium of the Human Skin Flora
Authors: Tauch Andreas , Kaiser Olaf , Hain Torsten , Goesmann Alexander , Weisshaar Bernd , Albersmeier Andreas , Bekel Thomas , Bischoff Nicole , Brune Iris , Chakraborty Trinad , Kalinowski Jörn , Meyer Folker , Rupp Oliver , Schneiker Susanne , Viehoever Prisca , Pühler Alfred 
Published: June 2005

ABSTRACTCorynebacterium jeikeiumis a “lipophilic” and multidrug-resistant bacterial species of the human skin flora that has been recognized with increasing frequency as a serious nosocomial pathogen. Here we report the genome sequence of the clinical isolateC. jeikeiumK411, which was initially recovered from the axilla of a bone marrow transplant patient. The genome ofC. jeikeiumK411 consists of a circular chromosome of 2,462,499 bp and the 14,323-bp bacteriocin-producing plasmid pKW4. The chromosome ofC. jeikeiumK411 contains 2,104 predicted coding sequences, 52% of which were considered to be orthologous with genes in theCorynebacterium glutamicum,Corynebacterium efficiens, andCorynebacterium diphtheriaegenomes. These genes apparently represent the chromosomal backbone that is conserved between the four corynebacteria. Among the genes that lack an ortholog in the known corynebacterial genomes, many are located close to transposable elements or revealed an atypical G+C content, indicating that horizontal gene transfer played an important role in the acquisition of genes involved in iron and manganese homeostasis, in multidrug resistance, in bacterium-host interaction, and in virulence. Metabolic analyses of the genome sequence indicated that the “lipophilic” phenotype ofC. jeikeiummost likely originates from the absence of fatty acid synthase and thus represents a fatty acid auxotrophy. Accordingly, both the complete gene repertoire and the deduced lifestyle ofC. jeikeiumK411 largely reflect the strict dependence of growth on the presence of exogenous fatty acids. The predicted virulence factors ofC. jeikeiumK411 are apparently involved in ensuring the availability of exogenous fatty acids by damaging the host tissue.
The
Helicobacter pylori
CrdRS Two-Component Regulation System (HP1364/HP1365) Is Required for Copper-Mediated Induction of the Copper Resistance Determinant CrdA
Authors: Waidner Barbara , Melchers Klaus , Stähler Frank Nils , Kist Manfred , Bereswill Stefan 
Published: June 2005

ABSTRACT

Here we describe that the
Helicobacter pylori
sensor kinase produced by HP1364 and the response regulator produced by HP1365 and designated CrdS and CrdR, respectively, are both required for transcriptional induction of the
H. pylori
copper resistance determinant CrdA by copper ions. CrdRS-deficient mutants lacked copper induction of
crdA
expression and were copper sensitive. A direct role of CrdR in transcriptional regulation of
crdA
was confirmed by in vitro binding of CrdR to the
crdA
upstream region. A 21-nucleotide sequence located near the
crdA
promoter was shown to be required for CrdR binding.
Mitochondrial DNA, allozymes, morphology and historical biogeography in the Podarcis vaucheri (Lacertidae) species complex
Authors: Busack Stephen , Lawson Robin , Arjo Wendy 
Published: June 2005

Abstract
Mitochondrial DNA analysis indicates that Podarcis vaucheri is a species
complex with one clade inhabiting both north and south shores of the Strait
of Gibraltar and one clade restricted to North Africa. While each clade
exhibits differing morphology, allozyme analysis suggests varying degrees of
reproductive contact among populations within clades. Ancestral P. vaucheri
appears to have been restricted to insular areas of the Betic-Rif Massif and
mainland Africa during Miocene, with major lineage differentiation occurring
during Pliocene.Our analysis further confirms that Podarcis atrata warrants
species status and suggests that it may be more widely distributed than
previously reported.
Intermediate-Depth Circulation of the Indian and South Pacific Oceans Measured by Autonomous Floats
Authors: Davis Russ E. 
Published: June 2005

Abstract
As part of the World Ocean Circulation Experiment, 306 autonomous floats were deployed in the tropical and South Pacific Ocean and 228 were deployed in the Indian Ocean to observe the basinwide circulation near 900-m depth. Mean velocities, seasonal variability, and lateral eddy diffusivity from the resultant 2583 float-years of data are presented. Area averages, local function fits, and a novel application of objective mapping are used to estimate the mean circulation. Patterns of mean circulation resemble those at the surface in both basins. Well-developed subtropical gyres, twice as strong in the Indian Ocean as in the Pacific, feed western boundary currents. Tropical gyres are separated by eastward flow along the equator in both hemispheres of both basins, although the Indian subcontinent splits the north Indian tropical gyre. The Antarctic Circumpolar Current (ACC) and west wind drifts are prominent in both basins, generally tending slightly southward but deviating to the north behind the Del Cano, Kerguelen, and Campbell Plateaus and, of course, South America. Remarkably, the eastern boundaries of the southern subtropical gyres in all three basins apparently occur in the ocean interior, away from land. The Indian Ocean’s subtropical gyre, and perhaps part of the South Atlantic’s, reaches east to a retroflection just upstream of the Campbell Plateau south of New Zealand. Seasonal variability at 900 m is focused around the equator with weaker variability found near certain bathymetric features. There is a remarkable agreement between the observed seasonable variability and that predicted by the Jet Propulsion Laboratory (JPL)–Estimating the Circulation and Climate of the Ocean (ECCO) data-assimilating numerical model. Aside from seasonal effects, eddy variability is greatest along the equator, in tropical and subtropical western basins, and along the ACC. Integrals of velocity across regional passages (Tasman Sea, Mozambique Channel) provide useful reference for hydrographic analyses of transport. Across whole ocean basins, however, the uncertainty associated with the appropriate continuity relation for horizontal flow (e.g., geostrophy vs nondivergence) is comparable to the mean flow.
Parameterizing the Sea Surface Roughness
Authors: Drennan William M. , Taylor Peter K. , Yelland Margaret J. 
Published: June 2005

Abstract
The concept of an “equivalent surface roughness” over the ocean is useful in understanding the relation between wind speed (at some height) and the net momentum flux from air to sea. The relative performance of different physics-motivated scalings for this roughness can provide valuable guidance as to which mechanisms are important under various conditions. Recently, two quite different roughness length scalings have been proposed. Taylor and Yelland presented a simple formula based on wave steepness, defined as the ratio of significant wave height to peak wavelength, to predict the surface roughness. A consequence of this formula is that roughness changes due to fetch or duration limitations are small, an order of 10%. The wave steepness formula was proposed as an alternative to the classical wave-age scaling first suggested by Kitaigorodskii and Volkov. Wave-age scaling, in contrast to steepness scaling, predicts order-of-magnitude changes in roughness associated with fetch or duration. The existence of two scalings, with different roughness predictions in certain conditions, has led to considerable confusion among certain groups. At several recent meetings, including the 2001 World Climate Research Program/Scientific Committee on Oceanic Research (WCRP/SCOR) workshop on the intercomparison and validation of ocean–atmosphere flux fields, proponents of the two scalings met with the goal of understanding the merits and limitations of each scaling. Here the results of these efforts are presented. The two sea-state scalings are tested using a composite of eight datasets representing a wide range of conditions. In conditions with a dominant wind-sea component, both scalings were found to yield improved estimates when compared with a standard bulk formulation. In general mixed sea conditions, the steepness formulation was preferred over both bulk and wave-age scalings, while for underdeveloped “young” wind sea, the wave-age formulation yields the best results. Neither sea-state model was seen to perform well in swell-dominated conditions where the steepness was small, but the steepness model did better than the wave-age model for swell-dominated conditions where the steepness exceeded a certain threshold.
The Behavior of Jet Currents over a Continental Slope Topography with a Possible Application to the Northern Current
Authors: Flexas M. M. , van Heijst G. J. F. , Trieling R. R. 
Published: June 2005

Abstract
The Northern Current is a slope current in the northwest Mediterranean that shows high mesoscale variability, generally associated with meander and eddy formation. A barotropic laboratory model of this current is used here to study the role of the bottom topography on the current variability. For this purpose, a source–sink setup in a cylindrical tank placed on a rotating table is used to generate an axisymmetric barotropic current. To study inviscid topographic effects, experiments are performed over a topographic slope and also over a constant-depth setup, the latter being used as a reference for the former. With the aim of obtaining a fully comprehensive view of the vorticity balance at play, the flow may be forced in either azimuthal direction, leading to a “westward” prograde current (similar to the Northern Current) or an “eastward” retrograde current. For slow flows, eastward and westward currents showed similar patterns, dominated by Kelvin–Helmholtz-type instabilities. For high-speed flows, eastward and westward currents showed very different behavior. In eastward currents, the variability is observed to concentrate toward the center of the jet and shows strong meandering formation. Westward currents, instead, showed major variability toward the edges of the jet, together with a strong variability over the uppermost slope, which has been associated here with a topographic Rossby wave trapped over the shelf break. The differences between eastward and westward jets are explained through the balance between shear-induced and topographically induced vorticity at play in each case. Moreover, a model of jets over a beta plane is successfully applied here, allowing its extension to any ambient potential vorticity gradient caused either by latitudinal or bottom depth changes.
Viscosity-Dependent Internal Variability in a Model of the North Pacific
Authors: Dawe Jordan T. , Thompson Lu Anne 
Published: June 2005

Abstract
A 2°-resolution isopycnal model of the North Pacific Ocean is shown to produce anomalies that propagate around the subtropical gyre on the decadal time scale that do not appear in a 1°-resolution version of the same model. A principal oscillation pattern (POP) analysis of the isopycnal interface anomaly is performed to examine the dynamics responsible for the anomaly generation. The POPs show a coherent oscillation around the entire subtropical gyre with two centers of action, one in the Central Mode Water (CMW) region, the other in the Subtropical Countercurrent (STCC). Lead–lag covariances between the subduction rate in the CMW and the layer thickness along the oscillation path indicate that anomalous subduction events are not the driving mechanism for the oscillation. A linearized quasigeostrophic mode analysis shows that the anomalies are generated by flow instability in the region of the STCC. The instability disappears in the 1° model because of changes in the horizontal viscosity, which is set in each model to the minimum value necessary to resolve the western boundary current and preserve numerical stability. A criterion for model resolution of an instability of a given length and time scale damped by biharmonic viscosity is derived. The enhancement of the large-scale instabilities in the low-resolution model emphasizes the importance of achieving mesoscale resolution in ocean models used for climate studies.
Wind-Driven Oceanic Rossby Waves in the Tropical South Indian Ocean with and without an Active ENSO
Authors: Baquero-Bernal Astrid , Latif Mojib 
Published: June 2005

Abstract
The interannual heat content variability in the tropical south Indian Ocean (SIO) and its relationship with El Niño–Southern Oscillation (ENSO) is studied. The baroclinic ocean response to stochastic wind stress predicted by a simple analytical model is compared with two integrations of the ECHO-G coupled general circulation model. In one integration, ocean–atmosphere interactions are suppressed in the tropical Pacific Ocean, so that this integration does not simulate ENSO. In the other integration, interactions are allowed everywhere and ENSO is simulated. The results show that basinwide variability in the SIO heat content can be produced by two mechanisms: 1) oscillatory forcing by ENSO-related wind stress and 2) temporally stochastic and spatially coherent wind stress forcing. Previous studies have shown that transmission of energy from the tropical Pacific to the southern Indian Ocean occurs through coastal Kelvin waves along the western coast of Australia. The results in this paper confirm the occurrence of such transmission. In the ECHO-G simulations, this transmission occurs both at the annual time scale and at interannual time scales. Generation of offshore Rossby waves by these coastal Kelvin waves at interannual time scales—and, in particular, at the ENSO time scale—was found.
Origins and Dynamics of the 90-Day and 30–60-Day Variations in the Equatorial Indian Ocean
Authors: Han Weiqing 
Published: June 2005

Abstract
Sea level observations in the equatorial Indian Ocean show a dominant spectral peak at 90 days and secondary peaks at 30–60 days over an intraseasonal period (20–90 days). A detailed investigation of the origins and dynamics of these variations is carried out using an ocean general circulation model, namely, the Hybrid Coordinate Ocean Model (HYCOM). Two parallel experiments are performed in the tropical Indian Ocean basin for the period 1988–2001: one is forced by NCEP 3-day mean forcing fields together with the Climate Prediction Center (CPC) Merged Analysis of Precipitation (CMAP) pentad precipitation, and the other is forced by monthly mean fields. To help to understand the role played by the wind-driven equatorial wave dynamics, a linear continuously stratified ocean model is also used. Both the observed and modeled 90-day sea level anomaly fields and HYCOM surface current clearly show equatorial Kelvin and first-meridional-mode Rossby wave structures that are forced by the 90-day winds. The wind amplitude at the 90-day period, however, is weaker than that for the 30–60-day period, suggesting that the equatorial Indian Ocean selectively responds to the 90-day winds. This selective response arises mainly from the resonant excitation of the second-baroclinic-mode (n = 2) waves by the 90-day winds. In this case, Rossby waves reflected from the eastern ocean boundary enhance the directly forced response in the ocean interior, strengthening the 90-day peak. In addition, the directly forced response increases monotonically with the increase of forcing period, contributing to the larger variances of currents and sea level at 90 days. Two factors account for this monotonic increase in directly forced response. First, at lower frequency, both Rossby and Kelvin waves associated with the low-order baroclinic modes have longer wavelengths, which are more efficiently excited by the larger-scale winds. Second, responses of the high-order modes directly follow the local winds, and their amplitudes are proportional to both forcing period and wind strength. Although most energy is surface trapped, there is a significant amount that propagates through the pycnocline into the deep ocean. The dominance of the 90-day peak occurs not only at the surface but also in the deeper layers down to 600 m. In the deeper ocean, both the directly forced response and reflected waves associated with the first two baroclinic modes contribute to the 90-day variation. Spectra of the observed sea surface temperature (SST) also show a 90-day peak, likely a result of the selective response of the equatorial Indian Ocean at the 90-day period. Near the surface, the spectral peaks of currents and sea level at the 30–60-day period are directly forced by winds that peak at 30–60 days. In the deeper layers, both directly forced and reflected waves associated with the first two baroclinic modes contribute. Oceanic instabilities can have significant contributions only near the western boundary and near 5°N south of Sri Lanka.
Brief Communication: Factors Affecting Rehospitalisation in Psychiatric Patients in Singapore
Authors: Mahendran Rathi , Mythily  , Chong Siow-Ann , Chan Yiong Huak 
Published: June 2005

Objectives: To study the patterns of readmission in Singapore using a cohort of first admission schizophrenia patients to the state mental health institute.Methods: A retrospective analysis of case records was done of first admission schizophrenia patients to the hospital from April 1993 to March 1994. Patients who had only one admission in the five years of follow up were compared to ‘revolving door patients’.Results: The cohort comprised 133 males (56.8%) and 101 females (43.2%). Seventy-eight patients (33.3%) had one admission to the hospital while 56 (23.9%) fulfilled the revolving door criteria. On performing a logistic regression we found sex (p1/4 0.02), shorter duration of illness (p1/4 0.01) and CPN referral (0.006) were significantly associated with revolving door phenomena.Conclusions: Our study has identified male gender, history of self-harm and a short duration of illness to be risk factors for ‘revolving door’ phenomena.
Psychiatric Disorders among the Mapuche in Chile
Authors: Vicente Benjamin , Kohn Robert , Rioseco Pedro , Saldivia Sandra , Torres Silverio 
Published: June 2005

Background: The Mapuche are the largest indigenous group in Chile; yet almost all data on the mental health of indigenous populations are from North America. Aim: The study examines the differential DSM-III-R prevalence rates of psychiatric disorders and service utilization among indigenous and non-indigenous community residence. Methods: The Composite International Diagnostic Interview (CIDI) was administered to a stratified random sample of 75 Mapuche and 434 non-Mapuche residents of the province of Cautín. Lifetime prevalence and 12-month prevalence rates were estimated. Results: Approximately 28.4% of the Mapuche population had a lifetime, and 15.7% a 12-month, prevalent psychiatric disorder compared to 38.0% and 25.7%, respectively, of the non-Mapuche. Few significant differences were noted between the two groups; however, generalized anxiety disorder, simple phobia, and drug dependence were less prevalent among the Mapuche. Service utilization among the Mapuche with mental illness was low. Conclusions: This is a preliminary study based on a small sample size. Further research on the mental health of indigenous populations of South America is needed.
Challenging Stigma and Discrimination in Communities: A Focus Group Study Identifying UK Mental Health Service Users’ Main Campaign Priorities
Authors: Pinfold Vanessa , Byrne Peter , Toulmin Hilary 
Published: June 2005

Background: Stigma and discrimination experienced by people with mental health problems have been identified as major obstacles to treatment and recovery. Less is known about how to effectively tackle stigma-discrimination, although there are numerous international, national and local programmes attempting to improve public mental health literacy and anti-discrimination evidenced based practice. Aims: To explore mental health service users’ views on how campaigns to address stigma and discrimination should prioritise their actions. Method: Qualitative study using focus group discussions, involving 33 persons aged between 25 and 75. Results: A triad of diminished credibility, dis-empowerment with particular reference to communication problems and avoidance by their social network defined experiences of stigma. Reactions to stigma can be placed in four categories: avoid stigma, resign yourself to it, challenge it, or distance yourself from others with a mental health problem. A range of solutions was discussed with most favouring changes within the health services that are currently supporting them over traditional educational programmes with the public. Conclusions: For mental health service users stigma must be tackled on many different levels reflecting the varied and complex impact that negative social reactions have on an individual’s life. When asked to prioritise one area, most service users in our sample highlighted reforms within the health service for tackling stigma and discrimination.