bluuebunny/crossref_metadata_2025_split huggingface dataset:
Aquaporin Expression and Freeze Tolerance in
Candida albicans
Authors: Tanghe An , Carbrey Jennifer M. , Agre Peter , Thevelein Johan M. , Van Dijck Patrick 
Published: October 2005

ABSTRACT

Aquaporins are members of the major intrinsic protein superfamily of integral membrane proteins which enable the transport of water, glycerol, and other solutes across membranes in various organisms. In microorganisms, the physiological role of aquaporins is not yet defined. We found a clear correlation between expression of the
Candida albicans
aquaporin-encoding gene
AQY1
and freeze tolerance. A connection with the function for the aquaporin in the natural environment of
C. albicans
is, however, not obvious.
Production of Ethanol from Starch by Respiration-Deficient Recombinant
Saccharomyces cerevisiae
Authors: Toksoy Öner Ebru , Oliver Stephen G. , Kırdar Betül 
Published: October 2005

ABSTRACT

A 100%-respiration-deficient nuclear petite amylolytic
Saccharomyces cerevisiae
NPB-G strain was generated, and its employment for direct fermentation of starch into ethanol was investigated. In a comparison of ethanol fermentation performances with the parental respiration-sufficient WTPB-G strain, the NPB-G strain showed an increase of ca. 48% in both ethanol yield and ethanol productivity.
Synthetic Aperture Radar (L band) and Optical Vegetation Indices for Discriminating the Brazilian Savanna Physiognomies: A Comparative Analysis
Authors: Sano Edson E. , Ferreira Laerte G. , Huete Alfredo R. 
Published: October 2005

Abstract
The all-weather capability, signal independence to the solar illumination angle, and response to 3D vegetation structures are the highlights of active radar systems for natural vegetation mapping and monitoring. However, they may present significant soil background effects. This study addresses a comparative analysis of the performance of L-band synthetic aperture radar (SAR) data and optical vegetation indices (VIs) for discriminating the Brazilian cerrado physiognomies. The study area was the Brasilia National Park, Brazil, one of the test sites of the Large-Scale Biosphere–Atmosphere (LBA) experiment in Amazonia. Seasonal Japanese Earth Resources Satellite-1 (JERS-1) SAR backscatter coefficients (σ°) were compared with two vegetation indices [normalized difference vegetation index (NDVI) and enhanced vegetation index (EVI)] over the five most dominant cerrados’ physiognomies plus gallery forest. In contrast to the VIs, σ° from dry and wet seasons did not change significantly, indicating primary response to vegetation structures. Discriminant analysis and analysis of variance (ANOVA) showed an overall higher performance of radar data. However, when both SAR and VIs are combined, the discrimination capability increased significantly, indicating that the fusion of the optical and radar backscatter observations provides overall improved classifications of the cerrado types. In addition, VIs showed good performance for monitoring the cerrado dynamics.
Observations of Small-Scale Processes Associated with the Internal Tide Encountering an Island
Authors: Stevens Craig L. , Abraham Edward R. , Moore C. Mark , Boyd Philip W. , Sharples Jonathan 
Published: October 2005

Abstract
Current-meter, temperature, and microstructure observations of the large-amplitude internal tide shoaling on the continental shelf of the east coast of northern New Zealand show the complexity of the internal kinematics and mixing. The propagation speed of the main internal wave was around 0.3 m s−1, and nonstationary time series analysis was used to locate the trailing short-wavelength internal waves in frequency (periods of around 40 min) and tidal-phase space. The average energy dissipation rate (5 × 10−8 m2 s−3) was an order of magnitude smaller than that observed on the open shelf in other studies, but peaks in dissipation rate were measured to be much greater. The vertical diffusivity of heat was around 10−4 m2 s−1, comparable to, or greater than, other studies. Examples of the scale and sporadic nature of larger mixing events were observed. The behavior was complicated by the nearby steeply shoaling coast of the Poor Knight Islands. Consistent reflected wave energy was not apparent.
Finite-Amplitude Evolution of Instabilities Associated with the Coastal Upwelling Front
Authors: Durski Scott M. , Allen J. S. 
Published: October 2005

Abstract
A primitive equation model is used to study the finite-amplitude evolution of instabilities associated with the coastal upwelling front. Simulations of increasing complexity are examined that represent idealizations of summer conditions off the Oregon coast, including cases with steady and with time-variable wind in a domain with alongshore-uniform bathymetry and with time-variable wind in a domain with realistic Oregon coast bathymetry. The numerical results indicate that the fastest-growing mode in this system has approximately an 8–10-km alongshore wavelength but that, once the disturbances grow to finite amplitude, the predominant alongfront scale increases rapidly because of nonlinear effects. Separation of the total kinetic energy into contributions from the alongshore average flow and perturbation about that average shows that the initial growth of the perturbation kinetic energy is due to potential energy conversion, but transfer of energy from the kinetic energy of the alongshore average flow becomes important once the disturbances reach large amplitude. The time-variable wind simulations again show initial growth of small-scale instabilities followed by evolution to larger scales. In this case, however, even after larger-scale disturbances have developed on the upwelling front, smaller-scale patterns amplify along the front in response to each upwelling-favorable wind event. Realistic coastal bathymetry introduces additional alongshore topographic scales into the problem, but the formation of instabilities on small scales and evolution to larger scales are still ubiquitous. Where instabilities encounter strong curvature in the upwelling front produced by bathymetric effects, the upwelling front becomes highly contorted and horizontal variability is significantly enhanced.
Direct Evidence of an Oceanic Inverse Kinetic Energy Cascade from Satellite Altimetry
Authors: Scott Robert B. , Wang Faming 
Published: October 2005

AbstractSea surface height measurements from satellites reveal the turbulent properties of the South Pacific Ocean surface geostrophic circulation, both supporting and challenging different aspects of geostrophic turbulence theory. A near-universal shape of the spectral kinetic energy flux is found and provides direct evidence of a source of kinetic energy near to or smaller than the deformation radius, consistent with linear instability theory. The spectral kinetic energy flux also reveals a net inverse cascade (i.e., a cascade to larger spatial scale), consistent with two-dimensional turbulence phenomenology. However, stratified geostrophic turbulence theory predicts an inverse cascade for the barotropic mode only; energy in the large-scale baroclinic modes undergoes a direct cascade toward the first-mode deformation scale. Thus if the surface geostrophic flow is predominately the first baroclinic mode, as expected for oceanic stratification profiles, then the observed inverse cascade contradicts geostrophic turbulence theory. The latter interpretation is argued for. Furthermore, and consistent with this interpretation, the inverse cascade arrest scale does not follow the Rhines arrest scale, as one would expect for the barotropic mode. A tentative revision of theory is proposed that would resolve the conflicts; however, further observations and idealized modeling experiments are needed to confirm, or refute, the revision. It is noted that no inertial range was found for the inverse cascade range of the spectrum, implying inertial range scaling, such as the established K−5/3 slope in the spectral kinetic energy density plot, is not applicable to the surface geostrophic flow.
Two-Layer Rotating Exchange Flow between Two Deep Basins: Theory and Application to the Strait of Gibraltar
Authors: Timmermans M-L. E. , Pratt L. J. 
Published: October 2005

Abstract
Rotating two-layer exchange flow over a sill in a strait separating two relatively deep and wide basins is analyzed. Upstream of the sill in the deep upstream basin, the infinitely deep dense lower layer is assumed to be inactive, while the relatively thin upper layer flowing away from the sill forms a detached boundary current in the upstream basin. This analysis emphasizes the importance of this upstream boundary current, incorporating its width as a key parameter in a formalism for deducing the volume exchange rate and discriminating between maximal and submaximal states. Hence, even for narrow straits in which rotation does not dominate the dynamics within the strait, the importance of rotation in the wide upstream basin can be exploited. It is shown that the maximal allowable exchange transport through straits wider than 1½ Rossby deformation radii increases as rotation increases, unlike for smaller rotations, where the exchange decreases as rotation increases. The theory is applied to the exchange flow through the Strait of Gibraltar. This application illustrates how images of the oceans taken from space showing the width of the upstream flow, in this case a space shuttle photograph, might be used to determine the exchange transport through a strait. Maximal exchange conditions in the Strait of Gibraltar are predicted to apply at the time the space shuttle photograph was taken.
Propagation of Tracer Signals in Boundary Currents
Authors: Waugh Darryn W. , Hall Timothy M. 
Published: October 2005

Abstract
The propagation of a range of tracer signals in a simple model of the deep western boundary current is examined. Analytical expressions are derived in certain limits for the transit-time distributions and the propagation times (tracer ages) of tracers with exponentially growing or periodic concentration histories at the boundary current’s origin. If mixing between the boundary current and the surrounding ocean is either very slow or very rapid, then all tracer signals propagate at the same rate. In contrast, for intermediate mixing rates tracer ages generally depend on the history of the tracer variations at the origin and range from the advective time along the current to the much larger mean age. Close agreement of the model with chlorofluorocarbon (CFC) and tritium observations in the North Atlantic deep western boundary current (DWBC) is obtained when the model is in the intermediate mixing regime, with current speed around 5 cm s−1 and mixing time scale around 1 yr. In this regime anomalies in temperature and salinity of decadal or shorter period will propagate downstream at roughly the current speed, which is much faster than the spreading rate inferred from CFC or tritium–helium ages (approximately 5 cm s−1 as compared with 2 cm s−1). This rapid propagation of anomalies is consistent with observations in the subpolar DWBC, but is at odds with inferences from measurements in the tropical DWBC. This suggests that observed tropical temperature and salinity anomalies are not simply propagated signals from the north. The sensitivity of the tracer spreading rates to tracer and mixing time scales in the model suggests that tight constraints on the flow and transport in real DWBCs may be obtained from simultaneous measurements of several different tracers—in particular, hydrographic anomalies and steadily increasing transient tracers.
In vitrostudies of lymphangioleiomyomatosis
Authors: Black J. L. , Ge Q. , Boustany S. , Johnson P. R. A. , Poniris M. H. , Glanville A. R. , Oliver B. G. G. , Moir L. M. , Burgess J. K. 
Published: October 2005

Lymphangioleiomyomatosis (LAM) is associated with abnormal airway smooth muscle that leads to the characteristic pathology of lung nodule formation and destruction of lung tissue. The current authors have previously identified abnormal behaviour of airway smooth muscle cells from patients with asthma.In this study, cells and tissue sections derived from patients with LAM (n = 7), asthma (n = 8), and nonasthmatic controls (n = 9) were compared. The presence of the antigen human melanosome (HM)B-45 was investigated, along with the proliferation and release of extracellular matrix proteins, release of endogenous prostaglandin E2(PGE2), vascular endothelial growth factor and connective tissue growth factor, and the expression of integrins.Positive HMB-45 staining was found in all LAM patients and no controls. Proliferation of LAM cells was not different from control cells nor was its inhibition by β-agonists, corticosteroids, rapamycin or PGE2. However, endogenous PGE2levels were markedly decreased in LAM cells, and this was associated with decreased expression of the inducible form of cyclooxygenase (COX-2). The increased levels of connective tissue growth factor seen in asthma cells were not observed in LAM. Elastin mRNA in response to transforming growth factor-β stimulation was markedly lower in LAM cells than either asthma or control cells.In conclusion, lymphangioleiomyomatosis cells exhibit abnormal propertiesin vitrothat may contribute to pathophysiology and symptomatology in patients with lymphangioleiomyomatosis.
Tumour necrosis factor gene polymorphisms and childhood wheezing
Authors: Bilolikar H. , Nam A. R. , Rosenthal M. , Davies J. C. , Henderson D. C. , Balfour-Lynn I. M. 
Published: October 2005

Tumour necrosis factor (TNF)-α is associated with childhood wheezing. A genetic predisposition to increased TNF-α production, influenced by single nucleotide gene polymorphisms, may be important.Frequencies of TNF-α-308G/A and lymphotoxin (LT)-α+252G/A polymorphisms were compared in 115 asthmatic children, 55 wheezy infants and 156 control school children from the UK. Genotype frequencies for the TNF-α-308 and LT-α+252 polymorphisms were significantly different from controls.Haplotype analysis showed that TNF-α-308G, LT-α+252A/TNF-α-308A, LT-α+252A was associated with a markedly increased risk for both asthma and infant wheezing. The TNF-α-308G, LT-α+252G/TNF-α-308G, LT-α+252A combination was protective for asthma and infant wheezing. These findings were confirmed by analysis of Caucasian data. Nasal TNF-α levels were measured in the infants during acute wheezing episodes and higher, but nonsignificant levels were produced in those with one or two LT-α+252A alleles. Unexpectedly, significantly lower nasal TNF-α levels were found in the presence of one or two TNF-α-308A alleles. TNF-α-308/LT-α+252 genotype combinations had a significant influence on nasal TNF-α levels.In conclusion, these findings may have implications for future early intervention studies by helping to identify infants at increased risk for wheezing and childhood asthma.
Factors associated with infection byPseudomonas aeruginosain adult cystic fibrosis
Authors: Chambers D. , Scott F. , Bangur R. , Davies R. , Lim A. , Walters S. , Smith G. , Pitt T. , Stableforth D. , Honeybourne D. 
Published: October 2005

Cross-infection withPseudomonas aeruginosais an emerging issue in the care of patients with cystic fibrosis (CF). This study sought to determine the extent of, and patient factors associated with, cross-infection in a tertiary referral adult CF centre.P. aeruginosaisolates were genotyped into two groups between November 2001 and February 2003, using pulsed-field gel electrophoresis after DNA digestion by theSpeI endonuclease, and identified as clustered if there was >80% homology in the macrorestriction profiles. Patient factors and measures of disease severity were identifieda priori.In total, 157 out of 227 patients had aP. aeruginosaisolate genotyped. Of these, 94 patients (60%) were infected with clustered genotypes and 47 (30%) were infected with the newly described “Midlands 1” (Md1) genotype. A further 18 patients were infected with the previously identified “Liverpool” genotype and two with the “Manchester” genotype. Logistic regression analysis revealed that the predominant predictor of infection with Md1 was age at the time of referral to the centre, suggesting that infection may have occurred prior to referral in some patients. Md1 demonstrated a relatively benign anti-biogram and did not appear to be associated with more severe disease.In conclusion, the present study provides further evidence of the emerging importance ofPseudomonas aeruginosacross-infection in cystic fibrosis.
Tumour necrosis factor-α (−308) gene polymorphism in obstructive sleep apnoea–hypopnoea syndrome
Authors: Riha R. L. , Brander P. , Vennelle M. , McArdle N. , Kerr S. M. , Anderson N. H. , Douglas N. J. 
Published: October 2005

Patients with obstructive sleep apnoea–hypopnoea syndrome (OSAHS) have elevated circulating levels of tumour necrosis factor (TNF)-α. The hypothesis in this study was that OSAHS might be associated with the TNF-α (−308A) gene polymorphism, which results in increased TNF-α production. This hypothesis was examined in OSAHS patients, their siblings and population controls.A total of 206 subjects were recruited. All underwent sleep studies and clinical review, and were subsequently classified as having OSAHS or not depending on apnoea–hypopnoea frequency, sex, age and symptoms. All subjects had blood collected and genotyping was performed on DNA extracted from peripheral leukocytes. Some 192 random UK blood donors were used as population controls.The results demonstrated a significant association for TNF-α (−308A) allele carriage with OSAHS (OR = 1.8; 95% Confidence interval: 1.18–2.75) when compared with population controls. Siblings with OSAHS were significantly more likely to carry the TNF-α (−308A) allele. In addition, 21 pairs of male siblings discordant for carriage of the −308A allele showed a significant level of discordance for the OSAHS phenotype.In conclusion, this study demonstrates an association of tumour necrosis factor-α (−308A) carriage with obstructive sleep apnoea–hypopnoea syndrome, suggesting that inflammation may be implicated in the pathogenesis of this condition.
Exacerbations of COPD: quantifying the patient's perspective using discrete choice modelling
Authors: Haughney J. , Partridge M. R. , Vogelmeier C. , Larsson T. , Kessler R. , Ståhl E. , Brice R. , Löfdahl C-G. 
Published: October 2005

Patient-centred care is the current vogue in chronic obstructive pulmonary disease (COPD), but it is only recently that robust techniques have become available to determine patients' values and preferences. In this international cross-sectional study, patients' concerns and expectations regarding COPD exacerbations were explored using discrete choice modelling.A fractional factorial design was used to develop scenarios comprising a combination of levels for nine different attributes. In face-to-face interviews, patients were presented with paired scenarios and asked to choose the least preferable. Multinomial logit (with hierarchical Bayes) methods were used to estimate utilities. A total of 125 patients (82 males; mean age 66 yrs; 4.6 mean exacerbations·yr−1) were recruited.The attributes of exacerbations considered most important were impact on everyday life (20%), need for medical care (16%), number of future attacks (12%) and breathlessness (11%). The next most important attributes were speed of recovery, productive cough and social impact (all 9%), followed by sleep disturbance and impact on mood (both 7%). Importantly, analysis of utility shifts showed that patients most feared being hospitalised, housebound or bedridden. These issues were more important than symptom improvement.Strategies for the clinical management of chronic obstructive pulmonary disease should clearly address patients' concerns and focus on preventing and treating exacerbations to avoid these feared outcomes.
Sepsis induces early phrenic nerve neuropathy in rats
Authors: Nayci A. , Atis S. , Comelekoglu U. , Ozge A. , Ogenler O. , Coskun B. , Zorludemir S. 
Published: October 2005

The aim of the present study was to investigate the electrophysiology of the phrenic nerve and the diaphragm muscle during sepsis.In total, 26 rats underwent either sham laparotomy or caecal ligation and puncture (CLP). Electrophysiology was evaluatedviaa phrenic nerve conduction study and needle electromyography of the diaphragm, prior to CLP, 6 and 24 h post-CLP and on day 7. The histopathology of the diaphragm muscle and phrenic nerve was also examined on day 7.In the sepsis group, the phrenic nerve conduction study showed decreased amplitude of compound action potential (CMAP), and prolongation in the duration and the latency of CMAP. The diaphragmatic needle electromyography showed decreased amplitude and frequency of the motor unit action potential (MUP), and prolongation in the duration of MUP, at all time points, compared with the pre-CLP values. The electrophysiological abnormalities were consistent with axonal and demyelinating phrenic nerve neuropathy. Electrophysiological abnormalities were present at 6 h with worsening at 24 h and on day 7. Histopathological examination showed normal muscular fibres and focally slight myelin degenerations of the phrenic nerve fibres.In conclusion, sepsis induced phrenic nerve neuropathy as early as the 6th h in rats.
Comparative analysis of RNA regulatory elements of amino acid metabolism genes in Actinobacteria
Authors: Seliverstov Alexander V , Putzer Harald , Gelfand Mikhail S , Lyubetsky Vassily A 
Published: October 2005

Abstract

Background
Formation of alternative structures in mRNA in response to external stimuli, either direct or mediated by proteins or other RNAs, is a major mechanism of regulation of gene expression in bacteria. This mechanism has been studied in detail using experimental and computational approaches in proteobacteria and Firmicutes, but not in other groups of bacteria.

Results
Comparative analysis of amino acid biosynthesis operons in Actinobacteria resulted in identification of conserved regions upstream of several operons. Classical attenuators were predicted upstream of trp operons in Corynebacterium spp. and Streptomyces spp., and trpS and leuS genes in some Streptomyces spp. Candidate leader peptides with terminators were observed upstream of ilvB genes in Corynebacterium spp., Mycobacterium spp. and Streptomyces spp. Candidate leader peptides without obvious terminators were found upstream of cys operons in Mycobacterium spp. and several other species. A conserved pseudoknot (named LEU element) was identified upstream of leuA operons in most Actinobacteria. Finally, T-boxes likely involved in the regulation of translation initiation were observed upstream of ileS genes from several Actinobacteria.

Conclusion
The metabolism of tryptophan, cysteine and leucine in Actinobacteria seems to be regulated on the RNA level. In some cases the mechanism is classical attenuation, but in many cases some components of attenuators are missing. The most interesting case seems to be the leuA operon preceded by the LEU element that may fold into a conserved pseudoknot or an alternative structure. A LEU element has been observed in a transposase gene from Bifidobacterium longum, but it is not conserved in genes encoding closely related transposases despite a very high level of protein similarity. One possibility is that the regulatory region of the leuA has been co-opted from some element involved in transposition. Analysis of phylogenetic patterns allowed for identification of ML1624 of M. leprae and its orthologs as the candidate regulatory proteins that may bind to the LEU element. T-boxes upstream of the ileS genes are unusual, as their regulatory mechanism seems to be inhibition of translation initiation via a hairpin sequestering the Shine-Dalgarno box.