bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of Mycobacteria by Matrix-Assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry
Authors: Pignone Michelle , Greth Kimberly M. , Cooper Jason , Emerson David , Tang Jane 
Published: June 2006

ABSTRACT

Classical methods for identification of
Mycobacterium
species rely on morphology and biochemical profiles. Speciation of a
Mycobacterium
isolate using these standard methods is a lengthy process based on subjective data interpretation. In this study,
Mycobacterium
species were characterized by utilizing matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS). This technology is designed to provide a characteristic mass spectral fingerprint based on desorbed ions from the cell surface. Thirty-seven strains were analyzed; these represented thirteen species and five subspecies that included the
Mycobacterium tuberculosis
complex and the
M. avium-M. intracellulare
complex, as well as rapid- and slow-growing mycobacteria. All 37 strains were analyzed in triplicate, and a database was generated. This method produced species-specific patterns for all but 1 of the 37 isolates and provided reliable differentiation at the strain level. The data suggest that whole-cell MALDI-TOF MS has potential as a rapid and reproducible method for the identification and characterization of
Mycobacterium
species.
Comparison of Flocked and Rayon Swabs for Collection of Respiratory Epithelial Cells from Uninfected Volunteers and Symptomatic Patients
Authors: Daley Peter , Castriciano Santina , Chernesky Max , Smieja Marek 
Published: June 2006

ABSTRACT
Significantly more epithelial cells were collected by flocked swabs than by rayon swabs in parallel nasopharyngeal and nasal swabs taken from 16 volunteers. Nasopharyngeal sampling of 61 symptomatic patients also yielded more cells by flocked than rayon swabs, providing better clinical specimens for diagnosis.
Isolation of
Corynebacterium xerosis
from Animal Clinical Specimens
Authors: Vela A. I. , Gracía E. , Fernández A. , Domínguez L. , Fernández-Garayzábal J. F. 
Published: June 2006

ABSTRACT

This article describes the first identification of
Corynebacterium xerosis
from animal clinical specimens, which was confirmed by microbiological and molecular genetic (16S rRNA gene sequencing) methods.
Genetic Determinants and Polymorphisms Specific for Human-Adapted Serovars of
Salmonella enterica
That Cause Enteric Fever
Authors: Tracz Dobryan M. , Tabor Helen , Jerome Morganne , Ng Lai-King , Gilmour Matthew W. 
Published: June 2006

ABSTRACT

Salmonella enterica
serovars Typhi, Paratyphi A, and Sendai are human-adapted pathogens that cause typhoid (enteric) fever. The acute prevalence in some global regions and the disease severity of typhoidal
Salmonella
have necessitated the development of rapid and specific detection tests. Most of the methodologies currently used to detect serovar Typhi do not identify serovars Paratyphi A or Sendai. To assist in this aim, comparative sequence analyses were performed at the loci of core bacterial genetic determinants and
Salmonella
pathogenicity island 2 genes encoded by clinically significant
S. enterica
serovars. Genetic polymorphisms specific for serovar Typhi (at
trpS
), as well as polymorphisms unique to human-adapted typhoidal serovars (at
sseC
and
sseF
), were observed. Furthermore, entire coding sequences unique to human-adapted typhoidal
Salmonella
strains (i.e., serovar-specific genetic loci rather than polymorphisms) were observed in publicly available comparative genomic DNA microarray data sets. These polymorphisms and loci were developed into real-time PCR, standard PCR, and liquid microsphere suspension array-based molecular protocols and tested for with a panel of clinical and reference subspecies I
S. enterica
strains. A proportion of the nontyphoidal
Salmonella
strains hybridized with the allele-specific oligonucleotide probes for
sseC
and
sseF
; but the
trpS
allele was unique to serovar Typhi (with a singular serovar Paratyphi B strain as an exception), and the coding sequences STY4220 and STY4221 were unique among serovars Typhi, Paratyphi A, and Sendai. These determinants provided phylogenetic data on the genetic relatedness of serovars Typhi, Paratyphi A, and Sendai; and the protocols developed might allow the rapid identification of these
Salmonella
serovars that cause enteric fever.
Cyanobacterial Two-Component Proteins: Structure,Diversity, Distribution, andEvolution
Authors: Ashby Mark K. , Houmard Jean 
Published: June 2006

SUMMARYA survey of the already characterized and potential two-component protein sequences that exist in the nine complete and seven partially annotated cyanobacterial genome sequences available (as of May 2005) showed that the cyanobacteria possess a much larger repertoire of such proteins than most other bacteria. By analysis of the domain structure of the 1,171 potential histidine kinases, response regulators, and hybrid kinases, many various arrangements of about thirty different modules could be distinguished. The number of two-component proteins is related in part to genome size but also to the variety of physiological properties and ecophysiologies of the different strains. Groups of orthologues were defined, only a few of which have representatives with known physiological functions. Based on comparisons with the proposed phylogenetic relationships between the strains, the orthology groups show that (i) a few genes, some of them clustered on the genome, have been conserved by all species, suggesting their very ancient origin and an essential role for the corresponding proteins, and (ii) duplications, fusions, gene losses, insertions, and deletions, as well as domain shuffling, occurred during evolution, leading to the extant repertoire. These mechanisms are put in perspective with the different genetic properties that cyanobacteria have to achieve genome plasticity. This review is designed to serve as a basis for orienting further research aimed at defining the most ancient regulatory mechanisms and understanding how evolution worked to select and keep the most appropriate systems for cyanobacteria to develop in the quite different environments that they have successfully colonized.
Biology ofPseudomonas stutzeri
Authors: Lalucat Jorge , Bennasar Antoni , Bosch Rafael , García-Valdés Elena , Palleroni Norberto J. 
Published: June 2006

SUMMARYPseudomonas stutzeriis a nonfluorescent denitrifying bacterium widely distributed in the environment, and it has also been isolated as an opportunistic pathogen from humans. Over the past 15 years, much progress has been made in elucidating the taxonomy of this diverse taxonomical group, demonstrating the clonality of its populations. The species has received much attention because of its particular metabolic properties: it has been proposed as a model organism for denitrification studies; many strains have natural transformation properties, making it relevant for study of the transfer of genes in the environment; several strains are able to fix dinitrogen; and others participate in the degradation of pollutants or interact with toxic metals. This review considers the history of the discovery, nomenclatural changes, and early studies, together with the relevant biological and ecological properties, ofP. stutzeri.
Predictive validity of a retrospective measure of noise exposure
Authors: McNamee R , Burgess G , Dippnall W M , Cherry N 
Published: June 2006

Aims:To investigate the validity of measures of noise exposure derived retrospectively for a cohort of nuclear energy workers for the period 1950–98, by investigating their ability to predict hearing loss.Methods:Subjects were men aged 45–65 chosen from a larger group of employees—assembled for a nested case-control study of noise and death from ischaemic heart disease—who had had at least one audiogram after at least five years’ work. Average hearing loss, across both ears and the frequencies 0.5, 1, 2, and 4 kHz, was calculated from the last audiogram for each man. Previous noise exposure at work was assessed retrospectively by three hygienists using work histories, noise survey records from 1965–98, and judgement about use of hearing protection devices. Smoking and age at the time of the audiogram were extracted from records. Differences in hearing loss between men categorised by cumulative noise exposure were assessed after controlling for age, smoking, year of test, and previous test experience.Results:There were 186 and 150 eligible subjects at sites A and B of the company respectively who were employed for an average of 20 years. Compared to men with less than one year’s exposure to levels of 85dB(A) or greater, hearing loss was greater by 3.7 dB (90% CI −2.6 to 10.1), 3.8 dB (90% CI −2.6 to 10.3), 7.0 dB (90% CI 1.1 to 12.9) and 10.1 dB (90% CI 4.2 to 16.0) in the lowest to highest categories of cumulative noise exposure at site B. In contrast, at site A, the corresponding figures were −2.2 dB, −2.4 dB, −1.8 dB, and −4.4 dB, with no confidence interval excluding zero.Conclusions:Noise estimation at one site was shown to have predictive validity in terms of hearing loss, but not at the other site. Reasons for the differences between sites are discussed.
Ambient particulate air pollution and cardiac arrhythmia in a panel of older adults in Steubenville, Ohio
Authors: Sarnat S E , Suh H H , Coull B A , Schwartz J , Stone P H , Gold D R 
Published: June 2006

Objectives:Ambient particulate air pollution has been associated with increased risk of cardiovascular morbidity and mortality. Pathways by which particles may act involve autonomic nervous system dysfunction or inflammation, which can affect cardiac rate and rhythm. The importance of these pathways may vary by particle component or source. In an eastern US location with significant regional pollution, the authors examined the association of air pollution and odds of cardiac arrhythmia in older adults.Methods:Thirty two non-smoking older adults were evaluated on a weekly basis for 24 weeks during the summer and autumn of 2000 with a standardised 30 minute protocol that included continuous electrocardiogram measurements. A central ambient monitoring station provided daily concentrations of fine particles (PM2.5, sulfate, elemental carbon) and gases. Sulfate was used as a marker of regional pollution. The authors used logistic mixed effects regression to examine the odds of having any supraventricular ectopy (SVE) or ventricular ectopy (VE) in association with increases in air pollution for moving average pollutant concentrations up to 10 days before the health assessment.Results:Participant specific mean counts of arrhythmia over the protocol varied between 0.1–363 for SVE and 0–350 for VE. The authors observed odds ratios for having SVE over the length of the protocol of 1.42 (95% CI 0.99 to 2.04), 1.70 (95% CI 1.12 to 2.57), and 1.78 (95% CI 0.95 to 3.35) for 10.0 μg/m3, 4.2 μg/m3, and 14.9 ppb increases in five day moving average PM2.5, sulfate, and ozone concentrations respectively. The other pollutants, including elemental carbon, showed no effect on arrhythmia. Participants reporting cardiovascular conditions (for example, previous myocardial infarction or hypertension) were the most susceptible to pollution induced SVE. The authors found no association of pollution with VE.Conclusion:Increased levels of ambient sulfate and ozone may increase the risk of supraventricular arrhythmia in the elderly.
Three dimensional reconstruction of the pancreas based on the virtual Chinese human—female number 1
Authors: Zhou Z M , Fang C H , Huang L W , Zhong S Z , Wang B L , Zhou W Y 
Published: June 2006

Abstract

Objective
To study the three dimensional (3D) reconstruction and 3D visualisation of the pancreas and create anatomy of the digitalised visual pancreas so as to construct a concrete basis for virtual operation and surgical operation on pancreas.

Methods
The digital imaging data of pancreas, duodenum, common bile duct, arteries, and veins were obtained from the virtual Chinese human—female 1 (VCH-F1). The image data were investigated and 380 images ascertained of pancreas picked up from images numbers 2617 to 2996. Finally, the images from number 2574 to 3017 were adopted to segment and processed using ACDSee and Photoshop so as to reconstruct 3D pancreas digitally. The data of pancreatic surfaces were transformed into Visualization Toolkit (VTK). The GUI program written with VC+ was used to display this VTK file and realise 3D visualisation of the pancreas.

Results
3D reconstruction and visualisation of the pancreas and the peri-pancreatic structures (the duodenum, the common bile duct,the inferior vena cava, the portal vein vessels, the aorta, the coeliac trunk vessels) was successful. The 3D and visualised pancreas manifested itself with its complete structure as well as its adjacency to other tissues.

Conclusion
The 3D reconstruction and 3D visualisation of the pancreas based on the digital data of VCH-F1 produces a digitally visualised pancreas, which promises a novel method for virtual operation on the pancreas, clinical operation on the pancreas, and anatomy of 3D visualised pancreas.
Determinants and consequences of smoke-free homes: findings from the International Tobacco Control (ITC) Four Country Survey
Authors: Borland R , Yong H-H , Cummings K M , Hyland A , Anderson S , Fong G T 
Published: June 2006

Objective:To report on prevalence, trends and determinants of smoke-free home policies in smokers’ homes in different countries and to estimate the effects of these policies on smoking cessation.Design:Two waves of the International Tobacco Control (ITC) Four Country Survey (ITC-4), a cohort survey of smokers conducted by telephone. Wave 1 was conducted in October/December 2002 with broadly representative samples of over 2000 adult (⩾ 18 years) cigarette smokers in each of the following four countries: Canada, the United States, the United Kingdom, and Australia, 75% of whom were followed up at Wave 2 on average seven months later.Key measures:Levels of smoking restrictions in homes (both waves).Results:Australian smokers were most likely to live in smoke-free homes and UK smokers least likely (34%v15% at Wave 1). Levels of smoke-free homes increased between waves. Logistic regressions indicated that the main independent predictors of smokers reporting smoke-free homes or implementation of a smoke-free policy between waves included household factors such as having a child, particularly a young child, and having other non-smoking adults in the household. Positive attitudes to smoke-free public places and/or reported presence of smoke-free public places were independent predictors of having or implementing smoke-free homes, supporting a social diffusion model for smoking restrictions. Intentions to quit at Wave 1 and quitting activity between survey waves were associated with implementing bans between Waves 1 and 2. Presence of bans at Wave 1 was associated with significantly greater proportions of quit attempts, and success among those who tried at Wave 2. There was no significant interaction between the predictive models and country.Conclusions:Smoke-free public places seem to stimulate adoption of smoke-free homes, a strategy associated with both increased frequency of quit attempts, and of the success of those attempts.
Strengthening the Role of the Special Rapporteur on Freedom of Religion or Belief
Authors: Evans Carolyn 
Published: June 2006

AbstractThe Special Rapporteur holds the key United Nations mandate for the protection of freedom of religion and belief. This article gives an overview of the establishment and developing role of the Rapporteur and considers the way in which the three individuals who have held the office so far have carried out their mandate. It assesses the effectiveness of the methodologies used by the Rapporteur and, in particular, questions the shift of emphasis from prevention to protection. It then analyses the way in which the Rapporteurs have dealt with some of the substantive issues required by their role. The example of religious defamation is given to demonstrate the dangers of Rapporteurs taking overly simplistic approaches to complex issues. Finally a number of areas where further consideration is needed—in particular with respect to funding, the development of a treaty on religious freedom and the relationship with States—are briefly overviewed. The article concludes that the performance of the Rapporteurs have been exceptional, particularly given the limited financial resources allocated to the mandate and the complexities of the problems with which the mandate deals.
Evaluating Aspects of the Community Land and Atmosphere Models (CLM3 and CAM3) Using a Dynamic Global Vegetation Model
Authors: Bonan Gordon B. , Levis Samuel 
Published: June 2006

Abstract
The Community Land Model version 3 (CLM3) Dynamic Global Vegetation Model (CLM–DGVM) is used diagnostically to identify land and atmospheric model biases that lead to biases in the simulated vegetation. The CLM–DGVM driven with observed atmospheric data (offline simulation) underestimates global forest cover, overestimates grasslands, and underestimates global net primary production. These results are consistent with earlier findings that the soils in CLM3 are too dry. In the offline simulation an increase in simulated transpiration by changing this variable's soil moisture dependence and by decreasing canopy-intercepted precipitation results in better global plant biogeography and global net primary production. When CLM–DGVM is coupled to the Community Atmosphere Model version 3 (CAM3), the same modifications do not improve simulated vegetation in the eastern United States and Amazonia where the most serious vegetation biases appear. The dry bias in eastern U.S. precipitation is so severe that the simulated vegetation is insensitive to changes in the hydrologic cycle. In Amazonia, strong coupling among soil moisture, vegetation, evapotranspiration, and precipitation produces a highly complex hydrologic cycle in which small perturbations in precipitation are accentuated by vegetation. These interactions in Amazonia lead to a dramatic precipitation decrease and a collapse of the forest. These results suggest that the accurate parameterization of convection poses a complex and challenging scientific issue for climate models that include dynamic vegetation. The results also emphasize the difficulties that may arise when coupling any two highly nonlinear systems that have only been tested uncoupled.
The Low-Resolution CCSM3
Authors: Yeager Stephen G. , Shields Christine A. , Large William G. , Hack James J. 
Published: June 2006

Abstract
The low-resolution fully coupled configuration of the Community Climate System Model version 3 (CCSM3) is described and evaluated. In this most economical configuration, an ocean at nominal 3° resolution is coupled to an atmosphere model at T31 resolution. There are climate biases associated with the relatively coarse grids, yet the coupled solution remains comparable to higher-resolution CCSM3 results. There are marked improvements in the new solution compared to the low-resolution configuration of CCSM2. In particular, the CCSM3 simulation maintains a robust meridional overturning circulation in the ocean, and it generates more realistic El Niño variability. The improved ocean solution was achieved with no increase in computational cost by redistributing deep ocean and midlatitude resolution into the upper ocean and the key water formation regions of the North Atlantic, respectively. Given its significantly lower resource demands compared to higher resolutions, this configuration shows promise for studies of paleoclimate and other applications requiring long, equilibrated solutions.
Monsoon Regimes in the CCSM3
Authors: Meehl Gerald A. , Arblaster Julie M. , Lawrence David M. , Seth Anji , Schneider Edwin K. , Kirtman Ben P. , Min Dughong 
Published: June 2006

Abstract
Simulations of regional monsoon regimes, including the Indian, Australian, West African, South American, and North American monsoons, are described for the T85 version of the Community Climate System Model version 3 (CCSM3) and compared to observations and Atmospheric Model Intercomparison Project (AMIP)-type SST-forced simulations with the Community Atmospheric Model version 3 (CAM3) at T42 and T85. There are notable improvements in the regional aspects of the precipitation simulations in going to the higher-resolution T85 compared to T42 where topography is important (e.g., Ethiopian Highlands, South American Andes, and Tibetan Plateau). For the T85 coupled version of CCSM3, systematic SST errors are associated with regional precipitation errors in the monsoon regimes of South America and West Africa, though some aspects of the monsoon simulations, particularly in Asia, improve in the coupled model compared to the SST-forced simulations. There is very little realistic intraseasonal monsoon variability in the CCSM3 consistent with earlier versions of the model. Teleconnections to the tropical Pacific are well simulated for the South Asian monsoon.
Atmospheric Circulation and Its Effect on Arctic Sea Ice in CCSM3 Simulations at Medium and High Resolution*
Authors: DeWeaver Eric , Bitz Cecilia M. 
Published: June 2006

Abstract
The simulation of Arctic sea ice and surface winds changes significantly when Community Climate System Model version 3 (CCSM3) resolution is increased from T42 (∼2.8°) to T85 (∼1.4°). At T42 resolution, Arctic sea ice is too thick off the Siberian coast and too thin along the Canadian coast. Both of these biases are reduced at T85 resolution. The most prominent surface wind difference is the erroneous North Polar summer anticyclone, present at T42 but absent at T85.
An offline sea ice model is used to study the effect of the surface winds on sea ice thickness. In this model, the surface wind stress is prescribed alternately from reanalysis and the T42 and T85 simulations. In the offline model, CCSM3 surface wind biases have a dramatic effect on sea ice distribution: with reanalysis surface winds annual-mean ice thickness is greatest along the Canadian coast, but with CCSM3 winds thickness is greater on the Siberian side. A significant difference between the two CCSM3-forced offline simulations is the thickness of the ice along the Canadian archipelago, where the T85 winds produce thicker ice than their T42 counterparts. Seasonal forcing experiments, with CCSM3 winds during spring and summer and reanalysis winds in fall and winter, relate the Canadian thickness difference to spring and summer surface wind differences. These experiments also show that the ice buildup on the Siberian coast at both resolutions is related to the fall and winter surface winds.
The Arctic atmospheric circulation is examined further through comparisons of the winter sea level pressure (SLP) and eddy geopotential height. At both resolutions the simulated Beaufort high is quite weak, weaker at higher resolution. Eddy heights show that the wintertime Beaufort high in reanalysis has a barotropic vertical structure. In contrast, high CCSM3 SLP in Arctic winter is found in association with cold lower-tropospheric temperatures and a baroclinic vertical structure.
In reanalysis, the summertime Arctic surface circulation is dominated by a polar cyclone, which is accompanied by surface inflow and a deep Ferrel cell north of the traditional polar cell. The Arctic Ferrel cell is accompanied by a northward flux of zonal momentum and a polar lobe of the zonal-mean jet. These features do not appear in the CCSM3 simulations at either resolution.