bluuebunny/crossref_metadata_2025_split huggingface dataset:
Compliance of Clinical Microbiology Laboratories in the United States with Current Recommendations for Processing Respiratory Tract Specimens from Patients with Cystic Fibrosis
Authors: Zhou Juyan , Garber Elizabeth , Desai Manisha , Saiman Lisa 
Published: April 2006

ABSTRACT

Respiratory tract specimens from patients with cystic fibrosis (CF) require unique processing by clinical microbiology laboratories to ensure detection of all potential pathogens. The present study sought to determine the compliance of microbiology laboratories in the United States with recently published recommendations for CF respiratory specimens. Microbiology laboratory protocols from 150 of 190 (79%) CF care sites were reviewed. Most described the use of selective media for
Burkholderia cepacia
complex (99%),
Staphylococcus aureus
(82%), and
Haemophilus influenzae
(89%) and identified the species of all gram-negative bacilli (87%). Only 52% delineated the use of agar diffusion assays for susceptibility testing of
Pseudomonas aeruginosa
. Standardizing laboratory practices will improve treatment, infection control, and our understanding of the changing epidemiology of CF microbiology.
Clonal Distribution and Differential Occurrence of the Enterotoxin Gene Cluster,
egc
, in Carriage- versus Bacteremia-Associated Isolates of
Staphylococcus aureus
Authors: van Belkum Alex , Melles Damian C. , Snijders Susan V. , van Leeuwen Willem B. , Wertheim Heiman F. L. , Nouwen Jan L. , Verbrugh Henri A. , Etienne Jerome 
Published: April 2006

ABSTRACT

The
Staphylococcus aureus
enterotoxin gene cluster,
egc
, was detected in isolates from healthy individuals and in those from patients with bacteremia. The
egc
genes cooccur and are slightly enriched in strains from healthy carriers (present in 63.7% of carriage-associated isolates versus 52.9% of invasive isolates;
P
= 0.03). Multilocus sequence typing revealed that successful staphylococcal clones usually harbor the
egc
locus.
Early Detection of Hepatitis C Virus Infection by Use of a New Combined Antigen-Antibody Detection Assay: Potential Use for High-Risk Individuals
Authors: Schnuriger A. , Dominguez S. , Valantin M.-A. , Tubiana R. , Duvivier C. , Ghosn J. , Simon A. , Katlama C. , Thibault V. 
Published: April 2006

ABSTRACT
The performance of a new combined antigen-antibody assay (Monolisa HCV Ag-Ab Ultra; Bio-Rad Laboratories) was evaluated in the context of acute hepatitis C in human immunodeficiency virus-infected patients. The combined assay became positive as early as the first PCR and earlier than a third-generation enzyme-linked immunosorbent assay in 65% of the cases. Reduction of the long period of HCV seronegativity should improve the diagnosis of hepatitis C infection, especially in high-risk populations.
Human Herpesvirus 6 Chromosomal Integration in Immunocompetent Patients Results in High Levels of Viral DNA in Blood, Sera, and Hair Follicles
Authors: Ward Katherine N. , Leong Hoe Nam , Nacheva Elisabeth P. , Howard Julie , Atkinson Claire E. , Davies Nicholas W. S. , Griffiths Paul D. , Clark Duncan A. 
Published: April 2006

ABSTRACT

Six immunocompetent patients with human herpesvirus 6 (HHV-6) chromosomal integration had HHV-6 and β-globin DNA quantified in various samples by PCR. The mean HHV-6 DNA concentration (log
10
copies/milliliter) in blood was 7.0 (≥1 HHV-6 DNA copies/leukocyte), and in serum it was 5.3 (≥1 HHV-6 DNA copies/lysed cell). The mean HHV-6 DNA load (log
10
copies)/hair follicle was 4.2 (≥1 copies/hair follicle cell), demonstrating that viral integration is not confined to blood cells. The characteristically high HHV-6 DNA levels in chromosomal integration may confound laboratory diagnosis of HHV-6 infection and should be given due consideration.
Molecular Characterization and Drug Resistance Testing of
Mycobacterium tuberculosis
Isolates from Chad
Authors: Diguimbaye Colette , Hilty Markus , Ngandolo Richard , Mahamat Hassane H. , Pfyffer Gaby E. , Baggi Franca , Tanner Marcel , Schelling Esther , Zinsstag Jakob 
Published: April 2006

ABSTRACT

The molecular characterizations of the first 40
Mycobacterium tuberculosis
isolates from Chad revealed a high proportion of isolates of the Cameroon family (33%), of which one isolate showed a monodrug resistance. In total, 9/33 (27%) isolates were resistant to isoniazid. The implications of these findings are discussed.
A 24-Hour Screening Protocol for Identification of Vancomycin-Resistant
Enterococcus faecium
Authors: Drews Steven J. , Johnson Grant , Gharabaghi Farhad , Roscoe Margaret , Matlow Anne , Tellier Raymond , Richardson Susan E. 
Published: April 2006

ABSTRACT

We describe a 24-h protocol for the identification of patients who are positive for vancomycin-resistant
Enterococcus faecium
(VRE), using stool and rectal swab samples and VRE screening broth, automated DNA extraction, and real-time PCR for
vanA
and
vanB
genes. Compared to conventional screening methods, this protocol had a high sensitivity and specificity and a negative predictive value.
Fulminant, Acyclovir-Resistant, Herpes Simplex Virus Type 2 Hepatitis in an Immunocompetent Woman
Authors: Czartoski Todd , Liu Charlie , Koelle David M. , Schmechel Stephen , Kalus Andrea , Wald Anna 
Published: April 2006

ABSTRACT
We report an immunocompetent woman with multisystem organ failure following herpes simplex virus type 2 (HSV-2) hepatitis. After she initially responded to intravenous acyclovir, she was switched to oral valacyclovir. She developed respiratory failure and opportunistic infections and died. Autopsy confirmed disseminated HSV infection, and lung tissue grew acyclovir-resistant HSV-2.
Fluoroquinolone Resistance in
Ureaplasma parvum
in the United States
Authors: Duffy Lynn , Glass John , Hall Geraldine , Avery Robin , Rackley Raymond , Peterson Scott , Waites Ken 
Published: April 2006

ABSTRACT

We report the first case of naturally occurring fluoroquinolone resistance in
Ureaplasma
spp. from the United States. Resistance in this case probably developed as a result of mutations in the
gyrA
and
parC
genes of the DNA gyrase/topoisomerase IV complex that occurred in the presence of antimicrobial selective pressure.
The patient with supine hypertension and orthostatic hypotension: a clinical dilemma
Authors: Naschitz J E , Slobodin G , Elias N , Rosner I 
Published: April 2006

Abstract
Coexistent supine hypertension and orthostatic hypotension (SH-OH) pose a particular therapeutic dilemma, as treatment of one aspect of the condition may worsen the other. Studies of SH-OH are to be found by and large on patients with autonomic nervous disorders as well as patients with chronic arterial hypertension. In medical practice, however, the aetiologies and clinical presentation of the syndrome seem to be more varied. In the most typical cases the diagnosis is straightforward and the responsible mechanism evident. In those patients with mild or non-specific symptoms, the diagnosis is more demanding and the investigation may benefit from results of the tilt test, bedside autonomic tests as well as haemodynamic assessment. Discrete patterns of SH-OH may be recognisable. This review focuses on the management of the patient with coexistent SH-OH.
Recognition of acute illness in people with chronic neurological disability
Authors: Bakheit A M O 
Published: April 2006

Abstract
Coincidental acute illness is common in patients with chronic progressive or stable neurological disability. Although the presentation of acute illness in these patients is often similar to that in people without pre-existing disability, sometimes it may be atypical. In addition, an adequate medical history is often difficult to obtain in patients with advanced neurological disease, for example because of the presence of aphasia, severe dysarthria, or cognitive impairment. In these circumstances early and accurate diagnosis of acute medical and surgical emergencies requires both clinical acumen and a high index of suspicion. The aim of this article is to describe the main atypical manifestations of acute illness in patients with chronic disabling neurological disorders.
COX-2 inhibitors and the heart: are all coxibs the same?
Authors: Sooriakumaran P 
Published: April 2006

Abstract
The selective COX-2 inhibitors (coxibs) were originally developed to minimise the adverse effects of conventional non-steroidal anti-inflammatory drugs (NSAIDs) while maintaining the same analgesic and anti-inflammatory properties. Many large studies confirmed the improved gastric side effect profile of coxibs compared with non-selective NSAIDs; however, reports of increased cardiovascular morbidity and mortality followed, and the manufacturer Merck was forced to withdraw rofecoxib (Vioxx) from the market. Other coxibs have also either perished or had restrictions placed on their use. However, there seem to be significant differences between coxibs regarding their cardiovascular profiles, and the evidence for a class effect is dubious. In this paper, the current body of knowledge regarding the cardiovascular toxicities of coxibs is reviewed. The take home message for prescribing NSAIDs and those coxibs still on the market seems to be one of caution rather than contraindication, except in patients with significant cardiovascular risk factors.
Management of inflammatory bowel diseases in Eastern Europe
Authors: Lakatos L , Lakatos P L 
Published: April 2006

Abstract
Limited data are available on the management of inflammatory bowel diseases (IBD) in East European countries. The diagnostic tools and most treatment options are also available in Eastern Europe. The diagnostic procedures commonly used became more sophisticated in the past few years, with a greater use of computed tomography/magnetic resonance imaging and serology testing; however, double contrast barium enema, enteroclysis, and endoscopy remained standard. The medical therapy and surgical strategies are also somewhat different from those applied in Western countries. In ulcerative colitis, besides mesalazine, the use of sulphasalazine is still frequent, while azathioprine is only used in a minority of patients. The use of conventional corticosteroids is common and the rate of non-colorectal cancer associated colectomies is low. In contrast, 5-aminosalicylates are still used for maintenance in Crohn's disease and azathioprine is generally less frequently given compared with Western Europe. Biological agents have also become available about five years ago, yet their use is restricted mainly to specialised centres.
Cloud-Resolving Satellite Data Assimilation: Information Content of IR Window Observations and Uncertainties in Estimation
Authors: Vukicevic T. , Sengupta M. , Jones A. S. , Haar T. Vonder 
Published: April 2006

Abstract
This study addresses the problem of four-dimensional (4D) estimation of a cloudy atmosphere on cloud-resolving scales using satellite remote sensing measurements. The motivation is to develop a methodology for accurate estimation of cloud properties and the associated atmospheric environment on small spatial scales but over large regions to aid in better understanding of the clouds and their role in the atmospheric system. The problem is initially approached by the study of the assimilation of the Geostationary Operational Environmental Satellite (GOES) imager observations into a cloud-resolving model with explicit bulk cloud microphysical parameterization. A new 4D variational data assimilation (4DVAR) research system with the cloud-resolving capability is applied to a case of a multilayered cloud evolution without convection. In the experiments the information content of the IR window channels is addressed as well as the sensitivity of estimation to lateral boundary condition errors, model first guess, decorrelation length in the background statistical error model, and the use of a generic linear model error. The assimilation results are compared with independent observations from the Atmospheric Radiation Measurement (ARM) central facility archive.
The modeled 3D spatial distribution and short-term evolution of the ice cloud mass is significantly improved by the assimilation of IR window channels when the model already contains conditions for the ice cloud formation. The assimilated ice cloud in this case is in good agreement with the independent cloud radar measurements. The simulation of liquid clouds below thick ice clouds is not influenced by the IR window observations. The assimilation results clearly demonstrate that increasing the observational constraint from individual to combined channel measurements and from less to more frequent observation times systematically improves the assimilation results. The experiments with the model error indicate that the current specification of this error in the form of a generic linear forcing, which was adopted from other data assimilation studies, is not suitable for the cloud-resolving data assimilation. Instead, a parameter estimation approach may need to be explored in the future. The experiments with varying decorrelation lengths suggest the need to use the model horizontal grid spacing that is several times smaller than the GOES imager native resolution to achieve equivalent spatial variability in the assimilation.
Trends in Stratospheric Ozone: Lessons Learned from a 3D Chemical Transport Model
Authors: Stolarski Richard S. , Douglass Anne R. , Steenrod Stephen , Pawson Steven 
Published: April 2006

Abstract
Stratospheric ozone is affected by external factors such as chlorofluorcarbons (CFCs), volcanoes, and the 11-yr solar cycle variation of ultraviolet radiation. Dynamical variability due to the quasi-biennial oscillation and other factors also contribute to stratospheric ozone variability. A research focus during the past two decades has been to quantify the downward trend in ozone due to the increase in industrially produced CFCs. During the coming decades research will focus on detection and attribution of the expected recovery of ozone as the CFCs are slowly removed from the atmosphere. A chemical transport model (CTM) has been used to simulate stratospheric composition for the past 30 yr and the next 20 yr using 50 yr of winds and temperatures from a general circulation model (GCM). The simulation includes the solar cycle in ultraviolet radiation, a representation of aerosol surface areas based on observations including volcanic perturbations from El Chichon in 1982 and Pinatubo in 1991, and time-dependent mixing ratio boundary conditions for CFCs, halons, and other source gases such as N2O and CH4. A second CTM simulation was carried out for identical solar flux and boundary conditions but with constant “background” aerosol conditions. The GCM integration included an online ozonelike tracer with specified production and loss that was used to evaluate the effects of interannual variability in dynamics. Statistical time series analysis was applied to both observed and simulated ozone to examine the capability of the analyses for the determination of trends in ozone due to CFCs and to separate these trends from the solar cycle and volcanic effects in the atmosphere. The results point out several difficulties associated with the interpretation of time series analyses of atmospheric ozone data. In particular, it is shown that lengthening the dataset reduces the uncertainty in derived trend due to interannual dynamic variability. It is further shown that interannual variability can make it difficult to accurately assess the impact of a volcanic eruption, such as Pinatubo, on ozone. Such uncertainties make it difficult to obtain an early proof of ozone recovery in response to decreasing chlorine.
Probability Distributions of Angle of Approach and Relative Velocity for Colliding Droplets in a Turbulent Flow
Authors: Wang Lian-Ping , Franklin Charmaine N. , Ayala Orlando , Grabowski Wojciech W. 
Published: April 2006

Abstract
Prediction of the effect of air turbulence on statistics relevant to a collision–coalescence process represents a key challenge in the modeling of cloud microphysics. In this paper, collision-related statistics for gravity-driven motion of droplets are considered and various probability distributions associated with geometric configuration and relative motion of colliding droplets are theoretically derived. The theoretical results agree well with numerical results obtained from direct numerical simulations (DNSs). In the absence of air turbulence, the probability distributions, calculated at the beginning of the time steps used for collision detection, nontrivially depend on the time step size. Next, a novel theory is developed to quantify the effect of turbulence on the angle-of-approach θ and radial relative velocity |wr,c| for colliding pairs. A logical decomposition is used to construct extended collision volumes for a specific level of radial motion caused by air turbulence. It is shown that the inward relative motion due to turbulent fluctuations dominates the effect of turbulence in modifying the probability distributions of θ and |wr,c|. Two key dimensionless parameters are identified in the theory: one measures the effect of finite time step size in numerical collision detection and the second measures the relative magnitude of air turbulence. The theory is compared with 11 numerical experiments from DNS. It is shown that the theory captures the essential physics of the effect of air turbulence and provides a quantitatively good representation of the statistics for θ. For most numerical experiments, the theory predicts 〈θ〉 to within 5%. The probability distribution of |wr,c| is more sensitive to the influence of air turbulence and shows larger intermittency at large |wr,c| than what is assumed in the theory. The theoretical framework developed here may be of value to other problems involving gravitational settling and weak turbulence, such as parameterization of collision kernel and hydrodynamic interactions of droplets in warm rain processes.
Influence of the Equatorial QBO on the Extratropical Stratosphere
Authors: Hampson John , Haynes Peter 
Published: April 2006

Abstract
The work described here examines the influence of the equatorial quasi-biennial oscillation (QBO) on the extratropics in a zonally truncated 3D mechanistic stratospheric model. Model results show that the extratropical response to the QBO depends critically on the phase alignment of the QBO with the annual cycle: the signal of extratropical response varies by a factor of 8 between the phase alignment that gives minimum response and that which gives maximum response. Model simulations in which the time and height structure of the QBO are varied suggest that, in this zonally truncated model, the equatorial height of 21–23 km is most influential for the extratropical response and that late autumn/early winter is the time at which the QBO has the most influence over the extratropical circulation. The correlation coefficient between the QBO (measured by zonal wind) and the extratropics (measured by zonal wind or potential temperature) is as high as 0.95. The correlation coefficient is largest for simulations with lower boundary wave forcing weaker than that which gives largest extratropical interannual variability. For stronger extratropical wave forcing, the correlation coefficient is slightly smaller, but the regression coefficient of the linear term in a least squares fit is significantly larger.
Rayleigh Wave–Internal Wave Coupling and Internal Wave Generation above a Model Jet Stream
Authors: Sutherland B. R. 
Published: April 2006

Abstract
Linear theory for modes in a nonuniformly stratified, semi-infinite shear flow demonstrates that Rayleigh waves (stable waves propagating in fluid with spatially varying shear) couple with evanescent internal waves. If the bulk Richardson number (the squared ratio of the buoyancy frequency and shear) lies between 1/4 and 1, the waves have infinite e-folding depth for waves with critical relative horizontal wavenumbers. Fully nonlinear numerical simulations examine the effect of Rayleigh wave–internal wave coupling when the shear layer is localized and is thus Kelvin–Helmholtz unstable. Diagnostics examining profiles of the wave-induced mean flow show that if the bulk Richardson number is of order unity, significant momentum is extracted from a shear layer as a consequence of transport by waves. The work is extended to the study of unstable jet flows and applications of this work for internal wave generation by dynamic instability of the upper flank of the jet stream are discussed.
The Seasonal Cycles in the Distribution of Precipitation around Cyclones in the Western North Pacific and Atlantic
Authors: Chang Edmund K. M. , Song Siwon 
Published: April 2006

Abstract
The seasonal cycles in the distribution of precipitation around the western North Pacific and Atlantic cyclones have been examined by compositing quantitative estimates of the precipitation rate relative to cyclone centers. The precipitation data sources considered include estimates produced by the 40-yr European Centre for Medium-Range Weather Forecasts (ECMWF) Re-Analysis (ERA-40) project, the satellite-based daily precipitation estimates produced by the Global Precipitation Climatology Project, and estimates derived based on observed weather reports contained in the Comprehensive Ocean–Atmosphere Data Set (COADS).
Results from all three datasets suggest that for Pacific cyclones, substantially more precipitation is found in the warm sector in fall than in winter and less precipitation is found behind the cold front in spring and summer than in winter. The seasonal cycle for Atlantic cyclones is found to be distinctly different. The distribution in precipitation around cyclones in fall and winter are not very different, while in spring and summer less precipitation is found over much of the cyclone.
The implications for the observed seasonal cycles are discussed. The seasonal cycle for Pacific cyclones suggests that diabatic contributions to the generation of eddy available potential energy (APE) due to latent heat release should be maximal in fall with a relative minimum in midwinter, while for Atlantic cyclones diabatic generation of eddy APE in fall and winter is nearly the same. This is suggested to be one of the factors that can contribute to the observed midwinter minimum in the Pacific storm track, and the absence of such a minimum in the Atlantic.
Possible reasons contributing to the differences in the seasonal cycle between the two basins are discussed. Preliminary analyses suggest that differences in static stability, availability of moisture, as well as dynamical forcing may all be contributing factors.
Issues on estimating rates of precipitation based on ship reports are addressed in appendix A. It is argued that it may be a good time to recalibrate existing schemes.