bluuebunny/crossref_metadata_2025_split huggingface dataset:
Species-Specific Identification of
Leptospiraceae
by 16S rRNA Gene Sequencing
Authors: Morey Roger E. , Galloway Renee L. , Bragg Sandra L. , Steigerwalt Arnold G. , Mayer Leonard W. , Levett Paul N. 
Published: October 2006

ABSTRACT

The genus
Leptospira
is classified into 13 named species and 4 genomospecies based upon DNA-DNA reassociation studies. Phenotypic tests are unable to distinguish between species of
Leptospira
, and there is a need for a simplified molecular approach to the identification of leptospires. 16S rRNA gene sequences are potentially useful for species identification of
Leptospira
, but there are a large number of sequences of various lengths and quality in the public databases. 16S rRNA gene sequences of near full length and bidirectional high redundancy were determined for all type strains of the species of the
Leptospiraceae
. Three clades were identified within the genus
Leptospira
, composed of pathogenic species, nonpathogenic species, and another clade of undetermined pathogenicity with intermediate 16S rRNA gene sequence relatedness. All type strains could be identified by 16S rRNA gene sequences, but within both pathogenic and nonpathogenic clades as few as two or three base pairs separated some species. Sequences within the nonpathogenic clade were more similar, and in most cases ≤10 bp distinguished these species. These sequences provide a reference standard for identification of
Leptospira
species and confirm previously established relationships within the genus. 16S rRNA gene sequencing is a powerful method for identification in the clinical laboratory and offers a simplified approach to the identification of
Leptospira
species.
Comparison of Phenotypic with Genotypic Procedures for Confirmation of Coagulase-Negative
Staphylococcus
Catheter-Related Bloodstream Infections
Authors: Aldea-Mansilla Carmen , García de Viedma Darío , Cercenado Emilia , Martín-Rabadán Pablo , Marín Mercedes , Bouza Emilio 
Published: October 2006

ABSTRACT
We sought here to review the present definition of catheter-related bloodstream infections (CR-BSI) due to coagulase-negative staphylococci (CNS) by comparing the routine phenotypic methods with a genotypic procedure that considers different morphotypes. Our phenotypic characterization of CNS isolates included routine identification with biotype and antibiotype. The genotypic diagnosis was based on longer incubation periods with the consideration of all morphotypes and molecular typing by pulsed-field gel electrophoresis techniques. We prospectively selected 61 episodes of suspected CR-BSI by CNS occurring during 1 year, based on the presence of a compatible clinical setting and the isolation of one or more CNS from blood and catheter tip. Of these episodes, 47 (77%) were identified as true episodes of CR-BSI based on the presence of microorganisms of the same genotype in the blood and on the catheter tip. The sensitivity, specificity, positive predictive, negative predictive, accuracy, positive likelihood ratio, and negative likelihood ratio values obtained by different phenotypic microbiological approaches to establish the diagnosis of CR-BSI were as follows: identity at species level (78.7%, 85.7%, 94.9%, 54.5%, 80.3%, 5.51, and 0.25, respectively); identity of species and biotype (59.6%, 92.9%, 96.6%, 40.6%, 67.2%, 8.34, and 0.44, respectively); identity of species and antibiotype (61.7%, 92.9%, 96.7%, 41.9%, 68.8%, 8.64, and 0.41, respectively); and identity of species, biotype, and antibiotype (48.9%, 92.9%, 95.8%, 35.1%, 59%, 6.85, and 0.55, respectively). Our study demonstrates the inaccuracy of the diagnosis of CNS CR-BSI when the current definition based on conventional routine microbiological practice is followed. A new definition of CNS CR-BSI is necessary, at least as an epidemiological and research tool.
Disseminated Gonococcal Infection in an Immunocompetent Patient Caused by an Imported
Neisseria gonorrhoeae
Multidrug-Resistant Strain
Authors: Dal Conte Ivano , Starnino Stefania , Di Perri Giovanni , Stefanelli Paola 
Published: October 2006

ABSTRACT

We herein report the microbiological features of a
Neisseria gonorrhoeae
strain isolated from an immunocompetent patient with disseminated gonococcal infection (DGI). The strain expressed the IA/IB serovar; was resistant to penicillin, tetracycline, and ciprofloxacin; and had presumably been acquired in Southeast Asia. To date, this is the first case reported in our country of DGI due to an imported multidrug-resistant strain.
Verification of the IDI-MRSA Assay for Detecting Methicillin-Resistant
Staphylococcus aureus
in Diverse Specimen Types in a Core Clinical Laboratory Setting
Authors: Drews Steven J. , Willey Barbara M. , Kreiswirth Nathan , Wang Min , Ianes Teresa , Mitchell Jayne , Latchford Mary , McGeer Allison J. , Katz Kevin C. 
Published: October 2006

ABSTRACT
The IDI-MRSA assay has a sensitivity of 96% and a specificity of 96% when used to screen patients at extranasal sites. This verification study used previously unverified swabs and was undertaken in a core medical laboratory using nonmicrobiology technologists trained in sample processing, molecular laboratory work flow, and PCR practice.
Enumeration of Bacterial Cell Numbers and Detection of Significant Bacteriuria by Use of a New Flow Cytometry-Based Device
Authors: Okada Hiroshi , Shirakawa Toshiro , Gotoh Akinobu , Kamiyama Yutaka , Muto Satoru , Ide Hisamitsu , Hamaguchi Yukio , Horie Shigeo 
Published: October 2006

ABSTRACT
A new, automated flow cytometry-based urine bacterium analyzer (UBA) was developed. We assessed the UBA for linearity of measurement, reproducibility of results, carryover rate, and correlation of measured results with those determined by urine culture. We also evaluated its ability to screen urine samples for significant bacteriuria. The UBA showed excellent linearity and a minor carryover rate. Results from the UBA were highly reproducible, and in between-run precision assays, the coefficients of variation for the UBA results were smaller than those for the urine culture results. Two hundred seventy-three urine specimens from patients attending the outpatient clinics of two university-based hospitals were examined. The results for the UBA were compared with those for urine culture. The UBA detected significant bacteriuria with a sensitivity of 96.6%, a specificity of 79.9%, a positive predictive value of 57.0%, a negative predictive value of 98.8%, a false-positive rate of 15.8%, a false-negative rate of 0.7%, and an accuracy of 83.5%. These results were comparable to or better than those obtained with previously reported screening procedures. The UBA can perform accurate enumeration of bacterial cells automatically in 90 seconds and can be used for the screening of significant bacteriuria.
Risk of leukaemia among children living near the Solway coast of Dumfries and Galloway Health Board area, Scotland, 1975–2002
Authors: Stark J M , Black R J , Brewster D H 
Published: October 2006

Objective:To investigate allegations of an excess risk of leukaemia among children living near the Solway Firth coast of Dumfries and Galloway Health Board area in Scotland, UK.Methods:Incident cases of childhood leukaemia (International Classification of Diseases, 10th revision, C91–C95, patients aged 0–14 years) for two almost equal calendar periods of diagnosis (1975–89 and 1990–2002) were selected from the Scottish Cancer Registry database and allocated to predetermined study areas, on the basis of proximity of residence to the Solway coast. Expected numbers of childhood leukaemia cases for the study areas were calculated by applying Scotland’s age-specific, sex-specific and calendar period-specific rates to estimates of the person-years at risk in each study area. The ratios of observed to expected cases or standardised incidence ratios (SIRs) were calculated overall and for each sex and calendar period category. Exact 95% confidence intervals (CIs) for the SIRs were calculated assuming a Poisson distribution for the observed number of cases of childhood leukaemia.Results:No statistically significantly increased SIRs were found in boys, girls or both combined for any of the areas or periods of diagnosis studied. For the total period of observation (1975–2002), and the more immediate coastal area studied, the SIR for both sexes combined was 1.22 (95% CI 0.53 to 2.40).Conclusion:No statistically significant evidence was found of an excess risk of childhood leukaemia in the vicinity of the Solway Firth coast of Dumfries and Galloway Health Board area in Scotland.
Pharmacogenetic Screening of CYP3A and ABCB1 in Relation to Population Pharmacokinetics of Docetaxel
Authors: Bosch Tessa M. , Huitema Alwin D.R. , Doodeman Valerie D. , Jansen Robert , Witteveen Els , Smit Wim M. , Jansen Rob L. , van Herpen Carla M. , Soesan Marcel , Beijnen Jos H. , Schellens Jan H.M. 
Published: October 2006

AbstractPurpose: Despite the extensive clinical experience with docetaxel, unpredictable interindividual variability in efficacy and toxicity remain important limitations associated with the use of this anticancer drug. Large interindividual pharmacokinetic variability has been associated with variation in toxicity profiles. Genetic polymorphisms in drug-metabolizing enzymes and drug transporters could possibly explain the observed pharmacokinetic variability. The aim of this study was therefore to investigate the influence of polymorphisms in the CYP3A and ABCB1 genes on the population pharmacokinetics of docetaxel.Experimental Design: Whole blood samples were obtained from patients with solid tumors and treated with docetaxel to quantify the exposure to docetaxel. DNA was collected to determine polymorphisms in the CYP3A and ABCB1 genes with DNA sequencing. A population pharmacokinetic analysis of docetaxel was done using nonlinear mixed-effect modeling.Results: In total, 92 patients were assessable for pharmacokinetic analysis of docetaxel. A three-compartmental model adequately described the pharmacokinetics of docetaxel. Several polymorphisms in the CYP3A and ABCB1 genes were found, with allele frequencies of 0.54% to 48.4%. The homozygous C1236T polymorphism in the ABCB1 gene (ABCB1*8) was significantly correlated with a decreased docetaxel clearance (−25%; P = 0.0039). No other relationships between polymorphisms and pharmacokinetic variables reached statistical significance. Furthermore, no relationship between haplotypes of CYP3A and ABCB1 and the pharmacokinetics could be identified.Conclusions: The polymorphism C1236T in the ABCB1 gene was significantly related to docetaxel clearance. Our current finding may provide a meaningful tool to explain interindividual differences in docetaxel treatment in daily practice.
Extracellular pH and P-31 Magnetic Resonance Spectroscopic Variables are Related to Outcome in Canine Soft Tissue Sarcomas Treated with Thermoradiotherapy
Authors: Lora-Michiels Michaël , Yu Daohai , Sanders Linda , Poulson Jean M. , Azuma Chieko , Case Beth , Vujaskovic Zeljko , Thrall Donald E. , Charles H. Cecil , Dewhirst Mark W. 
Published: October 2006

AbstractPurpose: The objective was to test whether tumor pH and 31P magnetic resonance spectroscopic end points were related to treatment outcome in pet canine patients with spontaneous soft tissue sarcomas treated with thermoradiotherapy.Experimental Design: Forty-two dogs with evaluable 31P magnetic resonance spectroscopic end points and pH data were included in this study. Tumor variables (grade and volume), extracellular pH (pHe), T2 relaxation times, intracellular pH, and selected phosphometabolite ratios were examined for correlation with clinical outcome.Results: From 39 dogs, pHe was a predictor of metastasis-free survival (MFS), with hazard ratio (HR, 0.29; P = 0.005) and overall survival (OS) with (HR, 0.36; P = 0.013). Tumor volume (&gt;19 cm3) was related to MFS (HR, 2.14; P = 0.04), time to local failure (HR, 3.4; P = 0.025), and OS (HR, 2.27; P = 0.03). There was no association between T2 or intracellular pH and clinical outcome. Tumor grade (high versus low/intermediate) and phosphodiester/βATP ratio were identified as significant predictors for MFS, with (HR, 2.66; P = 0.009) and (HR, 0.75; P = 0.027), respectively, and as predictors of OS with (HR, 2.66; P = 0.009) and (HR, 0.76; P = 0.03), respectively. The phosphodiester/phosphocreatinine ratio predicted time to local failure (HR, 1.24; P = 0.017).Conclusions: pHe was predictive of metastasis and OS in canine spontaneous sarcomas. To our knowledge, this is the first time that pHe has been shown to be predictive of clinical outcome. The results suggest that additional studies should be considered evaluating the prognostic significance of this variable. Phospholipid resonances, related to membrane metabolism, were related to clinical outcome, confirming recent results reported in human patients with soft tissue sarcomas treated with thermoradiotherapy.
YKL-40 and Matrix Metalloproteinase-9 as Potential Serum Biomarkers for Patients with High-Grade Gliomas
Authors: Hormigo Adília , Gu Bin , Karimi Sasan , Riedel Elyn , Panageas Katherine S. , Edgar Mark A. , Tanwar Meena K. , Rao Jasti S. , Fleisher Martin , DeAngelis Lisa M. , Holland Eric C. 
Published: October 2006

Abstract
Purpose: Biomarkers can facilitate diagnosis, monitor treatment response, and assess prognosis in some patients with cancer. YKL-40 and matrix metalloproteinase-9 (MMP-9) are two proteins highly differentially expressed by malignant gliomas. We obtained prospective longitudinal serum samples from patients with gliomas to determine whether YKL-40 or MMP-9 could be used as serum markers.
Experimental Design: Serum samples were obtained concurrently with magnetic resonance imaging scans. YKL-40 and MMP-9 were determined by ELISA and the values correlated with the patient's radiographic status and survival.
Results: High-grade glioma patients who underwent a surgical resection of their tumor had transient increase of both YKL-40 and MMP-9 serum levels in the postoperative period. Glioblastoma multiforme (GBM) patients with no radiographic evidence of disease (n = 10 patients, 50 samples) had a significantly lower level of YKL-40 and MMP-9 than patients with active tumor (n = 66 patients, 209 samples; P = 0.0003 and 0.0002, respectively). Anaplastic glioma patients with no radiographic evidence of disease (n = 32 patients, 107 samples) also had a significantly lower level of YKL-40 compared with those patients with active tumor (n = 48 patients, 199 samples; P = 0.04). There was a significant inverse association between YKL-40 and survival in GBM, hazard ratio (hazard ratio, 1.4; P = 0.02), and anaplastic astrocytoma patients (hazard ratio, 2.2; P = 0.05).
Conclusions: YKL-40 and MMP-9 can be monitored in patients' serum and help confirm the absence of active disease in GBM and YKL-40 in anaplastic glioma patients. YKL-40 can be used as predictor of survival in patients with high-grade glioma. Longitudinal studies with a larger patient population are needed to confirm these findings.
Isodeoxyelephantopin, a Novel Sesquiterpene Lactone, Potentiates Apoptosis, Inhibits Invasion, and Abolishes Osteoclastogenesis through Suppression of Nuclear Factor-κB (NF-κB) Activation and NF-κB-Regulated Gene Expression
Authors: Ichikawa Haruyo , Nair Mangalam S. , Takada Yasunari , Sheeja D.B. Alan , Kumar M.A. Suresh , Oommen Oommen V. , Aggarwal Bharat B. 
Published: October 2006

AbstractPurpose: Deoxyelephantopin (ESD) and isodeoxyelephantopin (ESI) are two sesquiterpene lactones derived from the medicinal plant Elephantopus scaber Linn. (Asteraceae). Although they are used for the treatment of a wide variety of proinflammatory diseases, very little is known about their mechanism of action. Because most genes that control inflammation are regulated by activation of the transcription factor nuclear factor-κB (NF-κB), we postulated that ESD and ESI mediate their activities through modulation of the NF-κB activation pathway.Experimental Design: We investigated the effect of ESI and ESD on NF-κB activation by electrophoretic mobility shift assay and NF-κB-regulated gene expression by Western blot analysis.Results: We found that ESI suppressed NF-κB activation induced by a wide variety of inflammatory agents, including tumor necrosis factor (TNF), interleukin-1β, phorbol 12-myristate 13-acetate, and lipopolysaccharide. The suppression was not cell type specific, and both inducible and constitutive NF-κB activation was blocked. ESI did not interfere with the binding of NF-κB to DNA but rather inhibited IκBα kinase, IκBα phosphorylation, IκBα degradation, p65 phosphorylation, and subsequent p65 nuclear translocation. ESI also suppressed the expression of TNF-induced NF-κB-regulated, proliferative, antiapoptotic, and metastatic gene products. These effects correlated with enhancement of apoptosis induced by TNF and suppression of TNF-induced invasion and receptor activator of NF-κB ligand-induced osteoclastogenesis.Conclusion: Our results indicate that ESI inhibits NF-κB activation and NF-κB-regulated gene expression, which may explain the ability of ESI to enhance apoptosis and inhibit invasion and osteoclastogenesis.
Cisplatin Preferentially Binds Mitochondrial DNA and Voltage-Dependent Anion Channel Protein in the Mitochondrial Membrane of Head and Neck Squamous Cell Carcinoma: Possible Role in Apoptosis
Authors: Yang Zejia , Schumaker Lisa M. , Egorin Merrill J. , Zuhowski Eleanor G. , Guo Zhongmin , Cullen Kevin J. 
Published: October 2006

AbstractPurpose: Cisplatin adducts to nuclear DNA (nDNA) are felt to be the molecular lesions that trigger apoptosis, but the mechanism linking nDNA adduct formation and cell death is unclear. Some literature in the last decade has suggested a possible direct effect of cisplatin on mitochondria independent of nDNA interaction. In this study, we define separately the sequelae of cisplatin interactions with nDNA and with mitochondria in head and neck squamous cell carcinoma (HNSCC) cell lines.Experimental Design: Cisplatin binding to mitochondrial DNA (mtDNA) and proteins was analyzed by atomic absorption spectroscopy and other methods.Results: Following 1 hour of exposure to cisplatin, platinum adducts to mtDNA were 300- to 500-fold more abundant than adducts to nDNA; these differences were not due to differences in rates of adduct repair. Whereas HNSCC cell cytoplasts free of nDNA retained the same dose-dependent cisplatin sensitivity as parental cells, HNSCC ρ0 cells free of mtDNA were 4- to 5-fold more resistant to cisplatin than parental cells. Isolated mitochondria released cytochrome c within minutes of exposure to cisplatin, and ultrastructural analysis of intact HNSCC cells by electron microscopy showed marked mitochondrial disruption after 4 hours of cisplatin treatment, whereas the nucleus and other cellular structures remain intact. The very prompt release of cytochrome c from isolated mitochondria implies that apoptosis does not require alteration in mitochondrial gene transcription. Further, cisplatin binds preferentially to mitochondrial membrane proteins, particularly the voltage-dependent anion channel.Conclusions: Cisplatin binding to nDNA is not necessary for induction of apoptosis in HNSCC, which can result from direct action of cisplatin on mitochondria.
Improvement in Determination of Ice Water Content from Two-Dimensional Particle Imagery. Part I: Image-to-Mass Relationships
Authors: Baker Brad , Lawson R. Paul 
Published: October 2006

Abstract
Ice water content in natural clouds is an important but difficult quantity to measure. The goal of a number of past studies was to find average relationships between the masses and lengths of ice particles to determine ice water content from in situ data, such as those routinely recorded with two-dimensional imaging probes. The general approach in these past studies was to measure maximum length L and mass M of a dataset of ice crystals collected at a ground site. Linear regression analysis was performed on the logarithms of the data to estimate an average mass-to-length relationship of the form M = αLβ. Relationships were determined for subsets of the dataset based on crystal habit (shape) as well as for the full dataset. In this study, alternative relationships for determining mass using the additional parameters of width W, area A, and perimeter P are explored. A 50% reduction in rms error in the determination of mass relative to using L alone is achieved using a single parameter that is a combination of L, W, A, and P. The new parameter is designed to take into account the shape of the ice particle without the need to classify the crystals first. An interesting result is that, when applied to the test dataset, the same reduction in rms error is also shown to be achievable using A alone. Using A alone facilitates the reanalysis and improvement of the determination of ice water content from large existing datasets of two-dimensional images, because A is simply the number of occulted pixels in the digital images. Possible sources of error in this study are investigated, as is the usefulness of first segregating the particles into crystal habits.
Numerical Simulations of the Wake of Kauai
Authors: Lane Todd P. , Sharman Robert D. , Frehlich Rod G. , Brown John M. 
Published: October 2006

Abstract
This study uses a series of numerical simulations to examine the structure of the wake of the Hawaiian island of Kauai. The primary focus is on the conditions on 26 June 2003, which was the day of the demise of the Helios aircraft within Kauai’s wake. The simulations show that, in an east-northeasterly trade wind flow, Kauai produces a well-defined wake that can extend 40 km downstream of the island. The wake is bounded to the north and south by regions of strong vertical and horizontal shear—that is, shear lines. These shear lines mark the edge of the wake in the horizontal plane and are aligned approximately parallel to the upstream flow direction at each respective height. The highest-resolution simulations show that these shear lines can become unstable and break down through Kelvin–Helmholtz instability. The breakdown generates turbulent eddies that are advected both downstream and into the recirculating wake flow. Turbulence statistics are estimated from the simulation using a technique that analyzes model-derived structure functions. A number of sensitivity studies are also completed to determine the influence of the upstream conditions on the structure of the wake. These simulations show that directional shear controls the tilt of the wake in the north–south plane with height. These simulations also show that at lower incident wind speeds the wake has a qualitatively similar structure but is less turbulent. At higher wind speeds, the flow regime changes, strong gravity waves are generated, and the wake is poorly defined. These results are consistent with previous idealized studies of stratified flow over isolated obstacles.
Development and Testing of Tropical Cyclone Parametric Wind Models Tailored for Midlatitude Application—Preliminary Results
Authors: MacAfee Allan W. , Pearson Garry M. 
Published: October 2006

Abstract
Over the years, researchers have developed parametric wind models to depict the surface winds within a tropical cyclone (TC). Most models were developed using data from aircraft flights into low-latitude (south of 30°N) TCs in the Atlantic Ocean, Gulf of Mexico, and Caribbean Sea. Such models may not adequately reproduce the midlatitude TC wind field where synoptic interaction and acceleration are more pronounced. To tailor these models for midlatitude application, latitude-dependent angular size and shape details were added by using new techniques to set values for model input parameters and by incorporating additional field-shaping procedures. A method to assess the different techniques and field-shaping procedures was developed in which qualitative and quantitative assessment was performed using five parametric models and samples of buoy and 2D surface wind data. Contingency tables and statistical scores such as mean absolute error and bias were used to select the techniques and procedures that create the most realistic depiction of low- and midlatitude TC surface wind fields.