bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of Alcaligin Siderophore Utilization on In Vivo Growth of
Bordetella pertussis
Authors: Brickman Timothy J. , Armstrong Sandra K. 
Published: August 2007

ABSTRACT

Bordetella pertussis
, the causative agent of human whooping cough, or pertussis, is an obligate human pathogen with diverse high-affinity transport systems for the assimilation of iron, a biometal that is essential for growth. Under iron starvation stress conditions,
B. pertussis
produces the siderophore alcaligin. The alcaligin siderophore gene cluster, consisting of the
alcABCDERS
and
fauA
genes, encodes activities required for alcaligin biosynthesis, the export of the siderophore from the cell, the uptake of the ferric alcaligin complex across the outer membrane, and the transcriptional activation of alcaligin system genes by an autogenous mechanism involving alcaligin sensing. The
fauA
gene encodes a 79-kDa TonB-dependent outer membrane receptor protein required for the uptake and utilization of ferric alcaligin as an iron source. In this study, using mixed-infection competition experiments in a mouse respiratory model, inactivation of the
B. pertussis
ferric alcaligin receptor protein was found to have a profound impact on in vivo growth and survival of a
fauA
mutant compared with a coinfecting wild-type strain. The attenuating effect of
fauA
inactivation was evident early in the course of the infection, suggesting that the contribution of ferric alcaligin transport to the ecological fitness of
B. pertussis
may be important for adaptation to iron-restricted host conditions that exist at the initial stages of infection. Alcaligin-mediated iron acquisition by
B. pertussis
may be critical for successful host colonization and establishment of infection.
Modulation of Host Innate Immune Response in the Bladder by UropathogenicEscherichia coli
Authors: Billips Benjamin K. , Forrestal Sarah G. , Rycyk Matthew T. , Johnson James R. , Klumpp David J. , Schaeffer Anthony J. 
Published: August 2007

ABSTRACTUropathogenicEscherichia coli(UPEC), the most frequent cause of urinary tract infection (UTI), is associated with an inflammatory response which includes the induction of cytokine/chemokine secretion by urothelial cells and neutrophil recruitment to the bladder. Recent studies indicate, however, that UPEC can evade the early activation of urothelial innate immune response in vitro. In this study, we report that infection with the prototypic UPEC strain NU14 suppresses tumor necrosis factor alpha (TNF-α)-mediated interleukin-8 (CXCL-8) and interleukin-6 (CXCL-6) secretion from urothelial cell cultures compared to infection with a type 1 piliatedE. coliK-12 strain. Furthermore, examination of a panel of clinicalE. coliisolates revealed that 15 of 17 strains also possessed the ability to suppress cytokine secretion. In a murine model of UTI, NU14 infection resulted in diminished levels of mRNAs encoding keratinocyte-derived chemokine, macrophage inflammatory peptide 2, and CXCL-6 in the bladder relative to infection with anE. coliK-12 strain. Furthermore, reduced stimulation of inflammatory chemokine production during NU14 infection correlated with decreased levels of bladder and urine myeloperoxidase and increased bacterial colonization. These data indicate that a broad phylogenetic range of clinicalE. coliisolates, including UPEC, may evade the activation of innate immune response in the urinary tract, thereby providing a pathogenic advantage.
Identification of LpxL, a Late Acyltransferase of
Francisella tularensis
Authors: McLendon Molly K. , Schilling Birgit , Hunt Jason R. , Apicella Michael A. , Gibson Bradford W. 
Published: August 2007

ABSTRACT

Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria, and the lipid A region of LPS mediates stimulation of the immune system in a structure-dependent manner. Unlike the LPS of many other gram-negative bacteria, the LPS of
Francisella tularensis
isolated from in vitro cultures is not proinflammatory. This observed lack of proinflammatory prowess may reflect structural features of the lipid A, such as the number and length of the acyl chains and the single-phosphate group. To better understand this phenotype, we have begun to elucidate LPS biosynthesis in
F. tularensis
. We present complementation, mutational, and chemical data demonstrating that
F. tularensis
FTT0232c encodes a functional late acyltransferase enzyme with specificity similar to that of the
Escherichia coli
LpxL ortholog. Expression of this late acyltransferase complemented the temperature-sensitive and hypoacylated lipid A phenotypes of an
E. coli lpxL
mutant, expression of FTT0232c is increased during intracellular growth relative to that during in vitro growth, and finally, LPS obtained from a mutant of
F. tularensis
lacking FTT0232c showed an abundant triacyl lipid A species after mass spectrometric analysis, consistent with the loss of an LpxL late acyltransferase.
Preparation of the HCP Nano-Sheet Cobalt via a Green-Solvothermal Route
Authors: Yuan Ding S. 
Published: August 2007

The nano-sheet cobalt has been prepared via a green- solvothermal route. The spectra of X-ray powder diffraction (XRD) prove that as-prepared cobalt is hexagonal close-packed cobalt (hcp) phase in this research. The saturated magnetization intensity (Ms), coercive force (Hc) and remanence (Br) of the hcp cobalt sheets with 59.2 nm thickness are 318 emu g-1, 199 Oe and 25 emu g-1	at 293K, respectively. The nano-size hcp cobalt with higher Ms and lower Hc is soft magnetic materials.
Scalable Implementations of Ensemble Filter Algorithms for Data Assimilation
Authors: Anderson Jeffrey L. , Collins Nancy 
Published: August 2007

Abstract
A variant of a least squares ensemble (Kalman) filter that is suitable for implementation on parallel architectures is presented. This parallel ensemble filter produces results that are identical to those from sequential algorithms already described in the literature when forward observation operators that relate the model state vector to the expected value of observations are linear (although actual results may differ due to floating point arithmetic round-off error). For nonlinear forward observation operators, the sequential and parallel algorithms solve different linear approximations to the full problem but produce qualitatively similar results. The parallel algorithm can be implemented to produce identical answers with the state variable prior ensembles arbitrarily partitioned onto a set of processors for the assimilation step (no caveat on round-off is needed for this result).
Example implementations of the parallel algorithm are described for environments with low (high) communication latency and cost. Hybrids of these implementations and the traditional sequential ensemble filter can be designed to optimize performance for a variety of parallel computing environments. For large models on machines with good communications, it is possible to implement the parallel algorithm to scale efficiently to thousands of processors while bit-wise reproducing the results from a single processor implementation. Timing results on several Linux clusters are presented from an implementation appropriate for machines with low-latency communication.
Most ensemble Kalman filter variants that have appeared in the literature differ only in the details of how a prior ensemble estimate of a scalar observation is updated given an observed value and the observational error distribution. These details do not impact other parts of either the sequential or parallel filter algorithms here, so a variety of ensemble filters including ensemble square root and perturbed observations filters can be used with all the implementations described.
Autocorrelation and Cross-Correlation Estimators of Polarimetric Variables
Authors: Melnikov Valery M. , Zrnić Dusan S. 
Published: August 2007

Abstract
Herein are proposed novel estimators of differential reflectivity ZDR and correlation coefficient ρhv between horizontally and vertically polarized echoes. The estimators use autocorrelations and cross correlations of the returned signals to avoid bias by omnipresent but varying white noise. These estimators are considered for implementation on the future polarimetric Weather Surveillance Radar-1988 Doppler (WSR-88D) network. On the current network the reflectivity factor is measured at signal-to-noise ratios (SNRs) as low as 2 dB and the same threshold is expected to hold for the polarimetric variables. At such low SNR and all the way up to SNR = 15 dB, the conventional estimators of differential reflectivity and the copolar correlation coefficient are prone to errors due to uncertainties in noise levels caused by instability of radar devices, thermal radiations of precipitation and the ground, and wideband radiation of electrically active clouds. Noise variations at SNR less than 15 dB can bias the estimates beyond apparatus accuracy. For brevity the authors refer to the estimators of ZDR and ρhv free from noise bias as the “1-lag estimators” because these are derived from 1-lag correlations. The estimators are quite robust and the only weak assumption for validity is that spectral widths of signals from vertically and horizontally polarized returns are equal. This assumption is verified on radar data. Radar observations demonstrate the validity of these estimator and lower sensitivity to interference signals than the conventional algorithms.
Comparisons of Raman Lidar Measurements of Tropospheric Water Vapor Profiles with Radiosondes, Hygrometers on the Meteorological Observation Tower, and GPS at Tsukuba, Japan
Authors: Sakai Tetsu , Nagai Tomohiro , Nakazato Masahisa , Matsumura Takatsugu , Orikasa Narihiro , Shoji Yoshinori 
Published: August 2007

Abstract
The vertical distribution profiles of the water vapor mixing ratio (w) were measured by Raman lidar at the Meteorological Research Institute, Japan, during the period from 2000 to 2004. The measured values were compared with those obtained with radiosondes, hygrometers on a meteorological observation tower, and global positioning system (GPS) antennas near the lidar site. The values of w obtained with the lidar were lower than those obtained with the corrected Meisei RS2-91 radiosonde by 1.2% on average and higher than those obtained with the corrected Vaisala RS80-A radiosonde by 17% for w ≥ 0.5 g kg−1. The lidar data were higher than those radiosondes’ data by 19% or 33% for w &lt; 0.5 g kg−1. The vertical variations of w obtained with the lidar differed from those obtained with the Meisei RS-01G radiosonde and Meteolabor Snow White radiosonde by 5% on average for w ≥ 0.5 g kg−1. The lidar data were lower than those radiosondes’ data by 37% or 39% for w &lt; 0.5 g kg−1. The temporal variations of w obtained with the lidar and the hygrometers on the meteorological tower agreed to within 0.4% at a height of 213 m, although the absolute values differed systematically by 9%–14% due to the incomplete overlap of the laser beam and the receiver’s field of view at heights between 50 and 150 m. The precipitable water vapor obtained with the lidar indicated a mean positive bias of 2 mm (9%–11%) relative to those obtained with GPS. The lidar water vapor calibration coefficient that was calculated using RS2-91 radiosonde data varied by 11% during an 18-month period. Therefore, it is necessary to develop an accurate, yet convenient, method for determining the calibration coefficient for the use of the lidar.
Design of the AmeriFlux Portable Eddy Covariance System and Uncertainty Analysis of Carbon Measurements
Authors: Ocheltree T. W. , Loescher H. W. 
Published: August 2007

AbstractThe AmeriFlux network continues to improve the understanding of carbon, water, and energy fluxes across temporal and spatial scales. The network includes ∼120 research sites that contribute to the understanding of processes within and among ecosystems. To improve the networks ability and confidence to synthesize data across multiple sites, the AmeriFlux quality assurance and quality control laboratory was established to reduce the within- and among-site uncertainties. This paper outlines the design of the portable eddy covariance system (PECS) and subsequent data processing procedures used for site comparisons. Because the PECS makes precision measurements of atmospheric CO2, the authors also present the results of uncertainty analyses in determining the polynomials for an infrared gas analyzer, estimating the CO2 in secondary standards, and estimating ambient CO2 in field measurements. Under field conditions, drift in the measurement of CO2 increased the uncertainty in flux measurements across 7 days by 5% and was not dependent on the magnitude or direction of the flux. The maximum relative flux measurement error for unstable conditions was 10.03 μmol CO2 m−2 s−1.
Targeted Dropwindsondes in Complex Terrain
Authors: Poulos Gregory S. , Wang Junhong , Lauritsen Dean K. , Cole Harold L. 
Published: August 2007

Abstract
The dropwindsonde (or dropsonde) is a frequently utilized tool in geophysical research and its use over ocean and flat terrain is a reliable and well-established practice. Its use in complex terrain, however, is complicated by signal acquisition challenges that can be directly related to the ground target location, local relief, and line of sight to flight tracks relevant to the observation sought. This note describes a straightforward technique to calculate the theoretical altitude above ground to which a ground-targeted dropsonde will provide data for a given airborne platform. It is found that this height HCq can be calculated from expected airborne platform horizontal velocity Uag, mean dropwindsonde vertical velocity Ws, the relevant barrier maximum HB, and the horizontal distance from the target area to the barrier maximum DB. Here, HCq is found to be weakly dependent on release altitude through Ws. An example from the Terrain-induced Rotor Experiment (T-REX) is used to show that for modern aircraft platforms and dropwindsondes signal loss can occur 1–2 km above ground if mitigation is not pursued. Practical mitigation techniques are described for those complex terrain cases where signal propagation problems would create a significant negative scientific impact.
High-Stiffness Distal Fixation Restores Anterior Laxity and Stiffness as Well as Joint Line Fixation with an Interference Screw
Authors: Liu-Barba David , Howell Stephen M. , Hull Maury L. 
Published: August 2007

Background Fixation of an anterior cruciate ligament graft at the joint line with an interference screw restores anterior laxity better than low-stiffness distal fixation with double staples and sutures tied to a post at implantation in porcine bone. Hypothesis Fixation of an anterior cruciate ligament graft with a high-stiffness distal fixation device restores anterior laxity and knee stiffness as well as joint line fixation with an interference screw in human bone. Study Design Controlled laboratory study. Methods Eleven cadaveric knees with foam reinforcement of the bone were reconstructed with a double-looped tendon graft and fixed with an interference screw and 3 high-stiffness methods of fixation (tandem washer, WasherLoc, and WasherLoc with bone dowel). Anterior laxity at 225 and 110 N of anterior load and knee stiffness were measured at 0°, 30°, 60°, 90°, and 120° of flexion with a 6 degrees of freedom load application system. Results The increase in anterior laxity and knee stiffness with the interference screw was not significantly different from that with the high-stiffness distal methods. Conclusion In the human knee, the use of high-stiffness fixation devices placed distal to the joint line restored anterior laxity and knee stiffness as well as joint line fixation with an interference screw at implantation. Clinical Relevance The stiffness provided by each method of fixation should be considered along with the length of the graft when determining anterior laxity and knee stiffness.
Donor Site Evaluation after Autologous Osteochondral Mosaicplasty for Cartilaginous Lesions of the Elbow Joint
Authors: Iwasaki Norimasa , Kato Hiroyuki , Kamishima Tamotsu , Suenaga Naoki , Minami Akio 
Published: August 2007

Background One significant disadvantage of autologous osteochondral mosaicplasty (mosaicplasty) is the harvesting of osteochondral grafts from the normal articular area of the knee joint. However, the effect of harvesting grafts on knee function remains unclear. Purpose To clarify the functional effects on the donor knee of harvesting osteochondral grafts and to perform magnetic resonance imaging evaluation of donor site repair after mosaicplasty for capitellar osteochondritis dissecans in young athletes. Study Design Case series; Level of evidence, 4. Methods Eleven male competitive athletes with advanced lesions of capitellar osteochondritis dissecans underwent mosaicplasties. The surgical technique involves obtaining small-sized cylindrical osteochondral grafts from the lateral periphery of the femoral condyle at the level of the patellofemoral joint and transplanting them to osteochondral defects in the capitellum. Assessment at a mean follow-up of 26 months included local findings of the donor knees, a Lysholm knee scoring scale, International Knee Documentation Committee standard evaluation form, and magnetic resonance imaging evaluation. Results All patients returned to a competitive level of their previous sports without any donor site disturbances. Based on the Lysholm knee score and International Knee Documentation Committee evaluation form, all knees were graded as excellent and normal, respectively. The magnetic resonance imaging showed 50% to 100% defect fill in 6 of 9 patients and normal or nearly normal signals in 4 patients at the donor sites. Conclusion No adverse effects of osteochondral graft harvest on donor knee function were found after mosaicplasty for capitellar osteochondritis dissecans in young athletes. However, magnetic resonance imaging indicates that the donor site is resurfaced with fibrous tissue.
Blunted hepcidin response to oral iron challenge in HFE-related hemochromatosis
Authors: Piperno Alberto , Girelli Domenico , Nemeth Elizabeta , Trombini Paola , Bozzini Claudia , Poggiali Erika , Phung Yen , Ganz Tomas , Camaschella Clara 
Published: August 2007

AbstractInadequate hepcidin synthesis leads to iron overload in HFE-related hemochromatosis. We explored the regulation of hepcidin by iron in 88 hemochromatosis patients (61 C282Y/C282Y, 27 C282Y/H63D) and 23 healthy controls by analyzing urinary hepcidin before and 24 hours after a 65-mg oral iron dose. Thirty-four patients were studied at diagnosis and had iron overload, and 54 patients were iron depleted. At diagnosis, hepcidin values in C282Y homozygotes were similar to controls, whereas values in C282Y/H63D heterozygotes were higher (P = .02). However, the hepcidin/ferritin ratio was decreased in both homozygotes (P < .001) and heterozygotes (P = .017), confirming the inadequate hepcidin production for the iron load with both genotypes. In iron-depleted patients of both genotypes studied at a time remote from phlebotomy, basal hepcidin was still lower than in controls (P < .001 for C282Y/C282Y and P = .002 for heterozygotes). After an iron challenge, mean urinary hepcidin excretion increased in controls (P = .001) but not patients, irrespective of genotype and iron status. Significant hepcidin increase ( ≥ 10 ng/mg creatinine) was observed in 74% of controls, 15% of homozygotes, and 32% of heterozygotes. The hepcidin response to oral iron is blunted in HFE-related hemochromatosis and not improved after iron depletion. The findings support the involvement of HFE in iron sensing and subsequent regulation of hepcidin.
Short-term oleoyl-estrone treatment affects capacity to manage lipids in rat adipose tissue
Authors: Salas Anna , Noé Véronique , Ciudad Carlos J , Romero M Mar , Remesar Xavier , Esteve Montserrat 
Published: August 2007

Abstract

Background
Short-term OE (oleoyl-estrone) treatment causes significant decreases in rat weight mainly due to adipose tissue loss. The aim of this work was to determine if OE treatment affects the expression of genes that regulate lipid metabolism in white adipose tissue.

Results
Gene expression in adipose tissue from female treated rats (48 hours) was analysed by hybridization to cDNA arrays and levels of specific mRNAs were determined by real-time PCR. Treatment with OE decreased the expression of 232 genes and up-regulated 75 other genes in mesenteric white adipose tissue. The use of real-time PCR validate that, in mesenteric white adipose tissue, mRNA levels for Lipoprotein Lipase (LPL) were decreased by 52%, those of Fatty Acid Synthase (FAS) by 95%, those of Hormone Sensible Lipase (HSL) by 32%, those of Acetyl CoA Carboxylase (ACC) by 92%, those of Carnitine Palmitoyltransferase 1b (CPT1b) by 45%, and those of Fatty Acid Transport Protein 1 (FATP1) and Adipocyte Fatty Acid Binding Protein (FABP4) by 52% and 49%, respectively. Conversely, Tumour Necrosis Factor (TNFα) values showed overexpression (198%).

Conclusion
Short-term treatment with OE affects adipose tissue capacity to extract fatty acids from lipoproteins and to deal with fatty acid transport and metabolism.
Regions of Diversity 8, 9 and 13 contribute to Streptococcus pneumoniae virulence
Authors: Embry Addie , Hinojosa Ernesto , Orihuela Carlos J 
Published: August 2007

Abstract

Background

Streptococcus pneumoniae is the leading cause of community-acquired pneumonia. Previously, using comparative genomic analyses, 13 regions of genomic plasticity have been identified in the S. pneumoniae genome. These "Regions of Diversity" (RDs) accounted for half the genomic variation observed amongst all pneumococci tested, moreover, were determined to encode a variety of putative virulence factors. To date, genes within 5 RDs have been unequivocally demonstrated to contribute to S. pneumoniae virulence. It is unknown if the remaining RDs also contribute to virulence.

Results
Using allelic exchange, we created S. pneumoniae mutants that were deficient in RD2, 5, 7, 8, 9, 12 and 13. Mutants deficient in RD8, 9 and 13 were attenuated in a mouse model of disease. RD8 is 40,358 nucleotides in length and encodes 37 genes. Using a panel of isogenic mutants, we determined that RD8b3 is the operon within RD8 that is responsible for virulence. Mice infected with mutants deficient in RD8, RD8b3, RD9 and RD13 had significantly less bacteria in the blood two days after intranasal challenge and improved survival over time versus mice infected with wild type. In all instances mutants colonized the nasopharynx at levels equivalent to wild type.

Conclusion
Genes within RD1, 3, 4, 6, and 10 have previously been shown to contribute to virulence. This study demonstrates that genes within RD8, 9 and 13 also contribute to virulence. The ability of mutants deficient in RD2, 5, 7, 8, 9, 12, and 13 to colonize the nasopharynx indicates that genes within these RDs are not required for asymptomatic carriage. Nonetheless, the observation that mutants deficient in RD8b3, 9 and 13 are attenuated indicates that genes within these loci are necessary for spread of the bacteria beyond the nasopharynx to normally sterile sites.