bluuebunny/crossref_metadata_2025 huggingface dataset:
Cosmic variance of weak lensing surveys in the non-Gaussian regime
Authors: Semboloni Elisabetta , Van Waerbeke Ludovic , Heymans Catherine , Hamana Takashi , Colombi Stephane , White Martin , Mellier Yannick
Published: December 2006

The results from weak gravitational lensing analyses are subject to a cosmic variance error term that has previously been estimated assuming Gaussian statistics. In this Letter we address the issue of estimating cosmic variance errors for weak lensing surveys in the non-Gaussian regime.

Using standard cold dark matter model ray-tracing simulations characterized by Ωm = 0.3, ΩΛ = 0.7, h = 0.7 and σ8 = 1 for different survey redshifts zs, we determine the variance of the two-point shear correlation function measured across 64 independent lines of sight. We compare the measured variance to the variance expected from a random Gaussian field and derive a redshift-dependent non-Gaussian calibration relation.

We find that the ratio between the non-Gaussian and Gaussian variance at 1 arcmin can be as high as ∼30 for a survey with source redshift zs ∼ 0.5 and ∼10 for zs ∼ 1. The transition scale ϑc above which the ratio is consistent with unity is found to be ϑc ∼ 20 arcmin for zs ∼ 0.5 and ϑc∼ 10 arcmin for zs∼ 1. We provide fitting formulae to our results permitting the estimation of non-Gaussian cosmic variance errors, and discuss the impact on current and future surveys.

A more extensive set of simulations will, however, be required to investigate the dependence of our results on cosmology, specifically on the amplitude of clustering.
Instability strips of slowly pulsating B stars and β Cephei stars: the effect of the updated OP opacities and of the metal mixture
Authors: Miglio Andrea , Montalbán Josefina , Dupret Marc-Antoine
Published: December 2006

The discovery of β Cephei stars in low-metallicity environments, as well as the difficulty in theoretically explaining the excitation of the pulsation modes observed in some β Cephei and hybrid slowly pulsating B–β Cephei pulsators, suggest that the ‘iron opacity bump’ provided by stellar models could be underestimated. We analyze the effect of uncertainties in the opacity computations and in the solar metal mixture on the excitation of pulsation modes in B-type stars. We carry out a pulsational stability analysis for four grids of main-sequence models with masses between 2.5 and 12M⊙ computed with OPAL and OP opacity tables and two different metal mixtures. We find that in a typical β Cephei model the OP opacity is 25 per cent larger than OPAL in the region where the driving of pulsation modes occurs. Furthermore, the difference in the Fe mass fraction between the two metal mixtures considered is of the order of 20 per cent. The implication on the excitation of pulsation modes is non-negligible: the blue border of the slowly pulsating B star (SPB) instability strip is displaced at higher effective temperatures, leading to a larger number of models being hybrid SPB-β Cephei pulsators. Moreover, higher overtone p-modes are excited in β Cephei models and unstable modes are found in a larger number of models for lower metallicities, in particular β Cephei pulsations are also found in models with Z = 0.01.
Application of an inverse kernel concept to Monte Carlo based IMRT
Authors: Bogner Ludwig , Hartmann Matthias , Rickhey Mark , Moravek Zdenek
Published: December 2006

Inverse treatment planning by means of pencil beam algorithms can lead to errors in the calculation of dose in areas without secondary electron equilibrium. Monte Carlo (MC) simulations give accurate results in such areas but result in increased computation times. We present a new, so‐called inverse kernel concept that offers MC precision in inverse treatment planning with acceptable computation times and memory consumption. Inverse kernels are matrices that describe the dose contribution from all bixels of a beam to a distinct voxel of the patient phantom. The concept is similar to other generalized pencil‐beam concepts, except that inverse kernel elements are precalculated using a single MC simulation and stored as binary trees. In this procedure a modified MC code (XVMC) is applied to trace the photon history for each dose deposition. Iterative optimization is then applied in a second step. The inverse process is separated into (i) a slower MC simulation and (ii) a faster iterative optimization, followed by (iii) the segmentation procedure, and (iv) a final MC dose calculation step including a segment weight reoptimization. Inverse kernel optimization, or IKO, with segmentation and reoptimization steps is demonstrated by means of a lung cancer case. To demonstrate the superiority of an inverse MC system over pencil‐beam or collapsed‐cone based systems, the final result of the IKO is compared to plans where all segments have been calculated by pencil beam or collapsed cone, respectively. Dose‐volume histograms and dose‐difference histograms show remarkable differences, which can be attributed to systematic errors in both algorithms. IKO is a precise, nonhybrid, inverse MC treatment planning system which suits current clinical needs, as several optimization steps can follow one single MC‐simulation step for a distinct beam setup.
Dosimetric characterization of a novel intracavitary mold applicator for high dose rate endorectal brachytherapy treatment
Authors: Poon Emily , Reniers Brigitte , Devic Slobodan , Vuong Té , Verhaegen Frank
Published: December 2006

The dosimetric properties of a novel intracavitary mold applicator for high dose rate (HDR) endorectal cancer treatment have been investigated using Monte Carlo (MC) simulations and experimental methods. The long applicator has a flexible structure made of silicone rubber for easy passage into cavities with deep‐seated tumors. It consists of eight source catheters arranged around a central cavity for shielding insertion, and is compatible for use with an endocavitary balloon. A phase space model of the HDR source has been validated for dose calculations using the GEANT4 MC code. EBT model film was used to measure dose distributions in water around shielded and unshielded applicators with two loading configurations, and to quantify the shielding effect of a balloon injected with an iodine solution . The film calibration procedure was performed in water using an HDR source. Ionization chamber measurements in a Lucite phantom show that placing a tungsten rod in the applicator attenuates the dose in the shielded region by up to 85%. Inserting the shielded applicator into a water‐filled balloon pushes the neighboring tissues away from the radiation source, and the resulting geometric displacement reduces the dose by up to 53%; another 8% dose reduction can be achieved when the balloon is injected with an iodine solution. All experimental results agree with the GEANT4 calculations within measurement uncertainties.
Low magnetic moment PIN diodes for high field MRI surface coils
Authors: Voskoboynik Pavel , Joos Ronald D. , Doherty W. E. , Goldfarb Ron B.
Published: December 2006

Positive‐intrinsic‐negative (PIN) silicon diodes are commonly used in magnetic resonance imaging (MRI) coils to perform active or passive blocking and detuning, or to disable circuit functions. However, diode packages with large magnetic moments are known to cause image artifacts in high field MRI systems. In this study, diode packages with low magnetic moment were designed by compensating components of ferromagnetic nickel and paramagnetic tungsten with diamagnetic silver. The new diodes have an initial positive susceptibility up to fields of and a negative susceptibility from . Their magnetic moments are one to two orders of magnitude smaller than those of standard diodes; moments as small as at were achieved.
An analysis of the treatment couch and control system dynamics for respiration‐induced motion compensation
Authors: D'Souza Warren D. , McAvoy Thomas J.
Published: December 2006

Sophisticated methods for real‐time motion compensation include using the linear accelerator, MLC, or treatment couch. To design such a couch, the required couch and control system dynamics need to be investigated. We used an existing treatment couch known as the to gain insight into couch dynamics and an internal model controller to simulate feedback control of respiration‐induced motion. The couch dynamics, described using time constants and dead times, were investigated using step inputs. The resulting data were modeled as first and second order systems with dead time. The couch was determined to have a linear response for step inputs . Motion data from 12 patients were obtained using a skin marker placed on the abdomen of the patient and the marker data were assumed to be an exact surrogate of tumor motion. The feedback system was modeled with the couch as a second‐ordersystem and the controller as a first order system. The time constants of the couch and controller and the dead times were varied starting with parameters obtained from the couch and the performance of the feedback system was evaluated. The resulting residual motion under feedback control was generally when a fast enough couch was simulated.
Estimation of white matter connectivity based on a three‐dimensional directional diffusion function in diffusion tensor MRI
Authors: Kumazawa Seiji , Yoshiura Takashi , Arimura Hidetaka , Mihara Futoshi , Honda Hiroshi , Higashida Yoshiharu , Toyofuku Fukai
Published: December 2006

Diffusion tensor (DT) magnetic resonance imaging (MRI) provides the directional information of local neuronal fibers, and has been used to estimate the neuroanatomical connectivity in the cerebral white matter. Several methods for white matter tractography have been developed based on DT‐MRI. However, it has been difficult to estimate the white matter tract pathways in the fiber crossing and branching region because of the ambiguity of the principal eigenvector and/or low anisotropy due to the partial volume effect. In this paper, we proposed a new method for white matter tractography, which permits fiber tract branching and passing through crossing regions. Our tractography method is based on a three‐dimensional (3D)directional diffusion function(DDF), which was given by a 3D anisotropic Gaussian function defined by normalized three eigenvalues and their corresponding eigenvectors of DT. The DDF was used for generation of a 3D directional diffusion field and for determination of the connectivity between the voxels in fiber tracking. To extract the white matter tract region, DDF‐based tractography (DDFT) method used the directional diffusion field instead of a threshold fractional anisotropy map, which has been used in the conventional methods, so that low anisotropy voxels in the branching and crossing regions may be included. We applied the DDFT method and two conventional tractography methods (a streamline technique and a tensorline algorithm) to DT‐MRI data of five normal subjects for visualizing the pyramidal tract. Our method visualized the pathways connected to a large portion of the primary motor cortex, including foot, hand and face motor areas, passing through the crossing regions with other white matter tracts in all subjects, whereas the conventional methods showed only a small portion of the pyramidal tract. The pyramidal tract pathways estimated by our method were consistent with the neuroanatomical knowledge. In conclusion, the DDFT method may be useful in assisting neuroradiologists in estimating the white matter tracts.
A dosimetric study on the high dose rate Flexisource
Authors: Granero D. , Pérez‐Calatayud J. , Casal E. , Ballester F. , Venselaar J.
Published: December 2006

In this work, the dose rate distribution of a new high dose rate source (Flexisource used in the afterloading Flexitron system, Isodose Control, Veenendaal, The Netherlands) is studied by means of Monte Carlo techniques using the GEANT4 code. The dosimetric parameters of the Task Group No. 43 Report (TG43) formalism and two‐dimensional rectangular look‐up tables have been obtained.
Targeted 2D/3D registration using ray normalization and a hybrid optimizer
Authors: Dey Joyoni , Napel Sandy
Published: December 2006

X‐ray images are often used to guide minimally invasive procedures in interventional radiology. The use of a preoperatively obtained 3D volume can enhance the visualization needed for guiding catheters and other surgical devices. However, for intraoperative usefulness, the 3D dataset needs to be registered to the 2D x‐ray images of the patient. We investigated the effect of targeting subvolumes of interest in the 3D datasets and registering the projections with C‐arm x‐ray images. We developed an intensity‐based 2D/3D rigid‐body registration using a Monte Carlo‐based hybrid algorithm as the optimizer, using a single view for registration. Pattern intensity (PI) and mutual information (MI) were two metrics tested. We used normalization of the rays to address the problems due to truncation in 3D necessary for targeting. We tested the algorithm on a C‐arm x‐ray image of a pig's head and a 3D dataset reconstructed from multiple views of the C‐arm. PI and MI were comparable in performance. For two subvolumes starting with a set of initial poses from in , from (random), in and and deg in the three angles, the robustness was 94% for PI and 91% for MI, with accuracy of (PI) and (MI), using the hybrid algorithm. The hybrid optimizer, when compared with a standard Powell's direction set method, increased the robustness from 59% (Powell) to 94% (hybrid). Another set of 50 random initial conditions from in and deg in the three angles, yielded robustness of 84% (hybrid) versus 38% (Powell) using PI as metric, with accuracies (hybrid) versus (Powell).
Monte Carlo and experimental dosimetry of an brachytherapy seed
Authors: Dolan James , Li Zuofeng , Williamson Jeffrey F.
Published: December 2006

We have performed a comprehensive dosimetric characterization of the model 6711 seed using both experimental [ thermoluminscent dosimetry (TLD)] and theoretical (Monte Carlo photon transport) methods. In addition to determining the dosimetric parameters of the 6711, this report quantified: (1) the angular dependence of TLD energy response functions for both point and volume detectors in water, poly(methylmethacrylate), and solid water media; and (2) the contribution of underlying geometric uncertainties to the overall uncertainty of Monte Carlo derived dosimetric parameters according to the National Institute of Standards and Technology Report 1297 methodology. The theoretical value for the dose rate constant in water was [combined standard uncertainty (CSU) with coverage factor ] and the experimental value was . Agreement between experimental and theoretical radial dose function values was well within the CSU, while agreement between experimental and theoretical anisotropy function values was within the CSU only after incorporating the use of polar angle‐dependent energy response functions. The angular dependence of the relative energy response was found to have a complex and significant dependence on measurement medium and internal geometry of the source.
Prospects for quantitative two‐dimensional radiochromic film dosimetry for low dose‐rate brachytherapy sources
Authors: Le Yi , Ali Imad , Dempsey James F. , Williamson Jeffrey F.
Published: December 2006

Radiochromic film (RCF) has been shown to be a precise and accurate two‐dimensional dosimeter for acute exposure radiation fields. However, “temporal history” mismatch between calibration and brachytherapy films due to RCF dose‐rate effects could introduce potentially large uncertainties in low dose‐rate (LDR) brachytherapy absolute dose measurement. This article presents a quantitative evaluation of the precision and accuracy of a laser scanner‐based RCF‐dosimetry system and the effect of the temporal history mismatch in LDR absolute dose measurement. MD‐55‐2 RCF was used to measure absolute dose for a low dose‐rate brachytherapy source using both single‐ and double‐exposure techniques. Dose‐measurement accuracy was evaluated by comparing RCF to Monte Carlo photon‐transport simulation. The temporal history mismatch effect was investigated by examining dependence of RCF accuracy on irradiation‐to‐densitometry time interval. The predictions of the empirical cumulative dose superposition model (CDSM) were compared with measurements. For the double‐exposure technique, the agreement between measurement and Monte Carlo simulation was better than 4% in the dose range with measurement precisions (coverage factor ) of and for the doses greater or less than , respectively. The overall uncertainty of dose rate/air‐kerma strength measurements achievable by this dosimetry system for a spatial resolution of is less than 4% for doses greater than . The measured temporal history mismatch systematic error is about 1.8% for a postexposure time when using the double exposure technique and agrees with CDSM's prediction qualitatively. This work demonstrates that the model MD‐55‐2 RCF detector has the potential to support quantitative dose measurements about LDR brachytherapy sources with precision and accuracy better than that of previously described dosimeters. The impacts of this work on the future use of new type of RCF were also discussed.
A dosimetric comparison of and for HDR brachytherapy of the breast, accounting for the effect of finite patient dimensions and tissue inhomogeneities
Authors: Lymperopoulou G. , Papagiannis P. , Angelopoulos A. , Karaiskos P. , Georgiou E. , Baltas D.
Published: December 2006

Monte Carlo simulation dosimetry is used to compare to for breast high dose rate (HDR) brachytherapy applications using multiple catheter implants. Results for bare point sources show that while delivers a greater dose rate per unit air kerma strength at the radial distance range of interest to brachytherapy in homogeneous water phantoms, it suffers a greater dose rate deficit in missing scatter conditions relative to . As a result of these two opposing factors, in the scatter conditions defined by the presence of the lung and the finite patient dimensions in breast brachytherapy the dose distributions calculated in a patient equivalent mathematical phantom by Monte Carlo simulations for the same implant of either or commercially available sources are found comparable. Dose volume histogram results support that could be at least as effective as delivering the same dose to the lung and slightly reduced dose to the breast skin. The current treatment planning systems’ approach of employing dosimetry data precalculated in a homogeneous water phantom of given shape and dimensions, however, is shown to notably overestimate the delivered dose distribution for . Especially at the skin and the lung, the treatment planning system dose overestimation is on the order of 15%–30%. These findings do not undermine the potential of HDR sources for breast brachytherapy relative to the most commonly used HDR sources. They imply, however, that there could be a need for the amendment of dose calculation algorithms employed in clinical treatment planning of particular brachytherapy applications, especially for intermediate photon energy sources such as .
Physics for Radiation Protection—A Handbook 2nd edition 2nd edition
Authors: Wen Chuan‐Dong
Published: December 2006

Physics for Radiation Protection—A Handbook Martin James E., WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim, 2006. ISBN 3‐527‐40611‐5. $250.00 (hardcopy). 822 pp.
Pharmacokinetics and Safety of Indinavir in Human Immunodeficiency Virus-Infected Pregnant Women
Authors: Unadkat Jashvant D. , Wara Diane W. , Hughes Michael D. , Mathias Anita A. , Holland Diane T. , Paul Mary E. , Connor James , Huang Sharon , Nguyen Bach-Yen , Watts D. Heather , Mofenson Lynne M. , Smith Elizabeth , Deutsch Paul , Kaiser Kathleen A. , Tuomala Ruth E.
Published: December 2006

Human immunodeficiency virus-infected women (n= 16) received indinavir (800 mg three times a day) plus zidovudine plus lamivudine from 14 to 28 weeks of gestation to 12 weeks postpartum. Two women and eight infants experienced grade 3 or 4 toxicities that were possibly treatment related. Indinavir area under the plasma concentration-time curve was 68% lower antepartum versus postpartum, suggesting increased intestinal and/or hepatic CYP3A activity during pregnancy.
Evaluation of Accessory Gene Regulator (
agr
) Group and Function in the Proclivity towards Vancomycin Intermediate Resistance in
Staphylococcus aureus
Authors: Tsuji Brian T. , Rybak Michael J. , Lau Kerry L. , Sakoulas George
Published: December 2006

Simulated therapeutic vancomycin exposures were evaluated against
agr
wild-type and knockout
Staphylococcus aureus
groups I, II, III, and IV using an in vitro pharmacodynamic model. All
agr
groups developed intermediate resistance to vancomycin after subtherapeutic exposure. The free unbound fraction of the area under the concentration-time curve (
f
AUC/MIC) required to suppress resistance was fourfold higher (
P
< 0.001) in
agr
dysfunctional strains (112 to 169) than that in parent wild-type strains (28).
Clinical Prediction Tool To Identify Patients withPseudomonas aeruginosaRespiratory Tract Infections at Greatest Risk for Multidrug Resistance
Authors: Lodise Thomas P. , Miller Christopher D. , Graves Jeffrey , Furuno Jon P. , McGregor Jessina C. , Lomaestro Ben , Graffunder Eileen , McNutt Louise-Anne
Published: December 2006

Despite the increasing prevalence of multiple-drug-resistant (MDR)Pseudomonas aeruginosa, the factors predictive of MDR have not been extensively explored. We sought to examine factors predictive of MDR among patients withP. aeruginosarespiratory tract infections and to develop a tool to estimate the probability of MDR among such high-risk patients. This was a single-site, case-control study of patients withP. aeruginosarespiratory tract infections. Multiple-drug resistance was defined as resistance to four or more antipseudomonal antimicrobial classes. Clinical data on demographics, antibiotic history, and microbiology were collected. Classification and regression tree analysis (CART) was used to identify the duration of antibiotic exposure associated with MDRP. aeruginosa. Log-binomial regression was used to model the probability of MDRP. aeruginosa. Among 351P. aeruginosa-infected patients, the proportion of MDRP. aeruginosawas 35%. A significant relationship between prior antibiotic exposure and MDRP. aeruginosawas found for all of the antipseudomonal antibiotics studied, but the duration of prior exposure associated with MDR varied between antibiotic classes; the shortest prior exposure duration was observed for carbapenems and fluoroquinolones, and the longest duration was noted for cefepime and piperacillin-tazobactam. Within the final model, the predicted MDRP. aeruginosalikelihood was most dependent upon length of hospital stay, prior culture sample collection, and number of CART-derived prior antibiotic exposures. A history of a prolonged hospital stay and exposure to antipseudomonal antibiotics predicts multidrug resistance among patients withP. aeruginosarespiratory tract infections at our institution. Identifying these risk factors enabled us to develop a prediction tool to assess the risk of resistance and thus guide empirical antibiotic therapy.
Caspofungin in Combination with Amphotericin B against
Candida parapsilosis
Authors: Barchiesi Francesco , Spreghini Elisabetta , Tomassetti Serena , Giannini Daniele , Scalise Giorgio
Published: December 2006

C
andida parapsilosis
has emerged as an important nosocomial pathogen. In the present study, a checkerboard broth microdilution method was performed to investigate the in vitro activities of caspofungin (CAS) in combination with amphotericin B (AMB) against three clinical isolates of
C. parapsilosis
. Although there was a significant reduction of the MIC of one or both drugs used in combination, an indifferent interaction (fractional inhibitory concentration index greater than 0.50 and less than or equal to 4.0) was observed in 100% of cases. This finding was confirmed by killing curve studies. By a disk diffusion assay, the halo diameters produced by antifungal agents in combination were often significantly greater than those produced by each drug alone. Antagonism was never observed. In a murine model of systemic candidiasis, CAS at either 0.25 or 1 mg/kg/day combined with AMB at 1 mg/kg/day was significantly more effective than each single drug at reducing the colony counts in kidneys. Higher doses of the echinocandin (i.e., 5 and 10 mg/kg/day) combined with the polyene did not show any advantage over CAS alone. Overall, our study showed a positive interaction of CAS and AMB against
C. parapsilosis
.
Role of Peptide Hydrophobicity in the Mechanism of Action of α-Helical Antimicrobial Peptides
Authors: Chen Yuxin , Guarnieri Michael T. , Vasil Adriana I. , Vasil Michael L. , Mant Colin T. , Hodges Robert S.
Published: December 2006

In the present study, the 26-residue amphipathic α-helical antimicrobial peptide V13KL(Y. Chen et al., J. Biol. Chem. 2005, 280:12316-12329, 2005) was used as the framework to study the effects of peptide hydrophobicity on the mechanism of action of antimicrobial peptides. Hydrophobicity was systematically decreased or increased by replacing leucine residues with less hydrophobic alanine residues or replacing alanine residues with more hydrophobic leucine residues on the nonpolar face of the helix, respectively. Hydrophobicity of the nonpolar face of the amphipathic helix was demonstrated to correlate with peptide helicity (measured by circular dichroism spectroscopy) and self-associating ability (measured by reversed-phase high-performance liquid chromatography temperature profiling) in aqueous environments. Higher hydrophobicity was correlated with stronger hemolytic activity. In contrast, there was an optimum hydrophobicity window in which high antimicrobial activity could be obtained. Decreased or increased hydrophobicity beyond this window dramatically decreased antimicrobial activity. The decreased antimicrobial activity at high peptide hydrophobicity can be explained by the strong peptide self-association which prevents the peptide from passing through the cell wall in prokaryotic cells, whereas increased peptide self-association had no effect on peptide access to eukaryotic membranes.
Antiparasitic Drug Nitazoxanide Inhibits the Pyruvate Oxidoreductases of
Helicobacter pylori
, Selected Anaerobic Bacteria and Parasites, and
Campylobacter jejuni
Authors: Hoffman Paul S. , Sisson Gary , Croxen Matthew A. , Welch Kevin , Harman W. Dean , Cremades Nunilo , Morash Michael G.
Published: December 2006

Nitazoxanide (NTZ) exhibits broad-spectrum activity against anaerobic bacteria and parasites and the ulcer-causing pathogen
Helicobacter pylori
. Here we show that NTZ is a noncompetitive inhibitor (

K
i

, 2 to 10 μM) of the pyruvate:ferredoxin/flavodoxin oxidoreductases (PFORs) of
Trichomonas vaginalis
,
Entamoeba histolytica
,
Giardia intestinalis
,
Clostridium difficile
,
Clostridium perfringens
,
H. pylori
, and
Campylobacter jejuni
and is weakly active against the pyruvate dehydrogenase of
Escherichia coli
. To further mechanistic studies, the PFOR operon of
H. pylori
was cloned and overexpressed in
E. coli
, and the multisubunit complex was purified by ion-exchange chromatography. Pyruvate-dependent PFOR activity with NTZ, as measured by a decrease in absorbance at 418 nm (spectral shift from 418 to 351 nm), unlike the reduction of viologen dyes, did not result in the accumulation of products (acetyl coenzyme A and CO
2
) and pyruvate was not consumed in the reaction. NTZ did not displace the thiamine pyrophosphate (TPP) cofactor of PFOR, and the 351-nm absorbing form of NTZ was inactive. Optical scans and
1
H nuclear magnetic resonance analyses determined that the spectral shift (
A
418
to
A
351
) of NTZ was due to protonation of the anion (NTZ
−
) of the 2-amino group of the thiazole ring which could be generated with the pure compound under acidic solutions (pK
a
= 6.18). We propose that NTZ
−
intercepts PFOR at an early step in the formation of the lactyl-TPP transition intermediate, resulting in the reversal of pyruvate binding prior to decarboxylation and in coordination with proton transfer to NTZ. Thus, NTZ might be the first example of an antimicrobial that targets the “activated cofactor” of an enzymatic reaction rather than its substrate or catalytic sites, a novel mechanism that may escape mutation-based drug resistance.
Cloning and Characterization of the Pyrrolomycin Biosynthetic Gene Clusters from
Actinosporangium vitaminophilum
ATCC 31673 and
Streptomyces
sp. Strain UC 11065
Authors: Zhang Xiujun , Parry Ronald J.
Published: December 2006

The pyrrolomycins are a family of polyketide antibiotics, some of which contain a nitro group. To gain insight into the nitration mechanism associated with the formation of these antibiotics, the pyrrolomycin biosynthetic gene cluster from
Actinosporangium vitaminophilum
was cloned. Sequencing of ca. 56 kb of
A. vitaminophilum
DNA revealed 35 open reading frames (ORFs). Sequence analysis revealed a clear relationship between some of these ORFs and the biosynthetic gene cluster for pyoluteorin, a structurally related antibiotic. Since a gene transfer system could not be devised for
A. vitaminophilum
, additional proof for the identity of the cloned gene cluster was sought by cloning the pyrrolomycin gene cluster from
Streptomyces
sp. strain UC 11065, a transformable pyrrolomycin producer. Sequencing of ca. 26 kb of UC 11065 DNA revealed the presence of 17 ORFs, 15 of which exhibit strong similarity to ORFs in the
A. vitaminophilum
cluster as well as a nearly identical organization. Single-crossover disruption of two genes in the UC 11065 cluster abolished pyrrolomycin production in both cases. These results confirm that the genetic locus cloned from UC 11065 is essential for pyrrolomycin production, and they also confirm that the highly similar locus in
A. vitaminophilum
encodes pyrrolomycin biosynthetic genes. Sequence analysis revealed that both clusters contain genes encoding the two components of an assimilatory nitrate reductase. This finding suggests that nitrite is required for the formation of the nitrated pyrrolomycins. However, sequence analysis did not provide additional insights into the nitration process, suggesting the operation of a novel nitration mechanism.
Coproduction of Novel 16S rRNA Methylase RmtD and Metallo-β-Lactamase SPM-1 in a Panresistant
Pseudomonas aeruginosa
Isolate from Brazil
Authors: Doi Yohei , de Oliveira Garcia Doroti , Adams Jennifer , Paterson David L.
Published: December 2006

Serious infections with
Pseudomonas aeruginosa
are frequently treated with the combination of a β-lactam antimicrobial and an aminoglycoside.
P. aeruginosa
strain PA0905 was isolated in 2005 from an inpatient in Brazil. It showed a panresistant phenotype that included resistance to β-lactams, aminoglycosides, and fluoroquinolones. The β-lactam resistance was conferred by the production of the metallo-β-lactamase SPM-1. No inhibitory zone was observed when a disk diffusion test was performed with the semisynthetic aminoglycoside arbekacin, raising suspicion of 16S rRNA methylase production. A cloning experiment subsequently revealed the presence of a novel 16S rRNA methylase, RmtD, which accounted for the high-level resistance to all 4,6-disubstituted deoxystreptamine aminoglycosides, such as amikacin, tobramycin, and gentamicin. RmtD shared a moderate degree of identity with RmtA, another 16S rRNA methylase that was initially reported to occur in
P. aeruginosa
in Japan in 2003. This is the first identification of aminoglycoside resistance mediated by a 16S rRNA methylase in South America. This is also the first report to document coproduction of a metallo-β-lactamase and a 16S rRNA methylase, a combination that would severely compromise therapeutic options for the infected patients.
Luminescent Whole-Cell Cyanobacterial Bioreporter for Measuring Fe Availability in Diverse Marine Environments
Authors: Boyanapalli Ramakrishna , Bullerjahn George S. , Pohl Christa , Croot Peter L. , Boyd Philip W. , McKay R. Michael L.
Published: December 2006

A
Synechococcus
sp. strain PCC 7002 Fe bioreporter was constructed containing the
isiAB
promoter fused to the
Vibrio harveyi luxAB
genes. Bioreporter luminescence was characterized with respect to the free ferric ion concentration in trace metal-buffered synthetic medium. The applicability of the Fe bioreporter to assess Fe availability in the natural environment was tested by using samples collected from the Baltic Sea and from the high-nutrient, low-chlorophyll subarctic Pacific Ocean. Parallel assessment of dissolved Fe and bioreporter response confirmed that direct chemical measurements of dissolved Fe should not be considered alone when assessing Fe availability to phytoplankton.
Use of Artificial Neural Networks and a Gamma-Concept-Based Approach To Model Growth of and Bacteriocin Production by
Streptococcus macedonicus
ACA-DC 198 under Simulated Conditions of Kasseri Cheese Production
Authors: Poirazi Panayiota , Leroy Frédéric , Georgalaki Marina D. , Aktypis Anastassios , De Vuyst Luc , Tsakalidou Effie
Published: December 2006

Growth of and bacteriocin production by
Streptococcus macedonicus
ACA-DC 198 were assessed and modeled under conditions simulating Kasseri cheese production. Controlled fermentations were performed in milk supplemented with yeast extract at different combinations of temperature (25, 40, and 55°C), constant pH (pHs 5 and 6), and added NaCl (at concentrations of 0, 2, and 4%, wt/vol). The data obtained were used to construct two types of predictive models, namely, a modeling approach based on the gamma concept, as well as a model based on artificial neural networks (ANNs). The latter computational methods were used on 36 control fermentations to quantify the complex relationships between the conditions applied (temperature, pH, and NaCl) and population behavior and to calculate the associated biokinetic parameters, i.e., maximum specific growth and cell count decrease rates and specific bacteriocin production. The functions obtained were able to estimate these biokinetic parameters for four validation fermentation experiments and obtained good agreement between modeled and experimental values. Overall, these experiments show that both methods can be successfully used to unravel complex kinetic patterns within biological data of this kind and to predict population kinetics. Whereas ANNs yield a better correlation between experimental and predicted results, the gamma-concept-based model is more suitable for biological interpretation. Also, while the gamma-concept-based model has not been designed for modeling of other biokinetic parameters than the specific growth rate, ANNs are able to deal with any parameter of relevance, including specific bacteriocin production.
Response ofNitrosospirasp. Strain AF-Like Ammonia Oxidizers to Changes in Temperature, Soil Moisture Content, and Fertilizer Concentration
Authors: Avrahami Sharon , Bohannan Brendan J. M.
Published: December 2006

Very little is known regarding the ecology ofNitrosospirasp. strain AF-like bacteria, a unique group of ammonia oxidizers within theBetaproteobacteria. We studied the response ofNitrosospirasp. strain AF-like ammonia oxidizers to changing environmental conditions by applying molecular methods and physiological measurements to Californian grassland soil manipulated in the laboratory. This soil is naturally high inNitrosospirasp. strain AF-like bacteria relative to the much-better-studiedNitrosospira multiformis-like ammonia-oxidizing bacteria. Increases in temperature, soil moisture, and fertilizer interacted to reduce the relative abundance ofNitrosospirasp. strain AF-like bacteria, although they remained numerically dominant. The overall abundance of ammonia-oxidizing bacteria increased with increasing soil moisture and decreased with increasing temperature. Potential nitrification activity was altered by interactions among temperature, soil moisture, and fertilizer, with activity tending to be higher when soil moisture and temperature were increased. The increase in potential nitrification activity with increased temperature was surprising, given that the overall abundance of ammonia-oxidizing bacteria decreased significantly under these conditions. This observation suggests that (i)Nitrosospirasp. strain AF-like bacteria may respond to increased temperature with an increase in activity, despite a decrease in abundance, or (ii) that potential nitrification activity in these soils may be due to organisms other than bacteria (e.g., archaeal ammonia oxidizers), at least under conditions of increased temperature.
Altered Metabolic Flux due to Deletion of
odhA
causes
l
-Glutamate Overproduction in
Corynebacterium glutamicum
Authors: Asakura Yoko , Kimura Eiichiro , Usuda Yoshihiro , Kawahara Yoshio , Matsui Kazuhiko , Osumi Tsuyoshi , Nakamatsu Tsuyoshi
Published: December 2006

l
-Glutamate overproduction in
Corynebacterium glutamicum
, a biotin auxotroph, is induced by biotin limitation or by treatment with certain fatty acid ester surfactants or with penicillin. We have analyzed the relationship between the inductions, 2-oxoglutarate dehydrogenase complex (ODHC) activity, and
l
-glutamate production. Here we show that a strain deleted for
odhA
and completely lacking ODHC activity produces
l
-glutamate as efficiently as the induced wild type (27.8 mmol/g [dry weight] of cells for the
ohdA
deletion strain compared with only 1.0 mmol/g [dry weight] of cells for the uninduced wild type). This level of production is achieved without any induction or alteration in the fatty acid composition of the cells, showing that
l
-glutamate overproduction can be caused by the change in metabolic flux alone. Interestingly, the
l
-glutamate productivity of the
odhA
-deleted strain is increased about 10% by each of the
l
-glutamate-producing inductions, showing that the change in metabolic flux resulting from the
odhA
deletion and the inductions have additive effects on
l
-glutamate overproduction. Tween 40 was indicated to induce drastic metabolic change leading to
l
-glutamate overproduction in the
odhA
-deleted strain. Furthermore, optimizing the metabolic flux from 2-oxoglutarate to
l
-glutamate by tuning glutamate dehydrogenase activity increased the
l
-glutamate production of the
odhA
-deleted strain.
Colonization, Persistence, and Tissue Tropism ofEscherichia coliO26 in Conventionally Reared Weaned Lambs
Authors: Aktan İlknur , La Ragione Roberto M. , Woodward Martin J.
Published: December 2006

Escherichia coliO26 is recognized as an emerging pathogen associated with disease in both ruminants and humans. Compared to those ofE. coliO157:H7, the shedding pattern and location ofE. coliO26 in the gastrointestinal tract (GIT) of ruminants are poorly understood. In the studies reported here, anstx-negativeE. coliO26 strain of ovine origin was inoculated orally into 6-week-old lambs and the shedding pattern of the O26 strain was monitored by serial bacteriological examination of feces. The location of colonization in the GIT was examined at necropsy at two time points. The numbers of O26 organisms excreted in feces declined from approximately 107to 104CFU per gram of feces by day 7 and continued at this level for a further 3 weeks. Beyond day 30, excretion was from few animals, intermittent, and just above the detection limit. By day 38, all fecal samples were negative, but at necropsy, O26 organisms were recovered from the upper GIT, specifically the ileum. However, no attaching-effacing (AE) lesions were observed. To identify the location ofE. coliO26 within the GIT early after inoculation, two lambs were examined postmortem, 4 days postinoculation. High numbers of O26 organisms were recovered from all GIT sites examined, and ∼109CFU were recovered from 1 gram of ileal tissue from one animal. Despite high numbers of O26 organisms, AE lesions were identified on the mucosa of the ascending colon of only one animal. These data indicate thatE. coliO26 readily colonizes 6-week-old lambs, but the sparseness of AE lesions suggests that O26 is well adapted to this host, and mechanisms other than those dependent upon intimin may play a role in persistence.
Prevalence of
Escherichia coli
O157:H7 in Gallbladders of Beef Cattle
Authors: Reinstein S. , Fox J. T. , Shi X. , Nagaraja T. G.
Published: December 2006

Gallbladders and rectal contents were collected from cattle (
n
= 933) at slaughter to determine whether the gallbladder harbors
Escherichia coli
O157:H7. Both gallbladder mucosal swabs and homogenized mucosal tissues were used for isolation. Only five gallbladders (0.54%) were positive for
E. coli
O157:H7. Fecal prevalence averaged 7.1%; however, none of the cattle that had
E. coli
O157:H7 in the gallbladder was positive for
E. coli
O157:H7 in feces. Therefore, the gallbladder does not appear to be a common site of colonization for
E. coli
O157:H7 in beef cattle.
Transcriptional Activation Domains of the
Candida albicans
Gcn4p and Gal4p Homologs
Authors: Martchenko Mikhail , Levitin Anastasia , Whiteway Malcolm
Published: December 2006

Many putative transcription factors in the pathogenic fungus
Candida albicans
contain sequence similarity to well-defined transcriptional regulators in the budding yeast
Saccharomyces cerevisiae
, but this sequence similarity is often limited to the DNA binding domains of the molecules. The Gcn4p and Gal4p proteins of
Saccharomyces cerevisiae
are highly studied and well-understood eukaryotic transcription factors of the basic leucine zipper (Gcn4p) and C
6
zinc cluster (Gal4p) families;
C. albicans
has
C. albicans
Gcn4p (CaGcn4p) and CaGal4p with DNA binding domains highly similar to their
S. cerevisiae
counterparts. Deletion analysis of the CaGcn4p protein shows that the N′ terminus is needed for transcriptional activation; an 81-amino-acid region is critical for this function, and this domain can be coupled to a
lexA
DNA binding module to provide transcription-activating function in a heterologous reporter system. Deletion analysis of the
C. albicans
Gal4p identifies a C-terminal 73-amino-acid-long transcription-activating domain that also can be transferred to a heterologous reporter construct to direct transcriptional activation. These two transcriptional activation regions show no sequence similarity to the respective domains in their
S. cerevisiae
homologs, and the two
C. albicans
transcription-activating domains themselves show little similarity.
Cryptococcus neoformans
Produces Authentic Prostaglandin E
2
without a Cyclooxygenase
Authors: Erb-Downward John R. , Huffnagle Gary B.
Published: December 2006

Many single-celled eukaryotes produce prostaglandin-like molecules, but these have not been absolutely verified by mass spectrometry. We have isolated, and identified by liquid chromatography-tandem mass spectrometry, authentic prostaglandin E
2
from
Cryptococcus neoformans
. Cyclooxygenase inhibitors did not inhibit prostaglandin synthesis, and the cryptococcal genome lacks a cyclooxygenase homolog. Thus, novel enzymes must exist.
The Anaphase-Promoting Complex/Cyclosome Is Required for Anaphase Progression in Multinucleated
Ashbya gossypii
Cells
Authors: Gladfelter Amy S. , Sustreanu Nicoleta , Hungerbuehler A. Katrin , Voegeli Sylvia , Galati Virginie , Philippsen Peter
Published: December 2006

Regulated protein degradation is essential for eukaryotic cell cycle progression. The anaphase-promoting complex/cyclosome (APC/C) is responsible for the protein destruction required for the initiation of anaphase and the exit from mitosis, including the degradation of securin and B-type cyclins. We initiated a study of the APC/C in the multinucleated, filamentous ascomycete
Ashbya gossypii
to understand the mechanisms underlying the asynchronous mitosis observed in these cells. These experiments were motivated by previous work which demonstrated that the mitotic cyclin AgClb1/2p persists through anaphase, suggesting that the APC/C may not be required for the division cycle in
A. gossypii
. We have now found that the predicted APC/C components AgCdc23p and AgDoc1p and the targeting factors AgCdc20p and AgCdh1p are essential for growth and nuclear division. Mutants lacking any of these factors arrest as germlings with nuclei blocked in mitosis. A likely substrate of the APC/C is the securin homologue AgPds1p, which is present in all nuclei in hyphae except those in anaphase. The destruction box sequence of AgPds1p is required for this timed disappearance. To investigate how the APC/C may function to degrade AgPds1p in only the subset of anaphase nuclei, we localized components and targeting subunits of the APC/C. Remarkably, AgCdc23p, AgDoc1p, and AgCdc16p were found in all nuclei in all cell cycle stages, as were the APC/C targeting factors AgCdc20p and AgCdh1p. These data suggest that the AgAPC/C may be constitutively active across the cell cycle and that proteolysis in these multinucleated cells may be regulated at the level of substrates rather than by the APC/C itself.
Mutations in Alternative Carbon Utilization Pathways in
Candida albicans
Attenuate Virulence and Confer Pleiotropic Phenotypes
Authors: Ramírez Melissa A. , Lorenz Michael C.
Published: December 2006

The interaction between
Candida albicans
and cells of the innate immune system is a key determinant of disease progression. Transcriptional profiling has revealed that
C. albicans
has a complex response to phagocytosis, much of which is similar to carbon starvation. This suggests that nutrient limitation is a significant stress in vivo, and we have shown that glyoxylate cycle mutants are less virulent in mice. To examine whether other aspects of carbon metabolism are important in vivo during an infection, we have constructed strains lacking
FOX2
and
FBP1
, which encode key components of fatty acid β-oxidation and gluconeogenesis, respectively. As expected,
fox2
Δ mutants failed to utilize several fatty acids as carbon sources. Surprisingly, however, these mutants also failed to grow in the presence of several other carbon sources, whose assimilation is independent of β-oxidation, including ethanol and citric acid. Mutants lacking the glyoxylate enzyme ICL1 also had more severe carbon utilization phenotypes than were expected. These results suggest that the regulation of alternative carbon metabolism in
C. albicans
is significantly different from that in other fungi. In vivo,
fox2
Δ mutants show a moderate but significant reduction in virulence in a mouse model of disseminated candidiasis, while disruption of the glyoxylate cycle or gluconeogenesis confers a severe attenuation in this model. These data indicate that
C. albicans
often encounters carbon-poor conditions during growth in the host and that the ability to efficiently utilize multiple nonfermentable carbon sources is a virulence determinant. Consistent with this in vivo requirement,
C. albicans
uniquely regulates carbon metabolism in a more integrated manner than in
Saccharomyces cerevisiae
, such that defects in one part of the machinery have wider impacts than expected. These aspects of alternative carbon metabolism may then be useful as targets for therapeutic intervention.