bluuebunny/crossref_metadata_2025 huggingface dataset:
Least squares parameter estimation methods for material decomposition with energy discriminating detectors
Authors: Le Huy Q. , Molloi Sabee
Published: December 2010

Purpose:

Energy resolving detectors provide more than one spectral measurement in one image acquisition. The purpose of this study is to investigate, with simulation, the ability to decompose four materials using energy discriminating detectors and least squares minimization techniques.

Methods:

Three least squares parameter estimation decomposition techniques were investigated for four‐material breast imaging tasks in the image domain. The first technique treats the voxel as if it consisted of fractions of all the materials. The second method assumes that a voxel primarily contains one material and divides the decomposition process into segmentation and quantification tasks. The third is similar to the second method but a calibration was used. The simulated computed tomography (CT) system consisted of an 80 kVp spectrum and a CdZnTe (CZT) detector that could resolve the x‐ray spectrum into five energy bins. A postmortem breast specimen was imaged with flat panel CT to provide a model for the digital phantoms. Hydroxyapatite (HA) (50, 150, 250, 350, 450, and 550 mg/ml) and iodine (4, 12, 20, 28, 36, and 44 mg/ml) contrast elements were embedded into the glandular region of the phantoms. Calibration phantoms consisted of a 30/70 glandular‐to‐adipose tissue ratio with embedded HA (100, 200, 300, 400, and 500 mg/ml) and iodine (5, 15, 25, 35, and 45 mg/ml). The x‐ray transport process was simulated where the Beer–Lambert law, Poisson process, and CZT absorption efficiency were applied. Qualitative and quantitative evaluations of the decomposition techniques were performed and compared. The effect of breast size was also investigated.

Results:

The first technique decomposed iodine adequately but failed for other materials. The second method separated the materials but was unable to quantify the materials. With the addition of a calibration, the third technique provided good separation and quantification of hydroxyapatite, iodine, glandular, and adipose tissues. Quantification with this technique was accurate with errors of 9.83% and 6.61% for HA and iodine, respectively. Calibration at one point (one breast size) showed increased errors as the mismatch in breast diameters between calibration and measurement increased. A four‐point calibration successfully decomposed breast diameter spanning the entire range from 8 to 20 cm. For a 14 cm breast, errors were reduced from 5.44% to 1.75% and from 6.17% to 3.27% with the multipoint calibration for HA and iodine, respectively.

Conclusions:

The results of the simulation study showed that a CT system based on CZT detectors in conjunction with least squares minimization technique can be used to decompose four materials. The calibrated least squares parameter estimation decomposition technique performed the best, separating and accurately quantifying the concentrations of hydroxyapatite and iodine.
Estimation of three‐dimensional intrinsic dosimetric uncertainties resulting from using deformable image registration for dose mapping
Authors: Salguero Francisco J. , Saleh‐Sayah Nahla K. , Yan Chenyu , Siebers Jeffrey V.
Published: December 2010

Purpose:

This article presents a general procedural framework to assess the point‐by‐point precision in mapped dose associated with the intrinsic uncertainty of a deformable image registration (DIR) for any arbitrary patient.

Methods:

Dose uncertainty is obtained via a three‐step process. In the first step, for each voxel in an imaging pair, a cluster of points is obtained by an iterative DIR procedure. In the second step, the dispersion of the points due to the imprecision of the DIR method is used to compute the spatial uncertainty. Two different ways to quantify the spatial uncertainty are presented in this work. Method A consists of a one‐dimensional analysis of the modules of the position vectors, whereas method B performs a more detailed 3D analysis of the coordinates of the points. In the third step, the resulting spatial uncertainty estimates are used in combination with the mapped dose distribution to compute the point‐by‐point dose standard deviation. The process is demonstrated to estimate the dose uncertainty induced by mapping a 62.6 Gy dose delivered on maximum exhale to maximum inhale of a ten‐phase four‐dimensional lung CT.

Results:

For the demonstration lung image pair, the standard deviation of inconsistency vectors is found to be up to 9.2 mm with a mean of 1.3 mm. This uncertainty results in a maximum estimated dose uncertainty of 29.65 Gy if method A is used and 21.81 Gy for method B. The calculated volume with dose uncertainty above 10.00 Gy is for method A and for method B.

Conclusions:

This procedure represents a useful tool to evaluate the precision of a mapped dose distribution due to the intrinsic DIR uncertainty in a patient. The procedure is flexible, allowing incorporation of alternative intrinsic error models.
On the impact of dose rate variation upon RapidArc® implementation of volumetric modulated arc therapy
Authors: Nicolini Giorgia , Clivio Alessandro , Cozzi Luca , Fogliata Antonella , Vanetti Eugenio
Published: December 2010

Purpose:

A study was carried out to evaluate the robustness and mutual interplay of two variables concurring to generate modulation patterns of the RapidArc® (RapidArc) implementation of volumetric modulated arc therapy. Dose rate (DR) and gantry speed (GS) are free parameters optimized alongside field aperture shape by the RapidArc engine; however, they are limited by machine constraints and mutually compensate in order to deliver the proper MU/deg during the gantry rotation.

Methods:

Four test cases (one geometrical and three clinical) were selected and RapidArc plans were optimized using maximum allowed dose rates from 100 to 600 MU/min. The maximum gantry speed was fixed at 4.8 deg/s. Qualitative analysis of DR and GS patterns from these cases was summarized together with quantitative assessment of delivery parameters. Pretreatment quality assurance measurements and scoring of plan quality aimed to determine whether preferable initial conditions might be identified or the optimization engine might be invariant to those variables and capable of providing adequate plans independently from the limits applied.

Results:

The results of the study were: (i) High dynamic range in MU/deg is achievable across all dose rates by means of gantry speed modulation; (ii) there is a robust compensation mechanism between the two variables; (iii) from a machine delivery point‐of‐view, slightly improved accuracy is achieved when lower DRs are applied; however, this does not have practical consequences since measurements and plan evaluation showed a lack of clinically relevant deviation; and (iv) reduced total treatment time is a major advantage of high DR.

Conclusions:

A trend toward improved plan quality for clinical cases was observed with high DR but cannot be generalized, due to the limited amount of cases investigated and the consequent limited significance of the observed differences. As a minimum benefit, the reduced total treatment time should be considered as well.
Calibration‐free device sizing using an inverse geometry x‐ray system
Authors: Tomkowiak Michael T. , Speidel Michael A. , Raval Amish N. , Van Lysel Michael S.
Published: December 2010

Purpose:

Quantitative coronary angiography (QCA) can be used to support device size selection for cardiovascular interventions. The accuracy of QCA measurements using conventional x‐ray fluoroscopy depends on proper calibration using a reference object and avoiding vessel foreshortening. The authors have developed a novel interventional device sizing method using the inverse geometry scanning‐beam digital x‐ray (SBDX) fluoroscopy system. The proposed method can measure the diameter and length of vessel segments without imaging a reference object and when vessels appear foreshortened.

Methods:

SBDX creates multiple tomosynthetic x‐ray images corresponding to planes through the patient volume. The structures that lie in the plane are in focus and the features above and below the plane are blurred. Three‐dimensional localization of the vessel edges was performed by examining the degree of blurring at each image plane. A 3D vessel centerline was created and used to determine vessel magnification and angulation relative to the image planes. Diameter measurements were performed using a model‐based method and length measurements were calculated from the 3D centerline. Phantom validation was performed by measuring the diameter and length of vessel segments with nominal diameters ranging from 0.5 to 2.8 mm and nominal lengths of 42 mm. The phantoms were imaged at a range of positions between the source and the detector ( relative to isocenter) and with a range of foreshortening angles (0°–75°).

Results:

Changes in vessel phantom position created magnifications ranging from 87% to 118% relative to isocenter magnification. Average diameter errors were less than 0.15 mm. Average length measurements were within 1% (0.3 mm) of the true length. No trends were observed between measurement accuracy and magnification. Changes in vessel phantom orientation resulted in decreased apparent length down to 28% of the original nonforeshortened length. Average diameter errors were less than 0.25 mm across all vessel angulations; errors were less than 0.1 mm for smaller diameter vessels and low to moderate vessel angles. Diameter errors increased with true diameter and vessel angle relative to the image plane. Average length measurement errors were also within 1% (0.3 mm) for each angulation.

Conclusions:

Tomosynthetic imaging with SBDX can accurately measure dimensions of vessels in various magnifications and angulations without calibration. This method may be more accurate and convenient than conventional QCA techniques.
Feasibility of using cone‐beam CT to verify and reposition the optically guided target localization of linear accelerator based stereotactic radiosurgery
Authors: Zhu Jingeng
Published: December 2010

Purpose:

The optically guided target localization had been developed for linear accelerator based stereotactic radiosurgery (SRS). Unlike the traditional laser localization, the optical guided target localization utilizes a digital system to position patient. Although the system has been proven accurate and robust, it takes away the capability of physicist to directly double check the target position prior to irradiation. Any error from system calibration, data transformation, or head ring position maintenance will not be caught. The purpose of this work is to investigate the possibility of using cone‐beam CT (CBCT) to double check the optically guided SRS target localization and reposition the patient.

Methods:

A SRS quality assurance (QA) phantom was used in the study. The phantom mounted with SRS head frame was scanned by computer tomography (CT) and planned according to the SRS radiation treatment planning process. A target isocenter is defined and transferred to the optically guided target localization system. The phantom was then transported to the linear accelerator room and localized at the initial position agreed by the optically guided target localization system and the CBCT system. Tests were conducted by moving/rotating the phantom to a set of preset offsets and taking CBCT images. Shifts detected by CBCT were compared with the preset offsets. Agreements between them were studied to see how well the CBCT was in discovering the optically guided target localization error.

Results:

Experiment results demonstrated good agreement between the CBCT detected phantom shift and the preset offset, when the offset is above 1 mm shift or 0.2 degree rotation. Offset less than 1 mm shift or 0.2 degree rotation was not detectable by CBCT.

Conclusions:

The study concludes that the CBCT is able to discover the optically guided target localization error due to the system calibration or had ring migration. It is a valuable second check tool for SRS target localization quality assurance. The accuracy of CBCT in estimating patient positioning deviation satisfies the SRS procedures with generous tumor size and margin that can tolerate 1 mm or 0.2 degree accuracy. This avoids sending patient home without treatment. CBCT can be neither used as a primary SRS target localization nor can it be used to reposition the patient that cannot tolerate 1 mm shift or 0.2 degree rotation.
Dosimetry revisited for the HDR brachytherapy source model mHDR‐v2
Authors: Granero Domingo , Vijande Javier , Ballester Facundo , Rivard Mark J.
Published: December 2010

Purpose:

Recently, the manufacturer of the HDR mHDR‐v2 brachytherapy source reported small design changes (referred to herein as mHDR‐v2r) that are within the manufacturing tolerances but may alter the existing dosimetric data for this source. This study aimed to (1) check whether these changes affect the existing dosimetric data published for this source; (2) obtain new dosimetric data in close proximity to the source, including the contributions from electrons and considering the absence of electronic equilibrium; and (3) obtain scatter dose components for collapsed cone treatment planning system implementation.

Methods:

Three different Monte Carlo (MC) radiation transport codes were used:MCNP5, PENELOPE2008, and GEANT4. The source was centrally positioned in a 40 cm radius water phantom. Absorbed dose and collision kerma were obtained using 0.1 mm (0.5 mm) thick voxels to provide high‐resolution dosimetry near (far from) the source. Dose‐rate distributions obtained with the three MC codes were compared.

Results:

Simulations of mHDR‐v2 and mHDR‐v2r designs performed with three radiation transport codes showed agreement typically within 0.2% for. Dosimetric contributions from source electrons were significant for . The dose‐rate constant and radial dose function were similar to those from previous MC studies of the mHDR‐v2 design. The 2D anisotropy function also coincided with that of the mHDR‐v2 design for . Detailed results of dose distributions and scatter components are presented for the modified source design.

Conclusions:

Comparison of these results to prior MC studies showed agreement typically within 0.5% for. If dosimetric data for are not needed, dosimetric results from the prior MC studies will be adequate.
Kinetics of Hydrothermal Inactivation of Endotoxins
Authors: Li Lixiong , Wilbur Chris L. , Mintz Kathryn L.
Published: December 2010

A kinetic model was established for the inactivation of endotoxins in water at temperatures ranging from 210°C to 270°C and a pressure of 6.2 × 10
6
Pa. Data were generated using a bench scale continuous-flow reactor system to process feed water spiked with endotoxin standard (
Escherichia coli
O113:H10). Product water samples were collected and quantified by the
Limulus
amebocyte lysate assay. At 250°C, 5-log endotoxin inactivation was achieved in about 1 s of exposure, followed by a lower inactivation rate. This non-log-linear pattern is similar to reported trends in microbial survival curves. Predictions and parameters of several non-log-linear models are presented. In the fast-reaction zone (3- to 5-log reduction), the Arrhenius rate constant fits well at temperatures ranging from 120°C to 250°C on the basis of data from this work and the literature. Both biphasic and modified Weibull models are comparable to account for both the high and low rates of inactivation in terms of prediction accuracy and the number of parameters used. A unified representation of thermal resistance curves for a 3-log reduction and a 3
D
value associated with endotoxin inactivation and microbial survival, respectively, is presented.
Metabolic Engineering of
Saccharomyces cerevisiae
for Production of Eicosapentaenoic Acid, Using a Novel Δ5-Desaturase from
Paramecium tetraurelia
Authors: Tavares Sabina , Grotkjær Thomas , Obsen Thomas , Haslam Richard P. , Napier Johnathan A. , Gunnarsson Nina
Published: December 2010

Very-long-chain polyunsaturated fatty acids, such as arachidonic acid (ARA), eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA), have well-documented importance in human health and nutrition. Sustainable production in robust host organisms that do not synthesize them naturally requires the coordinated expression of several heterologous desaturases and elongases. In the present study we show production of EPA in
Saccharomyces cerevisiae
using glucose as the sole carbon source through expression of five heterologous fatty acid desaturases and an elongase. Novel Δ5-desaturases from the ciliate protozoan
Paramecium tetraurelia
and from the microalgae
Ostreococcus tauri
and
Ostreococcus lucimarinus
were identified via a BLAST search, and their substrate preferences and desaturation efficiencies were assayed in a yeast strain producing the ω6 and ω3 fatty acid substrates for Δ5-desaturation. The Δ5-desaturase from
P. tetraurelia
was up-to-2-fold more efficient than the microalgal desaturases and was also more efficient than Δ5-desaturases from
Mortierella alpina
and
Leishmania major. In vivo
investigation of acyl carrier substrate specificities showed that the Δ5-desaturases from
P. tetraurelia
,
O. lucimarinus
,
O. tauri
, and
M. alpina
are promiscuous toward the acyl carrier substrate but prefer phospholipid-bound substrates. In contrast, the Δ5-desaturase from
L. major
showed no activity on phospholipid-bound substrate and thus appears to be an exclusively acyl coenzyme A-dependent desaturase.
Comparison of
Arcobacter
Isolation Methods, and Diversity of
Arcobacter
spp. in Cheshire, United Kingdom
Authors: Merga J. Y. , Leatherbarrow A. J. H. , Winstanley C. , Bennett M. , Hart C. A. , Miller W. G. , Williams N. J.
Published: December 2010

The aims of this study were, firstly, to compare five published methods for the isolation of
Arcobacter
spp. from animal feces in order to determine the most sensitive and specific method. Second, we analyzed the resulting isolates by multilocus sequence typing (MLST) in order to investigate the diversity of the isolates recovered. Third, we investigated the ability to recover
Arcobacter
spp. from frozen fecal samples. Seventy-seven fecal samples from cattle, sheep, and badgers were subjected to five isolation methods, based on published methods for the isolation of
Arcobacter
and
Campylobacter
spp. Thirty-nine
Arcobacter butzleri
isolates were analyzed using a multilocus sequence typing scheme. The survival of
Arcobacter
spp. in frozen samples was investigated by freezing the fecal samples at −80°C for 7 days and then applying the same five isolation methods. The most sensitive and specific method used an
Arcobacter
-specific broth in conjunction with modified charcoal cefoperazone deoxycholate agar (mCCDA) with added antibiotics. Freezing of fecal samples led to a reduction in the recovery of
Arcobacter
spp. by approximately 50%. The 39 allelic profiles obtained by MLST could be divided into 11 sequence types (STs). We have identified the most sensitive and specific method for the isolation of
Arcobacter
spp. from animal feces and demonstrated that the freezing of fecal samples prior to isolation reduces arcobacter recovery. MLST analysis of the isolates revealed a high level of diversity.
Biochemical Characteristics of the Novel Haloalkane Dehalogenase DatA, Isolated from the Plant Pathogen
Agrobacterium tumefaciens
C58
Authors: Hasan Khomaini , Fortova Andrea , Koudelakova Tana , Chaloupkova Radka , Ishitsuka Mayuko , Nagata Yuji , Damborsky Jiri , Prokop Zbynek
Published: December 2010

We report the biochemical characterization of a novel haloalkane dehalogenase, DatA, isolated from the plant pathogen
Agrobacterium tumefaciens
C58. DatA possesses a peculiar pair of halide-stabilizing residues, Asn-Tyr, which have not been reported to play this role in other known haloalkane dehalogenases. DatA has a number of other unique characteristics, including substrate-dependent and cooperative kinetics, a dimeric structure, and excellent enantioselectivity toward racemic mixtures of chiral brominated alkanes and esters.
Saccharomyces cerevisiae
Genome-Wide Mutant Screen for Sensitivity to 2,4-Diacetylphloroglucinol, an Antibiotic Produced by
Pseudomonas fluorescens
Authors: Kwak Youn-Sig , Han Sangjo , Thomashow Linda S. , Rice Jennifer T. , Paulitz Timothy C. , Kim Dongsup , Weller David M.
Published: December 2010

2,4-Diacetylphloroglucinol (2,4-DAPG), an antibiotic produced by
Pseudomonas fluorescens
, has broad-spectrum antibiotic activity, inhibiting organisms ranging from viruses, bacteria, and fungi to higher plants and mammalian cells. The biosynthesis and regulation of 2,4-DAPG in
P. fluorescens
are well described, but the mode of action against target organisms is poorly understood. As a first step to elucidate the mechanism, we screened a deletion library of
Saccharomyces cerevisiae
in broth and agar medium supplemented with 2,4-DAPG. We identified 231 mutants that showed increased sensitivity to 2,4-DAPG under both conditions, including 22 multidrug resistance-related mutants. Three major physiological functions correlated with an increase in sensitivity to 2,4-DAPG: membrane function, reactive oxygen regulation, and cell homeostasis. Physiological studies with wild-type yeast validated the results of the mutant screens. The chemical-genetic fitness profile of 2,4-DAPG resembled those of menthol, sodium azide, and hydrogen peroxide determined in previous high-throughput screening studies. Collectively, these findings indicate that 2,4-DAPG acts on multiple basic cellular processes.
Characterization of the Dictyostelium Homolog of Chromatin Binding Protein DET1 Suggests a Conserved Pathway Regulating Cell Type Specification and Developmental Plasticity
Authors: Dubin Manu J. , Kasten Sonja , Nellen Wolfgang
Published: December 2010

DET1 (De-etiolated 1) is a chromatin binding protein involved in developmental regulation in both plants and animals. DET1 is largely restricted to multicellular eukaryotes, and here we report the characterization of a DET1 homolog from the social amoeba
Dictyostelium discoideum
. As in other species,
Dictyostelium
DET1 is nuclear localized. In contrast to other species, where it is an essential protein, loss of DET1 is nonlethal in
Dictyostelium
, although viability is significantly reduced. The phenotype of the
det1
−
mutant is highly pleiotropic and results in a large degree of heterogeneity in developmental parameters. Loss of DET1 results in delayed and abnormal development with enlarged aggregation territories. Mutant slugs displayed cell type patterning with a bias toward the prestalk pathway. A number of DET1-interacting proteins are conserved in
Dictyostelium
, and the apparently conserved role of DET1 in regulatory pathways involving the bZIP transcription factors DimB, c-Jun, and HY5 suggests a highly conserved mechanism regulating development in multicellular eukaryotes. While the mechanism by which DET1 functions is unclear, it appears that it has a key role in regulation of developmental plasticity and integration of information on environmental conditions into the developmental program of an organism.
Molecular Characterization of Propolis-Induced Cell Death in Saccharomyces cerevisiae
Authors: de Castro Patrícia Alves , Savoldi Marcela , Bonatto Diego , Barros Mário Henrique , Goldman Maria Helena S. , Berretta Andresa A. , Goldman Gustavo Henrique
Published: December 2010

Propolis, a natural product of plant resins, is used by the bees to seal holes in their honeycombs and protect the hive entrance. However, propolis has also been used in folk medicine for centuries. Here, we apply the power ofSaccharomyces cerevisiaeas a model organism for studies of genetics, cell biology, and genomics to determine how propolis affects fungi at the cellular level. Propolis is able to induce an apoptosis cell death response. However, increased exposure to propolis provides a corresponding increase in the necrosis response. We showed that cytochromecbut not endonuclease G (Nuc1p) is involved in propolis-mediated cell death inS. cerevisiae. We also observed that the metacaspaseYCA1gene is important for propolis-mediated cell death. To elucidate the gene functions that may be required for propolis sensitivity in eukaryotes, the full collection of about 4,800 haploidS. cerevisiaedeletion strains was screened for propolis sensitivity. We were able to identify 138 deletion strains that have different degrees of propolis sensitivity compared to the corresponding wild-type strains. Systems biology revealed enrichment for genes involved in the mitochondrial electron transport chain, vacuolar acidification, negative regulation of transcription from RNA polymerase II promoter, regulation of macroautophagy associated with protein targeting to vacuoles, and cellular response to starvation. Validation studies indicated that propolis sensitivity is dependent on the mitochondrial function and that vacuolar acidification and autophagy are important for yeast cell death caused by propolis.
Control of Lipopolysaccharide Biosynthesis by FtsH-Mediated Proteolysis of LpxC Is Conserved in Enterobacteria but Not in All Gram-Negative Bacteria
Authors: Langklotz Sina , Schäkermann Michael , Narberhaus Franz
Published: December 2010

Despite the essential function of lipopolysaccharides (LPS) in Gram-negative bacteria, it is largely unknown how the exact amount of this molecule in the outer membrane is controlled. The first committed step in LPS biosynthesis is catalyzed by the LpxC enzyme. In
Escherichia coli
, the cellular concentration of LpxC is adjusted by the only essential protease in this organism, the membrane-anchored metalloprotease FtsH. Turnover of
E. coli
LpxC requires a length- and sequence-specific C-terminal degradation signal. LpxC proteins from
Salmonella
,
Yersinia
, and
Vibrio
species carry similar C-terminal ends and, like the
E. coli
enzyme, were degraded by FtsH. Although LpxC proteins are highly conserved in Gram-negative bacteria, there are striking differences in their C termini. The
Aquifex aeolicus
enzyme, which is devoid of the C-terminal extension, was stable in
E. coli
, whereas LpxC from the alphaproteobacteria
Agrobacterium tumefaciens
and
Rhodobacter capsulatus
was degraded by the Lon protease. Proteolysis of the
A. tumefaciens
protein required the C-terminal end of LpxC. High stability of
Pseudomonas aeruginosa
LpxC in
E. coli
and
P. aeruginosa
suggested that
Pseudomonas
uses a proteolysis-independent strategy to control its LPS content. The differences in LpxC turnover along with previously reported differences in susceptibility against antimicrobial compounds have important implications for the potential of LpxC as a drug target.
Exploring the Active Site of the Tungsten, Iron-Sulfur Enzyme Acetylene Hydratase
Authors: tenBrink Felix , Schink Bernhard , Kroneck Peter M. H.
Published: December 2010

The soluble tungsten, iron-sulfur enzyme acetylene hydratase (AH) from mesophilic
Pelobacter acetylenicus
is a member of the dimethyl sulfoxide (DMSO) reductase family. It stands out from its class as it catalyzes a nonredox reaction, the addition of H
2
O to acetylene (H—C≡C—H) to form acetaldehyde (CH
3
CHO). Caught in its active W(IV) state, the high-resolution three-dimensional structure of AH offers an excellent starting point to tackle its unique chemistry and to identify catalytic amino acid residues within the active site cavity: Asp13 close to W(IV) coordinated to two molybdopterin-guanosine-dinucleotide ligands, Lys48 which couples the [4Fe-4S] cluster to the W site, and Ile142 as part of a hydrophobic ring at the end of the substrate access channel designed to accommodate the substrate acetylene. A protocol was developed to express AH in
Escherichia coli
and to produce active-site variants which were characterized with regard to activity and occupancy of the tungsten and iron-sulfur centers. By this means, fusion of the N-terminal chaperone binding site of the
E. coli
nitrate reductase NarG to the AH gene improved the yield and activity of AH and its variants significantly. Results from site-directed mutagenesis of three key residues, Asp13, Lys48, and Ile142, document their important role in catalysis of this unusual tungsten enzyme.
Regulation of Acid Resistance by Connectors of Two-Component Signal Transduction Systems in
Escherichia coli
Authors: Eguchi Yoko , Ishii Eiji , Hata Kensuke , Utsumi Ryutaro
Published: December 2010

Two-component signal transduction systems (TCSs), utilized extensively by bacteria and archaea, are involved in the rapid adaptation of the organisms to fluctuating environments. A typical TCS transduces the signal by a phosphorelay between the sensor histidine kinase and its cognate response regulator. Recently, small-sized proteins that link TCSs have been reported and are called “connectors.” Their physiological roles, however, have remained elusive. SafA (

s

ensor

a

ssociating

f

actor A) (formerly B1500), a small (65-amino-acid [65-aa]) membrane protein, is among such connectors and links
Escherichia coli
TCSs EvgS/EvgA and PhoQ/PhoP. Since the activation of the EvgS/EvgA system induces acid resistance, we examined whether the SafA-activated PhoQ/PhoP system is also involved in the acid resistance induced by EvgS/EvgA. Using a constitutively active
evgS1
mutant for the activation of EvgS/EvgA, we found that SafA, PhoQ, and PhoP all contributed to the acid resistance phenotype. Moreover, EvgS/EvgA activation resulted in the accumulation of cellular RpoS in the exponential-phase cells in a SafA-, PhoQ-, and PhoP-dependent manner. This RpoS accumulation was caused by another connector, IraM, expression of which was induced by the activation of the PhoQ/PhoP system, thus preventing RpoS degradation by trapping response regulator RssB. Acid resistance assays demonstrated that IraM also participated in the EvgS/EvgA-induced acid resistance. Therefore, we propose a model of a signal transduction cascade proceeding from EvgS/EvgA to PhoQ/PhoP and then to RssB (connected by SafA and IraM) and discuss its contribution to the acid resistance phenotype.
Replisome Trafficking in Growing Vegetative Hyphae ofStreptomyces coelicolorA3(2)
Authors: Wolánski Marcin , Wali Rashmi , Tilley Emma , Jakimowicz Dagmara , Zakrzewska-Czerwińska Jolanta , Herron Paul
Published: December 2010

We observed movies of replisome trafficking duringStreptomyces coelicolorgrowth. A replisome(s) in the spore served as a replication center(s) until hyphae reached a certain length, when a tip-proximal replisome formed and moved at a fixed distance behind the tip at a speed equivalent to the extension rate of the tip.
Effect of daily noise exposure monitoring on annual rates of hearing loss in industrial workers
Authors: Rabinowitz Peter M , Galusha Deron , Kirsche Sharon R , Cullen Mark R , Slade Martin D , Dixon-Ernst Christine
Published: December 2010

Objectives

Occupational noise-induced hearing loss (NIHL) is prevalent, yet evidence on the effectiveness of preventive interventions is lacking. The effectiveness of a new technology allowing workers to monitor daily at-ear noise exposure was analysed.

Methods

Workers in the hearing conservation program of an aluminium smelter were recruited because of accelerated rates of hearing loss. The intervention consisted of daily monitoring of at-ear noise exposure and regular feedback on exposures from supervisors. The annual rate of change in high frequency hearing average at 2, 3 and 4 KHz before intervention (2000–2004) and 4 years after intervention (2006–2009) was determined. Annual rates of loss were compared between 78 intervention subjects and 234 controls in other company smelters matched for age, gender and high frequency hearing threshold level in 2005.

Results

Individuals monitoring daily noise exposure experienced on average no further worsening of high frequency hearing (average rate of hearing change at 2, 3 and 4 KHz=–0.5 dB/year). Matched controls also showed decelerating hearing loss, the difference in rates between the two groups being significant (p<0.0001). Analysis of a subset of intervention subjects matched to controls for initial rate of hearing loss showed a similar trend but the difference was not statistically significant (p=0.06).

Conclusion

Monitoring daily occupational noise exposure inside hearing protection with ongoing administrative feedback apparently reduces the risk of occupational NIHL in industrial workers. Longer follow-up of these workers will help determine the significance of the intervention effect. Intervention studies for the prevention of NIHL need to include appropriate control groups.
The contribution of major risk factors and job strain to occupational class differences in coronary heart disease incidence: the MONICA Brianza and PAMELA population-based cohorts
Authors: Ferrario Marco M , Veronesi Giovanni , Chambless Lloyd E , Sega Roberto , Fornari Carla , Bonzini Matteo , Cesana Giancarlo
Published: December 2010

Objectives

We investigated the contribution of major coronary heart disease (CHD) risk factors and job strain to occupational class differences in CHD incidence in a pooled-cohort prospective study in northern Italy.

Methods

2964 men aged 25–74 from four northern Italian population-based cohorts were investigated at baseline and followed for first fatal or non-fatal CHD event (171 events). Standardised procedures were used for baseline risk factor measurements, follow-up and validation of CHD events. Four occupational classes were derived from the Erikson–Goldthorpe–Portocarero social class scheme: higher and lower professionals and administrators, non-manual workers, skilled and unskilled manual workers, and the self-employed. HRs were estimated with Cox models.

Results

Among CHD-free subjects, with non-manual workers as the reference group, age-adjusted excess risks were found for professionals and administrators (+84%, p=0.02), the self-employed (+72%, p=0.04) and manual workers (+63%, p=0.04). The relationship was consistent across different CHD diagnostic categories. Adjusting for major risk factors only slightly reduced the reported excess risks. In a sub-sample of currently employed subjects, adjusting for major risk factors, sport physical activity and job strain reduced the excess risk for manual workers (relative change = −71.4%) but did not substantially modify the excess risks of professionals and administrators and the self-employed.

Conclusions

In our study, we found higher CHD incidence rates for manual workers, professionals and administrators, and the self-employed, compared to non-manual workers. When the entire spectrum of job categories is considered, the job strain model helped explain the CHD excess risk for manual workers but not for other occupational classes.
Diagnostic performance of PCR and ELISA on blood and milk samples and serological survey for small ruminant lentiviruses in central Spain
Authors: Barquero N. , Arjona A. , Domenech A. , Toural C. , de las Heras A. , Fernández‐Garayzabal J. F. , Ruiz‐Santa Quiteria J. A. , Gomez‐Lucia E.
Published: January 2011

The diagnostic performance of an ELISA for the detection of antibodies to the small ruminant lentiviruses (SRLVs) maedi‐visna virus and caprine arthritis‐encephalitis virus in milk and corresponding blood samples was evaluated in 50 sheep. The agreement between ELISA results in blood and milk was 90 per cent, and the κ value was 0.79. In addition, a serological survey in the central zone of Spain was performed using milk samples from 413 animals (250 sheep and 163 goats) from 12 flocks/herds. All flocks/herds had some animals that were positive for SRLV. Among the animals, 60.0 per cent of the sheep and 8.0 per cent of the goats tested were seropositive. Each sample was also tested using a PCR technique, which increased the percentage of positive animals detected. Using a combination of ELISA and PCR gave a total of 72.2 per cent of sheep and 28.8 per cent of goats positive for SRLV.
Theoretical investigation of second-order nonlinear optical response — Hexamolybdate as a superior donor over metal carbonyl complexes in the D–π–A model
Authors: Song Ping , Liu Chunguang , Guan Wei , Yan Likai , Sun Xiaolei , Yao Chan , Su Zhongmin
Published: January 2011

Density functional theory (DFT) calculations were carried out to investigate the nonlinear optical (NLO) response for the donor-conjugated bridge-accepter (D–π–A) model of p-nitroaniline (PNA) – hexamolybdate derivatives and PNA–metal–carbonyl complexes. The bond length alternation (BLA) values decrease with lengthening of the π-conjugated bridge, especially for PNA–hexamolybdate derivatives, which dramatically enhances the NLO response. In addition, the introduction of Mo≡N in PNA–hexamolybdate derivatives is expected to provide a better electron transition channel, consequently generating lower BLA values and an outstanding NLO response compared with PNA–metal–carbonyl complexes. It is shown that the hexamolybdate acts as an electron donor when incorporating metal–carbonyl complexes into one molecule. All these behaviors reflect the superiority of hexamolybdate as a donor moiety in the D–π–A model for the design of potential NLO materials.
Synthesis of a new chiral auxiliary — Non-cross-linked polystyrene-supported oxazolidine-2-selone
Authors: He Xiping , Li Jia , Lu Cuifen , Chen Zuxin , Yang Guichun
Published: January 2011

A new chiral auxiliary, non-cross-linked polystyrene-supported oxazolidine-2-selone was synthesized using N-Boc-l-tyrosine ethyl ester as starting material. The structure of the target product was detected by IR, NMR, elemental analysis, and the spectrum result was consistent with the molecular structure.
AN ONTOLOGY-BASED MODEL FOR REPRESENTING IMAGE PROCESSING APPLICATION OBJECTIVES
Authors: CLOUARD RÉGIS , RENOUF ARNAUD , REVENU MARINETTE
Published: January 2011

This paper investigates the types of information that are necessary and sufficient to design and evaluate image processing software programs, and proposes a representation of these information elements using a computational language performable by vision systems and understandable by experts. The language is built upon a formulation model which distinguishes the specification of a goal and the definition of an input image class. Goals are stated in terms of tasks together with result samples. Image classes are defined by both linguistic and iconic descriptions. The model is implemented as an OWL domain ontology which provides the primitives for the formulation language.
A SEMI-GENERAL METHOD TO SOLVE THE COMBINATORIAL OPTIMIZATION PROBLEMS BASED ON NANOCOMPUTING
Authors: DAREHMIRAKI MAJID
Published: January 2011

Nanocomputing describes computing that uses nanoscale devices. It is reasonable to search for nanoscale particles, such as molecules, that do not require difficult fabrication steps. DNA is recognized as a nanomaterial, not as a biological material, in the research field of nanotechnology. This paper proposes a semi-general method to solve combinatorial optimization problems based on DNA computing. It is obvious that the DNA molecule is one of the most promising functional nanomaterials. However, the application of DNA molecules is still under study because of the big gap that exists between theory and practice.
STRUCTURAL AND MORPHOLOGICAL CHARACTERIZATION OF GOLD NANOPARTICLES BY TEM AND DIGITAL CIS TECHNIQUE
Authors: EL-DALY A. A.
Published: January 2011

In this paper, we report a convenient and informative procedure for detecting the morphology and surface structure of individual gold nanocrystals using digital Crystal Image Software (CIS) processing of transmission electron microscopy (TEM) image, which comprises coalescence phenomena of these nanoparticles. The results show that the internal structure of Au nanoparticles has a core of gold atoms arranged as a Marks decahedron, surrounded by additional gold–organic compound layers forming a rigid surface layer, and its outer layer comprises four staple motif bridge molecules that resemble handles, formed an unusual pattern. The obtained results improved our understanding of the basics of the coalescence phenomena such as the driving mechanisms acting at different particle sizes. However, these discrete natures of the nanoparticles will assist in the understanding of principles of nanocore assembly and opens a new window for nanoparticles chemistry.
Real-time performance analysis of multiprocessor systems with shared memory
Authors: Schliecker Simon , Ernst Rolf
Published: January 2011

Predicting timing behavior is key to reliable real-time system design and verification, but becomes increasingly difficult for current multiprocessor systems on chip. The integration of formerly separate functionality into a single multicore system introduces new intercore timing dependencies resulting from the common use of the now shared resources. This feedback of system timing on local timing makes traditional performance analysis approaches inappropriate.

This article presents a general methodology to model the shared resource traffic and consider its effect on the local task execution. The aggregate busy time captures the timing of multiple accesses to a shared memory far better than the traditional models that focus on the timing of individual events. An iterative approach is proposed to tackle the analysis dependencies that exist in systems with event-driven task activation and dynamic resource arbitration.
Collective Hydrodynamics of Swimming Microorganisms: Living Fluids
Authors: Koch Donald L. , Subramanian Ganesh
Published: January 2011

Experimental observations indicate that, at sufficiently high cell densities, swimming bacteria exhibit coordinated motions on length scales (10 to 100 μm) that are large compared with the size of an individual cell but too small to yield significant gravitational or inertial effects. We discuss simulations of hydrodynamically interacting self-propelled particles as well as stability analyses and numerical solutions of averaged equations of motion for low Reynolds number swimmers. It has been found that spontaneous motions can arise in such systems from the coupling between the stresses the bacteria induce in the fluid as they swim and the rotation of the bacteria due to the resulting fluid velocity disturbances.
Discrete Conservation Properties of Unstructured Mesh Schemes
Authors: Perot J. Blair
Published: January 2011

Numerical methods with discrete conservation statements are useful because they cannot produce solutions that violate important physical constraints. A large number of numerical methods used in computational fluid dynamics (CFD) have either global or local conservation statements for some of the primary unknowns of the method. This review suggests that local conservation of primary unknowns often follows from global conservation of those quantities. Secondary conservation involves the conservation of derived quantities, such as kinetic energy, entropy, and vorticity, which are not directly unknowns of the numerical system. Secondary conservation can further improve physical fidelity of a numerical solution, but it is typically much harder to achieve. We consider current approaches to secondary conservation and techniques used outside of CFD that are potentially related. Finally, the review concludes with a discussion of how secondary conservation properties might be included automatically.
Numerical Methods for High-Speed Flows
Authors: Pirozzoli Sergio
Published: January 2011

We review numerical methods for direct numerical simulation (DNS) and large-eddy simulation (LES) of turbulent compressible flow in the presence of shock waves. Ideal numerical methods should be accurate and free from numerical dissipation in smooth parts of the flow, and at the same time they must robustly capture shock waves without significant Gibbs ringing, which may lead to nonlinear instability. Adapting to these conflicting goals leads to the design of strongly nonlinear numerical schemes that depend on the geometrical properties of the solution. For low-dissipation methods for smooth flows, numerical stability can be based on physical conservation principles for kinetic energy and/or entropy. Shock-capturing requires the addition of artificial dissipation, in more or less explicit form, as a surrogate for physical viscosity, to obtain nonoscillatory transitions. Methods suitable for both smooth and shocked flows are discussed, and the potential for hybridization is highlighted. Examples of the application of advanced algorithms to DNS/LES of turbulent, compressible flows are presented.
Shock-Bubble Interactions
Authors: Ranjan Devesh , Oakley Jason , Bonazza Riccardo
Published: January 2011

When a shock wave propagates through a medium of nonuniform thermodynamic properties, several processes occur simultaneously that alter the geometry of the shock wave and the thermodynamic state of the medium. These include shock compression and acceleration of the medium, refraction of the shock, and vorticity generation within the medium. The interaction of a shock wave with a cylinder or a sphere (both referred to as a bubble in this review) is the simplest configuration in which all these processes take place and can be studied in detail. Shock acceleration leads to an initial compression and distortion of the bubble, followed by the formation of a vortex pair in the two-dimensional (2D) case and a vortex ring in the 3D case. At later times, for appropriate combinations of the incident shock strength and density contrast between the bubble and ambient materials, secondary vortices are formed, mass is stripped away from the original bubble, and mixing of the bubble and ambient fluids occurs.
Transition and Stability of High-Speed Boundary Layers
Authors: Fedorov Alexander
Published: January 2011

This article reviews stability and laminar-turbulent transition in high-speed boundary-layer flows, emphasizing qualitative features of the disturbance spectrum leading to new mechanisms of receptivity and instability. It is shown that the extension of subsonic and low-supersonic stability concepts and transition prediction methods to hypersonic speeds is not straightforward. The discussion focuses on theoretical models providing insights into the physics of instability and helping make proper decisions on transition control strategies.
Differential effects of mineralocorticoid blockade on the hypothalamo-pituitary-adrenal axis in pregnant and nonpregnant ewes
Authors: Lingis Melissa , Richards Elaine M. , Keller-Wood Maureen
Published: January 2011

During pregnancy, plasma ACTH and cortisol are chronically increased; this appears to occur through a reset of hypothalamo-pituitary-adrenal (HPA) activity. We have hypothesized that differences in mineralocorticoid receptor activity in pregnancy may alter feedback inhibition of the HPA axis. We tested the effect of MR antagonism in pregnant and nonpregnant ewes infused for 4 h with saline or the MR antagonist canrenoate. Pregnancy significantly increased plasma ACTH, cortisol, angiotensin II, and aldosterone. Infusion of canrenoate increased plasma ACTH, cortisol, and aldosterone in both pregnant and nonpregnant ewes; however, the temporal pattern of these responses differed between these two reproductive states. In nonpregnant ewes, plasma ACTH and cortisol transiently increased at 1 h of infusion, whereas in pregnant ewes the levels gradually increased and were significantly elevated from 2 to 4 h of infusion. MR blockade increased plasma aldosterone from 2 to 4 h in the pregnant ewes but only at 4 h in the nonpregnant ewes. In both pregnant and nonpregnant ewes, the increase in plasma aldosterone was significantly related to the timing and magnitude of the increase in plasma potassium. The results indicate a differential effect of MR activity in pregnant and nonpregnant ewes and suggest that the slow changes in ACTH, cortisol, and aldosterone are likely to be related to blockade of MR effects in the kidney rather than to effects of MR blockade in hippocampus or hypothalamus.