bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACTPropolis, 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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACTWe 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.