bluuebunny/crossref_metadata_2025_split huggingface dataset:
Anatomical background and generalized detectability in tomosynthesis and cone‐beam CT
Authors: Gang G. J. , Tward D. J. , Lee J. , Siewerdsen J. H. 
Published: April 2010

Purpose:Anatomical background presents a major impediment to detectability in 2D radiography as well as 3D tomosynthesis and cone‐beam CT (CBCT). This article incorporates theoretical and experimental analysis of anatomical background “noise” in cascaded systems analysis of 2D and 3D imaging performance to yield “generalized” metrics of noise‐equivalent quanta (NEQ) and detectability index as a function of the orbital extent of the (circular arc) source‐detector orbit.Methods:A physical phantom was designed based on principles of fractal self‐similarity to exhibit power‐law spectral density comparable to various anatomical sites (e.g., breast and lung). Background power spectra were computed as a function of source‐detector orbital extent, including tomosynthesis and CBCT ( to 360°) under two acquisition schemes: (1) Constant angular separation between projections (variable dose) and (2) constant total number of projections (constant dose). The resulting was incorporated in the generalized NEQ, and detectability index was computed from 3D cascaded systems analysis for a variety of imaging tasks.Results:The phantom yielded power‐law spectra within the expected spatial frequency range, quantifying the dependence of clutter magnitude and correlation with increasing tomosynthesis angle. Incorporation of in the 3D NEQ provided a useful framework for analyzing the tradeoffs among anatomical, quantum, and electronic noise with dose and orbital extent. Distinct implications are posed for breast and chest tomosynthesis imaging system design—applications varying significantly in and , and imaging task and, therefore, in optimal selection of orbital extent, number of projections, and dose. For example, low‐frequency tasks (e.g., soft‐tissue masses or nodules) tend to benefit from larger orbital extent and more fully 3D tomographic imaging, whereas high‐frequency tasks (e.g., microcalcifications) require careful, application‐specific selection of orbital extent and number of projections to minimize negative effects of quantum and electronic noise.Conclusions:The complex tradeoffs among anatomical background, quantum noise, and electronic noise in projection imaging, tomosynthesis, and CBCT can be described by generalized cascaded systems analysis, providing a useful framework for system design and optimization.
A comparative study on the risk of second primary cancers in out‐of‐field organs associated with radiotherapy of localized prostate carcinoma using Monte Carlo‐based accelerator and patient models
Authors: Bednarz Bryan , Athar Basit , Xu X. George 
Published: April 2010

Purpose:A physician's decision regarding an ideal treatment approach (i.e., radiation, surgery, and/or hormonal) for prostate carcinoma is traditionally based on a variety of metrics. One of these metrics is the risk of radiation‐induced second primary cancer following radiation treatments. The aim of this study was to investigate the significance of second cancer risks in out‐of‐field organs from 3D‐CRT and IMRT treatments of prostate carcinoma compared to baseline cancer risks in these organs.Methods:Monte Carlo simulations were performed using a detailed medical linear accelerator model and an anatomically realistic adult male whole‐body phantom. A four‐field box treatment, a four‐field box treatment plus a six‐field boost, and a seven‐field IMRT treatment were simulated. Using BEIR VII risk models, the age‐dependent lifetime attributable risks to various organs outside the primary beam with a known predilection for cancer were calculated using organ‐averaged equivalent doses.Results:The four‐field box treatment had the lowest treatment‐related second primary cancer risks to organs outside the primary beam ranging from to depending on the patients age at exposure and second primary cancer site. The risks to organs outside the primary beam from the four‐field box and six‐field boost and the seven‐field IMRT were nearly equivalent. The risks from the four‐field box and six‐field boost ranged from to , and from the seven‐field IMRT ranged from to . The second cancer risks in all organs considered from each plan were below the baseline risks.Conclusions:The treatment‐related second cancer risks in organs outside the primary beam due to 3D‐CRT and IMRT is small. New risk assessment techniques need to be investigated to address the concern of radiation‐induced second cancers from prostate treatments, particularly focusing on risks to organs inside the primary beam.
Imaging performance of a hybrid x‐ray computed tomography‐fluorescence molecular tomography system using priors
Authors: Ale Angelique , Schulz Ralf B. , Sarantopoulos Athanasios , Ntziachristos Vasilis 
Published: April 2010

Purpose:The performance is studied of two newly introduced and previously suggested methods that incorporate priors into inversion schemes associated with data from a recently developed hybrid x‐ray computed tomography and fluorescence molecular tomography system, the latter based on CCD camera photon detection. The unique data set studied attains accurately registered data of high spatially sampled photon fields propagating through tissue along 360° projections.Methods:Approaches that incorporate structural prior information were included in the inverse problem by adding a penalty term to the minimization function utilized for image reconstructions. Results were compared as to their performance with simulated and experimental data from a lung inflammation animal model and against the inversions achieved when not using priors.Results:The importance of using priors over stand‐alone inversions is also showcased with high spatial sampling simulated and experimental data. The approach of optimal performance in resolving fluorescent biodistribution in small animals is also discussed.Conclusions:Inclusion of prior information from x‐ray CT data in the reconstruction of the fluorescence biodistribution leads to improved agreement between the reconstruction and validation images for both simulated and experimental data.
Absorption spectra time evolution of EBT‐2 model GAFCHROMIC™ film
Authors: Devic Slobodan , Aldelaijan Saad , Mohammed Huriyyah , Tomic Nada , Liang Li‐Heng , DeBlois Francois , Seuntjens Jan 
Published: April 2010

Purpose: One of the major drawbacks of the current radiochromic film dosimetry protocols is the postirradiation waiting time. In this article, the authors study the postirradiation time evolution of the absorption spectrum of radiochromic EBT‐2 GAFCHROMIC™ film model.Methods: Postirradiation scanning times range from 3 min to 5 days and a dose range extends from 0 to 6 Gy. The authors compare the results of absorption spectra measurements for the latest GAFCHROMIC™ EBT‐2 film model to the absorption spectra of the previous EBT GAFCHROMIC™ film model. The authors also describe a method that can establish the time error constraints on the postirradiation scanning time that will still provide an acceptable dose error for clinical applications if the protocol employing the shorter postirradiation scanning time is implemented in the clinic.Results: The two film models experience the very same dose change in net absorbance with sensitivity of the latest EBT‐2 model GAFCHROMIC™ film being slightly lower than its predecessor. The authors show that for two postirradiation scanning times of 30 min and 24 h, the 1% dose error can be achieved if the scanning time window is less than ±5 min and ±2 h, respectively.Conclusions: By comparing the resultant change in net absorbance between the latest EBT‐2 and previous EBT GAFCHROMIC™ film models, the authors conclude that the addition of the yellow marker dye to the sensitive layer does not affect dosimetric properties of the latest film model. The authors also describe a procedure by which one can establish an acceptable time window around chosen postirradiation scanning time protocol that would provide an acceptable dose error for practical purposes.
Dosimetric evaluation of a novel polymer gel dosimeter for proton therapy
Authors: Zeidan O. A. , Sriprisan S. I. , Lopatiuk‐Tirpak O. , Kupelian P. A. , Meeks S. L. , Hsi W. C. , Li Z. , Palta J. R. , Maryanski M. J. 
Published: April 2010

Purpose:The aim of this study is to evaluate the dosimetric performance of a newly developed proton‐sensitive polymer gel formulation for proton therapy dosimetry.Methods:Using passive scattered modulated and nonmodulated proton beams, the dose response of the gel was assessed. A next‐generation optical CT scanner is used as the readout mechanism of the radiation‐induced absorbance in the gel medium. Comparison of relative dose profiles in the gel to ion chamber profiles in water is performed. A simple and easily reproducible calibration protocol is established for routine gel batch calibrations. Relative stopping power ratio measurement of the gel medium was performed to ensure accurate water‐equivalent depth dose scaling. Measured dose distributions in the gel were compared to treatment planning system for benchmark irradiations and quality of agreement is assessed using clinically relevant gamma index criteria.Results:The dosimetric response of the gel was mapped up to 600 cGy using an electron‐based calibration technique. Excellent dosimetric agreement is observed between ion chamber data and gel. The most notable result of this work is the fact that this gel has no observed dose quenching in the Bragg peak region. Quantitative dose distribution comparisons to treatment planning system calculations show that most of the gel dose maps pass the 3%/3 mm gamma criterion.Conclusions:This study shows that the new proton‐sensitive gel dosimeter is capable of reproducing ion chamber dose data for modulated and nonmodulated Bragg peak beams with different clinical beam energies. The findings suggest that the gel dosimeter can be used as QA tool for millimeter range verification of proton beam deliveries in the dosimeter medium.
Dose and detectability for a cone‐beam C‐arm CT system revisited
Authors: Ganguly Arundhuti , Yoon Sungwon , Fahrig Rebecca 
Published: April 2010

Purpose:The authors had previously published measurements of the detectability of disk‐shaped contrast objects in images obtained from a C‐arm CT system. A simple approach based on Rose's criterion was used to scale the date, assuming the threshold for the smallest diameter detected should be inversely proportional to. A more detailed analysis based on recent theoretical modeling of C‐arm CT images is presented in this work.Methods:The signal and noise propagations in a C‐arm based CT system have been formulated by other authors using cascaded systems analysis. They established a relationship between detectability and the noise equivalent quanta. Based on this model, the authors obtained a relation between x‐ray dose and the diameter of the smallest disks detected. A closed form solution was established by assuming no rebinning and no resampling of data, with low additive noise and using a ramp filter. For the case when no such assumptions were made, a numerically calculated solution using previously reported imaging and reconstruction parameters was obtained. The detection probabilities for a range of dose and kVp values had been measured previously. These probabilities were normalized to a single dose of 56.6 mGy using the Rose‐criteria‐based relation to obtain a universal curve. Normalizations based on the new numerically calculated relationship were compared to the measured results.Results:The theoretical and numerical calculations have similar results and predict the detected diameter size to be inversely proportional to and , respectively. The normalized experimental curves and the associated universal plot using the new relation were not significantly different from those obtained using the Rose‐criterion‐based normalization.Conclusions:From numerical simulations, the authors found that the diameter of detected disks depends inversely on the cube root of the dose. For observer studies for disks larger than 4 mm, the cube root as well as square root relations appear to give similar results when used for normalization.
Adaptive Evolution ofEscherichia coliK-12 MG1655 during Growth on a Nonnative Carbon Source,l-1,2-Propanediol
Authors: Lee Dae-Hee , Palsson Bernhard Ø. 
Published: May 2010

ABSTRACTLaboratory adaptive evolution studies can provide key information to address a wide range of issues in evolutionary biology. Such studies have been limited thus far by the inability of workers to readily detect mutations in evolved microbial strains on a genome scale. This limitation has now been overcome by recently developed genome sequencing technology that allows workers to identify all accumulated mutations that appear during laboratory adaptive evolution. In this study, we evolvedEscherichia coliK-12 MG1655 with a nonnative carbon source,l-1,2-propanediol (l-1,2-PDO), for ∼700 generations. We found that (i) experimental evolution ofE. colifor ∼700 generations in 1,2-PDO-supplemented minimal medium resulted in acquisition of the ability to usel-1,2-PDO as a sole carbon and energy source so that the organism changed from an organism that did not grow at all initially to an organism that had a growth rate of 0.35 h−1; (ii) six mutations detected by whole-genome resequencing accumulated in the evolvedE. colimutant over the course of adaptive evolution onl-1,2-PDO; (iii) five of the six mutations were within coding regions, and IS5was inserted between twofucregulons; (iv) two major mutations (mutations infucOand its promoter) involved inl-1,2-PDO catabolism appeared early during adaptive evolution; and (v) multiple defined knock-in mutant strains with all of the mutations had growth rates essentially matching that of the evolved strain. These results provide insight into the genetic basis underlying microbial evolution for growth on a nonnative substrate.
Iron-Dependent Remodeling of Fungal Metabolic Pathways Associated with Ferrichrome Biosynthesis
Authors: Mercier Alexandre , Labbé Simon 
Published: May 2010

ABSTRACT

The fission yeast
Schizosaccharomyces pombe
excretes and accumulates the hydroxamate-type siderophore ferrichrome. The
sib1

+

and
sib2

+

genes encode, respectively, a siderophore synthetase and an
l
-ornithine N
5
-oxygenase that participate in ferrichrome biosynthesis. In the present report, we demonstrate that
sib1

+

and
sib2

+

are repressed by the GATA-type transcriptional repressor Fep1 in response to high levels of iron. We further found that the loss of Fep1 results in increased ferrichrome production. We showed that a
sib1Δ sib2Δ
mutant strain exhibits a severe growth defect on iron-poor media. We determined that two metabolic pathways are involved in biosynthesis of ornithine, an obligatory precursor of ferrichrome. Ornithine is produced by hydrolysis of arginine by the Car1 and Car3 proteins. Although
car3

+

was constitutively expressed,
car1

+

transcription levels were repressed upon exposure to iron, with a concomitant decrease of Car1 arginase activity. Ornithine is also generated by transformation of glutamate, which itself is produced by two separate biosynthetic pathways which are transcriptionally regulated by iron in an opposite fashion. In one pathway, the glutamate dehydrogenase Gdh1, which produces glutamate from 2-ketoglutarate, was repressed under iron-replete conditions in a Fep1-dependent manner. The other pathway involves two coupled enzymes, glutamine synthetase Gln1 and Fe-S cluster-containing glutamate synthase Glt1, which were both repressed under iron-limiting conditions but were expressed under iron-replete conditions. Collectively, these results indicate that under conditions of iron deprivation, yeast remodels metabolic pathways linked to ferrichrome synthesis in order to limit iron utilization without compromising siderophore production and its ability to sequester iron from the environment.
Improvement of the Representation of Bifidobacteria in Fecal Microbiota Metagenomic Libraries by Application of thecpn60Universal Primer Cocktail
Authors: Hill Janet E. , Fernando W. M. Ursla , Zello Gordon A. , Tyler Robert T. , Dahl Wendy J. , Van Kessel Andrew G. 
Published: May 2010

ABSTRACTActinobacteria, particularly bifidobacteria, are widely observed to be underrepresented in metagenomic studies of microbial communities. We have compared human fecal microbiota clone libraries based on 16S rRNA andcpn60PCR products. Taxonomic profiles were similar except that thecpn60libraries contained large numbers of bifidobacterial sequences.
Gene Expression in Proliferating Cells of the Dinoflagellate
Alexandrium catenella
(Dinophyceae)
Authors: Toulza Eve , Shin Mi-Sun , Blanc Guillaume , Audic Stéphane , Laabir Mohamed , Collos Yves , Claverie Jean-Michel , Grzebyk Daniel 
Published: May 2010

ABSTRACT

Understanding the conditions leading to harmful algal blooms, especially those produced by toxic dinoflagellate species, is important for environmental and health safety. In addition to investigations into the environmental conditions necessary for the formation of toxic blooms, we postulate that investigating gene expression in proliferating cells is essential for understanding bloom dynamics. Expressed sequence tags were produced from cultured cells of the toxic dinoflagellate
Alexandrium catenella
sampled during the initiation phase of growth using Sanger's method and by 454 pyrosequencing. A significant proportion of identified genes (ca. 25%) represented enzymes and proteins that participate in a variety of cellular regulatory mechanisms that may characterize proliferating cells, e.g., control of the cell cycle and division, regulation of transcription, translation and posttranslational protein modifications, signaling, intracellular trafficking, and transport. All of the several genes selected for gene expression assays due to their involvement in metabolism and the cell cycle were overexpressed during exponential growth. These data will be useful for investigating the mechanisms underlying growth and toxin production in toxic
Alexandrium
species and for studying and monitoring the development of toxic blooms.
Characterization of Strains unlike
Mesorhizobium loti
That Nodulate
Lotus
spp. in Saline Soils of Granada, Spain
Authors: Lorite María J. , Muñoz Socorro , Olivares José , Soto María J. , Sanjuán Juan 
Published: May 2010

ABSTRACT

Lotus
species are forage legumes with potential as pastures in low-fertility and environmentally constrained soils, owing to their high persistence and yield under those conditions. The aim of this work was the characterization of phenetic and genetic diversity of salt-tolerant bacteria able to establish efficient symbiosis with
Lotus
spp. A total of 180 isolates able to nodulate
Lotus corniculatus
and
Lotus tenuis
from two locations in Granada, Spain, were characterized. Molecular identification of the isolates was performed by repetitive extragenic palindromic PCR (REP-PCR) and 16S rRNA,
atpD
, and
recA
gene sequence analyses, showing the presence of bacteria related to different species of the genus
Mesorhizobium
:
Mesorhizobium tarimense
/
Mesorhizobium tianshanense
,
Mesorhizobium chacoense
/
Mesorhizobium albiziae
, and the recently described species,
Mesorhizobium alhagi
. No
Mesorhizobium loti
-like bacteria were found, although most isolates carried
nodC
and
nifH
symbiotic genes closely related to those of
M. loti
, considered the type species of bacteria nodulating
Lotus
, and other
Lotus
rhizobia. A significant portion of the isolates showed both high salt tolerance and good symbiotic performance with
L. corniculatus
, and many behaved like salt-dependent bacteria, showing faster growth and better symbiotic performance when media were supplemented with Na or Ca salts.
An Old Yellow Enzyme Gene Controls the Branch Point between
Aspergillus fumigatus
and
Claviceps purpurea
Ergot Alkaloid Pathways
Authors: Coyle Christine M. , Cheng Johnathan Z. , O'Connor Sarah E. , Panaccione Daniel G. 
Published: May 2010

ABSTRACT

Ergot fungi in the genus
Claviceps
and several related fungal groups in the family Clavicipitaceae produce toxic ergot alkaloids. These fungi produce a variety of ergot alkaloids, including clavines as well as lysergic acid derivatives. Ergot alkaloids are also produced by the distantly related, opportunistic human pathogen
Aspergillus fumigatus
. However, this fungus produces festuclavine and fumigaclavines A, B, and C, which collectively differ from clavines of clavicipitaceous fungi in saturation of the last assembled of four rings in the ergoline ring structure. The two lineages are hypothesized to share early steps of the ergot alkaloid pathway before diverging at some point after the synthesis of the tricyclic intermediate chanoclavine-I. Disruption of
easA
, a gene predicted to encode a flavin-dependent oxidoreductase of the old yellow enzyme class, in
A. fumigatus
led to accumulation of chanoclavine-I and chanoclavine-I-aldehyde. Complementation of the
A. fumigatus easA
mutant with a wild-type allele from the same fungus restored the wild-type profile of ergot alkaloids. These data demonstrate that the product of
A. fumigatus easA
is required for incorporation of chanoclavine-I-aldehyde into more-complex ergot alkaloids, presumably by reducing the double bond conjugated to the aldehyde group, thus facilitating ring closure. Augmentation of the
A. fumigatus easA
mutant with a homologue of
easA
from
Claviceps purpurea
resulted in accumulation of ergot alkaloids typical of clavicipitaceous fungi (agroclavine, setoclavine, and its diastereoisomer isosetoclavine). These data indicate that functional differences in the
easA
-encoded old yellow enzymes of
A. fumigatus
and
C. purpurea
result in divergence of their respective ergot alkaloid pathways.
Diverse Bacteria Inhabit Living Hyphae of Phylogenetically Diverse Fungal Endophytes
Authors: Hoffman Michele T. , Arnold A. Elizabeth 
Published: April 2010

ABSTRACT

Both the establishment and outcomes of plant-fungus symbioses can be influenced by abiotic factors, the interplay of fungal and plant genotypes, and additional microbes associated with fungal mycelia. Recently bacterial endosymbionts were documented in soilborne Glomeromycota and Mucoromycotina and in at least one species each of mycorrhizal Basidiomycota and Ascomycota. Here we show for the first time that phylogenetically diverse endohyphal bacteria occur in living hyphae of diverse foliar endophytes, including representatives of four classes of Ascomycota. We examined 414 isolates of endophytic fungi, isolated from photosynthetic tissues of six species of cupressaceous trees in five biogeographic provinces, for endohyphal bacteria using microscopy and molecular techniques. Viable bacteria were observed within living hyphae of endophytic Pezizomycetes, Dothideomycetes, Eurotiomycetes, and Sordariomycetes from all tree species and biotic regions surveyed. A focus on 29 fungus/bacterium associations revealed that bacterial and fungal phylogenies were incongruent with each other and with taxonomic relationships of host plants. Overall, eight families and 15 distinct genotypes of endohyphal bacteria were recovered; most were members of the
Proteobacteria
, but a small number of
Bacillaceae
also were found, including one that appears to occur as an endophyte of plants. Frequent loss of bacteria following subculturing suggests a facultative association. Our study recovered distinct lineages of endohyphal bacteria relative to previous studies, is the first to document their occurrence in foliar endophytes representing four of the most species-rich classes of fungi, and highlights for the first time their diversity and phylogenetic relationships with regard both to the endophytes they inhabit and the plants in which these endophyte-bacterium symbiota occur.