bluuebunny/crossref_metadata_2025_split huggingface dataset:
MO‐E‐L100F‐01: Real‐Time Soft Tissue Elasticity Imaging with Ultrasound
Authors: Hall T 
Published: July 2007

Methods for imaging the elastic properties of soft tissues have undergone rapid development in recent years. This is in part facilitated by the ever‐increasing capabilities of ultrasound imaging systems. This presentation will describe the basic mechanics of soft tissues and terminology used in elasticity imaging (e.g., stress, strain, elastic modulus). Key developments in motion tracking for elasticity imaging will be reviewed with emphasis on the current state of the art in motion tracking algorithms for accurate estimation of displacement fields. That discussion sets the stage for an analysis of observations of soft tissue mechanics as seen via real‐time elasticity (mechanical strain) images of breast tissues during relatively large deformations. For example, many benign lesions tend to lose contrast in strain images as deformation increases. That behavior can be understood given the measured mechanical properties of in vitro tissue samples. Unlike benign lesions most cancerous tumors tend to maintain a large negative contrast with increasing deformation, and that too can be understood from in vitro measurements. The utility of this information is summarized with a review of recent clinical trials of breast elasticity imaging. Specifically, a recent multi‐institutional, multi‐observer study has demonstrated that elasticity imaging increases the diagnostic confidence of breast ultrasound radiologists when attempting to classify a tumor as either “benign” or “malignant”. The presentation will conclude with a brief discussion of the prospects for future enhancements and improvements in elasticity image formation and information content.Educational Objectives1. Understand the basic vocabulary used to describe simple solid mechanics.2. Understand the methods used to form real‐time elasticity images using ultrasound and the potential for significant improvements in the future.3. Understand the basic criteria for interpreting breast elasticity images.
MO‐E‐M100J‐02: Functional Imaging
Authors: Xing L 
Published: July 2007

Functional imaging is being increasingly used in radiation therapy for target definition and treatment planning. In this talk I will summarize recent advances in functional and molecular imaging techniques and discuss various issues related to the integration of the newly emerged imaging data into radiation therapy planning. In particular, techniques of time resolved 4D PET acquisition will be discussed and a few method of enhancing 4D PET images will be described. It is anticipated that the new imaging modalities will make significant impact in cancer diagnosis, staging, treatment planning, and monitoring of therapeutic response. The potential impact of biologically conformal radiation therapy (BCRT) or biologically guided radiation therapy (BGRT) will be discussed. Finally, issues related to the quality assurance of functional and molecular imaging and BCRT will also be addressed.Educational Objectives:1. Introduce the concept of functional and molecular imaging.2. Illustrate the steps involved in integrating molecular imaging such as PET and MRSI into treatment planning process.3. Introduce PET/MRI/MRSI and CT image fusion techniques (including deformable image registration).4. 4D PET data acquisition and image enhancement.5. Provide an overview on recent advances in PET/CT and MRSI, and update on the development of new PET tracers and data acquisition techniques.This work was supported in part by NCI 5R01 CA98523‐01.
MO‐E‐M100J‐03: Gross Tumor Volume and Normal Structure Definition
Authors: Balter J 
Published: July 2007

Regardless of the degree to which positioning is maintained later in treatment, the critical step in the radiation therapy process involves definition of the initial patient model. Many factors influence this process, most notably the sources of differential contrast in images used, the knowledge and experience of the users defining both normal tissue as well as targeted structures, and distracting factors such as organ movement and imaging artifacts. Significant attention has recently focused on the interobserver variation in target definition, with differences observed that exceed the gains expected through in‐room target localization and potentially through gating/tracking. While Radiation Oncology departments are consumers of advanced imaging information, we have yet to find ways to truly optimize imaging to aid in consistent definition of targeted and avoidance tissues.The objectives of this talk are to:1. Review the process of initial definition of target and avoidance tissues.2. Discuss observed variances in target definition.3. Describe the impact of motion and advances such as 4DCT in the process.4. Suggest potential areas for improving consistency in these processes.
MO‐E‐M100J‐06: Intra‐Fraction Target‐Beam Positioning
Authors: Keall P , Sawant A 
Published: July 2007

The problem of intrafraction tumor‐target positioning can be divided into two separate processes: (1) estimating the real‐time target position and (2) repositioning the beam to account for intrafraction target motion. Several solutions exist for both target position estimation and beam repositioning, however in principal any method of position estimation could be integrated with any method of beam repositioning. Note that beam repositioning can include moving the target to align with the beam (e.g. couch motion), which in the target reference is the same as moving the beam to align with the target.There are several common features in target position estimation systems. First, that in the absence of a real‐time volumetric imaging system, the target position is estimated from surrogates and thus there is uncertainty in the position of the target with respect to the surrogates. Second, for all but EPID‐based methods target position estimation is independent of the treatment beam and therefore careful quality assurance is required to ensure the accurate position estimation with respect to the treatment beam.There are also several common features of the beam repositioning systems. First, control systems with secondary feedback are required to ensure accurate and precise real time mechanical motion. Second, that there is a delay between the target motion and the beam repositioning. This delay causes delay‐time dependent errors which can be reduced with prediction algorithms.The various target position estimation and beam repositioning processes either in development or available for clinical use will be described and contrasted.Educational Objectives:1. Understand the separation of the target position estimation and beam repositioning processes.2. Understand the advantages and disadvantages of several real‐time target position estimation systems.3. Understand the advantages and disadvantages of several beam repositioning systems.Some research in this area at Stanford is supported by Varian Medical stems.
MO‐E‐AUD‐04: Automated Linear Accelerator Quality Assurance Using a Commercial Cylindrical Calibration Phantom
Authors: Mamalui‐Hunter M , Li H , Low D 
Published: July 2007

Purpose: Precise mechanical operation of a linear accelerator is critical for accurate dose delivery. Available quantitative procedures for the linac mechanical quality assurance (QA) are time consuming and therefore conducted on a relatively infrequent basis. We present a method for evaluating the mechanical performance of a linac based on a series of projection portal images of a prototype cylindrical calibration phantom with embedded markers.Method and Materials: We used non‐linear multiobjective optimization of information extracted from the images to determine a number of geometric parameters of interest. The markers detection included modeling the imager response to radiation beams where significantly non‐uniform background was expected. Results: The average results for the parameters of our geometric linac model were: gantry angle deviation 0.066 ± 0.085° (1 SD), gantry sag 0.026 ± 0.02°, imager in‐plane rotation 0.026 ± 0.055°, roll — 0.082 ± 0.16° and pitch −0.9 ± 0.604°, SDD 1489.7 ± 5 mm, SAD 998 .3 ± 1.7 mm, and the imager shift [− 0.66,3.9]±[0.30,1.6] mm. The results were corrected for the phantom center shift relative to the linac rotational center. The average rotational center was . The average couch height and angle variations were 0.15±0.9 mm and 0.154±0.1°, respectively. The image analysis quality was examined by comparing the detected set of marker coordinates to its simulated counterpart for three regions of the phantom image: central, near the edge and the intermediate region (relative to the central line of the cylinder). The upper limit of the mean difference was less than 0.25 mm with the cumulative mean of 0.146 mm and SD of 0.07 mm. The results of the primary optimization of directly detected marker coordinates virtually coincided with their counterparts based on the simulated coordinates for all the geometric parameters of the model.Conclusion: This procedure is accurate and automated, which allows precise mechanic QA to be performed more frequently.Conflict of Interest: partially supported by Varian Medical Systems.
WE‐D‐M100J‐05: Estimation of Tumor Control Probability Model Parameters for Early Stage Non‐Small‐Cell Lung Cancer (NSCLC)
Authors: Semenenko V , Gore E , Li X 
Published: July 2007

Purpose: To estimate parameters for the tumor control probability (TCP) model based on the linear‐quadratic (LQ) cell survival formalism from published clinical data for early stage NSCLC and to investigate potential outcomes of alternate dose fractionation schemes. Method and Materials: A comprehensive literature search was performed to identify studies reporting local control after conventionally fractionated 3DCRT and hypofractionated stereotactic body radiation therapy (SBRT) for T1‐2N0M0 NSCLC. Parameters of the LQ‐based TCP model were estimated by fitting the selected clinical data sets using the maximum likelihood method. Fits were obtained and compared for three versions of the TCP model: without the time effect, with an exponential growth of clonogens, and with delayed onset of clonogen proliferation. Obtained parameter estimates were used to compare different fractionation schemes that take advantage of increase in tumor control as the overall treatment time is reduced. Results: A fit to the exponential growth model was significantly better (p < 0.0001) than a fit to the model with no time effect. Also, the model with delayed onset provided a significantly better fit (p = 0.0142) to the data than the exponential growth model assuming no delay in clonogen repopulation. Parameter estimates for the model with delayed onset were: α = 0.066 Gy−1, α/β = 21.1 Gy, γ = 1.85 Gy/day, Tk = 32.2 days, and k (the number of clonogens) = 6.3. Our analysis of different hypofractionated regiments confirms observations by others and suggests that a moderate reduction in the number of fractions (with the increase in the dose per fraction) may result in better tumor control for the same level of late complications.Conclusion: The derived TCP model parameter estimates may prove useful for biologically based treatment planning of Stage I NSCLC, especially when unconventional fractionation schemes, such as in SBRT, are employed.
WE‐E‐M100F‐01: 3D Interfraction Position Verification for Patients Undergoing Partial Breast Irradiation: Comparing Digital Tomosynthesis to Cone‐Beam CT
Authors: Zhang J , Wu Q , Godfrey D , Yin F 
Published: July 2007

Purpose: This clinical study evaluates digital tomosynthesis (DTS) technology for daily imaging guidance for partial breast irradiation (PBI) and compares its positioning accuracy to the 3D CBCT technique. Compared to CBCT, DTS offers lower imaging dose and the geometrical flexibility that particularly suits PBI. Methods and Material: Ten patients undergoing PBI were imaged using an on‐board‐imager mounted on a Varian 21EX linear accelerator. Following the initials setup using skin markers and 2D KV/MV radiographs, a CBCT scan was acquired to provide 3D positioning guidance. A subset of the CBCT projections were used to reconstruct a stack of DTS image slices using the Feldkamp filtered back‐projection algorithm. To optimize soft tissue contrast, the DTS images were reconstructed for the 45‐degree oblique view along which the tumor bed, breast tissues, bones, and lung were well separated. Coronal and sagittal DTS views were also reconstructed for comparison. The inter‐fraction position deviations between the 1st fraction and each of the subsequent fractions were measured by coronal‐DTS, sagittal‐DTS, oblique‐DTS and CBCT as four independent technologies. Differences between these technologies and their clinical impact were evaluated. The evaluator was well trained for DTS technology. Results: Eighty‐five imaging datasets were obtained from 10 patients. Surgical clips (when present) were visible in all three DTS views. The tumor bed had the best contrast in the oblique‐DTS. One‐dimensional positioning differences between DTS (averaged over 3 DTS views) and CBCT were ∼0.1 cm when surgical clips were used in the registration and ∼0.2 cm when the tumor bed were used in the registration. Conclusion: DTS is equivalent to CBDT as a 3D imaging technique for daily patient positioning of PBI but with less mechanical constraints and imaging dose.Partially supported by a research grant from Varian Medical Systems.
Legionella pneumophila
in Cooling Towers: Fluctuations in Counts, Determination of Genetic Variability by Pulsed-Field Gel Electrophoresis (PFGE), and Persistence of PFGE Patterns
Authors: Ragull Sonia , Garcia-Nuñez Marian , Pedro-Botet Maria Luisa , Sopena Nieves , Esteve Maria , Montenegro Rafael , Sabrià Miquel 
Published: June 2007

ABSTRACT

The concentrations of
Legionella pneumophila
in cooling towers may vary considerably over short periods of time, producing significant fluctuations throughout the year. Despite genetic variability, in small geographical areas the same indistinguishable pulsed-field gel electrophoresis patterns may be shared among different cooling towers and persist over time.
Effects of Intranasal Administration of a Leptin-Secreting
Lactococcus lactis
Recombinant on Food Intake, Body Weight, and Immune Response of Mice
Authors: Bermúdez-Humarán Luis G. , Nouaille Sébastien , Zilberfarb Vladimir , Corthier Gérard , Gruss Alexandra , Langella Philippe , Issad Tarik 
Published: June 2007

ABSTRACT

Leptin is an adipocyte-derived pleiotropic hormone that modulates a large number of physiological functions, including control of body weight and regulation of the immune system. In this work, we show that a recombinant strain of the food-grade lactic acid bacterium
Lactococcus lactis
(LL-lep) can produce and efficiently secrete human leptin. The secreted leptin is a fully biologically active hormone, as demonstrated by its capacity to stimulate a STAT3 reporter gene in HEK293 cells transfected with the Ob-Rb leptin receptor. The immunomodulatory activity of leptin-secreting
L. lactis
was evaluated in vivo by coexpression with the human papillomavirus type 16 E7 protein. In C57BL/6 mice immunized intranasally with a recombinant
L. lactis
strain coproducing leptin and E7 antigen, the adaptive immune response was significantly higher than in mice immunized with recombinant
L. lactis
producing only E7 antigen, demonstrating adjuvanticity of leptin. We then analyzed the effects of intranasally administered LL-lep in obese
ob
/
ob
mice. We observed that daily administration of LL-lep to these mice significantly reduced body weight gain and food intake. These results demonstrate that leptin can be produced and secreted in an active form by
L. lactis
and that leptin-producing
L. lactis
regulates in vivo antigen-specific immune responses, as well as body weight and food consumption.
Interpreting Ecological Diversity Indices Applied to Terminal Restriction Fragment Length Polymorphism Data: Insights from Simulated Microbial Communities
Authors: Blackwood Christopher B. , Hudleston Deborah , Zak Donald R. , Buyer Jeffrey S. 
Published: June 2007

ABSTRACT

Ecological diversity indices are frequently applied to molecular profiling methods, such as terminal restriction fragment length polymorphism (T-RFLP), in order to compare diversity among microbial communities. We performed simulations to determine whether diversity indices calculated from T-RFLP profiles could reflect the true diversity of the underlying communities despite potential analytical artifacts. These include multiple taxa generating the same terminal restriction fragment (TRF) and rare TRFs being excluded by a relative abundance (fluorescence) threshold. True community diversity was simulated using the lognormal species abundance distribution. Simulated T-RFLP profiles were generated by assigning each species a TRF size based on an empirical or modeled TRF size distribution. With a typical threshold (1%), the only consistently useful relationship was between Smith and Wilson evenness applied to T-RFLP data (TRF-
E
var
) and true Shannon diversity (
H
′), with correlations between 0.71 and 0.81. TRF-
H
′ and true
H
′ were well correlated in the simulations using the lowest number of species, but this correlation declined substantially in simulations using greater numbers of species, to the point where TRF-
H
′ cannot be considered a useful statistic. The relationships between TRF diversity indices and true indices were sensitive to the relative abundance threshold, with greatly improved correlations observed using a 0.1% threshold, which was investigated for comparative purposes but is not possible to consistently achieve with current technology. In general, the use of diversity indices on T-RFLP data provides inaccurate estimates of true diversity in microbial communities (with the possible exception of TRF-
E
var
). We suggest that, where significant differences in T-RFLP diversity indices were found in previous work, these should be reinterpreted as a reflection of differences in community composition rather than a true difference in community diversity.
Identification of Internal Transcribed Spacer Sequence Motifs in Truffles: a First Step toward Their DNA Bar Coding
Authors: El Karkouri Khalid , Murat Claude , Zampieri Elisa , Bonfante Paola 
Published: June 2007

ABSTRACT

This work presents DNA sequence motifs from the internal transcribed spacer (ITS) of the nuclear rRNA repeat unit which are useful for the identification of five European and Asiatic truffles (
Tuber magnatum
,
T. melanosporum
,
T. indicum
,
T. aestivum
, and
T. mesentericum
). Truffles are edible mycorrhizal ascomycetes that show similar morphological characteristics but that have distinct organoleptic and economic values. A total of 36 out of 46 ITS1 or ITS2 sequence motifs have allowed an accurate in silico distinction of the five truffles to be made (i.e., by pattern matching and/or BLAST analysis on downloaded GenBank sequences and directly against GenBank databases). The motifs considered the intraspecific genetic variability of each species, including rare haplotypes, and assigned their respective species from either the ascocarps or ectomycorrhizas. The data indicate that short ITS1 or ITS2 motifs (≤50 bp in size) can be considered promising tools for truffle species identification. A dot blot hybridization analysis of
T. magnatum
and
T. melanosporum
compared with other close relatives or distant lineages allowed at least one highly specific motif to be identified for each species. These results were confirmed in a blind test which included new field isolates. The current work has provided a reliable new tool for a truffle oligonucleotide bar code and identification in ecological and evolutionary studies.
Distribution and Expression of Elicitin Genes in the Interspecific Hybrid OomycetePhytophthora alni
Authors: Ioos Renaud , Panabières Franck , Industri Benoît , Andrieux Axelle , Frey Pascal 
Published: June 2007

ABSTRACTPhytophthora alnisubsp.alni,P. alnisubsp.multiformis, andP. alnisubsp.uniformisare responsible for alder disease in Europe. Class I and II elicitin gene patterns ofP. alnisubsp.alni,P. alnisubsp.multiformis,P. alnisubsp.uniformis, and the phylogenetically close speciesP. cambivoraandP. fragariaewere studied through mRNA sequencing and 3′ untranslated region (3′UTR)-specific PCRs and sequencing. The occurrence of multiple 3′UTR sequences in association with identical elicitin-encoding sequences inP. alnisubsp.alniindicated duplication/recombination events. The mRNA pattern displayed byP. alnisubsp.alnidemonstrated that elicitin genes from all the parental genomes are actually expressed in this allopolyploid taxon. The complementary elicitin patterns resolved confirmed the possible involvement ofP. alnisubsp.multiformisandP. alnisubsp.uniformisin the genesis of the hybrid speciesP. alnisubsp.alni. The occurrence of multiple and common elicitin gene sequences throughoutP. cambivora,P. fragariae, andP. alnisensu lato, not observed in otherPhytophthoraspecies, suggests that duplication of these genes occurred before the radiation of these species.
Use of a Dominant
rpsL
Allele Conferring Streptomycin Dependence for Positive and Negative Selection in
Thermus thermophilus
Authors: Blas-Galindo Emilio , Cava Felipe , López-Viñas Eduardo , Mendieta Jesús , Berenguer José 
Published: June 2007

ABSTRACT

A spontaneous
rpsL
mutant of
Thermus thermophilus
was isolated in a search for new selection markers for this organism. This new allele, named
rpsL1
, encodes a K47R/K57E double mutant S12 ribosomal protein that confers a streptomycin-dependent (SD) phenotype to
T. thermophilus
. Models built on the available three-dimensional structures of the 30S ribosomal subunit revealed that the K47R mutation directly affects the streptomycin binding site on S12, whereas the K57E does not apparently affect this binding site. Either of the two mutations conferred the SD phenotype individually. The presence of the
rpsL1
allele, either as a single copy inserted into the chromosome as part of suicide plasmids or in multicopy as replicative plasmids, produced a dominant SD phenotype despite the presence of a wild-type
rpsL
gene in a host strain. This dominant character allowed us to use the
rpsL1
allele not only for positive selection of plasmids to complement a kanamycin-resistant mutant strain, but also more specifically for the isolation of deletion mutants through a single step of negative selection on streptomycin-free growth medium.
Saccharomyces cerevisiaeSignature Genes for Predicting Nitrogen Deficiency during Alcoholic Fermentation
Authors: Mendes-Ferreira A. , del Olmo M. , García-Martínez J. , Jiménez-Martí E. , Leão C. , Mendes-Faia A. , Pérez-Ortín J. E. 
Published: June 2007

ABSTRACTGenome-wide analysis of the wine yeast strainSaccharomyces cerevisiaePYCC4072 identified 36 genes highly expressed under conditions of low or absent nitrogen in comparison with a nitrogen-replete condition. Reverse transcription-PCR analysis for four of these transcripts with this strain and its validation with another wine yeast strain underlines the usefulness of these signature genes for predicting nitrogen deficiency and therefore the diagnosis of wine stuck/sluggish fermentations.