bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical experience of the importance of daily portal imaging for head and neck IMRT treatments
Authors: Court Laurence E , Wolfsberger Luciant , Allen Aaron M , James Steven , Tishler Roy B 
Published: August 2008

The purpose of this study was to evaluate patient setup in head and neck IMRT using daily portal imaging. At our institution, orthogonal digital portal images are taken daily to check patient positioning prior to head and neck IMRT treatment. Isocenter misalignments are corrected using a couch shift (3 mm action level). Therapists also compare the DRRs and portal images looking at points more distant from the isocenter, particularly in the supraclavicular region, and re‐position the patient's shoulders in the mask if considered necessary. The daily isocenter shifts (C2 region) and frequency of patient repositioning were investigated by review of record‐and‐verify records for 15 patients. The magnitude of the shoulder repositioning was evaluated for 10 of these patients by comparing portal images and plan DRRs for a point 8 cm inferior of isocenter (T2‐T4).For all patients, pretreatment isocenter discrepancies 3 mm or smaller were recorded for a median of 92.5% of fractions (range: 71.4 – 100%). Patients were repositioned in the immobilization mask before treatment for a median of 14% of fractions (3–34%). Thirty percent of these were for shoulder shifts of 1 cm or larger. Twenty percent of patients needed shoulder shifts of 1 cm or more for more than 7/35 fractions, meaning that without setup based on daily imaging, parts of the CTV would have received less than 95% of the prescribed dose. In conclusion, with our current immobilization, isocenter positioning accuracy is excellent, while correct shoulder position is more variable, particularly for a small subset of patients. Frequent imaging of head and neck IMRT patients is essential to accurate delivery of therapy, with shoulder position an important factor.PACS number: 87.53.Oq
Comparison of breath‐hold and free‐breathing positions of an external fiducial by analysis of respiratory traces
Authors: Hunjan Sandeep , Starkschall George , Rosen Isaac , Prado Karl , Tolani Naresh , Balter Peter 
Published: August 2008

An internal target volume (ITV) accounting for respiratory‐induced tumor motion is best obtained using 4DCT. However, when 4DCT is not available, inspiratory/expiratory breath‐hold CT images have been suggested as an alternative. In such cases, an external fiducial on the abdomen can be used as a substitute for tumor motion and CT images are acquired when the marker position matches – as judged by the therapist/physicist ‐ its positions at previously determined free‐breathing (FB) respiratory extrema . In this study we retrospectively determined the accuracy of these matches. Free breathing 4DCT images were acquired, followed by and CT images for 25 patients with non‐small‐cell lung cancer. Respiration was monitored using a commercial external fiducial system, which generates positional information while CT studies are conducted. Software was written for statistically analyzing the displacement of the external fiducial during and CT acquisition and comparing these displacements with corresponding mean FB extrema positions using a Student's t‐test. In 72% of patients, mean positions at differed significantly from mean positions at . In 92% of patients, mean positions at differed significantly from mean positions at , although this difference was smaller than 0.5 cm in many cases . Our findings indicate that relying solely on abdominal external markers for accurate BH CT imaging in order to accurately estimate FB extrema positions may be subject to significant error.PACS numbers 87.53.bd, 87.57.C‐, 87.59.Fm, 87.55.Gh
Comparison of the KonRad IMRT and XiO treatment planning systems
Authors: Reitz Bodo , Miften Moyed 
Published: August 2008

Reducing the treatment time for IMRT patients is highly desirable. The objective of this work was to evaluate the new clinical Siemens KonRad inverse treatment planning system (TPS) and compare it to the CMS XiO TPS with special emphasis on the segmentation efficiency. For head and neck, liver and prostate cancer patients, step‐and‐shoot IMRT plans were designed using both CMS XiO and Siemens KonRad TPS. Number, direction and energy of beams used were the same in the plans from both systems for each treatment site. The plans were optimized to achieve the same clinical objectives concerning dose to the target volume and to the relevant organs‐at‐risk (OARs). The number of intensity levels were minimized until the clinical objectives could not be achieved anymore. Dose‐volume histograms (DVHs), mean and maximum doses were compared, as well as the number of beam segments and monitor units (MUs). The beams of each plan were delivered individually on a MapCheck device to verify the agreement between calculations and measurements to be less than 3%–3 mm distance‐to‐agreement. Plans optimized with KonRad resulted in fewer segments and lower number of MUs and therefore reduced delivery time on average by 28% or 3.6 min, while achieving similar dose distributions. CMS XiO plans exhibited a slightly steeper dose fall‐off outside the target volumes; however the difference was not clinically significant. DVHs to OARs were comparable. All calculated dose distributions passed the 3%–3 mm verification check.PACS numbers: 87.55.D
A commissioning procedure for breast intracavitary electronic brachytherapy systems
Authors: Hiatt Jessica , Cardarelli Gene , Hepel Jaroslaw , Wazer David , Sternick Edward 
Published: August 2008

In this work, we report a comprehensive quality assurance (QA) process for the commissioning of an Electronic Brachytherapy (EB) system at one of the first U.S. sites to apply the device clinically. Thus far, EB systems have been released only for intracavitary breast treatments. As such, EB as an Accelerated Partial Breast Irradiation (APBI) treatment modality is relatively unstudied and is unfamiliar to many medical physicists. We present our documented experience as a guide for other institutions' EB commissioning process. Our tests included eight elements: A) well‐chamber constancy, B) beam stability, C) source positional accuracy, D) output stability, E) timer linearity, F) dummy marker/source position coincidence, G) controller functionality and safety interlocks, and H) treatment planning data verification following the AAPM TG‐43 recommendations. Together with TG‐43, our methodology provides a comprehensive EB system check for medical physicists commissioning such a device.PACS Numbers: 87.53.Jw, 87.53.Xd
Image guided IMRT dosimetry using anatomy specific MOSFET configurations
Authors: Amin Md Nurul , Norrlinger Bern , Heaton Robert , Islam Mohammad 
Published: August 2008

We have investigated the feasibility of using a set of multiple MOSFETs in conjunction with the mobileMOSFET wireless dosimetry system, to perform a comprehensive and efficient quality assurance (QA) of IMRT plans. Anatomy specific MOSFET configurations incorporating 5 MOSFETs have been developed for a specially designed IMRT dosimetry phantom. Kilovoltage cone beam computed tomography (kV CBCT) imaging was used to increase the positional precision and accuracy of the detectors and phantom, and so minimize dosimetric uncertainties in high dose gradient regions. The effectiveness of the MOSFET based dose measurements was evaluated by comparing the corresponding doses measured by an ion chamber. For 20 head and neck IMRT plans the agreement between the MOSFET and ionization chamber dose measurements was found to be within and (1σ) for measurement points in the high dose and low dose respectively. A precision of 1 mm in detector positioning was achieved by using the X‐Ray Volume Imaging (XVI) kV CBCT system available with the Elekta Synergy Linear Accelerator. Using the anatomy specific MOSFET configurations, simultaneous measurements were made at five strategically located points covering high dose and low dose regions. The agreement between measurements and calculated doses by the treatment planning system for head and neck and prostate IMRT plans was found to be within . The results indicate that a cylindrical phantom incorporating multiple MOSFET detectors arranged in an anatomy specific configuration, in conjunction with image guidance, can be utilized to perform a comprehensive and efficient quality assurance of IMRT plans.PACS number: 87.55.Qr
Radiation transmission, leakage and beam penumbra measurements of a micro‐multileaf collimator using GafChromic EBT film
Authors: García‐Garduño Olivia Amanda , Celis Miguel Ángel , Lárraga‐Gutiérrez José Manuel , Moreno‐Jiménez Sergio , Martínez‐Dávalos Arnulfo , Rodríguez‐Villafuerte Mercedes 
Published: August 2008

Micro‐multileaf collimator systems coupled to linear accelerators for radioneurosurgery treatments require a rigorous dosimetric characterization in order to be used in 3D conformal and intensity modulated stereotactic radiosurgery and radiotherapy applications. This characterization involves high precision measurements of leaf transmission, leakage and beam penumbra through the collimation system and requires the use of detectors with high spatial resolution, high sensitivity and practically no energy dependence. In this work the use of GafChromic EBT radiochromic film to measure the basic dosimetric properties of the m3‐mMLC (BrainLAB, Germany) micro‐multileaf collimator system integrated to a 6 MV linear accelerator, is reported. Results show that average values of transmission and leakage radiation areand, respectively. The 80–20% beam penumbra were found to bealong the leaf side (perpendicular to leaf motion) andalong the leaf end (parallel to leaf motion) using square field sizes ranging from 9.1 to 1.8 cm. These measurements are in agreement with values reported in the literature for the same type of mMLC using different radiation detectors.PACS number: 87.56.N‐
Dosimetric verification of micro‐MLC based intensity modulated radiation therapy
Authors: Basran Parminder , Yeboah Collins 
Published: August 2008

A methodology for the dosimetric verification of micro‐multileaf collimator (mMLC) based intensity modulated radiation therapy (IMRT) plans intended for stereotactic applications is described. The method is similar to that of conventional IMRT patient‐specific quality assurance (QA) with some notable exceptions, particularly, mechanical tests that verify the mMLC positioning with respect to the isocenter and individual leaf calibration prior to use. Relative dosimetry measurements are performed with radiographic film, a commercial film‐scanning system and a dose‐image registration program. Film dosimetry results are within of calculated distributions or within 2.0 mm distance to agreement. Absolute dosimetry measurements are performed with a small volume ion chamber and a commercially available stereotactic phantom. The cumulative dose from all beams is within of the prescribed dose. Large deviations may be observed from individual beams since the smaller IMRT fields tend to have very few high‐dose and low‐gradient regions. An independent program that examines the treatment mMLC file is used to estimate the central axis dose from each beam and provide a dose image that can be assessed alongside the intended fluence distribution prior to treatment. Tolerances for relative and absolute dosimetry of mMLC‐based IMRT treatments are tighter than what is typically reported for conventional MLC‐based IMRT. Also, the time commitment for the IMRT QA is slightly longer than of conventional MLC‐based IMRT due to QA processes that check the mechanical alignment of the mMLC device with the laser and radiation isocenter.PACS Number: 87.53Dq, 87.53Ly, 87.53Tf
Controlled Expression of the Dominant Flocculation Genes
FLO1
,
FLO5
, and
FLO11
in
Saccharomyces cerevisiae
Authors: Govender Patrick , Domingo Jody L. , Bester Michael C. , Pretorius Isak S. , Bauer Florian F. 
Published: August 2008

ABSTRACT

In many industrial fermentation processes, the
Saccharomyces cerevisiae
yeast should ideally meet two partially conflicting demands. During fermentation, a high suspended yeast count is required to maintain a satisfactory rate of fermentation, while at completion, efficient settling is desired to enhance product clarification and recovery. In most fermentation industries, currently used starter cultures do not satisfy this ideal, probably because nonflocculent yeast strains were selected to avoid fermentation problems. In this paper, we assess molecular strategies to optimize the flocculation behavior of
S. cerevisiae
. For this purpose, the chromosomal copies of three dominant flocculation genes,
FLO1
,
FLO5
, and
FLO11
, of the haploid nonflocculent, noninvasive, and non-flor-forming
S. cerevisiae
FY23 strain were placed under the transcriptional control of the promoters of the
ADH2
and
HSP30
genes. All six promoter-gene combinations resulted in specific flocculation behaviors in terms of timing and intensity. The strategy resulted in stable expression patterns providing a platform for the direct comparison and assessment of the specific impact of the expression of individual dominant
FLO
genes with regard to cell wall characteristics, such as hydrophobicity, biofilm formation, and substrate adhesion properties. The data also clearly demonstrate that the flocculation behavior of yeast strains can be tightly controlled and fine-tuned to satisfy specific industrial requirements.
Real-Time PCR Method for Detection of Pathogenic
Yersinia enterocolitica
in Food
Authors: Lambertz S. Thisted , Nilsson C. , Hallanvuo S. , Lindblad M. 
Published: August 2008

ABSTRACT

The current methods for the detection of pathogenic
Yersinia enterocolitica
bacteria in food are time consuming and inefficient. Therefore, we have developed and evaluated in-house a TaqMan probe-based real-time PCR method for the detection of this pathogen. The complete method comprises overnight enrichment, DNA extraction, and real-time PCR amplification. Also included in the method is an internal amplification control. The selected primer-probe set was designed to use a 163-bp amplicon from the chromosomally located gene
ail
(attachment and invasion locus). The selectivity of the PCR method was tested with a diverse range (
n
= 152) of related and unrelated strains, and no false-negative or false-positive PCR results were obtained. The sensitivity of the PCR amplification was 85 fg purified genomic DNA, equivalent to 10 cells per PCR tube. Following the enrichment of 10 g of various food samples (milk, minced beef, cold-smoked sausage, fish, and carrots), the sensitivity ranged from 0.5 to 55 CFU
Y. enterocolitica
. Good precision, robustness, and efficiency of the PCR amplification were also established. In addition, the method was tested on naturally contaminated food; in all, 18 out of 125 samples were positive for the
ail
gene. Since no conventional culture method could be used as a reference method, the PCR products amplified from these samples were positively verified by using conventional PCR and sequencing of the amplicons. A rapid and specific real-time PCR method for the detection of pathogenic
Y. enterocolitica
bacteria in food, as presented here, provides a superior alternative to the currently available detection methods and makes it possible to identify the foods at risk for
Y. enterocolitica
contamination.
O
2
- and NO-Sensing Mechanism through the DevSR Two-Component System in
Mycobacterium smegmatis
Authors: Lee Jin-Mok , Cho Ha Yeon , Cho Hyo Je , Ko In-Jeong , Park Sae Woong , Baik Hyung-Suk , Oh Jee-Hyun , Eom Chi-Yong , Kim Young Min , Kang Beom Sik , Oh Jeong-Il 
Published: August 2008

ABSTRACT

The DevS histidine kinase of
Mycobacterium smegmatis
contains tandem GAF domains (GAF-A and GAF-B) in its N-terminal sensory domain. The heme iron of DevS is in the ferrous state when purified and is resistant to autooxidation from a ferrous to a ferric state in the presence of O
2
. The redox property of the heme and the results of sequence comparison analysis indicate that DevS of
M. smegmatis
is more closely related to DosT of
Mycobacterium tuberculosis
than DevS of
M. tuberculosis
. The binding of O
2
to the deoxyferrous heme led to a decrease in the autokinase activity of DevS, whereas NO binding did not. The regulation of DevS autokinase activity in response to O
2
and NO was not observed in the DevS derivatives lacking its heme, indicating that the ligand-binding state of the heme plays an important role in the regulation of DevS kinase activity. The redox state of the quinone/quinol pool of the respiratory electron transport chain appears not to be implicated in the regulation of DevS activity. Neither cyclic GMP (cGMP) nor cAMP affected DevS autokinase activity, excluding the possibility that the cyclic nucleotides serve as the effector molecules to modulate DevS kinase activity. The three-dimensional structure of the putative GAF-B domain revealed that it has a GAF folding structure without cyclic nucleotide binding capacity.
Involvement of an Essential Gene,mviN, in Murein Synthesis inEscherichia coli
Authors: Inoue Azusa , Murata Yoshimitsu , Takahashi Hiroshi , Tsuji Naoko , Fujisaki Shingo , Kato Jun-ichi 
Published: August 2008

ABSTRACTWe isolated a temperature-sensitive mutant with a mutation inmviN, an essential gene inEscherichia coli. At the nonpermissive temperature,mviNmutant cells swelled and burst. An intermediate in murein synthesis, polyprenyl diphosphate-N-acetylmuramic acid-(pentapeptide)-N-acetyl-glucosamine, accumulated in mutant cells. These results indicated that MviN is involved in murein synthesis.
Sinorhizobium melilotiMutants Deficient in Phosphatidylserine Decarboxylase Accumulate Phosphatidylserine and Are Strongly Affected during Symbiosis with Alfalfa
Authors: Vences-Guzmán Miguel Angel , Geiger Otto , Sohlenkamp Christian 
Published: August 2008

ABSTRACTSinorhizobium meliloticontains phosphatidylglycerol, cardiolipin, phosphatidylcholine, and phosphatidylethanolamine (PE) as major membrane lipids. PE is formed in two steps. In the first step, phosphatidylserine synthase (Pss) condenses serine with CDP-diglyceride to form phosphatidylserine (PS), and in the second step, PS is decarboxylated by phosphatidylserine decarboxylase (Psd) to form PE. In this study we identified the sinorhizobialpsdgene coding for Psd. A sinorhizobial mutant deficient inpsdis unable to form PE but accumulates the anionic phospholipid PS. Properties of PE-deficient mutants lacking either Pss or Psd were compared with those of theS. melilotiwild type. Whereas both PE-deficient mutants grew in a wild-type-like manner on many complex media, they were unable to grow on minimal medium containing high phosphate concentrations. Surprisingly, thepsd-deficient mutant could grow on minimal medium containing low concentrations of inorganic phosphate, while thepss-deficient mutant could not. Addition of choline to the minimal medium rescued growth of thepss-deficient mutant, CS111, to some extent but inhibited growth of thepsd-deficient mutant, MAV01. When the two distinct PE-deficient mutants were analyzed for their ability to form a nitrogen-fixing root nodule symbiosis with their alfalfa host plant, they behaved strikingly differently. The Pss-deficient mutant, CS111, initiated nodule formation at about the same time point as the wild type but did form about 30% fewer nodules than the wild type. In contrast, the PS-accumulating mutant, MAV01, initiated nodule formation much later than the wild type and formed 90% fewer nodules than the wild type. The few nodules formed by MAV01 seemed to be almost devoid of bacteria and were unable to fix nitrogen. Leaves of alfalfa plants inoculated with the mutant MAV01 were yellowish, indicating that the plants were starved for nitrogen. Therefore, changes in lipid composition, including the accumulation of bacterial PS, prevent the establishment of a nitrogen-fixing root nodule symbiosis.
Role of Premature Stop Codons in Bacterial Evolution
Authors: Wong Tit-Yee , Fernandes Sanjit , Sankhon Naby , Leong Patrick P. , Kuo Jimmy , Liu Jong-Kang 
Published: August 2008

ABSTRACT

When the stop codons TGA, TAA, and TAG are found in the second and third reading frames of a protein-encoding gene, they are considered premature stop codons (PSC).
Deinococcus radiodurans
disproportionately favored TGA more than the other two triplets as a PSC. The TGA triplet was also found more often in noncoding regions and as a stop codon, though the bias was less pronounced. We investigated this phenomenon in 72 bacterial species with widely differing chromosomal GC contents. Although TGA and TAG were compositionally similar, we found a great variation in use of TGA but a very limited range of use of TAG. The frequency of use of TGA in the gene sequences generally increased with the GC content of the chromosome, while the frequency of use of TAG, like that of TAA, was inversely proportional to the GC content of the chromosome. The patterns of use of TAA, TGA and TAG as real stop codons were less biased and less influenced by the GC content of the chromosome. Bacteria with higher chromosomal GC contents often contained fewer PSC trimers in their genes. Phylogenetically related bacteria often exhibited similar PSC ratios. In addition, metabolically versatile bacteria have significantly fewer PSC trimers in their genes. The bias toward TGA but against TAG as a PSC could not be explained either by the preferential usage of specific codons or by the GC contents of individual chromosomes. We proposed that the quantity and the quality of the PSC in the genome might be important in bacterial evolution.
Molecular Characterization of a
Clostridium difficile
Bacteriophage and Its Cloned Biologically Active Endolysin
Authors: Mayer Melinda J. , Narbad Arjan , Gasson Michael J. 
Published: August 2008

ABSTRACT

Clostridium difficile
infection is increasing in both frequency and severity, with the emergence of new highly virulent strains highlighting the need for more rapid and effective methods of control. Here, we show that bacteriophage endolysin can be used to inhibit and kill
C. difficile
. The genome sequence of a novel bacteriophage that is active against
C. difficile
was determined, and the bacteriophage endolysin gene was subcloned and expressed in
Escherichia coli
. The partially purified endolysin was active against 30 diverse strains of
C. difficile
, and importantly, this group included strains of the major epidemic ribotype 027 (B1/NAP1). In contrast, a range of commensal species that inhabit the gastrointestinal tract, including several representatives of the clostridium-like
Firmicutes
, were insensitive to the endolysin. This endolysin provides a platform for the generation of both therapeutic and detection systems to combat the
C. difficile
problem. To investigate a method for the protected delivery and production of the lysin in the gastrointestinal tract, we demonstrated the expression of active CD27L endolysin in the lactic acid bacterium
Lactococcus lactis
MG1363.