bluuebunny/crossref_metadata_2025 huggingface dataset:
Hepatic oxidant/antioxidant status in cholesterol‐fed rabbits: Effects of garlic extract
Authors: Arhan Mehmet , Öztürk H. Serdar , Turhan Nesrin , Aytac Bilal , Güven M. Cengiz , Olcay Ekmel , Durak İlker
Published: August 2008

Aim: The investigation of oxidant/antioxidant status in hepatic tissues from cholesterol‐fed rabbits and the establishment of possible protective effects of aqueous garlic extract on cholesterol‐induced hepatic steatosis.

Methods: Twenty‐two of 31 white New Zealand rabbits were given cholesterol (0.5 g/kg/day) for 4 months. Seven of them were then killed (cholesterol group). The remaining 15 animals were divided into two groups. Seven were fed on a normal laboratory diet (normal diet group) and the others (extract group) on a normal diet plus garlic extract (1.5 ml/kg/day) for an additional 3 months. Superoxide dismutase (SOD), glutathione peroxidase (GSH‐Px), catalase (CAT) enzyme activities, antioxidant potential (AOP) value, malondialdehyde (MDA), cholesterol and triglyceride levels in the liver tissues and total cholesterol and triglyceride levels in serum samples were measured. An histological evaluation was also done.

Results: An impaired antioxidant system, reduced antioxidant defence potential and increased peroxidation were found in hepatic steatotic tissues from cholesterol‐fed animals. Treatment with garlic extract caused a significant increase in antioxidant potential and partly eliminated peroxidation damage in the hepatic tissue. Additionally, the extract caused significant reductions in the cholesterol levels of blood and hepatic tissues. The histological evaluations were in accordance with these results.

Conclusion: The results suggest that cholesterol‐induced steatosis leads to a weakened antioxidant defence system and causes peroxidation in the hepatic tissue. Treatment with garlic extract may contribute to significant amelioration in the hepatic steatosis and peroxidation processes.
Liver regeneration is impaired by FK778 in partially hepatectomized rats, while supplemental uridine restores both liver growth and hepatocyte proliferation
Authors: Biglarnia Ali‐Reza , Lorant Tomas , Lee Hyon‐Soek , Tufveson Gunnar , Tötsch Martin , Malagó Massimo
Published: August 2008

Aim:  The impact of mandatory immunosuppression on liver regeneration after segmental liver transplantation is of clinical importance. FK778, a novel immunosuppressant, inhibits pyrimidine biosynthesis and prevents rejection after organ transplantation in a dose‐dependent manner. We investigated the effect of FK778 at a highly effective dose on liver regeneration in a small animal model.

Methods:  Inbred Lewis rats were subjected to 70% partial hepatectomy (PH) and treated with saline (n = 28), uridine (n = 16), FK778 alone (n = 28) or in combination with uridine (n = 16). FK778 was given intravenously daily at a dose of 25 mg/kg bodyweight (bw) and uridine was given daily intraperitoneally at a dose of 250 mg/kg bw. Liver bodyweight ratio (LBR), hepatocyte proliferation index (PI), blood chemistry and morphological analysis were incorporated. PI was determined by Ki‐67 immunostaining. De Ritis ratio was calculated to assess the extent of liver damage.

Results:  In FK778‐treated animals PI was decreased at 24 h and 72 h and LBR was lower at 48 h and 72 h (P < 0.05) after the PH. In addition, morphological analysis showed confluent central lobular necrosis at 72 h in four of seven animals. Uridine supplementation restored PI, LBR and the de Ritis ratio in FK778‐treated animals and no confluent necroses were observed.

Conclusion:  FK778 is antihepatotrophic as well as antiproliferative during rat liver regeneration. Both liver growth and hepatocyte proliferation are completely restored by supplementation with uridine. In addition, supplemental uridine markedly reduces the severity of morphological abnormalities consistent with FK778 toxicity.
Frequency and distribution of hepatitis B virus genotypes among eastern Indian voluntary blood donors: Association with precore and basal core promoter mutations
Authors: Biswas Avik , Chandra Partha K , Datta Sibnarayan , Panigrahi Rajesh , Banerjee Arup , Chakrabarti Shekhar , Biswas Kalidas , Patra Dipak , Bhattacharya Prasun , Biswas Kuntal , Chakravarty Runu
Published: August 2008

Aim:  To screen hepatitis B virus (HBV) genotypes and associated basal core promoter (BCP; T1762/A1764) and precore (PreC; A1896) mutations among the HBV surface antigen (HBsAg) positive voluntary blood donors in eastern India.

Methods:  HBV genotypes, BCP and PreC mutations of 141 HBsAg positive voluntary blood donors were determined by the restriction fragment length polymorphism (RFLP) method and a phylogenetic tree was constructed from surface (S) gene region sequences of representative HBsAg positive donors to confirm the results.

Results:  HBV/D was the most predominant (79, 56.0%) genotype followed by HBV/C (33, 23.4%) and HBV/A (29, 20.6%). HBV/C infected blood donors are mostly young (18–25 years). The occurrence of BCP mutation was found to be significantly higher in HBV/C (24, 72.7%) than in HBV/A (7, 24.1%, P < 0.001) and HBV/D (17, 21.5%, P < 0.001), whereas PreC mutation was more frequent in HBV/D (28, 35.4%) than in HBV/C (9, 27.3%). However, the simultaneous presence of BCP and PreC mutations was more common in HBV/C (8/33, 24.2%), followed by HBV/D (6/79, 7.6%).

Conclusion:  In addition to HBV/D and HBV/A, a significant proportion of HBV/C (23.4%) was also present among the voluntary blood donors from eastern India, most frequently in the 18–25 year age group. BCP mutation was more common in HBV/C infected donors.
Effect of porto‐systemic shunting on NOS expression after extended hepatectomy in rats
Authors: Hayashi Hironori , Shimizu Koichi , Tani Takashi , Takamura Hiroyuki , Takeshita Masaki , Nakamura Keishi , Ninomiya Itasu , Fushida Sachio , Harada Shin‐ichi , Kayahara Masato
Published: August 2008

Aim:  Several surgical procedures have been developed for reducing portal vein pressure to prevent postoperative liver injury. Nitric oxide synthase expression (NOS) induced by elevation of portal vein pressure is thought to play an important role in liver regeneration, but the details are not well understood.

Methods:  Rats in the control group and in the subcutaneous splenic transposition (SST) group underwent 90% partial hepatectomy. Survival and portal vein pressure were analyzed. The serum IL‐6 and TNF‐α levels were measured by enzyme‐linked immunosorbent assay (ELISA). Hepatocyte proliferation and apoptosis 12 hours after hepatectomy were analyzed immunohistochemically. The protein and messenger RNA expression of inducible and endothelial NOS were analyzed using Western blotting and quantitative reverse transcriptase polymerase chain reaction, respectively.

Results:  The survival rate of the SST group was significantly higher. Portal vein pressure, TNF‐α level and the apoptotic index were significantly lower in the SST group. Twelve hours after surgery, liver inducible NOS (iNOS) protein expression was significantly lower in the SST group. However, protein expression of endothelial NOS was not significantly different between the groups.

Conclusion:  Inducible NOS expression after extended hepatectomy is related to the effects of porto‐systemic shunting on the splanchnic circulation. Also, iNOS induction and concomitant nitric oxide generation appear to participate in the cytotoxicity of excessive portal pressure after extended hepatectomy.
Dynamic Performance and Modular Design of Redundant Macro-/Minimanipulators
Authors: Bowling Alan P. , Khatib Oussama
Published: August 2008

This paper presents methodologies for the analysis and design of redundant manipulators, especially macro-/ministructures, for improved dynamic performance. Herein, the dynamic performance of a redundant manipulator is characterized by the end-effector inertial and acceleration properties. The belted inertia ellipsoid is used to characterize inertial properties, and the recently developed dynamic capability equations are used to analyze acceleration capability. The approach followed here is to design the ministructure to achieve the task performance and then to design the macrostructure to support and complement the ministructure, referred to here as modular design. The methodology is illustrated in the design of a six-degree-of-freedom planar manipulator.
The Influence of a Cracked Blade on Rotor’s Free Vibration
Authors: Chiu Yi-Jui , Huang Shyh-Chin
Published: August 2008

The influence on the coupled vibrations among shaft, disk, and blades of a rotor system due to a cracked blade was investigated analytically. On the shaft-disk-blade system, without a cracked blade, there exist three types of coupled modes, shaft disk blade (SDB), disk blade (DB), and blade-blade. A cracked blade was found to change not only the natural frequencies but also the types of coupled modes. First, the DB modes disappeared and were replaced by SDB modes. Second, in some modes the disk experienced mode localization due to the cracked blade. Numerical results showed that natural frequencies varied with the blade’s crack location and depth. At no bending moment places the crack imposed no effect. The crack affected the natural frequency slightly until its depth reached as deep as 70% then the frequency dropped abruptly.
Design of a Combined Solar Dryer: Thermal-Photovoltaic for the Treatment of Grains
Authors: Pilatowsky I. , Gama D. , Ortega J. , Campos J. , Best R. , Oskam A. H. , Finck A.
Published: August 2008

Solar drying is one of the most vastly used technologies in rural areas, especially in developing countries, allowing for self provision and commercialization of products with an added value. Among the technical problems encountered, is the control of the operating conditions, due mainly to the intermittency of solar radiation which in turn produces a non homogeneous treatment of the product making it necessary to control both temperature and air velocity. Considering these facts, the design of a dryer for the treatment of grains is proposed, with the intention of obtaining control on the kinetics of drying using direct or indirect solar heating and electrical energy storage from a solar photovoltaic system within established air velocities and temperatures ranges. The energy required for the grain treatment is provided by a solar thermal-photovoltaic multipurpose solar unit installed in the solar testing platform at CIE-UNAM. Solar heating can be carried out by indirect heating of air using a thermo hydronic system with a water to air heat exchanger or by means of an one pass solar air heater. The heating of air can be direct during the day or using thermal storage both at night as well as the following day. The dryer can be operated during the day or the night or 24 hours a day if it is required, depending on the thermal and photovoltaic system configurations. The photovoltaic system is composed of photovoltaic panels, batteries and a charge controller and it has been designed to operate the fan motor as well as the lamps in the night time, however a total solar operation is possible by activating circulation pumps between the solar array and the dryer, between the solar collectors field and the thermal storage tank and between the storage tank and the dryer. Part of the electricity generated is for day use for the fan and the other electric components and the rest is stored for night utilization. This paper presents the conditions and parameters for the design of the grain dryer, the different heating circuits and the integration aspects of measurement and control devices of the multipurpose solar unit, as well as the operating modes.
Thermal Analysis of a Conical Receiver in a Parabolloid Dish to be Used as Generator in an Advanced Solar Thermal Cooling System
Authors: Sauceda D. , Vela´zquez N. , Beltra´n R. , Quintero M.
Published: August 2008

In this paper an experimental thermal analysis made to a conical receiver attached to a solar parabolloid dish concentrator is presented, the purpose of this study is to know if it fulfills the requirements as far as quality and amount of energy demanded by a generator of a solar thermal cooling system (Solar-Branched-GAX Cycle). The analyzed system consists of a conical receiver of 19 cm of diameter by 20 cm of height, which was mounted to a focal length of 80 cm in a communications conventional antenna of 190 cm diameter, prepared with a reflecting coat. The concentrator was mounted in a multipurpose proving stand of solar collectors, with a solar tracking system in two axes. The analysis was carried out by evaluating experimentally three cases, which consisted of: A) receiver smooth, B) Receiver smooth with glass cover and C) Receiver with fins in the inner tail cone. According to the obtained results it can be concluded that the system of parabolloid disc concentrator using a conical receiver with fins is a very interesting option to be used as a generator of a solar thermal refrigeration system, since steam for a volumetric flow of 0.480 l/min can be generated.
Single molecule measurements with photoelectron emission microscopy
Authors: Kong Xianhua , Rowe J. E. , Nemanich R. J.
Published: August 2008

In this research, variable wavelength photoelectron emission microscopy (PEEM) with tunable UV light from the Duke University free electron laser is applied to image single fibrinogen molecules adsorbed onto n-type silicon surfaces. High resolution PEEM images (∼10nm) are obtained with photon energies from 4to6eV. Wavelength-dependent image sequences are analyzed to determine the photoionization spectrum and the photoelectron emission threshold of individual molecules. The experimental data are fitted using temperature dependent Fowler law, square-root law, and cube-root law. The details of the theoretical models are discussed. The square-root and cube-root fittings reveal the ionization threshold of 5.0eV for fibrinogen adsorbed onto n-type silicon, while temperature dependent Fowler law shows a threshold of 4.9eV. The accuracy of the measurements is calculated to be ±0.2eV. The authors conclude that no significant difference is observed from the three theoretical fitting approaches.
Conformal filling of silicon micropillar platform with b10oron
Authors: Deo N. , Brewer J. R. , Reinhardt C. E. , Nikolić R. J. , Cheung C. L.
Published: August 2008

A recently proposed micropillar semiconductor platform filled with a high volume of isotopic b10oron (B10) has great potential to yield efficient thermal neutron detectors because B10 has a high thermal neutron cross section. Here, the authors report the development of conformal filling of high aspect ratio silicon micropillar platforms with B10 by low pressure chemical vapor deposition (LPCVD) using B10-enriched decaborane (B10H14). The relationships between the pillar structure and the key process parameters including reaction temperature, process pressure, and buffer gas flow rates were investigated to optimize the conformal filling on these structures. Reaction temperature of 420–530 °C, process pressure of 50–450 mTorr, 0.3 SCCM (SCCM denotes cubic centimeter per minute at STP) B10H14 flow rate, and argon buffer gas flow rate of 0–200 SCCM were used to deposit B10 materials into the micropillar structures with aspect ratios of 3:1, 6:1, and 10:1. All three mentioned pillar structures were found to be completely (∼100%) filled with B10 at 420 °C and 50 mTorr. At higher process temperatures, the fill factors of the three pillar structures decreased significantly. The effect of reaction temperature, process pressure, and buffer gas flow rates on the LPCVD deposition mechanism with respect to the structure geometry are also discussed.
Surface bonding effects in compound semiconductor nanoparticles: II
Authors: Farrell H. H.
Published: August 2008

Small nanoparticles have a large proportion of their atoms either at or near the surface, and those in clusters are essentially all on the surface. As a consequence, the details of the surface structure are of paramount importance in governing the overall stability of the particle. Just as with bulk materials, factors that determine this stability include “bulk” structure, surface reconstruction, charge balance and hybridization, ionicity, strain, stoichiometry, and the presence of adsorbates. Needless to say, many of these factors, such as charge balance, hybridization, and strain, are interdependent. These factors all contribute to the overall binding energy of clusters and small nanoparticles and play a role in determining the deviations from an inverse size dependence that the authors have previously reported for compound semiconductor materials. Using first-principles density functional theory calculations, the authors have explored how these factors influence particle stability under a variety of conditions.
Evaluation of an electron Monte Carlo dose calculation algorithm for electron beams
Authors: Hu Ye Angela , Song Haijun , Chen Zhe , Zhou Sumin , Yin Fang‐Fang
Published: August 2008

The electron Monte Carlo (eMC) dose calculation algorithm of the Eclipse treatment planning system is based heavily upon Monte Carlo simulation of the linac head and modeling of the linac beam characteristics with minimal measurement of beam data. Commissioning of the eMC algorithm on multiple identical linacs provided a unique opportunity to systematically evaluate the algorithm with actual measurements of clinically relevant beam and dose parameters. In this study, measured and eMC calculated dose distributions were compared both along and perpendicular to electron beam direction for electron energy/applicator/depth combination using measurement data from four Varian CLINAC 21EX linear accelerators (Varian Medical Systems, Palo Alto, CA). Cutout factors for sizes down to were also compared. Comparisons between the measurement and the eMC calculated values show that the , , , and values mostly agree within 3 mm. Measure and calculated bremsstrahlung dose Dx correlates well statistically although eMC calculated values are consistently smaller than the measured, with maximum discrepancy of 1% for the 20 MeV electron beams. Surface dose agrees mostly within 2%. Field width and penumbra agree mostly within 3 mm. Calculation grid size is found to have a significant effect on the dose calculation. A grid size of 5 mm can produce erroneous dose distributions. Using a grid size of 2.5 mm and a 3% accuracy specified for the eMC to stop calculation iteration, the absolute output agrees with measurements within 3% for field sizes of or larger. For cutout of , however, the output disagreement can reach 8%. Our results indicate that the eMC algorithm in Eclipse provides acceptable agreement with measurement data for most clinical situations. Calculation grid size of 2.5 mm or smaller is recommended.
Establishing action levels for EPID‐based QA for IMRT
Authors: Howell Rebecca M. , Smith Iris P. N. , Jarrio Christie S.
Published: August 2008

Although portal dosimetry is used to provide quality assurance (QA) for intensity‐modulated radiation therapy (IMRT) treatment plans, trends in agreement between the portal dose prediction (PDP) and the measured dose have not been clarified. In this work, we evaluated three scalar parameters of agreement for 152 treatment plans (1152 treatment fields): maximum gamma , average gamma , and percentage of the field area with a gamma value greater than 1.0 . These data were then used to set clinical action levels based on the institutional mean and standard deviations. We found that agreement between measured dose and PDP was improved by recalculating the fields at lower dose rates. We conclude that action levels are a useful tool for standardizing the evaluation of EPID‐based IMRT QA.

PACS numbers: 87.53.Oq, 87.53.Mr, 87.53.Xd
Time‐course of effects of external beam radiation on [18F]FDG uptake in healthy tissue and bone marrow
Authors: Kesner Adam L , Lau Victoria K , Speiser Michael , Hsueh Wei‐Ann , Agazaryan Nzhde , DeMarco John J , Czernin Johannes , Silverman Daniel HS
Published: August 2008

The utility of PET for monitoring responses to radiation therapy have been complicated by metabolically active processes in surrounding normal tissues. We examined the time‐course of [18F]FDG uptake in normal tissues using small animal‐dedicated PET during the 2 month period following external beam radiation. Four mice received 12 Gy of external beam radiation, in a single fraction to the left half of the body. Small animal [18F]FDG‐PET scans were acquired for each mouse at 0 (pre‐radiation), 1, 2, 3, 4, 5, 8, 12, 19, 24, and 38 days following irradiation. [18F]FDG activity in various tissues was compared between irradiated and non‐irradiated body halves before, and at each time point after irradiation. Radiation had a significant impact on [18F]FDG uptake in previously healthy tissues, and time‐course of effects differed in different types of tissues. For example, liver tissue demonstrated increased uptake, particularly over days 3–12, with the mean left to right uptake ratio increasing 52% over mean baseline values . In contrast, femoral bone marrow uptake demonstrated decreased uptake, particularly over days 2–8, with the mean left to right uptake ratio decreasing 26% below mean baseline values . Significant effects were also seen in lung and brain tissue. Radiation had diverse effects on [18F]FDG uptake in previously healthy tissues. These kinds of data may help lay groundwork for a systematically acquired database of the time‐course of effects of radiation on healthy tissues, useful for animal models of cancer therapy imminently, as well as interspecies extrapolations pertinent to clinical application eventually.

PACs Number: 87.50.‐a
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‐
Unified dosimetry index (UDI): a figure of merit for ranking treatment plans
Authors: Akpati Hilary , Kim ChangSeon , Kim Bong , Park Tae , Meek Allen
Published: August 2008

We have formulated a unified dosimetry index (UDI) that computes, for any given treatment plan, its deviations in terms of dose coverage, conformity, homogeneity, and dose gradient vis‐à‐vis an ideal plan (which we define as a dosimetry plan of perfect dose coverage, conformity, homogeneity, and step‐wise fall‐off to zero dose outside the planning target volume). In order to validate the UDI scoring system, 21 stereotactic cranial radiosurgery cases were evaluated retrospectively. The cases were planned on the BrainSCAN treatment planning system (BrainLAB, Feldkirchen, Germany) using 6 to 8 non‐coplanar static beams collimated with the micro multi‐leaf collimator (mMLC). We suggest a technique for creating a ranking system that can be utilized for plan evaluation and comparison between multiple plans. Under this system treatment plans are classified as “excellent”, “good”, “average”, or “poor”. The proposed ranking system can be utilized as a general guide for generating an optimal dosimetry plan for external beam radiation therapy.
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
Variability and Robustness in T Cell Activation from Regulated Heterogeneity in Protein Levels
Authors: Feinerman Ofer , Veiga Joël , Dorfman Jeffrey R. , Germain Ronald N. , Altan-Bonnet Grégoire
Published: August 2008

In T cells, the stochasticity of protein expression could contribute to the useful diversification of biological functions within a clonal population or interfere with accurate antigen discrimination. Combining computer modeling and single-cell measurements, we examined how endogenous variation in the expression levels of signaling proteins might affect antigen responsiveness during T cell activation. We found that the CD8 co-receptor fine-tunes activation thresholds, whereas the soluble hematopoietic phosphatase 1 (SHP-1) digitally regulates cell responsiveness. Stochastic variation in the expression of these proteins generates substantial diversity of activation within a clonal population of T cells, but co-regulation of CD8 and SHP-1 levels ultimately limits this very diversity. These findings reveal how eukaryotic cells can draw on regulated variation in gene expression to achieve phenotypic variability in a controlled manner.
The Global Atmospheric Circulation on Moist Isentropes
Authors: Pauluis Olivier , Czaja Arnaud , Korty Robert
Published: August 2008

The global atmospheric circulation transports energy from the equatorial regions to higher latitudes through a poleward flow of high-energy and -entropy parcels and an equatorward flow of air with lower energy and entropy content. Because of its turbulent nature, this circulation can only be described in some averaged sense. Here, we show that the total mass transport by the circulation is twice as large when averaged on moist isentropes than when averaged on dry isentropes. The additional mass transport on moist isentropes corresponds to a poleward flow of warm moist air near Earth's surface that rises into the upper troposphere within mid-latitudes and accounts for up to half of the air in the upper troposphere in polar regions.
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

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

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

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

We 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

Sinorhizobium 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

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

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.