bluuebunny/crossref_metadata_2025_split huggingface dataset:
BrachyView, A novel inbody imaging system for HDR prostate brachytherapy: Design and Monte Carlo feasibility study
Authors: Safavi‐Naeini M. , Han Z. , Cutajar D. , Guatelli S. , Petasecca M. , Lerch M. L. F. , Franklin D. R. , Jakubek J. , Pospisil S. , Bucci J. , Zaider M. , Rosenfeld A. B. 
Published: June 2013

Purpose:High dose rate (HDR) brachytherapy is a form of radiation therapy for treating prostate cancer whereby a high activity radiation source is moved between predefined positions inside applicators inserted within the treatment volume. Accurate positioning of the source is essential in delivering the desired dose to the target area while avoiding radiation injury to the surrounding tissue. In this paper,HDR BrachyView, a novel inbody dosimetric imaging system for real time monitoring and verification of the radioactive seed position in HDR prostate brachytherapy treatment is introduced. The current prototype consists of a 15 × 60 mm2 silicon pixel detector with a multipinhole tungsten collimator placed 6.5 mm above the detector. Seven identical pinholes allow full imaging coverage of the entire treatment volume. The combined pinhole and pixel sensor arrangement is geometrically designed to be able to resolve the three‐dimensional location of the source. The probe may be rotated to keep the whole prostate within the transverse plane. The purpose of this paper is to demonstrate the efficacy of the design through computer simulation, and to estimate the accuracy in resolving the source position (in detector plane and in 3D space) as part of the feasibility study for the BrachyView project.Methods:Monte Carlo simulations were performed using the GEANT4 radiation transport model, with a192Ir source placed in different locations within a prostate phantom. A geometrically accurate model of the detector and collimator were constructed. Simulations were conducted with a single pinhole to evaluate the pinhole design and the signal to background ratio obtained. Second, a pair of adjacent pinholes were simulated to evaluate the error in calculated source location.Results:Simulation results show that accurate determination of the true source position is easily obtainable within the typical one second source dwell time. The maximum error in the estimated projection position was found to be 0.95 mm in the imaging (detector) plane, resulting in a maximum source positioning estimation error of 1.48 mm.Conclusions:HDR BrachyView is a feasible design for real‐time source tracking in HDR prostate brachytherapy. It is capable of resolving the source position within a subsecond dwell time. In combination with anatomical information obtained from transrectal ultrasound imaging, HDR BrachyView adds a significant quality assurance capability to HDR brachytherapy treatment systems.
Dosimetric comparison of helical tomotherapy treatment plans for total marrow irradiation created using GPU and CPU dose calculation engines
Authors: Nalichowski Adrian , Burmeister Jay 
Published: June 2013

Purpose:To compare optimization characteristics, plan quality, and treatment delivery efficiency between total marrow irradiation (TMI) plans using the new TomoTherapy graphic processing unit (GPU) based dose engine and CPU/cluster based dose engine.Methods:Five TMI plans created on an anthropomorphic phantom were optimized and calculated with both dose engines. The planning treatment volume (PTV) included all the bones from head to mid femur except for upper extremities. Evaluated organs at risk (OAR) consisted of lung, liver, heart, kidneys, and brain. The following treatment parameters were used to generate the TMI plans: field widths of 2.5 and 5 cm, modulation factors of 2 and 2.5, and pitch of either 0.287 or 0.43. The optimization parameters were chosen based on the PTV and OAR priorities and the plans were optimized with a fixed number of iterations. The PTV constraint was selected to ensure that at least 95% of the PTV received the prescription dose. The plans were evaluated based on D80 and D50 (dose to 80% and 50% of the OAR volume, respectively) and hotspot volumes within the PTVs. Gamma indices (Γ) were also used to compare planar dose distributions between the two modalities. The optimization and dose calculation times were compared between the two systems. The treatment delivery times were also evaluated.Results:The results showed very good dosimetric agreement between the GPU and CPU calculated plans for any of the evaluated planning parameters indicating that both systems converge on nearly identical plans. All D80 and D50 parameters varied by less than 3% of the prescription dose with an average difference of 0.8%. A gamma analysis Γ(3%, 3 mm) < 1 of the GPU plan resulted in over 90% of calculated voxels satisfying Γ < 1 criterion as compared to baseline CPU plan. The average number of voxels meeting the Γ < 1 criterion for all the plans was 97%. In terms of dose optimization/calculation efficiency, there was a 20‐fold reduction in planning time with the new GPU system. The average optimization/dose calculation time utilizing the traditional CPU/cluster based system was 579 vs 26.8 min for the GPU based system. There was no difference in the calculated treatment delivery time per fraction. Beam‐on time varied based on field width and pitch and ranged between 15 and 28 min.Conclusions:The TomoTherapy GPU based dose engine is capable of calculating TMI treatment plans with plan quality nearly identical to plans calculated using the traditional CPU/cluster based system, while significantly reducing the time required for optimization and dose calculation.
Conditions for reliable time‐resolved dosimetry of electronic portal imaging devices for fixed‐gantry IMRT and VMAT
Authors: Yeo Inhwan Jason , Jung Jae Won , Patyal Baldev , Mandapaka Anant , Yong Yi Byong , Oh Kim Jong 
Published: June 2013

Purpose:The continuous scanning mode of electronic portal imaging devices (EPID) that offers time‐resolved information has been newly explored for verifying dynamic radiation deliveries. This study seeks to determine operating conditions (dose rate stability and time resolution) under which that mode can be used accurately for the time‐resolved dosimetry of intensity‐modulated radiation therapy (IMRT) beams.Methods:The authors have designed the following test beams with variable beam holdoffs and dose rate regulations: a 10 × 10 cm open beam to serve as a reference beam; a sliding window (SW) beam utilizing the motion of a pair of multileaf collimator (MLC) leaves outside the 10 × 10 cm jaw; a step and shoot (SS) beam to move the pair in step; a volumetric modulated arc therapy (VMAT) beam. The beams were designed in such a way that they all produce the same open beam output of 10 × 10 cm. Time‐resolved ion chamber measurements at isocenter and time‐resolved and integrating EPID measurements were performed for all beams. The time‐resolved EPID measurements were evaluated through comparison with the ion chamber and integrating EPID measurements, as the latter are accepted procedures. For two‐dimensional, time‐resolved evaluation, a VMAT beam with an infield MLC travel was designed. Time‐resolved EPID measurements and Monte Carlo calculations of such EPID dose images for this beam were performed and intercompared.Results:For IMRT beams (SW and SS), the authors found disagreement greater than 2%, caused by frame missing of the time‐resolved mode. However, frame missing disappeared, yielding agreement better than 2%, when the dose rate of irradiation (and thus the frame acquisition rates) reached a stable and planned rate as the dose of irradiation was raised past certain thresholds (a minimum 12 s of irradiation per shoot used for SS IMRT). For VMAT, the authors found that dose rate does not affect the frame acquisition rate, thereby causing no frame missing. However, serious inplanar nonuniformities were found. This could be overcome by sacrificing temporal resolution (10 frames or 0.95 s/image): the continuous images agreed with ion chamber responses at the center of EPID and the calculation two‐dimensionally in a time‐resolved manner.Conclusions:The authors have determined conditions under which the continuous mode can be used for time‐resolved dosimetry of fixed‐gantry IMRT and VMAT and demonstrated it for VMAT.
In vivo evaluation of a breast‐specific magnetic resonance guided focused ultrasound system in a goat udder model
Authors: Payne A. , Todd N. , Minalga E. , Wang Y. , Diakite M. , Hadley R. , Merrill R. , Factor R. , Neumayer L. , Parker D. L. 
Published: June 2013

Purpose:This work further evaluates the functionality, efficacy, and safety of a new breast‐specific magnetic resonance guided high intensity focused ultrasound (MRgFUS) system in anin vivo goat udder model.Methods:Eight female goats underwent an MRgFUS ablation procedure using the breast‐specific MRgFUS system. Tissue classification was achieved through the 3D magnetic resonance imaging (MRI) acquisition of several contrasts (T1w, T2w, PDw, 3‐point Dixon). The MRgFUS treatment was performed with a grid trajectory executed in one or two planes within the glandular tissue of the goat udder. Temperature was monitored using a 3D proton resonance frequency (PRF) MRI technique. Delayed contrast enhanced‐MR images were acquired immediately and 14 days post MRgFUS treatment. A localized tissue excision was performed in one animal and histological analysis was performed. Animals were available for adoption at the conclusion of the study.Results:The breast‐specific MRgFUS system was able to ablate regions ranging in size from 0.4 to 3.6 cm3 in the goat udder model. Tissue damage was confirmed through the correlation of thermal dose measurements obtained with realtime 3D MR thermometry to delayed contrast enhanced‐MR images immediately after the treatment and 14 days postablation. In general, lesions were longer in the ultrasound propagation direction, which is consistent with the dimensions of the ultrasound focal spot. Thermal dose volumes had better agreement with nonenhancing areas of the DCE‐MRI images obtained 14 days after the MRgFUS treatment.Conclusions:The system was able to successfully ablate lesions up to 3.6 cm3. The thermal dose volume was found to correlate better with the 14‐day postablation nonenhancing delayed contrast enhanced‐MR image volumes. While the goat udder is not an ideal model for the human breast, this study has proven the feasibility of using this system on a wide variety of udder shapes and sizes, demonstrating the flexibility that would be required in order to treat human subjects.
Acoustic measurements and the individual subjective evaluation for sound fields
Authors: Sakai Hiroyuki 
Published: June 2013

Acoustical measurements and individual subjective evaluations for sound fields were performed based on a model of the human auditory-brain system and subjective preference theory. In the acoustic measurement section, orthogonal factors in historical opera houses and outdoor sound fields in forests are discussed. In the subjective evaluation section, individual differences and intra-individual changes of subjective preference are described in terms of the orthogonal factors. The main conclusions are as follows: (1) In acoustic measurements in a forest and in a bamboo forest, it is found that multiple scattering effects between trees or bamboo improve IACC; (2) Results of a preference test in an existing opera house show that subjective preference theory can be applied to opera houses, including the orchestra pit and the box seats; (3) Coefficient is introduced for individual preference in a sound field; and (4) The investigations of preference tests in relation to listening level (LL) and subsequent reverberation time (Tsub) for a simulated sound field show that subjects with a large value of α have small intra-individual changes, so the range of its preferred value is small. On the other hand, subjects with small value have minor preference as its parameter is changed.
Thesis advisor: Yoichi Ando
Copies of this thesis written in English can be obtained from Hiroyuki Sakai, Graduate School of Science and Technology, Kobe University, Rokkodai, Nada, Kobe 657-8501 Japan. E-mail address: sakaih@kobe-u.ac.jp.
Being a badger's advocate
Authors: Cousquer Glen 
Published: June 2013

THIS series gives readers the opportunity to consider and contribute to discussion of some of the ethical dilemmas that can arise in veterinary practice. Each month, a case scenario is presented, followed by discussion of some of the issues involved. In addition, a possible way forward is suggested; however, there is rarely a cut‐and‐dried answer in such cases, and readers may wish to suggest an alternative approach. This month's dilemma, ‘Being a badger's advocate’, is presented and discussed by Glen Cousquer. Readers with comments to contribute are invited to send them as soon as possible, so that they can be considered for publication in the next issue. Discussion of the dilemma ‘Anaesthetic death: who pays?’, which was published in the May issue of In Practice, appears on page 351.The series is being coordinated by Siobhan Mullan, of the University of Bristol. It is hoped it will provide a framework that will help practices find solutions when facing similar dilemmas.
Five-year workplace wellness intervention in the NHS
Authors: Blake Holly , Zhou Dingyuan , Batt Mark E 
Published: June 2013

Aims: Poor health and well-being has been observed among NHS staff and has become a key focus in current public health policy. The objective of this study was to deliver and evaluate a five-year employee wellness programme aimed at improving the health and well-being of employees in a large NHS workplace. Method: A theory-driven multi-level ecological workplace wellness intervention was delivered including health campaigns, provision of facilities and health-promotion activities to encourage employees to make healthy lifestyle choices and sustained behaviour changes. An employee questionnaire survey was distributed at baseline ( n = 1,452) and at five years ( n = 1,134), including measures of physical activity, BMI, diet, self-efficacy, social support, perceived general health and mood, smoking behaviours, self-reported sickness absence, perceived work performance and job satisfaction. Results: Samples were comparable at baseline and follow-up. At five years, significantly more respondents actively travelled (by walking or cycling both to work and for non-work trips) and more were active while at work. Significantly more respondents met current recommendations for physical activity at five years than at baseline. Fewer employers reported ‘lack of time’ as a barrier to being physically active following the intervention. Significantly lower sickness absence, greater job satisfaction and greater organisational commitment was reported at five years than at baseline. Conclusions: Improvements in health behaviours, reductions in sickness absence and improvements in job satisfaction and organisational commitment were observed following five years of a workplace wellness intervention for NHS employees. These findings suggest that health-promoting programmes should be embedded within NHS infrastructure.
Determinants of Stamp Duty Revenue in Indian States
Authors: Mukherjee Vivekananda 
Published: June 2013

This article exploits a panel data set from 18 Indian states over the period between 1993–1994 and 2009–2010 and identifies a set of parameters significantly affecting stamp duty revenue collection in the states. It turns out that among all the parameters, the per capita income of the state has the most significant impact on stamp duty revenue collection. The administrative reforms at the states’ stamp duty and registration departments, like introduction of franking machines and e-governance, have a positive impact on stamp duty revenue collection as well. It is found that the central government’s choice of capital gains tax rate creates an externality on stamp duty revenue collection in the states. The results are used to critically assess the policy of lowering of stamp duty rates and introducing administrative reforms as part of the Urban Reform Incentive Fund implemented by the central government since 2003–2004 (later subsumed under the Jawaharlal Nehru National Urban Renewal Mission (JNNURM)). JEL Classification: H21, H71, H77, C33
Mobilomics in Saccharomyces cerevisiaestrains
Authors: Menconi Giulia , Battaglia Giovanni , Grossi Roberto , Pisanti Nadia , Marangoni Roberto 
Published: June 2013

Abstract

Background
Mobile Genetic Elements (MGEs) are selfish DNA integrated in the genomes. Their detection is mainly based on consensus-like searches by scanning the investigated genome against the sequence of an already identified MGE. Mobilomics aims at discovering all the MGEs in a genome and understanding their dynamic behavior: The data for this kind of investigation can be provided by comparative genomics of closely related organisms. The amount of data thus involved requires a strong computational effort, which should be alleviated.

Results
Our approach proposes to exploit the high similarity among homologous chromosomes of different strains of the same species, following a progressive comparative genomics philosophy. We introduce a software tool based on our new fast algorithm, called regender, which is able to identify the conserved regions between chromosomes. Our case study is represented by a unique recently available dataset of 39 different strains of S.cerevisiae, which regender is able to compare in few minutes. By exploring the non-conserved regions, where MGEs are mainly retrotransposons called Tys, and marking the candidate Tys based on their length, we are able to locate a priori and automatically all the already known Tys and map all the putative Tys in all the strains. The remaining putative mobile elements (PMEs) emerging from this intra-specific comparison are sharp markers of inter-specific evolution: indeed, many events of non-conservation among different yeast strains correspond to PMEs. A clustering based on the presence/absence of the candidate Tys in the strains suggests an evolutionary interconnection that is very similar to classic phylogenetic trees based on SNPs analysis, even though it is computed without using phylogenetic information.

Conclusions
The case study indicates that the proposed methodology brings two major advantages: (a) it does not require any template sequence for the wanted MGEs and (b) it can be applied to infer MGEs also for low coverage genomes with unresolved bases, where traditional approaches are largely ineffective.
Genetic heterogeneity revealed by sequence analysis of Mycobacterium tuberculosis isolates from extra-pulmonary tuberculosis patients
Authors: Das Sarbashis , Roychowdhury Tanmoy , Kumar Parameet , Kumar Anil , Kalra Priya , Singh Jitendra , Singh Sarman , Prasad HK , Bhattacharya Alok 
Published: June 2013

Abstract

Background
Tuberculosis remains a major public health problem. Clinical tuberculosis manifests often as pulmonary and occasionally as extra-pulmonary tuberculosis. The emergence of drug resistant tubercle bacilli and its association with HIV is a formidable challenge to curb the spread of tuberculosis. There have been concerted efforts by whole genome sequencing and bioinformatics analysis to identify genomic patterns and to establish a relationship between the genotype of the organism and clinical manifestation of tuberculosis. Extra-pulmonary TB constitutes 15–20 percent of the total clinical cases of tuberculosis reported among immunocompetent patients, whereas among HIV patients the incidence is more than 50 percent. Genomic analysis of M. tuberculosis isolates from extra pulmonary patients has not been explored.

Results
The genomic DNA of 5 extra-pulmonary clinical isolates of M. tuberculosis derived from cerebrospinal fluid, lymph node fine needle aspirates (FNAC) / biopsies, were sequenced. Next generation sequencing approach (NGS) was employed to identify Single Nucleotide Variations (SNVs) and computational methods used to predict their consequence on functional genes. Analysis of distribution of SNVs led to the finding that there are mixed genotypes in patient isolates and that many SNVs are likely to influence either gene function or their expression. Phylogenetic relationship between the isolates correlated with the origin of the isolates. In addition, insertion sites of IS elements were identified and their distribution revealed a variation in number and position of the element in the 5 extra-pulmonary isolates compared to the reference M. tuberculosis H37Rv strain.

Conclusions
The results suggest that NGS sequencing is able to identify small variations in genomes of M. tuberculosis isolates including changes in IS element insertion sites. Moreover, variations in isolates of M. tuberculosis from non-pulmonary sites were documented. The analysis of our results indicates genomic heterogeneity in the clinical isolates.
Community acquisition of β-lactamase producing Enterobacteriaceae in neonatal gut
Authors: Kothari Charu , Gaind Rajni , Singh Laishram Chandreshwor , Sinha Anju , Kumari Vidya , Arya Sugandha , Chellani Harish , Saxena Sunita , Deb Monorama 
Published: June 2013

Abstract

Background
Commensal flora constitutes a reservoir of antibiotic resistance. The increasing variety of β-lactamases and the emergence of Carbapenem resistant Enterobacteriaceae (CRE) in community, raise concerns regarding efficacy of β-lactams. It is important to know the exact load of antibiotic resistance in the absence of any antibiotic selection pressure including via food and water.
In the present study gut colonization in neonates with no direct antibiotic pressure was used as a model to evaluate β-lactam resistance in the community.

Results
In this prospective study, 75 healthy, vaginally delivered, antibiotic naive, breast fed neonates were studied for gut colonization by Extended spectrum β-lactamases (ESBL), AmpC β-lactamases hyperproducing Enterobacteriaceae and CRE on day 0, 21 and 60. Total 267 Enterobacteriaceae were isolated and E.coli was the predominant flora. ESBL, AmpC and coproduction was seen in 20.6%, 19.9% and 11.2% isolates respectively. ESBL carriage increased threefold from day 1 to 60 showing predominance of CTX-M group 15 (82.5%), ampC genes were heterogeneous. Colonization with CRE was rare, only one baby harboured Enterobacter sp positive for kpc-2. The reservoirs for these genes are likely to be mother and the environment.

Conclusions
Data strongly suggests that in absence of any antibiotic pressure there is tremendous load of antibiotic resistance to β-lactam drugs. Wide spread presence of ESBL and AmpC can drive rapid emergence and dissemination of CRE. This is the first report from India which depicts the smaller picture of true antibiotic pressure present in the Indian community.