bluuebunny/crossref_metadata_2025_split huggingface dataset:
The effect of small field output factor measurements on IMRT dosimetry
Authors: Azimi Rezvan , Alaei Parham , Higgins Patrick 
Published: July 2012

Purpose:To evaluate how changes in the measured small field output factors affect the doses in intensity‐modulated treatment planning.Methods:IMRT plans were created using Philips Pinnacle treatment planning system. The plans were optimized to treat a cylindrical target 2 cm in diameter and 2 cm in length. Output factors for 2 × 2 and 3 × 3 cm2 field sizes were changed by ±5%, ±10%, and ±20% increments from the baseline measurements and entered into the planning system. The treatment units were recommissioned in the treatment planning system after each modification of the output factors and treatment plans were reoptimized. All plans were delivered to a solid water phantom and dose measurements were made using an ionization chamber. The percentage differences between measured and computed doses were calculated. An Elekta Synergy and a Varian 2300CD linear accelerator were separately evaluated.Results:For the Elekta unit, decreasing the output factors resulted in higher measured than computed doses by 0.8% for −5%, 3.6% for −10%, and 8.7% for −20% steps. Increasing the output factors resulted in lower doses by 2.9% for +5%, 5.4% for +10%, and 8.3% for +20% steps. For the Varian unit no changes were observed for either increased or decreased output factors.Conclusions:The measurement accuracy of small field output factors are of importance especially when the treatment plan consists of small segments as in IMRT. The method proposed here could be used to verify the accuracy of the measured small field output factors for certain linear accelerators as well as to test the beam model. The Pinnacle treatment planning system model uses output factors as a function of jaw setting. Consequently, plans using the Elekta unit, which conforms the jaws to the segments, are sensitive to small field measurement accuracy. On the other hand, for the Varian unit, jaws are fixed and segments are modeled as blocked fields hence, the impact of small field output factors on IMRT monitor unit calculation is not evaluable by this method.
Improvements in dose calculation accuracy for small off‐axis targets in high dose per fraction tomotherapy
Authors: Hardcastle Nicholas , Bayliss Adam , Wong Jeannie Hsiu Ding , Rosenfeld Anatoly B. , Tomé Wolfgang A. 
Published: July 2012

Purpose:A recent field safety notice from TomoTherapy detailed the underdosing of small, off‐axis targets when receiving high doses per fraction. This is due to angular undersampling in the dose calculation gantry angles. This study evaluates a correction method to reduce the underdosing, to be implemented in the current version (v4.1) of the TomoTherapy treatment planning software.Methods:The correction method, termed “Super Sampling” involved the tripling of the number of gantry angles from which the dose is calculated during optimization and dose calculation. Radiochromic film was used to measure the dose to small targets at various off‐axis distances receiving a minimum of 21 Gy in one fraction. Measurements were also performed for single small targets at the center of the Lucy phantom, using radiochromic film and the dose magnifying glass (DMG).Results:Without super sampling, the peak dose deficit increased from 0% to 18% for a 10 mm target and 0% to 30% for a 5 mm target as off‐axis target distances increased from 0 to 16.5 cm. When super sampling was turned on, the dose deficit trend was removed and all peak doses were within 5% of the planned dose. For measurements in the Lucy phantom at 9.7 cm off‐axis, the positional and dose magnitude accuracy using super sampling was verified using radiochromic film and the DMG.Conclusions:A correction method implemented in the TomoTherapy treatment planning system which triples the angular sampling of the gantry angles used during optimization and dose calculation removes the underdosing for targets as small as 5 mm diameter, up to 16.5 cm off‐axis receiving up to 21 Gy.
Fast DRR generation for 2D to 3D registration on GPUs
Authors: Tornai Gábor János , Cserey György , Pappas Ion 
Published: July 2012

Purpose: The generation of digitally reconstructed radiographs (DRRs) is the most time consuming step on the CPU in intensity based two‐dimensional x‐ray to three‐dimensional (CT or 3D rotational x‐ray) medical image registration, which has application in several image guided interventions. This work presents optimized DRR rendering on graphical processor units (GPUs) and compares performance achievable on four commercially available devices.Methods: A ray‐cast based DRR rendering was implemented for a 512 × 512 × 72 CT volume. The block size parameter was optimized for four different GPUs for a region of interest (ROI) of 400 × 225 pixels with different sampling ratios (1.1%–9.1% and 100%). Performance was statistically evaluated and compared for the four GPUs. The method and the block size dependence were validated on the latest GPU for several parameter settings with a public gold standard dataset (512 × 512 × 825 CT) for registration purposes.Results: Depending on the GPU, the full ROI is rendered in 2.7–5.2 ms. If sampling ratio of 1.1%–9.1% is applied, execution time is in the range of 0.3–7.3 ms. On all GPUs, the mean of the execution time increased linearly with respect to the number of pixels if sampling was used.Conclusions: The presented results outperform other results from the literature. This indicates that automatic 2D to 3D registration, which typically requires a couple of hundred DRR renderings to converge, can be performed quasi on‐line, in less than a second or depending on the application and hardware in less than a couple of seconds. Accordingly, a whole new field of applications is opened for image guided interventions, where the registration is continuously performed to match the real‐time x‐ray.
Design, construction, and evaluation of a dynamic MR compatible cardiac left ventricle model
Authors: Dieringer Matthias A. , Hentschel Jan , de Quadros Thiago , von Knobelsdorff‐Brenkenhoff Florian , Hoffmann Werner , Niendorf Thoralf , Schulz‐Menger Jeanette 
Published: July 2012

Purpose:Development of magnetic resonance (MR) sequences is important to answer clinical questions and to overcome current limitations. To meet the challenges of cardiac MR, dynamic and reproducible testing conditions are required. We aimed at developing a dynamic MR‐compatible cardiac left ventricle model that imitates myocardial tissue properties and simulates dynamic motion.Methods:A dynamic left ventricle silicone model was designed to match myocardial T1 and T2 relaxation times. Silicone mixtures were explored to replicate T2 values of myocardial edema. A controllable piston pump was constructed to produce pulsatile flow paradigms. They were validated against flow sensors and MR data, including SSFP‐based and phase‐contrast‐based sequences. A dedicated software interface was developed for the control.Results:Model dimensions represented cardiac left ventricle dimensions of healthy men. The range of end diastolic volumes was 85–175 ml, depending on the driven stroke volume. Stroke volume quantification for flow paradigms of 30/60/90/120 ml resulted in 29.2/57.6/88.8/118.4 ml by MR volumetry, 29.6/59.9/89.4/119.0 ml by phase contrast measurements, and 29.9/60.4/91.1/120.9 ml by flow meter revealing consistency. The system accurately replicated physiological and pathophysiological flow paradigms. The silicon model exhibited T1 of 1002 ± 8 ms, T2 of 58 ± 1 ms. Signal intensities (a.u.) of the ventricle model were 128 ± 23 for FGRE (vs 138 ± 17 in vivo) and 1156 ± 37 for b‐SSFP (vs 991 ± 96 in vivo). T2 of 75 ± 2 ms was achieved for the myocardial pathology.Conclusions:We developed a controllable left ventricle model resembling MR signal characteristics of human myocardium, including pathological conditions, and allowing for the replication of contraction and flow paradigms.
Complete Genome Sequence of Geobacillus thermoglucosidans TNO-09.020, a Thermophilic Sporeformer Associated with a Dairy-Processing Environment
Authors: Zhao Yu , Caspers Martien P. , Abee Tjakko , Siezen Roland J. , Kort Remco 
Published: July 2012

ABSTRACT

Thermophilic spore-forming bacteria are a common cause of contamination in dairy products. We isolated the thermophilic strain
Geobacillus thermoglucosidans
TNO-09.020 from a milk processing plant and report the complete genome of a dairy plant isolate consisting of a single chromosome of 3.75 Mb.
The Breadth and Titer of Maternal HIV-1-Specific Heterologous Neutralizing Antibodies Are Not Associated with a Lower Rate of Mother-to-Child Transmission of HIV-1
Authors: Chaillon Antoine , Wack Thierry , Braibant Martine , Mandelbrot Laurent , Blanche Stéphane , Warszawski Josiane , Barin Francis 
Published: July 2012

ABSTRACT
It has been hypothesized that neutralizing antibodies (NAbs) should have broad specificity to be effective in protection against diverse HIV-1 variants. The mother-to-child transmission model of HIV-1 provides the opportunity to examine whether the breadth of maternal NAbs is associated with protection of infants from infection. Samples were obtained at delivery from 57 transmitting mothers (T) matched with 57 nontransmitting mothers (NT) enrolled in the multicenter French perinatal cohort (ANRS EPF CO1) between 1990 and 1996. Sixty-eight (59.6%) and 46 (40.4%) women were infected by B and non-B viruses, respectively. Neutralization assays were carried out with TZM-bl cells, using a panel of 10 primary isolates of 6 clades (A, B, C, F, CRF01_AE, and CRF02_AG), selected for their moderate or low sensitivity to neutralization. Neutralization breadths were not statistically different between T and NT mothers. However, a few statistically significant differences were observed, with higher frequencies or titers of NAbs toward several individual strains for NT mothers when the clade B-infected or non-clade B-infected mothers were analyzed separately. Our study confirms that the breadth of maternal NAbs is not associated with protection of infants from infection.
Selective Modification of Adenovirus Replication Can Be Achieved through Rational Mutagenesis of the Adenovirus Type 5 DNA Polymerase
Authors: Capella Cristina , Beltejar Michael-John , Brown Caitlin , Fong Vincent , Daddacha Waaqo , Kim Baek , Dewhurst Stephen 
Published: July 2012

ABSTRACT
Mutations that reduce the efficiency of deoxynucleoside (dN) triphosphate (dNTP) substrate utilization by the HIV-1 DNA polymerase prevent viral replication in resting cells, which contain low dNTP concentrations, but not in rapidly dividing cells such as cancer cells, which contain high levels of dNTPs. We therefore tested whether mutations in regions of the adenovirus type 5 (Ad5) DNA polymerase that interact with the dNTP substrate or DNA template could alter virus replication. The majority of the mutations created, including conservative substitutions, were incompatible with virus replication. Five replication-competent mutants were recovered from 293 cells, but four of these mutants failed to replicate in A549 lung carcinoma cells and Wi38 normal lung cells. Purified polymerase proteins from these viruses exhibited only a 2- to 4-fold reduction in their dNTP utilization efficiency but nonetheless could not be rescued, even when intracellular dNTP concentrations were artificially raised by the addition of exogenous dNs to virus-infected A549 cells. The fifth mutation (I664V) reduced biochemical dNTP utilization by the viral polymerase by 2.5-fold. The corresponding virus replicated to wild-type levels in three different cancer cell lines but was significantly impaired in all normal cell lines in which it was tested. Efficient replication and virus-mediated cell killing were rescued by the addition of exogenous dNs to normal lung fibroblasts (MRC5 cells), confirming the dNTP-dependent nature of the polymerase defect. Collectively, these data provide proof-of-concept support for the notion that conditionally replicating, tumor-selective adenovirus vectors can be created by modifying the efficiency with which the viral DNA polymerase utilizes dNTP substrates.
Observational evidence that urbanisation and neighbourhood deprivation are associated with escalation in chronic pharmacological pain treatment: a longitudinal population-based study in the Netherlands
Authors: Leue Carsten , Buijs Servaas , Strik Jacqueline , Lousberg Richel , Smit Jasper , van Kleef Maarten , van Os Jim 
Published: July 2012

ObjectiveTo examine, in the light of the association between urban environment and poor mental health, whether urbanisation and neighbourhood deprivation are associated with analgesic escalation in chronic pharmacological pain treatment and whether escalation is associated with prescriptions of psychotropic medication.DesignLongitudinal analysis of a population-based routine dispensing database in the Netherlands.SettingRepresentative sample of pharmacies, covering 73% of the Dutch nationwide medication consumption in the primary care and hospital outpatient settings.Participants449 410 patients aged 15–85 years were included, of whom 166 374 were in theStarter groupand 283 036 in theContinuation groupof chronic analgesic treatment.Main outcome measureEscalation of analgesics (ie, change to a higher level of analgesic potency, classified across five levels) in association with urbanisation (five levels) and dichotomous neighbourhood deprivation was analysed over a 6-month observation period.MethodsOrdered logistic multivariate model evaluating analgesic treatment.ResultsIn bothStarterandContinuationgroups, escalation was positively associated with urbanisation in a dose–response fashion (Starter group: OR (urbanisation level 1 compared with level 5): 1.24, 95% CI 1.18 to 1.30; Continuation group: OR 1.18, 95% CI 1.14 to 1.23). An additional association was apparent with neighbourhood deprivation (Starter group: OR 1.07, 95% CI 1.02 to 1.11; Continuation group: OR 1.04, 95% CI 1.01 to 1.08). Use of somatic and particularly psychotropic co-medication was associated with escalation in both groups.ConclusionsEscalation of chronic analgesic treatment is associated with urban and deprived environments and occurs in a context of adding psychotropic medication prescriptions. These findings suggest that pain outcomes and mental health outcomes share factors that increase risk and remedy suffering.
An evaluation of overnight fixation to facilitate neuropathological examination in Coroner's autopsies: our experience of over 200 cases
Authors: Scott Ian Stuart , MacDonald Alastair Wray 
Published: July 2012

AimsFollowing recent changes in Coroner's Rules, there has been a desire to examine brains at the time of autopsy, rather than after a prolonged period of immersion fixation. Examination of the fresh brain at postmortem can yield unsatisfactory results where detailed histological examination is required. We aim to provide a compromise, where detailed examination of the brain is possible, without the requirement for prolonged fixation, interference with funeral arrangements and delay in the Coronial process.MethodsA retrospective audit of over 200 neuropathology cases requested by HM Coroner for the East Riding of Yorkshire between 2007 and 2010 was performed. The cases consisted of full neuropathology autopsies (n=212) and brains referred by general pathology colleagues (n=26).ResultsOf the 238 brains examined, approximately half (n=109) of the brains were sectioned fresh in the mortuary. The remaining brains (n=129) were immersion fixed overnight in 20% formalin prior to cutting and sampling for histology (n=127). The median time for reporting was 31 days (range 1–167; n=101) for brains requiring histology. This equates to a median turnaround time of 1 month for a neuropathological autopsy requiring detailed histology. In all cases, the report was prepared and available to HM Coroner in advance of the Inquest.ConclusionsThis method provides reliable histological diagnoses in neuropathological autopsies and does not interfere with funeral arrangements for bereaved families following deaths falling under Coronial jurisdiction. In all cases, the body could be released to relatives, at Coroner's discretion, within two working days of the autopsy.
Efficacy of intranasal vaccination of field buffaloes against haemorrhagic septicaemia with a live gdhA derivative Pasteurella multocida B:2
Authors: Rafidah O. , Zamri‐Saad M. , Shahirudin S. , Nasip E. 
Published: July 2012

The efficacy of an intranasal haemorrhagic septicaemia vaccine containing live gdhA derivative Pasteurella multocida B:2 was tested in buffaloes in Sabah. Sixty buffaloes, kept grazing in the field with minimal human intervention were devided into three groups of 20 buffaloes per group. Buffaloes of group 1 were exposed intranasal to 5 ml vaccine containing 106 CFU/ml of live gdhA derivative P multocida B:2. Buffaloes of group 2 were not exposed to the vaccine but exposed to PBS and were allowed to commingle and graze in the same field as the buffaloes of group 1 while buffaloes of group 3 were similarly exposed to PBS and were grazing separately. Booster was on group 1, two weeks later. Twelve months after the first vaccination, three buffaloes from each group were brought into the experimental house and challenged subcutaneously with 109 CFU/ml of live wild‐type P multocida B:2. All challenged buffaloes of groups 1 and 2 survived with only mild, transient signs while all control unvaccinated buffaloes developed severe signs of haemorrhagic septicaemia and were euthanased between 28 hours and 38 hours postchallenge with signs and lesions typical of haemorrhagic septicaemia. These data showed that the gdhA mutant strain, given intranasally as two doses two weeks apart, successfully induced systemic immunity in exposed buffaloes and also led to spread of vaccine strain to the in‐contact animals, where it acted as an effective live vaccine to protect both exposed buffaloes and in‐contact buffaloes against challenge with the virulent parent strain.
Modelling volume growth response of young Scots pine (Pinus sylvetris) stands to N, P, and K fertilization in drained peatland sites in Finland
Authors: Hökkä Hannu , Repola Jaakko , Moilanen Mikko 
Published: July 2012

Fertilizers are applied in drained peatland forests to correct nutrient imbalances, but few models have been developed for predicting the stand growth response. We used 10- to 34-year-long stem growth increment data from 51 fertilization experiments involving ash, PK, and NPK treatments (doses of P, K, and N varying between 35 and 45, 60 and 80, and 80 and 90 kg·ha–1, respectively) and controls to model the volume growth response of young Scots pine (Pinus sylvetris L.) stands to fertilization in drained peatland sites of middle and northern Finland. We used the linear mixed models method to express the stand-level growth response as a function of time (5-year periods), site type group, location, and the fertilization treatment (ash–PK combined and NPK). Different growth responses were obtained for nitrogen-rich sites with PK treatment and nitrogen-poor sites with NPK treatment. The PK fertilization in nitrogen-rich sites resulted in the largest volume growth response and longest temporal effect (1.0–2.0 m3·ha–1·a–1 higher mean growth for at least 35 years), with quicker and stronger effects in more southern conditions where average temperature sums were greater than 1000 degree-days (°C). NPK fertilization in nitrogen-poor sites gave a modest response (0.4–0.8 m3·ha–1·a–1 in 35 years).
MicroRNA-101 Inhibited Postinfarct Cardiac Fibrosis and Improved Left Ventricular Compliance via the FBJ Osteosarcoma Oncogene/Transforming Growth Factor-β1 Pathway
Authors: Pan Zhenwei , Sun Xuelin , Shan Hongli , Wang Ning , Wang Jinghao , Ren Jinshuai , Feng Shuya , Xie Liangjun , Lu Chunying , Yuan Ye , Zhang Yang , Wang Ying , Lu Yanjie , Yang Baofeng 
Published: July 2012

Background—
Cardiac interstitial fibrosis is a major cause of the deteriorated performance of the heart in patients with chronic myocardial infarction. MicroRNAs (miRs) have recently been proven to be a novel class of regulators of cardiovascular diseases, including those associated with cardiac fibrosis. This study aimed to explore the role of miR-101 in cardiac fibrosis and the underlying mechanisms.

Methods and Results—
Four weeks after coronary artery ligation of rats, the expression of miR-101a and miR-101b (miR-101a/b) in the peri-infarct area was decreased. Treatment of cultured rat neonatal cardiac fibroblasts with angiotensin II also suppressed the expression of miR-101a/b. Forced expression of miR-101a/b suppressed the proliferation and collagen production in rat neonatal cardiac fibroblasts, as revealed by cell counting, MTT assay, and quantitative reverse transcription–polymerase chain reaction. The effect was abrogated by cotransfection with AMO-101a/b, the antisense inhibitors of miR-101a/b. c-Fos was found to be a target of miR-101a because overexpression of miR-101a decreased the protein and mRNA levels of c-Fos and its downstream protein transforming growth factor-β1. Silencing c-Fos by siRNA mimicked the antifibrotic action of miR-101a, whereas forced expression of c-Fos protein canceled the effect of miR-101a in cultured cardiac fibroblasts. Strikingly, echocardiography and hemodynamic measurements indicated remarkable improvement of the cardiac performance 4 weeks after adenovirus-mediated overexpression of miR-101a in rats with chronic myocardial infarction. Furthermore, the interstitial fibrosis was alleviated and the expression of c-Fos and transforming growth factor-β1 was inhibited.

Conclusion—
Overexpression of miR-101a can mitigate interstitial fibrosis and the deterioration of cardiac performance in postinfarct rats, indicating the therapeutic potential of miR-101a for cardiac disease associated with fibrosis.
The impact of occupational therapy in Parkinson’s disease: a randomized controlled feasibility study
Authors: Sturkenboom Ingrid H , Graff Maud J , Borm George F , Veenhuizen Yvonne , Bloem Bastiaan R , Munneke Marten , Nijhuis-van der Sanden Maria W 
Published: July 2012

Aim: To evaluate the feasibility of a randomized controlled trial including process and potential impact of occupational therapy in Parkinson’s disease. Design: Process and outcome were quantitatively and qualitatively evaluated in an exploratory multicentre, two-armed randomized controlled trial at three months. Participants: Forty-three community-dwelling patients with Parkinson’s disease and difficulties in daily activities, their primary caregivers and seven occupational therapists. Intervention: Ten weeks of home-based occupational therapy according to the Dutch guidelines of occupational therapy in Parkinson’s disease versus no occupational therapy in the control group. Main measures: Process evaluation measured accrual, drop-out, intervention delivery and protocol adherence. Primary outcome measures of patients assessed daily functioning: Canadian Occupational Performance Measure (COPM) and Assessment of Motor and Process Skills. Primary outcome for caregivers was caregiver burden: Zarit Burden Inventory. Participants’ perspectives of the intervention were explored using questionnaires and in-depth interviews. Results: Inclusion was 23% (43/189), drop-out 7% (3/43) and unblinding of assessors 33% (13/40). Full intervention protocol adherence was 74% (20/27), but only 60% (71/119) of baseline Canadian Occupational Performance Measure priorities were addressed in the intervention. The outcome measures revealed negligible to small effects in favour of the intervention group. Almost all patients and caregivers of the intervention group were satisfied with the results. They perceived: ‘more grip on the situation’ and used ‘practical advices that make life easier’. Therapists were satisfied, but wished for a longer intervention period. Conclusions: The positive perceived impact of occupational therapy warrants a large-scale trial. Adaptations in instructions and training are needed to use the Canadian Occupational Performance Measure as primary outcome measure.