Modeling of couch transmission in the RayStation treatment planning system

PurposeTo present our methods and results regarding the modeling of a carbon fiber couch (Varian Exact IGRT) in the RayStation treatment planning system (TPS).MethodsThree geometrical-models (GMs) were implemented in the TPS to represent the three different regions of the couch (thick, medium and thin). The materials and densities of each GM component were tuned to maximize the agreement between measured and calculated attenuations. Moreover, a couch computed-tomography (CT) scan was acquired and dosimetrically compared with the GMs. For validation, plan-specific quality assurance (QA) of VMAT plans (TG-119 cases, 5 prostate and 5 H&N clinical cases) was performed by comparing measured dose distributions with doses computed with and without including the GMs in the TPS.ResultsCouch attenuations up to 4.3% were measured (energy: 6MV). Compared to couch CT, GMs could be modified to optimize the agreement with measurements and reduce dependence on the dose grid resolution. For both couch CT and GM, absolute deviations between measured and calculated attenuations were within 1.0%. When including the GMs in plan-specific QA, global 2%/2 mm γ-pass rates showed an average improvement of 4.8% (p-value < 0.001, max +18.6%). The couch reduced the mean dose to targets by up to 2.4% of the prescribed dose for prostate cases and up to 1.4% for H&N cases.ConclusionsRayStation accurately considers the implemented couch GMs replicating measured attenuations within an uncertainty of 1.0%. Materials and densities are proposed for the Varian Exact IGRT couch. The results obtained justify introducing couch GMs in clinical routine.     

A patient immobilization device for prone breast radiotherapy: Dosimetric effects and inclusion in the treatment planning system

PurposeTo assess the dosimetric impact of a patient positioning device for prone breast radiotherapy and assess the accuracy of a treatment planning system (TPS) in predicting this impact.MethodsBeam attenuation and build-up dose perturbations, quantified by ionization chamber and radiochromic film dosimetry, were evaluated for 3 components of the patient positioning device: the carbon fiber baseplate, the support cushions and the support wedge for the contralateral breast. Dose calculations were performed using the XVMC dose engine implemented in the Monaco TPS. All components were included during planning CT acquisition.ResultsBeam attenuation amounted to 7.57% (6 MV) and 5.33% (15 MV) for beams obliquely intersecting the couchtop–baseplate combination. Beams traversing large sections of the support wedge were attenuated by 12.28% (6 MV) and 9.37% (15 MV). For the support cushion foam, beam attenuation remained limited to 0.11% (6 MV) and 0.08% (15 MV) per centimeter thickness. A substantial loss of dose build-up was detected when irradiating through any of the investigated components. TPS dose calculations accurately predicted beam attenuation by the baseplate and support wedge. A manual density overwrite was needed to model attenuation by the support cushion foam. TPS dose calculations in build-up regions differed considerably from measurements for both open beams and beams traversing the device components.ConclusionsIrradiating through the components of the positioning device resulted in a considerable degradation of skin sparing. Inclusion of the device components in the treatment planning CT allowed to accurately model the most important attenuation effect, but failed to accurately predict build-up doses.     

Required transition from research to clinical application: Report on the 4D treatment planning workshops 2014 and 2015

Since 2009, a 4D treatment planning workshop has taken place annually, gathering researchers working on the treatment of moving targets, mainly with scanned ion beams. Topics discussed during the workshops range from problems of time resolved imaging, the challenges of motion modelling, the implementation of 4D capabilities for treatment planning, up to different aspects related to 4D dosimetry and treatment verification.This report gives an overview on topics discussed at the 4D workshops in 2014 and 2015. It summarizes recent findings, developments and challenges in the field and discusses the relevant literature of the recent years. The report is structured in three parts pointing out developments in the context of understanding moving geometries, of treating moving targets and of 4D quality assurance (QA) and 4D dosimetry.The community represented at the 4D workshops agrees that research in the context of treating moving targets with scanned ion beams faces a crucial phase of clinical translation. In the coming years it will be important to define standards for motion monitoring, to establish 4D treatment planning guidelines and to develop 4D QA tools. These basic requirements for the clinical application of scanned ion beams to moving targets could e.g. be determined by a dedicated ESTRO task group.Besides reviewing recent research results and pointing out urgent needs when treating moving targets with scanned ion beams, the report also gives an outlook on the upcoming 4D workshop organized at the University Medical Center Groningen (UMCG) in the Netherlands at the end of 2016.     

Identifying mismatches between conservation area networks and vulnerable populations using spatial randomization

Grassland birds are among the most globally threatened bird groups due to substantial degradation of native grassland habitats. However, the current network of grassland conservation areas may not be adequate for halting population declines and biodiversity loss. Here, we evaluate a network of grassland conservation areas within Wisconsin, U.S.A., that includes both large Focal Landscapes and smaller targeted conservation areas (e.g., Grassland Bird Conservation Areas, GBCAs) established within them. To date, this conservation network has lacked baseline information to assess whether the current placement of these conservation areas aligns with population hot spots of grassland‐dependent taxa. To do so, we fitted data from thousands of avian point‐count surveys collected by citizen scientists as part of Wisconsin''s Breeding Bird Atlas II with multinomial N‐mixture models to estimate habitat–abundance relationships, develop spatially explicit predictions of abundance, and establish ecological baselines within priority conservation areas for a suite of obligate grassland songbirds. Next, we developed spatial randomization tests to evaluate the placement of this conservation network relative to randomly placed conservation networks. Overall, less than 20% of species statewide populations were found within the current grassland conservation network. Spatial tests demonstrated a high representation of this bird assemblage within the entire conservation network, but with a bias toward birds associated with moderately tallgrasses relative to those associated with shortgrasses or tallgrasses. We also found that GBCAs had higher representation at Focal Landscape rather than statewide scales. Here, we demonstrated how combining citizen science data with hierarchical modeling is a powerful tool for estimating ecological baselines and conducting large‐scale evaluations of an existing conservation network for multiple grassland birds. Our flexible spatial randomization approach offers the potential to be applied to other protected area networks and serves as a complementary tool for conservation planning efforts globally.     

The first baleen whale marine protected area proposed for Bryde's whales in the Beibu Gulf,China

The establishment of marine protected areas (MPAs) for cetaceans is an important strategy to mitigate human disturbance and protect biodiversity. Despite abundant cetacean species, there are only a few MPAs dedicated to cetacean conservation in China, all of which are for inshore dolphins. Bryde's whales, the only nearshore baleen whale population in mainland China, are conflicting with intensive human activities, yet an effective conservation strategy is lacking. This study used species distribution models to analyze distribution patterns and suitable habitats of Bryde's whales in the Beibu Gulf and proposes the first baleen whale MPA in China. Our results showed Bryde's whales have a seasonal distribution pattern in the Beibu Gulf, and that the waters around Weizhou Island and the southeastern coast of Vietnam were their core habitats. The seasonal nighttime light data indicated a negative relationship between the number of ship lights and Bryde's whale sightings and suggest that Bryde's whales might be threatened by fisheries. We proposed an MPA based on the results, suggesting that the waters within 20 km around Weizhou Island should be declared a protected area. Furthermore, we recommend that anthropogenic activities in the waters around Weizhou Island are better managed to reduce negative impacts on marine life.     

呼和浩特白塔机场春季鸟类的鸟击危险等级评估(英文)

2005年3—5月采用样带法对呼和浩特白塔机场4个样区的鸟类进行了调查,共记录到鸟类59种,隶属于10目26科。通过分析春季鸟类群落中各鸟种的相对重要值、分布系数、密度和种间相遇概率等群落特征参数,结合鸟类在机场及周边地区的活动行为等综合因素确定影响飞机飞行安全的危险鸟类。其结果表明构成飞行安全威胁有两类喜鹊和红隼等23种鸟类为最危险的鸟类,雀鹰和金翅雀等8种鸟类为较危险的鸟类。     

Knowledge-based planning using pseudo-structures for volumetric modulated arc therapy (VMAT) of postoperative uterine cervical cancer: a multi-institutional study

BackgroundThe aim of this study was to investigate the performance of the RapidPlan (RP ) using models registered pseudostructures, and to determine how many structures are required for automatic optimization of volumetric modulated arc therapy (VMAT) for postoperative uterine cervical cancer.Materials and methodsPseudo-structures around the PTV were retrospectively contoured for patients who had completed treatment at five institutions. For 22 common patients, plans were generated with a single optimization for models with two (RP_2), four (RP_4), and five (RP_5) registered structures, and the dosimetric parameters of these models were compared with a clinical plan with several optimizations.ResultsMost dosimetric parameters showed no major differences between each RP model. In particular, the rectum D_max, V_50Gy, and V_40Gy with RP_2, RP_4, and RP_5 were not significantly different, and were lower than those of the clinical plan. The average proportions of plans achieving acceptable criteria for dosimetric parameters were close to 100% for all models. Using RP_2, the average time for the VMAT planning was reduced by 88 minutes compared with the clinical plan.ConclusionThe RapidPlan model with two registered pseudo-structures could generate clinically acceptable plans while saving time.     

Frustration‐guided motion planning reveals conformational transitions in proteins

Proteins exist as conformational ensembles, exchanging between substates to perform their function. Advances in experimental techniques yield unprecedented access to structural snapshots of their conformational landscape. However, computationally modeling how proteins use collective motions to transition between substates is challenging owing to a rugged landscape and large energy barriers. Here, we present a new, robotics‐inspired motion planning procedure called dCC‐RRT that navigates the rugged landscape between substates by introducing dynamic, interatomic constraints to modulate frustration. The constraints balance non‐native contacts and flexibility, and instantaneously redirect the motion towards sterically favorable conformations. On a test set of eight proteins determined in two conformations separated by, on average, 7.5 Å root mean square deviation (RMSD), our pathways reduced the Cα atom RMSD to the goal conformation by 78%, outperforming peer methods. We then applied dCC‐RRT to examine how collective, small‐scale motions of four side‐chains in the active site of cyclophilin A propagate through the protein. dCC‐RRT uncovered a spatially contiguous network of residues linked by steric interactions and collective motion connecting the active site to a recently proposed, non‐canonical capsid binding site 25 Å away, rationalizing NMR and multi‐temperature crystallography experiments. In all, dCC‐RRT can reveal detailed, all‐atom molecular mechanisms for small and large amplitude motions. Source code and binaries are freely available at https://github.com/ExcitedStates/KGS/ .     

Incorporating zoning and socioeconomic costs in planning for bird conservation

New systematic conservation approaches have high potential in evaluation of different conservation scenarios and can be used as decision support tools for managers and planners with multiple goals. The present study focused on two major issues in conservation planning including socioeconomic costs and zoning procedure. The goal was to prioritize and identify representative areas for bird conservation, while minimizing the economic cost for the silvicultural sector and resolve conflicts with recreational activities. The study was conducted in forest areas of Golestan Province as part of Hyrcanian mixed forests, located along the southern coasts of the Caspian Sea and northern slopes of the Alborz Mountains, northern Iran. We used systematic conservation software Marxan with Zones to select candidate areas for conservation. Two types of conservation networks were defined, one with high and partial protection zones and the other with high protection zones only. We focused on four conservation scenarios varying in targets, costs, and multiple zones. The results showed that incorporation of socioeconomic costs significantly decreases the potential impacts on the silvicultural and recreational sectors without significant change in the area of protection zones. Furthermore, we found that design of multiple zone conservation areas facilitates evaluation of a wider range of conservation scenarios that can reduce potential socioeconomic impacts on other interests.