Purpose
Real‐time high soft‐tissue contrast magnetic resonance imaging (MRI) from the MR‐Linac offers the best opportunity for accurate motion tracking during radiation therapy delivery via ...high‐frequency two‐dimensional (2D) cine imaging. This work investigates the efficacy of real‐time organ motion tracking based on the registration of MRI acquired on MR‐Linac.
Methods
Algorithms based on image intensity were developed to determine the three‐dimensional (3D) translation of abdominal targets. 2D and 3D abdominal MRIs were acquired for 10 healthy volunteers using a high‐field MR‐Linac. For each volunteer, 3D respiration‐gated T2 and 2D T2/T1‐weighted cine in sagittal, coronal, and axial planes with a planar temporal resolution of 0.6 for 60 s was captured. Datasets were also collected on MR‐compatible physical and virtual four‐dimensional (4D) motion phantoms. Target contours for the liver and pancreas from the 3D T2 were populated to the cine and assumed as the ground‐truth motion. We performed image registration using a research software to track the target 3D motion. Standard deviations of the error (SDE) between the ground‐truth and tracking were analyzed.
Results
Algorithms using a research software were demonstrated to be capable of tracking arbitrary targets in the abdomen at 5 Hz with an overall accuracy of 0.6 mm in phantom studies and 2.1 mm in volunteers. However, this value is subject to patient‐specific considerations, namely motion amplitude. Calculation times of < 50 ms provide a pathway of real‐time motion tracking integration. A major challenge in using 2D cine MRI to track the target is handling the full 3D motion of the target.
Conclusions
Feasibility to track organ motion using intensity‐based registration of MRIs was demonstrated for abdominal targets. Tracking accuracy of about 2 mm was achieved for the motion of the liver and pancreatic head for typical patient motion. Further development is ongoing to improve the tracking algorithm for large and complex motions.
Background
Real‐time motion monitoring (RTMM) is necessary for accurate motion management of intrafraction motions during radiation therapy (RT).
Purpose
Building upon a previous study, this work ...develops and tests an improved RTMM technique based on real‐time orthogonal cine magnetic resonance imaging (MRI) acquired during magnetic resonance‐guided adaptive RT (MRgART) for abdominal tumors on MR‐Linac.
Methods
A motion monitoring research package (MMRP) was developed and tested for RTMM based on template rigid registration between beam‐on real‐time orthogonal cine MRI and pre‐beam daily reference 3D‐MRI (baseline). The MRI data acquired under free‐breathing during the routine MRgART on a 1.5T MR‐Linac for 18 patients with abdominal malignancies of 8 liver, 4 adrenal glands (renal fossa), and 6 pancreas cases were used to evaluate the MMRP package. For each patient, a 3D mid‐position image derived from an in‐house daily 4D‐MRI was used to define a target mask or a surrogate sub‐region encompassing the target. Additionally, an exploratory case reviewed for an MRI dataset of a healthy volunteer acquired under both free‐breathing and deep inspiration breath‐hold (DIBH) was used to test how effectively the RTMM using the MMRP can address through‐plane motion (TPM). For all cases, the 2D T2/T1‐weighted cine MRIs were captured with a temporal resolution of 200 ms interleaved between coronal and sagittal orientations. Manually delineated contours on the cine frames were used as the ground‐truth motion. Common visible vessels and segments of target boundaries in proximity to the target were used as anatomical landmarks for reproducible delineations on both the 3D and the cine MRI images. Standard deviation of the error (SDE) between the ground‐truth and the measured target motion from the MMRP package were analyzed to evaluate the RTMM accuracy. The maximum target motion (MTM) was measured on the 4D‐MRI for all cases during free‐breathing.
Results
The mean (range) centroid motions for the 13 abdominal tumor cases were 7.69 (4.71–11.15), 1.73 (0.81–3.05), and 2.71 (1.45–3.93) mm with an overall accuracy of <2 mm in the superior–inferior (SI), the left‐right (LR), and the anterior‐posterior (AP) directions, respectively. The mean (range) of the MTM from the 4D‐MRI was 7.38 (2–11) mm in the SI direction, smaller than the monitored motion of centroid, demonstrating the importance of the real‐time motion capture. For the remaining patient cases, the ground‐truth delineation was challenging under free‐breathing due to the target deformation and the large TPM in the AP direction, the implant‐induced image artifacts, and/or the suboptimal image plane selection. These cases were evaluated based on visual assessment. For the healthy volunteer, the TPM of the target was significant under free‐breathing which degraded the RTMM accuracy. RTMM accuracy of <2 mm was achieved under DIBH, indicating DIBH is an effective method to address large TPM.
Conclusions
We have successfully developed and tested the use of a template‐based registration method for an accurate RTMM of abdominal targets during MRgART on a 1.5T MR‐Linac without using injected contrast agents or radio‐opaque implants. DIBH may be used to effectively reduce or eliminate TPM of abdominal targets during RTMM.
The number of planted trees per hectare influences individual volume growth, which in turn can affect wood properties. The objective of this study was to assess the effect of six different plantation ...spacings of jack pine (Pinus banksiana Lamb.) 25 years following planting on tree growth, morphology, and wood properties. Stem analyses were performed to calculate annual and cumulative diameter, height, and volume growth. For morphological and wood property measurements several parameters were analyzed: diameter of the largest branch, live crown ratio, wood density, and the moduli of elasticity and rupture on small clear samples. The highest volume growth for individual trees was obtained in the 1111 trees/ha plantation, while the lowest was in the 4444 trees/ha plantation. Wood density and the moduli of elasticity and rupture did not change significantly between the six plantation spacings, but the largest branch diameter was significantly higher in the 1111 trees/ha (3.26 cm mean diameter) compared with the 4444 trees/ha spacing (2.03 cm mean diameter). Based on this study, a wide range of spacing induced little negative effect on the measured wood properties, except for the size of knots. Increasing the initial spacing of jack pine plantations appears to be a good choice if producing large, fast-growing stems is the primary goal, but lumber mechanical and visual properties could be decreased due to the larger branch diameter.
Direct In Vivo Microbial Transcriptomics During Infection Hébert, François-Olivier; Boyle, Brian; Levesque, Roger C.
Trends in microbiology (Regular ed.),
September 2018, 2018-09-00, 20180901, Letnik:
26, Številka:
9
Journal Article
Recenzirano
The challenge in infectious diseases is monitoring infection in the host. Omics-based genomics and transcriptomics can define microbial genes expressed during infection and treatment with ...antimicrobials. Recent studies pinpoint a direct in situ in vivo approach revolutionizing infection monitoring and optimizing antimicrobial therapy using machine learning.
Sticklebacks infected by the parasitic flatworm Schistocephalus solidus show dramatic changes in phenotype, including a loss of species-typical behavioural responses to predators. The timing of host ...behaviour change coincides with the development of infectivity of the parasite to the final host (a piscivorous bird), making it an ideal model for studying the mechanisms of infection-induced behavioural modification. However, whether the loss of host anti-predator behaviour results from direct manipulation by the parasite, or is a by-product (e.g. host immune response) or side effect of infection (e.g. energetic loss), remains controversial. To understand the physiological mechanisms that generate these behavioural changes, we quantified the behavioural profiles of experimentally infected fish and attempted to replicate these in non-parasitized fish by exposing them to treatments including immunity activation and fasting, or by pharmacologically inhibiting the stress axis. All fish were screened for the following behaviours: activity, water depth preference, sociability, phototaxis, anti-predator response and latency to feed. We were able to change individual behaviours with certain treatments. Our results suggest that the impact of S. solidus on the stickleback might be of a multifactorial nature. The behaviour changes observed in infected fish might result from the combined effects of modifying the serotonergic axis, lack of energy and activation of the immune system.
Because they generate more wood per area and time, short rotation plantations are likely to play an increasing role in meeting the global increase in the demand for wood fiber. To be successful, ...high-yield plantations require costly intensive silviculture regimes to ensure the survival and maximize yields. While hybrid poplar (Populus spp.) is frequently used in intensive, short rotation forestry, it is particularly sensitive to competition and resource levels. Mechanical site preparation is thus of great importance to create microsites that provide sufficient light levels and adequate soil water and nutrient availability. We conducted an experiment in Québec (Canada) to compare two intensive site preparation treatments commonly used to establish hybrid poplar. We compared the effects of double-blade site preparation (V-blade), mounding and a control on hybrid poplar growth and nutritional status four growing seasons after planting on recently harvested forested sites. We also evaluated the effects of site preparation and planted poplar on inorganic soil N. Our results confirmed general positive effects of site preparation on the early growth of hybrid poplar clones. After four growing seasons, survival was higher in the mounding treatment (99%) than in the V-blade (91%) and the control (48%). Saplings planted in the V-blade and in the mounding treatments had mean diameters that were respectively 91% and 155% larger than saplings planted in the control plots. Saplings were 68% taller in the mounding treatment than the control plots, but differences between the V-blade and controls were not significant. We did not detect significant effects of site preparation or the presence of planted hybrid poplar on soil inorganic N. Sapling foliar nutrient concentrations were not influenced by the site preparation treatments. Based on these results, mounding appears to be a good management approach to establish hybrid poplar plantations under the ecological conditions we have studied, as it is less likely to cause erosion because of the localized nature of the treatment. However, these environmental benefits need to be balanced against economic and social considerations.
Discontinuous Galerkin methods are popular because they can achieve high order where the solution is smooth, because they can capture shocks while needing only nearest-neighbor communication, and ...because they are relatively easy to formulate on complex meshes. We perform a detailed comparison of various limiting strategies presented in the literature applied to the equations of general relativistic magnetohydrodynamics. We compare the standard minmod /ΛΠN limiter, the hierarchical limiter of Krivodonova, the simple WENO limiter, the HWENO limiter, and a discontinuous Galerkin-finite-difference hybrid method. The ultimate goal is to understand what limiting strategies are able to robustly simulate magnetized Tolman-Oppenheimer-Volkoff stars without any fine-tuning of parameters. Among the limiters explored in the paper, the only limiting strategy we can endorse is a discontinuous Galerkin-finite-difference hybrid method.
Abstract Magnetic resonance imaging (MRI) studies have identified aberrant cortical structure in Alzheimer's disease (AD). The association between MRI-derived cortical morphometry measures and ...β-amyloid, however, remains poorly understood. In this study, we explored the potential relationship between early alterations in cortical thickness and later stage β-amyloid deposition, using a novel approach, in a transgenic AD mouse model. We acquired longitudinal anatomical MRI scans from mutant amyloid precursor protein (APP) transgenic mice and age-matched wild-type mice at 1 and 3.5 months-of-age, and employed fully-automated image processing methods to derive objective, quantitative measures of cortical thickness on a region-of-interest basis. We also generated 3D quantitative immunohistochemistry (qIHC) volumes of deposited β-amyloid burden from 18 month-old transgenic mice using an automated, production-level process. These studies revealed thinner cortex in most regions in the 1 month-old transgenic mice relative to age-matched wild-types, with the exception of the frontal, perirhinal/entorhinal, posterior cingulate, and retrosplenial cortical regions. Between 1 and 3.5 months-of-age, the transgenic mice demonstrated stable or increasing cortical thickness, while the wild-type mice showed cortical thinning. Based on data from co-registered 3D MRI and qIHC volumes, we identified an association between abnormal, early, regional cortical thickness change over 2.5 months and later β-amyloid deposition. These observations suggest that the spatio-temporal pattern of early (pre-plaque) alterations in cerebral cortical structure is indicative of regional predisposition to later β-amyloid pathology in a transgenic AD mouse model.
Intraspecific trait variability (ITV) provides the material for species' adaptation to environmental changes. To advance our understanding of how ITV can contribute to species' adaptation to a wide ...range of environmental conditions, we studied five widespread understorey forest species exposed to both continental‐scale climate gradients, and local soil and disturbance gradients. We investigated the environmental drivers of between‐site leaf and root trait variation, and tested whether higher between‐site ITV was associated with increased trait sensitivity to environmental variation (i.e. environmental fit).
We measured morphological (specific leaf area: SLA, specific root length: SRL) and chemical traits (Leaf and Root N, P, K, Mg, Ca) of five forest understorey vascular plant species at 78 sites across Canada. A total of 261 species‐by‐site combinations spanning ~4300 km were sampled, capturing important abiotic and biotic environmental gradients (neighbourhood composition, canopy structure, soil conditions, climate). We used multivariate and univariate linear mixed models to identify drivers of ITV and test the association of between‐site ITV with environmental fit.
Between‐site ITV of leaf traits was primarily driven by canopy structure and climate. Comparatively, environmental drivers explained only a small proportion of variability in root traits: these relationships were trait specific and included soil conditions (Root P), canopy structure (Root N) and neighbourhood composition (SRL, Root K). Between‐site ITV was associated with increased environmental fit only for a minority of traits, primarily in response to climate (SLA, Leaf N, SRL).
Synthesis. By studying how ITV is structured along environmental gradients among species adapted to a wide range of conditions, we can begin to understand how individual species might respond to environmental change. Our results show that generalisable trait–environment relationships occur primarily aboveground, and only accounted for a small proportion of variability. For our group of species with broad ecological niches, variability in traits was only rarely associated with higher environmental fit, and primarily along climatic gradients. These results point to promising research avenues on the various ways in which trait variation can affect species' performance along different environmental gradients.
Résumé
La variabilité intraspécifique des traits (VIT) fournit le matériel nécessaire à l'adaptation des espèces aux changements environnementaux. Pour mieux comprendre comment la VIT peut contribuer à l'adaptation des espèces à un large éventail de conditions environnementales, nous avons étudié cinq espèces forestières de sous‐bois très répandues, exposées à la fois à des gradients climatiques à l'échelle continentale et à des gradients locaux de conditions édaphiques et de perturbation. Nous avons étudié les déterminants environnementaux de la variation intraspécifique des traits foliaires et racinaires. Nous avons ensuite testé si une VIT inter‐site (d'un site à l'autre) plus élevée était associée à une sensibilité accrue des traits à la variation environnementale (c.‐à‐d. un ajustement environnemental).
Nous avons mesuré les traits morphologiques (surface foliaire spécifique, SFS; longueur racinaire spécifique, LRS) et chimiques (N, P, K, Mg, Ca des feuilles et des racines) de cinq espèces vasculaires de sous‐bois dans 78 sites au Canada. Un total de 261 combinaisons d'espèces par site couvrant approx. 4300 km a été échantillonné, représentant d'importants gradients abiotiques et biotiques (composition du voisinage, structure de la canopée, conditions du sol, climat). Nous avons utilisé des modèles linéaires mixtes univariés et multivariés pour identifier les déterminants de la VIT inter‐site et tester l'association de la VIT inter‐site avec l'ajustement environnemental.
La VIT inter‐site des traits foliaires était principalement déterminée par la structure de la canopée et le climat. En comparaison, les facteurs environnementaux n'expliquaient qu'une faible proportion de la variabilité des traits racinaires : ces relations étaient spécifiques à chaque trait, incluant les conditions du sol (P racinaire), la structure de la canopée (N racinaire) et la composition du voisinage (LRS, K racinaire). La VIT inter‐site n'était associée à un ajustement environnemental accru que pour une minorité de traits, principalement en réponse au climat (SFS, N foliaire, LRS).
Synthèse. En étudiant la façon dont la VIT est structurée le long des gradients environnementaux parmi des espèces adaptées à un large éventail de conditions, nous pouvons commencer à comprendre comment ces espèces peuvent répondre aux changements environnementaux. Nos résultats montrent que des associations trait‐environnement généralisables existent principalement au‐dessus du sol et ne représentent qu'une faible proportion de la variabilité. Pour notre groupe d'espèces ubiquistes, la variabilité des traits n'était que rarement associée à un meilleur ajustement environnemental, et principalement le long des gradients climatiques. Ces résultats soulèvent des pistes de recherche prometteuses sur les différentes façons dont la variation des traits peut affecter la performance des espèces le long de différents gradients environnementaux.
By studying how ITV is structured along environmental gradients among species adapted to a wide range of conditions, we can begin to understand how individual species might respond to environmental change. Our results show that generalisable trait–environment relationships occur primarily aboveground, and only accounted for a small proportion of variability. For our group of species with broad ecological niches, variability in traits was only rarely associated with higher environmental fit, and primarily along climatic gradients. These results point to promising research avenues on the various ways in which trait variation can affect species' performance along different environmental gradients.
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