CORE-Deblur: Parallel MRI Reconstruction by Deblurring Using Compressed Sensing

In this work we introduce a new method that combines Parallel MRI and Compressed Sensing (CS) for accelerated image reconstruction from subsampled k-space data. The method first computes a convolved image, which gives the convolution between a user-defined kernel and the unknown MR image, and then reconstructs the image by CS-based image deblurring, in which CS is applied for removing the inherent blur stemming from the convolution process. This method is hence termed CORE-Deblur. Retrospective subsampling experiments with data from a numerical brain phantom and in-vivo 7T brain scans showed that CORE-Deblur produced high-quality reconstructions, comparable to those of a conventional CS method, while reducing the number of iterations by a factor of 10 or more. The average Normalized Root Mean Square Error (NRMSE) obtained by CORE-Deblur for the in-vivo datasets was 0.016. CORE-Deblur also exhibited robustness regarding the chosen kernel and compatibility with various k-space subsampling schemes, ranging from regular to random. In summary, CORE-Deblur enables high quality reconstructions and reduction of the CS iterations number by 10-fold.Comment: 11 pages, 6 figures, 1 tabl

The Variable Stars and Blue Horizontal Branch of the Metal-Rich Globular Cluster NGC 6441

We present time-series VI photometry of the metal-rich ([Fe/H] = -0.53) globular cluster NGC 6441. Our color-magnitude diagram shows that the extended blue horizontal branch seen in Hubble Space Telescope data exists in the outermost reaches of the cluster. The red clump slopes nearly parallel to the reddening vector. A component of this slope is due to differential reddening, but part is intrinsic. The blue horizontal branch stars are more centrally concentrated than the red clump stars. We have discovered about 50 new variable stars near NGC 6441, among them eight or more RR Lyrae stars which are very probably cluster members. Comprehensive period searches over the range 0.2-1.0 days yielded unusually long periods (0.5-0.9 days) for the fundamental pulsators compared with field RR Lyrae of the same metallicity. Three similar long-period RR Lyrae are known in other metal-rich globulars. With over ten examples in hand, it seems that a distinct sub-class of RR Lyrae is emerging. The observed properties of the horizontal branch stars are in reasonable agreement with recent models which invoke deep mixing to enhance the atmospheric helium abundance, while they conflict with models which assume high initial helium abundance. The light curves of the c-type RR Lyrae seem to have unusually long rise times and sharp minima. Reproducing these light curves in stellar pulsation models may provide another means of constraining the physical variables responsible for the anomalous blue horizontal branch extension and sloped red clump observed in NGC 6441.Comment: 30 pages plus 6 EPS and 6 JPEG figures; uses AAS TeX. Accepted by the Astronomical Journal. Minor changes include computing He abundance, modifications to Figs 1 and 8, and expansion on idea that blue HB stars may be produced in binarie

Parsimonious continuous time random walk models and kurtosis for diffusion in magnetic resonance of biological tissue

In this paper, we provide a context for the modeling approaches that have been developed to describe non-Gaussian diffusion behavior, which is ubiquitous in diffusion weighted magnetic resonance imaging of water in biological tissue. Subsequently, we focus on the formalism of the continuous time random walk theory to extract properties of subdiffusion and superdiffusionthrough novel simplifications of the Mittag-Leffler function. For the case of time-fractional subdiffusion, we compute the kurtosis for the Mittag-Leffler function, which provides both a connection and physical context to the much-used approach of diffusional kurtosis imaging. We provide Monte Carlo simulations to illustrate the concepts of anomalous diffusion as stochastic processes of the random walk. Finally, we demonstrate the clinical utility of the Mittag-Leffler function as a model to describe tissue microstructure through estimations of subdiffusion and kurtosis with diffusion MRI measurements in the brain of a chronic ischemic stroke patient

Reconstructing Velocities of Migrating Birds from Weather Radar – A Case Study in Computational Sustainability

Bird migration occurs at the largest of global scales, but monitoring such movements can be challenging. In the US there is an operational network of weather radars providing freely accessible data for monitoring meteorological phenomena in the atmosphere. Individual radars are sensitive enough to detect birds, and can provide insight into migratory behaviors of birds at scales that are not possible using other sensors. Archived data from the WSR-88D network of US weather radars hold valuable and detailed information about the continent-scale migratory movements of birds over the last 20 years. However, significant technical challenges must be overcome to understand this information and harness its potential for science and conservation. We describe recent work on an AI system to quantify bird migration using radar data, which is part of the larger BirdCast project to model and forecast bird migration at large scales using radar, weather, and citizen science data

Heterogeneous models place the root of the placental mammal phylogeny

Heterogeneity among life traits in mammals has resulted in considerable phylogenetic conflict, particularly concerning the position of the placental root. Layered upon this are gene- and lineage-specific variation in amino acid substitution rates and compositional biases. Life trait variations that may impact upon mutational rates are longevity, metabolic rate, body size, and germ line generation time. Over the past 12 years, three main conflicting hypotheses have emerged for the placement of the placental root. These hypotheses place the Atlantogenata (common ancestor of Xenarthra plus Afrotheria), the Afrotheria, or the Xenarthra as the sister group to all other placental mammals. Model adequacy is critical for accurate tree reconstruction and by failing to account for these compositional and character exchange heterogeneities across the tree and data set, previous studies have not provided a strongly supported hypothesis for the placental root. For the first time, models that accommodate both tree and data set heterogeneity have been applied to mammal data. Here, we show the impact of accurate model assignment and the importance of data sets in accommodating model parameters while maintaining the power to reject competing hypotheses. Through these sophisticated methods, we demonstrate the importance of model adequacy, data set power and provide strong support for the Atlantogenata over other competing hypotheses for the position of the placental root

Chemoradiotherapy screening in a novel biomimetic polymer based pancreatic cancer model

Pancreatic Ductal Adenocarcinoma (PDAC) is a deadly and aggressive disease with a very low survival rate. This is partly due to the resistance of the disease to currently available treatment options. Herein, we report for the first time the use of a novel polyurethane scaffold based PDAC model for screening the short and relatively long term (1 and 17 days post-treatment) responses of chemotherapy, radiotherapy and their combination. We show a dose dependent cell viability reduction and apoptosis induction for both chemotherapy and radiotherapy. Furthermore, we observe a change in the impact of the treatment depending on the time-frame, especially for radiation for which the PDAC scaffolds showed resistance after 1 day but responded more 17 days post-treatment. This is the first study to report a viable PDAC culture in a scaffold for more than 2 months and the first to perform long-term (17 days) post-treatment observations in vitro. This is particularly important as a longer time-frame is much closer to animal studies and to patient treatment regimes, highlighting that our scaffold system has great potential to be used as an animal free model for screening of PDAC

Long-Chain ω-3 Levels Are Associated With Increased Alcohol Sensitivity in a Population-Based Sample of Adolescents.

BackgroundThe levels of the ω-3 long-chain polyunsaturated fatty acids (ω-3 LC-PUFAs), including eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), have been associated with alcohol sensitivity in vertebrate and invertebrate model systems, but prior studies have not examined this association in human samples despite evidence of associations between ω-3 LC-PUFA levels and alcohol-related phenotypes. Both alcohol sensitivity and ω-3 LC-PUFA levels are impacted by genetic factors, and these influences may contribute to observed associations between phenotypes. Given the potential for using EPA and DHA supplementation in adjuvant care for alcohol misuse and other outcomes, it is important to clarify how ω-3 LC-PUFA levels relate to alcohol sensitivity.MethodsAnalyses were conducted using data from the Avon Longitudinal Study of Parents and Children. Plasma ω-3 LC-PUFA levels were measured at ages 15.5 and 17.5. Participants reported on their initial alcohol sensitivity using the early drinking Self-Rating of the Effects of Alcohol (SRE-5) scale, for which more drinks needed for effects indicates lower levels of response per drink, at ages 15.5, 16.5, and 17.5. Polygenic liability for alcohol consumption, alcohol problems, EPA levels, and DHA levels was derived using summary statistics from large, publicly available datasets. Linear regressions were used to examine the cross-sectional and longitudinal associations between ω-3 LC-PUFA levels and SRE scores.ResultsAge 15.5 ω-3 LC-PUFA levels were negatively associated with contemporaneous SRE scores and with age 17.5 SRE scores. One modest association (p = 0.02) between polygenic liability and SRE scores was observed, between alcohol problems-based polygenic risk scores (PRS) and age 16.5 SRE scores. Tests of moderation by genetic liability were not warranted.ConclusionsPlasma ω-3 LC-PUFA levels may be related to initial sensitivity to alcohol during adolescence. These data indicate that diet-related factors have the potential to impact humans' earliest responses to alcohol exposure

Off-resonance saturation as an MRI method to quantify mineral- iron in the post-mortem brain

PURPOSE: To employ an off‐resonance saturation method to measure the mineral‐iron pool in the postmortem brain, which is an endogenous contrast agent that can give information on cellular iron status. METHODS: An off‐resonance saturation acquisition protocol was implemented on a 7 Tesla preclinical scanner, and the contrast maps were fitted to an established analytical model. The method was validated by correlation and Bland‐Altman analysis on a ferritin‐containing phantom. Mineral‐iron maps were obtained from postmortem tissue of patients with neurological diseases characterized by brain iron accumulation, that is, Alzheimer disease, Huntington disease, and aceruloplasminemia, and validated with histology. Transverse relaxation rate and magnetic susceptibility values were used for comparison. RESULTS: In postmortem tissue, the mineral‐iron contrast colocalizes with histological iron staining in all the cases. Iron concentrations obtained via the off‐resonance saturation method are in agreement with literature. CONCLUSIONS: Off‐resonance saturation is an effective way to detect iron in gray matter structures and partially mitigate for the presence of myelin. If a reference region with little iron is available in the tissue, the method can produce quantitative iron maps. This method is applicable in the study of diseases characterized by brain iron accumulation and can complement existing iron‐sensitive parametric methods