Variations in boundary layer stability across Antarctica: a comparison between coastal and interior sites

The range of boundary layer stability profiles, from the surface to 500 m a.g.l. (above ground level), present in radiosonde observations from two continental-interior (South Pole Station and Dome Concordia Station) and three coastal (McMurdo Station, Georg von Neumayer Station III, and Syowa Station) Antarctic sites, is examined using the self-organizing maps (SOMs) neural network algorithm. A wide range of potential temperature profiles is revealed, from shallow boundary layers with strong near-surface stability to deeper boundary layers with weaker or near-neutral stability, as well as profiles with weaker near-surface stability and enhanced stability aloft, above the boundary layer. Boundary layer regimes were defined based on the range of profiles revealed by the SOM analysis; 20 boundary layer regimes were identified to account for differences in stability near the surface as well as above the boundary layer. Strong, very strong, or extremely strong stability, with vertical potential temperature gradients of 5 to in excess of 30 K per 100 m, occurred more than 80 % of the time at South Pole and Dome Concordia in the winter. Weaker stability was found in the winter at the coastal sites, with moderate and strong stability (vertical potential temperature gradients of 1.75 to 15 K per 100 m) occurring 70 % to 85 % of the time. Even in the summer, moderate and strong stability is found across all five sites, either immediately near the surface or aloft, just above the boundary layer. While the mean boundary layer height at the continental-interior sites was found to be approximately 50 m, the mean boundary layer height at the coastal sites was deeper, around 110 m. Further, a commonly described two-stability-regime system in the Arctic associated with clear or cloudy conditions was applied to the 20 boundary layer regimes identified in this study to understand if the two-regime behavior is also observed in the Antarctic. It was found that moderate and strong stability occur more often with clear- than cloudy-sky conditions, but weaker stability regimes occur almost equally for clear and cloudy conditions.</p

Modelling the Distribution of 3D Brain MRI using a 2D Slice VAE

Probabilistic modelling has been an essential tool in medical image analysis, especially for analyzing brain Magnetic Resonance Images (MRI). Recent deep learning techniques for estimating high-dimensional distributions, in particular Variational Autoencoders (VAEs), opened up new avenues for probabilistic modeling. Modelling of volumetric data has remained a challenge, however, because constraints on available computation and training data make it difficult effectively leverage VAEs, which are well-developed for 2D images. We propose a method to model 3D MR brain volumes distribution by combining a 2D slice VAE with a Gaussian model that captures the relationships between slices. We do so by estimating the sample mean and covariance in the latent space of the 2D model over the slice direction. This combined model lets us sample new coherent stacks of latent variables to decode into slices of a volume. We also introduce a novel evaluation method for generated volumes that quantifies how well their segmentations match those of true brain anatomy. We demonstrate that our proposed model is competitive in generating high quality volumes at high resolutions according to both traditional metrics and our proposed evaluation.Comment: accepted for publication at MICCAI 2020. Code available https://github.com/voanna/slices-to-3d-brain-vae

Learning an atlas of a cognitive process in its functional geometry

Proceedings of the 22nd International Conference, IPMI 2011, Kloster Irsee, Germany, July 3-8, 2011.In this paper we construct an atlas that captures functional characteristics of a cognitive process from a population of individuals. The functional connectivity is encoded in a low-dimensional embedding space derived from a diffusion process on a graph that represents correlations of fMRI time courses. The atlas is represented by a common prior distribution for the embedded fMRI signals of all subjects. The atlas is not directly coupled to the anatomical space, and can represent functional networks that are variable in their spatial distribution. We derive an algorithm for fitting this generative model to the observed data in a population. Our results in a language fMRI study demonstrate that the method identifies coherent and functionally equivalent regions across subjects.National Science Foundation (U.S.) (IIS/CRCNS 0904625)National Science Foundation (U.S.) (CAREER grant 0642971)National Institutes of Health (U.S.) (NCRR NAC P41- RR13218)National Institute of Biomedical Imaging and Bioengineering (U.S.) (U54-EB005149)National Institutes of Health (U.S.) (U41RR019703)National Institutes of Health (U.S.) (P01CA067165)Seventh Framework Programme (European Commission) (n◦257528 (KHRESMOI)

LNCS

Concurrent accesses to shared data structures must be synchronized to avoid data races. Coarse-grained synchronization, which locks the entire data structure, is easy to implement but does not scale. Fine-grained synchronization can scale well, but can be hard to reason about. Hand-over-hand locking, in which operations are pipelined as they traverse the data structure, combines fine-grained synchronization with ease of use. However, the traditional implementation suffers from inherent overheads. This paper introduces snapshot-based synchronization (SBS), a novel hand-over-hand locking mechanism. SBS decouples the synchronization state from the data, significantly improving cache utilization. Further, it relies on guarantees provided by pipelining to minimize synchronization that requires cross-thread communication. Snapshot-based synchronization thus scales much better than traditional hand-over-hand locking, while maintaining the same ease of use

Molecular basis for passive immunotherapy of Alzheimer's disease

Amyloid aggregates of the amyloid-{beta} (A{beta}) peptide are implicated in the pathology of Alzheimer's disease. Anti-A{beta} monoclonal antibodies (mAbs) have been shown to reduce amyloid plaques in vitro and in animal studies. Consequently, passive immunization is being considered for treating Alzheimer's, and anti-A{beta} mAbs are now in phase II trials. We report the isolation of two mAbs (PFA1 and PFA2) that recognize A{beta} monomers, protofibrils, and fibrils and the structures of their antigen binding fragments (Fabs) in complex with the A{beta}(1–8) peptide DAEFRHDS. The immunodominant EFRHD sequence forms salt bridges, hydrogen bonds, and hydrophobic contacts, including interactions with a striking WWDDD motif of the antigen binding fragments. We also show that a similar sequence (AKFRHD) derived from the human protein GRIP1 is able to cross-react with both PFA1 and PFA2 and, when cocrystallized with PFA1, binds in an identical conformation to A{beta}(1–8). Because such cross-reactivity has implications for potential side effects of immunotherapy, our structures provide a template for designing derivative mAbs that target A{beta} with improved specificity and higher affinity

Asymmetric Image-Template Registration

Authors Manuscript received: 2010 May 4. 12th International Conference, London, UK, September 20-24, 2009, Proceedings, Part IA natural requirement in pairwise image registration is that the resulting deformation is independent of the order of the images. This constraint is typically achieved via a symmetric cost function and has been shown to reduce the effects of local optima. Consequently, symmetric registration has been successfully applied to pairwise image registration as well as the spatial alignment of individual images with a template. However, recent work has shown that the relationship between an image and a template is fundamentally asymmetric. In this paper, we develop a method that reconciles the practical advantages of symmetric registration with the asymmetric nature of image-template registration by adding a simple correction factor to the symmetric cost function. We instantiate our model within a log-domain diffeomorphic registration framework. Our experiments show exploiting the asymmetry in image-template registration improves alignment in the image coordinates.NAMIC (NIH NIBIB NAMIC U54-EB005149)NAC (NIH NCRR NAC P41- RR13218)mBIRN (NIH NCRR mBIRN U24-RR021382)NIH NINDS (R01-NS051826 Grant)National Science Foundation (U.S.) (CAREER Grant 0642971)NIBIB (R01 EB001550)NIBIB (R01EB006758)NCRR (R01 RR16594-01A1)NCRR (P41-RR14075)NINDS (R01 NS052585-01)Singapore. Agency for Science, Technology and Researc

Temporal Registration in In-Utero Volumetric MRI Time Series

We present a robust method to correct for motion and deformations in in-utero volumetric MRI time series. Spatio-temporal analysis of dynamic MRI requires robust alignment across time in the presence of substantial and unpredictable motion. We make a Markov assumption on the nature of deformations to take advantage of the temporal structure in the image data. Forward message passing in the corresponding hidden Markov model (HMM) yields an estimation algorithm that only has to account for relatively small motion between consecutive frames. We demonstrate the utility of the temporal model by showing that its use improves the accuracy of the segmentation propagation through temporal registration. Our results suggest that the proposed model captures accurately the temporal dynamics of deformations in in-utero MRI time series.National Institutes of Health (U.S.) (NIH NIBIB NAC P41EB015902)National Institutes of Health (U.S.) (NIH NICHD U01HD087211)National Institutes of Health (U.S.) (NIH NIBIB R01EB017337)Wistron CorporationMerrill Lynch Wealth Management (Fellowship

Temporal Registration in In-Utero Volumetric MRI Time Series

We present a robust method to correct for motion and deformations in in-utero volumetric MRI time series. Spatio-temporal analysis of dynamic MRI requires robust alignment across time in the presence of substantial and unpredictable motion. We make a Markov assumption on the nature of deformations to take advantage of the temporal structure in the image data. Forward message passing in the corresponding hidden Markov model (HMM) yields an estimation algorithm that only has to account for relatively small motion between consecutive frames. We demonstrate the utility of the temporal model by showing that its use improves the accuracy of the segmentation propagation through temporal registration. Our results suggest that the proposed model captures accurately the temporal dynamics of deformations in in-utero MRI time series.National Institutes of Health (U.S.) (NIH NIBIB NAC P41EB015902)National Institutes of Health (U.S.) (NIH NICHD U01HD087211)National Institutes of Health (U.S.) (NIH NIBIB R01EB017337)Wistron CorporationMerrill Lynch Wealth Management (Fellowship

On Correctness of Data Structures under Reads-Write Concurrency

Abstract. We study the correctness of shared data structures under reads-write concurrency. A popular approach to ensuring correctness of read-only operations in the presence of concurrent update, is read-set validation, which checks that all read variables have not changed since they were first read. In practice, this approach is often too conserva-tive, which adversely affects performance. In this paper, we introduce a new framework for reasoning about correctness of data structures under reads-write concurrency, which replaces validation of the entire read-set with more general criteria. Namely, instead of verifying that all read conditions over the shared variables, which we call base conditions. We show that reading values that satisfy some base condition at every point in time implies correctness of read-only operations executing in parallel with updates. Somewhat surprisingly, the resulting correctness guarantee is not equivalent to linearizability, and is instead captured through two new conditions: validity and regularity. Roughly speaking, the former re-quires that a read-only operation never reaches a state unreachable in a sequential execution; the latter generalizes Lamport’s notion of regular-ity for arbitrary data structures, and is weaker than linearizability. We further extend our framework to capture also linearizability. We illus-trate how our framework can be applied for reasoning about correctness of a variety of implementations of data structures such as linked lists.

Organizing XML data in a wireless broadcast system by exploiting structural similarities

Wireless data broadcast is an efficient way of delivering data of common interest to a large population of mobile devices within a proximate area, such as smart cities, battle fields, etc. In this work, we focus ourselves on studying the data placement problem of periodic XML data broadcast in mobile and wireless environments. This is an important issue, particularly when XML becomes prevalent in today’s ubiquitous and mobile computing devices and applications. Taking advantage of the structured characteristics of XML data, effective broadcast programs can be generated based on the XML data on the server only. An XML data broadcast system is developed and a theoretical analysis on the XML data placement on a wireless channel is also presented, which forms the basis of the novel data placement algorithm in this work. The proposed algorithm is validated through a set of experiments. The results show that the proposed algorithm can effectively place XML data on air and significantly improve the overall access efficiency