MR image reconstruction using deep density priors

Algorithms for Magnetic Resonance (MR) image reconstruction from undersampled measurements exploit prior information to compensate for missing k-space data. Deep learning (DL) provides a powerful framework for extracting such information from existing image datasets, through learning, and then using it for reconstruction. Leveraging this, recent methods employed DL to learn mappings from undersampled to fully sampled images using paired datasets, including undersampled and corresponding fully sampled images, integrating prior knowledge implicitly. In this article, we propose an alternative approach that learns the probability distribution of fully sampled MR images using unsupervised DL, specifically Variational Autoencoders (VAE), and use this as an explicit prior term in reconstruction, completely decoupling the encoding operation from the prior. The resulting reconstruction algorithm enjoys a powerful image prior to compensate for missing k-space data without requiring paired datasets for training nor being prone to associated sensitivities, such as deviations in undersampling patterns used in training and test time or coil settings. We evaluated the proposed method with T1 weighted images from a publicly available dataset, multi-coil complex images acquired from healthy volunteers (N=8) and images with white matter lesions. The proposed algorithm, using the VAE prior, produced visually high quality reconstructions and achieved low RMSE values, outperforming most of the alternative methods on the same dataset. On multi-coil complex data, the algorithm yielded accurate magnitude and phase reconstruction results. In the experiments on images with white matter lesions, the method faithfully reconstructed the lesions. Keywords: Reconstruction, MRI, prior probability, machine learning, deep learning, unsupervised learning, density estimationComment: Published in IEEE TMI. Main text and supplementary material, 19 pages tota

Quantum Spin Lenses in Atomic Arrays

We propose and discuss `quantum spin lenses', where quantum states of delocalized spin excitations in an atomic medium are `focused' in space in a coherent quantum process down to (essentially) single atoms. These can be employed to create controlled interactions in a quantum light-matter interface, where photonic qubits stored in an atomic ensemble are mapped to a quantum register represented by single atoms. We propose Hamiltonians for quantum spin lenses as inhomogeneous spin models on lattices, which can be realized with Rydberg atoms in 1D, 2D and 3D, and with strings of trapped ions. We discuss both linear and non-linear quantum spin lenses: in a non-linear lens, repulsive spin-spin interactions lead to focusing dynamics conditional to the number of spin excitations. This allows the mapping of quantum superpositions of delocalized spin excitations to superpositions of spatial spin patterns, which can be addressed by light fields and manipulated. Finally, we propose multifocal quantum spin lenses as a way to generate and distribute entanglement between distant atoms in an atomic lattice array.Comment: 13 pages, 9 figure

Higgs Boson Masses in the Complex NMSSM at One-Loop Level

The Next-to-Minimal Supersymmetric Extension of the Standard Model (NMSSM) with a Higgs sector containing five neutral and two charged Higgs bosons allows for a rich phenomenology. In addition, the plethora of parameters provides many sources of CP violation. In contrast to the Minimal Supersymmetric Extension, CP violation in the Higgs sector is already possible at tree-level. For a reliable understanding and interpretation of the experimental results of the Higgs boson search, and for a proper distinction of Higgs sectors provided by the Standard Model or possible extensions, the Higgs boson masses have to be known as precisely as possible including higher-order corrections. In this paper we calculate the one-loop corrections to the neutral Higgs boson masses in the complex NMSSM in a Feynman diagrammatic approach adopting a mixed renormalization scheme based on on-shell and $\bar{DR}$ conditions. We study various scenarios where we allow for tree-level CP-violating phases in the Higgs sector and where we also study radiatively induced CP violation due to a non-vanishing phase of the trilinear coupling $A_t$ in the stop sector. The effects on the Higgs boson phenomenology are found to be significant. We furthermore estimate the theoretical error due to unknown higher-order corrections by both varying the renormalization scheme of the top and bottom quark masses and by adopting different renormalization scales. The residual theoretical error can be estimated to about 10%

Comparison of digital and conventional impression techniques: evaluation of patients’ perception, treatment comfort, effectiveness and clinical outcomes

Background: The purpose of this study was to compare two impression techniques from the perspective of patient preferences and treatment comfort.Methods: Twenty-four (12 male, 12 female) subjects who had no previous experience with either conventional or digital impression participated in this study. Conventional impressions of maxillary and mandibular dental arches were taken with a polyether impression material (Impregum, 3 M ESPE), and bite registrations were made with polysiloxane bite registration material (Futar D, Kettenbach). Two weeks later, digital impressions and bite scans were performed using an intra-oral scanner (CEREC Omnicam, Sirona). Immediately after the impressions were made, the subjects' attitudes, preferences and perceptions towards impression techniques were evaluated using a standardized questionnaire. The perceived source of stress was evaluated using the State-Trait Anxiety Scale. Processing steps of the impression techniques (tray selection, working time etc.) were recorded in seconds. Statistical analyses were performed with the Wilcoxon Rank test, and p < 0.05 was considered significant.Results: There were significant differences among the groups (p < 0.05) in terms of total working time and processing steps. Patients stated that digital impressions were more comfortable than conventional techniques.Conclusions: Digital impressions resulted in a more time-efficient technique than conventional impressions. Patients preferred the digital impression technique rather than conventional techniques

A case study of controlling crossover in a selection hyper-heuristic framework using the multidimensional knapsack problem

Hyper-heuristics are high-level methodologies for solving complex problems that operate on a search space of heuristics. In a selection hyper-heuristic framework, a heuristic is chosen from an existing set of low-level heuristics and applied to the current solution to produce a new solution at each point in the search. The use of crossover low-level heuristics is possible in an increasing number of general-purpose hyper-heuristic tools such as HyFlex and Hyperion. However, little work has been undertaken to assess how best to utilise it. Since a single-point search hyper-heuristic operates on a single candidate solution, and two candidate solutions are required for crossover, a mechanism is required to control the choice of the other solution. The frameworks we propose maintain a list of potential solutions for use in crossover. We investigate the use of such lists at two conceptual levels. First, crossover is controlled at the hyper-heuristic level where no problem-specific information is required. Second, it is controlled at the problem domain level where problem-specific information is used to produce good-quality solutions to use in crossover. A number of selection hyper-heuristics are compared using these frameworks over three benchmark libraries with varying properties for an NP-hard optimisation problem: the multidimensional 0-1 knapsack problem. It is shown that allowing crossover to be managed at the domain level outperforms managing crossover at the hyper-heuristic level in this problem domain. © 2016 Massachusetts Institute of Technolog

Enhanced snoMEN Vectors Facilitate Establishment of GFP–HIF-1α Protein Replacement Human Cell Lines

The snoMEN (snoRNA Modulator of gene ExpressioN) vector technology was developed from a human box C/D snoRNA, HBII-180C, which contains an internal sequence that can be manipulated to make it complementary to RNA targets, allowing knock-down of targeted genes. Here we have screened additional human nucleolar snoRNAs and assessed their application for gene specific knock-downs to improve the efficiency of snoMEN vectors. We identify and characterise a new snoMEN vector, termed 47snoMEN, that is derived from box C/D snoRNA U47, demonstrating its use for knock-down of both endogenous cellular proteins and G/YFP-fusion proteins. Using multiplex 47snoMEM vectors that co-express multiple 47snoMEN in a single transcript, each of which can target different sites in the same mRNA, we document &#62;3-fold increase in knock-down efficiency when compared with the original HBII-180C based snoMEN. The multiplex 47snoMEM vector allowed the construction of human protein replacement cell lines with improved efficiency, including the establishment of novel GFP–HIF-1α replacement cells. Quantitative mass spectrometry analysis confirmed the enhanced efficiency and specificity of protein replacement using the 47snoMEN-PR vectors. The 47snoMEN vectors expand the potential applications for snoMEN technology in gene expression studies, target validation and gene therapy

Nitrosylation of Myoglobin and Nitrosation of Cysteine by Nitrite in a Model System Simulating Meat Curing

Demand is growing for meat products cured without the addition of sodium nitrite. Instead of the direct addition of nitrite to meat in formulation, nitrite is supplied by bacterial reduction of natural nitrate often added as vegetable juice/powder. However, the rate of nitrite formation in this process is relatively slow, and the total ingoing nitrite is typically less than in conventional curing processes. The objective of this study was to determine the impact of the rate of addition of nitrite and the amount of nitrite added on nitrosylation/nitrosation reactions in a model meat curing system. Myoglobin was preferentially nitrosylated as no decrease in sulfhydryl groups was found until maximum nitrosylmyoglobin color was achieved. The cysteine–myoglobin model retained more sulfhydryl groups than the cysteine-only model (p \u3c 0.05). The rate of nitrite addition did not alter nitrosylation/nitrosation reactions (p \u3e 0.05). These data suggest that the amount of nitrite but not the rate of addition impacts the nitrosylation/nitrosation reactions this syste

Regulation of microRNA biogenesis and turnover by animals and their viruses

Item does not contain fulltextMicroRNAs (miRNAs) are a ubiquitous component of gene regulatory networks that modulate the precise amounts of proteins expressed in a cell. Despite their small size, miRNA genes contain various recognition elements that enable specificity in when, where and to what extent they are expressed. The importance of precise control of miRNA expression is underscored by functional studies in model organisms and by the association between miRNA mis-expression and disease. In the last decade, identification of the pathways by which miRNAs are produced, matured and turned-over has revealed many aspects of their biogenesis that are subject to regulation. Studies in viral systems have revealed a range of mechanisms by which viruses target these pathways through viral proteins or non-coding RNAs in order to regulate cellular gene expression. In parallel, a field of study has evolved around the activation and suppression of antiviral RNA interference (RNAi) by viruses. Virus encoded suppressors of RNAi can impact miRNA biogenesis in cases where miRNA and small interfering RNA pathways converge. Here we review the literature on the mechanisms by which miRNA biogenesis and turnover are regulated in animals and the diverse strategies that viruses use to subvert or inhibit these processes

DGCR8 HITS-CLIP reveals novel functions for the Microprocessor

The Drosha-DGCR8 complex (Microprocessor) is required for microRNA (miRNA) biogenesis. DGCR8 recognizes the RNA substrate, whereas Drosha functions as the endonuclease. High-throughput sequencing and crosslinking immunoprecipitation (HITS-CLIP) was used to identify RNA targets of DGCR8 in human cells. Unexpectedly, miRNAs were not the most abundant targets. DGCR8-bound RNAs also comprised several hundred mRNAs as well as snoRNAs and long non-coding RNAs. We found that the Microprocessor controls the abundance of several mRNAs as well as of MALAT-1. By contrast, DGCR8-mediated cleavage of snoRNAs is independent of Drosha, suggesting the involvement of DGCR8 in cellular complexes with other endonucleases. Interestingly, binding of DGCR8 to cassette exons, acts as a novel mechanism to regulate the relative abundance of alternatively spliced isoforms. Collectively, these data provide new insights in the complex role of DGCR8 in controlling the fate of several classes of RNAs