A subspace-based resolution-enhancing image reconstruction method for few-view differential phase-contrast tomography

It is well known that properly designed image reconstruction methods can facilitate reductions in imaging doses and data-acquisition times in tomographic imaging. The ability to do so is particularly important for emerging modalities, such as differential x-ray phase-contrast tomography (D-XPCT), which are currently limited by these factors. An important application of D-XPCT is high-resolution imaging of biomedical samples. However, reconstructing high-resolution images from few-view tomographic measurements remains a challenging task due to the high-frequency information loss caused by data incompleteness. In this work, a subspace-based reconstruction strategy is proposed and investigated for use in few-view D-XPCT image reconstruction. By adopting a two-step approach, the proposed method can simultaneously recover high-frequency details within a certain region of interest while suppressing noise and/or artifacts globally. The proposed method is investigated by the use of few-view experimental data acquired by an edge-illumination D-XPCT scanner

A joint-reconstruction approach for single-shot edge illumination x-ray phase-contrast tomography

Edge illumination X-ray phase-contrast tomography (EIXPCT) is an imaging technique that estimates the spatially variant X-ray refractive index and absorption distribution within an object while seeking to circumvent the limitations of previous benchtop implementations of X-ray phase-contrast tomography. As with gratingor analyzer-based methods, conventional image reconstruction methods for EIXPCT require that two or more images be acquired at each tomographic view angle. This requirement leads to increased data acquisition times, hindering in vivo applications. To circumvent these limitations, a joint reconstruction (JR) approach is proposed that concurrently produces estimates of the refractive index and absorption distributions from a tomographic data set containing only a single image per tomographic view angle. The JR reconstruction method solves a nonlinear optimization problem by use of a novel iterative gradient-based algorithm. The JR method is demonstrated in both computer-simulated and experimental EIXPCT studies

Comparison of data-acquisition designs for single-shot edge-illumination X-ray phase-contrast tomography

Edge-illumination X-ray phase-contrast tomography (EIXPCT) is an emerging technique that enables practical phase-contrast imaging with laboratory-based X-ray sources. A joint reconstruction method was proposed for reconstructing EIXPCT images, enabling novel flexible data-acquisition designs. However, only limited efforts have been devoted to optimizing data-acquisition designs for use with the joint reconstruction method. In this study, several promising designs are introduced, such as the constant aperture position (CAP) strategy and the alternating aperture position (AAP) strategy covering different angular ranges. In computer-simulation studies, these designs are analyzed and compared. Experimental data are employed to test the designs in real-world applications. All candidate designs are also compared for their implementation complexity. The tradeoff between data-acquisition time and image quality is discussed

Genomic Context of Azole Resistance Mutations in Aspergillus fumigatus Determined Using Whole-Genome Sequencing.

A rapid and global emergence of azole resistance has been observed in the pathogenic fungus Aspergillus fumigatus over the past decade. The dominant resistance mechanism appears to be of environmental origin and involves mutations in the cyp51A gene, which encodes a protein targeted by triazole antifungal drugs. Whole-genome sequencing (WGS) was performed for high-resolution single-nucleotide polymorphism (SNP) analysis of 24 A. fumigatus isolates, including azole-resistant and susceptible clinical and environmental strains obtained from India, the Netherlands, and the United Kingdom, in order to assess the utility of WGS for characterizing the alleles causing resistance. WGS analysis confirmed that TR34/L98H (a mutation comprising a tandem repeat [TR] of 34 bases in the promoter of the cyp51A gene and a leucine-to-histidine change at codon 98) is the sole mechanism of azole resistance among the isolates tested in this panel of isolates. We used population genomic analysis and showed that A. fumigatus was panmictic, with as much genetic diversity found within a country as is found between continents. A striking exception to this was shown in India, where isolates are highly related despite being isolated from both clinical and environmental sources across >1,000 km; this broad occurrence suggests a recent selective sweep of a highly fit genotype that is associated with the TR34/L98H allele. We found that these sequenced isolates are all recombining, showing that azole-resistant alleles are segregating into diverse genetic backgrounds. Our analysis delineates the fundamental population genetic parameters that are needed to enable the use of genome-wide association studies to identify the contribution of SNP diversity to the generation and spread of azole resistance in this medically important fungus. IMPORTANCE: Resistance to azoles in the ubiquitous ascomycete fungus A. fumigatus was first reported from clinical isolates collected in the United States during the late 1980s. Over the last decade, an increasing number of A. fumigatus isolates from the clinic and from nature have been found to show resistance to azoles, suggesting that resistance is emerging through selection by the widespread usage of agricultural azole antifungal compounds. Aspergillosis is an emerging clinical problem, with high rates of treatment failures necessitating the development of new techniques for surveillance and for determining the genome-wide basis of azole resistance in A. fumigatus

Correction: Selective particle and cell capture in a continuous flow using micro-vortex acoustic streaming

The authors regret that a citation to a relevant paper was missed. The following sentence and reference (ref. 1 shown below) should be added in the Introduction after the sentence ending "...of the applied flow rate.5,37": "For example, Lee et al. acoustically oscillate air/liquid interfaces using a ∼50 kHz piezoelectric transducer to produce acoustic streaming fields for size-based separation of cells and particles".1 The Royal Society of Chemistry apologises for these errors and any consequent inconvenience to authors and readers

Single-shot edge illumination x-ray phase-contrast tomography enabled by joint image reconstruction

Edge illumination x-ray phase-contrast tomography (EIXPCT) is an emerging x-ray phase-contrast tomography technique for reconstructing the complex-valued x-ray refractive index distribution of an object. Conventional image reconstruction approaches for EIXPCT require multiple images to be acquired at each tomographic view angle. This contributes to prolonged data-acquisition times and elevated radiation doses, which can hinder in vivo applications. In this work, a new “single-shot” method is proposed for joint reconstruction (JR) of the real and imaginaryvalued components of the refractive index distribution from a tomographic data set that contains only a single image acquired at each view angle. The proposed method is predicated on a nonlinear formulation of the inverse problem that is solved by using a gradient-based optimization method. The method is validated and investigated using computersimulated and experimental EIXPCT data sets

Supersymmetric Extension of GCA in 2d

We derive the infinite dimensional Supersymmetric Galilean Conformal Algebra (SGCA) in the case of two spacetime dimensions by performing group contraction on 2d superconformal algebra. We also obtain the representations of the generators in terms of superspace coordinates. Here we find realisations of the SGCA by considering scaling limits of certain 2d SCFTs which are non-unitary and have their left and right central charges become large in magnitude and opposite in sign. We focus on the Neveu-Schwarz sector of the parent SCFTs and develop, in parallel to the GCA studies recently in (arXiv:0912.1090), the representation theory based on SGCA primaries, Ward identities for their correlation functions and their descendants which are null states.Comment: La TeX file, 32 pages; v2: typos corrected, journal versio

Nonlinear Elasticity, Fluctuations and Heterogeneity of Nematic Elastomers

Liquid crystal elastomers realize a fascinating new form of soft matter that is a composite of a conventional crosslinked polymer gel (rubber) and a liquid crystal. These {\em solid} liquid crystal amalgams, quite similarly to their (conventional, fluid) liquid crystal counterparts, can spontaneously partially break translational and/or orientational symmetries, accompanied by novel soft Goldstone modes. As a consequence, these materials can exhibit unconventional elasticity characterized by symmetry-enforced vanishing of some elastic moduli. Thus, a proper description of such solids requires an essential modification of the classical elasticity theory. In this work, we develop a {\em rotationally invariant}, {\em nonlinear} theory of elasticity for the nematic phase of ideal liquid crystal elastomers. We show that it is characterized by soft modes, corresponding to a combination of long wavelength shear deformations of the solid network and rotations of the nematic director field. We study thermal fluctuations of these soft modes in the presence of network heterogeneities and show that they lead to a large variety of anomalous elastic properties, such as singular length-scale dependent shear elastic moduli, a divergent elastic constant for splay distortion of the nematic director, long-scale incompressibility, universal Poisson ratios and a nonlinear stress-strain relation fo arbitrary small strains. These long-scale elastic properties are {\em universal}, controlled by a nontrivial zero-temperature fixed point and constitute a qualitative breakdown of the classical elasticity theory in nematic elastomers. Thus, nematic elastomers realize a stable ``critical phase'', characterized by universal power-law correlations, akin to a critical point of a continuous phase transition, but extending over an entire phase.Comment: 61 pages, 24 eps pages, submitted to Annals of Physic

Detailed Balance and Intermediate Statistics

We present a theory of particles, obeying intermediate statistics ("anyons"), interpolating between Bosons and Fermions, based on the principle of Detailed Balance. It is demonstrated that the scattering probabilities of identical particles can be expressed in terms of the basic numbers, which arise naturally and logically in this theory. A transcendental equation determining the distribution function of anyons is obtained in terms of the statistics parameter, whose limiting values 0 and 1 correspond to Bosons and Fermions respectively. The distribution function is determined as a power series involving the Boltzmann factor and the statistics parameter and we also express the distribution function as an infinite continued fraction. The last form enables one to develop approximate forms for the distribution function, with the first approximant agreeing with our earlier investigation.Comment: 13 pages, RevTex, submitted for publication; added references; added sentence