Astrophysical Fluid Dynamics via Direct Statistical Simulation

In this paper we introduce the concept of Direct Statistical Simulation (DSS) for astrophysical flows. This technique may be appropriate for problems in astrophysical fluids where the instantaneous dynamics of the flows are of secondary importance to their statistical properties. We give examples of such problems including mixing and transport in planets, stars and disks. The method is described for a general set of evolution equations, before we consider the specific case of a spectral method optimised for problems on a spherical surface. The method is illustrated for the simplest non-trivial example of hydrodynamics and MHD on a rotating spherical surface. We then discuss possible extensions of the method both in terms of computational methods and the range of astrophysical problems that are of interest.Comment: 26 pages, 11 figures, added clarifying remarks and references, and corrected typos. This version is accepted for publication in The Astrophysical Journa

An in silico MS/MS library for automatic annotation of novel FAHFA lipids.

BackgroundA new lipid class named 'fatty acid esters of hydroxyl fatty acids' (FAHFA) was recently discovered in mammalian adipose tissue and in blood plasma and some FAHFAs were found to be associated with type 2 diabetes. To facilitate the automatic annotation of FAHFAs in biological specimens, a tandem mass spectra (MS/MS) library is needed. Due to the limitation of the commercial available standard compounds, we proposed building an in silico MS/MS library to extend the coverage of molecules.ResultsWe developed a computer-generated library with 3267 tandem mass spectra (MS/MS) for 1089 FAHFA species. FAHFA spectra were generated based on authentic standards with negative mode electrospray ionization and 10, 20, and 40 V collision induced dissociation at 4 spectra/s as used in in ultra-high performance liquid chromatography-QTOF mass spectrometry studies. However, positional information of the hydroxyl group is only obtained either at lower QTOF spectra acquisition rates of 1 spectrum/s or at the MS(3) level in ion trap instruments. Therefore, an additional set of 4290 fragment-rich MS/MS spectra was created to enable distinguishing positional FAHFA isomers. The library was generated based on ion fragmentations and ion intensities of FAHFA external reference standards, developing a heuristic model for fragmentation rules and extending these rules to large swaths of computer-generated structures of FAHFAs with varying chain lengths, degrees of unsaturation and hydroxyl group positions. Subsequently, we validated the new in silico library by discovering several new FAHFA species in egg yolk, showing that this library enables high-throughput screening of FAHFA lipids in various biological matrices.ConclusionsThe developed library and templates are freely available for commercial or noncommercial use at http://fiehnlab.ucdavis.edu/staff/yanma/fahfa-lipid-library. This in silico MS/MS library allows users to annotate FAHFAs from accurate mass tandem mass spectra in an easy and fast manner with NIST MS Search or PepSearch software. The developing template is provided for advanced users to modify the parameters and export customized libraries according to their instrument features. Graphical abstractExample of experimental and in silico MS/MS spectra for FAHFA lipids

Non-Poissonian statistics from Poissonian light sources with application to passive decoy state quantum key distribution

We propose a method to prepare different non-Poissonian signal pulses from sources of Poissonian photon number distribution using only linear optical elements and threshold photon detectors. This method allows a simple passive preparation of decoy states for quantum key distribution. We show that the resulting key rates are comparable to the performance of active choices of intensities of Poissonian signals.Comment: 7 pages, 3 figures, accepted for publication in Opt. Let

Shearlet-based compressed sensing for fast 3D cardiac MR imaging using iterative reweighting

High-resolution three-dimensional (3D) cardiovascular magnetic resonance (CMR) is a valuable medical imaging technique, but its widespread application in clinical practice is hampered by long acquisition times. Here we present a novel compressed sensing (CS) reconstruction approach using shearlets as a sparsifying transform allowing for fast 3D CMR (3DShearCS). Shearlets are mathematically optimal for a simplified model of natural images and have been proven to be more efficient than classical systems such as wavelets. Data is acquired with a 3D Radial Phase Encoding (RPE) trajectory and an iterative reweighting scheme is used during image reconstruction to ensure fast convergence and high image quality. In our in-vivo cardiac MRI experiments we show that the proposed method 3DShearCS has lower relative errors and higher structural similarity compared to the other reconstruction techniques especially for high undersampling factors, i.e. short scan times. In this paper, we further show that 3DShearCS provides improved depiction of cardiac anatomy (measured by assessing the sharpness of coronary arteries) and two clinical experts qualitatively analyzed the image quality

MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis.

Data-independent acquisition (DIA) in liquid chromatography (LC) coupled to tandem mass spectrometry (MS/MS) provides comprehensive untargeted acquisition of molecular data. We provide an open-source software pipeline, which we call MS-DIAL, for DIA-based identification and quantification of small molecules by mass spectral deconvolution. For a reversed-phase LC-MS/MS analysis of nine algal strains, MS-DIAL using an enriched LipidBlast library identified 1,023 lipid compounds, highlighting the chemotaxonomic relationships between the algal strains

Endoscopic laser-ablation for the treatment of orthotopic and ectopic ureteroceles in dogs: 13 cases (2008-2017).

BACKGROUND: Ureteroceles are a rare condition in dogs in which conventional treatments can result in substantial morbidity. Cystoscopic and fluoroscopic-guided laser ablation (CLA) of ureteroceles can successfully relieve obstruction. OBJECTIVES: To describe the technique and outcomes of attempting CLA for treatment of ureteroceles in dogs. ANIMALS: Thirteen client-owned dogs that underwent CLA for treatment of ureteroceles. METHODS: Retrospective multicentered study. Medical records were reviewed in all dogs that underwent CLA for ureterocele(s). A laser was used to extend the opening of the ureteral orifice (UO) unless surgical conversion was necessary. Data collected included signalment, clinicopathologic data, imaging, procedural findings, complications, and short- and long-term outcome. RESULTS: Thirteen dogs with 13 ureteroceles associated with 14 UOs resulting in ureteral obstruction were included. One ureterocele extended bilaterally. Treatment was initiated via retrograde cystoscopy (7 females), percutaneous perineal urethrocystoscopy (4 males), or percutaneous antegrade cystoscopy (2 males). Surgical conversion was necessary in 2 males. Ten of 14 (71%) UOs associated with the ureteroceles were ectopic. Thirteen of 14 had stenotic or imperforate UOs. No postoperative complications were noted. Preoperative incontinence or pollakiuria was present in 9 of 13 and 3 of 13 dogs and resolved in 8 of 9 and 3 of 3 dogs, respectively. Follow-up imaging showed resolution of all ureteroceles and improved ureteral/renal pelvic dilatation. Median follow-up time was 27 months (range, 3-96 months). CONCLUSIONS AND CLINICAL IMPORTANCE: Cystoscopic-guided laser ablation was effective for the treatment of ureteroceles(s) in 11 of 13 dogs

Drug-eluting Bead Chemoembolization for the Treatment of Nonresectable Hepatic Carcinoma in Dogs: A Prospective Clinical Trial

Abstract Background Effective treatment options for nonresectable hepatic carcinoma (HC) in dogs are limited. Hypothesis/Objective Objectives were to report outcomes, complications, and tumor responses via computed tomography (CT) assessment after drug‐eluting bead transarterial chemoembolization (DEB‐TACE) for nonresectable HC in dogs. The authors hypothesized that major complications would be uncommon and short‐term CT assessment would demonstrate stable disease or partial response. Animals Client‐owned dogs (n = 16) with nonresectable HC. Methods Prospective, single‐arm clinical trial. Drug‐eluting bead transarterial chemoembolization was performed to varying levels of blood flow stasis. Computed tomography imaging was compared before and approximately 12 weeks after initial treatment. Results Drug‐eluting bead transarterial chemoembolization was successfully administered in all attempts. Based on percent change in elliptical tumor volume response (mL), stable disease (8/13; 62%) was the most common outcome followed by partial response (3/13; 23%) and progressive disease (2/13; 15%) with a median of 74 days (range, 39‐125) after initial treatment. Median tumor volume (mL) after DEB‐TACE decreased in volume by 13% (range, 56% decrease to 77% increase). Mild complications consistent with postembolization syndrome occurred after 7/27 (26%) treatments. Major complications occurred after 3/27 (11%) treatments: hepatic abscess/septicemia (2) and cholecystitis/death (1), resulting in treatment‐induced death after 2/27 (7%) treatments. Median survival time after treatment was 337 days (range, 22‐1061). Dogs with a presenting complaint of weight loss (P = .02) had a significantly shorter median survival time (126 days; range, 46‐337) than those dogs without prior history of weight loss (582 days; range, 22‐1061). Conclusions Drug‐eluting bead transarterial chemoembolization for nonresectable HC is a feasible procedure, which promoted stable disease or partial response in 85% of dogs in this study sample