Diffeomorphic random sampling using optimal information transport

In this article we explore an algorithm for diffeomorphic random sampling of nonuniform probability distributions on Riemannian manifolds. The algorithm is based on optimal information transport (OIT)---an analogue of optimal mass transport (OMT). Our framework uses the deep geometric connections between the Fisher-Rao metric on the space of probability densities and the right-invariant information metric on the group of diffeomorphisms. The resulting sampling algorithm is a promising alternative to OMT, in particular as our formulation is semi-explicit, free of the nonlinear Monge--Ampere equation. Compared to Markov Chain Monte Carlo methods, we expect our algorithm to stand up well when a large number of samples from a low dimensional nonuniform distribution is needed.Comment: 8 pages, 3 figure

Investigation of Er3+ Ions Reinforced Zinc-Phosphate Glasses for Ionizing Radiation Shielding Applications

Melt quenching technique is used for preparing glasses with chemical formula (70P2 O5)– (16 − x)CdO–(14ZnO)–(xEr2 O3), (x = 1–6 mol%). These glasses were named Er1, Er2, Er3, Er4, Er5, and Er6, respectively. Photon buildup factors, fast neutron absorption, and electron stopping of the prepared glasses were examined. Glasses’ density was varied from 3.390 ± 0.003 for the Er1 glass sample to 3.412 ± 0.003 for the Er6 glass sample. The Buildup factor (BUF) spectra have relatively higher values in the Compton Scattering (CS) dominated areas compared to both Photoelectric effect (PE), and Pair Production (PP) dominated energy regions. The highest BUF appeared at the Er atom K-absorption edge, whose intensity increases as the molar concentration of Er2 O3 in the glasses increases. The photon absorption efficiency (PAE) of the glasses increases according to the trend (PAE)Er1 < (PAE)Er2 < (PAE)Er3 < (PAE)Er4 < (PAE)Er5 < (PAE)Er6. Fast neutron removal cross-section, FNRC (ΣR) values of the glasses obtained via calculation varied from 0.1045–0.1039 cm−1 for Er1–Er6. Furthermore, the continuous slowing down approximation mode (CSDA) range enhances the kinetic energy of electrons for all glasses. Generally, results revealed that the investigated glasses could be applied for radiation shielding and dosimetric media. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.Taif University Researchers Supporting Project number (TURSP-2020/23), Taif University, Taif Saudi Arabia. "The APC was covered by "Dunarea de Jos" University of Galati, Romania, through grant no. RF3621/2021

Fabrication and characterization of dual function nanoscale pH-scanning ion conductance microscopy (SICM) probes for high resolution pH mapping

The easy fabrication and use of nanoscale dual function pH-scanning ion conductance microscopy (SICM) probes is reported. These probes incorporate an iridium oxide coated carbon electrode for pH measurement and an SICM barrel for distance control, enabling simultaneous pH and topography mapping. These pH-SICM probes were fabricated rapidly from laser pulled theta quartz pipets, with the pH electrode prepared by in situ carbon filling of one of the barrels by the pyrolytic decomposition of butane, followed by electrodeposition of a thin layer of hydrous iridium oxide. The other barrel was filled with an electrolyte solution and Ag/AgCl electrode as part of a conductance cell for SICM. The fabricated probes, with pH and SICM sensing elements typically on the 100 nm scale, were characterized by scanning electron microscopy, energy-dispersive X-ray spectroscopy, and various electrochemical measurements. They showed a linear super-Nernstian pH response over a range of pH (pH 2–10). The capability of the pH-SICM probe was demonstrated by detecting both pH and topographical changes during the dissolution of a calcite microcrystal in aqueous solution. This system illustrates the quantitative nature of pH-SICM imaging, because the dissolution process changes the crystal height and interfacial pH (compared to bulk), and each is sensitive to the rate. Both measurements reveal similar dissolution rates, which are in agreement with previously reported literature values measured by classical bulk methods

Robust Online Hamiltonian Learning

In this work we combine two distinct machine learning methodologies, sequential Monte Carlo and Bayesian experimental design, and apply them to the problem of inferring the dynamical parameters of a quantum system. We design the algorithm with practicality in mind by including parameters that control trade-offs between the requirements on computational and experimental resources. The algorithm can be implemented online (during experimental data collection), avoiding the need for storage and post-processing. Most importantly, our algorithm is capable of learning Hamiltonian parameters even when the parameters change from experiment-to-experiment, and also when additional noise processes are present and unknown. The algorithm also numerically estimates the Cramer-Rao lower bound, certifying its own performance.Comment: 24 pages, 12 figures; to appear in New Journal of Physic

Inference of Experimental Radial Impurity Transport on Alcator C-Mod: Bayesian Parameter Estimation and Model Selection

We present a fully Bayesian approach for the inference of radial profiles of impurity transport coefficients and compare its results to neoclassical, gyrofluid and gyrokinetic modeling. Using nested sampling, the Bayesian Impurity Transport InferencE (BITE) framework can handle complex parameter spaces with multiple possible solutions, offering great advantages in interpretative power and reliability with respect to previously demonstrated methods. BITE employs a forward model based on the pySTRAHL package, built on the success of the well-known STRAHL code [Dux, IPP Report, 2004], to simulate impurity transport in magnetically-confined plasmas. In this paper, we focus on calcium (Ca, Z=20) Laser Blow-Off injections into Alcator C-Mod plasmas. Multiple Ca atomic lines are diagnosed via high-resolution X-ray Imaging Crystal Spectroscopy and Vacuum Ultra-Violet measurements. We analyze a sawtoothing I-mode discharge for which neoclassical and turbulent (quasilinear and nonlinear) predictions are also obtained. We find good agreement in diffusion across the entire radial extent, while turbulent convection and density profile peaking are estimated to be larger in experiment than suggested by theory. Efforts and challenges associated with the inference of experimental pedestal impurity transport are discussed.Comment: 38 pages, 19 figures, submitted for publication in Nuclear Fusio

How Different Preparation Techniques Affect MRI-Induced Anxiety of MRI Patients: A Preliminary Study

Background: Magnetic resonance imaging (MRI) exams may cause patients to feel anxious before or during the scan, which affects the scanning outcome and leads to motion artifacts. Adequate preparation can effectively alleviate patients’ anxiety before the scan. We aimed to assess the effect of different preparation methods on MRI-induced anxiety: We conducted a prospective randomized study on MRI patients between March and May 2022. We divided 30 patients into two groups: the control group, which received routine preparation (RP), and the experimental group, which received video preparation (VP).We used the State-Trait Anxiety Inventory (STAI) to measure anxiety levels before and after the interventions. We assessed patients’ self-satisfaction after the scan: After preparation, VP (STAI mean = 10.7500) and RP (STAI mean = 12.7857), we observed a significant association between the pre- and post-STAI results in VP (p = 0.025). The effects of both methods in decreasing anxiety were more significant for first-timers (p = 0.009 in RP/0.014 in VP). We noted high satisfaction levels for both forms of preparation. The VP technique was superior in reducing patient anxiety, especially in first-time MRI patients. Hence, VP techniques can be used in different clinical settings to reduce anxiety and facilitate patients’ understanding of the instructions given

Cooperativity Dominates the Genomic Organization of p53-Response Elements: A Mechanistic View

p53-response elements (p53-REs) are organized as two repeats of a palindromic DNA segment spaced by 0 to 20 base pairs (bp). Several experiments indicate that in the vast majority of the human p53-REs there are no spacers between the two repeats; those with spacers, particularly with sizes beyond two nucleotides, are rare. This raises the question of what it indicates about the factors determining the p53-RE genomic organization. Clearly, given the double helical DNA conformation, the orientation of two p53 core domain dimers with respect to each other will vary depending on the spacer size: a small spacer of 0 to 2 bps will lead to the closest p53 dimer-dimer orientation; a 10-bp spacer will locate the p53 dimers on the same DNA face but necessitate DNA looping; while a 5-bp spacer will position the p53 dimers on opposite DNA faces. Here, via conformational analysis we show that when there are 0–2 bp spacers, p53-DNA binding is cooperative; however, cooperativity is greatly diminished when there are spacers with sizes beyond 2 bp. Cooperative binding is broadly recognized to be crucial for biological processes, including transcriptional regulation. Our results clearly indicate that cooperativity of the p53-DNA association dominates the genomic organization of the p53-REs, raising questions of the structural organization and functional roles of p53-REs with larger spacers. We further propose that a dynamic landscape scenario of p53 and p53-REs can better explain the selectivity of the degenerate p53-REs. Our conclusions bear on the evolutionary preference of the p53-RE organization and as such, are expected to have broad implications to other multimeric transcription factor response element organization

Modelling the COVID-19 pandemic in context : An international participatory approach

Funding RA is funded by the Bill and Melinda Gates Foundation (OPP1193472). LW is funded by the Li Ka Shing Foundation. CF is funded by grant #2017/26770-8, São Paulo Research Foundation (FAPESP). The CoMo Consortium has support from the Oxford University COVID-19 Research Response Fund (ref: 0009280). Scientific writing assistance and editorial support was provided by Adam Bodley, according to Good Publication Practice guidelines.Peer reviewedPublisher PD

Injection Drug Use Is a Risk Factor for HCV Infection in Urban Egypt

OBJECTIVE: To identify current risk factors for hepatitis C virus (HCV) transmission in Greater Cairo. DESIGN AND SETTING: A 1:1 matched case-control study was conducted comparing incident acute symptomatic hepatitis C patients in two "fever" hospitals of Greater Cairo with two control groups: household members of the cases and acute hepatitis A patients diagnosed at the same hospitals. Controls were matched on the same age and sex to cases and were all anti-HCV antibody negative. Iatrogenic, community and household exposures to HCV in the one to six months before symptoms onset for cases, and date of interview for controls, were exhaustively assessed. RESULTS: From 2002 to 2007, 94 definite acute symptomatic HCV cases and 188 controls were enrolled in the study. In multivariate analysis, intravenous injections (OR = 5.0; 95% CI = 1.2-20.2), medical stitches (OR = 4.2; 95% CI = 1.6-11.3), injection drug use (IDU) (OR = 7.9; 95% CI = 1.4-43.5), recent marriage (OR = 3.3; 95% CI = 1.1-9.9) and illiteracy (OR = 3.9; 95% CI = 1.8-8.5) were independently associated with an increased HCV risk. CONCLUSION: In urban Cairo, invasive health care procedures remain a source of HCV transmission and IDU is an emerging risk factor. Strict application of standard precautions during health care is a priority. Implementation of comprehensive infection prevention programs for IDU should be considered

Potential health and economic impacts of dexamethasone treatment for patients with COVID-19

Acknowledgements We thank all members of the COVID-19 International Modelling Consortium and their collaborative partners. This work was supported by the COVID-19 Research Response Fund, managed by the Medical Sciences Division, University of Oxford. L.J.W. is supported by the Li Ka Shing Foundation. R.A. acknowledges funding from the Bill and Melinda Gates Foundation (OPP1193472).Peer reviewedPublisher PD