School of Physics - Research Publications
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ItemX-ray fluorescence spectroscopy (XRF) for metallome analysis of herbarium specimens(BMC, 2022-12-19)BACKGROUND: "Herbarium X-ray Fluorescence (XRF) Ionomics" is a new quantitative approach for extracting the elemental concentrations from herbarium specimens using handheld XRF devices. These instruments are principally designed for dense sample material of infinite thickness (such as rock or soil powder), and their built-in algorithms and factory calibrations perform poorly on the thin dry plant leaves encountered in herbaria. While empirical calibrations have been used for 'correcting' measured XRF values post hoc, this approach has major shortcomings. As such, a universal independent data analysis pipeline permitting full control and transparency throughout the quantification process is highly desirable. Here we have developed such a pipeline based on Dynamic Analysis as implemented in the GeoPIXE package, employing a Fundamental Parameters approach requiring only a description of the measurement hardware and derivation of the sample areal density, based on a universal standard. RESULTS: The new pipeline was tested on potassium, calcium, manganese, iron, cobalt, nickel, and zinc concentrations in dry plant leaves. The Dynamic Analysis method can correct for complex X-ray interactions and performs better than both the built-in instrument algorithms and the empirical calibration approach. The new pipeline is also able to identify and quantify elements that are not detected and reported by the device built-in algorithms and provides good estimates of elemental concentrations where empirical calibrations are not straightforward. CONCLUSIONS: The new pipeline for processing XRF data of herbarium specimens has a greater accuracy and is more robust than the device built-in algorithms and empirical calibrations. It also gives access to all elements detected in the XRF spectrum. The new analysis pipeline has made Herbarium XRF approach even more powerful to study the metallome of existing plant collections.
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ItemPhoton extraction enhancement of praseodymium ions in gallium nitride nanopillars(NATURE PORTFOLIO, 2022-12-08)Lanthanoid-doped Gallium Nitride (GaN) integrated into nanophotonic technologies is a promising candidate for room-temperature quantum photon sources for quantum technology applications. We manufactured praseodymium (Pr)-doped GaN nanopillars of varying size, and showed significantly enhanced room-temperature photon extraction efficiency compared to unstructured Pr-doped GaN. Implanted Pr ions in GaN show two main emission peaks at 650.3 nm and 651.8 nm which are attributed to 3P0-3F2 transition in the 4f-shell. The maximum observed enhancement ratio was 23.5 for 200 nm diameter circular pillars, which can be divided into the emitted photon extraction enhancement by a factor of 4.5 and the photon collection enhancement by a factor of 5.2. The enhancement mechanism is explained by the eigenmode resonance inside the nanopillar. Our study provides a pathway for Lanthanoid-doped GaN nano/micro-scale photon emitters and quantum technology applications.
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ItemNo Preview AvailableRedshift Evolution of the Feedback-Cooling Equilibrium in the Core of 48 SPT Galaxy Clusters: A Joint Chandra-SPT-ATCA Analysis(IOP Publishing Ltd, 2023-05-01)Abstract We analyze the cooling and feedback properties of 48 galaxy clusters at redshifts 0.4 < z < 1.3 selected from the South Pole Telescope (SPT) catalogs to evolve like the progenitors of massive and well-studied systems at z ∼ 0. We estimate the radio power at the brightest cluster galaxy (BCG) location of each cluster from an analysis of Australia Telescope Compact Array data. Assuming that the scaling relation between the radio power and active galactic nucleus (AGN) cavity power P cav observed at low redshift does not evolve with redshift, we use these measurements in order to estimate the expected AGN cavity power in the core of each system. We estimate the X-ray luminosity within the cooling radius L cool of each cluster from a joint analysis of the available Chandra X-ray and SPT Sunyaev–Zel’dovich (SZ) data. This allows us to characterize the redshift evolution of the P cav/L cool ratio. When combined with low-redshift results, these constraints enable investigations of the properties of the feedback–cooling cycle across 9 Gyr of cluster growth. We model the redshift evolution of this ratio measured for cool-core clusters by a log-normal distribution Log - ( α + β z , σ 2 ) and constrain the slope of the mean evolution to β = −0.05 ± 0.47. This analysis improves the constraints on the slope of this relation by a factor of two. We find no evidence of redshift evolution of the feedback–cooling equilibrium in these clusters, which suggests that the onset of radio-mode feedback took place at an early stage of cluster formation. High values of P cav/L cool are found at the BCG location of noncool-core clusters, which might suggest that the timescales of the AGN feedback cycle and the cool core–noncool core transition are different. This work demonstrates that the joint analysis of radio, SZ, and X-ray data solidifies the investigation of AGN feedback at high redshifts.
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ItemNo Preview AvailableEvidence for AGN-regulated Cooling in Clusters at z similar to 1.4: A Multiwavelength View of SPT-CL J0607-4448(IOP Publishing Ltd, 2023-02-01)Abstract We present a multiwavelength analysis of the galaxy cluster SPT-CL J0607-4448 (SPT0607), which is one of the most distant clusters discovered by the South Pole Telescope at z = 1.4010 ± 0.0028. The high-redshift cluster shows clear signs of being relaxed with well-regulated feedback from the active galactic nucleus (AGN) in the brightest cluster galaxy (BCG). Using Chandra X-ray data, we construct thermodynamic profiles and determine the properties of the intracluster medium. The cool-core nature of the cluster is supported by a centrally peaked density profile and low central entropy ( K 0 = 18 − 9 + 11 keV cm2), which we estimate assuming an isothermal temperature profile due to the limited spectral information given the distance to the cluster. Using the density profile and gas cooling time inferred from the X-ray data, we find a mass-cooling rate M ̇ cool = 100 − 60 + 90 M ⊙ yr−1. From optical spectroscopy and photometry around the [O ii] emission line, we estimate that the BCG star formation rate is SFR [ O II ] = 1.7 − 0.6 + 1.0 M ⊙ yr−1, roughly two orders of magnitude lower than the predicted mass-cooling rate. In addition, using ATCA radio data at 2.1 GHz, we measure a radio jet power P cav = 3.2 − 1.3 + 2.1 × 10 44 erg s−1, which is consistent with the X-ray cooling luminosity ( L cool = 1.9 − 0.5 + 0.2 × 10 44 erg s−1 within r cool = 43 kpc). These findings suggest that SPT0607 is a relaxed, cool-core cluster with AGN-regulated cooling at an epoch shortly after cluster formation, implying that the balance between cooling and feedback can be reached quickly. We discuss the implications for these findings on the evolution of AGN feedback in galaxy clusters.
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ItemNo Preview AvailableMid-infrared spectral reconstruction with dielectric metasurfaces and dictionary learning(Optica Publishing Group, 2022-05-15)Mid-infrared (MIR) spectroscopy has numerous industrial applications and is usually performed with Fourier-transform infrared (FTIR) spectrometers. While these work well for many purposes, there is currently much interest in alternative approaches that are smaller and lighter, i.e., MIR microspectrometers. Here we investigate all-dielectric metasurfaces as spectral filters for MIR microspectrometers. Two metasurface types are studied. For the first, we design, fabricate, and test a metasurface with a narrow and angularly tunable transmission stop band. We use it to reconstruct the transmission spectra of various materials. The second metasurface, investigated theoretically, possesses narrow passband features via symmetry-protected bound states in the continuum.
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ItemNo Preview AvailablePerceptual Grouping Explains Similarities in Constellations Across Cultures(SAGE PUBLICATIONS INC, 2022-03)Cultures around the world organize stars into constellations, or asterisms, and these groupings are often considered to be arbitrary and culture specific. Yet there are striking similarities in asterisms across cultures, and groupings such as Orion, the Big Dipper, the Pleiades, and the Southern Cross are widely recognized across many different cultures. Psychologists have informally suggested that these shared patterns are explained by Gestalt laws of grouping, but there have been no systematic attempts to catalog asterisms that recur across cultures or to explain the perceptual basis of these groupings. Here, we compiled data from 27 cultures around the world and found that a simple computational model of perceptual grouping accounts for many of the recurring cross-cultural asterisms. Our results suggest that basic perceptual principles account for more of the structure of asterisms across cultures than previously acknowledged and highlight ways in which specific cultures depart from this shared baseline.
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ItemNo Preview AvailableDynamic responses of renal oxygenation at the onset of cardiopulmonary bypass in sheep and man(SAGE PUBLICATIONS LTD, 2022-09-01)INTRODUCTION: The renal medulla is susceptible to hypoxia during cardiopulmonary bypass (CPB), which may contribute to the development of acute kidney injury. But the speed of onset of renal medullary hypoxia remains unknown. METHODS: We continuously measured renal medullary oxygen tension (MPO2) in 24 sheep, and urinary PO2 (UPO2) as an index of MPO2 in 92 patients, before and after induction of CPB. RESULTS: In laterally recumbent sheep with a right thoracotomy (n = 20), even before CPB commenced MPO2 fell from (mean ± SEM) 52 ± 4 to 41 ±5 mmHg simultaneously with reduced arterial pressure (from 108 ± 5 to 88 ± 5 mmHg). In dorsally recumbent sheep with a medial sternotomy (n = 4), MPO2 was even more severely reduced (to 12 ± 12 mmHg) before CPB. In laterally recumbent sheep in which a crystalloid prime was used (n = 7), after commencing CPB, MPO2 fell abruptly to 24 ±6 mmHg within 20-30 minutes. MPO2 during CPB was not improved by adding donor blood to the prime (n = 13). In patients undergoing cardiac surgery, UPO2 fell by 4 ± 1 mmHg and mean arterial pressure fell by 7 ± 1 mmHg during the 30 minutes before CPB. UPO2 then fell by a further 12 ± 2 mmHg during the first 30 minutes of CPB but remained relatively stable for the remaining 24 minutes of observation. CONCLUSIONS: Renal medullary hypoxia is an early event during CPB. It starts to develop even before CPB, presumably due to a pressure-dependent decrease in renal blood flow. Medullary hypoxia during CPB appears to be promoted by hypotension and is not ameliorated by increasing blood hemoglobin concentration.
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ItemNo Preview AvailableQuantitative proteomics of tau and A beta in n detergent fractions from Alzheimer's disease brains(WILEY, 2022-11-22)The two hallmarks of Alzheimer's disease (AD) are amyloid-β (Aβ) plaques and neurofibrillary tangles marked by phosphorylated tau. Increasing evidence suggests that aggregating Aβ drives tau accumulation, a process that involves synaptic degeneration leading to cognitive impairment. Conversely, there is a realization that non-fibrillar (oligomeric) forms of Aβ mediate toxicity in AD. Fibrillar (filamentous) aggregates of proteins across the spectrum of the primary and secondary tauopathies were the focus of recent structural studies with a filament structure-based nosologic classification, but less emphasis was given to non-filamentous co-aggregates of insoluble proteins in the fractions derived from post-mortem human brains. Here, we revisited sarkosyl-soluble and -insoluble extracts to characterize tau and Aβ species by quantitative targeted mass spectrometric proteomics, biochemical assays, and electron microscopy. AD brain sarkosyl-insoluble pellets were greatly enriched with Aβ42 at almost equimolar levels to N-terminal truncated microtubule-binding region (MTBR) isoforms of tau with multiple site-specific post-translational modifications (PTMs). MTBR R3 and R4 tau peptides were most abundant in the sarkosyl-insoluble materials with a 10-fold higher concentration than N-terminal tau peptides. This indicates that the major proportion of the enriched tau was the aggregation-prone N-terminal and proline-rich region (PRR) of truncated mixed 4R and 3R tau with more 4R than 3R isoforms. High concentration and occupancies of site-specific phosphorylation pT181 (~22%) and pT217 (~16%) (key biomarkers of AD) along with other PTMs in the PRR and MTBR indicated a regional susceptibility of PTMs in aggregated tau. Immunogold labelling revealed that tau may exist in globular non-filamentous form (N-terminal intact tau) co-localized with Aβ in the sarkosyl-insoluble pellets along with tau filaments (N-truncated MTBR tau). Our results suggest a model that Aβ and tau interact forming globular aggregates, from which filamentous tau and Aβ emerge. These characterizations contribute towards unravelling the sequence of events which lead to end-stage AD changes.
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ItemNo Preview AvailableDetection and Estimation of Randomly Phase Modulated Signals(IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC, 2023)
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ItemNo Preview AvailableA Novel Optical Assay System for Bilirubin Concentration Measurement in Whole Blood(IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC, 2022-02-01)As a biomarker for liver disease, bilirubin has been utilized in prognostic scoring systems for cirrhosis. While laboratory-based methods are used to determine bilirubin levels in clinical settings, they do not readily lend themselves to applications outside of hospitals. Consequently, bilirubin monitoring for cirrhotic patients is often performed only intermittently; thus, episodes requiring clinical interventions could be missed. This work investigates the feasibility of measuring bilirubin concentration in whole porcine blood samples using dual-wavelength transmission measurement. A compact and low-cost dual-wavelength transmission measurement setup is developed and optimized to measure whole blood bilirubin concentrations. Using small volumes of whole porcine blood (72 µL), we measured the bilirubin concentration within a range corresponding to healthy individuals and cirrhotic patients (1.2-30 mg/dL). We demonstrate that bilirubin levels can be estimated with a positive correlation (R-square > 0.95) and an accuracy of ±1.7 mg/dL, with higher reliability in cirrhotic bilirubin concentrations (> 4 mg/dL) - critical for high-risk patients. The optical and electronic components utilized are economical and can be readily integrated into a miniature, low-cost, and user-friendly system. This could provide a pathway for point-of-care monitoring of blood bilirubin outside of medical facilities (e.g., patient's home).