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Knappett JBM, Haydon B, Cowie BCC, Kewish CM, van Riessen GA. Evaluation of the X-ray/EUV Nanolithography Facility at AS through wavefront propagation simulations. JOURNAL OF SYNCHROTRON RADIATION 2024; 31:485-492. [PMID: 38630438 DOI: 10.1107/s1600577524002534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 03/18/2024] [Indexed: 05/08/2024]
Abstract
Synchrotron light sources can provide the required spatial coherence, stability and control to support the development of advanced lithography at the extreme ultraviolet and soft X-ray wavelengths that are relevant to current and future fabricating technologies. Here an evaluation of the optical performance of the soft X-ray (SXR) beamline of the Australian Synchrotron (AS) and its suitability for developing interference lithography using radiation in the 91.8 eV (13.5 nm) to 300 eV (4.13 nm) range are presented. A comprehensive physical optics model of the APPLE-II undulator source and SXR beamline was constructed to simulate the properties of the illumination at the proposed location of a photomask, as a function of photon energy, collimation and monochromator parameters. The model is validated using a combination of experimental measurements of the photon intensity distribution of the undulator harmonics. It is shown that the undulator harmonics intensity ratio can be accurately measured using an imaging detector and controlled using beamline optics. Finally, the photomask geometric constraints and achievable performance for the limiting case of fully spatially coherent illumination are evaluated.
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Affiliation(s)
- Jerome B M Knappett
- Department of Mathematical and Physical Sciences, School of Computing, Engineering and Mathematical Sciences, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Blair Haydon
- Department of Mathematical and Physical Sciences, School of Computing, Engineering and Mathematical Sciences, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Bruce C C Cowie
- Australian Synchrotron, Australian Nuclear Science and Technology Organisation (ANSTO), Clayton, Victoria 3168, Australia
| | - Cameron M Kewish
- Department of Mathematical and Physical Sciences, School of Computing, Engineering and Mathematical Sciences, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Grant A van Riessen
- Department of Mathematical and Physical Sciences, School of Computing, Engineering and Mathematical Sciences, La Trobe University, Bundoora, Victoria 3086, Australia
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2
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Boseley RE, Sylvain NJ, Peeling L, Kelly ME, Pushie MJ. A review of concepts and methods for FTIR imaging of biomarker changes in the post-stroke brain. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184287. [PMID: 38266967 DOI: 10.1016/j.bbamem.2024.184287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 01/26/2024]
Abstract
Stroke represents a core area of study in neurosciences and public health due to its global contribution toward mortality and disability. The intricate pathophysiology of stroke, including ischemic and hemorrhagic events, involves the interruption in oxygen and nutrient delivery to the brain. Disruption of these crucial processes in the central nervous system leads to metabolic dysregulation and cell death. Fourier transform infrared (FTIR) spectroscopy can simultaneously measure total protein and lipid content along with a number of key biomarkers within brain tissue that cannot be observed using conventional techniques. FTIR imaging provides the opportunity to visualize this information in tissue which has not been chemically treated prior to analysis, thus retaining the spatial distribution and in situ chemical information. Here we present a review of FTIR imaging methods for investigating the biomarker responses in the post-stroke brain.
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Affiliation(s)
- Rhiannon E Boseley
- Department of Surgery, University of Saskatchewan, Saskatoon, SK S7N 0W8, Canada
| | - Nicole J Sylvain
- Department of Surgery, University of Saskatchewan, Saskatoon, SK S7N 0W8, Canada
| | - Lissa Peeling
- Department of Surgery, University of Saskatchewan, Saskatoon, SK S7N 0W8, Canada
| | - Michael E Kelly
- Department of Surgery, University of Saskatchewan, Saskatoon, SK S7N 0W8, Canada
| | - M Jake Pushie
- Department of Surgery, University of Saskatchewan, Saskatoon, SK S7N 0W8, Canada.
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3
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Szczerbowska-Boruchowska M, Stec P, Czyzycki M, Szczerbowski Z, Simon R, Baumbach T, Ziomber-Lisiak A. The applicability of Fourier transform infrared microspectroscopy for correction against matrix effects in X-ray fluorescence microimaging of tissues. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 293:122468. [PMID: 36787676 DOI: 10.1016/j.saa.2023.122468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 02/04/2023] [Indexed: 06/18/2023]
Abstract
X-ray fluorescence (XRF) and Fourier transform infrared (FTIR) microscopy techniques are now considered popular for rapid and label-free complementary spectrochemical analysis of chemical elements and molecular systems in biological specimens. The morphological heterogeneity but also the inhomogeneities associated with the thickness/density of biological samples demonstrate challenges for the quantitative XRF microimaging. Therefore, in the present work, we proposed for the first time the application of the total absorbance under the FTIR spectra as a mass surface correction procedure for two-dimensional (2D) XRF microimaging of tissues. We also evaluated the equivalence of the developed correction method based on total absorbance of FTIR spectra with the proposed approaches based on incoherent scattering of primary X-rays as well as on the membrane Si-Kα transmission signal, on the example of selected rat organ tissues. Thin cryo-sections taken from various organs of Wistar rats were deposited on silicon nitride membranes (Si3N4). The FTIR microscopy studies were performed to collect infrared absorption spectra, used then for the determination of total absorbance values in the selected areas of tissue samples. In turn, hard X-ray imaging based on synchrotron radiation allowed the determination of characteristic radiation intensities of the elements detectable from the tissue, as well as the characteristic radiation of the membrane Si and incoherently scattered X-ray photons (Compton scattering). The latter served as correction factors for the surface mass of the sample alongside the FTIR total absorbance. The qualitative and quantitative analyses showed a high agreement between the results of elemental surface mass correction using total absorbance under FTIR spectra of tissues with those obtained using surface mass correction factors determined directly from XRF spectra. Therefore, the proposed procedure is a good alternative in cases where the surface mass effect of the sample cannot be eliminated based on the information provided directly by the XRF spectrum, as in the case of using polymer films as sample support. We have also proposed a procedure for synchronizing SRXRF and FTIR images, not limited to visual inspection of imaging/mapping data, but also enabling quantitative analysis. We found that the total absorbance determined from FTIR spectra can be successfully used as a correction factor for eliminating the surface mass effect in XRF microimaging of thin freeze-fried tissues and therefore to obtain the surface mass-independent elemental quantities. The proposed approach for 2D-FTIR-XRF analysis can also be a powerful and versatile tool for fostering a correlation and co-localization analysis to search for common distribution patterns between molecular arrangements and chemical elements.
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Affiliation(s)
| | - Patryk Stec
- AGH University of Science and Technology, Faculty of Physics and Applied Computer Science, Al. Mickiewicza 30, 30-059 Krakow, Poland
| | - Mateusz Czyzycki
- AGH University of Science and Technology, Faculty of Physics and Applied Computer Science, Al. Mickiewicza 30, 30-059 Krakow, Poland; Karlsruhe Institute of Technology, Institute for Photon Science and Synchrotron Radiation, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Zbigniew Szczerbowski
- AGH University of Science and Technology, Faculty of Geo-Data Science, Geodesy, and Environmental Enginiering, Al. Mickiewicza 30, 30-059 Krakow, Poland
| | - Rolf Simon
- Karlsruhe Institute of Technology, Institute for Photon Science and Synchrotron Radiation, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Tilo Baumbach
- Karlsruhe Institute of Technology, Institute for Photon Science and Synchrotron Radiation, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Agata Ziomber-Lisiak
- Chair of Pathophysiology, Faculty of Medicine, Jagiellonian University Medical College, ul. Czysta 18, 31-121 Krakow, Poland
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Wilk A, Drozdz A, Olbrich K, Janik-Olchawa N, Setkowicz Z, Chwiej J. Influence of measurement mode on the results of glioblastoma multiforme analysis with the FTIR microspectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 287:122086. [PMID: 36423418 DOI: 10.1016/j.saa.2022.122086] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 11/02/2022] [Accepted: 11/03/2022] [Indexed: 06/16/2023]
Abstract
Fourier Transform Infrared (FTIR) microspectroscopy is well known for its effectiveness in spectral and biochemical analyses of various materials. It enables to determine the sample biochemical composition by assigning detected frequencies, characteristic for functional groups of main biological macromolecules. In analysis of tissue sections one of two measurement modes, namely transmission and transflection, is usually applied. The first one has relatively straightforward geometry, hence it is considered to be more precise and accurate. However, IR-transparent media are very fragile and expensive. Transflection does not require expensive substrates, but is more prone to disruptive influence of Mie scattering as well as electric field standing wave effect. The excessive comparison of spectra' characteristics, obtained via both measurement modes, was performed in this paper. By the means of Mann-Whitney non-parametrical U test and PCA, the comparison of results obtained with both modes and assessment of usefulness of IR spectra obtained with transmission and transflection modes to differentiate between healthy and GBM-affected tissue, were performed. The main objective of the presented research is to compare the results of FTIR analysis of unfixed biological samples performed with transflection and transmission mode. In frame of the study we demonstrated the discrepancies between results of biochemical analysis performed based on data obtained with transmission and transflection. Such observation suggests that caution should be taken in drawing conclusions from the results obtained with transflection geometry, as its more prone to disruptive effects. Despite that, IR spectra developed with both modes allowed to distinguish GBM area from healthy tissue, which proves their diagnostic potential. Especially, application of the ME-EMSC correction of spectra before PCA enhances the performance of both methods to distinguish the analysed tissue areas.
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Affiliation(s)
- Aleksandra Wilk
- Faculty of Physics and Applied Computer Science, AGH University of Science and Technology, Mickiewicza 30, 30-059 Krakow, Poland
| | - Agnieszka Drozdz
- Faculty of Physics and Applied Computer Science, AGH University of Science and Technology, Mickiewicza 30, 30-059 Krakow, Poland; Faculty of Biology and Biotechnology, Maria Curie-Sklodowska University, Akademicka 19, 20-033 Lublin, Poland.
| | - Karolina Olbrich
- Faculty of Physics and Applied Computer Science, AGH University of Science and Technology, Mickiewicza 30, 30-059 Krakow, Poland
| | - Natalia Janik-Olchawa
- Faculty of Physics and Applied Computer Science, AGH University of Science and Technology, Mickiewicza 30, 30-059 Krakow, Poland
| | - Zuzanna Setkowicz
- Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa 9, 30-387 Krakow, Poland
| | - Joanna Chwiej
- Faculty of Physics and Applied Computer Science, AGH University of Science and Technology, Mickiewicza 30, 30-059 Krakow, Poland
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Balerna A, Ferrario M, Stellato F. The INFN-LNF present and future accelerator-based light facilities. EUROPEAN PHYSICAL JOURNAL PLUS 2023; 138:37. [PMID: 36686496 PMCID: PMC9843097 DOI: 10.1140/epjp/s13360-022-03611-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 12/18/2022] [Indexed: 06/17/2023]
Abstract
The INFN-Frascati National Laboratory (LNF) is nowadays running a 0.51 GeV electron-positron collider, DA Φ NE, that also represents the synchrotron radiation source of the beamlines of the DA Φ NE-Light facility. Not being DA Φ NE dedicated to synchrotron radiations activities, the DA Φ NE-Light facility can use it mainly in parasitic mode. Particle accelerators and high energy physics (HEP) have been and are the main core of the LNF research activity, but like other HEP international laboratories also LNF is now moving in the direction of developing a dedicated free electron laser (FEL) user facility, EuPRAXIA@SPARC_Lab, based on plasma acceleration. This new facility in the framework of the EuPRAXIA (European Plasma Research Accelerator with eXcellence in Applications) EU project should produce FEL radiation beams for a wide range of applications using a smaller accelerator compared to actual radio frequency-based accelerator sources dimensions.
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Affiliation(s)
- Antonella Balerna
- Laboratori Nazionali di Frascati, INFN, Via Enrico Fermi 54, 00044 Frascati, RM Italy
| | - Massimo Ferrario
- Laboratori Nazionali di Frascati, INFN, Via Enrico Fermi 54, 00044 Frascati, RM Italy
| | - Francesco Stellato
- Physics Department, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Roma, Italy
- Sezione di Roma Tor Vergata, INFN, Via della Ricerca Scientifica 1, 00133 Roma, Italy
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Surowka AD, Czyzycki M, Ziomber-Lisiak A, Migliori A, Szczerbowska-Boruchowska M. On 2D-FTIR-XRF microscopy - A step forward correlative tissue studies by infrared and hard X-ray radiation. Ultramicroscopy 2021; 232:113408. [PMID: 34706307 DOI: 10.1016/j.ultramic.2021.113408] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 09/14/2021] [Accepted: 10/03/2021] [Indexed: 11/28/2022]
Abstract
Correlative Fourier Transform Infra-Red (FTIR) and hard X-Ray Fluorescence (XRF) microscopy studies of thin biological samples have recently evolved as complementary methods for biochemical fingerprinting of animal/human tissues. These are seen particularly useful for tracking the mechanisms of neurological diseases, i.e., in Alzheimer/Parkinson disease, in the brain where mishandling of trace metals (Fe, Cu, Zn) seems to be often associated with ongoing damage to molecular components via, among others, oxidative/reductive stress neurotoxicity. Despite substantial progress in state-of-the-art detection and data analysis methods, combined FTIR-XRF experiments have never benefited from correlation and co-localization analysis of molecular moieties and chemical elements, respectively. We here propose for the first time a completely novel data analysis pipeline, utilizing the idea of 2D correlation spectrometry for brain tissue analysis. In this paper, we utilized combined benchtop FTIR - synchrotron XRF mapping experiments on thin brain samples mounted on polypropylene membranes. By implementing our recently developed Multiple Linear Regression Multi-Reference (MLR-MR) algorithm, along with advanced image processing, artifact-free 2D FTIR-XRF spectra could be obtained by mitigating the impact of spectral artifacts, such as Etalon fringes and mild scattering Mie-like signatures, in the FTIR data. We demonstrated that the method is a powerful tool for co-localizing and correlating molecular arrangements and chemical elements (and vice versa) using visually attractive 2D correlograms. Moreover, the methods' applicability for fostering the identification of distinct (biological) materials, involving chemical elements and molecular arrangements, is also shown. Taken together, the 2D FTIR-XRF method opens up for new measures for in-situ investigating hidden complex biochemical correlations, and yet unraveled mechanisms in a biological sample. This step seems crucial for developing new strategies for facilitating the research on the interaction of metals/nonmetals with organic components. This is particularly important for enhancing our understanding of the diseases associated with metal/nonmetal mishandling.
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Affiliation(s)
- Artur D Surowka
- Faculty of Physics and Applied Computer Science, AGH University of Science and Technology, al. A. Mickiewicza 30, Krakow 30-059, Poland.
| | - Mateusz Czyzycki
- Faculty of Physics and Applied Computer Science, AGH University of Science and Technology, al. A. Mickiewicza 30, Krakow 30-059, Poland; Laboratory for Applications of Synchrotron Radiation, Karlsruhe Institute of Technology, Kaiser Str. 12, Karlsruhe 76131, Germany; Nuclear Science and Instrumentation Laboratory, International Atomic Energy Agency (IAEA) Laboratories, Seibersdorf, Austria
| | - Agata Ziomber-Lisiak
- Department of Pathophysiology, Jagiellonian University, Medical College, Czysta 18, Krakow 31-121, Poland
| | - Alessandro Migliori
- Nuclear Science and Instrumentation Laboratory, International Atomic Energy Agency (IAEA) Laboratories, Seibersdorf, Austria
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Surowka AD, Gianoncelli A, Birarda G, Sala S, Cefarin N, Matruglio A, Szczerbowska-Boruchowska M, Ziomber-Lisiak A, Vaccari L. Soft X-ray induced radiation damage in thin freeze-dried brain samples studied by FTIR microscopy. JOURNAL OF SYNCHROTRON RADIATION 2020; 27:1218-1226. [PMID: 32876596 DOI: 10.1107/s1600577520010103] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 07/21/2020] [Indexed: 06/11/2023]
Abstract
In order to push the spatial resolution limits to the nanoscale, synchrotron-based soft X-ray microscopy (XRM) experiments require higher radiation doses to be delivered to materials. Nevertheless, the associated radiation damage impacts on the integrity of delicate biological samples. Herein, the extent of soft X-ray radiation damage in popular thin freeze-dried brain tissue samples mounted onto Si3N4 membranes, as highlighted by Fourier transform infrared microscopy (FTIR), is reported. The freeze-dried tissue samples were found to be affected by general degradation of the vibrational architecture, though these effects were weaker than those observed in paraffin-embedded and hydrated systems reported in the literature. In addition, weak, reversible and specific features of the tissue-Si3N4 interaction could be identified for the first time upon routine soft X-ray exposures, further highlighting the complex interplay between the biological sample, its preparation protocol and X-ray probe.
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Affiliation(s)
- Artur D Surowka
- Elettra-Sincrotrone Trieste SCpA, SS 14, km 163.5, Basovizza, TS 34149 Trieste, Italy
| | - A Gianoncelli
- Elettra-Sincrotrone Trieste SCpA, SS 14, km 163.5, Basovizza, TS 34149 Trieste, Italy
| | - G Birarda
- Elettra-Sincrotrone Trieste SCpA, SS 14, km 163.5, Basovizza, TS 34149 Trieste, Italy
| | - S Sala
- Elettra-Sincrotrone Trieste SCpA, SS 14, km 163.5, Basovizza, TS 34149 Trieste, Italy
| | - N Cefarin
- Elettra-Sincrotrone Trieste SCpA, SS 14, km 163.5, Basovizza, TS 34149 Trieste, Italy
| | - A Matruglio
- Department of Chemical Engineering, University College London, London, United Kingdom
| | - M Szczerbowska-Boruchowska
- AGH University of Science and Technology, Faculty of Physics and Applied Computer Science, al. Mickiewicza 30, Krakow 30-059, Poland
| | - A Ziomber-Lisiak
- Chair of Pathophysiology, Faculty of Medicine, Jagiellonian University, ul. Czysta 18, Kraków 31-121, Poland
| | - L Vaccari
- Elettra-Sincrotrone Trieste SCpA, SS 14, km 163.5, Basovizza, TS 34149 Trieste, Italy
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Synthesis, structural characterization, DFT, kinetics and mechanism of oxidation of bromothymol blue: application to textile industrial wastewater treatment. CHEMICAL PAPERS 2020. [DOI: 10.1007/s11696-020-01299-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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