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Jan 2022 • bioRxiv

In vitro and in vivo NIR Fluorescence Lifetime Imaging with a time-gated SPAD camera

Jason T Smith, Alena Rudkouskaya, Shan Gao, Juhi M Gupta, Arin Ulku, Claudio Bruschini, Edoardo Charbon, Shimon Weiss, Margarida Barroso, Xavier Intes, Xavier Michalet

Near-infrared (NIR) fluorescence lifetime imaging (FLI) provides a unique contrast mechanism to monitor biological parameters and molecular events in vivo. Single-photon avalanche photodiode (SPAD) cameras have been recently demonstrated in FLI microscopy (FLIM) applications, but their suitability for in vivo macroscopic FLI (MFLI) in deep tissues remains to be demonstrated. Herein, we report in vivo NIR MFLI measurement with SwissSPAD2, a large time-gated SPAD camera. We first benchmark its performance in well-controlled in vitro experiments, ranging from monitoring environmental effects on fluorescence lifetime, to quantifying Förster Resonant Energy Transfer (FRET) between dyes. Next, we use it for in vivo studies of target-drug engagement in live and intact tumor xenografts using FRET. Information obtained with SwissSPAD2 was successfully compared to that obtained with a gated-ICCD camera, using two different approaches. Our results demonstrate that SPAD cameras offer a powerful technology for in vivo preclinical applications in the NIR window.

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Jan 2022 • ACS Photonics

Tunable Metasurface Using Thin-Film Lithium Niobate in the Telecom Regime

Aharon Weiss, Christian Frydendahl, Jonathan Bar-David, Roy Zektzer, Eitan Edrei, Jacob Engelberg, Noa Mazurski, Boris Desiatov, Uriel Levy

Metasurfaces have seen a great evolution over the last few years, demonstrating a high degree of control over the amplitude, phase, polarization, and spectral properties of reflected or transmitted electromagnetic waves. Nevertheless, the inherent limitation of static metasurface realizations, which cannot be controlled after their fabrication, engages an ongoing pursuit for reconfigurable metasurfaces with profound tunability. In this paper, we mitigate this grand challenge by demonstrating a new method for free-space rapid optical tunability and modulation, utilizing a planar aluminum nanodisk metasurface coated with indium tin oxide (ITO) on a thin film of lithium niobate (LiNbO) with a chromium/gold (Cr/Au) substrate. Resonance coupling gives rise to an enhanced, confined electromagnetic field residing in the thin film, leading to a narrow and high contrast dip in reflectance of around 1.55 μm. The precise spectral …

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Jan 2022 • Science advances

Peroxisome function relies on organelle-associated mRNA translation

Noa Dahan, Yury S Bykov, Elizabeth A Boydston, Amir Fadel, Zohar Gazi, Hodaya Hochberg-Laufer, James Martenson, Vlad Denic, Yaron Shav-Tal, Jonathan S Weissman, Naama Aviram, Einat Zalckvar, Maya Schuldiner

Crucial metabolic functions of peroxisomes rely on a variety of peroxisomal membrane proteins (PMPs). While mRNA transcripts of PMPs were shown to be colocalized with peroxisomes, the process by which PMPs efficiently couple translation with targeting to the peroxisomal membrane remained elusive. Here, we combine quantitative electron microscopy with proximity-specific ribosome profiling and reveal that translation of specific PMPs occurs on the surface of peroxisomes in the yeast Saccharomyces cerevisiae. This places peroxisomes alongside chloroplasts, mitochondria, and the endoplasmic reticulum as organelles that use localized translation for ensuring correct insertion of hydrophobic proteins into their membranes. Moreover, the correct targeting of these transcripts to peroxisomes is crucial for peroxisomal and cellular function, emphasizing the importance of localized translation for cellular physiology.

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Jan 2022 • ACS Omega

CVD-Assisted Synthesis of 2D Layered MoSe2 on Mo Foil and Low Frequency Raman Scattering of Its Exfoliated Few-Layer Nanosheets on CaF2 Substrates

Rajashree Konar, Bharathi Rajeswaran, Atanu Paul, Eti Teblum, Hagit Aviv, Ilana Perelshtein, Ilya Grinberg, Yaakov Raphael Tischler, Gilbert Daniel Nessim

Transition-metal dichalcogenides (TMDCs) are unique layered materials with exotic properties. So, examining their structures holds tremendous importance. 2H-MoSe2 (analogous to MoS2; Gr. 6 TMDC) is a crucial optoelectronic material studied extensively using Raman spectroscopy. In this regard, low-frequency Raman (LFR) spectroscopy can probe this material’s structure as it reveals distinct vibration modes. Here, we focus on understanding the microstructural evolution of different 2H-MoSe2 morphologies and their layers using LFR scattering. We grew phase-pure 2H-MoSe2 (with variable microstructures) directly on a Mo foil using a two-furnace ambient-pressure chemical vapor deposition (CVD) system by carefully controlling the process parameters. We analyzed the layers of exfoliated flakes after ultrasonication and drop-cast 2H-MoSe2 of different layer thicknesses by choosing different concentrations of …

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Jan 2022 • Journal of Composites Science 6 (1), 15, 2022

A Review on Synthesis Methods of Phyllosilicate-and Graphene-Filled Composite Hydrogels

Sayan Ganguly, Shlomo Margel

This review discusses, in brief, the various synthetic methods of two widely-used nanofillers; phyllosilicate and graphene. Both are 2D fillers introduced into hydrogel matrices to achieve mechanical robustness and water uptake behavior. Both the fillers are inserted by physical and chemical gelation methods where most of the chemical gelation, i.e., covalent approaches, results in better physical properties compared to their physical gels. Physical gels occur due to supramolecular assembly, van der Waals interactions, electrostatic interactions, hydrophobic associations, and H-bonding. For chemical gelation, in situ radical triggered gelation mostly occurs.

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Jan 2022 • bioRxiv

The conformational plasticity of the selectivity filter methionines controls the in-cell Cu (I) uptake through the CTR1 transporter

Pavel Janoš, Jana Aupič, Sharon Ruthstein, Alessandra Magistrato

Copper is a trace element vital to many cellular functions. Yet its abnormal levels are toxic to cells, provoking a variety of severe diseases. The high affinity Copper Transporter 1 (CTR1), being the main in-cell copper (Cu(I)) entry route, tightly regulates its cellular uptake via a still elusive mechanism. Here, all-atoms simulations unlock the molecular terms of Cu(I) transport in eukaryotes disclosing that the two Methionine triads, forming the selectivity filter, play an unprecedented dual role both enabling selective Cu(I) transport and regulating its uptake-rate thanks to an intimate coupling between the conformational plasticity of their bulky side chains and the number of bound Cu(I) ions. Namely, the Met residues act as a gate reducing the Cu(I) import-rate when two ions simultaneously bind to CTR1. This may represent an elegant autoregulatory mechanism through which CTR1 protects the cells from excessively high, and hence toxic, in-cell Cu(I) levels. Overall, these outcomes resolve fundamental questions in CTR1 biology and open new windows of opportunity to tackle diseases associated with an imbalanced copper uptake.

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Jan 2022 • ACS Applied Energy Materials

Precious-Group-Metal-Free Energy-Efficient Urea Electrolysis: Membrane Electrode Assembly Cell Using Ni3N Nanoparticles as Catalyst

Vineesh Thazhe Veettil, Anagha Usha Vijayakumar, Aviv Ashdot, David Zitoun

The sluggish kinetics of the anodic oxygen evolution reaction (OER) limit the overall efficiency of green hydrogen production. The proposed strategy to overcome this is to replace OER with other kinetically favorable anodic reactions like urea oxidation reaction (UOR). Herein, we develop an organometallic synthesis of nickel nitride nanoparticles supported on carbon (Ni3N–C) as the catalyst for both UOR and hydrogen evolution reaction (HER). A precious group metal-free electrolyzer based on Ni3N–C catalyst (as both anode and cathode) is implemented for the first time, and the urea electrolyzer cell has a 200 mV lower overpotential compared to that of the water electrolyzer.

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Jan 2022 • BMJ Open

External validation and recalibration of an incidental meningioma prognostic model - IMPACT: protocol for an international multicentre retrospective cohort study.

International Consortium on Meningioma (ICOM) and British Neurosurgical Trainee Research Collaborative (BNTRC) IMPACT Study Investigators


Jan 2022 • ACS Catalysis

Recent Progress and Viability of PGM-Free Catalysts for Hydrogen Evolution Reaction and Hydrogen Oxidation Reaction

Wenjamin Moschkowitsch, Oran Lori, Lior Elbaz

The global energy demand is expected to rise continuously in the foreseeable future, and this demand cannot be fulfilled with fossil fuels if the ambitious goals for global reduction in greenhouse gas emissions are to be met. 1, 2 Therefore, it is necessary to switch to energy production from sustainable energy sources such as solar and wind. 3, 4 These sources suffer from intermittent production, producing a surplus of energy at certain hours and seasons and little to none at others. Hence, large energy storage solutions are necessary in order to store the excess energy in peak times and compensate at the lowand down-times. 4, 5One of the most promising energy storage solutions today is chemical, in the form of hydrogen, which can be used with fuel cells to generate electricity or burned to generate heat, as well as being used in the chemical industry for various applications. 5 It can be easily produced with various …

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Jan 2022 • bioRxiv

Characterization of the continuous transcriptional heterogeneity in Wilms’ tumors using unsupervised machine learning

Yaron Trink, Achia Urbach, Benjamin Dekel, Peter Hohenstein, Jacob Goldberger, Tomer Kalisky

Wilms′ tumors are pediatric malignancies that are thought to arise from faulty kidney development. To date, the course of treatment depends on manual histopathological classification which is difficult since the tumors differ between patients in a continuous manner. Here, we used three computational approaches to characterize the continuous heterogeneity of Wilms′ tumors. We first chose a published dataset of microarray gene expression measurements from high-risk blastemal-type Wilms′ tumors. Then, we used Pareto Task Inference to show that the tumors form a triangle-shaped continuum in latent space that is bounded by three tumor archetypes with ″stromal″, ″epithelial″, and ″blastemal″ characteristics, that resemble the un-induced mesenchyme, the Cap mesenchyme, and early epithelial structures of the fetal kidney. We confirmed this by fitting a generative probabilistic ″grade of membership″ model whereby each tumor is represented as a unique mixture of three hidden ″topics″ with blastemal, stromal, and epithelial characteristics. Finally, we used cellular deconvolution to show that each tumor is composed of a unique mixture of cell populations resembling the un-induced mesenchyme, the cap mesenchyme, and the early epithelial structures of the fetal kidney. We anticipate that these methodologies will pave the way for more quantitative strategies for tumor stratification and classification.

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Jan 2022 • bioRxiv

Sex-specific regulation of metabolic health and vertebrate lifespan by AMP biosynthesis

Gwendoline Astre, Tehila Atlan, Uri Goshtchevsky, Kobi Shapira, Adi Oron-Gottesman, Tomer Levy, Ariel Velan, Erez Y Levanon, Joris Deelen, Itamar Harel

The loss of energy homeostasis seen during aging, is causally linked to multiple age-related pathologies. The AMP-activated protein kinase (AMPK) directly senses cellular energy levels, which are reflected in the ratio between AMP:ATP. However, the genetic regulation of vertebrate aging by the AMPK pathway remains poorly understood. Here, we manipulate ATP production by mutating APRT, a key enzyme in AMP biosynthesis, and extend vertebrate lifespan in a male-specific manner. Using a multi-omics approach, we demonstrate that the APRT mutation restores metabolic plasticity, and identify a distinct transcriptional signature linking mitochondria with the sex-related differences in longevity. Accordingly, APRT mutant cells display a reduction in mitochondrial functions and ATP levels, and an increase in AMPK activity, resembling a persistent state of energy starvation. In-vivo, a fasting-like response was observed exclusively in male mutants, including resistance to a high-fat diet. Finally, intermittent fasting eliminated the longevity benefits mediated by the APRT mutation in males. Together, these data identify AMP biosynthesis as a sex-specific mediator of vertebrate longevity and metabolic health.

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Jan 2022 • arXiv preprint arXiv:2201.12749

Large-scale behavior of energy spectra of the quantum random antiferromagnetic Ising chain with mixed transverse and longitudinal fields

Richard Berkovits

In recent years it became clear that the metallic regime of systems that exhibit a many body localization (MBL) behavior show properties which are quite different than the vanilla metallic region of the single particle Anderson regime. Here we show that the large scale energy spectrum of a canonical microscopical model featuring MBL, displays a non-universal behavior at intermediate scales, which is distinct from the deviation from universality seen in the single particle Anderson regime. The crucial step in revealing this behavior is a global unfolding of the spectrum performed using the singular value decomposition (SVD) which takes into account the sample to sample fluctuations of the spectra. The spectrum properties may be observed directly in the singular value amplitudes via the scree plot, or by using the SVD to unfold the spectra and then perform a number of states variance calculation. Both methods reveal an intermediate scale of energies which follow super Posissonian statistics.

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Jan 2022 • Polymers

Chiral Porous Carbon Surfaces for Enantiospecific Synthesis

Sapir Shekef Aloni, Molhm Nassir, Yitzhak Mastai

Chiral surfaces, developed in the last decade, serve as media for enantioselective chemical reactions. Until today, they have been based mostly on developments in silica templating, and are made mainly from imprints of silicate materials developed a long time ago. Here, a chiral porous activated carbon surface was developed based on a chiral ionic liquid, and the surface chemistry and pore structure were studied to lay a new course of action in the field. The enantioselectivities of surfaces are examined by using variety of methods such as circular dichroism, linear sweep voltammetry and catalysis. These techniques revealed a 28.1% preference for the D enantiomer of the amino acid proline, and linear sweep voltammetry confirmed chirality recognition by another probe. An aldol surface chiral catalytic reaction was devised and allowed to determine the root of the enantiomeric excess. These results affirm the path toward a new type of chiral surface. View Full-Text

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Jan 2022 • The Journal of Chemical Physics

Membrane potential sensing: Material design and method development for single particle optical electrophysiology

Debjit Roy, Zehavit Shapira, Shimon Weiss

We review the development of 'single' nanoparticle-based inorganic and organic voltage sensors which can eventually become a viable tool for 'non-genetic optogenetics'. The voltage sensing is accomplished with optical imaging at the fast temporal response and high spatial resolutions in a large field of view. Inorganic voltage nanosensors utilize the Quantum Confined Stark effect (QCSE) to sense local electric fields. Engineered nanoparticles achieve substantial single-particle voltage sensitivity (~2% Δ spectral Stark shift, up to ~30% ΔF/F per 160 mV) at room temperature due to enhanced charge separation. A dedicated home build fluorescence microscope records spectrally resolved images to measure QCSE induced spectral shift at the single-particle level. Biomaterial based surface ligands are designed and developed based on theoretical simulations. The hybrid nanobiomaterials satisfies anisotropic …

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Jan 2022 • bioRxiv

An in cell site-specific labeling methodology reveals conformational changes of proteins in bacteria

Yulia Shenberger, Lada Gevorkyan-Airapetov, Melanie Hirsch, Lukas Hofmann, Sharon Ruthstein

Gaining new structural information on proteins in their native cellular environments will shed light on many enzymatic reaction mechanisms and encourage the development of new therapeutic approaches. During the last decade, in cell electron paramagnetic resonance (EPR) spectroscopy experiments have provided high-resolution data on conformational changes of proteins within the cell. However, one of the major obstacles of EPR spectroscopy is the spin-labeling process, which until now was performed only outside the cellular environment (i.e., exogenously). The spin-labeled protein is then injected into the cell, which limits the protein size and the cellular system that can be used. Here, we describe a new spin-labeling approach that can be applied to over-expressed proteins in Escherichia coli (i.e., endogenously). This approach uses a Cu(II) ion bound to a ligand, which has high affinity to a dHis site in the protein of interest. The presence of a nearby 19F-phenylalanine residue can be exploited to verify that the Cu(II)-ligand indeed bound to the protein target. This new methodology allows for the study of any protein, regardless of size or the cellular system used.

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Jan 2022 • ACS Applied Energy Materials

Precious-Group-Metal-Free Energy-Efficient Urea Electrolysis: Membrane Electrode Assembly Cell Using Ni3N Nanoparticles as Catalyst

Vineesh Thazhe Veettil, Anagha Usha Vijayakumar, Aviv Ashdot, David Zitoun

The sluggish kinetics of the anodic oxygen evolution reaction (OER) limit the overall efficiency of green hydrogen production. The proposed strategy to overcome this is to replace OER with other kinetically favorable anodic reactions like urea oxidation reaction (UOR). Herein, we develop an organometallic synthesis of nickel nitride nanoparticles supported on carbon (Ni3N–C) as the catalyst for both UOR and hydrogen evolution reaction (HER). A precious group metal-free electrolyzer based on Ni3N–C catalyst (as both anode and cathode) is implemented for the first time, and the urea electrolyzer cell has a 200 mV lower overpotential compared to that of the water electrolyzer.

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Jan 2022 • bioRxiv

Electrically Controlling and Optically Observing the Membrane Potential of Supported Lipid Bilayers

Shimon Yudovich, Adan Marzouqe, Joseph Kantorovitsch, Eti Teblum, Tao Chen, Jorg Enderlein, Evan W Miller, Shimon Weiss

Supported lipid bilayers are a well-developed model system for the study of membranes and their associated proteins, such as membrane channels, enzymes, and receptors. These versatile model membranes can be made from various components, ranging from simple synthetic phospholipids to complex mixtures of constituents, mimicking the cell membrane with its relevant physiochemical and molecular phenomena. In addition, the high stability of supported lipids bilayers allows for their study via a wide array of experimental probes. In this work, we describe a platform for supported lipid bilayers that is accessible both electrically and optically. We show that the polarization of the supported membrane can be electrically controlled and optically probed using voltage-sensitive dyes. Membrane polarization dynamics is understood through electrochemical impedance spectroscopy and the analysis of the equivalent electrical circuit. We also describe the effect of the conducting electrode layer on the fluorescence of the optical probe through metal-induced energy transfer. We conclude with a discussion on possible applications of this platform for the study of voltage-dependent membrane proteins and other processes in membrane biology and surface science.

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Jan 2022 • bioRxiv

A BALB/c IGHV Reference Set, defined by haplotype analysis of long-read VDJ-C sequences from F1 (BALB/c/C57BL/6) mice

Katherine JL Jackson, Justin T Kos, William Lees, William S Gibson, Melissa Laird Smith, Ayelet Peres, Gur Yaari, Martin Corcoran, Christian E Busse, Mats Ohlin, Corey T Watson, Andrew M Collins

The immunoglobulin genes of inbred mouse strains that are commonly used in models of antibody-mediated human diseases are poorly characterized. This compromises data analysis. To infer the immunoglobulin genes of BALB/c mice, we used long-read SMRT sequencing to amplify VDJ-C sequences from F1 (BALB/c x C57BL/6) hybrid animals. Previously unreported strain variations were identified in the Ighm and Ighg2b genes, and analysis of VDJ rearrangements led to the inference of 278 germline IGHV alleles. 169 alleles are not present in the C57BL/6 genome reference sequence. To establish a set of expressed BALB/c IGHV germline gene sequences, we computationally retrieved IGHV haplotypes from the IgM dataset. Haplotyping led to the confirmation of 162 BALB/c IGHV gene sequences. A musIGHV398 pseudogene variant also appears to be present in the BALB/cByJ substrain, while a functional musIGHV398 gene is highly expressed in the BALB/cJ substrain. Only four of the BALB/c alleles were also observed in the C57BL/6 haplotype. The full set of inferred BALB/c sequences has been used to establish a BALB/c IGHV reference set, hosted at https://ogrdb.airr-community.org. We assessed whether assemblies from the Mouse Genome Project (MGP) are suitable for the determination of the genes of the IGH loci. Only 37 (43.5%) of the 85 confirmed IMGT-named BALB/c IGHV and 33 (42.9%) of the 77 confirmed non-IMGT IGHV were found in a search of the MGP BALB/cJ genome assembly. This suggests that Adaptive Immune Receptor Repertoire sequencing (AIRR-Seq) data, but not currently-available genome assemblies …

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Jan 2022 • bioRxiv

Altered somatic hypermutation patterns in COVID-19 patients classifies disease severity

Modi Safra, Zvi Tamari, Pazit Polak, Shachaf Shiber, Moshe Matan, Hani Karameh, Yigal Helviz, Adva Levy-Barda, Vered Yahalom, Avi Peretz, Eli Ben-Chetrit, Baruch Brenner, Tamir Tuller, Meital Gal-Tanamy, Gur Yaari

The success of the human body in fighting SARS-CoV-2 infection relies on lymphocytes and their antigen receptors. Identifying and characterizing clinically relevant receptors is of utmost importance. We report here the application of a machine learning approach, utilizing B cell receptor repertoire sequencing data from severely and mildly infected individuals with SARS-CoV-2 compared with uninfected controls. In contrast to previous studies, our approach successfully stratifies non-infected from infected individuals, as well as disease level of severity. The features that drive this classification are based on somatic hypermutation patterns, and point to alterations in the somatic hypermutation process in COVID-19 patients. These features may be used to build and adapt therapeutic strategies to COVID-19, in particular to quantitatively assess potential diagnostic and therapeutic antibodies. These results constitute a proof of concept for future epidemiological challenges.

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Jan 2022 • Optics Express

Single-shot analysis of amplified correlated light

Sara Meir, Avi Klein, Hamootal Duadi, Eliahu Cohen, Moti Fridman

Correlated beams are important in classical and quantum communication as well as other technologies. However, classical amplifiers, which are essential for long transmission of correlated beams, degrade the correlation due to noise and due to the amplifier spectral response. We measure, with a novel high resolution single-shot measurement system, the impact of amplifiers on correlated beams. We develop a new method for analyzing the correlation between the signal and idler beams by choosing peaks in the pulses according to their power levels. We demonstrate how to tailor the correlation after the amplifier to obtain either higher or lower correlation. Our research may influence the future use of amplifiers in non-classical communication systems as well as the transmission of quantum information over long distances.

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Jan 2022 • Journal of The Electrochemical Society

A Study of Composite Solid Electrolytes: The Effect of Inorganic Additives on the Polyethylene Oxide-Sodium Metal Interface

Shaul Bublil, Yuval Elias, Diana Golodnitsky, Miryam Fayena-Greenstein, Doron Aurbach

High electrolyte-electrode interface stability is essential for solid state batteries to avoid side reactions that form interphases and voids, leading to loss of contact and increased impedance. Such detrimental situations increase overvoltage, reduce cycling efficiency, and shorten battery cycle life. While composite solid electrolytes were studied extensively, the effect of inorganic additives in the polymer matrix on the electrolyte-anode interface remains unclear. Here, solid electrolyte was studied for batteries with sodium metal anode based on polyethylene oxide (PEO) polymeric matrix containing ceramic additive. Extensive electrochemical analyses under both AC and DC conditions were performed, and chemical reactions between sodium metal and the PEO matrix, which produce interphases at the electrode-electrolyte interface, were investigated. Addition of sodium beta aluminate in the matrix appears to mitigate …

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