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Nov 2023 • bioRxiv

Characterization of alternative splicing in high-risk Wilms’ tumors

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

The significant heterogeneity of Wilms’ tumors between different patients is thought to arise from genetic and epigenetic distortions that occur during various stages of fetal kidney development in a way that is poorly understood. To address this, we characterized the heterogeneity of alternative mRNA splicing in Wilms’ tumors using a publicly available RNAseq dataset of high-risk Wilms’ tumors and normal kidney samples. Through Pareto task inference and cell deconvolution, we found that the tumors and normal kidney samples are organized according to progressive stages of kidney development within a triangle-shaped region in latent space, whose vertices, or “archetypes,” resemble the cap mesenchyme, the nephrogenic stroma, and epithelial tubular structures of the fetal kidney. We identified a set of genes that are alternatively spliced between tumors located in different regions of latent space and found that many of these genes are associated with the Epithelial to Mesenchymal Transition (EMT) and muscle development. Using motif enrichment analysis, we identified putative splicing regulators, some of which are associated with kidney development. Our findings provide new insights into the etiology of Wilms’ tumors and suggest that specific splicing mechanisms in early stages of development may contribute to tumor development in different patients.

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Nov 2023 • Gels 9 (11), 895, 2023

Engineering of PVA/PVP hydrogels for Agricultural Applications

Eyal Malka, Shlomo Margel

Hydrogels have gained significant popularity in agricultural applications in terms of minimizing waste and mitigating the negative environmental impact of agrochemicals. This review specifically examines the utilization of environmentally friendly, shapable hydrogels composed of polyvinyl alcohol (PVA) and polyvinylpyrrolidone (PVP) in various casings for crop protection against different pests, fertilizing, and watering. To activate their effectiveness, PVA/PVP hydrogels were loaded with both hydrophilic and hydrophobic environmentally friendly pesticides, namely hydrogen peroxide (HP), the essential oil thymol, and urea as a fertilizer, either separately or in combination. This review covers various physical and chemical approaches used for loading, shaping, and controlling the release profiles of pesticides and fertilizers. Additionally, it explores the evaluation of the chemical composition, structure, classification, rheology, and morphology of the hydrogels as well as their impact on the thermal stability of the encapsulated pesticides and fertilizer, followed by biological tests. These hydrogels significantly contribute to the stabilization and controlled release of essential nutrients and biocides for plants, while maintaining excellent biocidal and fertilizing properties as well as sustainability characteristics. By shedding light on the latest insights into the concepts, applications, and results of these hydrogels, this review demonstrates their immense potential for widespread future use in agriculture.

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Nov 2023 • APL Photonics

Supercontinuum generation by saturated second-order nonlinear interactions

Marc Jankowski, Carsten Langrock, Boris Desiatov, Marko Lončar, MM Fejer

We propose a new approach to supercontinuum generation and carrier-envelope-offset detection based on saturated second-order nonlinear interactions in dispersion-engineered nanowaveguides. The technique developed here broadens the interacting harmonics by forming stable bifurcations of the pulse envelopes due to an interplay between phase-mismatch and pump depletion. We first present an intuitive heuristic model for spectral broadening by second-harmonic generation of femtosecond pulses and show that this model agrees well with experiments. Then, having established strong agreement between theory and experiment, we develop scaling laws that determine the energy required to generate an octave of bandwidth as a function of input pulse duration, device length, and input pulse chirp. These scaling laws suggest that future realization based on this approach could enable supercontinuum …

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Nov 2023 • Molecular Reproduction and Development 90 (12), 785-803, 2023

Epigenetic aging of mammalian gametes

Michael Klutstein, Nitzan Gonen

The process of aging refers to physiological changes that occur to an organism as time progresses and involves changes to DNA, proteins, metabolism, cells, and organs. Like the rest of the cells in the body, gametes age, and it is well established that there is a decline in reproductive capabilities in females and males with aging. One of the major pathways known to be involved in aging is epigenetic changes. The epigenome is the multitude of chemical modifications performed on DNA and chromatin that affect the ability of chromatin to be transcribed. In this review, we explore the effects of aging on female and male gametes with a focus on the epigenetic changes that occur in gametes throughout aging. Quality decline in oocytes occurs at a relatively early age. Epigenetic changes constitute an important part of oocyte aging. DNA methylation is reduced with age, along with reduced expression of DNA …

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Nov 2023 • Journal of the American Chemical Society

Near-Temperature-Independent Electron Transport Well beyond Expected Quantum Tunneling Range via Bacteriorhodopsin Multilayers

Sudipta Bera, Jerry A Fereiro, Shailendra K Saxena, Domenikos Chryssikos, Koushik Majhi, Tatyana Bendikov, Lior Sepunaru, David Ehre, Marc Tornow, Israel Pecht, Ayelet Vilan, Mordechai Sheves, David Cahen

A key conundrum of biomolecular electronics is efficient electron transport (ETp) through solid-state junctions up to 10 nm, often without temperature activation. Such behavior challenges known charge transport mechanisms, especially via nonconjugated molecules such as proteins. Single-step, coherent quantum-mechanical tunneling proposed for ETp across small protein, 2–3 nm wide junctions, but it is problematic for larger proteins. Here we exploit the ability of bacteriorhodopsin (bR), a well-studied, 4–5 nm long membrane protein, to assemble into well-defined single and multiple bilayers, from ∼9 to 60 nm thick, to investigate ETp limits as a function of junction width. To ensure sufficient signal/noise, we use large area (∼10–3 cm2) Au–protein–Si junctions. Photoemission spectra indicate a wide energy separation between electrode Fermi and the nearest protein-energy levels, as expected for a polymer of …

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Nov 2023 • Micromachines 14 (12), 2173, 2023

Fabrication and Applications of Magnetic Polymer Composites for Soft Robotics

Sayan Ganguly, Shlomo Margel

The emergence of magnetic polymer composites has had a transformative impact on the field of soft robotics. This overview will examine the various methods by which innovative materials can be synthesized and utilized. The advancement of soft robotic systems has been significantly enhanced by the utilization of magnetic polymer composites, which amalgamate the pliability of polymers with the reactivity of magnetic materials. This study extensively examines the production methodologies involved in dispersing magnetic particles within polymer matrices and controlling their spatial distribution. The objective is to gain insights into the strategies required to attain the desired mechanical and magnetic properties. Additionally, this study delves into the potential applications of these composites in the field of soft robotics, encompassing various devices such as soft actuators, grippers, and wearable gadgets. The study emphasizes the transformative capabilities of magnetic polymer composites, which offer a novel framework for the advancement of biocompatible, versatile soft robotic systems that utilize magnetic actuation.

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Nov 2023 • Materials Today Energy

Evolution of ternary LixSnyOz artificial cathode-electrolyte interphase (ACEI) through ALD: a surface strengthened NCM811 with enhanced electrochemical performances for Li-ion …

Arka Saha, Ortal Shalev, Sandipan Maiti, Longlong Wang, Sri Harsha Akella, Bruria Schmerling, Sarah Targin, Maria Tkachev, Xiulin Fan, Malachi Noked

[(LiNi0.8Co0.1Mn0.1)O2], or NCM811, a member of the LixNi1−y−zCoyMnzO2 (NCM) family of cathode active materials (CAMs), is gaining recognition in the battery community as the CAM of choice for future high energy density lithium-ion batteries, given its high nickel content of c. 80%. Yet, its commercialization is impeded by its mechanochemical instability at a high state of charge (SOC), which results in severe capacity fading and active lithium loss during cycling. In this contribution, we report conformal nanometer-thick (c. 4–7 nm) lithiated tin-oxide ternary coatings (LixSnyOz) deposited on NCM811 cathode powder using the atomic layer deposition (ALD) technique. The first-of-its-kind ALD coating, where Li is being accompanied by a second metal ion (Sn); provides a combination of benefits: (i) it stabilizes the crystal structure, (ii) suppresses electrode polarization, (iii) lowers the voltage hysteresis, and (iv …

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Nov 2023 • Angewandte Chemie

Is “Water in Salt” Electrolytes the Ultimate Solution? Achieving High Stability of Organic Anodes in Diluted Electrolyte Solutions Via a Wise Anions Selection

Amey Nimkar, Khorsed Alam, Gil Bergman, Mikhael D Levi, Dan Thomas Major, Netanel Shpigel, Doron Aurbach

The introduction of the water‐in‐salt (WIS) electrolytes concept to prevent water splitting and widen the electrochemical stability window, has spurred extensive research efforts toward development of improved aqueous batteries. The successful implementation of these electrolyte solutions in many electrochemical systems shifts the focus from diluted to WIS electrolyte solutions. Considering the high costs and the tendency of these nearly saturated solutions to crystallize, this trend can be carefully re‐evaluated. Herein we show that the stability of organic electrodes comprising the active material perylene‐3,4,9,10‐tetracarboxylic dianhydride (PTCDA), is strongly influenced by the solvation character of the anions rather than the concentration of the electrolyte solution. Even though the charging process of PTCDA involves solely insertion of cations (i.e., principal counter‐ions), surprisingly, the dominant factor …

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Nov 2023 • Gels 9 (11), 895, 2023

Engineering of PVA/PVP Hydrogels for Agricultural Applications

Eyal Malka, Shlomo Margel

Hydrogels have gained significant popularity in agricultural applications in terms of minimizing waste and mitigating the negative environmental impact of agrochemicals. This review specifically examines the utilization of environmentally friendly, shapable hydrogels composed of polyvinyl alcohol (PVA) and polyvinylpyrrolidone (PVP) in various casings for crop protection against different pests, fertilizing, and watering. To activate their effectiveness, PVA/PVP hydrogels were loaded with both hydrophilic and hydrophobic environmentally friendly pesticides, namely hydrogen peroxide (HP), the essential oil thymol, and urea as a fertilizer, either separately or in combination. This review covers various physical and chemical approaches used for loading, shaping, and controlling the release profiles of pesticides and fertilizers. Additionally, it explores the evaluation of the chemical composition, structure, classification, rheology, and morphology of the hydrogels as well as their impact on the thermal stability of the encapsulated pesticides and fertilizer, followed by biological tests. These hydrogels significantly contribute to the stabilization and controlled release of essential nutrients and biocides for plants, while maintaining excellent biocidal and fertilizing properties as well as sustainability characteristics. By shedding light on the latest insights into the concepts, applications, and results of these hydrogels, this review demonstrates their immense potential for widespread future use in agriculture.

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Nov 2023 • Advanced Sensor Research

Modular Droplet‐Based Fluidics for Large Volume Libraries of Individual Multiparametric Codes in Lab‐On‐Chip Systems (Adv. Sensor Res. 11/2023)

Julian Schütt, Hariharan Nhalil, Jürgen Fassbender, Lior Klein, Asaf Grosz, Denys Makarov

In article 2300101, Julian Schütt, Hariharan Nhalil, Jürgen Fassbender, Lior Klein, Asaf Grosz, and Denys Makarov propose a new concept of multiparametric coding in droplet-based fluidics relying on different sensing units and targeted tailoring of the fluidic circuit and its complexification. The possibility to prepare up to 3 million unique codes is demonstrated experimentally, which is relevant for pharmaceutical and biotechnological assays including drug discovery.

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Nov 2023 • Nature Communications

A single pseudouridine on rRNA regulates ribosome structure and function in the mammalian parasite Trypanosoma brucei

K Shanmugha Rajan, Hava Madmoni, Anat Bashan, Masato Taoka, Saurav Aryal, Yuko Nobe, Tirza Doniger, Beathrice Galili Kostin, Amit Blumberg, Smadar Cohen-Chalamish, Schraga Schwartz, Andre Rivalta, Ella Zimmerman, Ron Unger, Toshiaki Isobe, Ada Yonath, Shulamit Michaeli

Trypanosomes are protozoan parasites that cycle between insect and mammalian hosts and are the causative agent of sleeping sickness. Here, we describe the changes of pseudouridine (Ψ) modification on rRNA in the two life stages of the parasite using four different genome-wide approaches. CRISPR-Cas9 knock-outs of all four snoRNAs guiding Ψ on helix 69 (H69) of the large rRNA subunit were lethal. A single knock-out of a snoRNA guiding Ψ530 on H69 altered the composition of the 80S monosome. These changes specifically affected the translation of only a subset of proteins. This study correlates a single site Ψ modification with changes in ribosomal protein stoichiometry, supported by a high-resolution cryo-EM structure. We propose that alteration in rRNA modifications could generate ribosomes preferentially translating state-beneficial proteins.

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Nov 2023 • Micromachines 14 (12), 2173, 2023

Fabrication and Applications of Magnetic Polymer Composites for Soft Robotics

Sayan Ganguly, Shlomo Margel

The emergence of magnetic polymer composites has had a transformative impact on the field of soft robotics. This overview will examine the various methods by which innovative materials can be synthesized and utilized. The advancement of soft robotic systems has been significantly enhanced by the utilization of magnetic polymer composites, which amalgamate the pliability of polymers with the reactivity of magnetic materials. This study extensively examines the production methodologies involved in dispersing magnetic particles within polymer matrices and controlling their spatial distribution. The objective is to gain insights into the strategies required to attain the desired mechanical and magnetic properties. Additionally, this study delves into the potential applications of these composites in the field of soft robotics, encompassing various devices such as soft actuators, grippers, and wearable gadgets. The study emphasizes the transformative capabilities of magnetic polymer composites, which offer a novel framework for the advancement of biocompatible, versatile soft robotic systems that utilize magnetic actuation.

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Nov 2023 • Bulletin of the American Physical Society

Generating Correlated X-ray Pairs as a Low-Noise Low-Damage Probe

Nicholas Hartley, Daniel Hodge, Eric Christie, Arianna Gleason, Siegfried Glenzer, Aliaksei Halavanau, Abigail Mae Hardy, Colin Recker, Sean Sheehan, Sharon Shwartz, Michael Ware, Richard Sandberg, Gary Walker

PM10. 00002: Generating Correlated X-ray Pairs as a Low-Noise Low-Damage Probe*

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Nov 2023 • Physical Review B

Periodically driven open quantum systems with vibronic interaction: Resonance effects and vibrationally mediated decoupling

Jakob Bätge, Yu Wang, Amikam Levy, Wenjie Dou, Michael Thoss

Periodic driving and Floquet engineering have emerged as invaluable tools for controlling and uncovering novel phenomena in quantum systems. In this study, we adopt these methods to manipulate nonequilibrium processes within electronic-vibronic open quantum systems. Through resonance mechanisms and by focusing on the limit-cycle dynamics and quantum thermodynamic properties, we illustrate the intricate interplay between the driving field and vibronic states and its overall influence on the electronic system. Specifically, we observe an effective decoupling of the electronic system from the periodic driving at specific frequencies, a phenomenon that is mediated by the vibrational mode interaction. Additionally, we engineer the driving field to obtain a partial removal of the Franck-Condon blockade. These insights hold promise for efficient charge current control. Our results are obtained from numerically …

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Nov 2023 • Ultrasonics Sonochemistry

Ultrasonic-assisted synthesis of lignin-capped Cu2O nanocomposite with antibiofilm properties

Moorthy Maruthapandi, Akanksha Gupta, Arumugam Saravanan, Gila Jacobi, Ehud Banin, John HT Luong, Aharon Gedanken

Under ultrasonication, cuprous oxide (Cu2O) microparticles (<5 µm) were fragmented into nanoparticles (NPs, ranging from 10 to 30 nm in diameter), and interacted strongly with alkali lignin (Mw= 10 kDa) to form a nanocomposite. The ultrasonic wave generates strong binding interaction between lignin and Cu2O. The L-Cu nanocomposite exhibited synergistic effects with enhanced antibiofilm activities against E. coli, multidrug-resistant (MDR) E. coli, S. aureus (SA), methicillin-resistant SA, and P. aeruginosa (PA). The lignin-Cu2O (L-Cu) nanocomposite also imparted notable eradication of such bacterial biofilms. Experimental evidence unraveled the destruction of bacterial cell walls by L-Cu, which interacted strongly with the bacterial membrane. After exposure to L-Cu, the bacterial cells lost the integrated structural morphology. The estimated MIC for biofilm inhibition for the five tested pathogens was 1 mg/mL L …

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Nov 2023 • arXiv preprint arXiv:2311.12980

Nonlinear Self-Calibrated Spectrometer with Single GeSe-InSe Heterojunction Device

Rana Darweesh, Rajesh Kumar Yadav, Elior Adler, Michal Poplinger, Adi Levi, Jea-Jung Lee, Amir Leshem, Ashwin Ramasubramaniam, Fengnian Xia, Doron Naveh

Optical spectroscopy the measurement of electromagnetic spectra is fundamental to various scientific domains and serves as the building block of numerous technologies. Computational spectrometry is an emerging field that employs an array of photodetectors with different spectral responses or a single photodetector device with tunable spectral response, in conjunction with numerical algorithms, for spectroscopic measurements. Compact single photodetectors made from layered materials are particularly attractive, since they eliminate the need for bulky mechanical and optical components used in traditional spectrometers and can easily be engineered as heterostructures to optimize device performance. However, compact tunable photodetectors are typically nonlinear devices and this adds complexity to extracting optical spectra from the device response. Here, we report on the training of an artificial neural network (ANN) to recover the full nonlinear spectral photoresponse of a nonlinear problem of high dimensionality of a single GeSe-InSe p-n heterojunction device. We demonstrate the functionality of a calibrated spectrometer in the spectral range of 400-1100 nm, with a small device footprint of ~25X25 micrometers, and we achieve a mean reconstruction error of 0.0002 for the power-spectrum at a spectral resolution of 0.35 nm. Using our device, we demonstrate a solution to metamerism, an apparent matching of colors with different power spectral distributions, which is a fundamental problem in optical imaging.

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Nov 2023 • Scientific Reports

Integration of high-resolution imaging through scattering medium into a disposable micro-endoscope via projection of 2D spots-array

Shimon Elkabetz, Oran Herman, Amihai Meiri, Asaf Shahmoon, Zeev Zalevsky

The objective of this research includes integration of high-resolution imaging through scattering medium, such as blood, into a disposable micro-endoscope. A fiber laser integrated into the micro-endoscope as part of its illumination channel, allows to project a tunable array of spots of light onto an object, that is located behind the scattering medium. We have a laser fiber as part of the illumination channel of a disposable micro-endoscope. By using proper optics, we convert the temporal modulation of the laser into spatial distribution. Thus, the result is generation of spatial spots when using a pulsed laser. The detection channel is a holographic recording of the collected back scattered light, that allows extraction of the electrical field. By time integrating the field we obtain the realization of the spatial array of illumination spots formed on top of the inspected object and behind the scattering medium. By changing the …

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Nov 2023 • Light, science & applications

Weak measurements and quantum-to-classical transitions in free electron-photon interactions

Yiming Pan, Eliahu Cohen, Ebrahim Karimi, Avraham Gover, Norbert Schönenberger, Tomáš Chlouba, Kangpeng Wang, Saar Nehemia, Peter Hommelhoff, Ido Kaminer, Yakir Aharonov

How does the quantum-to-classical transition of measurement occur? This question is vital for both foundations and applications of quantum mechanics. Here, we develop a new measurement-based framework for characterizing the classical and quantum free electron–photon interactions and then experimentally test it. We first analyze the transition from projective to weak measurement in generic light–matter interactions and show that any classical electron-laser-beam interaction can be represented as an outcome of weak measurement. In particular, the appearance of classical point-particle acceleration is an example of an amplified weak value resulting from weak measurement. A universal factor, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek …

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Nov 2023 • Langmuir

Kinetics and Optimization of Hexagonal Palladium Nanosheets: Unveiling Insights into CO-Mediated Synthesis Strategies and Mechanistic Understanding

Mike Rozenberg, Melina Zysler, David Zitoun

Nanoparticles with unique shapes and structures have attracted significant attention due to their distinctive properties and potential applications, but their growth mechanism is often overlooked. Hexagonal palladium nanosheets (HPNS) were synthesized through a CO-mediated reduction approach. Herein, we investigate the kinetics of the HPNS formation and modify the experimental conditions consistently by changing the carbon monoxide (CO) precursor, temperature, and stirring speed. The CO precursor plays a major role in HPNS formation with an emphasis on the kinetics of the release of CO in the solution. Slow-release and atmosphere CO precursors resulted in the highest shape yield of HPNS relative to tetrahedrons, while the fast-release CO precursor leads to the formation of a higher percentage of tetrahedrons. Additionally, an increase of the addition temperature of the CO precursor and a higher …

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Nov 2023 • Light, science & applications

Weak measurements and quantum-to-classical transitions in free electron-photon interactions

Yiming Pan, Eliahu Cohen, Ebrahim Karimi, Avraham Gover, Norbert Schönenberger, Tomáš Chlouba, Kangpeng Wang, Saar Nehemia, Peter Hommelhoff, Ido Kaminer, Yakir Aharonov

How does the quantum-to-classical transition of measurement occur? This question is vital for both foundations and applications of quantum mechanics. Here, we develop a new measurement-based framework for characterizing the classical and quantum free electron–photon interactions and then experimentally test it. We first analyze the transition from projective to weak measurement in generic light–matter interactions and show that any classical electron-laser-beam interaction can be represented as an outcome of weak measurement. In particular, the appearance of classical point-particle acceleration is an example of an amplified weak value resulting from weak measurement. A universal factor, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek …

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Nov 2023 • ACS Applied Bio Materials

Zirconium-Coated β-Cyclodextrin Nanomaterials for Biofilm Eradication

Akanksha Gupta, John HT Luong, Aharon Gedanken

Under alkaline treatment, zirconyl chloride (ZrOCl2.8H2O) became a zirconia gel and formed a stable complex with beta-cyclodextrin (βCD). This complex was highly active in reactive oxygen species (ROS) formation via H2O2 decomposition. Its surface with numerous hydroxyl groups acts as an ionic sponge to capture the charged reaction intermediates, including superoxide (O2–•) and the hydroxyl radical (•OH). ROS, especially •OH radicals, are harmful to living microorganisms because of their kinetic instability, high oxidation potential, and chemical nonselectivity. Therefore, •OH radicals can engage in fast reactions with virtually any adjacent biomolecule. With H2O2, the complex with cationic and hydrophobic moieties interacted with the anionic bacterial membrane of two Gram-positive (Staphylococcus aureus and S. epidermidis) and two Gram-negative (Escherichia coli and Klebsiella pneumoniae) strains …

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