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Apr 2024 • RNA

Computational analysis of super-resolved in situ sequencing data reveals genes modified by immune–tumor contact events

Michal Danino-Levi, Tal Goldberg, Maya Keter, Nikol Akselrod, Noa Shprach-Buaron, Modi Safra, Gonen Singer, Shahar Alon

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Apr 2024 • Desalination

A single-electrode evaluation method used for analyzing the working mechanism and capability of integrated membrane capacitive deionization

Qinghao Wu, Qifeng Wang, Chen Yu, Shanfu Lu, Kun Lin, Yan Xiang, Kuichang Zuo, Doron Aurbach, Dawei Liang

The evaluation of capacitive deionization (CDI) often relies on indicators like salt adsorption capacity and rate. However, these indicators encompass the entire system, including the anode and cathode. In practice scenarios, differences in specific capacitance, weight, and potential of zero charge result in varying theoretical ion adsorption capacity (IAC) and electrode potential. Hence, it is crucial to assess the deionization performance of individual electrodes. In this study, by introducing a reference electrode into the desalination device and enhancing the effective area and mass loading of the counter electrode, a single-electrode evaluation device was established to specifically analyze the deionization performance of the working electrode. Through this evaluation method, the single-electrode deionization performances of the anodic and cathodic integrated membrane electrodes (IMEs) were investigated …

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Apr 2024 • Advanced Quantum Technologies

Photon Number Splitting Attack–Proposal and Analysis of an Experimental Scheme

Ariel Ashkenazy, Yuval Idan, Dor Korn, Dror Fixler, Barak Dayan, Eliahu Cohen

Photon‐number‐splitting (PNS) is a well‐known theoretical attack on quantum key distribution (QKD) protocols that employ weak coherent states produced by attenuated laser pulses. However, beyond the fact that it has not yet been demonstrated experimentally, its plausibility and effect on quantum bit error rate are questioned. In this work, an experimental scheme is presented for PNS attack employing demonstrated technological capabilities, specifically a single‐photon Raman interaction (SPRINT) in a cavity‐enhanced three‐level atomic system. Several aspects of the proposed implementation are addressed, analytically and simulatively, and the eavesdropper's information gain by the attack is calculated. Furthermore, it is analytically shown that the scheme results in a small (yet non‐zero) quantum bit error rate, and a comparison to purely theoretical analyses in the literature is presented. It is believed that the …

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Apr 2024 • Proceedings

High-Frequency Grating-Based Microelectromechanical Systems Actuator

Inês Pires, Inês S Garcia, João Vieira, Zeev Zalevsky, Carlos Calaza, Filipe S Alves, Rosana A Dias

A silicon mechanical-photonic wavelength converter, not based on absorption, has been recently proposed to address the need for all-silicon photodetectors in the infrared spectrum. Its implementation requires high-frequency modulation, from hundreds of kHz to 1 MHz, of a light beam over an area of a few hundred microns. Since the displacement amplitudes of tens of microns at these frequencies are unfeasible, a moving grate is proposed to locally modulate the light. The MEMS actuator, an array of 1 µm-wide 1 µm-spaced beams (100 × 100 µm2 area), achieved displacements of 70 nm at atmospheric pressure and 350 nm under low vacuum, with 10 Vpp actuation at 290 kHz (FOM displacement × frequency2 above previously reported works).

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Mar 2024 • Nature Communications

Reshaped three-body interactions and the observation of an Efimov state in the continuum

Yaakov Yudkin, Roy Elbaz, José P D’Incao, Paul S Julienne, Lev Khaykovich

Efimov trimers are exotic three-body quantum states that emerge from the different types of three-body continua in the vicinity of two-atom Feshbach resonances. In particular, as the strength of the interaction is decreased to a critical point, an Efimov state merges into the atom-dimer threshold and eventually dissociates into an unbound atom-dimer pair. Here we explore the Efimov state in the vicinity of this critical point using coherent few-body spectroscopy in 7Li atoms using a narrow two-body Feshbach resonance. Contrary to the expectation, we find that the 7Li Efimov trimer does not immediately dissociate when passing the threshold, and survives as a metastable state embedded in the atom-dimer continuum. We identify this behavior with a universal phenomenon related to the emergence of a repulsive interaction in the atom-dimer channel which reshapes the three-body interactions in any system …

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Mar 2024 • Angewandte Chemie International Edition

Differential Substrate Sensing in Terpene Synthases from Plants and Microorganisms. Insights from Structural, Bioinformatic, and EnzyDock Analyses

Renana Schwartz, Shani Zev, Dan T Major

Terpene synthases (TPS) catalyze the first step in the formation of terpenoids, which comprise the largest class of natural products in nature. TPS employ a family of universal natural substrates, composed of isoprenoid units bound to a diphosphate moiety. The intricate structures generated by TPS are the result of substrate binding and folding in the active site, enzyme‐controlled carbocation reaction cascades, and final reaction quenching. A key unaddressed question in class I TPS is the asymmetric nature of the diphosphate‐(Mg2+)3 cluster, which forms a critical part of the active site. In this asymmetric ion‐cluster, two diphosphate oxygens protrude into the active site pocket. The substrate hydrocarbon tail, which is eventually molded into terpenes, can bind to either of these oxygens, yet to which is unknown. Here, we employ structural, bioinformatics, and EnzyDock docking tools to address this enigma. We bring …

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Mar 2024 • Surfaces and Interfaces

In-depth investigation into defect-induced Raman lines in irradiated graphene

Nahum Shabi, Madina Telkhozhayeva, Olga Girshevitz, Moshe Kaveh, Issai Shlimak

Identifying the type of structural defects and determining their concentration is crucial for effective defect engineering strategies since they govern various physical, chemical, and optoelectronic properties of graphene. Here, we study the effects of Ga ion irradiation on freestanding monolayer graphene, specifically focusing on the behavior of three defect-induced Raman lines (D, D' and (D+ D')). By employing a modified approach of the local activation model, we determine the key defect parameters of each line and show their dependence on different vibrational configurations of the iTO and iLO phonons emitted during scattering. The redshift of the lines and the broadening of their width, observed with an increase in the concentration of radiation defects over Nd ≈ 1013cm−2, are explained by the tensile stress of the graphene film and a decrease in the phonon lifetime, respectively. The resulting intensity ratio I(D)/I …

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Mar 2024 • Circulation

Small extracellular vesicles from infarcted and failing heart accelerate tumor growth

Tal Caller, Itai Rotem, Olga Shaihov-Teper, Daria Lendengolts, Yeshai Schary, Ruty Shai, Efrat Glick-Saar, Dan Dominissini, Menachem Motiei, Idan Katzir, Rachela Popovtzer, Merav Nahmoud, Alex Boomgarden, Crislyn D’Souza-Schorey, Nili Naftali-Shani, Jonathan Leor

BACKGROUND Myocardial infarction (MI) and heart failure are associated with an increased incidence of cancer. However, the mechanism is complex and unclear. Here, we aimed to test our hypothesis that cardiac small extracellular vesicles (sEVs), particularly cardiac mesenchymal stromal cell–derived sEVs (cMSC-sEVs), contribute to the link between post-MI left ventricular dysfunction (LVD) and cancer. METHODS We purified and characterized sEVs from post-MI hearts and cultured cMSCs. Then, we analyzed cMSC-EV cargo and proneoplastic effects on several lines of cancer cells, macrophages, and endothelial cells. Next, we modeled heterotopic and orthotopic lung and breast cancer tumors in mice with post-MI LVD. We transferred cMSC-sEVs to assess sEV biodistribution and its effect on tumor growth. Finally, we tested the effects of sEV depletion and spironolactone treatment on cMSC-EV release …

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Mar 2024 • Advanced Functional Materials

Guided Search to Self‐Healing in Semiconductors

Alexandre Py‐Renaudie, Yahel Soffer, Pallavi Singh, Sujit Kumar, Davide R Ceratti, Yuval Mualem, Irit Rosenhek‐Goldian, Dan Oron, Sidney R Cohen, Philip Schulz, David Cahen, Jean‐François Guillemoles

Self‐healing (SH) of (opto)electronic material damage can have a huge impact on resource sustainability. The rising interest in halide perovskite (HaP) compounds over the past decade is due to their excellent semiconducting properties for crystals and films, even if made by low‐temperature solution‐based processing. Direct proof of self‐healing in Pb‐based HaPs is demonstrated through photoluminescence recovery from photodamage, fracture healing and their use as high‐energy radiation and particle detectors. Here, the question of how to find additional semiconducting materials exhibiting SH, in particular lead‐free ones is addressed. Applying a data‐mining approach to identify semiconductors with favorable mechanical and thermal properties, for which Pb HaPs are clear outliers, it is found that the Cs2AuIAuIIIX6, (X = I, Br, Cl) family, which is synthesized and tested for SH. This is the first demonstration of …

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Mar 2024 • Biosensors

A Self-Calibrated Single Wavelength Biosensor for Measuring Oxygen Saturation

Michal Katan, Ori Pearl, Alon Tzroya, Hamootal Duadi, Dror Fixler

Traditional methods for measuring blood oxygen use multiple wavelengths, which produce an intrinsic error due to ratiometric measurements. These methods assume that the absorption changes with the wavelength, but in fact the scattering changes as well and cannot be neglected. We found that if one measures in a specific angle around a cylindrical tissue, called the iso-pathlength (IPL) point, the reemitted light intensity is unaffected by the tissue’s scattering. Therefore, the absorption can be isolated from the scattering, which allows the extraction of the subject’s oxygen saturation. In this work, we designed an optical biosensor for reading the light intensity reemitted from the tissue, using a single light source and multiple photodetectors (PDs), with one of them in the IPL point’s location. Using this bio-device, we developed a methodology to extract the arterial oxygen saturation using a single wavelength light source. We proved this method is not dependent on the light source and is applicable to different measurement locations on the body, with an error of 0.5%. Moreover, we tested thirty-eight males and females with the biosensor under normal conditions. Finally, we show the results of measuring subjects in a hypoxic chamber that simulates extreme conditions with low oxygen.

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Mar 2024 • Molecular Therapy-Nucleic Acids

A pipeline for identifying guide RNA sequences that promote RNA editing of nonsense mutations that cause inherited retinal diseases

Nina Schneider, Ricky Steinberg, Amit Ben-David, Johanna Valensi, Galit David-Kadoch, Zohar Rosenwasser, Eyal Banin, Erez Y Levanon, Dror Sharon, Shay Ben-Aroya

Adenosine deaminases acting on RNA (ADARs) are endogenous enzymes catalyzing the deamination of adenosines to inosines, which are then read as guanosines during translation. This ability to recode makes ADAR an attractive therapeutic tool to edit genetic mutations and reprogram genetic information at the mRNA level. Using the endogenous ADARs and guiding them to a selected target has promising therapeutic potential. Indeed, different studies have reported several site-directed RNA-editing approaches for making targeted base changes in RNA molecules. The basic strategy has been to use guide RNAs (gRNAs) that hybridize and form a double-stranded RNA (dsRNA) structure with the desired RNA target because of ADAR activity in regions of dsRNA formation. Here we report on a novel pipeline for identifying disease-causing variants as candidates for RNA editing, using a yeast-based screening …

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Mar 2024 • Nanoscale Imaging, Sensing, and Actuation for Biomedical Applications XXI …, 2024

Self-calibrated biosensor for measuring multiple physiological parameters

Michal Katan, Hamootal Duadi, Dror Fixler

Nanophotonic techniques for diagnosis of a physiological tissue state are useful due to their noninvasive nature. Yet, light reflectance from a tissue is determined by the medium optical properties, absorption and scattering. Therefore, evaluating physiological parameters that correlate with absorption exclusively requires calibration of the scattering. While finding pulse rate is possible in a single wavelength, other parameters, such as oxygen saturation, require more than one light source and ratiometric measurements. As a result, the differences in the optical pathlength of the different wavelengths produce an inherent error. We have previously discovered the iso-path length (IPL) point, a specific position around a cylindrical media where the light intensity is not affected by the scattering. It was found by measuring the full scattering profile (FSP), meaning the angular distribution of light intensity of cylindrical tissues …

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Mar 2024 • Journal of The Electrochemical Society

Misuse of XPS in Analyzing Solid Polymer Electrolytes for Lithium Batteries

Ortal Breuer, Yosef Gofer, Yuval Elias, Miryam Fayena-Greenstein, Doron Aurbach

One of the most powerful spectroscopic tools for battery analysis is X-ray photoelectron spectroscopy (XPS); however, its great power, must be accompanied by great responsibility for authenticity. Fluorine is documented to be unstable under XPS conditions, and fluorinated salts used in Li batteries show photodecomposition. As all-solid-state batteries advance, demand for surface characterization is increasing. Here, a popular solid polymer electrolyte comprising a fluorinated salt in a PEO matrix was measured by XPS. Rapid photodecomposition after few minutes produced mainly LiF, initially not found on the surface. Not being aware of such artifacts may lead to an erroneous analysis of the characterized electrochemical system.

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Mar 2024 • Physical Review A

Nonrelativistic spatiotemporal quantum reference frames

Michael Suleymanov, Ismael L Paiva, Eliahu Cohen

Quantum reference frames have attracted renewed interest recently, as their exploration is relevant and instructive in many areas of quantum theory. Among the different types, position and time reference frames have captivated special attention. Here, we introduce and analyze a nonrelativistic framework in which each system contains an internal clock in addition to its external (spatial) degree of freedom and, hence, can be used as a spatiotemporal quantum reference frame. We present expressions for expectation values and variances of relevant observables in different perspectives, as well as relations between these quantities in different perspectives in scenarios with no interactions. In particular, we show that even in these simple scenarios the relative uncertainty between clocks affects the relative spatial spread of the systems.

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Mar 2024 • Journal of Physics: Energy

Roadmap on Multivalent Batteries

M Rosa Palacin, Patrik Johansson, Robert Dominko, Ben Dlugatch, Doron Aurbach, Zhenyou Li, Maximilian Fichtner, Olivera Lužanin, Jan Bitenc, Zhixuan Wei, Clarissa Glaser, Jürgen Janek, Ana Fernández-Barquín, Aroa R Mainar, Olatz Leonet, Idoia Urdampilleta, J Alberto Blázquez, Deyana S Tchitchekova, Alexandre Ponrouch, Pieremanuele Canepa, Gopalakrishnan Sai Gautam, Raúl San Román Gallego Casilda, Cynthia S Martinez-Cisneros, Nieves Ureña Torres, Alejandro Varez, Jean-Yves Sanchez, Kostiantyn V Kravchyk, Maksym V Kovalenko, Anastasia A Teck, Huw Shiel, Ifan EL Stephens, Mary P Ryan, Eugen Zemlyanushin, Sonia Dsoke, Rebecca Grieco, Nagaraj Patil, Rebeca Marcilla, Xuan Gao, Claire J Carmalt, Guanjie He, Maria-Magdalena Titirici

Battery technologies based in multivalent charge carriers with ideally two or three electrons transferred per ion exchanged between the electrodes have large promises in raw performance numbers, most often expressed as high energy density, and are also ideally based on raw materials that are widely abundant and less expensive. Yet, these are still globally in their infancy, with some concepts (e.g., Mg metal) being more technologically mature. The challenges to address are derived on one side from the highly polarizing nature of multivalent ions when compared to single valent concepts such as Li+ or Na+ present in Li-ion or Na-ion batteries, and on the other, from the difficulties in achieving efficient metal plating/stripping (which remains the holy grail for lithium). Nonetheless, research performed to date has given some fruits and a clearer view of the challenges ahead. These include technological topics …

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Mar 2024 • arXiv preprint arXiv:2403.03050

Microscopic origin of abrupt transition in interdependent superconducting networks

Bnaya Gross, Irina Volotsenko, Ivan Bonamassa, Shlomo Havlin, Aviad Frydman

The paradigm of interdependent networks has recently been manifested in experimentally testable lab setup of interdependent superconducting networks. This system experiences an abrupt transition due to the thermal dissipation between the networks but its underlying mechanism remains elusive. Here we study the critical behavior and the underlying mechanism of the transition, unveiling its unique microscopic nature. The microscopic characteristics of the transition result in a macroscopic long-living plateau that lasts for thousands of seconds and increases with the size of the system. We characterize the critical behavior of the transition and find that the critical exponents are consistent with those predicted theoretically for percolation of abstract interdependent networks and interdependent ferromagnetic networks, supporting a common universal origin of interdependent systems.

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Mar 2024 • Phytobiomes Journal

Persistence and microbiome modification in Rhizoctonia solani inoculated rhizosphere following amendment of a Bacillus biocontrol agent

Maya Moshe, Omer Frenkel, Noa Sela, Chagai Davidovich, Hildah Amutuhaire, Ehud Banin, Eddie Cytryn

Background Bacterial biocontrol agents that antagonize soilborne pathogens are increasingly considered as alternatives to chemical pesticides, but their in-vivo efficacy is often inconsistent, restricting commercial use. The efficacy of a biocontrol agent can depend on rhizosphere competence and its interaction with native microbiomes, which can effect ecosystem functioning. This study investigated the capacity of a Bacillus cereus sensu lato (Bcsl) biocontrol strain (S-25) to persist on roots and in the rhizosphere of cucumber, and evaluated its impact on bacterial and fungal community composition in the rhizosphere, in the absence and presence of Rhizoctonia solani, the causative agent of damping-off disease in young seedlings. Results Following amendment, S-25 abundance in the cucumber rhizosphere decreased by two orders of magnitude, but remained relatively high for the duration of the experiment, in …

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Mar 2024 • Real-time Measurements, Rogue Phenomena, and Single-Shot Applications IX …, 2024

Quantum temporal optics

Moti Fridman, Eliahu Cohen

This manuscript introduces and shares MATLAB code for simulating the behavior of a temporal SU(1,1) interferometer, offering a valuable resource for researchers and practitioners in the field. The provided code facilitates comprehensive simulations of the interferometer’s dynamics, enabling the exploration of its response to various parameters and scenarios. The simulations delve into the interferometer’s performance, emphasizing its sensitivity to ultrafast phase changes and its concurrent operation in both the time and spectral domains. By making the MATLAB code openly available, this contribution aims to foster collaboration, enhance reproducibility, and serve as a foundational tool for researchers delving into the design and analysis of temporal SU(1,1) interferometers. The manuscript provides detailed documentation on code usage, empowering users to adapt and extend the simulations for their specific …

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Mar 2024 • Nucleic Acids Research

Two redundant transcription factor binding sites in a single enhancer are essential for mammalian sex determination

Meshi Ridnik, Elisheva Abberbock, Veronica Alipov, Shelly Ziv Lhermann, Shoham Kaufman, Maor Lubman, Francis Poulat, Nitzan Gonen

Male development in mammals depends on the activity of the two SOX gene: Sry and Sox9, in the embryonic testis. As deletion of Enhancer 13 (Enh13) of the Sox9 gene results in XY male-to-female sex reversal, we explored the critical elements necessary for its function and hence, for testis and male development. Here, we demonstrate that while microdeletions of individual transcription factor binding sites (TFBS) in Enh13 lead to normal testicular development, combined microdeletions of just two SRY/SOX binding motifs can alone fully abolish Enh13 activity leading to XY male-to-female sex reversal. This suggests that for proper male development to occur, these few nucleotides of non-coding DNA must be intact. Interestingly, we show that depending on the nature of these TFBS mutations, dramatically different phenotypic outcomes can occur, providing a molecular explanation for the distinct clinical …

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Mar 2024 • Nanoscale Imaging, Sensing, and Actuation for Biomedical Applications XXI …, 2024

Endoscope-based scattering measurements of esophagus phantoms

Natanel Ovadia Sr, Hamootal Duadi, Dror Fixler

In today's medical world, endoscopy is one of the most common methods for assessing a patient's health status, yet in most cases, endoscopy is not sufficient and usually requires other examinations as well. It is widely known that healthy, and diseased tissues possess different optical properties like scattering and absorption. By finding the changes in those optical properties it's possible to determine the tissue status by endoscopy only. This poster suggests an alternative self-calibrated endoscopy examination for finding these properties and quantitatively assessing the tissue. Implementing the physical phenomenon called the iso pathlength (IPL) point, makes it possible to extract the tissue absorption property since it simplifies the problem into an easily solvable first-order problem. The phenomenon claims the existence of physical positions on the surface tissue, in which the light reflected from, isn't affected by the …

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Mar 2024 • Journal of The Electrochemical Society

Specific Removal and Recovery of Bromide Ions: The Search for Stable Electrodes and Operation Modes

Izaak Cohen, Barak Shapira, Alexey Shopin, Yuval Elias, Eran Avraham, Doron Aurbach

In previous work, we introduced an elegant approach for bromide recovery from water by the introduction of a hybrid physical adsorption and capacitive deionization processes for selective removal and recovery of boron from water. In this paper, we show that the harsh environment of water contaminated with bromine-moieties adversely affects the longevity of relevant electrodes, with close to 100 consecutive work hours of bromides removal without noticeable degradation. To extend the lifespan of electrodes, we used an asymmetric CDI cell with a 1:5 positive/negative electrodes ratio in which a polarity switch between electrodes is applied every six adsorption-desorption cycles in a way that in each adsorption-desorption cycle, a different electrode of the six electrodes, functions as the positive electrode. We deduce that the polarity switch reduces oxidation and subsequent degradation of the positive electrodes …

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