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Jul 2020 • RNA biology

The large repertoire of 2’-O-methylation guided by C/D snoRNAs on Trypanosoma brucei rRNA

K Shanmugha Rajan, Yinzhou Zhu, Katerina Adler, Tirza Doniger, Smadar Cohen-Chalamish, Ankita Srivastava, Moran Shalev-Benami, Donna Matzov, Ron Unger, Christian Tschudi, Arthur Günzl, Gordon G Carmichael, Shulamit Michaeli

The parasite Trypanosoma brucei cycles between insect and mammalian hosts, and is the causative agent of sleeping sickness. Here, we performed genome-wide mapping of 2ʹ-O-methylations (Nms) on trypanosome rRNA using three high-throughput sequencing methods; RibOxi-seq, RiboMeth-seq and 2ʹ-OMe-seq. This is the first study using three genome-wide mapping approaches on rRNA from the same species showing the discrepancy among the methods. RibOxi-seq detects all the sites, but RiboMeth-seq is the only method to evaluate the level of a single Nm site. The sequencing revealed at least ninety-nine Nms guided by eighty-five snoRNAs among these thirty-eight Nms are trypanosome specific sites. We present the sequence and target of the C/D snoRNAs guiding on rRNA. This is the highest number of Nms detected to date on rRNA of a single cell parasite. Based on RiboMeth-seq, several Nm …

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Jul 2020 • Physical Review Letters

Helical Edge States and Quantum Phase Transitions in Tetralayer Graphene

Shi Che, Yanmeng Shi, Jiawei Yang, Haidong Tian, Ruoyu Chen, Takashi Taniguchi, Kenji Watanabe, Dmitry Smirnov, Chun Ning Lau, Efrat Shimshoni, Ganpathy Murthy, Herbert A Fertig

Helical conductors with spin-momentum locking are promising platforms for Majorana fermions. Here we report observation of two topologically distinct phases supporting helical edge states in charge neutral Bernal-stacked tetralayer graphene in Hall bar and Corbino geometries. As the magnetic field B⊥ and out-of-plane displacement field D are varied, we observe a phase diagram consisting of an insulating phase and two metallic phases, with 0, 1, and 2 helical edge states, respectively. These phases are accounted for by a theoretical model that relates their conductance to spin-polarization plateaus. Transitions between them arise from a competition among interlayer hopping, electrostatic and exchange interaction energies. Our work highlights the complex competing symmetries and the rich quantum phases in few-layer graphene.

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Jul 2020 • Journal of The Electrochemical Society

Enhancement of electrochemical performance of lithium and manganese-rich cathode materials via thermal treatment with SO2

Hadar Sclar, Johannes Sicklinger, Evan M Erickson, Sandipan Maiti, Judith Grinblat, Michael Talianker, Francis Amalraj Susai, Larisa Burstein, Hans Beyer, Louis Hartmann, Gregory Avruschenko, Hubert A Gasteiger, Boris Markovsky, Doron Aurbach

In this study, we present a novel surface modification approach via SO 2 gas treatment at 200 C–400 C to enhance the electrochemical performance of Li and Mn-rich cathode materials 0.35 Li 2 MnO 3 centerdot 0.65 LiNi 0.35 Mn 0.45 Co 0.20 O 2 (HE-NCM) for advanced lithium-ion batteries. It was established by X-ray photoelectron spectroscopy that the SO 2 treatment leads to the formation of surface sulfates and sulfites on the material, while the bulk remains unaffected, as confirmed by X-ray and electron diffraction studies. Based on the results obtained, we proposed possible mechanisms of the SO 2 thermal treatment that include partial reduction of manganese (however, we could not find any substantial evidence for it in the XPS data) and oxidation of sulfur. The electrochemical performance was evaluated by testing the materials as cathodes in coin-type half-cells with metallic lithium anodes at 25 C and 30 C …

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Jul 2020 • Electrochimica Acta 354, 136771, 2020

On the challenge of large energy storage by electrochemical devices

Satyanarayana Maddukuri, David Malka, Munseok S Chae, Yuval Elias, Shalom Luski, Doron Aurbach

This paper reviews work that promotes the effective use of renewable energy sources (solar and wind) by developing technologies for large energy storage, concentrating on electrochemical devices. Unfortunately, we are not far from a non-return situation related to global warming due to green-house gasses emission, 88% of which is contributed through release of CO2 by combusting fossil fuels. Major contributors to CO2 emission are power stations that produce electricity. Only a massive replacement of fossil fuels combustion by photovoltaic solar panels and wind turbines for electricity production can reduce drastically the detrimental CO2 emission. The success of using renewable energy depends on the availability of technologies for large energy storage. We believe that modern electrochemistry can provide them. We review herein relevant options. While hydrogen based technology using fuel cells and flow …

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Jul 2020 • arXiv preprint arXiv:2007.10384

Off-resonant coherent electron transport over three nanometers in multi-heme protein bioelectronic junctions

Zdenek Futera, Ichiro Ide, Ben Kayser, Kavita Garg, Xiuyun Jiang, Jessica H van Wonderen, Julea N Butt, Hisao Ishii, Israel Pecht, Mordechai Sheves, David Cahen, Jochen Blumberger

Multi-heme cytochromes (MHC) are fascinating proteins used by bacterial organisms to shuttle electrons within and between their cells. When placed in a solid state electronic junction, they support temperature-independent currents over several nanometers that are three orders of magnitude higher compared to other redox proteins of comparable size. To gain microscopic insight into their astonishingly high conductivities, we present herein the first current-voltage calculations of its kind, for a MHC sandwiched between two Au(111) electrodes, complemented by photo-emission spectroscopy experiments. We find that conduction proceeds via off-resonant coherent tunneling mediated by a large number of protein valence-band orbitals that are strongly delocalized over heme and protein residues, effectively "gating" the current between the two electrodes. This picture is profoundly different from the dominant electron hopping mechanism supported by the same protein in aqueous solution. Our results imply that current output in MHC junctions could be even further increased in the resonant regime, e.g. by application of a gate voltage, making these proteins extremely interesting for next-generation bionanoelectronic devices.

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Jul 2020 • IEEE Photonics Technology Letters

Integrated high-resolution optical spectrum analyzer with broad operational bandwidth

Arijit Misra, Stefan Preußler, Dvir Munk, Moshe Katzman, Linjie Zhou, Avi Zadok, Thomas Schneider

Precise optical spectrum analysis with high resolution by an economical and reliable device is of much interest in optical science and technology. In this work, we propose a silicon-photonic integrated optical spectrum analyzer comprised of two cascaded filters. A first ring resonator stage selects multiple ultra-narrow spectral bands of equal spacing. The set of bands may be scanned across the spectrum of interest through thermal tuning. A second filter stage separates the multiple sampled bands into different output ports. The free spectral ranges of the two stages are matched. The spectrum is reconstructed using simple, low bandwidth photodiodes. In a proof of concept experiment, the proposed integrated optical spectrum analyzer shows a wide operational range with 128MHz resolution.

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Jul 2020 • Journal of biophotonics

Reducing data acquisition for light‐sheet microscopy by extrapolation between imaged planes

Ziv Shemesh, Gal Chaimovich, Liron Gino, Nisan Ozana, Jonathan Nylk, Kishan Dholakia, Zeev Zalevsky

Light‐sheet fluorescence microscopy (LSFM) is a powerful technique that can provide high‐resolution images of biological samples. Therefore, this technique offers significant improvement for three‐dimensional (3D) imaging of living cells. However, producing high‐resolution 3D images of a single cell or biological tissues, normally requires high acquisition rate of focal planes, which means a large amount of sample sections. Consequently, it consumes a vast amount of processing time and memory, especially when studying real‐time processes inside living cells. We describe an approach to minimize data acquisition by interpolation between planes using a phase retrieval algorithm. We demonstrate this approach on LSFM data sets and show reconstruction of intermediate sections of the sparse samples. Since this method diminishes the required amount of acquisition focal planes, it also reduces acquisition time …

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Jul 2020 • Nature Reviews Materials 5 (7), 517-538, 2020

Charge-transfer materials for electrochemical water desalination, ion separation and the recovery of elements

Pattarachai Srimuk, Xiao Su, Jeyong Yoon, Doron Aurbach, Volker Presser

Reversible electrochemical processes are a promising technology for energy-efficient water treatment. Electrochemical desalination is based on the compensation of electric charge by ionic species, through which the ions are immobilized and, thereby, removed from a feed-water stream flowing through a desalination cell. For decades, electrochemical desalination has focused on the use of carbon electrodes, but their salt-removal ability is limited by the mechanism of ion electrosorption at low molar concentrations and low charge-storage capacity. Recently, charge-transfer materials, often found in batteries, have demonstrated much larger charge-storage capacities and energy-efficient desalination at both low and high molar strengths. In this Review, we assess electrochemical-desalination mechanisms and materials, including ion electrosorption and charge-transfer processes, namely, ion binding with redox …

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Jul 2020 • Nanomaterials

Bifunctional Carbon Dots—Magnetic and Fluorescent Hybrid Nanoparticles for Diagnostic Applications

Ilana Perelshtein, Nina Perkas, Shai Rahimipour, Aharon Gedanken

There is a huge demand for materials capable of simple detection or separation after conjugation with specific biologic substances when applied as a diagnostic tools. Taking into account the photoluminescence properties of C-dots and the highly magnetic properties of Fe (0), a new hybrid composite of these components was synthesized via ultrasound irradiation. The material was fully characterized by various physicochemical techniques. The main goal of the current study was to obtain a highly magnetic and intense fluorescent hybrid material. The goal was achieved. In addition, magnetic particles tended to agglomerate. The new hybrid can be suspended in ethanol, which is an additional feature of the current research. The dispersion of the hybrid nanoparticles in ethanol was achieved by utilizing the interaction of iron particles with C-dots which were decorated with functional groups on their surface. The newly formed hybrid material has potential applications in diagnostic by conjugating with specific antibodies or with any other biologic compounds. Such application may be useful in detection of various diseases such as: cancer, tuberculosis, etc. View Full-Text

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Jul 2020 • ACS Applied Nano Materials

Gold Nanorod-Based Bio-Barcode Sensor Array for Enzymatic Detection in Biomedical Applications

Marianna Beiderman, Ariel Ashkenazy, Elad Segal, Eran A Barnoy, Menachem Motiei, Tamar Sadan, Adi Salomon, Shai Rahimipour, Dror Fixler, Rachela Popovtzer

Early diagnosis of disease onset requires sensor systems that detect multiple disease-related processes within the body. However, major obstacles must be surmounted for in vivo sensor use, including size, biocompatibility, sensitivity, and selectivity. As an initial study, here we fabricated a multidimensional gold nanorod (GNR)-based bio-barcode sensing array for sensitive and selective detection of biological events. The sensor comprises an array of gold nanocavities and GNRs that are bound to the array as well as to fluorescein via bio-barcode peptides. Exposure of the sensor to peptide-specific enzymes as inputs led to bio-barcode cleavage, which produced distinct optical-based output, that is, changes in fluorescence lifetime and surface plasmon resonance. The sensor showed sensitivity and selectivity to each biomarker input alone, as well as simultaneous distinguishable responses to their combination. By …

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Jul 2020 • Advanced Materials

Ferroelectric exchange bias affects interfacial electronic states

Gal Tuvia, Yiftach Frenkel, Prasanna K Rout, Itai Silber, Beena Kalisky, Yoram Dagan

In polar oxide interfaces phenomena such as superconductivity, magnetism, 1D conductivity, and quantum Hall states can emerge at the polar discontinuity. Combining controllable ferroelectricity at such interfaces can affect the superconducting properties and sheds light on the mutual effects between the polar oxide and the ferroelectric oxide. Here, the interface between the polar oxide LaAlO3 and the ferroelectric Ca‐doped SrTiO3 is studied by means of electrical transport combined with local imaging of the current flow with the use of scanning a superconducting quantum interference device (SQUID). Anomalous behavior of the interface resistivity is observed at low temperatures. The scanning SQUID maps of the current flow suggest that this behavior originates from an intrinsic bias induced by the polar LaAlO3 layer. Such intrinsic bias combined with ferroelectricity can constrain the possible structural domain …

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Jun 2020 • MRS Bulletin

Defects in halide perovskites: The lattice as a boojum?

Sujit Kumar, Gary Hodes, David Cahen

Although halide perovskites (HaPs) are synthesized in ways that appear antithetical to those required for yielding high-quality semiconductors, the properties of the resulting materials imply, particularly for single crystals, ultralow densities of optoelectronically active defects. This article provides different views of this unusual behavior. We pose the question: Can present models of point defects in solids be used to interpret the experimental data and provide predictive power? The question arises because the measured ultralow densities refer to static defects using our present methods and models, while dynamic defect densities are ultrahigh, a result of the material being relatively soft, with a shallow electrostatic energy landscape, and with anharmonic lattice dynamics. All of these factors make the effects of dynamic defects on the materials’ optoelectronic properties minimal. We hope this article will stimulate …

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Jun 2020 • Ultrasonics Sonochemistry 64, 105009, 2020

Sonochemical synthesis of carbon dots, mechanism, effect of parameters, and catalytic, energy, biomedical and tissue engineering applications

Raj Kumar, Vijay Bhooshan Kumar, Aharon Gedanken

Carbon-based nanomaterials are gaining more and more interest because of their wide range of applications. Carbon dots (CDs) have shown exclusive interest due to unique and novel physicochemical, optical, electrical, and biological properties. Since their discovery, CDs became a promising material for wide range of research applications from energy to biomedical and tissue engineering applications. At same time several new methods have been developed for the synthesis of CDs. Compared to many of these methods, the sonochemical preparation is a green method with advantages such as facile, mild experimental conditions, green energy sources, and feasibility to formulate CDs and doped CDs with controlled physicochemical properties and lower toxicity. In the last five years, the sonochemically synthesized CDs were extensively studied in a wide range of applications. In this review, we discussed the …

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Jun 2020 • Scientific reports

All-optical, an ultra-thin endoscopic photoacoustic sensor using multi-mode fiber

Nadav Shabairou, Benjamin Lengenfelder, Martin Hohmann, Florian Klämpfl, Michael Schmidt, Zeev Zalevsky

Photoacoustic endoscopy (PAE) is a method of in-vivo imaging that uses tissue absorption properties. In PAE, the main tools used to detect the acoustic signal are mechanical ultrasound transducers, which require direct contact and which are difficult to miniaturize. All-optic photoacoustic sensors can challenge this issue as they can provide contact-free sensing. Here, we demonstrate sensing of photo-acoustic signals through a multimode fiber (MMF) which can provide an ultra-thin endoscopic photoacoustic sensor. Furthermore, we show the advantage of using the optical-flow method for speckle sensing and extract the photoacoustic signal despite the mode-mixing along the MMF. Moreover, it is demonstrated for the first time that the speckle reconstruction method can be used without the need for imaging of the speckles as this enables the use of multimode fibers for the speckle method.

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Jun 2020 • Colloids and Surfaces B: Biointerfaces

Cooperative crystallization effect in the formation of sonochemically grafted active materials based on polysaccharides

Yevgenia Shebis, Vijay Bhooshan Kumar, Aharon Gedanken, Elena Poverenov

The current study explores the formation of active eco-friendly materials capable of preventing microbial contamination using in situ ultrasonic grafting of vanillin, curcumin and a curcumin-vanillin mixture on the surfaces of carboxymethylcellulose (CMC) and chitosan films. Spectroscopic, microscopic, physical and mechanical studies revealed that the films grafted with curcumin-vanillin mixture demonstrate improved mechanical properties and higher degree of order. The bioactivity of the prepared films was tested on food model, fresh-cut melons and films with a deposited curcumin-vanillin mixture showed superior antibacterial properties. For instance, this mixture-grafted on CMC films demonstrated a total inhibition of yeast/mold proliferation during 12 days. The HR-SEM studies of the mixture-grafted films revealed the presence of crystalline structures. Cooperative crystallization effect between the curcumin (the …

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Jun 2020 • ACS Energy Letters

Oxidation Stability of Organic Redox Mediators as Mobile Catalysts in Lithium–Oxygen Batteries

Won-Jin Kwak, Jiwon Park, Hun Kim, Jung Min Joo, Doron Aurbach, Hye Ryung Byon, Yang-Kook Sun

Employing organic redox mediators (ORMs) for lithium–oxygen (Li–O2) batteries has emerged as an important strategy to suppress charging overpotentials. Judicious molecular designs of ORMs can also tailor their redox potential and electron-transfer rate to optimize the catalytic efficiency. However, the stability of ORMs in Li–O2 cells was scarcely studied. Here, the catalytic efficiency and stability of several important ORMs are assessed through in situ gas analysis and reactivity tests with singlet oxygen. Some well-known ORMs are detrimentally decomposed during the first cycle in Li–O2 cells, whereas nitroxyl-radical-based ORMs bear the most stable and efficient response. Analogous nitroxyl-radical derivatives further increase round-trip energy efficiency and electron-transfer kinetics. This study underlines chemical stability aspects of ORMs, which are mandatory for the long-term cyclability in Li–O2 cells. We …

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Jun 2020 • Entropy

Large deviations for continuous time random walks

Wanli Wang, Eli Barkai, Stanislav Burov

Recently observation of random walks in complex environments like the cell and other glassy systems revealed that the spreading of particles, at its tails, follows a spatial exponential decay instead of the canonical Gaussian. We use the widely applicable continuous time random walk model and obtain the large deviation description of the propagator. Under mild conditions that the microscopic jump lengths distribution is decaying exponentially or faster ie, Lévy like power law distributed jump lengths are excluded, and that the distribution of the waiting times is analytical for short waiting times, the spreading of particles follows an exponential decay at large distances, with a logarithmic correction. Here we show how anti-bunching of jump events reduces the effect, while bunching and intermittency enhances it. We employ exact solutions of the continuous time random walk model to test the large deviation theory. View Full-Text

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Jun 2020 • Batteries & Supercaps

Effect of Crystal Structure and Morphology on Na3V2(PO4)2F3 Performances for Na‐Ion Batteries

Ayan Mukherjee, Tali Sharabani, Rosy Sharma, Sivan Okashy, Malachi Noked

Na-ion batteries (SIB) are considered promising systems for energy storage devices, however diversity of available cathode materials is lower compared to lithium ion batteries. Recently, Na3V2 (PO4) 2F3 (NVPF) has been demonstrated as promising cathode material for SIB owing to high specific capacity and electrochemical reversibility. However, most of reports demonstrates capacities lower than theoretical value and optimization of electrochemical performances by controlled morphology and crystal structure was not demonstrated yet. Here, we demonstrate a scalable synthesis strategy to tailor the crystal structure and morphology of NVPF and showed that our approach enables to optimize the Na+ ion accommodation, diffusion and stability. A flower morphology (NVPF-F) crystalizes in tetragonal structure, demonstrates discharge capacity of 109.5 mA. hg À 1 and 98.1% columbic efficiency whereas a hollow spherical morphology (NVPF-S) with orthorhombic structure exhibits discharge capacity of 124.8 mA. hg À 1 (very close to theoretical value) and 99.5% columbic efficiency. The observed discharge capacity for NVPF-S is highest reported value which is ascribed due to stable crystal structure and monodispersed morphology. Long term stability with negligible capacity loss is demonstrated over 550 cycles. Our findings shed light on importance of crystal structure and morphology of NVPF on electrochemical response, and realization as cathode material for SIB.

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Jun 2020 • Physical Review Research

Uncertainty and symmetry bounds for the quantum total detection probability

Felix Thiel, Itay Mualem, David A Kessler, Eli Barkai

We investigate a generic discrete quantum system prepared in state| ψ in〉 under repeated detection attempts, aimed to find the particle in state| d〉, for example, a quantum walker on a finite graph searching for a node. For the corresponding classical random walk, the total detection probability P det is unity. Due to destructive interference, one may find initial states| ψ in〉 with P det< 1. We first obtain an uncertainty relation which yields insight on this deviation from classical behavior, showing the relation between P det and energy fluctuations: Δ P Var [H ̂] d≥|〈 d|[H ̂, D ̂]| ψ in〉| 2, where Δ P= P det−|〈 ψ in| d〉| 2 and D ̂=| d〉〈 d| is the measurement projector. Secondly, exploiting symmetry we show that P det≤ 1/ν, where the integer ν is the number of states equivalent to the initial state. These bounds are compared with the exact solution for small systems, obtained from an analysis of the dark and bright …

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Jun 2020 • Nucleic acids research

Polymorphisms in human immunoglobulin heavy chain variable genes and their upstream regions

Ivana Mikocziova, Moriah Gidoni, Ida Lindeman, Ayelet Peres, Omri Snir, Gur Yaari, Ludvig M Sollid

Germline variations in immunoglobulin genes influence the repertoire of B cell receptors and antibodies, and such polymorphisms may impact disease susceptibility. However, the knowledge of the genomic variation of the immunoglobulin loci is scarce. Here, we report 25 potential novel germline IGHV alleles as inferred from rearranged naïve B cell cDNA repertoires of 98 individuals. Thirteen novel alleles were selected for validation, out of which ten were successfully confirmed by targeted amplification and Sanger sequencing of non-B cell DNA. Moreover, we detected a high degree of variability upstream of the V-REGION in the 5′UTR, L-PART1 and L-PART2 sequences, and found that identical V-REGION alleles can differ in upstream sequences. Thus, we have identified a large genetic variation not only in the V-REGION but also in the upstream sequences of IGHV genes. Our findings provide a new …

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Jun 2020 • Current Opinion in Colloid & Interface Science 49, 107-117, 2020

Polyhedral liquid droplets: Recent advances in elucidation and application

Orlando Marin, Maria Tkachev, Eli Sloutskin, Moshe Deutsch

The re-discovery of temperature-controlled self-faceting, shaping, and splitting transitions in liquid oil-in-water emulsion droplets, has recently led to a significant progress in the fundamental understanding of these counterintuitive phenomena, sparking scientific controversies, and opening new routes towards their technological applications. These recent developments are reviewed here. The faceting transitions were demonstrated to occur in a wide range of oil: surfactant combinations, for broad temperature ranges, and in droplets of sizes spanning an incredible 13 decades in volume, from nano (11× 10− 9) to yocto (300× 10− 24) liters. Droplets’ polymerization enables forming solid faceted particles, of shapes and sizes otherwise unachievable. Colloids and nanoparticles adsorbed controllably onto the faceted liquid droplets’ interfaces self-position at their vertices and self-expel into the aqueous medium. The self …

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