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Jan 2020 • Sensors

Microcavity Enhanced Raman Spectroscopy of Fullerene C60 Bucky Balls

Vinayaka H Damle, Miri Sinwani, Hagit Aviv, Yaakov R Tischler

Raman spectroscopy is a widely used characterization technique in material science. It is a non-destructive tool with relatively simple instrumentation, and provides intrinsic qualitative information of analytes by probing their vibrational modes. In many cases, Raman enhancement is essential for detecting low-intensity signals in high-noise environments, spectrally unresolved features, and hidden modes. Here we present optical and Raman spectroscopic characterization of fullerene C 60 in a gold microcavity. The fabrication of single-layered gold mirrors is facile, low cost and direct but was proven to give considerably significant enhancement. The findings of this work demonstrate the cavity resonance as a powerful tool in obtaining tunability over individual peak for selective enhancement in the tuned spectral range. The PL of the material within the cavity has demonstrated a red shift assumed to be caused by the low-energy transitions. These transitions are induced by virtual low-energy states generated by the cavity. We further observe that adopting this principle enables resolution of active Raman modes that until now were unobserved. Finally, we assigned the new experimentally observed modes to the corresponding motions calculated by DFT. View Full-Text

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Jan 2020 • bioRxiv

Fe (III) heme sets an activation threshold for processing distinct groups of pri-miRNAs in mammalian cells

Sara H Weitz, Jen Quick-Cleveland, Jose P Jacob, Ian Barr, Rachel Senturia, Kikuye Koyano, Xinshu Xiao, Shimon Weiss, Feng Guo

The essential biological cofactor heme is synthesized in cells in the Fe(II) form. Oxidized Fe(III) heme is specifically required for processing primary transcripts of microRNAs (pri-miRNAs) by the RNA-binding protein DGCR8, a core component of the Microprocessor complex. It is unknown how readily available Fe(III) heme is in the largely reducing environment in human cells and how changes in cellular Fe(III) heme availability alter microRNA (miRNA) expression. Here we address the first question by characterizing DGCR8 mutants with various degrees of deficiency in heme-binding. We observed a strikingly simple correlation between Fe(III) heme affinity in vitro and the Microprocessor activity in HeLa cells, with the heme affinity threshold for activation estimated to be between 0.6-5 pM under typical cell culture conditions. The threshold is strongly influenced by cellular heme synthesis and uptake. We suggest that the threshold reflects a labile Fe(III) heme pool in cells. Based on our understanding of DGCR8 mutants, we reanalyzed recently reported miRNA sequencing data and conclude that heme is generally required for processing canonical pri-miRNAs, that heme modulates the specificity of Microprocessor, and that cellular heme level and differential DGCR8 heme occupancy alter the expression of distinct groups of miRNAs in a hierarchical fashion. Overall, our study provides the first glimpse of a labile Fe(III) heme pool important for a fundamental physiological function and reveal principles governing how Fe(III) heme modulates miRNA maturation at a genomic scale. We also discuss potential states and biological significance of the labile …

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Jan 2020 • Journal of chemical theory and computation

Role of Microsolvation and Quantum Effects in the Accurate Prediction of Kinetic Isotope Effects: The Case of Hydrogen Atom Abstraction in Ethanol by Atomic Hydrogen in Aqueous …

Suraj Kannath, Paweł Adamczyk, David Ferro-Costas, Antonio Fernández-Ramos, Dan Thomas Major, Agnieszka Dybala-Defratyka

Hydrogen abstraction from ethanol by atomic hydrogen in aqueous solution is studied using two theoretical approaches: the multipath variational transition state theory (MP-VTST) and a path-integral formalism in combination with free-energy perturbation and umbrella sampling (PI-FEP/UM). The performance of the models is compared to experimental values of H kinetic isotope effects (KIE). Solvation models used in this study ranged from purely implicit, via mixed–microsolvation treated quantum mechanically via the density functional theory (DFT) to fully explicit representation of the solvent, which was incorporated using a combined quantum mechanical-molecular mechanical (QM/MM) potential. The effects of the transition state conformation and the position of microsolvating water molecules interacting with the solute on the KIE are discussed. The KIEs are in good agreement with experiment when MP-VTST is …

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Jan 2020 • Materials Chemistry and Physics

Sol-gel approach to incorporate millimeter-long carbon nanotubes into fabrics for the development of electrical-conductive textiles

Valentina Trovato, Eti Teblum, Yulia Kostikov, Andrea Pedrana, Valerio Re, Gilbert D Nessim, Giuseppe Rosace

In this paper, a new and versatile approach to obtain a good dispersion in water-based paste of short (≅ 1.5 mm) and long (≅ 3.0 mm) millimeter-sized carbon nanotubes (CNT) for the fabrication of electroconductive textiles is reported. With this aim, N-[3-(triethoxysilyl)propyl]ethylenediamine (EDAES) was used in combination with a waterborne thermo-degradable surfactant to stabilize the dispersion of two different kinds of carbon nanotubes (CNT) in hydroalcoholic solutions. A polyurethane thickener was added to each CNT dispersion to obtain dense pastes that were deposited onto cotton fabrics using the knife-over-roll technique. High magnification images confirm that the nanotubes are well dispersed in both coatings, furthermore appearing homogeneously distributed on the cotton surface. The conductivity of the long CNT-coated fabrics was confirmed by the electrical resistance of 2.61 × 104 Ω/sq which …

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Jan 2020 • Sensors

Reduction in Irradiation Dose in Aperture Coded Enhanced Computed Tomography Imager Using Super-Resolution Techniques

Yossef Danan, Doron Avraham, Zeev Zalevsky

One of the main concerns regarding medical imaging is the danger tissue’s ionizing due to the applied radiation. Many medical procedures are based on this ionizing radiation (such as X-rays and Gamma radiation). This radiation allows the physician to perform diagnosis inside the human body. Still, the main concern is stochastic effects to the DNA, particularly the cause of cancer. The radiation dose endangers not only the patient but also the medical staff, who might be close to the patient and be exposed to this dangerous radiation in a daily manner. This paper presents a novel concept of radiation reduced Computed Tomography (CT) scans. The proposed concept includes two main methods: minification to enhance the energy concertation per pixel and subpixel resolution enhancement, using shifted images, to preserve resolution. The proposed process uses several pinhole masks as the base of the imaging modality. The proposed concept was validated numerically and experimentally and has demonstrated the capability of reducing the radiation efficiency by factor 4, being highly significant to the world of radiology and CT scans. This dose reduction allows a safer imaging process for the patient and the medical staff. This method simplifies the system and improves the obtained image quality. The proposed method can contribute additively to standard existing dose reduction or super-resolution techniques to achieve even better performance. View Full-Text

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Jan 2020 • Nucleic acids research

OGRDB: a reference database of inferred immune receptor genes

William Lees, Christian E Busse, Martin Corcoran, Mats Ohlin, Cathrine Scheepers, Frederick A Matsen IV, Gur Yaari, Corey T Watson, AIRR Community, Andrew Collins, Adrian J Shepherd

High-throughput sequencing of the adaptive immune receptor repertoire (AIRR-seq) is providing unprecedented insights into the immune response to disease and into the development of immune disorders. The accurate interpretation of AIRR-seq data depends on the existence of comprehensive germline gene reference sets. Current sets are known to be incomplete and unrepresentative of the degree of polymorphism and diversity in human and animal populations. A key issue is the complexity of the genomic regions in which they lie, which, because of the presence of multiple repeats, insertions and deletions, have not proved tractable with short-read whole genome sequencing. Recently, tools and methods for inferring such gene sequences from AIRR-seq datasets have become available, and a community approach has been developed for the expert review and publication of such inferences. Here, we …

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Jan 2020 • Sensors

Design of surface enhanced Raman scattering (SERS) nanosensor array

Y Mandelbaum, R Mottes, Z Zalevsky, D Zitoun, A Karsenty

An advanced Surface-Enhanced Raman Scattering (SERS) Nanosensor Array, dedicated to serve in the future as a pH imager for the real-time detection of chemical reaction, is presented. The full flow of elementary steps—architecture, design, simulations, fabrication, and preliminary experimental results of structural characterization (Focused Ion Beam (FIB), TEM and SEM)—show an advanced SERS pixel array that is capable of providing spatially resolved measurements of chemical pH in a fluid target that became more than desirable in this period. Ultimately, the goal will be to provide real-time monitoring of a chemical reaction. The pixels consist of a nanostructured substrate composed of an array of projections or cavities. The shape of the nanostructures and the thickness of the metallic (Ag or Au) layer can be tuned to give maximal enhancement at the desired wavelength. The number and arrangement of nanostructures is optimized to obtain maximal responsivity. View Full-Text

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Jan 2020 • Langmuir

Fabrication of dipole-aligned thin films of Porphyrin J-aggregates over large surfaces

Adam Weissman, Hodaya Klimovsky, Dor Harel, Racheli Ron, Martin Oheim, Adi Salomon

We report a new approach for large-scale alignment of micron-sized J-aggregates of a derivative of porphyrin onto planar glass substrates. We applied a unidirectional nitrogen flow to an aqueous dye drop deposited onto a glass substrate to form an about 5 nm thick film of aligned J-aggregates over macroscopic surface areas up to several millimeters. The inter-aggregate distance is ∼500 nm, and it scales with the nitrogen pressure. We verified the film thickness and J-aggregate alignment using multimodal microscopy and spectroscopy techniques. Our technique is fast, simple, and cost-effective for producing large two-dimensional (2-D) arrays of aligned emitters.

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Jan 2020 • Applied Sciences

Double Slit with an Einstein–Podolsky–Rosen Pair

Bar Y Peled, Amit Te’eni, Danko Georgiev, Eliahu Cohen, Avishy Carmi

In this somewhat pedagogical paper we revisit complementarity relations in bipartite quantum systems. Focusing on continuous-variable systems, we examine the influential class of EPR-like states through a generalization to Gaussian states and present some new quantitative relations between entanglement and local interference within symmetric and asymmetric double-double-slit scenarios. This approach is then related to ancilla-based quantum measurements, and weak measurements in particular. Finally, we tie up the notions of distinguishability, predictability, coherence and visibility while drawing some specific connections between them. View Full-Text

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Jan 2020 • Materials

Electrochemical activation of Li2MnO3 electrodes at 0° c and its impact on the subsequent performance at higher temperatures

Francis Amalraj Susai, Michael Talianker, Jing Liu, Tanmoy Paul, Yehudit Grinblat, Evan Erickson, Malachi Noked, Larisa Burstein, Anatoly I Frenkel, Yoed Tsur, Boris Markovsky, Doron Aurbach

Jan 2020 • Chemistry of Materials 32 (3), 915-952, 2020

Layered Cathode Materials for Lithium-Ion Batteries: Review of Computational Studies on LiNi1–x–yCoxMnyO2 and LiNi1–x–yCoxAlyO2

Arup Chakraborty, Sooraj Kunnikuruvan, Sandeep Kumar, Boris Markovsky, Doron Aurbach, Mudit Dixit, Dan Thomas Major

At present the most successful rechargeable battery is the Li-ion battery, due to the small size, high energy density, and low reduction potential of Li. Computational materials science has become an increasingly important tool to study these batteries, and in particular cathode properties. In silico studies of cathode materials have proven to be a valuable tool to understand the workings of cathodes, without having to do sophisticated experiments. First-principles and empirical computations have been used by various groups to study key properties, such as structural stability, electronic structure, ion diffusion mechanisms, equilibrium cell voltage, thermal and electrochemical stability, and surface behavior of Li-ion battery cathode materials. Arguably, the most practical and promising Li-ion cathode materials today are layered oxide materials, and in particular LiNi1–x–yCoxMnyO2 (NCM) and LiNi1–x–yCoxAlyO2 (NCA …

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Jan 2020 • Beilstein journal of organic chemistry

Understanding the role of active site residues in CotB2 catalysis using a cluster model

Keren Raz, Ronja Driller, Thomas Brück, Bernhard Loll, Dan T Major

Terpene cyclases are responsible for the initial cyclization cascade in the multistep synthesis of a large number of terpenes. CotB2 is a diterpene cyclase from Streptomyces melanosporofaciens, which catalyzes the formation of cycloocta-9-en-7-ol, a precursor to the next-generation anti-inflammatory drug cyclooctatin. In this work, we present evidence for the significant role of the active site's residues in CotB2 on the reaction energetics using quantum mechanical calculations in an active site cluster model. The results revealed the significant effect of the active site residues on the relative electronic energy of the intermediates and transition state structures with respect to gas phase data. A detailed understanding of the role of the enzyme environment on the CotB2 reaction cascade can provide important information towards a biosynthetic strategy for cyclooctatin and the biomanufacturing of related terpene structures.

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Jan 2020 • ChemElectroChem

Electrochemical oxidation of glycine with bimetallic nickel− manganese oxide catalysts

Roopathy Mohan, Arindam Modak, Palaniappan Subramanian, Rivka Cahan, P Sivakumar, Aharon Gedanken, Alex Schechter

A simple template‐free hydrothermal route followed by high‐temperature (800 °C) annealing in air forms Ni–Mn bimetallic oxides, namely NiMn2O4, Ni1.5Mn1.5O4, and MnNi2O4, which are characterized by XRD, Raman, EDS, and SEM analysis. The electrocatalytic activity of these metal oxides toward the oxidation of glycine molecules in alkaline condition was studied by cyclic voltammetry and linear sweep voltammetry methods. Among other nickel manganese bimetallic oxides and monometallic oxides (Mn2O3, NiO), Ni1.5Mn1.5O4 shows excellent redox characteristics with high oxidation current density (310 μA cm−2 at 0.43 V vs. Ag/AgCl) and lower onset potential (0.22 V vs. Ag/AgCl). Additionally, Ni1.5Mn1.5O4 exhibits a moderate Tafel slope (78 mV dec−1) and is electrochemically stable, as confirmed from chronoamperometry, indicating its potential for glycine oxidation. The linear dependence of …

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Jan 2020 • Sensors

Gamma Radiation Imaging System via Variable and Time-Multiplexed Pinhole Arrays

Ariel Schwarz, Amir Shemer, Yossef Danan, Rachel Bar-Shalom, Hemy Avraham, Alex Zlotnik, Zeev Zalevsky

Biomedical planar imaging using gamma radiation is a very important screening tool for medical diagnostics. Since lens imaging is not available in gamma imaging, the current methods use lead collimator or pinhole techniques to perform imaging. However, due to ineffective utilization of the gamma radiation emitted from the patient’s body and the radioactive dose limit in patients, poor image signal to noise ratio (SNR) and long image capturing time are evident. Furthermore, the resolution is related to the pinhole diameter, thus there is a tradeoff between SNR and resolution. Our objectives are to reduce the radioactive dose given to the patient and to preserve or improve SNR, resolution and capturing time while incorporating three-dimensional capabilities in existing gamma imaging systems. The proposed imaging system is based on super-resolved time-multiplexing methods using both variable and moving pinhole arrays. Simulations were performed both in MATLAB and GEANT4, and gamma single photon emission computed tomography (SPECT) experiments were conducted to support theory and simulations. The proposed method is able to reduce the radioactive dose and image capturing time and to improve SNR and resolution. The results and method enhance the gamma imaging capabilities that exist in current systems, while providing three-dimensional data on the object. View Full-Text

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Jan 2020 • Optica

Ultrabroadband nonlinear optics in nanophotonic periodically poled lithium niobate waveguides

Marc Jankowski, Carsten Langrock, Boris Desiatov, Alireza Marandi, Cheng Wang, Mian Zhang, Christopher R Phillips, Marko Lončar, MM Fejer

Quasi-phase-matched interactions in waveguides with quadratic nonlinearities enable highly efficient nonlinear frequency conversion. In this paper, we demonstrate the first generation of devices that combine the dispersion engineering available in nanophotonic waveguides with quasi-phase-matched nonlinear interactions available in periodically poled lithium niobate (PPLN). This combination enables quasi-static interactions of femtosecond pulses, reducing the pulse energy requirements by several orders of magnitude compared to conventional devices, from picojoules to femtojoules. We experimentally demonstrate two effects associated with second harmonic generation (SHG). First, we observe efficient quasi-phase-matched SHG with <100fJ of pulse energy. Second, in the limit of strong phase-mismatch, we observe spectral broadening of both harmonics with as little as 2 pJ of pulse energy. These …

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Jan 2020 • Journal of The Electrochemical Society

Improved Performance of Li-metal∣ LiNi0. 8Co0. 1Mn0. 1O2 Cells with High-Loading Cathodes and Small Amounts of Electrolyte Solutions Containing Fluorinated Carbonates at 30° C …

Elena Markevich, Gregory Salitra, Michal Afri, Yosef Talyosef, Doron Aurbach

Herein, we report on the performance of stable lithium metal mid LiNi 0.8 Co 0.1 Mn 0.1 O 2 (NCM 811) cells with practical electrodes loading of 3.4 mAh cm− 2 and small amounts of electrolyte solutions, at 30–55 C. The latter contained 1 M LiPF 6 in fluoroethylene carbonate (FEC)/difluoroethylene carbonates (DFEC)/dimethyl carbonate (DMC) 1: 1: 8, around 0.7–1.7 μl mg− 1 of active cathode material (14–33 μl cm− 2). Using DFEC as a co-solvent enables to overcome drastic capacity fading of Li metal mid NCM cells containing practical amounts (≤ 1.2 μl mg− 1 NCM 811) of electrolyte solutions based on FEC/DMC. The lithium metal anodes were characterized by scanning electron microscope (SEM), Energy Dispersive X-ray Spectroscopy (EDS) and Fourier transform infrared spectroscopy (FTIR). The surface films formed on Li anodes cycled in solutions containing FEC and DFEC are composed mainly of their …

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Jan 2020 • bioRxiv

Lytic Reactivation of the Kaposi’s sarcoma-associated herpesvirus (KSHV) is Accompanied by Major Nucleolar Alterations

Nofar Atari, K Shanmugha Rajan, Vaibhav Chikne, Smadar Cohen-Chalamish, Odelia Orbaum, Avi Jacob, Inna Kalt, Shulamit Michaeli, Ronit Sarid

The nucleolus is a sub-nuclear compartment whose primary function is the biogenesis of ribosomal subunits. Certain viral infections affect the morphology and composition of the nucleolar compartment and influence ribosomal RNA (rRNA) transcription and maturation. However, no description of nucleolar morphology and function during infection with Kaposi’s sarcoma-associated herpesvirus (KSHV) is available to date. Using immunofluorescence microscopy, we documented extensive destruction of the nuclear and nucleolar architecture during lytic reactivation of KSHV. This was manifested by redistribution of key nucleolar proteins, including the rRNA transcription factor, UBF, the essential pre-rRNA processing factor Fibrillarin, and the nucleolar multifunctional phosphoproteins Nucleophosmin (NPM1) and Nucleolin. Distinct delocalization patterns were evident; certain nucleolar proteins remained together whereas others dissociated, implying that nucleolar proteins undergo nonrandom programmed dispersion. Of note, neither Fibrillarin nor UBF colocalized with promyelocytic leukemia (PML) nuclear bodies or with the viral protein LANA-1, and their redistribution was not dependent on viral DNA replication or late viral gene expression. No significant changes in pre-rRNA levels and no accumulation of pre-rRNA intermediates were found by RT-qPCR and Northern blot analysis, respectively. Furthermore, fluorescent in situ hybridization (FISH), combined with immunofluorescence, revealed an overlap between Fibrillarin and internal transcribed spacer 1 (ITS1), which represents the primary product of the pre-rRNA, suggesting that the …

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Jan 2020 • Journal of Superconductivity and Novel Magnetism

Magnetism and conductivity along structural domain walls of SrTiO3

Yiftach Frenkel, Yanwu Xie, Harold Y Hwang, Beena Kalisky

The interface between the oxide insulators LaAlO3 and SrTiO3 (LAO/STO) hosts a two-dimensional electron gas. The combination of interfacial conductivity and superconductivity at ultra-low temperatures with the physical phenomena of the oxide parent materials has fueled extensive research in the field since its discovery in 2004. Scanning superconducting quantum interference device (SQUID) measurements have shown that structural domain walls, formed below 105 K, modulate the current flow at the interface and recently revealed weak magnetic signals along the same domain structure. Here we use scanning SQUID to investigate the temperature dependence of different electronic properties of the LAO/STO interface. We find correlation between magnetism and conductivity, which are both spatially modulated on the domain structure. This data suggests a possible relation between the populations of …

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Jan 2020 • Scientific reports

Sensitive readout for microfluidic high-throughput applications using scanning SQUID microscopy

Shai Wissberg, Maria Ronen, Ziv Oren, Doron Gerber, Beena Kalisky

Microfluidic chips provide a powerful platform for high-throughput screening of diverse biophysical systems. The most prevalent detection methods are fluorescence based. Developing new readout techniques for microfluidics focusing on quantitative information in the low signal regime is desirable. In this work, we combine the well-established immunoassay approach, with magnetic nanoparticles, with a highly sensitive magnetic imaging technique. We offer to integrate a microfluidic array into a scanning superconducting quantum interference device (SQUID) microscope, to image nanoparticles that were moved through the microfluidic device. We demonstrate the technique on protein-protein interactions (PPI). We compare sensitivity to that of a conventional readout, quantify the amount of interactions, and demonstrate 0.1 atto-mole sensitivity. Our work serves as a proof of concept that will promote the …

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Jan 2020 • Current Biology

Cortical Interactions between Prosthetic and Natural Vision

Tamar Arens-Arad, Nairouz Farah, Rivkah Lender, Avital Moshkovitz, Thomas Flores, Daniel Palanker, Yossi Mandel

Outer retinal degenerative diseases, such as retinitis pigmentosa (RP) and age-related macular degeneration (AMD), are among the leading causes of incurable blindness in the Western world [1]. Retinal prostheses have been shown to restore some useful vision by electrically stimulating the remaining retinal neurons [2]. In contrast to inherited retinal degenerative diseases (e.g., RP), typically leading to a complete loss of the visual field, in AMD patients the disease is localized to the macula, leaving the peripheral vision intact. Implanting a retinal prosthesis in the central macula in AMD patients [3, 4] leads to an intriguing situation where the patient’s central retina is stimulated electrically, whereas the peripheral healthy retina responds to natural light stimulation. An important question is whether the visual cortex responds to these two concurrent stimuli similarly to the interaction between two adjacent natural light …

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Jan 2020 • Biochemical Journal 477 (1), 23-44, 2020

Into the basket and beyond: the journey of mRNA through the nuclear pore complex

Asaf Ashkenazy-Titelman, Yaron Shav-Tal, Ralph H Kehlenbach

The genetic information encoded in nuclear mRNA destined to reach the cytoplasm requires the interaction of the mRNA molecule with the nuclear pore complex (NPC) for the process of mRNA export. Numerous proteins have important roles in the transport of mRNA out of the nucleus. The NPC embedded in the nuclear envelope is the port of exit for mRNA and is composed of ∼30 unique proteins, nucleoporins, forming the distinct structures of the nuclear basket, the pore channel and cytoplasmic filaments. Together, they serve as a rather stationary complex engaged in mRNA export, while a variety of soluble protein factors dynamically assemble on the mRNA and mediate the interactions of the mRNA with the NPC. mRNA export factors are recruited to and dissociate from the mRNA at the site of transcription on the gene, during the journey through the nucleoplasm and at the nuclear pore at the final stages of …

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