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Dec 2019 • Scientific reports

Switching of multi-state magnetic structures via domain wall propagation triggered by spin-orbit torques

Shubhankar Das, Ariel Zaig, Hariharan Nhalil, Liran Avraham, Moty Schultz, Lior Klein

Spin-orbit torques emerge as a promising method for manipulating magnetic configurations of spintronic devices. Here, we show that these torques can induce a magnetization reversal via domain wall propagation which may open new ways in developing novel spintronic devices and in particular in realizing high-density multi-level magnetic memory. Our devices are bi-layer heterostructures of Ni 0.8 Fe 0.2 on top of β-Ta patterned in the form of two or three crossing ellipses which exhibit in the crossing area shape-induced biaxial and triaxial magnetic anisotropy, respectively. We demonstrate field-free switching between discrete remanent magnetic states of the structures by spin-orbit torques induced by flowing electrical current through one of the ellipses. We note switchings induced by the coupling between the ellipses where current flowing in one ellipse triggers a reversal in a neighboring ellipse which …

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Dec 2019 • Small, 2019

Interfacing the Cell with “Biomimetic Membrane Proteins”

Asaf Grupi, Idan Ashur, Nurit Degani‐Katzav, Shimon Yudovich, Zehavit Shapira, Adan Marzouq, Lion Morgenstein, Yossi Mandel, Shimon Weiss

Integral membrane proteins mediate a myriad of cellular processes and are the target of many therapeutic drugs. Enhancement and extension of the functional scope of membrane proteins can be realized by membrane incorporation of engineered nanoparticles designed for specific diagnostic and therapeutic applications. In contrast to hydrophobic insertion of small amphiphilic molecules, delivery and membrane incorporation of particles on the nanometric scale poses a crucial barrier for technological development. In this perspective, the transformative potential of biomimetic membrane proteins (BMPs), current state of the art, and the barriers that need to be overcome in order to advance the field are discussed.

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Nov 2019 • EPL (Europhysics Letters)

Embedding information in physically generated random bit sequences while maintaining certified randomness

Shira Sardi, Herut Uzan, Shiri Otmazgin, Yaara Aviad, Michael Rosenbluh, Ido Kanter

Ultrafast physical random bit generation at hundreds of Gb/s rates, with verified randomness, is a crucial ingredient in secure communication and has recently emerged using optics-based physical systems. Here we examine the inverse problem and measure the ratio of information bits that can be systematically embedded in a random bit sequence without degrading its certified randomness. These ratios exceed 0.01 in experimentally obtained long random bit sequences. Based on these findings we propose a high-capacity private-key cryptosystem with a finite key length, where the existence as well as the content of the communication is concealed in the random sequence. Our results call for a rethinking of the current quantitative definition of practical classical randomness as well as the measure of randomness generated by quantum methods, which have to include bounds using the proposed inverse …

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Nov 2019 • Journal of biophotonics

Detecting nucleic acid fragments in serum using a magnetically modulated sandwich assay

Michael Margulis, Saar Ashri, Meir Cohen, Amos Danielli

We present a novel assay for rapid and highly sensitive detection of specific nucleic acid fragments in human serum. In a magnetic modulation biosensing (MMB) system, magnetic beads and fluorescently labeled probes are attached to the target analyte and form a “sandwich” complex. An alternating external magnetic field gradient condenses the magnetic beads (and hence the target molecules with the fluorescently labeled probes) to the detection volume and sets them in a periodic motion, in and out of a laser beam. A synchronous detection enables the removal of background signal from the oscillating target signal without complicated sample preparation. The high sensitivity of the MMB system, combined with the specificity of a sandwich hybridization assay, enables detection of DNA fragments without enzymatic signal amplification. Here, we demonstrate the sensitivity of the assay by directly detecting the …

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Nov 2019 • Small

Neuroprotective effect of nerve growth factor loaded in porous silicon nanostructures in an Alzheimer's Disease model and potential delivery to the brain

Neta Zilony‐Hanin, Michal Rosenberg, Michal Richman, Ronen Yehuda, Hadas Schori, Menachem Motiei, Shai Rahimipour, Alexander Groisman, Ester Segal, Orit Shefi

Nerve growth factor (NGF) plays a vital role in reducing the loss of cholinergic neurons in Alzheimer's disease (AD). However, its delivery to the brain remains a challenge. Herein, NGF is loaded into degradable oxidized porous silicon (PSiO2) carriers, which are designed to carry and continuously release the protein over a 1 month period. The released NGF exhibits a substantial neuroprotective effect in differentiated rat pheochromocytoma PC12 cells against amyloid‐beta (Aβ)‐induced cytotoxicity, which is associated with Alzheimer's disease. Next, two potential localized administration routes of the porous carriers into murine brain are investigated: implantation of PSiO2 chips above the dura mater, and biolistic bombardment of PSiO2 microparticles through an opening in the skull using a pneumatic gene gun. The PSiO2‐implanted mice are monitored for a period of 8 weeks and no inflammation or adverse …

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Nov 2019 • Ultrasonics sonochemistry

Sonochemically modified ovalbumin enhances enantioenrichment of some amino acids

Amruta Mutalikdesai, Molhm Nassir, Abed Saady, Alfred Hassner, Aharon Gedanken

As part of our efforts to develop a new method for chiral resolution of amino acids with sonochemically modified proteins, we present result that indicates how ovalbumin microspheres (OAMS) interact specifically with l-amino acids from a racemate in solution, leaving an excess of d-enantiomer in the permeate solution. Among different amino acids that interacted with the OAMS, tryptophan (Trp) was the most successfully resolved with 65% enantiomeric excess. A control experiment with native ovalbumin in solution did not show any chiral resolution of amino acids. Interestingly, when the OAMS were pretreated with racemic lysine (Lys) solution and then used for resolution of tryptophan the enantiomeric enrichment of d-tryptophan was raised to 98%. This unanticipated positive effect is discussed in terms of the structural correlation between Trp and Lys, which is less apparent in other amino acids such as …

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Nov 2019 • Frontiers in immunology

Methods and Applications of Computational Immunology

Benny Chain, Victor Greiff, Johannes Textor, Gur Yaari

Understanding the immune system is of paramount importance for the prevention and treatment of disease as well as the development of novel immunotherapies and immunodiagnostics in the framework of precision immunology and medicine. Recently, the advent of high-throughput biological methods has provided unprecedented insight into the molecular mechanisms underlying immune cell dynamics. The immense complexity of innate and adaptive immunity spanning several orders of spatial and temporal scales may, however, only be grasped by a systems computational immunology approach—specifically, by developing powerful computational approaches, which process, model, and integrate these big immunological data.

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Nov 2019 • Journal of Raman Spectroscopy

Microcavity enhancement of low‐frequency Raman scattering from a CsPbI3 thin film

Tal Ben Uliel, Laxman Gouda, Hagit Aviv, Anat Itzhak, Yaakov R Tischler

Low‐frequency Raman (LFR) spectroscopy is a powerful, nondestructive method used for chemical and structural characterization of materials. Typically, the signal intensity of LFR is relatively low, resulting significantly longer signal acquisition duration. Here, we show a photonic structure based on a planar optical microcavity consists of two distributed Bragg reflectors that is capable of enhancing the LFR signal of the material placed in between the mirrors. CsPbI3 forms smooth and uniform thin films and has distinct LFR signatures; thus, we chose to use it for investigating the microcavity enhancement capabilities. By compromising the quality factor of the cavity, we achieved a broader transmission peak and essentially earned enhancement from the double‐resonance effect. Measurements on a CsPbI3 thin film inside a cavity compared with a bare film spin coated on glass demonstrated two orders of magnitude …

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Nov 2019 • ACS applied materials & interfaces

Magnetic targeting of mTHPC to improve the selectivity and efficiency of photodynamic therapy

Elina Haimov-Talmoud, Yifat Harel, Hadas Schori, Menachem Motiei, Ayelet Atkins, Rachela Popovtzer, Jean-Paul Lellouche, Orit Shefi

Photodynamic therapy (PDT) is a promising recognized treatment for cancer. To date, PDT drugs are injected systemically, and the tumor area is irradiated to induce cell death. Current clinical protocols have several drawbacks, including limited accessibility to solid tumors and insufficient selectivity of drugs. Herein, we propose an alternative approach to improve PDT effectiveness by magnetic targeting of responsive carriers conjugated to the PDT drug. We coordinatively attached a meso-tetrahydroxyphenylchlorin (mTHPC) photosensitizer to Ce-doped-γ-Fe2O3 maghemite nanoparticles (MNPs). These MNPs are superparamagnetic and biocompatible, and the resulting mTHPC–MNPs nanocomposites are stable in aqueous suspensions. MDA-MB231 (human breast cancer) cells incubated with the mTHPC–MNPs showed high uptake and high death rates in cell population after PDT. The exposure to external …

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Nov 2019 • Cell

Clonal decomposition and DNA replication states defined by scaled single-cell genome sequencing

Emma Laks, Andrew McPherson, Hans Zahn, Daniel Lai, Adi Steif, Jazmine Brimhall, Justina Biele, Beixi Wang, Tehmina Masud, Jerome Ting, Diljot Grewal, Cydney Nielsen, Samantha Leung, Viktoria Bojilova, Maia Smith, Oleg Golovko, Steven Poon, Peter Eirew, Farhia Kabeer, Teresa Ruiz de Algara, So Ra Lee, M Jafar Taghiyar, Curtis Huebner, Jessica Ngo, Tim Chan, Spencer Vatrt-Watts, Pascale Walters, Nafis Abrar, Sophia Chan, Matt Wiens, Lauren Martin, R Wilder Scott, T Michael Underhill, Elizabeth Chavez, Christian Steidl, Daniel Da Costa, Yussanne Ma, Robin JN Coope, Richard Corbett, Stephen Pleasance, Richard Moore, Andrew J Mungall, Colin Mar, Fergus Cafferty, Karen Gelmon, Stephen Chia, Gregory J Hannon, Giorgia Battistoni, Dario Bressan, Ian Cannell, Hannah Casbolt, Cristina Jauset, Tatjana Kovačević, Claire Mulvey, Fiona Nugent, Marta Paez Ribes, Isabella Pearsall, Fatime Qosaj, Kirsty Sawicka, Sophia Wild, Elena Williams, Samuel Aparicio, Yangguang Li, Ciara O’Flanagan, Austin Smith, Teresa Ruiz, Shankar Balasubramanian, Maximillian Lee, Bernd Bodenmiller, Marcel Burger, Laura Kuett, Sandra Tietscher, Jonas Windager, Edward Boyden, Shahar Alon, Yi Cui, Amauche Emenari, Dan Goodwin, Emmanouil Karagiannis, Anubhav Sinha, Asmamaw T Wassie, Carlos Caldas, Alejandra Bruna, Maurizio Callari, Wendy Greenwood, Giulia Lerda, Yaniv Lubling, Alastair Marti, Oscar Rueda, Abigail Shea, Owen Harris, Robby Becker, Flaminia Grimaldi, Suvi Harris, Sara Vogl, Johanna A Joyce, Jean Hausser, Spencer Watson, Sorhab Shah, Ignacio Vázquez-García, Simon Tavaré, Khanh Dinh, Eyal Fisher, Russell Kunes, Nicolas A Walton, Mohammad Al Sa’d, Nick Chornay, Ali Dariush, Eduardo Gonzales Solares, Carlos Gonzalez-Fernandez, Aybuke Kupcu Yoldas, Neil Millar, Xiaowei Zhuang, Jean Fan, Hsuan Lee, Leonardo Sepulveda Duran, Chenglong Xia, Pu Zheng, Marco A Marra, Carl Hansen, Sohrab P Shah

Accurate measurement of clonal genotypes, mutational processes, and replication states from individual tumor-cell genomes will facilitate improved understanding of tumor evolution. We have developed DLP+, a scalable single-cell whole-genome sequencing platform implemented using commodity instruments, image-based object recognition, and open source computational methods. Using DLP+, we have generated a resource of 51,926 single-cell genomes and matched cell images from diverse cell types including cell lines, xenografts, and diagnostic samples with limited material. From this resource we have defined variation in mitotic mis-segregation rates across tissue types and genotypes. Analysis of matched genomic and image measurements revealed correlations between cellular morphology and genome ploidy states. Aggregation of cells sharing copy number profiles allowed for calculation of single …

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Nov 2019 • The Journal of Physical Chemistry C

Combined experimental and theoretical study of cobalt corroles as catalysts for oxygen reduction reaction

Jennifer S Shpilman, Ariel Friedman, Noam Zion, Naomi Levy, Dan T Major, Lior Elbaz

Bioinspired transition-metal complexes may serve as efficient and low-cost potential catalysts for oxygen reduction reaction (ORR) in fuel cells, instead of precious group metal-free (PGM-free) materials. Herein, we present a study of the ORR electrocatalytic activity of different mesosubstituted Co-corroles with varying electronegativity using both experimental and theoretical methods. Specifically, we studied the influence of different mesosubstituted Co-corroles on catalytic activity. Using density functional theory (DFT), we computed lowest unoccupied molecular orbital (LUMO) energies, vertical excitation energies, electrostatic potentials, and O2 adsorption energies and compared them with the ORR catalytic activity obtained from cyclic voltammetry and rotating ring-disk electrode measurements. We found that the first one-electron reduction for all the corroles occurs at the Co-center based on computed LUMOs …

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Nov 2019 • Quantum Views

Quantum measurements-yet another surprise

Eliahu Cohen

When you measure a quantum system, the outcome will be one of the eigenvalues of the measured (Hermitian) operator. If you perform this measurement over an ensemble of (normalized) pure states , you will readily find the expectation value of the measured operator , which obviously resides within its spectrum. That at least, was what most of us were taught in our first quantum mechanics course. It turns out, however, that the above depends on how exactly your perform your measurement and what is the statistical analysis you make.In 1988 Aharonov, Albert and Vaidman (AAV) proposed a new quantum measurement scheme known as weak measurement [1]. Instead of the above strong, projective measurement, they suggested to weakly couple the measured system with the measuring pointer. One can still use the von Neumann measurement scheme, but one ought to make sure that the shift of the pointer is much smaller than its uncertainty. In that case, the amount of information one acquires with each strong measurement of the pointer is typically very small, so one will customarily need to repeat the measurement many times over similarly prepared quantum system (some exceptions do exist). But importantly, and unlike the standard paradigm, these strong measurements of the pointer barely change the states of the measured systems (this is often denoted as the non-invasiveness property of weak measurements).

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Nov 2019 • Physical Review Research

Large fluctuations of the first detected quantum return time

Ruoyu Yin, Klaus Ziegler, Felix Thiel, Eli Barkai

How long does it take a quantum particle to return to its origin? As shown previously under repeated projective measurements aimed to detect the return, the closed cycle yields a geometrical phase which shows that the average first detected return time is quantized. For critical sampling times or when parameters of the Hamiltonian are tuned this winding number is modified. These discontinuous transitions exhibit gigantic fluctuations of the return time. While the general formalism of this problem was studied at length, the magnitude of the fluctuations, which is quantitatively essential, remains poorly characterized. Here, we derive explicit expressions for the variance of the return time, for quantum walks in finite Hilbert space. A classification scheme of the diverging variance is presented, for four different physical effects: the Zeno regime, when the overlap of an energy eigenstate and the detected state is small, and …

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Nov 2019 • Bioinformatics

RAbHIT: R antibody haplotype inference tool

Ayelet Peres, Moriah Gidoni, Pazit Polak, Gur Yaari

Summary Antibody haplotype inference (chromosomal phasing) may have clinical implications for the identification of genetic predispositions to diseases. Yet, our knowledge of the genomic loci encoding for the variable regions of the antibody is only partial, mostly due to the challenge of aligning short reads from genome sequencing to these highly repetitive loci. A powerful approach to infer the content of these loci relies on analyzing repertoires of rearranged V(D)J sequences. We present here RAbHIT, an R Haplotype Antibody Inference Tool, that implements a novel algorithm to infer V(D)J haplotypes by adapting a Bayesian framework. RAbHIT offers inference of haplotype and gene deletions. It may be applied to sequences from naïve and non-naïve B-cells, sequenced by different library preparation protocols. Availability and implementation RAbHIT is freely available for …

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Nov 2019 • Optics express

Photonic human identification based on deep learning of back scattered laser speckle patterns

Zeev Kalyzhner, Or Levitas, Felix Kalichman, Ron Jacobson, Zeev Zalevsky

The analysis of the dynamics of speckle patterns that are generated when laser light is back scattered from a tissue has been recently shown as very applicable for remote sensing of various bio-medical parameters. In this work, we present how the analysis of a static single speckle pattern scattered from the forehead of a subject, together with advanced machine learning techniques based on multilayered neural networks, can offer novel approach to accurate identification within a small predefined number of classes (e.g., a ‘smart home’ setting which restricts its operations for family members only). Processing the static scattering speckle pattern by neural networks enables extraction of unique features with no previous expert knowledge being required. Using the right model allows for a very accurate differentiation between desirable categories, and that model can form a basis for using speckles patterns as a form of …

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Nov 2019 • Israel Journal of Chemistry 59 (11-12), 980-989, 2019

EPR Distance Measurements as a Tool to Characterize Protein‐DNA Interactions

Hila Sameach, Sharon Ruthstein

Over recent decades, electron paramagnetic resonance (EPR) spectroscopy has become an essential tool for exploring complex biological systems. Herein, we discuss the potential of pulsed EPR spectroscopy to shed light on the mechanisms of protein‐DNA interactions. To this end, we first provide an overview of pulsed EPR methodology (and specifically, double electron electron resonance; DEER), with a focus on the various spin‐labeling methods used today both for protein labeling and for DNA labeling. Next, after briefly discussing recent applications of DEER in protein‐DNA studies, we introduce a detailed case study, an example of how EPR spectroscopy has been used to resolve the transcription mechanism of the CueR copper regulator.

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Nov 2019 • Physical Review B

Quasiperiodic magnetic flux avalanches in doubly connected superconductors

J Shvartzberg, A Shaulov, Y Yeshurun

Magneto-optical imaging of Nb rings, open rings, and strips reveals that the topology affects the dendritic flux avalanches in the samples. In particular, dendrites crossing the entire width of the sample appear only in the rings. Such dendrites appear when the difference between the applied field and the average field inside the central hole reaches a certain threshold level Δ H th. With increasing applied field, this condition is reached quasiperiodically as a crossing dendrite creates momentarily a hot channel through which flux flows into the central hole, balancing the field inside the hole with that outside the ring. The threshold Δ H th differs in magnitude from the onset field H th of magnetic instability, and exhibits qualitatively different dependence on the rim width.

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Nov 2019 • ACS combinatorial science

FTO Darkening Rate as a Qualitative, High-Throughput Mapping Method for Screening Li-Ionic Conduction in Thin Solid Electrolytes

Shay Tirosh, Niv Aloni, Simcha Meir, Arie Zaban, David Cahen, Diana Golodnitsky

We present a high-throughput (combinatorial) method to screen thin ceramic films as Li-ion conductors by mapping an optical effect of Li-ion conduction. The method, while qualitative, is fast and simple to implement, provides a planar (XY) map of Li-ion conductivity through different parts of the film. The effect, FTO darkening, is an optoelectrochemical one that relies on darkening of the FTO (F-doped tin oxide) substrate, onto which the investigated film is deposited. The rate of color change of the FTO reflects the rate of Li-ion migration through the film. The method is validated by testing two model systems, a Li–La–S–O film with uniform composition and varying thickness, and a Li–La–P–O film with varying thickness and lateral composition. The darkening rate, obtained from optical transmission, correlates linearly with inverse film thickness. The darkening rate map can be compared with a resistance map obtained by …

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Nov 2019 • blood

Chromatin occupancy and epigenetic analysis reveal new insights into the function of the GATA1 N terminus in erythropoiesis

Te Ling, Yehudit Birger, Monika J Stankiewicz, Nissim Ben-Haim, Tomer Kalisky, Avigail Rein, Eitan Kugler, Wei Chen, Chunling Fu, Kevin Zhang, Hiral Patel, Jacek W Sikora, Young Ah Goo, Neil Kelleher, Lihua Zou, Shai Izraeli, John D Crispino

Mutations in GATA1, which lead to expression of the GATA1s isoform that lacks the GATA1 N terminus, are seen in patients with Diamond-Blackfan anemia (DBA). In our efforts to better understand the connection between GATA1s and DBA, we comprehensively studied erythropoiesis in Gata1s mice. Defects in yolks sac and fetal liver hematopoiesis included impaired terminal maturation and reduced numbers of erythroid progenitors. RNA-sequencing revealed that both erythroid and megakaryocytic gene expression patterns were altered by the loss of the N terminus, including aberrant upregulation of Gata2 and Runx1. Dysregulation of global H3K27 methylation was found in the erythroid progenitors upon loss of N terminus of GATA1. Chromatin-binding assays revealed that, despite similar occupancy of GATA1 and GATA1s, there was a striking reduction of H3K27me3 at regulatory elements of the Gata2 …

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Nov 2019 • Journal of Applied Physics

Irradiation-induced broadening of the Raman spectra in monolayer graphene

I Shlimak, A Butenko, E Kogan, M Kaveh

Broadening of the Raman scattering (RS) spectra was studied in monolayer graphene samples irradiated with various doses of ions followed by annealing of radiation damage at different temperatures. It is shown that the width Γ (full width at half maximum) of three main RS lines (G, D, and 2D) increases linearly with the increase of the density of irradiation-induced point defects Nd: ΔΓ = mNd. The slope m is the same for one-phonon emitting G-line and D-line and almost double for a two-phonon emitting 2D-line. It is observed that the width of the D-line for slightly irradiated samples is larger than one half of the width of the 2D-line, which shows that, in the case of the D-line, elastic electron scattering on point defects leads to an additional linewidth. This difference decreases with the increase of Nd, which shows the decrease of the role of scattering on a single point defect because of the spreading of this …

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Nov 2019 • The Journal of Physical Chemistry C

Visualization of plasmon-induced hot electrons by scanning electron microscopy

Elad Segal, Matan Galanty, Hannah Aharon, Adi Salomon

We show that scanning electron microscopy imaging can indicate hot-electron formation in aluminum plasmonic nanostructures composed of five triangular cavities. A very strong secondary electron emission was observed, up to 150 nm from the plasmonic structure. The secondary electron emission depends on the acceleration voltage, the distance between the plasmonic cavities, the metal type, and the roughness of the surface. Furthermore, the formation of hot electrons was used to increase the efficiency of an optoelectronic device.

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