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Oct 2020 • Biomedical optics express

Single wavelength measurements of absorption coefficients based on iso-pathlength point

I Feder, H Duadi, D Fixler

In optical sensing, to reveal the chemical composition of tissues, the main challenge is isolating absorption from scattering. Most techniques use multiple wavelengths, which adds an error due to the optical pathlength differences. We suggest using a unique measurement angle for cylindrical tissues, the iso-pathlength (IPL) point, which depends on tissue geometry only (specifically the effective radius). We present a method for absorption assessment from a single wavelength at multiple measurement angles. The IPL point presented similar optical pathlengths for different tissues, both in simulation and experiments, hence it is optimal. Finally, in vivo measurements validated our proposed method.

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Oct 2020 • Physical Review B

Twinned nanostructure of thin films grown on r-cut sapphire

Anatoly G Shabalin, Elihu Anouchi, Nelson Hua, Yimin A Wu, Martin V Holt, Amos Sharoni, Oleg G Shpyrko

Due to strong electron-phonon interactions, strain engineering is a powerful tool to control quantum critical phenomena in strongly correlated oxides. Exploring this possibility requires understanding the nanoscale structure of quantum materials and the role it plays in forming the strain landscape. Here, we used a combination of x-ray nanoimaging and reciprocal space mapping to study the nanostructure of the archetypal Mott insulator VO 2, featuring an insulator-to-metal and structural phase transitions. We found that VO 2 thin films grown on r-cut sapphire consist of two intertwined crystal lattices, permanently inclined with respect to each other. This persistent pattern of twin domains stands out from the symmetry breaking induced by the structural phase transition and conceivably originates from the post-growth strain relaxation process. We propose a model explaining the formation of twin domains and the …

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Oct 2020 • Royal Society of Chemistry, 2020

New magnetically responsive polydicarbazole-magnetite nanoparticlesElectronic supplementary information (ESI) available: experimental details including analyses. See http://www …

Jean-Paul Lellouche, Nurit Perlman, Augustine Joseph, Senthil Govindaraji, Ludmila Buzhansky, Aline Yakir, Ian Bruce

Magnetically responsive COOH-polydicarbazole-magnetite nanocomposites have been prepared by chemical oxidation of three COOH-dicarbazole monomers 1 and 4â 5 in the presence of magnetite nanoparticles. These functionalized nanoparticles have been tested for DNA hybridization experiments.

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Oct 2020 • Bioessays

Speculating on the roles of nuclear speckles: how RNA‐protein nuclear assemblies affect gene expression

Sarah E Hasenson, Yaron Shav‐Tal

Nuclear speckles are eukaryotic nuclear bodies enriched in splicing factors. Their exact purpose has been a matter of debate. The different proposed roles of nuclear speckles are reviewed and an additional layer of function is put forward, suggesting that by accumulating splicing factors within them, nuclear speckles can buffer the nucleoplasmic levels of splicing factors available for splicing and thereby modulate splicing rates. These findings build on the already established model that nuclear speckles function as a storage/recycling site for splicing factors. Many studies have demonstrated proximity between nuclear speckles and sites of active transcription, suggesting that this juxtaposition can enhance the rates of gene expression. It is found that nuclear speckle disassembly increases splicing factor availability in the nucleoplasm, leading to an increase in splicing rates and faster release of nascent transcripts …

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Oct 2020 • arXiv preprint arXiv:2010.12220

Classical and wave chaos in the transformation from curved to flat surfaces

Chenni Xu, Itzhack Dana, Li-Gang Wang, Patrick Sebbah

We study classical and wave chaotic dynamics of light both on a curved surface and on a table billiard with nonuniform distribution of refractive index. Inspired by the concept of transformation optics, we demonstrate that these two systems are fundamentally equivalent in terms of both light rays and waves, under a conformal coordinate transformation. This total equivalency allows us to study simultaneously a typical family of curved surfaces and their corresponding transformed billiards. Here we consider the truncated Tannery's pear and its equivalent flat billiard with non-uniform distribution of refractive index, when an off-centered hole is pierced to introduce chaos. We find that the degree of chaos is fully controlled by the single geometric parameter of Tannery's pears. This is proved by exploring in the transformed billiard the dependence with this geometric parameter of the Poincar\'{e} surface of section, the Lyapunov exponent and the the statistics of eigenmodes and eigenfrequency spectrum. Finally, a simple interpretation of our findings naturally emerges when considering transformed billiards, which allows to extend our prediction to other class of curved surfaces. The powerful analogy we reveal here between two a priori unrelated systems not only brings forward a novel approach to control the degree of chaos, but also provides potentialities for further studies and applications in various fields, such as billiards design, optical fibers, or laser microcavities.

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Oct 2020 • Physical Review B

Twinned nanostructure of thin films grown on r-cut sapphire

Anatoly G Shabalin, Elihu Anouchi, Nelson Hua, Yimin A Wu, Martin V Holt, Amos Sharoni, Oleg G Shpyrko

Due to strong electron-phonon interactions, strain engineering is a powerful tool to control quantum critical phenomena in strongly correlated oxides. Exploring this possibility requires understanding the nanoscale structure of quantum materials and the role it plays in forming the strain landscape. Here, we used a combination of x-ray nanoimaging and reciprocal space mapping to study the nanostructure of the archetypal Mott insulator VO 2, featuring an insulator-to-metal and structural phase transitions. We found that VO 2 thin films grown on r-cut sapphire consist of two intertwined crystal lattices, permanently inclined with respect to each other. This persistent pattern of twin domains stands out from the symmetry breaking induced by the structural phase transition and conceivably originates from the post-growth strain relaxation process. We propose a model explaining the formation of twin domains and the …

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Oct 2020 • Ternary and Multinary Compounds, 741-744, 2020

Investigation of the defect chemistry of CuInSe2 by positron lifetime and electrical measurements

J Klais, HJ Müller, R Krause-Rehberg, David Cahen, Vera Lyakhovitskaya

In this study we present the determination of the defect chemistry and the electrical properties of CuInSe2 after controlled annealing steps. The samples were investigated with the positron annihilation method and the admittance spectroscopy.

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Oct 2020 • Advanced Materials Interfaces

Magnetic Organization of Neural Networks via Micro‐Patterned Devices

Michal Marcus, Ganit Indech, Naor Vardi, Itay Levy, Alexandra Smith, Shlomo Margel, Orit Shefi, Amos Sharoni

Guiding neuronal migration and outgrowth has great importance for therapeutic applications and for bioelectronics interfaces. Many efforts have been devoted to the development of tools to form predesigned structured neuronal networks. Here, a unique approach to localize cell bodies and direct neurite outgrowth is described based on local magnetic manipulations. Inspired by spintronic devices, a multi‐layer deposition process is developed to generate nanometric‐thick films with perpendicular magnetization that provide stable attraction forces toward the entire magnetic pads. PC12 cells, a common neuronal model, are transformed to magnetic units by incubation with superparamagnetic nanoparticles, which are then plated and differentiated atop the substrates. The vast majority of MNPs‐loaded cells adhere to the magnetic pads, showing high affinity to the magnetic patterns in correlation with numerical …

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Oct 2020 • Physical Review E

Extreme value theory for constrained physical systems

Marc Höll, Wanli Wang, Eli Barkai

We investigate extreme value theory for physical systems with a global conservation law which describes renewal processes, mass transport models, and long-range interacting spin models. As shown previously, a special feature is that the distribution of the extreme value exhibits a nonanalytical point in the middle of the support. We expose exact relationships between constrained extreme value theory and well-known quantities of the underlying stochastic dynamics, all valid beyond the midpoint in general, ie, even far from the thermodynamic limit. For example, for renewal processes the distribution of the maximum time between two renewal events is exactly related to the mean number of these events. In the thermodynamic limit, we show how our theory is suitable to describe typical and rare events which deviate from classical extreme value theory. For example, for the renewal process we unravel dual scaling of …

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Oct 2020 • Nature Communications

Optical framed knots as information carriers

Hugo Larocque, Alessio D’Errico, Manuel F Ferrer-Garcia, Avishy Carmi, Eliahu Cohen, Ebrahim Karimi

Modern beam shaping techniques have enabled the generation of optical fields displaying a wealth of structural features, which include three-dimensional topologies such as Möbius, ribbon strips and knots. However, unlike simpler types of structured light, the topological properties of these optical fields have hitherto remained more of a fundamental curiosity as opposed to a feature that can be applied in modern technologies. Due to their robustness against external perturbations, topological invariants in physical systems are increasingly being considered as a means to encode information. Hence, structured light with topological properties could potentially be used for such purposes. Here, we introduce the experimental realization of structures known as framed knots within optical polarization fields. We further develop a protocol in which the topological properties of framed knots are used in conjunction with …

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Oct 2020 • Physical Review B

Super-Poissonian behavior of the Rosenzweig-Porter model in the nonergodic extended regime

Richard Berkovits

The Rosenzweig-Porter model has seen a resurgence in interest as it exhibits a nonergodic extended phase between the ergodic extended metallic phase and the localized phase. Such a phase is relevant to many physical models from the Sachdev-Ye-Kitaev model in high-energy physics and quantum gravity to the interacting many-body localization in condensed-matter physics and quantum computing. This phase is characterized by fractal behavior of the wave functions and a postulated correlated miniband structure of the energy spectrum. Here we will seek evidence for the latter in the spectrum. Since this behavior is expected on intermediate energy scales, spectral rigidity or number variance is a natural way to tease it out. Nevertheless, due to the Thouless energy and ambiguities in the unfolding procedure, the results are inconclusive. On the other hand, by using the singular-value decomposition method …

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Oct 2020 • Journal of the American Society of Nephrology

Single-cell RNA sequencing reveals mRNA splice isoform switching during kidney development

Yishay Wineberg, Tali Hana Bar-Lev, Anna Futorian, Nissim Ben-Haim, Leah Armon, Debby Ickowicz, Sarit Oriel, Efrat Bucris, Yishai Yehuda, Naomi Pode-Shakked, Shlomit Gilad, Sima Benjamin, Peter Hohenstein, Benjamin Dekel, Achia Urbach, Tomer Kalisky

Background During mammalian kidney development, nephron progenitors undergo a mesenchymal-to-epithelial transition and eventually differentiate into the various tubular segments of the nephron. Recently, Drop-seq single-cell RNA sequencing technology for measuring gene expression from thousands of individual cells identified the different cell types in the developing kidney. However, that analysis did not include the additional layer of heterogeneity that alternative mRNA splicing creates.Methods Full transcript length single-cell RNA sequencing characterized the transcriptomes of 544 individual cells from mouse embryonic kidneys.Results Gene expression levels measured with full transcript length single-cell RNA sequencing identified each cell type. Further analysis comprehensively characterized splice isoform switching during the transition between mesenchymal and epithelial cellular states, which is …

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Oct 2020 • Physical Review Research

Regularized Boltzmann-Gibbs statistics for a Brownian particle in a nonconfining field

Lucianno Defaveri, Celia Anteneodo, David A Kessler, Eli Barkai

We consider an overdamped Brownian particle subject to an asymptotically flat potential with a trap of depth U 0 around the origin. When the temperature is small compared to the trap depth (ξ= k B T/U 0≪ 1), there exists a range of timescales over which physical observables remain practically constant. This range can be very long, of the order of the Arrhenius factor e 1/ξ. For these quasiequilibrium states, the usual Boltzmann-Gibbs recipe does not work since the partition function is divergent due to the flatness of the potential at long distances. However, we show that the standard Boltzmann-Gibbs statistical framework and thermodynamic relations can still be applied through proper regularization. This can be a valuable tool for the analysis of metastability in the nonconfining potential fields that characterize a vast number of systems.

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Oct 2020 • Advanced Energy Materials

Vacancy‐Driven High Rate Capabilities in Calcium‐Doped Na0.4MnO2 Cathodes for Aqueous Sodium‐Ion Batteries

Munseok S Chae, Arup Chakraborty, Sooraj Kunnikuruvan, Ran Attias, Satyanarayana Maddukuri, Yosef Gofer, Dan Thomas Major, Doron Aurbach

Aqueous sodium‐ion batteries are expected to be low‐cost, safe, and environmentally friendly systems for large scale energy storage due to the abundance and low cost of sodium. However, only a few candidates have been reported for cathodes and there is a need to develop new practical host materials with improved electrochemical performance. Here, tunnel‐type, calcium‐doped, sodium manganese oxide is demonstrated as a novel cathode material, ultrafast rate capabilities and superior high‐rate cycling stability—98.8% capacity retention at the 1000th cycle—for aqueous sodium‐ion batteries. Advanced structural analysis of the Ca0.07Na0.26MnO2 material using X‐ray diffraction and ab initio calculations identify the calcium sites and indicate a plausible sodium diffusion mechanism. Calcium preferentially substitutes at the Na(1) sites among the three different types of Na sites. This substitution creates …

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Oct 2020 • Nano letters

Cathodoluminescence nanoscopy of 3D plasmonic networks

Racheli Ron, Marcin Stefan Zielinski, Adi Salomon

Nanoporous metallic networks are endowed with the distinctive optical properties of strong field enhancement and spatial localization, raising the necessity to map the optical eigenmodes with high spatial resolution. In this work, we used cathodoluminescence (CL) to map the local electric fields of a three-dimensional (3D) silver network made of nanosized ligaments and holes over a broad spectral range. A multitude of neighboring hotspots at different frequencies and intensities are observed at subwavelength distances over the network. In contrast to well-defined plasmonic structures, the hotspots do not necessarily correlate with the network morphology, emphasizing the complexity and energy dissipation through the network. In addition, we show that the inherent connectivity of the networked structure plays a key optical role because a ligament with a single connected linker shows localized modes whereas an …

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Oct 2020 • Ultrasonics Sonochemistry

Ultrasonic assisted synthesis of styrylpyridinium dyes: Optical properties and DFT calculations

Abed Saady, Pagidi Sudhakar, Molhm Nassir, Aharon Gedanken

The ultrasonic technique has received considerable attention in several fields; in particular, it gained rapid momentum in organic synthesis due to the larger reaction rates, milder reaction conditions, and better yields. We report herein a facile synthesis of a series of styrylpyridinium based dyes under ultrasonic irradiation. Within short reaction time (15 min) under ultrasonic irradiation, compared to normal laboratory conditions, (4–16 h), we can achieve good to excellent yields. The reaction time is shortened because ultrasound can accelerate the generation of the nucleophile of the pyridinium salt and subsequently a nucleophilic addition of an aldehyde followed by dehydration affords the styrylpyridinium dye, (Knoevenagel condensation). The photophysical properties of all compounds are comprehensively investigated in different solvents. All the compounds exhibit negative solvatochromism both in absorption and …

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Oct 2020 • Current Opinion in Systems Biology 24, 100-108, 2020

Germline immunoglobulin genes: disease susceptibility genes hidden in plain sight?

Andrew M Collins, Gur Yaari, Adrian J Shepherd, William Lees, Corey T Watson

Immunoglobulin genes are rarely considered as disease susceptibility genes despite their obvious and central contributions to immune function. This appears to be a consequence of historical views on antibody repertoire formation that no longer stand, and of difficulties that until recently surrounded the documentation of the suite of antibody genes in any individual. If these important genes are to be accessible to GWAS studies, allelic variation within the human population needs to be better documented, and a curated set of genomic variations associated with antibody genes needs to be formulated. Repertoire studies arising from the COVID-19 pandemic provide an opportunity to meet these needs, and may provide insights into the profound variability that is seen in outcomes to this infection.

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Oct 2020 • Desalination

Thermally reduced graphene oxide as an electrode for CDI processes: A compromise between performance and scalability?

Ayelet Kalfa, Tirupathi Rao Penki, Izaak Cohen, Netanel Shpigel, Eran Avraham, Doron Aurbach, Dawei Liang, Qinghao Wu, Haining Wang, Yan Xiang

Capacitive deionization (CDI) is an alternative water desalination technology, which was investigated extensively in the last decade. The choice of electrodes' materials plays a major role in the electrosorption performance, affecting the whole desalination process. Graphene-based nanostructures in various types were extensively studied owing to their superior inherent physico-chemical properties. Whereas excellent electrosorption performance was reported – expressed in terms of salt adsorption capacity (SAC) or average salt adsorption rate (ASAR) – the cost-benefit of graphene-based electrodes, considering total production cost and much lower price of commercial activated carbon, is still controversial.Here, we explore partially exfoliated thermally reduced graphene oxide (GO) – denoted as PE-rGO – prepared by scalable low-temperature thermal exfoliation of GO under air atmosphere. PE-rGO displays a …

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Oct 2020 • Current opinion in biotechnology 65, 248-258, 2020

Enzymatic control of product distribution in terpene synthases: insights from multiscale simulations

Keren Raz, Shani Levi, Prashant Kumar Gupta, Dan Thomas Major

In this opinion, we review some recent work on terpene biosynthesis using multiscale simulation approaches, with special focus on contributions from our group. Terpene synthases generate terpenes employing rich carbocation chemistry, including highly specific ring formations, proton, hydride, methyl, and methylene migrations, followed by reaction quenching. In these enzymes, the main catalytic challenge is not rate enhancement, but rather control of intrinsically reactive carbocations and the resulting product distribution. Herein, we review multiscale simulations of selected mono-, sesqui-, and diterpene synthases. We point to the many tools adopted by terpene synthases to achieve correct substrate fold, carbocation formation, carbocation reaction environment, and reaction quenching. A better understanding of the toolbox employed by terpene synthases is expected to aid in the search for new enzymatic and …

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Oct 2020 • ACS omega

Mechanism underlying the emission of gases during the low-temperature oxidation of bituminous and lignite coal piles: The involvement of radicals

Tze’ela Taub, Aviv Hassid, Sharon Ruthstein, Haim Cohen

Coal is one of the major fuels for power generation, and it will continue in this capacity for the next several decades. Two types of coal are mainly used: lignite and bituminous coals. When exposed to air, post-mining, the coal surface undergoes LTO (low-temperature oxidation) at RT-150 °C according to the atmospheric oxygen level. The LTO process decreases the calorific value of the coal, and consequently, different gases are released [mainly carbon oxides (CO, CO2), water vapor, hydrogen (H2), and also some low molecular-weight organic gases (C1–5)]. Some of these gases are toxic and flammable. In extreme cases, fires erupt. The mechanism by which the molecular oxygen oxidizes the coal macromolecule at the temperature range of 30–150 °C (LTO process) is complex and also involves a chain of radical reactions that take place; however, the exact underlying mechanism is not yet clear. The LTO …

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Oct 2020 • Nano letters

The scattering of gold nanorods combined with differential uptake, paving a new detection method for macrophage subtypes using flow cytometery

R Chakraborty, D Leshem-Lev, R Kornowski, D Fixler

The strategy of identification for M1 and M2 macrophages both in vivo and in vitro would help to predict the health condition of the individual. Here, we introduced a solution to this problem with the advantage of both the phagocytic nature of macrophages and the scattering effect of gold nanorods (GNRs). The internalized GNRs, relating to their extent of intake, caused a conspicuous scattering profile at the red channel in flow cytometry, overruling the contribution of the cellular side scatters. This internalization is solely governed by the surface chemistry of GNRs. The PAH-GNRs showed maximum intake potency followed by Cit-, PSS-, and PEG-GNRs. On a substantial note, PAH-GNRs lead to differential uptake between M1 and M2 cells, with three times higher intake in M2 cells over M1. This is the first report of employing the scattering of unlabeled GNRs to discriminate M1 and M2 cell types using a flow cytometer.

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