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Oct 2020 • Ternary and Multinary Compounds, 67-70, 2020

Single crystal synchrotron X-ray diffraction of CuInSe2

Felix Frolow, Leonid Chernyak, David Cahen, Hanna Hallak, Jamal Gabboun, Åke Kvick, Heinz Graafsma

The structure of CuInSe2 was redetermined, using synchrotron X-radiation with 0.15Å wavelength, thus eliminating problems of uncertainties introduced by absorption corrections. This allowed us to look at the effect of subjecting crystals to strong electric fields, a process known to be able to type convert the material under relatively mild conditions. Proper refinement became possible after correcting for twinning. The main results are relatively high Cu temperature factors and significant electron density in octahedral interstitial sites. The main results of electric field application are a decrease in structure quality (increased R factor) and a slight increase in electron density on Cu sites. These preliminary results point to the need for further work with twin-free crystals.

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Oct 2020 • Scientific reports

Fibers-based temporal super-resolved imaging

Sagie Asraf, Moti Fridman, Zeev Zalevsky

In this paper we present a new technique for a fiber-based temporal super resolving system allowing to improve the resolution of a temporal imaging system. The proposed super resolving concept is based upon translating the field of view multiplexing method that is used to increase resolution in spatial imaging systems from the spatial domain to the temporal domain. In this paper, an optical realization of our proposed system is presented, using optical fibers and electro-optic modulators. In addition, we show how one can apply this method using low-rate electronics for the required modulation. We also show simulation results that demonstrate the high resolution accepted in our method compares to the basic temporal imaging system. Experimental results which demonstrate resolution improvement by a factor of 1.5 based on the proposed method are presented together with an additional experiment that shows the …

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Oct 2020 • Scientific reports

Fibers-based temporal super-resolved imaging

Sagie Asraf, Moti Fridman, Zeev Zalevsky

In this paper we present a new technique for a fiber-based temporal super resolving system allowing to improve the resolution of a temporal imaging system. The proposed super resolving concept is based upon translating the field of view multiplexing method that is used to increase resolution in spatial imaging systems from the spatial domain to the temporal domain. In this paper, an optical realization of our proposed system is presented, using optical fibers and electro-optic modulators. In addition, we show how one can apply this method using low-rate electronics for the required modulation. We also show simulation results that demonstrate the high resolution accepted in our method compares to the basic temporal imaging system. Experimental results which demonstrate resolution improvement by a factor of 1.5 based on the proposed method are presented together with an additional experiment that shows the …

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Oct 2020 • Royal Society of Chemistry, 2020

The sonochemical preparation of tungsten oxide nanoparticlesElectronic supplementary information (ESI) available: Table S1; elemental analysis values of the product of W (CO) 6 …

Yu Koltypin, SI Nikitenko, A Gedanken

Amorphous tungsten oxide has been prepared by ultrasound irradiation of a solution of tungsten hexacarbonyl W (CO) 6 in diphenylmethane (DPhM) in the presence of an Ar (80%) â O2 (20%) gaseous mixture at 90 ÂC. Heating this amorphous powder at 550 ÂC under Ar yields snowflake-like dendritic particles consisting of a mixture of monoclinic and orthorhombic WO2 crystals. Annealing of the as-prepared product in Ar at 1000 ÂC causes the formation of a WO2â WO3 mixture containing nanorods (around 50 nm in diameter) and packs of these nanorods. Heating the product in air for 3 hours leads to triclinic WO3 crystal formation, with a basic size of 50â 70 nm. The prepared oxides have been characterized by elemental analysis, X-ray powder diffraction measurements, FTIR spectroscopy, differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), transmission electron microscopy (TEM), scanning electron microscopy (SEM), and energy dispersive X-ray analysis (EDX).

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Oct 2020 • MBio

Sensing Host Arginine Is Essential for Leishmania Parasites’ Intracellular Development

Adele Goldman-Pinkovich, Sriram Kannan, Roni Nitzan-Koren, Madhu Puri, Harsh Pawar, Yael Bar-Avraham, Jacquelyn McDonald, Aakash Sur, Wen-Wei Zhang, Greg Matlashewski, Rentala Madhubala, Shulamit Michaeli, Peter J Myler, Dan Zilberstein

Arginine homeostasis in lysosomes is critical for the growth and metabolism of mammalian cells. Phagolysosomes of macrophages are the niche where the parasitic protozoan Leishmania resides and causes human leishmaniasis. During infection, parasites encounter arginine deprivation, which is monitored by a sensor on the parasite cell surface. The sensor promptly activates a mitogen-activated protein kinase 2 (MAPK2)-mediated arginine deprivation response (ADR) pathway, resulting in upregulating the abundance and activity of the Leishmania arginine transporter (AAP3). Significantly, the ADR is also activated during macrophage infection, implying that arginine levels within the host phagolysosome are limiting for growth. We hypothesize that ADR-mediated upregulation of AAP3 activity is necessary to withstand arginine starvation, suggesting that the ADR is essential for parasite intracellular development …

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Oct 2020 • Neuroinformatics

Axonal tree morphology and signal propagation dynamics improve interneuron classification

Netanel Ofer, Orit Shefi, Gur Yaari

Neurons are diverse and can be differentiated by their morphological, electrophysiological, and molecular properties. Current morphology-based classification approaches largely rely on the dendritic tree structure or on the overall axonal projection layout. Here, we use data from public databases of neuronal reconstructions and membrane properties to study the characteristics of the axonal and dendritic trees for interneuron classification. We show that combining signal propagation patterns observed by biophysical simulations of the activity along ramified axonal trees with morphological parameters of the axonal and dendritic trees, significantly improve classification results compared to previous approaches. The classification schemes introduced here can be utilized for robust neuronal classification. Our work paves the way for understanding and utilizing form-function principles in realistic neuronal …

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Oct 2020 • Earth Sci

The Impact of Atmospheric and Tectonic Constraints on Radon-222 and Carbon Dioxide Flow in Geological Porous Media-A Dozen-Year Research Summary. Front

H Zafrir, S Barbosa, E Levintal, N Weisbrod, Y Ben Horin, Z Zalevsky

Long-term monitoring of Rn-222 and CO2 at a depth of several dozen meter at the Sde-Eliezer site, located within one of the Dead Sea Fault Zone segments in northern Israel, has led to the discovery of the clear phenomenon that both gases are affected by underground tectonic activity along the Dead Sea Fault Zone. It may relate to pre-seismic processes associated with the accumulation and relaxation of lithospheric stress and strain producing earthquakes. This approach assumes that meteorological influences on physico-chemical parameters are limited at depth since its strength diminishes with the increase of the overlay layer thickness. Hence, the monitoring of natural gases in deep boreholes above the water table enables to reduce the climatic-induced periodic contributions, and thus to identify the specific portion of the radon signals that could be related to regional tectonic pre-seismic activity. The plausible pre-seismic local movement of the two gases at depthis identified by the appearance of discrete, random, non-cyclical signals, wider in time duration than 20 h and clearly wider than the sum of the width of the periodic diurnal and semidiurnal signals driven by ambient meteorological parameters. These non-cyclical signals may precede, by one day or more, a forthcoming seismic event. Hence, it is plausible to conclude that monitoring of any other natural gas that is present at depth may show a similar broadening signal and may serve as a precursor too. The necessary technical conditions enabling to distinguish between anomalous signals of gases that may be induced locally by pre-seismic processes at depth, and the relatively low …

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Oct 2020 • Current Opinion in Systems Biology 24, 109-119, 2020

Mining adaptive immune receptor repertoires for biological and clinical information using machine learning

Victor Greiff, Gur Yaari, Lindsay Cowell

The adaptive immune system stores invaluable information about current and past immune responses and may serve as an ultrasensitive biosensor. Given the immune system’s critical role in a wide variety of disease types, this has broad implications for biomedicine. Machine and deep learning is being leveraged to decipher how information is encoded in adaptive immune receptor repertoires to enable prediction from adaptive immune responses and fast-track vaccine, therapeutics, and diagnostics development. Recent advances include predicting the presence of immunity post-vaccination or infection, predicting the presence of disease, and designing antibody-based therapeutics. Outstanding challenges encompass increasing our knowledge of the feature space structure that encodes relevant immune information, addressing the lack of ground-truth-labeled data, and improving our handling of genetic and …

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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 • 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 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 • 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 • 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 • 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 • 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 • Nature communications

Increased RNA editing in maternal immune activation model of neurodevelopmental disease

Hadas Tsivion-Visbord, Eli Kopel, Ariel Feiglin, Tamar Sofer, Ran Barzilay, Tali Ben-Zur, Orly Yaron, Daniel Offen, Erez Y Levanon

The etiology of major neurodevelopmental disorders such as schizophrenia and autism is unclear, with evidence supporting a combination of genetic factors and environmental insults, including viral infection during pregnancy. Here we utilized a mouse model of maternal immune activation (MIA) with the viral mimic PolyI: C infection during early gestation. We investigated the transcriptional changes in the brains of mouse fetuses following MIA during the prenatal period, and evaluated the behavioral and biochemical changes in the adult brain. The results reveal an increase in RNA editing levels and dysregulation in brain development-related gene pathways in the fetal brains of MIA mice. These MIA-induced brain editing changes are not observed in adulthood, although MIA-induced behavioral deficits are observed. Taken together, our findings suggest that MIA induces transient dysregulation of RNA editing at a …

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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 • 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 • 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 • 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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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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