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Feb 2019 • Multiphoton Microscopy in the Biomedical Sciences XIX 10882, 70-77, 2019

Phasor-based widefield FLIM using a gated 512× 512 single-photon SPAD imager

Arin Can Ulku, Claudio Bruschini, Ivan Michel Antolovic, Shimon Weiss, Xavier Michalet, Edoardo Charbon

Single-photon avalanche diode (SPAD) imagers can perform fast time-resolved imaging in a compact form factor, by exploiting the processing capability and speed of integrated CMOS electronics. Developments in SPAD imagers have recently made them compatible with widefield microscopy, thanks to array formats approaching one megapixel and sensitivity and noise levels approaching those of established technologies. In this paper, phasor-based FLIM is demonstrated with a gated binary 512×512 SPAD imager, which can operate with a gate length as short as 5.75 ns, a minimum gate step of 17.9 ps, and up to 98 kfps readout rate (1-bit frames). Lifetimes of ATTO 550 and Rhodamine 6G (R6G) solutions were measured across a 472×256 sub-array using phasor analysis, acquiring data by shifting a 13.1 ns gate window across the 50 ns laser period. The measurement accuracy obtained when employing such …

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Feb 2019 • Biophysical Journal

Cusp Artifacts in High Order Superresolution Optical Fluctuation Imaging (SOFI)

Xiyu Yi, Shimon Weiss

Since its introduction, Super-resolution Optical Fluctuation Imaging (SOFI) has attracted interest due to its simplicity and affordability. Many applications, methodology enhancements, and derivative methods have since been introduced. One of the most important and attractive features of SOFI is its high order cumulant image reconstruction, which could potentially yield unlimited resolution enhancement.Practical application of high order (higher than 4) SOFI has been, however, limited. The reasons for such limitation have never been fully understood (nor fully discussed). In this work, careful analysis of the artifacts of high order SOFI cumulants is provided. We have identified that there is a portion of highly non-intuitive artifacts (dubbed here as ‘cusp’artifacts) hidden in the high order SOFI cumulants, which have been overlooked in previous studies. A series of realistic simulations were performed to study cusp …

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Feb 2019 • ECS Meeting Abstracts

(Keynote) Updates in Non-Aqueous Mg Electrochemistry, Biu Corner.

Doron Aurbach

Developing practical rechargeable magnesium batteries (RMB) is very attractive. The first rechargeable magnesium battery prototype was demonstrated almost two decade ago. It comprised magnesium metal anode, Mo6S8 Chevrel phase cathode, and complex ethereal solutions that included THF or glymes and ionic organo-metallic species formed by complicated reactions between a RnMgCl2-n Lewis base and an AlClnR3-n Lewis acid (R = alkyl or aryl groups). These prototypes exhibited very prolonged cycle life at 100% cycling efficiency (no side reactions). However the low abundance of molybdenum and the low energy density (1.1V, 120mAh/g cathode capacity) avoided any practical development of these first systems. Unfortunately, we are not aware of any practically promising RMB that that could show better electrochemical performance that the 19 years old first prototype. A main challenge related to …

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Feb 2019 • Journal of The Electrochemical Society

The Ratio between the Surface Charge and Electrode's Capacitance as a Fast Tool for Assessing the Charge Efficiency in Capacitive Deionization Processes

Ayelet Kalfa, Izaak Cohen, Eran Avraham, Doron Aurbach

This paper suggests an effective approach to evaluate carbon electrodes that can be effective in capacitive de-ionization processes of salty aqueous solutions. The first assessment of any electrode material, before its assembly in a CDI cell, includes its specific capacitance and its electric conductivity among other physical properties. These properties may bring a sense whether the electrode can be suitable for electro-adsorption processes, but can hardly tell about the efficiency of the process which is related to the charge utilization. A new term is discussed-the ratio between the specific capacity of an electrode and the specific charge related to the electrode's surface groups. A close inspection of the amphoteric modified Donnan model of the electric double layer shows that the ratio between the surface charge density and the integral specific capacitance, namely, the overall charge density, of the carbon electrodes …

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Feb 2019 • Nano letters

Comparing transcriptome profiles of neurons interfacing adjacent cells and nanopatterned substrates reveals fundamental neuronal interactions

Koby Baranes, Dror Hibsh, Sharon Cohen, Tony Yamin, Sol Efroni, Amos Sharoni, Orit Shefi

Developing neuronal axons are directed by chemical and physical signals toward a myriad of target cells. According to current dogma, the resulting network architecture is critically shaped by electrical interconnections, the synapses; however, key mechanisms translating neuronal interactions into neuronal growth behavior during network formation are still unresolved. To elucidate these mechanisms, we examined neurons interfacing nanopatterned substrates and compared them to natural interneuron interactions. We grew similar neuronal populations under three connectivity conditions, (1) the neurons are isolated, (2) the neurons are interconnected, and (3) the neurons are connected only to artificial substrates, then quantitatively compared both the cell morphologies and the transcriptome-expression profiles. Our analysis shows that whereas axon-guidance signaling pathways in isolated neurons are …

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Feb 2019 • Journal of The Electrochemical Society

Introduction to the focus issue on selected papers from IMLB 2018

Doron Aurbach

There is no doubt that Li-ion batteries are the most important and impressive success of modern electrochemistry. Commercialization of high energy density primary Li metal-based batteries more than 40 years ago promoted development of rechargeable Li-ion batteries, which became a practical reality during the 1990s. Because Li-ion batteries now power most of our mobile electronic devices, and because those devices are used for so many things, it is difficult to imagine our daily lives without rechargeable Li-ion batteries. Increasing our confidence in this technology from all points of view has led to improvement in their durability, energy content, safety, and is now promoting intensive ongoing efforts to develop Li-ion batteries for electrochemical propulsion. In fact, thanks to recent development in this field, electro-mobility is no longer just a dream. We face here a revolution in ground transportation that promotes …

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Feb 2019 • arXiv preprint arXiv:1903.00043

Experimental Observation of Acceleration-Induced Thermality

Morgan H Lynch, Eliahu Cohen, Yaron Hadad, Ido Kaminer

We examine the radiation emitted by high-energy positrons channeled into silicon crystal samples. The positrons are modeled as semiclassical vector currents coupled to an Unruh-DeWitt detector to incorporate any local change in the energy of the positron. In the subsequent accelerated QED analysis, we discover a Larmor formula and power spectrum that are both thermalized by the acceleration. Thus, these systems explicitly exhibit thermalization of the detector energy gap at the celebrated Fulling-Davies-Unruh (FDU) temperature. Our derived power spectrum, with a nonzero energy gap, is then shown to have an excellent statistical agreement with high-energy channeling experiments and also provides a method to directly measure the FDU temperature. We also investigate the Rindler horizon dynamics and confirm that the Bekenstein-Hawking area-entropy law is satisfied in these experiments. As such, we …

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Feb 2019 • Journal of immunological methods

A primer set for comprehensive amplification of V-genes from rhesus macaque origin based on repertoire sequencing

Ronit Rosenfeld, Anat Zvi, Eitan Winter, Ronen Hope, Ofir Israeli, Ohad Mazor, Gur Yaari

Recombinant antibodies serve as therapeutic molecules for a broad range of applications. High affinity antibodies are typically isolated following an active and effective immunization. Human-like antibodies may be obtained from immunized nonhuman primates (NHP), such as rhesus macaque, when immunized human origin is not available. For the isolation of such antibodies, strategies like phage and yeast display, are employed. These strategies are primarily based on the amplification of the rearranged variable (V) regions coded by mRNA, obtained from lymphatic source of immunized animals. To amplify these genomic sequences, designated set of primers are required, ideally covering the immune animal V-gene repertoire. Such primer sets are commonly designed based on the germline repertoire of specific animals according to immunoglobulin databases. However, In case of rhesus macaque, however, the …

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Feb 2019 • Elife

Macrophages restrict the nephrogenic field and promote endothelial connections during kidney development

David AD Munro, Yishay Wineberg, Julia Tarnick, Chris S Vink, Zhuan Li, Clare Pridans, Elaine Dzierzak, Tomer Kalisky, Peter Hohenstein, Jamie A Davies

The origins and functions of kidney macrophages in the adult have been explored, but their roles during development remain largely unknown. Here we characterise macrophage arrival, localisation, heterogeneity, and functions during kidney organogenesis. Using genetic approaches to ablate macrophages, we identify a role for macrophages in nephron progenitor cell clearance as mouse kidney development begins. Throughout renal organogenesis, most kidney macrophages are perivascular and express F4/80 and CD206. These macrophages are enriched for mRNAs linked to developmental processes, such as blood vessel morphogenesis. Using antibody-mediated macrophage-depletion, we show macrophages support vascular anastomoses in cultured kidney explants. We also characterise a subpopulation of galectin-3+ (Gal3+) myeloid cells within the developing kidney. Our findings may stimulate research into macrophage-based therapies for renal developmental abnormalities and have implications for the generation of bioengineered kidney tissues.

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Feb 2019 • Nature communications

Mosaic deletion patterns of the human antibody heavy chain gene locus shown by Bayesian haplotyping

Moriah Gidoni, Omri Snir, Ayelet Peres, Pazit Polak, Ida Lindeman, Ivana Mikocziova, Vikas Kumar Sarna, Knut EA Lundin, Christopher Clouser, Francois Vigneault, Andrew M Collins, Ludvig M Sollid, Gur Yaari

Analysis of antibody repertoires by high-throughput sequencing is of major importance in understanding adaptive immune responses. Our knowledge of variations in the genomic loci encoding immunoglobulin genes is incomplete, resulting in conflicting VDJ gene assignments and biased genotype and haplotype inference. Haplotypes can be inferred using IGHJ6 heterozygosity, observed in one third of the people. Here, we propose a robust novel method for determining VDJ haplotypes by adapting a Bayesian framework. Our method extends haplotype inference to IGHD-and IGHV-based analysis, enabling inference of deletions and copy number variations in the entire population. To test this method, we generated a multi-individual data set of naive B-cell repertoires, and found allele usage bias, as well as a mosaic, tiled pattern of deleted IGHD and IGHV genes. The inferred haplotypes may have clinical …

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Feb 2019 • Optics Express

Interaction-free ghost-imaging of structured objects

Yingwen Zhang, Alicia Sit, Frédéric Bouchard, Hugo Larocque, Florence Grenapin, Eliahu Cohen, Avshalom C Elitzur, James L Harden, Robert W Boyd, Ebrahim Karimi

Quantum – or classically correlated – light can be employed in various ways to improve resolution and measurement sensitivity. In an “interaction-free” measurement, a single photon can be used to reveal the presence of an object placed within one arm of an interferometer without being absorbed by it. With a technique known as “ghost-imaging”, entangled photon pairs are used for detecting an opaque object with significantly improved signal-to-noise ratio while preventing over-illumination. Here, we integrate these two methods to obtain a new imaging technique which we term “interaction-free ghost-imaging” (IFGI). With this new technique, we reduce photon illumination on the object by up to 26.5% while still maintaining at least the same image quality of conventional ghost-imaging. Alternatively, IFGI can improve image signal-to-noise ratio by 18% when given the same number of interacting photons as in …

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Feb 2019 • Proceedings of the National Academy of Sciences

Illuminating spatial A-to-I RNA editing signatures within the Drosophila brain

Anne L Sapiro, Anat Shmueli, Gilbert Lee Henry, Qin Li, Tali Shalit, Orly Yaron, Yoav Paas, Jin Billy Li, Galit Shohat-Ophir

Adenosine-to-inosine (A-to-I) RNA editing, catalyzed by ADAR enzymes, is a ubiquitous mechanism that generates transcriptomic diversity. This process is particularly important for proper neuronal function; however, little is known about how RNA editing is dynamically regulated between the many functionally distinct neuronal populations of the brain. Here, we present a spatial RNA editing map in the Drosophila brain and show that different neuronal populations possess distinct RNA editing signatures. After purifying and sequencing RNA from genetically marked groups of neuronal nuclei, we identified a large number of editing sites and compared editing levels in hundreds of transcripts across nine functionally different neuronal populations. We found distinct editing repertoires for each population, including sites in repeat regions of the transcriptome and differential editing in highly conserved and likely functional …

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Feb 2019 • Optics letters

Phase retrieval by an array of overlapping time-lenses

Hamootal Duadi, Tomer Yaron, Avi Klein, Sara Meir, Moti Fridman

Temporal imaging of both the intensity and the phase is important for investigating ultra-short events such as rogue waves or mode-locked laser dynamics in a record high resolution. We developed a temporal phase retrieval scheme based on several overlapping time-lenses, where all the time-lenses use the same fibers and detectors leading to high stability and low noise levels. We show that our phase retrieval technique converges faster than techniques that resort to a single time-lens, together with the Fourier transform of the signal.

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Feb 2019 • Journal of colloid and interface science

Directed assembly of nanoparticles into continuous microstructures by standing surface acoustic waves

Haim Sazan, Silvia Piperno, Michael Layani, Shlomo Magdassi, Hagay Shpaisman

Directed-assembly by standing surface acoustic waves (SSAWs) only requires an acoustic contrast between particles and their surrounding medium. It is therefore highly attractive as this requirement is fulfilled by almost all dispersed systems. Previous studies utilizing SSAWs demonstrated mainly reversible microstructure arrangements from nanoparticles. The surface chemistry of colloids dramatically influences their tendency to aggregate and sinter; therefore, it should be possible to form permanent microstructures with intimate contact between nanoparticles by controlling this property.Dispersed silver nanoparticles in a microfluidic channel were exposed to SSAWs and reversibly accumulated at the pressure nodes. We show that addition of chloride ions that remove the polyacrylic capping of the nanoparticles trigger their sintering and the formation of stable conducting silver microstructures. Moreover, if the …

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Feb 2019 • Scientific reports

Cardioprotection from stress conditions by weak magnetic fields in the Schumann Resonance band

G Elhalel, C Price, D Fixler, A Shainberg

The Schumann Resonances (ScR) are Extremely Low Frequency (ELF) electromagnetic resonances in the Earth-ionosphere cavity excited by global lightning discharges. This natural electromagnetic noise has likely existed on the Earth ever since the Earth had an atmosphere and an ionosphere, hence surrounding us throughout our evolutionary history. The purpose of this study was to examine the influence of extremely weak magnetic fields in the ScR first mode frequency range on the spontaneous contractions, calcium transients and Creatine Kinase (CK) release of rat cardiac cell cultures. We show that applying 7.8 Hz, 90 nT magnetic fields (MF) causes a gradual decrease in the spontaneous calcium transients’ amplitude, reaching 28% of the initial amplitude after 40 minutes of MF application, and accompanied with a gradual decrease in the calcium transients’ rise time. The mechanical spontaneous …

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Feb 2019 • Frontiers in immunology

Identification of subject-specific immunoglobulin alleles from expressed repertoire sequencing data

Daniel Gadala-Maria, Moriah Gidoni, Susanna Marquez, Jason A Vander Heiden, Justin T Kos, Corey T Watson, Kevin C O'Connor, Gur Yaari, Steven H Kleinstein

The adaptive immune receptor repertoire (AIRR) contains information on an individuals' immune past, present and potential in the form of the evolving sequences that encode the B cell receptor (BCR) repertoire. AIRR sequencing (AIRR-seq) studies rely on databases of known BCR germline variable (V), diversity (D) and joining (J) genes to detect somatic mutations in AIRR-seq data via comparison to the best-aligning database alleles. However, it has been shown that these databases are far from complete, leading to systematic misidentification of mutated positions in subsets of sample sequences. We previously presented TIgGER, a computational method to identify subject-specific V gene genotypes, including the presence of novel V gene alleles, directly from AIRR-seq data. However, the original algorithm was unable to detect alleles that differed by more than 5 single nucleotide polymorphisms (SNPs) from a database allele. Here we present and apply an improved version of the TIgGER algorithm which can detect alleles that differ by any number of SNPs from the nearest database allele, and can construct subject-specific genotypes with minimal prior information. TIgGER predictions are validated both computationally (using a leave-one-out strategy) and experimentally (using genomic sequencing), resulting in the addition of three new immunoglobulin heavy chain V (IGHV) gene alleles to the IMGT repertoire. Finally, we develop a Bayesian strategy to provide a confidence estimate associated with genotype calls. All together, these methods allow for much higher accuracy in germline allele assignment, an essential step in AIRR-seq studies.

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Feb 2019 • International Society for Optics and Photonics

Tunable prism based upon novel piezoelectric nanoparticle/sol-gel design used for active solar cells concentrators

Gilad Rachamim, Margarita Ritenberg, Raz Jelinek, Zeev Zalevsky

Active solar concentrators attract significant interest in photovoltaic (PV) research activity since they can substantially reduce the area of PV cells while still collecting significant amount of solar energy via large aperture collecting optics. Solar concentrators include lenses or curved mirrors directing light from the sun into a smaller spatial spot falling on the PV cell. However, the main problem of active concentrators, severely limiting their practicality, is the high cost and low angular accuracy of sun tracking apparatuses. Specifically, tracking of the sun in existing concentrators is currently done through elaborate and expensive mechanical/optical systems, which exhibit lower performance over time and require energy input by themselves. In this paper we develop a novel active solar concentrator without any mechanical tracking. We aim to accomplish this goal through designing tunable prisms via novel chemical system …

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Feb 2019 • WILEY

FLOW SENSING IN-DEPTH OF A TISSUE VIA ANALYSIS OF THE SPATIAL STATISTICS OF THE BACK SCATTERED LASER ILLUMINATION

Mark Goldberg, Ran Califa, Sagi Polani, Javier Garcia-Monreal, Zeev Zalevsky


Feb 2019 • International Society for Optics and Photonics

Bio-sensor based on multiclass support vector machine with a reject option

Stav Buchsbaum, Yossi Keshet, Nisan Ozana, Zeev Zalevsky

In this work we explore the problem of multiclass classification where the classifier may abstain from classifying on some observation. We derivate a new surrogate loss function and a multiclass decision rule by using a reject threshold on posterior probabilities in the Bayes decision rule, known as Chow's rule. The goal of the decision rule is to minimize the value of given misprediction and rejection cost functions specified by the user. We suggest a general training algorithm by plug-in the surrogate loss in to Support Vector Machine (SVM) structure. We then test the algorithm on various real -life problem in the photonic medical sensing field where accuracy is critical. We present an example of a non-invasive way of detecting glucose level in blood to help patients with Diabetes mellitus diseases while the sensing is performed with speckle-based approach to analyze remote sensing of biomedical parameters. The …

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Feb 2019 • Physical Review A

Structured quantum projectiles

Hugo Larocque, Robert Fickler, Eliahu Cohen, Vincenzo Grillo, Rafal E Dunin-Borkowski, Gerd Leuchs, Ebrahim Karimi

Matter wave interferometry is becoming an increasingly important technique in quantum metrology. However, unlike its photonic counterpart, this technique relies on the interference of particles possessing a nonzero rest mass and an electric charge. Matter waves can therefore experience alterations in their wavelike features while propagating through uniform fields to which a linear potential can be attributed, eg, the Newtonian gravitational potential. Here, we derive the propagation kernel attributed to matter waves within such a potential. This kernel thereafter allows us to provide analytical formulations for structured matter waves subjected to a linear potential. Our formulations are in agreement with both the classical dynamics attributed to such waves and with previous interferometry experiments. Eigenbasis representations of structured matter waves are also introduced along with their application to enhanced …

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Feb 2019 • JOSA B

Signal-dependent pump-to-probe noise transfer due to Kerr nonlinearity in silicon ring resonators

Tomer Yeminy, Zeev Zalevsky, Dan Sadot

The pump-probe configuration has been extensively implemented in silicon ring resonators (RRs) for all-optical switching and wavelength conversion. While the pump’s influence on the probe’s signal is well known, the effect of the pump on the probe’s noise has not been studied. Here, we analytically and numerically analyze the impact of the pump’s signal and noise on the probe’s noise distribution. We show that the probe’s output noise has two sources: the probe’s input noise passing through the RR’s transfer function and a new noise term generated by the RR’s transfer function fluctuations caused by the pump’s noise via the Kerr effect. Furthermore, this pump-induced noise can significantly reduce the probe’s output optical signal-to-noise ratio by up to 15 dB. As the new noise term strongly depends on the pump’s power, wavelength conversion of optical communications signals with amplitude modulation …

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