BINA

4691 articles

79 publishers

Join mailing list

Dec 2025 • Methods in enzymology 713, 255-270, 2025

Global quantification of off-target activity by base editors

Michelle Eidelman, Eli Eisenberg, Erez Y Levanon

Base editors are engineered deaminases combined with CRISPR components. These engineered deaminases are designed to target specific sites within DNA or RNA to make a precise change in the molecule. In therapeutics, they hold promise for correcting mutations associated with genetic diseases. However, a key challenge is minimizing unintended edits at off-target sites, which could lead to harmful mutations. Researchers are actively addressing this concern through a variety of optimization efforts that aim to improve the precision of base editors and minimize off-target activity. Here, we examine the various types of off-target activity, and the methods used to evaluate them. Current methods for finding off-target activity focus on identifying similar sequences in the genome or in the transcriptome, assuming the guide RNA misdirects the editor. The main method presented here, that was originally developed to …

Show more

Nov 2025 • arXiv preprint arXiv:2311.00845

Floquet engineering with spatially nonuniform driving fields

Stella Tallula Schindler, Hanan Herzig Sheinfux

We generalize the scope of Floquet engineering to include spatially-dependent modulations of an optical system. As an application, we show that we can transform large classes of Hamiltonians into one another by driving them in a time-periodic but spatially non-uniform manner. We propose several experimental realizations in 1D optical lattices, including freeing disordered lattices from Anderson localization, as well as effectively disconnecting all their sites. These techniques straightforwardly extend to more complex classes of systems.

Show more

Nov 2025 • ChemElectroChem

The Impact of Sinusoidal Amplitude on Visualising Thermodynamic Dispersion in Fourier Transformed AC Voltammetry

Alister R Dale-Evans, Nick Yates, Rifael Snitkoff-Sol, Lior Elbaz, Alan M Bond, David J Gavaghan, Alison Parkin

Mathematical models of voltammetric experiments commonly contain a singular point value for the reversible potential, whereas experimental data for surface-confined redox-active species is often interpreted to contain thermodynamic dispersion, meaning the population of molecules on the electrode possess a distribution of reversible potential values. Large amplitude ramped Fourier Transformed Alternating Current Voltammetry (FTacV), a technique in which a sinusoidal potential-time oscillation is overlaid onto a linear potential-time ramp, is known to provide access to higher order harmonic components that are largely devoid of non-Faradaic current. Initially, a theoretical study reveals that the use of very large amplitude sinusoidal oscillations reduces the apparent effects of thermodynamic dispersion; conversely, frequency can be varied to change the sensitivity of the measurement to kinetic dispersion. Subsequently, FTacV measurements are used to probe a highly thermodynamically dispersed surface-confined ferrocene derivative attached to a glassy carbon electrode, with amplitudes ranging from 25 to 300 mV and low frequency, which minimises the impact of kinetic dispersion. The results from the experimental study validate the theoretical predictions, demonstrating that we can vary the amplitude in FTacV experiments to tune in and out of thermodynamic dispersion.

Show more

Nov 2025 • arXiv preprint arXiv:2311.13915

First passage times in compact domains exhibit biscaling

Talia Baravi, Eli Barkai

The study of first passage times for diffusing particles reaching target states is foundational in various practical applications, including diffusion-controlled reactions. In this work, we present a bi-scaling theory for the probability density function of first passage times in confined compact processes, applicable to both Euclidean and Fractal domains, diverse geometries, and scenarios with or without external force fields, accommodating Markovian and semi-Markovian random walks. In large systems, first passage time statistics exhibit a bi-scaling behavior, challenging the use of a single time scale. Our theory employs two distinct scaling functions: one for short times, capturing initial dynamics in unbounded systems, and the other for long times is sensitive to finite size effects. The combined framework provides a complete expression for first passage time statistics across all time scales.

Show more

Nov 2025 • Optics & Laser Technology

Modulating incoherence for phase recovery with single-pixel intensity correlation

Tanushree Karmakar, Aditya Chandra Mandal, Prateek Agrawal, Zeev Zalevsky, Rakesh Kumar Singh

Recovery of missing phase information from the intensity correlation is crucial in various applications ranging from astronomy to biology. Interferometry and phase retrieval algorithms are common methods for phase recovery. Here, we present a non-interferometric and iteration-free approach for recovering the phase of the Fourier spectrum. This is implemented in an in-line configuration with a structured illumination and a single-pixel estimation of the intensity correlations. Instead of many temporal measurements, single exposure speckle is used to acquire the complex Fourier spectrum from the intensity correlation. Mapping of the complex Fourier spectrum is demonstrated by discretely varying the frequency of the structured illumination and then extracting the intensity correlations for a set of three phase-shifted structured illuminations at each frequency. Furthermore, the recovered Fourier spectrum is used to …

Show more

Oct 2025 • arXiv preprint arXiv:2410.07034

Exploring non-Euclidean photonics: Pseudosphere microlaser

H Girin, S Bittner, X Checoury, D Decanini, B Dietz, A Grigis, C Lafargue, J Zyss, C Xu, P Sebbah, M Lebental

Classical and wave properties of pseudosphere-shape microlasers are investigated through experiments and numerical simulations. These pseudosphere microlasers are surface-like organic microlasers with constant negative curvature, which were fabricated with high optical quality by direct laser writing. It is shown that they behave, in many ways, similar to two-dimensional flat disks, regardless of the different Gaussian curvature of the two systems. Indeed, it is evidenced that, due to rotational symmetry, the pseudosphere is an integrable system with marginally stable dynamics.

Show more

Oct 2025 • Electrochimica Acta 512, 145472, 2025

Boosting urea electro-oxidation activity by pairing nanoporous nickel with borate anions

Bibhudatta Malik, Johannes Bartl, Nophar Tubul, Hannah-Noa Barad

In this work, we elucidate the crucial role of borate anions ([B(OH)4]-) for the electrocatalytic urea oxidation reaction (UOR) using a nanoporous metallic nickel (NP-Ni) catalyst grown on Si substrates. The UOR activity of the NP-Ni catalyst has been studied at various boric acid (H3BO3) concentrations, demonstrating superior activity at a specific electrolytic composition of 0.5 M KOH, 0.33 M urea, and 50 mM of H3BO3. Based on a wide range of electrochemical techniques, such as, cyclic voltammetry (CV), linear sweep voltammetry (LSV), Pb-anodic deposition, and chronoamperometry (CA), we develop a potential mechanism for the [B(OH)4]--mediated UOR. The high double layer capacitance, surface density of Ni redox sites, and urea oxidation currents, clearly demonstrate the significant impact of [B(OH)4]- during electrolysis. Furthermore, we find that UOR catalyzed by the NP-Ni is controlled by diffusion both in presence and absence of [B(OH)4]-. Finally, a set of physical characterizations, including XPS, SEM, and TEM were performed to correlate the composition and structure of the NP-Ni to the [B(OH)4]--mediated increased UOR activity. The boosted UOR we obtain can open new avenues for treatment of wastewater and assist with environmental remediation.

Show more

Oct 2025 • arXiv preprint arXiv:2410.11264

Change in Magnetic Order in NiPS3 Single Crystals Induced by a Molecular Intercalation

Nirman Chakraborty, Adi Harchol, Azhar Abu-Hariri, Rajesh Kumar Yadav, Muhamed Dawod, Diksha Prabhu Gaonkar, Kusha Sharma, Anna Eyal, Yaron Amouyal, Doron Naveh, Efrat Lifshitz

Intercalation is a robust method for tuning the physical properties of a vast number of van der Waals (vdW) materials. However, the prospects of using intercalation to modify magnetism in vdWs systems and the associated mechanisms have not been investigated adequately. In this work, we modulate magnetic order in an XY antiferromagnet NiPS3 single crystals by introducing pyridine molecules into the vdWs gap under different thermal conditions. X-ray diffraction measurements indicated pronounced changes in the lattice parameter beta, while magnetization measurements at in-plane and out-of-plane configurations exposed reversal trends in the crystals Neel temperatures through intercalation-de-intercalation processes. The changes in magnetic ordering were also supported by three-dimensional thermal diffusivity experiments. The preferred orientation of the pyridine dipoles within vdW gaps was deciphered via polarized Raman spectroscopy. The results highlight the relation between the preferential alignment of the intercalants, thermal transport, and crystallographic disorder along with the modulation of anisotropy in the magnetic order. The theoretical concept of double-exchange interaction in NiPS3 was employed to explain the intercalation-induced magnetic ordering. The study uncovers the merit of intercalation as a foundation for spin switches and spin transistors in advanced quantum devices.

Show more

Sep 2025 • Angewandte Chemie 137 (5), e202418792, 2025

Formation of H2O2 in Near‐Neutral Zn‐air Batteries Enables Efficient Oxygen Evolution Reaction

Roman Kapaev, Nicole Leifer, Alagar Raja Kottaichamy, Amit Ohayon, Langyuan Wu, Menny Shalom, Malachi Noked

Rechargeable Zn-air batteries with near-neutral electrolytes hold promise as cheap, safe and sustainable devices, but they suffer from slow charge kinetics and remain poorly studied. Here we reveal a charge storage mechanism of near-neutral Zn-air batteries that is mediated by H2O2 formation upon cell discharge and its oxidation upon charge. The manifestation of this mechanism strongly depends on the electrolyte composition and positive electrode material, being pronounced when ZnSO4 solutions and carbon nanotubes are employed. Oxidation of dissolved H2O2 is facile, enabling oxygen evolution reaction (OER) at low potentials (~1.5 V vs. Zn2+/Zn) which, in contrast to conventional four-electron OER, does not induce corrosion of carbon electrodes. Facilitation of the H2O2-mediated pathway might therefore be helpful for developing high-performance near-neutral Zn-air batteries.

Show more

Sep 2025 • Optics & Laser Technology

Cascade time-lens

Sara Meir, Hamootal Duadi, Yuval Tamir, Moti Fridman

Temporal optics rises from the equivalence between light diffraction in free space and pulse dispersion in dispersive media, paving the way for the development of temporal devices and applications, such as time-lenses. A Four-wave mixing based time-lens allows single-shot measurements of ultra-short signals in high temporal resolution by imaging signals, and inducing temporal Fourier transform. We introduce a cascade time-lens by utilizing a cascade FWM process within the time-lens. We theoretically develop and experimentally demonstrate the cascade time-lens, and confirm that different cascade orders correspond to different effective temporal systems, leading to measuring in various temporal imaging configurations simultaneously with a single optical setup. This approach can simplify experiments and provide a more comprehensive view of a signal’s phase and temporal structure. Such capabilities are …

Show more

Aug 2025 • Small Methods 9 (4), 2401204, 2025

Protein Electronic Energy Transport Levels Derived from High‐Sensitivity Near‐UV and Constant Final State Yield Photoemission Spectroscopy

Jerry Alfred Fereiro, Masaki Tomita, Tatyana Bendikov, Sudipta Bera, Israel Pecht, Mordechai Sheves, David Cahen, Hisao Ishii

Proteins are attractive as functional components in molecular junctions. However, control-ling the electronic charge transport via proteins, held between two electrodes, requires in-formation on their frontier orbital energy level alignment relative to the electrodes’ Fermi level (EF), which normally requires studies of UV Photoemission Spectroscopy (UPS) with HeI excitation. Such excitation is problematic for proteins, which can denature under stand-ard measuring conditions. Here we use high-sensitivity soft UV photoemission spectroscopy (HS-UPS) combined with Constant Final State Yield Spectroscopy (CFS-YS) to get this in-formation for electrode/protein contacts. Monolayers of the redox protein Azurin, (Az) and its Apo-form on Au substrates, have HOMO onset energies, obtained from CFS-YS, differ by ~ 0.2 eV, showing crucial role of the Cu redox centre in the electron transport process. We find that combined HS-UPS / CFS-YS measurements agree with the Photoelectron Yield Spectroscopy (PYS), showing potential of the HS-UPS + CFS-YS as a powerful tool to char-acterize and map the energetics of a protein-electrode interfaces, which will aid optimizing design of devices with targeted electronic properties, as well as for novel applications.

Show more

Jul 2025 • arXiv preprint arXiv:2407.16598

A tale of three approaches: dynamical phase transitions for weakly bound Brownian particles

Lucianno Defaveri, Eli Barkai, David A Kessler

We investigate a system of Brownian particles weakly bound by attractive parity-symmetric potentials that grow at large distances as , with . The probability density function at long times reaches the Boltzmann-Gibbs equilibrium state, with all moments finite. However, the system's relaxation is not exponential, as is usual for a confining system with a well-defined equilibrium, but instead follows a stretched exponential with exponent . This problem is studied from three perspectives. First, we propose a straightforward and general scaling rate-function solution for . This rate-function, which is an important tool from large deviation theory, also displays anomalous time scaling and a dynamical phase transition. Second, through the eigenfunctions of the Fokker-Planck operator, we obtain, using the WKB method, more complete solutions that reproduce the rate function approach. Finally, we show how the alternative path-integral formalism allows us to recover the same results, with the above rate-function being the solution of the classical Hamilton-Jacobi equation describing the most probable path. Properties such as parity, the role of initial conditions, and the dynamical phase transition are thoroughly studied in all three approaches.

Show more

Jul 2025 • Journal of Power Sources

Oxygen and ion transporter co-polymer shell on silver oxygen reduction reaction catalyst in alkaline exchange membrane fuel cell

Anna Kitayev, Anya Muzikansky, Ervin Tal-Gutelmacher, David Zitoun

The intrinsic sluggishness of oxygen reduction reaction (ORR) limits the widespread adoption of low-temperature anion exchange membrane fuel cells (AEMFCs) technology, and effective ORR electrocatalysts and methods for ORR enhancement are needed. Herein, we investigate the mechanism behind the improvement of ORR activity of Ag electrocatalyst coated with a shell based on polydopamine (PDA) crosslinked with polyethylene imine (PEI) during AEMFC operation. We show a correlation between electrochemical and physical properties of the PDA/PEI Ag catalyst, with its performance within membrane-electrode assembly (MEA) in practical fuel cell operating environments. Higher current density observed in a catalytic region of polarization curve in AEMFC, matches the positive shift in the half-wave potential of ORR on Ag PDA/PEI as measured by rotating disc electrode (RDE) experiments. Additionally …

Show more

Jun 2025 • Molecular Metabolism

RNA editing deficiency models differential immunogenicity of pancreatic α-and β-cells

Shani Peleg, Liza Zamashanski, Jonathan Belin, Roy Novoselsky, Roni Cohen-Fultheim, Udi Ehud Knebel, Benjamin Glaser, Shalev Itzkovitz, Klaus H Kaestner, Alvin C Powers, Erez Y Levanon, Agnes Klochendler, Yuval Dor

A longstanding question in type 1 diabetes (T1D) research pertains to the selective loss of β-cells whilst neighboring islet α-cells remain unharmed. Here we demonstrate differential sensitivity of mouse α- and β-cells to deficient RNA editing, a cellular process that prevents double-stranded RNA (dsRNA)-mediated activation of a type I interferon (IFN) response. Mosaic disruption of the RNA editing enzyme Adar in mouse β-cells triggers a massive interferon response, islet inflammation and mutant β-cell destruction. Surprisingly, wild type β-cells are also eliminated while neighboring α-cells are unaffected. α-cell Adar deletion leads to only a slight elevation in interferon signature and does not elicit inflammation nor a metabolic phenotype. Concomitant deletion of Adar in α- and β-cells leads to elimination of both cell populations, suggesting that in contrast to β-cells, α-cell death requires both cell autonomous …

Show more

Jun 2025 • Science Translational Medicine

Germline-encoded recognition of peanut underlies development of convergent antibodies in humans

Orlee Marini-Rapoport, Léna Andrieux, Tarun Keswani, Guangning Zong, Dylan Duchen, Gur Yaari, Jungki Min, Isabelle R Lytle, Alexander F Rosenberg, Christopher Fucile, James J Kobie, Michael S Piepenbrink, Timothy Sun, Victoria M Martin, Qian Yuan, Wayne G Shreffler, Antti E Seppo, Kirsi M Järvinen, Johannes R Loeffler, Andrew B Ward, Steven H Kleinstein, Lars C Pedersen, Monica L Fernández-Quintero, Geoffrey A Mueller, Sarita U Patil

Humans develop immunoglobulin G (IgG) antibodies to the foods they consume. In the context of food allergy, allergen-specific IgG antibodies can sequentially class-switch to pathogenic IgE. However, the mechanism underlying the antigenicity of food proteins remains uncharacterized. Here, we identified convergent antibodies arising from different antibody gene rearrangements that bind to the immunodominant peanut allergen Ara h 2 and characterized allelic and junctional constraints on germline antibody specificity. Structurally, we found similar epitope-paratope interactions across multiple gene rearrangements. We demonstrate that these germline-encoded epitope-specific convergent antibodies to peanut occur commonly in the population because of the worldwide prevalence of the relevant gene rearrangements, allelic independence, and junctional malleability. As a result, serum IgG to this public epitope …

Show more

Jun 2025 • IEEE Transactions on Radar Systems

Advanced RCS Measurements Processing using Multi-Basis Dictionary Framework

Gavriel B Aminov, Zeev Zalevsky

Accurate extraction of Radar Cross Section (RCS) from real-world measurements is crucial for various radar applications yet challenged by noise, clutter, near-field effects, and complex scattering phenomena. This paper introduces the Dictionary Pursuit (DP) method based on Compressive Sensing (CS) principles and presents a comprehensive comparison with the classical Fourier-based approach. The DP method employs multiple physical bases—specifically Image and range-Doppler bases—to represent distinct scattering phenomena within a single optimization framework. By leveraging weighted L1-norm regularization through Basis Pursuit Denoising (BPDN), the proposed method effectively separates target signals from environmental contamination while reducing manual intervention requirements. Validation through both numerical simulations and experimental measurements demonstrates that the DP …

Show more

Jun 2025 • NAR cancer

A systematic evaluation of the therapeutic potential of endogenous-ADAR editors in cancer prevention and treatment

Rona Merdler-Rabinowicz, Ariel Dadush, Sumeet Patiyal, Padma Sheila Rajagopal, Gulzar N Daya, Shay Ben-Aroya, Alejandro A Schäffer, Eli Eisenberg, Eytan Ruppin, Erez Y Levanon

Adenosine deaminases acting on RNA (ADAR) enzymes constitute a natural cellular mechanism that induces A-to-I(G) editing, introducing genetic changes at the RNA level. Recently, interest in the endogenous-ADAR editor has emerged for correcting genetic mutations, consisting of a programmed oligonucleotide that attracts the native ADAR, thereby offering opportunities for medical therapy. Here, we systematically chart the scope of cancer mutations that endogenous-ADAR can correct. First, analyzing germline single nucleotide variants in cancer predisposition genes, we find that endogenous-ADAR can revert a fifth of them, reducing the risk of cancer development later in life. Second, examining somatic mutations across various cancer types, we find that it has the potential to correct at least one driver mutation in over a third of the samples, suggesting a promising future treatment strategy. We also …

Show more

Jun 2025 • IEEE Journal of Microwaves

Penetrating Barriers: Microwave-Based Remote Sensing and Reconstruction of Audio Signals Through Walls

Kobi Aflalo, Zeev Zalevsky

This study investigate the remote detection and reconstruction of audio signals using Radio Frequency (RF) emissions, focusing on the implications for eavesdropping detection and prevention. Utilizing the widely used 2.4 GHz continuous wave microwave radiation directed at a speaker membrane, we successfully reassembled human speech and music signals, demonstrating the feasibility of audio reconstruction in real-world scenarios. A series of denoising techniques, including Robust locally weighted scatterplot smoothing (LOWESS), Moving Median, and Wavelet Denoising, were evaluated for their effectiveness in enhancing signal quality, with performance metrics such as root mean square error (RMSE) and signal-to-noise ratio SNR employed for comparison. Our findings reveal that Wavelet denoising outperforms other methods in preserving the integrity of speech signals, while also highlighting the …

Show more

Jun 2025 • Journal of Biomedical Optics

Combined optical-electromechanical wearable sensors for cardiac health monitoring

Michal Katan, Rui MR Pinto, Shiran Arol-Wiegand, Bar Atuar, Alon Tzroya, Hamootal Duadi, KB Vinayakumar, Dror Fixler

Significance Integrating multiple biosensors improves the sensitivity and precision of physiological measurements in healthcare monitoring. By combining sensors that target different physiological parameters, a more comprehensive assessment of a subject’s health can be achieved. Aim We evaluate the performance of two biosensors for extracting cardiac parameters: a textile-based strain sensor for measuring respiratory rate and an optical sensor for measuring heart rate, , and respiratory rate. The objective is to determine optimal placement conditions for each sensor and assess their feasibility for integration into a single wearable system. Approach Two experimental setups were tested. In the first, the strain sensor was placed on the subject’s shirt, while the optical sensor was positioned on the external wrist. In the second, both sensors were placed on the chest, under the shirt. The accuracy and performance …

Show more

Jun 2025 • Nutrients

Application of PIXE for Tear Analysis: Impact of Mineral Supplementation on Iron and Magnesium Levels in Athletes

Tal Zobok, Yulia Sheinfeld, Basel Obied, Yoav Vardizer, Alon Zahavi, Yakov Rabinovich, Olga Girshevitz, Nahum Shabi, Dror Fixler, Nitza Goldenberg-Cohen

Background/Objectives: To evaluate the concentrations of trace elements in tear fluid among athletes using particle-induced X-ray emission (PIXE), and to assess the associations with gender, sports intensity, and nutritional supplement intake. Methods: In this cohort study, 84 athletes engaged in high- or low-intensity sports completed a demographic and supplement-use questionnaire. Tear samples were collected using Schirmer strips and analyzed for elemental composition with PIXE, a high-sensitivity technique suited for small biological samples. Multivariate and nonparametric statistical analyses were used to compare groups. Results: There were 46 males and 38 females, aged 17–63 years (mean 30.21 years). Tear phosphorus, potassium, and sulfur concentrations were higher in women than men and higher in women participating in low-intensity compared to high-intensity sports. Tear concentrations of magnesium were higher in men participating in high-intensity sports compared to low-intensity sports. They were higher in men than women regardless of supplement intake. Iron concentrations were higher in men than women only when neither group was taking supplements. Smoking had a slight inverse relationship to iron values. Iron levels were particularly high in men participating in intense sports and low in smokers. Magnesium supplements were associated with raised magnesium levels in tears. Conclusions: This study demonstrates an association between trace element levels in human tears and gender, sports intensity, and food supplement intake. PIXE enables the evaluation of trace element concentration in tears, which may …

Show more

Jun 2025 • Molecular Therapy Methods & Clinical Development

Precise measurement of CRISPR genome editing outcomes through single-cell DNA sequencing

Nechama Kalter, Saurabh Gulati, Michael Rosenberg, Qawer Ayaz, Joanne Nguyen, Shu Wang, Benjamin Schroeder, Chieh-Yuan Li, Ayal Hendel

Gene therapy for clinical applications necessitates a comprehensive, accurate, and precise measurement of gene-edited drug products. State-of-the-art pipelines for evaluating editing outcomes rely primarily on bulk sequencing approaches, which are limited to population-level assessment. Here, we leveraged Tapestri, a single-cell sequencing technology for an in-depth analysis of editing outcomes. Using this platform, we characterized the genotype of triple-edited cells simultaneously at more than 100 loci, including editing zygosity, structural variations, and cell clonality. Our findings revealed a unique editing pattern in nearly every edited cell, highlighting the importance of single-cell resolution measurement to ensure the highest safety standards.

Show more

logo
Articali

Powered by Articali

TermsPrivacy