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2024 • bioRxiv

An unbiased comparison of immunoglobulin sequence aligners

Thomas Konstantinovsky, Ayelet Peres, Pazit Polak, Gur Yaari

Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) is critical for our understanding of the adaptive immune system's dynamics in health and disease. Reliable analysis of AIRR-seq data depends on accurate Immunoglobulin (Ig) sequence alignment. Various Ig sequence aligners exist, but there is no unified benchmarking standard representing the complexities of AIRR-seq data, obscuring objective comparisons of aligners across tasks. Here, we introduce GenAIRR, an efficient simulation framework for generating Ig sequences alongside their ground truths. GenAIRR realistically simulates the intricacies of V(D)J recombination, somatic hypermutation, and an array of sequence corruptions. We comprehensively assessed prominent Ig sequence aligners across various metrics, unveiling unique performance characteristics for each aligner. The GenAIRR-produced datasets, combined with the proposed rigorous evaluation criteria, establish a solid basis for unbiased benchmarking of immunogenetics computational tools. It sets up the ground for further improving the crucial task of Ig sequence alignment, ultimately enhancing our understanding of adaptive immunity.

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2024 • Advanced Quantum Technologies

Photon Number Splitting Attack–Proposal and Analysis of an Experimental Scheme

Ariel Ashkenazy, Yuval Idan, Dor Korn, Dror Fixler, Barak Dayan, Eliahu Cohen

Photon‐number‐splitting (PNS) is a well‐known theoretical attack on quantum key distribution (QKD) protocols that employ weak coherent states produced by attenuated laser pulses. However, beyond the fact that it has not yet been demonstrated experimentally, its plausibility and effect on quantum bit error rate are questioned. In this work, an experimental scheme is presented for PNS attack employing demonstrated technological capabilities, specifically a single‐photon Raman interaction (SPRINT) in a cavity‐enhanced three‐level atomic system. Several aspects of the proposed implementation are addressed, analytically and simulatively, and the eavesdropper's information gain by the attack is calculated. Furthermore, it is analytically shown that the scheme results in a small (yet non‐zero) quantum bit error rate, and a comparison to purely theoretical analyses in the literature is presented. It is believed that the …

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Dec 2023 • Nature Catalysis

Modifying Fe–N interaction to boost catalytic performance

Ulrike I Kramm, Lior Elbaz

Iron–nitrogen–carbon (FeNC) catalysts are a viable alternative to platinum, but still lack the necessary performance. Now, pyrolysis under forming gas is found as a path to boosting their site density, activity and durability.

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Dec 2023 • EJIFCC

A novel score-based approach by using routine laboratory tests for accurate diagnosis of spontaneous bacterial peritonitis (SBP) in cirrhotic patients

George Abdo, Uri Nir, Rasha Rawajdey, Wadie Abu Dahoud, Jammal Massalha, Taleb Hajouj, Mohammad H Assadi, Nseir William

BackgroundSpontaneous Bacterial Peritonitis (SBP) poses a significant risk to cirrhosis patients with ascites, emphasizing the critical need for early detection and intervention. This retrospective observational study spanning a decade aimed to devise predictive models for SBP using routine laboratory tests. Additionally, it aimed to propose a novel scoring system to aid SBP diagnosis.MethodsData analysis encompassed 229 adult cirrhotic patients hospitalized for ascites between 2012 and 2021. Exclusions eliminated cases of secondary ascites unrelated to liver cirrhosis. Patients were categorized into SBP-positive (n= 110) and SBP-negative (n= 119) groups. Comparative analysis of demographic details and various laboratory indicators (Neutrophil-to-Lymphocyte Ratio (NLR), Mean Platelet Volume (MPV), C-Reactive Protein (CRP), Platelet (PLT), Alanine Transaminase (ALT), Aspartate Amino Transferase (AST …

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Dec 2023 • ACS omega

Monte Carlo-Simulated Annealing and Machine Learning-Based Funneled Approach for Finding the Global Minimum Structure of Molecular Clusters

Michal Roth, Yoni Toker, Dan T Major

Understanding the physical underpinnings and geometry of molecular clusters is of great importance in many fields, ranging from studying the beginning of the universe to the formation of atmospheric particles. To this end, several approaches have been suggested, yet identifying the most stable cluster geometry (i.e., global potential energy minimum) remains a challenge, especially for highly symmetric clusters. Here, we suggest a new funneled Monte Carlo-based simulated annealing (SA) approach, which includes two key steps: generation of symmetrical clusters and classification of the clusters according to their geometry using machine learning (MCSA-ML). We demonstrate the merits of the MCSA-ML method in comparison to other approaches on several Lennard-Jones (LJ) clusters and four molecular clusters─Ser8(Cl–)2, H+(H2O)6, Ag+(CO2)8, and Bet4Cl–. For the latter of these clusters, the correct …

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Dec 2023 • International Journal of Molecular Sciences

Nicotinamide-expanded allogeneic natural killer cells with CD38 deletion, expressing an enhanced CD38 chimeric antigen receptor, target multiple myeloma cells

Avishay Edri, Nimrod Ben-Haim, Astar Hailu, Nurit Brycman, Orit Berhani-Zipori, Julia Rifman, Sherri Cohen, Dima Yackoubov, Michael Rosenberg, Ronit Simantov, Hideshima Teru, Keiji Kurata, Kenneth Carl Anderson, Ayal Hendel, Aviad Pato, Yona Geffen

Natural killer (NK) cells are a vital component of cancer immune surveillance. They provide a rapid and potent immune response, including direct cytotoxicity and mobilization of the immune system, without the need for antigen processing and presentation. NK cells may also be better tolerated than T cell therapy approaches and are susceptible to various gene manipulations. Therefore, NK cells have become the focus of extensive translational research. Gamida Cell’s nicotinamide (NAM) platform for cultured NK cells provides an opportunity to enhance the therapeutic potential of NK cells. CD38 is an ectoenzyme ubiquitously expressed on the surface of various hematologic cells, including multiple myeloma (MM). It has been selected as a lead target for numerous monoclonal therapeutic antibodies against MM. Monoclonal antibodies target CD38, resulting in the lysis of MM plasma cells through various antibody-mediated mechanisms such as antibody-dependent cellular cytotoxicity (ADCC), complement-dependent cytotoxicity, and antibody-dependent cellular phagocytosis, significantly improving the outcomes of patients with relapsed or refractory MM. However, this therapeutic strategy has inherent limitations, such as the anti-CD38-induced depletion of CD38-expressing NK cells, thus hindering ADCC. We have developed genetically engineered NK cells tailored to treat MM, in which CD38 was knocked-out using CRISPR-Cas9 technology and an enhanced chimeric antigen receptor (CAR) targeting CD38 was introduced using mRNA electroporation. This combined genetic approach allows for an improved cytotoxic activity directed against …

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Dec 2023 • Journal of Biological Engineering

A streptavidin–biotin system combined with magnetic actuators for remote neuronal guidance

Dafna Rivka Levenberg, Eli Varon, Ganit Indech, Tal Ben Uliel, Lidor Geri, Amos Sharoni, Orit Shefi

The ability to control neuronal mobility and organization is of great importance in developing neuronal interfaces and novel therapeutic approaches. An emerging promising method is the manipulation of neuronal cells from afar via magnetic forces. Nevertheless, using magnetic iron oxide nanoparticles as internal actuators may lead to biotoxicity, adverse influence on intracellular processes, and thus requires prerequisite considerations for therapeutic approaches. Magnetizing the cells via the incorporation of magnetic particles that can be applied extracellularly is advantageous. Herein, we have developed a magnetic system based on streptavidin–biotin interaction to decorate cellular membrane with magnetic elements. In this model, superparamagnetic microparticles, coated with streptavidin, were specifically bound to biotinylated PC12 cells. We demonstrated that cell movement can be directed remotely by the forces produced by pre-designed magnetic fields. First, using time lapse imaging, we analyzed the kinetics of cell migration towards the higher flux zone. Next, to form organized networks of cells we designed and fabricated micro-patterned magnetic devices. The fabricated devices were composed of a variety of ferromagnetic shapes, sputter-deposited onto glass substrates. Cells that were conjugated to the magnetic particles were plated atop the micro-patterned substrates, attracted to the magnetic actuators and became fixed onto the magnetic patterns. In all, our study presents a novel system based on a well-known molecular technology combined with nanotechnology that may well lead to the expansion of implantable magnetic …

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Dec 2023 • Electrocatalysis for Membrane Fuel Cells: Methods, Modeling and Applications …, 2023

Design of PGM‐free ORR Catalysts: From Molecular to the State of the Art

Naomi Levy, Lior Elbaz

The state‐of‐the‐art Platinum group metal (PGM)‐free oxygen reduction reaction (ORR) catalysts have been synthesized using the pyrolysis of iron, nitrogen, and carbon precursors, and result in highly active ORR catalysts, but their undefined structure limits their further development. Since the inspiration for these catalysts came from well‐defined structures of transition metal complexes, it is important to understand the various parameters that govern the reaction potential, selectivity, and the stability with well‐defined catalysts and try to extrapolate them to the pyrolyzed catalysts. In this chapter, we give an overview of the parameters that influence the catalysis of ORR with well‐defined ORR catalysts. These can later be used to further enhance the performance of the state‐of‐the‐art PGM‐free ORR catalysts.

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Dec 2023 • Advanced Materials Technologies

Biolistic Delivery of Photosensitizer‐Loaded Porous Si Carriers for Localized Photodynamic Therapy (Adv. Mater. Technol. 23/2023)

Elina Haimov‐Talmoud, Michal Rosenberg, Sofia Arshavsky‐Graham, Eli Varon, Orit Shefi, Ester Segal

Highly localized photodynamic therapy (PDT) is achieved by biolistic delivery of photosensitizer-loaded porous silicon microparticles directly into solid tumors, as demonstrated by Orit Shefi, Ester Segal, and co-workers in article 2300877. PDT irradiation following the uptake of the released photosensitizer payload induce substantial inhibition of tumor growth in vivo, opening new possibilities for an improved clinical PDT treatment.

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Dec 2023 • Electrochimica Acta

Iron doped cobalt nickel layered double hydroxide supported on nickel foam as a robust electrocatalyst for highly efficient water oxidation in alkaline sea water

Akanksha Gupta, Hari Krishna Sadhanala, Aharon Gedanken

The seawater electrolysis is an economically favorable approach for water splitting application because seawater is one of the plentiful abundant natural resources on our earth. In water splitting pathway, the anodic half-cell reaction from seawater stills a challenging task due to anodic corrosion and the competitive chloride oxidation process. In the current study, we prepared flower-shaped porous nanorods of iron doped cobalt nickel layered double hydroxide supported on nickel foam (Fe0.05 CoNi LDH/NF), which require very less oxygen evolution reaction (OER) overpotential in 1M KOH (212mV) and alkaline seawater (287mV) to deliver 10 mAcm−2 current density and exhibited remarkable 14h durability. At the same time, post treated sample reveals the better OER activity after chronopotentiometry analysis, because of superior conductivity and corrosion-resistance of the electrocatalyst. The doping of Fe cation …

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Dec 2023 • APL Photonics

Tensor characteristics of forward Brillouin sensors in bare and coated fibers

Alon Bernstein, Elad Zehavi, Yosef London, Mirit Hen, Rafael Suna, Shai Ben-Ami, Avi Zadok

Forward Brillouin scattering fiber sensors can detect and analyze media outside the cladding of standard fibers, where guided light does not reach. Nearly all such sensors reported to-date have relied on the radially symmetric guided acoustic modes of the fiber. Wave motion in these modes is strictly dilatational. However, forward Brillouin scattering also takes place through torsional–radial guided acoustic modes of the fiber. Torsional–radial modes exhibit more complex tensor characteristics, and they consist of both dilatational and shear wave contributions. In this work, we show that forward Brillouin sensing through torsional–radial acoustic modes is qualitatively different from processes based on the radial ones. While dilatational wave components may dissipate toward liquids outside the fiber cladding, shear waves do not. Consequently, the effect of outside liquids varies among torsional–radial modes. Those …

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Dec 2023 • Nature Communications

Dissecting the basis for differential substrate specificity of ADAR1 and ADAR2

Marlon S Zambrano-Mila, Monika Witzenberger, Zohar Rosenwasser, Anna Uzonyi, Ronit Nir, Shay Ben-Aroya, Erez Y Levanon, Schraga Schwartz

Millions of adenosines are deaminated throughout the transcriptome by ADAR1 and/or ADAR2 at varying levels, raising the question of what are the determinants guiding substrate specificity and how these differ between the two enzymes. We monitor how secondary structure modulates ADAR2 vs ADAR1 substrate selectivity, on the basis of systematic probing of thousands of synthetic sequences transfected into cell lines expressing exclusively ADAR1 or ADAR2. Both enzymes induce symmetric, strand-specific editing, yet with distinct offsets with respect to structural disruptions: −26 nt for ADAR2 and −35 nt for ADAR1. We unravel the basis for these differences in offsets through mutants, domain-swaps, and ADAR homologs, and find it to be encoded by the differential RNA binding domain (RBD) architecture. Finally, we demonstrate that this offset-enhanced editing can allow an improved design of ADAR2 …

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Dec 2023 • Applied Optics

Multi-harmonic structured illumination-based optical diffraction tomography

Ruihua Liu, Kai Wen, Jiaoyue Li, Ying Ma, Juanjuan Zheng, Sha An, Junwei Min, Zeev Zalevsky, Baoli Yao, Peng Gao

Imaging speed and spatial resolution are key factors in optical diffraction tomography (ODT), while they are mutually exclusive in 3D refractive index imaging. This paper presents a multi-harmonic structured illumination-based optical diffraction tomography (MHSI-ODT) to acquire 3D refractive index (RI) maps of transparent samples. MHSI-ODT utilizes a digital micromirror device (DMD) to generate structured illumination containing multiple harmonics. For each structured illumination orientation, four spherical spectral crowns are solved from five phase-shifted holograms, meaning that the acquisition of each spectral crown costs 1.25 raw images. Compared to conventional SI-ODT, which retrieves two spectral crowns from three phase-shifted raw images, MHSI-ODT enhances the imaging speed by 16.7% in 3D RI imaging. Meanwhile, MHSI-ODT exploits both the 1st-order and the 2nd-order harmonics; therefore, it …

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Dec 2023 • Molecular Reproduction and Development 90 (12), 785-803, 2023

Epigenetic aging of mammalian gametes

Michael Klutstein, Nitzan Gonen

The process of aging refers to physiological changes that occur to an organism as time progresses and involves changes to DNA, proteins, metabolism, cells, and organs. Like the rest of the cells in the body, gametes age, and it is well established that there is a decline in reproductive capabilities in females and males with aging. One of the major pathways known to be involved in aging is epigenetic changes. The epigenome is the multitude of chemical modifications performed on DNA and chromatin that affect the ability of chromatin to be transcribed. In this review, we explore the effects of aging on female and male gametes with a focus on the epigenetic changes that occur in gametes throughout aging. Quality decline in oocytes occurs at a relatively early age. Epigenetic changes constitute an important part of oocyte aging. DNA methylation is reduced with age, along with reduced expression of DNA …

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Dec 2023 • Genome Research

A somatic hypermutation–based machine learning model stratifies individuals with Crohn's disease and controls

Modi Safra, Lael Werner, Pazit Polak, Ayelet Peres, Naomi Salamon, Michael Schvimer, Batia Weiss, Iris Barshack, Dror S Shouval, Gur Yaari


Dec 2023 • arXiv preprint arXiv:2312.10367

Covariant field lines: a geometrical approach to electrodynamics

Yaron Hadad, Ido Kaminer, Aharon Elitzur, Eliahu Cohen

This paper revisits the geometric foundations of electromagnetic theory, by studying Faraday's concept of field lines. We introduce "covariant electromagnetic field lines," a novel construct that extends traditional field line concepts to a covariant framework. Our work includes the derivation of a closed-form formula for the field line curvature in proximity to a moving electric charge, showcasing the curvature is always non-singular, including nearby a point charge. Our geometric framework leads to a geometric derivation of the Lorentz force equation and its first-order corrections, circumventing the challenges of self-force singularities and providing insights into the problem of radiation-reaction. This study not only provides a fresh geometric perspective on electromagnetic field lines but also opens avenues for future research in fields like quantum electrodynamics, gravitational field theory, and beyond.

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Dec 2023 • Molecular Cancer Therapeutics

Abstract C105: A systematic evaluation of the therapeutic potential of base editing in cancer prevention and treatment

Rona Merdler-Rabinowicz, Ariel Dadush, Sumeet Patiyal, Gulzar Daya, Lipika Ray, Padma Sheila Rajagopal, Alejandro A Schaffer, Eytan Ruppin, Erez Y Levanon

Base editing (BE) techniques offer efficient means to modify specific nucleotides in the genome. While current research mainly focuses on applying BE for treating genetic diseases caused by single-nucleotide variants (SNVs), its potential in cancer is worth exploring, as many tumors arise from an accumulation of various mutations. BE techniques primarily consist of a fusion between a Cas nuclease and a deaminase (Cas-BE), that enables A-to-G or C-to-T edits. This allows for the correction of G>A and T>C SNVs at the DNA or RNA level. Additionally, BE can correct C>T and A>G SNVs at the DNA level through the cellular DNA repair response. Precise targeting is aimed by a programmed guide RNA (gRNA), which engages in Watson-Crick base pairing with the desired region. However, a remaining concern is gRNA binding to additional locations in the genome, leading to unintended off-target edits. An …

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Dec 2023 • NAR Genomics and Bioinformatics

Elevated A-to-I RNA editing in COVID-19 infected individuals

Rona Merdler-Rabinowicz, David Gorelik, Jiwoon Park, Cem Meydan, Jonathan Foox, Miriam Karmon, Hillel S Roth, Roni Cohen-Fultheim, Galit Shohat-Ophir, Eli Eisenberg, Eytan Ruppin, Christopher E Mason, Erez Y Levanon

Given the current status of coronavirus disease 2019 (COVID-19) as a global pandemic, it is of high priority to gain a deeper understanding of the disease's development and how the virus impacts its host. Adenosine (A)-to-Inosine (I) RNA editing is a post-transcriptional modification, catalyzed by the ADAR family of enzymes, that can be considered part of the inherent cellular defense mechanism as it affects the innate immune response in a complex manner. It was previously reported that various viruses could interact with the host's ADAR enzymes, resulting in epigenetic changes both to the virus and the host. Here, we analyze RNA-seq of nasopharyngeal swab specimens as well as whole-blood samples of COVID-19 infected individuals and show a significant elevation in the global RNA editing activity in COVID-19 compared to healthy controls. We also detect specific coding sites that exhibit higher editing …

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Dec 2023 • Angewandte Chemie 135 (50), e202306904, 2023

Polyimide compounds for post‐lithium energy storage applications

Amey Nimkar, Gil Bergman, Elad Ballas, Nophar Tubul, Noam Levi, Fyodor Malchik, Idan Kukurayeve, Munseok S Chae, Daniel Sharon, Mikhael Levi, Netanel Shpigel, Guoxiu Wang, Doron Aurbach

The exploration of cathode and anode materials that enable reversible storage of mono and multivalent cations has driven extensive research on organic compounds. In this regard, polyimide (PI)‐based electrodes have emerged as a promising avenue for the development of post‐lithium energy storage systems. This review article provides a comprehensive summary of the syntheses, characterizations, and applications of PI compounds as electrode materials capable of hosting a wide range of cations. Furthermore, the review also delves into the advancements in PI based solid state batteries, PI‐based separators, current collectors, and their effectiveness as polymeric binders. By highlighting the key findings in these areas, this review aims at contributing to the understanding and advancement of PI‐based structures paving the way for the next generation of energy storage systems.

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Dec 2023 • Israel Journal of Chemistry 63 (12), e202400002, 2023

Advancing the Understanding of Surface Science through Nonlinear Optics and Electrochemistry

Adi Salomon, Malachi Noked, Menny Shalom

Surface characterization is essential for understanding chemical and electrochemical transformations occurring on surfaces or at interfaces. Battery electrode aging processes, biofilm growth, crystallization, and transport/signaling across cellular membranes are only a few examples of such phenomena. This special issue delves into applied electrochemistry and nonlinear optical techniques applicable to surface characterization.

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Dec 2023 • Optics Letters

Synchrotron-based x ray fluorescence ghost imaging

Mathieu Manni, Adi Ben-Yehuda, Yishai Klein, Bratislav Lukic, Andrew Kingston, Alexander Rack, Sharon Shwartz, Nicola Viganò

X ray fluorescence ghost imaging (XRF-GI) was recently demonstrated for x ray lab sources. It has the potential to reduce the acquisition time and deposited dose by choosing their trade-off with a spatial resolution while alleviating the focusing constraints of the probing beam. Here, we demonstrate the realization of synchrotron-based XRF-GI: we present both an adapted experimental setup and its corresponding required computational technique to process the data. This extends the above-mentioned potential advantages of GI to synchrotron XRF imaging. In addition, it enables new strategies to improve resilience against drifts at all scales and the study of previously inaccessible samples, such as liquids.

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