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May 2024 • arXiv preprint arXiv:2305.12468

High-resolution computed tomography with scattered X-ray radiation and a single pixel detector

A Ben Yehuda, O Sefi, Y Klein, RH Shukrun, H Schwartz, E Cohen, S Shwartz

X-ray imaging is a prevalent technique for non-invasively visualizing the interior of the human body and opaque instruments. In most commercial x-ray modalities, an image is formed by measuring the x-rays that pass through the object of interest. However, despite the potential of scattered radiation to provide additional information about the object, it is often disregarded due to its inherent tendency to cause blurring. Consequently, conventional imaging modalities do not measure or utilize these valuable data. In contrast, we propose and experimentally demonstrate a high-resolution technique for x-ray computed tomography (CT) that measures scattered radiation by exploiting computational ghost imaging (CGI). We show that our method can provide sub-200 {\mu}m resolution, exceeding the capabilities of most existing x-ray imaging modalities. Our research reveals a promising technique for incorporating scattered radiation data in CT scans to improve image resolution and minimize radiation exposure for patients. The findings of our study suggest that our technique could represent a significant advancement in the fields of medical and industrial imaging, with the potential to enhance the accuracy and safety of diagnostic imaging procedures.

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May 2024 • Briefings in Bioinformatics

Guidelines for reproducible analysis of adaptive immune receptor repertoire sequencing data

Ayelet Peres, Vered Klein, Boaz Frankel, William Lees, Pazit Polak, Mark Meehan, Artur Rocha, João Correia Lopes, Gur Yaari

Enhancing the reproducibility and comprehension of adaptive immune receptor repertoire sequencing (AIRR-seq) data analysis is critical for scientific progress. This study presents guidelines for reproducible AIRR-seq data analysis, and a collection of ready-to-use pipelines with comprehensive documentation. To this end, ten common pipelines were implemented using ViaFoundry, a user-friendly interface for pipeline management and automation. This is accompanied by versioned containers, documentation and archiving capabilities. The automation of pre-processing analysis steps and the ability to modify pipeline parameters according to specific research needs are emphasized. AIRR-seq data analysis is highly sensitive to varying parameters and setups; using the guidelines presented here, the ability to reproduce previously published results is demonstrated. This work promotes transparency …

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May 2024 • American Chemical Society

Mechanisms and Barriers in Nanomedicine: Progress in the Field and Future Directions

Thomas Anchordoquy, Natalie Artzi, Irina V Balyasnikova, Yechezkel Barenholz, Ninh M La-Beck, Jacob S Brenner, Warren CW Chan, Paolo Decuzzi, Agata A Exner, Alberto Gabizon, Biana Godin, Samuel K Lai, Twan Lammers, Michael J Mitchell, S Moein Moghimi, Vladimir R Muzykantov, Dan Peer, Juliane Nguyen, Rachela Popovtzer, Madison Ricco, Natalie J Serkova, Ravi Singh, Avi Schroeder, Anna A Schwendeman, Joelle P Straehla, Tambet Teesalu, Scott Tilden, Dmitri Simberg

In recent years, steady progress has been made in synthesizing and characterizing engineered nanoparticles, resulting in several approved drugs and multiple promising candidates in clinical trials. Regulatory agencies such as the Food and Drug Administration and the European Medicines Agency released important guidance documents facilitating nanoparticle-based drug product development, particularly in the context of liposomes and lipid-based carriers. Even with the progress achieved, it is clear that many barriers must still be overcome to accelerate translation into the clinic. At the recent conference workshop “Mechanisms and Barriers in Nanomedicine” in May 2023 in Colorado, U.S.A., leading experts discussed the formulation, physiological, immunological, regulatory, clinical, and educational barriers. This position paper invites open, unrestricted, nonproprietary discussion among senior faculty, young …

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May 2024 • Advances in Cement Research

Enhancing cement hydration by core/shell PS@SiO2 nanoparticles

Meytal Shalit, Maya Radune, Yaniv Knop, Yitzhak Mastai

Nanoparticles are widely used in construction. Here, nano-SiO2 is employed, in a way that prevents agglomeration of the nanoparticles, as pozzolanic material to improve Portland cement hydration and to improve the properties of the concrete. To explore the effect of nano-SiO2 and core-shell PS@SiO2 on cement properties, spherical polystyrene particles were prepared by dispersion polymerization of styrene in polar solvents and characterized by FTIR and E-SEM. The core shells PS@SiO2 were synthesized by Stöber method. The results showed an amorphous nano-SiO2 layer can be deposited uniformly on polystyrene particles. This core/shell structure was reducing the aggregation of nano-SiO2 effectively. It was shown that PS@SiO2 particles improved the concrete performances compared to blended cement with nano-SiO2 due to the agglomeration affect. Highlights •Core/shell PS@SiO2 nanoparticles …

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May 2024 • 245th ECS Meeting (May 26-30, 2024)

Direct Hydroquinone Fuel Cells

Lior Elbaz, Yan Yurko


May 2024 • ChemistrySelect

Performance of CuP2 Negative Electrode for Na‐Ion Batteries with CNTs As Stabilizer

En Zhang, Arka Saha, Guangshen Jiang, Xiaosa Xu, Alina Yarmolenko, Tarik Aziz, Grothe Julia, Gilbert Daniel Nessim, Stefan Kaskel

Transition metal phosphides (TMPs) are promising anode materials for sodium ion battery, thanks to their high theoretical specific capacities. Nevertheless, they suffer from large volume change and from poor conductivity during prolonged cycling. Here we systematically investigate the role of different kinds of single/multi‐wall carbon nanotubes (SWCNTs/MWCNTs) as additives in order to stabilize copper phosphide particles (CuP2) as anode materials in sodium ion batteries (SIBs). All composites show enhancement in the overall capacity and cycling stability compared to the pristine CuP2 due to the well‐connected CNTs on and between the CuP2 particles. At a high currency density of 1 A g−1, CuP2@SWCNTs composite with 13 wt.% SWCNTs can deliver a specific capacity over 400 mAh g−1 for more than 60 cycles, much better than conventional hard carbon materials. The CNTs enhance the …

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May 2024 • Energy Storage Materials

Self-discharge in flowless Zn-Br2 batteries and its mitigation

Elad Ballas, Amey Nimkar, Gil Bergman, Ran Elazari, Racheli Wakshlak, Daniel Sharon, Mikhael D Levi, Dan Thomas Major, Daniel Mandler, Netanel Shpigel, Doron Aurbach

Several decades after the invention of the flow Zn-Br2 systems persistent attempts have been made to develop stationary Zn-Br2 batteries. Such development should increase the energy density of the system simultaneously significantly reducing their cost and opening new challenges associated with the cell design and its performance. One of the major concerns is the rapid self-discharge of stationary systems leading to spontaneous charge loss during battery storage time. While self-discharge in flow cells is generally attributed to the chemical oxidation of the Zn anode, we show that the origin of self-discharge in a static configuration is completely different. By systematic investigations of activated carbon with different surface areas under varied charging conditions, mechanistic insights into this phenomenon were provided. Based on this understanding, we proposed herein an effective way to suppress the cathode …

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May 2024 • Histochemistry and Cell Biology

CCAT1 lncRNA is chromatin-retained and post-transcriptionally spliced

Chaya Bohrer, Eli Varon, Eldar Peretz, Gita Reinitz, Noa Kinor, David Halle, Aviram Nissan, Yaron Shav-Tal

Super-enhancers are unique gene expression regulators widely involved in cancer development. Spread over large DNA segments, they tend to be found next to oncogenes. The super-enhancer c-MYC locus forms long-range chromatin looping with nearby genes, which brings the enhancer and the genes into proximity, to promote gene activation. The colon cancer-associated transcript 1 (CCAT1) gene, which is part of the MYC locus, transcribes a lncRNA that is overexpressed in colon cancer cells through activation by MYC. Comparing different types of cancer cell lines using RNA fluorescence in situ hybridization (RNA FISH), we detected very prominent CCAT1 expression in HeLa cells, observed as several large CCAT1 nuclear foci. We found that dozens of CCAT1 transcripts accumulate on the gene locus, in addition to active transcription occurring from the gene. The accumulating transcripts are released …

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May 2024 • Academic Press, 2024

Mechanistic docking in terpene synthases using EnzyDock

Renana Schwartz, Shani Zev, Dan T Major

Terpene Synthases (TPS) catalyze the formation of multicyclic, complex terpenes and terpenoids from linear substrates. Molecular docking is an important research tool that can further our understanding of TPS multistep mechanisms and guide enzyme design. Standard docking programs are not well suited to tackle the unique challenges of TPS, like the many chemical steps which form multiple stereo-centers, the weak dispersion interactions between the isoprenoid chain and the hydrophobic region of the active site, description of carbocation intermediates, and finding mechanistically meaningful sets of docked poses. To address these and other unique challenges, we developed the multistate, multiscale docking program EnzyDock and used it to study many TPS and other enzymes. In this review we discuss the unique challenges of TPS, the special features of EnzyDock developed to address these challenges …

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May 2024 • Angewandte Chemie International Edition

Differential Substrate Sensing in Terpene Synthases from Plants and Microorganisms: Insight from Structural, Bioinformatic, and EnzyDock Analyses

Renana Schwartz, Shani Zev, Dan T Major

Terpene synthases (TPSs) catalyze the first step in the formation of terpenoids, which comprise the largest class of natural products in nature. TPSs employ a family of universal natural substrates, composed of isoprenoid units bound to a diphosphate moiety. The intricate structures generated by TPSs are the result of substrate binding and folding in the active site, enzyme‐controlled carbocation reaction cascades, and final reaction quenching. A key unaddressed question in class I TPSs is the asymmetric nature of the diphosphate‐(Mg2+)3 cluster, which forms a critical part of the active site. In this asymmetric ion cluster, two diphosphate oxygen atoms protrude into the active site pocket. The substrate hydrocarbon tail, which is eventually molded into terpenes, can bind to either of these oxygen atoms, yet to which is unknown. Herein, we employ structural, bioinformatics, and EnzyDock docking tools to address this …

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May 2024 • ACS Catalysis

Fourier-Transformed Alternating Current Voltammetry (FTacV) for Analysis of Electrocatalysts

Rifael Z Snitkoff-Sol, Alan M Bond, Lior Elbaz

Electrocatalysts play a critical role in energy technologies, but the development of active, efficient, and durable catalysts is impeded by the lack of methodologies to deconvolute the complex interplay between various aspects influencing the activity of the catalysts, e.g., the number of active sites, turnover frequency, and the reaction pathways. Fourier-transformed alternating current voltammetry (FTacV) is an emerging tool for the analysis of electroactive species and has been successfully applied to a variety of reactions such as the oxygen reduction reaction, oxygen evolution reaction, carbon dioxide reduction reaction, hydrogen evolution reaction, and hydrogen oxidation reaction. The harmonics generated from FTacV measurements neatly detect underlaying processes not visible by other, more commonly employed techniques for analysis of electrocatalysts, such as the rotating disc electrode and dc voltammetry …

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May 2024 • Biotechnology Journal

DNA origami scaffold promoting nerve guidance and regeneration

Jonathan Giron, Merav Antman‐Passig, Neta Zilony, Hadas Schori, Ido Bachelet, Orit Shefi

Self‐assembly of biological elements into biomimetic cargo carriers for targeting and delivery is a promising approach. However, it still holds practical challenges. We developed a functionalization approach of DNA origami (DO) nanostructures with neuronal growth factor (NGF) for manipulating neuronal systems. NGF bioactivity and its interactions with the neuronal system were demonstrated in vitro and in vivo models. The DO elements fabricated by molecular self‐assembly have manipulated the surrounding environment through static spatially and temporally controlled presentation of ligands to the cell surface receptors. Our data showed effective bioactivity in differentiating PC12 cells in vitro. Furthermore, the DNA origami NGF (DON) affected the growth directionality and spatial capabilities of dorsal root ganglion neurons in culture by introducing a chemotaxis effect along a gradient of functionalized DO …

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May 2024 • Cell Reports

Structural and mechanistic insights into the function of Leishmania ribosome lacking a single pseudouridine modification

K Shanmugha Rajan, Saurav Aryal, Disha-Gajanan Hiregange, Anat Bashan, Hava Madmoni, Mika Olami, Tirza Doniger, Smadar Cohen-Chalamish, Pascal Pescher, Masato Taoka, Yuko Nobe, Aliza Fedorenko, Tanaya Bose, Ella Zimermann, Eric Prina, Noa Aharon-Hefetz, Yitzhak Pilpel, Toshiaki Isobe, Ron Unger, Gerald F Späth, Ada Yonath, Shulamit Michaeli

Leishmania is the causative agent of cutaneous and visceral diseases affecting millions of individuals worldwide. Pseudouridine (Ψ), the most abundant modification on rRNA, changes during the parasite life cycle. Alterations in the level of a specific Ψ in helix 69 (H69) affected ribosome function. To decipher the molecular mechanism of this phenotype, we determine the structure of ribosomes lacking the single Ψ and its parental strain at ∼2.4–3 Å resolution using cryo-EM. Our findings demonstrate the significance of a single Ψ on H69 to its structure and the importance for its interactions with helix 44 and specific tRNAs. Our study suggests that rRNA modification affects translation of mRNAs carrying codon bias due to selective accommodation of tRNAs by the ribosome. Based on the high-resolution structures, we propose a mechanism explaining how the ribosome selects specific tRNAs.

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May 2024 • 245th ECS Meeting (May 26-30, 2024)

Elucidating the Hydrogen Evolution Reaction Mechanism of Immobilized Iron Porphyrin Electrocatalysts

Nils Heppe, Charlotte Gallenkamp, Rifael Z Snitkoff-Sol, Stephen Daniel Paul, Nicole Segura Salas, Vasily Potapkin, Atefeh Jafari, Olaf Leupold, Volker Schuenemann, Lior Elbaz, Vera Krewald, Ulrike I Kramm


May 2024 • arXiv preprint arXiv:2405.02036

Spontaneous Conducting Boundary Channels in 1T-TaS

TR Devidas, Jonathan T Reichanadter, Shannon C Haley, Matan Sterenberg, Joel E Moore, Jeffrey B Neaton, James G Analytis, Beena Kalisky, Eran Maniv

Materials that transition between metal and insulator, the two opposing states that distinguish all solids, are fascinating because they underlie many mysteries in the physics of the solid state. In 1T-TaS, the metal-insulator transition is linked to a series of metastable states of a chiral charge density wave whose basic nature is still an open question. In this work, we show that pulses of current through these materials create current-carrying boundary channels that distinguish the metallic and insulating states. We demonstrate electrical control of these channels' properties, suggesting their formation could be due to the complex interplay of the formation of domain walls and the viscous flow of electrons. Our findings show that physical boundaries play a key role in the properties of the metastable states of the metal-insulator transition, highlighting new possibilities for in-situ electrical design and active manipulation of electrical components.

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May 2024 • Nature Communications

Extreme magnetoresistance at high-mobility oxide heterointerfaces with dynamic defect tunability

DV Christensen, TS Steegemans, T D. Pomar, YZ Chen, A Smith, VN Strocov, B Kalisky, N Pryds

Magnetic field-induced changes in the electrical resistance of materials reveal insights into the fundamental properties governing their electronic and magnetic behavior. Various classes of magnetoresistance have been realized, including giant, colossal, and extraordinary magnetoresistance, each with distinct physical origins. In recent years, extreme magnetoresistance (XMR) has been observed in topological and non-topological materials displaying a non-saturating magnetoresistance reaching 103−108% in magnetic fields up to 60 T. XMR is often intimately linked to a gapless band structure with steep bands and charge compensation. Here, we show that a linear XMR of 80,000% at 15 T and 2 K emerges at the high-mobility interface between the large band-gap oxides γ-Al2O3 and SrTiO3. Despite the chemically and electronically very dissimilar environment, the temperature/field phase diagrams of γ-Al2O …

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May 2024 • arXiv preprint arXiv:2305.16017

Experimental evidence for defect tolerance in Pb-halide perovskites

Naga Prathibha Jasti, Igal Levine, Yishay Feldman, Sigalit Aharon, David Cahen

The term defect tolerance (DT) is used often to rationalize the exceptional optoelectronic properties of Halide Perovskites, HaPs, and their devices. Even though DT lacked direct experimental evidence, it became fact in the field. DT in semiconductors implies tolerance to structural defects without the electrical and optical effects (e.g., traps), associated with such defects. We present first direct experimental evidence for DT in Pb HaPs by comparing the structural quality of 2D, 2D_3D, and 3D Pb HaP crystals with their optoelectronic characteristics using high sensitivity methods. Importantly, we get information from the material bulk, because we sample at least a few 100 nm, up to several micrometer, from the sample surface, which allows assessing intrinsic bulk (and not only surface) properties of HaPs. The results point to DT in 3D, to a lesser extent in 2D_3D, but not in 2D Pb HaPs. We ascribe such dimension dependent DT to the higher number of (near)neighboring species, available to compensate for structural defect effects in the 3D than in the 2D HaP crystals. Overall, our data provide an experimental basis to rationalize DT in Pb HaPs. These experiments and findings can guide the search for, and design of other materials with DT.

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May 2024 • arXiv preprint arXiv:2305.12468

High-resolution computed tomography with scattered X-ray radiation and a single pixel detector

A Ben Yehuda, O Sefi, Y Klein, RH Shukrun, H Schwartz, E Cohen, S Shwartz

X-ray imaging is a prevalent technique for non-invasively visualizing the interior of the human body and opaque instruments. In most commercial x-ray modalities, an image is formed by measuring the x-rays that pass through the object of interest. However, despite the potential of scattered radiation to provide additional information about the object, it is often disregarded due to its inherent tendency to cause blurring. Consequently, conventional imaging modalities do not measure or utilize these valuable data. In contrast, we propose and experimentally demonstrate a high-resolution technique for x-ray computed tomography (CT) that measures scattered radiation by exploiting computational ghost imaging (CGI). We show that our method can provide sub-200 {\mu}m resolution, exceeding the capabilities of most existing x-ray imaging modalities. Our research reveals a promising technique for incorporating scattered radiation data in CT scans to improve image resolution and minimize radiation exposure for patients. The findings of our study suggest that our technique could represent a significant advancement in the fields of medical and industrial imaging, with the potential to enhance the accuracy and safety of diagnostic imaging procedures.

Show more

May 2024 • Energy Storage Materials

Self-discharge in flowless Zn-Br2 batteries and its mitigation

Elad Ballas, Amey Nimkar, Gil Bergman, Ran Elazari, Racheli Wakshlak, Daniel Sharon, Mikhael D Levi, Dan Thomas Major, Daniel Mandler, Netanel Shpigel, Doron Aurbach

Several decades after the invention of the flow Zn-Br2 systems persistent attempts have been made to develop stationary Zn-Br2 batteries. Such development should increase the energy density of the system simultaneously significantly reducing their cost and opening new challenges associated with the cell design and its performance. One of the major concerns is the rapid self-discharge of stationary systems leading to spontaneous charge loss during battery storage time. While self-discharge in flow cells is generally attributed to the chemical oxidation of the Zn anode, we show that the origin of self-discharge in a static configuration is completely different. By systematic investigations of activated carbon with different surface areas under varied charging conditions, mechanistic insights into this phenomenon were provided. Based on this understanding, we proposed herein an effective way to suppress the cathode …

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May 2024 • Molecular Catalysis

Effect of heat treatment on improving OER activity of NiFeOOH based aerogels: A combined experimental and theoretical study

Or Rimon, Wenjamin Moschkowitsch, Gili Cohen Taguri, Lior Elbaz, Maytal Caspary Toroker


Apr 2024 • Heliyon

PemB, a type III secretion effector in Pseudomonas aeruginosa, affects Caenorhabditis elegans life span

Shira Zelikman, Reut Dudkevich, Hadar Korenfeld-Tzemach, Esther Shmidov, Mor Levi-Ferber, Sivan Shoshani, Shay Ben-Aroya, Sivan Henis-Korenblit, Ehud Banin

Pseudomonas aeruginosa is one of the leading nosocomial opportunistic pathogens causing acute and chronic infections. Among its main virulent factors is the Type III secretion system (T3SS) which enhances disease severity by delivering effectors to the host in a highly regulated manner. Despite its importance for virulence, only six T3SS-dependent effectors have been discovered so far. Previously, we identified two new potential effectors using a machine-learning algorithm approach. Here we demonstrate that one of these effectors, PemB, is indeed virulent. Using a live Caenorhabditis elegans infection model, we demonstrate this effector damages the integrity of the intestine barrier leading to the death of the host. Implementing a high-throughput assay using Saccharomyces cerevisiae, we identified several candidate proteins that interact with PemB. One of them, EFT1, has an ortholog in C. elegans (eef-2 …

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