Nov 2024 • arXiv preprint arXiv:2411.04684
Ohad Vilk, Motti Charter, Sivan Toledo, Eli Barkai, Ran Nathan
Natural and anomalous diffusion are widely observed and used to explore causes and consequences of movement across organisms, resulting in extensive use of the mean and mean-squared displacement (MSD). Using high-resolution data from over 70 million localizations of young and adult free-ranging Barn Owls (\textit{Tyto alba}), we demonstrate the necessity of a broad spectrum of displacement moments to characterize bird movement across scales. The mean and MSD -- interchangeable with moments and 2 -- are insufficient special cases. We reveal empirical strong anomalous diffusion as a nonlinear growth of displacement moments according to . The moment spectrum function displays piecewise linearity with a critical moment marking the crossover point between two scaling regimes, linked to a combination of age-specific behavioral modes. A critical timescale of five minutes marks an unexpected transition from a convex to a concave , related to environmental and behavioral constraints. Using two stochastic models of varying ecological complexity, we demonstrate that strong anomalous diffusion may be widespread in animal movement, underscoring the importance of expanding analysis beyond the average and MSD.
Show moreNov 2024 • arXiv preprint arXiv:2411.12702
Yishai Klein, Edward Strizhevsky, Haim Aknin, Moshe Deutsch, Eliahu Cohen, Avi Pe'er, Kenji Tamasaku, Tobias Schulli, Ebrahim Karimi, Sharon Shwartz
The invention of X-ray interferometers has led to advanced phase-sensing devices that are invaluable in various applications. These include the precise measurement of universal constants, e.g. the Avogadro number, of lattice parameters of perfect crystals, and phase-contrast imaging, which resolves details that standard absorption imaging cannot capture. However, the sensitivity and robustness of conventional X-ray interferometers are constrained by factors, such as fabrication precision, beam quality, and, importantly, noise originating from external sources or the sample itself. In this work, we demonstrate a novel X-ray interferometric method of phase measurement with enhanced immunity to various types of noise, by extending, for the first time, the concept of the SU(1,1) interferometer into the X-ray regime. We use a monolithic silicon perfect crystal device with two thin lamellae to generate correlated photon pairs via spontaneous parametric down-conversion (SPDC). Arrival time coincidence and sum-energy filtration allow a high-precision separation of the correlated photon pairs, which carry the phase information from orders-of-magnitude larger uncorrelated photonic noise. The novel SPDC-based interferometric method presented here is anticipated to exhibit enhanced immunity to vibrations as well as to mechanical and photonic noise, compared to conventional X-ray interferometers. Therefore, this SU(1,1) X-ray interferometer should pave the way to unprecedented precision in phase measurements, with transformative implications for a wide range of applications.
Show moreNov 2024 • bioRxiv
Yaron Trink, Achia Urbach, Benjamin Dekel, Peter Hohenstein, Jacob Goldberger, Tomer Kalisky
The significant heterogeneity of Wilms’ tumors between different patients is thought to arise from genetic and epigenetic distortions that occur during various stages of fetal kidney development in a way that is poorly understood. To address this, we characterized the heterogeneity of alternative mRNA splicing in Wilms’ tumors using a publicly available RNAseq dataset of high-risk Wilms’ tumors and normal kidney samples. Through Pareto task inference and cell deconvolution, we found that the tumors and normal kidney samples are organized according to progressive stages of kidney development within a triangle-shaped region in latent space, whose vertices, or “archetypes,” resemble the cap mesenchyme, the nephrogenic stroma, and epithelial tubular structures of the fetal kidney. We identified a set of genes that are alternatively spliced between tumors located in different regions of latent space and found that many of these genes are associated with the Epithelial to Mesenchymal Transition (EMT) and muscle development. Using motif enrichment analysis, we identified putative splicing regulators, some of which are associated with kidney development. Our findings provide new insights into the etiology of Wilms’ tumors and suggest that specific splicing mechanisms in early stages of development may contribute to tumor development in different patients.
Show moreNov 2024 • ChemCatChem
Stephanie Himpich, Marion Ringel, Renana Schwartz, Nicole Dimos, Ronja Driller, Carl PO Helmer, Prashant Kumar Gupta, Martina Haack, Dan Thomas Major, Thomas Brück, Bernhard Loll
Structural diversity of diterpenes is mediated by the enigmatic family of diterpene synthases. The overall enzymatic contribution hereby lies in a carefully concerted chemistry of highly reactive carbocation intermediates mainly guided by aromatic and polar amino acid side chains and the pyrophosphate cofactor. To date several studies aimed to shed light on the mechanism underlining terpene synthases chemistry. Specifically, the diterpene synthase CotB2 serves as model enzyme for detailed mutagenesis studies. Here we investigate the catalytic mechanism of CotB2 variant V80L in a holistic, biochemical, structural, and computational biology approach. We were able to identify an altered product profile compared to CotB2WT for the substrates geranylgeranyl diphosphate and farnesyl diphosphate. Moreover, we solved the crystal structure, and shed further light on terpene synthase chemistry by modelling of the …
Show moreNov 2024 • synthesis 20 (20of), 20country, 2024
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Show moreNov 2024
Yogendra Kumar, BEN Dlugatch, Ananya Maddegalla, Yuri Glagovsky, Natalia Fridman, Sri Harsha Akella, Nicole Leifer, Doron Aurbach, Dmitry Bravo-Zhivotovski, Malachi Noked
The development of efficient electrolytes is crucial for advancing magnesium (Mg) batteries, which hold promise for next-generation energy storage systems. Previously, electrolytes such as [Mg2(µ-Cl)3•6THF]+ [Ph4Al]-, A, and [Mg2(µ-Cl)3•6THF]+ [Ph3AlCl]-, B, have been studied, but their performance has been limited by issues related to ion dissociation and electrochemical stability. In this study, we report the synthesis of novel electrolytes by introducing polydentate ligands to these known systems, leading to the formation of [DME•MgCl•3THF]+ [Ph4Al]- 1 and [DG•MgCl•2THF]+ [Ph4Al]- 2, [Mg•3DME]2+ [Ph3AlCl-]2 3 and [Mg•2DG]2+ [Ph3AlCl-]2 4. These firstly discovered compounds were thoroughly characterized using X-ray crystallography and NMR spectroscopy. Our findings reveal that the choice of counter anion plays a pivotal role in the products and mechanism of the dissociation of the bridged [Mg2(µ-Cl)3•6THF]+ cation upon the addition of polydentate ligands. Specifically, with the [Ph4Al]- counter anion (precursor A), the dissociation results in a [MgCl]+ mono-cation, while with the [Ph3AlCl]- counter anion (precursor B), a [Mg]2+ divalent cation is formed. The resultant MgCl2 byproduct enhances solubility, expands electrochemical windows, and improves cyclic stability, leading to superior electrochemical performance of the new electrolytes (1, 2, 3, and 4) compared to the original precursors. These insights offer valuable guidelines for the design and synthesis of advanced electrolytes for rechargeable magnesium batteries, potentially paving the way for more efficient and stable energy storage solutions.
Show moreNov 2024 • Nature communications
Lior Peri, Donna Matzov, Dominic R Huxley, Alon Rainish, Fabrizio Fierro, Liel Sapir, Tara Pfeiffer, Lukas Waterloo, Harald Hübner, Yoav Peleg, Peter Gmeiner, Peter J McCormick, Dorothee Weikert, Masha Y Niv, Moran Shalev-Benami
Bitter taste receptors (TAS2Rs), a subfamily of G-protein coupled receptors (GPCRs) expressed orally and extraorally, elicit signaling in response to a large set of tastants. Among 25 functional TAS2Rs encoded in the human genome, TAS2R14 is the most promiscuous, and responds to hundreds of chemically diverse ligands. Here we present the cryo–electron microscopy (cryo-EM) structure of the human TAS2R14 in complex with its signaling partner gustducin, and bound to flufenamic acid (FFA), a clinically approved nonsteroidal anti-inflammatory drug. The structure reveals an unusual binding mode, where two copies of FFA are bound at distinct pockets: one at the canonical receptor site within the trans-membrane bundle, and the other in the intracellular facet, bridging the receptor with gustducin. Together with a pocket-specific BRET-based ligand binding assay, these results illuminate bitter taste signaling and …
Show moreNov 2024 • Heliyon
Saja Nasser, Gili Cohen-Taguri, Tali Mass, Iddo Pinkas, Gil Goobes
In the original published version of this article, the graphical abstract was omitted. The authors wish to update the article with the graphical abstract included. The authors apologize for the error. Both the HTML and PDF versions of the article have been updated to correct the error.
Show moreNov 2024 • Journal of the American Chemical Society
Qidi Wang, Chenglong Zhao, Xia Hu, Jianlin Wang, Swapna Ganapathy, Stephen Eustace, Xuedong Bai, Baohua Li, Hong Li, Doron Aurbach, Marnix Wagemaker
The formation of stable interphases on the electrodes is crucial for rechargeable lithium (Li) batteries. However, next-generation high-energy batteries face challenges in controlling interphase formation due to the high reactivity and structural changes of electrodes, leading to reduced stability and slow ion transport, which accelerate battery degradation. Here, we report an approach to address these issues by introducing multicomponent grain-boundary-rich interphase that boosts the rapid transport of ions and enhances passivation toward prolonged lifespan. This is guided by fundamental principles of solid-state ionics and geological crystallization differentiation theory, achieved through improved solvation chemistry. Demonstrations showcase how the introduction of the interphase substantially impacts the Li-ion transport across the interphase and the electrode–electrolyte compatibility in cost-effective electrolyte …
Show moreNov 2024 • arXiv preprint arXiv:2311.00590
Ilya Olevsko, Omer Shavit, Moshe Feldberg, Yossi Abulafia, Adi Salomon, Martin Oheim
Recent progress has boosted the resolving power of optical microscopies to spatial dimensions well below the diffraction limit. Yet, axial super-resolution and axial single-molecule localisation typically require more complicated implementations than their lateral counterparts. In the present work, we propose a simple solution for axial metrology by providing a multi-layered single-excitation, dual-emission test slide, in which axial distance is colour-encoded. Our test slide combines on a standard microscope coverslip substrate two flat, thin, uniform and brightly emitting fluorophore layers, separated by a nanometric transparent spacer layer having a refractive index close to a biological cell. The ensemble is sealed in an index-matched protective polymer. As a proof-of-principle, we estimate the light confinement resulting from evanescent-wave excitation in total internal reflection fluorescence (TIRF) microscopy. Our test sample permits, even for the non-expert user, a facile axial metrology at the sub-100-nm scale, a critical requirement for axial super-resolution, as well as near-surface imaging, spectroscopy and sensing.
Show moreNov 2024 • Investigative Ophthalmology & Visual Science
Basel Obied, Stephen Richard, Alon Zahavi, Hila Kreizman-Shefer, Jacob Bajar, Dror Fixler, Matea Krmpotić, Olga Girshevitz, Nitza Goldenberg-Cohen
Nov 2024 • Nucleic Acids Research, gkae1083, 2024
Pietro D’Addabbo, Roni Cohen-Fultheim, Itamar Twersky, Adriano Fonzino, Domenico Alessandro Silvestris, Ananth Prakash, Pietro Luca Mazzacuva, Juan Antonio Vizcaino, Andrew Green, Blake Sweeney, Andy Yates, Yvonne Lussi, Jie Luo, Maria-Jesus Martin, Eli Eisenberg, Erez Y Levanon, Graziano Pesole, Ernesto Picardi
A-to-I RNA editing is the most common non-transient epitranscriptome modification. It plays several roles in human physiology and has been linked to several disorders. Large-scale deep transcriptome sequencing has fostered the characterization of A-to-I editing at the single nucleotide level and the development of dedicated computational resources. REDIportal is a unique and specialized database collecting ∼16 million of putative A-to-I editing sites designed to face the current challenges of epitranscriptomics. Its running version has been enriched with sites from the TCGA project (using data from 31 studies). REDIportal provides an accurate, sustainable and accessible tool enriched with interconnections with widespread ELIXIR core resources such as Ensembl, RNAcentral, UniProt and PRIDE. Additionally, REDIportal now includes information regarding RNA editing in putative double-stranded RNAs …
Show moreNov 2024 • Oxford University Press
Pietro D’Addabbo, Roni Cohen-Fultheim, Itamar Twersky, Adriano Fonzino, Domenico Alessandro Silvestris, Ananth Prakash, Pietro Luca Mazzacuva, Juan Antonio Vizcaino, Andrew Green, Blake Sweeney, Andy Yates, Yvonne Lussi, Jie Luo, Maria-Jesus Martin, Eli Eisenberg, Erez Y Levanon, Graziano Pesole, Ernesto Picardi
A-to-I RNA editing is the most common non-transient epitranscriptome modification. It plays several roles in human physiology and has been linked to several disorders. Large-scale deep transcriptome sequencing has fostered the characterization of A-to-I editing at the single nucleotide level and the development of dedicated computational resources. REDIportal is a unique and specialized database collecting ∼16 million of putative A-to-I editing sites designed to face the current challenges of epitranscriptomics. Its running version has been enriched with sites from the TCGA project (using data from 31 studies). REDIportal provides an accurate, sustainable and accessible tool enriched with interconnections with widespread ELIXIR core resources such as Ensembl, RNAcentral, UniProt and PRIDE. Additionally, REDIportal now includes information regarding RNA editing in putative double-stranded RNAs …
Show moreOct 2024 • Nature Nanotechnology
Lorenzo Orsini, Hanan Herzig Sheinfux, Yandong Li, Seojoo Lee, Gian Marcello Andolina, Orazio Scarlatella, Matteo Ceccanti, Karuppasamy Soundarapandian, Eli Janzen, James H Edgar, Gennady Shvets, Frank HL Koppens
Topological photonics offers the opportunity to control light propagation in a way that is robust from fabrication disorders and imperfections. However, experimental demonstrations have remained on the order of the vacuum wavelength. Theoretical proposals have shown topological edge states that can propagate robustly while embracing deep subwavelength confinement that defies diffraction limits. Here we show the experimental proof of these deep subwavelength topological edge states by implementing periodic modulation of hyperbolic phonon polaritons within a van der Waals heterostructure composed of isotopically pure hexagonal boron nitride flakes on patterned gold films. The topological edge state is confined in a subdiffraction volume of 0.021 µm3, which is four orders of magnitude smaller than the free-space excitation wavelength volume used to probe the system, while maintaining the resonance …
Show moreOct 2024 • Journal of Magnesium and Alloys, 2024
Dedy Setiawan, Hyeonjun Lee, Jangwook Pyun, Amey Nimkar, Netanel Shpigel, Daniel Sharon, Seung-Tae Hong, Doron Aurbach, Munseok S Chae
Magnesium-ion batteries (MIBs) are promising candidates for lithium-ion batteries because of their abundance, non-toxicity, and favorable electrochemical properties. This review explores the reaction mechanisms and electrochemical characteristics of Mg-alloy anode materials. While Mg metal anodes provide high volumetric capacity and dendrite-free electrodeposition, their practical application is hindered by challenges such as sluggish Mg²⁺ ion diffusion and electrolyte compatibility. Alloy-type anodes that incorporate groups XIII, XIV, and XV elements have the potential to overcome these limitations. We review various Mg alloys, emphasizing their alloying/dealloying reaction mechanisms, their theoretical capacities, and the practical aspects of MIBs. Furthermore, we discuss the influence of the electrolyte composition on the reversibility and efficiency of these alloy anodes. Emphasis is placed on overcoming …
Show moreOct 2024 • Small
Naresh Vangapally, David Lusztig, Suman Rathod, Amreen Bano, Hadar Scalar, Sri Harsha Akella, Malachi Noked, Dan T Major, Ion C Halalay, Suresh Sriramulu, Shalom Luski, Doron Aurbach
Li‐ion batteries based on high specific capacity LixSiO‐Graphite anodes and LiNi0.89Co0.05 Mn0.05Al0.01O2 (NCMA) cathodes may have numerous practical applications owing to high energy density without a necessary compromise on safety. SiO, which is an attractive Li insertion anode material, offers more cycling stability than Si and a higher capacity than graphite. Therefore, a new trend has emerged for developing composite C‐Si anodes, possessing the excellent cyclability of graphite coupled with high capacity SiO. The composite structure described herein prevents the volume expansion of SiO and maintains the structural integrity during prolonged cycling. However, graphite electrodes suffer from exfoliation in propylene carbonate (PC) based electrolyte solutions, which avoids well known safety benefits related to a possible use of PC based electrolyte solutions in all kinds of Li batteries. Herein, it is …
Show moreOct 2024 • Nature Medicine
Johanna Klughammer, Daniel L Abravanel, Åsa Segerstolpe, Timothy R Blosser, Yury Goltsev, Yi Cui, Daniel R Goodwin, Anubhav Sinha, Orr Ashenberg, Michal Slyper, Sébastien Vigneau, Judit Jané‐Valbuena, Shahar Alon, Chiara Caraccio, Judy Chen, Ofir Cohen, Nicole Cullen, Laura K DelloStritto, Danielle Dionne, Janet Files, Allison Frangieh, Karla Helvie, Melissa E Hughes, Stephanie Inga, Abhay Kanodia, Ana Lako, Colin MacKichan, Simon Mages, Noa Moriel, Evan Murray, Sara Napolitano, Kyleen Nguyen, Mor Nitzan, Rebecca Ortiz, Miraj Patel, Kathleen L Pfaff, Caroline Porter, Asaf Rotem, Sarah Strauss, Robert Strasser, Aaron R Thorner, Madison Turner, Isaac Wakiro, Julia Waldman, Jingyi Wu, Jorge Gómez Tejeda Zañudo, Diane Zhang, Nancy U Lin, Sara M Tolaney, Eric P Winer, Edward S Boyden, Fei Chen, Garry P Nolan, Scott J Rodig, Xiaowei Zhuang, Orit Rozenblatt-Rosen, Bruce E Johnson, Aviv Regev, Nikhil Wagle
Although metastatic disease is the leading cause of cancer-related deaths, its tumor microenvironment remains poorly characterized due to technical and biospecimen limitations. In this study, we assembled a multi-modal spatial and cellular map of 67 tumor biopsies from 60 patients with metastatic breast cancer across diverse clinicopathological features and nine anatomic sites with detailed clinical annotations. We combined single-cell or single-nucleus RNA sequencing for all biopsies with a panel of four spatial expression assays (Slide-seq, MERFISH, ExSeq and CODEX) and H&E staining of consecutive serial sections from up to 15 of these biopsies. We leveraged the coupled measurements to provide reference points for the utility and integration of different experimental techniques and used them to assess variability in cell type composition and expression as well as emerging spatial expression …
Show moreOct 2024 • Active Photonic Platforms (APP) 2024 13110, 1311002, 2024
T Bucher, Y Kurman, K Wang, Q Yan, A Niedermayr, R Ruimy, H Nahari, R Dahan, H Herzig Sheinfux, GM Vanacore, I Kaminer
Recent advancements in ultrafast electron microscopy have provided direct access to polariton dynamics, visualizing such dynamics in space and time. This work presents new experimental results revealing a myriad of phenomena involving interactions of vortex-anti-vortex pairs, their creation and annihilation. We show new behaviors that became accessible thanks to a new development in electron microscopy - Free-Electron Ramsey Imaging (FERI) - which enabled extracting both the sub-cycle and group dynamics of polariton wavepackets. Our demonstrations involve optical phonon-polaritons in hexagonal boron nitride (hBN) and Molybdenum oxide, renowned for their unique dispersion and novel wavepacket propagations behaviors. These discoveries not only enhance our understanding of vortex phenomena across various systems, but also offer promising avenues for accessing new kinds of light-matter …
Show moreOct 2024 • Journal of Magnesium and Alloys, 2024
Dedy Setiawan, Hyeonjun Lee, Jangwook Pyun, Amey Nimkar, Netanel Shpigel, Daniel Sharon, Seung-Tae Hong, Doron Aurbach, Munseok S Chae
Magnesium-ion batteries (MIBs) are promising candidates for lithium-ion batteries because of their abundance, non-toxicity, and favorable electrochemical properties. This review explores the reaction mechanisms and electrochemical characteristics of Mg-alloy anode materials. While Mg metal anodes provide high volumetric capacity and dendrite-free electrodeposition, their practical application is hindered by challenges such as sluggish Mg²⁺ ion diffusion and electrolyte compatibility. Alloy-type anodes that incorporate groups XIII, XIV, and XV elements have the potential to overcome these limitations. We review various Mg alloys, emphasizing their alloying/dealloying reaction mechanisms, their theoretical capacities, and the practical aspects of MIBs. Furthermore, we discuss the influence of the electrolyte composition on the reversibility and efficiency of these alloy anodes. Emphasis is placed on overcoming …
Show moreOct 2024 • bioRxiv
Eric Engelbrecht, Oscar L Rodriguez, Kaitlyn Shields, Steven Schulze, David Tieri, Uddalok Jana, Gur Yaari, William Lees, Melissa L Smith, Corey T Watson
Immunoglobulins (IGs), critical components of the human immune system, are composed of heavy and light protein chains encoded at three genomic loci. The IG Kappa (IGK) chain locus consists of two large, inverted segmental duplications. The complexity of IG loci has hindered effective use of standard high-throughput methods for characterizing genetic variation within these regions. To overcome these limitations, we leverage long-read sequencing to create haplotype-resolved IGK assemblies in an ancestrally diverse cohort (n=36), representing the first comprehensive description of IGK haplotype variation at population-scale. We identify extensive locus polymorphism, including novel single nucleotide variants (SNVs) and a common novel ~24.7 Kbp structural variant harboring a functional IGKV gene. Among 47 functional IGKV genes, we identify 141 alleles, 64 (45.4%) of which were not previously curated. We report inter-population differences in allele frequencies for 14 of the IGKV genes, including alleles unique to specific populations within this dataset. Finally, we identify haplotypes carrying signatures of gene conversion that associate with enrichment of SNVs in the IGK distal region. These data provide a critical resource of curated genomic reference information from diverse ancestries, laying a foundation for advancing our understanding of population-level genetic variation in the IGK locus.
Show moreOct 2024 • Nature nanotechnology
Longlong Wang, Ayan Mukherjee, Chang-Yang Kuo, Sankalpita Chakrabarty, Reut Yemini, Arrelaine A Dameron, Jaime W DuMont, Sri Harsha Akella, Arka Saha, Sarah Taragin, Hagit Aviv, Doron Naveh, Daniel Sharon, Ting-Shan Chan, Hong-Ji Lin, Jyh-Fu Lee, Chien-Te Chen, Boyang Liu, Xiangwen Gao, Suddhasatwa Basu, Zhiwei Hu, Doron Aurbach, Peter G Bruce, Malachi Noked
A critical current challenge in the development of all-solid-state lithium batteries (ASSLBs) is reducing the cost of fabrication without compromising the performance. Here we report a sulfide ASSLB based on a high-energy, Co-free LiNiO2 cathode with a robust outside-in structure. This promising cathode is enabled by the high-pressure O2 synthesis and subsequent atomic layer deposition of a unique ultrathin LixAlyZnzOδ protective layer comprising a LixAlyZnzOδ surface coating region and an Al and Zn near-surface doping region. This high-quality artificial interphase enhances the structural stability and interfacial dynamics of the cathode as it mitigates the contact loss and continuous side reactions at the cathode/solid electrolyte interface. As a result, our ASSLBs exhibit a high areal capacity (4.65 mAh cm−2), a high specific cathode capacity (203 mAh g−1), superior cycling stability (92% capacity retention …
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