--- OA_place: repository OA_type: green _id: '21685' abstract: - lang: eng text: Nonlinear optics has become the workhorse for countless applications in classical and quantum optics, from optical bistability to single photon pair generation. However, the intrinsic weakness of optical nonlinearity has meant that large input powers and weak output powers are often a necessity in nonlinear frequency conversion. Here, motivated by recent advances in using non-Hermitian photonics and gain/loss engineering to enable non-reciprocal light transport, we explore how the interplay between non-Hermiticity and optical nonlinearity leads to a fundamentally new regime of nonlinear frequency conversion. We show how non-Hermitian coupling between discrete frequency modes can result in non-reciprocal flow of energy in the frequency dimension, closely resembling the non-Hermitian skin effect (NHSE). Applying our theory to a multimode nonlinear cavity supporting cascaded nonlinear processes, we create an asymmetric infrared (IR) comb that features a ``skin'' frequency mode populated with efficiency exceeding 85\%. Furthermore, we demonstrate how three-wave mixing processes in the non-reciprocal infrared comb we generate enables terahertz (THz) generation exceeding the Manley-Rowe limit. We then show how the non-reciprocal frequency conversion is robust against cavity defects and disorder that cause random fluctuations in the dissipation rate for different modes. Moreover, in certain regimes, the nonlinear, non-Hermitian system supports stable limit cycles that can enable multimode pulsing with picosecond pulse widths and GHz repetition rates. Finally, we explore how the system can be applied to generate simultaneous IR and THz frequency combs, potentially unlocking novel applications in spectroscopy and metrology. article_number: '2409.14299' article_processing_charge: No arxiv: 1 author: - first_name: Sahil full_name: Pontula, Sahil last_name: Pontula - first_name: Sachin full_name: Vaidya, Sachin last_name: Vaidya - first_name: Charles full_name: Roques-Carmes, Charles id: e2e68fc9-6505-11ef-a541-eb4e72cc3e82 last_name: Roques-Carmes - first_name: Shiekh Zia full_name: Uddin, Shiekh Zia last_name: Uddin - first_name: Marin full_name: Soljacic, Marin last_name: Soljacic - first_name: Yannick full_name: Salamin, Yannick last_name: Salamin citation: ama: Pontula S, Vaidya S, Roques-Carmes C, Uddin SZ, Soljacic M, Salamin Y. Non-reciprocal frequency conversion in a multimode nonlinear system. arXiv. doi:10.48550/arXiv.2409.14299 apa: Pontula, S., Vaidya, S., Roques-Carmes, C., Uddin, S. Z., Soljacic, M., & Salamin, Y. (n.d.). Non-reciprocal frequency conversion in a multimode nonlinear system. arXiv. https://doi.org/10.48550/arXiv.2409.14299 chicago: Pontula, Sahil, Sachin Vaidya, Charles Roques-Carmes, Shiekh Zia Uddin, Marin Soljacic, and Yannick Salamin. “Non-Reciprocal Frequency Conversion in a Multimode Nonlinear System.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2409.14299. ieee: S. Pontula, S. Vaidya, C. Roques-Carmes, S. Z. Uddin, M. Soljacic, and Y. Salamin, “Non-reciprocal frequency conversion in a multimode nonlinear system,” arXiv. . ista: Pontula S, Vaidya S, Roques-Carmes C, Uddin SZ, Soljacic M, Salamin Y. Non-reciprocal frequency conversion in a multimode nonlinear system. arXiv, 2409.14299. mla: Pontula, Sahil, et al. “Non-Reciprocal Frequency Conversion in a Multimode Nonlinear System.” ArXiv, 2409.14299, doi:10.48550/arXiv.2409.14299. short: S. Pontula, S. Vaidya, C. Roques-Carmes, S.Z. Uddin, M. Soljacic, Y. Salamin, ArXiv (n.d.). date_created: 2026-04-09T09:10:41Z date_published: 2024-09-22T00:00:00Z date_updated: 2026-04-13T10:49:12Z day: '22' doi: 10.48550/arXiv.2409.14299 extern: '1' external_id: arxiv: - '2409.14299' fulldoi: https://doi.org/10.48550/arXiv.2409.14299 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2409.14299 month: '09' oa: 1 oa_version: Preprint publication: arXiv publication_status: submitted scopus_import: '1' status: public title: Non-reciprocal frequency conversion in a multimode nonlinear system type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- OA_place: repository OA_type: green _id: '21686' abstract: - lang: eng text: Scintillation describes the conversion of high-energy particles into light in transparent media and finds diverse applications such as high-energy particle detection and industrial and medical imaging. This process operates on multiple timescales, with the final radiative step consisting of spontaneous emission, which can be modeled within the framework of quasi-equilibrium fluctuational electrodynamics. Scintillation can therefore be controlled and enhanced via nanophotonic effects, which has been proposed and experimentally demonstrated. Such designs have thus far obeyed Lorentz reciprocity, meaning there is a direct equivalence between scintillation emission and absorption by the scintillator. However, scintillators that do not obey Lorentz reciprocity have not been explored, even though they represent a novel platform for probing emission which is both nonequilibrium and nonreciprocal in nature. In this work, we propose to harness nonreciprocity to achieve directional control of scintillation emission, granting an additional degree of control over scintillation. Such directionality of light output is important in improving collection efficiencies along the directions where detectors are located. We present the design of a nonreciprocal scintillator using a one-dimensional magnetophotonic crystal in the Voigt configuration. Our work demonstrates the potential of controlling nonequilibrium emission such as scintillation by breaking reciprocity and expands the space of nanophotonic design for achieving such control. article_number: '2409.17002' article_processing_charge: No arxiv: 1 author: - first_name: Olivia Y. full_name: Long, Olivia Y. last_name: Long - first_name: Simo full_name: Pajovic, Simo last_name: Pajovic - first_name: Charles full_name: Roques-Carmes, Charles id: e2e68fc9-6505-11ef-a541-eb4e72cc3e82 last_name: Roques-Carmes - first_name: Yoichiro full_name: Tsurimaki, Yoichiro last_name: Tsurimaki - first_name: Nicholas full_name: Rivera, Nicholas last_name: Rivera - first_name: Marin full_name: Soljačić, Marin last_name: Soljačić - first_name: Svetlana V. full_name: Boriskina, Svetlana V. last_name: Boriskina - first_name: Shanhui full_name: Fan, Shanhui last_name: Fan citation: ama: Long OY, Pajovic S, Roques-Carmes C, et al. Nonreciprocal scintillation using one-dimensional magneto-optical photonic crystals. arXiv. doi:10.48550/arXiv.2409.17002 apa: Long, O. Y., Pajovic, S., Roques-Carmes, C., Tsurimaki, Y., Rivera, N., Soljačić, M., … Fan, S. (n.d.). Nonreciprocal scintillation using one-dimensional magneto-optical photonic crystals. arXiv. https://doi.org/10.48550/arXiv.2409.17002 chicago: Long, Olivia Y., Simo Pajovic, Charles Roques-Carmes, Yoichiro Tsurimaki, Nicholas Rivera, Marin Soljačić, Svetlana V. Boriskina, and Shanhui Fan. “Nonreciprocal Scintillation Using One-Dimensional Magneto-Optical Photonic Crystals.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2409.17002. ieee: O. Y. Long et al., “Nonreciprocal scintillation using one-dimensional magneto-optical photonic crystals,” arXiv. . ista: Long OY, Pajovic S, Roques-Carmes C, Tsurimaki Y, Rivera N, Soljačić M, Boriskina SV, Fan S. Nonreciprocal scintillation using one-dimensional magneto-optical photonic crystals. arXiv, 2409.17002. mla: Long, Olivia Y., et al. “Nonreciprocal Scintillation Using One-Dimensional Magneto-Optical Photonic Crystals.” ArXiv, 2409.17002, doi:10.48550/arXiv.2409.17002. short: O.Y. Long, S. Pajovic, C. Roques-Carmes, Y. Tsurimaki, N. Rivera, M. Soljačić, S.V. Boriskina, S. Fan, ArXiv (n.d.). date_created: 2026-04-09T09:10:41Z date_published: 2024-09-25T00:00:00Z date_updated: 2026-04-13T10:48:09Z day: '25' doi: 10.48550/arXiv.2409.17002 extern: '1' external_id: arxiv: - '2409.17002' fulldoi: https://doi.org/10.48550/arXiv.2409.17002 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2409.17002 month: '09' oa: 1 oa_version: Preprint publication: arXiv publication_status: submitted scopus_import: '1' status: public title: Nonreciprocal scintillation using one-dimensional magneto-optical photonic crystals type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- OA_place: repository OA_type: green _id: '21689' abstract: - lang: eng text: Metasurfaces -- ultrathin structures composed of subwavelength optical elements -- have revolutionized light manipulation by enabling precise control over electromagnetic waves' amplitude, phase, polarization, and spectral properties. Concurrently, computational imaging leverages algorithms to reconstruct images from optically processed signals, overcoming limitations of traditional imaging systems. This review explores the synergistic integration of metaoptics and computational imaging, "computational metaoptics," which combines the physical wavefront shaping ability of metasurfaces with advanced computational algorithms to enhance imaging performance beyond conventional limits. We discuss how computational metaoptics addresses the inherent limitations of single-layer metasurfaces in achieving multifunctionality without compromising efficiency. By treating metasurfaces as physical preconditioners and co-designing them with reconstruction algorithms through end-to-end (inverse) design, it is possible to jointly optimize the optical hardware and computational software. This holistic approach allows for the automatic discovery of optimal metasurface designs and reconstruction methods that significantly improve imaging capabilities. Advanced applications enabled by computational metaoptics are highlighted, including phase imaging and quantum state measurement, which benefit from the metasurfaces' ability to manipulate complex light fields and the computational algorithms' capacity to reconstruct high-dimensional information. We also examine performance evaluation challenges, emphasizing the need for new metrics that account for the combined optical and computational nature of these systems. Finally, we identify new frontiers in computational metaoptics which point toward a future where computational metaoptics may play a central role in advancing imaging science and technology. article_number: '2411.09133' article_processing_charge: No arxiv: 1 author: - first_name: Charles full_name: Roques-Carmes, Charles id: e2e68fc9-6505-11ef-a541-eb4e72cc3e82 last_name: Roques-Carmes - first_name: Kai full_name: Wang, Kai last_name: Wang - first_name: Yuanmu full_name: Yang, Yuanmu last_name: Yang - first_name: Arka full_name: Majumdar, Arka last_name: Majumdar - first_name: Zin full_name: Lin, Zin last_name: Lin citation: ama: Roques-Carmes C, Wang K, Yang Y, Majumdar A, Lin Z. Computational metaoptics for imaging. arXiv. doi:10.48550/arXiv.2411.09133 apa: Roques-Carmes, C., Wang, K., Yang, Y., Majumdar, A., & Lin, Z. (n.d.). Computational metaoptics for imaging. arXiv. https://doi.org/10.48550/arXiv.2411.09133 chicago: Roques-Carmes, Charles, Kai Wang, Yuanmu Yang, Arka Majumdar, and Zin Lin. “Computational Metaoptics for Imaging.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2411.09133. ieee: C. Roques-Carmes, K. Wang, Y. Yang, A. Majumdar, and Z. Lin, “Computational metaoptics for imaging,” arXiv. . ista: Roques-Carmes C, Wang K, Yang Y, Majumdar A, Lin Z. Computational metaoptics for imaging. arXiv, 2411.09133. mla: Roques-Carmes, Charles, et al. “Computational Metaoptics for Imaging.” ArXiv, 2411.09133, doi:10.48550/arXiv.2411.09133. short: C. Roques-Carmes, K. Wang, Y. Yang, A. Majumdar, Z. Lin, ArXiv (n.d.). date_created: 2026-04-09T09:10:41Z date_published: 2024-11-14T00:00:00Z date_updated: 2026-04-13T09:53:49Z day: '14' doi: 10.48550/arXiv.2411.09133 extern: '1' external_id: arxiv: - '2411.09133' fulldoi: https://doi.org/10.48550/arXiv.2411.09133 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2411.09133 month: '11' oa: 1 oa_version: Preprint publication: arXiv publication_status: submitted scopus_import: '1' status: public title: Computational metaoptics for imaging type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- OA_place: repository OA_type: green _id: '21690' abstract: - lang: eng text: Many quantum systems exhibit high sensitivity to their initial conditions, where microscopic quantum fluctuations can significantly influence macroscopic observables. Understanding how quantum states may influence the behavior of nonlinear dynamic systems may open new avenues in controlling light-matter interactions. To explore this issue, we analyze the sensitivity of a fundamental quantum optical process - parametric oscillation - to quantum initializations. Focusing on optical parametric oscillators (OPOs), we demonstrate that the quantum statistics of arbitrary initial states are imprinted in the early-stage dynamics and can persist in the steady-state probabilities. We derive the "quantum sensitivity" of parametric oscillators, linking the initial quantum state to the system's steady-state outcomes, highlighting how losses and parametric gain govern the system's quantum sensitivity. Moreover, we show that these findings extend beyond OPOs to a broader class of nonlinear systems, including Josephson junction based superconducting circuits. Our work opens the way to a new class of experiments that can test the sensitivity of macroscopic systems to quantum initial conditions and offers a pathway for controlling systems with quantum degrees of freedom. article_number: :2412.02887 article_processing_charge: No arxiv: 1 author: - first_name: Alex full_name: Gu, Alex last_name: Gu - first_name: Jamison full_name: Sloan, Jamison last_name: Sloan - first_name: Charles full_name: Roques-Carmes, Charles id: e2e68fc9-6505-11ef-a541-eb4e72cc3e82 last_name: Roques-Carmes - first_name: Seou full_name: Choi, Seou last_name: Choi - first_name: Eric I. full_name: Rosenthal, Eric I. last_name: Rosenthal - first_name: Michael full_name: Horodynski, Michael last_name: Horodynski - first_name: Yannick full_name: Salamin, Yannick last_name: Salamin - first_name: Jelena full_name: Vučković, Jelena last_name: Vučković - first_name: Marin full_name: Soljačić, Marin last_name: Soljačić citation: ama: Gu A, Sloan J, Roques-Carmes C, et al. Quantum sensitivity of parametric oscillators. arXiv. doi:10.48550/arXiv.2412.02887 apa: Gu, A., Sloan, J., Roques-Carmes, C., Choi, S., Rosenthal, E. I., Horodynski, M., … Soljačić, M. (n.d.). Quantum sensitivity of parametric oscillators. arXiv. https://doi.org/10.48550/arXiv.2412.02887 chicago: Gu, Alex, Jamison Sloan, Charles Roques-Carmes, Seou Choi, Eric I. Rosenthal, Michael Horodynski, Yannick Salamin, Jelena Vučković, and Marin Soljačić. “Quantum Sensitivity of Parametric Oscillators.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2412.02887. ieee: A. Gu et al., “Quantum sensitivity of parametric oscillators,” arXiv. . ista: Gu A, Sloan J, Roques-Carmes C, Choi S, Rosenthal EI, Horodynski M, Salamin Y, Vučković J, Soljačić M. Quantum sensitivity of parametric oscillators. arXiv, :2412.02887. mla: Gu, Alex, et al. “Quantum Sensitivity of Parametric Oscillators.” ArXiv, :2412.02887, doi:10.48550/arXiv.2412.02887. short: A. Gu, J. Sloan, C. Roques-Carmes, S. Choi, E.I. Rosenthal, M. Horodynski, Y. Salamin, J. Vučković, M. Soljačić, ArXiv (n.d.). date_created: 2026-04-09T09:10:41Z date_published: 2024-12-03T00:00:00Z date_updated: 2026-04-13T09:52:34Z day: '03' doi: 10.48550/arXiv.2412.02887 extern: '1' external_id: arxiv: - '2412.02887' fulldoi: https://doi.org/10.48550/arXiv.2412.02887 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2412.02887 month: '12' oa: 1 oa_version: Preprint publication: arXiv publication_status: submitted scopus_import: '1' status: public title: Quantum sensitivity of parametric oscillators type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- OA_place: repository OA_type: green _id: '21691' abstract: - lang: eng text: Light-matter interaction with squeezed vacuum has received much interest for the ability to enhance the native interaction strength between an atom and a photon with a reservoir assumed to have an infinite bandwidth. Here, we study a model of parametrically driven cavity quantum electrodynamics (cavity QED) for enhancing light-matter interaction while subjected to a finite-bandwidth squeezed vacuum drive. Our method is capable of unveiling the effect of relative bandwidth as well as squeezing required to observe the anticipated anti-crossing spectrum and enhanced cooperativity without the ideal squeezed bath assumption. Furthermore, we analyze the practicality of said models when including intrinsic photon loss due to resonators imperfection. With these results, we outline the requirements for experimentally implementing an effectively squeezed bath in solid-state platforms such as InAs quantum dot cavity QED such that \textit{in situ} control and enhancement of light-matter interaction could be realized. article_number: '2412.15068' article_processing_charge: No arxiv: 1 author: - first_name: Trung Kiên full_name: Lê, Trung Kiên last_name: Lê - first_name: Daniil M. full_name: Lukin, Daniil M. last_name: Lukin - first_name: Charles full_name: Roques-Carmes, Charles id: e2e68fc9-6505-11ef-a541-eb4e72cc3e82 last_name: Roques-Carmes - first_name: Aviv full_name: Karnieli, Aviv last_name: Karnieli - first_name: Eran full_name: Lustig, Eran last_name: Lustig - first_name: Melissa A. full_name: Guidry, Melissa A. last_name: Guidry - first_name: Shanhui full_name: Fan, Shanhui last_name: Fan - first_name: Jelena full_name: Vučković, Jelena last_name: Vučković citation: ama: Lê TK, Lukin DM, Roques-Carmes C, et al. Cavity quantum electrodynamics in finite-bandwidth squeezed reservoir. arXiv. doi:10.48550/arXiv.2412.15068 apa: Lê, T. K., Lukin, D. M., Roques-Carmes, C., Karnieli, A., Lustig, E., Guidry, M. A., … Vučković, J. (n.d.). Cavity quantum electrodynamics in finite-bandwidth squeezed reservoir. arXiv. https://doi.org/10.48550/arXiv.2412.15068 chicago: Lê, Trung Kiên, Daniil M. Lukin, Charles Roques-Carmes, Aviv Karnieli, Eran Lustig, Melissa A. Guidry, Shanhui Fan, and Jelena Vučković. “Cavity Quantum Electrodynamics in Finite-Bandwidth Squeezed Reservoir.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2412.15068. ieee: T. K. Lê et al., “Cavity quantum electrodynamics in finite-bandwidth squeezed reservoir,” arXiv. . ista: Lê TK, Lukin DM, Roques-Carmes C, Karnieli A, Lustig E, Guidry MA, Fan S, Vučković J. Cavity quantum electrodynamics in finite-bandwidth squeezed reservoir. arXiv, 2412.15068. mla: Lê, Trung Kiên, et al. “Cavity Quantum Electrodynamics in Finite-Bandwidth Squeezed Reservoir.” ArXiv, 2412.15068, doi:10.48550/arXiv.2412.15068. short: T.K. Lê, D.M. Lukin, C. Roques-Carmes, A. Karnieli, E. Lustig, M.A. Guidry, S. Fan, J. Vučković, ArXiv (n.d.). date_created: 2026-04-09T09:10:41Z date_published: 2024-12-19T00:00:00Z date_updated: 2026-04-13T09:50:09Z day: '19' doi: 10.48550/arXiv.2412.15068 extern: '1' external_id: arxiv: - '2412.15068' fulldoi: https://doi.org/10.48550/arXiv.2412.15068 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2412.15068 month: '12' oa: 1 oa_version: Preprint publication: arXiv publication_status: submitted scopus_import: '1' status: public title: Cavity quantum electrodynamics in finite-bandwidth squeezed reservoir type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- OA_place: repository OA_type: green _id: '21692' abstract: - lang: eng text: Scintillation, the process of converting high-energy radiation to detectable visible light, is pivotal in advanced technologies spanning from medical diagnostics to fundamental scientific research. Despite significant advancements toward faster and more efficient scintillators, there remains a fundamental limit arising from the intrinsic properties of scintillating materials. The scintillation process culminates in spontaneous emission of visible light, which is restricted in rate by the oscillator strength of individual emission centers. Here, we observe a novel collective emission phenomenon under X-ray excitation, breaking this limit and accelerating the emission. Our observation reveals that strong interactions between simultaneously excited coupled perovskite quantum dots can create collective radioluminescence. This effect is characterized by a spectral shift and an enhanced rate of emission, with an average lifetime of 230 ps, 14 times faster than their room temperature spontaneous emission. It has been established that such quantum dots exhibit superfluorescence under UV excitation. However, X-ray superfluorescence is inherently different, as each high-energy photon creates multiple synchronized excitation events, triggered by a photoelectron and resulting in even faster emission rates, a larger spectral shift, and a broader spectrum. This observation is consistent with a quantum-optical analysis explaining both the UV-driven and X-ray-driven effects. We use a Hanbury-Brown-Twiss g^(2) (τ) setup to analyze the temperature-dependent temporal response of these scintillators. Collective radioluminescence breaks the limit of scintillation lifetime based on spontaneous emission and could dramatically improve time-of-flight detector performance, introducing quantum enhancements to scintillation science. article_number: '2412.21101' article_processing_charge: No arxiv: 1 author: - first_name: Shaul full_name: Katznelson, Shaul last_name: Katznelson - first_name: Shai full_name: Levy, Shai last_name: Levy - first_name: Alexey full_name: Gorlach, Alexey last_name: Gorlach - first_name: Nathan full_name: Regev, Nathan last_name: Regev - first_name: Michael full_name: Birk, Michael last_name: Birk - first_name: Chen full_name: Mechel, Chen last_name: Mechel - first_name: Offek full_name: Tziperman, Offek last_name: Tziperman - first_name: Roman full_name: Schuetz, Roman last_name: Schuetz - first_name: Rotem full_name: Strassberg, Rotem last_name: Strassberg - first_name: Georgy full_name: Dosovitsky, Georgy last_name: Dosovitsky - first_name: Charles full_name: Roques-Carmes, Charles id: e2e68fc9-6505-11ef-a541-eb4e72cc3e82 last_name: Roques-Carmes - first_name: Yehonadav full_name: Bekenstein, Yehonadav last_name: Bekenstein - first_name: Ido full_name: Kaminer, Ido last_name: Kaminer citation: ama: Katznelson S, Levy S, Gorlach A, et al. Superfluorescent scintillation from coupled perovskite quantum dots. arXiv. doi:10.48550/arXiv.2412.21101 apa: Katznelson, S., Levy, S., Gorlach, A., Regev, N., Birk, M., Mechel, C., … Kaminer, I. (n.d.). Superfluorescent scintillation from coupled perovskite quantum dots. arXiv. https://doi.org/10.48550/arXiv.2412.21101 chicago: Katznelson, Shaul, Shai Levy, Alexey Gorlach, Nathan Regev, Michael Birk, Chen Mechel, Offek Tziperman, et al. “Superfluorescent Scintillation from Coupled Perovskite Quantum Dots.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2412.21101. ieee: S. Katznelson et al., “Superfluorescent scintillation from coupled perovskite quantum dots,” arXiv. . ista: Katznelson S, Levy S, Gorlach A, Regev N, Birk M, Mechel C, Tziperman O, Schuetz R, Strassberg R, Dosovitsky G, Roques-Carmes C, Bekenstein Y, Kaminer I. Superfluorescent scintillation from coupled perovskite quantum dots. arXiv, 2412.21101. mla: Katznelson, Shaul, et al. “Superfluorescent Scintillation from Coupled Perovskite Quantum Dots.” ArXiv, 2412.21101, doi:10.48550/arXiv.2412.21101. short: S. Katznelson, S. Levy, A. Gorlach, N. Regev, M. Birk, C. Mechel, O. Tziperman, R. Schuetz, R. Strassberg, G. Dosovitsky, C. Roques-Carmes, Y. Bekenstein, I. Kaminer, ArXiv (n.d.). date_created: 2026-04-09T09:10:41Z date_published: 2024-12-30T00:00:00Z date_updated: 2026-04-13T09:48:01Z day: '30' doi: 10.48550/arXiv.2412.21101 extern: '1' external_id: arxiv: - '2412.21101' fulldoi: https://doi.org/10.48550/arXiv.2412.21101 language: - iso: eng main_file_link: - open_access: '1' url: ' https://doi.org/10.48550/arXiv.2412.21101' month: '12' oa: 1 oa_version: Preprint publication: arXiv publication_status: submitted scopus_import: '1' status: public title: Superfluorescent scintillation from coupled perovskite quantum dots type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- OA_type: closed access _id: '21806' abstract: - lang: eng text: Light-responsive liquid crystal elastomer networks (LCNs) have received significant interest due to their potential application in soft robotics and shape-morphing devices. Here, we present a systematic examination of light-responsive LCNs prepared using a catalyst-free Diels–Alder cycloaddition and a new azobenzene functionalized monomer for main-chain incorporation. The networks have robust mechanical stiffness that can be reversibly modulated by 1 GPa by turning the UV light on and off. This study highlights the contribution of photothermal softening to reversibly control rheological properties of the newly developed LCNs and demonstrates the ability to tune the modulus on demand. We believe this work will guide future developments of light-responsive LCNs based on the newly developed Diels–Alder cycloaddition. article_processing_charge: No article_type: original author: - first_name: Minwook full_name: Park, Minwook last_name: Park - first_name: Jesus full_name: Guillen Campos, Jesus last_name: Guillen Campos - first_name: Friedrich J full_name: Stricker, Friedrich J id: 7aca2cfc-46cf-11f0-abd3-8c96b5186745 last_name: Stricker - first_name: Javier full_name: Read de Alaniz, Javier last_name: Read de Alaniz citation: ama: Park M, Guillen Campos J, Stricker FJ, Read de Alaniz J. Photo-responsive Diels-Alder based azobenzene-functionalized main-chain liquid crystal networks. Journal of Materials Chemistry C. 2024;12(31):11976-11981. doi:10.1039/d4tc01281j apa: Park, M., Guillen Campos, J., Stricker, F. J., & Read de Alaniz, J. (2024). Photo-responsive Diels-Alder based azobenzene-functionalized main-chain liquid crystal networks. Journal of Materials Chemistry C. Royal Society of Chemistry. https://doi.org/10.1039/d4tc01281j chicago: Park, Minwook, Jesus Guillen Campos, Friedrich J Stricker, and Javier Read de Alaniz. “Photo-Responsive Diels-Alder Based Azobenzene-Functionalized Main-Chain Liquid Crystal Networks.” Journal of Materials Chemistry C. Royal Society of Chemistry, 2024. https://doi.org/10.1039/d4tc01281j. ieee: M. Park, J. Guillen Campos, F. J. Stricker, and J. Read de Alaniz, “Photo-responsive Diels-Alder based azobenzene-functionalized main-chain liquid crystal networks,” Journal of Materials Chemistry C, vol. 12, no. 31. Royal Society of Chemistry, pp. 11976–11981, 2024. ista: Park M, Guillen Campos J, Stricker FJ, Read de Alaniz J. 2024. Photo-responsive Diels-Alder based azobenzene-functionalized main-chain liquid crystal networks. Journal of Materials Chemistry C. 12(31), 11976–11981. mla: Park, Minwook, et al. “Photo-Responsive Diels-Alder Based Azobenzene-Functionalized Main-Chain Liquid Crystal Networks.” Journal of Materials Chemistry C, vol. 12, no. 31, Royal Society of Chemistry, 2024, pp. 11976–81, doi:10.1039/d4tc01281j. short: M. Park, J. Guillen Campos, F.J. Stricker, J. Read de Alaniz, Journal of Materials Chemistry C 12 (2024) 11976–11981. date_created: 2026-05-06T10:43:33Z date_published: 2024-07-10T00:00:00Z date_updated: 2026-05-12T06:50:12Z day: '10' ddc: - '540' doi: 10.1039/d4tc01281j extern: '1' fulldoi: https://doi.org/10.1039/d4tc01281j intvolume: ' 12' issue: '31' language: - iso: eng month: '07' oa_version: None page: 11976-11981 publication: Journal of Materials Chemistry C publication_identifier: eissn: - 2050-7534 issnl: - 2050-7526 publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: Photo-responsive Diels-Alder based azobenzene-functionalized main-chain liquid crystal networks type: journal_article user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd volume: 12 year: '2024' ... --- OA_type: closed access _id: '21817' abstract: - lang: eng text: 'Ambidirectionality, which is the ability of structural elements to move beyond a reference state in two opposite directions, is common in nature. However, conventional soft materials are typically limited to a single, unidirectional deformation unless complex hybrid constructs are used. We exploited the combination of mesogen self-assembly, polymer chain elasticity, and polymerization-induced stress to design liquid crystalline elastomers that exhibit two mesophases: chevron smectic C (cSmC) and smectic A (SmA). Inducing the cSmC-SmA–isotropic phase transition led to an unusual inversion of the strain field in the microstructure, resulting in opposite deformation modes (e.g., consecutive shrinkage or expansion and right-handed or left-handed twisting and tilting in opposite directions) and high-frequency nonmonotonic oscillations. This ambidirectional movement is scalable and can be used to generate Gaussian transformations at the macroscale.' article_processing_charge: No article_type: original author: - first_name: Yuxing full_name: Yao, Yuxing last_name: Yao - first_name: Atalaya Milan full_name: Wilborn, Atalaya Milan last_name: Wilborn - first_name: Baptiste full_name: Lemaire, Baptiste last_name: Lemaire - first_name: Foteini full_name: Trigka, Foteini last_name: Trigka - first_name: Friedrich J full_name: Stricker, Friedrich J id: 7aca2cfc-46cf-11f0-abd3-8c96b5186745 last_name: Stricker - first_name: Alan H. full_name: Weible, Alan H. last_name: Weible - first_name: Shucong full_name: Li, Shucong last_name: Li - first_name: Robert K. A. full_name: Bennett, Robert K. A. last_name: Bennett - first_name: Tung Chun full_name: Cheung, Tung Chun last_name: Cheung - first_name: Alison full_name: Grinthal, Alison last_name: Grinthal - first_name: Mikhail full_name: Zhernenkov, Mikhail last_name: Zhernenkov - first_name: Guillaume full_name: Freychet, Guillaume last_name: Freychet - first_name: Patryk full_name: Wąsik, Patryk last_name: Wąsik - first_name: Boris full_name: Kozinsky, Boris last_name: Kozinsky - first_name: Michael M. full_name: Lerch, Michael M. last_name: Lerch - first_name: Xiaoguang full_name: Wang, Xiaoguang last_name: Wang - first_name: Joanna full_name: Aizenberg, Joanna last_name: Aizenberg citation: ama: Yao Y, Wilborn AM, Lemaire B, et al. Programming liquid crystal elastomers for multistep ambidirectional deformability. Science. 2024;386(6726):1161-1168. doi:10.1126/science.adq6434 apa: Yao, Y., Wilborn, A. M., Lemaire, B., Trigka, F., Stricker, F. J., Weible, A. H., … Aizenberg, J. (2024). Programming liquid crystal elastomers for multistep ambidirectional deformability. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.adq6434 chicago: Yao, Yuxing, Atalaya Milan Wilborn, Baptiste Lemaire, Foteini Trigka, Friedrich J Stricker, Alan H. Weible, Shucong Li, et al. “Programming Liquid Crystal Elastomers for Multistep Ambidirectional Deformability.” Science. American Association for the Advancement of Science, 2024. https://doi.org/10.1126/science.adq6434. ieee: Y. Yao et al., “Programming liquid crystal elastomers for multistep ambidirectional deformability,” Science, vol. 386, no. 6726. American Association for the Advancement of Science, pp. 1161–1168, 2024. ista: Yao Y, Wilborn AM, Lemaire B, Trigka F, Stricker FJ, Weible AH, Li S, Bennett RKA, Cheung TC, Grinthal A, Zhernenkov M, Freychet G, Wąsik P, Kozinsky B, Lerch MM, Wang X, Aizenberg J. 2024. Programming liquid crystal elastomers for multistep ambidirectional deformability. Science. 386(6726), 1161–1168. mla: Yao, Yuxing, et al. “Programming Liquid Crystal Elastomers for Multistep Ambidirectional Deformability.” Science, vol. 386, no. 6726, American Association for the Advancement of Science, 2024, pp. 1161–68, doi:10.1126/science.adq6434. short: Y. Yao, A.M. Wilborn, B. Lemaire, F. Trigka, F.J. Stricker, A.H. Weible, S. Li, R.K.A. Bennett, T.C. Cheung, A. Grinthal, M. Zhernenkov, G. Freychet, P. Wąsik, B. Kozinsky, M.M. Lerch, X. Wang, J. Aizenberg, Science 386 (2024) 1161–1168. date_created: 2026-05-06T10:54:51Z date_published: 2024-12-06T00:00:00Z date_updated: 2026-05-12T09:48:12Z day: '06' ddc: - '540' doi: 10.1126/science.adq6434 extern: '1' external_id: pmid: - '39636998' fulldoi: https://doi.org/10.1126/science.adq6434 intvolume: ' 386' issue: '6726' language: - iso: eng month: '12' oa_version: None page: 1161-1168 pmid: 1 publication: Science publication_identifier: eissn: - 1095-9203 issn: - 0036-8075 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' scopus_import: '1' status: public title: Programming liquid crystal elastomers for multistep ambidirectional deformability type: journal_article user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd volume: 386 year: '2024' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '21913' abstract: - lang: eng text: 'The HIRA histone chaperone complex is comprised of four protein subunits: HIRA, UBN1, CABIN1, and transiently associated ASF1a. All four subunits have been demonstrated to play a role in the deposition of the histone variant H3.3 onto areas of actively transcribed euchromatin in cells. The mechanism by which these subunits function together to drive histone deposition has remained poorly understood. Here we present biochemical and biophysical data supporting a model whereby ASF1a delivers histone H3.3/H4 dimers to the HIRA complex, H3.3/H4 tetramerization drives the association of two HIRA/UBN1 complexes, and the affinity of the histones for DNA drives release of ASF1a and subsequent histone deposition. These findings have implications for understanding how other histone chaperone complexes may mediate histone deposition.' acknowledgement: We would like to acknowledge Elliot Dean and Christina Freeman for technical assistance with recombinant protein expression in insect cells and members of the Marmorstein laboratory for many discussions related to this work. Schematic Figures were created with BioRender.com. article_number: '107604' article_processing_charge: Yes article_type: original author: - first_name: Austin full_name: Vogt, Austin last_name: Vogt - first_name: Mary full_name: Szurgot, Mary last_name: Szurgot - first_name: Lauren full_name: Gardner, Lauren id: f9dedd98-6d15-11f0-88a5-a7b4143fdec5 last_name: Gardner orcid: 0009-0000-5733-1546 - first_name: David C. full_name: Schultz, David C. last_name: Schultz - first_name: Ronen full_name: Marmorstein, Ronen last_name: Marmorstein citation: ama: Vogt A, Szurgot M, Gardner L, Schultz DC, Marmorstein R. HIRA complex deposition of histone H3.3 is driven by histone tetramerization and histone-DNA binding. Journal of Biological Chemistry. 2024;300(9). doi:10.1016/j.jbc.2024.107604 apa: Vogt, A., Szurgot, M., Gardner, L., Schultz, D. C., & Marmorstein, R. (2024). HIRA complex deposition of histone H3.3 is driven by histone tetramerization and histone-DNA binding. Journal of Biological Chemistry. Elsevier. https://doi.org/10.1016/j.jbc.2024.107604 chicago: Vogt, Austin, Mary Szurgot, Lauren Gardner, David C. Schultz, and Ronen Marmorstein. “HIRA Complex Deposition of Histone H3.3 Is Driven by Histone Tetramerization and Histone-DNA Binding.” Journal of Biological Chemistry. Elsevier, 2024. https://doi.org/10.1016/j.jbc.2024.107604. ieee: A. Vogt, M. Szurgot, L. Gardner, D. C. Schultz, and R. Marmorstein, “HIRA complex deposition of histone H3.3 is driven by histone tetramerization and histone-DNA binding,” Journal of Biological Chemistry, vol. 300, no. 9. Elsevier, 2024. ista: Vogt A, Szurgot M, Gardner L, Schultz DC, Marmorstein R. 2024. HIRA complex deposition of histone H3.3 is driven by histone tetramerization and histone-DNA binding. Journal of Biological Chemistry. 300(9), 107604. mla: Vogt, Austin, et al. “HIRA Complex Deposition of Histone H3.3 Is Driven by Histone Tetramerization and Histone-DNA Binding.” Journal of Biological Chemistry, vol. 300, no. 9, 107604, Elsevier, 2024, doi:10.1016/j.jbc.2024.107604. short: A. Vogt, M. Szurgot, L. Gardner, D.C. Schultz, R. Marmorstein, Journal of Biological Chemistry 300 (2024). date_created: 2026-05-24T08:25:45Z date_published: 2024-09-01T00:00:00Z date_updated: 2026-06-02T14:52:50Z day: '01' ddc: - '572' doi: 10.1016/j.jbc.2024.107604 extern: '1' external_id: pmid: - '39059488' fulldoi: https://doi.org/10.1016/j.jbc.2024.107604 has_accepted_license: '1' intvolume: ' 300' issue: '9' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.jbc.2024.107604 month: '09' oa: 1 oa_version: Published Version pmid: 1 publication: Journal of Biological Chemistry publication_identifier: eissn: - 1083-351X issn: - 0021-9258 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: HIRA complex deposition of histone H3.3 is driven by histone tetramerization and histone-DNA binding tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 300 year: '2024' ... --- OA_type: green _id: '21967' abstract: - lang: eng text: "Selection against deleterious mutations, called purifying selection, plays a central role in evolution and acts in all populations. It is known that the genetic patterns observed in genomic regions undergoing purifying selection differ from those resulting from neutral evolution. However, a comprehensive understanding of the underlying mechanisms shaping those patterns is still lacking.\r\n\r\nIn the present work, we use simulations combined with a genealogical approach to identify the effect of purifying selection on the ancestry and thus on the genetic diversity. Our analysis relies on the postulate that the genealogy belongs to the universality class of Beta-coalescents. Under this assumption, we derive statistics measuring the distortion of the genealogy. This approach allows us to consider a wide range of regimes (i.e. arbitrary selection and mutation strengths) and uncover a rich phase diagram. We find that, for strong selection, the limiting genealogy is given by Kingman’s coalescent on a polynomial timescale. As selection gets weaker, Muller’s ratchet starts operating, setting off the emergence of multiple mergers in the genealogical structures. Our results show that while multiple-merger coalescents are often interpreted as the signature of selective sweeps in rapidly adapting populations, these structures can also appear in the context of Muller’s ratchet." acknowledgement: This work was supported by the Austrian Academy of Science, DOC fellowship No 26293 (K.K.) and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101034413 (J.T.). Simulations were performed on the ISTA High-performance Computing Cluster. article_processing_charge: No author: - first_name: Kseniia full_name: Khudiakova, Kseniia id: 4E6DC800-AE37-11E9-AC72-31CAE5697425 last_name: Khudiakova orcid: 0000-0002-6246-1465 - first_name: Florin full_name: Boenkost, Florin last_name: Boenkost - first_name: Julie N full_name: Tourniaire, Julie N id: 5dc06dd8-8e51-11ec-9170-8d9c450cc216 last_name: Tourniaire citation: ama: Khudiakova K, Boenkost F, Tourniaire JN. Genealogies under purifying selection. bioRxiv. doi:10.1101/2024.10.15.618444 apa: Khudiakova, K., Boenkost, F., & Tourniaire, J. N. (n.d.). Genealogies under purifying selection. bioRxiv. https://doi.org/10.1101/2024.10.15.618444 chicago: Khudiakova, Kseniia, Florin Boenkost, and Julie N Tourniaire. “Genealogies under Purifying Selection.” BioRxiv, n.d. https://doi.org/10.1101/2024.10.15.618444. ieee: K. Khudiakova, F. Boenkost, and J. N. Tourniaire, “Genealogies under purifying selection,” bioRxiv. . ista: Khudiakova K, Boenkost F, Tourniaire JN. Genealogies under purifying selection. bioRxiv, 10.1101/2024.10.15.618444. mla: Khudiakova, Kseniia, et al. “Genealogies under Purifying Selection.” BioRxiv, doi:10.1101/2024.10.15.618444. short: K. Khudiakova, F. Boenkost, J.N. Tourniaire, BioRxiv (n.d.). corr_author: '1' date_created: 2026-06-09T12:14:08Z date_published: 2024-10-18T00:00:00Z date_updated: 2026-06-12T12:43:34Z day: '18' department: - _id: NiBa - _id: JaMa doi: 10.1101/2024.10.15.618444 ec_funded: 1 fulldoi: https://doi.org/10.1101/2024.10.15.618444 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2024.10.15.618444 month: '10' oa: 1 oa_version: Preprint project: - _id: 34d33d68-11ca-11ed-8bc3-ec13763c0ca8 grant_number: '26293' name: The impact of deleterious mutations on small populations - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: bioRxiv publication_status: draft related_material: record: - id: '21918' relation: dissertation_contains status: public status: public title: Genealogies under purifying selection tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: preprint user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2024' ... --- OA_place: repository OA_type: green _id: '13974' abstract: - lang: eng text: The Tverberg theorem is one of the cornerstones of discrete geometry. It states that, given a set X of at least (d+1)(r−1)+1 points in Rd, one can find a partition X=X1∪⋯∪Xr of X, such that the convex hulls of the Xi, i=1,…,r, all share a common point. In this paper, we prove a trengthening of this theorem that guarantees a partition which, in addition to the above, has the property that the boundaries of full-dimensional convex hulls have pairwise nonempty intersections. Possible generalizations and algorithmic aspects are also discussed. As a concrete application, we show that any n points in the plane in general position span ⌊n/3⌋ vertex-disjoint triangles that are pairwise crossing, meaning that their boundaries have pairwise nonempty intersections; this number is clearly best possible. A previous result of Álvarez-Rebollar et al. guarantees ⌊n/6⌋pairwise crossing triangles. Our result generalizes to a result about simplices in Rd, d≥2. acknowledgement: "Part of the research leading to this paper was done during the 16th Gremo Workshop on Open Problems (GWOP), Waltensburg, Switzerland, June 12–16, 2018. We thank Patrick Schnider for suggesting the problem, and Stefan Felsner, Malte Milatz, and Emo Welzl for fruitful discussions during the workshop. We also thank Stefan Felsner and Manfred Scheucher for finding, communicating the example from Sect. 3.3, and the kind permission to include their visualization of the point set. We thank Dömötör Pálvölgyi, the SoCG reviewers, and DCG reviewers for various helpful comments.\r\nR. Fulek gratefully acknowledges support from Austrian Science Fund (FWF), Project M2281-N35. A. Kupavskii was supported by the Advanced Postdoc.Mobility Grant no. P300P2_177839 of the Swiss National Science Foundation. Research by P. Valtr was supported by the Grant no. 18-19158 S of the Czech Science Foundation (GAČR)." article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Radoslav full_name: Fulek, Radoslav id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87 last_name: Fulek orcid: 0000-0001-8485-1774 - first_name: Bernd full_name: Gärtner, Bernd last_name: Gärtner - first_name: Andrey full_name: Kupavskii, Andrey last_name: Kupavskii - first_name: Pavel full_name: Valtr, Pavel last_name: Valtr - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 citation: ama: Fulek R, Gärtner B, Kupavskii A, Valtr P, Wagner U. The crossing Tverberg theorem. Discrete and Computational Geometry. 2024;72:831-848. doi:10.1007/s00454-023-00532-x apa: Fulek, R., Gärtner, B., Kupavskii, A., Valtr, P., & Wagner, U. (2024). The crossing Tverberg theorem. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-023-00532-x chicago: Fulek, Radoslav, Bernd Gärtner, Andrey Kupavskii, Pavel Valtr, and Uli Wagner. “The Crossing Tverberg Theorem.” Discrete and Computational Geometry. Springer Nature, 2024. https://doi.org/10.1007/s00454-023-00532-x. ieee: R. Fulek, B. Gärtner, A. Kupavskii, P. Valtr, and U. Wagner, “The crossing Tverberg theorem,” Discrete and Computational Geometry, vol. 72. Springer Nature, pp. 831–848, 2024. ista: Fulek R, Gärtner B, Kupavskii A, Valtr P, Wagner U. 2024. The crossing Tverberg theorem. Discrete and Computational Geometry. 72, 831–848. mla: Fulek, Radoslav, et al. “The Crossing Tverberg Theorem.” Discrete and Computational Geometry, vol. 72, Springer Nature, 2024, pp. 831–48, doi:10.1007/s00454-023-00532-x. short: R. Fulek, B. Gärtner, A. Kupavskii, P. Valtr, U. Wagner, Discrete and Computational Geometry 72 (2024) 831–848. date_created: 2023-08-06T22:01:12Z date_published: 2024-09-01T00:00:00Z date_updated: 2025-04-14T13:52:36Z day: '01' department: - _id: UlWa doi: 10.1007/s00454-023-00532-x external_id: arxiv: - '1812.04911' isi: - '001038546500001' fulldoi: https://doi.org/10.1007/s00454-023-00532-x intvolume: ' 72' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.1812.04911 month: '09' oa: 1 oa_version: Preprint page: 831-848 project: - _id: 261FA626-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02281 name: Eliminating intersections in drawings of graphs publication: Discrete and Computational Geometry publication_identifier: eissn: - 1432-0444 issn: - 0179-5376 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '6647' relation: earlier_version status: public scopus_import: '1' status: public title: The crossing Tverberg theorem type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 72 year: '2024' ... --- _id: '14400' abstract: - lang: eng text: "We consider the problem of computing the maximal probability of satisfying an \r\n-regular specification for stochastic, continuous-state, nonlinear systems evolving in discrete time. The problem reduces, after automata-theoretic constructions, to finding the maximal probability of satisfying a parity condition on a (possibly hybrid) state space. While characterizing the exact satisfaction probability is open, we show that a lower bound on this probability can be obtained by (I) computing an under-approximation of the qualitative winning region, i.e., states from which the parity condition can be enforced almost surely, and (II) computing the maximal probability of reaching this qualitative winning region.\r\nThe heart of our approach is a technique to symbolically compute the under-approximation of the qualitative winning region in step (I) via a finite-state abstraction of the original system as a \r\n-player parity game. Our abstraction procedure uses only the support of the probabilistic evolution; it does not use precise numerical transition probabilities. We prove that the winning set in the abstract -player game induces an under-approximation of the qualitative winning region in the original synthesis problem, along with a policy to solve it. By combining these contributions with (a) a symbolic fixpoint algorithm to solve \r\n-player games and (b) existing techniques for reachability policy synthesis in stochastic nonlinear systems, we get an abstraction-based algorithm for finding a lower bound on the maximal satisfaction probability.\r\nWe have implemented the abstraction-based algorithm in Mascot-SDS, where we combined the outlined abstraction step with our tool Genie (Majumdar et al., 2023) that solves \r\n-player parity games (through a reduction to Rabin games) more efficiently than existing algorithms. We evaluated our implementation on the nonlinear model of a perturbed bistable switch from the literature. We show empirically that the lower bound on the winning region computed by our approach is precise, by comparing against an over-approximation of the qualitative winning region. Moreover, our implementation outperforms a recently proposed tool for solving this problem by a large margin." acknowledgement: "We thank Daniel Hausmann and Nir Piterman for their valuable comments on an earlier version of the manuscript of our other paper [22] where we present, among other things, the parity fixpoint for 2 1/2-player games (for a slightly more general class of games) with a different and indirect proof of correctness. Based on their comments we observed that, unlike the other fixpoints that we present in [22], the parity fixpoint does not follow the exact same structure as its counterpart for 2-player games, which we also use int his paper.\r\nWe also thank Thejaswini Raghavan for observing that our symbolic parity fixpoint algorithm can be solved in quasi-polynomial time using recent improved algorithms for solving \r\n-calculus expressions. This significantly improved the complexity bounds of our algorithm in this paper.\r\nThe work of R. Majumdar and A.-K. Schmuck are partially supported by DFG, Germany project 389792660 TRR 248–CPEC. A.-K. Schmuck is additionally funded through DFG, Germany project (SCHM 3541/1-1). K. Mallik is supported by the ERC project ERC-2020-AdG 101020093. S. Soudjani is supported by the following projects: EPSRC EP/V043676/1, EIC 101070802, and ERC 101089047." article_number: '101430' article_processing_charge: Yes (in subscription journal) article_type: original arxiv: 1 author: - first_name: Rupak full_name: Majumdar, Rupak last_name: Majumdar - first_name: Kaushik full_name: Mallik, Kaushik id: 0834ff3c-6d72-11ec-94e0-b5b0a4fb8598 last_name: Mallik orcid: 0000-0001-9864-7475 - first_name: Anne Kathrin full_name: Schmuck, Anne Kathrin last_name: Schmuck - first_name: Sadegh full_name: Soudjani, Sadegh last_name: Soudjani citation: ama: 'Majumdar R, Mallik K, Schmuck AK, Soudjani S. Symbolic control for stochastic systems via finite parity games. Nonlinear Analysis: Hybrid Systems. 2024;51(2). doi:10.1016/j.nahs.2023.101430' apa: 'Majumdar, R., Mallik, K., Schmuck, A. K., & Soudjani, S. (2024). Symbolic control for stochastic systems via finite parity games. Nonlinear Analysis: Hybrid Systems. Elsevier. https://doi.org/10.1016/j.nahs.2023.101430' chicago: 'Majumdar, Rupak, Kaushik Mallik, Anne Kathrin Schmuck, and Sadegh Soudjani. “Symbolic Control for Stochastic Systems via Finite Parity Games.” Nonlinear Analysis: Hybrid Systems. Elsevier, 2024. https://doi.org/10.1016/j.nahs.2023.101430.' ieee: 'R. Majumdar, K. Mallik, A. K. Schmuck, and S. Soudjani, “Symbolic control for stochastic systems via finite parity games,” Nonlinear Analysis: Hybrid Systems, vol. 51, no. 2. Elsevier, 2024.' ista: 'Majumdar R, Mallik K, Schmuck AK, Soudjani S. 2024. Symbolic control for stochastic systems via finite parity games. Nonlinear Analysis: Hybrid Systems. 51(2), 101430.' mla: 'Majumdar, Rupak, et al. “Symbolic Control for Stochastic Systems via Finite Parity Games.” Nonlinear Analysis: Hybrid Systems, vol. 51, no. 2, 101430, Elsevier, 2024, doi:10.1016/j.nahs.2023.101430.' short: 'R. Majumdar, K. Mallik, A.K. Schmuck, S. Soudjani, Nonlinear Analysis: Hybrid Systems 51 (2024).' corr_author: '1' date_created: 2023-10-08T22:01:15Z date_published: 2024-02-01T00:00:00Z date_updated: 2025-04-14T07:55:55Z day: '01' ddc: - '000' department: - _id: ToHe doi: 10.1016/j.nahs.2023.101430 ec_funded: 1 external_id: arxiv: - '2101.00834' isi: - '001093188100001' file: - access_level: open_access checksum: 4eab70274d1004ea411f7f0e74c033ac content_type: application/pdf creator: dernst date_created: 2024-07-16T10:26:41Z date_updated: 2024-07-16T10:26:41Z file_id: '17258' file_name: 2024_NonlinearAnalysis_Majumdar.pdf file_size: 1787569 relation: main_file success: 1 file_date_updated: 2024-07-16T10:26:41Z fulldoi: https://doi.org/10.1016/j.nahs.2023.101430 has_accepted_license: '1' intvolume: ' 51' isi: 1 issue: '2' language: - iso: eng month: '02' oa: 1 oa_version: Published Version project: - _id: 62781420-2b32-11ec-9570-8d9b63373d4d call_identifier: H2020 grant_number: '101020093' name: Vigilant Algorithmic Monitoring of Software publication: 'Nonlinear Analysis: Hybrid Systems' publication_identifier: issn: - 1751-570X publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Symbolic control for stochastic systems via finite parity games tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 51 year: '2024' ... --- OA_place: publisher OA_type: hybrid _id: '14463' abstract: - lang: eng text: Inversions are thought to play a key role in adaptation and speciation, suppressing recombination between diverging populations. Genes influencing adaptive traits cluster in inversions, and changes in inversion frequencies are associated with environmental differences. However, in many organisms, it is unclear if inversions are geographically and taxonomically widespread. The intertidal snail, Littorina saxatilis, is one such example. Strong associations between putative polymorphic inversions and phenotypic differences have been demonstrated between two ecotypes of L. saxatilis in Sweden and inferred elsewhere, but no direct evidence for inversion polymorphism currently exists across the species range. Using whole genome data from 107 snails, most inversion polymorphisms were found to be widespread across the species range. The frequencies of some inversion arrangements were significantly different among ecotypes, suggesting a parallel adaptive role. Many inversions were also polymorphic in the sister species, L. arcana, hinting at an ancient origin. acknowledgement: We would like to thank members of the Littorina team for their advice and feedback during this project. In particular, we thank Alan Le Moan, who inspired us to look at heterozygosity differences to identify inversions, and Katherine Hearn for helping with the PCA scripts. We thank Edinburgh Genomics for library preparation and sequencing. Sample collections, sequencing and data preparation were supported by the European Research Council (ERC-2015-AdG-693030- BARRIERS) and the Natural Environment Research Council (NE/P001610/1). The analysis was supported by the Swedish Research Council (vetenskaprådet; 2018-03695_VR) and the Portuguese Foundation for Science and Technology (Fundación para a Ciência e Tecnologia) through a research project (PTDC/BIA-EVL/1614/2021) and CEEC contract (2020.00275.CEECIND). article_number: e17160 article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: James full_name: Reeve, James last_name: Reeve - first_name: Roger K. full_name: Butlin, Roger K. last_name: Butlin - first_name: Eva L. full_name: Koch, Eva L. last_name: Koch - first_name: Sean full_name: Stankowski, Sean id: 43161670-5719-11EA-8025-FABC3DDC885E last_name: Stankowski - first_name: Rui full_name: Faria, Rui last_name: Faria citation: ama: Reeve J, Butlin RK, Koch EL, Stankowski S, Faria R. Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana). Molecular Ecology. 2024;33(24). doi:10.1111/mec.17160 apa: Reeve, J., Butlin, R. K., Koch, E. L., Stankowski, S., & Faria, R. (2024). Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana). Molecular Ecology. Wiley. https://doi.org/10.1111/mec.17160 chicago: Reeve, James, Roger K. Butlin, Eva L. Koch, Sean Stankowski, and Rui Faria. “Chromosomal Inversion Polymorphisms Are Widespread across the Species Ranges of Rough Periwinkles (Littorina Saxatilis and L. Arcana).” Molecular Ecology. Wiley, 2024. https://doi.org/10.1111/mec.17160. ieee: J. Reeve, R. K. Butlin, E. L. Koch, S. Stankowski, and R. Faria, “Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana),” Molecular Ecology, vol. 33, no. 24. Wiley, 2024. ista: Reeve J, Butlin RK, Koch EL, Stankowski S, Faria R. 2024. Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana). Molecular Ecology. 33(24), e17160. mla: Reeve, James, et al. “Chromosomal Inversion Polymorphisms Are Widespread across the Species Ranges of Rough Periwinkles (Littorina Saxatilis and L. Arcana).” Molecular Ecology, vol. 33, no. 24, e17160, Wiley, 2024, doi:10.1111/mec.17160. short: J. Reeve, R.K. Butlin, E.L. Koch, S. Stankowski, R. Faria, Molecular Ecology 33 (2024). date_created: 2023-10-29T23:01:17Z date_published: 2024-12-01T00:00:00Z date_updated: 2025-01-09T07:53:18Z day: '01' ddc: - '570' department: - _id: NiBa doi: 10.1111/mec.17160 external_id: isi: - '001085119000001' pmid: - '37843465' file: - access_level: open_access checksum: 686576036663f489c2d079df3079d126 content_type: application/pdf creator: dernst date_created: 2025-01-09T07:52:12Z date_updated: 2025-01-09T07:52:12Z file_id: '18785' file_name: 2024_MolecularEcology_Reeve.pdf file_size: 6228700 relation: main_file success: 1 file_date_updated: 2025-01-09T07:52:12Z fulldoi: https://doi.org/10.1111/mec.17160 has_accepted_license: '1' intvolume: ' 33' isi: 1 issue: '24' language: - iso: eng month: '12' oa: 1 oa_version: Published Version pmid: 1 publication: Molecular Ecology publication_identifier: eissn: - 1365-294X issn: - 0962-1083 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana) tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 33 year: '2024' ... --- APC_amount: 3040,36 EUR OA_place: publisher OA_type: hybrid _id: '14478' abstract: - lang: eng text: Entire chromosomes are typically only transmitted vertically from one generation to the next. The horizontal transfer of such chromosomes has long been considered improbable, yet gained recent support in several pathogenic fungi where it may affect the fitness or host specificity. To date, it is unknown how these transfers occur, how common they are and whether they can occur between different species. In this study, we show multiple independent instances of horizontal transfers of the same accessory chromosome between two distinct strains of the asexual entomopathogenic fungusMetarhizium robertsiiduring experimental co-infection of its insect host, the Argentine ant. Notably, only the one chromosome – but no other – was transferred from the donor to the recipient strain. The recipient strain, now harboring the accessory chromosome, exhibited a competitive advantage under certain host conditions. By phylogenetic analysis we further demonstrate that the same accessory chromosome was horizontally transferred in a natural environment betweenM. robertsiiand another congeneric insect pathogen,M. guizhouense. Hence horizontal chromosome transfer is not limited to the observed frequent events within species during experimental infections but also occurs naturally across species. The transferred accessory chromosome contains genes that might be involved in its preferential horizontal transfer, encoding putative histones and histone-modifying enzymes, but also putative virulence factors that may support its establishment. Our study reveals that both intra- and interspecies horizontal transfer of entire chromosomes is more frequent than previously assumed, likely representing a not uncommon mechanism for gene exchange.Significance StatementThe enormous success of bacterial pathogens has been attributed to their ability to exchange genetic material between one another. Similarly, in eukaryotes, horizontal transfer of genetic material allowed the spread of virulence factors across species. The horizontal transfer of whole chromosomes could be an important pathway for such exchange of genetic material, but little is known about the origin of transferable chromosomes and how frequently they are exchanged. Here, we show that the transfer of accessory chromosomes - chromosomes that are non-essential but may provide fitness benefits - is common during fungal co-infections and is even possible between distant pathogenic species, highlighting the importance of horizontal gene transfer via chromosome transfer also for the evolution and function of eukaryotic pathogens. acknowledgement: We thank Bernhardt Steinwender, Jorgen Eilenberg, and Nicolai V. Meyling for the fungal strains. We further thank Chengshu Wang for providing the short sequencing reads for M. guizhouense ARESF977 he used for his published genome assembly, and Kristian Ullrich for help in the bioinformatics analysis for methylation pattern in Nanopore reads, and the VBC and the Max Planck Society for the use of their sequencing centers. We thank Barbara Milutinović and Hinrich Schulenburg for discussion, and Tal Dagan and Jens Rolff for comments on a previous version of the manuscript. Fig. 1A was created with BioRender.com. This study received funding by the European Research Council under the European Union’s Horizon 2020 Research and Innovation Programme (No. 771402; EPIDEMICSonCHIP) to S.C. and by the German Research Foundation (DFG grant HA9263/1-1) to M.H. article_number: e2316284121 article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Michael full_name: Habig, Michael last_name: Habig - first_name: Anna V full_name: Grasse, Anna V id: 406F989C-F248-11E8-B48F-1D18A9856A87 last_name: Grasse - first_name: Judith full_name: Müller, Judith last_name: Müller - first_name: Eva H. full_name: Stukenbrock, Eva H. last_name: Stukenbrock - first_name: Hanna full_name: Leitner, Hanna id: 8fc5c6f6-5903-11ec-abad-c83f046253e7 last_name: Leitner - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: ama: Habig M, Grasse AV, Müller J, Stukenbrock EH, Leitner H, Cremer S. Frequent horizontal chromosome transfer between asexual fungal insect pathogens. Proceedings of the National Academy of Sciences of the United States of America. 2024;121(11). doi:10.1073/pnas.2316284121 apa: Habig, M., Grasse, A. V., Müller, J., Stukenbrock, E. H., Leitner, H., & Cremer, S. (2024). Frequent horizontal chromosome transfer between asexual fungal insect pathogens. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2316284121 chicago: Habig, Michael, Anna V Grasse, Judith Müller, Eva H. Stukenbrock, Hanna Leitner, and Sylvia Cremer. “Frequent Horizontal Chromosome Transfer between Asexual Fungal Insect Pathogens.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2316284121. ieee: M. Habig, A. V. Grasse, J. Müller, E. H. Stukenbrock, H. Leitner, and S. Cremer, “Frequent horizontal chromosome transfer between asexual fungal insect pathogens,” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 11. National Academy of Sciences, 2024. ista: Habig M, Grasse AV, Müller J, Stukenbrock EH, Leitner H, Cremer S. 2024. Frequent horizontal chromosome transfer between asexual fungal insect pathogens. Proceedings of the National Academy of Sciences of the United States of America. 121(11), e2316284121. mla: Habig, Michael, et al. “Frequent Horizontal Chromosome Transfer between Asexual Fungal Insect Pathogens.” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 11, e2316284121, National Academy of Sciences, 2024, doi:10.1073/pnas.2316284121. short: M. Habig, A.V. Grasse, J. Müller, E.H. Stukenbrock, H. Leitner, S. Cremer, Proceedings of the National Academy of Sciences of the United States of America 121 (2024). corr_author: '1' date_created: 2023-10-31T13:30:00Z date_published: 2024-03-12T00:00:00Z date_updated: 2025-08-05T13:30:51Z day: '12' ddc: - '570' department: - _id: SyCr doi: 10.1073/pnas.2316284121 ec_funded: 1 external_id: isi: - '001207630200005' pmid: - '38442176' file: - access_level: open_access checksum: f5e871db617b682edc71fcd08670dc81 content_type: application/pdf creator: dernst date_created: 2024-03-19T09:02:57Z date_updated: 2024-03-19T09:02:57Z file_id: '15124' file_name: 2024_PNAS_Habig.pdf file_size: 5750361 relation: main_file success: 1 file_date_updated: 2024-03-19T09:02:57Z fulldoi: https://doi.org/10.1073/pnas.2316284121 has_accepted_license: '1' intvolume: ' 121' isi: 1 issue: '11' language: - iso: eng month: '03' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 2649B4DE-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '771402' name: Epidemics in ant societies on a chip publication: Proceedings of the National Academy of Sciences of the United States of America publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: Frequent horizontal chromosome transfer between asexual fungal insect pathogens tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 121 year: '2024' ... --- _id: '14479' abstract: - lang: eng text: 'In animals, parasitic infections impose significant fitness costs.1,2,3,4,5,6 Infected animals can alter their feeding behavior to resist infection,7,8,9,10,11,12 but parasites can manipulate animal foraging behavior to their own benefits.13,14,15,16 How nutrition influences host-parasite interactions is not well understood, as studies have mainly focused on the host and less on the parasite.9,12,17,18,19,20,21,22,23 We used the nutritional geometry framework24 to investigate the role of amino acids (AA) and carbohydrates (C) in a host-parasite system: the Argentine ant, Linepithema humile, and the entomopathogenic fungus, Metarhizium brunneum. First, using 18 diets varying in AA:C composition, we established that the fungus performed best on the high-amino-acid diet 1:4. Second, we found that the fungus reached this optimal diet when given various diet pairings, revealing its ability to cope with nutritional challenges. Third, we showed that the optimal fungal diet reduced the lifespan of healthy ants when compared with a high-carbohydrate diet but had no effect on infected ants. Fourth, we revealed that infected ant colonies, given a choice between the optimal fungal diet and a high-carbohydrate diet, chose the optimal fungal diet, whereas healthy colonies avoided it. Lastly, by disentangling fungal infection from host immune response, we demonstrated that infected ants foraged on the optimal fungal diet in response to immune activation and not as a result of parasite manipulation. Therefore, we revealed that infected ant colonies chose a diet that is costly for survival in the long term but beneficial in the short term—a form of collective self-medication.' acknowledgement: We are sincerely grateful to the referees for their valuable comments and suggestions, which helped us to improve the paper. We are thankful to Jorgen Eilenberg and Nicolai V. Meyling for the fungal strain, to Simon Tragust, Abel Bernadou, and Brian Lazarro for insightful discussions, to Iago Sanmartín-Villar, Léa Briard, Céline Maitrel, and Nolwenn Rissen for their help with the experiments. Furthermore, we thank Anna V. Grasse for help with the immune gene expression analyses. We thank Sergio Ibarra for creating the graphical abstract. E.C. was supported by a Fyssen Foundation grant and the Alexander von Humboldt Foundation. A.D. was supported by the CNRS. article_processing_charge: No article_type: original author: - first_name: Eniko full_name: Csata, Eniko last_name: Csata - first_name: Alfonso full_name: Perez-Escudero, Alfonso last_name: Perez-Escudero - first_name: Emmanuel full_name: Laury, Emmanuel last_name: Laury - first_name: Hanna full_name: Leitner, Hanna id: 8fc5c6f6-5903-11ec-abad-c83f046253e7 last_name: Leitner - first_name: Gerard full_name: Latil, Gerard last_name: Latil - first_name: Juerge full_name: Heinze, Juerge last_name: Heinze - first_name: Stephen full_name: Simpson, Stephen last_name: Simpson - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 - first_name: Audrey full_name: Dussutour, Audrey last_name: Dussutour citation: ama: Csata E, Perez-Escudero A, Laury E, et al. Fungal infection alters collective nutritional intake of ant colonies. Current Biology. 2024;34(4):902-909.e6. doi:10.1016/j.cub.2024.01.017 apa: Csata, E., Perez-Escudero, A., Laury, E., Leitner, H., Latil, G., Heinze, J., … Dussutour, A. (2024). Fungal infection alters collective nutritional intake of ant colonies. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2024.01.017 chicago: Csata, Eniko, Alfonso Perez-Escudero, Emmanuel Laury, Hanna Leitner, Gerard Latil, Juerge Heinze, Stephen Simpson, Sylvia Cremer, and Audrey Dussutour. “Fungal Infection Alters Collective Nutritional Intake of Ant Colonies.” Current Biology. Elsevier, 2024. https://doi.org/10.1016/j.cub.2024.01.017. ieee: E. Csata et al., “Fungal infection alters collective nutritional intake of ant colonies,” Current Biology, vol. 34, no. 4. Elsevier, p. 902–909.e6, 2024. ista: Csata E, Perez-Escudero A, Laury E, Leitner H, Latil G, Heinze J, Simpson S, Cremer S, Dussutour A. 2024. Fungal infection alters collective nutritional intake of ant colonies. Current Biology. 34(4), 902–909.e6. mla: Csata, Eniko, et al. “Fungal Infection Alters Collective Nutritional Intake of Ant Colonies.” Current Biology, vol. 34, no. 4, Elsevier, 2024, p. 902–909.e6, doi:10.1016/j.cub.2024.01.017. short: E. Csata, A. Perez-Escudero, E. Laury, H. Leitner, G. Latil, J. Heinze, S. Simpson, S. Cremer, A. Dussutour, Current Biology 34 (2024) 902–909.e6. date_created: 2023-10-31T13:30:20Z date_published: 2024-02-26T00:00:00Z date_updated: 2025-08-05T13:29:38Z day: '26' department: - _id: SyCr doi: 10.1016/j.cub.2024.01.017 external_id: isi: - '001195884300001' pmid: - '38307022' fulldoi: https://doi.org/10.1016/j.cub.2024.01.017 intvolume: ' 34' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2023.10.26.564092 month: '02' oa: 1 oa_version: Preprint page: 902-909.e6 pmid: 1 publication: Current Biology publication_identifier: eissn: - 1879-0445 issn: - 0960-9822 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Fungal infection alters collective nutritional intake of ant colonies type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 34 year: '2024' ... --- _id: '14543' abstract: - lang: eng text: The acyl-CoA-binding domain-containing protein 6 (ACBD6) is ubiquitously expressed, plays a role in the acylation of lipids and proteins, and regulates the N-myristoylation of proteins via N-myristoyltransferase enzymes (NMTs). However, its precise function in cells is still unclear, as is the consequence of ACBD6 defects on human pathophysiology. Utilizing exome sequencing and extensive international data sharing efforts, we identified 45 affected individuals from 28 unrelated families (consanguinity 93%) with bi-allelic pathogenic, predominantly loss-of-function (18/20) variants in ACBD6. We generated zebrafish and Xenopus tropicalis acbd6 knockouts by CRISPR/Cas9 and characterized the role of ACBD6 on protein N-myristoylation with YnMyr chemical proteomics in the model organisms and human cells, with the latter also being subjected further to ACBD6 peroxisomal localization studies. The affected individuals (23 males and 22 females), with ages ranging from 1 to 50 years old, typically present with a complex and progressive disease involving moderate-to-severe global developmental delay/intellectual disability (100%) with significant expressive language impairment (98%), movement disorders (97%), facial dysmorphism (95%), and mild cerebellar ataxia (85%) associated with gait impairment (94%), limb spasticity/hypertonia (76%), oculomotor (71%) and behavioural abnormalities (65%), overweight (59%), microcephaly (39%) and epilepsy (33%). The most conspicuous and common movement disorder was dystonia (94%), frequently leading to early-onset progressive postural deformities (97%), limb dystonia (55%), and cervical dystonia (31%). A jerky tremor in the upper limbs (63%), a mild head tremor (59%), parkinsonism/hypokinesia developing with advancing age (32%), and simple motor and vocal tics were among other frequent movement disorders. Midline brain malformations including corpus callosum abnormalities (70%), hypoplasia/agenesis of the anterior commissure (66%), short midbrain and small inferior cerebellar vermis (38% each), as well as hypertrophy of the clava (24%) were common neuroimaging findings. acbd6-deficient zebrafish and Xenopus models effectively recapitulated many clinical phenotypes reported in patients including movement disorders, progressive neuromotor impairment, seizures, microcephaly, craniofacial dysmorphism, and midbrain defects accompanied by developmental delay with increased mortality over time. Unlike ACBD5, ACBD6 did not show a peroxisomal localisation and ACBD6-deficiency was not associated with altered peroxisomal parameters in patient fibroblasts. Significant differences in YnMyr-labelling were observed for 68 co- and 18 post-translationally N-myristoylated proteins in patient-derived fibroblasts. N-Myristoylation was similarly affected in acbd6-deficient zebrafish and Xenopus tropicalis models, including Fus, Marcks, and Chchd-related proteins implicated in neurological diseases. The present study provides evidence that bi-allelic pathogenic variants in ACBD6 lead to a distinct neurodevelopmental syndrome accompanied by complex and progressive cognitive and movement disorders. article_processing_charge: No article_type: original author: - first_name: Rauan full_name: Kaiyrzhanov, Rauan last_name: Kaiyrzhanov - first_name: Aboulfazl full_name: Rad, Aboulfazl last_name: Rad - first_name: Sheng-Jia full_name: Lin, Sheng-Jia last_name: Lin - first_name: Aida full_name: Bertoli-Avella, Aida last_name: Bertoli-Avella - first_name: Wouter W full_name: Kallemeijn, Wouter W last_name: Kallemeijn - first_name: Annie full_name: Godwin, Annie last_name: Godwin - first_name: Maha S full_name: Zaki, Maha S last_name: Zaki - first_name: Kevin full_name: Huang, Kevin id: 3b3d2888-1ff6-11ee-9fa6-8f209ca91fe3 last_name: Huang orcid: 0000-0002-2512-7812 - first_name: Tracy full_name: Lau, Tracy last_name: Lau - first_name: Cassidy full_name: Petree, Cassidy last_name: Petree - first_name: Stephanie full_name: Efthymiou, Stephanie last_name: Efthymiou - first_name: Ehsan full_name: Ghayoor Karimiani, Ehsan last_name: Ghayoor Karimiani - first_name: Maja full_name: Hempel, Maja last_name: Hempel - first_name: Elizabeth A full_name: Normand, Elizabeth A last_name: Normand - first_name: Sabine full_name: Rudnik-Schöneborn, Sabine last_name: Rudnik-Schöneborn - first_name: Ulrich A full_name: Schatz, Ulrich A last_name: Schatz - first_name: Marc P full_name: Baggelaar, Marc P last_name: Baggelaar - first_name: Muhammad full_name: Ilyas, Muhammad last_name: Ilyas - first_name: Tipu full_name: Sultan, Tipu last_name: Sultan - first_name: Javeria Raza full_name: Alvi, Javeria Raza last_name: Alvi - first_name: Manizha full_name: Ganieva, Manizha last_name: Ganieva - first_name: Ben full_name: Fowler, Ben last_name: Fowler - first_name: Ruxandra full_name: Aanicai, Ruxandra last_name: Aanicai - first_name: Gulsen full_name: Akay Tayfun, Gulsen last_name: Akay Tayfun - first_name: Abdulaziz full_name: Al Saman, Abdulaziz last_name: Al Saman - first_name: Abdulrahman full_name: Alswaid, Abdulrahman last_name: Alswaid - first_name: Nafise full_name: Amiri, Nafise last_name: Amiri - first_name: Nilufar full_name: Asilova, Nilufar last_name: Asilova - first_name: Vorasuk full_name: Shotelersuk, Vorasuk last_name: Shotelersuk - first_name: Patra full_name: Yeetong, Patra last_name: Yeetong - first_name: Matloob full_name: Azam, Matloob last_name: Azam - first_name: Meisam full_name: Babaei, Meisam last_name: Babaei - first_name: Gholamreza full_name: Bahrami Monajemi, Gholamreza last_name: Bahrami Monajemi - first_name: Pouria full_name: Mohammadi, Pouria last_name: Mohammadi - first_name: Saeed full_name: Samie, Saeed last_name: Samie - first_name: Selina Husna full_name: Banu, Selina Husna last_name: Banu - first_name: Jorge Pinto full_name: Basto, Jorge Pinto last_name: Basto - first_name: Fanny full_name: Kortüm, Fanny last_name: Kortüm - first_name: Mislen full_name: Bauer, Mislen last_name: Bauer - first_name: Peter full_name: Bauer, Peter last_name: Bauer - first_name: Christian full_name: Beetz, Christian last_name: Beetz - first_name: Masoud full_name: Garshasbi, Masoud last_name: Garshasbi - first_name: Awatif full_name: Hameed Issa, Awatif last_name: Hameed Issa - first_name: Wafaa full_name: Eyaid, Wafaa last_name: Eyaid - first_name: Hind full_name: Ahmed, Hind last_name: Ahmed - first_name: Narges full_name: Hashemi, Narges last_name: Hashemi - first_name: Kazem full_name: Hassanpour, Kazem last_name: Hassanpour - first_name: Isabella full_name: Herman, Isabella last_name: Herman - first_name: Sherozjon full_name: Ibrohimov, Sherozjon last_name: Ibrohimov - first_name: Ban A full_name: Abdul-Majeed, Ban A last_name: Abdul-Majeed - first_name: Maria full_name: Imdad, Maria last_name: Imdad - first_name: Maksudjon full_name: Isrofilov, Maksudjon last_name: Isrofilov - first_name: Qassem full_name: Kaiyal, Qassem last_name: Kaiyal - first_name: Suliman full_name: Khan, Suliman last_name: Khan - first_name: Brian full_name: Kirmse, Brian last_name: Kirmse - first_name: Janet full_name: Koster, Janet last_name: Koster - first_name: Charles Marques full_name: Lourenço, Charles Marques last_name: Lourenço - first_name: Tadahiro full_name: Mitani, Tadahiro last_name: Mitani - first_name: Oana full_name: Moldovan, Oana last_name: Moldovan - first_name: David full_name: Murphy, David last_name: Murphy - first_name: Maryam full_name: Najafi, Maryam last_name: Najafi - first_name: Davut full_name: Pehlivan, Davut last_name: Pehlivan - first_name: Maria Eugenia full_name: Rocha, Maria Eugenia last_name: Rocha - first_name: Vincenzo full_name: Salpietro, Vincenzo last_name: Salpietro - first_name: Miriam full_name: Schmidts, Miriam last_name: Schmidts - first_name: Adel full_name: Shalata, Adel last_name: Shalata - first_name: Mohammad full_name: Mahroum, Mohammad last_name: Mahroum - first_name: Jawabreh Kassem full_name: Talbeya, Jawabreh Kassem last_name: Talbeya - first_name: Robert W full_name: Taylor, Robert W last_name: Taylor - first_name: Dayana full_name: Vazquez, Dayana last_name: Vazquez - first_name: Annalisa full_name: Vetro, Annalisa last_name: Vetro - first_name: Hans R full_name: Waterham, Hans R last_name: Waterham - first_name: Mashaya full_name: Zaman, Mashaya last_name: Zaman - first_name: Tina A full_name: Schrader, Tina A last_name: Schrader - first_name: Wendy K full_name: Chung, Wendy K last_name: Chung - first_name: Renzo full_name: Guerrini, Renzo last_name: Guerrini - first_name: James R full_name: Lupski, James R last_name: Lupski - first_name: Joseph full_name: Gleeson, Joseph last_name: Gleeson - first_name: Mohnish full_name: Suri, Mohnish last_name: Suri - first_name: Yalda full_name: Jamshidi, Yalda last_name: Jamshidi - first_name: Kailash P full_name: Bhatia, Kailash P last_name: Bhatia - first_name: Barbara full_name: Vona, Barbara last_name: Vona - first_name: Michael full_name: Schrader, Michael last_name: Schrader - first_name: Mariasavina full_name: Severino, Mariasavina last_name: Severino - first_name: Matthew full_name: Guille, Matthew last_name: Guille - first_name: Edward W full_name: Tate, Edward W last_name: Tate - first_name: Gaurav K full_name: Varshney, Gaurav K last_name: Varshney - first_name: Henry full_name: Houlden, Henry last_name: Houlden - first_name: Reza full_name: Maroofian, Reza last_name: Maroofian citation: ama: Kaiyrzhanov R, Rad A, Lin S-J, et al. Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders. Brain. 2024;147(4):1436-1456. doi:10.1093/brain/awad380 apa: Kaiyrzhanov, R., Rad, A., Lin, S.-J., Bertoli-Avella, A., Kallemeijn, W. W., Godwin, A., … Maroofian, R. (2024). Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders. Brain. Oxford University Press. https://doi.org/10.1093/brain/awad380 chicago: Kaiyrzhanov, Rauan, Aboulfazl Rad, Sheng-Jia Lin, Aida Bertoli-Avella, Wouter W Kallemeijn, Annie Godwin, Maha S Zaki, et al. “Bi-Allelic ACBD6 Variants Lead to a Neurodevelopmental Syndrome with Progressive and Complex Movement Disorders.” Brain. Oxford University Press, 2024. https://doi.org/10.1093/brain/awad380. ieee: R. Kaiyrzhanov et al., “Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders,” Brain, vol. 147, no. 4. Oxford University Press, pp. 1436–1456, 2024. ista: Kaiyrzhanov R, Rad A, Lin S-J, Bertoli-Avella A, Kallemeijn WW, Godwin A, Zaki MS, Huang K, Lau T, Petree C, Efthymiou S, Ghayoor Karimiani E, Hempel M, Normand EA, Rudnik-Schöneborn S, Schatz UA, Baggelaar MP, Ilyas M, Sultan T, Alvi JR, Ganieva M, Fowler B, Aanicai R, Akay Tayfun G, Al Saman A, Alswaid A, Amiri N, Asilova N, Shotelersuk V, Yeetong P, Azam M, Babaei M, Bahrami Monajemi G, Mohammadi P, Samie S, Banu SH, Basto JP, Kortüm F, Bauer M, Bauer P, Beetz C, Garshasbi M, Hameed Issa A, Eyaid W, Ahmed H, Hashemi N, Hassanpour K, Herman I, Ibrohimov S, Abdul-Majeed BA, Imdad M, Isrofilov M, Kaiyal Q, Khan S, Kirmse B, Koster J, Lourenço CM, Mitani T, Moldovan O, Murphy D, Najafi M, Pehlivan D, Rocha ME, Salpietro V, Schmidts M, Shalata A, Mahroum M, Talbeya JK, Taylor RW, Vazquez D, Vetro A, Waterham HR, Zaman M, Schrader TA, Chung WK, Guerrini R, Lupski JR, Gleeson J, Suri M, Jamshidi Y, Bhatia KP, Vona B, Schrader M, Severino M, Guille M, Tate EW, Varshney GK, Houlden H, Maroofian R. 2024. Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders. Brain. 147(4), 1436–1456. mla: Kaiyrzhanov, Rauan, et al. “Bi-Allelic ACBD6 Variants Lead to a Neurodevelopmental Syndrome with Progressive and Complex Movement Disorders.” Brain, vol. 147, no. 4, Oxford University Press, 2024, pp. 1436–56, doi:10.1093/brain/awad380. short: R. Kaiyrzhanov, A. Rad, S.-J. Lin, A. Bertoli-Avella, W.W. Kallemeijn, A. Godwin, M.S. Zaki, K. Huang, T. Lau, C. Petree, S. Efthymiou, E. Ghayoor Karimiani, M. Hempel, E.A. Normand, S. Rudnik-Schöneborn, U.A. Schatz, M.P. Baggelaar, M. Ilyas, T. Sultan, J.R. Alvi, M. Ganieva, B. Fowler, R. Aanicai, G. Akay Tayfun, A. Al Saman, A. Alswaid, N. Amiri, N. Asilova, V. Shotelersuk, P. Yeetong, M. Azam, M. Babaei, G. Bahrami Monajemi, P. Mohammadi, S. Samie, S.H. Banu, J.P. Basto, F. Kortüm, M. Bauer, P. Bauer, C. Beetz, M. Garshasbi, A. Hameed Issa, W. Eyaid, H. Ahmed, N. Hashemi, K. Hassanpour, I. Herman, S. Ibrohimov, B.A. Abdul-Majeed, M. Imdad, M. Isrofilov, Q. Kaiyal, S. Khan, B. Kirmse, J. Koster, C.M. Lourenço, T. Mitani, O. Moldovan, D. Murphy, M. Najafi, D. Pehlivan, M.E. Rocha, V. Salpietro, M. Schmidts, A. Shalata, M. Mahroum, J.K. Talbeya, R.W. Taylor, D. Vazquez, A. Vetro, H.R. Waterham, M. Zaman, T.A. Schrader, W.K. Chung, R. Guerrini, J.R. Lupski, J. Gleeson, M. Suri, Y. Jamshidi, K.P. Bhatia, B. Vona, M. Schrader, M. Severino, M. Guille, E.W. Tate, G.K. Varshney, H. Houlden, R. Maroofian, Brain 147 (2024) 1436–1456. date_created: 2023-11-16T12:36:51Z date_published: 2024-04-01T00:00:00Z date_updated: 2024-07-16T08:23:24Z day: '01' ddc: - '570' department: - _id: GradSch doi: 10.1093/brain/awad380 extern: '1' external_id: pmid: - '37951597' file: - access_level: open_access checksum: 0ee7a8ab9300225d60968f7a3e3cfa0d content_type: application/pdf creator: dernst date_created: 2024-07-16T08:22:13Z date_updated: 2024-07-16T08:22:13Z file_id: '17254' file_name: 2024_Brain_Kaiyrzhanov.pdf file_size: 2641456 relation: main_file success: 1 file_date_updated: 2024-07-16T08:22:13Z fulldoi: https://doi.org/10.1093/brain/awad380 has_accepted_license: '1' intvolume: ' 147' issue: '4' keyword: - Neurology (clinical) language: - iso: eng month: '04' oa: 1 oa_version: Submitted Version page: 1436-1456 pmid: 1 publication: Brain publication_identifier: eissn: - 1460-2156 issn: - 0006-8950 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 147 year: '2024' ... --- _id: '14660' abstract: - lang: eng text: "The classical Steinitz theorem states that if the origin belongs to the interior of the convex hull of a set \U0001D446⊂ℝ\U0001D451, then there are at most 2\U0001D451 points of \U0001D446 whose convex hull contains the origin in the interior. Bárány, Katchalski,and Pach proved the following quantitative version of Steinitz’s theorem. Let \U0001D444 be a convex polytope in ℝ\U0001D451 containing the standard Euclidean unit ball \U0001D401\U0001D451. Then there exist at most 2\U0001D451 vertices of \U0001D444 whose convex hull \U0001D444′ satisfies \U0001D45F\U0001D401\U0001D451⊂\U0001D444′ with \U0001D45F⩾\U0001D451−2\U0001D451. They conjectured that \U0001D45F⩾\U0001D450\U0001D451−1∕2 holds with a universal constant \U0001D450>0. We prove \U0001D45F⩾15\U0001D4512, the first polynomial lower bound on \U0001D45F. Furthermore, we show that \U0001D45F is not greater than 2/√\U0001D451." acknowledgement: M.N. was supported by the János Bolyai Scholarship of the Hungarian Academy of Sciences aswell as the National Research, Development and Innovation Fund (NRDI) grants K119670 andK131529, and the ÚNKP-22-5 New National Excellence Program of the Ministry for Innovationand Technology from the source of the NRDI as well as the ELTE TKP 2021-NKTA-62 fundingscheme article_processing_charge: Yes (via OA deal) article_type: original arxiv: 1 author: - first_name: Grigory full_name: Ivanov, Grigory id: 87744F66-5C6F-11EA-AFE0-D16B3DDC885E last_name: Ivanov - first_name: Márton full_name: Naszódi, Márton last_name: Naszódi citation: ama: 'Ivanov G, Naszódi M. Quantitative Steinitz theorem: A polynomial bound. Bulletin of the London Mathematical Society. 2024;56(2):796-802. doi:10.1112/blms.12965' apa: 'Ivanov, G., & Naszódi, M. (2024). Quantitative Steinitz theorem: A polynomial bound. Bulletin of the London Mathematical Society. London Mathematical Society. https://doi.org/10.1112/blms.12965' chicago: 'Ivanov, Grigory, and Márton Naszódi. “Quantitative Steinitz Theorem: A Polynomial Bound.” Bulletin of the London Mathematical Society. London Mathematical Society, 2024. https://doi.org/10.1112/blms.12965.' ieee: 'G. Ivanov and M. Naszódi, “Quantitative Steinitz theorem: A polynomial bound,” Bulletin of the London Mathematical Society, vol. 56, no. 2. London Mathematical Society, pp. 796–802, 2024.' ista: 'Ivanov G, Naszódi M. 2024. Quantitative Steinitz theorem: A polynomial bound. Bulletin of the London Mathematical Society. 56(2), 796–802.' mla: 'Ivanov, Grigory, and Márton Naszódi. “Quantitative Steinitz Theorem: A Polynomial Bound.” Bulletin of the London Mathematical Society, vol. 56, no. 2, London Mathematical Society, 2024, pp. 796–802, doi:10.1112/blms.12965.' short: G. Ivanov, M. Naszódi, Bulletin of the London Mathematical Society 56 (2024) 796–802. corr_author: '1' date_created: 2023-12-10T23:00:58Z date_published: 2024-02-01T00:00:00Z date_updated: 2025-09-04T11:31:49Z day: '01' ddc: - '510' department: - _id: UlWa doi: 10.1112/blms.12965 external_id: arxiv: - '2212.04308' isi: - '001113277100001' file: - access_level: open_access checksum: 30ea0694757bc668cf7cd15ae357b35e content_type: application/pdf creator: dernst date_created: 2024-07-16T10:35:10Z date_updated: 2024-07-16T10:35:10Z file_id: '17259' file_name: 2024_BulletinLondonMathSoc_Ivanov.pdf file_size: 111756 relation: main_file success: 1 file_date_updated: 2024-07-16T10:35:10Z fulldoi: https://doi.org/10.1112/blms.12965 has_accepted_license: '1' intvolume: ' 56' isi: 1 issue: '2' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 796-802 publication: Bulletin of the London Mathematical Society publication_identifier: eissn: - 1469-2120 issn: - 0024-6093 publication_status: published publisher: London Mathematical Society quality_controlled: '1' scopus_import: '1' status: public title: 'Quantitative Steinitz theorem: A polynomial bound' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 56 year: '2024' ... --- _id: '14683' abstract: - lang: eng text: "Mosaic analysis with double markers (MADM) technology enables the generation of genetic mosaic tissue in mice and high-resolution phenotyping at the individual cell level. Here, we present a protocol for isolating MADM-labeled cells with high yield for downstream molecular analyses using fluorescence-activated cell sorting (FACS). We describe steps for generating MADM-labeled mice, perfusion, single-cell suspension, and debris removal. We then detail procedures for cell sorting by FACS and downstream analysis. This protocol is suitable for embryonic to adult mice.\r\nFor complete details on the use and execution of this protocol, please refer to Contreras et al. (2021).1" acknowledged_ssus: - _id: Bio - _id: PreCl acknowledgement: This research was supported by the Scientific Service Units (SSU) at IST Austria through resources provided by the Imaging & Optics Facility (IOF) and Preclinical Facilities (PCF). N.A. received support from FWF Firnberg-Programme (T 1031). G.C. received support from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 754411 as an ISTplus postdoctoral fellow. This work was also supported by IST Austria institutional funds, FWF SFB F78 to S.H., and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 725780 LinPro) to S.H. article_number: '102771' article_processing_charge: Yes (in subscription journal) article_type: review author: - first_name: Nicole full_name: Amberg, Nicole id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87 last_name: Amberg orcid: 0000-0002-3183-8207 - first_name: Giselle T full_name: Cheung, Giselle T id: 471195F6-F248-11E8-B48F-1D18A9856A87 last_name: Cheung orcid: 0000-0001-8457-2572 - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 citation: ama: Amberg N, Cheung GT, Hippenmeyer S. Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry. STAR Protocols. 2024;5(1). doi:10.1016/j.xpro.2023.102771 apa: Amberg, N., Cheung, G. T., & Hippenmeyer, S. (2024). Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry. STAR Protocols. Elsevier. https://doi.org/10.1016/j.xpro.2023.102771 chicago: Amberg, Nicole, Giselle T Cheung, and Simon Hippenmeyer. “Protocol for Sorting Cells from Mouse Brains Labeled with Mosaic Analysis with Double Markers by Flow Cytometry.” STAR Protocols. Elsevier, 2024. https://doi.org/10.1016/j.xpro.2023.102771. ieee: N. Amberg, G. T. Cheung, and S. Hippenmeyer, “Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry,” STAR Protocols, vol. 5, no. 1. Elsevier, 2024. ista: Amberg N, Cheung GT, Hippenmeyer S. 2024. Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry. STAR Protocols. 5(1), 102771. mla: Amberg, Nicole, et al. “Protocol for Sorting Cells from Mouse Brains Labeled with Mosaic Analysis with Double Markers by Flow Cytometry.” STAR Protocols, vol. 5, no. 1, 102771, Elsevier, 2024, doi:10.1016/j.xpro.2023.102771. short: N. Amberg, G.T. Cheung, S. Hippenmeyer, STAR Protocols 5 (2024). corr_author: '1' date_created: 2023-12-13T11:48:05Z date_published: 2024-03-15T00:00:00Z date_updated: 2025-04-15T08:23:06Z day: '15' ddc: - '570' department: - _id: SiHi doi: 10.1016/j.xpro.2023.102771 ec_funded: 1 external_id: pmid: - '38070137' file: - access_level: open_access checksum: 3f0ee62e04bf5a44b45b035662826e95 content_type: application/pdf creator: dernst date_created: 2024-07-16T11:50:03Z date_updated: 2024-07-16T11:50:03Z file_id: '17260' file_name: 2024_STARProtoc_Amberg.pdf file_size: 8871807 relation: main_file success: 1 file_date_updated: 2024-07-16T11:50:03Z fulldoi: https://doi.org/10.1016/j.xpro.2023.102771 has_accepted_license: '1' intvolume: ' 5' issue: '1' keyword: - General Immunology and Microbiology - General Biochemistry - Genetics and Molecular Biology - General Neuroscience language: - iso: eng month: '03' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 268F8446-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: T01031 name: Role of Eed in neural stem cell lineage progression - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: 059F6AB4-7A3F-11EA-A408-12923DDC885E grant_number: F7805 name: Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression - _id: 260018B0-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '725780' name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development publication: STAR Protocols publication_identifier: issn: - 2666-1667 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2024' ... --- _id: '14701' article_processing_charge: No article_type: letter_note author: - first_name: Lynden A. full_name: Archer, Lynden A. last_name: Archer - first_name: Peter G. full_name: Bruce, Peter G. last_name: Bruce - first_name: Ernesto J. full_name: Calvo, Ernesto J. last_name: Calvo - first_name: Daniel full_name: Dewar, Daniel last_name: Dewar - first_name: James H. J. full_name: Ellison, James H. J. last_name: Ellison - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: Xiangwen full_name: Gao, Xiangwen last_name: Gao - first_name: Laurence J. full_name: Hardwick, Laurence J. last_name: Hardwick - first_name: Gabriela full_name: Horwitz, Gabriela last_name: Horwitz - first_name: Jürgen full_name: Janek, Jürgen last_name: Janek - first_name: Lee R. full_name: Johnson, Lee R. last_name: Johnson - first_name: Jack W. full_name: Jordan, Jack W. last_name: Jordan - first_name: Shoichi full_name: Matsuda, Shoichi last_name: Matsuda - first_name: Svetlana full_name: Menkin, Svetlana last_name: Menkin - first_name: Soumyadip full_name: Mondal, Soumyadip id: d25d21ef-dc8d-11ea-abe3-ec4576307f48 last_name: Mondal - first_name: Qianyuan full_name: Qiu, Qianyuan last_name: Qiu - first_name: Thukshan full_name: Samarakoon, Thukshan last_name: Samarakoon - first_name: Israel full_name: Temprano, Israel last_name: Temprano - first_name: Kohei full_name: Uosaki, Kohei last_name: Uosaki - first_name: Ganesh full_name: Vailaya, Ganesh last_name: Vailaya - first_name: Eric D. full_name: Wachsman, Eric D. last_name: Wachsman - first_name: Yiying full_name: Wu, Yiying last_name: Wu - first_name: Shen full_name: Ye, Shen last_name: Ye citation: ama: 'Archer LA, Bruce PG, Calvo EJ, et al. Towards practical metal–oxygen batteries: General discussion. Faraday Discussions. 2024;248:392-411. doi:10.1039/d3fd90062b' apa: 'Archer, L. A., Bruce, P. G., Calvo, E. J., Dewar, D., Ellison, J. H. J., Freunberger, S. A., … Ye, S. (2024). Towards practical metal–oxygen batteries: General discussion. Faraday Discussions. Royal Society of Chemistry. https://doi.org/10.1039/d3fd90062b' chicago: 'Archer, Lynden A., Peter G. Bruce, Ernesto J. Calvo, Daniel Dewar, James H. J. Ellison, Stefan Alexander Freunberger, Xiangwen Gao, et al. “Towards Practical Metal–Oxygen Batteries: General Discussion.” Faraday Discussions. Royal Society of Chemistry, 2024. https://doi.org/10.1039/d3fd90062b.' ieee: 'L. A. Archer et al., “Towards practical metal–oxygen batteries: General discussion,” Faraday Discussions, vol. 248. Royal Society of Chemistry, pp. 392–411, 2024.' ista: 'Archer LA, Bruce PG, Calvo EJ, Dewar D, Ellison JHJ, Freunberger SA, Gao X, Hardwick LJ, Horwitz G, Janek J, Johnson LR, Jordan JW, Matsuda S, Menkin S, Mondal S, Qiu Q, Samarakoon T, Temprano I, Uosaki K, Vailaya G, Wachsman ED, Wu Y, Ye S. 2024. Towards practical metal–oxygen batteries: General discussion. Faraday Discussions. 248, 392–411.' mla: 'Archer, Lynden A., et al. “Towards Practical Metal–Oxygen Batteries: General Discussion.” Faraday Discussions, vol. 248, Royal Society of Chemistry, 2024, pp. 392–411, doi:10.1039/d3fd90062b.' short: L.A. Archer, P.G. Bruce, E.J. Calvo, D. Dewar, J.H.J. Ellison, S.A. Freunberger, X. Gao, L.J. Hardwick, G. Horwitz, J. Janek, L.R. Johnson, J.W. Jordan, S. Matsuda, S. Menkin, S. Mondal, Q. Qiu, T. Samarakoon, I. Temprano, K. Uosaki, G. Vailaya, E.D. Wachsman, Y. Wu, S. Ye, Faraday Discussions 248 (2024) 392–411. date_created: 2023-12-20T10:48:09Z date_published: 2024-01-29T00:00:00Z date_updated: 2025-09-04T11:34:30Z day: '29' department: - _id: StFr doi: 10.1039/d3fd90062b external_id: isi: - '001130090400001' pmid: - '38112202' fulldoi: https://doi.org/10.1039/d3fd90062b intvolume: ' 248' isi: 1 keyword: - Physical and Theoretical Chemistry language: - iso: eng month: '01' oa_version: None page: 392-411 pmid: 1 publication: Faraday Discussions publication_identifier: eissn: - 1364-5498 issn: - 1359-6640 publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: 'Towards practical metal–oxygen batteries: General discussion' type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 248 year: '2024' ... --- _id: '14702' article_processing_charge: No article_type: letter_note author: - first_name: Gary A. full_name: Attard, Gary A. last_name: Attard - first_name: Ernesto J. full_name: Calvo, Ernesto J. last_name: Calvo - first_name: Larry A. full_name: Curtiss, Larry A. last_name: Curtiss - first_name: Daniel full_name: Dewar, Daniel last_name: Dewar - first_name: James H. J. full_name: Ellison, James H. J. last_name: Ellison - first_name: Xiangwen full_name: Gao, Xiangwen last_name: Gao - first_name: Clare P. full_name: Grey, Clare P. last_name: Grey - first_name: Laurence J. full_name: Hardwick, Laurence J. last_name: Hardwick - first_name: Gabriela full_name: Horwitz, Gabriela last_name: Horwitz - first_name: Juergen full_name: Janek, Juergen last_name: Janek - first_name: Lee R. full_name: Johnson, Lee R. last_name: Johnson - first_name: Jack W. full_name: Jordan, Jack W. last_name: Jordan - first_name: Shoichi full_name: Matsuda, Shoichi last_name: Matsuda - first_name: Soumyadip full_name: Mondal, Soumyadip id: d25d21ef-dc8d-11ea-abe3-ec4576307f48 last_name: Mondal - first_name: Alex R. full_name: Neale, Alex R. last_name: Neale - first_name: Nagore full_name: Ortiz-Vitoriano, Nagore last_name: Ortiz-Vitoriano - first_name: Israel full_name: Temprano, Israel last_name: Temprano - first_name: Ganesh full_name: Vailaya, Ganesh last_name: Vailaya - first_name: Eric D. full_name: Wachsman, Eric D. last_name: Wachsman - first_name: Hsien-Hau full_name: Wang, Hsien-Hau last_name: Wang - first_name: Yiying full_name: Wu, Yiying last_name: Wu - first_name: Shen full_name: Ye, Shen last_name: Ye citation: ama: 'Attard GA, Calvo EJ, Curtiss LA, et al. Materials for stable metal–oxygen battery cathodes: general discussion. Faraday Discussions. 2024;248:75-88. doi:10.1039/d3fd90059b' apa: 'Attard, G. A., Calvo, E. J., Curtiss, L. A., Dewar, D., Ellison, J. H. J., Gao, X., … Ye, S. (2024). Materials for stable metal–oxygen battery cathodes: general discussion. Faraday Discussions. Royal Society of Chemistry. https://doi.org/10.1039/d3fd90059b' chicago: 'Attard, Gary A., Ernesto J. Calvo, Larry A. Curtiss, Daniel Dewar, James H. J. Ellison, Xiangwen Gao, Clare P. Grey, et al. “Materials for Stable Metal–Oxygen Battery Cathodes: General Discussion.” Faraday Discussions. Royal Society of Chemistry, 2024. https://doi.org/10.1039/d3fd90059b.' ieee: 'G. A. Attard et al., “Materials for stable metal–oxygen battery cathodes: general discussion,” Faraday Discussions, vol. 248. Royal Society of Chemistry, pp. 75–88, 2024.' ista: 'Attard GA, Calvo EJ, Curtiss LA, Dewar D, Ellison JHJ, Gao X, Grey CP, Hardwick LJ, Horwitz G, Janek J, Johnson LR, Jordan JW, Matsuda S, Mondal S, Neale AR, Ortiz-Vitoriano N, Temprano I, Vailaya G, Wachsman ED, Wang H-H, Wu Y, Ye S. 2024. Materials for stable metal–oxygen battery cathodes: general discussion. Faraday Discussions. 248, 75–88.' mla: 'Attard, Gary A., et al. “Materials for Stable Metal–Oxygen Battery Cathodes: General Discussion.” Faraday Discussions, vol. 248, Royal Society of Chemistry, 2024, pp. 75–88, doi:10.1039/d3fd90059b.' short: G.A. Attard, E.J. Calvo, L.A. Curtiss, D. Dewar, J.H.J. Ellison, X. Gao, C.P. Grey, L.J. Hardwick, G. Horwitz, J. Janek, L.R. Johnson, J.W. Jordan, S. Matsuda, S. Mondal, A.R. Neale, N. Ortiz-Vitoriano, I. Temprano, G. Vailaya, E.D. Wachsman, H.-H. Wang, Y. Wu, S. Ye, Faraday Discussions 248 (2024) 75–88. date_created: 2023-12-20T10:49:43Z date_published: 2024-01-29T00:00:00Z date_updated: 2025-09-04T11:35:09Z day: '29' department: - _id: StFr doi: 10.1039/d3fd90059b external_id: isi: - '001130029600001' pmid: - '38109098' fulldoi: https://doi.org/10.1039/d3fd90059b intvolume: ' 248' isi: 1 keyword: - Physical and Theoretical Chemistry language: - iso: eng month: '01' oa_version: None page: 75-88 pmid: 1 publication: Faraday Discussions publication_identifier: eissn: - 1364-5498 issn: - 1359-6640 publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: 'Materials for stable metal–oxygen battery cathodes: general discussion' type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 248 year: '2024' ...