@misc{18837, abstract = {Super-resolution methods provide far better spatial resolution than the optical diffraction limit of about half the wavelength of light (∼200-300 nm). Nevertheless, they have yet to attain widespread use in plants, largely due to plants’ challenging optical properties. Expansion microscopy improves effective resolution by isotropically increasing the physical distances between sample structures while preserving relative spatial arrangements and clearing the sample. However, its application to plants has been hindered by the rigid, mechanically cohesive structure of plant tissues. Here, we report on whole-mount expansion microscopy of thale cress (Arabidopsis thaliana) root tissues (PlantEx), achieving a four-fold resolution increase over conventional microscopy. Our results highlight the microtubule cytoskeleton organization and interaction between molecularly defined cellular constituents. Combining PlantEx with stimulated emission depletion (STED) microscopy, we increase nanoscale resolution and visualize the complex organization of subcellular organelles from intact tissues by example of the densely packed COPI-coated vesicles associated with the Golgi apparatus and put these into a cellular structural context. Our results show that expansion microscopy can be applied to increase effective imaging resolution in Arabidopsis root specimens.}, author = {Danzl, Johann G and Kreuzinger, Caroline}, publisher = {Institute of Science and Technology Austria}, title = {{Research Data for the publication "Super-resolution expansion microscopy in plant roots"}}, doi = {10.15479/AT:ISTA:18837}, year = {2025}, } @article{18848, abstract = {Type II CRISPR endonucleases are widely used programmable genome editing tools. Recently, CRISPR-Cas systems with highly compact nucleases have been discovered, including Cas9d (a type II-D nuclease). Here, we report the cryo-EM structures of a Cas9d nuclease (747 amino acids in length) in multiple functional states, revealing a stepwise process of DNA targeting involving a conformational switch in a REC2 domain insertion. Our structures provide insights into the intricately folded guide RNA which acts as a structural scaffold to anchor small, flexible protein domains for DNA recognition. The sgRNA can be truncated by up to ~25% yet still retain activity in vivo. Using ancestral sequence reconstruction, we generated compact nucleases capable of efficient genome editing in mammalian cells. Collectively, our results provide mechanistic insights into the evolution and DNA targeting of diverse type II CRISPR-Cas systems, providing a blueprint for future re-engineering of minimal RNA-guided DNA endonucleases.}, author = {Ocampo, Rodrigo Fregoso and Bravo, Jack Peter Kelly and Dangerfield, Tyler L. and Nocedal, Isabel and Jirde, Samatar A. and Alexander, Lisa M. and Thomas, Nicole C. and Das, Anjali and Nielson, Sarah and Johnson, Kenneth A. and Brown, Christopher T. and Butterfield, Cristina N. and Goltsman, Daniela S.A. and Taylor, David W.}, issn = {2041-1723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{DNA targeting by compact Cas9d and its resurrected ancestor}}, doi = {10.1038/s41467-024-55573-4}, volume = {16}, year = {2025}, } @article{18849, abstract = {Many biological systems operate near the physical limits to their performance, suggesting that aspects of their behavior and underlying mechanisms could be derived from optimization principles. However, such principles have often been applied only in simplified models. Here, we explore a detailed mechanistic model of the gap gene network in the Drosophila embryo, optimizing its 50+ parameters to maximize the information that gene expression levels provide about nuclear positions. This optimization is conducted under realistic constraints, such as limits on the number of available molecules. Remarkably, the optimal networks we derive closely match the architecture and spatial gene expression profiles observed in the real organism. Our framework quantifies the tradeoffs involved in maximizing functional performance and allows for the exploration of alternative network configurations, addressing the question of which features are necessary and which are contingent. Our results suggest that multiple solutions to the optimization problem might exist across closely related organisms, offering insights into the evolution of gene regulatory networks.}, author = {Sokolowski, Thomas R and Gregor, Thomas and Bialek, William and Tkačik, Gašper}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences}, number = {1}, publisher = {National Academy of Sciences}, title = {{Deriving a genetic regulatory network from an optimization principle}}, doi = {10.1073/pnas.2402925121}, volume = {122}, year = {2025}, } @article{18850, abstract = {Biophysical constraints limit the specificity with which transcription factors (TFs) can target regulatory DNA. While individual nontarget binding events may be low affinity, the sheer number of such interactions could present a challenge for gene regulation by degrading its precision or possibly leading to an erroneous induction state. Chromatin can prevent nontarget binding by rendering DNA physically inaccessible to TFs, at the cost of energy-consuming remodeling orchestrated by pioneer factors (PFs). Under what conditions and by how much can chromatin reduce regulatory errors on a global scale? We use a theoretical approach to compare two scenarios for gene regulation: one that relies on TF binding to free DNA alone and one that uses a combination of TFs and chromatin-regulating PFs to achieve desired gene expression patterns. We find, first, that chromatin effectively silences groups of genes that should be simultaneously OFF, thereby allowing more accurate graded control of expression for the remaining ON genes. Second, chromatin buffers the deleterious consequences of nontarget binding as the number of OFF genes grows, permitting a substantial expansion in regulatory complexity. Third, chromatin-based regulation productively co-opts nontarget TF binding for ON genes in order to establish a “leaky” baseline expression level, which targeted activator or repressor binding subsequently up- or down-modulates. Thus, on a global scale, using chromatin simultaneously alleviates pressure for high specificity of regulatory interactions and enables an increase in genome size with minimal impact on global expression error.}, author = {Perkins, Mindy Liu and Crocker, Justin and Tkačik, Gašper}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences}, number = {1}, publisher = {National Academy of Sciences}, title = {{Chromatin enables precise and scalable gene regulation with factors of limited specificity}}, doi = {10.1073/pnas.2411887121}, volume = {122}, year = {2025}, } @article{18851, abstract = {We present volume-limited samples of cataclysmic variables (CVs) and AM CVn binaries jointly selected from SRG/eROSITA eRASS1 and Gaia DR3 using an X-ray + optical color–color diagram (the "X-ray Main Sequence"). This tool identifies all CV subtypes, including magnetic and low-accretion rate systems, in contrast to most previous surveys. We find 23 CVs, 3 of which are AM CVns, out to 150 pc in the Western Galactic Hemisphere. Our 150 pc sample is spectroscopically verified and complete down to LX = 1.3 × 1029 erg s−1 in the 0.2–2.3 keV band, and we also present CV candidates out to 300 pc and 1000 pc. We discovered two previously unknown systems in our 150 pc sample: the third nearest AM CVn and a magnetic period bouncer. We find the mean LX of CVs to be 〈LX〉 ≈ 4.6 × 1030 erg s−1, in contrast to previous surveys which yielded 〈LX〉 ∼ 1031−1032 erg s−1. We construct X-ray luminosity functions that, for the first time, flatten out at LX ∼ 1030 erg s−1. We infer average number, mass, and luminosity densities of ρN,CV = (3.7 ± 0.7) × 10−6pc−3, (math formular), and (math formular), respectively, in the solar neighborhood. Our uniform selection method also allows us to place meaningful estimates on the space density of AM CVns, ρN,AM CVn = (5.5 ± 3.7) × 10−7 pc−3. Magnetic CVs and period bouncers make up 35% and 25% of our sample, respectively. This work, through a novel discovery technique, shows that the observed number densities of CVs and AM CVns, as well as the fraction of period bouncers, are still in tension with population synthesis estimates.}, author = {Rodriguez, Antonio C. and El-Badry, Kareem and Suleimanov, Valery and Pala, Anna F. and Kulkarni, Shrinivas R. and Gaensicke, Boris and Mori, Kaya and Rich, R. Michael and Sarkar, Arnab and Bao, Tong and De Oliveira, Raimundo Lopes and Ramsay, Gavin and Szkody, Paula and Graham, Matthew and Prince, Thomas A. and Caiazzo, Ilaria and Vanderbosch, Zachary P. and Roestel, Jan Van and Das, Kaustav K. and Qin, Yu Jing and Kasliwal, Mansi M. and Wold, Avery and Groom, Steven L. and Reiley, Daniel and Riddle, Reed}, issn = {0004-6280}, journal = {Publications of the Astronomical Society of the Pacific}, number = {1}, publisher = {IOP Publishing}, title = {{Cataclysmic variables and AM CVn binaries in SRG/eROSITA + Gaia: Volume limited samples, X-ray luminosity functions, and space densities}}, doi = {10.1088/1538-3873/ada185}, volume = {137}, year = {2025}, } @article{18852, abstract = {Recent observations have found a growing number of hypervelocity stars with speeds of ≈1500 − 2500 km s−1 that could have only been produced through thermonuclear supernovae in white dwarf binaries. Most of the observed hypervelocity runaways in this class display a surprising inflated structure: their current radii are roughly an order of magnitude greater than they would have been as white dwarfs filling their Roche lobe. While many simulations exist studying the dynamical phase leading to supernova detonation in these systems, no detailed calculations of the long-term structure of the runaways have yet been performed. We used an existing AREPO hydrodynamical simulation of a supernova in a white dwarf binary as a starting point for the evolution of these stars with the one-dimensional stellar evolution code MESA. We show that the supernova shock is not energetic enough to inflate the white dwarf over timescales longer than a few thousand years, significantly shorter than the 105 − 6 year lifetimes inferred for observed hypervelocity runaways. Although they experience a shock from a supernova less than ≈0.02 R⊙ away, our models do not experience significant interior heating, and all contract back to radii of around 0.01 R⊙ within about 104 years. Explaining the observed inflated states requires either an additional source of significant heating or some other physics that is not yet accounted for in the subsequent evolution.}, author = {Bhat, Aakash and Bauer, Evan B. and Pakmor, Rüdiger and Shen, Ken J. and Caiazzo, Ilaria and Rajamuthukumar, Abinaya Swaruba and El-Badry, Kareem and Kerzendorf, Wolfgang E.}, issn = {1432-0746}, journal = {Astronomy & Astrophysics}, number = {1}, publisher = {EDP Sciences}, title = {{Supernova shocks cannot explain the inflated state of hypervelocity runaways from white dwarf binaries}}, doi = {10.1051/0004-6361/202451371}, volume = {693}, year = {2025}, } @article{18853, abstract = {Electrolyte additives are extensively validated effective in mitigating dendrite growth and parasitic reactions in aqueous zinc-ion batteries (AZIBs). Nonetheless, the mechanisms by which additives influence the formation and characteristics of the inorganic solid–electrolyte interphase (SEI) are not yet fully elucidated. Herein, we investigate how Zn(CF3COO)2 additives influence solvation structure and elucidate the mechanism by which these additives promote the dual reduction of anions. Through cryo-transmission electron microscopy analysis, we identified the SEI as a highly amorphous ZnS/ZnF2 phase. This amorphous hybrid SEI demonstrates exceptional stability, mechanical robustness, and high Zn2+ conductivity, effectively mitigating parasitic reactions and enhancing Zn plating/stripping reversibility. Even under elevated current densities, the Zn anode exhibits ultra-stable longevity and ultra-high reversibility. This study provides a comprehensive understanding of the intrinsic mechanisms governing solvation structure modulation that lead to the formation of amorphous hybrid SEI, underscoring their efficacy in enhancing the performance and durability of AZIBs.}, author = {Zeng, Guifang and Sun, Qing and Horta, Sharona and Martínez-Alanis, Paulina R. and Wu, Peng and Li, Jing and Wang, Shang and Ibáñez, Maria and Tian, Yanhong and Ci, Lijie and Cabot, Andreu}, issn = {1754-5706}, journal = {Energy and Environmental Science}, number = {4}, pages = {1683--1695}, publisher = {Royal Society of Chemistry}, title = {{Modulating the solvation structure to enhance amorphous solid electrolyte interface formation for ultra-stable aqueous zinc anode}}, doi = {10.1039/d4ee03750b}, volume = {18}, year = {2025}, } @article{18854, abstract = {Context. One of the surprising early findings with JWST has been the discovery of a strong “roll-over” or a softening of the absorption edge of Lyα in a large number of galaxies at z ≳ 6, in addition to systematic offsets from photometric redshift estimates and fundamental galaxy scaling relations. This has been interpreted as strong cumulative damped Lyα absorption (DLA) wings from high column densities of neutral atomic hydrogen (H I), signifying major gas accretion events in the formation of these galaxies. Aims. To explore this new phenomenon systematically, we assembled the JWST/NIRSpec PRImordial gas Mass AssembLy (PRIMAL) legacy survey of 584 galaxies at z = 5.0 − 13.4, designed to study the physical properties and gas in and around galaxies during the reionization epoch. Methods. We characterized this benchmark sample in full and spectroscopically derived the galaxy redshifts, metallicities, star formation rates, and ultraviolet (UV) slopes. We defined a new diagnostic, the Lyα damping parameter DLyα, to measure and quantify the net effect of Lyα emission strength, the H I fraction in the intergalactic medium, or the local H I column density for each source. The JWST-PRIMAL survey is based on the spectroscopic DAWN JWST Archive (DJA-Spec). We describe DJA-Spec in this paper, detailing the reduction methods, the post-processing steps, and basic analysis tools. All the software, reduced spectra, and spectroscopically derived quantities and catalogs are made publicly available in dedicated repositories. Results. We find that the fraction of galaxies showing strong integrated DLAs with NHI > 1021 cm−2 only increases slightly from ≈60% at z ≈ 6 up to ≈65 − 90% at z > 8. Similarly, the prevalence and prominence of Lyα emission is found to increase with decreasing redshift, in qualitative agreement with previous observational results. Strong Lyα emitters (LAEs) are predominantly found to be associated with low-metallicity and UV faint galaxies. By contrast, strong DLAs are observed in galaxies with a variety of intrinsic physical properties, but predominantly at high redshifts and low metallicities. Conclusions. Our results indicate that strong DLAs likely reflect a particular early assembly phase of reionization-era galaxies, at which point they are largely dominated by pristine H I gas accretion. At z = 8 − 10, this gas gradually cools and forms into stars that ionize their local surroundings, forming large ionized bubbles and producing strong observed Lyα emission at z < 8.}, author = {Heintz, K. E. and Brammer, G. B. and Watson, D. and Oesch, P. A. and Keating, L. C. and Hayes, M. J. and Abdurro'Uf, Unknown and Arellano-Córdova, K. Z. and Carnall, A. C. and Christiansen, C. R. and Cullen, F. and Davé, R. and Dayal, P. and Ferrara, A. and Finlator, K. and Fynbo, J. P.U. and Flury, S. R. and Gelli, V. and Gillman, S. and Gottumukkala, R. and Gould, K. and Greve, T. R. and Hardin, S. E. and Hsiao, T. Y.Y. and Hutter, A. and Jakobsson, P. and Killi, M. and Khosravaninezhad, N. and Laursen, P. and Lee, M. M. and Magdis, G. E. and Matthee, Jorryt J and Naidu, R. P. and Narayanan, D. and Pollock, C. and Prescott, M. K.M. and Rusakov, V. and Shuntov, M. and Sneppen, A. and Smit, R. and Tanvir, N. R. and Terp, C. and Toft, S. and Valentino, F. and Vijayan, A. P. and Weaver, J. R. and Wise, J. H. and Witstok, J.}, issn = {1432-0746}, journal = {Astronomy & Astrophysics}, publisher = {EDP Sciences}, title = {{The JWST-PRIMAL archival survey: A JWST/NIRSpec reference sample for the physical properties and Lyman-α absorption and emission of ∼600 galaxies at z = 5.0-13.4}}, doi = {10.1051/0004-6361/202450243}, volume = {693}, year = {2025}, } @article{18855, abstract = {A central problem in computational statistics is to convert a procedure for sampling combinatorial objects into a procedure for counting those objects, and vice versa. We consider sampling problems which come from Gibbs distributions, which are families of probability distributions over a discrete space Ω with probability mass function of the form μ^Ω_β(ω) ∝ e^{β H(ω)} for β in an interval [β_min, β_max] and H(ω) ∈ {0} ∪ [1, n]. Two important parameters are the partition function, which is the normalization factor Z(β) = ∑_{ω ∈ Ω} e^{β H(ω)}, and the vector of pre-image counts c_x=|H^-1(x)|. We develop black-box sampling algorithms to estimate the counts roughly Õ(n²/ε²) samples for integer-valued distributions and Õ(q/ε²) samples for general distributions, where q = (log Z(β_max))/Z(β_min) (ignoring some second-order terms and parameters). We show this is optimal up to logarithmic factors. We illustrate with improved algorithms for counting connected subgraphs, independent sets, and perfect matchings. As a key subroutine, we estimate all values of the partition function using Õ(n²/ε²) samples for integer-valued distributions and Õ(q/ε²) samples for general distributions. This improves over a prior algorithm of Huber (2015) which computes a single point estimate Z(β_max) and which uses a slightly larger amount of samples. We show matching lower bounds, demonstrating this complexity is optimal as a function of n and q up to logarithmic terms.}, author = {Harris, David G. and Kolmogorov, Vladimir}, issn = {1549-6333}, journal = {ACM Transactions on Algorithms}, number = {1}, publisher = {Association for Computing Machinery}, title = {{Parameter estimation for Gibbs distributions}}, doi = {10.1145/3685676}, volume = {21}, year = {2025}, } @article{18878, abstract = {Thermoelectric (TE) materials, with the ability to convert heat into electrical energy, can generate micro-electrical fields at electronic interfaces with biological systems, making them applicable in electric-catalyzing as nanozymes, and modulate the infected microenvironment of skin wounds. Thereby, by harnessing temperature differences in vitro or in vivo, TE nanomaterials can provide antimicrobial reactive oxygen species (ROS) by catalyzing redox reactions, thereby accelerating wound healing by suppressing infection. However, despite their promising potential, there is still a lack of comprehensive understanding of the antimicrobial mechanisms, biocompatibility, and practical applications of TE nanomaterials in wound healing, as this is a newly-emerged sub-area of energy-related biomedical applications. This review aims to address this gap by highlighting the emerging progress of TE materials in wound healing, clarifying their mechanism and advances, emphasizing their potential challenges for commercialization and clinical use, and proposing novel design strategies of TE nanomaterials for effective antibacterial performance.}, author = {Jia, Shiyu and Qi, Cai and Xu, Shengduo and Yang, Lei and Sun, Qiang}, issn = {1005-0302}, journal = {Journal of Materials Science and Technology}, number = {08}, pages = {212--226}, publisher = {Elsevier}, title = {{Advancements of thermoelectric nanomaterials in ROS-mediated broad-spectrum antibacterial therapies for wound healing}}, doi = {10.1016/j.jmst.2024.11.039}, volume = {225}, year = {2025}, } @article{18880, abstract = {In this paper, we provide a rate of convergence for a version of the Carathéodory convergence for the multiple SLE model with a Dyson Brownian motion driver towards its hydrodynamic limit, for β=1 and β=2. The results are obtained by combining techniques from the field of Schramm–Loewner Evolutions with modern techniques from random matrices. Our approach shows how one can apply modern tools used in the proof of universality in random matrix theory to the field of Schramm–Loewner Evolutions.}, author = {Campbell, Andrew J and Luh, Kyle and Margarint, Vlad}, issn = {2010-3271}, journal = {Random Matrices: Theory and Application}, number = {1}, publisher = {World Scientific Publishing}, title = {{Rate of convergence in multiple SLE using random matrix theory}}, doi = {10.1142/S201032632450028X}, volume = {14}, year = {2025}, } @article{18881, abstract = {The determination of the intrinsic properties of solid active material candidates is essential for their performance optimization. However, macroscopic electrodes and related analytical techniques show challenges concerning the number of additional influencing parameters. We explore recessed microelectrodes (rME) as a platform that allows for a binder-free investigation of Prussian Blue analogues (PBA), a family of promising battery materials. The enhanced diffusion using microelectrochemical tools is indispensable to assess the intrinsic material performance, overcoming the limitation of cation diffusion from the electrolyte to the solid interface during (dis)charging cycles and allowing the investigation of limiting steps in the coupled ion-electron transfer process. The intrinsic electrochemical performance of PBAs was studied in a three-electrode configuration by means of cyclic voltammetry and galvanostatic (dis)charging in aqueous Na+-containing electrolyte. We extended the evaluation to the role of the electrolyte on the performance of cathodic and anodic processes of a Mn-based PBA. Ex-situ and operando chemical characterization were coupled to support the microelectrochemical results.}, author = {Jiyane, Nomnotho and Santana Santos, Carla and Echevarria Poza, Igor and Palacios Corella, Mario and Abdillah Mahbub, Muhammad Adib and Marin-Tajadura, Gimena and Quast, Thomas and Ibáñez, Maria and Ventosa, Edgar and Schuhmann, Wolfgang}, issn = {2566-6223}, journal = {Batteries & Supercaps}, number = {3}, publisher = {Wiley}, title = {{Recessed microelectrodes as a platform to investigate the intrinsic redox process of Prussian blue analogs for energy storage application}}, doi = {10.1002/batt.202400743}, volume = {8}, year = {2025}, } @article{18882, abstract = {Ternary liquid-like thermoelectric materials have garnered significant attention due to their ultra-low lattice thermal conductivity. Among these, Ag8SnSe6 stands out for its exceptionally low sound velocity and thermal conductivity. However, the inherent poor electrical conductivity and suboptimal thermoelectric properties of Ag8SnSe6 necessitate further improvement. Here, a novel approach is initiated to enhance the thermoelectric properties of Ag8SnSe6 by combining low-dimensionalization with intrinsic doping. For the first time, this work successfully synthesizes single-phase Ag8SnSe6 nanocrystals, ≈10 nm in size, with the correct phase and composition using a robust and reliable colloidal method. This approach represents a significant improvement over previous reports on this material. Reducing the crystal domains of Ag8SnSe6 to the nanoscale induces quantum confinement effects, increasing the density of states near the Fermi surface. It also introduces additional grain boundaries, which lower the lattice thermal conductivity and simplify structural design. Moreover, incorporating small amounts of Sn nanopowder into the Ag8SnSe6 nanocrystals before consolidation further enhances the thermoelectric performance. Sn acts as a donor dopant, increasing the electronic concentration while at the same time improving their mobility by reducing interface barriers, thus significantly improving the material transport properties. Additionally, the presence of Sn leads to the formation of point defects, dislocations, and secondary phases, which increase phonon scattering and further reduce the thermal conductivity. Through this synergistic optimization, the figure of merit shows a significant increase across a wide temperature range. Overall, a strategy is presented for the controlled preparation of Ag8SnSe6 nanocrystals, the decoupling of their electrical and thermal transport, and the practical application of this material to thermoelectric single-leg modules.}, author = {Zhao, Xueke and Li, Mengyao and Jia, Mochen and Fiedler, Christine and Nan, Bingfei and Yang, Dongwen and Li, Lei and Yuan, Zicheng and Song, Hongzhang and Liu, Yu and Ibáñez, Maria and Wang, Ziyu and Shan, Chongxin and Cabot, Andreu}, issn = {1616-3028}, journal = {Advanced Functional Materials}, number = {24}, publisher = {Wiley}, title = {{Low-dimensional structure modulation in Ag8SnSe6 for enhanced thermoelectric performance}}, doi = {10.1002/adfm.202421449}, volume = {35}, year = {2025}, } @article{18984, abstract = {Although planets have been found orbiting binary systems, whether they can survive binary interactions is debated. While the tightest-orbit binaries should host the most dynamically stable and long-lived circumbinary planetary systems, they are also the systems that are expected to experience mass transfer, common envelope evolution, or stellar mergers. In this study, we explore the effect of stable non-conservative mass transfer on the dynamical evolution of circumbinary planets. We present a new script that seamlessly integrates binary evolution data from the 1D binary stellar evolution code MESA into the N-body simulation code REBOUND. This integration framework enables a comprehensive examination of the dynamical evolution of circumbinary planets orbiting mass-transferring binaries, while simultaneously accounting for the detailed stellar structure evolution. In addition, we introduce a recalibration method to mitigate numerical errors from updates of binary properties during the system's dynamical evolution. We construct a reference binary model in which a 2.21M⊙ star loses its hydrogen-rich envelope through non-conservative mass transfer to the 1.76M⊙ companion star, creating a 0.38M⊙ subdwarf. We find the tightest stable orbital separation for circumbinary planets to be ≃2.5 times the binary separation after mass transfer. Accounting for tides by using the interior stellar structure, we find that tidal effects become apparent after the rapid mass transfer phase and start to fade away during the latter stage of the slow mass transfer phase. Our research provides a new framework for exploring circumbinary planet dynamics in interacting binary systems.}, author = {Xing, Zepei and Torres Rodriguez, Santiago and Götberg, Ylva Louise Linsdotter and Trani, Alessandro A. and Korol, Valeriya and Cuadra, Jorge}, issn = {1365-2966}, journal = {Monthly Notices of the Royal Astronomical Society}, number = {1}, pages = {285--292}, publisher = {Oxford University Press}, title = {{Combining REBOUND and MESA: Dynamical evolution of planets orbiting interacting binaries}}, doi = {10.1093/mnras/stae2820}, volume = {537}, year = {2025}, } @article{18985, abstract = {Persistent multiyear drought (MYD) events pose a growing threat to nature and humans in a changing climate. We identified and inventoried global MYDs by detecting spatiotemporally contiguous climatic anomalies, showing that MYDs have become drier, hotter, and led to increasingly diminished vegetation greenness. The global terrestrial land affected by MYDs has increased at a rate of 49,279 ± 14,771 square kilometers per year from 1980 to 2018. Temperate grasslands have exhibited the greatest declines in vegetation greenness during MYDs, whereas boreal and tropical forests have had comparably minor responses. With MYDs becoming more common, this global quantitative inventory of the occurrence, severity, trend, and impact of MYDs provides an important benchmark for facilitating more effective and collaborative preparedness toward mitigation of and adaptation to such extreme events.}, author = {Chen, Liangzhi and Brun, Philipp and Buri, Pascal and Fatichi, Simone and Gessler, Arthur and Mccarthy, Michael and Pellicciotti, Francesca and Stocker, Benjamin and Karger, Dirk Nikolaus}, issn = {1095-9203}, journal = {Science}, number = {6731}, pages = {278--284}, publisher = {AAAS}, title = {{Global increase in the occurrence and impact of multiyear droughts}}, doi = {10.1126/science.ado4245}, volume = {387}, year = {2025}, } @article{18986, abstract = {We consider a prototypical problem of Bayesian inference for a structured spiked model: a low-rank signal is corrupted by additive noise. While both information-theoretic and algorithmic limits are well understood when the noise is a Gaussian Wigner matrix, the more realistic case of structured noise still remains challenging. To capture the structure while maintaining mathematical tractability, a line of work has focused on rotationally invariant noise. However, existing studies either provide suboptimal algorithms or are limited to a special class of noise ensembles. In this paper, using tools from statistical physics (replica method) and random matrix theory (generalized spherical integrals) we establish the characterization of the information-theoretic limits for a noise matrix drawn from a general trace ensemble. Remarkably, our analysis unveils the asymptotic equivalence between the rotationally invariant model and a surrogate Gaussian one. Finally, we show how to saturate the predicted statistical limits using an efficient algorithm inspired by the theory of adaptive Thouless-Anderson-Palmer (TAP) equations.}, author = {Barbier, Jean and Camilli, Francesco and Xu, Yizhou and Mondelli, Marco}, issn = {2643-1564}, journal = {Physical Review Research}, publisher = {American Physical Society}, title = {{Information limits and Thouless-Anderson-Palmer equations for spiked matrix models with structured noise}}, doi = {10.1103/PhysRevResearch.7.013081}, volume = {7}, year = {2025}, } @article{18987, abstract = {Biallelic variants in NADH (nicotinamide adenine dinucleotide (NAD) + hydrogen (H))-ubiquinone oxidoreductase 1 alpha subcomplex 13 have been linked to mitochondrial complex I deficiency, nuclear type 28, based on three affected individuals from two families. With only two families reported, the clinical and molecular spectrum of NADH-ubiquinone oxidoreductase 1 alpha subcomplex 13–related diseases remains unclear. We report 10 additional affected individuals from nine independent families, identifying four missense variants (including recurrent c.170G > A) and three ultra-rare or novel predicted loss-of-function biallelic variants. Updated clinical–radiological data from previously reported families and a literature review compiling clinical features of all reported patients with isolated complex I deficiency caused by 43 genes encoding complex I subunits and assembly factors are also provided. Our cohort (mean age 7.8 ± 5.4 years; range 2.5–18) predominantly presented a moderate-to-severe neurodevelopmental syndrome with oculomotor abnormalities (84%), spasticity/hypertonia (83%), hypotonia (69%), cerebellar ataxia (66%), movement disorders (58%) and epilepsy (46%). Neuroimaging revealed bilateral symmetric T2 hyperintense substantia nigra lesions (91.6%) and optic nerve atrophy (66.6%). Protein modeling suggests missense variants destabilize a critical junction between the hydrophilic and membrane arms of complex I. Fibroblasts from two patients showed reduced complex I activity and compensatory complex IV activity increase. This study characterizes NADH-ubiquinone oxidoreductase 1 alpha subcomplex 13–related disease in 13 individuals, highlighting genotype–phenotype correlations.}, author = {Kaiyrzhanov, Rauan and Thompson, Kyle and Efthymiou, Stephanie and Mukushev, Askhat and Zharylkassyn, Akbota and Prasad, Chitra and Karimiani, Ehsan Ghayoor and Alvi, Javeria Raza and Niyazov, Dmitriy and Alahmad, Ahmad and Babaei, Meisam and Tajsharghi, Homa and Albash, Buthaina and Alaqeel, Ahmad and Charif, Majida and Hashemi, Narges and Heidari, Morteza and Kalantar, Seyed Mehdi and Lenaers, Guy and Mehrjardi, Mohammad Yahya Vahidi and Srinivasan, Varunvenkat M. and Gowda, Vykuntaraju K. and Mirabutalebi, Seyed Hamidreza and Carere, Deanna Alexis and Movahedinia, Mojtaba and Murphy, David and Mcfarland, Robert and Abdel-Hamid, Mohamed S. and Elhossini, Rasha M. and Alavi, Shahryar and Napier, Melanie and Belanger-Quintana, Amaya and Prasad, Asuri N. and Jakobczyk, Jessica and Roubertie, Agathe and Rupar, Tony and Sultan, Tipu and Toosi, Mehran Beiraghi and Sazanov, Leonid A and Severino, Mariasavina and Houlden, Henry and Taylor, Robert W. and Maroofian, Reza}, issn = {2632-1297}, journal = {Brain Communications}, number = {1}, publisher = {Oxford University Press}, title = {{Biallelic NDUFA13 variants lead to a neurodevelopmental phenotype with gradual neurological impairment}}, doi = {10.1093/braincomms/fcae453}, volume = {7}, year = {2025}, } @misc{18991, abstract = {Research data for the article "Learning reshapes the hippocampal representation hierarchy" from Chiossi et al. (PNAS, 2025). The data includes hippocampal CA1 unit activity and behaviour tracking of 5 Long Evans rats during the learning of an associative memory task. Detailed information can be found in the 'readme.txt' file.}, author = {Chiossi, Heloisa}, keywords = {hippocampus, electrophysiology, behavior}, publisher = {Institute of Science and Technology Austria}, title = {{Research data for the publication "Learning reshapes the hippocampal representation hierarchy"}}, doi = {10.15479/AT:ISTA:18991}, year = {2025}, } @article{19002, abstract = {A k-subcolouring of a graph G is a function f : V (G) → {0,...,k − 1} such that the set of vertices coloured i induce a disjoint union of cliques. The subchromatic number, χsub(G), is the minimum k such that G admits a k-subcolouring. Nešetril, ˇ Ossona de Mendez, Pilipczuk, and Zhu (2020), recently raised the problem of finding tight upper bounds for χsub(G2) when G is planar. We show that χsub(G2) ≤ 43 when G is planar, improving their bound of 135. We give even better bounds when the planar graph G has larger girth. Moreover, we show that χsub(G3) ≤ 95, improving the previous bound of 364. For these we adapt some recent techniques of Almulhim and Kierstead (2022), while also extending the decompositions of triangulated planar graphs of Van den Heuvel, Ossona de Mendez, Quiroz, Rabinovich and Siebertz (2017), to planar graphs of arbitrary girth. Note that these decompositions are the precursors of the graph product structure theorem of planar graphs. We give improved bounds for χsub(Gp) for all p ≥ 2, whenever G has bounded treewidth, bounded simple treewidth, bounded genus, or excludes a clique or biclique as a minor. For this we introduce a family of parameters which form a gradation between the strong and the weak colouring numbers. We give upper bounds for these parameters for graphs coming from such classes. Finally, we give a 2-approximation algorithm for the subchromatic number of graphs having a layering in which each layer has bounded cliquewidth and this layering is computable in polynomial time (like the class of all dth powers of planar graphs, for fixed d). This algorithm works even if the power p and the graph G is unknown.}, author = {Cortés, Pedro P. and Kumar, Pankaj and Moore, Benjamin and Ossona de Mendez, Patrice and Quiroz, Daniel A.}, issn = {0012-365X}, journal = {Discrete Mathematics}, number = {4}, publisher = {Elsevier}, title = {{Subchromatic numbers of powers of graphs with excluded minors}}, doi = {10.1016/j.disc.2024.114377}, volume = {348}, year = {2025}, } @article{19012, abstract = {False vacuum decay—the transition from a metastable quantum state to a true vacuum state—plays an important role in quantum field theory and non-equilibrium phenomena such as phase transitions and dynamical metastability. The non-perturbative nature of false vacuum decay and the limited experimental access to this process make it challenging to study, leaving several open questions regarding how true vacuum bubbles form, move and interact. Here we observe quantized bubble formation in real time, a key feature of false vacuum decay dynamics, using a quantum annealer with 5,564 superconducting flux qubits. We develop an effective model that captures both initial bubble creation and subsequent interactions, and remains accurate under dissipation. The annealer reveals coherent scaling laws in the driven many-body dynamics for more than 1,000 intrinsic qubit time units. This work provides a method for investigating false vacuum dynamics of large quantum systems in quantum annealers.}, author = {Vodeb, Jaka and Desaules, Jean-Yves Marc and Hallam, Andrew and Rava, Andrea and Humar, Gregor and Willsch, Dennis and Jin, Fengping and Willsch, Madita and Michielsen, Kristel and Papić, Zlatko}, issn = {1745-2481}, journal = {Nature Physics}, pages = {386--392}, publisher = {Springer Nature}, title = {{Stirring the false vacuum via interacting quantized bubbles on a 5,564-qubit quantum annealer}}, doi = {10.1038/s41567-024-02765-w}, volume = {21}, year = {2025}, }