@article{19443, abstract = {In cryo-electron microscopy, accurate particle localization and classification are imperative. Recent deep learning solutions, though successful, require extensive training datasets. The protracted generation time of physics-based models, often employed to produce these datasets, limits their broad applicability. We introduce FakET, a method based on neural style transfer, capable of simulating the forward operator of any cryo transmission electron microscope. It can be used to adapt a synthetic training dataset according to reference data producing high-quality simulated micrographs or tilt-series. To assess the quality of our generated data, we used it to train a state-of-the-art localization and classification architecture and compared its performance with a counterpart trained on benchmark data. Remarkably, our technique matches the performance, boosts data generation speed 750x, uses 33x less memory, and scales well to typical transmission electron microscope detector sizes. It leverages GPU acceleration and parallel processing. The source code is available at https://github.com/paloha/faket/.}, author = {Harar, Pavol and Herrmann, Lukas and Grohs, Philipp and Haselbach, David}, issn = {1878-4186}, journal = {Structure}, number = {4}, pages = {820--827.e4}, publisher = {Cell Press}, title = {{FakET: Simulating cryo-electron tomograms with neural style transfer}}, doi = {10.1016/j.str.2025.01.020}, volume = {33}, year = {2025}, } @article{20154, abstract = {In long-lived mammals, including humans, brain cell homeostasis is critical for maintaining brain function throughout life. Most neurons are generated during development and must maintain their cellular identity and plasticity to preserve brain function. Although extensive studies indicate the importance of recycling and regenerating cellular molecules to maintain cellular homeostasis, recent evidence has shown that some proteins and RNAs do not turn over for months and even years. We propose that these long-lived cellular molecules may be the basis for maintaining brain function in the long term, but also a potential convergent target of brain aging. We highlight key discoveries and challenges, and propose potential directions to unravel the mystery of brain cell longevity.}, author = {Hetzer, Martin W and Toda, Tomohisa}, issn = {1878-108X}, journal = {Trends in Neurosciences}, number = {9}, pages = {645--654}, publisher = {Cell Press}, title = {{Long-lived cellular molecules in the brain}}, doi = {10.1016/j.tins.2025.07.004}, volume = {48}, year = {2025}, } @article{20427, abstract = {Animal cells migrating up chemotactic gradients often show speed oscillations. A new study describes a molecular circuit that switches zebrafish germ cells between phases of straight runs, tumbling and directional reorientation.}, author = {Li, Ziqiang and Sixt, Michael K}, issn = {1879-0445}, journal = {Current Biology}, number = {18}, pages = {R890--R892}, publisher = {Cell Press}, title = {{Cell migration: How animal cells run and tumble}}, doi = {10.1016/j.cub.2025.08.016}, volume = {35}, year = {2025}, } @article{15016, abstract = {Amphibians, by virtue of their phylogenetic position, provide invaluable insights on nervous system evolution, development, and remodeling. The genetic toolkit for amphibians, however, remains limited. Recombinant adeno-associated viral vectors (AAVs) are a powerful alternative to transgenesis for labeling and manipulating neurons. Although successful in mammals, AAVs have never been shown to transduce amphibian cells efficiently. We screened AAVs in three amphibian species—the frogs Xenopus laevis and Pelophylax bedriagae and the salamander Pleurodeles waltl—and identified at least two AAV serotypes per species that transduce neurons. In developing amphibians, AAVs labeled groups of neurons generated at the same time during development. In the mature brain, AAVrg retrogradely traced long-range projections. Our study introduces AAVs as a tool for amphibian research, establishes a generalizable workflow for AAV screening in new species, and expands opportunities for cross-species comparisons of nervous system development, function, and evolution.}, author = {Jaeger, Eliza C.B. and Vijatovic, David and Deryckere, Astrid and Zorin, Nikol and Nguyen, Akemi L. and Ivanian, Georgiy and Woych, Jamie and Arnold, Rebecca C and Ortega Gurrola, Alonso and Shvartsman, Arik and Barbieri, Francesca and Toma, Florina-Alexandra and Gorbsky, Gary J. and Horb, Marko E. and Cline, Hollis T. and Shay, Timothy F. and Kelley, Darcy B. and Yamaguchi, Ayako and Shein-Idelson, Mark and Tosches, Maria Antonietta and Sweeney, Lora Beatrice Jaeger}, issn = {1878-1551}, journal = {Developmental Cell}, number = {5}, pages = {794--812.e6}, publisher = {Cell Press}, title = {{Adeno-associated viral tools to trace neural development and connectivity across amphibians}}, doi = {10.1016/j.devcel.2024.10.025}, volume = {60}, year = {2025}, } @article{18619, abstract = {Brassinosteroids (BRs) are steroidal phytohormones indispensable for plant growth, development, and responses to environmental stresses. The export of bioactive BRs to the apoplast is essential for BR signalling initiation, which requires binding of BR molecule to the extracellular domains of the plasma membrane-localized receptor complex. We have previously shown that the Arabidopsis thaliana ATP-binding cassette (ABC) transporter, ABCB19, functions as a BR exporter, and together with its close homologue, ABCB1, positively regulate BR signalling. Here, we demonstrate that ABCB1 is another BR transporter. The ATP hydrolysis activity of ABCB1 was stimulated by bioactive BRs, and its transport activity was confirmed in proteoliposomes and protoplasts. Structures of ABCB1 in substrate-unbound (apo), brassinolide (BL)-bound, and ATP plus BL-bound states were determined. In the BL-bound structure, BL was bound to the hydrophobic cavity formed by the transmembrane domain, and triggered local conformational changes. Together, our data provide additional insights into the ABC transporter-mediated BR export.}, author = {Wei, H and Zhu, H and Ying, W and Janssens, H and Kvasnica, M and Winne, JM and Gao, Y and Friml, Jiří and Ma, Q and Tan, S and Liu, X and Russinova, E and Sun, L}, issn = {2590-3462}, journal = {Plant Communications}, number = {1}, publisher = {Cell Press}, title = {{Structural insights into brassinosteroid export mediated by the Arabidopsis ABC transporter ABCB1}}, doi = {10.1016/j.xplc.2024.101181}, volume = {6}, year = {2025}, } @article{19003, 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 = {Gallei, Michelle C and Truckenbrodt, Sven M and Kreuzinger, Caroline and Inumella, Syamala and Vistunou, Vitali and Sommer, Christoph M and Tavakoli, Mojtaba and Agudelo Duenas, Nathalie and Vorlaufer, Jakob and Jahr, Wiebke and Randuch, Marek and Johnson, Alexander J and Benková, Eva and Friml, Jiří and Danzl, Johann G}, issn = {1532-298X}, journal = {The Plant Cell}, number = {4}, publisher = {Oxford University Press}, title = {{Super-resolution expansion microscopy in plant roots}}, doi = {10.1093/plcell/koaf006}, volume = {37}, year = {2025}, } @article{20452, abstract = {Accurate modeling of long-range forces is critical in atomistic simulations, as they play a central role in determining the properties of material and chemical systems. However, standard machine learning interatomic potentials (MLIPs) often rely on short-range approximations, limiting their applicability to systems with significant electrostatics and dispersion forces. We recently introduced the Latent Ewald Summation (LES) method, which captures long-range electrostatics without explicitly learning atomic charges or charge equilibration. We benchmark LES on diverse and challenging systems, including charged molecules, ionic liquids, electrolyte solutions, polar dipeptides, surface adsorption, electrolyte/solid interfaces, and solid-solid interfaces. Here we show that LES can reproduce the exact atomic charges for classical systems with fixed charges and can infer dipole and quadrupole moments, as well as the dipole derivative with respect to atomic positions, for quantum mechanical systems. Moreover, LES can achieve better accuracy in energy and force predictions compared to methods that explicitly learn from charges.}, author = {King, Daniel S. and Kim, Dongjin and Zhong, Peichen and Cheng, Bingqing}, issn = {2041-1723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{Machine learning of charges and long-range interactions from energies and forces}}, doi = {10.1038/s41467-025-63852-x}, volume = {16}, year = {2025}, } @misc{22770, author = {Cheng, Bingqing and King, Daniel and Kim, Dongjin and Zhong, Peichen}, publisher = {Zenodo}, title = {{BingqingCheng/cace-lr-fit: V0}}, doi = {10.5281/zenodo.16415060}, year = {2025}, } @article{18710, abstract = {We present an ab initio theoretical method to calculate the resonant Auger spectrum in the presence of ultrafast dissociation. The method is demonstrated by deriving the L-VV resonant Auger spectrum mediated by the 2p3/2−1σ* resonance in HCl, where the electronic Auger decay and nuclear dissociation occur on the same time scale. The Auger decay rates are calculated within the one-center approximation and are shown to vary significantly with the inter-nuclear distance. A quantum-mechanical description of dissociation is effectuated by propagating the corresponding Franck–Condon factors. The calculated profiles of Auger spectral lines resemble those of atomic Auger decay but here the characteristic tails extend towards lower electron kinetic energies, which reflect specific features of the potential energy curves. The presented method can describe the resonant Auger spectrum for an arbitrary speed of dissociation and simplifies to known approximations in the limiting cases.}, author = {Hrast, Mateja and Ljubotina, Marko and Zitnik, Matjaz}, issn = {1463-9076}, journal = {Physical Chemistry Chemical Physics}, number = {3}, pages = {1473--1482}, publisher = {Royal Society of Chemistry}, title = {{Ab initio Auger spectrum of the ultrafast dissociating 2p3/2−1σ* resonance in HCl}}, doi = {10.1039/d4cp03727h}, volume = {27}, year = {2025}, } @article{17459, abstract = {Atopic dermatitis (AD) is the most common chronic inflammatory skin disease worldwide. AD is a highly complex disease with different subtypes. Many elements of AD pathophysiology have been described, but if/how they interact with each other or which mechanisms are important in which patients is still unclear. Langerhans cells (LCs) are antigen-presenting cells (APCs) in the epidermis. Depending on the context, they can act either pro- or anti-inflammatory. Many different studies have investigated LCs in the context of AD and found them to be connected to all major mechanisms of AD pathophysiology. As APCs, LCs recruit other immune cells and shape the immune response, especially adaptive immunity via polarization of T cells. As sentinel cells, LCs are primary sensors of the skin microbiome and are important for the decision of immunity versus tolerance. LCs are also involved with the integrity of the skin barrier by influencing tight junctions. Finally, LCs are important cells in the neuro-immune crosstalk in the skin. In this review, we provide an overview about the many different roles of LCs in AD. Understanding LCs might bring us closer to a more complete understanding of this highly complex disease. Potentially, modulating LCs might offer new options for targeted therapies for AD patients.}, author = {Pan, Yi and Hochgerner, Mathias and Cichon, Malgorzata Anna and Benezeder, Theresa and Bieber, Thomas and Wolf, Peter}, issn = {1468-3083}, journal = {Journal of the European Academy of Dermatology and Venereology}, number = {2}, pages = {278--289}, publisher = {Wiley}, title = {{Langerhans cells: Central players in the pathophysiology of atopic dermatitis}}, doi = {10.1111/jdv.20291}, volume = {39}, year = {2025}, } @article{15121, abstract = {We present an auction algorithm using multiplicative instead of constant weight updates to compute a (1-E)-approximate maximum weight matching (MWM) in a bipartite graph with n vertices and m edges in time 0(mE-1), beating the running time of the fastest known approximation algorithm of Duan and Pettie [JACM ’14] that runs in 0(mE-1 log E-1). Our algorithm is very simple and it can be extended to give a dynamic data structure that maintains a (1-E)-approximate maximum weight matching under (1) one-sided vertex deletions (with incident edges) and (2) one-sided vertex insertions (with incident edges sorted by weight) to the other side. The total time time used is 0(mE-1), where m is the sum of the number of initially existing and inserted edges.}, author = {Zheng, Da Wei and Henzinger, Monika H}, issn = {1436-4646}, journal = {Mathematical Programming}, pages = {881--894}, publisher = {Springer Nature}, title = {{Multiplicative auction algorithm for approximate maximum weight bipartite matching}}, doi = {10.1007/s10107-024-02066-3}, volume = {210}, year = {2025}, } @article{17293, abstract = {Voltage-gated CaV2.1 (P/Q-type) Ca2+ channels play a crucial role in regulating neurotransmitter release, thus contributing to synaptic plasticity and to processes such as learning and memory. Despite their recognized importance in neural function, there is limited information on their potential involvement in neurodegenerative conditions such as Alzheimer's disease (AD). Here, we aimed to explore the impact of AD pathology on the density and nanoscale compartmentalization of CaV2.1 channels in the hippocampus in association with GABAB receptors. Histoblotting experiments showed that the density of CaV2.1 channel was significantly reduced in the hippocampus of APP/PS1 mice in a laminar-dependent manner. CaV2.1 channel was enriched in the active zone of the axon terminals and was present at a very low density over the surface of dendritic tree of the CA1 pyramidal cells, as shown by quantitative SDS-digested freeze-fracture replica labelling (SDS-FRL). In APP/PS1 mice, the density of CaV2.1 channel in the active zone was significantly reduced in the strata radiatum and lacunosum-moleculare, while it remained unaltered in the stratum oriens. The decline in Cav2.1 channel density was found to be associated with a corresponding impairment in the GABAergic synaptic function, as evidenced by electrophysiological experiments carried out in the hippocampus of APP/PS1 mice. Remarkably, double SDS-FRL showed a co-clustering of CaV2.1 channel and GABAB1 receptor in nanodomains (~40–50 nm) in wild type mice, while in APP/PS1 mice this nanoarchitecture was absent. Together, these findings suggest that the AD pathology-induced reduction in CaV2.1 channel density and CaV2.1-GABAB1 de-clustering may play a role in the synaptic transmission alterations shown in the AD hippocampus. Therefore, uncovering these layer-dependent changes in P/Q calcium currents associated with AD pathology can benefit the development of future strategies for AD management.}, author = {Martín‐Belmonte, Alejandro and Aguado, Carolina and Alfaro‐Ruiz, Rocío and Kulik, Akos and de la Ossa, Luis and Moreno‐Martínez, Ana Esther and Alberquilla, Samuel and García‐Carracedo, Lucía and Fernández, Miriam and Fajardo‐Serrano, Ana and Aso, Ester and Shigemoto, Ryuichi and Martín, Eduardo D. and Fukazawa, Yugo and Ciruela, Francisco and Luján, Rafael}, issn = {1750-3639}, journal = {Brain Pathology}, number = {2}, publisher = {Wiley}, title = {{Nanoarchitecture of CaV>2.1 channels and GABAB receptors in the mouse hippocampus: Impact of APP/PS1 pathology}}, doi = {10.1111/bpa.13279}, volume = {35}, year = {2025}, } @article{17240, abstract = {We prove an upper bound on the energy density of the dilute spin-\(\frac {1}{2}\) Fermi gas capturing the leading correction to the kinetic energy\(8\pi a\rho _\uparrow\rho _\downarrow\) with an error of size smaller than\(a\rho^{2}(a^ 3\rho)^{1/3-\varepsilon}\) for any\(\varepsilon> 0\), where a denotes the scattering length of the interaction. The result is valid for a large class of interactions including interactions with a hard core. A central ingredient in the proof is a rigorous version of a fermionic cluster expansion adapted from the formal expansion of Gaudin et al. (Nucl Phys A 176(2):237–260, 1971. https://doi.org/10.1016/0375-9474(71)90267-3).}, author = {Lauritsen, Asbjørn Bækgaard}, issn = {1424-0637}, journal = {Annales Henri Poincare}, pages = {203--243}, publisher = {Springer Nature}, title = {{Almost optimal upper bound for the ground state energy of a dilute Fermi gas via cluster expansion}}, doi = {10.1007/s00023-024-01450-1}, volume = {26}, year = {2025}, } @phdthesis{20203, abstract = {Tribocharging, or contact electrification, is the phenomenon in which two initially neutral materials exchange electric charge through contact and subsequent separation. While it is widely observed in everyday life and crucial to numerous natural processes, even the most basic aspects of tribocharging are still a mystery—what are the charge carriers involved and what drives their exchange? This work spans three separate projects that address different aspects of tribocharging. First, we introduce a novel strategy combining Finite Element Method (FEM) simulations with Kelvin Probe Force Microscopy (KPFM) to quantitatively extract surface charge density from surface voltage maps. Second, we present a simple theoretical model that allows for the existence of triboelectric cycles, under the assumption that multiple charge carrying species are involved. Third, we present experimental evidence that identical materials can spontaneously evolve into a triboelectric series, driven by contact history. Modeling this behavior enables the replication of experimental results with simulations, and even experimentally forcing the appearance of a pre-designed series by manipulating contact history. Together, the findings from these projects challenge traditional views on tribocharging, provide new tools for probing it, and open up new avenues of research—all with the hopes of bringing us closer to understanding this puzzling phenomenon.}, author = {Sobarzo Ponce, Juan Carlos A}, isbn = {978-3-99078-062-6}, issn = {2663-337X}, pages = {96}, publisher = {Institute of Science and Technology Austria}, title = {{Tribocharging of identical insulators: Triboelectric series, triboelectric cycles and surface charges}}, doi = {10.15479/AT-ISTA-20203}, year = {2025}, } @phdthesis{20607, author = {Mondal, Soumyadip}, isbn = {978-3-99078-071-8}, issn = {2663-337X}, pages = {71}, publisher = {Institute of Science and Technology Austria}, title = {{Oxygen and sulfur redox: Conversion kinetics and phase equilibria}}, doi = {10.15479/AT-ISTA-20607}, year = {2025}, } @article{18892, abstract = {Sick individuals often conceal their disease status to group members, thereby preventing social exclusion or aggression. Here we show by behavioural, chemical, immunological and infection load analyses that sick ant pupae instead actively emit a chemical signal that in itself is sufficient to trigger their own destruction by colony members. In our experiments, this altruistic disease-signalling was performed only by worker but not queen pupae. The lack of signalling by queen pupae did not constitute cheating behaviour, but reflected their superior immune capabilities. Worker pupae suffered from extensive pathogen replication whereas queen pupae were able to restrain their infection. Our data suggest the evolution of a finely-tuned signalling system in which it is not the induction of an individual’s immune response, but rather its failure to overcome the infection, that triggers pupal signalling for sacrifice. This demonstrates a balanced interplay between individual and social immunity that efficiently achieves whole-colony health.}, author = {Dawson, Erika and Hönigsberger, Michaela and Kampleitner, Niklas and Grasse, Anna V and Lindorfer, Lukas and Robb, Jennifer and Beikzadeh Abbasi, Farnaz and Strahodinsky, Florian and Leitner, Hanna and Rajendran, Harikrishnan and Schmitt, Thomas and Cremer, Sylvia}, issn = {2041-1723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{Altruistic disease signalling in ant colonies}}, doi = {10.1038/s41467-025-66175-z}, volume = {16}, year = {2025}, } @misc{20471, abstract = {Sick individuals often conceal their disease status to group members, thereby preventing social exclusion or aggression. Here we show by behavioural, chemical, immunological and infection load analyses that sick ant pupae instead actively emit a chemical signal that in itself is sufficient to trigger their own destruction by colony members. In our experiments, this altruistic disease-signalling was performed only by worker but not queen pupae. The lack of signalling by queen pupae did not constitute cheating behaviour, but reflected their superior immune capabilities. Worker pupae suffered from extensive pathogen replication whereas queen pupae were able to restrain their infection. Our data suggest the evolution of a finely-tuned signalling system in which it is not the induction of an individual’s immune response, but rather its failure to overcome the infection, that triggers pupal signalling for sacrifice. This demonstrates a balanced interplay between individual and social immunity that efficiently achieves whole-colony health. }, author = {Cremer, Sylvia}, keywords = {host-parasite interactions, social insects, social immunity, chemical communication, cooperation}, publisher = {Institute of Science and Technology Austria}, title = {{Altruistic disease signalling in ant colonies}}, doi = {10.15479/AT-ISTA-20471}, year = {2025}, } @article{12311, abstract = {In this note, we prove a formula for the cancellation exponent kv,n between division polynomials ψn and ϕn associated with a sequence {nP}n∈N of points on an elliptic curve E defined over a discrete valuation field K. The formula greatly generalizes the previously known special cases and treats also the case of non-standard Kodaira types for non-perfect residue fields.}, author = {Naskręcki, Bartosz and Verzobio, Matteo}, issn = {1473-7124}, journal = {Proceedings of the Royal Society of Edinburgh Section A: Mathematics}, keywords = {Elliptic curves, Néron models, division polynomials, height functions, discrete valuation rings}, number = {5}, pages = {1646--1660}, publisher = {Cambridge University Press}, title = {{Common valuations of division polynomials}}, doi = {10.1017/prm.2024.7}, volume = {155}, year = {2025}, } @article{18705, abstract = {Given a non-singular diagonal cubic hypersurface X⊂Pn−1 over Fq(t) with char(Fq)≠3, we show that the number of rational points of height at most |P| is O(|P|3+ε) for n=6 and O(|P|2+ε) for n=4. In fact, if n=4 and char(Fq)>3 we prove that the number of rational points away from any rational line contained in X is bounded by O(|P|3/2+ε). From the result in 6 variables we deduce weak approximation for diagonal cubic hypersurfaces for n≥7 over Fq(t) when char(Fq)>3 and handle Waring's problem for cubes in 7 variables over Fq(t) when char(Fq)≠3. Our results answer a question of Davenport regarding the number of solutions of bounded height to x31+x32+x33=x34+x35+x36 with xi∈Fq[t].}, author = {Glas, Jakob and Hochfilzer, Leonhard}, issn = {1432-1807}, journal = {Mathematische Annalen}, pages = {5485--5533}, publisher = {Springer Nature}, title = {{On a question of Davenport and diagonal cubic forms over Fq(t)}}, doi = {10.1007/s00208-024-03035-z}, volume = {391}, year = {2025}, } @article{17094, abstract = {Contract-based design is a promising methodology for taming the complexity of developing sophisticated systems. A formal contract distinguishes between assumptions, which are constraints that the designer of a component puts on the environments in which the component can be used safely, and guarantees, which are promises that the designer asks from the team that implements the component. A theory of formal contracts can be formalized as an interface theory, which supports the composition and refinement of both assumptions and guarantees. Although there is a rich landscape of contract-based design methods that address functional and extra-functional properties, we present the first interface theory designed to ensure system-wide security properties. Our framework provides a refinement relation and a composition operation that support both incremental design and independent implementability. We develop our theory for both stateless and stateful interfaces. Additionally, we introduce information-flow contracts where assumptions and guarantees are sets of flow relations. We use these contracts to illustrate how to enrich information-flow interfaces with a semantic view. We illustrate the applicability of our framework with two examples inspired by the automotive domain.}, author = {Bartocci, Ezio and Ferrere, Thomas and Henzinger, Thomas A and Nickovic, Dejan and Oliveira da Costa, Ana}, issn = {1572-8102}, journal = {Formal Methods in System Design}, pages = {3--48}, publisher = {Springer Nature}, title = {{Information-flow interfaces}}, doi = {10.1007/s10703-024-00447-0}, volume = {66}, year = {2025}, }