@article{8125, abstract = {Biological memory is known to be flexible—memory formation and recall depend on factors such as the behavioral context of the organism. However, this property is often ignored in associative memory models, leaving it unclear how memories can be organized and recalled when subject to contextual control. Because of the lack of a rigorous analytical framework, it is also unknown how contextual control affects memory stability, storage capacity, and information content. Here, we bring the dynamic nature of memory to the fore by introducing a novel model of associative memory, which we refer to as the context-modular memory network. In our model, stored memory patterns are associated to one of several background network states, or contexts. Memories are accessible when their corresponding context is active, and are otherwise inaccessible. Context modulates the effective network connectivity by imposing a specific configuration of neuronal and synaptic gating—gated neurons (synapses) have their activity (weights) momentarily silenced, thereby reducing interference from memories belonging to other contexts. Memory patterns are randomly and independently chosen, while neuronal and synaptic gates may be selected randomly or optimized through a process of contextual synaptic refinement. Through analytic and numerical results, we show that context-modular memory networks can exhibit both improved memory capacity and differential control of memory stability with random gating (especially for neuronal gating). For contextual synaptic refinement, we devise a method in which synapses are gated off for a given context if they destabilize the memory patterns in that context, drastically improving memory capacity and enabling even more precise control over memory stability. Notably, synaptic refinement allows for patterns to be accessible in multiple contexts, stabilizing memory patterns even for weight matrices that alone do not contain any information about the memory patterns, such as Gaussian random matrices. Overall, our model integrates recent ideas about context-dependent memory organization with classic associative memory models and proposes a rigorous theory which can act as a framework for future work. Furthermore, our work carries important implications for the understanding of biological memory storage and recall in the brain, such as highlighting an intriguing trade-off between memory capacity and accessibility.}, author = {Podlaski, William F. and Agnes, Everton J. and Vogels, Tim P}, issn = {2160-3308}, journal = {Physical Review X}, publisher = {American Physical Society}, title = {{High capacity and dynamic accessibility in associative memory networks with context-dependent neuronal and synaptic gating}}, doi = {10.1103/PhysRevX.15.011057}, volume = {15}, year = {2025}, } @article{8616, abstract = {The brain vasculature supplies neurons with glucose and oxygen, but little is known about how vascular plasticity contributes to brain function. Using longitudinal in vivo imaging, we report that a substantial proportion of blood vessels in the adult mouse brain sporadically occlude and regress. Their regression proceeds through sequential stages of blood-flow occlusion, endothelial cell collapse, relocation or loss of pericytes, and retraction of glial endfeet. Regressing vessels are found to be widespread in mouse, monkey and human brains. We further reveal that blood vessel regression cause a reduction of neuronal activity due to a dysfunction in mitochondrial metabolism and glutamate production. Our results elucidate the mechanism of vessel regression and its role in neuronal function in the adult brain.}, author = {Gao, Xiaofei and Li, Jun-Liszt and Chen, Xingjun and Ci, Bo and Chen, Fei and Lu, Nannan and Shen, Bo and Zheng, Lijun and Jia, Jie-Min and Yi, Yating and Zhang, Shiwen and Shi, Ying-Chao and Shi, Kaibin and Propson, Nicholas E and Huang, Yubin and Poinsatte, Katherine and Zhang, Zhaohuan and Yue, Yuanlei and Bosco, Dale B and Lu, Ying-mei and Yang, Shi-bing and Adams, Ralf H. and Lindner, Volkhard and Huang, Fen and Wu, Long-Jun and Zheng, Hui and Han, Feng and Hippenmeyer, Simon and Stowe, Ann M. and Peng, Bo and Margeta, Marta and Wang, Xiaoqun and Liu, Qiang and Körbelin, Jakob and Trepel, Martin and Lu, Hui and Zhou, Bo O. and Zhao, Hu and Su, Wenzhi and Bachoo, Robert M. and Ge, Woo-ping}, issn = {2041-1723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{Reduction of neuronal activity mediated by blood-vessel regression in the brain}}, doi = {10.1038/s41467-025-60308-0}, volume = {16}, 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}, } @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{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{17468, abstract = {Oxygen redox chemistry is central to life1 and many human-made technologies, such as in energy storage2,3,4. The large energy gain from oxygen redox reactions is often connected with the occurrence of harmful reactive oxygen species3,5,6. Key species are superoxide and the highly reactive singlet oxygen3,4,5,6,7, which may evolve from superoxide. However, the factors determining the formation of singlet oxygen, rather than the relatively unreactive triplet oxygen, are unknown. Here we report that the release of triplet or singlet oxygen is governed by individual Marcus normal and inverted region behaviour. We found that as the driving force for the reaction increases, the initially dominant evolution of triplet oxygen slows down, and singlet oxygen evolution becomes predominant with higher maximum kinetics. This behaviour also applies to the widely observed superoxide disproportionation, in which one superoxide is oxidized by another, in both non-aqueous and aqueous systems, with Lewis and Brønsted acidity controlling the driving forces. Singlet oxygen yields governed by these conditions are relevant, for example, in batteries or cellular organelles in which superoxide forms. Our findings suggest ways to understand and control spin states and kinetics in oxygen redox chemistry, with implications for fields, including life sciences, pure chemistry and energy storage.}, author = {Mondal, Soumyadip and Nguyen, Huyen T.K. and Hauschild, Robert and Freunberger, Stefan Alexander}, issn = {1476-4687}, journal = {Nature}, number = {8085}, pages = {601–605}, publisher = {Springer Nature}, title = {{Marcus kinetics control singlet and triplet oxygen evolving from superoxide}}, doi = {10.1038/s41586-025-09587-7}, volume = {646}, year = {2025}, } @article{17884, abstract = {Human T cell leukemia virus type 1 (HTLV-1) immature particles differ in morphology from other retroviruses, suggesting a distinct way of assembly. Here we report the results of cryo-electron tomography studies of HTLV-1 virus-like particles assembled in vitro, as well as derived from cells. This work shows that HTLV-1 uses a distinct mechanism of Gag–Gag interactions to form the immature viral lattice. Analysis of high-resolution structural information from immature capsid (CA) tubular arrays reveals that the primary stabilizing component in HTLV-1 is the N-terminal domain of CA. Mutagenesis analysis supports this observation. This distinguishes HTLV-1 from other retroviruses, in which the stabilization is provided primarily by the C-terminal domain of CA. These results provide structural details of the quaternary arrangement of Gag for an immature deltaretrovirus and this helps explain why HTLV-1 particles are morphologically distinct.}, author = {Obr, Martin and Percipalle, Mathias and Chernikova, Darya and Yang, Huixin and Thader, Andreas and Pinke, Gergely and Porley, Dario J and Mansky, Louis M. and Dick, Robert A. and Schur, Florian KM}, issn = {1545-9985}, journal = {Nature Structural & Molecular Biology}, pages = {268--276}, publisher = {Springer Nature}, title = {{Distinct stabilization of the human T cell leukemia virus type 1 immature Gag lattice}}, doi = {10.1038/s41594-024-01390-8}, volume = {32}, year = {2025}, } @article{18074, abstract = {The Aharonov–Casher theorem is a result on the number of the so-called zero modes of a system described by the magnetic Pauli operator in R2. In this paper we address the same question for the Dirac operator on a flat two-dimensional manifold with boundary and Atiyah–Patodi–Singer boundary condition. More concretely we are interested in the plane and a disc with a finite number of circular holes cut out. We consider a smooth compactly supported magnetic field on the manifold and an arbitrary magnetic field inside the holes.}, author = {Fialova, Marie}, issn = {1424-0637}, journal = {Annales Henri Poincare}, pages = {2859--2900}, publisher = {Springer Nature}, title = {{Aharonov–Casher theorems for Dirac operators on manifolds with boundary and APS boundary condition}}, doi = {10.1007/s00023-024-01482-7}, volume = {26}, year = {2025}, } @article{18154, abstract = {In 1976, Deligne and Lusztig realized the representation theory of finite groups of Lie type inside étale cohomology of certain algebraic varieties. Recently, a p-adic version of this theory started to emerge: there are p-adic Deligne–Lusztig spaces, whose cohomology encodes representation theoretic information for p-adic groups – for instance, it partially realizes the local Langlands correspondence with characteristic zero coefficients. However, the parallel case of coefficients of positive characteristic ℓ≠p has not been inspected so far. The purpose of this article is to initiate such an inspection. In particular, we relate cohomology of certain p-adic Deligne–Lusztig spaces to Vignéras's modular local Langlands correspondence for GLn.}, author = {Löwit, Jakub}, issn = {1090-266X}, journal = {Journal of Algebra}, number = {2}, pages = {81--118}, publisher = {Elsevier}, title = {{On modulo ℓ cohomology of p-adic Deligne–Lusztig varieties for GLn}}, doi = {10.1016/j.jalgebra.2024.08.033}, volume = {663}, year = {2025}, } @article{18157, abstract = {Interest in sliding block puzzles dates back to the 15-puzzle, seemingly invented by Noyes Chapman in 1874 (see [23] for an account of the fascinating history of the puzzle). The game consists of fifteen movable square blocks numbered and arranged within a square box, leaving one empty space (see Figure 1). The task at hand is to start from a given configuration of the numbered blocks and reach the desired target configuration, where the only allowed move is to slide a numbered block into an adjacent empty space. This task seemed to be unpredictably either very easy to accomplish, or completely impossible, and the puzzle turned into a worldwide sensation in the spring of 1880. A particularly challenging instance, known as the 13-15-14 puzzle, consisted of initial and target configurations that differed by a single swap (historically this swap involved the blocks labeled 14 and 15). The craze of this puzzle was such that it consistently made newspaper headlines in 1880, with an article in the New York Times lamenting that it was “threatening our free institutions” [23, p. 9]. Various prizes were offered for anyone who could solve this challenge, beginning with a $25 set of teeth and culminating with Sam Loyd’s famous $1,000 cash prize.}, author = {Brunck, Florestan R and Kwan, Matthew Alan}, issn = {0343-6993}, journal = {Mathematical Intelligencer}, pages = {52--65}, publisher = {Springer Nature}, title = {{Books, Hallways, and social butterflies: A note on sliding block puzzles}}, doi = {10.1007/s00283-024-10358-x}, volume = {47}, year = {2025}, } @article{18169, abstract = {As the complexity and criticality of software increase every year, so does the importance of runtime monitoring. Third-party and best-effort monitoring are especially valuable, yet under-explored areas of runtime monitoring. In this context, third-party monitoring means monitoring with a limited knowledge of the monitored software (as it has been developed by a third party). Best-effort monitoring keeps pace with the monitored software at the cost of possibly imprecise verdicts when keeping up with the monitored software would not be feasible. Most existing monitoring frameworks do not support the combination of third-party and best-effort monitoring because they either require the full access to the monitored code or the ability to process all observable events, or both. We present a middleware framework, Vamos, for the runtime monitoring of software. Vamos is explicitly designed to support third-party and best-effort scenarios. The design goals of Vamos are (i) efficiency (tracing events with low overhead), (ii) flexibility (the ability to monitor a variety of different event channels, and to connect to a wide range of monitors), and (iii) ease-of-use. To achieve its goals, Vamos combines aspects of event broker and event recognition systems with aspects of stream processing systems. We implemented a prototype toolchain for Vamos and conducted a set of experiments demonstrating the usability of the scheme. The results indicate that Vamos enables writing useful yet efficient monitors, and simplifies key aspects of setting up a monitoring system from scratch.}, author = {Chalupa, Marek and Mühlböck, Fabian and Muroya Lei, Stefanie and Henzinger, Thomas A}, issn = {0167-6423}, journal = {Science of Computer Programming}, number = {2}, publisher = {Elsevier}, title = {{VAMOS: Middleware for best-effort third-party monitoring}}, doi = {10.1016/j.scico.2024.103212}, volume = {240}, year = {2025}, } @article{18170, abstract = {This study presents a graphene field-effect transistor (gFET) biosensor with dual detection capabilities for SARS-CoV-2: one RNA detection assay to confirm viral positivity and the other for nucleocapsid (N-)protein detection as a proxy for infectiousness of the patient. This technology can be rapidly adapted to emerging infectious diseases, making an essential tool to contain future pandemics. To detect viral RNA, the highly conserved E-gene of the virus was targeted, allowing for the determination of SARS-CoV-2 presence or absence using nasopharyngeal swab samples. For N-protein detection, specific antibodies were used. Tested on 213 clinical nasopharyngeal samples, the gFET biosensor showed good correlation with RT-PCR cycle threshold values, proving its high sensitivity in detecting SARS-CoV-2 RNA. Specificity was confirmed using 21 pre-pandemic samples positive for other respiratory viruses. The gFET biosensor had a limit of detection (LOD) for N-protein of 0.9 pM, establishing a foundation for the development of a sensitive tool for monitoring active viral infection. Results of gFET based N-protein detection corresponded to the results of virus culture in all 16 available clinical samples and thus it also proved its capability to serve as a proxy for infectivity. Overall, these findings support the potential of the gFET biosensor as a point-of-care device for rapid diagnosis of SARS-CoV-2 infection and indirect assessment of infectiousness in patients, providing additional information for clinical and public health decision-making.}, author = {Herdina, Anna Nele and Bozdogan, Anil and Aspermair, Patrik and Dostalek, Jakub and Klausberger, Miriam and Lingg, Nico and Cserjan-Puschmann, Monika and Aguilar, Patricia Pereira and Auer, Simone and Demirtas, Halil and Andersson, Jakob and Lötsch, Felix and Holzer, Barbara and Steinrigl, Adi and Thalhammer, Florian and Schellnegger, Julia and Breuer, Monika and Knoll, Wolfgang and Strassl, Robert}, issn = {1873-4235}, journal = {Biosensors and Bioelectronics}, publisher = {Elsevier}, title = {{Bridging basic science and applied diagnostics: Comprehensive viral diagnostics enabled by graphene-based electronic biosensor technology advancements}}, doi = {10.1016/j.bios.2024.116807}, volume = {267}, year = {2025}, } @inproceedings{22120, author = {Muñoz Hermosilla, José M and Miles, Evan and McCarthy, Michael and Hardmeier, Florian and Melo Velasco, Juan Vicente and Jouvet, Guillaume and Pellicciotti, Francesca}, booktitle = {EGU General Assembly 2025}, location = {Vienna, Austria & Virtual}, publisher = {European Geosciences Union}, title = {{Towards reconstructing debris supply to reproduce the historic changes in debris extent at a Swiss glacier}}, doi = {10.5194/egusphere-egu25-17446}, year = {2025}, } @article{21263, abstract = {Two landmark results in combinatorial random matrix theory, due to Komlós and Costello–Tao–Vu, show that discrete random matrices and symmetric discrete random matrices are typically nonsingular. In particular, in the language of graph theory, when p is a fixed constant, the biadjacency matrix of a random Erdős–Rényi bipartite graph G(n,n,p) and the adjacency matrix of an Erdős–Rényi random graph G(n,p) are both nonsingular with high probability. However, very sparse random graphs (i.e., where p is allowed to decay rapidly with n) are typically singular, due to the presence of “local” dependencies such as isolated vertices and pairs of degree-1 vertices with the same neighbour. In this paper, we give a combinatorial description of the rank of a sparse random graph G(n,n,c/n) or G(n,c/n) in terms of such local dependencies, for all constants c=e (and we present some evidence that the situation is very different for c=e). This gives an essentially complete answer to a question raised by Vu (2014). As applications of our main theorem and its proof, we also determine the asymptotic singularity probability of the 2-core of a sparse random graph, we show that the rank of a sparse random graph is extremely well approximated by its matching number, and we deduce a central limit theorem for the rank of G(n,c/n).}, author = {Glasgow, Margalit and Kwan, Matthew Alan and Sah, Ashwin and Sawhney, Mehtaab}, issn = {1435-9863}, journal = {Journal of the European Mathematical Society}, publisher = {EMS Press}, title = {{The exact rank of sparse random graphs}}, doi = {10.4171/jems/1692}, year = {2025}, } @unpublished{21427, abstract = {While tumor malignancy has been extensively studied under the prism of genetic and epigenetic heterogeneity, tumor cell states also critically depend on reciprocal interactions with the microenvironment. This raises the hitherto untested possibility that heterogeneity of the untransformed tumor stroma can actively fuel malignant progression. As biological heterogeneity is inherently difficult to control, we adopted a reductionist approach and let tumor cells invade micro-engineered environments harboring obstacles with precision-controlled geometry. We find that not only the presence of obstacles, but more surprisingly their spatial disorder, causes a drastic shift from a collective to a single-cell mode of invasion – comparable in strength to cadherin loss. Combining live-imaging and perturbation experiments with minimal biophysical modeling, we demonstrate that cell detachments result both from local geometrical constraints and a global integration of spatial disorder over time. We show that different types of microenvironments map onto different universality classes of invasion dynamics - homogeneous substrates follow Kardar–Parisi–Zhang (KPZ) scaling, while disordered ones exhibit exponents consistent with KPZ with quenched disorder (KPZq). Our findings highlight generic physical principles for how the mode of cancer cell invasion depends on environmental heterogeneity, with potential implications to understand tumor evolution in vivo.}, author = {Dunajova, Zuzana and Tasciyan, Saren and Majek, Juraj and Merrin, Jack and Sahai, Erik and Sixt, Michael K and Hannezo, Edouard B}, booktitle = {bioRxiv}, title = {{Substrate heterogeneity promotes cancer cell dissemination through interface roughening}}, doi = {10.1101/2025.05.20.655037}, year = {2025}, } @article{20656, abstract = {Phytohormone auxin and its directional transport mediate much of the remarkably plastic development of higher plants. Positive feedback between auxin signaling and transport is a prerequisite for (1) self-organizing processes, including vascular tissue formation, and (2) directional growth responses such as gravitropism. Here, we identify a mechanism by which auxin signaling directly targets PIN auxin transporters. Via the cell-surface AUXIN-BINDING PROTEIN1 (ABP1)-TRANSMEMBRANE KINASE 1 (TMK1) receptor module, auxin rapidly induces phosphorylation and thus stabilization of PIN2. Following gravistimulation, initial auxin asymmetry activates autophosphorylation of the TMK1 kinase. This induces TMK1 interaction with and phosphorylation of PIN2, stabilizing PIN2 at the lower root side, thus reinforcing asymmetric auxin flow for root bending. Upstream of TMK1 in this regulation, ABP1 acts redundantly with the root-expressed ABP1-LIKE 3 (ABL3) auxin receptor. Such positive feedback between cell-surface auxin signaling and PIN-mediated polar auxin transport is fundamental for robust root gravitropism and presumably for other self-organizing developmental phenomena.}, author = {Rodriguez Solovey, Lesia and Fiedler, Lukas and Zou, Minxia and Giannini, Caterina and Monzer, Aline and Vladimirtsev, Dmitrii and Randuch, Marek and Yu, Yongfan and Gelová, Zuzana and Verstraeten, Inge and Hajny, Jakub and Chen, Meng and Tan, Shutang and Hörmayer, Lukas and Li, Lanxin and Marques-Bueno, Maria Mar and Quddoos, Zainab and Molnar, Gergely and Kulich, Ivan and Jaillais, Yvon and Friml, Jiří}, issn = {0092-8674}, journal = {Cell}, number = {22}, pages = {6138--6150.e17}, publisher = {Elsevier}, title = {{ABP1/ABL3-TMK1 cell-surface auxin signaling targets PIN2-mediated auxin fluxes for root gravitropism}}, doi = {10.1016/j.cell.2025.08.026}, volume = {188}, year = {2025}, } @phdthesis{20364, author = {Giannini, Caterina}, issn = {2663-337X}, keywords = {Auxin Signaling, Plant Development}, pages = {151}, publisher = {Institute of Science and Technology Austria}, title = {{Nuclear and cell surface auxin signaling in A. thaliana developmental transitions}}, doi = {10.15479/AT-ISTA-20364}, year = {2025}, } @phdthesis{20441, abstract = {Epithelial spreading plays a pivotal role in the development of organisms especially those such as zebrafish which require the epithelial enveloping layer (EVL) to spread to cover the substantial yolk surface during gastrulation. Epiboly requires the transition of the epithelium with cuboidal cells to form a thin, flat squamous epithelial sheet. During this transition, the cells show tissue-scale mechanosensation with mechanisms such as direct mechanical control over the axis of cell division. Cytoskeletal intermediate filaments play a crucial role in vertebrate cells, not only facilitating mechanical stability but also helping facilitate the mechanosensitive response of the cell. Mechanosenstivity displayed by intermediate filaments is due not just to their interesting physical properties but also to their interactions with other cytoskeletal elements such as actin and microtubules. Keratin is the predominant intermediate filament expressed in the EVL. It expresses concomitantly with the gastrulation movements of the developing embryo. Our work focuses on understanding the role and dynamics of the keratin cytoskeletal network in modulating the physical aspects of EVL spreading. We demonstrated with the combination of physical characterisation and manipulations of the EVL, utilising a variety of biophysical tools and microscopy, the mechanistic role of keratin in tissue spreading. Generating novel genetic morphants and mutants, we probe the effect that the loss of the keratin network has on the physiology of the epithelium and the developing embryo. We show that the changing organisation of the keratin network is important for changing EVL physical properties as the stress imposed on the EVL increases during epiboly. By modelling the epithelium, we study how the mechanical heterogeneity in an epithelium can feed back into a mechanical loop to the maturation of the keratin network and hence affect the mechanics of the epithelium. However, unlike what would be predicted by the effect of intermediate filaments in acting as a security belt and increasing the resistance of the epithelium, we observe that loss of keratin leads to a delay in the EVL movement. Using both local aspirations of the YSL and EVL ablations, we demonstrate the mechanistic facilitation of actin mechanosensation in a keratin-dependent manner. Furthermore, using chemical inhibitors of microtubule polymerisation, we provide insight into the mechanisms underlying the organisation and distribution of keratin. Interestingly, the phenotype observed upon this loss of microtubules shows that keratins interact with the nucleus through microtubular interactions. Together with these diverse observations, we describe the mechanosensory feedback between resilience and that is critical for uniform and robust spreading of the epithelium.}, author = {Naik, Suyash}, isbn = {978-3-99078-069-5}, issn = {2663-337X}, pages = {105}, publisher = {Institute of Science and Technology Austria}, title = {{Keratins act as global coordinators of tissue spreading through mechanosensitive feedback}}, doi = {10.15479/AT-ISTA-20441}, year = {2025}, } @phdthesis{19478, author = {Chen, Huihuang}, issn = {2663-337X}, pages = {118}, publisher = {Institute of Science and Technology Austria}, title = {{The cAMP second messenger in auxin signalling}}, doi = {10.15479/AT-ISTA-19478}, year = {2025}, } @phdthesis{20920, abstract = {Verifiable Delay Functions (VDFs) introduced by Boneh et al. (CRYPTO'18) are functions that require a prescribed number of sequential steps T to evaluate, yet their output can be verified in time much faster than T. Since their introduction, VDFs have gained a lot of attention due to their applications in blockchain protocols, randomness beacons, timestamping and deniability. This thesis explores the theory and applications of VDFs, focusing on enhancing their soundness, efficiency and practicality. The only practical VDFs known to date are based on repeated squaring in hidden order groups. Consider the function VDF(x,T)=x^(2^T). The iterated squaring assumption states that, for a random group element x, the result of VDF cannot be computed significantly faster than performing T sequential squarings if the group order is unknown. To make the result verifiable a prover can compute a proof of exponentiation (PoE) \pi. Given \pi, the output of VDF can be verified in time much less than T. We first present new constructions of statistically sound proofs of exponentiation, which are an important building block in the construction of SNARKs (Succinct Non-Interactive Argument of Knowledge). Statistical soundness means that the proofs remain secure against computationally unbounded adversaries, in particular, it remains secure even when the group order is known. We thereby address limitations in previous PoE protocols which either required (non-standard) hardness assumptions or a lot of parallel repetitions. Our construction significantly reduces the proof size of statistically sound PoEs that allow for a structured exponent, which leads to better efficiency of SNARKs and other applications. Secondly, we introduce improved batching techniques for PoEs, which allow multiple proofs to be aggregated and verified with minimal overhead. These protocols optimize communication and computation complexity in large-scale blockchain environments and enable scalable remote benchmarking of parallel computation resources. We then construct VDFs with enhanced properties such as zero-knowledge and watermarkability. It was shown by Arun, Bonneau and Clark (ASIACRYPT'22) that these features enable new cryptographic primitives called short-lived proofs and signatures. The validity of such proofs and signatures expires after a predefined amount of time T, i.e., they are deniable after time T. Our constructions improve upon the constructions by Arun, Bonneau and Clark in several dimensions (faster forging times, arguably weaker assumptions). Finally, we apply PoEs in the realm of primality testing, providing cryptographically sound proofs of non-primality for large Proth numbers. This work gives a surprising application of VDFs in the area of computational number theory. Together, our contributions advance both the theoretical foundations and the real-world usability of VDFs in general and in particular of PoEs, making them more adaptable and secure for current and emerging cryptographic applications.}, author = {Hoffmann, Charlotte}, issn = {2663-337X}, pages = {116}, publisher = {Institute of Science and Technology Austria}, title = {{Theory and applications of verifiable delay functions}}, doi = {10.15479/AT-ISTA-20920}, year = {2025}, }