@article{20342,
  abstract     = {Safety and liveness stand as fundamental concepts in formal languages, playing a key role in verification. The safety-liveness classification of boolean properties characterizes whether a given property can be falsified by observing a finite prefix of an infinite computation trace (always for safety, never for liveness). In the quantitative setting, properties are arbitrary functions from infinite words to partially-ordered domains. Extending this paradigm to the quantitative domain, where properties are arbitrary functions mapping infinite words to partially-ordered domains, we introduce and study the notions of quantitative safety and liveness. First, we formally define quantitative safety and liveness, and prove that our definitions induce conservative quantitative generalizations of both the safety-progress hierarchy and the safety-liveness decomposition of boolean properties. Consequently, like their boolean counterparts, quantitative properties can be min-decomposed into safety and liveness parts, or alternatively, max-decomposed into co-safety and co-liveness parts. We further establish a connection between quantitative safety and topological continuity and provide alternative characterizations of quantitative safety and liveness in terms of their boolean analogs. Second, we instantiate our framework with the specific classes of quantitative properties expressed by automata. These quantitative automata contain finitely many states and rational-valued transition weights, and their common value functions Inf, Sup, LimInf, LimSup, LimInfAvg, LimSupAvg, and DSum map infinite words into the totally-ordered domain of real numbers. For all common value functions, we provide a procedure for deciding whether a given automaton is safe or live, we show how to construct its safety closure, and we present a min-decomposition into safe and live automata.},
  author       = {Boker, Udi and Henzinger, Thomas A and Mazzocchi, Nicolas Adrien and Sarac, Naci E},
  issn         = {1860-5974},
  journal      = {Logical Methods in Computer Science},
  number       = {2},
  publisher    = {EPI Sciences},
  title        = {{Safety and liveness of quantitative properties and automata}},
  doi          = {10.46298/lmcs-21(2:2)2025},
  volume       = {21},
  year         = {2025},
}

@phdthesis{20147,
  abstract     = {Quantitative properties offer a framework for specifying and verifying system behaviors beyond the traditional boolean perspective. For example, while a boolean property may specify whether a server eventually grants every request it receives, a quantitative one may map each server execution to its average response time. This quantitative view is relatively well-studied in the context of static verification. However, although such properties often appear in practice as performance or robustness measures in a dynamic verification context, a general theoretical framework for their analysis and classification from a monitoring perspective is still missing.

In this thesis, we aim to develop such a framework that takes resource-precision tradeoffs of monitors as a central consideration. We present the first theory of monitorability for quantitative properties where monitors can be naturally approximate and compared regarding their precision and resource use. In particular, we show that additional monitor resources such as registers or states lead to strictly better approximations for some properties. To enable such analyses in a machine-model independent way, we describe an abstract notion of monitors that can be instantiated with concrete models of monitors. Within this framework, we study how abstract monitors behave and identify classes of properties amenable to approximate monitoring with resource-precision considerations. We then extend the boolean safety-liveness dichotomy and safety-progress hierarchy to the quantitative setting with a monitoring perspective. In particular, we prove that every property is the pointwise minimum of a safety property and a liveness property, and properties that are both safe and co-safe can be approximately monitored arbitrarily precisely using only finitely many states. We also study the classes of quantitative properties definable by finite-state quantitative automata and provide algorithms for deciding their safety or liveness as well as their safety-liveness decompositions. Finally, we present the first general-purpose tool for automating the analysis, verification, and monitoring of quantitative automata.


},
  author       = {Sarac, Naci E},
  issn         = {2663-337X},
  pages        = {149},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{A monitoring-oriented theory and classification of quantitative specifications}},
  doi          = {10.15479/AT-ISTA-20147},
  year         = {2025},
}

@article{19701,
  abstract     = {Living systems are characterized by controlled flows of matter, energy, and information. While the biophysics community has productively engaged with the first two, addressing information flows has been more challenging, with some scattered success in evolutionary theory and a more coherent track record in neuroscience. Nevertheless, interdisciplinary work of the past two decades at the interface of biophysics, quantitative biology, and engineering has led to an emerging mathematical language for describing information flows at the molecular scale. This is where the central processes of life unfold: from detection and transduction of environmental signals to the readout or copying of genetic information and the triggering of adaptive cellular responses. Such processes are coordinated by complex biochemical reaction networks that operate at room temperature, are out of equilibrium, and use low copy numbers of diverse molecular species with limited interaction specificity. Here we review how flows of information through biochemical networks can be formalized using information-theoretic quantities, quantified from data, and computed within various modeling frameworks. Optimization of information flows is presented as a candidate design principle that navigates the relevant time, energy, crosstalk, and metabolic constraints to predict reliable cellular signaling and gene regulation architectures built of individually noisy components.},
  author       = {Tkačik, Gašper and Wolde, Pieter Rein Ten},
  issn         = {1936-1238},
  journal      = {Annual Review of Biophysics},
  pages        = {249--274},
  publisher    = {Annual Reviews},
  title        = {{Information processing in biochemical networks}},
  doi          = {10.1146/annurev-biophys-060524-102720},
  volume       = {54},
  year         = {2025},
}

@article{20048,
  abstract     = {During embryonic development, cell behaviors need to be tightly regulated in time and space. Yet how the temporal and spatial regulations of cell behaviors are interconnected during embryonic development remains elusive. To address this, we turned to zebrafish gastrulation, the process whereby dynamic cell behaviors generate the three principal germ layers of the early embryo. Here, we show that Hoxb cluster genes are expressed in a temporally collinear manner at the blastoderm margin, where mesodermal and endodermal (mesendoderm) progenitor cells are specified and ingress to form mesendoderm/hypoblast. Functional analysis shows that these Hoxb genes regulate the timing of cell ingression: under- or overexpression of Hoxb genes perturb the timing of mesendoderm cell ingression and, consequently, the positioning of these cells along the forming anterior-posterior body axis after gastrulation. Finally, we found that Hoxb genes control the timing of mesendoderm ingression by regulating cellular bleb formation and cell surface fluctuations in the ingressing cells. Collectively, our findings suggest that Hoxb genes interconnect the temporal and spatial pattern of cell behaviors during zebrafish gastrulation by controlling cell surface fluctuations.},
  author       = {Moriyama, Yuuta and Mitsui, Toshiyuki and Heisenberg, Carl-Philipp J},
  issn         = {1477-9129},
  journal      = {Development},
  number       = {12},
  publisher    = {Company of Biologists},
  title        = {{Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation}},
  doi          = {10.1242/dev.204261},
  volume       = {152},
  year         = {2025},
}

@article{21343,
  abstract     = {The large sieve is used to estimate the density of quadratic polynomials Q ∈ Z[x],
such that there exists an odd degree polynomial defined over Z which has resultant ±1 with Q.
Given a monic polynomial R ∈ Z[x] of odd degree, this is used to show that for almost all
quadratic polynomials Q ∈ Z[x], there exists a prime p such that Q and R share a common
root in Fp. Using recent work of Landesman, an application to the average size of the odd part
of the class group of quadratic number fields is also given},
  author       = {Browning, Timothy D and Chan, Yik Tung},
  issn         = {2270-518X},
  journal      = {Journal de l'Ecole Polytechnique - Mathematiques},
  pages        = {1677--1691},
  publisher    = {Ecole Polytechnique},
  title        = {{Solubility of a resultant equation and applications}},
  doi          = {10.5802/jep.320},
  volume       = {12},
  year         = {2025},
}

@article{20249,
  abstract     = {We develop a heuristic for the density of integer points on affine cubic surfaces. Our heuristic applies to smooth surfaces defined by cubic polynomials that are log K3, but it can also be adjusted to handle singular cubic surfaces. We compare our heuristic to Heath-Brown’s prediction for sums of three cubes, as well as to asymptotic formulae in the literature around Zagier’s work on the Markoff cubic surface, and work of Baragar and Umeda on further surfaces of Markoff-type. We also test our heuristic against numerical data for several families of cubic surfaces.},
  author       = {Browning, Timothy D and Wilsch, Florian Alexander},
  issn         = {1420-9020},
  journal      = {Selecta Mathematica New Series},
  number       = {4},
  publisher    = {Springer Nature},
  title        = {{Integral points on cubic surfaces: heuristics and numerics}},
  doi          = {10.1007/s00029-025-01074-1},
  volume       = {31},
  year         = {2025},
}

@article{20218,
  abstract     = {Humanity has long sought inspiration from nature to innovate materials and devices. As science advances, nature-inspired materials are becoming part of our lives. Animate materials, characterized by their activity, adaptability, and autonomy, emulate properties of living systems. While only biological materials fully embody these principles, artificial versions are advancing rapidly, promising transformative impacts in the circular economy, health and climate resilience within a generation. This roadmap presents authoritative perspectives on animate materials across different disciplines and scales, highlighting their interdisciplinary nature and potential applications in diverse fields including nanotechnology, robotics and the built environment. It underscores the need for concerted efforts to address shared challenges such as complexity management, scalability, evolvability, interdisciplinary collaboration, and ethical and environmental considerations. The framework defined by classifying materials based on their level of animacy can guide this emerging field to encourage cooperation and responsible development. By unravelling the mysteries of living matter and leveraging its principles, we can design materials and systems that will transform our world in a more sustainable manner.},
  author       = {Volpe, Giorgio and Araújo, Nuno A.M. and Guix, Maria and Miodownik, Mark and Martin, Nicolas and Alvarez, Laura and Simmchen, Juliane and Leonardo, Roberto Di and Pellicciotta, Nicola and Martinet, Quentin and Palacci, Jérémie A and Ng, Wai Kit and Saxena, Dhruv and Sapienza, Riccardo and Nadine, Sara and Mano, João F. and Mahdavi, Reza and Beck Adiels, Caroline and Forth, Joe and Santangelo, Christian and Palagi, Stefano and Seok, Ji Min and Webster-Wood, Victoria A. and Wang, Shuhong and Yao, Lining and Aghakhani, Amirreza and Barois, Thomas and Kellay, Hamid and Coulais, Corentin and Van Hecke, Martin and Pierce, Christopher J. and Wang, Tianyu and Chong, Baxi and Goldman, Daniel I. and Reina, Andreagiovanni and Trianni, Vito and Volpe, Giovanni and Beckett, Richard and Nair, Sean P. and Armstrong, Rachel},
  issn         = {1361-648X},
  journal      = {Journal of Physics: Condensed Matter},
  number       = {33},
  publisher    = {IOP Publishing},
  title        = {{Roadmap for animate matter}},
  doi          = {10.1088/1361-648X/adebd3},
  volume       = {37},
  year         = {2025},
}

@article{20453,
  abstract     = {Magnetotropic susceptibility is the thermodynamic coefficient that maps the curvature of free energy with respect to an applied magnetic field orientation, providing a means to quantify the magnetic anisotropy of a crystal. In this context, non-linear magnetic torque behavior has been reported in FePS3, motivating the investigation of similar non-linear characteristics in its magnetotropic susceptibility. In this work, we derive the non-linear magnetotropic susceptibility expressions for FePS3 in both ac*-and bc*-planes using complementary approaches: by taking the first derivative of torque and through the formal calculation of the magnetotropic susceptibility. Higher-order terms in the magnetization are included, and the final equations are obtained by applying symmetry constraints imposed by the C2h point group of the material. We analyze the behavior of the resulting non-linear expressions and identify the contributions of each parameter. Our theoretical results show good agreement with preliminary, unpublished experimental data, offering meaningful guidance for ongoing and future experimental work.},
  author       = {Farooq, Hamza and Nauman, Muhammad},
  issn         = {1361-648X},
  journal      = {Journal of Physics: Condensed Matter},
  number       = {40},
  publisher    = {IOP Publishing},
  title        = {{Non-linear magnetotropic susceptibility in FePS3}},
  doi          = {10.1088/1361-648X/ae0913},
  volume       = {37},
  year         = {2025},
}

@article{20219,
  abstract     = {Reproduction is a fundamental biological process, with organisms reproducing sexually, asexually, and, in some cases, utilizing both modes of reproduction within the same population. Does the ability to reproduce through a combination of asexual and sexual modes offer an evolutionary advantage over relying on either mode alone? Here, we introduce an empirically driven theoretical model to examine the dynamics and interplay between sexual and asexual reproduction in stick insect populations. We analyse it using a novel phase transition approach and corroborate it using published experimental data. We find that the presence of males can either increase or decrease the overall population size. However, maintaining an optimal ratio of parthenogenetic to sexual reproduction is crucial for male resilience, effectively delaying male extinction. Conversely, extreme levels of parthenogenetic reproduction—whether too high or too low—can lead to male extinction, emphasizing the need for a balanced number of virgin females to ensure the persistence of males. Our model also explains male absence in Carausius morosus and persistence in Extatosoma tiaratum. Our findings provide valuable insights into the interplay of reproductive strategies and contribute to broader discussions on the transitions between sexual and asexual reproduction.},
  author       = {Ayalon, Oran and Rajendran, Harikrishnan},
  issn         = {1742-5662},
  journal      = {Journal of the Royal Society Interface},
  number       = {229},
  publisher    = {Royal Society},
  title        = {{Interplay of asexual and sexual reproduction in bifunctional insects}},
  doi          = {10.1098/rsif.2025.0202},
  volume       = {22},
  year         = {2025},
}

@unpublished{19762,
  abstract     = {The cerebral cortex must contain the appropriate numbers of neurons in each layer to acquire its proper functional organization. Accordingly, neurogenesis requires precise regulation along development. Cortical neurons are made either directly by Radial Glia Cells (RGCs) that self- consume, or indirectly from RGCs via Intermediate Progenitor Cells (IPCs) and largely preserving the RGC pool. According to the standing model of cortical development, Direct Neurogenesis predominates at early stages of development, and progressively shifts to Indirect Neurogenesis, which predominates at late stages. However, neurogenesis at early stages should be compatible with RGC amplification, and neurogenesis at late stages needs to involve RGC consumption, which seems in conflict with the standing model. Here we studied the modes of neurogenesis along cortical development using multiple approaches, including birthdating, live imaging and MADM clone labeling. Contrary to the established dogma, our data show that Indirect Neurogenesis clearly predominates at early developmental stages, gradually shifting to Direct Neurogenesis at late stages. These findings challenge the current model of cortical neurogenesis, and prompt a re-evaluation of previous and ongoing work about the genetic and molecular mechanisms regulating this process.},
  author       = {Cárdenas, Adrián and Çelik, Irem and Espinós, Alexandre and Streicher, Carmen and López-González, Lara and del-Valle-Anton, Lucia and Fernández, Virginia and Amin, Salma and Negri, Enrico and Ortuño, Eduardo Fernández and Hippenmeyer, Simon and Borrell, Víctor},
  booktitle    = {bioRxiv},
  title        = {{Early indirect neurogenesis transitions to late direct neurogenesis in mouse cerebral cortex development}},
  doi          = {10.1101/2025.05.22.655488},
  year         = {2025},
}

@unpublished{19717,
  abstract     = {Radial glial progenitors (RGPs) generate all projection neurons (PNs) in the cerebral cortex through incompletely understood processes. Herein, we combine Mosaic Analysis with Double Markers (MADM)-based clonal analysis at embryonic days 12.5 and 13.5 with early postnatal callosal tracing to reveal a lineage progression that challenges the inside-outside model of cortical development and the conventional view of an invariable sequence of asymmetric neurogenic divisions. Our data demonstrate that early multipotent RGPs generate all extra-telencephalic (ET) and intra-telencephalic (IT) PNs across all layers through parallel sublineages and the random specification, during the earliest neurogenic divisions, of fate-restricted daughter RGPs. While the neuronal production of the parental multipotent RGPs consists of small ET-PN or IT-PN outputs, fate-restricted RGPs produce larger translaminar outputs spanning deep and upper layers of only IT-PNs, the predominant mammalian PN subtype. We further show that the emergence of IT-PN fate-restricted RGPs also leads to quantitatively and temporally stereotyped neurogenesis population-wise.},
  author       = {Varela-Martínez, I and Villalba Requena, Ana and Garcia-Marqués, J. and Hippenmeyer, Simon and Nieto, M.},
  booktitle    = {bioRxiv},
  title        = {{Early emergence of projection-subtype fate-restricted radial glial progenitors orchestrates neocortical neurogenesis}},
  doi          = {10.1101/2025.05.07.652665},
  year         = {2025},
}

@unpublished{19674,
  abstract     = {When examined through the lens of their residual streams, a puzzling property emerges in transformer networks: residual contributions (e.g., attention heads) sometimes specialize in specific tasks or input attributes. In this paper, we analyze this phenomenon in vision transformers, focusing on the spectral geometry of residuals, and explore its implications for modality alignment in vision-language models. First, we link it to the intrinsically low-dimensional structure of visual head representations, zooming into their principal components and showing that they encode specialized roles across a wide variety of input data distributions. Then, we analyze the effect of head specialization in multimodal models, focusing on how improved alignment between text and specialized heads impacts zero-shot classification performance. This specialization-performance link consistently holds across diverse pre-training data, network sizes, and objectives, demonstrating a powerful new mechanism for boosting zero-shot classification through targeted alignment. Ultimately, we translate these insights into actionable terms by introducing ResiDual, a technique for spectral alignment of the residual stream. Much like panning for gold, it lets the noise from irrelevant unit principal components (i.e., attributes) wash away to amplify task-relevant ones. Remarkably, this dual perspective on modality alignment yields fine-tuning level performance on different data distributions while modelling an extremely interpretable and parameter-efficient transformation, as we extensively show on 70 pre-trained network-dataset combinations (7 models, 10 datasets).},
  author       = {Basile, Lorenzo and Maiorca, Valentino and Bortolussi, Luca and Rodolà, Emanuele and Locatello, Francesco},
  booktitle    = {arXiv},
  title        = {{ResiDual transformer alignment with spectral decomposition}},
  doi          = {10.48550/arXiv.2411.00246},
  year         = {2025},
}

@phdthesis{20167,
  author       = {Schön, Hanna},
  isbn         = {978-3-99078-061-9},
  issn         = {2663-337X},
  pages        = {171},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs}},
  doi          = {10.15479/AT-ISTA-20167},
  year         = {2025},
}

@article{20538,
  abstract     = {In this study, we describe an integrated approach for methyl group assignment comprising precursor-based selective methyl group labeling, a novel pulse sequence for methyl to backbone coherence transfer and chemical shift predictions using UCBShift 2.0. The utility of this novel α-ketoacid isotopologue is shown by the adaptation of an HMBC-HMQC pulse sequence that simultaneously connects geminal methyl groups of leucine and valine residues to each other and to the protein backbone. By additional 13C,2H-labeling of residues other than valine and leucine residues of the protein, important chemical shift information about neighboring residues (following valine and leucine residues) can be achieved. Thus, different valine and leucine residues in a protein can be characterized as a specific chemical shift vector. Frequency matching with predicted chemical shifts via UCBShift 2.0 using experimental data taken from a subset of the BMRB database revealed a correct assignment performance of about 90%. With applications to proteins of 60.2 kDa and 134 kDa (4 × 33.5 kDa) in size, we demonstrate that the approach provides valuable information even for very large proteins.},
  author       = {Knödlstorfer, Sonja and Toscano, Giorgia and Ptaszek, Aleksandra L. and Kontaxis, Georg and Napoli, Federico and Schneider, Jakob and Maier, Katharina and Kapitonova, Anna and Lichtenecker, Roman J. and Schanda, Paul and Konrat, Robert},
  issn         = {1089-8638},
  journal      = {Journal of Molecular Biology},
  number       = {23},
  publisher    = {Elsevier},
  title        = {{A novel HMBC-CC-HMQC NMR strategy for methyl assignment using triple-13C-labeled α-ketoisovalerate integrated with UCBShift 2.0}},
  doi          = {10.1016/j.jmb.2025.169465},
  volume       = {437},
  year         = {2025},
}

@article{20258,
  abstract     = {The specific introduction of ^1H-^13C or ^1H-^15N moieties into otherwise deuterated proteins holds great potential for high-resolution solution and magic-angle spinning (MAS) NMR studies of protein structure and dynamics. Arginine residues play key roles for example at active sites of enzymes. Taking advantage of a chemically synthesized Arg with a ^13C-^1H2 group in an otherwise deuterated backbone, we demonstrate here the usefulness of proton-detected MAS NMR approaches to probe arginine dynamics. In experiments with crystalline ubiquitin and the 134 kDa tetrameric enzyme malate dehydrogenase we detected a wide range of motions, from sites that are rigid on time scales of at least tens of milliseconds to residues undergoing predominantly nanosecond motions. Spin-relaxation and dipolar-coupling measurements enabled quantitative determination of these dynamics. We observed microsecond dynamics of residue Arg54 in crystalline ubiquitin, whose backbone is known to sample different β-turn conformations on this time scale. The labeling scheme and experiments presented here expand the toolkit for high-resolution proton-detected MAS NMR.},
  author       = {Rohden, Darja and Napoli, Federico and Kapitonova, Anna and Tatman, Benjamin and Lichtenecker, Roman J. and Schanda, Paul},
  issn         = {1089-8638},
  journal      = {Journal of Molecular Biology},
  number       = {23},
  publisher    = {Elsevier},
  title        = {{Arginine dynamics probed by magic-angle spinning NMR with a specific isotope-labeling scheme}},
  doi          = {10.1016/j.jmb.2025.169379},
  volume       = {437},
  year         = {2025},
}

@misc{19956,
  abstract     = {The specific introduction of 1H-13C or 1H-15N moieties into otherwise deuterated proteins holds great potential for high-resolution solution and magic-angle spinning (MAS) NMR studies of protein structure and dynamics. Arginine residues play key roles for example at active sites of enzymes. Taking advantage of a chemically synthesized Arg with a 13C-1H2 group in an otherwise deuterated backbone, we demonstrate here the usefulness of proton-detected arginine MAS NMR approaches to probe arginine dynamics. In experiments on crystalline ubiquitin and the 134 kDa tetrameric enzyme malate dehydrogenase we detected a wide range of motions, from sites that are rigid on time scales of at least tens of milliseconds to residues undergoing predominantly nanosecond motions. Spin-relaxation and dipolar-coupling measurements enabled quantitative determination of these dynamics. We observed microsecond dynamics of residue Arg54 in crystalline ubiquitin, whose backbone is known to sample different β-turn conformations on this time scale. The labeling scheme and experiments presented here expand the toolkit for high-resolution proton-detected MAS NMR},
  author       = {Schanda, Paul},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Arginine Dynamics Probed by Magic-Angle Spinning NMR with a Specific Isotope-Labeling Scheme}},
  doi          = {10.15479/AT-ISTA-19956},
  year         = {2025},
}

@phdthesis{19395,
  abstract     = {Plant growth and development rely significantly on phytohormones, with auxin serving as a master regulator, orchestrating processes from embryogenesis to organogenesis, vascular patterning, and environmental adaptation. Since its conceptual proposition by Charles Darwin in 1880 as an endogenous chemical signal influencing phototropism in grass, auxin has captivated scientists seeking to understand how such a small molecule exerts a profound influence on plant development.
One particularly fascinating aspect of auxin function is its ability to self-organize its transport. Through a feedback mechanism between auxin perception and directional transport—primarily mediated by PIN auxin transporters—auxin establishes narrow transport channels. This phenomenon, known as auxin canalization, is fundamental to vascular formation, regeneration, and other key developmental processes. Despite advances in our understanding, driven by experimental studies and computational models, auxin canalization remains an enigma, with many unanswered questions.
Like other hormones, auxin functions through intricate signaling pathways. It operates through at least two distinct signaling mechanisms: the well-characterized canonical pathway and the less understood non-canonical pathway. While significant progress has been made in elucidating the canonical pathway, the non-canonical mechanisms remain less defined and require further investigation.
In this study, we revisit the non-canonical auxin signaling pathway mediated by the cell-surface complex Auxin Binding Protein 1-Transmembrane Kinase 1 (ABP1-TMK1), with a particular focus on its downstream phosphorylation events. We reveal that this auxin-mediated phosphorylation is conserved across the green lineage, underscoring its fundamental role in plant development. We explore key phosphorylation targets, particularly PIN2, which is essential for root gravitropism. To further understand TMK1’s role in diverse developmental processes, we identified and investigated its interactors as potential co-receptors or regulatory components within its signaling network.
Given the previously established role of ABP1-TMK1 in auxin canalization, we sought to further investigate this process and identified several TMK1 interactors also involved in this intricate mechanism.
These findings provide new insights into the complex regulation of auxin canalization, highlighting a broader and more interconnected signaling framework than previously understood.},
  author       = {Monzer, Aline},
  issn         = {2663-337X},
  pages        = {160},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Cell-surface auxin signaling: Linking molecular pathways to plant development}},
  doi          = {10.15479/AT-ISTA-19395},
  year         = {2025},
}

@unpublished{19399,
  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 key prerequisite for (i) self-organizing processes including vascular tissue formation and (ii) directional growth responses such as gravitropism. Here we identify a mechanism, by which auxin signaling directly targets PIN auxin transporters. Via the cell-surface ABP1-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 auxin receptor ABL3. Such positive feedback between cell-surface auxin signaling and PIN-mediated polar auxin transport is fundamental for robust root gravitropism and presumably also 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 Xu, Tongda and Kulich, Ivan and Jaillais, Yvon and Friml, Jiří},
  booktitle    = {bioRxiv},
  title        = {{ABP1/ABL3-TMK1 cell-surface auxin signaling directly targets PIN2-mediated auxin fluxes for root gravitropism}},
  doi          = {10.1101/2022.11.30.518503},
  year         = {2025},
}

@unpublished{19398,
  abstract     = {Receptor-like kinases (RLKs), particularly the Transmembrane Kinase (TMK) family, play essential roles in signaling and development, with TMKs being key components of auxin perception and downstream phosphorylation events. While TMKs’ involvement in auxin canalization, a process essential for vasculature formation and regeneration, has been established, nonetheless, the additional signaling and regulatory partners remain poorly understood. In this study, we identify and characterize seven leucine-rich repeat RLKs (TINT1–TINT7) as novel interactors of TMK1, revealing their diverse evolutionary, structural, and functional characteristics. Our results show that TINTs interact with TMK1 and highlight their roles in regulating various developmental processes. Majority of TINTs contributes, together with TMK1, to auxin canalization, with TINT5 linking TMK1 to other canalization component CAMEL. Beyond canalization, we also establish the role of TINT-TMK1 interactions in processes such as stomatal movement and the hypocotyl’s gravitropic response. These findings suggest that TINTs, through their interaction with TMK1, are integral components of various signaling networks, contributing to both auxin canalization and broader plant development.},
  author       = {Monzer, Aline and Mazur, Ewa and Rodriguez Solovey, Lesia and Gallei, Michelle C and Zou, Minxia and Smejkal, Michael and Cervenova, Ema and Friml, Jiří},
  booktitle    = {bioRxiv},
  title        = {{TMK interacting network of receptor like kinases for auxin canalization and beyond}},
  doi          = {10.1101/2025.02.28.640727},
  year         = {2025},
}

@inproceedings{21280,
  abstract     = {We give an algorithm that, with high probability, maintains a (1-ε)-approximate s-t maximum flow in undirected, uncapacitated n-vertex graphs undergoing m edge insertions in Õ(m+ n F^*/ε) total update time, where F^{*} is the maximum flow on the final graph. This is the first algorithm to achieve polylogarithmic amortized update time for dense graphs (m = Ω(n²)), and more generally, for graphs where F^* = Õ(m/n). At the heart of our incremental algorithm is the residual graph sparsification technique of Karger and Levine [SICOMP '15], originally designed for computing exact maximum flows in the static setting. Our main contributions are (i) showing how to maintain such sparsifiers for approximate maximum flows in the incremental setting and (ii) generalizing the cut sparsification framework of Fung et al. [SICOMP '19] from undirected graphs to balanced directed graphs.},
  author       = {Goranci, Gramoz and Henzinger, Monika H and Räcke, Harald and Sricharan, A.},
  booktitle    = {52nd International Colloquium on Automata, Languages, and Programming},
  isbn         = {9783959773720},
  location     = {Aarhus, Denmark},
  pages        = {91:1--91:20},
  publisher    = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
  title        = {{Incremental approximate maximum flow via residual graph sparsification}},
  doi          = {10.4230/lipics.icalp.2025.91},
  volume       = {334},
  year         = {2025},
}