@article{21015,
  abstract     = {Early embryo geometry is one of the most invariant species-specific traits, yet its role in ensuring developmental reproducibility and robustness remains underexplored. Here we show that in zebrafish, the geometry of the fertilized egg—specifically its curvature and volume—serves as a critical initial condition triggering a cascade of events that influence development. The embryo geometry guides patterned asymmetric cell divisions in the blastoderm, generating radial gradients of cell volume and nucleocytoplasmic ratio. These gradients generate mitotic phase waves, with the nucleocytoplasmic ratio determining individual cell cycle periods independently of other cells. We demonstrate that reducing cell autonomy reshapes these waves, emphasizing the instructive role of geometry-derived volume patterns in setting the intrinsic period of the cell cycle oscillator. In addition to organizing cell cycles, early embryo geometry spatially patterns zygotic genome activation at the midblastula transition, a key step in establishing embryonic autonomy. Disrupting the embryo shape alters the zygotic genome activation pattern and causes ectopic germ layer specification, underscoring the developmental significance of geometry. Together, our findings reveal a symmetry-breaking function of early embryo geometry in coordinating cell cycle and transcriptional patterning.},
  author       = {Mishra, Nikhil and Li, Yuting I and Hannezo, Edouard B and Heisenberg, Carl-Philipp J},
  issn         = {1745-2481},
  journal      = {Nature Physics},
  pages        = {139--150},
  publisher    = {Springer Nature},
  title        = {{Geometry-driven asymmetric cell divisions pattern cell cycles and zygotic genome activation in the zebrafish embryo}},
  doi          = {10.1038/s41567-025-03122-1},
  volume       = {22},
  year         = {2026},
}

@article{21485,
  abstract     = {Insulating oxides are among the most abundant solid materials in the universe1,2,3. Of the many ways in which they influence natural phenomena, perhaps the most consequential is their capacity to transfer electrical charge during contact4,5,6,7,8,9,10—which occurs even between samples of the same oxide—yet the symmetry-breaking parameter that causes this remains unidentified11,12. Here we show that adventitious carbonaceous molecules adsorbed from the environment are the symmetry-breaking factor in same-material oxide contact electrification (CE). We use acoustic levitation to measure charge exchange between a sphere and a plate composed of identical amorphous silicon dioxide (SiO2). Although charging polarity is random for co-prepared samples, we control it with baking or plasma treatment. Observing the charge-exchange relaxation afterwards, we see dynamics over a timescale of hours and connect this directly to the presence of adventitious carbon with time-of-flight mass spectrometry, low-energy ion scattering and infrared spectroscopy. Going further, we confirm that adventitious carbon can even determine charge exchange among different oxides. Our results identify the symmetry-breaking parameter that causes insulating oxides to exchange charge in settings ranging from desert sands4 to volcanic plumes5,6, while simultaneously highlighting an overlooked factor in CE more broadly.},
  author       = {Grosjean, Galien M and Ostermann, Markus and Sauer, Markus and Hahn, Michael and Pichler, Christian M. and Fahrnberger, Florian and Pertl, Felix and Balazs, Daniel and Link, Mason M. and Kim, Seong H. and Schrader, Devin L. and Blanco, Adriana and Gracia, Francisco and Mujica, Nicolás and Waitukaitis, Scott R},
  issn         = {1476-4687},
  journal      = {Nature},
  number       = {8106},
  pages        = {626--631},
  publisher    = {Springer Nature},
  title        = {{Adventitious carbon breaks symmetry in oxide contact electrification}},
  doi          = {10.1038/s41586-025-10088-w},
  volume       = {651},
  year         = {2026},
}

@article{21894,
  abstract     = {The Dean–Kawasaki equation—one of the most fundamental SPDEs of
fluctuating hydrodynamics—has been proposed as a model for density fluctuations in weakly interacting particle systems. In its original form, it is highly
singular and fails to be renormalizable, even by approaches such as regularity structures and paracontrolled distributions, hindering mathematical approaches to its rigorous justification. It has been understood recently that it is
natural to introduce a suitable regularization, for example, by applying a formal spatial discretization or by truncating high-frequency noise: This yields
well-posed equations that should still precisely approximate the law of the
particle density fluctuations.
In the present work, we prove that a regularization in the form of a formal
discretization of the Dean–Kawasaki equation indeed accurately describes
density fluctuations in systems of weakly interacting diffusing particles: We
show that, in suitable weak metrics, the law of fluctuations as predicted by
the discretized Dean–Kawasaki SPDE approximates the law of fluctuations
of the original particle system, up to an error that is of arbitrarily high order in
the inverse particle number and a discretization error. In particular, the Dean–
Kawasaki equation provides a means for efficient and accurate simulations of
density fluctuations in weakly interacting particle systems.},
  author       = {Cornalba, Federico and Fischer, Julian L and Ingmanns, Jonas and Raithel, Claudia},
  issn         = {2168-894X},
  journal      = {The Annals of Probability},
  keywords     = {Weakly interacting particle systems, fluctuating hydrodynamics, Dean-Kawasaki equation, stochastic PDEs, numerical approximation},
  number       = {1},
  pages        = {155--215},
  publisher    = {Institute of Mathematical Statistics},
  title        = {{Density fluctuations in weakly interacting particle systems via the Dean–Kawasaki equation}},
  doi          = {10.1214/25-aop1763},
  volume       = {54},
  year         = {2026},
}

@article{22229,
  abstract     = {Hippocampal CA3 pyramidal neurons (PNs) form the largest autoassociative network in the mammalian brain. Whether CA3–CA3 recurrent connectivity is genetically preconfigured or environmentally shaped during ongoing memory storage is currently unknown. To address this question, we performed multicellular patch-clamp-based circuit mapping of up to eight CA3 PNs in the mouse hippocampus at multiple postnatal time points (P7–8, P18–25, and P45–50). Here, we show that the hippocampal CA3 network undergoes a developmental transformation from local, dense, and random connectivity to a distributed, sparse, and structured configuration. Thus, sparse and structured connectivity may emerge via experience-dependent mechanisms. In parallel, the strength of single synapses is downregulated; single synaptic events are sufficient to trigger postsynaptic spiking early in development, whereas spatial summation of several inputs is required at later time points. Biologically inspired models of memory storage by Hebbian synaptic plasticity and retrieval via pattern completion suggest that developmental changes improve specific aspects of memory storage and retrieval. Our results imply a developmental transformation of the neuronal code and the memory functions in the hippocampal CA3 network.</jats:p>},
  author       = {Vargas Barroso, Victor M and Watson, Jake and Navas Olivé, Andrea C and Schlögl, Alois and Jonas, Peter M},
  issn         = {2041-1723},
  journal      = {Nature Communications},
  publisher    = {Springer Nature},
  title        = {{Developmental emergence of sparse and structured synaptic connectivity in the hippocampal CA3 memory circuit}},
  doi          = {10.1038/s41467-026-71914-x},
  volume       = {17},
  year         = {2026},
}

@article{22967,
  abstract     = {Alkali salts are widely used in solution processing, yet the corresponding cations are often assumed to remain in the liquid phase. Here, we show that alkali ions introduced during the solution synthesis of SnSe are retained through particle isolation and continue to influence the material during subsequent thermal processing, where they shape the evolution of the final polycrystalline material. Different SnSe powders were prepared using Li+, Na+, and K+ precursors, as well as tetramethylammonium (TMA+) precursors as a nonalkali reference for comparison, and all samples were consolidated under identical conditions. Although all three alkali ions were found in the matrix, at grain boundaries, and in segregated nanoscale regions, they partitioned differently and resulted in distinct grain sizes, defect distributions, and therefore transport properties. Li induced the strongest grain size heterogeneity and the lowest energy barriers, Na the best overall balance between carrier concentration and mobility, and K the broadest alkali-rich grain boundary regions along with the strongest interfacial penalty to charge carrier transport. These results show that residual alkali ions are not just remnants of solution synthesis but active determinants of microstructure and thermoelectric performance in SnSe.},
  author       = {Fiedler, Christine and Horta, Sharona and Navita, Navita and Maji, Krishnendu and Kleinhanns, Tobias and Llorca, Jordi and Wang, Qi and Ramon, Maria Garcia and Das, Sambit and Gavini, Vikram and Liu, Yu and Ibáñez, Maria},
  issn         = {1520-5002},
  journal      = {Chemistry of Materials},
  number       = {18},
  pages        = {9323–9332},
  publisher    = {American Chemical Society},
  title        = {{Alkali ions retained from synthesis govern microstructure and transport in solution-processed SnSe}},
  doi          = {10.1021/acs.chemmater.6c01284},
  volume       = {38},
  year         = {2026},
}

@article{20869,
  abstract     = {Premise: What maintains trait divergence in the face of gene flow? Two varieties of wild snapdragon (Antirrhinum majus) characterized by divergent flower color hybridize in their native range. Selection on flower color genes is indicated by sharp clines, but the selective agents have not been demonstrated. Although previous work has focused on pollinators, pigmentation genes can also contribute to abiotic stress tolerance. We hypothesized that pigmentation in A. majus mediates stress tolerance, which could contribute to hybrid zone maintenance through parental niche divergence or hybrid maladaptation. Specifically, we tested whether morphotype mediates drought tolerance in an experiment comparing magenta-flowered var. pseudomajus, yellow-flowered var. striatum, and their pink-flowered hybrid cross.
Methods: We experimentally compared drought tolerance of each morphotype from allopatric crosses within and between varieties using three greenhouse treatments. Control plants were watered as needed, while drought-treated plants were watered half as often, either from the transplant stage (“early” drought), or from flowering onset (“late” drought).
Results: Parental morphotypes responded identically to drought in fitness and most phenotypic traits. However, hybrids had lower survival (14%) under late drought stress than parental morphotypes (70%). All hybrids that flowered in the late drought treatment died, compared to ~20% of flowering parental morphotypes.
Conclusions: Hybrid maladaptation to abiotic stress could potentially contribute to flower color divergence in the face of gene flow in A. majus. Further research should test the relevance of our results to field conditions and explicitly probe the role of flower color genes in drought tolerance.},
  author       = {Fuster‐Calvo, Alexandre and Jaworski, Coline C. and Ellis, Thomas and Baskett, Carina},
  issn         = {1537-2197},
  journal      = {American Journal of Botany},
  number       = {12},
  publisher    = {Wiley},
  title        = {{Reduced fitness under drought stress in F1 hybrids of Antirrhinum majus varieties with divergent flower colors}},
  doi          = {10.1002/ajb2.70129},
  volume       = {112},
  year         = {2025},
}

@article{20929,
  abstract     = {Insulin/insulin-like growth factor signaling inhibits FOXO transcription factors to control development, homeostasis, and aging. Here, we use proximity labeling to identify proteins interacting with the C. elegans FOXO DAF-16. We show that in well-fed, unstressed animals harboring active insulin signaling, DAF-16 forms a complex with the PAR-1/MARK serine/threonine kinase, a key regulator of cell polarity. PAR-1 inhibits DAF-16 accumulation and promotes DAF-16 phosphorylation at S249, at a conserved motif that PAR-1/human MARK2 phosphorylates in vitro. DAF-2 insulin-like receptor signaling stimulates DAF-16 S249 phosphorylation, suggesting DAF-2 activates PAR-1. DAF-2 also promotes PAR-1 expression by inhibiting DAF-16. PAR-1 knockdown, or DAF-16 S249A, prolong lifespan, whereas phosphomimetic DAF-16 S249D suppresses the longevity of daf-2 mutants. At low insulin signaling, DAF-16 proximity labeling highlights transcription factors, chromatin regulators, and DNA repair proteins. One interactor, the zinc finger/homeobox protein ZFH-2/ZFHX3, forms a complex with DAF-16 and prolongs lifespan. Our work provides entry points for hypothesis-driven studies of FOXO function and longevity.},
  author       = {Artan, Murat and Schön, Hanna and De Bono, Mario},
  issn         = {2041-1723},
  journal      = {Nature Communications},
  publisher    = {Springer Nature},
  title        = {{Proximity labeling of DAF-16 FOXO highlights aging regulatory proteins}},
  doi          = {10.1038/s41467-025-66409-0},
  volume       = {16},
  year         = {2025},
}

@inbook{18765,
  abstract     = {Mosaic Analysis with Double Markers (MADM) represents a mouse genetic approach coupling differential fluorescent labeling to genetic manipulations in dividing cells and their lineages. MADM uniquely enables the generation and visualization of individual control or homozygous mutant cells in a heterozygous genetic environment. Among its diverse applications, MADM has been used to dissect cell-autonomous gene functions important for cortical development and neural development in general. The high cellular resolution offered by MADM also permits the analysis of transcriptomic changes of individual cells upon genetic manipulations. In this chapter, we describe an experimental protocol combining the generation and isolation of MADM-labeled cells with downstream single-cell RNA-sequencing technologies to probe cell-type specific phenotypes due to genetic mutations at single-cell resolution.},
  author       = {Cheung, Giselle T and Pauler, Florian and Hippenmeyer, Simon},
  booktitle    = {Lineage Tracing},
  editor       = {Garcia-Marques, Jorge and Lee, Tzumin},
  isbn         = {9781071643099},
  issn         = {1940-6029},
  pages        = {139--151},
  publisher    = {Springer Nature},
  title        = {{Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM)}},
  doi          = {10.1007/978-1-0716-4310-5_7},
  volume       = {2886},
  year         = {2025},
}

@article{20260,
  abstract     = {The medial axis of a set consists of the points in the ambient space without a unique closest point in the original set. Since its introduction, the medial axis has been used extensively in many applications as a method of computing a skeleton topologically equivalent to the original set. Unfortunately, one limiting factor in the use of the medial axis of a smooth manifold is that it is not necessarily topologically stable under small perturbations of the manifold. To counter these instabilities, various prunings of the medial axis have been proposed in the computational geometry community. Here, we examine one type of pruning, called burning. Because of the good experimental results it was hoped that the burning method of simplifying the medial axis would be stable. In this work, we show a simple example that dashes such hopes. Based on Bing’s house with two rooms, we demonstrate an isotopy of a shape where the medial axis goes from collapsible to non-collapsible. More precisely, we consider the standard deformation retract from the closed ball to Bing’s house with two rooms, but stop just short of the point where Bing’s house becomes two dimensional. This way we obtain an isotopy from the 3-ball to a thickened version of Bing’s house. Under this isotopy, the medial axis goes from collapsible to non-collapsible. We stress that this isotopy can be made generic, in the sense of singularity theory, as developed by Arnol’d and Thom.},
  author       = {Chambers, Erin Wolf and Fillmore, Christopher D and Stephenson, Elizabeth R and Wintraecken, Mathijs},
  issn         = {2730-9657},
  journal      = {La Matematica},
  pages        = {811--828},
  publisher    = {Springer Nature},
  title        = {{Burning or collapsing the medial axis is unstable}},
  doi          = {10.1007/s44007-025-00170-0},
  volume       = {4},
  year         = {2025},
}

@article{20099,
  abstract     = {The hippocampus, critical for learning and memory, is dogmatically described as a trisynaptic circuit where dentate gyrus granule cells (GCs), CA3 pyramidal neurons (PNs), and CA1 PNs are serially connected. However, CA3 also forms an autoassociative network, and its PNs have diverse morphologies, intrinsic properties, and GC input levels. How PN subtypes compose this recurrent network is unknown. To determine the synaptic arrangement of identified CA3 PNs, we combine multicellular patch-clamp recording and post hoc morphological analysis in mouse hippocampal slices. PNs can be divided into distinct “superficial” and “deep” subclasses, the latter including previously reported “athorny” cells. Subclasses have distinct input-output transformations and asymmetric connectivity, which is more abundant from superficial to deep PNs, splitting CA3 locally into two parallel recurrent networks. Coincident spontaneous inhibition occurs frequently within but not between subclasses, implying subclass-specific inhibitory innervation. Our results suggest two separately controlled sublayers for parallel information processing in hippocampal CA3.},
  author       = {Watson, Jake and Vargas Barroso, Victor M and Jonas, Peter M},
  issn         = {2211-1247},
  journal      = {Cell Reports},
  number       = {8},
  publisher    = {Elsevier},
  title        = {{Cell-specific wiring routes information flow through hippocampal CA3}},
  doi          = {10.1016/j.celrep.2025.116080},
  volume       = {44},
  year         = {2025},
}

@article{19074,
  abstract     = {The public goods game is among the most studied metaphors of cooperation in groups. In this game, individuals can use their endowments to make contributions towards a good that benefits everyone. Each individual, however, is tempted to free-ride on the contributions of others. Herein, we study repeated public goods games among asymmetric players. Previous work has explored to which extent asymmetry allows for full cooperation, such that players contribute their full endowment each round. However, by design that work focusses on equilibria where individuals make the same contribution each round. Instead, here we consider players whose contributions along the equilibrium path can change from one round to the next. We do so for three different models – one without any budget constraints, one with endowment constraints, and one in which individuals can save their current endowment to be used in subsequent rounds. In each case, we explore two key quantities: the welfare and the resource efficiency that can be achieved in equilibrium. Welfare corresponds to the sum of all players’ payoffs. Resource efficiency relates this welfare to the total contributions made by the players. Compared to constant contribution sequences, we find that time-dependent contributions can improve resource efficiency across all three models. Moreover, they can improve the players’ welfare in the model with savings.},
  author       = {Hübner, Valentin and Hilbe, Christian and Staab, Manuel and Kleshnina, Maria and Chatterjee, Krishnendu},
  issn         = {2153-0793},
  journal      = {Dynamic Games and Applications},
  pages        = {1617--1645},
  publisher    = {Springer Nature},
  title        = {{Time-dependent strategies in repeated asymmetric public goods games}},
  doi          = {10.1007/s13235-025-00627-5},
  volume       = {15},
  year         = {2025},
}

@article{20324,
  abstract     = {We report relaxation oscillations in a one-dimensional array of Josephson junctions, wherein the array dynamically switches between low-current and high-current states. The oscillations are current-voltage dual to those ordinarily observed in single junctions. The current-voltage dual circuit quantitatively accounts for temporal dynamics of the array, including the dependence on biasing conditions. Injection locking of the oscillations results in well-developed current plateaux. A thermal model explains the self-consistent reduction of the superconducting gap due to overheating of the array in the high-current state. Our work suggests that overheating determines the switching from the high-current state to the low-current state.},
  author       = {Mukhopadhyay, Soham and Lancheros Naranjo, Diego A and Senior, Jorden L and Higginbotham, Andrew P},
  issn         = {2331-7019},
  journal      = {Physical Review Applied},
  publisher    = {American Physical Society},
  title        = {{Dual relaxation oscillations in a Josephson-junction array}},
  doi          = {10.1103/qvls-7s3q},
  volume       = {24},
  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},
}

@phdthesis{19903,
  abstract     = {Cooperation, that is, one person paying a cost for another's benefit, is a fundamental principle without which no form of society could exist. The extent to which humans cooperate with each other is also an essential feature that differentiates them from other animals. Cooperation occurs even in the absence of altruistic motivations, when it is selfishly incentivised by the expectation of a future reward. For example, many economic interactions are well described that way. This kind of cooperation requires that people exhibit reciprocal behaviour that acts as a mechanism that rewards cooperation.
With game-theoretic models, it is possible to formally study potential such mechanisms and under what conditions they can exist. This thesis contributes to this effort by analysing recently introduced models of cooperation that advance on previous work by taking into account the potential for pre-existing inequality among cooperating individuals as well as the different forms that reciprocity can take.
Individuals may differ both intrinsically, in their abilities, as well as extrinsically, in the amount of resources they have available. Allowing for such differences in a model of cooperation helps to understand how inequality affects the potential for, and outcomes of, cooperation among unequals. In this thesis, it is shown that in the presence of intrinsic inequality, a similar unequal distribution of resources can increase the potential for cooperation. This effect is stronger the smaller the group is in which cooperation takes place. It is also shown that under particular assumptions, if the unequal members of a group vary the size of their contributions to a cooperative effort over time, they can thereby increase their efficiency and improve the collective outcome.
Cooperative behaviour in a two-person interaction can be rewarded either by direct reciprocation whenever the same two people interact again, or indirectly by a third party who observed the interaction. In the latter case of indirect reciprocity, individuals are proximally rewarded by a good reputation, which ultimately translates to being rewarded with cooperative behaviour by others. This mechanism can enable selfishly motivated cooperation even in circumstances where individuals are unlikely to meet again, akin to how money facilitates trade. While these two forms of reciprocity have mostly been studied in isolation, this thesis analyses both direct and indirect reciprocity in a general model in order to compare their relative effectiveness under different circumstances. The contribution of this thesis is an extension of previous work regarding a specific kind of interaction, whose parameters allow for convenient mathematical analysis, to the most general set of possible interactions.},
  author       = {Hübner, Valentin},
  issn         = {2663-337X},
  pages        = {157},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Reciprocity and inequality in social dilemmas}},
  doi          = {10.15479/AT-ISTA-19903},
  year         = {2025},
}

@article{14683,
  abstract     = {Mosaic analysis with double markers (MADM) technology enables the generation of genetic mosaic tissue in mice and high-resolution phenotyping at the individual cell level. Here, we present a protocol for isolating MADM-labeled cells with high yield for downstream molecular analyses using fluorescence-activated cell sorting (FACS). We describe steps for generating MADM-labeled mice, perfusion, single-cell suspension, and debris removal. We then detail procedures for cell sorting by FACS and downstream analysis. This protocol is suitable for embryonic to adult mice.
For complete details on the use and execution of this protocol, please refer to Contreras et al. (2021).1},
  author       = {Amberg, Nicole and Cheung, Giselle T and Hippenmeyer, Simon},
  issn         = {2666-1667},
  journal      = {STAR Protocols},
  keywords     = {General Immunology and Microbiology, General Biochemistry, Genetics and Molecular Biology, General Neuroscience},
  number       = {1},
  publisher    = {Elsevier},
  title        = {{Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry}},
  doi          = {10.1016/j.xpro.2023.102771},
  volume       = {5},
  year         = {2024},
}

@article{17187,
  abstract     = {The generation of diverse cell types during development is fundamental to brain
functions. We outline a protocol to quantitatively assess the clonal output of individual neural progenitors using mosaic analysis with double markers (MADM) in
mice. We first describe steps to acquire and reconstruct adult MADM clones in
the superior colliculus. Then we detail analysis pipelines to determine clonal
composition and architecture. This protocol enables the buildup of quantitative
frameworks of lineage progression with precise spatial resolution in the brain.
For complete details on the use and execution of this protocol, please refer to
Cheung et al.1},
  author       = {Cheung, Giselle T and Streicher, Carmen and Hippenmeyer, Simon},
  issn         = {2666-1667},
  journal      = {STAR Protocols},
  number       = {3},
  publisher    = {Elsevier},
  title        = {{Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice}},
  doi          = {10.1016/j.xpro.2024.103157},
  volume       = {5},
  year         = {2024},
}

@article{17235,
  abstract     = {We demonstrate ion irradiation by argon or gallium as a wafer-scale post-processing method to increase disorder in superconducting thin films. We study several widely used superconductors, both single-elements and compounds. We show that ion irradiation increases normal-state resistivity in all our films, which is expected to enable tuning their superconducting properties, for example, toward a higher kinetic inductance. We observe an increase in superconducting transition temperature for Al and MoSi and a decrease for Nb, NbN, and TiN. In MoSi, ion irradiation also improves the mixing of the two materials. We demonstrate the fabrication of an amorphous and homogeneous film of MoSi with uniform thickness, which is promising, for example, for superconducting nanowire single-photon detectors.},
  author       = {Kohopää, Katja and Ronzani, Alberto and Jabdaraghi, Robab Najafi and Bera, Arijit and Ribeiro, Mário and Hazra, Dibyendu and Senior, Jorden L and Prunnila, Mika and Govenius, Joonas and Lehtinen, Janne S. and Kemppinen, Antti},
  issn         = {2166-532X},
  journal      = {APL Materials},
  number       = {7},
  publisher    = {AIP Publishing},
  title        = {{Effect of ion irradiation on superconducting thin films}},
  doi          = {10.1063/5.0202851},
  volume       = {12},
  year         = {2024},
}

@article{17888,
  abstract     = {Context: Biotic resource exploitation is a critical determinant of species’ distributions. However, quantifying resource exploitation patterns through space and time can be difficult, complicating their incorporation in spatial ecology studies. Therefore, understanding the local drivers of spatial patterns of resource exploitation may contribute to better large-scale species distribution models.
Objectives: We investigated (1) how the resource exploitation patterns of two trophic interactions (plant–insect) are explained by insect behaviour, resource aggregation, and potential insect-insect interactions. We also analyzed how (2) resource patch size and (3) resource accessibility in a heterogeneous landscape affected host exploitation patterns.
Methods: We quantified nectar robbing by insects in the genus Bombus (bumblebees) and seed predation by Brachypterolus vestitus larvae (Antirrhinum beetle) on Antirrhinum majus L. (wild snapdragons) in the Pyrenees Mountains, Catalonia, Spain. We tested hypotheses about resource exploitation by integrating spatial analyses at multiple scales.
Results: Both trophic interactions were aggregated, explained by the aggregation of their resource. At some scales, nectar robbing is more aggregated than the resource. Trophic interaction abundance is proportional to resource patch size, following the ideal free distribution model. Landscape features do not explain the locations exploited. Nectar robbing and seed predation occur together more often than expected.
Conclusions: Our findings suggest that multiple biotic and ecological spatial factors may simultaneously affect resource exploitation at a local scale. These findings should be considered when developing agricultural projects, management plans and conservation policies.},
  author       = {Pocull Belles, Guillem and Baskett, Carina and Barton, Nicholas H},
  issn         = {1572-9761},
  journal      = {Landscape Ecology},
  number       = {9},
  publisher    = {Springer Nature},
  title        = {{Multiscale spatial analysis of two plant–insect interactions: Effects of landscape, resource distribution, and other insects}},
  doi          = {10.1007/s10980-024-01899-9},
  volume       = {39},
  year         = {2024},
}

@inproceedings{17170,
  abstract     = {In this article we extend and strengthen the seminal work by Niyogi, Smale, and Weinberger on the learning of the homotopy type from a sample of an underlying space. In their work, Niyogi, Smale, and Weinberger studied samples of C² manifolds with positive reach embedded in ℝ^d. We extend their results in the following ways: - As the ambient space we consider both ℝ^d and Riemannian manifolds with lower bounded sectional curvature. - In both types of ambient spaces, we study sets of positive reach - a significantly more general setting than C² manifolds - as well as general manifolds of positive reach. - The sample P of a set (or a manifold) 𝒮 of positive reach may be noisy. We work with two one-sided Hausdorff distances - ε and δ - between P and 𝒮. We provide tight bounds in terms of ε and δ, that guarantee that there exists a parameter r such that the union of balls of radius r centred at the sample P deformation-retracts to 𝒮. We exhibit their tightness by an explicit construction. We carefully distinguish the roles of δ and ε. This is not only essential to achieve tight bounds, but also sensible in practical situations, since it allows one to adapt the bound according to sample density and the amount of noise present in the sample separately.},
  author       = {Attali, Dominique and Kourimska, Hana and Fillmore, Christopher D and Ghosh, Ishika and Lieutier, André and Stephenson, Elizabeth R and Wintraecken, Mathijs},
  booktitle    = {40th International Symposium on Computational Geometry},
  isbn         = {9783959773164},
  issn         = {1868-8969},
  location     = {Athens, Greece},
  pages        = {11:1--11:19},
  publisher    = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
  title        = {{Tight bounds for the learning of homotopy à la Niyogi, Smale, and Weinberger for subsets of euclidean spaces and of Riemannian manifolds}},
  doi          = {10.4230/LIPIcs.SoCG.2024.11},
  volume       = {293},
  year         = {2024},
}

@unpublished{18689,
  abstract     = {Multiplexed fluorescence microscopy imaging is widely used in biomedical applications. However, simultaneous imaging of multiple fluorophores can result in spectral leaks and overlapping, which greatly degrades image quality and subsequent analysis. Existing popular spectral unmixing methods are mainly based on computational intensive linear models and the performance is heavily dependent on the reference spectra, which may greatly preclude its further applications. In this paper, we propose a deep learning-based blindly spectral unmixing method, termed AutoUnmix, to imitate the physical spectral mixing process. A tranfer learning framework is further devised to allow our AutoUnmix adapting to a variety of imaging systems without retraining the network. Our proposed method has demonstrated real-time unmixing capabilities, surpassing existing methods by up to 100-fold in terms of unmixing speed. We further validate the reconstruction performance on both synthetic datasets and biological samples. The unmixing results of AutoUnmix achieve a highest SSIM of 0.99 in both three- and four-color imaging, with nearly up to 20% higher than other popular unmixing methods. Due to the desirable property of data independency and superior blind unmixing performance, we believe AutoUnmix is a powerful tool to study the interaction process of different organelles labeled by multiple fluorophores.},
  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},
  booktitle    = {bioRxiv},
  title        = {{Super-resolution expansion microscopy in plant roots}},
  doi          = {10.1101/2024.02.21.581330},
  year         = {2024},
}