@article{19404, abstract = {Cell migration is a fundamental process during embryonic development. Most studies in vivo have focused on the migration of cells using the extracellular matrix (ECM) as their substrate for migration. In contrast, much less is known about how cells migrate on other cells, as found in early embryos when the ECM has not yet formed. Here, we show that lateral mesendoderm (LME) cells in the early zebrafish gastrula use the ectoderm as their substrate for migration. We show that the lateral ectoderm is permissive for the animal-pole-directed migration of LME cells, while the ectoderm at the animal pole halts it. These differences in permissiveness depend on the lateral ectoderm being more cohesive than the animal ectoderm, a property controlled by bone morphogenetic protein (BMP) signaling within the ectoderm. Collectively, these findings identify ectoderm tissue cohesion as one critical factor in regulating LME migration during zebrafish gastrulation.}, author = {Tavano, Ste and Brückner, David and Tasciyan, Saren and Tong, Xin and Kardos, Roland and Schauer, Alexandra and Hauschild, Robert and Heisenberg, Carl-Philipp J}, issn = {2211-1247}, journal = {Cell Reports}, number = {3}, publisher = {Elsevier}, title = {{BMP-dependent patterning of ectoderm tissue material properties modulates lateral mesendoderm cell migration during early zebrafish gastrulation}}, doi = {10.1016/j.celrep.2025.115387}, volume = {44}, year = {2025}, } @article{19405, abstract = {In the third APOKASC catalog, we present data for the complete sample of 15,808 evolved stars with APOGEE spectroscopic parameters and Kepler asteroseismology. We used 10 independent asteroseismic analysis techniques and anchor our system on fundamental radii derived from Gaia L and spectroscopic Teff. We provide evolutionary state, asteroseismic surface gravity, mass, radius, age, and the data used to derive them for 12,418 stars. This includes 10,036 exceptionally precise measurements, with median fractional uncertainties in vmax, Δν, mass, radius, and age of 0.6%, 0.6%, 3.8%, 1.8%, and 11.1%, respectively. We provide more limited data for 1624 additional stars that either have lower-quality data or are outside of our primary calibration domain. Using lower red giant branch (RGB) stars, we find a median age for the chemical thick disk of 9.14 ± 0.05(ran) ± 0.9(sys) Gyr with an age dispersion of 1.1 Gyr, consistent with our error model. We calibrate our red clump (RC) mass loss to derive an age consistent with the lower RGB and provide asymptotic GB and RGB ages for luminous stars. We also find a sharp upper-age boundary in the chemical thin disk. We find that scaling relations are precise and accurate on the lower RGB and RC, but they become more model dependent for more luminous giants and break down at the tip of the RGB. We recommend the use of multiple methods, calibration to a fundamental scale, and the use of stellar models to interpret frequency spacings.}, author = {Pinsonneault, Marc H. and Zinn, Joel C. and Tayar, Jamie and Serenelli, Aldo and García, Rafael A. and Mathur, Savita and Vrard, Mathieu and Elsworth, Yvonne P. and Mosser, Benoit and Stello, Dennis and Bell, Keaton J. and Bugnet, Lisa Annabelle and Corsaro, Enrico and Gaulme, Patrick and Hekker, Saskia and Hon, Marc and Huber, Daniel and Kallinger, Thomas and Cao, Kaili and Johnson, Jennifer A. and Liagre, Bastien and Patton, Rachel A. and Santos, Ângela R.G. and Basu, Sarbani and Beck, Paul G. and Beers, Timothy C. and Chaplin, William J. and Cunha, Katia and Frinchaboy, Peter M. and Girardi, Léo and Godoy-Rivera, Diego and Holtzman, Jon A. and Jönsson, Henrik and Mészáros, Szabolcs and Reyes, Claudia and Rix, Hans Walter and Shetrone, Matthew and Smith, Verne V. and Spoo, Taylor and Stassun, Keivan G. and Wang, Ji}, issn = {0067-0049}, journal = {Astrophysical Journal, Supplement Series}, number = {2}, publisher = {IOP Publishing}, title = {{APOKASC-3: The third joint spectroscopic and asteroseismic catalog for evolved stars in the Kepler fields}}, doi = {10.3847/1538-4365/ad9fef}, volume = {276}, year = {2025}, } @article{19406, abstract = {Polyploidization is a common occurrence in the evolutionary history of flowering plants, significantly contributing to their adaptability and diversity. However, the molecular mechanisms behind these adaptive advantages are not well understood. Through comprehensive phenotyping of diploid and tetraploid clones from Citrus and Poncirus genera, we discovered that genome doubling significantly enhances salt stress resilience. Epigenetic and transcriptomic analyses revealed that increased ethylene production in the roots of tetraploid plants was associated with hypomethylation and enhanced chromatin accessibility of the ACO1 gene. This increased ethylene production activates the transcription of reactive oxygen species scavenging genes and stress-related hormone biosynthesis genes. Consequently, tetraploid plants exhibited superior root functionality under salt stress, maintaining improved cytosolic K+/Na+ homeostasis. To genetically validate the link between salt stress resilience and ACO1 expression, we generated overexpression and knockout lines, confirming the central role of ACO1 expression regulation following genome doubling in salt stress resilience. Our work elucidates the molecular mechanisms underlying the role of genome doubling in stress resilience. We also highlight the importance of chromatin dynamics in fine-tuning ethylene gene expression and activating salt stress resilience pathways, offering valuable insights into plant adaptation and crop genome evolution.}, author = {Song, Xin and Zhang, Miao and Wang, Ting Ting and Duan, Yao Yuan and Ren, Jie and Gao, Hu and Fan, Yan Jie and Xia, Qiang Ming and Cao, Hui Xiang and Xie, Kai Dong and Wu, Xiao Meng and Zhang, Fei and Zhang, Si Qi and Huang, Ying and Boualem, Adnane and Bendahmane, Abdelhafid and Tan, Feng Quan and Guo, Wen Wu}, issn = {1469-8137}, journal = {New Phytologist}, number = {1}, pages = {176--191}, publisher = {Wiley}, title = {{Polyploidization leads to salt stress resilience via ethylene signaling in citrus plants}}, doi = {10.1111/nph.20428}, volume = {246}, year = {2025}, } @article{19407, abstract = {We discuss, in a non-Archimedean setting, the distribution of the coefficients of L-polynomials of curves of genus g over Fq . Among other results, this allows us to prove that the Q-vector space spanned by such characteristic polynomials has dimension g + 1. We also state a conjecture about the Archimedean distribution of the number of rational points of curves over finite fields.}, author = {Ballini, Francesco and Lombardo, Davide and Verzobio, Matteo}, issn = {1473-7124}, journal = {Proceedings of the Royal Society of Edinburgh Section A: Mathematics}, publisher = {Cambridge University Press}, title = {{On the L-polynomials of curves over finite fields}}, doi = {10.1017/prm.2025.7}, year = {2025}, } @article{19416, abstract = {Recently, Biagioli and Tompkins (2023, https://doi.org/10.1029/2022ms003231) used a simple stochastic model to derive a dimensionless parameter to predict convective self aggregation (SA) development, which was based on the derivation of the maximum free convective distance ($d_{clr}$) expected in the pre-aggregated, random state. Our goal is to test and further investigate this hypothesis, namely that $d_{clr}$ can predict SA occurrence, using an ensemble of twenty-four distinct combinations of horizontal mixing, planetary boundary layer (PBL), and microphysical parameterizations. We conclude that the key impact of parameterization schemes on SA is through their control of the number of convective cores and their relative spacing, $d_{clr}$, which itself is impacted by cold-pool (CP) properties and mean updraft core size. SA is more likely when the convective core count is small, while CPs modify convective spacing via suppression in their interiors and triggering by gust-front convergence and collisions. Each parameterization scheme emphasizes a different mechanism. Subgrid-scale horizontal turbulent mixing mainly affects SA through the determination of convective core size and thus spacing. The sensitivity to the microphysics is mainly through rain evaporation and the subsequent impact on CPs, while perturbations to the ice cloud microphysics have a limited effect. Non-local PBL mixing schemes promote SA primarily by increasing convective inhibition through inversion entrainment and altering low cloud amounts, leading to fewer convective cores and larger $d_{clr}$. }, author = {Casallas Garcia, Alejandro and Tompkins, A.M. and Muller, Caroline J and Thompson, G.}, issn = {1942-2466}, journal = {Journal of Advances in Modeling Earth Systems}, number = {3}, publisher = {Wiley}, title = {{Sensitivity of self-aggregation and the key role of the free convection distance}}, doi = {10.1029/2024MS004791}, volume = {17}, year = {2025}, } @article{19418, abstract = {The size-Ramsey number r^(H) of a graph H is the smallest number of edges a (host) graph G can have, such that for any red/blue colouring of G, there is a monochromatic copy of H in G. Recently, Conlon, Nenadov and Trujić showed that if H is a graph on n vertices and maximum degree three, then r^(H)=O(n8/5), improving upon the upper bound of n5/3+o(1) by Kohayakawa, Rödl, Schacht and Szemerédi. In this paper we show that r^(H)≤n3/2+o(1). While the previously used host graphs were vanilla binomial random graphs, we prove our result using a novel host graph construction. Our bound hits a natural barrier of the existing methods.}, author = {Draganić, Nemanja and Petrova, Kalina H}, issn = {1469-7750}, journal = {Journal of the London Mathematical Society}, number = {3}, publisher = {Wiley}, title = {{Size‐Ramsey numbers of graphs with maximum degree three}}, doi = {10.1112/jlms.70116}, volume = {111}, year = {2025}, } @article{19420, abstract = {Auxin and its PIN-FORMED (PIN) exporters are essential for tissue repair and regeneration in flowering plants. To gain insight into the evolution of this mechanism, we investigated their roles in leaves excised from Physcomitrium patens, a bryophyte known for its remarkable cell reprogramming capacity. We used various approaches to manipulate auxin levels, including exogenous application, pharmacological manipulations, and auxin biosynthesis mutants. We observed no significant effect on the rate of cell reprogramming. Rather, our analysis of auxin dynamics revealed a decrease in auxin levels upon excision, which was followed by a local increase before the reprogramming process began. Mutant analysis revealed that PpPINs are required for effective cell reprogramming, and endogenously expressed PpPINA-GFP accumulates polarly at sites that will develop into future filamentous stem cells. In addition, hyperpolarized PpPINA variants carrying mutated phosphorylation sites showed a marked delay in reprogramming, whereas endogenous or nonpolar versions do not have this effect. These results underscore that both the levels and the polarity of PpPINA are important for efficient cell reprogramming. Overall, these findings highlight the pivotal role of PIN polarity in plant regeneration. Furthermore, they suggest that understanding polarity mechanisms could have broader implications for improving regenerative processes across various plant species.}, author = {Tang, Han and Chen, L and Friml, Jiří}, issn = {1471-9053}, journal = {Plant and Cell Physiology}, publisher = {Oxford University Press}, title = {{Auxin fluctuation and PIN polarization in moss leaf cell reprogramming.}}, doi = {10.1093/pcp/pcaf008}, year = {2025}, } @article{19422, abstract = {Nitrogen (N) is an essential macronutrient for plant development and, ultimately, yield. Identifying the genetic components and mechanisms underlying N use efficiency in maize (Zea mays L.) is thus of great importance. Nitrate (NO3−) is the preferred inorganic N source in maize. Here we performed a genome-wide association study of shoot NO3− accumulation in maize seedlings grown under low-NO3− conditions, identifying the ferredoxin family gene ZmFd4 as a major contributor to this trait. ZmFd4 interacts and co-localizes with nitrite reductases (ZmNiRs) in chloroplasts to promote their enzymatic activity. Furthermore, ZmFd4 forms a high-affinity heterodimer with its closest paralogue, ZmFd9, in a NO3−-sensitive manner. Although ZmFd4 exerts similar biochemical functions as ZmFd9, ZmFd4 and ZmFd9 interaction limits their ability to associate with ZmNiRs and stimulate their activity. Knockout lines for ZmFd4 with decreased NO3− contents exhibit more efficient NO3− assimilation, and field experiments show consistently improved N utilization and grain yield under N-deficient conditions. Our work thus provides molecular and mechanistic insights into the natural variation in N utilization, instrumental for genetic improvement of yield in maize and, potentially, in other crops.}, author = {Jia, G and Chen, G and Zhang, Z and Tian, C and Wang, Y and Luo, J and Zhang, K and Zhao, X and Zhao, X and Li, Z and Sun, L and Yang, W and Guo, Y and Friml, Jiří and Gong, Z and Zhang, J}, issn = {2055-0278}, journal = {Nature Plants}, publisher = {Springer Nature}, title = {{Ferredoxin-mediated mechanism for efficient nitrogen utilization in maize}}, doi = {10.1038/s41477-025-01934-w}, volume = {11}, year = {2025}, } @article{19423, abstract = {Auxin, indole-3-acetic acid (IAA), is a key phytohormone with diverse morphogenic roles in land plants, but its function and transport mechanisms in algae remain poorly understood. We therefore aimed to explore the role of IAA in a complex, streptophyte algae Chara braunii. Here, we described novel responses of C. braunii to IAA and characterized two homologs of PIN auxin efflux carriers: CbPINa and CbPINc. We determined their localization in C. braunii using epitope-specific antibodies and tested their function in heterologous land plant models. Further, using phosphoproteomic analysis, we identified IAA-induced phosphorylation events. The thallus regeneration assay showed that IAA promotes thallus elongation and side branch development. Immunolocalization of CbPINa and CbPINc confirmed their presence on the plasma membrane of vegetative and generative cells of C. braunii. However, functional assays in tobacco BY-2 cells demonstrated that CbPINa affects auxin transport, whereas CbPINc does not. The IAA is effective in the acceleration of cytoplasmic streaming and the phosphorylation of evolutionary conserved targets such as homolog of RAF-like kinase. These findings suggest that, although canonical PIN-mediated auxin transport mechanisms might not be fully conserved in Chara, IAA is involved in morphogenesis and fast signaling processes.}, author = {Kurtović, K and Vosolsobě, S and Nedvěd, D and Müller, K and Dobrev, PI and Schmidt, V and Piszczek, P and Kuhn, A and Smoljan, Adrijana and Fisher, TJ and Weijers, D and Friml, Jiří and Bowman, JL and Petrášek, J}, issn = {1469-8137}, journal = {New Phytologist}, number = {3}, pages = {1066--1083}, publisher = {Wiley}, title = {{The role of indole-3-acetic acid and characterization of PIN transporters in complex streptophyte alga Chara braunii}}, doi = {10.1111/nph.70019}, volume = {246}, year = {2025}, } @article{19433, abstract = {An ordered r-matching is an r-uniform hypergraph matching equipped with an ordering on its vertices. These objects can be viewed as natural generalisations of r-dimensional orders. The theory of ordered 2-matchings is well developed and has connections and applications to extremal and enumerative combinatorics, probability and geometry. On the other hand, in the case r≥3 much less is known, largely due to a lack of powerful bijective tools. Recently, Dudek, Grytczuk and Ruciński made some first steps towards a general theory of ordered r-matchings, and in this paper we substantially improve several of their results and introduce some new directions of study. Many intriguing open questions remain.}, author = {Anastos, Michael and Jin, Zhihan and Kwan, Matthew Alan and Sudakov, Benny}, issn = {2050-5094}, journal = {Forum of Mathematics, Sigma}, publisher = {Cambridge University Press}, title = {{Extremal, enumerative and probabilistic results on ordered hypergraph matchings}}, doi = {10.1017/fms.2024.144}, volume = {13}, year = {2025}, } @article{19436, abstract = {Dynamic DNA methylation represses transposable elements (TEs) and regulates gene activity, playing a pivotal role in plant development. Although substantial progress has been made in understanding DNA methylation reprogramming during germline development in Arabidopsis thaliana, whether similar mechanisms exist in other dicot plants remains unclear. Here, we analyzed DNA methylation levels in meiocytes, microspores, and pollens of Brassica Rapa using whole-genome bisulfite sequencing (WGBS). Global DNA methylation analysis revealed similar CHH methylation reprogramming compared to Arabidopsis, while distinct patterns were observed in the dynamics of global CG and CHG methylation in B. rapa. Differentially methylated region (DMR) analysis identified specifically methylated loci in the male sex cells of B. Rapa with a stronger tendency to target genes, similar to observations in Arabidopsis. Additionally, we found that the activity and genomic targeting preference of the small RNA-directed DNA methylation (RdDM) were altered during B. Rapa male germline development. A subset of long terminal repeat (LTR) TEs were activated, possibly due to the dynamic regulation of DNA methylation during male sexual development in B. Rapa. These findings provided new insights into the evolution of epigenetic reprogramming mechanisms in plants.}, author = {Zhang, Jun and Wu, Di and Zhang, Yating and Feng, Xiaoqi and Gao, Hongbo}, issn = {2730-9401}, journal = {Molecular Horticulture}, publisher = {Springer Nature}, title = {{DNA methylation dynamics in male germline development in Brassica Rapa}}, doi = {10.1186/s43897-024-00137-9}, volume = {5}, year = {2025}, } @article{19437, abstract = {We demonstrate the formation of ferroelectric domain-wall polarons in a minimal two-dimensional lattice model of electrons interacting with rotating dipoles. Along the domain wall, the rotors polarize in opposite directions, causing the electron to localize along a particular lattice direction. The rotor-electron coupling is identified as the origin of a structural instability in the crystal that leads to the domain-wall formation via a symmetry-breaking process. Our results provide the first theoretical description of ferroelectric polarons, as discussed in the context of soft semiconductors.}, author = {Kluibenschedl, Florian and Koutentakis, Georgios and Al Hyder, Ragheed and Lemeshko, Mikhail}, issn = {1079-7114}, journal = {Physical Review Letters}, number = {9}, publisher = {American Physical Society}, title = {{Domain-wall ferroelectric polarons in a two-dimensional rotor lattice model}}, doi = {10.1103/PhysRevLett.134.096302}, volume = {134}, year = {2025}, } @article{19438, abstract = {Polymorphic short insertions and deletions (INDELs 50 bp) are abundant, although less common than single nucleotide polymorphisms (SNPs). Evidence from model organisms shows INDELs to be more strongly influenced by purifying selection than SNPs. Partly for this reason, INDELs are rarely used as markers for demographic processes or to detect divergent selection. Here, we compared INDELs and SNPs in the intertidal snail Littorina saxatilis, focussing on hybrid zones between ecotypes, in order to test the utility of INDELs in the detection of divergent selection. We computed INDEL and SNP site frequency spectra using capture sequencing data. We assessed the impact of divergent selection by analyzing allele frequency clines across habitat boundaries. We also examined the influence of GC-biased gene conversion because it may be confounded with signatures of selection. We show evidence that short INDELs are affected more by purifying selection than SNPs, but part of the observed site frequency spectra difference can be attributed to GC-biased gene conversion. We did not find a difference in the impact of divergent selection between short INDELs and SNPs. Short INDELs and SNPs were similarly distributed across the genome and so are likely to respond to indirect selection in the same way. A few regions likely affected by divergent selection were revealed by INDELs and not by SNPs. Short INDELs can be useful (additional) genetic markers helping to identify genomic regions important for adaptation and population divergence.}, author = {Perini, Samuel and Johannesson, Kerstin and Butlin, Roger K. and Westram, Anja M}, issn = {1420-9101}, journal = {Journal of Evolutionary Biology}, number = {3}, pages = {367--378}, publisher = {Oxford University Press}, title = {{Short INDELs and SNPs as markers of evolutionary processes in hybrid zones}}, doi = {10.1093/jeb/voaf002}, volume = {38}, year = {2025}, } @article{19439, abstract = {White dwarfs (WDs) are the most abundant compact objects, and recent surveys have suggested that over a third of WDs in accreting binaries host a strong (B ≳ 1 MG) magnetic field. However, the origin and evolution of WD magnetism remain under debate. Two WD pulsars, AR Sco and J191213.72–441045.1 (J1912), have been found, which are non-accreting binaries hosting rapidly spinning (1.97 minutes and 5.30 minutes, respectively) magnetic WDs. The WD in AR Sco is slowing down on a (math formular) yr timescale. It is believed they will eventually become polars, accreting systems in which a magnetic WD (B ≈ 10−240 MG) accretes from a Roche lobe-filling donor spinning in sync with the orbit (≳78 minutes). Here, we present multiwavelength data and analysis of Gaia22ayj, which outbursted in 2022 March. We find that Gaia22ayj is a magnetic accreting WD that is rapidly spinning down (math formular yr) like WD pulsars, but shows clear evidence of accretion, like polars. Strong linear polarization (40%) is detected in Gaia22ayj; such high levels have only been seen in the WD pulsar AR Sco and demonstrate the WD is magnetic. High speed photometry reveals a 9.36 minutes period accompanying a high amplitude (∼2 mag) modulation. We associate this with a WD spin or spin–orbit beat period, not an orbital period as was previously suggested. Fast (60 s) optical spectroscopy reveals a broad "hump," reminiscent of cyclotron emission in polars, between 4000 and 8000 Å. We find an X-ray luminosity of (math formular) in the 0.3–8 keV energy range, while two very large array radio campaigns resulted in a non-detection with a Fr < 15.8 μJy 3σ upper limit. The shared properties of both WD pulsars and polars suggest that Gaia22ayj is a missing link between the two classes of magnetic WD binaries.}, author = {Rodriguez, Antonio C. and El-Badry, Kareem and Hakala, Pasi and Rodríguez-Gil, Pablo and Bao, Tong and Galiullin, Ilkham and Kurlander, Jacob A. and Law, Casey J. and Pelisoli, Ingrid and Schreiber, Matthias R. and Burdge, Kevin and Caiazzo, Ilaria and Roestel, Jan Van and Szkody, Paula and Drake, Andrew J. and Buckley, David A.H. and Potter, Stephen B. and Gaensicke, Boris and Mori, Kaya and Bellm, Eric C. and Kulkarni, Shrinivas R. and Prince, Thomas A. and Graham, Matthew and Kasliwal, Mansi M. and Rose, Sam and Sharma, Yashvi and Ahumada, Tomás and Anand, Shreya and Viitanen, Akke and Wold, Avery and Chen, Tracy X. and Riddle, Reed and Smith, Roger}, issn = {0004-6280}, journal = {Publications of the Astronomical Society of the Pacific}, number = {2}, publisher = {IOP Publishing}, title = {{A link between White Dwarf pulsars and polars: Multiwavelength observations of the 9.36-minute period variable Gaia22ayj}}, doi = {10.1088/1538-3873/adb0f1}, volume = {137}, year = {2025}, } @article{19440, abstract = {Let μ(G) denote the minimum number of edges whose addition to G results in a Hamiltonian graph, and let μ^(G) denote the minimum number of edges whose addition to G results in a pancyclic graph. We study the distributions of μ(G),μ^(G) in the context of binomial random graphs. Letting d=d(n):=n⋅p, we prove that there exists a function f:R+→[0,1] of order f(d)=12de−d+e−d+O(d6e−3d) such that, if G∼G(n,p) with 20≤d(n)≤0.4logn, then with high probability μ(G)=(1+o(1))⋅f(d)⋅n. Let ni(G) denote the number of degree i vertices in G. A trivial lower bound on μ(G) is given by the expression n0(G)+⌈12n1(G)⌉. In the denser regime of random graphs, we show that if np−13logn−2loglogn→∞ and G∼G(n,p) then, with high probability, μ(G)=n0(G)+⌈12n1(G)⌉. For completion to pancyclicity, we show that if G∼G(n,p) and np≥20 then, with high probability, μ^(G)=μ(G). Finally, we present a polynomial time algorithm such that, if G∼G(n,p) and np≥20, then, with high probability, the algorithm returns a set of edges of size μ(G) whose addition to G results in a pancyclic (and therefore also Hamiltonian) graph.}, author = {Alon, Yahav and Anastos, Michael}, issn = {1098-2418}, journal = {Random Structures and Algorithms}, number = {2}, publisher = {Wiley}, title = {{The completion numbers of hamiltonicity and pancyclicity in random graphs}}, doi = {10.1002/rsa.21286}, volume = {66}, year = {2025}, } @article{19441, abstract = {Catalytic microswimmers convert the chemical energy from fuel into motion. They sustain chemical gradients and fluid flows that propel them by phoresis. This leads to unconventional behavior and collective dynamics, such as self-organization into complex structures. Characterizing the nonequilibrium interactions of microswimmers is crucial for advancing our understanding of active systems. However, this remains a challenge owing to the importance of fluctuations at the microscale and the difficulty in disentangling the different contributions to the interactions. Here, we show a massive dependence of the nonequilibrium interactions on the shape of catalytic microswimmers. We perform tracking experiments at high throughput to map interactions between nanocolloidal tracers and dimeric microswimmers of various aspect ratios. Our method leverages dual tracers with differing phoretic mobilities to quantitatively disentangle phoretic motion from hydrodynamic advection. This approach is validated through experiments on single chemically active sites and on immobilized catalytic microswimmers. We further investigate the activity-driven interactions of free microswimmers and directly measure their phoretic interactions. When compared to standard models, our findings highlight the important role of osmotic flows for microswimmers near surfaces and reveal an enhanced contribution of hydrodynamic advection relative to phoretic motion as the size of the microswimmer increases. Our study provides robust measurements of the nonequilibrium interactions from catalytic microswimmers and lays the groundwork for a realistic description of active systems.}, author = {Carrasco, Celso and Martinet, Quentin and Shen, Zaiyi and Lintuvuori, Juho and Palacci, Jérémie A and Aubret, Antoine}, issn = {1936-086X}, journal = {ACS Nano}, number = {11}, pages = {11133--11145}, publisher = {American Chemical Society}, title = {{Characterization of nonequilibrium interactions of catalytic microswimmers using phoretically responsive nanotracers}}, doi = {10.1021/acsnano.4c18078}, volume = {19}, year = {2025}, } @article{19442, abstract = {1. Climate change is expected to induce shifts in the composition, structure and functioning of Arctic tundra ecosystems. Increases in the frequency and severity of tundra fires have the potential to catalyse vegetation transitions with far-reaching local, regional and global consequences. 2. We propose that post-fire tundra recovery, coupled with climate change, may not necessarily lead to pre-fire conditions. Our hypothesis, based on surveys and literature, suggests two climate–fire driven trajectories. One trajectory results in increased woody vegetation under low fire frequency; the other results in grass dominance under high frequency. 3. Future research should address uncertainties regarding possible tundra ecosystem shifts linked to fires, using methods that encompass greater temporal and spatial scales than previously addressed. More case studies, especially in underrepresented regions and ecosystem types, are essential to broaden the empirical basis for forecasts and potential fire management strategies. 4. Synthesis. Our review synthesises current knowledge on post-fire vegetation trajectories in Arctic tundra ecosystems, highlighting potential transitions and alternative ecosystem states and their implications. We discuss challenges in defining and predicting these trajectories as well as future directions.}, author = {Heim, Ramona Julia and Rocha, Adrian V. and Zemlianskii, Vitalii and Barrett, Kirsten and Bültmann, Helga and Breen, Amy and Frost, Gerald Verner and Hollingsworth, Teresa Nettleton and Jandt, Randi and Kozlova, Maria and Kurka, Anastasiya and Jorgenson, Mark Torre and Landhäusser, Simon M. and Loranty, Michael Mark and Miller, Eric A. and Narita, Kenji and Pravdolyubova, Evgeniya and Hölzel, Norbert and Schaepman-Strub, Gabriela}, issn = {1365-2745}, journal = {Journal of Ecology}, number = {5}, pages = {1042--1056}, publisher = {Wiley}, title = {{Arctic tundra ecosystems under fire—Alternative ecosystem states in a changing climate?}}, doi = {10.1111/1365-2745.70022}, volume = {113}, year = {2025}, } @article{19443, abstract = {In cryo-electron microscopy, accurate particle localization and classification are imperative. Recent deep learning solutions, though successful, require extensive training datasets. The protracted generation time of physics-based models, often employed to produce these datasets, limits their broad applicability. We introduce FakET, a method based on neural style transfer, capable of simulating the forward operator of any cryo transmission electron microscope. It can be used to adapt a synthetic training dataset according to reference data producing high-quality simulated micrographs or tilt-series. To assess the quality of our generated data, we used it to train a state-of-the-art localization and classification architecture and compared its performance with a counterpart trained on benchmark data. Remarkably, our technique matches the performance, boosts data generation speed 750x, uses 33x less memory, and scales well to typical transmission electron microscope detector sizes. It leverages GPU acceleration and parallel processing. The source code is available at https://github.com/paloha/faket/.}, author = {Harar, Pavol and Herrmann, Lukas and Grohs, Philipp and Haselbach, David}, issn = {1878-4186}, journal = {Structure}, number = {4}, pages = {820--827.e4}, publisher = {Elsevier}, title = {{FakET: Simulating cryo-electron tomograms with neural style transfer}}, doi = {10.1016/j.str.2025.01.020}, volume = {33}, year = {2025}, } @article{19444, abstract = {As the field of neural organoids and assembloids expands, there is an emergent need for guidance and advice on designing, conducting and reporting experiments to increase the reproducibility and utility of these models. In this Perspective, we present a framework for the experimental process that encompasses ensuring the quality and integrity of human pluripotent stem cells, characterizing and manipulating neural cells in vitro, transplantation techniques and considerations for modelling human development, evolution and disease. As with all scientific endeavours, we advocate for rigorous experimental designs tailored to explicit scientific questions as well as transparent methodologies and data sharing to provide useful knowledge for current research practices and for developing regulatory standards.}, author = {Pașca, Sergiu P. and Arlotta, Paola and Bateup, Helen S. and Camp, J. Gray and Cappello, Silvia and Gage, Fred H. and Knoblich, Jürgen A. and Kriegstein, Arnold R. and Lancaster, Madeline A. and Ming, Guo Li and Novarino, Gaia and Okano, Hideyuki and Parmar, Malin and Park, In Hyun and Reiner, Orly and Song, Hongjun and Studer, Lorenz and Takahashi, Jun and Temple, Sally and Testa, Giuseppe and Treutlein, Barbara and Vaccarino, Flora M. and Vanderhaeghen, Pierre and Young-Pearse, Tracy}, issn = {1476-4687}, journal = {Nature}, number = {8054}, pages = {315--320}, publisher = {Springer Nature}, title = {{A framework for neural organoids, assembloids and transplantation studies}}, doi = {10.1038/s41586-024-08487-6}, volume = {639}, year = {2025}, } @inproceedings{19445, abstract = {In reconfiguration, we are given two solutions to a graph problem, such as Vertex Cover or Dominating Set, with each solution represented by a placement of tokens on vertices of the graph. Our task is to reconfigure one into the other using small steps while ensuring the intermediate configurations of tokens are also valid solutions. The two commonly studied settings are Token Jumping and Token Sliding, which allows moving a single token to an arbitrary or an adjacent vertex, respectively. We introduce new rules that generalize Token Jumping, parameterized by the number of tokens allowed to move at once and by the maximum distance of each move. Our main contribution is identifying minimal rules that allow reconfiguring any possible given solution into any other for Independent Set, Vertex Cover, and Dominating Set. For each minimal rule, we also provide an efficient algorithm that finds a corresponding reconfiguration sequence. We further focus on the rule that allows each token to move to an adjacent vertex in a single step. This natural variant turns out to be the minimal rule that guarantees reconfigurability for Vertex Cover. We determine the computational complexity of deciding whether a (shortest) reconfiguration sequence exists under this rule for the three studied problems. While reachability for Vertex Cover is shown to be in P, finding a shortest sequence is shown to be NP-complete. For Independent Set and Dominating Set, even reachability is shown to be PSPACE-complete.}, author = {Křišťan, Jan Matyáš and Svoboda, Jakub}, booktitle = {19th International Conference and Workshops on Algorithms and Computation}, isbn = {9789819628445}, issn = {1611-3349}, location = {Chengdu, China}, pages = {244--265}, publisher = {Springer Nature}, title = {{Reconfiguration using generalized token jumping}}, doi = {10.1007/978-981-96-2845-2_16}, volume = {15411}, year = {2025}, }