@article{18172, abstract = {Red Giant stars host solar-like oscillations which have mixed character, being sensitive to conditions both in the outer convection zone and deep within the interior. The properties of these modes are sensitive to both core rotation and magnetic fields. While asteroseismic studies of the former have been done on a large scale, studies of the latter are currently limited to tens of stars. We aim to produce the first large catalogue of both magnetic and rotational perturbations. We jointly constrain these parameters by devising an automated method for fitting the power spectra directly. We successfully apply the method to 302 low-luminosity red giants. We find a clear bimodality in core rotation rate. The primary peak is at δνrot = 0.32 μHz, and the secondary at δνrot = 0.47 μHz. Combining our results with literature values, we find that the percentage of stars rotating much more rapidly than the population average increases with evolutionary state. We measure magnetic splittings of 2σ significance in 23 stars. While the most extreme magnetic splitting values appear in stars with masses > 1.1M⊙, implying they formerly hosted a convective core, a small but statistically significant magnetic splitting is measured at lower masses. Asymmetry between the frequencies of a rotationally split multiplet has previously been used to diagnose the presence of a magnetic perturbation. We find that of the stars with a significant detection of magnetic perturbation, 43\% do not show strong asymmetry. We find no strong evidence of correlation between the rotation and magnetic parameters.}, author = {Hatt, Emily J. and Ong, J. M.Joel and Nielsen, Martin B. and Chaplin, William J. and Davies, Guy R. and Deheuvels, Sébastien and Ballot, Jérôme and Li, Gang and Bugnet, Lisa Annabelle}, issn = {1365-2966}, journal = {Monthly Notices of the Royal Astronomical Society}, number = {2}, pages = {1060--1076}, publisher = {Oxford University Press}, title = {{Asteroseismic signatures of core magnetism and rotation in hundreds of low-luminosity red giants}}, doi = {10.1093/mnras/stae2053}, volume = {534}, year = {2024}, } @article{18174, abstract = {We investigate the phase ordering (pattern formation) of systems of two-dimensional core–shell particles using Monte Carlo (MC) computer simulations and classical density functional theory (DFT). The particles interact via a pair potential having a hard core and a repulsive square shoulder. Our simulations show that on cooling, the liquid state structure becomes increasingly characterized by long wavelength density modulations and on further cooling forms a variety of other phases, including clustered, striped, and other patterned phases. In DFT, the hard core part of the potential is treated using either fundamental measure theory or a simple local density approximation, whereas the soft shoulder is treated using the random phase approximation. The different DFTs are benchmarked using large-scale grand-canonical-MC and Gibbs-ensemble-MC simulations, demonstrating their predictive capabilities and shortcomings. We find that having the liquid state static structure factor S(k) for wavenumber k is sufficient to identify the Fourier modes governing both the liquid and solid phases. This allows us to identify from easier-to-obtain liquid state data the wavenumbers relevant to the periodic phases and to predict roughly where in the phase diagram these patterned phases arise.}, author = {Wassermair, Michael and Kahl, Gerhard and Roth, Roland and Archer, Andrew J.}, issn = {1089-7690}, journal = {The Journal of chemical physics}, number = {12}, publisher = {AIP Publishing}, title = {{Fingerprints of ordered self-assembled structures in the liquid phase of a hard-core, square-shoulder system}}, doi = {10.1063/5.0226954}, volume = {161}, year = {2024}, } @inproceedings{18175, abstract = {Large-scale software repositories are a source of insights for software engineering. They offer an unmatched window into the software development process at scale. Their sheer number and size holds the promise of broadly applicable results. At the same time, that very size presents practical challenges for scaling tools and algorithms to millions of projects. A reasonable approach is to limit studies to representative samples of the population of interest. Broadly applicable conclusions can then be obtained by generalizing to the entire population. The contribution of this paper is a standardized experimental design methodology for choosing the inputs of studies working with large-scale repositories. We advocate for a methodology that clearly lays out what the population of interest is, how to sample it, and that fosters reproducibility. Along the way, we discourage researchers from using extrinsic attributes of projects such as stars, that measure some unclear notion of popularity.}, author = {Maj, Petr and Muroya Lei, Stefanie and Siek, Konrad and Di Grazia, Luca and Vitek, Jan}, booktitle = {38th European Conference on Object-Oriented Programming}, isbn = {9783959773416}, issn = {1868-8969}, location = {Vienna, Austria}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{The fault in our stars: Designing reproducible large-scale code analysis experiments}}, doi = {10.4230/LIPIcs.ECOOP.2024.27}, volume = {313}, year = {2024}, } @article{18176, abstract = {Introducing a class of SU(2) invariant quantum unitary circuits generating chiral transport, we examine the role of broken space-reflection and time-reversal symmetries on spin-transport properties. Upon adjusting parameters of local unitary gates, the dynamics can be either chaotic or integrable. The latter corresponds to a generalization of the space-time discretized (Trotterized) higher-spin quantum Heisenberg chain. We demonstrate that breaking of space-reflection symmetry results in a drift in the dynamical spin susceptibility. Remarkably, we find a universal drift velocity given by a simple formula, which, at zero average magnetization, depends only on the values of SU(2) Casimir invariants associated with local spins. In the integrable case, the drift velocity formula is confirmed analytically based on the exact solution of thermodynamic Bethe ansatz equations. Finally, by inspecting the large fluctuations of the time-integrated current between two halves of the system in stationary maximum-entropy states, we demonstrate violation of the Gallavotti-Cohen symmetry, implying that such states cannot be regarded as equilibrium ones. We show that the scaled cumulant generating function of the time-integrated current instead obeys a generalized fluctuation relation.}, author = {Zadnik, Lenart and Ljubotina, Marko and Krajnik, Žiga and Ilievski, Enej and Prosen, Tomaž}, issn = {2691-3399}, journal = {PRX Quantum}, number = {3}, publisher = {American Physical Society}, title = {{Quantum many-body spin ratchets}}, doi = {10.1103/PRXQuantum.5.030356}, volume = {5}, year = {2024}, } @inproceedings{18177, abstract = {Partially Specified Boolean Networks (PSBNs) represent a family of Boolean models resulting from possible interpretations of unknown update logics. Hybrid extension of CTL (HCTL) has the power to express complex dynamical phenomena, such as oscillations or stability. We present BNClassifier to classify Boolean Networks corresponding to a given PSBN according to criteria specified in HCTL. The implementation of the tool is fully symbolic (based on BDDs). The results are visualised using the machine-learning-based technology of decision trees.}, author = {Beneš, Nikola and Brim, Luboš and Huvar, Ondřej and Pastva, Samuel and Šafránek, David}, booktitle = {Computational Methods in Systems Biology}, isbn = {9783031716706}, issn = {1611-3349}, pages = {19--26}, publisher = {Springer Nature}, title = {{BNClassifier: Classifying boolean models by dynamic properties}}, doi = {10.1007/978-3-031-71671-3_2}, volume = {14971}, year = {2024}, } @article{18187, abstract = {Quasicrystals are ordered but not periodic, which makes them fascinating objects at the interface between order and disorder. Experiments with ultracold atoms zoom in on this interface by driving a quasicrystal and exploring its fractal properties.}, author = {Leonard, Julian}, issn = {1745-2481}, journal = {Nature Physics}, number = {3}, pages = {351--352}, publisher = {Springer Nature}, title = {{A kicked quasicrystal}}, doi = {10.1038/s41567-023-02357-0}, volume = {20}, year = {2024}, } @article{18188, abstract = {New generations of ultracold-atom experiments are continually raising the demand for efficient solutions to optimal control problems. Here, we apply Bayesian optimization to improve a state-preparation protocol recently implemented in an ultracold-atom system to realize a two-particle fractional quantum Hall state. Compared to manual ramp design, we demonstrate the superior performance of our optimization approach in a numerical simulation – resulting in a protocol that is 10x faster at the same fidelity, even when taking into account experimentally realistic levels of disorder in the system. We extensively analyze and discuss questions of robustness and the relationship between numerical simulation and experimental realization, and how to make the best use of the surrogate model trained during optimization. We find that numerical simulation can be expected to substantially reduce the number of experiments that need to be performed with even the most basic transfer learning techniques. The proposed protocol and workflow will pave the way toward the realization of more complex many-body quantum states in experiments.}, author = {Blatz, Tizian and Kwan, Joyce and Leonard, Julian and Bohrdt, Annabelle}, issn = {2521-327X}, journal = {Quantum}, publisher = {Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften}, title = {{Bayesian optimization for robust state preparation in quantum many-body systems}}, doi = {10.22331/q-2024-06-27-1388}, volume = {8}, year = {2024}, } @unpublished{18202, abstract = {We report on adiabatic state preparation in the one-dimensional quantum Ising model using ultracold bosons in a tilted optical lattice. We prepare many-body ground states of controllable system sizes and observe enhanced fluctuations around the transition between paramagnetic and antiferromagnetic states, marking the precursor of quantum critical behavior. Furthermore, we find evidence for superpositions of domain walls and study their effect on the many-body ground state by measuring the populations of each spin configuration across the transition. These results shed new light on the effect of boundary conditions in finite-size quantum systems.}, author = {Kim, Sooshin and Lukin, Alexander and Rispoli, Matthew and Tai, M. Eric and Kaufman, Adam M. and Segura, Perrin and Li, Yanfei and Kwan, Joyce and Leonard, Julian and Brice Bakkali-Hassani, Brice Bakkali-Hassani and Greiner, Markus}, booktitle = {arXiv}, title = {{Adiabatic state preparation in a quantum Ising spin chain}}, doi = {10.48550/arXiv.2404.07481}, year = {2024}, } @article{18203, abstract = {Protein Data Bank (PDB) files list the relative spatial location of atoms in a protein structure as the final output of the process of fitting and refining to experimentally determined electron density measurements. Where experimental evidence exists for multiple conformations, atoms are modelled in alternate locations. Programs reading PDB files commonly ignore these alternate conformations by default leaving users oblivious to the presence of alternate conformations in the structures they analyze. This has led to underappreciation of their prevalence, under characterisation of their features and limited the accessibility to this high-resolution data representing structural ensembles. We have trawled PDB files to extract structural features of residues with alternately located atoms. The output includes the distance between alternate conformations and identifies the location of these segments within the protein chain and in proximity of all other atoms within a defined radius. This dataset should be of use in efforts to predict multiple structures from a single sequence and support studies investigating protein flexibility and the association with protein function.}, author = {Rosenberg, Aviv A. and Marx, Ailie and Bronstein, Alexander}, issn = {2052-4463}, journal = {Scientific Data}, publisher = {Springer Nature}, title = {{A dataset of alternately located segments in protein crystal structures}}, doi = {10.1038/s41597-024-03595-4}, volume = {11}, year = {2024}, } @article{18204, abstract = {Non-linear dynamical systems describe numerous real-world phenomena, ranging from the weather, to financial markets and disease progression. Individual systems may share substantial common information, for example patients’ anatomy. Lately, deep-learning has emerged as a leading method for data-driven modeling of non-linear dynamical systems. Yet, despite recent breakthroughs, prior works largely ignored the existence of shared information between different systems. However, such cases are quite common, for example, in medicine: we may wish to have a patient-specific model for some disease, but the data collected from a single patient is usually too small to train a deep-learning model. Hence, we must properly utilize data gathered from other patients. Here, we explicitly consider such cases by jointly modeling multiple systems. We show that the current single-system models consistently fail when trying to learn simultaneously from multiple systems. We suggest a framework for jointly approximating the Koopman operators of multiple systems, while intrinsically exploiting common information. We demonstrate how we can adapt to a new system using order-of-magnitude less new data and show the superiority of our model over competing methods, in terms of both forecasting ability and statistical fidelity, across chaotic, cardiac, and climate systems.}, author = {Elul, Yonatan and Rozenberg, Eyal and Boyarski, Amit and Yaniv, Yael and Schuster, Assaf and Bronstein, Alexander}, issn = {2399-3650}, journal = {Communications Physics}, publisher = {Springer Nature}, title = {{Data-driven modeling of interrelated dynamical systems}}, doi = {10.1038/s42005-024-01626-5}, volume = {7}, year = {2024}, } @article{18205, abstract = {We explore numerically an unsupervised, physics-informed, deep learning-based reconstruction technique for time-resolved imaging by multiplexed ptychography. In our method, the untrained deep learning model replaces the iterative algorithm’s update step, yielding superior reconstructions of multiple dynamic object frames compared to conventional methodologies. More precisely, we demonstrate improvements in image quality and resolution, while reducing sensitivity to the number of recorded frames, the mutual orthogonality of different probe modes, overlap between neighboring probe beams and the cutoff frequency of the ptychographic microscope – properties that are generally of paramount importance for ptychographic reconstruction algorithms.}, author = {Wengrowicz, Omri and Bronstein, Alexander and Cohen, Oren}, issn = {1094-4087}, journal = {Optics Express}, number = {6}, pages = {8791--8803}, publisher = {Optica Publishing Group}, title = {{Unsupervised physics-informed deep learning-based reconstruction for time-resolved imaging by multiplexed ptychography}}, doi = {10.1364/oe.515445}, volume = {32}, year = {2024}, } @inproceedings{18206, abstract = {In the context of in vitro fertilization (IVF), selecting embryos for transfer is critical in determining pregnancy outcomes, with implantation as the essential first milestone for a successful pregnancy. This study introduces the Bonna algorithm, an advanced deep-learning framework engineered to predict embryo implantation probabilities. The algorithm employs a sophisticated integration of machine-learning techniques, utilizing MobileNetV2 for pixel and context embedding, a custom Pix2Pix model for precise segmentation, and a Vision Transformer for additional depth in embedding. MobileNetV2 was chosen for its robust feature extraction capabilities, focusing on textures and edges. The custom Pix2Pix model is adapted for precise segmentation of significant biological features such as the zona pellucida and blastocyst cavity. The Vision Transformer adds a global perspective, capturing complex patterns not apparent in local image segments. Tested on a dataset of images of human blastocysts collected from Ukraine, Israel, and Spain, the Bonna algorithm was rigorously validated through 10-fold cross-validation to ensure its robustness and reliability. It demonstrates superior performance with a mean area under the receiver operating characteristic curve (AUC) of 0.754, significantly outperforming existing models. The study not only advances predictive accuracy in embryo selection but also highlights the algorithm’s clinical applicability due to reliable confidence reporting.}, author = {Rave, Gilad and Fordham, Daniel E. and Bronstein, Alexander and Silver, David H.}, booktitle = {First International Conference on Artificial Intelligence in Healthcare}, isbn = {9783031672842}, issn = {1611-3349}, location = {Swansea, United Kingdom}, pages = {160--171}, publisher = {Springer Nature}, title = {{Enhancing predictive accuracy in embryo implantation: The Bonna algorithm and its clinical implications}}, doi = {10.1007/978-3-031-67285-9_12}, volume = {14976}, year = {2024}, } @article{18305, abstract = {Motor circuits represent the main output of the central nervous system and produce dynamic behaviors ranging from relatively simple rhythmic activities like swimming in fish and breathing in mammals to highly sophisticated dexterous movements in humans. Despite decades of research, the development and function of motor circuits remain poorly understood. Breakthroughs in the field recently provided new tools and tractable model systems that set the stage to discover the molecular mechanisms and circuit logic underlying motor control. Here, we describe recent advances from both vertebrate (mouse, frog) and invertebrate (nematode, fruit fly) systems on cellular and molecular mechanisms that enable motor circuits to develop and function and highlight conserved and divergent mechanisms necessary for motor circuit development.}, author = {Kratsios, Paschalis and Zampieri, Niccolò and Carrillo, Robert and Mizumoto, Kota and Sweeney, Lora Beatrice Jaeger and Philippidou, Polyxeni}, issn = {1529-2401}, journal = {The Journal of Neuroscience}, number = {40}, publisher = {Society for Neuroscience}, title = {{Molecular and cellular mechanisms of motor circuit development}}, doi = {10.1523/JNEUROSCI.1238-24.2024}, volume = {44}, year = {2024}, } @article{18306, abstract = {Neutral sodium (Na i) is an alkali metal with a favorable absorption cross section such that tenuous gases are easily illuminated at select transiting exoplanet systems. We examine both the time-averaged and time-series alkali spectral flux individually, over 4 nights at a hot Saturn system on a ∼2.8 day orbit about a Sun-like star WASP-49 A. Very Large Telescope/ESPRESSO observations are analyzed, providing new constraints. We recover the previously confirmed residual sodium flux uniquely when averaged, whereas night-to-night Na i varies by more than an order of magnitude. On HARPS/3.6 m Epoch II, we report a Doppler redshift at vΓ,NaD = + 9.7 ± 1.6 km s−1 with respect to the planet's rest frame. Upon examining the lightcurves, we confirm night-to-night variability, on the order of ∼1%–4% in NaD, rarely coinciding with exoplanet transit, not readily explained by stellar activity, starspots, tellurics, or the interstellar medium. Coincident with the ∼+10 km s−1 Doppler redshift, we detect a transient sodium absorption event dFNaD/F⋆ = 3.6% ± 1% at a relative difference of ΔFNaD(t) ∼ 4.4% ± 1%, lasting ΔtNaD ≳ 40 minutes. Since exoplanetary alkali signatures are blueshifted due to the natural vector of radiation pressure, estimated here at roughly ∼−5.7 km s−1, the radial velocity is rather at +15.4 km s−1, far larger than any known exoplanet system. Given that the redshift magnitude vΓ is in between the Roche limit and dynamically stable satellite orbits, the transient sodium may be a putative indication of a natural satellite orbiting WASP-49 A b.}, author = {Oza, Apurva V. and Seidel, Julia V. and Hoeijmakers, H. Jens and Unni, Athira and Kesseli, Aurora Y. and Schmidt, Carl A. and Sivarani, Thirupathi and Bello-Arufe, Aaron and Gebek, Andrea and Meyer Zu Westram, Moritz and Sousa, Sérgio G. and Lopes, Rosaly M.C. and Hu, Renyu and De Kleer, Katherine and Fisher, Chloe and Charnoz, Sébastien and Baker, Ashley D. and Halverson, Samuel P. and Schneider, Nick M. and Psaridi, Angelica and Wyttenbach, Aurélien and Torres Rodriguez, Santiago and Bhatnagar, Ishita and Johnson, Robert E.}, issn = {2041-8213}, journal = {Astrophysical Journal Letters}, number = {2}, publisher = {IOP Publishing}, title = {{Redshifted sodium transient near exoplanet transit}}, doi = {10.3847/2041-8213/ad6b29}, volume = {973}, year = {2024}, } @inproceedings{18308, abstract = {We study in this paper the problem of maintaining a solution to k-median and k-means clustering in a fully dynamic setting. To do so, we present an algorithm to efficiently maintain a coreset, a compressed version of the dataset, that allows easy computation of a clustering solution at query time. Our coreset algorithm has near-optimal update time of Õ(k) in general metric spaces, which reduces to Õ(d) in the Euclidean space ℝ^d. The query time is O(k²) in general metrics, and O(kd) in ℝ^d. To maintain a constant-factor approximation for k-median and k-means clustering in Euclidean space, this directly leads to an algorithm with update time Õ(d), and query time Õ(kd + k²). To maintain a O(polylog k)-approximation, the query time is reduced to Õ(kd).}, author = {La Tour, Max Dupré and Henzinger, Monika H and Saulpic, David}, booktitle = {32nd Annual European Symposium on Algorithms}, isbn = {9783959773386}, issn = {1868-8969}, location = {London, United Kingdom}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Fully dynamic k-means coreset in near-optimal update time}}, doi = {10.4230/LIPIcs.ESA.2024.100}, volume = {308}, year = {2024}, } @inproceedings{18309, abstract = {The problem of designing connectivity oracles supporting vertex failures is one of the basic data structures problems for undirected graphs. It is already well understood: previous works [Duan-Pettie STOC'10; Long-Saranurak FOCS'22] achieve query time linear in the number of failed vertices, and it is conditionally optimal as long as we require preprocessing time polynomial in the size of the graph and update time polynomial in the number of failed vertices. We revisit this problem in the paradigm of algorithms with predictions: we ask if the query time can be improved if the set of failed vertices can be predicted beforehand up to a small number of errors. More specifically, we design a data structure that, given a graph G = (V,E) and a set of vertices predicted to fail D̂ ⊆ V of size d = |D̂|, preprocesses it in time Õ(d|E|) and then can receive an update given as the symmetric difference between the predicted and the actual set of failed vertices D̂△D = (D̂ ⧵ D) ∪ (D ⧵ D̂) of size η = |D̂△D|, process it in time Õ(η⁴), and after that answer connectivity queries in G ⧵ D in time O(η). Viewed from another perspective, our data structure provides an improvement over the state of the art for the fully dynamic subgraph connectivity problem in the sensitivity setting [Henzinger-Neumann ESA'16]. We argue that the preprocessing time and query time of our data structure are conditionally optimal under standard fine-grained complexity assumptions.}, author = {Hu, Bingbing and Kosinas, Evangelos and Polak, Adam}, booktitle = {32nd Annual European Symposium on Algorithms}, isbn = {9783959773386}, issn = {1868-8969}, location = {London, United Kingdom}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Connectivity oracles for predictable vertex failures}}, doi = {10.4230/LIPIcs.ESA.2024.72}, volume = {308}, year = {2024}, } @article{18310, author = {Kitsara, Maria and Smajlhodžić-Deljo, Merima and Gurbeta Pokvic, Lejla and Bert, Bettina and Bubalo, Nataliia and Erden, Sevilay and Franco, Nuno Henrique and Chirico, Giuseppe and Gómez Raja, Jonathan and Gonzalez-Uarquin, Fernando and Lang, Annemarie and Linklater, Nicole and Mojsova, Sandra and Olsson, I. Anna S. and Sandvig, Ioanna and Schaffert, Alexandra and Schmit, Marthe and Schober, Sophie and Sevastre, Bogdan and Wilflingseder, Doris and Ahluwalia, Arti and Neuhaus, Winfried}, issn = {2632-3559}, journal = {Alternatives to Laboratory Animals}, number = {6}, pages = {326--333}, publisher = {SAGE Publications}, title = {{Introducing the COST action ‘Improving the Quality of Biomedical Science with 3Rs Concepts’ (IMPROVE)}}, doi = {10.1177/02611929241286024}, volume = {52}, year = {2024}, } @article{18311, abstract = {Local wound signaling in plants informs the surrounding tissues about an injury and initiates the regeneration process. In a recent paper published in Cell, Yang and colleagues show the involvement of a single Pep family member from tomato in wound signaling and how exogenous application of this regeneration factor enhances transformation efficiency in crops.}, author = {Hörmayer, Lukas and Friml, Jiří}, issn = {1748-7838}, journal = {Cell Research}, pages = {761--762}, publisher = {Springer Nature}, title = {{Feeling the danger: Local wound signaling in plants}}, doi = {10.1038/s41422-024-01035-x}, volume = {34}, year = {2024}, } @article{18445, abstract = {Acquisition of specialized cellular features is controlled by the ordered expression of transcription factors (TFs) along differentiation trajectories. Here, we find a member of the Onecut TF family, ONECUT3, expressed in postmitotic neurons that leave their Ascl1+/Onecut1/2+ proliferative domain in the vertebrate hypothalamus to instruct neuronal differentiation. We combined single-cell RNA-seq and gain-of-function experiments for gene network reconstruction to show that ONECUT3 affects the polarization and morphogenesis of both hypothalamic GABA-derived dopamine and thyrotropin-releasing hormone (TRH)+ glutamate neurons through neuron navigator-2 (NAV2). In vivo, siRNA-mediated knockdown of ONECUT3 in neonatal mice reduced NAV2 mRNA, as well as neurite complexity in Onecut3-containing neurons, while genetic deletion of Onecut3/ceh-48 in C. elegans impaired neurocircuit wiring, and sensory discrimination-based behaviors. Thus, ONECUT3, conserved across neuronal subtypes and many species, underpins the polarization and morphological plasticity of phenotypically distinct neurons that descend from a common pool of Ascl1+ progenitors in the hypothalamus.}, author = {Zupančič, Maja and Keimpema, Erik and Tretiakov, Evgenii O. and Eder, Stephanie J. and Lev, Itamar and Englmaier, Lukas and Bhandari, Pradeep and Fietz, Simone A. and Härtig, Wolfgang and Renaux, Estelle and Villunger, Andreas and Hökfelt, Tomas and Zimmer, Manuel and Clotman, Frédéric and Harkany, Tibor}, issn = {2041-1723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{Concerted transcriptional regulation of the morphogenesis of hypothalamic neurons by ONECUT3}}, doi = {10.1038/s41467-024-52762-z}, volume = {15}, year = {2024}, } @article{18446, abstract = {How living systems achieve precision in form and function despite their intrinsic stochasticity is a fundamental yet ongoing question in biology. We generated morphomaps of preimplantation embryogenesis in mouse, rabbit, and monkey embryos, and these morphomaps revealed that although blastomere divisions desynchronized passively, 8-cell embryos converged toward robust three-dimensional shapes. Using topological analysis and genetic perturbations, we found that embryos progressively changed their cellular connectivity to a preferred topology, which could be predicted by a physical model in which actomyosin contractility and noise facilitate topological transitions, lowering surface energy. This mechanism favored regular embryo packing and promoted a higher number of inner cells in the 16-cell embryo. Synchronized division reduced embryo packing and generated substantially more misallocated cells and fewer inner-cell–mass cells. These findings suggest that stochasticity in division timing contributes to robust patterning.}, author = {Fabrèges, Dimitri and Corominas-Murtra, Bernat and Moghe, Prachiti and Kickuth, Alison and Ichikawa, Takafumi and Iwatani, Chizuru and Tsukiyama, Tomoyuki and Daniel, Nathalie and Gering, Julie and Stokkermans, Anniek and Wolny, Adrian and Kreshuk, Anna and Duranthon, Véronique and Uhlman, Virginie and Hannezo, Edouard B and Hiiragi, Takashi}, issn = {1095-9203}, journal = {Science}, number = {6718}, publisher = {AAAS}, title = {{Temporal variability and cell mechanics control robustness in mammalian embryogenesis}}, doi = {10.1126/science.adh1145}, volume = {386}, year = {2024}, }