@article{18481, abstract = {A tight regulation of morphogen production is key for morphogen gradient formation and thereby for reproducible and organised organ development. Although many genetic interactions involved in the establishment of morphogen production domains are known, the biophysical mechanisms of morphogen source formation are poorly understood. Here we addressed this by focusing on the morphogen Sonic hedgehog (Shh) in the vertebrate neural tube. Shh is produced by the adjacently located notochord and by the floor plate of the neural tube. Using a data-constrained computational screen, we identified different possible mechanisms by which floor plate formation can occur, only one of which is consistent with experimental data. In this mechanism, the floor plate is established rapidly in response to Shh from the notochord and the dynamics of regulatory interactions within the neural tube. In this process, uniform activators and Shh-dependent repressors are key for establishing the floor plate size. Subsequently, the floor plate becomes insensitive to Shh and increases in size due to tissue growth, leading to scaling of the floor plate with neural tube size. In turn, this results in scaling of the Shh amplitude with tissue growth. Thus, this mechanism ensures a separation of time scales in floor plate formation, so that the floor plate domain becomes growth-dependent after an initial rapid establishment phase. Our study raises the possibility that the time scale separation between specification and growth might be a common strategy for scaling the morphogen gradient amplitude in growing organs. The model that we developed provides a new opportunity for quantitative studies of morphogen source formation in growing tissues.}, author = {Ho, Richard D.J.G. and Kishi, Kasumi and Majka, Maciej and Kicheva, Anna and Zagórski, Marcin P}, issn = {1553-7358}, journal = {PLoS Computational Biology}, publisher = {Public Library of Science}, title = {{Dynamics of morphogen source formation in a growing tissue}}, doi = {10.1371/journal.pcbi.1012508}, volume = {20}, year = {2024}, } @article{18482, abstract = {This paper is dedicated to an optimization problem. Let A, B ⊂ Rn be compact convex sets. Consider the minimal number t0 > 0 such that t0B covers A after a shift to a vector x0 ∈ Rn. The goal is to find t0 and x0. In the special case of B being a unit ball centered at zero, x0 and t0 are known as the Chebyshev center and the Chebyshev radius of A. This paper focuses on the case in which A and B are defined with their black-box support functions. An algorithm for solving such problems efficiently is suggested. The algorithm has a superlinear convergence rate, and it can solve hundred-dimensional test problems in a reasonable time, but some additional conditions on A and B are required to guarantee the presence of convergence. Additionally, the behavior of the algorithm for a simple special case is investigated, which leads to a number of theoretical results. Perturbations of this special case are also studied.}, author = {Arkhipov, Pavel}, issn = {1608-3032}, journal = {Automation and Remote Control}, number = {6}, pages = {522--532}, publisher = {Springer Nature}, title = {{An algorithm for finding the generalized Chebyshev center of sets defined via their support functions}}, doi = {10.1134/S0005117924060031}, volume = {85}, year = {2024}, } @article{18483, abstract = {In this paper we prove a perturbative version of a remarkable Bialy–Mironov (Ann. Math. 196(1):389–413, 2022) result. They prove non perturbative Birkhoff conjecture for centrally-symmetric convex domains, namely, a centrally-symmetric convex domain with integrable billiard is ellipse. We combine techniques from Bialy–Mironov (Ann. Math. 196(1):389–413, 2022) with a local result by Kaloshin–Sorrentino (Ann. Math. 188(1):315–380, 2018) and show that a domain close enough to a centrally symmetric one with integrable billiard is ellipse. To combine these results we derive a slight extension of Bialy–Mironov (Ann. Math. 196(1):389–413, 2022) by proving that a notion of rational integrability is equivalent to the C0-integrability condition used in their paper.}, author = {Kaloshin, Vadim and Koudjinan, Edmond and Zhang, Ke}, issn = {1420-8970}, journal = {Geometric and Functional Analysis}, pages = {1973--2007}, publisher = {Springer Nature}, title = {{Birkhoff conjecture for nearly centrally symmetric domains}}, doi = {10.1007/s00039-024-00695-6}, volume = {34}, year = {2024}, } @article{18488, abstract = {The advancement of quantum simulators motivates the development of a theoretical framework to assist with efficient state preparation in quantum many-body systems. Generally, preparing a target entangled state via unitary evolution with time-dependent couplings is a challenging task and very little is known about the existence of solutions and their properties. In this work we develop a constructive approach for preparing matrix product states (MPS) via continuous unitary evolution. We provide an explicit construction of the operator that exactly implements the evolution of a given MPS along a specified direction in its tangent space. This operator can be written as a sum of local terms of finite range, yet it is in general non-Hermitian. Relying on the explicit construction of the non-Hermitian generator of the dynamics, we demonstrate the existence of a Hermitian sequence of operators that implements the desired MPS evolution with an error that decreases exponentially with the operator range. The construction is benchmarked on an explicit periodic trajectory in a translationally invariant MPS manifold. We demonstrate that the Floquet unitary generating the dynamics over one period of the trajectory features an approximate MPS-like eigenstate embedded among a sea of thermalizing eigenstates. These results show that our construction is not only useful for state preparation and control of many-body systems, but also provides a generic route towards Floquet scars—periodically driven models with quasilocal generators of dynamics that have exact MPS eigenstates in their spectrum.}, author = {Ljubotina, Marko and Petrova, Elena and Schuch, Norbert and Serbyn, Maksym}, issn = {2691-3399}, journal = {PRX Quantum}, number = {4}, publisher = {American Physical Society}, title = {{Tangent space generators of matrix product states and exact floquet quantum scars}}, doi = {10.1103/prxquantum.5.040311}, volume = {5}, year = {2024}, } @article{18490, abstract = {For large classes of even-dimensional Riemannian manifolds (Formula presented.), we construct and analyze conformally invariant random fields. These centered Gaussian fields (Formula presented.), called co-polyharmonic Gaussian fields, are characterized by their covariance kernels k which exhibit a precise logarithmic divergence: (Formula presented.). They share a fundamental quasi-invariance property under conformal transformations. In terms of the co-polyharmonic Gaussian field (Formula presented.), we define the Liouville Quantum Gravity measure, a random measure on (Formula presented.), heuristically given as (Formula presented.) and rigorously obtained as almost sure weak limit of the right-hand side with (Formula presented.) replaced by suitable regular approximations (Formula presented.). In terms on the Liouville Quantum Gravity measure, we define the Liouville Brownian motion on (Formula presented.) and the random GJMS operators. Finally, we present an approach to a conformal field theory in arbitrary even dimension with an ansatz based on Branson's (Formula presented.) -curvature: we give a rigorous meaning to the Polyakov–Liouville measure (Formula presented.) and we derive the corresponding conformal anomaly. The set of admissible manifolds is conformally invariant. It includes all compact 2-dimensional Riemannian manifolds, all compact non-negatively curved Einstein manifolds of even dimension, and large classes of compact hyperbolic manifolds of even dimension. However, not every compact even-dimensional Riemannian manifold is admissible. Our results concerning the logarithmic divergence of the kernel (Formula presented.) rely on new sharp estimates for heat kernels and higher order Green kernels on arbitrary closed manifolds. }, author = {Dello Schiavo, Lorenzo and Herry, Ronan and Kopfer, Eva and Sturm, Karl Theodor}, issn = {1469-7750}, journal = {Journal of the London Mathematical Society}, number = {5}, publisher = {London Mathematical Society}, title = {{Conformally invariant random fields, Liouville quantum gravity measures, and random Paneitz operators on Riemannian manifolds of even dimension}}, doi = {10.1112/jlms.70003}, volume = {110}, year = {2024}, } @article{18491, abstract = {Predicting the outcomes of adaptation is a major goal of evolutionary biology. When temporal changes in the environment mirror spatial gradients, it opens up the potential for predicting the course of adaptive evolution over time based on patterns of spatial genetic and phenotypic variation. We assessed this approach in a 30-year transplant experiment in the intertidal snail Littorina saxatilis. In 1992, snails were transplanted from a predation-dominated environment to one dominated by wave action. On the basis of spatial patterns, we predicted transitions in shell size and morphology, allele frequencies at positions throughout the genome, and chromosomal rearrangement frequencies. Observed changes closely agreed with predictions and transformation was both dramatic and rapid. Hence, adaptation can be predicted from knowledge of the phenotypic and genetic variation among populations.}, author = {Garcia Castillo, Diego Fernando and Barton, Nicholas H and Faria, Rui and Larsson, Jenny and Stankowski, Sean and Butlin, Roger and Johannesson, Kerstin and Westram, Anja M}, issn = {2375-2548}, journal = {Science Advances}, number = {41}, publisher = {AAAS}, title = {{Predicting rapid adaptation in time from adaptation in space: A 30-year field experiment in marine snails}}, doi = {10.1126/sciadv.adp2102}, volume = {10}, year = {2024}, } @article{18492, abstract = {Surveys in the Milky Way and Large Magellanic Cloud have revealed that the majority of massive stars will interact with companions during their lives. However, knowledge of the binary properties of massive stars at low metallicity, and therefore in conditions approaching those of the Early Universe, remain sparse. We present the Binarity at LOw Metallicity (BLOeM) campaign, an ESO large programme designed to obtain 25 epochs of spectroscopy for 929 massive stars in the Small Magellanic Cloud, allowing us to probe multiplicity in the lowest-metallicity conditions to date (Z = 0.2 Z⊙). BLOeM will provide (i) the binary fraction, (ii) the orbital configurations of systems with periods of P ≲ 3 yr, (iii) dormant black-hole binary candidates (OB+BH), and (iv) a legacy database of physical parameters of massive stars at low metallicity. Main sequence (OB-type) and evolved (OBAF-type) massive stars are observed with the LR02 setup of the GIRAFFE instrument of the Very Large Telescope (3960–4570 Å resolving power R = 6200; typical signal-to-noise ratio(S/N) ≈70–100). This paper utilises the first nine epochs obtained over a three-month time period. We describe the survey and data reduction, perform a spectral classification of the stacked spectra, and construct a Hertzsprung-Russell diagram of the sample via spectral-type and photometric calibrations. Our detailed classification reveals that the sample covers spectral types from O4 to F5, spanning the effective temperature and luminosity ranges 6.5 ≲ Teff/kK ≲ 45 and 3.7 < log L/L⊙ < 6.1 and initial masses of 8 ≲ Mini ≲ 80 M⊙. The sample comprises 159 O-type stars, 331 early B-type (B0–3) dwarfs and giants (luminosity classes V–III), 303 early B-type supergiants (II–I), and 136 late-type BAF supergiants. At least 82 stars are OBe stars: 20 O-type and 62 B-type (13% and 11% of the respective samples). In addition, the sample includes 4 high-mass X-ray binaries, 3 stars resembling luminous blue variables, 2 bloated stripped-star candidates, 2 candidate magnetic stars, and 74 eclipsing binaries.}, author = {Shenar, T. and Bodensteiner, J. and Sana, H. and Crowther, P. A. and Lennon, D. J. and Abdul-Masih, M. and Almeida, L. A. and Backs, F. and Berlanas, S. R. and Bernini-Peron, M. and Bestenlehner, J. M. and Bowman, D. M. and Bronner, V. A. and Britavskiy, N. and De Koter, A. and De Mink, S. E. and Deshmukh, K. and Evans, C. J. and Fabry, M. and Gieles, M. and Gilkis, A. and González-Torà, G. and Gräfener, G. and Götberg, Ylva Louise Linsdotter and Hawcroft, C. and Hénault-Brunet, V. and Herrero, A. and Holgado, G. and Janssens, S. and Johnston, C. and Josiek, J. and Justham, S. and Kalari, V. M. and Katabi, Z. Z. and Keszthelyi, Z. and Klencki, J. and Kubát, J. and Kubátová, B. and Langer, N. and Lefever, R. R. and Ludwig, B. and Mackey, J. and Mahy, L. and Maíz Apellániz, J. and Mandel, I. and Maravelias, G. and Marchant, P. and Menon, A. and Najarro, F. and Oskinova, L. M. and O'Grady, A. J.G. and Ovadia, R. and Patrick, L. R. and Pauli, D. and Pawlak, M. and Ramachandran, V. and Renzo, M. and Rocha, D. F. and Sander, A. A.C. and Sayada, T. and Schneider, F. R.N. and Schootemeijer, A. and Schösser, E. C. and Schürmann, C. and Sen, K. and Shahaf, S. and Simón-Díaz, S. and Stoop, M. and Toonen, S. and Tramper, F. and Van Loon, J. Th and Valli, R. and Van Son, L. A.C. and Vigna-Gómez, A. and Villaseñor, J. I. and Vink, J. S. and Wang, C. and Willcox, R.}, issn = {1432-0746}, journal = {Astronomy and Astrophysics}, publisher = {EDP Sciences}, title = {{Binarity at LOw Metallicity (BLOeM): A spectroscopic VLT monitoring survey of massive stars in the SMC}}, doi = {10.1051/0004-6361/202451586}, volume = {690}, year = {2024}, } @article{18493, abstract = {Context. The escape of Lyman-α photons at redshifts greater than two is an ongoing subject of study and an important quantity to further understanding of Lyman-α emitters (LAEs), the transmission of Lyman-α photons through the interstellar medium and intergalactic medium, and the impact these LAEs have on cosmic reionisation. Aims. This study aims to assess the Lyman-α escape fraction, fesc, Lyα, over the redshift range 2.9 < z < 6.7, focusing on Very Large Telescope/Multi Unit Spectroscopic Explorer (VLT/MUSE) selected, gravitationally lensed, intrinsically faint LAEs. These galaxies are of particular interest as the potential drivers of cosmic reionisation. Methods. We assessed fesc, Lyα in two ways: through an individual study of 96 LAEs behind the A2744 lensing cluster, with James Webb Space Telescope/Near-Infrared Camera (JWST/NIRCam) and HST data, and through a study of the global evolution of fesc, Lyα using the state-of-the-art luminosity functions for LAEs and the UV-selected ‘parent’ population (dust-corrected). We compared these studies to those in the literature based on brighter samples. Results. We find a negligible redshift evolution of fesc, Lyα for our individual galaxies; it is likely that it was washed out by significant intrinsic scatter. We observed a more significant evolution towards higher escape fractions with decreasing UV magnitude and fit this relation. When comparing the two luminosity functions to derive fesc, Lyα in a global sense, we saw agreement with previous literature when integrating the luminosity functions to a bright limit. However, when integrating using a faint limit equivalent to the observational limits of our samples, we observed enhanced values of fesc, Lyα, particularly around z ∼ 6, where fesc, Lyα becomes consistent with 100% escape. This indicates for the faint regimes we sampled that galaxies towards reionisation tend to allow very large fractions of Lyman-α photons to escape. We interpret this as evidence of a lack of any significant dust in these populations; our sample is likely dominated by young, highly star-forming chemically unevolved galaxies. Finally, we assessed the contribution of the LAE population to reionisation using our latest values for fesc, Lyα and the LAE luminosity density. The dependence on the escape fraction of Lyman continuum photons is strong, but for values similar to those observed recently in z ∼ 3 LAEs and high-redshift analogues, LAEs could provide all the ionising emissivity necessary for reionisation.}, author = {Goovaerts, I. and Thai, T. T. and Pello, R. and Tuan-Anh, P. and Laporte, N. and Matthee, Jorryt J and Nanayakkara, T. and Pharo, J.}, issn = {1432-0746}, journal = {Astronomy and Astrophysics}, publisher = {EDP Sciences}, title = {{Charting the Lyman-α escape fraction in the range 2.9 < z < 6.7 and consequences for the LAE reionisation contribution}}, doi = {10.1051/0004-6361/202451432}, volume = {690}, year = {2024}, } @article{18494, abstract = {We expect luminous (M 1450 ≲ −26.5) high-redshift quasars to trace the highest-density peaks in the early Universe. Here, we present observations of four z ≳ 6 quasar fields using JWST/NIRCam in the imaging and wide-field slitless spectroscopy mode and report a wide range in the number of detected [O iii]-emitting galaxies in the quasars’ environments, ranging between a density enhancement of δ ≈ 65 within a 2 cMpc radius—one of the largest protoclusters during the Epoch of Reionization discovered to date—to a density contrast consistent with zero, indicating the presence of a UV-luminous quasar in a region comparable to the average density of the Universe. By measuring the two-point cross-correlation function of quasars and their surrounding galaxies, as well as the galaxy autocorrelation function, we infer a correlation length of quasars at 〈z〉 = 6.25 of r 0 QQ = 22.0 − 2.9 + 3.0 cMpc h − 1 , while we obtain a correlation length of the [O iii]-emitting galaxies of r 0 GG = 4.1 ± 0.3 cMpc h − 1 . By comparing the correlation functions to dark-matter-only simulations we estimate the minimum mass of the quasars’ host dark matter halos to be log 10 ( M halo , min / M ⊙ ) = 12.43 − 0.15 + 0.13 (and log 10 ( M halo , min [ OIII ] / M ⊙ ) = 10.56 − 0.03 + 0.05 for the [O iii] emitters), indicating that (a) luminous quasars do not necessarily reside within the most overdense regions in the early Universe, and that (b) the UV-luminous duty cycle of quasar activity at these redshifts is f duty ≪ 1. Such short quasar activity timescales challenge our understanding of early supermassive black hole growth and provide evidence for highly dust-obscured growth phases or episodic, radiatively inefficient accretion rates.}, author = {Eilers, Anna Christina and Mackenzie, Ruari and Pizzati, Elia and Matthee, Jorryt J and Hennawi, Joseph F. and Zhang, Haowen and Bordoloi, Rongmon and Kashino, Daichi and Lilly, Simon J. and Naidu, Rohan P. and Simcoe, Robert A. and Yue, Minghao and Frenk, Carlos S. and Helly, John C. and Schaller, Matthieu and Schaye, Joop}, issn = {1538-4357}, journal = {Astrophysical Journal}, number = {2}, publisher = {IOP Publishing}, title = {{EIGER. VI. The correlation function, host halo mass, and duty cycle of luminous quasars at z ≳ 6}}, doi = {10.3847/1538-4357/ad778b}, volume = {974}, year = {2024}, } @misc{18498, abstract = {Scripts and data used in the research study Predicting rapid adaptation in time from adaptation in space: a 30-year field experiment in marine snails. https://doi.org/10.1101/2023.09.27.559715}, author = {Garcia Castillo, Diego Fernando and Barton, Nicholas H and Faria, Rui and Larsson, Jenny and Stankowski, Sean and Butlin, Roger and Johannesson, Kerstin and Westram, Anja M}, publisher = {Zenodo}, title = {{Data and code for: Predicting rapid adaptation in time from adaptation in space: a 30-year field experiment in marine snails}}, doi = {10.5281/ZENODO.12159343}, year = {2024}, } @inproceedings{18503, abstract = {In 1996, Karger [Kar96] gave a startling randomized algorithm that finds a minimum-cut in a (weighted) graph in time O(m log3 n) which he termed near-linear time meaning linear (in the size of the input) times a polylogarthmic factor. In this paper, we give the first deterministic algorithm which runs in near-linear time for weighted graphs. Previously, the breakthrough results of Kawarabayashi and Thorup [KT19] gave a near-linear time algorithm for simple graphs (which was improved to have running time O(m log2 n log log n) in [HRW20].) The main technique here is a clustering procedure that perfectly preserves minimum cuts. Recently, Li [Li21] gave an m1+o(1) deterministic minimum-cut algorithm for weighted graphs; this form of running time has been termed “almost-linear”. Li uses almost-linear time deterministic expander decompositions which do not perfectly preserve minimum cuts, but he can use these clusterings to, in a sense, “derandomize” the methods of Karger. In terms of techniques, we provide a structural theorem that says there exists a sparse clustering that preserves minimum cuts in a weighted graph with o(1) error. In addition, we construct it deterministically in near linear time. This was done exactly for simple graphs in [KT19, HRW20] and with polylogarithmic error for weighted graphs in [Li21]. Extending the techniques in [KT19, HRW20] to weighted graphs presents significant challenges, and moreover, the algorithm can only polylogarithmically approximately preserve minimum cuts. A remaining challenge is to reduce the polylogarithmic-approximate clusterings to 1 + o(1/ log n)-approximate so that they can be applied recursively as in [Li21] over O(log n) many levels. This is an additional challenge that requires building on properties of tree-packings in the presence of a wide range of edge weights to, for example, find sources for local flow computations which identify minimum cuts that cross clusters.}, author = {Henzinger, Monika H and Li, Jason and Rao, Satish and Wang, Di}, booktitle = {35th Annual ACM-SIAM Symposium on Discrete Algorithms}, location = {Alexandria, VA, United States}, pages = {3089--3139}, publisher = {Society for Industrial and Applied Mathematics}, title = {{Deterministic near-linear time minimum cut in weighted graphs}}, doi = {10.1137/1.9781611977912.111}, year = {2024}, } @phdthesis{18515, abstract = {Understanding the role of evolutionary processes in shaping genetic variation has been a primary goal in evolutionary genetics. In this regard, a key question is how genetically distinct populations evolve in the face of gene flow, thereby generating genetic and phenotypic divergence and reproductive isolation (RI). This requires quantifying the role and relative contributions of prezygotic and postzygotic isolating mechanisms on the reduction of gene exchange between populations, and identifying regions in the genome that mediate RI, which is often polygenic. Further, this needs distinguishing neutral and selected regions in the genome, and discerning how selection influences patterns of neutral divergence. Population structure, defined as any deviation from panmixia, such as geographic distribution, movement and mating patterns of individuals, influences how genetic variation is structured in space and shapes the neutral null model. Availability of large scale spatial genomic datasets now enables us to detect signatures of population structure in genetic data and infer population genetic parameters. Such inferences are crucial and have wide applications in biodiversity, conservation genetics, population management and medical genetics. However, inferences are based on assumptions that do not always match the complex reality, thus leading to erroneous conclusions. Moreover, the role and interaction of heterogeneous population density and dispersal, which are ubiquitous in nature, has been challenging to study owing to their mathematical complexity. In such scenarios, feedback between theory, data and simulations can prove to be useful. In this thesis, I examine the effect of population structure on neutral genetic variation and barriers to gene exchange in hybridising populations, thereby bridging together the fields of spatial population genetics and speciation. Despite being a key concept in speciation, reproductive isolation (RI) lacks a quantitative definition and has been used and measured differently across different fields. Chapter 2 gives a quantitative definition of RI, in terms of the effect of genetic differences on gene flow. We give analytical predictions for RI in a range of scenarios, in terms of effective migration rates for discrete populations and barrier strength for continuous populations. In addition to this, we discuss current measures of RI and their limitations, and propose the need for new measures that combine organismal and genetic perspectives of RI. In chapter 3, I examine the combined effect of assortative mating, sexual selection and viability selection on RI. For this, we consider a polygenic ‘magic’ trait under a mainland-island model. We obtain novel theoretical predictions for molecular divergence in terms of effective migration rates, which bears a simple relationship to measurable fitness components of migrants and various early generation hybrids. We explore the conditions under which local adaptation can be maintained despite maladaptive gene flow and quantify the relative contributions of viability and sexual selection to genome-wide barriers to gene flow. The next two chapters of the thesis focus on a hybrid zone of Antirrhinum majus that consist of two subspecies- the magenta flowered A. m. pseudomajus and the yellow flowered A.m. striatum. Previous studies have suggested that flower colour is target of pollinator mediated selection and is influenced only by few genes. While these regions show high genetic differentiation between the subspecies, the rest of the genome is seen to be well mixed. Chapter 4 examines the effects of heterogeneous population density and leptokurtic dispersal on isolation by distance and the distribution of heterozygosity by focusing on non-flower colour markers. Chapter 5 analyses cline shapes and associations among 6 focal flower colour markers to understand how selection and dispersal maintain this hybrid zone. We see sharp coincident stepped clines at all loci and positive associations throughout the hybrid zone, contrary to the expected patterns from diffusive gene flow. With a novel scheme of inferring dispersal combined with multilocus simulations, we show that stepped clines do not reflect genetic barriers to gene flow, but are rather a result of long-distance migration. This framework allows us to get realistic estimates gene flow and selection and shows how traditional cline analysis may lead to inaccurate conclusions when assumptions of the theory are not met. Overall, this thesis investigates how different features of population structure leave detectable signatures in genetic variation, namely in patterns of isolation by distance, linkage disequilibrium and genetic divergence. It also highlights how effective migration rates provide useful way of analysing polygenic architectures and shed new light into hybrid zones. In doing so, I identify scenarios when simple models become insufficient and suggest possibe directions by combining genetic data with simulations.}, author = {Surendranadh, Parvathy}, issn = {2663-337X}, pages = {219}, publisher = {Institute of Science and Technology Austria}, title = {{Effect of population structure on neutral genetic variation and barriers to gene exchange}}, doi = {10.15479/at:ista:18515}, year = {2024}, } @inproceedings{18521, abstract = {In distributed systems with processes that do not share a global clock, partial synchrony is achieved by clock synchronization that guarantees bounded clock skew among all applications. Existing solutions for distributed runtime verification under partial synchrony against temporal logic specifications are exact but suffer from significant computational overhead. In this paper, we propose an approximate distributed monitoring algorithm for Signal Temporal Logic (STL) that mitigates this issue by abstracting away potential interleaving behaviors. This conservative abstraction enables a significant speedup of the distributed monitors, albeit with a tradeoff in accuracy. We address this tradeoff with a methodology that combines our approximate monitor with its exact counterpart, resulting in enhanced efficiency without sacrificing precision. We evaluate our approach with multiple experiments, showcasing its efficacy in both real-world applications and synthetic examples.}, author = {Bonakdarpour, Borzoo and Momtaz, Anik and Nickovic, Dejan and Sarac, Naci E}, booktitle = {24th International Conference on Runtime Verification}, isbn = {9783031742330}, issn = {1611-3349}, location = {Istanbul, Turkey}, pages = {282--301}, publisher = {Springer Nature}, title = {{Approximate distributed monitoring under partial synchrony: Balancing speed & accuracy}}, doi = {10.1007/978-3-031-74234-7_18}, volume = {15191}, year = {2024}, } @article{18522, abstract = {The Golgi apparatus is essential for protein sorting, yet its quality control mechanisms are poorly understood. Here we show that the Dsc ubiquitin ligase complex uses its rhomboid pseudo-protease subunit, Dsc2, to assess the hydrophobic length of α-helical transmembrane domains (TMDs) at the Golgi. Thereby the Dsc complex likely interacts with orphaned ER and Golgi proteins that have shorter TMDs and ubiquitinates them for targeted degradation. Some Dsc substrates will be extracted by Cdc48 for endosome and Golgi associated proteasomal degradation (EGAD), while others will undergo ESCRT dependent vacuolar degradation. Some substrates are degraded by both, EGAD- or ESCRT pathways. The accumulation of Dsc substrates entails a specific increase in glycerophospholipids with shorter and asymmetric fatty acyl chains. Hence, the Dsc complex mediates the selective degradation of orphaned proteins at the sorting center of cells, which prevents their spreading across other organelles and thereby preserves cellular membrane protein and lipid composition.}, author = {Weyer, Yannick and Schwabl, Sinead I. and Tang, Xuechen and Purwar, Astha and Siegmann, Konstantin and Ruepp, Angela and Dunzendorfer-Matt, Theresia and Widerin, Michael A. and Niedrist, Veronika and Mutsters, Noa J.M. and Tettamanti, Maria G. and Weys, Sabine and Sarg, Bettina and Kremser, Leopold and Liedl, Klaus R. and Schmidt, Oliver and Teis, David}, issn = {2041-1723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{The Dsc ubiquitin ligase complex identifies transmembrane degrons to degrade orphaned proteins at the Golgi}}, doi = {10.1038/s41467-024-53676-6}, volume = {15}, year = {2024}, } @article{18523, abstract = {Recent observations from the EIGER JWST program have measured for the first time the quasar–galaxy cross-correlation function at z ≈ 6. The autocorrelation function of faint z ≈ 6 quasars was also recently estimated. These measurements provide key insights into the properties of quasars and galaxies at high redshift and their relation with the host dark matter haloes. In this work, we interpret these data building upon an empirical quasar population model that has been applied successfully to quasar clustering and demographic measurements at z ≈ 2–4. We use a new, large-volume N-body simulation with more than a trillion particles, FLAMINGO-10k, to model quasars and galaxies simultaneously. We successfully reproduce observations of z ≈ 6 quasars and galaxies (i.e. their clustering properties and luminosity functions), and infer key quantities such as their luminosity–halo mass relation, the mass function of their host haloes, and their duty cycle/occupation fraction. Our key findings are (i) quasars reside on average in ≈ 1012.5 M haloes (corresponding to ≈ 5σ fluctuations in the initial conditions of the linear density field), but the distribution of host halo masses is quite broad; (ii) the duty cycle of (UV-bright) quasar activity is relatively low (≈ 1 per cent); (iii) galaxies (that are bright in [O III]) live in much smaller haloes (≈ 1010.9 M) and have a larger duty cycle (occupation fraction) of ≈ 13 per cent. Finally, we focus on the inferred properties of quasars and present a homogeneous analysis of their evolution with redshift. The picture that emerges reveals a strong evolution of the host halo mass and duty cycle of quasars at z ≈ 2–6, and calls for new investigations of the role of quasar activity across cosmic time.}, author = {Pizzati, Elia and Hennawi, Joseph F. and Schaye, Joop and Schaller, Matthieu and Eilers, Anna Christina and Wang, Feige and Frenk, Carlos S. and Elbers, Willem and Helly, John C. and Mackenzie, Ruari and Matthee, Jorryt J and Bordoloi, Rongmon and Kashino, Daichi and Naidu, Rohan P. and Yue, Minghao}, issn = {1365-2966}, journal = {Monthly Notices of the Royal Astronomical Society}, number = {4}, pages = {3155--3175}, publisher = {Oxford University Press}, title = {{A unified model for the clustering of quasars and galaxies at z ≈ 6}}, doi = {10.1093/mnras/stae2307}, volume = {534}, year = {2024}, } @article{18524, abstract = {Recent works have constrained the binary fraction of evolved populations of massive stars in local galaxies such as red supergiants and Wolf–Rayet stars, but the binary fraction of yellow supergiants (YSGs) in the Hertzsprung gap remains unconstrained. Binary evolution theory predicts that the Hertzsprung gap is home to multiple populations of binary systems with varied evolutionary histories. In this paper, we develop a method to distinguish single YSGs from YSG plus O- or B-type main-sequence binaries using optical and ultraviolet photometry, and then apply this method to identify candidate YSG binaries in the Magellanic Clouds. After constructing a set of combined stellar atmosphere models, we find that optical photometry is, given typical measurement and reddening uncertainties, sufficient to discern single YSGs from YSG+OB binaries if the OB-star is at least ∼5M⊙ for Teff,YSG ∼ 4000 K, but requires a ∼20M⊙ OB star for YSGs up to Teff,YSG ∼ 9000 K. For these hotter YSG temperatures, ultraviolet photometry allows binaries with OB companions as small as ∼7M⊙ to be identified. We use color–color spaces developed from these models to search for evidence of excess blue or ultraviolet light in a set of ∼1000 YSG candidates in the Magellanic Clouds. We identify hundreds of candidate YSG binary systems and report a preliminary fraction of YSGs that show a blue/UV color excess of 20%–60%. Spectroscopic follow-up is now required to confirm the true nature of this population.}, author = {O’Grady, Anna J.G. and Drout, Maria R. and Neugent, Kathryn F. and Ludwig, Bethany and Götberg, Ylva Louise Linsdotter and Gaensler, B. M.}, issn = {1538-4357}, journal = {Astrophysical Journal}, publisher = {IOP Publishing}, title = {{Binary yellow supergiants in the Magellanic Clouds. I. Photometric candidate identification}}, doi = {10.3847/1538-4357/ad778a}, volume = {975}, year = {2024}, } @article{18525, abstract = {As their statistical power grows, genome-wide association studies (GWAS) have identified an increasing number of loci underlying quantitative traits of interest. These loci are scattered throughout the genome and are individually responsible only for small fractions of the total heritable trait variance. The recently proposed omnigenic model provides a conceptual framework to explain these observations by postulating that numerous distant loci contribute to each complex trait via effect propagation through intracellular regulatory networks. We formalize this conceptual framework by proposing the “quantitative omnigenic model” (QOM), a statistical model that combines prior knowledge of the regulatory network topology with genomic data. By applying our model to gene expression traits in yeast, we demonstrate that QOM achieves similar gene expression prediction performance to traditional GWAS with hundreds of times less parameters, while simultaneously extracting candidate causal and quantitative chains of effect propagation through the regulatory network for every individual gene. We estimate the fraction of heritable trait variance in cis- and in trans-, break the latter down by effect propagation order, assess the trans- variance not attributable to transcriptional regulation, and show that QOM correctly accounts for the low-dimensional structure of gene expression covariance. We furthermore demonstrate the relevance of QOM for systems biology, by employing it as a statistical test for the quality of regulatory network reconstructions, and linking it to the propagation of nontranscriptional (including environmental) effects.}, author = {Ruzickova, Natalia and Hledik, Michal and Tkačik, Gašper}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {44}, publisher = {National Academy of Sciences}, title = {{Quantitative omnigenic model discovers interpretable genome-wide associations}}, doi = {10.1073/pnas.2402340121}, volume = {121}, year = {2024}, } @article{18526, abstract = {Multivesicular endosomes (MVEs) sequester membrane proteins destined for degradation within intralumenal vesicles (ILVs), a process mediated by the membrane-remodeling action of Endosomal Sorting Complex Required for Transport (ESCRT) proteins. In Arabidopsis, endosomal membrane constriction and scission are uncoupled, resulting in the formation of extensive concatenated ILV networks and enhancing cargo sequestration efficiency. Here, we used a combination of electron tomography, computer simulations, and mathematical modeling to address the questions of when concatenated ILV networks evolved in plants and what drives their formation. Through morphometric analyses of tomographic reconstructions of endosomes across yeast, algae, and various land plants, we have found that ILV concatenation is widespread within plant species, but only prevalent in seed plants, especially in flowering plants. Multiple budding sites that require the formation of pores in the limiting membrane were only identified in hornworts and seed plants, suggesting that this mechanism has evolved independently in both plant lineages. To identify the conditions under which these multiple budding sites can arise, we used particle-based molecular dynamics simulations and found that changes in ESCRT filament properties, such as filament curvature and membrane binding energy, can generate the membrane shapes observed in multiple budding sites. To understand the relationship between membrane budding activity and ILV network topology, we performed computational simulations and identified a set of membrane remodeling parameters that can recapitulate our tomographic datasets.}, author = {Weiner, Ethan and Berryman, Elizabeth and Frey, Felix F and Solís, Ariadna González and Leier, André and Lago, Tatiana Marquez and Šarić, Anđela and Otegui, Marisa S.}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {44}, publisher = {National Academy of Sciences}, title = {{Endosomal membrane budding patterns in plants}}, doi = {10.1073/pnas.2409407121}, volume = {121}, year = {2024}, } @article{18527, abstract = {Context. Galaxies evolve through a dynamic exchange of material with their immediate surrounding environment, the so-called circumgalactic medium (CGM). Understanding the physics of gas flows and the nature of the CGM is fundamental to studying galaxy evolution, especially at 4 ≤ z ≤ 6 (i.e., after the Epoch of Reionization) when galaxies rapidly assembled their masses and reached their chemical maturity. Galactic outflows are predicted to enrich the CGM with metals, although it has also been suggested that gas stripping in systems undergoing a major merger may play a role. Aims. In this work, we explore the metal enrichment of the medium around merging galaxies at z ∼ 4.5, observed by the ALMA Large Program to INvestigate [CII] at Early times (ALPINE). To do so, we study the nature of the [CII] 158 μm emission in the CGM around these systems, using simulations to help disentangle the mechanisms contributing to the CGM metal pollution. Methods. By adopting an updated classification of major merger systems in the ALPINE survey, we selected and analyzed merging galaxies whose components can be spatially and/or spectrally resolved in a robust way. This makes it possible to distinguish between the [CII] emission coming from the single components of the system and that coming from the system as a whole. We also made use of the dustyGadget cosmological simulation to select synthetic analogs of observed galaxies and guide the interpretation of the observational results. Results. We find a large diffuse [CII] envelope (≳20 kpc) embedding all the merging systems, with at least 25% of the total [CII] emission coming from the medium between the galaxies. Using predictions from dustyGadget, we suggest that this emission has a multi-fold nature, with dynamical interactions between galaxies playing a major role in stripping the gas and enriching the medium with heavy elements.}, author = {Di Cesare, Claudia and Ginolfi, M. and Graziani, L. and Schneider, R. and Romano, M. and Popping, G.}, issn = {1432-0746}, journal = {Astronomy and Astrophysics}, publisher = {EDP Sciences}, title = {{Carbon envelopes around merging galaxies at z ~ 4.5}}, doi = {10.1051/0004-6361/202449164}, volume = {690}, year = {2024}, } @article{18528, abstract = {The recent measurement of magnetic field strength inside the radiative interior of red giant stars has opened the way toward full 3D characterization of the geometry of stable large-scale magnetic fields. However, current measurements, which are limited to dipolar (ℓ = 1) mixed modes, do not properly constrain the topology of magnetic fields due to degeneracies on the observed magnetic field signature on such ℓ = 1 mode frequencies. Efforts focused toward unambiguous detections of magnetic field configurations are now key to better understand angular momentum transport in stars. We investigated the detectability of complex magnetic field topologies (such as the ones observed at the surface of stars with a radiative envelope with spectropolarimetry) inside the radiative interior of red giants. We focused on a field composed of a combination of a dipole and a quadrupole (quadrudipole) and on an offset field. We explored the potential of probing such magnetic field topologies from a combined measurement of magnetic signatures on ℓ = 1 and quadrupolar (ℓ = 2) mixed mode oscillation frequencies. We first derived the asymptotic theoretical formalism for computing the asymmetric signature in the frequency pattern for ℓ = 2 modes due to a quadrudipole magnetic field. To access asymmetry parameters for more complex magnetic field topologies, we numerically performed a grid search over the parameter space to map the degeneracy of the signatures of given topologies. We demonstrate the crucial role played by ℓ = 2 mixed modes in accessing internal magnetic fields with a quadrupolar component. The degeneracy of the quadrudipole compared to pure dipolar fields is lifted when considering magnetic asymmetries in both ℓ = 1 and ℓ = 2 mode frequencies. In addition to the analytical derivation for the quadrudipole, we present the prospect for complex magnetic field inversions using magnetic sensitivity kernels from standard perturbation analysis for forward modeling. Using this method, we explored the detectability of offset magnetic fields from ℓ = 1 and ℓ = 2 frequencies and demonstrate that offset fields may be mistaken for weak and centered magnetic fields, resulting in underestimating the magnetic field strength in stellar cores. We emphasize the need to characterize ℓ = 2 mixed-mode frequencies, (along with the currently characterized ℓ = 1 mixed modes), to unveil the higher-order components of the geometry of buried magnetic fields and to better constrain angular momentum transport inside stars.}, author = {Das, Srijan B and Einramhof, Lukas and Bugnet, Lisa Annabelle}, issn = {1432-0746}, journal = {Astronomy and Astrophysics}, publisher = {EDP Sciences}, title = {{Unveiling complex magnetic field configurations in red giant stars}}, doi = {10.1051/0004-6361/202450918}, volume = {690}, year = {2024}, }