@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{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{18553, abstract = {Transcription-coupled nucleotide excision repair (TC-NER) efficiently eliminates DNA damage that impedes gene transcription by RNA polymerase II (RNA Pol II). TC-NER is initiated by the recognition of lesion-stalled RNA Pol II by CSB, which recruits the CRL4CSA ubiquitin ligase and UVSSA. RNA Pol II ubiquitylation at RPB1-K1268 by CRL4CSA serves as a critical TC-NER checkpoint, governing RNA Pol II stability and initiating DNA damage excision by TFIIH recruitment. However, the precise regulatory mechanisms of CRL4CSA activity and TFIIH recruitment remain elusive. Here, we reveal human serine/threonine-protein kinase 19 (STK19) as a TC-NER factor, which is essential for correct DNA damage removal and subsequent transcription restart. Cryogenic electron microscopy (cryo-EM) studies demonstrate that STK19 is an integral part of the RNA Pol II-TC-NER complex, bridging CSA, UVSSA, RNA Pol II, and downstream DNA. STK19 stimulates TC-NER complex stability and CRL4CSA activity, resulting in efficient RNA Pol II ubiquitylation and correct UVSSA and TFIIH binding. These findings underscore the crucial role of STK19 as a core TC-NER component.}, author = {Ramadhin, Anisha R. and Lee, Shun-Hsiao and Zhou, Di and Testa Salmazo, Anita P and Gonzalo-Hansen, Camila and van Sluis, Marjolein and Blom, Cindy M.A. and Janssens, Roel C. and Raams, Anja and Dekkers, Dick and Bezstarosti, Karel and Slade, Dea and Vermeulen, Wim and Pines, Alex and Demmers, Jeroen A.A. and Bernecky, Carrie A and Sixma, Titia K. and Marteijn, Jurgen A.}, issn = {1097-2765}, journal = {Molecular Cell}, number = {24}, pages = {4740--4757.e12}, publisher = {Elsevier}, title = {{STK19 drives transcription-coupled repair by stimulating repair complex stability, RNA Pol II ubiquitylation, and TFIIH recruitment}}, doi = {10.1016/j.molcel.2024.10.030}, volume = {84}, year = {2024}, } @article{18554, abstract = {We prove the Eigenstate Thermalization Hypothesis for general Wigner-type matrices in the bulk of the self-consistent spectrum, with optimal control on the fluctuations for obs ervables of arbitrary rank. As the main technical ingredient, we prove rank-uniform optimal local laws for one and two resolvents of a Wigner-type matrix with regular observables. Our results hold under very general conditions on the variance profile, even allowing many vanishing entries, demonstrating that Eigenstate Thermalization occurs robustly across a diverse class of random matrix ensembles, for which the underlying quantum system has a non-trivial spatial structure.}, author = {Erdös, László and Riabov, Volodymyr}, issn = {1432-0916}, journal = {Communications in Mathematical Physics}, number = {12}, publisher = {Springer Nature}, title = {{Eigenstate Thermalization Hypothesis for Wigner-type matrices}}, doi = {10.1007/s00220-024-05143-y}, volume = {405}, year = {2024}, } @inproceedings{18556, abstract = {Given a finite set, A ⊆ ℝ², and a subset, B ⊆ A, the MST-ratio is the combined length of the minimum spanning trees of B and A⧵B divided by the length of the minimum spanning tree of A. The question of the supremum, over all sets A, of the maximum, over all subsets B, is related to the Steiner ratio, and we prove this sup-max is between 2.154 and 2.427. Restricting ourselves to 2-dimensional lattices, we prove that the sup-max is 2, while the inf-max is 1.25. By some margin the most difficult of these results is the upper bound for the inf-max, which we prove by showing that the hexagonal lattice cannot have MST-ratio larger than 1.25.}, author = {Cultrera di Montesano, Sebastiano and Draganov, Ondrej and Edelsbrunner, Herbert and Saghafian, Morteza}, booktitle = {32nd International Symposium on Graph Drawing and Network Visualization}, isbn = {9783959773430}, issn = {1868-8969}, location = {Vienna, Austria}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{The Euclidean MST-ratio for bi-colored lattices}}, doi = {10.4230/LIPIcs.GD.2024.3}, volume = {320}, year = {2024}, } @article{18559, abstract = {We prove a 1973 conjecture due to Erdős on the existence of Steiner triple systems with arbitrarily high girth.}, author = {Kwan, Matthew Alan and Sah, Ashwin and Sawhney, Mehtaab and Simkin, Michael}, issn = {1939-8980}, journal = {Annals of Mathematics}, number = {3}, pages = {1059--1156}, publisher = {Princeton University}, title = {{High-girth Steiner triple systems}}, doi = {10.4007/annals.2024.200.3.4}, volume = {200}, year = {2024}, } @inbook{18563, abstract = {I give a personal account about the wave of new research activities that rose in the 1990s on the specification, verification, and control of real-time systems.}, author = {Henzinger, Thomas A}, booktitle = {Real Time and Such}, editor = {Graf, Susanne and Pettersson, Paul and Steffen, Bernhard}, isbn = {9783031737503}, issn = {1611-3349}, pages = {154--164}, publisher = {Springer Nature}, title = {{Reminiscences of a Real-Time Researcher}}, doi = {10.1007/978-3-031-73751-0_12}, volume = {15230}, year = {2024}, } @phdthesis{18568, abstract = {Locomotion is ubiquitous in the animal kingdom because an animal's survival depends on its ability to navigate its environment to find food, avoid predators and locate potential mates. These behaviours require control mechanisms that can extract information from the environment, particularly visual cues. Selective evolutionary pressures have thus refined such visuomotor transformations in a species-specific manner to meet the specific ecological and ethological challenges of each organism. However, a common challenge across organisms as visual information processing becomes increasingly detailed is the mechanisms required to synthesise disparate pieces of information into a coherent percept or unified picture of the world. In this thesis, I investigate how disparate visual information is combined in the brain of Drosophila melanogaster to effectively guide locomotion. For this, I first designed and built a behavioural setup to record locomotion and present visual stimuli to freely-walking fruit flies in a closed-loop manner. This setup allowed the investigation of innate visually-guided behaviours, including the optomotor reflex and courtship. Second, taking advantage of my system I investigated the optomotor response, a reflexive visual stabilisation behaviour in which flies turn in the direction of global motion to minimise retinal slip. This behaviour is thought to be mediated by Lobula plate tangential cells (LPTCs); a complex network of optic-flow-sensitive neurons essential for self-motion estimation. Using a novel genetic mutant, I demonstrate that electrical coupling between two LPTC subtypes, contralateral HS and H2 neurons, regulates the balance between smooth optomotor turning and saccadic anti-optomotor responses. These findings underscore the critical role of binocular motion cue integration in guiding course control. Finally, I developed a novel behavioural paradigm in which a sexually aroused male fruit fly is presented with an optomotor distractor. This setup creates competition between two visual behaviours, courtship tracking and the optomotor response, enabling me to explore how the visual system resolves this conflict. In this setting, males engaged in courtship selectively suppress their optomotor response based on the female's location. Furthermore, when this experiment is replicated with an “artificial female”, optogenetically aroused males alternate between tracking and optomotor responses. The probability and dynamics of this switching are determined by the relative strengths of the two competing stimuli. In summary, the results presented in this thesis explore two mechanisms – integration and competition - through which visual information is combined in the brain of the fruit fly to drive locomotion.}, author = {Satapathy, Roshan K}, isbn = {978-3-99078-047-3}, issn = {2663-337X}, pages = {114}, publisher = {Institute of Science and Technology Austria}, title = {{Mechanisms of visual integration and competition in innate behaviours in Drosophila melanogaster}}, doi = {10.15479/at:ista:18568}, year = {2024}, } @misc{18579, abstract = {Electrophysiological, calcium two-photon recordings and behavioral data for Vega-Zuniga et al. Relevant information can be found in the 'README.txt' files. }, author = {Vega Zuniga, Tomas A and Sumser, Anton L and Symonova, Olga and Koppensteiner, Peter and Schmidt, Florian and Jösch, Maximilian A}, publisher = {Institute of Science and Technology Austria}, title = {{A thalamic hub-and-spoke network enables visual perception during action by coordinating visuomotor dynamics}}, doi = {10.15479/AT:ISTA:18579}, year = {2024}, } @article{18581, abstract = {Background: Human induced pluripotent stem cells represent a scalable source of youthful tissue progenitors and secretomes for regenerative therapies. The aim of our study was to investigate the potential of conditioned medium (CM) from hiPSC-mesenchymal progenitors (hiPSC-MPs) to stimulate osteogenic differentiation of human bone marrow-derived mesenchymal stromal cells (MSCs). We also investigated whether prolonged cultivation or osteogenic pre-differentiation of hiPSC-MPs could enhance the stimulatory activity of CM. Methods: MSCs were isolated from 13 donors (age 20–90 years). CM derived from hiPSC-MPs was added to the MSC cultures and the effects on proliferation and osteogenic differentiation were examined after 14 days and 6 weeks. The stimulatory activity of hiPSC-MP-CM was compared with the activity of MSC-derived CM and with the activity of CM prepared from hiPSC-MPs pre-cultured in growth or osteogenic medium for 14 days. Comparative proteomic analysis of CM was performed to gain insight into the molecular components responsible for the stimulatory activity. Results: Primary bone marrow-derived MSC exhibited variability, with a tendency towards lower proliferation and tri-lineage differentiation in older donors. hiPSC-MP-CM increased the proliferation and alkaline phosphatase activity of MSC from several adult/aged donors after 14 days of continuous supplementation under osteogenic conditions. However, CM supplementation failed to improve the mineralization of MSC pellets after 6 weeks under osteogenic conditions. hiPSC-MP-CM showed greater enhancement of proliferation and ALP activity than CM derived from bone marrow-derived MSCs. Moreover, 14-day cultivation but not osteogenic pre-differentiation of hiPSC-MPs strongly enhanced CM stimulatory activity. Quantitative proteomic analysis of d14-CM revealed a distinct profile of components that formed a highly interconnected associations network with two clusters, one functionally associated with binding and organization of actin/cytoskeletal components and the other with structural constituents of the extracellular matrix, collagen, and growth factor binding. Several hub proteins were identified that were reported to have functions in cell-extracellular matrix interaction, osteogenic differentiation and development. Conclusions: Our data show that hiPSC-MP-CM enhances early osteogenic differentiation of human bone marrow-derived MSCs and that prolonged cultivation of hiPSC-MPs enhances CM-stimulatory activity. Proteomic analysis of the upregulated protein components provides the basis for further optimization of hiPSC-MP-CM for bone regenerative therapies.}, author = {Marolt Presen, Darja and Goeschl, Vanessa and Hanetseder, Dominik and Ogrin, Laura and Stetco, Alexandra Larissa and Tansek, Anja and Pozenel, Laura and Bruszel, Bella and Mitulovic, Goran and Oesterreicher, Johannes and Zipperle, Johannes and Schaedl, Barbara and Holnthoner, Wolfgang and Grillari, Johannes and Redl, Heinz}, issn = {1757-6512}, journal = {Stem Cell Research and Therapy}, publisher = {Springer Nature}, title = {{Prolonged cultivation enhances the stimulatory activity of hiPSC mesenchymal progenitor-derived conditioned medium}}, doi = {10.1186/s13287-024-03960-5}, volume = {15}, year = {2024}, } @article{18582, abstract = {Identification of PIN exporters for auxin, the major coordinative signal in plants, some 25 years ago, signifies a landmark in our understanding of plant-specific mechanisms underlying development and adaptation. Auxin is directionally transported throughout the plant body; a unique feature already envisioned by Darwin and solidified by PINs’ discovery and characterization. The PIN-based auxin distribution network with its complex regulations of PIN expression, localization and activity turned out to underlie a remarkable multitude of developmental processes and represents means to integrate endogenous and environmental signals. Given the recent anniversary, we here summarize past and current developments in this exciting field.}, author = {Luschnig, Christian and Friml, Jiří}, issn = {2041-1723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{Over 25 years of decrypting PIN-mediated plant development}}, doi = {10.1038/s41467-024-54240-y}, volume = {15}, year = {2024}, } @article{18583, abstract = {There are a number of well-known problems and conjectures about partitioning graphs to satisfy local constraints. For example, the majority colouring conjecture of Kreutzer, Oum, Seymour, van der Zypen and Wood states that every directed graph has a 3-colouring such that for every vertex v, at most half of the out-neighbours of v have the same colour as . As another example, the internal partition conjecture, due to DeVos and to Ban and Linial, states that for every d, all but finitely many d-regular graphs have a partition into two non-empty parts such that for every vertex v, at least half of the neighbours of v lie in the same part as v. We prove several results in this spirit: in particular, two of our results are that the majority colouring conjecture holds for Erdős–Rényi random directed graphs (of any density), and that the internal partition conjecture holds if we permit a tiny number of ‘exceptional vertices’. Our proofs involve a variety of techniques, including several different methods to analyse random recolouring processes. One highlight is a personality-changing scheme: we ‘forget’ certain information based on the state of a Markov chain, giving us more independence to work with.}, author = {Anastos, Michael and Cooley, Oliver and Kang, Mihyun and Kwan, Matthew Alan}, issn = {1469-7750}, journal = {Journal of the London Mathematical Society}, number = {6}, publisher = {Wiley}, title = {{Partitioning problems via random processes}}, doi = {10.1112/jlms.70010}, volume = {110}, year = {2024}, } @article{18584, abstract = {In this paper, we describe the "Medium Bands, Mega Science" JWST Cycle 2 survey (JWST-GO-4111) and demonstrate the power of these data to reveal both the spatially integrated and spatially resolved properties of galaxies from the local Universe to the era of cosmic dawn. Executed in 2023 November, MegaScience obtained ∼30 arcmin2 of deep multiband NIRCam imaging centered on the z ∼ 0.3 A2744 cluster, including 11 medium-band filters and the two shortest-wavelength broadband filters, F070W and F090W. Together, MegaScience and the UNCOVER Cycle 1 treasury program provide a complete set of deep (∼28–30 magAB) images in all NIRCam medium- and broadband filters. This unique data set allows us to precisely constrain photometric redshifts, map stellar populations and dust attenuation for large samples of distant galaxies, and examine the connection between galaxy structures and formation histories. MegaScience also includes ∼17 arcmin2 of NIRISS parallel imaging in two broadband and four medium-band filters from 0.9 to 4.8 μm, expanding the footprint where robust spectral energy distribution (SED) fitting is possible. We provide example SEDs and multiband cutouts at a variety of redshifts, and use a catalog of JWST spectroscopic redshifts to show that MegaScience improves both the scatter and catastrophic outlier rate of photometric redshifts by factors of 2–3. Additionally, we demonstrate the spatially resolved science enabled by MegaScience by presenting maps of the [O iii] line emission and continuum emission in three spectroscopically confirmed z > 6 galaxies. We show that line emission in reionization-era galaxies can be clumpy, extended, and spatially offset from continuum emission, implying that galaxy assembly histories are complex even at these early epochs. We publicly release fully reduced mosaics and photometric catalogs for both the NIRCam primary and NIRISS parallel fields (jwst-uncover.github.io/megascience).}, author = {Suess, Katherine A. and Weaver, John R. and Price, Sedona H. and Pan, Richard and Wang, Bingjie and Bezanson, Rachel and Brammer, Gabriel and Cutler, Sam E. and Labbé, Ivo and Leja, Joel and Williams, Christina C. and Whitaker, Katherine E. and Atek, Hakim and Dayal, Pratika and De Graaff, Anna and Feldmann, Robert and Franx, Marijn and Fudamoto, Yoshinobu and Fujimoto, Seiji and Furtak, Lukas J. and Goulding, Andy D. and Greene, Jenny E. and Khullar, Gourav and Kokorev, Vasily and Kriek, Mariska and Lorenz, Brian and Marchesini, Danilo and Maseda, Michael V. and Matthee, Jorryt J and Miller, Tim B. and Mitsuhashi, Ikki and Mowla, Lamiya A. and Muzzin, Adam and Naidu, Rohan P. and Nanayakkara, Themiya and Nelson, Erica J. and Oesch, Pascal A. and Setton, David J. and Shipley, Heath and Smit, Renske and Spilker, Justin S. and Van Dokkum, Pieter and Zitrin, Adi}, issn = {1538-4357}, journal = {Astrophysical Journal}, number = {1}, publisher = {IOP Publishing}, title = {{Medium bands, mega science: A JWST/NIRCam medium-band imaging survey of A2744}}, doi = {10.3847/1538-4357/ad75fe}, volume = {976}, year = {2024}, } @article{18585, abstract = {We present the census of Hβ+[OIII] 4960,5008 Åemitters at 6.87 galaxies. We report a rapid decline of the [OIII] luminosity density at z≳6−7 which cannot be explained by the evolution of the cosmic star-formation rate density. Finally we find that FRESCO detects in only 2h galaxies likely accounting for ∼10−20% of the ionising budget at z=7−8 (assuming an escape fraction of 10%), raising the prospect of directly detecting a significant fraction of the sources of reionisation with JWST.}, author = {Meyer, R. A. and Oesch, P. A. and Giovinazzo, E. and Weibel, A. and Brammer, G. and Matthee, Jorryt J and Naidu, R. P. and Bouwens, R. J. and Chisholm, J. and Covelo-Paz, A. and Fudamoto, Y. and Maseda, M. and Nelson, E. and Shivaei, I. and Xiao, M. and Herard-Demanche, T. and Illingworth, G. D. and Kerutt, J. and Kramarenko, Ivan and Labbe, I. and Leonova, E. and Magee, D. and Matharu, J. and Prieto Lyon, G. and Reddy, N. and Schaerer, D. and Shapley, A. and Stefanon, M. and Wozniak, M. A. and Wuyts, S.}, issn = {1365-2966}, journal = {Monthly Notices of the Royal Astronomical Society}, number = {1}, pages = {1067--1094}, publisher = {Oxford University Press}, title = {{JWST FRESCO: A comprehensive census of H β + [O iii] emitters at 6.8 < z < 9.0 in the GOODS fields}}, doi = {10.1093/mnras/stae2353}, volume = {535}, year = {2024}, } @article{18586, abstract = {We prove the Central Limit Theorem and superpolynomial mixing for environment viewed from the particle process in quasi periodic Diophantine random environment. The main ingredients are smoothness estimates for the solution of the Poisson equation and local limit asymptotics for certain accelerated walks.}, author = {Czudek, Klaudiusz S and Dolgopyat, Dmitry}, issn = {1980-0436}, journal = {Alea}, number = {2}, pages = {1853--1865}, publisher = {Instituto Nacional de Matematica Pura e Aplicada}, title = {{The central limit theorem and rate of mixing for simple random walks on the circle}}, doi = {10.30757/ALEA.V21-70}, volume = {21}, year = {2024}, }